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Cates J, Powell H, Platts-Mills J, Nasrin D, Panchalingam S, Sow SO, Traore A, Sur D, Ramamurthy T, Zaidi AKM, Kabir F, Faruque ASG, Ahmed D, Breiman RF, Omore R, Ochieng JB, Hossain MJ, Antonio M, Mandomando I, Vubil D, Nataro JP, Levine MM, Parashar UD, Kotloff KL, Tate JE. Clinical severity of enteric viruses detected using a quantitative molecular assay compared to conventional assays in the Global Enteric Multicenter Study. J Infect Dis 2024:jiae201. [PMID: 38637321 DOI: 10.1093/infdis/jiae201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/13/2024] [Accepted: 04/15/2024] [Indexed: 04/20/2024] Open
Abstract
BACKGROUND Quantitative molecular assays are increasingly used for detection of enteric viruses. METHODS We compared the clinical severity using modified Vesikari score (mVS) of enteric viruses detected by conventional assays (enzyme immunoassays [EIA] for rotavirus and adenovirus 40/41 and conventional polymerase chain reaction for astrovirus, sapovirus, and norovirus) and a quantitative molecular assay (TaqMan Array Card [TAC]) among children aged 0-59 months in the Global Enteric Multicenter Study. For rotavirus and adenovirus 40/41, we compared severity between EIA-positive and TAC-positive cases assigned etiologies using different cycle threshold (CT) cutoffs. RESULTS Using conventional assays, the median (interquartile range) mVS was 10 (8, 11) for rotavirus, 9 (7, 11) for adenovirus 40/41, 8 (6, 10) for astrovirus, sapovirus, and norovirus GII, and 7 (6, 9) for norovirus GI. Compared to rotavirus EIA-positive cases, the median mVS was 2 and 3 points lower for EIA-negative/TAC-positive cases with CT<32.6 and 32.6≤CT<35, respectively (p-value<.0001). Adenovirus 40/41 EIA-positive and EIA-negative/TAC-positive cases were similar, regardless of CT cutoff. CONCLUSIONS Quantitative molecular assays compared to conventional assays, such as EIA, may influence severity of identified cases, especially for rotavirus. Cutoffs to assign etiology for quantitative assays should be considered in the design and interpretation of enteric virus studies.
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Affiliation(s)
- Jordan Cates
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Helen Powell
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - James Platts-Mills
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Dilruba Nasrin
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Sandra Panchalingam
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Samba O Sow
- Centre pour le Développement des Vaccins, Bamako, Mali
| | - Awa Traore
- Centre pour le Développement des Vaccins, Bamako, Mali
| | - Dipika Sur
- National Institute of Cholera and Enteric Diseases, Kolkata, India
| | | | - Anita K M Zaidi
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Furqan Kabir
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Abu S G Faruque
- International Centre for Diarrhoeal Disease Research, Mohakhali, Dhaka, Bangladesh
| | - Dilruba Ahmed
- International Centre for Diarrhoeal Disease Research, Mohakhali, Dhaka, Bangladesh
| | - Robert F Breiman
- Department of Global Health, Rollins School of Public Health, Emory University, USA
- Infectious Diseases and Oncology Research Institute, University of the Witwatersrand, Johannesburg, South Africa
| | - Richard Omore
- Kenya Medical Research Institute, Centers for Global Health Research (KEMRI-CGHR), Kisumu, Kenya
| | - John Benjamin Ochieng
- Kenya Medical Research Institute, Centers for Global Health Research (KEMRI-CGHR), Kisumu, Kenya
| | - M Jahangir Hossain
- Medical Research Council (UK) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Martin Antonio
- Medical Research Council (UK) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
- Centre for Epidemic Preparedness and Response, London School of Hygiene & Tropical Medicine, London, UK
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | | | - Delfino Vubil
- Centro de Investigação em Saúde da Manhiça, Maputo, Mozambique
| | - James P Nataro
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Pediatrics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Myron M Levine
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Umesh D Parashar
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Karen L Kotloff
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Jacqueline E Tate
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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2
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Pavlinac PB, Platts-Mills JA, Liu J, Atlas HE, Gratz J, Operario D, Rogawski McQuade ET, Ahmed D, Ahmed T, Alam T, Ashorn P, Badji H, Bahl R, Bar-Zeev N, Chisti MJ, Cornick J, Chauhan A, De Costa A, Deb S, Dhingra U, Dube Q, Duggan CP, Freyne B, Gumbi W, Hotwani A, Kabir M, Islam O, Kabir F, Kasumba I, Kibwana U, Kotloff KL, Khan SS, Maiden V, Manji K, Mehta A, Ndeketa L, Praharaj I, Qamar FN, Sazawal S, Simon J, Singa BO, Somji S, Sow SO, Tapia MD, Tigoi C, Toure A, Walson JL, Yousafzai MT, Houpt ER. Azithromycin for Bacterial Watery Diarrhea: A Reanalysis of the AntiBiotics for Children With Severe Diarrhea (ABCD) Trial Incorporating Molecular Diagnostics. J Infect Dis 2024; 229:988-998. [PMID: 37405406 PMCID: PMC11011181 DOI: 10.1093/infdis/jiad252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 05/25/2023] [Accepted: 07/03/2023] [Indexed: 07/06/2023] Open
Abstract
BACKGROUND Bacterial pathogens cause substantial diarrhea morbidity and mortality among children living in endemic settings, yet antimicrobial treatment is only recommended for dysentery or suspected cholera. METHODS AntiBiotics for Children with severe Diarrhea was a 7-country, placebo-controlled, double-blind efficacy trial of azithromycin in children 2-23 months of age with watery diarrhea accompanied by dehydration or malnutrition. We tested fecal samples for enteric pathogens utilizing quantitative polymerase chain reaction to identify likely and possible bacterial etiologies and employed pathogen-specific cutoffs based on genomic target quantity in previous case-control diarrhea etiology studies to identify likely and possible bacterial etiologies. RESULTS Among 6692 children, the leading likely etiologies were rotavirus (21.1%), enterotoxigenic Escherichia coli encoding heat-stable toxin (13.3%), Shigella (12.6%), and Cryptosporidium (9.6%). More than one-quarter (1894 [28.3%]) had a likely and 1153 (17.3%) a possible bacterial etiology. Day 3 diarrhea was less common in those randomized to azithromycin versus placebo among children with a likely bacterial etiology (risk difference [RD]likely, -11.6 [95% confidence interval {CI}, -15.6 to -7.6]) and possible bacterial etiology (RDpossible, -8.7 [95% CI, -13.0 to -4.4]) but not in other children (RDunlikely, -0.3% [95% CI, -2.9% to 2.3%]). A similar association was observed for 90-day hospitalization or death (RDlikely, -3.1 [95% CI, -5.3 to -1.0]; RDpossible, -2.3 [95% CI, -4.5 to -.01]; RDunlikely, -0.6 [95% CI, -1.9 to .6]). The magnitude of risk differences was similar among specific likely bacterial etiologies, including Shigella. CONCLUSIONS Acute watery diarrhea confirmed or presumed to be of bacterial etiology may benefit from azithromycin treatment. CLINICAL TRIALS REGISTRATION NCT03130114.
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Affiliation(s)
- Patricia B Pavlinac
- Department of Global Health
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - James A Platts-Mills
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Jie Liu
- School of Public Health, Qingdao University, Qingdao, China
| | | | - Jean Gratz
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Darwin Operario
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia, USA
| | | | | | - Tahmeed Ahmed
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Tahmina Alam
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Per Ashorn
- Center for Child, Adolescent, and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University and Tampere University Hospital, Tampere, Finland
| | - Henry Badji
- Centre pour le Développement des Vaccines, Bamako, Mali
| | - Rajiv Bahl
- Department of Maternal, Newborn, Child, and Adolescent Health and Aging, World Health Organization, Geneva, Switzerland
| | - Naor Bar-Zeev
- International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Mohammod Jobayer Chisti
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Jen Cornick
- Clinical Research Programme, Malawi Liverpool Wellcome Trust, Blantyre, Malawi
| | | | - Ayesha De Costa
- Department of Maternal, Newborn, Child, and Adolescent Health and Aging, World Health Organization, Geneva, Switzerland
| | - Saikat Deb
- Center for Public Health Kinetics, New Delhi, India
| | - Usha Dhingra
- Center for Public Health Kinetics, New Delhi, India
| | - Queen Dube
- Department of Pediatrics, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Christopher P Duggan
- Division of Gastroenterology, Hepatology and Nutrition, Department of Nutrition, Boston Children's Hospital, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Bridget Freyne
- Clinical Research Programme, Malawi Liverpool Wellcome Trust, Blantyre, Malawi
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Department of Women and Children's Health, School of Medicine, University College Dublin, Dublin, Ireland
| | - Wilson Gumbi
- Kenya Medical Research Institute–Wellcome Trust Research Programme, Kilifi, Kenya
| | - Aneeta Hotwani
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Mamun Kabir
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Ohedul Islam
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Furqan Kabir
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Irene Kasumba
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Upendo Kibwana
- Department of Pediatrics and Child Health, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Karen L Kotloff
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Pediatrics, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Shaila S Khan
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Victor Maiden
- Clinical Research Programme, Malawi Liverpool Wellcome Trust, Blantyre, Malawi
| | - Karim Manji
- Department of Pediatrics and Child Health, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Ashka Mehta
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Latif Ndeketa
- Clinical Research Programme, Malawi Liverpool Wellcome Trust, Blantyre, Malawi
| | - Ira Praharaj
- Department of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | - Farah Naz Qamar
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | | | - Jonathon Simon
- Department of Maternal, Newborn, Child, and Adolescent Health and Aging, World Health Organization, Geneva, Switzerland
| | - Benson O Singa
- Center for Clinical Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Sarah Somji
- Department of Pediatrics and Child Health, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Samba O Sow
- Centre pour le Développement des Vaccines, Bamako, Mali
| | - Milagritos D Tapia
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Caroline Tigoi
- Kenya Medical Research Institute–Wellcome Trust Research Programme, Kilifi, Kenya
| | - Aliou Toure
- Centre pour le Développement des Vaccines, Bamako, Mali
| | - Judd L Walson
- Department of Global Health
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Infectious Diseases, Department of Pediatrics and Medicine, University of Washington, Seattle
| | | | - Eric R Houpt
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia, USA
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3
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Liu J, Garcia Bardales PF, Islam K, Jarju S, Juma J, Mhango C, Naumanga Q, Qureshi S, Sonye C, Ahmed N, Aziz F, Bhuiyan MTR, Charles M, Cunliffe NA, Abdou M, Galagan SR, Gitteh E, Guindo I, Jahangir Hossain M, Jabang AMJ, Jere KC, Kawonga F, Keita M, Keita NY, Kotloff KL, Shapiama Lopez WV, Munga S, Paredes Olortegui M, Omore R, Pavlinac PB, Qadri F, Qamar FN, Azadul Alam Raz SM, Riziki L, Schiaffino F, Stroup S, Traore SN, Pinedo Vasquez T, Yousafzai MT, Antonio M, Cornick JE, Kabir F, Khanam F, Kosek MN, Ochieng JB, Platts-Mills JA, Tennant SM, Houpt ER. Shigella Detection and Molecular Serotyping With a Customized TaqMan Array Card in the Enterics for Global Health (EFGH): Shigella Surveillance Study. Open Forum Infect Dis 2024; 11:S34-S40. [PMID: 38532960 PMCID: PMC10962731 DOI: 10.1093/ofid/ofad574] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024] Open
Abstract
Background Quantitative polymerase chain reaction (qPCR) targeting ipaH has been proven to be highly efficient in detecting Shigella in clinical samples compared to culture-based methods, which underestimate Shigella burden by 2- to 3-fold. qPCR assays have also been developed for Shigella speciation and serotyping, which is critical for both vaccine development and evaluation. Methods The Enterics for Global Health (EFGH) Shigella surveillance study will utilize a customized real-time PCR-based TaqMan Array Card (TAC) interrogating 82 targets, for the detection and differentiation of Shigella spp, Shigella sonnei, Shigella flexneri serotypes, other diarrhea-associated enteropathogens, and antimicrobial resistance (AMR) genes. Total nucleic acid will be extracted from rectal swabs or stool samples, and assayed on TAC. Quantitative analysis will be performed to determine the likely attribution of Shigella and other particular etiologies of diarrhea using the quantification cycle cutoffs derived from previous studies. The qPCR results will be compared to conventional culture, serotyping, and phenotypic susceptibility approaches in EFGH. Conclusions TAC enables simultaneous detection of diarrheal etiologies, the principal pathogen subtypes, and AMR genes. The high sensitivity of the assay enables more accurate estimation of Shigella-attributed disease burden, which is critical to informing policy and in the design of future clinical trials.
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Affiliation(s)
- Jie Liu
- School of Public Health, Qingdao University, Qingdao, China
| | | | - Kamrul Islam
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Sheikh Jarju
- Medical Research Council Unit The Gambia, London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Jane Juma
- Centre pour le Développement des Vaccins du Mali (CVD-Mali), Bamako, Mali
| | | | - Queen Naumanga
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Sonia Qureshi
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Catherine Sonye
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Naveed Ahmed
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Fatima Aziz
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Md Taufiqur Rahman Bhuiyan
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Mary Charles
- Malawi Liverpool Wellcome Research Programme, Blantyre, Malawi
| | - Nigel A Cunliffe
- Institute of Infection, Veterinary and Ecological Sciences, Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, United Kingdom
| | - Mahamadou Abdou
- Centre pour le Développement des Vaccins du Mali (CVD-Mali), Bamako, Mali
| | - Sean R Galagan
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Ensa Gitteh
- Medical Research Council Unit The Gambia, London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Ibrehima Guindo
- Centre pour le Développement des Vaccins du Mali (CVD-Mali), Bamako, Mali
| | - M Jahangir Hossain
- Medical Research Council Unit The Gambia, London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Abdoulie M J Jabang
- Medical Research Council Unit The Gambia, London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Khuzwayo C Jere
- Malawi Liverpool Wellcome Research Programme, Blantyre, Malawi
- Institute of Infection, Veterinary and Ecological Sciences, Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, United Kingdom
- Department of Medical Laboratory Sciences, School of Life Sciences and Health Professions, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Flywell Kawonga
- Malawi Liverpool Wellcome Research Programme, Blantyre, Malawi
| | - Mariama Keita
- Medical Research Council Unit The Gambia, London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | | | - Karen L Kotloff
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | | | - Stephen Munga
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | | | - Richard Omore
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Patricia B Pavlinac
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Firdausi Qadri
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Farah Naz Qamar
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - S M Azadul Alam Raz
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Laura Riziki
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Francesca Schiaffino
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
- Faculty of Veterinary Medicine, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Suzanne Stroup
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | | | | | | | - Martin Antonio
- Medical Research Council Unit The Gambia, London School of Hygiene and Tropical Medicine, Fajara, The Gambia
- Centre for Epidemic Preparedness and Response, London School of Hygiene & Tropical Medicine, London, UK
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Jennifer E Cornick
- Malawi Liverpool Wellcome Research Programme, Blantyre, Malawi
- Institute of Infection, Veterinary and Ecological Sciences, Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, United Kingdom
| | - Furqan Kabir
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Farhana Khanam
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Margaret N Kosek
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | | | - James A Platts-Mills
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Sharon M Tennant
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Eric R Houpt
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
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4
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Ali K, Meyer E, Kabir F. Editorial: Biorisk management, laboratory acquired infections and clinical containment, volume II. Front Public Health 2024; 12:1368828. [PMID: 38439752 PMCID: PMC10910501 DOI: 10.3389/fpubh.2024.1368828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 02/07/2024] [Indexed: 03/06/2024] Open
Affiliation(s)
- Kashif Ali
- Department of Biosciences, Faculty of Life Sciences, Shaheed Zulfikar Ali Bhutto Institute of Science and Technology, Karachi, Pakistan
| | - Esmeralda Meyer
- Department of Research Compliance and Regulatory Affairs, Institutional Animal Care and Use Committee, Emory University, Atlanta, GA, United States
| | - Furqan Kabir
- Infectious Diseases Research Laboratory (IDRL), Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
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5
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Ansari N, Kabir F, Khan W, Khalid F, Malik AA, Warren JL, Mehmood U, Kazi AM, Yildirim I, Tanner W, Kalimuddin H, Kanwar S, Aziz F, Memon A, Alam MM, Ikram A, Meschke JS, Jehan F, Omer SB, Nisar MI. Environmental surveillance for COVID-19 using SARS-CoV-2 RNA concentration in wastewater - a study in District East, Karachi, Pakistan. Lancet Reg Health Southeast Asia 2024; 20:100299. [PMID: 38234701 PMCID: PMC10794106 DOI: 10.1016/j.lansea.2023.100299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 04/18/2023] [Accepted: 09/28/2023] [Indexed: 01/19/2024]
Abstract
Background Wastewater-based surveillance is used to track the temporal patterns of the SARS-CoV-2 virus in communities. Viral RNA particle detection in wastewater samples can indicate an outbreak within a catchment area. We describe the feasibility of using a sewage network to monitor SARS-CoV-2 trend and use of genomic sequencing to describe the viral variant abundance in an urban district in Karachi, Pakistan. This was among the first studies from Pakistan to demonstrate the surveillance for SARS-CoV-2 from a semi-formal sewage system. Methods Four sites draining into the Lyari River in District East, Karachi, were identified and included in the current study. Raw sewage samples were collected early morning twice weekly from each site between June 10, 2021 and January 17, 2022, using Bag Mediated Filtration System (BMFS). Secondary concentration of filtered samples was achieved by ultracentrifugation and skim milk flocculation. SARS-CoV-2 RNA concentrations in the samples were estimated using PCR (Qiagen ProMega kits for N1 & N2 genes). A distributed-lag negative binomial regression model within a hierarchical Bayesian framework was used to describe the relationship between wastewater RNA concentration and COVID-19 cases from the catchment area. Genomic sequencing was performed using Illumina iSeq100. Findings Among the 151 raw sewage samples included in the study, 123 samples (81.5%) tested positive for N1 or N2 genes. The average SARS-CoV-2 RNA concentrations in the sewage samples at each lag (1-14 days prior) were associated with the cases reported for the respective days, with a peak association observed on lag day 10 (RR: 1.15; 95% Credible Interval: 1.10-1.21). Genomic sequencing showed that the delta variant dominated till September 2022, while the omicron variant was identified in November 2022. Interpretation Wastewater-based surveillance, together with genomic sequencing provides valuable information for monitoring the community temporal trend of SARS-CoV-2. Funding PATH, Bill & Melinda Gates Foundation, and Global Innovation Fund.
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Affiliation(s)
- Nadia Ansari
- Faculty of Health Sciences, Department of Paediatrics and Child Health, Medical College, The Aga Khan University, Stadium Road, Karachi 74800, Pakistan
| | - Furqan Kabir
- Faculty of Health Sciences, Department of Paediatrics and Child Health, Medical College, The Aga Khan University, Stadium Road, Karachi 74800, Pakistan
| | - Waqasuddin Khan
- CITRIC Centre for Bioinformatics and Computational Biology, Department of Paediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Stadium Road, Karachi 74800, Pakistan
| | - Farah Khalid
- Faculty of Health Sciences, Department of Paediatrics and Child Health, Medical College, The Aga Khan University, Stadium Road, Karachi 74800, Pakistan
| | - Amyn Abdul Malik
- Yale Institute for Global Health, Yale University, New Haven, CT, USA
- Section of Infectious Diseases and Global Health, Department of Paediatrics, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Joshua L. Warren
- Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Usma Mehmood
- Faculty of Health Sciences, Department of Paediatrics and Child Health, Medical College, The Aga Khan University, Stadium Road, Karachi 74800, Pakistan
| | - Abdul Momin Kazi
- Faculty of Health Sciences, Department of Paediatrics and Child Health, Medical College, The Aga Khan University, Stadium Road, Karachi 74800, Pakistan
| | - Inci Yildirim
- Yale Institute for Global Health, Yale University, New Haven, CT, USA
- Section of Infectious Diseases and Global Health, Department of Paediatrics, Yale School of Medicine, Yale University, New Haven, CT, USA
- Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Windy Tanner
- Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Hussain Kalimuddin
- Faculty of Health Sciences, Department of Paediatrics and Child Health, Medical College, The Aga Khan University, Stadium Road, Karachi 74800, Pakistan
| | - Samiah Kanwar
- Faculty of Health Sciences, Department of Paediatrics and Child Health, Medical College, The Aga Khan University, Stadium Road, Karachi 74800, Pakistan
- CITRIC Centre for Bioinformatics and Computational Biology, Department of Paediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Stadium Road, Karachi 74800, Pakistan
| | - Fatima Aziz
- Faculty of Health Sciences, Department of Paediatrics and Child Health, Medical College, The Aga Khan University, Stadium Road, Karachi 74800, Pakistan
| | - Arslan Memon
- District Health Office (East), Karachi, Pakistan
| | | | - Aamer Ikram
- National Institutes of Health, Chak Shahzad, Islamabad, Pakistan
| | | | - Fyezah Jehan
- Faculty of Health Sciences, Department of Paediatrics and Child Health, Medical College, The Aga Khan University, Stadium Road, Karachi 74800, Pakistan
- CITRIC Centre for Bioinformatics and Computational Biology, Department of Paediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Stadium Road, Karachi 74800, Pakistan
| | - Saad B. Omer
- Yale Institute for Global Health, Yale University, New Haven, CT, USA
- Section of Infectious Diseases and Global Health, Department of Paediatrics, Yale School of Medicine, Yale University, New Haven, CT, USA
- Yale School of Public Health, Yale University, New Haven, CT, USA
- Yale School of Nursing, Orange, CT, USA
| | - Muhammad Imran Nisar
- Faculty of Health Sciences, Department of Paediatrics and Child Health, Medical College, The Aga Khan University, Stadium Road, Karachi 74800, Pakistan
- CITRIC Centre for Bioinformatics and Computational Biology, Department of Paediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Stadium Road, Karachi 74800, Pakistan
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6
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Javaid N, Lo SW, Nisar MI, Basharat A, Jaleel H, Rasool K, Sultana Q, Kabir F, Hotwani A, Breiman RF, Bentley SD, Shakoor S, Mirza S. Strain features of pneumococcal isolates in the pre- and post-PCV10 era in Pakistan. Microb Genom 2024; 10:001163. [PMID: 38270581 PMCID: PMC10868622 DOI: 10.1099/mgen.0.001163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 12/06/2023] [Indexed: 01/26/2024] Open
Abstract
Pakistan is amongst the four countries with the highest number of pneumococcal deaths. While the PCV10 vaccine was introduced in Pakistan in October 2012, data regarding the impact of the vaccine on the population dynamics of Streptococcus pneumoniae in Pakistan remain obscure. Using whole genome sequencing of 190 isolates (nasopharyngeal carriage=75, disease=113, unknown sites=2) collected between 2002 and 2020, this study presents characteristics of pneumococcal strains in Pakistan in the pre- and post-vaccine era. The isolates were characterized on the basis of serotype distribution, genetic lineages (or Global Pneumococcal Sequence Cluster, GPSC) and antibiotic resistance. A high level of diversity in serotype and genetic lineages of pneumococci was observed in Pakistan. Among 190 isolates, we identified 54 serotypes, 67 GPSCs and 116 sequence types (STs) including 23 new STs. The most prevalent GPSCs and their associated serotypes in nasopharyngeal carriage were GPSC54 (expressing serotype 9V), GPSC5 (15A and 7B, and serogroup 24), GPSC25 (15B/15C), GPSC67 (18C) and GPSC376 (6A and 6D). Similarly, among 113 disease-causing isolates, the most prevalent GPSC/serotype combinations were GPSC2 (serotype 1), GPSC10 (serotypes 14, 10A, 19A and 19F), GPSC43 (serotypes 13, 11A, 23B, 35A and 9V), GPSC67 (serotypes 18A and 18C) and GPSC642 (serotype 11A). Of the 190 isolates, the highest levels of resistance were observed against penicillin (58.9 %, n=122), erythromycin (29.5 %, n=56), clindamycin (13.2 %, n=25), co-trimoxazole (94.2 %, n=179) and tetracycline/doxycycline (53.2 %, n=101). A higher proportion of disease-causing isolates were multidrug resistant as compared to carriage isolates (54 % vs 25 %). Our data suggest limited coverage of PCV10 in nasopharyngeal (21.6 %, 16/74) as well as disease-causing (38.1 %, 16/42) isolates among children ≤5 years old; however, higher valent vaccine PCV13 would increase the coverage rates to 33.8 % in nasopharyngeal and 54.8 % in disease-causing isolates, whereas PCV24/25 would offer the highest coverage rates. Owing to the diversity of serotypes observed during the post-vaccine period, the suggested inclusion of serotype in future vaccine formulations will require investigations with larger data sets with an extended temporal window. This article contains data hosted by Microreact.
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Affiliation(s)
- Nida Javaid
- Department of Life Sciences, School of Science and Engineering, Lahore University of Management Science, Lahore, Pakistan
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK
| | - Stephanie W. Lo
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK
- Milner Centre for Evolution, Department of Life Science, University of Bath, Bath, UK
| | - Muhammad Imran Nisar
- Departments of Pathology, Pediatrics, and Medicine, Aga Khan University, Karachi, Pakistan
| | - Asma Basharat
- Department of Life Sciences, School of Science and Engineering, Lahore University of Management Science, Lahore, Pakistan
| | - Hadiqa Jaleel
- Department of Life Sciences, School of Science and Engineering, Lahore University of Management Science, Lahore, Pakistan
| | - Karam Rasool
- Department of Microbiology, Chughtai Lab/Chughtai Institute of Pathology, Lahore, Pakistan
| | - Qamar Sultana
- Department of Microbiology, Chughtai Lab/Chughtai Institute of Pathology, Lahore, Pakistan
| | - Furqan Kabir
- Infectious Diseases Research Laboratory (IDRL), Dept. of Paediatrics & Child Health, Aga Khan University, Karachi, Pakistan
| | - Aneeta Hotwani
- Departments of Pathology, Pediatrics, and Medicine, Aga Khan University, Karachi, Pakistan
| | - Robert F. Breiman
- Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | | | - Sadia Shakoor
- Departments of Pathology, Pediatrics, and Medicine, Aga Khan University, Karachi, Pakistan
| | - Shaper Mirza
- Department of Life Sciences, School of Science and Engineering, Lahore University of Management Science, Lahore, Pakistan
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7
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Nowshin I, Akber EB, Kabir F, Ahmed M. Ship Breaking Workers and Their Pattern of Work-Related Respiratory Problems: A Cross-sectional Study at Sitakunda Ship Breaking Industrial Area of Bangladesh. Mymensingh Med J 2024; 33:146-153. [PMID: 38163786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
A cross-sectional study was conducted from March 2019 to August 2019 to determine the pattern of work-related respiratory problems among workers in ship breaking industry at Sitakunda, Chittagong, Bangladesh as many unskilled and semiskilled worker are working there without having minimum knowledge and idea about the possible adverse health effect of different pollutants which also pose threats to the ambient environment. Total 120 male respondents were selected purposively. Majority 80.8% (97) of the workers were below 30 years. About 71.0% (85) respondents were working for less than five years. Majority of respondents worked 8 hours daily. Most of them worked each of the days in a week. About 66.0% (80) had smoking habit. Among 120 respondents, 95.8% (115) had no previous respiratory problem. But 63.3% (76) felt that their respiratory problems were increasing day by day due to current job (ship breaking). There were 85.0% (102) respondents who felt cold or sneeze mostly in working place. About 80.0% (96) of respondents felt better during holiday. There were different respiratory symptoms among the respondents like nasal irritation, hoarseness of voice, cough during cold, cough without cold, bringing up phlegm when catch cold, bringing up phlegm without cold, tightness of chest where the prevalence was 54.2% (65), 85.0% (102), 93.3% (112), 28.3% (34), 70.0% (84), 39.0% (27) and 67.5% (81) respectively among the workers. Majority respondents 96.7% (116) were conscious about using PPE. Only 17.5% (21) used mask during work. Different pulmonary lung function test like forced vital capacity (FVC), forced expiratory volume in 1 second (FEV1), FEV1%, peak expiratory flow rate (PFER) was done. Mean of FVC, FEV1 was 3.76 and 1.09 respectively. According to pulmonary statuses of workers as per spirometric findings 20.83% (25) had normal pulmonary function, 58.33% (45) had obstruction and 20.83% (25) had combined obstructive parameters. So in light of the study it is clear that the work organization has not developed in this particular industry. In every steps of their work ship breaking workers are facing violations of industrial codes which correspond with safe working environment. In long run the workers have to pay with their health and life about which they are unaware.
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Affiliation(s)
- I Nowshin
- Dr Iffat Nowshin, Associate Professor, Department of Community Medicine, Shaheed Monsur Ali Medical College, Uttara, Dhaka, Bangladesh; E-mail:
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8
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Monangi NK, Xu H, Fan YM, Khanam R, Khan W, Deb S, Pervin J, Price JT, Kaur L, Al Mahmud A, Thanh LQ, Care A, Landero JA, Combs GF, Belling E, Chappell J, Chen J, Kong F, Lacher C, Ahmed S, Chowdhury NH, Rahman S, Kabir F, Nisar I, Hotwani A, Mehmood U, Nizar A, Khalid J, Dhingra U, Dutta A, Ali SM, Aftab F, Juma MH, Rahman M, Ahmed T, Islam MM, Vwalika B, Musonda P, Ashorn U, Maleta K, Hallman M, Goodfellow L, Gupta JK, Alfirevic A, Murphy SK, Rand L, Ryckman KK, Murray JC, Bahl R, Litch JA, Baruch-Gravett C, Sopory S, Chandra Mouli Natchu U, Kumar PV, Kumari N, Thiruvengadam R, Singh AK, Kumar P, Alfirevic Z, Baqui AH, Bhatnagar S, Hirst JE, Hoyo C, Jehan F, Jelliffe-Pawlowski L, Rahman A, Roth DE, Sazawal S, Stringer JSA, Ashorn P, Zhang G, Muglia LJ. Association of maternal prenatal copper concentration with gestational duration and preterm birth: a multicountry meta-analysis. Am J Clin Nutr 2024; 119:221-231. [PMID: 37890672 PMCID: PMC10808817 DOI: 10.1016/j.ajcnut.2023.10.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 09/29/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Copper (Cu), an essential trace mineral regulating multiple actions of inflammation and oxidative stress, has been implicated in risk for preterm birth (PTB). OBJECTIVES This study aimed to determine the association of maternal Cu concentration during pregnancy with PTB risk and gestational duration in a large multicohort study including diverse populations. METHODS Maternal plasma or serum samples of 10,449 singleton live births were obtained from 18 geographically diverse study cohorts. Maternal Cu concentrations were determined using inductively coupled plasma mass spectrometry. The associations of maternal Cu with PTB and gestational duration were analyzed using logistic and linear regressions for each cohort. The estimates were then combined using meta-analysis. Associations between maternal Cu and acute-phase reactants (APRs) and infection status were analyzed in 1239 samples from the Malawi cohort. RESULTS The maternal prenatal Cu concentration in our study samples followed normal distribution with mean of 1.92 μg/mL and standard deviation of 0.43 μg/mL, and Cu concentrations increased with gestational age up to 20 wk. The random-effect meta-analysis across 18 cohorts revealed that 1 μg/mL increase in maternal Cu concentration was associated with higher risk of PTB with odds ratio of 1.30 (95% confidence interval [CI]: 1.08, 1.57) and shorter gestational duration of 1.64 d (95% CI: 0.56, 2.73). In the Malawi cohort, higher maternal Cu concentration, concentrations of multiple APRs, and infections (malaria and HIV) were correlated and associated with greater risk of PTB and shorter gestational duration. CONCLUSIONS Our study supports robust negative association between maternal Cu and gestational duration and positive association with risk for PTB. Cu concentration was strongly correlated with APRs and infection status suggesting its potential role in inflammation, a pathway implicated in the mechanisms of PTB. Therefore, maternal Cu could be used as potential marker of integrated inflammatory pathways during pregnancy and risk for PTB.
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Affiliation(s)
- Nagendra K Monangi
- Division of Neonatology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States; Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center and March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati, Ohio, United States; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States.
| | - Huan Xu
- Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center and March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati, Ohio, United States; Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Yue-Mei Fan
- Center for Child, Adolescent and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.
| | - Rasheeda Khanam
- International Center for Maternal and Newborn Health, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States
| | - Waqasuddin Khan
- Biorepository and Omics Research Group, Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, Aga Khan University, Karachi, Sindh, Pakistan
| | - Saikat Deb
- Research Division, Public Health Laboratory, Center for Public Health Kinetics, Chake Chake, Tanzania
| | - Jesmin Pervin
- Maternal and Child Health Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka District, Bangladesh
| | - Joan T Price
- Obstetrics and Gynecology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States
| | - Lovejeet Kaur
- Child and Maternal Health Program, Translational Health Science and Technology Institute (THSTI), Faridabad, India
| | - Abdullah Al Mahmud
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka, Bangladesh
| | | | - Angharad Care
- Department of Women's and Children's Health, The University of Liverpool, Liverpool, United Kingdom
| | - Julio A Landero
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, United States
| | - Gerald F Combs
- Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA, United States
| | - Elizabeth Belling
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Joanne Chappell
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Jing Chen
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio.
| | - Fansheng Kong
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Craig Lacher
- USDA-ARS, Grand Forks Human Nutrition Research Center, Grand Forks, ND, United States
| | | | | | | | - Furqan Kabir
- Biorepository and Omics Research Group, Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, Aga Khan University, Karachi, Sindh, Pakistan
| | - Imran Nisar
- Biorepository and Omics Research Group, Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, Aga Khan University, Karachi, Sindh, Pakistan
| | - Aneeta Hotwani
- Biorepository and Omics Research Group, Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, Aga Khan University, Karachi, Sindh, Pakistan
| | - Usma Mehmood
- Biorepository and Omics Research Group, Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, Aga Khan University, Karachi, Sindh, Pakistan
| | - Ambreen Nizar
- Biorepository and Omics Research Group, Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, Aga Khan University, Karachi, Sindh, Pakistan
| | - Javairia Khalid
- Biorepository and Omics Research Group, Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, Aga Khan University, Karachi, Sindh, Pakistan
| | - Usha Dhingra
- Center for Public Health Kinetics, New Delhi, India
| | - Arup Dutta
- Center for Public Health Kinetics, New Delhi, India
| | - Said Mohamed Ali
- Research Division, Public Health Laboratory, Center for Public Health Kinetics, Chake Chake, Tanzania
| | - Fahad Aftab
- Research Division, Public Health Laboratory, Center for Public Health Kinetics, Chake Chake, Tanzania
| | - Mohammed Hamad Juma
- Research Division, Public Health Laboratory, Center for Public Health Kinetics, Chake Chake, Tanzania
| | - Monjur Rahman
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Tahmeed Ahmed
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - M Munirul Islam
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka, Bangladesh
| | | | - Patrick Musonda
- School of Public Health, University of Zambia, Lusaka, Zambia
| | - Ulla Ashorn
- Center for Child, Adolescent and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Kenneth Maleta
- School of Public Health and Family Medicine, University of Malawi College of Medicine, Blantyre, Malawi
| | - Mikko Hallman
- School of Public Health and Family Medicine, University of Malawi College of Medicine, Blantyre, Malawi; Medical Research Centre Oulu, PEDEGO Research Unit, University of Oulu, Oulu, Pohjois-Pohjanmaa, Finland
| | - Laura Goodfellow
- Department of Women's and Children's Health, The University of Liverpool, Liverpool, United Kingdom
| | - Juhi K Gupta
- Department of Women's and Children's Health, The University of Liverpool, Liverpool, United Kingdom
| | - Ana Alfirevic
- Department of Women's and Children's Health, The University of Liverpool, Liverpool, United Kingdom
| | - Susan K Murphy
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, United States
| | - Larry Rand
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Francisco School of Medicine, San Francisco, CA, United States
| | - Kelli K Ryckman
- Department of Epidemiology, University of Iowa College of Public Health, Iowa City, IA, United States
| | - Jeffrey C Murray
- Department of Pediatrics, University of Iowa, Iowa City, IA, United States
| | - Rajiv Bahl
- Department of Maternal, Newborn, Child and Adolescent Health, World Health Organization, Geneva, Switzerland
| | - James A Litch
- Global Alliance to Prevent Prematurity and Stillbirth, Lynnwood, WA, United States
| | | | - Shailaja Sopory
- Child and Maternal Health Program, Translational Health Science and Technology Institute (THSTI), Faridabad, India
| | | | - Pavitra V Kumar
- Geochronology Group, Inter University Accelerator Centre (IUAC), Delhi, India
| | - Neha Kumari
- Child and Maternal Health Program, Translational Health Science and Technology Institute (THSTI), Faridabad, India
| | - Ramachandran Thiruvengadam
- Child and Maternal Health Program, Translational Health Science and Technology Institute (THSTI), Faridabad, India
| | - Atul Kumar Singh
- Geochronology Group, Inter University Accelerator Centre (IUAC), Delhi, India
| | - Pankaj Kumar
- Geochronology Group, Inter University Accelerator Centre (IUAC), Delhi, India
| | - Zarko Alfirevic
- Department of Women's and Children's Health, The University of Liverpool, Liverpool, United Kingdom
| | - Abdullah H Baqui
- International Center for Maternal and Newborn Health, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States
| | - Shinjini Bhatnagar
- Child and Maternal Health Program, Translational Health Science and Technology Institute (THSTI), Faridabad, India
| | - Jane E Hirst
- Tu Du Hospital, Ho Chi Ming City, Vietnam; Nuffield Department of Women's & Reproductive Health, University of Oxford, Oxford, United Kingdom
| | - Cathrine Hoyo
- Department of Biological Sciences and Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina, United States
| | - Fyezah Jehan
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Laura Jelliffe-Pawlowski
- Department of Epidemiology and Biostatistics, University of California San Francisco School of Medicine, San Francisco, CA, United States
| | - Anisur Rahman
- Maternal and Child Health Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka District, Bangladesh
| | - Daniel E Roth
- Centre for Global Child Health, Hospital for Sick Children, University of Toronto, Toronto, Canada; Department of Pediatrics, University of Toronto, Toronto, Canada
| | - Sunil Sazawal
- Research Division, Public Health Laboratory, Center for Public Health Kinetics, Chake Chake, Tanzania; Center for Public Health Kinetics, New Delhi, India
| | - Jeffrey S A Stringer
- Obstetrics and Gynecology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States
| | - Per Ashorn
- Center for Child, Adolescent and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Department of Pediatrics, Tampere University Hospital, Tampere, Finland
| | - Ge Zhang
- Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center and March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati, Ohio, United States; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States; Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.
| | - Louis J Muglia
- Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center and March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati, Ohio, United States; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States; Burroughs Wellcome Fund, Research Triangle Park, NC, United States
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9
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Khan W, Kabir F, Kanwar S, Aziz F, Muneer S, Kalam A, Rajab Ali MN, Ansari N, Vanaerschot M, Ahyong V, Fahsbender L, Kalantar K, Black A, Glascock A, Gil J, Ayscue P, Tato C, Jehan F, Nisar I. Building up a genomic surveillance platform for SARS-CoV-2 in the middle of a pandemic: a true North-South collaboration. BMJ Glob Health 2023; 8:e012589. [PMID: 37984892 PMCID: PMC10660681 DOI: 10.1136/bmjgh-2023-012589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 09/09/2023] [Indexed: 11/22/2023] Open
Abstract
Next-generation sequencing technology has revolutionised pathogen surveillance over the last two decades. However, the benefits are not equitably distributed, with developing countries lagging far behind in acquiring the required technology and analytical capacity. Recent declines in the cost associated with sequencing-equipment and running consumables have created an opportunity for broader adoption. During the COVID-19 pandemic, rapid diagnostics development and DNA sequencing revolutionised the ability to diagnose and sequence SARS-CoV-2 rapidly. Socioeconomic inequalities substantially impact the ability to sequence SARS-CoV-2 strains and undermine a developing country's pandemic preparedness. Low- and middle-income countries face additional challenges in establishing, maintaining and expanding genomic surveillance. We present our experience of establishing a genomic surveillance system at the Aga Khan University, Karachi, Pakistan. Despite being at a leading health sciences research institute in the country, we encountered significant challenges. These were related to collecting standardised contextual data for SARS-CoV-2 samples, procuring sequencing reagents and consumables, and challenges with library preparation, sequencing and submission of high-quality SARS-CoV-2 genomes. Several technical roadblocks ensued during the implementation of the genomic surveillance framework, which were resolved in collaboration with our partners. High-quality genome sequences were then deposited on open-access platforms per the best practices. Subsequently, these efforts culminated in deploying Pakistan's first SARS-CoV-2 phyllo surveillance map as a Nextstrain build. Our experience offers lessons for the successful development of Genomic Surveillance Infrastructure in resource-limited settings struck by a pandemic.
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Affiliation(s)
- Waqasuddin Khan
- Pediatrics and Child Health, The Aga Khan University, Karachi, Sindh, Pakistan
- Biorepository and Omics Research Group, Medical College Pakistan, The Aga Khan University, Karachi, Sindh, Pakistan
| | - Furqan Kabir
- Pediatrics and Child Health, The Aga Khan University, Karachi, Sindh, Pakistan
- Biorepository and Omics Research Group, Medical College Pakistan, The Aga Khan University, Karachi, Sindh, Pakistan
| | - Samiah Kanwar
- Pediatrics and Child Health, The Aga Khan University, Karachi, Sindh, Pakistan
| | - Fatima Aziz
- Pediatrics and Child Health, The Aga Khan University, Karachi, Sindh, Pakistan
| | - Sahrish Muneer
- Pediatrics and Child Health, The Aga Khan University, Karachi, Sindh, Pakistan
| | - Adil Kalam
- Pediatrics and Child Health, The Aga Khan University, Karachi, Sindh, Pakistan
| | | | - Nadia Ansari
- Pediatrics and Child Health, The Aga Khan University, Karachi, Sindh, Pakistan
| | | | - Vida Ahyong
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Liz Fahsbender
- The Chan Zuckerberg Initiative, Palo Alto, California, USA
| | | | - Allison Black
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | | | - Juliana Gil
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | | | - Cristina Tato
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Fyezah Jehan
- Pediatrics and Child Health, The Aga Khan University, Karachi, Sindh, Pakistan
- Biorepository and Omics Research Group, Medical College Pakistan, The Aga Khan University, Karachi, Sindh, Pakistan
| | - Imran Nisar
- Pediatrics and Child Health, The Aga Khan University, Karachi, Sindh, Pakistan
- Biorepository and Omics Research Group, Medical College Pakistan, The Aga Khan University, Karachi, Sindh, Pakistan
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10
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Bukhari AR, Ashraf J, Kanji A, Rahman YA, Trovão NS, Thielen PM, Yameen M, Kanwar S, Khan W, Kabir F, Nisar MI, Merritt B, Hasan R, Spiro D, Rasmussen Z, Aamir UB, Hasan Z. Sequential viral introductions and spread of BA.1 across Pakistan provinces during the Omicron wave. BMC Genomics 2023; 24:432. [PMID: 37532989 PMCID: PMC10399012 DOI: 10.1186/s12864-023-09539-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 07/27/2023] [Indexed: 08/04/2023] Open
Abstract
BACKGROUND COVID-19 waves caused by specific SARS-CoV-2 variants have occurred globally at different times. We focused on Omicron variants to understand the genomic diversity and phylogenetic relatedness of SARS-CoV-2 strains in various regions of Pakistan. METHODS We studied 276,525 COVID-19 cases and 1,031 genomes sequenced from December 2021 to August 2022. Sequences were analyzed and visualized using phylogenetic trees. RESULTS The highest case numbers and deaths were recorded in Sindh and Punjab, the most populous provinces in Pakistan. Omicron variants comprised 93% of all genomes, with BA.2 (32.6%) and BA.5 (38.4%) predominating. The first Omicron wave was associated with the sequential identification of BA.1 in Sindh, then Islamabad Capital Territory, Punjab, Khyber Pakhtunkhwa (KP), Azad Jammu Kashmir (AJK), Gilgit-Baltistan (GB) and Balochistan. Phylogenetic analysis revealed Sindh to be the source of BA.1 and BA.2 introductions into Punjab and Balochistan during early 2022. BA.4 was first introduced in AJK and BA.5 in Punjab. Most recent common ancestor (MRCA) analysis revealed relatedness between the earliest BA.1 genome from Sindh with Balochistan, AJK, Punjab and ICT, and that of first BA.1 from Punjab with strains from KPK and GB. CONCLUSIONS Phylogenetic analysis provides insights into the introduction and transmission dynamics of the Omicron variant in Pakistan, identifying Sindh as a hotspot for viral dissemination. Such data linked with public health efforts can help limit surges of new infections.
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Affiliation(s)
- Ali Raza Bukhari
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, 74800, Pakistan
| | - Javaria Ashraf
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, 74800, Pakistan
| | - Akbar Kanji
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, 74800, Pakistan
| | - Yusra Abdul Rahman
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, 74800, Pakistan
| | - Nídia S Trovão
- Fogarty International Center, U.S. National Institutes of Health, 16 Center Drive, Bethesda, MD, 20892, USA
| | - Peter M Thielen
- Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, MD, 20723, USA
| | - Maliha Yameen
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, 74800, Pakistan
| | - Samiah Kanwar
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, 74800, Pakistan
| | - Waqasuddin Khan
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, 74800, Pakistan
| | - Furqan Kabir
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, 74800, Pakistan
| | - Muhammad Imran Nisar
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, 74800, Pakistan
| | - Brian Merritt
- Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, MD, 20723, USA
| | - Rumina Hasan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, 74800, Pakistan
| | - David Spiro
- Fogarty International Center, U.S. National Institutes of Health, 16 Center Drive, Bethesda, MD, 20892, USA
| | - Zeba Rasmussen
- Fogarty International Center, U.S. National Institutes of Health, 16 Center Drive, Bethesda, MD, 20892, USA
| | - Uzma Bashir Aamir
- World Health Organization Country Office, Park Road, Chak Shahzad, Islamabad, Pakistan
| | - Zahra Hasan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, 74800, Pakistan.
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11
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Espinosa CA, Khan W, Khanam R, Das S, Khalid J, Pervin J, Kasaro MP, Contrepois K, Chang AL, Phongpreecha T, Michael B, Ellenberger M, Mehmood U, Hotwani A, Nizar A, Kabir F, Wong RJ, Becker M, Berson E, Culos A, De Francesco D, Mataraso S, Ravindra N, Thuraiappah M, Xenochristou M, Stelzer IA, Marić I, Dutta A, Raqib R, Ahmed S, Rahman S, Hasan ASMT, Ali SM, Juma MH, Rahman M, Aktar S, Deb S, Price JT, Wise PH, Winn VD, Druzin ML, Gibbs RS, Darmstadt GL, Murray JC, Stringer JSA, Gaudilliere B, Snyder MP, Angst MS, Rahman A, Baqui AH, Jehan F, Nisar MI, Vwalika B, Sazawal S, Shaw GM, Stevenson DK, Aghaeepour N. Multiomic signals associated with maternal epidemiological factors contributing to preterm birth in low- and middle-income countries. Sci Adv 2023; 9:eade7692. [PMID: 37224249 DOI: 10.1126/sciadv.ade7692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 04/20/2023] [Indexed: 05/26/2023]
Abstract
Preterm birth (PTB) is the leading cause of death in children under five, yet comprehensive studies are hindered by its multiple complex etiologies. Epidemiological associations between PTB and maternal characteristics have been previously described. This work used multiomic profiling and multivariate modeling to investigate the biological signatures of these characteristics. Maternal covariates were collected during pregnancy from 13,841 pregnant women across five sites. Plasma samples from 231 participants were analyzed to generate proteomic, metabolomic, and lipidomic datasets. Machine learning models showed robust performance for the prediction of PTB (AUROC = 0.70), time-to-delivery (r = 0.65), maternal age (r = 0.59), gravidity (r = 0.56), and BMI (r = 0.81). Time-to-delivery biological correlates included fetal-associated proteins (e.g., ALPP, AFP, and PGF) and immune proteins (e.g., PD-L1, CCL28, and LIFR). Maternal age negatively correlated with collagen COL9A1, gravidity with endothelial NOS and inflammatory chemokine CXCL13, and BMI with leptin and structural protein FABP4. These results provide an integrated view of epidemiological factors associated with PTB and identify biological signatures of clinical covariates affecting this disease.
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Affiliation(s)
- Camilo A Espinosa
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Waqasuddin Khan
- Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Karachi, Pakistan
| | - Rasheda Khanam
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Sayan Das
- Centre for Public Health Kinetics, New Delhi, Delhi, India
| | - Javairia Khalid
- Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Karachi, Pakistan
| | - Jesmin Pervin
- Maternal and Child Health Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Margaret P Kasaro
- University of North Carolina Global Projects Zambia, Lusaka, Zambia
- Department of Obstetrics and Gynecology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Kévin Contrepois
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Alan L Chang
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Thanaphong Phongpreecha
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Basil Michael
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Mathew Ellenberger
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Usma Mehmood
- Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Karachi, Pakistan
| | - Aneeta Hotwani
- Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Karachi, Pakistan
| | - Ambreen Nizar
- Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Karachi, Pakistan
| | - Furqan Kabir
- Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Karachi, Pakistan
| | - Ronald J Wong
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Martin Becker
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Eloise Berson
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Anthony Culos
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
- Department of Computer Science, Columbia University, New York, NY, USA
| | - Davide De Francesco
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Samson Mataraso
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Neal Ravindra
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Melan Thuraiappah
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Maria Xenochristou
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Ina A Stelzer
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Ivana Marić
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Arup Dutta
- Centre for Public Health Kinetics, New Delhi, Delhi, India
| | - Rubhana Raqib
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | | | | | | | - Said M Ali
- Public Health Laboratory-Ivo de Carneri, Pemba, Zanzibar, Tanzania
| | - Mohamed H Juma
- Public Health Laboratory-Ivo de Carneri, Pemba, Zanzibar, Tanzania
| | - Monjur Rahman
- Maternal and Child Health Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Shaki Aktar
- Maternal and Child Health Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Saikat Deb
- Centre for Public Health Kinetics, New Delhi, Delhi, India
- Public Health Laboratory-Ivo de Carneri, Pemba, Zanzibar, Tanzania
| | - Joan T Price
- Department of Obstetrics and Gynecology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
- Department of Obstetrics and Gynaecology, University of Zambia School of Medicine, Lusaka, Zambia
| | - Paul H Wise
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Virginia D Winn
- Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, CA, USA
| | - Maurice L Druzin
- Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ronald S Gibbs
- Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, CA, USA
| | - Gary L Darmstadt
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Jeffrey C Murray
- Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | - Jeffrey S A Stringer
- Department of Obstetrics and Gynecology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Brice Gaudilliere
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Martin S Angst
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Anisur Rahman
- Maternal and Child Health Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Abdullah H Baqui
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Fyezah Jehan
- Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Karachi, Pakistan
| | - Muhammad Imran Nisar
- Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Karachi, Pakistan
| | - Bellington Vwalika
- Department of Obstetrics and Gynecology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
- Department of Obstetrics and Gynaecology, University of Zambia School of Medicine, Lusaka, Zambia
| | - Sunil Sazawal
- Centre for Public Health Kinetics, New Delhi, Delhi, India
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Gary M Shaw
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - David K Stevenson
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Nima Aghaeepour
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
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12
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Shahid S, Nisar MI, Jehan F, Ahmed S, Kabir F, Hotwani A, Muneer S, Qazi MF, Muhammad S, Ali A, Zaidi AK, Iqbal NT. Co-carriage of Staphylococcus aureus and Streptococcus pneumoniae among children younger than 2 years of age in a rural population in Pakistan. Clin Epidemiol Glob Health 2023; 21:None. [PMID: 37337613 PMCID: PMC10276771 DOI: 10.1016/j.cegh.2023.101293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 03/07/2023] [Accepted: 03/27/2023] [Indexed: 03/31/2023] Open
Abstract
Objectives Staphylococcus aureus and Streptococcus pneumoniae are common colonizers of the human nasopharynx. In this study, we describe S. aureus nasopharyngeal carriage and evaluate its association with S. pneumoniae carriage post-10-valent pneumococcal conjugate vaccine (PCV10) introduction in Pakistan. Methods A serial cross-sectional study was undertaken from 2014 to 2018, children <2 years were randomly selected, and nasopharyngeal swabs were collected using standard WHO guidelines. S. aureus and S. pneumoniae isolates were identified using standard methods and tested for antimicrobial susceptibility by the standard Kirby-Bauer disk-diffusion method as per Clinical & Laboratory Standards Institute (CLSI) recommendations. Regression analysis was used to determine predictors associated with S. aureus carriage. Results We enrolled 3140 children. S. aureus carriage prevalence was 5.6% (176/3140), and 50.1% (81/176) of the isolates were methicillin-resistant S. aureus (MRSA). S. aureus carriage was higher in the absence of pneumococcus compared to isolates in which pneumococcus was present (7.5% vs 5.0%). S. aureus carriage was negatively associated with pneumococcal carriage, being in 3rd and 4th year of enrollment, and vaccination with two and three PCV10 doses, in addition, fast breathing, ≥2 outpatients visits, and rainy season were positively associated. The following resistance rates were observed: 98.9% for penicillin, 74.4% for fusidic acid, and 23.3% for gentamicin, 10.2% for erythromycin, and 8.5% for cotrimoxazole. All isolates were susceptible to amikacin. Conclusions Overall S. aureus carriage prevalence was low, PCV10 vaccine was protective against the carriage. The proportion of MRSA carriage and antimicrobial resistance was high in this community warranting continuous monitoring for invasive infections.
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Affiliation(s)
- Shahira Shahid
- Department of Pediatric and Child Health, Aga Khan University, Karachi, Pakistan
| | - Muhammad Imran Nisar
- Department of Pediatric and Child Health, Aga Khan University, Karachi, Pakistan
| | - Fyezah Jehan
- Department of Pediatric and Child Health, Aga Khan University, Karachi, Pakistan
| | - Sheraz Ahmed
- Department of Pediatric and Child Health, Aga Khan University, Karachi, Pakistan
| | - Furqan Kabir
- Department of Pediatric and Child Health, Aga Khan University, Karachi, Pakistan
| | - Aneeta Hotwani
- Department of Pediatric and Child Health, Aga Khan University, Karachi, Pakistan
| | - Sahrish Muneer
- Department of Pediatric and Child Health, Aga Khan University, Karachi, Pakistan
| | | | - Sajid Muhammad
- Department of Pediatric and Child Health, Aga Khan University, Karachi, Pakistan
| | - Asad Ali
- Department of Pediatric and Child Health, Aga Khan University, Karachi, Pakistan
| | - Anita K.M. Zaidi
- Department of Pediatric and Child Health, Aga Khan University, Karachi, Pakistan
- Bill & Melinda Gates Foundation, Seattle, WA, USA
| | - Najeeha T. Iqbal
- Department of Pediatric and Child Health, Aga Khan University, Karachi, Pakistan
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13
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Ali K, Kabir F, Meyer E. Editorial: Biorisk management, laboratory acquired infections and clinical containment. Front Public Health 2023; 11:1127856. [PMID: 36733903 PMCID: PMC9887301 DOI: 10.3389/fpubh.2023.1127856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 01/02/2023] [Indexed: 01/18/2023] Open
Affiliation(s)
- Kashif Ali
- Department of Biosciences, Faculty of Life Sciences, Shaheed Zulfiqar Ali Bhutto Institute of Science and Technology, Karachi, Pakistan,*Correspondence: Kashif Ali ✉
| | - Furqan Kabir
- Infectious Diseases Research Laboratory (IDRL), Department of Paediatrics and Child Health, The Aga Khan University, Karachi, Pakistan,Furqan Kabir ✉
| | - Esmeralda Meyer
- Institutional Animal Care and Use Committee (IACUC), Research Compliance & Regulatory Affairs, Emory University, Atlanta, CO, United States
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14
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Kabir F, Iqbal J, Jamil Z, Iqbal NT, Mallawaarachchi I, Aziz F, Kalam A, Muneer S, Hotwani A, Ahmed S, Umrani F, Syed S, Sadiq K, Ma JZ, Moore SR, Ali A. Impact of enteropathogens on faltering growth in a resource-limited setting. Front Nutr 2023; 9:1081833. [PMID: 36704796 PMCID: PMC9871909 DOI: 10.3389/fnut.2022.1081833] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 12/08/2022] [Indexed: 01/12/2023] Open
Abstract
Introduction Environmental enteropathy is an important contributor to childhood malnutrition in the developing world. Chronic exposure to fecal pathogens leads to alteration in intestinal structure and function, resulting in impaired gut immune function, malabsorption, and growth faltering leading to environmental enteropathy. Methods A community-based intervention study was carried out on children till 24 months of age in Matiari district, Pakistan. Blood and fecal specimens were collected from the enrolled children aged 3-6 and 9 months. A real-time PCR-based TaqMan array card (TAC) was used to detect enteropathogens. Results Giardia, Campylobacter spp., enteroaggregative Escherichia coli (EAEC), Enteropathogenic Escherichia coli (EPEC), Enterotoxigenic Escherichia coli (ETEC), and Cryptosporidium spp. were the most prevailing enteropathogens in terms of overall positivity at both time points. Detection of protozoa at enrollment and 9 months was negatively correlated with rate of change in height-for-age Z (ΔHAZ) scores during the first and second years of life. A positive association was found between Giardia, fecal lipocalin (LCN), and alpha 1-Acid Glycoprotein (AGP), while Campylobacter spp. showed positive associations with neopterin (NEO) and myeloperoxidase (MPO). Conclusion Protozoal colonization is associated with a decline in linear growth velocity during the first 2 years of life in children living in Environmental enteric dysfunction (EED) endemic settings. Mechanistic studies exploring the role of cumulative microbial colonization, their adaptations to undernutrition, and their influence on gut homeostasis are required to understand symptomatic enteropathogen-induced growth faltering.
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Affiliation(s)
- Furqan Kabir
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Junaid Iqbal
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan,Department of Biological and Biomedical Sciences, The Aga Khan University, Karachi, Pakistan
| | - Zehra Jamil
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan,Department of Biological and Biomedical Sciences, The Aga Khan University, Karachi, Pakistan
| | - Najeeha Talat Iqbal
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan,Department of Biological and Biomedical Sciences, The Aga Khan University, Karachi, Pakistan
| | - Indika Mallawaarachchi
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, United States
| | - Fatima Aziz
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Adil Kalam
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Sahrish Muneer
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Aneeta Hotwani
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Sheraz Ahmed
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Fayaz Umrani
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Sana Syed
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan,Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Virginia, Charlottesville, VA, United States
| | - Kamran Sadiq
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Jennie Z. Ma
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, United States
| | - Sean R. Moore
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Virginia, Charlottesville, VA, United States,*Correspondence: Sean R. Moore,
| | - Asad Ali
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan,Asad Ali,
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15
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Contrepois K, Chen S, Ghaemi MS, Wong RJ, Jehan F, Sazawal S, Baqui AH, Stringer JSA, Rahman A, Nisar MI, Dhingra U, Khanam R, Ilyas M, Dutta A, Mehmood U, Deb S, Hotwani A, Ali SM, Rahman S, Nizar A, Ame SM, Muhammad S, Chauhan A, Khan W, Raqib R, Das S, Ahmed S, Hasan T, Khalid J, Juma MH, Chowdhury NH, Kabir F, Aftab F, Quaiyum A, Manu A, Yoshida S, Bahl R, Pervin J, Price JT, Rahman M, Kasaro MP, Litch JA, Musonda P, Vwalika B, Shaw G, Stevenson DK, Aghaeepour N, Snyder MP. Author Correction: Prediction of gestational age using urinary metabolites in term and preterm pregnancies. Sci Rep 2022; 12:19753. [PMID: 36396676 PMCID: PMC9671899 DOI: 10.1038/s41598-022-23715-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Kévin Contrepois
- grid.168010.e0000000419368956Department of Genetics, Stanford University School of Medicine, Stanford, CA USA ,grid.168010.e0000000419368956Stanford Cardiovascular Institute, Stanford University, Stanford, CA USA
| | - Songjie Chen
- grid.168010.e0000000419368956Department of Genetics, Stanford University School of Medicine, Stanford, CA USA
| | - Mohammad S. Ghaemi
- grid.168010.e0000000419368956Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA USA ,grid.24433.320000 0004 0449 7958Digital Technologies Research Centre, National Research Council Canada, Toronto, ON Canada
| | - Ronald J. Wong
- grid.168010.e0000000419368956Department of Pediatrics, Division of Neonatal and Developmental Medicine, Stanford University School of Medicine, Stanford, CA USA
| | - Fyezah Jehan
- grid.7147.50000 0001 0633 6224Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan ,grid.7147.50000 0001 0633 6224Biorepository and Omics Research Group, Faculty of Health Sciences, Medical College, Aga Khan University, Karachi, Pakistan
| | - Sunil Sazawal
- Center for Public Health Kinetics, New Delhi, India ,Public Health Laboratory IdC, Pemba, Zanzibar, Tanzania
| | - Abdullah H. Baqui
- grid.21107.350000 0001 2171 9311International Center for Maternal and Newborn Health, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA
| | - Jeffrey S. A. Stringer
- grid.10698.360000000122483208Department of Obstetrics and Gynecology, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Anisur Rahman
- grid.414142.60000 0004 0600 7174Maternal and Child Health Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Muhammad I. Nisar
- grid.7147.50000 0001 0633 6224Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan ,grid.7147.50000 0001 0633 6224Biorepository and Omics Research Group, Faculty of Health Sciences, Medical College, Aga Khan University, Karachi, Pakistan
| | - Usha Dhingra
- Center for Public Health Kinetics, New Delhi, India
| | - Rasheda Khanam
- grid.21107.350000 0001 2171 9311International Center for Maternal and Newborn Health, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA
| | - Muhammad Ilyas
- grid.7147.50000 0001 0633 6224Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Arup Dutta
- Center for Public Health Kinetics, New Delhi, India
| | - Usma Mehmood
- grid.7147.50000 0001 0633 6224Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Saikat Deb
- Center for Public Health Kinetics, New Delhi, India ,Public Health Laboratory IdC, Pemba, Zanzibar, Tanzania
| | - Aneeta Hotwani
- grid.7147.50000 0001 0633 6224Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Said M. Ali
- Public Health Laboratory IdC, Pemba, Zanzibar, Tanzania
| | - Sayedur Rahman
- Projahnmo Research Foundation, Abanti, Banani, Dhaka, Bangladesh
| | - Ambreen Nizar
- grid.7147.50000 0001 0633 6224Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Shaali M. Ame
- Public Health Laboratory IdC, Pemba, Zanzibar, Tanzania
| | - Sajid Muhammad
- grid.7147.50000 0001 0633 6224Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | | | - Waqasuddin Khan
- grid.7147.50000 0001 0633 6224Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan ,grid.7147.50000 0001 0633 6224Biorepository and Omics Research Group, Faculty of Health Sciences, Medical College, Aga Khan University, Karachi, Pakistan
| | - Rubhana Raqib
- International Center for Diarroheal Disease Research, Mohakhali, Dhaka, Bangladesh
| | - Sayan Das
- Center for Public Health Kinetics, New Delhi, India
| | - Salahuddin Ahmed
- Projahnmo Research Foundation, Abanti, Banani, Dhaka, Bangladesh
| | - Tarik Hasan
- Projahnmo Research Foundation, Abanti, Banani, Dhaka, Bangladesh
| | - Javairia Khalid
- grid.7147.50000 0001 0633 6224Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan ,grid.7147.50000 0001 0633 6224Biorepository and Omics Research Group, Faculty of Health Sciences, Medical College, Aga Khan University, Karachi, Pakistan
| | | | | | - Furqan Kabir
- grid.7147.50000 0001 0633 6224Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Fahad Aftab
- Center for Public Health Kinetics, New Delhi, India
| | - Abdul Quaiyum
- International Center for Diarroheal Disease Research, Mohakhali, Dhaka, Bangladesh
| | - Alexander Manu
- grid.3575.40000000121633745Maternal, Newborn, Child and Adolescent Health Research, World Health Organization, Geneva, Switzerland
| | - Sachiyo Yoshida
- grid.3575.40000000121633745Maternal, Newborn, Child and Adolescent Health Research, World Health Organization, Geneva, Switzerland
| | - Rajiv Bahl
- grid.3575.40000000121633745Maternal, Newborn, Child and Adolescent Health Research, World Health Organization, Geneva, Switzerland
| | - Jesmin Pervin
- grid.414142.60000 0004 0600 7174Maternal and Child Health Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Joan T. Price
- grid.10698.360000000122483208Department of Obstetrics and Gynecology, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Monjur Rahman
- grid.414142.60000 0004 0600 7174Maternal and Child Health Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | | | - James A. Litch
- grid.507550.20000 0004 8512 7499Global Alliance to Prevent Prematurity and Stillbirth, Seattle, USA
| | - Patrick Musonda
- grid.12984.360000 0000 8914 5257Department of Biostatistics, University of Zambia, Lusaka, Zambia
| | - Bellington Vwalika
- grid.12984.360000 0000 8914 5257Department of Obstetrics and Gynecology, University of Zambia School of Medicine, Lusaka, Zambia
| | - Gary Shaw
- grid.168010.e0000000419368956Department of Pediatrics, Division of Neonatal and Developmental Medicine, Stanford University School of Medicine, Stanford, CA USA
| | - David K. Stevenson
- grid.168010.e0000000419368956Department of Pediatrics, Division of Neonatal and Developmental Medicine, Stanford University School of Medicine, Stanford, CA USA
| | - Nima Aghaeepour
- grid.168010.e0000000419368956Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA USA
| | - Michael P. Snyder
- grid.168010.e0000000419368956Department of Genetics, Stanford University School of Medicine, Stanford, CA USA ,grid.168010.e0000000419368956Stanford Cardiovascular Institute, Stanford University, Stanford, CA USA
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16
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Shahid S, Khan A, Nisar MI, Khalid F, Qazi MF, Ahmed S, Kabir F, Hotwani A, Muneer S, Ali SA, Whitney CG, Zaidi AKM, Jehan F. Pneumococcal Carriage in Infants Post-PCV10 Introduction in Pakistan: Results from Serial Cross-Sectional Surveys. Vaccines (Basel) 2022; 10:vaccines10060971. [PMID: 35746579 PMCID: PMC9230137 DOI: 10.3390/vaccines10060971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/30/2022] [Accepted: 06/02/2022] [Indexed: 11/16/2022] Open
Abstract
The 10-valent pneumococcal vaccine was introduced in Pakistan’s Expanded Program on Immunization (EPI) in 2013 as a 3 + 0 schedule without catchup. We conducted three annual cross-sectional surveys from 2014−2016 to measure vaccine-type (VT) carriage in infants from a rural part of Pakistan. Nasopharyngeal specimens were collected by random sampling of infants from two union councils of Matiari. Samples were then transported to the Infectious Disease Research Laboratory (IDRL) at the Aga Khan University within 6−8 h of collection. Serotypes were established using sequential multiplex PCR. Of the 665 children enrolled across three surveys, 547 were culture-positive for pneumococcus. VT carriage decreased from 21.8% in 2014 to 12.7% in 2016 (p-value for trend <0.001). Those who were not vaccinated or partially vaccinated were found to be at higher risk of carrying a VT serotype ((aOR 2.53, 95% CI 1.39, 4.63 for non-vaccinated) and (aOR 3.35, 95% CI 1.82, 6.16 for partially vaccinated)). On the other hand, being enrolled in the most recent survey was negatively associated with VT carriage (aOR 0.51, 95% CI 0.28, 0.93). We found that PCV10 was effective in decreasing the carriage of vaccine-type serotypes in Pakistani infants.
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Affiliation(s)
- Shahira Shahid
- Department of Pediatric and Child Health, Aga Khan University, Karachi 74800, Pakistan; (S.S.); (A.K.); (F.K.); (M.F.Q.); (S.A.); (F.K.); (A.H.); (S.M.); (S.A.A.); (A.K.M.Z.); (F.J.)
| | - Amala Khan
- Department of Pediatric and Child Health, Aga Khan University, Karachi 74800, Pakistan; (S.S.); (A.K.); (F.K.); (M.F.Q.); (S.A.); (F.K.); (A.H.); (S.M.); (S.A.A.); (A.K.M.Z.); (F.J.)
| | - Muhammad Imran Nisar
- Department of Pediatric and Child Health, Aga Khan University, Karachi 74800, Pakistan; (S.S.); (A.K.); (F.K.); (M.F.Q.); (S.A.); (F.K.); (A.H.); (S.M.); (S.A.A.); (A.K.M.Z.); (F.J.)
- Correspondence: ; Tel.: +92-333-217-7911
| | - Farah Khalid
- Department of Pediatric and Child Health, Aga Khan University, Karachi 74800, Pakistan; (S.S.); (A.K.); (F.K.); (M.F.Q.); (S.A.); (F.K.); (A.H.); (S.M.); (S.A.A.); (A.K.M.Z.); (F.J.)
| | - Muhammad Farrukh Qazi
- Department of Pediatric and Child Health, Aga Khan University, Karachi 74800, Pakistan; (S.S.); (A.K.); (F.K.); (M.F.Q.); (S.A.); (F.K.); (A.H.); (S.M.); (S.A.A.); (A.K.M.Z.); (F.J.)
| | - Sheraz Ahmed
- Department of Pediatric and Child Health, Aga Khan University, Karachi 74800, Pakistan; (S.S.); (A.K.); (F.K.); (M.F.Q.); (S.A.); (F.K.); (A.H.); (S.M.); (S.A.A.); (A.K.M.Z.); (F.J.)
| | - Furqan Kabir
- Department of Pediatric and Child Health, Aga Khan University, Karachi 74800, Pakistan; (S.S.); (A.K.); (F.K.); (M.F.Q.); (S.A.); (F.K.); (A.H.); (S.M.); (S.A.A.); (A.K.M.Z.); (F.J.)
| | - Aneeta Hotwani
- Department of Pediatric and Child Health, Aga Khan University, Karachi 74800, Pakistan; (S.S.); (A.K.); (F.K.); (M.F.Q.); (S.A.); (F.K.); (A.H.); (S.M.); (S.A.A.); (A.K.M.Z.); (F.J.)
| | - Sahrish Muneer
- Department of Pediatric and Child Health, Aga Khan University, Karachi 74800, Pakistan; (S.S.); (A.K.); (F.K.); (M.F.Q.); (S.A.); (F.K.); (A.H.); (S.M.); (S.A.A.); (A.K.M.Z.); (F.J.)
| | - Syed Asad Ali
- Department of Pediatric and Child Health, Aga Khan University, Karachi 74800, Pakistan; (S.S.); (A.K.); (F.K.); (M.F.Q.); (S.A.); (F.K.); (A.H.); (S.M.); (S.A.A.); (A.K.M.Z.); (F.J.)
| | | | - Anita K. M. Zaidi
- Department of Pediatric and Child Health, Aga Khan University, Karachi 74800, Pakistan; (S.S.); (A.K.); (F.K.); (M.F.Q.); (S.A.); (F.K.); (A.H.); (S.M.); (S.A.A.); (A.K.M.Z.); (F.J.)
- Bill & Melinda Gates Foundation, Seattle, WA 98102, USA
| | - Fyezah Jehan
- Department of Pediatric and Child Health, Aga Khan University, Karachi 74800, Pakistan; (S.S.); (A.K.); (F.K.); (M.F.Q.); (S.A.); (F.K.); (A.H.); (S.M.); (S.A.A.); (A.K.M.Z.); (F.J.)
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17
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Contrepois K, Chen S, Ghaemi MS, Wong RJ, Jehan F, Sazawal S, Baqui AH, Nisar MI, Dhingra U, Khanam R, Ilyas M, Dutta A, Mehmood U, Deb S, Hotwani A, Ali SM, Rahman S, Nizar A, Ame SM, Muhammad S, Chauhan A, Khan W, Raqib R, Das S, Ahmed S, Hasan T, Khalid J, Juma MH, Chowdhury NH, Kabir F, Aftab F, Quaiyum MA, Manu A, Yoshida S, Bahl R, Rahman A, Pervin J, Price JT, Rahman M, Kasaro MP, Litch JA, Musonda P, Vwalika B, Stringer JSA, Shaw G, Stevenson DK, Aghaeepour N, Snyder MP. Prediction of gestational age using urinary metabolites in term and preterm pregnancies. Sci Rep 2022; 12:8033. [PMID: 35577875 PMCID: PMC9110694 DOI: 10.1038/s41598-022-11866-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 04/25/2022] [Indexed: 11/23/2022] Open
Abstract
Assessment of gestational age (GA) is key to provide optimal care during pregnancy. However, its accurate determination remains challenging in low- and middle-income countries, where access to obstetric ultrasound is limited. Hence, there is an urgent need to develop clinical approaches that allow accurate and inexpensive estimations of GA. We investigated the ability of urinary metabolites to predict GA at time of collection in a diverse multi-site cohort of healthy and pathological pregnancies (n = 99) using a broad-spectrum liquid chromatography coupled with mass spectrometry (LC–MS) platform. Our approach detected a myriad of steroid hormones and their derivatives including estrogens, progesterones, corticosteroids, and androgens which were associated with pregnancy progression. We developed a restricted model that predicted GA with high accuracy using three metabolites (rho = 0.87, RMSE = 1.58 weeks) that was validated in an independent cohort (n = 20). The predictions were more robust in pregnancies that went to term in comparison to pregnancies that ended prematurely. Overall, we demonstrated the feasibility of implementing urine metabolomics analysis in large-scale multi-site studies and report a predictive model of GA with a potential clinical value.
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Abtahi S, Sailer A, Sadiq K, Iqbal N, Ahmed K, Kabir F, Ali SA, Turner JR. Abnormal transporter and tight junction protein expression in environmental enteric dysfunction. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.r5615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Shabnam Abtahi
- PathologyBrigham and women's Hospital, Harvard Medical SchoolBostonMA
| | | | - Kamran Sadiq
- Department of Paediatrics and Child HealthAga Khan UniversityKarachi
| | - Najeeha Iqbal
- Department of Paediatrics and Child HealthAga Khan UniversityKarachi
| | - Kumail Ahmed
- Department of Paediatrics and Child HealthAga Khan UniversityKarachi
| | - Furqan Kabir
- Department of Paediatrics and Child HealthAga Khan UniversityKarachi
| | - S A. Ali
- Department of Paediatrics and Child HealthAga Khan UniversityKarachi
| | - Jerrold R. Turner
- PathologyUniversity of ChicagoChicagoIL
- Brigham and Women's Hospital, Harvard Medical SchoolBostonMA
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19
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Nisar MI, Jehan F, Shahid S, Ahmed S, Shakoor S, Kabir F, Hotwani A, Muneer S, Khalid F, Muhammad S, Althouse BM, Hu H, Whitney CG, Ali A, Zaidi AKM, Omer SB, Iqbal N. Serotype-specific effectiveness against pneumococcal carriage and serotype replacement after ten-valent Pneumococcal Conjugate Vaccine (PCV10) introduction in Pakistan. PLoS One 2022; 17:e0262466. [PMID: 35061793 PMCID: PMC8782386 DOI: 10.1371/journal.pone.0262466] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 12/23/2021] [Indexed: 11/19/2022] Open
Abstract
Objective
Pakistan was one of the first South-Asian countries to introduce the ten-valent pneumococcal conjugate vaccine (PCV10) at the national level, using a 3+0 schedule without catchup, in 2013.
Methods
From 2014–18, fifteen children <2 years old were recruited every week in Matiari, Sindh, and nasopharyngeal swabs were collected. The samples were cultured, and pneumococcus was further serotyped through multiplex PCR at the Aga Khan University Hospital as per the method described by the Centers for Disease Control and Prevention, USA.
Results
Pneumococcus was detected in 2370/3140 (75%) children. Vaccine type (VT) and non-vaccine type (NVT) serotypes were carried by 379 and 1990 children. There was a significant decline in VT carriage (by 40.3%, p-value <0.001), whereas overall NVT carriage remained the same. The prevalence of VT serotypes 6B, 9V/9A, and 19F showed a significant decline by 58.8%, 79.3%, and 56%, respectively. The prevalence of NVT serotypes 19A, 21, and 10A increased by 70%, 33.3%, and 65.6%, respectively, whereas serotypes 13 and 9N/9L decreased by 53.4% and 51.8%, respectively. Serotype-specific vaccine effectiveness estimates that reached statistical significance were for 9V/9A (VE = 65.0, 95% CI 26.0–83.5%), 19F (VE = 55.3, 95% CI 15.5–76.4%) and for the vaccine related serotype 6A (VE = 28.4, 95% CI 0.9–48.2%).
Conclusion
The emergence of NVT serotypes, primarily 19A replacing VT serotypes in this rural community, necessitates continuous monitoring of serotypes in the carriage and invasive disease to evaluate the utility of existing vaccine formulations.
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Affiliation(s)
- Muhammad Imran Nisar
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
- * E-mail:
| | - Fyezah Jehan
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Shahira Shahid
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Sheraz Ahmed
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Sadia Shakoor
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Furqan Kabir
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Aneeta Hotwani
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Sahrish Muneer
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Farah Khalid
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Sajid Muhammad
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | | | - Hao Hu
- Bill & Melinda Gates Foundation, Seattle, WA, United States of America
| | | | - Asad Ali
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Anita K. M. Zaidi
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
- Bill & Melinda Gates Foundation, Seattle, WA, United States of America
| | - Saad B. Omer
- Yale Institute for Global Health, New Haven, CT, United States of America
| | - Najeeha Iqbal
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
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20
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Colston JM, Taniuchi M, Ahmed T, Ferdousi T, Kabir F, Mduma E, Nshama R, Iqbal NT, Haque R, Ahmed T, Ali Bhutta Z, Kosek MN, Platts-Mills JA. Intestinal Colonization With Bifidobacterium longum Subspecies Is Associated With Length at Birth, Exclusive Breastfeeding, and Decreased Risk of Enteric Virus Infections, but Not With Histo-Blood Group Antigens, Oral Vaccine Response or Later Growth in Three Birth Cohorts. Front Pediatr 2022; 10:804798. [PMID: 35252058 PMCID: PMC8888871 DOI: 10.3389/fped.2022.804798] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 01/13/2022] [Indexed: 11/30/2022] Open
Abstract
Bifidobacterium longum subspecies detected in infant stool have been associated with numerous subsequent health outcomes and are potential early markers of deviation from healthy developmental trajectories. This analysis derived indicators of carriage and early colonization with B. infantis and B. longum and quantified their associations with a panel of early-life exposures and outcomes. In a sub-study nested within a multi-site birth cohort, extant stool samples from infants in Bangladesh, Pakistan and Tanzania were tested for presence and quantity of two Bifidobacterium longum subspecies. The results were matched to indicators of nutritional status, enteropathogen infection, histo-blood group antigens, vaccine response and feeding status and regression models were fitted to test for associations while adjusting for covariates. B. infantis was associated with lower quantity of and decreased odds of colonization with B. longum, and vice versa. Length at birth was associated with a 0.36 increase in log10 B. infantis and a 0.28 decrease in B. longum quantity at 1 month of age. B. infantis colonization was associated with fewer viral infections and small reductions in the risk of rotavirus and sapovirus infections, but not reduced overall diarrheal disease risk. No associations with vaccine responses, HBGAs or later nutritional status were identified. Suboptimal intrauterine growth and a shorter duration of exclusive breastfeeding may predispose infants to early intestinal colonization with the B. longum subspecies at the expense of B. infantis, thus denying them potential benefits of reduced enteric virus episodes.
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Affiliation(s)
- Josh M Colston
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, United States
| | - Mami Taniuchi
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, United States
| | - Tahmina Ahmed
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, United States
| | - Tania Ferdousi
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Furqan Kabir
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Estomih Mduma
- Haydom Global Health Research Centre, Haydom, Tanzania
| | | | - Najeeha Talat Iqbal
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Rashidul Haque
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Zulfiqar Ali Bhutta
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Margaret N Kosek
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, United States.,Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, United States
| | - James A Platts-Mills
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, United States
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21
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Ahmed T, Chisti MJ, Rahman MW, Alam T, Ahmed D, Parvin I, Kabir MF, Sazawal S, Dhingra P, Dutta A, Deb S, Chouhan A, Sharma AK, Jaiswal VK, Dhingra U, Walson JL, Singa BO, Pavlinac PB, McGrath CJ, Nyabinda C, Deichsel EL, Anyango M, Kariuki KM, Rwigi D, Tornberg-Belanger SN, Kotloff KL, Sow SO, Tapia MD, Haidara FC, Mehta A, Coulibaly F, Badji H, Permala-Booth J, Tennant SM, Malle D, Bar-Zeev N, Dube Q, Freyne B, Cunliffe N, Ndeketa L, Witte D, Ndamala C, Cornick J, Qamar FN, Yousafzai MT, Qureshi S, Shakoor S, Thobani R, Hotwani A, Kabir F, Mohammed J, Manji K, Duggan CP, Kisenge R, Sudfeld CR, Kibwana U, Somji S, Bakari M, Msemwa C, Samma A, Bahl R, De Costa A, Simon J, Ashorn P. Effect of 3 Days of Oral Azithromycin on Young Children With Acute Diarrhea in Low-Resource Settings: A Randomized Clinical Trial. JAMA Netw Open 2021; 4:e2136726. [PMID: 34913980 PMCID: PMC8678692 DOI: 10.1001/jamanetworkopen.2021.36726] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 09/21/2021] [Indexed: 12/25/2022] Open
Abstract
Importance World Health Organization (WHO) guidelines do not recommend routine antibiotic use for children with acute watery diarrhea. However, recent studies suggest that a significant proportion of such episodes have a bacterial cause and are associated with mortality and growth impairment, especially among children at high risk of diarrhea-associated mortality. Expanding antibiotic use among dehydrated or undernourished children may reduce diarrhea-associated mortality and improve growth. Objective To determine whether the addition of azithromycin to standard case management of acute nonbloody watery diarrhea for children aged 2 to 23 months who are dehydrated or undernourished could reduce mortality and improve linear growth. Design, Setting, and Participants The Antibiotics for Children with Diarrhea (ABCD) trial was a multicountry, randomized, double-blind, clinical trial among 8266 high-risk children aged 2 to 23 months presenting with acute nonbloody diarrhea. Participants were recruited between July 1, 2017, and July 10, 2019, from 36 outpatient hospital departments or community health centers in a mixture of urban and rural settings in Bangladesh, India, Kenya, Malawi, Mali, Pakistan, and Tanzania. Each participant was followed up for 180 days. Primary analysis included all randomized participants by intention to treat. Interventions Enrolled children were randomly assigned to receive either oral azithromycin, 10 mg/kg, or placebo once daily for 3 days in addition to standard WHO case management protocols for the management of acute watery diarrhea. Main Outcomes and Measures Primary outcomes included all-cause mortality up to 180 days after enrollment and linear growth faltering 90 days after enrollment. Results A total of 8266 children (4463 boys [54.0%]; mean [SD] age, 11.6 [5.3] months) were randomized. A total of 20 of 4133 children in the azithromycin group (0.5%) and 28 of 4135 children in the placebo group (0.7%) died (relative risk, 0.72; 95% CI, 0.40-1.27). The mean (SD) change in length-for-age z scores 90 days after enrollment was -0.16 (0.59) in the azithromycin group and -0.19 (0.60) in the placebo group (risk difference, 0.03; 95% CI, 0.01-0.06). Overall mortality was much lower than anticipated, and the trial was stopped for futility at the prespecified interim analysis. Conclusions and Relevance The study did not detect a survival benefit for children from the addition of azithromycin to standard WHO case management of acute watery diarrhea in low-resource settings. There was a small reduction in linear growth faltering in the azithromycin group, although the magnitude of this effect was not likely to be clinically significant. In low-resource settings, expansion of antibiotic use is not warranted. Adherence to current WHO case management protocols for watery diarrhea remains appropriate and should be encouraged. Trial Registration ClinicalTrials.gov Identifier: NCT03130114.
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Affiliation(s)
- Tahmeed Ahmed
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Mohammod Jobayer Chisti
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Muhammad Waliur Rahman
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Tahmina Alam
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Dilruba Ahmed
- Laboratory Sciences and Services Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Irin Parvin
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Md Farhad Kabir
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Sunil Sazawal
- Center for Public Health Kinetics, New Delhi, Delhi, India
| | | | - Arup Dutta
- Center for Public Health Kinetics, New Delhi, Delhi, India
| | - Saikat Deb
- Center for Public Health Kinetics, New Delhi, Delhi, India
| | | | | | | | - Usha Dhingra
- Center for Public Health Kinetics, New Delhi, Delhi, India
| | - Judd L Walson
- Childhood Acute Illness and Nutrition Network, Nairobi, Kenya
- Department of Global Health, University of Washington, Seattle
- Department of Pediatrics, University of Washington, Seattle
- Department of Medicine (Allergy and Infectious Diseases), University of Washington, Seattle
| | - Benson O Singa
- Childhood Acute Illness and Nutrition Network, Nairobi, Kenya
- Kenya Medical Research Institute, Nairobi, Kenya
| | | | | | | | - Emily L Deichsel
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore
| | | | | | - Doreen Rwigi
- Kenya Medical Research Institute, Nairobi, Kenya
| | | | - Karen L Kotloff
- Department of Pediatrics, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore
- Department of Medicine, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore
| | - Samba O Sow
- Centre pour le Développement des Vaccins, Bamako, Mali
| | - Milagritos D Tapia
- Department of Pediatrics, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore
- Department of Medicine, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore
| | - Fadima Cheick Haidara
- Division of Advanced Primary Health Care Research and Clinical Trials, Centre pour le Développement des Vaccins, Bamako, Mali
| | - Ashka Mehta
- Department of Pediatrics, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore
- Department of Medicine, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore
| | - Flanon Coulibaly
- Division of Advanced Primary Health Care Research and Clinical Trials, Centre pour le Développement des Vaccins, Bamako, Mali
| | - Henry Badji
- Division of Clinical Microbiology and Molecular Biology, Centre pour le Développement des Vaccins, Bamako, Mali
| | - Jasnehta Permala-Booth
- Department of Medicine, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore
| | - Sharon M Tennant
- Department of Medicine, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore
| | - Dramane Malle
- Division of Clinical Microbiology and Molecular Biology, Centre pour le Développement des Vaccins, Bamako, Mali
| | - Naor Bar-Zeev
- International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Queen Dube
- Department of Pediatrics, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Bridget Freyne
- Malawi Liverpool Wellcome Trust Clinical Research Programme, Institute of Infection, Veterinary and Ecological Sciences, The University of Liverpool, Blantyre, Malawi
| | - Nigel Cunliffe
- National Institutes of Health Research Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, United Kingdom
| | - Latif Ndeketa
- Malawi Liverpool Wellcome Trust Clinical Research Programme, Liverpool School of Tropical Medicine, Blantyre, Malawi
| | - Desiree Witte
- Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Chifundo Ndamala
- Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Jennifer Cornick
- Malawi Liverpool Wellcome Trust Clinical Research Programme, Institute of Infection, Veterinary and Ecological Sciences, The University of Liverpool, Blantyre, Malawi
| | - Farah Naz Qamar
- Department of Pediatrics and Child Heath, Aga Khan University, Karachi, Pakistan
| | | | - Shahida Qureshi
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Sadia Shakoor
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Rozina Thobani
- Department of Pediatrics and Child Heath, Aga Khan University, Karachi, Pakistan
| | - Aneeta Hotwani
- Department of Pediatrics and Child Heath, Aga Khan University, Karachi, Pakistan
| | - Furqan Kabir
- Department of Pediatrics and Child Heath, Aga Khan University, Karachi, Pakistan
| | - Jan Mohammed
- Department of Pediatrics and Child Heath, Aga Khan University, Karachi, Pakistan
| | - Karim Manji
- Department of Pediatrics and Child Health, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Christopher P Duggan
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Rodrick Kisenge
- Department of Pediatrics and Child Health, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Christopher R Sudfeld
- Department of Global Health and Population, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Upendo Kibwana
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Sarah Somji
- Department of Pediatrics and Child Health, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Mohamed Bakari
- Department of Pediatrics and Child Health, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Cecylia Msemwa
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Abraham Samma
- Department of Global Health and Population, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Rajiv Bahl
- Department of Maternal, Child, and Adolescent Health and Aging, World Health Organization, Geneva, Switzerland
| | - Ayesha De Costa
- Department of Maternal, Child, and Adolescent Health and Aging, World Health Organization, Geneva, Switzerland
| | - Jonathon Simon
- Department of Maternal, Child, and Adolescent Health and Aging, World Health Organization, Geneva, Switzerland
| | - Per Ashorn
- Department of Maternal, Child, and Adolescent Health and Aging, World Health Organization, Geneva, Switzerland
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22
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Kabir F, Liu Z, Anderson J, Crossman D, Sasaki S, Huang L, Guo S, Guimbellot J, Rowe S, Harris W. 602: Antisense oligonucleotide target site blockade of miR-145 binding selectively enhances CFTR correction in airway epithelial cells and nasal organoids. J Cyst Fibros 2021. [DOI: 10.1016/s1569-1993(21)02025-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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23
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Monangi N, Xu H, Khanam R, Khan W, Deb S, Pervin J, Price JT, Kennedy SH, Al Mahmud A, Fan Y, Le TQ, Care A, Landero JA, Combs GF, Belling E, Chappell J, Kong F, Lacher C, Ahmed S, Chowdhury NH, Rahman S, Kabir F, Nisar I, Hotwani A, Mehmood U, Nizar A, Khalid J, Dhingra U, Dutta A, Ali S, Aftab F, Juma MH, Rahman M, Vwalika B, Musonda P, Ahmed T, Islam MM, Ashorn U, Maleta K, Hallman M, Goodfellow L, Gupta JK, Alfirevic A, Murphy S, Rand L, Ryckman KK, Murray JC, Bahl R, Litch JA, Baruch-Gravett C, Alfirevic Z, Ashorn P, Baqui A, Hirst J, Hoyo C, Jehan F, Jelliffe-Pawlowski LL, Rahman A, Roth DE, Sazawal S, Stringer J, Zhang G, Muglia L. Association of maternal prenatal selenium concentration and preterm birth: a multicountry meta-analysis. BMJ Glob Health 2021; 6:bmjgh-2021-005856. [PMID: 34518202 PMCID: PMC8438754 DOI: 10.1136/bmjgh-2021-005856] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 08/04/2021] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Selenium (Se), an essential trace mineral, has been implicated in preterm birth (PTB). We aimed to determine the association of maternal Se concentrations during pregnancy with PTB risk and gestational duration in a large number of samples collected from diverse populations. METHODS Gestational duration data and maternal plasma or serum samples of 9946 singleton live births were obtained from 17 geographically diverse study cohorts. Maternal Se concentrations were determined by inductively coupled plasma mass spectrometry analysis. The associations between maternal Se with PTB and gestational duration were analysed using logistic and linear regressions. The results were then combined using fixed-effect and random-effect meta-analysis. FINDINGS In all study samples, the Se concentrations followed a normal distribution with a mean of 93.8 ng/mL (SD: 28.5 ng/mL) but varied substantially across different sites. The fixed-effect meta-analysis across the 17 cohorts showed that Se was significantly associated with PTB and gestational duration with effect size estimates of an OR=0.95 (95% CI: 0.9 to 1.00) for PTB and 0.66 days (95% CI: 0.38 to 0.94) longer gestation per 15 ng/mL increase in Se concentration. However, there was a substantial heterogeneity among study cohorts and the random-effect meta-analysis did not achieve statistical significance. The largest effect sizes were observed in UK (Liverpool) cohort, and most significant associations were observed in samples from Malawi. INTERPRETATION While our study observed statistically significant associations between maternal Se concentration and PTB at some sites, this did not generalise across the entire cohort. Whether population-specific factors explain the heterogeneity of our findings warrants further investigation. Further evidence is needed to understand the biologic pathways, clinical efficacy and safety, before changes to antenatal nutritional recommendations for Se supplementation are considered.
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Affiliation(s)
- Nagendra Monangi
- Division of Neonatology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center and March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Huan Xu
- Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center and March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati, Ohio, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Rasheda Khanam
- International Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Waqasuddin Khan
- Biorepository and Omics Research Group, Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Karachi, Sindh, Pakistan
| | - Saikat Deb
- Center for Public Health Kinetics, New Delhi, India
- Research Division, Public Health Laboratory, Center for Public Health Kinetics, Chake Chake, Tanzania
| | - Jesmin Pervin
- Maternal and Child Health Division, International Centre for Diarrhoeal Disease Research Bangladesh, Dhaka, Dhaka District, Bangladesh
| | - Joan T Price
- Obstetrics and Gynecology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Stephen H Kennedy
- INTERBIO-21st Study Consortium, Nuffield Department of Women's & Reproductive Health, University of Oxford, Oxford, UK
| | - Abdullah Al Mahmud
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research Bangladesh, Dhaka, Dhaka District, Bangladesh
| | - Yuemei Fan
- Center for Child Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Pirkanmaa, Finland
| | - Thanh Q Le
- Benh Vien Tu Du, Ho Chi Minh City, Viet Nam
| | - Angharad Care
- Department of Women's and Children's Health, University of Liverpool, Liverpool, UK
| | - Julio A Landero
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, USA
| | - Gerald F Combs
- Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, Medford, Massachusetts, USA
| | - Elizabeth Belling
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Joanne Chappell
- Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center and March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati, Ohio, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Fansheng Kong
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Criag Lacher
- Grand Forks Human Nutrition Research Center, USDA ARS, Grand Forks, North Dakota, USA
| | | | | | | | - Furqan Kabir
- Biorepository and Omics Research Group, Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Karachi, Sindh, Pakistan
| | - Imran Nisar
- Biorepository and Omics Research Group, Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Karachi, Sindh, Pakistan
| | - Aneeta Hotwani
- Biorepository and Omics Research Group, Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Karachi, Sindh, Pakistan
| | - Usma Mehmood
- Biorepository and Omics Research Group, Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Karachi, Sindh, Pakistan
| | - Ambreen Nizar
- Biorepository and Omics Research Group, Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Karachi, Sindh, Pakistan
| | - Javairia Khalid
- Biorepository and Omics Research Group, Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Karachi, Sindh, Pakistan
| | - Usha Dhingra
- Center for Public Health Kinetics, New Delhi, India
| | - Arup Dutta
- Center for Public Health Kinetics, New Delhi, India
| | - Said Ali
- Research Division, Public Health Laboratory, Center for Public Health Kinetics, Chake Chake, Tanzania
| | - Fahad Aftab
- Research Division, Public Health Laboratory, Center for Public Health Kinetics, Chake Chake, Tanzania
| | - Mohammed Hamad Juma
- Research Division, Public Health Laboratory, Center for Public Health Kinetics, Chake Chake, Tanzania
| | - Monjur Rahman
- Nutritional and Clinical Services Division, International Centre for Diarrhoeal Disease Research Bangladesh, Dhaka, Dhaka District, Bangladesh
| | | | - Patrick Musonda
- School of Public Health, University of Zambia, Lusaka, Zambia
| | | | - Md Munirul Islam
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research Bangladesh, Dhaka, Bangladesh
| | - Ulla Ashorn
- University of Tampere, Tampere, Pirkanmaa, Finland
| | - Kenneth Maleta
- School of Public Health, University of Malawi College of Medicine, Blantyre, Malawi
| | - Mikko Hallman
- Medical Research Centre Oulu, PEDEGO Research Unit, University of Oulu, Oulu, Pohjois-Pohjanmaa, Finland
| | - Laura Goodfellow
- Department of Women's and Children's Health, University of Liverpool, Liverpool, Merseyside, UK
| | - Juhi K Gupta
- Department of Women's and Children's Health, University of Liverpool, Liverpool, Merseyside, UK
| | - Ana Alfirevic
- Department of Women's and Children's Health, University of Liverpool, Liverpool, Merseyside, UK
| | - Susan Murphy
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, North Carolina, USA
| | - Larry Rand
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Francisco, San Francisco, California, USA
| | - Kelli K Ryckman
- Department of Epidemiology, University of Iowa, Iowa City, Iowa, USA
| | - Jeffrey C Murray
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, USA
| | - Rajiv Bahl
- Department of Medicine, World Health Organization, Geneva, Switzerland
| | - James A Litch
- Global Alliance to Prevent Prematurity and Stillbirth, Lynnwood, Washington, USA
| | | | - Zarko Alfirevic
- Division of Perinatal Medicine, University of Liverpool, Liverpool, UK
| | - Per Ashorn
- Center for Child Health Research, Faculty of Medicine and Health Technology, University of Tampere, Tampere, Pirkanmaa, Finland
- Department of Pediatrics, Tampere University Hospital, Tampere, Finland
| | - Abdullah Baqui
- International Center for Maternal and Newborn Health, Department of International Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Jane Hirst
- Nuffield Department of Women's and Reproductive Health, University of Oxford, Oxford, UK
| | - Cathrine Hoyo
- Department of Biological Sciences and Center for Human Health and the Enivironment, North Carolina State University, Raleigh, North Carolina, USA
| | - Fyezah Jehan
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Laura L Jelliffe-Pawlowski
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, USA
| | - Anisur Rahman
- Maternal and Child Health Division, International Centre for Diarrhoeal Disease Research Bangladesh, Dhaka, Dhaka District, Bangladesh
| | - Daniel E Roth
- Department of Paediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Sunil Sazawal
- Center for Public Health Kinetics, New Delhi, India
- Research Division, Public Health Laboratory, Center for Public Health Kinetics, Chake Chake, Tanzania
| | - Jeffrey Stringer
- Obstetrics and Gynecology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ge Zhang
- Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center and March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Louis Muglia
- Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center and March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Burroughs Wellcome Fund, Research Triangle Park, North Carolina, USA
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Nisar MI, Jehan F, Shahid S, Shakoor S, Kabir F, Hotwani A, Muneer S, Ahmed S, Whitney C, Ali A, Zaidi AK, Omer SB, Iqbal N. Methods for estimating the direct and indirect effect of 10 valent pneumococcal vaccine on nasopharyngeal carriage in children under 2 years in Matiari, Pakistan. MethodsX 2021; 8:101357. [PMID: 34430258 PMCID: PMC8374347 DOI: 10.1016/j.mex.2021.101357] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/12/2021] [Indexed: 11/29/2022] Open
Abstract
Pneumonia is the leading cause of morbidity and mortality in children worldwide. The ten valent pneumococcal vaccine (PCV10) was introduced in Pakistan's Expanded Program on Immunization (EPI) in 2012 as a 3 + 0 schedule without catchup immunization. Nasopharyngeal carriage is taken as a surrogate marker to measure the impact of pneumococcal vaccine on populations. Carriage surveys are necessary to monitor the persistence of Vaccine Type (VT) serotypes, the emergence of Non-Vaccine Type (NVT) serotypes, and their role in both transmission and disease. This article describes various troubleshooting measures which we undertook to adopt the protocol to our setting. We also used an innovative approach to describe various epidemiological parameters of vaccine effectiveness against carriage. It is important to publish these methods to allow for valid regional and temporal comparisons of results in different settings. Thus, in this article, we describe the following methods for isolating upper airway pneumococcal carriage:•Methods for the collection, transport, and storage of nasopharyngeal samples.•Methods for identification and serotyping of pneumococci.•Methods for estimation of the direct and indirect effects of pneumococcal vaccines on nasopharyngeal carriage.
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Affiliation(s)
- Muhammad Imran Nisar
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Fyezah Jehan
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Shahira Shahid
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Sadia Shakoor
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Furqan Kabir
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Aneeta Hotwani
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Sahrish Muneer
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Sheraz Ahmed
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | | | - Asad Ali
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Anita Km Zaidi
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan.,Bill & Melinda Gates Foundation, Seattle, WA, United States
| | - Saad B Omer
- Yale Institute for Global Health, New Haven, CT, United States
| | - Najeeha Iqbal
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
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25
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Qureshi S, Yousafzai MT, Rozi S, Qureshi S, Hotwani A, Sadiq K, Parkash O, Kazi AM, Kabir F, Usmani H, Qamar FN. Detection of typhoid carriers by duodenal fluid culture in a tertiary care hospital, Karachi: A cross-sectional study. J PAK MED ASSOC 2021; 71:2069-2072. [PMID: 34418032 DOI: 10.47391/jpma.580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
We aimed to detect typhoid carriers by performing duodenal fluid culture in patients in a tertiary care hospital in Pakistan. A cross-sectional study was conducted during 2017 at the Aga Khan University Hospital, Karachi. Patients who underwent upper gastrointestinal endoscopy were included. Participants were interviewed, and duodenal fluid samples were taken for culture to detect Salmonella typhi (S. typhi) and paratyphi. A polymerase chain reaction on 100 randomly selected sub-samples was also conducted. A total of 477 participants were enrolled. The mean age was 42.4±15.5 years. History of typhoid fever was present in 73 (15.3%) participants. Out of the 477 duodenal fluid cultures tested for various micro-organisms, 250 (52.4%) were positive. Neither S. typhi nor paratyphi were isolated. S. typhi was also not detected by PCR. To better detect S. typhi carriage in general population, future studies should target people with gall bladder diseases and screen them using culture and PCR based methods.
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Affiliation(s)
- Sonia Qureshi
- Department of Paediatrics, Aga Khan University Hospital, Karachi
| | | | - Shafquat Rozi
- Department of Community Health, Aga Khan University Hospital, Karachi, Pakistan
| | - Shahida Qureshi
- Department of Paediatric, Aga Khan University Hospital, Karachi, Pakistan
| | - Aneeta Hotwani
- Department of Paediatric, Aga Khan University Hospital, Karachi, Pakistan
| | - Kamran Sadiq
- Department of Paediatrics and Child Health, Aga Khan University Hospital, Karachi, Pakistan
| | - Om Parkash
- Department of Medicine, The Aga Khan University & Hospital, Karachi
| | - Abdul Momin Kazi
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Furqan Kabir
- Department of Paediatric, Aga Khan University Hospital, Karachi, Pakistan
| | - Hadi Usmani
- Department of Paediatric, Aga Khan University Hospital, Karachi, Pakistan
| | - Farah Naz Qamar
- Department of Paediatrics and Child Health, Aga Khan University Hospital, Karachi, Pakistan
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26
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Pavlinac PB, Platts-Mills JA, Tickell KD, Liu J, Juma J, Kabir F, Nkeze J, Okoi C, Operario DJ, Uddin J, Ahmed S, Alonso PL, Antonio M, Becker SM, Breiman RF, Faruque ASG, Fields B, Gratz J, Haque R, Hossain A, Hossain MJ, Jarju S, Qamar F, Iqbal NT, Kwambana B, Mandomando I, McMurry TL, Ochieng C, Ochieng JB, Ochieng M, Onyango C, Panchalingam S, Kalam A, Aziz F, Qureshi S, Ramamurthy T, Roberts JH, Saha D, Sow SO, Stroup SE, Sur D, Tamboura B, Taniuchi M, Tennant SM, Roose A, Toema D, Wu Y, Zaidi A, Nataro JP, Levine MM, Houpt ER, Kotloff KL. The Clinical Presentation of Culture-positive and Culture-negative, Quantitative Polymerase Chain Reaction (qPCR)-Attributable Shigellosis in the Global Enteric Multicenter Study and Derivation of a Shigella Severity Score: Implications for Pediatric Shigella Vaccine Trials. Clin Infect Dis 2021; 73:e569-e579. [PMID: 33044509 PMCID: PMC8326551 DOI: 10.1093/cid/ciaa1545] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 10/08/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Shigella is a leading cause of childhood diarrhea and target for vaccine development. Microbiologic and clinical case definitions are needed for pediatric field vaccine efficacy trials. METHODS We compared characteristics of moderate to severe diarrhea (MSD) cases in the Global Enteric Multicenter Study (GEMS) between children with culture positive Shigella to those with culture-negative, quantitative polymerase chain reaction (qPCR)-attributable Shigella (defined by an ipaH gene cycle threshold <27.9). Among Shigella MSD cases, we determined risk factors for death and derived a clinical severity score. RESULTS Compared to culture-positive Shigella MSD cases (n = 745), culture-negative/qPCR-attributable Shigella cases (n = 852) were more likely to be under 12 months, stunted, have a longer duration of diarrhea, and less likely to have high stool frequency or a fever. There was no difference in dehydration, hospitalization, or severe classification from a modified Vesikari score. Twenty-two (1.8%) Shigella MSD cases died within the 14-days after presentation to health facilities, and 59.1% of these deaths were in culture-negative cases. Age <12 months, diarrhea duration prior to presentation, vomiting, stunting, wasting, and hospitalization were associated with mortality. A model-derived score assigned points for dehydration, hospital admission, and longer diarrhea duration but was not significantly better at predicting 14-day mortality than a modified Vesikari score. CONCLUSIONS A composite severity score consistent with severe disease or dysentery may be a pragmatic clinical endpoint for severe shigellosis in vaccine trials. Reliance on culture for microbiologic confirmation may miss a substantial number of Shigella cases but is currently required to measure serotype specific immunity.
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Affiliation(s)
- Patricia B Pavlinac
- Department of Global Health, University of Washington, Seattle, Washington,USA
- Correspondence: Patricia B. Pavlinac, University of Washington, Seattle, WA, United States ()
| | - James A Platts-Mills
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia,USA
| | - Kirkby D Tickell
- Department of Global Health, University of Washington, Seattle, Washington,USA
| | - Jie Liu
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia,USA
| | - Jane Juma
- Center for Global Health Research, Kenya Medical Research Institute (KEMRI), Kenya
| | - Furqan Kabir
- Department of Paediatrics and Child Health, Aga Khan University, Karachi,Pakistan
| | - Joseph Nkeze
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland,USA
| | - Catherine Okoi
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Banjul,The Gambia
| | - Darwin J Operario
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia,USA
| | - Jashim Uddin
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia,USA
| | - Shahnawaz Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR, B), Dhaka,Bangladesh
| | - Pedro L Alonso
- Barcelona Centre for International Health Research (CRESIB), Hospital Clínic, Universitat de Barcelona, Barcelona,Spain
- Centro de Investigação em Saúde da Manhiça, Maputo,Mozambique
| | - Martin Antonio
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Banjul,The Gambia
| | - Stephen M Becker
- Science Applications International Corporation (SAIC), Richmond, Virginia,USA
| | - Robert F Breiman
- Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Abu S G Faruque
- International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR, B), Dhaka,Bangladesh
| | - Barry Fields
- Global Disease Detection Division, Kenya Office of the US Centers for Disease Control and Prevention, Nairobi,Kenya
| | - Jean Gratz
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia,USA
| | - Rashidul Haque
- International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR, B), Dhaka,Bangladesh
| | - Anowar Hossain
- International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR, B), Dhaka,Bangladesh
| | - M Jahangir Hossain
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Banjul,The Gambia
| | - Sheikh Jarju
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Banjul,The Gambia
| | - Farah Qamar
- Department of Paediatrics and Child Health, Aga Khan University, Karachi,Pakistan
| | - Najeeha Talat Iqbal
- Department of Paediatrics and Child Health, Aga Khan University, Karachi,Pakistan
| | - Brenda Kwambana
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Banjul,The Gambia
| | | | - Timothy L McMurry
- Public Health Sciences, University of Virginia, Charlottesville, Virginia,USA
| | - Caroline Ochieng
- Center for Global Health Research, Kenya Medical Research Institute (KEMRI), Kenya
| | - John B Ochieng
- Center for Global Health Research, Kenya Medical Research Institute (KEMRI), Kenya
| | - Melvin Ochieng
- Center for Global Health Research, Kenya Medical Research Institute (KEMRI), Kenya
| | - Clayton Onyango
- Global Disease Detection Division, Kenya Office of the US Centers for Disease Control and Prevention, Nairobi,Kenya
| | - Sandra Panchalingam
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland,USA
| | - Adil Kalam
- Department of Paediatrics and Child Health, Aga Khan University, Karachi,Pakistan
| | - Fatima Aziz
- Department of Paediatrics and Child Health, Aga Khan University, Karachi,Pakistan
| | - Shahida Qureshi
- Department of Paediatrics and Child Health, Aga Khan University, Karachi,Pakistan
| | | | - James H Roberts
- Public Health Sciences, University of Virginia, Charlottesville, Virginia,USA
| | - Debasish Saha
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Banjul,The Gambia
| | - Samba O Sow
- Centre pour le Développement des Vaccins, Bamako,Mali
| | - Suzanne E Stroup
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia,USA
| | - Dipika Sur
- National Institute of Cholera and Enteric Diseases, Kolkata,India
| | | | - Mami Taniuchi
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia,USA
| | - Sharon M Tennant
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland,USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland,USA
| | - Anna Roose
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland,USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland,USA
| | - Deanna Toema
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland,USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland,USA
| | - Yukun Wu
- Sanofi Pasteur, Swiftwater, Pennsylvania,USA
| | - Anita Zaidi
- Bill and Melinda Gates Foundation, Seattle, Washington,USA
| | - James P Nataro
- Public Health Sciences, University of Virginia, Charlottesville, Virginia,USA
| | - Myron M Levine
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland,USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland,USA
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, Maryland,USA
| | - Eric R Houpt
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia,USA
| | - Karen L Kotloff
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland,USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland,USA
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, Maryland,USA
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27
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Jamil Z, Iqbal NT, Idress R, Ahmed Z, Sadiq K, Mallawaarachchi I, Iqbal J, Syed S, Hotwani A, Kabir F, Ahmed K, Ahmed S, Umrani F, Ma JZ, Aziz F, Kalam A, Moore SR, Ali SA. Gut integrity and duodenal enteropathogen burden in undernourished children with environmental enteric dysfunction. PLoS Negl Trop Dis 2021; 15:e0009584. [PMID: 34264936 PMCID: PMC8352064 DOI: 10.1371/journal.pntd.0009584] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 08/09/2021] [Accepted: 06/17/2021] [Indexed: 11/18/2022] Open
Abstract
Environmental enteric dysfunction (EED) is a subclinical condition of intestinal inflammation, barrier dysfunction and malabsorption associated with growth faltering in children living in poverty. This study explores association of altered duodenal permeability (lactulose, rhamnose and their ratio) with higher burden of enteropathogen in the duodenal aspirate, altered histopathological findings and higher morbidity (diarrhea) that is collectively associated with linear growth faltering in children living in EED endemic setting. In a longitudinal birth cohort, 51 controls (WHZ > 0, HAZ > −1.0) and 63 cases (WHZ< -2.0, refractory to nutritional intervention) were recruited. Anthropometry and morbidity were recorded on monthly bases up to 24 months of age. Dual sugar assay of urine collected after oral administration of lactulose and rhamnose was assessed in 96 children from both the groups. Duodenal histopathology (n = 63) and enteropathogen analysis of aspirate via Taqman array card (n = 60) was assessed in only cases. Giardia was the most frequent pathogen and was associated with raised L:R ratio (p = 0.068). Gastric microscopy was more sensitive than duodenal aspirate in H. pylori detection. Microscopically confirmed H. pylori negatively correlated with HAZ at 24 months (r = −0.313, p = 0.013). Regarding histopathological parameters, goblet cell reduction significantly correlated with decline in dual sugar excretion (p< 0.05). Between cases and controls, there were no significant differences in the median (25th, 75th percentile) of urinary concentrations (μg/ml) of lactulose [27.0 (11.50, 59.50) for cases vs. 38.0 (12.0, 61.0) for controls], rhamnose [66.0 (28.0, 178.0) vs. 86.5 (29.5, 190.5)] and L:R ratio [0.47 (0.24, 0.90) vs. 0.51 (0.31, 0.71)] respectively. In multivariable regression model, 31% of variability in HAZ at 24 months of age among cases and controls was explained by final model including dual sugars. In conclusion, enteropathogen burden is associated with altered histopathological features and intestinal permeability. In cases and controls living in settings of endemic enteropathy, intestinal permeability test may predict linear growth. However, for adoption as a screening tool for EED, further validation is required due to its complex intestinal pathophysiology. EED is a subclinical condition of compromised gut integrity secondary to frequent and repeated exposure to enteropathogens in global settings with a high prevalence of undernutrition. In this study, we reported association of gut mucosal architecture with a dual sugar intestinal permeability assay (lactulose-rhamnose) in Pakistani children. In the presence of duodenal enteropathogens, features such as chronic inflammation, intra-epithelial lymphocytosis, enterocyte injury and Paneth cell reduction were consistently observed. When comparing undernourished cases and controls living in the same setting, we found urinary excretion of the sugars was similar among groups; however, variability in HAZ among children at 24 months was partially explained by a model that includes excretion values.
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Affiliation(s)
- Zehra Jamil
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Najeeha Talat Iqbal
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Romana Idress
- Department of Pathology & Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Zubair Ahmed
- Department of Pathology & Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Kamran Sadiq
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Indika Mallawaarachchi
- Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, United States of America
| | - Junaid Iqbal
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Sana Syed
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition; Department of Pediatrics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Aneeta Hotwani
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Furqan Kabir
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Kumail Ahmed
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Sheraz Ahmed
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Fayaz Umrani
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Jennie Z. Ma
- Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, United States of America
| | - Fatima Aziz
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Adil Kalam
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Sean R. Moore
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition; Department of Pediatrics, University of Virginia, Charlottesville, Virginia, United States of America
- * E-mail: (SRM); (SAA)
| | - Syed Asad Ali
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
- * E-mail: (SRM); (SAA)
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Muneer S, Kayani HA, Ali K, Asif E, Zohra RR, Kabir F. Laboratory biosafety and biosecurity related education in Pakistan: Engaging students through the Socratic method of learning. Journal of Biosafety and Biosecurity 2021. [DOI: 10.1016/j.jobb.2021.03.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Nisar MI, Shahid S, Muhammad S, Khalid F, Hussain A, Ahmed S, Shakoor S, Kabir F, Hotwani A, Ali A, Zaidi AK, Omer SB, Jehan F, Iqbal N. Impact of 10-valent Pneumococcal Conjugate Vaccine (PCV10) on nasopharyngeal carriage in children 2 years of age: Data from a four-year time series cross-sectional study from Pakistan. Data Brief 2021; 35:106828. [PMID: 33614873 PMCID: PMC7881212 DOI: 10.1016/j.dib.2021.106828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/28/2021] [Accepted: 01/29/2021] [Indexed: 11/10/2022] Open
Abstract
The dataset described in this paper was collected for a time-series cross-sectional study exploring the impact of 10-valent Pneumococcal Conjugate Vaccine (PCV10) on nasopharyngeal (NP) carriage in children under 2 years of age from a rural population in Sindh, Pakistan. The study was carried out in two union councils of Matiari - Khyber and Shah Alam Shah Jee Wasi (Latitude 25.680298 / Longitude 68.502711). Data was collected on socio-demographics, clinical characteristics and vaccination status using android phone-based application. NP samples were collected using standard World Health Organisation (WHO) techniques, culture and serotyping was done using sequential Multiplex PCR described by Centre for Disease Control, USA. We looked at the carriage rate of vaccine type (VT) and non-vaccine type (NVT) serotypes over time in vaccinated and unvaccinated children. We additionally looked at the predictors for pneumococcal carriage. The uploaded dataset, available on Mendeley data repository (Nisar, Muhammad Imran (2021), “Impact of PCV10 on nasopharyngeal carriage in children in Pakistan”, Mendeley Data, V1, doi:10.17632/t79h6g97gr.1), has 3140 observations in CSV format. Additional files uploaded include a data dictionary and the set of questionnaires. The dataset and accompanying files can be used by other interested researchers to replicate our analysis, carry similar analysis under varying set of assumptions or perform additional exploratory or metanalysis
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Affiliation(s)
- Muhammad Imran Nisar
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Shahira Shahid
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Sajid Muhammad
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Farah Khalid
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Amjad Hussain
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Sheraz Ahmed
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Sadia Shakoor
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Furqan Kabir
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Aneeta Hotwani
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Asad Ali
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Anita Km Zaidi
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan.,Bill & Melinda Gates Foundation, Seattle, WA, USA
| | - Saad B Omer
- Yale Institute for Global Health, New Haven, CT, USA
| | - Fyezah Jehan
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Najeeha Iqbal
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
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Nisar MI, Ahmed S, Jehan F, Shahid S, Shakoor S, Kabir F, Hotwani A, Munir S, Muhammad S, Khalid F, Althouse B, Hu H, Whitney C, Ali A, Zaidi AKM, Omer SB, Iqbal N. Direct and indirect effect of 10 valent pneumococcal vaccine on nasopharyngeal carriage in children under 2 years of age in Matiari, Pakistan. Vaccine 2021; 39:1319-1327. [PMID: 33422379 PMCID: PMC7910277 DOI: 10.1016/j.vaccine.2020.12.066] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 12/21/2020] [Accepted: 12/22/2020] [Indexed: 12/26/2022]
Abstract
Background Pakistan introduced Ten-valent pneumococcal-conjugate-vaccine PCV10 in 2012 as a 3 + 0 schedule without catch-up. Methods Children <2 years old in Matiari, Sindh provided nasopharyngeal swabs between 2014 and 2018, which were cultured for pneumococcus and serotyped through multiplex PCR at the Aga Khan University Hospital. Carriage rates over time for Vaccine-Type (VT) and Non-VT (NVT) serotypes were used to estimate direct, indirect, total and overall effects of vaccination. Regression analysis was used to determine factors associated with VT carriage. Results Pneumococcus was detected in 2370/3140 (75%). VT carriage decreased overall, 16.1–9.6% (p-trend <0.001); vaccinated (all 3 doses of PCV10 received) 11.3–8.1% (p-trend 0.031) and unvaccinated (no PCV10 dose received) 17.4–10.3% (p-trend 0.003) with a decline in serotypes 6B, 9V/9A and 19F. Immunization increased from 41.0% to 68.4% (p-trend 0.001). Direct effect of vaccine was 32.8% (95% CI 14.7–47.0%) and indirect effect 44.6%(95% CI 40.6–48.6%). Factors associated with decreased VT colonization were education 1–5 years (aOR 0.7, 95%CI 0.6–1.0), history of difficulty breathing (aOR 0.7, 95%CI 0.5–1.0), exposure to smoke (aOR 0.8, 95% CI 0.6–1.0), child fully immunized (aOR 0.7, 95%CI 0.5–1.0) and enrolled in 3rd (aOR 0.6, 95%CI 0.4–0.8) and 4th (aOR 0.6, 95%CI 0.5–0.9) year of the study whereas history of runny nose (aOR 1.5, 95% CI 1.2–1.9) was positively associated. Conclusions Decrease in VT pneumococcal carriage in vaccinated and unvaccinated children indicates herd immunity. Sustained increase in vaccine coverage and close long-term surveillance is warranted.
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Affiliation(s)
- Muhammad Imran Nisar
- Department of Pediatric and Child Health, Aga Khan University, Karachi, Pakistan.
| | - Sheraz Ahmed
- Department of Pediatric and Child Health, Aga Khan University, Karachi, Pakistan
| | - Fyezah Jehan
- Department of Pediatric and Child Health, Aga Khan University, Karachi, Pakistan
| | - Shahira Shahid
- Department of Pediatric and Child Health, Aga Khan University, Karachi, Pakistan
| | - Sadia Shakoor
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Furqan Kabir
- Department of Pediatric and Child Health, Aga Khan University, Karachi, Pakistan
| | - Aneeta Hotwani
- Department of Pediatric and Child Health, Aga Khan University, Karachi, Pakistan
| | - Sahrish Munir
- Department of Pediatric and Child Health, Aga Khan University, Karachi, Pakistan
| | - Sajid Muhammad
- Department of Pediatric and Child Health, Aga Khan University, Karachi, Pakistan
| | - Farah Khalid
- Department of Pediatric and Child Health, Aga Khan University, Karachi, Pakistan
| | | | - Hao Hu
- Bill & Melinda Gates Foundation, Seattle, WA, USA
| | | | - Asad Ali
- Department of Pediatric and Child Health, Aga Khan University, Karachi, Pakistan
| | - Anita K M Zaidi
- Department of Pediatric and Child Health, Aga Khan University, Karachi, Pakistan; Bill & Melinda Gates Foundation, Seattle, WA, USA
| | - Saad B Omer
- Yale Institute for Global Health, New Haven, CT, USA
| | - Najeeha Iqbal
- Department of Pediatric and Child Health, Aga Khan University, Karachi, Pakistan
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Jehan F, Sazawal S, Baqui AH, Nisar MI, Dhingra U, Khanam R, Ilyas M, Dutta A, Mitra DK, Mehmood U, Deb S, Mahmud A, Hotwani A, Ali SM, Rahman S, Nizar A, Ame SM, Moin MI, Muhammad S, Chauhan A, Begum N, Khan W, Das S, Ahmed S, Hasan T, Khalid J, Rizvi SJR, Juma MH, Chowdhury NH, Kabir F, Aftab F, Quaiyum A, Manu A, Yoshida S, Bahl R, Rahman A, Pervin J, Winston J, Musonda P, Stringer JSA, Litch JA, Ghaemi MS, Moufarrej MN, Contrepois K, Chen S, Stelzer IA, Stanley N, Chang AL, Hammad GB, Wong RJ, Liu C, Quaintance CC, Culos A, Espinosa C, Xenochristou M, Becker M, Fallahzadeh R, Ganio E, Tsai AS, Gaudilliere D, Tsai ES, Han X, Ando K, Tingle M, Marić I, Wise PH, Winn VD, Druzin ML, Gibbs RS, Darmstadt GL, Murray JC, Shaw GM, Stevenson DK, Snyder MP, Quake SR, Angst MS, Gaudilliere B, Aghaeepour N. Multiomics Characterization of Preterm Birth in Low- and Middle-Income Countries. JAMA Netw Open 2020; 3:e2029655. [PMID: 33337494 PMCID: PMC7749442 DOI: 10.1001/jamanetworkopen.2020.29655] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
IMPORTANCE Worldwide, preterm birth (PTB) is the single largest cause of deaths in the perinatal and neonatal period and is associated with increased morbidity in young children. The cause of PTB is multifactorial, and the development of generalizable biological models may enable early detection and guide therapeutic studies. OBJECTIVE To investigate the ability of transcriptomics and proteomics profiling of plasma and metabolomics analysis of urine to identify early biological measurements associated with PTB. DESIGN, SETTING, AND PARTICIPANTS This diagnostic/prognostic study analyzed plasma and urine samples collected from May 2014 to June 2017 from pregnant women in 5 biorepository cohorts in low- and middle-income countries (LMICs; ie, Matlab, Bangladesh; Lusaka, Zambia; Sylhet, Bangladesh; Karachi, Pakistan; and Pemba, Tanzania). These cohorts were established to study maternal and fetal outcomes and were supported by the Alliance for Maternal and Newborn Health Improvement and the Global Alliance to Prevent Prematurity and Stillbirth biorepositories. Data were analyzed from December 2018 to July 2019. EXPOSURES Blood and urine specimens that were collected early during pregnancy (median sampling time of 13.6 weeks of gestation, according to ultrasonography) were processed, stored, and shipped to the laboratories under uniform protocols. Plasma samples were assayed for targeted measurement of proteins and untargeted cell-free ribonucleic acid profiling; urine samples were assayed for metabolites. MAIN OUTCOMES AND MEASURES The PTB phenotype was defined as the delivery of a live infant before completing 37 weeks of gestation. RESULTS Of the 81 pregnant women included in this study, 39 had PTBs (48.1%) and 42 had term pregnancies (51.9%) (mean [SD] age of 24.8 [5.3] years). Univariate analysis demonstrated functional biological differences across the 5 cohorts. A cohort-adjusted machine learning algorithm was applied to each biological data set, and then a higher-level machine learning modeling combined the results into a final integrative model. The integrated model was more accurate, with an area under the receiver operating characteristic curve (AUROC) of 0.83 (95% CI, 0.72-0.91) compared with the models derived for each independent biological modality (transcriptomics AUROC, 0.73 [95% CI, 0.61-0.83]; metabolomics AUROC, 0.59 [95% CI, 0.47-0.72]; and proteomics AUROC, 0.75 [95% CI, 0.64-0.85]). Primary features associated with PTB included an inflammatory module as well as a metabolomic module measured in urine associated with the glutamine and glutamate metabolism and valine, leucine, and isoleucine biosynthesis pathways. CONCLUSIONS AND RELEVANCE This study found that, in LMICs and high PTB settings, major biological adaptations during term pregnancy follow a generalizable model and the predictive accuracy for PTB was augmented by combining various omics data sets, suggesting that PTB is a condition that manifests within multiple biological systems. These data sets, with machine learning partnerships, may be a key step in developing valuable predictive tests and intervention candidates for preventing PTB.
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Affiliation(s)
- Fyezah Jehan
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Sunil Sazawal
- Centre for Public Health Kinetics, New Delhi, Delhi, India
| | - Abdullah H. Baqui
- International Center for Maternal and Newborn Health, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Muhammad Imran Nisar
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Usha Dhingra
- Centre for Public Health Kinetics, New Delhi, Delhi, India
| | - Rasheda Khanam
- International Center for Maternal and Newborn Health, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Muhammad Ilyas
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Arup Dutta
- Centre for Public Health Kinetics, New Delhi, Delhi, India
| | - Dipak K. Mitra
- International Center for Maternal and Newborn Health, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Usma Mehmood
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Saikat Deb
- Centre for Public Health Kinetics, New Delhi, Delhi, India
- Public Health Laboratory-Ivo de Carneri, Pemba Island, Zanzibar
| | - Arif Mahmud
- International Center for Maternal and Newborn Health, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Aneeta Hotwani
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | | | - Sayedur Rahman
- International Center for Maternal and Newborn Health, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Ambreen Nizar
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | | | - Mamun Ibne Moin
- International Center for Maternal and Newborn Health, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Sajid Muhammad
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | | | - Nazma Begum
- International Center for Maternal and Newborn Health, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Waqasuddin Khan
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Sayan Das
- Centre for Public Health Kinetics, New Delhi, Delhi, India
| | - Salahuddin Ahmed
- International Center for Maternal and Newborn Health, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Tarik Hasan
- International Center for Maternal and Newborn Health, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Javairia Khalid
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Syed Jafar Raza Rizvi
- International Center for Maternal and Newborn Health, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | | | - Nabidul Haque Chowdhury
- International Center for Maternal and Newborn Health, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Furqan Kabir
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Fahad Aftab
- Centre for Public Health Kinetics, New Delhi, Delhi, India
| | - Abdul Quaiyum
- International Center for Maternal and Newborn Health, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Alexander Manu
- Maternal, Newborn, Child and Adolescent Health Research, World Health Organization, Geneva, Switzerland
| | - Sachiyo Yoshida
- Maternal, Newborn, Child and Adolescent Health Research, World Health Organization, Geneva, Switzerland
| | - Rajiv Bahl
- Maternal, Newborn, Child and Adolescent Health Research, World Health Organization, Geneva, Switzerland
| | - Anisur Rahman
- Matlab Health Research Centre, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Jesmin Pervin
- Maternal and Child Health Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Jennifer Winston
- Department of Obstetrics and Gynecology, University of North Carolina at Chapel Hill, Chapel Hill
| | - Patrick Musonda
- School of Public Health, University of Zambia, Lusaka, Zambia
| | - Jeffrey S. A. Stringer
- Department of Obstetrics and Gynecology, University of North Carolina at Chapel Hill, Chapel Hill
| | - James A. Litch
- Global Alliance to Prevent Prematurity and Stillbirth, Seattle, Washington
| | - Mohammad Sajjad Ghaemi
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California
- Digital Technologies Research Centre, National Research Council Canada, Toronto, Ontario, Canada
| | - Mira N. Moufarrej
- Department of Bioengineering, Stanford University, Stanford, California
| | - Kévin Contrepois
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Songjie Chen
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Ina A. Stelzer
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California
| | - Natalie Stanley
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California
| | - Alan L. Chang
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California
| | - Ghaith Bany Hammad
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California
| | - Ronald J. Wong
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - Candace Liu
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California
| | | | - Anthony Culos
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California
| | - Camilo Espinosa
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California
| | - Maria Xenochristou
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California
| | - Martin Becker
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California
| | - Ramin Fallahzadeh
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California
| | - Edward Ganio
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California
| | - Amy S. Tsai
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California
| | - Dyani Gaudilliere
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California
| | - Eileen S. Tsai
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California
| | - Xiaoyuan Han
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California
| | - Kazuo Ando
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California
| | - Martha Tingle
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California
| | - Ivana Marić
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - Paul H. Wise
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - Virginia D. Winn
- Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, California
| | - Maurice L. Druzin
- Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, California
| | - Ronald S. Gibbs
- Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, California
| | - Gary L. Darmstadt
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | | | - Gary M. Shaw
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - David K. Stevenson
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - Michael P. Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Stephen R. Quake
- Department of Bioengineering, Stanford University, Stanford, California
| | - Martin S. Angst
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California
| | - Brice Gaudilliere
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - Nima Aghaeepour
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, California
- Department of Biomedical Informatics, Stanford University School of Medicine, Stanford, California
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Rogawski McQuade ET, Shaheen F, Kabir F, Rizvi A, Platts-Mills JA, Aziz F, Kalam A, Qureshi S, Elwood S, Liu J, Lima AAM, Kang G, Bessong P, Samie A, Haque R, Mduma ER, Kosek MN, Shrestha S, Leite JP, Bodhidatta L, Page N, Kiwelu I, Shakoor S, Turab A, Soofi SB, Ahmed T, Houpt ER, Bhutta Z, Iqbal NT. Epidemiology of Shigella infections and diarrhea in the first two years of life using culture-independent diagnostics in 8 low-resource settings. PLoS Negl Trop Dis 2020; 14:e0008536. [PMID: 32804926 PMCID: PMC7451981 DOI: 10.1371/journal.pntd.0008536] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 08/27/2020] [Accepted: 06/29/2020] [Indexed: 02/06/2023] Open
Abstract
Culture-independent diagnostics have revealed a larger burden of Shigella among children in low-resource settings than previously recognized. We further characterized the epidemiology of Shigella in the first two years of life in a multisite birth cohort. We tested 41,405 diarrheal and monthly non-diarrheal stools from 1,715 children for Shigella by quantitative PCR. To assess risk factors, clinical factors related to age and culture positivity, and associations with inflammatory biomarkers, we used log-binomial regression with generalized estimating equations. The prevalence of Shigella varied from 4.9%-17.8% in non-diarrheal stools across sites, and the incidence of Shigella-attributable diarrhea was 31.8 cases (95% CI: 29.6, 34.2) per 100 child-years. The sensitivity of culture compared to qPCR was 6.6% and increased to 27.8% in Shigella-attributable dysentery. Shigella diarrhea episodes were more likely to be severe and less likely to be culture positive in younger children. Older age (RR: 1.75, 95% CI: 1.70, 1.81 per 6-month increase in age), unimproved sanitation (RR: 1.15, 95% CI: 1.03, 1.29), low maternal education (<10 years, RR: 1.14, 95% CI: 1.03, 1.26), initiating complementary foods before 3 months (RR: 1.10, 95% CI: 1.01, 1.20), and malnutrition (RR: 0.91, 95% CI: 0.88, 0.95 per unit increase in weight-for-age z-score) were risk factors for Shigella. There was a linear dose-response between Shigella quantity and myeloperoxidase concentrations. The burden of Shigella varied widely across sites, but uniformly increased through the second year of life and was associated with intestinal inflammation. Culture missed most clinically relevant cases of severe diarrhea and dysentery. Shigella is the second leading cause of diarrhea morbidity and mortality among children in low and middle-income countries. We characterized the epidemiology of Shigella using highly sensitive diagnostic methods in 41,405 diarrheal and monthly non-diarrheal stools from the first two years of life in a multisite birth cohort. The prevalence of Shigella varied from 4.9%-17.8% across sites, and the incidence of Shigella-attributable diarrhea was 31.8 cases (95% CI: 29.6, 34.2) per 100 child-years. Shigella diarrhea episodes were more likely to be severe and less likely to be culture positive in younger children. Older age, unimproved sanitation, low maternal education, initiating complementary foods before 3 months, and malnutrition were risk factors for Shigella. There was a linear dose-response between Shigella quantity and myeloperoxidase, a marker of intestinal inflammation, which suggests a potential mechanism for the impact of Shigella on child growth. Because culture missed most clinically relevant cases of severe diarrhea and dysentery, molecular diagnostics may be important tools in upcoming Shigella vaccine trials.
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Affiliation(s)
- Elizabeth T. Rogawski McQuade
- Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, United States of America
- Division of Infectious Diseases & International Health, University of Virginia, Charlottesville, Virginia, United States of America
- * E-mail: (ETRM); (NTI)
| | - Fariha Shaheen
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Furqan Kabir
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Arjumand Rizvi
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - James A. Platts-Mills
- Division of Infectious Diseases & International Health, University of Virginia, Charlottesville, Virginia, United States of America
| | - Fatima Aziz
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Adil Kalam
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Shahida Qureshi
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Sarah Elwood
- Division of Infectious Diseases & International Health, University of Virginia, Charlottesville, Virginia, United States of America
| | - Jie Liu
- Division of Infectious Diseases & International Health, University of Virginia, Charlottesville, Virginia, United States of America
| | | | | | | | | | - Rashidul Haque
- International Centre for Diarrheal Disease Research, Bangladesh, Dhaka, Bangladesh
| | | | - Margaret N. Kosek
- Division of Infectious Diseases & International Health, University of Virginia, Charlottesville, Virginia, United States of America
- Asociación Benéfica PRISMA, Iquitos, Peru
| | | | | | - Ladaporn Bodhidatta
- Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand
| | - Nicola Page
- National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Ireen Kiwelu
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
| | - Sadia Shakoor
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Ali Turab
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Sajid Bashir Soofi
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Tahmeed Ahmed
- International Centre for Diarrheal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Eric R. Houpt
- Division of Infectious Diseases & International Health, University of Virginia, Charlottesville, Virginia, United States of America
| | - Zulfiqar Bhutta
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Najeeha Talat Iqbal
- Department of Pediatrics and Child Health and Biological & Biomedical Sciences, Aga Khan University, Karachi, Pakistan
- * E-mail: (ETRM); (NTI)
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Burnett E, Kabir F, Van Trang N, Rayamajhi A, Satter SM, Liu J, Yousafzai MT, Anh DD, Basnet AT, Flora MS, Houpt E, Qazi SH, Canh TM, Rayamajhi AK, Saha BK, Saddal NS, Muneer S, Hung PH, Islam T, Ali SA, Tate JE, Yen C, Parashar UD. Infectious Etiologies of Intussusception Among Children <2 Years Old in 4 Asian Countries. J Infect Dis 2020; 221:1499-1505. [PMID: 31754717 PMCID: PMC7371463 DOI: 10.1093/infdis/jiz621] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 11/20/2019] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The etiology of intussusception, the leading cause of bowel obstruction in infants, is unknown in most cases. Adenovirus has been associated with intussusception and slightly increased risk of intussusception with rotavirus vaccination has been found. We conducted a case-control study among children <2 years old in Bangladesh, Nepal, Pakistan, and Vietnam to evaluate infectious etiologies of intussusception before rotavirus vaccine introduction. METHODS From 2015 to 2017, we enrolled 1-to-1 matched intussusception cases and hospital controls; 249 pairs were included. Stool specimens were tested for 37 infectious agents using TaqMan Array technology. We used conditional logistic regression to estimate odds ratio (OR) and 95% confidence interval (CI) of each pathogen associated with intussusception in a pooled analysis and quantitative subanalyses. RESULTS Adenovirus (OR, 2.67; 95% CI, 1.75-4.36) and human herpes virus 6 (OR, 3.50; 95% CI, 1.15-10.63) were detected more frequently in cases than controls. Adenovirus C detection <20 quantification cycles was associated with intussusception (OR, 18.59; 95% CI, 2.45-140.89). Wild-type rotavirus was not associated with intussusception (OR, 1.07; 95% CI, 0.52-2.22). CONCLUSIONS In this comprehensive evaluation, adenovirus and HHV-6 were associated with intussusception. Future research is needed to better understand mechanisms leading to intussusception, particularly after rotavirus vaccination.
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Affiliation(s)
- Eleanor Burnett
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, USA
| | - Furqan Kabir
- Dept. of Pediatrics and Child Health, Aga Khan University Karachi, Pakistan
| | | | - Ajit Rayamajhi
- Janak Medical and Research Center, Balaju, Kathmandu, Nepal
- Kanti Children’s Hospital, Maharajgunj, Kathmandu, Nepal
| | | | - Jie Liu
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, USA
| | | | - Dang Duc Anh
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | | | - Meerjady S. Flora
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka, Bangladesh
| | - Eric Houpt
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, USA
| | - Saqib Hamid Qazi
- Dept. of Pediatrics and Child Health, Aga Khan University Karachi, Pakistan
| | | | | | - Bablu K Saha
- Rangpur Medical College Hospital, Rangpur, Bangladesh
| | | | - Sehrish Muneer
- Dept. of Pediatrics and Child Health, Aga Khan University Karachi, Pakistan
| | | | - Towhidul Islam
- Sher E Bangla Medical College Hospital, Barisal, Bangladesh
| | - Syed Asad Ali
- Dept. of Pediatrics and Child Health, Aga Khan University Karachi, Pakistan
| | - Jacqueline E. Tate
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, USA
| | - Catherine Yen
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, USA
| | - Umesh D. Parashar
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, USA
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Kuhn KD, Edamura K, Bhatia N, Cheng I, Clark SA, Haynes CV, Heffner DL, Kabir F, Velasquez J, Spano AJ, Deppmann CD, Keeler AB. Molecular dissection of TNFR-TNFα bidirectional signaling reveals both cooperative and antagonistic interactions with p75 neurotrophic factor receptor in axon patterning. Mol Cell Neurosci 2020; 103:103467. [PMID: 32004684 PMCID: PMC7682658 DOI: 10.1016/j.mcn.2020.103467] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 12/18/2019] [Accepted: 01/13/2020] [Indexed: 11/25/2022] Open
Abstract
During neural development, complex organisms rely on progressive and regressive events whereby axons, synapses, and neurons are overproduced followed by selective elimination of a portion of these components. Tumor necrosis factor α (TNFα) together with its cognate receptor (Tumor necrosis factor receptor 1; TNFR1) have been shown to play both regressive (i.e. forward signaling from the receptor) and progressive (i.e. reverse signaling from the ligand) roles in sympathetic neuron development. In contrast, a paralog of TNFR1, p75 neurotrophic factor receptor (p75NTR) promotes mainly regressive developmental events in sympathetic neurons. Here we examine the interplay between these paralogous receptors in the regulation of axon branch elimination and arborization. We confirm previous reports that these TNFR1 family members are individually capable of promoting ligand-dependent suppression of axon growth and branching. Remarkably, p75NTR and TNFR1 physically interact and p75NTR requires TNFR1 for ligand-dependent axon suppression of axon branching but not vice versa. We also find that p75NTR forward signaling and TNFα reverse signaling are functionally antagonistic. Finally, we find that TNFα reverse signaling is necessary for nerve growth factor (NGF) dependent axon growth. Taken together these findings demonstrate several levels of synergistic and antagonistic interactions using very few signaling pathways and that the balance of these synergizing and opposing signals act to ensure proper axon growth and patterning.
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Affiliation(s)
- K D Kuhn
- Department of Biology, University of Virginia, Charlottesville, VA 22903, USA
| | - K Edamura
- Department of Biology, University of Virginia, Charlottesville, VA 22903, USA
| | - N Bhatia
- Department of Biology, University of Virginia, Charlottesville, VA 22903, USA
| | - I Cheng
- Neuroscience Graduate Program, University of Virginia, Charlottesville, VA 22903, USA
| | - S A Clark
- Neuroscience Graduate Program, University of Virginia, Charlottesville, VA 22903, USA
| | - C V Haynes
- Department of Biology, University of Virginia, Charlottesville, VA 22903, USA
| | - D L Heffner
- Department of Biology, University of Virginia, Charlottesville, VA 22903, USA
| | - F Kabir
- Department of Biology, University of Virginia, Charlottesville, VA 22903, USA
| | - J Velasquez
- Blue Ridge Virtual Governor's School, Palmyra, VA 22963, USA
| | - A J Spano
- Department of Biology, University of Virginia, Charlottesville, VA 22903, USA
| | - C D Deppmann
- Department of Biology, University of Virginia, Charlottesville, VA 22903, USA; Neuroscience Graduate Program, University of Virginia, Charlottesville, VA 22903, USA; Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22903, USA; Department of Cell Biology, University of Virginia, Charlottesville, VA 22903, USA.
| | - A B Keeler
- Department of Biology, University of Virginia, Charlottesville, VA 22903, USA.
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Iqbal NT, Syed S, Kabir F, Jamil Z, Akhund T, Qureshi S, Liu J, Ma JZ, Guleria S, Gewirtz A, Duggan CP, Hughes MA, Sadiq K, Ali A. Pathobiome driven gut inflammation in Pakistani children with Environmental Enteric Dysfunction. PLoS One 2019; 14:e0221095. [PMID: 31442248 PMCID: PMC6707605 DOI: 10.1371/journal.pone.0221095] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 07/30/2019] [Indexed: 01/05/2023] Open
Abstract
Environmental Enteric Dysfunction (EED) is an acquired small intestinal inflammatory condition underlying high rates of stunting in children <5 years of age in low- and middle-income countries. Children with EED are known to have repeated exposures to enteropathogens and environmental toxins that leads to malabsorptive syndrome. We aimed to characterize association of linear growth faltering with enteropathogen burden and subsequent changes in EED biomarkers. In a longitudinal birth cohort (n = 272), monthly anthropometric measurements (Length for Age Z score- LAZ) of asymptomatic children were obtained up to 18 months. Biological samples were collected at 6 and 9 months for the assessment of biomarkers. A customized TaqMan array card was used to target 40 enteropathogens in fecal samples. Linear regression was applied to study the effect of specific enteropathogen infection on change in linear growth (ΔLAZ). Presence of any pathogen in fecal sample correlated with serum flagellin IgA (6 mo, r = 0.19, p = 0.002), fecal Reg 1b (6 mo, r = 0.16, p = 0.01; 9mo, r = 0.16, p = 0.008) and serum Reg 1b (6 mo, r = 0.26, p<0.0001; 9 mo, r = 0.15, p = 0.008). At 6 months, presence of Campylobacter [β (SE) 7751.2 (2608.5), p = 0.003] and ETEC LT [β (SE) 7089.2 (3015.04), p = 0.019] was associated with increase in MPO. Giardia was associated with increase in Reg1b [β (SE) 72.189 (26.394), p = 0.006] and anti-flic IgA[β (SE) 0.054 (0.021), p = 0.0091]. Multiple enteropathogen infections in early life negatively correlated with ΔLAZ, and simultaneous changes in gut inflammatory and permeability markers. A combination vaccine targeting enteropathogens in early life could help in the prevention of future stunting.
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Affiliation(s)
- Najeeha T. Iqbal
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
- Department of Biological & Biomedical Sciences, Aga Khan University, Karachi, Pakistan
| | - Sana Syed
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
- Department of Pediatrics, University of Virginia, Charlottesville, VA, United States of America
| | - Furqan Kabir
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Zehra Jamil
- Department of Biological & Biomedical Sciences, Aga Khan University, Karachi, Pakistan
| | - Tauseef Akhund
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Shahida Qureshi
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Jie Liu
- Department of Medicine, University of Virginia, Charlottesville, VA, United States of America
| | - Jennie Z. Ma
- Department of Medicine, University of Virginia, Charlottesville, VA, United States of America
| | - Shan Guleria
- Department of Pediatrics, University of Virginia, Charlottesville, VA, United States of America
| | - Andrew Gewirtz
- Center for Inflammation Immunity & Infection, Georgia State University, Atlanta, Georgia, United States of America
| | - Christopher P. Duggan
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children’s Hospital, Boston, Massachusetts, United States of America
- Departments of Global Health and Population, and Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Molly A. Hughes
- Department of Medicine, University of Virginia, Charlottesville, VA, United States of America
| | - Kamran Sadiq
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Asad Ali
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
- * E-mail:
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36
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Nisar MI, Nayani K, Akhund T, Riaz A, Irfan O, Shakoor S, Muneer S, Muslim S, Hotwani A, Kabir F, Whitney C, Kim L, Srinivasan V, Ali A, Zaidi AKM, Jehan F. Correction to: Nasopharyngeal carriage of Streptococcus pneumoniae in children under 5 years of age before introduction of pneumococcal vaccine (PCV10) in urban and rural districts in Pakistan. BMC Infect Dis 2019; 19:114. [PMID: 30722782 PMCID: PMC6362562 DOI: 10.1186/s12879-019-3733-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 01/17/2019] [Indexed: 11/10/2022] Open
Affiliation(s)
- Muhammad Imran Nisar
- Department of Pediatrics and Child Health, Aga Khan University, Stadium Road, Karachi, 74800, Pakistan
| | - Kanwal Nayani
- Department of Pediatrics and Child Health, Aga Khan University, Stadium Road, Karachi, 74800, Pakistan
| | - Tauseef Akhund
- Department of Pediatrics and Child Health, Aga Khan University, Stadium Road, Karachi, 74800, Pakistan
| | - Atif Riaz
- Department of Pediatrics and Child Health, Aga Khan University, Stadium Road, Karachi, 74800, Pakistan
| | - Omar Irfan
- Department of Pediatrics and Child Health, Aga Khan University, Stadium Road, Karachi, 74800, Pakistan
| | - Sadia Shakoor
- Department of Pediatrics and Child Health, Aga Khan University, Stadium Road, Karachi, 74800, Pakistan
| | - Sehrish Muneer
- Department of Pediatrics and Child Health, Aga Khan University, Stadium Road, Karachi, 74800, Pakistan
| | - Sana Muslim
- Department of Pediatrics and Child Health, Aga Khan University, Stadium Road, Karachi, 74800, Pakistan
| | - Aneeta Hotwani
- Department of Pediatrics and Child Health, Aga Khan University, Stadium Road, Karachi, 74800, Pakistan
| | - Furqan Kabir
- Department of Pediatrics and Child Health, Aga Khan University, Stadium Road, Karachi, 74800, Pakistan
| | | | - Lindsay Kim
- Centre for Disease Control and Prevention, Atlanta, USA
| | | | - Asad Ali
- Department of Pediatrics and Child Health, Aga Khan University, Stadium Road, Karachi, 74800, Pakistan
| | - Anita K M Zaidi
- Department of Pediatrics and Child Health, Aga Khan University, Stadium Road, Karachi, 74800, Pakistan.,Bill & Melinda Gates Foundation, Seattle, USA
| | - Fyezah Jehan
- Department of Pediatrics and Child Health, Aga Khan University, Stadium Road, Karachi, 74800, Pakistan.
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37
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Nisar MI, Nayani K, Akhund T, Riaz A, Irfan O, Shakoor S, Muneer S, Muslim S, Hotwani A, Kabir F, Whitney C, Kim L, Srinivasan V, Ali A, Zaidi AKM, Jehan F. Nasopharyngeal carriage of Streptococcus pneumoniae in children under 5 years of age before introduction of pneumococcal vaccine (PCV10) in urban and rural districts in Pakistan. BMC Infect Dis 2018; 18:672. [PMID: 30563483 PMCID: PMC6299586 DOI: 10.1186/s12879-018-3608-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 12/10/2018] [Indexed: 11/10/2022] Open
Abstract
Background Benefits of pneumococcal conjugate vaccine programs have been linked to the vaccine’s ability to disrupt nasopharyngeal carriage and transmission. The 10-valent pneumococcal vaccine (PCV10) was included in the Expanded Program on Immunization (EPI) in Sindh, Pakistan in February 2013. This study was carried out immediately before PCV10 introduction to establish baseline pneumococcal carriage and prevalent serotypes in young children and to determine if carriage differed in urban and rural communities. Methods Nasopharyngeal specimens were collected from a random sample of children 3-11 and 12-59 months of age in an urban community (Karachi) and children 3-11 months of age in a rural community (Matiari). Samples were processed in a research laboratory in Karachi. Samples were transported in STGG media, enriched in Todd Hewitt broth, rabbit serum and yeast extract, cultured on 5% sheep blood agar, and serotyped using the CDC standardized sequential multiplex PCR assay. Serotypes were categorized into PCV10-type and non-vaccine types. Results We enrolled 670 children. Pneumococci were detected in 73.6% and 79.5 % of children in the infant group in Karachi and Matiari, respectively, and 78.2% of children 12 to 59 months of age in Karachi. In infants, 38.9% and 33.5% of those carrying pneumococci in Karachi and Matiari, respectively, had PCV10 types. In the older age group in Karachi, the proportion was 30.7%, not significantly different from infants. The most common serotypes were 6A, 23F, 19A, 6B and 19F. Conclusion We found that about 3 of 4 children carried pneumococci, and this figure did not vary with age group or urban or rural residence. Planned annual surveys in the same communities will inform change in carriage of PCV10 serotype pneumococci after the introduction and uptake of PCV10 in these communities Electronic supplementary material The online version of this article (10.1186/s12879-018-3608-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Muhammad Imran Nisar
- Department of Pediatrics and Child Health, Aga Khan University, Stadium Road, Karachi, 74800, Pakistan
| | - Kanwal Nayani
- Department of Pediatrics and Child Health, Aga Khan University, Stadium Road, Karachi, 74800, Pakistan
| | - Tauseef Akhund
- Department of Pediatrics and Child Health, Aga Khan University, Stadium Road, Karachi, 74800, Pakistan
| | - Atif Riaz
- Department of Pediatrics and Child Health, Aga Khan University, Stadium Road, Karachi, 74800, Pakistan
| | - Omar Irfan
- Department of Pediatrics and Child Health, Aga Khan University, Stadium Road, Karachi, 74800, Pakistan
| | - Sadia Shakoor
- Department of Pediatrics and Child Health, Aga Khan University, Stadium Road, Karachi, 74800, Pakistan
| | - Sehrish Muneer
- Department of Pediatrics and Child Health, Aga Khan University, Stadium Road, Karachi, 74800, Pakistan
| | - Sana Muslim
- Department of Pediatrics and Child Health, Aga Khan University, Stadium Road, Karachi, 74800, Pakistan
| | - Aneeta Hotwani
- Department of Pediatrics and Child Health, Aga Khan University, Stadium Road, Karachi, 74800, Pakistan
| | - Furqan Kabir
- Department of Pediatrics and Child Health, Aga Khan University, Stadium Road, Karachi, 74800, Pakistan
| | | | - Lindsay Kim
- Centre for Disease Control and Prevention, Atlanta, USA
| | | | - Asad Ali
- Department of Pediatrics and Child Health, Aga Khan University, Stadium Road, Karachi, 74800, Pakistan
| | - Anita K M Zaidi
- Department of Pediatrics and Child Health, Aga Khan University, Stadium Road, Karachi, 74800, Pakistan.,Bill & Melinda Gates Foundation, Seattle, USA
| | - Fyezah Jehan
- Department of Pediatrics and Child Health, Aga Khan University, Stadium Road, Karachi, 74800, Pakistan.
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38
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Platts-Mills JA, Liu J, Rogawski ET, Kabir F, Lertsethtakarn P, Siguas M, Khan SS, Praharaj I, Murei A, Nshama R, Mujaga B, Havt A, Maciel IA, McMurry TL, Operario DJ, Taniuchi M, Gratz J, Stroup SE, Roberts JH, Kalam A, Aziz F, Qureshi S, Islam MO, Sakpaisal P, Silapong S, Yori PP, Rajendiran R, Benny B, McGrath M, McCormick BJJ, Seidman JC, Lang D, Gottlieb M, Guerrant RL, Lima AAM, Leite JP, Samie A, Bessong PO, Page N, Bodhidatta L, Mason C, Shrestha S, Kiwelu I, Mduma ER, Iqbal NT, Bhutta ZA, Ahmed T, Haque R, Kang G, Kosek MN, Houpt ER. Use of quantitative molecular diagnostic methods to assess the aetiology, burden, and clinical characteristics of diarrhoea in children in low-resource settings: a reanalysis of the MAL-ED cohort study. Lancet Glob Health 2018; 6:e1309-e1318. [PMID: 30287127 PMCID: PMC6227251 DOI: 10.1016/s2214-109x(18)30349-8] [Citation(s) in RCA: 215] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 06/28/2018] [Accepted: 07/11/2018] [Indexed: 12/17/2022]
Abstract
Background Optimum management of childhood diarrhoea in low-resource settings has been hampered by insufficient data on aetiology, burden, and associated clinical characteristics. We used quantitative diagnostic methods to reassess and refine estimates of diarrhoea aetiology from the Etiology, Risk Factors, and Interactions of Enteric Infections and Malnutrition and the Consequences for Child Health and Development (MAL-ED) cohort study. Methods We re-analysed stool specimens from the multisite MAL-ED cohort study of children aged 0–2 years done at eight locations (Dhaka, Bangladesh; Vellore, India; Bhaktapur, Nepal; Naushero Feroze, Pakistan; Venda, South Africa; Haydom, Tanzania; Fortaleza, Brazil; and Loreto, Peru), which included active surveillance for diarrhoea and routine non-diarrhoeal stool collection. We used quantitative PCR to test for 29 enteropathogens, calculated population-level pathogen-specific attributable burdens, derived stringent quantitative cutoffs to identify aetiology for individual episodes, and created aetiology prediction scores using clinical characteristics. Findings We analysed 6625 diarrhoeal and 30 968 non-diarrhoeal surveillance stools from 1715 children. Overall, 64·9% of diarrhoea episodes (95% CI 62·6–71·2) could be attributed to an aetiology by quantitative PCR compared with 32·8% (30·8–38·7) using the original study microbiology. Viral diarrhoea (36·4% of overall incidence, 95% CI 33·6–39·5) was more common than bacterial (25·0%, 23·4–28·4) and parasitic diarrhoea (3·5%, 3·0–5·2). Ten pathogens accounted for 95·7% of attributable diarrhoea: Shigella (26·1 attributable episodes per 100 child-years, 95% CI 23·8–29·9), sapovirus (22·8, 18·9–27·5), rotavirus (20·7, 18·8–23·0), adenovirus 40/41 (19·0, 16·8–23·0), enterotoxigenic Escherichia coli (18·8, 16·5–23·8), norovirus (15·4, 13·5–20·1), astrovirus (15·0, 12·0–19·5), Campylobacter jejuni or C coli (12·1, 8·5–17·2), Cryptosporidium (5·8, 4·3–8·3), and typical enteropathogenic E coli (5·4, 2·8–9·3). 86·2% of the attributable incidence for Shigella was non-dysenteric. A prediction score for shigellosis was more accurate (sensitivity 50·4% [95% CI 46·7–54·1], specificity 84·0% [83·0–84·9]) than current guidelines, which recommend treatment only of bloody diarrhoea to cover Shigella (sensitivity 14·5% [95% CI 12·1–17·3], specificity 96·5% [96·0–97·0]). Interpretation Quantitative molecular diagnostics improved estimates of pathogen-specific burdens of childhood diarrhoea in the community setting. Viral causes predominated, including a substantial burden of sapovirus; however, Shigella had the highest overall burden with a high incidence in the second year of life. These data could improve the management of diarrhoea in these low-resource settings. Funding Bill & Melinda Gates Foundation.
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Affiliation(s)
- James A Platts-Mills
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA.
| | - Jie Liu
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - Elizabeth T Rogawski
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA; Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | | | | | | | - Shaila S Khan
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | | | | | | | - Buliga Mujaga
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
| | | | | | - Timothy L McMurry
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Darwin J Operario
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - Mami Taniuchi
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - Jean Gratz
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - Suzanne E Stroup
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - James H Roberts
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | | | | | | | - M Ohedul Islam
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Pimmada Sakpaisal
- Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand
| | - Sasikorn Silapong
- Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand
| | - Pablo P Yori
- Asociación Benéfica PRISMA, Iquitos, Peru; Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | | | | | - Monica McGrath
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA; Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | | | - Jessica C Seidman
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Dennis Lang
- Foundation for the National Institutes of Health, Bethesda, MD, USA
| | - Michael Gottlieb
- Foundation for the National Institutes of Health, Bethesda, MD, USA
| | - Richard L Guerrant
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | | | | | | | | | - Nicola Page
- National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Ladaporn Bodhidatta
- Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand
| | - Carl Mason
- Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand
| | - Sanjaya Shrestha
- Walter Reed/AFRIMS Research Unit, Nepal, Kathmandu, Nepal; University of Bergen, Bergen, Norway
| | - Ireen Kiwelu
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
| | | | | | | | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Rashidul Haque
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | | | - Margaret N Kosek
- Asociación Benéfica PRISMA, Iquitos, Peru; Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Eric R Houpt
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
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Rogawski ET, Liu J, Platts-Mills JA, Kabir F, Lertsethtakarn P, Siguas M, Khan SS, Praharaj I, Murei A, Nshama R, Mujaga B, Havt A, Maciel IA, Operario DJ, Taniuchi M, Gratz J, Stroup SE, Roberts JH, Kalam A, Aziz F, Qureshi S, Islam MO, Sakpaisal P, Silapong S, Yori PP, Rajendiran R, Benny B, McGrath M, Seidman JC, Lang D, Gottlieb M, Guerrant RL, Lima AAM, Leite JP, Samie A, Bessong PO, Page N, Bodhidatta L, Mason C, Shrestha S, Kiwelu I, Mduma ER, Iqbal NT, Bhutta ZA, Ahmed T, Haque R, Kang G, Kosek MN, Houpt ER. Use of quantitative molecular diagnostic methods to investigate the effect of enteropathogen infections on linear growth in children in low-resource settings: longitudinal analysis of results from the MAL-ED cohort study. Lancet Glob Health 2018; 6:e1319-e1328. [PMID: 30287125 PMCID: PMC6227248 DOI: 10.1016/s2214-109x(18)30351-6] [Citation(s) in RCA: 213] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 06/28/2018] [Accepted: 07/11/2018] [Indexed: 12/15/2022]
Abstract
BACKGROUND Enteropathogen infections in early childhood not only cause diarrhoea but contribute to poor growth. We used molecular diagnostics to assess whether particular enteropathogens were associated with linear growth across seven low-resource settings. METHODS We used quantitative PCR to detect 29 enteropathogens in diarrhoeal and non-diarrhoeal stools collected from children in the first 2 years of life obtained during the Etiology, Risk Factors, and Interactions of Enteric Infections and Malnutrition and the Consequences for Child Health and Development (MAL-ED) multisite cohort study. Length was measured monthly. We estimated associations between aetiology-specific diarrhoea and subclinical enteropathogen infection and quantity and attained length in 3 month intervals, at age 2 and 5 years, and used a longitudinal model to account for temporality and time-dependent confounding. FINDINGS Among 1469 children who completed 2 year follow-up, 35 622 stool samples were tested and yielded valid results. Diarrhoeal episodes attributed to bacteria and parasites, but not viruses, were associated with small decreases in length after 3 months and at age 2 years. Substantial decrements in length at 2 years were associated with subclinical, non-diarrhoeal, infection with Shigella (length-for-age Z score [LAZ] reduction -0·14, 95% CI -0·27 to -0·01), enteroaggregative Escherichia coli (-0·21, -0·37 to -0·05), Campylobacter (-0·17, -0·32 to -0·01), and Giardia (-0·17, -0·30 to -0·05). Norovirus, Cryptosporidium, typical enteropathogenic E coli, and Enterocytozoon bieneusi were also associated with small decrements in LAZ. Shigella and E bieneusi were associated with the largest decreases in LAZ per log increase in quantity per g of stool (-0·13 LAZ, 95% CI -0·22 to -0·03 for Shigella; -0·14, -0·26 to -0·02 for E bieneusi). Based on these models, interventions that successfully decrease exposure to Shigella, enteroaggregative E coli, Campylobacter, and Giardia could increase mean length of children by 0·12-0·37 LAZ (0·4-1·2 cm) at the MAL-ED sites. INTERPRETATION Subclinical infection and quantity of pathogens, particularly Shigella, enteroaggregative E coli, Campylobacter, and Giardia, had a substantial negative association with linear growth, which was sustained during the first 2 years of life, and in some cases, to 5 years. Successfully reducing exposure to certain pathogens might reduce global stunting. FUNDING Bill & Melinda Gates Foundation.
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Affiliation(s)
- Elizabeth T Rogawski
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA; Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Jie Liu
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - James A Platts-Mills
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | | | | | | | - Shaila S Khan
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | | | | | | | - Buliga Mujaga
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
| | | | | | - Darwin J Operario
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - Mami Taniuchi
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - Jean Gratz
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - Suzanne E Stroup
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - James H Roberts
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | | | | | | | - M Ohedul Islam
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Pimmada Sakpaisal
- Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand
| | - Sasikorn Silapong
- Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand
| | - Pablo P Yori
- Asociación Benéfica PRISMA, Iquitos, Peru; Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | | | | | - Monica McGrath
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA; Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Jessica C Seidman
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Dennis Lang
- Foundation for the National Institutes of Health, Bethesda, MD, USA
| | - Michael Gottlieb
- Foundation for the National Institutes of Health, Bethesda, MD, USA
| | - Richard L Guerrant
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | | | | | | | | | - Nicola Page
- National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Ladaporn Bodhidatta
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Carl Mason
- Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand
| | - Sanjaya Shrestha
- Walter Reed/AFRIMS Research Unit, Nepal, Kathmandu, Nepal; University of Bergen, Bergen, Norway
| | - Ireen Kiwelu
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
| | | | | | | | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Rashidul Haque
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | | | - Margaret N Kosek
- Asociación Benéfica PRISMA, Iquitos, Peru; Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Eric R Houpt
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA.
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Saha SK, Schrag SJ, El Arifeen S, Mullany LC, Shahidul Islam M, Shang N, Qazi SA, Zaidi AKM, Bhutta ZA, Bose A, Panigrahi P, Soofi SB, Connor NE, Mitra DK, Isaac R, Winchell JM, Arvay ML, Islam M, Shafiq Y, Nisar I, Baloch B, Kabir F, Ali M, Diaz MH, Satpathy R, Nanda P, Padhi BK, Parida S, Hotwani A, Hasanuzzaman M, Ahmed S, Belal Hossain M, Ariff S, Ahmed I, Ibne Moin SM, Mahmud A, Waller JL, Rafiqullah I, Quaiyum MA, Begum N, Balaji V, Halen J, Nawshad Uddin Ahmed ASM, Weber MW, Hamer DH, Hibberd PL, Sadeq-Ur Rahman Q, Mogan VR, Hossain T, McGee L, Anandan S, Liu A, Panigrahi K, Abraham AM, Baqui AH. Causes and incidence of community-acquired serious infections among young children in south Asia (ANISA): an observational cohort study. Lancet 2018; 392:145-159. [PMID: 30025808 PMCID: PMC6053599 DOI: 10.1016/s0140-6736(18)31127-9] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 05/08/2018] [Accepted: 05/15/2018] [Indexed: 12/11/2022]
Abstract
BACKGROUND More than 500 000 neonatal deaths per year result from possible serious bacterial infections (pSBIs), but the causes are largely unknown. We investigated the incidence of community-acquired infections caused by specific organisms among neonates in south Asia. METHODS From 2011 to 2014, we identified babies through population-based pregnancy surveillance at five sites in Bangladesh, India, and Pakistan. Babies were visited at home by community health workers up to ten times from age 0 to 59 days. Illness meeting the WHO definition of pSBI and randomly selected healthy babies were referred to study physicians. The primary objective was to estimate proportions of specific infectious causes by blood culture and Custom TaqMan Array Cards molecular assay (Thermo Fisher, Bartlesville, OK, USA) of blood and respiratory samples. FINDINGS 6022 pSBI episodes were identified among 63 114 babies (95·4 per 1000 livebirths). Causes were attributed in 28% of episodes (16% bacterial and 12% viral). Mean incidence of bacterial infections was 13·2 (95% credible interval [CrI] 11·2-15·6) per 1000 livebirths and of viral infections was 10·1 (9·4-11·6) per 1000 livebirths. The leading pathogen was respiratory syncytial virus (5·4, 95% CrI 4·8-6·3 episodes per 1000 livebirths), followed by Ureaplasma spp (2·4, 1·6-3·2 episodes per 1000 livebirths). Among babies who died, causes were attributed to 46% of pSBI episodes, among which 92% were bacterial. 85 (83%) of 102 blood culture isolates were susceptible to penicillin, ampicillin, gentamicin, or a combination of these drugs. INTERPRETATION Non-attribution of a cause in a high proportion of patients suggests that a substantial proportion of pSBI episodes might not have been due to infection. The predominance of bacterial causes among babies who died, however, indicates that appropriate prevention measures and management could substantially affect neonatal mortality. Susceptibility of bacterial isolates to first-line antibiotics emphasises the need for prudent and limited use of newer-generation antibiotics. Furthermore, the predominance of atypical bacteria we found and high incidence of respiratory syncytial virus indicated that changes in management strategies for treatment and prevention are needed. Given the burden of disease, prevention of respiratory syncytial virus would have a notable effect on the overall health system and achievement of Sustainable Development Goal. FUNDING Bill & Melinda Gates Foundation.
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Affiliation(s)
- Samir K Saha
- Department of Microbiology, Child Health Research Foundation, Dhaka Shishu Hospital, Sher-E-Bangla Nagar, Dhaka, Bangladesh.
| | - Stephanie J Schrag
- Centers for Disease Control and Prevention, Respiratory Diseases Branch, Atlanta, GA, USA
| | - Shams El Arifeen
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Luke C Mullany
- Johns Hopkins Bloomberg, School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Mohammad Shahidul Islam
- Department of Microbiology, Child Health Research Foundation, Dhaka Shishu Hospital, Sher-E-Bangla Nagar, Dhaka, Bangladesh
| | - Nong Shang
- Centers for Disease Control and Prevention, Respiratory Diseases Branch, Atlanta, GA, USA
| | - Shamim A Qazi
- Department of Child and Adolescent Health and Development, World Health Organization, Geneva, Switzerland
| | - Anita K M Zaidi
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Zulfiqar A Bhutta
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | | | - Pinaki Panigrahi
- Center for Global Health and Development, College of Public Health, University of Nebraska Medical Center, Omaha, NE, USA
| | - Sajid B Soofi
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Nicholas E Connor
- Department of Microbiology, Child Health Research Foundation, Dhaka Shishu Hospital, Sher-E-Bangla Nagar, Dhaka, Bangladesh
| | - Dipak K Mitra
- Maternal and Child Health Division, icddr,b, Dhaka, Bangladesh
| | - Rita Isaac
- Christian Medical College, Bagayam, Vellore, India
| | - Jonas M Winchell
- Centers for Disease Control and Prevention, Respiratory Diseases Branch, Atlanta, GA, USA
| | - Melissa L Arvay
- Centers for Disease Control and Prevention, Respiratory Diseases Branch, Atlanta, GA, USA
| | - Maksuda Islam
- Department of Microbiology, Child Health Research Foundation, Dhaka Shishu Hospital, Sher-E-Bangla Nagar, Dhaka, Bangladesh
| | - Yasir Shafiq
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Imran Nisar
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Benazir Baloch
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Furqan Kabir
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Murtaza Ali
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Maureen H Diaz
- Centers for Disease Control and Prevention, Respiratory Diseases Branch, Atlanta, GA, USA
| | | | - Pritish Nanda
- Asian Institute of Public Health, Bhubaneswar, India
| | | | | | - Aneeta Hotwani
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - M Hasanuzzaman
- Department of Microbiology, Child Health Research Foundation, Dhaka Shishu Hospital, Sher-E-Bangla Nagar, Dhaka, Bangladesh
| | - Sheraz Ahmed
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Mohammad Belal Hossain
- Department of Microbiology, Child Health Research Foundation, Dhaka Shishu Hospital, Sher-E-Bangla Nagar, Dhaka, Bangladesh
| | - Shabina Ariff
- Department of Microbiology, Child Health Research Foundation, Dhaka Shishu Hospital, Sher-E-Bangla Nagar, Dhaka, Bangladesh
| | - Imran Ahmed
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Syed Mamun Ibne Moin
- Johns Hopkins Bloomberg, School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Arif Mahmud
- Johns Hopkins Bloomberg, School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Jessica L Waller
- Centers for Disease Control and Prevention, Respiratory Diseases Branch, Atlanta, GA, USA
| | - Iftekhar Rafiqullah
- Department of Microbiology, Child Health Research Foundation, Dhaka Shishu Hospital, Sher-E-Bangla Nagar, Dhaka, Bangladesh
| | | | - Nazma Begum
- Johns Hopkins Bloomberg, School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | | | - Jasmin Halen
- Christian Medical College, Bagayam, Vellore, India
| | - A S M Nawshad Uddin Ahmed
- Department of Microbiology, Child Health Research Foundation, Dhaka Shishu Hospital, Sher-E-Bangla Nagar, Dhaka, Bangladesh
| | - Martin W Weber
- Child and Adolescent Health and Development Division, World Health Organization Regional Office for Europe, Copenhagen, Denmark
| | - Davidson H Hamer
- Department of Global Health and Center for Global Health and Development, Boston University School of Public Health, Boston, MA, USA
| | - Patricia L Hibberd
- Department of Global Health and Center for Global Health and Development, Boston University School of Public Health, Boston, MA, USA
| | | | | | - Tanvir Hossain
- Maternal and Child Health Division, icddr,b, Dhaka, Bangladesh
| | - Lesley McGee
- Centers for Disease Control and Prevention, Respiratory Diseases Branch, Atlanta, GA, USA
| | | | - Anran Liu
- Centers for Disease Control and Prevention, Respiratory Diseases Branch, Atlanta, GA, USA
| | - Kalpana Panigrahi
- Center for Global Health and Development, College of Public Health, University of Nebraska Medical Center, Omaha, NE, USA
| | | | - Abdullah H Baqui
- Johns Hopkins Bloomberg, School of Public Health, Johns Hopkins University, Baltimore, MD, USA
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Syed S, Yeruva S, Herrmann J, Sailer A, Sadiq K, Iqbal N, Kabir F, Ahmed K, Qureshi S, Moore SR, Turner J, Ali SA. Environmental Enteropathy in Undernourished Pakistani Children: Clinical and Histomorphometric Analyses. Am J Trop Med Hyg 2018; 98:1577-1584. [PMID: 29611507 PMCID: PMC6086170 DOI: 10.4269/ajtmh.17-0306] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Despite nutrition interventions, stunting thought to be secondary to underlying environmental enteropathy (EE) remains pervasive among infants residing in resource-poor countries and remains poorly characterized. From a birth cohort of 380 children, 65 malnourished infants received 12 weeks of nutritional supplementation with ready-to-use therapeutic food (RUTF). Eleven children with insufficient response to RUTF underwent upper endoscopy with duodenal biopsies, which were compared with U.S., age-matched specimens for healthy, celiac disease, non-celiac villous atrophy, non-celiac intraepithelial lymphocytosis, and graft-versus-host disease patients. Of the 11 children biopsied, EE was found in 10 (91%) with one subject with celiac disease. Morphometry demonstrated decreased villus-to-crypt (V:C) ratios in EE relative to healthy and non-celiac lymphocytosis patients. Environmental enteropathy villus volumes were significantly decreased relative to healthy controls. In EE, average CD3+ cells per 100 epithelial cells and per 1,000 µm2 of lamina propria and the number of lamina propria CD20+ B-cell aggregates were increased relative to all other groups. Our results indicate that V:C ratios are reduced in EE but are less severe than in celiac disease. Environmental enteropathy intraepithelial and lamina propria T lymphocytosis is of greater magnitude than that in celiac disease. The increases in lamina propria B and T lymphocytes suggest that non-cytolytic lymphocytic activation may be a more prominent feature of EE relative to celiac disease. These results provide new insights into shared yet distinct histological and immunological features of EE and celiac disease in children.
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Affiliation(s)
- Sana Syed
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.,Department of Pediatrics, University of Virginia, Charlottesville, Virginia.,Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan.,Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Sunil Yeruva
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jeremy Herrmann
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Anne Sailer
- Department of Pathology, University of Chicago, Chicago, Illinois
| | - Kamran Sadiq
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Najeeha Iqbal
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Furqan Kabir
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Kumail Ahmed
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Shahida Qureshi
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Sean R Moore
- Department of Pediatrics, University of Virginia, Charlottesville, Virginia
| | - Jerrold Turner
- Department of Pathology, University of Chicago, Chicago, Illinois.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.,Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - S Asad Ali
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
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Olortegui MP, Rouhani S, Yori PP, Salas MS, Trigoso DR, Mondal D, Bodhidatta L, Platts-Mills J, Samie A, Kabir F, Lima A, Babji S, Shrestha SK, Mason CJ, Kalam A, Bessong P, Ahmed T, Mduma E, Bhutta ZA, Lima I, Ramdass R, Moulton LH, Lang D, George A, Zaidi AK, Kang G, Houpt ER, Kosek MN. Astrovirus Infection and Diarrhea in 8 Countries. Pediatrics 2018; 141:peds.2017-1326. [PMID: 29259078 PMCID: PMC9923568 DOI: 10.1542/peds.2017-1326] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/12/2017] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND AND OBJECTIVES Astroviruses are important drivers of viral gastroenteritis but remain understudied in community settings and low- and middle-income countries. We present data from 8 countries with high prevalence of diarrhea and undernutrition to describe astrovirus epidemiology and assess evidence for protective immunity among children 0 to 2 years of age. METHODS We used 25 898 surveillance stools and 7077 diarrheal stools contributed by 2082 children for enteropathogen testing, and longitudinal statistical analysis to describe incidence, risk factors, and protective immunity. RESULTS Thirty-five percent of children experienced astrovirus infections. Prevalence in diarrheal stools was 5.6%, and severity exceeded all enteropathogens except rotavirus. Incidence of infection and diarrhea were 2.12 and 0.88 episodes per 100 child-months, respectively. Children with astrovirus infection had 2.30 times the odds of experiencing diarrhea after adjustment for covariates (95% confidence interval [CI], 2.01-2.62; P < .001). Undernutrition was a risk factor: odds of infection and diarrhea were reduced by 10% and 13%, respectively, per increase in length-for-age z score (infection: odds ratio, 0.90 [95% CI, 0.85-0.96]; P < .001; diarrhea: odds ratio, 0.87 [95% CI, 0.79-0.96]; P = .006). Some evidence of protective immunity to infection was detected (hazard ratio, 0.84 [95% CI, 0.71-1.00], P = .052), although this was heterogeneous between sites and significant in India and Peru. CONCLUSIONS Astrovirus is an overlooked cause of diarrhea among vulnerable children worldwide. With the evidence presented here, we highlight the need for future research as well as the potential for astrovirus to be a target for vaccine development.
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Affiliation(s)
| | - Saba Rouhani
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Pablo Peñataro Yori
- Asociación Benéfica PRISMA, Iquitos, Peru;,Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | | | | | | | | | - James Platts-Mills
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia
| | | | | | - Aldo Lima
- Universidade Federal do Ceará, Fortaleza, Brazil
| | | | - Sanjaya Kumar Shrestha
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand;,Centre for International Health, University of Bergen, Bergen, Norway
| | - Carl J. Mason
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Adil Kalam
- Aga Khan University, Naushahro Feroze, Pakistan
| | | | | | | | | | - Ila Lima
- Universidade Federal do Ceará, Fortaleza, Brazil
| | | | - Lawrence H. Moulton
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Dennis Lang
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland; and,Foundation for the National Institutes of Health, Bethesda, Maryland
| | | | | | | | - Eric R. Houpt
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia
| | - Margaret N. Kosek
- Asociación Benéfica PRISMA, Iquitos, Peru;,Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland;,Address correspondence to Margaret N. Kosek, MD, Department of International Health, Johns Hopkins Bloomberg School of Public Health, 615 N Wolfe St, Baltimore, MD 21205. E-mail
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Liu J, Platts-Mills JA, Juma J, Kabir F, Nkeze J, Okoi C, Operario DJ, Uddin J, Ahmed S, Alonso PL, Antonio M, Becker SM, Blackwelder WC, Breiman RF, Faruque ASG, Fields B, Gratz J, Haque R, Hossain A, Hossain MJ, Jarju S, Qamar F, Iqbal NT, Kwambana B, Mandomando I, McMurry TL, Ochieng C, Ochieng JB, Ochieng M, Onyango C, Panchalingam S, Kalam A, Aziz F, Qureshi S, Ramamurthy T, Roberts JH, Saha D, Sow SO, Stroup SE, Sur D, Tamboura B, Taniuchi M, Tennant SM, Toema D, Wu Y, Zaidi A, Nataro JP, Kotloff KL, Levine MM, Houpt ER. Use of quantitative molecular diagnostic methods to identify causes of diarrhoea in children: a reanalysis of the GEMS case-control study. Lancet 2016; 388:1291-301. [PMID: 27673470 PMCID: PMC5471845 DOI: 10.1016/s0140-6736(16)31529-x] [Citation(s) in RCA: 538] [Impact Index Per Article: 67.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 07/18/2016] [Accepted: 07/19/2016] [Indexed: 12/13/2022]
Abstract
BACKGROUND Diarrhoea is the second leading cause of mortality in children worldwide, but establishing the cause can be complicated by diverse diagnostic approaches and varying test characteristics. We used quantitative molecular diagnostic methods to reassess causes of diarrhoea in the Global Enteric Multicenter Study (GEMS). METHODS GEMS was a study of moderate to severe diarrhoea in children younger than 5 years in Africa and Asia. We used quantitative real-time PCR (qPCR) to test for 32 enteropathogens in stool samples from cases and matched asymptomatic controls from GEMS, and compared pathogen-specific attributable incidences with those found with the original GEMS microbiological methods, including culture, EIA, and reverse-transcriptase PCR. We calculated revised pathogen-specific burdens of disease and assessed causes in individual children. FINDINGS We analysed 5304 sample pairs. For most pathogens, incidence was greater with qPCR than with the original methods, particularly for adenovirus 40/41 (around five times), Shigella spp or enteroinvasive Escherichia coli (EIEC) and Campylobactor jejuni o C coli (around two times), and heat-stable enterotoxin-producing E coli ([ST-ETEC] around 1·5 times). The six most attributable pathogens became, in descending order, Shigella spp, rotavirus, adenovirus 40/41, ST-ETEC, Cryptosporidium spp, and Campylobacter spp. Pathogen-attributable diarrhoeal burden was 89·3% (95% CI 83·2-96·0) at the population level, compared with 51·5% (48·0-55·0) in the original GEMS analysis. The top six pathogens accounted for 77·8% (74·6-80·9) of all attributable diarrhoea. With use of model-derived quantitative cutoffs to assess individual diarrhoeal cases, 2254 (42·5%) of 5304 cases had one diarrhoea-associated pathogen detected and 2063 (38·9%) had two or more, with Shigella spp and rotavirus being the pathogens most strongly associated with diarrhoea in children with mixed infections. INTERPRETATION A quantitative molecular diagnostic approach improved population-level and case-level characterisation of the causes of diarrhoea and indicated a high burden of disease associated with six pathogens, for which targeted treatment should be prioritised. FUNDING Bill & Melinda Gates Foundation.
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Affiliation(s)
- Jie Liu
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - James A Platts-Mills
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - Jane Juma
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Furqan Kabir
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Joseph Nkeze
- Center for Vaccine Development and Institute of Global Health, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - Darwin J Operario
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - Jashim Uddin
- International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR, B), Dhaka, Bangladesh
| | - Shahnawaz Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR, B), Dhaka, Bangladesh
| | - Pedro L Alonso
- Centro de Investigação em Saúde da Manhiça, Maputo, Mozambique; Barcelona Centre for International Health Research (CRESIB, Hospital Clinic-Universitat de Barcelona), Barcelona, Spain
| | | | - Stephen M Becker
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - William C Blackwelder
- Center for Vaccine Development and Institute of Global Health, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Robert F Breiman
- Global Disease Detection Division, Kenya Office of the US Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Abu S G Faruque
- International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR, B), Dhaka, Bangladesh
| | - Barry Fields
- Global Disease Detection Division, Kenya Office of the US Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Jean Gratz
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - Rashidul Haque
- International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR, B), Dhaka, Bangladesh
| | - Anowar Hossain
- International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR, B), Dhaka, Bangladesh
| | | | - Sheikh Jarju
- Medical Research Council Unit, Banjul, The Gambia
| | - Farah Qamar
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Najeeha Talat Iqbal
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | | | | | - Timothy L McMurry
- Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Caroline Ochieng
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - John B Ochieng
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Melvin Ochieng
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Clayton Onyango
- Global Disease Detection Division, Kenya Office of the US Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Sandra Panchalingam
- Center for Vaccine Development and Institute of Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Adil Kalam
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Fatima Aziz
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Shahida Qureshi
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | | | - James H Roberts
- Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | | | - Samba O Sow
- Centre pour le Développement des Vaccins, Bamako, Mali
| | - Suzanne E Stroup
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - Dipika Sur
- National Institute of Cholera and Enteric Diseases, Kolkata, India
| | | | - Mami Taniuchi
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - Sharon M Tennant
- Center for Vaccine Development and Institute of Global Health, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Deanna Toema
- Center for Vaccine Development and Institute of Global Health, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Yukun Wu
- Center for Vaccine Development and Institute of Global Health, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Anita Zaidi
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - James P Nataro
- Department of Pediatrics, University of Virginia, Charlottesville, VA, USA
| | - Karen L Kotloff
- Center for Vaccine Development and Institute of Global Health, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Myron M Levine
- Center for Vaccine Development and Institute of Global Health, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Eric R Houpt
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA.
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Rouhani S, Peñataro Yori P, Paredes Olortegui M, Siguas Salas M, Rengifo Trigoso D, Mondal D, Bodhidatta L, Platts-Mills J, Samie A, Kabir F, Lima A, Babji S, Mason CJ, Kalam A, Bessong P, Ahmed T, Mduma E, Bhutta ZA, Lima I, Ramdass R, Lang D, George A, Zaidi AKM, Kang G, Houpt E, Kosek MN. Norovirus Infection and Acquired Immunity in 8 Countries: Results From the MAL-ED Study. Clin Infect Dis 2016; 62:1210-7. [PMID: 27013692 PMCID: PMC4845786 DOI: 10.1093/cid/ciw072] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 12/22/2015] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Norovirus is an important cause of childhood diarrhea. We present data from a longitudinal, multicountry study describing norovirus epidemiology during the first 2 years of life. METHODS A birth cohort of 1457 children across 8 countries contributed 7077 diarrheal stools for norovirus testing. A subset of 199 children contributed additional asymptomatic samples (2307) and diarrheal stools (770), which were used to derive incidence rates and evaluate evidence for acquired immunity. RESULTS Across sites, 89% of children experienced at least 1 norovirus infection before 24 months, and 22.7% of all diarrheal stools were norovirus positive. Severity of norovirus-positive diarrhea was comparable to other enteropathogens, with the exception of rotavirus. Incidence of genogroup II (GII) infection was higher than genogroup I and peaked at 6-11 months across sites. Undernutrition was a risk factor for symptomatic norovirus infection, with an increase in 1 standard deviation of length-for-age z score associated with a 17% reduction (odds ratio, 0.83 [95% confidence interval, .72-.97]; P = .011) in the odds of experiencing diarrhea when norovirus was present, after accounting for genogroup, rotavirus vaccine, and age. Evidence of acquired immunity was observed among GII infections only: Children with prior GII infection were found to have a 27% reduction in the hazard of subsequent infection (hazard ratio, 0.727; P = .010). CONCLUSIONS The high prevalence of norovirus across 8 sites in highly variable epidemiologic settings and demonstration of protective immunity for GII infections provide support for investment in vaccine development.
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Affiliation(s)
| | | | | | | | | | - Dinesh Mondal
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka
| | | | | | | | | | - Aldo Lima
- Universidade Federal do Ceará, Fortaleza, Brazil
| | | | - Carl J Mason
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Adil Kalam
- Aga Khan University, Naushahro Feroze, Pakistan
| | | | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka
| | | | | | - Ila Lima
- Universidade Federal do Ceará, Fortaleza, Brazil
| | | | - Dennis Lang
- Foundation for the National Institutes of Health, Bethesda, Maryland
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Platts-Mills JA, Babji S, Bodhidatta L, Gratz J, Haque R, Havt A, McCormick BJ, McGrath M, Olortegui MP, Samie A, Shakoor S, Mondal D, Lima IF, Hariraju D, Rayamajhi BB, Qureshi S, Kabir F, Yori PP, Mufamadi B, Amour C, Carreon JD, Richard SA, Lang D, Bessong P, Mduma E, Ahmed T, Lima AA, Mason CJ, Zaidi AK, Bhutta ZA, Kosek M, Guerrant RL, Gottlieb M, Miller M, Kang G, Houpt ER. Pathogen-specific burdens of community diarrhoea in developing countries: a multisite birth cohort study (MAL-ED). Lancet Glob Health 2015. [PMID: 26202075 DOI: 10.1016/s2214-109x(15)00151-5] [Citation(s) in RCA: 587] [Impact Index Per Article: 65.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
BACKGROUND Most studies of the causes of diarrhoea in low-income and middle-income countries have looked at severe disease in people presenting for care, and there are few estimates of pathogen-specific diarrhoea burdens in the community. METHODS We undertook a birth cohort study with not only intensive community surveillance for diarrhoea but also routine collection of non-diarrhoeal stools from eight sites in South America, Africa, and Asia. We enrolled children within 17 days of birth, and diarrhoeal episodes (defined as maternal report of three or more loose stools in 24 h, or one loose stool with visible blood) were identified through twice-weekly home visits by fieldworkers over a follow-up period of 24 months. Non-diarrhoeal stool specimens were also collected for surveillance for months 1-12, 15, 18, 21, and 24. Stools were analysed for a broad range of enteropathogens using culture, enzyme immunoassay, and PCR. We used the adjusted attributable fraction (AF) to estimate pathogen-specific burdens of diarrhoea. FINDINGS Between November 26, 2009, and February 25, 2014, we tested 7318 diarrhoeal and 24 310 non-diarrhoeal stools collected from 2145 children aged 0-24 months. Pathogen detection was common in non-diarrhoeal stools but was higher with diarrhoea. Norovirus GII (AF 5·2%, 95% CI 3·0-7·1), rotavirus (4·8%, 4·5-5·0), Campylobacter spp (3·5%, 0·4-6·3), astrovirus (2·7%, 2·2-3·1), and Cryptosporidium spp (2·0%, 1·3-2·6) exhibited the highest attributable burdens of diarrhoea in the first year of life. The major pathogens associated with diarrhoea in the second year of life were Campylobacter spp (7·9%, 3·1-12·1), norovirus GII (5·4%, 2·1-7·8), rotavirus (4·9%, 4·4-5·2), astrovirus (4·2%, 3·5-4·7), and Shigella spp (4·0%, 3·6-4·3). Rotavirus had the highest AF for sites without rotavirus vaccination and the fifth highest AF for sites with the vaccination. There was substantial variation in pathogens according to geography, diarrhoea severity, and season. Bloody diarrhoea was primarily associated with Campylobacter spp and Shigella spp, fever and vomiting with rotavirus, and vomiting with norovirus GII. INTERPRETATION There was substantial heterogeneity in pathogen-specific burdens of diarrhoea, with important determinants including age, geography, season, rotavirus vaccine usage, and symptoms. These findings suggest that although single-pathogen strategies have an important role in the reduction of the burden of severe diarrhoeal disease, the effect of such interventions on total diarrhoeal incidence at the community level might be limited.
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Affiliation(s)
- James A Platts-Mills
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | | | | | - Jean Gratz
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA; Haydom Lutheran Hospital, Haydom, Tanzania
| | - Rashidul Haque
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Alexandre Havt
- Clinical Research Unit and Institute of Biomedicine, Federal University of Ceara, Fortaleza, Brazil
| | | | - Monica McGrath
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | | | | | | | - Dinesh Mondal
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Ila Fn Lima
- Clinical Research Unit and Institute of Biomedicine, Federal University of Ceara, Fortaleza, Brazil
| | | | | | | | | | | | | | | | - J Daniel Carreon
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Stephanie A Richard
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Dennis Lang
- Foundation for the National Institutes of Health, Bethesda, MD, USA
| | | | - Esto Mduma
- Haydom Lutheran Hospital, Haydom, Tanzania
| | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Aldo Aam Lima
- Clinical Research Unit and Institute of Biomedicine, Federal University of Ceara, Fortaleza, Brazil
| | - Carl J Mason
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | | | | | - Margaret Kosek
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA; Asociación Benéfica PRISMA, Iquitos, Peru
| | - Richard L Guerrant
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - Michael Gottlieb
- Foundation for the National Institutes of Health, Bethesda, MD, USA
| | - Mark Miller
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | | | - Eric R Houpt
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA.
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Liu J, Kabir F, Manneh J, Lertsethtakarn P, Begum S, Gratz J, Becker SM, Operario DJ, Taniuchi M, Janaki L, Platts-Mills JA, Haverstick DM, Kabir M, Sobuz SU, Nakjarung K, Sakpaisal P, Silapong S, Bodhidatta L, Qureshi S, Kalam A, Saidi Q, Swai N, Mujaga B, Maro A, Kwambana B, Dione M, Antonio M, Kibiki G, Mason CJ, Haque R, Iqbal N, Zaidi AKM, Houpt ER. Development and assessment of molecular diagnostic tests for 15 enteropathogens causing childhood diarrhoea: a multicentre study. Lancet Infect Dis 2014; 14:716-724. [PMID: 25022434 DOI: 10.1016/s1473-3099(14)70808-4] [Citation(s) in RCA: 224] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
BACKGROUND Childhood diarrhoea can be caused by many pathogens that are difficult to assay in the laboratory. Molecular diagnostic techniques provide a uniform method to detect and quantify candidate enteropathogens. We aimed to develop and assess molecular tests for identification of enteropathogens and their association with disease. METHODS We developed and assessed molecular diagnostic tests for 15 enteropathogens across three platforms-PCR-Luminex, multiplex real-time PCR, and TaqMan array card-at five laboratories worldwide. We judged the analytical and clinical performance of these molecular techniques against comparator methods (bacterial culture, ELISA, and PCR) using 867 diarrhoeal and 619 non-diarrhoeal stool specimens. We also measured molecular quantities of pathogens to predict the association with diarrhoea, by univariate logistic regression analysis. FINDINGS The molecular tests showed very good analytical and clinical performance at all five laboratories. Comparator methods had limited sensitivity compared with the molecular techniques (20-85% depending on the target) but good specificity (median 97·3%, IQR 96·5-98·9; mean 95·2%, SD 9·1). Positive samples by comparator methods usually had higher molecular quantities of pathogens than did negative samples, across almost all platforms and for most pathogens (p<0·05). The odds ratio for diarrhoea at a given quantity (measured by quantification cycle, Cq) showed that for most pathogens associated with diarrhoea-including Campylobacter jejuni and Campylobacter coli, Cryptosporidium spp, enteropathogenic Escherichia coli, heat-stable enterotoxigenic E coli, rotavirus, Shigella spp and enteroinvasive E coli, and Vibrio cholerae-the strength of association with diarrhoea increased at higher pathogen loads. For example, Shigella spp at a Cq range of 15-20 had an odds ratio of 8·0 (p<0·0001), but at a Cq range of 25-30 the odds ratio fell to 1·7 (p=0·043). INTERPRETATION Molecular diagnostic tests can be implemented successfully and with fidelity across laboratories around the world. In the case of diarrhoea, these techniques can detect pathogens with high sensitivity and ascribe diarrhoeal associations based on quantification, including in mixed infections, providing rich and unprecedented measurements of infectious causes. FUNDING Bill & Melinda Gates Foundation Next Generation Molecular Diagnostics Project.
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Affiliation(s)
- Jie Liu
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - Furqan Kabir
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | | | - Paphavee Lertsethtakarn
- Department of Enteric Diseases, Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand
| | - Sharmin Begum
- International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR, B), Dhaka, Bangladesh
| | - Jean Gratz
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA; Kilimanjaro Clinical Research Institute, Moshi, Tanzania
| | - Steve M Becker
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - Darwin J Operario
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - Mami Taniuchi
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - Lalitha Janaki
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - James A Platts-Mills
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - Doris M Haverstick
- Department of Pathology, University of Virginia, Charlottesville, VA, USA
| | - Mamun Kabir
- International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR, B), Dhaka, Bangladesh
| | - Shihab U Sobuz
- International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR, B), Dhaka, Bangladesh
| | - Kaewkanya Nakjarung
- Department of Enteric Diseases, Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand
| | - Pimmada Sakpaisal
- Department of Enteric Diseases, Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand
| | - Sasikorn Silapong
- Department of Enteric Diseases, Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand
| | - Ladaporn Bodhidatta
- Department of Enteric Diseases, Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand
| | - Shahida Qureshi
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Adil Kalam
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Queen Saidi
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
| | - Ndealilia Swai
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
| | | | - Athanasia Maro
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
| | | | - Michel Dione
- Medical Research Council Unit, Banjul, The Gambia
| | | | - Gibson Kibiki
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
| | - Carl J Mason
- Department of Enteric Diseases, Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand
| | - Rashidul Haque
- International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR, B), Dhaka, Bangladesh
| | - Najeeha Iqbal
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Anita K M Zaidi
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Eric R Houpt
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA.
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Shakoor S, Kabir F, Khowaja AR, Qureshi SM, Jehan F, Qamar F, Whitney CG, Zaidi AKM. Pneumococcal serotypes and serogroups causing invasive disease in Pakistan, 2005-2013. PLoS One 2014; 9:e98796. [PMID: 24892937 PMCID: PMC4043782 DOI: 10.1371/journal.pone.0098796] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 05/06/2014] [Indexed: 11/19/2022] Open
Abstract
While pneumococcal conjugate vaccines have been implemented in most countries worldwide, use in Asia has lagged in part because of a lack of data on the amount of disease that is vaccine preventable in the region. We describe pneumococcal serotypes elicited from 111 episodes of invasive pneumococcal disease (IPD) from 2005 to 2013 among children and adults in Pakistan. Seventy-three percent (n = 81) of 111 IPD episodes were cases of meningitis (n = 76 in children 0–15 years and n = 5 among adults). Serotypes were determined by target amplification of DNA extracted from pneumococcal isolates (n = 52) or CSF specimens (n = 59). Serogroup 18 was the most common serogroup causing meningitis in children <5 years, accounting for 21% of cases (n = 13). The 10-valent pneumococcal conjugate vaccine (PCV 10) or PCV10- related serotypes were found in 61% (n = 47) of childhood (age 0–15 years) meningitis episodes. PCV-13 increased this coverage to 63% (one additional serotype 19A; n = 48). Our data indicate that use of PCVs would prevent a large proportion of serious pneumococcal disease.
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Affiliation(s)
- Sadia Shakoor
- Department of Pediatrics and Child Health, the Aga Khan University Hospital, Karachi, Pakistan
- Department of Pathology and Microbiology, the Aga Khan University Hospital, Karachi, Pakistan
| | - Furqan Kabir
- Department of Pediatrics and Child Health, the Aga Khan University Hospital, Karachi, Pakistan
| | - Asif R. Khowaja
- Department of Pediatrics and Child Health, the Aga Khan University Hospital, Karachi, Pakistan
| | - Shahida M. Qureshi
- Department of Pediatrics and Child Health, the Aga Khan University Hospital, Karachi, Pakistan
| | - Fyezah Jehan
- Department of Pediatrics and Child Health, the Aga Khan University Hospital, Karachi, Pakistan
| | - Farah Qamar
- Department of Pediatrics and Child Health, the Aga Khan University Hospital, Karachi, Pakistan
| | - Cynthia G. Whitney
- National Center for Immunization and Respiratory Diseases, CDC, Atlanta, Georgia, United States of America
| | - Anita K. M. Zaidi
- Department of Pediatrics and Child Health, the Aga Khan University Hospital, Karachi, Pakistan
- * E-mail:
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Kabir F, . MS, . GM, . MR, . MK, . MA. Study on Production System of Existing Ducks at Potuakhali District of Bangladesh and Development of a Self-sustainable Ducks Rearing Model Under Semi-scavenging System at Farmer`s Condition. ACTA ACUST UNITED AC 2007. [DOI: 10.3923/jbs.2007.327.332] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Wang J, Satoh M, Kabir F, Shaw M, Domingo MA, Mansoor R, Behney KM, Dong X, Lahita RG, Richards HB, Reeves WH. Increased prevalence of autoantibodies to ku antigen in African American versus white patients with systemic lupus erythematosus. Arthritis Rheum 2001; 44:2367-70. [PMID: 11665978 DOI: 10.1002/1529-0131(200110)44:10<2367::aid-art400>3.0.co;2-i] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
OBJECTIVE To investigate whether the widely varying estimates of the prevalence of anti-Ku autoantibodies are explained by racial/ethnic differences. METHODS Consecutive African American or white patients who met the 1982 criteria for systemic lupus erythematosus (SLE) and who were evaluated over 10 years in North Carolina, Florida, and New York were tested by immunoprecipitation of K562 cell extract for anti-Ku as well as anti-nuclear RNP (nRNP)/Sm, anti-Ro/SSA, and anti-La/SSB autoantibodies. RESULTS Anti-Ku autoantibodies were detected in sera from 18 of 155 African American patients with SLE (12%) versus 0 of 126 white patients (P < 0.0001, by Fisher's exact test). Anti-nRNP (63% versus 16%; P < 0.0001) and anti-Sm (23% versus 7%; P < 0.0004) autoantibodies were also more common in the African American subset. The 2 groups had comparable frequencies of anti-Ro/SSA and anti-La/SSB autoantibodies. CONCLUSION Anti-Ku antibodies are common in African American patients with SLE but rare in whites, probably explaining the different estimates of their prevalence. In African Americans, the frequency is comparable with that of anti-La/SSB. Along with anti-Ku, anti-nRNP and anti-Sm autoantibodies are also overrepresented in African Americans, suggesting that a group of specificities is characteristically associated with SLE in African Americans.
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Affiliation(s)
- J Wang
- Medical College of Georgia, Augusta, USA
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Kabir F, Wilson JE. Mitochondrial hexokinase in brain: coexistence of forms differing in sensitivity to solubilization by glucose-6-phosphate on the same mitochondria. Arch Biochem Biophys 1994; 310:410-6. [PMID: 8179326 DOI: 10.1006/abbi.1994.1186] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Hexokinase (ATP:D-hexose 6-phosphotransferase, EC 2.7.1.1) is associated with mitochondria from brain of various species. The fraction of the bound activity that can be released in soluble form after incubation of the mitochondria with glucose-6-phosphate (Glc-6-P) has been shown to vary markedly among species (F. Kabir and J.E. Wilson, Arch. Biochem. Biophys. 300, 641-650, 1993). A method has been developed by which mitochondria bearing significant amounts of bound hexokinase can be selectively immunoprecipitated by Staphylococcus aureus cells coated with anti-Type I hexokinase antibodies. Treatment of mitochondria from guinea pig, bovine, and human brain with Glc-6-P solubilized approximately 60, 40, and 20% of the bound hexokinase activity, respectively, but had no effect on the extent to which the mitochondria could be immunoprecipitated. This is consistent with the view that the residual hexokinase, resistant to solubilization with Glc-6-P, coexists on the same mitochondria bearing the Glc-6-P-sensitive form, i.e., removal of the latter does not prevent immunoprecipitation mediated by the Glc-6-P-resistant form. Mitochondrial porin has previously been shown to be involved in binding of hexokinase to mitochondria. Four porin species, having a common molecular weight but differing in isoelectric point, were detected, in the same relative amounts, in mitochondria from bovine and rat brain. The extent to which Glc-6-P solubilizes hexokinase from rat and bovine brain mitochondria is approximately 90 and approximately 40%, respectively. Thus the marked difference in sensitivity to solubilization with Glc-6-P cannot be attributed to differences in the relative amounts of different porin species present in rat and bovine mitochondria.
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Affiliation(s)
- F Kabir
- Department of Biochemistry, Michigan State University, East Lansing 48824
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