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Kakaraskoska Boceska B, Vilken T, Xavier BB, Kostyanev T, Lin Q, Lammens C, Ellis S, O'Brien S, da Costa RMA, Cook A, Russell N, Bielicki J, Riddell A, Stohr W, Walker AS, Berezin EN, Roilides E, De Luca M, Romani L, Ballot D, Dramowski A, Wadula J, Lochindarat S, Boonkasidecha S, Namiiro F, Ngoc HTB, Tran MD, Cressey TR, Preedisripipat K, Berkley JA, Musyimi R, Zarras C, Nana T, Whitelaw A, da Silva CB, Jaglal P, Ssengooba W, Saha SK, Islam MS, Mussi-Pinhata MM, Carvalheiro CG, Piddock LJV, Heath PT, Malhotra-Kumar S, Sharland M, Glupczynski Y, Goossens H. Assessment of three antibiotic combination regimens against Gram-negative bacteria causing neonatal sepsis in low- and middle-income countries. Nat Commun 2024; 15:3947. [PMID: 38729951 PMCID: PMC11087563 DOI: 10.1038/s41467-024-48296-z] [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: 11/27/2023] [Accepted: 04/26/2024] [Indexed: 05/12/2024] Open
Abstract
Gram-negative bacteria (GNB) are a major cause of neonatal sepsis in low- and middle-income countries (LMICs). Although the World Health Organization (WHO) reports that over 80% of these sepsis deaths could be prevented through improved treatment, the efficacy of the currently recommended first- and second-line treatment regimens for this condition is increasingly affected by high rates of drug resistance. Here we assess three well known antibiotics, fosfomycin, flomoxef and amikacin, in combination as potential antibiotic treatment regimens by investigating the drug resistance and genetic profiles of commonly isolated GNB causing neonatal sepsis in LMICs. The five most prevalent bacterial isolates in the NeoOBS study (NCT03721302) are Klebsiella pneumoniae, Acinetobacter baumannii, E. coli, Serratia marcescens and Enterobacter cloacae complex. Among these isolates, high levels of ESBL and carbapenemase encoding genes are detected along with resistance to ampicillin, gentamicin and cefotaxime, the current WHO recommended empiric regimens. The three new combinations show excellent in vitro activity against ESBL-producing K. pneumoniae and E. coli isolates. Our data should further inform and support the clinical evaluation of these three antibiotic combinations for the treatment of neonatal sepsis in areas with high rates of multidrug-resistant Gram-negative bacteria.
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Affiliation(s)
- Biljana Kakaraskoska Boceska
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium.
| | - Tuba Vilken
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Basil Britto Xavier
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
- Department of Medical Microbiology and Infection Control, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Tomislav Kostyanev
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
- Research Group for Global Capacity Building, National Food Institute, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Qiang Lin
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Christine Lammens
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Sally Ellis
- Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland
| | - Seamus O'Brien
- Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland
| | | | - Aislinn Cook
- Centre for Neonatal and Pediatric Infection, Institute for Infection & Immunity, St. George's University of London, London, UK
| | - Neal Russell
- Centre for Neonatal and Pediatric Infection, Institute for Infection & Immunity, St. George's University of London, London, UK
| | - Julia Bielicki
- Centre for Neonatal and Pediatric Infection, Institute for Infection & Immunity, St. George's University of London, London, UK
- Paediatric Research Centre, University of Basel Children's Hospital, Basel, Switzerland
| | - Amy Riddell
- Centre for Neonatal and Pediatric Infection, Institute for Infection & Immunity, St. George's University of London, London, UK
| | - Wolfgang Stohr
- MRC Clinical Trials Unit, University College London, London, UK
| | | | | | - Emmanuel Roilides
- Infectious Diseases Unit, 3rd Dept Paediatrics, School of Medicine, Faculty of Health Sciences, Aristotle University and Hippokration General Hospital, Thessaloniki, Greece
| | - Maia De Luca
- Infectious Disease Unit, Bambino Gesu Children's Hospital, Rome, Italy
| | - Lorenza Romani
- Infectious Disease Unit, Bambino Gesu Children's Hospital, Rome, Italy
| | - Daynia Ballot
- Department of Pediatrics and Child Health, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Angela Dramowski
- Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Jeannette Wadula
- Department of Clinical Microbiology & Infectious Diseases, National Health Laboratory Services, CH Baragwanath Academic Hospital, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | | | | | - Flavia Namiiro
- Mulago Specialized Women's and Neonatal Hospital, Kampala, Uganda
| | | | | | - Tim R Cressey
- AMS-PHPT Research Collaboration, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | | | - James A Berkley
- Clinical Research Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine & Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- The Childhood Acute Illness & Nutrition (CHAIN) Network, Nairobi, Kenya
| | - Robert Musyimi
- Department of Microbiology, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Charalampos Zarras
- Microbiology Department, Hippokration General Hospital, Thessaloniki, Greece
| | - Trusha Nana
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Andrew Whitelaw
- Division of Medical Microbiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Microbiology Laboratory, National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
| | - Cely Barreto da Silva
- Infection Control and Prevention Service, Santa Casa de Sao Paulo, Sao Paulo, Brazil
| | - Prenika Jaglal
- Department of Clinical Microbiology & Infectious Diseases, National Health Laboratory Services, CH Baragwanath Academic Hospital, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - Willy Ssengooba
- Makerere University, Department of Medical Microbiology, Kampala, Uganda
| | - Samir K Saha
- Child Health Research Foundation (CHRF), Dhaka, Bangladesh
| | | | | | | | - Laura J V Piddock
- Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland
| | - Paul T Heath
- Centre for Neonatal and Pediatric Infection, Institute for Infection & Immunity, St. George's University of London, London, UK
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Michael Sharland
- Centre for Neonatal and Pediatric Infection, Institute for Infection & Immunity, St. George's University of London, London, UK
| | - Youri Glupczynski
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium.
| | - Herman Goossens
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
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Cook A, Ferreras-Antolin L, Adhisivam B, Ballot D, Berkley JA, Bernaschi P, Carvalheiro CG, Chaikittisuk N, Chen Y, Chibabhai V, Chitkara S, Chiurchiu S, Chorafa E, Dien TM, Dramowski A, de Matos SF, Feng J, Jarovsky D, Kaur R, Khamjakkaew W, Laoyookhong P, Machanja E, Mussi-Pinhata MM, Namiiro F, Natraj G, Naziat H, Ngoc HTB, Ondongo-Ezhet C, Preedisripipat K, Rahman H, Riddell A, Roilides E, Russell N, Sastry AS, Tasimwa HB, Tongzhen J, Wadula J, Wang Y, Whitelaw A, Wu D, Yadav V, Yang G, Stohr W, Bielicki JA, Ellis S, Warris A, Heath PT, Sharland M. Neonatal invasive candidiasis in low- and middle-income countries: Data from the NeoOBS study. Med Mycol 2023; 61:myad010. [PMID: 36881725 PMCID: PMC10026246 DOI: 10.1093/mmy/myad010] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 08/19/2022] [Revised: 01/11/2023] [Accepted: 03/03/2023] [Indexed: 03/09/2023] Open
Abstract
Neonatal invasive candidiasis (NIC) has significant morbidity and mortality. Reports have shown a different profile of those neonates affected with NIC and of fluconazole-resistant Candida spp. isolates in low- and middle-income countries (LMICs) compared to high-income countries (HICs). We describe the epidemiology, Candida spp. distribution, treatment, and outcomes of neonates with NIC from LMICs enrolled in a global, prospective, longitudinal, observational cohort study (NeoOBS) of hospitalized infants <60 days postnatal age with sepsis (August 2018-February 2021). A total of 127 neonates from 14 hospitals in 8 countries with Candida spp. isolated from blood culture were included. Median gestational age of affected neonates was 30 weeks (IQR: 28-34), and median birth weight was 1270 gr (interquartile range [IQR]: 990-1692). Only a minority had high-risk criteria, such as being born <28 weeks, 19% (24/127), or birth weight <1000 gr, 27% (34/127). The most common Candida species were C. albicans (n = 45, 35%), C. parapsilosis (n = 38, 30%), and Candida auris (n = 18, 14%). The majority of C. albicans isolates were fluconazole susceptible, whereas 59% of C. parapsilosis isolates were fluconazole-resistant. Amphotericin B was the most common antifungal used [74% (78/105)], followed by fluconazole [22% (23/105)]. Death by day 28 post-enrollment was 22% (28/127). To our knowledge, this is the largest multi-country cohort of NIC in LMICs. Most of the neonates would not have been considered at high risk for NIC in HICs. A substantial proportion of isolates was resistant to first choice fluconazole. Understanding the burden of NIC in LMIC is essential to guide future research and treatment guidelines.
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Affiliation(s)
- Aislinn Cook
- Centre for Neonatal and Paediatric Infection, St. George's University of London, London, UK
| | - Laura Ferreras-Antolin
- Centre for Neonatal and Paediatric Infection, St. George's University of London, London, UK
- MRC Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - Bethou Adhisivam
- Department of Neonatology, Jawaharlal Institute of Postgraduate Medical Education & Research (JIPMER), Pondicherry, India
| | - Daynia Ballot
- School of Clinical Medicine, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
- Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
| | - James A Berkley
- Clinical Research Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine & Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- The Childhood Acute Illness & Nutrition (CHAIN) Network, Nairobi, Kenya
| | - Paola Bernaschi
- Microbiology Unit, Bambino Gesù Children's Hospital, Rome, Italy
| | - Cristina G Carvalheiro
- Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | | | - Yunsheng Chen
- Clinical Laboratory, Shenzhen Children's Hospital, Shenzhen, China
| | - Vindana Chibabhai
- Department of Clinical Microbiology & Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
- NHLS Microbiology Laboratory, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
| | - Shweta Chitkara
- Lady Hardinge Medical College & Associated SSK & KSC Hospitals, New Delhi, India
| | - Sara Chiurchiu
- Academic Hospital Paediatric Department, Bambino Gesù Children's Hospital, Rome, Italy
| | - Elisavet Chorafa
- Infectious Diseases Unit, 3rd Department of Pediatrics, School of Medicine, Faculty of Health Sciences, Aristotle University and Hippokration General Hospital, Thessaloniki, Greece
| | - Tran Minh Dien
- Vice Director Vietnam National Children's Hospital, Hanoi, Vietnam
- Department of Surgery, Vietnam National Children's Hospital, Hanoi, Vietnam
| | - Angela Dramowski
- Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | | | - Jinxing Feng
- Department of Neonatology, Shenzhen Children's Hospital, Shenzhen, China
| | | | - Ravinder Kaur
- Lady Hardinge Medical College & Associated SSK & KSC Hospitals, New Delhi, India
| | | | | | - Edwin Machanja
- Department of Microbiology, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Marisa M Mussi-Pinhata
- Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Flavia Namiiro
- Mulago Specialised Women and Neonatal Hospital, Kampala, Uganda
| | - Gita Natraj
- Seth G. S. Medical College & KEM Hospital, Mumbai, India
| | - Hakka Naziat
- Child Health Research Foundation, Dhaka, Bangladesh
| | - Hoang Thi Bich Ngoc
- Department of Microbiology, Vietnam National Children's Hospital, Hanoi, Vietnam
| | - Claude Ondongo-Ezhet
- School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | | | - Amy Riddell
- Centre for Neonatal and Paediatric Infection, St. George's University of London, London, UK
| | - Emmanuel Roilides
- Infectious Diseases Unit, 3rd Department of Pediatrics, School of Medicine, Faculty of Health Sciences, Aristotle University and Hippokration General Hospital, Thessaloniki, Greece
| | - Neal Russell
- Centre for Neonatal and Paediatric Infection, St. George's University of London, London, UK
| | - Apurba S Sastry
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education & Research (JIPMER), Pondicherry, India
| | | | - Ji Tongzhen
- Beijing Obstetrics and Gynecology Hospital, Capital Medical University,Beijing, China
- Beijing Maternal and Child Health Care Hospital, Beijing, China
| | - Jeannette Wadula
- National Health Laboratory Services, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Yajuan Wang
- Department of Neonatology, Children's Hospital, Capital Institute of Pediatrics, 2# Yabao Road, Chaoyang District, Beijing, China
- Department of Neonatology, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Andrew Whitelaw
- Division of Medical Microbiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
| | - Dan Wu
- Department of Neonatology, Children's Hospital, Capital Institute of Pediatrics, 2# Yabao Road, Chaoyang District, Beijing, China
| | - Varsha Yadav
- Seth G. S. Medical College & KEM Hospital, Mumbai, India
| | - Gao Yang
- Beijing Obstetrics and Gynecology Hospital, Capital Medical University,Beijing, China
- National Health Laboratory Services, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Wolfgang Stohr
- MRC Clinical Trials Unit at UCL, Institute of Clinical Trials & Methodology, University College London, London, UK
| | - Julia Anna Bielicki
- Centre for Neonatal and Paediatric Infection, St. George's University of London, London, UK
| | - Sally Ellis
- Global Antibiotic Research & Development Partnership (GARDP), Geneva, Switzerland
| | - Adilia Warris
- MRC Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - Paul T Heath
- Centre for Neonatal and Paediatric Infection, St. George's University of London, London, UK
| | - Michael Sharland
- Centre for Neonatal and Paediatric Infection, St. George's University of London, London, UK
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Koel BF, Vigeveno RM, Pater M, Koekkoek SM, Han AX, Tuan HM, Anh TTN, Hung NT, Thinh LQ, Hai LT, Ngoc HTB, Chau NVV, Ngoc NM, Chokephaibulkit K, Puthavathana P, Kinh NV, Trinh T, Lee RTC, Maurer-Stroh S, Eggink D, Thanh TT, Tan LV, van Doorn HR, de Jong MD. Longitudinal sampling is required to maximize detection of intrahost A/H3N2 virus variants. Virus Evol 2020; 6:veaa088. [PMID: 33343927 PMCID: PMC7733607 DOI: 10.1093/ve/veaa088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Seasonal human influenza viruses continually change antigenically to escape from neutralizing antibodies. It remains unclear how genetic variation in the intrahost virus population and selection at the level of individual hosts translates to the fast-paced evolution observed at the global level because emerging intrahost antigenic variants are rarely detected. We tracked intrahost variants in the hemagglutinin and neuraminidase surface proteins using longitudinally collected samples from 52 patients infected by A/H3N2 influenza virus, mostly young children, who received oseltamivir treatment. We identified emerging putative antigenic variants and oseltamivir-resistant variants, most of which remained detectable in samples collected at subsequent days, and identified variants that emerged intrahost immediately prior to increases in global rates. In contrast to most putative antigenic variants, oseltamivir-resistant variants rapidly increased to high frequencies in the virus population. Importantly, the majority of putative antigenic variants and oseltamivir-resistant variants were first detectable four or more days after onset of symptoms or start of treatment, respectively. Our observations demonstrate that de novo variants emerge, and may be positively selected, during the course of infection. Additionally, based on the 4–7 days post-treatment delay in emergence of oseltamivir-resistant variants in six out of the eight individuals with such variants, we find that limiting sample collection for routine surveillance and diagnostic testing to early timepoints after onset of symptoms can potentially preclude detection of emerging, positively selected variants.
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Affiliation(s)
- B F Koel
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - R M Vigeveno
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - M Pater
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - S M Koekkoek
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - A X Han
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | | | | | - N T Hung
- Children's Hospital 1, Ho Chi Minh City, Vietnam
| | - L Q Thinh
- Children's Hospital 1, Ho Chi Minh City, Vietnam
| | - L T Hai
- Vietnam National Children's Hospital, Hanoi, Vietnam
| | - H T B Ngoc
- Vietnam National Children's Hospital, Hanoi, Vietnam
| | - N V V Chau
- Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - N M Ngoc
- Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | | | | | - N V Kinh
- National Hospital of Tropical Diseases, Hanoi, Vietnam
| | - T Trinh
- National Hospital of Tropical Diseases, Hanoi, Vietnam
| | - R T C Lee
- Bioinformatics Institute, Agency for Science Technology and Research, Singapore 138671 Singapore
| | - S Maurer-Stroh
- Bioinformatics Institute, Agency for Science Technology and Research, Singapore 138671 Singapore.,Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore.,National Public Health Laboratory, National Centre for Infectious Diseases, Ministry of Health, Singapore 308442, Singapore
| | - D Eggink
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - T T Thanh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - L V Tan
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - H R van Doorn
- Oxford University Clinical Research Unit, Hanoi, Vietnam.,Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - M D de Jong
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
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