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Juliet R, Loganathan A, Neeravi A, Bakthavatchalam YD, Veeraraghavan B, Manohar P, Nachimuthu R. Characterization of Salmonella phage of the genus Kayfunavirus isolated from sewage infecting clinical strains of Salmonella enterica. Front Microbiol 2024; 15:1391777. [PMID: 38887719 PMCID: PMC11180730 DOI: 10.3389/fmicb.2024.1391777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 05/20/2024] [Indexed: 06/20/2024] Open
Abstract
The emergence of multi-drug resistance in Salmonella, causing food-borne infections, is a significant issue. With over 2,600 serovars in in Salmonella sp., it is crucial to identify specific solutions for each serovar. Phage therapy serves as an alternate treatment option. In this study, vB_SalP_792 phage was obtained from sewage, forming plaques in eight out of 13 tested clinical S. enterica isolates. Transmission electron microscopy (TEM) examination revealed a T7-like morphotype. The phage was characterized by its stability, life cycle, antibiofilm, and lytic ability in food sources. The phage remains stable throughout a range of temperatures (-20 to 70°C), pH levels (3-11), and in chloroform and ether. It also exhibited lytic activity within a range of MOIs from 0.0001 to 100. The life cycle revealed that 95% of the phages attached to their host within 3 min, followed by a 5-min latent period, resulting in a 50 PFU/cell burst size. The vB_SalP_792 phage genome has a dsDNA with a length of 37,281 bp and a GC content of 51%. There are 42 coding sequences (CDS), with 24 having putative functions and no resistance or virulence-related genes. The vB_SalP_792 phage significantly reduced the bacterial load in the established biofilms and also in egg whites. Thus, vB_SalP_792 phage can serve as an effective biocontrol agent for preventing Salmonella infections in food, and its potent lytic activity against the clinical isolates of S. enterica, sets out vB_SalP_792 phage as a successful candidate for future in vivo studies and therapeutical application against drug-resistant Salmonella infections.
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Affiliation(s)
- Ramya Juliet
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Archana Loganathan
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Ayyanraj Neeravi
- Department of Clinical Microbiology, Christian Medical College, Vellore, India
| | | | | | - Prasanth Manohar
- Department of Biochemistry and Biophysics, Texas A&M AgriLife Research, Texas A&M University, College Station, TX, United States
- Center for Phage Technology, Texas A&M AgriLife Research, Texas A&M University, College Station, TX, United States
| | - Ramesh Nachimuthu
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
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Gichuyia CM, Thomas LF, Makena C, Ochieng L, Gathura PB, Onono JO, Fèvre EM. Non-typhoidal salmonella contamination along the pork value chain in a rural East African setting: a cross-sectional study. Trans R Soc Trop Med Hyg 2023; 117:811-813. [PMID: 37490020 PMCID: PMC10629947 DOI: 10.1093/trstmh/trad046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 06/16/2023] [Accepted: 07/07/2023] [Indexed: 07/26/2023] Open
Abstract
BACKGROUND Non-typhoidal Salmonella (NTS) is a serious foodborne pathogen that has previously been isolated from pigs presented for slaughter in a rural pork value chain in western Kenya. METHODS To understand varying NTS contamination along the value chain we assessed prevalence at slaughter, transport and retail. Suspect isolates from culture were confirmed using matrix-assisted laser desorption-ionization time of flight mass spectrometry. RESULTS Prevalence on pig carcasses, meat transportation containers, retailed raw and cooked pork and accompanying side salads was 18.1%, 23.9%, 28.0%, 1.9% and 8.6%, respectively. CONCLUSION NTS contamination is propagated along the pork value chain in rural western Kenya, demonstrating the need for improved hygiene measures to prevent human exposure.
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Affiliation(s)
- Cianjo M Gichuyia
- Department of Public Health, Pharmacology and Toxicology, University of Nairobi, P. O. Box 29053-00625, Kangemi, Kenya
- International Livestock Research Institute (ILRI), P.O. Box 30709-00100, Nairobi, Kenya
| | - Lian F Thomas
- International Livestock Research Institute (ILRI), P.O. Box 30709-00100, Nairobi, Kenya
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 3BX, UK
| | - Christine Makena
- Department of Public Health, Pharmacology and Toxicology, University of Nairobi, P. O. Box 29053-00625, Kangemi, Kenya
- International Livestock Research Institute (ILRI), P.O. Box 30709-00100, Nairobi, Kenya
| | - Linnet Ochieng
- International Livestock Research Institute (ILRI), P.O. Box 30709-00100, Nairobi, Kenya
| | - Peter B Gathura
- Department of Public Health, Pharmacology and Toxicology, University of Nairobi, P. O. Box 29053-00625, Kangemi, Kenya
| | - Joshua O Onono
- Department of Public Health, Pharmacology and Toxicology, University of Nairobi, P. O. Box 29053-00625, Kangemi, Kenya
| | - Eric M Fèvre
- International Livestock Research Institute (ILRI), P.O. Box 30709-00100, Nairobi, Kenya
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 3BX, UK
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Nessle CN, Njuguna F, Dettinger J, Koima R, Nyamusi L, Kisembe E, Kinja S, Ndung'u M, Njenga D, Langat S, Olbara G, Moyer C, Vik T. Barriers to and facilitators of effective management of fever episodes in hospitalised Kenyan children with cancer: protocol for convergent mixed methods study. BMJ Open 2023; 13:e078124. [PMID: 37918936 PMCID: PMC10626801 DOI: 10.1136/bmjopen-2023-078124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 09/27/2023] [Indexed: 11/04/2023] Open
Abstract
INTRODUCTION Febrile neutropenia is an oncological emergency in children with cancer, associated with serious infections and complications. In low-resourced settings, death from infections in children with cancer is 20 times higher than in high-resourced treatment settings, thought to be related to delays in antibiotic administration and management. The barriers to effective management of fever episodes in children with cancer have not previously been described. This convergent mixed-methods study will provide the evidence to develop fever treatment guidelines and to inform their effective implementation in children with cancer at Moi Teaching and Referral Hospital (MTRH), a level 6 referral hospital in western Kenya. METHODS AND ANALYSIS Prospective data collection of paediatric patients with cancer with new fever episodes admitted to MTRH will be performed during routine treatment. Clinical variables will be collected from 50 fever episodes, including cancer diagnosis and infectious characteristics of the fever episode, and elapsed time from fever onset to various milestones in the management workflow. Semistructured qualitative interviews with healthcare providers (estimated 20 to reach saturation) will explore the barriers to and facilitators of appropriate management of fever episodes in children with cancer. The interview guide was informed by a theoretical framework and Consolidated Framework for Implementation Research. A mixed-methods analysis use of joint display tables and process mapping will link and integrate the two types of data with meta-inferences. ETHICS AND DISSEMINATION Institutional review board approval was obtained from the MTRH (0004273) and the University of Michigan (HUM0225674), and the study was registered with National Commission for Science Technology and Innovation (P/23/22885). Written consent will be obtained from all participants. Results will be formally shared with local and national policy leadership and local end users, presented at relevant national academic conferences and submitted for publication in a peer-reviewed journal.
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Affiliation(s)
- Charles Nathaniel Nessle
- Department of Pediatrics, Division of Hematology-Oncology, University of Michigan, Ann Arbor, Michigan, USA
- Fogarty International Center, National Institute of Health, Bethesda, Maryland, USA
| | - Festus Njuguna
- Department of Child Health and Pediatrics, Moi University, Eldoret, Kenya
| | - Julia Dettinger
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Raphael Koima
- Department of Child Health and Pediatrics, Moi University, Eldoret, Kenya
| | - Lenah Nyamusi
- Department of Child Health and Pediatrics, Moi University, Eldoret, Kenya
| | - Evelynn Kisembe
- School of Arts and Social Sciences, Moi University, Eldoret, Kenya
- Behavioral and Social Science Research, Moi University, Eldoret, Kenya
| | - Sarah Kinja
- Department of Child Health and Pediatrics, Moi University, Eldoret, Kenya
| | - Mercy Ndung'u
- Department of Child Health and Pediatrics, Moi University, Eldoret, Kenya
| | - Dennis Njenga
- Department of Child Health and Pediatrics, Moi University, Eldoret, Kenya
| | - Sandra Langat
- Department of Child Health and Pediatrics, Moi University, Eldoret, Kenya
| | - Gilbert Olbara
- Department of Child Health and Pediatrics, Moi Teaching and Referral Hospital, Eldoret, Kenya
| | - Cheryl Moyer
- Medical School, Learning Health Sciences, University of Michigan, Ann Arbor, Michigan, USA
| | - Terry Vik
- Department of Child Health and Pediatrics, Moi University, Eldoret, Kenya
- Department of Pediatrics, Division of Hematology-Oncology, Indiana University School of Medicine, Indianapolis, Indiana, USA
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Chirwa EB, Dale H, Gordon MA, Ashton PM. What is the Source of Infections Causing Invasive Nontyphoidal Salmonella Disease? Open Forum Infect Dis 2023; 10:ofad086. [PMID: 36910696 PMCID: PMC10004642 DOI: 10.1093/ofid/ofad086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
Invasive nontyphoidal Salmonella (iNTS) disease is a clinical condition distinct from Salmonella gastroenteritis. With an overall case-fatality rate of 14.5%, iNTS remains a major cause of morbidity and mortality, particularly in sub-Saharan Africa. However, the sources of infections that lead to cases of iNTS remain unclear. Broadly, there are 2 hypotheses as to the source of infections: (i) transmission from a zoonotic reservoir, similar to other nontyphoidal salmonelloses; or (ii) person-to-person transmission. Here we review several recent studies that have asked, "What is the source of infections causing invasive nontyphoidal Salmonella disease?" Two studies reported isolates in the stool of household members of iNTS cases that were very closely related (<3 single-nucleotide polymorphisms) to the iNTS case isolates; this is consistent with the hypothesis of person-to-person transmission, but infection from a common source (eg, a foodstuff) cannot be excluded. On the other hand, thorough investigations of the domestic environment of iNTS cases and the food pathway found only a single iNTS-associated Salmonella Enteritidis isolate. Therefore, we recommend that future studies test the hypothesis that iNTS is transmitted between people within the domestic environment. Further studies of food and water pathways are also warranted.
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Affiliation(s)
- Esmeda B Chirwa
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom.,Salmonella group, Malawi Liverpool Wellcome Programme, Blantyre, Malawi
| | - Helen Dale
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom.,Salmonella group, Malawi Liverpool Wellcome Programme, Blantyre, Malawi
| | - Melita A Gordon
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom.,Salmonella group, Malawi Liverpool Wellcome Programme, Blantyre, Malawi
| | - Philip M Ashton
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom.,Salmonella group, Malawi Liverpool Wellcome Programme, Blantyre, Malawi
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Koolman L, Prakash R, Diness Y, Msefula C, Nyirenda TS, Olgemoeller F, Wigley P, Perez-Sepulveda B, Hinton JCD, Owen SV, Feasey NA, Ashton PM, Gordon MA. Case-control investigation of invasive Salmonella disease in Malawi reveals no evidence of environmental or animal transmission of invasive strains, and supports human to human transmission. PLoS Negl Trop Dis 2022; 16:e0010982. [PMID: 36508466 PMCID: PMC9779717 DOI: 10.1371/journal.pntd.0010982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 12/22/2022] [Accepted: 11/23/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Invasive Salmonella infections cause significant morbidity and mortality in Sub-Saharan Africa. However, the routes of transmission are uncertain. We conducted a case-control study of index-case and geographically-matched control households in Blantyre, Malawi, sampling Salmonella isolates from index cases, healthy people, animals, and the household environment. METHODOLOGY Sixty index cases of human invasive Salmonella infection were recruited (March 2015-Oct 2016). Twenty-eight invasive Non-Typhoidal Salmonella (iNTS) disease and 32 typhoid patients consented to household sampling. Each index-case household was geographically matched to a control household. Extensive microbiological sampling included stool sampling from healthy household members, stool or rectal swabs from household-associated animals and boot-sock sampling of the household environment. FINDINGS 1203 samples from 120 households, yielded 43 non-Typhoidal Salmonella (NTS) isolates from 25 households (overall sample positivity 3.6%). In the 28 iNTS patients, disease was caused by 3 STs of Salmonella Typhimurium, mainly ST313. In contrast, the isolates from households spanned 15 sequence types (STs). Two S. Typhimurium isolates from index cases closely matched isolates from their respective asymptomatic household members (2 and 3 SNP differences respectively). Despite the recovery of a diverse range of NTS, there was no overlap between the STs causing iNTS disease with any environmental or animal isolates. CONCLUSIONS The finding of NTS strains from index cases that matched household members, coupled with lack of related animal or environmental isolates, supports a hypothesis of human to human transmission of iNTS infections in the household. The breadth of NTS strains found in animals and the household environment demonstrated the robustness of NTS sampling and culture methodology, and suggests a diverse ecology of Salmonella in this setting. Healthy typhoid (S. Typhi) carrier state was not detected. The lack of S. Typhi isolates from the household environment suggests that further methodological development is needed to culture S. Typhi from the environment.
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Affiliation(s)
- Leonard Koolman
- Malawi-Liverpool Wellcome Programme, Blantyre, Malawi
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Reenesh Prakash
- Malawi-Liverpool Wellcome Programme, Blantyre, Malawi
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Yohane Diness
- Malawi-Liverpool Wellcome Programme, Blantyre, Malawi
| | | | | | - Franziska Olgemoeller
- Malawi-Liverpool Wellcome Programme, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Paul Wigley
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Blanca Perez-Sepulveda
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Jay C. D. Hinton
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Siân V. Owen
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Nicholas A. Feasey
- Malawi-Liverpool Wellcome Programme, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Philip M. Ashton
- Malawi-Liverpool Wellcome Programme, Blantyre, Malawi
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- * E-mail:
| | - Melita A. Gordon
- Malawi-Liverpool Wellcome Programme, Blantyre, Malawi
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Kamuzu University of Health Sciences, Blantyre, Malawi
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Hengkrawit K, Tangjade C. Factors Associated with Multi-Drug-Resistant Non-Typhoidal Salmonella in the Invasive Disease, Thailand. Infect Drug Resist 2022; 15:6563-6576. [PMID: 36386407 PMCID: PMC9662010 DOI: 10.2147/idr.s387037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 10/29/2022] [Indexed: 12/18/2023] Open
Abstract
PURPOSE Invasive non-typhoidal Salmonella disease, iNTS is a major global health concern, especially multi-drug resistant non-typhoidal Salmonella, MDR-NTS. Information about risk factors of MDR-NTS in the invasive disease patient group was limited. This study aimed to identify those risk factors. METHODS This retrospective study examined data from patients who had non-typhoidal Salmonella, NTS infection, from 10 hospitals between June 2011 and June 2020. The multivariate regression analysis included demographic data, clinical data, culture reports, and antimicrobial susceptibility. RESULTS A total of 166 patients were invasive salmonellosis. where the median age was 8.3 years (IQR 1.8-79). 52% were the under-15-years-old group. Most of the patient data, 64.5% (107/166), was from a tertiary hospital. The majority of cases were bacteremia 95.7% (159/166). Serogroup C was the most common serogroup (39%). MDR-NTS was present in 68.8% (95% CI 7.17-11.06) of patients. Univariate analysis showed that onset of illness >3 days PTA (p=0.11), age over 60 years old (0.014), diabetic (p=0.002), or serogroup C infection (p=0.43) were significant factors for MDR-NTS infection. Multivariate analysis showed that the onset of symptoms more than 3 days before admission (p=0.001), and age over 60 years were significant factors. The patient who had white blood cells >15,000 cells/uL (p<0.001), a peak of fever ≥39 C° (p=001), and illness for more than 3 days before admission (p=0.035) were significantly related to invasive infection by multivariate analyses. CONCLUSION The iNTS patients who were over 60 years old or had onset of illness more than 3 days before admission were associated with MDR-NTS infection. Therefore, the choice of antimicrobials selected must be appropriate for the local prevalence and epidemiology of MDR-NTS including clinical correlation.
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Affiliation(s)
- Kitchawan Hengkrawit
- Pediatric Infectious Disease Unit, Department of Pediatrics, Panyananthaphikkhu Chonprathan Medical Center, Srinakarinwirot University, Nonthaburi, Thailand
| | - Chidchanok Tangjade
- Pediatrics Gastroenterology and Hepatology Unit, Department of Pediatrics, Panyananthaphikkhu Chonprathan Medical Center, Srinakarinwirot University, Nonthaburi, Thailand
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Siriphap A, Suwancharoen C, Laenoi W, Kraivuttinun P, Suthienkul O, Prapasawat W. First study on virulence genes, antimicrobial resistance, and integrons in Escherichia coli isolated from cage, free-range, and organic commercial eggs in Phayao Province, Thailand. Vet World 2022; 15:2293-2301. [PMID: 36341073 PMCID: PMC9631383 DOI: 10.14202/vetworld.2022.2293-2301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/02/2022] [Indexed: 11/23/2022] Open
Abstract
Background and Aim: Antimicrobial resistance (AMR) is a global problem that affects human and animal health, and eggs can act as a vehicle for pathogenic and non-pathogenic resistant bacteria in the food chain. Escherichia coli is an indicator of food contamination with fecal materials as well as the occurrence and levels of AMR. This study aimed to investigate the presence of AMR, integrons, and virulence genes in E. coli isolated from eggshell samples of three egg production systems, from supermarkets in Thailand. Materials and Methods: A total of 750 hen’s egg samples were purchased from supermarkets in Phayao Province: Cage eggs (250), free-range eggs (250), and organic eggs (250). Each sample was soaked in buffered peptone water (BPW), and the BPW samples were incubated at 37°C for 18–24 h. All samples were tested for E. coli by the standard conventional culture method. Then, all identified E. coli were tested for antimicrobial susceptibility to 15 antimicrobial agents by the agar disk diffusion method. All E. coli strains were subsequently found to have virulence genes and Classes 1 and 2 integrons by polymerase chain reaction. Results: Among the eggshell samples, 91 samples were identified as having E. coli (cage eggs, 24 strains; free-range eggs, 27 strains; and organic eggs, 40 strains). Then, among the E. coli strains, 47 (51.6%) were positive for at least one virulence gene. The proportion of AMR in the eggshell samples was 91.2% (83/91), and streptomycin (STR), ampicillin (AMP), and tetracycline (TET) had a high degree of resistance. Among the E. coli strains, 27 (29.7%) strains were positive for class 1 or 2 integrons, and integron-positive strains were commonly found in STR-, AMP-, and TET-resistant strains. Multidrug resistance (MDR) was detected in 57.1% (52/91) of the E. coli strains, with STR-AMP-TET (5.5%) as the most frequent pattern. The proportion of MDR in cage eggs was 75.0% (18/24), which was higher than in both free-range and organic eggs. On the other hand, 53.2% (25/47) of E. coli carrying virulence genes had MDR, distributed across the production systems as follows: Cage eggs, 76.9% (10/13); free-range eggs, 63.6% (7/11); and organic eggs, 34.8% (8/23). Conclusion: Escherichia coli was detected in eggshell samples from all three egg production systems. The high level of virulence genes, AMR, and integrons indicated the possibility of dissemination of AMR among pathogenic and commensal E. coli through eggshells. These findings could be a major concern to farmers, food handlers, and consumers, especially regarding raw egg consumption.
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Affiliation(s)
- Achiraya Siriphap
- Division of Microbiology and Parasitology, School of Medical Sciences, University of Phayao, Phayao 56000, Thailand
| | - Chittakun Suwancharoen
- Division of Microbiology and Parasitology, School of Medical Sciences, University of Phayao, Phayao 56000, Thailand
| | - Watchara Laenoi
- Division of Animal Science, School of Agriculture and Natural Resources, University of Phayao, Phayao 56000, Thailand
| | - Parinya Kraivuttinun
- Program in Environment, Faculty of Science and Technology, Uttaradit Rajabhat University, Uttaradit 53000, Thailand
| | - Orasa Suthienkul
- Faculty of Public Health, Mahidol University, Bangkok 10400, Thailand
| | - Watsawan Prapasawat
- Department of Clinic, Faculty of Veterinary Medicine, Mahanakorn University of Technology, Bangkok 10530, Thailand
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Ikhimiukor OO, Oaikhena AO, Afolayan AO, Fadeyi A, Kehinde A, Ogunleye VO, Aboderin AO, Oduyebo OO, Elikwu CJ, Odih EE, Komolafe I, Argimón S, Egwuenu A, Adebiyi I, Sadare OA, Okwor T, Kekre M, Underwood A, Ihekweazu C, Aanensen DM, Okeke IN. Genomic characterization of invasive typhoidal and non-typhoidal Salmonella in southwestern Nigeria. PLoS Negl Trop Dis 2022; 16:e0010716. [PMID: 36026470 PMCID: PMC9455843 DOI: 10.1371/journal.pntd.0010716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 09/08/2022] [Accepted: 08/03/2022] [Indexed: 11/25/2022] Open
Abstract
Background Salmonellosis causes significant morbidity and mortality in Africa. Information on lineages of invasive Salmonella circulating in Nigeria is sparse. Methods Salmonella enterica isolated from blood (n = 60) and cerebrospinal fluid (CSF, n = 3) between 2016 and 2020 from five tertiary hospitals in southwest Nigeria were antimicrobial susceptibility-tested and Illumina-sequenced. Genomes were analysed using publicly-available bioinformatic tools. Results Isolates and sequence types (STs) from blood were S. Typhi [ST1, n = 1 and ST2, n = 43] and invasive non-typhoidal Salmonella (iNTS) (S. Enteritidis [ST11, n = 7], S. Durham [ST10, n = 2], S. Rissen [ST8756, n = 2], S. Chester [ST2063, n = 1], S. Dublin [ST10, n = 1], S. Infantis [ST603, n = 1], S. Telelkebir [ST8757, n = 1] and S. Typhimurium [ST313, n = 1]). S. Typhi ST2 (n = 2) and S. Adabraka ST8757 (n = 1) were recovered from CSF. Most S. Typhi belonged to genotype 3.1.1 (n = 44), carried an IncY plasmid, had several antibiotic resistance genes (ARGs) including blaTEM-1 (n = 38), aph(6)-Id (n = 32), tet(A) (n = 33), sul2 (n = 32), dfrA14 (n = 30) as well as quinolone resistance-conferring gyrA_S83Y single-nucleotide polymorphisms (n = 37). All S. Enteritidis harboured aph(3”)-Ib, blaTEM-1, catA1, dfrA7, sul1, sul2, tet(B) genes, and a single ARG, qnrB19, was detected in S. Telelkebir. Typhoidal toxins cdtB, pltA and pltB were detected in S. Typhi, Rissen, Chester, and Telelkebir. Conclusion Most invasive salmonelloses in southwest Nigeria are vaccine-preventable infections due to multidrug-resistant, West African dominant S. Typhi lineage 3.1.1. Invasive NTS serovars, including some harbouring typhoidal toxin or resistance genes, represented a third of the isolates emphasizing the need for better diagnosis and surveillance. Whole genome sequencing of 63 invasive Salmonella from 5 tertiary hospitals in Nigeria revealed multiple serovars including a dominant antibiotic-resistance-gene harbouring S. Typhi 3.1.1 genotype comprising a gyrA_S83Y and IncY plasmid. We also report invasive non-typhoidal Salmonella harbouring typhoidal toxins.
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Affiliation(s)
- Odion O. Ikhimiukor
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Anderson O. Oaikhena
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Ayorinde O. Afolayan
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Abayomi Fadeyi
- Department of Medical Microbiology and Parasitology, University of Ilorin, Ilorin, Kwara State, Nigeria
| | - Aderemi Kehinde
- Department of Medical Microbiology and Parasitology, University College Hospital, Ibadan, Oyo State, Nigeria
| | - Veronica O. Ogunleye
- Department of Medical Microbiology and Parasitology, University College Hospital, Ibadan, Oyo State, Nigeria
| | - Aaron O. Aboderin
- Department of Medical Microbiology and Parasitology, Obafemi Awolowo University Teaching Hospitals Complex, Ile-Ife, Nigeria
| | - Oyinlola O. Oduyebo
- Department of Medical Microbiology and Parasitology, Faculty of Basic Medical Sciences, College of Medicine, University of Lagos, Lagos, Nigeria
| | - Charles J. Elikwu
- Department of Medical Microbiology, School of Basic Clinical Sciences, Benjamin Carson College of Health and Medical Sciences, Babcock University & Teaching Hospital, Ilishan-Remo, Ogun State, Nigeria
| | - Erkison Ewomazino Odih
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Ifeoluwa Komolafe
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Silvia Argimón
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, United Kingdom
| | | | - Ini Adebiyi
- Department of Medical Microbiology and Parasitology, University College Hospital, Ibadan, Oyo State, Nigeria
| | - Oluwadamilola A. Sadare
- Department of Medical Microbiology, School of Basic Clinical Sciences, Benjamin Carson College of Health and Medical Sciences, Babcock University & Teaching Hospital, Ilishan-Remo, Ogun State, Nigeria
| | - Tochi Okwor
- Nigeria Centre for Disease Control, Jabi, Abuja, Nigeria
| | - Mihir Kekre
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Anthony Underwood
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, United Kingdom
| | | | - David M. Aanensen
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Iruka N. Okeke
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
- * E-mail:
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9
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Multidrug-Resistant Nontyphoidal Salmonella Associated with Invasive Disease in an Immunocompetent Child. Indian J Pediatr 2021; 88:1266. [PMID: 34398414 DOI: 10.1007/s12098-021-03923-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 07/30/2021] [Indexed: 10/20/2022]
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10
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Kasumba IN, Pulford CV, Perez-Sepulveda BM, Sen S, Sayed N, Permala-Booth J, Livio S, Heavens D, Low R, Hall N, Roose A, Powell H, Farag T, Panchalingham S, Berkeley L, Nasrin D, Blackwelder WC, Wu Y, Tamboura B, Sanogo D, Onwuchekwa U, Sow SO, Ochieng JB, Omore R, Oundo JO, Breiman RF, Mintz ED, O’Reilly CE, Antonio M, Saha D, Hossain MJ, Mandomando I, Bassat Q, Alonso PL, Ramamurthy T, Sur D, Qureshi S, Zaidi AKM, Hossain A, Faruque ASG, Nataro JP, Kotloff KL, Levine MM, Hinton JCD, Tennant SM. Characteristics of Salmonella Recovered From Stools of Children Enrolled in the Global Enteric Multicenter Study. Clin Infect Dis 2021; 73:631-641. [PMID: 33493332 PMCID: PMC8366818 DOI: 10.1093/cid/ciab051] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 01/21/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The Global Enteric Multicenter Study (GEMS) determined the etiologic agents of moderate-to-severe diarrhea (MSD) in children under 5 years old in Africa and Asia. Here, we describe the prevalence and antimicrobial susceptibility of nontyphoidal Salmonella (NTS) serovars in GEMS and examine the phylogenetics of Salmonella Typhimurium ST313 isolates. METHODS Salmonella isolated from children with MSD or diarrhea-free controls were identified by classical clinical microbiology and serotyped using antisera and/or whole-genome sequence data. We evaluated antimicrobial susceptibility using the Kirby-Bauer disk-diffusion method. Salmonella Typhimurium sequence types were determined using multi-locus sequence typing, and whole-genome sequencing was performed to assess the phylogeny of ST313. RESULTS Of 370 Salmonella-positive individuals, 190 (51.4%) were MSD cases and 180 (48.6%) were diarrhea-free controls. The most frequent Salmonella serovars identified were Salmonella Typhimurium, serogroup O:8 (C2-C3), serogroup O:6,7 (C1), Salmonella Paratyphi B Java, and serogroup O:4 (B). The prevalence of NTS was low but similar across sites, regardless of age, and was similar among both cases and controls except in Kenya, where Salmonella Typhimurium was more commonly associated with cases than controls. Phylogenetic analysis showed that these Salmonella Typhimurium isolates, all ST313, were highly genetically related to isolates from controls. Generally, Salmonella isolates from Asia were resistant to ciprofloxacin and ceftriaxone, but African isolates were susceptible to these antibiotics. CONCLUSIONS Our data confirm that NTS is prevalent, albeit at low levels, in Africa and South Asia. Our findings provide further evidence that multidrug-resistant Salmonella Typhimurium ST313 can be carried asymptomatically by humans in sub-Saharan Africa.
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Affiliation(s)
- Irene N Kasumba
- Center for Vaccine Development and Global Health
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Caisey V Pulford
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | | | - Sunil Sen
- Center for Vaccine Development and Global Health
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Nurulla Sayed
- Center for Vaccine Development and Global Health
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Jasnehta Permala-Booth
- Center for Vaccine Development and Global Health
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Sofie Livio
- Center for Vaccine Development and Global Health
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Darren Heavens
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Ross Low
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Neil Hall
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Anna Roose
- Center for Vaccine Development and Global Health
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Helen Powell
- Center for Vaccine Development and Global Health
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Tamer Farag
- Center for Vaccine Development and Global Health
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Sandra Panchalingham
- Center for Vaccine Development and Global Health
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Lynette Berkeley
- Center for Vaccine Development and Global Health
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Dilruba Nasrin
- Center for Vaccine Development and Global Health
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - William C Blackwelder
- Center for Vaccine Development and Global Health
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Yukun Wu
- Center for Vaccine Development and Global Health
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | | | - Doh Sanogo
- Centre pour le Developpement des Vaccins, Bamako, Mali
| | | | - Samba O Sow
- Centre pour le Developpement des Vaccins, Bamako, Mali
| | - John B Ochieng
- Kenya Medical Research Institute/US Centers for Disease Control and Prevention, Kisumu, Kenya
| | - Richard Omore
- Kenya Medical Research Institute/US Centers for Disease Control and Prevention, Kisumu, Kenya
| | - Joseph O Oundo
- Kenya Medical Research Institute/US Centers for Disease Control and Prevention, Kisumu, Kenya
| | - Robert F Breiman
- Kenya Medical Research Institute/US Centers for Disease Control and Prevention, Kisumu, Kenya
| | - Eric D Mintz
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Ciara E O’Reilly
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Martin Antonio
- Medical Research Council Unit, The Gambia at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Debasish Saha
- Medical Research Council Unit, The Gambia at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - M Jahangir Hossain
- Medical Research Council Unit, The Gambia at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Inacio Mandomando
- Centro de Investigacao em Saude da Manhica (CISM), Maputo, Mozambique
| | - Quique Bassat
- Centro de Investigacao em Saude da Manhica (CISM), Maputo, Mozambique
- Catalan Institution for Research and Advanced Studies (ICREA), Pg. Lluís Companys 23, Barcelona, Spain
- Pediatric Infectious Diseases Unit, Pediatrics Department, Hospital Sant Joan de Déu (University of Barcelona), Barcelona, Spain
- Consorcio de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- ISGlobal, Hospital Clínic–Universitat de Barcelona, Barcelona, Spain
| | - Pedro L Alonso
- Centro de Investigacao em Saude da Manhica (CISM), Maputo, Mozambique
- ISGlobal, Hospital Clínic–Universitat de Barcelona, Barcelona, Spain
- Instituto Nacional de Saúde, Ministério de Saúde, Maputo, Mozambique
| | - T Ramamurthy
- National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Dipika Sur
- National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Shahida Qureshi
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Anita K M Zaidi
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Anowar Hossain
- International Centre for Diarrhoeal Disease Research, Mohakhali, Dhaka, Bangladesh
| | - Abu S G Faruque
- International Centre for Diarrhoeal Disease Research, Mohakhali, Dhaka, Bangladesh
| | | | - Karen L Kotloff
- Center for Vaccine Development and Global Health
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Myron M Levine
- Center for Vaccine Development and Global Health
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Jay C D Hinton
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Sharon M Tennant
- Center for Vaccine Development and Global Health
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
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11
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Park SE, Pham DT, Pak GD, Panzner U, Maria Cruz Espinoza L, von Kalckreuth V, Im J, Mogeni OD, Schütt-Gerowitt H, Crump JA, Breiman RF, Adu-Sarkodie Y, Owusu-Dabo E, Rakotozandrindrainy R, Bassiahi Soura A, Aseffa A, Gasmelseed N, Sooka A, Keddy KH, May J, Aaby P, Biggs HM, Hertz JT, Montgomery JM, Cosmas L, Olack B, Fields B, Sarpong N, Razafindrabe TJL, Raminosoa TM, Kabore LP, Sampo E, Teferi M, Yeshitela B, El Tayeb MA, Krumkamp R, Dekker DM, Jaeger A, Tall A, Gassama A, Niang A, Bjerregaard-Andersen M, Løfberg SV, Deerin JF, Park JK, Konings F, Carey ME, Van Puyvelde S, Ali M, Clemens J, Dougan G, Baker S, Marks F. The genomic epidemiology of multi-drug resistant invasive non-typhoidal Salmonella in selected sub-Saharan African countries. BMJ Glob Health 2021; 6:bmjgh-2021-005659. [PMID: 34341020 PMCID: PMC8330565 DOI: 10.1136/bmjgh-2021-005659] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 07/06/2021] [Indexed: 01/23/2023] Open
Abstract
Background Invasive non-typhoidal Salmonella (iNTS) is one of the leading causes of bacteraemia in sub-Saharan Africa. We aimed to provide a better understanding of the genetic characteristics and transmission patterns associated with multi-drug resistant (MDR) iNTS serovars across the continent. Methods A total of 166 iNTS isolates collected from a multi-centre surveillance in 10 African countries (2010–2014) and a fever study in Ghana (2007–2009) were genome sequenced to investigate the geographical distribution, antimicrobial genetic determinants and population structure of iNTS serotypes–genotypes. Phylogenetic analyses were conducted in the context of the existing genomic frameworks for various iNTS serovars. Population-based incidence of MDR-iNTS disease was estimated in each study site. Results Salmonella Typhimurium sequence-type (ST) 313 and Salmonella Enteritidis ST11 were predominant, and both exhibited high frequencies of MDR; Salmonella Dublin ST10 was identified in West Africa only. Mutations in the gyrA gene (fluoroquinolone resistance) were identified in S. Enteritidis and S. Typhimurium in Ghana; an ST313 isolate carrying blaCTX-M-15 was found in Kenya. International transmission of MDR ST313 (lineage II) and MDR ST11 (West African clade) was observed between Ghana and neighbouring West African countries. The incidence of MDR-iNTS disease exceeded 100/100 000 person-years-of-observation in children aged <5 years in several West African countries. Conclusions We identified the circulation of multiple MDR iNTS serovar STs in the sampled sub-Saharan African countries. Investment in the development and deployment of iNTS vaccines coupled with intensified antimicrobial resistance surveillance are essential to limit the impact of these pathogens in Africa.
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Affiliation(s)
- Se Eun Park
- International Vaccine Institute, Seoul, Republic of Korea.,Graduate School of Public Health, Yonsei University, Seoul, Republic of Korea
| | - Duy Thanh Pham
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Gi Deok Pak
- International Vaccine Institute, Seoul, Republic of Korea
| | - Ursula Panzner
- International Vaccine Institute, Seoul, Republic of Korea
| | | | | | - Justin Im
- International Vaccine Institute, Seoul, Republic of Korea
| | | | - Heidi Schütt-Gerowitt
- International Vaccine Institute, Seoul, Republic of Korea.,Institute of Medical Microbiology, University of Cologne, Cologne, Germany
| | - John A Crump
- Centre for International Health, University of Otago, Dunedin, New Zealand.,Division of Infectious Diseases and International Health, Duke University Medical Center, Durham, North Carolina, USA.,Duke Global Health Institute, Duke University, Durham, North Carolina, USA.,Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Robert F Breiman
- Centers for Disease Control and Prevention, KEMRI Complex, Nairobi, Kenya.,Global Health Institute, Emory University, Atlanta, Georgia, USA
| | - Yaw Adu-Sarkodie
- Kwame Nkrumah University of Science and Technology, Kumasi, Ghana.,Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana
| | - Ellis Owusu-Dabo
- Kwame Nkrumah University of Science and Technology, Kumasi, Ghana.,Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana
| | | | - Abdramane Bassiahi Soura
- Institut Supérieur des Sciences de la Population, University of Ouagadougou, Ouagadougou, Burkina Faso
| | - Abraham Aseffa
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Nagla Gasmelseed
- Faculty of Medicine, University of Gezira, Wad Medani, Sudan.,Faculty of Science, University of Hafr Al Batin, Hafr Albatin, Saudi Arabia
| | - Arvinda Sooka
- National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Karen H Keddy
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jürgen May
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research, Braunschweig, Germany
| | - Peter Aaby
- Bandim Health Project, Bissau, Guinea-Bissau.,Research Center for Vitamins and Vaccines, Bandim Health Project, Statens Serum Institut, Copenhagen, Denmark
| | - Holly M Biggs
- Division of Infectious Diseases and International Health, Duke University Medical Center, Durham, North Carolina, USA.,Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Julian T Hertz
- Division of Infectious Diseases and International Health, Duke University Medical Center, Durham, North Carolina, USA.,Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Joel M Montgomery
- Centers for Disease Control and Prevention, KEMRI Complex, Nairobi, Kenya
| | - Leonard Cosmas
- Centers for Disease Control and Prevention, KEMRI Complex, Nairobi, Kenya
| | | | - Barry Fields
- Centers for Disease Control and Prevention, KEMRI Complex, Nairobi, Kenya
| | - Nimako Sarpong
- Kwame Nkrumah University of Science and Technology, Kumasi, Ghana.,German Center for Infection Research, Braunschweig, Germany
| | | | | | | | | | | | | | | | - Ralf Krumkamp
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research, Braunschweig, Germany
| | - Denise Myriam Dekker
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research, Braunschweig, Germany
| | - Anna Jaeger
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research, Braunschweig, Germany
| | - Adama Tall
- Institute Pasteur de Dakar, Dakar, Senegal
| | - Amy Gassama
- Institute Pasteur de Dakar, Dakar, Senegal.,Université Cheikh Anta Diop de Dakar, Dakar, Senegal
| | | | - Morten Bjerregaard-Andersen
- Bandim Health Project, Bissau, Guinea-Bissau.,Research Center for Vitamins and Vaccines, Bandim Health Project, Statens Serum Institut, Copenhagen, Denmark
| | - Sandra Valborg Løfberg
- Bandim Health Project, Bissau, Guinea-Bissau.,Research Center for Vitamins and Vaccines, Bandim Health Project, Statens Serum Institut, Copenhagen, Denmark
| | | | - Jin Kyung Park
- International Vaccine Institute, Seoul, Republic of Korea
| | - Frank Konings
- International Vaccine Institute, Seoul, Republic of Korea
| | - Megan E Carey
- Department of Medicine, University of Cambridge, Cambridge, Cambridgeshire, UK
| | - Sandra Van Puyvelde
- Medicine, Cambridge University, Cambridge, UK.,Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.,Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Mohammad Ali
- International Vaccine Institute, Seoul, Republic of Korea.,Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - John Clemens
- International Vaccine Institute, Seoul, Republic of Korea.,International Centre for Diarrheal Disease Research, Dhaka, Bangladesh.,University of California, Fielding School of Public Health, Los Angeles, California, USA
| | - Gordon Dougan
- Department of Medicine, University of Cambridge, Cambridge, Cambridgeshire, UK
| | - Stephen Baker
- Department of Medicine, University of Cambridge, Cambridge, Cambridgeshire, UK
| | - Florian Marks
- International Vaccine Institute, Seoul, Republic of Korea
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12
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Luo L, Payne M, Kaur S, Hu D, Cheney L, Octavia S, Wang Q, Tanaka MM, Sintchenko V, Lan R. Elucidation of global and national genomic epidemiology of Salmonella enterica serovar Enteritidis through multilevel genome typing. Microb Genom 2021; 7. [PMID: 34292145 PMCID: PMC8477392 DOI: 10.1099/mgen.0.000605] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Salmonella enterica serovar Enteritidis is a major cause of foodborne Salmonella infections and outbreaks in humans. Effective surveillance and timely outbreak detection are essential for public health control. Multilevel genome typing (MGT) with multiple levels of resolution has been previously demonstrated as a promising tool for this purpose. In this study, we developed MGT with nine levels for S. Enteritidis and characterised the genomic epidemiology of S. Enteritidis in detail. We examined 26 670 publicly available S. Enteritidis genome sequences from isolates spanning 101 years from 86 countries to reveal their spatial and temporal distributions. Using the lower resolution MGT levels, globally prevalent and regionally restricted sequence types (STs) were identified; avian associated MGT4-STs were found that were common in human cases in the USA; temporal trends were observed in the UK with MGT5-STs from 2014 to 2018 revealing both long lived endemic STs and the rapid expansion of new STs. Using MGT3 to MGT6, we identified multidrug resistance (MDR) associated STs at various MGT levels, which improves precision of detection and global tracking of MDR clones. We also found that the majority of the global S. Enteritidis population fell within two predominant lineages, which had significantly different propensity of causing large scale outbreaks. An online open MGT database has been established for unified international surveillance of S. Enteritidis. We demonstrated that MGT provides a flexible and high-resolution genome typing tool for S. Enteritidis surveillance and outbreak detection.
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Affiliation(s)
- Lijuan Luo
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Michael Payne
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Sandeep Kaur
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Dalong Hu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Liam Cheney
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Sophie Octavia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Qinning Wang
- Centre for Infectious Diseases and Microbiology-Public Health, Institute of Clinical Pathology and Medical Research - NSW Health Pathology, Westmead Hospital, New South Wales, Australia
| | - Mark M Tanaka
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology-Public Health, Institute of Clinical Pathology and Medical Research - NSW Health Pathology, Westmead Hospital, New South Wales, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School, University of Sydney, New South Wales, Australia
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
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13
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Kubicek-Sutherland JZ, Xie G, Shakya M, Dighe PK, Jacobs LL, Daligault H, Davenport K, Stromberg LR, Stromberg ZR, Cheng Q, Kempaiah P, Ong’echa JM, Otieno V, Raballah E, Anyona S, Ouma C, Chain PSG, Perkins DJ, Mukundan H, McMahon BH, Doggett NA. Comparative genomic and phenotypic characterization of invasive non-typhoidal Salmonella isolates from Siaya, Kenya. PLoS Negl Trop Dis 2021; 15:e0008991. [PMID: 33524010 PMCID: PMC7877762 DOI: 10.1371/journal.pntd.0008991] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 02/11/2021] [Accepted: 11/17/2020] [Indexed: 02/07/2023] Open
Abstract
Non-typhoidal Salmonella (NTS) is a major global health concern that often causes bloodstream infections in areas of the world affected by malnutrition and comorbidities such as HIV and malaria. Developing a strategy to control the emergence and spread of highly invasive and antimicrobial resistant NTS isolates requires a comprehensive analysis of epidemiological factors and molecular pathogenesis. Here, we characterize 11 NTS isolates that caused bloodstream infections in pediatric patients in Siaya, Kenya from 2003-2010. Nine isolates were identified as S. Typhimurium sequence type 313 while the other two were S. Enteritidis. Comprehensive genotypic and phenotypic analyses were performed to compare these isolates to those previously identified in sub-Saharan Africa. We identified a S. Typhimurium isolate referred to as UGA14 that displayed novel plasmid, pseudogene and resistance features as compared to other isolates reported from Africa. Notably, UGA14 is able to ferment both lactose and sucrose due to the acquisition of insertion elements on the pKST313 plasmid. These findings show for the first time the co-evolution of plasmid-mediated lactose and sucrose metabolism along with cephalosporin resistance in NTS further elucidating the evolutionary mechanisms of invasive NTS phenotypes. These results further support the use of combined genomic and phenotypic approaches to detect and characterize atypical NTS isolates in order to advance biosurveillance efforts that inform countermeasures aimed at controlling invasive and antimicrobial resistant NTS.
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Affiliation(s)
| | - Gary Xie
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States
| | - Migun Shakya
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States
| | - Priya K. Dighe
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States
| | - Lindsey L. Jacobs
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States
| | | | - Karen Davenport
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States
| | | | | | - Qiuying Cheng
- Center for Global Health, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Prakasha Kempaiah
- Center for Global Health, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - John Michael Ong’echa
- University of New Mexico/KEMRI Laboratories of Parasitic and Viral Diseases, Kenya Medical Research Institute, Kisumu, Kenya
| | - Vincent Otieno
- University of New Mexico/KEMRI Laboratories of Parasitic and Viral Diseases, Kenya Medical Research Institute, Kisumu, Kenya
| | - Evans Raballah
- University of New Mexico/KEMRI Laboratories of Parasitic and Viral Diseases, Kenya Medical Research Institute, Kisumu, Kenya
- Department of Medical Laboratory Science, School of Public Health, Biomedical Sciences and Technology, Masinde Muliro University of Science and Technology, Kakamega, Kenya
| | - Samuel Anyona
- University of New Mexico/KEMRI Laboratories of Parasitic and Viral Diseases, Kenya Medical Research Institute, Kisumu, Kenya
- Department of Medical Biochemistry, School of Medicine, Maseno University, Maseno, Kenya
| | - Collins Ouma
- University of New Mexico/KEMRI Laboratories of Parasitic and Viral Diseases, Kenya Medical Research Institute, Kisumu, Kenya
- Department of Biomedical Sciences and Technology, School of Public Health and Community Development, Maseno University, Maseno, Kenya
| | | | - Douglas J. Perkins
- Center for Global Health, University of New Mexico, Albuquerque, New Mexico, United States of America
- University of New Mexico/KEMRI Laboratories of Parasitic and Viral Diseases, Kenya Medical Research Institute, Kisumu, Kenya
| | - Harshini Mukundan
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States
- * E-mail:
| | | | - Norman A. Doggett
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States
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14
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Antimicrobial resistance and genomic characterisation of Escherichia coli isolated from caged and non-caged retail table eggs in Western Australia. Int J Food Microbiol 2021; 340:109054. [PMID: 33465549 DOI: 10.1016/j.ijfoodmicro.2021.109054] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 01/05/2021] [Accepted: 01/07/2021] [Indexed: 01/15/2023]
Abstract
Foodborne exposure to antimicrobial-resistant bacteria is a growing global health concern. Escherichia coli (E. coli) is well recognised as an indicator of food contamination with faecal materials. In the present study, we investigated the occurrence of E. coli in table eggs sold at retail supermarkets in Western Australia (WA). A total of 2172 visually clean and intact retail eggs were purchased between October 2017 and June 2018. A single carton containing a dozen eggs was considered as a single sample resulting a total of 181 samples. The shells and contents of each sample were separately pooled and tested using standard culture-based methods. Overall, generic E. coli was detected in 36 (19.8%; 95% confidence interval: 14.3; 26.4) of the 181 tested retail egg samples. We characterised 100 of the recovered E. coli isolates for their phenotypic antimicrobial resistance using minimum inhibitory concentration (MIC). A subset of E. coli isolates (n = 14) were selected on the basis of their MIC patterns, and were further characterised using whole genome sequencing (WGS). Fifty-seven (57%) of the recovered generic E. coli isolates (n = 100) were resistant to at least one of the 14 antimicrobials included in the MIC testing panel, of which 22 isolates (22%) showed multi-class resistance. The highest frequencies of non-susceptibility of E. coli isolated from WA retailed eggs were against tetracycline (49%) and ampicillin (36%). WGS revealed that tet(A) and blaTEM-1B genes were present in most of the isolates exhibiting phenotypic resistance to tetracycline and ampicillin, respectively. The majority (98%) of the characterised E. coli isolates were susceptible to ciprofloxacin and azithromycin, and none were resistant to the cephalosporin antimicrobials included in the MIC panel. Two isolates demonstrated reduced susceptibility to ciprofloxacin, with MICs of 0.125 and 0.25 mg/L, and WGS revealed the presence of plasmid mediated qnrs1 gene in both isolates. This is the first report on detection of non-wild-type resistance to fluoroquinolones in supermarket eggs in Australia; one of the two isolates was from a cage-laid eggs sample while the other was from a barn-laid retail eggs sample. Fluoroquinolones have never been permitted for use in poultry farms in Australia. Thus, the detection of low-level ciprofloxacin-resistant E. coli in the absence of local antimicrobial selection pressure at the Australian layer farms warrants further research on the potential role of the environment or human-related factors in the transmission of antimicrobial resistance. The results of this study add to the local and global understanding of antimicrobial resistance spread in foods of animal origin.
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15
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Crump JA, Thomas KM, Benschop J, Knox MA, Wilkinson DA, Midwinter AC, Munyua P, Ochieng JB, Bigogo GM, Verani JR, Widdowson MA, Prinsen G, Cleaveland S, Karimuribo ED, Kazwala RR, Mmbaga BT, Swai ES, French NP, Zadoks RN. Investigating the meat pathway as a source of human nontyphoidal Salmonella bloodstream infections and diarrhea in East Africa. Clin Infect Dis 2020; 73:e1570-e1578. [PMID: 32777036 PMCID: PMC8492120 DOI: 10.1093/cid/ciaa1153] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 08/04/2020] [Indexed: 11/29/2022] Open
Abstract
Background Salmonella Enteritidis and Salmonella Typhimurium are major causes of bloodstream infection and diarrheal disease in East Africa. Sources of human infection, including the role of the meat pathway, are poorly understood. Methods We collected cattle, goat, and poultry meat pathway samples from December 2015 through August 2017 in Tanzania and isolated Salmonella using standard methods. Meat pathway isolates were compared with nontyphoidal serovars of Salmonella enterica (NTS) isolated from persons with bloodstream infections and diarrheal disease from 2007 through 2017 from Kenya by core genome multi-locus sequence typing (cgMLST). Isolates were characterized for antimicrobial resistance, virulence genes, and diversity. Results We isolated NTS from 164 meat pathway samples. Of 172 human NTS isolates, 90 (52.3%) from stool and 82 (47.7%) from blood, 53 (30.8%) were Salmonella Enteritidis sequence type (ST) 11 and 62 (36.0%) were Salmonella Typhimurium ST313. We identified cgMLST clusters within Salmonella Enteritidis ST11, Salmonella Heidelberg ST15, Salmonella Typhimurium ST19, and Salmonella II 42:r:- ST1208 that included both human and meat pathway isolates. Salmonella Typhimurium ST313 was isolated exclusively from human samples. Human and poultry isolates bore more antimicrobial resistance and virulence genes and were less diverse than isolates from other sources. Conclusions Our findings suggest that the meat pathway may be an important source of human infection with some clades of Salmonella Enteritidis ST11 in East Africa, but not of human infection by Salmonella Typhimurium ST313. Research is needed to systematically examine the contributions of other types of meat, animal products, produce, water, and the environment to nontyphoidal Salmonella disease in East Africa.
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Affiliation(s)
- John A Crump
- Centre for International Health, University of Otago, Dunedin, New Zealand.,Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania.,Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Kate M Thomas
- Centre for International Health, University of Otago, Dunedin, New Zealand
| | - Jackie Benschop
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Matthew A Knox
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - David A Wilkinson
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Anne C Midwinter
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Peninah Munyua
- Division of Global Health Protection, US Centers for Disease Control and Prevention, Nairobi, Kenya
| | - John B Ochieng
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Godfrey M Bigogo
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Jennifer R Verani
- Division of Global Health Protection, US Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Marc-Alain Widdowson
- Division of Global Health Protection, US Centers for Disease Control and Prevention, Nairobi, Kenya.,Institute of Tropical Medicine, Antwerp, Belgium
| | - Gerard Prinsen
- School of People, Environment and Planning, Massey University, Palmerston North, New Zealand
| | - Sarah Cleaveland
- Institute of Biodiversity, Animal Health, and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Esron D Karimuribo
- College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Rudovick R Kazwala
- College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Blandina T Mmbaga
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania.,Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Emanuel S Swai
- Department of Veterinary Services, Ministry of Livestock and Fisheries, Dodoma, Tanzania
| | - Nigel P French
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Ruth N Zadoks
- Institute of Biodiversity, Animal Health, and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom.,Sydney School of Veterinary Science, University of Sydney, Sydney, Australia
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16
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Piccini G, Montomoli E. Pathogenic signature of invasive non-typhoidal Salmonella in Africa: implications for vaccine development. Hum Vaccin Immunother 2020; 16:2056-2071. [PMID: 32692622 PMCID: PMC7553687 DOI: 10.1080/21645515.2020.1785791] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Invasive non-typhoidal Salmonella (iNTS) infections are a leading cause of bacteremia in Sub-Saharan Africa (sSA), thereby representing a major public health threat. Salmonella Typhimurium clade ST313 and Salmonella Enteriditis lineages associated with Western and Central/Eastern Africa are among the iNTS serovars which are of the greatest concern due to their case-fatality rate, especially in children and in the immunocompromised population. Identification of pathogen-associated features and host susceptibility factors that increase the risk for invasive non-typhoidal salmonellosis would be instrumental for the design of targeted prevention strategies, which are urgently needed given the increasing spread of multidrug-resistant iNTS in Africa. This review summarizes current knowledge of bacterial traits and host immune responses associated with iNTS infections in sSA, then discusses how this knowledge can guide vaccine development while providing a summary of vaccine candidates in preclinical and early clinical development.
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Affiliation(s)
| | - Emanuele Montomoli
- VisMederi srl , Siena, Italy.,Department of Molecular and Developmental Medicine, University of Siena , Siena, Italy
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17
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Abstract
Patients returning from travel to a foreign country often present with atypical infections that can present as diagnostic challenges. Although rarely seen in the United States, Salmonella infections are commonly seen in Sub-Saharan Africa. The common clinical manifestations of Salmonella infection include fever and diarrhea; however, about 5% of cases of non-typhi Salmonella progress to bacteremia. Here, we present a case of a unique presentation of Salmonella infection manifesting as a prostatic abscess in an immunocompetent patient.
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Affiliation(s)
- Christina Lin
- Internal Medicine, University of California Los Angeles, Los Angeles, USA
| | - Satya Patel
- Internal Medicine, University of California Los Angeles, Los Angeles, USA
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18
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Breurec S, Reynaud Y, Frank T, Farra A, Costilhes G, Weill FX, Le Hello S. Serotype distribution and antimicrobial resistance of human Salmonella enterica in Bangui, Central African Republic, from 2004 to 2013. PLoS Negl Trop Dis 2019; 13:e0007917. [PMID: 31790418 PMCID: PMC6907862 DOI: 10.1371/journal.pntd.0007917] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 12/12/2019] [Accepted: 11/11/2019] [Indexed: 01/30/2023] Open
Abstract
Background Limited epidemiological and antimicrobial resistance data are available on Salmonella enterica from sub-Saharan Africa. We determine the prevalence of resistance to antibiotics in isolates in the Central African Republic (CAR) between 2004 and 2013 and the genetic basis for resistance to third-generation cephalosporin (C3G). Methodology/Principal findings A total of 582 non-duplicate human clinical isolates were collected. The most common serotype was Typhimurium (n = 180, 31% of the isolates). A randomly selected subset of S. Typhimurium isolates were subtyped by clustered regularly interspaced short palindromic repeat polymorphism (CRISPOL) typing. All but one invasive isolate tested (66/68, 96%) were associated with sequence type 313. Overall, the rates of resistance were high to traditional first-line drugs (18–40%) but low to many other antimicrobials, including fluoroquinolones (one resistant isolate) and C3G (only one ESBL-producing isolate). The extended-spectrum beta-lactamase (ESBL)-producing isolate and three additional ESBL isolates from West Africa were studied by whole genome sequencing. The blaCTX-M-15 gene and the majority of antimicrobial resistance genes found in the ESBL isolate were present in a large conjugative IncHI2 plasmid highly similar (> 99% nucleotide identity) to ESBL-carrying plasmids found in Kenya (S. Typhimurium ST313) and also in West Africa (serotypes Grumpensis, Havana, Telelkebir and Typhimurium). Conclusions/Significance Although the prevalence of ESBL-producing Salmonella isolates was low in CAR, we found that a single IncHI2 plasmid-carrying blaCTX-M-15 was widespread among Salmonella serotypes from sub-Saharan Africa, which is of concern. Salmonella enterica infections are common causes of bloodstream infection in sub-Saharan Africa and associated with a high mortality rate. Levels of multidrug resistance have become alarmingly high. Then, third-generation cephalosporin (C3G) and fluoroquinolones have become standard for first-line empirical treatment. Recently, C3G-resistant Salmonella populations have emerged and spread over all continents. This resistance is mainly mediated by acquired extended-spectrum beta-lactamase (ESBL) genes carried by mobile genetic elements such as plasmids. We report here the prevalence of resistance to antibiotics in isolates in the Central African Republic (CAR) between 2004 and 2013 and the genetic basis for resistance to C3G. Overall, resistance rates to antimicrobials were low during the study period, for all classes other than conventional antimicrobials, confirming recommendations for first-line treatment based on C3G and fluoroquinolones. Only one ESBL-producing isolate was recovered. The ESBL gene and the majority of antimicrobial resistance genes found were present in a large plasmid highly similar to ESBL-carrying plasmids found in East and West Africa, highlighting its significant role in the spread of ESBL genes in Salmonella isolates in sub-Saharan Africa. These finding have implications for treatment of salmonellosis and support the growing necessity for increased microbiological surveillance based on networks of clinical laboratories in order to control dissemination of antibiotic resistance among Salmonella isolates.
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Affiliation(s)
- Sebastien Breurec
- Laboratoire de Bactériologie, Institut Pasteur, Bangui, Central African Republic
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, France
- Faculté de Médecine Hyacinthe Bastaraud, Université des Antilles, Pointe-à-Pitre, France
- Laboratoire de Microbiologie clinique et environnementale, Centre Hospitalier Universitaire de Pointe-à-Pitre/les Abymes, Pointe-à-Pitre, France
- * E-mail:
| | - Yann Reynaud
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, France
| | - Thierry Frank
- Laboratoire de Bactériologie, Institut Pasteur, Bangui, Central African Republic
| | - Alain Farra
- Laboratoire de Bactériologie, Institut Pasteur, Bangui, Central African Republic
| | - Geoffrey Costilhes
- Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, World Health Organization Collaborative Centre for typing and antibiotic resistance of Salmonella, Institut Pasteur, Paris, France
| | - François-Xavier Weill
- Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, World Health Organization Collaborative Centre for typing and antibiotic resistance of Salmonella, Institut Pasteur, Paris, France
| | - Simon Le Hello
- Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, World Health Organization Collaborative Centre for typing and antibiotic resistance of Salmonella, Institut Pasteur, Paris, France
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19
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The global burden of non-typhoidal salmonella invasive disease: a systematic analysis for the Global Burden of Disease Study 2017. THE LANCET. INFECTIOUS DISEASES 2019; 19:1312-1324. [PMID: 31562022 PMCID: PMC6892270 DOI: 10.1016/s1473-3099(19)30418-9] [Citation(s) in RCA: 283] [Impact Index Per Article: 56.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 04/15/2019] [Accepted: 06/19/2019] [Indexed: 12/22/2022]
Abstract
Background Non-typhoidal salmonella invasive disease is a major cause of global morbidity and mortality. Malnourished children, those with recent malaria or sickle-cell anaemia, and adults with HIV infection are at particularly high risk of disease. We sought to estimate the burden of disease attributable to non-typhoidal salmonella invasive disease for the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2017. Methods We did a systematic review of scientific databases and grey literature, and estimated non-typhoidal salmonella invasive disease incidence and mortality for the years 1990 to 2017, by age, sex, and geographical location using DisMod-MR, a Bayesian meta-regression tool. We estimated case fatality by age, HIV status, and sociodemographic development. We also calculated the HIV-attributable fraction and estimated health gap metrics, including disability-adjusted life-years (DALYs). Findings We estimated that 535 000 (95% uncertainty interval 409 000–705 000) cases of non-typhoidal salmonella invasive disease occurred in 2017, with the highest incidence in sub-Saharan Africa (34·5 [26·6–45·0] cases per 100 000 person-years) and in children younger than 5 years (34·3 [23·2–54·7] cases per 100 000 person-years). 77 500 (46 400–123 000) deaths were estimated in 2017, of which 18 400 (12 000–27 700) were attributable to HIV. The remaining 59 100 (33 300–98 100) deaths not attributable to HIV accounted for 4·26 million (2·38–7·38) DALYs in 2017. Mean all-age case fatality was 14·5% (9·2–21·1), with higher estimates among children younger than 5 years (13·5% [8·4–19·8]) and elderly people (51·2% [30·2–72·9] among those aged ≥70 years), people with HIV infection (41·8% [30·0–54·0]), and in areas of low sociodemographic development (eg, 15·8% [10·0–22·9] in sub-Saharan Africa). Interpretation We present the first global estimates of non-typhoidal salmonella invasive disease that have been produced as part of GBD 2017. Given the high disease burden, particularly in children, elderly people, and people with HIV infection, investigating the sources and transmission pathways of non-typhoidal salmonella invasive disease is crucial to implement effective preventive and control measures. Funding Bill & Melinda Gates Foundation.
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20
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Kumar A, Ellermann M, Sperandio V. Taming the Beast: Interplay between Gut Small Molecules and Enteric Pathogens. Infect Immun 2019; 87:IAI.00131-19. [PMID: 31262983 PMCID: PMC6704596 DOI: 10.1128/iai.00131-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The overuse of antibiotics has led to the evolution of drug-resistant bacteria that are becoming increasingly dangerous to human health. According to the Centers for Disease Control and Prevention, antibiotic-resistant bacteria cause at least 2 million illnesses and 23,000 deaths in the United States annually. Traditionally, antibiotics are bactericidal or bacteriostatic agents that place selective pressure on bacteria, leading to the expansion of antibiotic-resistant strains. In addition, antibiotics that are effective against some pathogens can also exacerbate their pathogenesis and may lead to severe progression of the disease. Therefore, alternative strategies are needed to treat antibiotic-resistant bacterial infections. One novel approach is to target bacterial virulence to prevent or limit pathogen colonization, while also minimizing tissue damage and disease comorbidities in the host. This review focuses on the interactions between enteric pathogens and naturally occurring small molecules in the human gut as potential therapeutic targets for antivirulence strategies. Individual small molecules in the intestines modulate enteric pathogen virulence and subsequent intestinal fitness and colonization. Targeted interruption of pathogen sensing of these small molecules could therefore attenuate their virulence. This review highlights the paths of discovery for new classes of antimicrobials that could potentially mitigate the urgent problem of antibiotic resistance.
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Affiliation(s)
- Aman Kumar
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Melissa Ellermann
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Vanessa Sperandio
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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21
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Sodagari HR, Mohammed AB, Wang P, O'Dea M, Abraham S, Robertson I, Habib I. Non-typhoidal Salmonella contamination in egg shells and contents from retail in Western Australia: Serovar diversity, multilocus sequence types, and phenotypic and genomic characterizations of antimicrobial resistance. Int J Food Microbiol 2019; 308:108305. [PMID: 31476731 DOI: 10.1016/j.ijfoodmicro.2019.108305] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 07/30/2019] [Accepted: 08/09/2019] [Indexed: 11/24/2022]
Abstract
In recent years, the number of human salmonellosis cases in Western Australia (WA) has increased more dramatically than in any other Australian state. In 2017, the number of cases in WA was more than double the five-year average, and eggs had emerged as the key culprit for several Salmonella foodborne disease outbreaks. To better understand such an epidemiologically intriguing situation, our research goal was to investigate the prevalence, serovar diversity, multilocus sequence types, and antimicrobial resistance of non-typhoidal Salmonella contamination in retail eggs produced and sold in WA. A total of 200 visually clean and intact retail egg samples (each containing a dozen eggs) were purchased for one year (2017-2018) from supermarkets in metropolitan Perth, the capital of WA. For each sample, the contents and shells of the 12 eggs were separately pooled and cultured according to standard methods. Overall, Salmonella was detected in 11.5% (23/200) of the tested egg samples. Salmonella was isolated from 4.5% (9/200) and 3% (6/200) of eggshells and egg contents, respectively. In 4% (8/200) of the samples, Salmonella was recovered from both eggshell and egg contents. Isolates from positive retail egg samples were serotyped as either S. Typhimurium (52.2% [12/23]) or S. Infantis (39.1% [9/23]). Both serotypes were concurrently recovered from two different retail egg samples. We retained a set of both S. Typhimurium (n = 29) and S. Infantis (n = 12) isolates from all Salmonella-positive retail packs (n = 23) for further characterization. Only two (S. Typhimurium) isolates showed resistance to ampicillin, of which one carried β-lactamase resistance gene blaTEM-1b. The remaining isolates (39/41) were susceptible to all 14 antimicrobials included in the minimum inhibitory concentrations (MICs) testing panel. Multilocus sequence typing and serotyping were perfectly mirrored, as all S. Typhimurium isolates were characterized as sequence type (ST)-19, and all S. Infantis isolates were ST-32. This study points to the noteworthy Salmonella prevalence rate in retail egg samples in WA. Our results illustrate minimal public health risks arising from antimicrobial resistance Salmonella from Australian eggs.
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Affiliation(s)
- Hamid Reza Sodagari
- School of Veterinary Medicine, College of Science, Health, Engineering and Education, Murdoch University, Perth, Australia
| | - Arkan Baraa Mohammed
- School of Veterinary Medicine, College of Science, Health, Engineering and Education, Murdoch University, Perth, Australia
| | - Penghao Wang
- School of Veterinary Medicine, College of Science, Health, Engineering and Education, Murdoch University, Perth, Australia
| | - Mark O'Dea
- School of Veterinary Medicine, College of Science, Health, Engineering and Education, Murdoch University, Perth, Australia
| | - Sam Abraham
- School of Veterinary Medicine, College of Science, Health, Engineering and Education, Murdoch University, Perth, Australia
| | - Ian Robertson
- School of Veterinary Medicine, College of Science, Health, Engineering and Education, Murdoch University, Perth, Australia
| | - Ihab Habib
- School of Veterinary Medicine, College of Science, Health, Engineering and Education, Murdoch University, Perth, Australia; Veterinary Medicine Department, College of Food and Agriculture, United Arab of Emirates University (UAEU), Al Ain, United Arab Emirates.
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22
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Aldrich C, Hartman H, Feasey N, Chattaway MA, Dekker D, Al-Emran HM, Larkin L, McCormick J, Sarpong N, Le Hello S, Adu-Sarkodie Y, Panzner U, Park SE, Im J, Marks F, May J, Dallman TJ, Eibach D. Emergence of phylogenetically diverse and fluoroquinolone resistant Salmonella Enteritidis as a cause of invasive nontyphoidal Salmonella disease in Ghana. PLoS Negl Trop Dis 2019; 13:e0007485. [PMID: 31220112 PMCID: PMC6605661 DOI: 10.1371/journal.pntd.0007485] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 07/02/2019] [Accepted: 05/22/2019] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Salmonella enterica serovar Enteritidis is a cause of both poultry- and egg-associated enterocolitis globally and bloodstream-invasive nontyphoidal Salmonella (iNTS) disease in sub-Saharan Africa (sSA). Distinct, multi-drug resistant genotypes associated with iNTS disease in sSA have recently been described, often requiring treatment with fluoroquinolone antibiotics. In industrialised countries, antimicrobial use in poultry production has led to frequent fluoroquinolone resistance amongst globally prevalent enterocolitis-associated lineages. METHODOLOGY/PRINCIPAL FINDINGS Twenty seven S. Enteritidis isolates from patients with iNTS disease and two poultry isolates, collected between 2007 and 2015 in the Ashanti region of Ghana, were whole-genome sequenced. These isolates, notable for a high rate of diminished ciprofloxacin susceptibility (DCS), were placed in the phyletic context of 1,067 sequences from the Public Health England (PHE) S. Enteritidis genome database to understand whether DCS was associated with African or globally-circulating clades of S. Enteritidis. Analysis showed four of the major S. Enteritidis clades were represented, two global and two African. All thirteen DCS isolates, containing a single gyrA mutation at codon 87, belonged to a global PT4-like clade responsible for epidemics of poultry-associated enterocolitis. Apart from two DCS isolates, which clustered with PHE isolates associated with travel to Spain and Brazil, the remaining DCS isolates, including one poultry isolate, belonged to two monophyletic clusters in which gyrA 87 mutations appear to have developed within the region. CONCLUSIONS/SIGNIFICANCE Extensive phylogenetic diversity is evident amongst iNTS disease-associated S. Enteritidis in Ghana. Antimicrobial resistance profiles differed by clade, highlighting the challenges of devising empirical sepsis guidelines. The detection of fluoroquinolone resistance in phyletically-related poultry and human isolates is of major concern and surveillance and control measures within the region's burgeoning poultry industry are required to protect a human population at high risk of iNTS disease.
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Affiliation(s)
- Cassandra Aldrich
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich (LMU), Munich, Germany
| | - Hassan Hartman
- National Infections Service, Public Health England, Colindale, United Kingdom
| | - Nicholas Feasey
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | | | - Denise Dekker
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Centre for Infection Research (DZIF), Hamburg-Borstel-Luebeck, Germany
| | - Hassan M. Al-Emran
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Jessore University of Science and Technology, Jessore, Bangladesh
| | - Lesley Larkin
- National Infections Service, Public Health England, Colindale, United Kingdom
| | - Jacquelyn McCormick
- National Infections Service, Public Health England, Colindale, United Kingdom
| | - Nimako Sarpong
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana
| | - Simon Le Hello
- Institut Pasteur, French National Reference Center for Escherichia coli, Shigella and Salmonella, Paris, France
| | - Yaw Adu-Sarkodie
- Department of Clinical Microbiology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Ursula Panzner
- International Vaccine Institute, Seoul, Republic of Korea
| | - Se Eun Park
- International Vaccine Institute, Seoul, Republic of Korea
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Justin Im
- International Vaccine Institute, Seoul, Republic of Korea
| | - Florian Marks
- International Vaccine Institute, Seoul, Republic of Korea
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Jürgen May
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Centre for Infection Research (DZIF), Hamburg-Borstel-Luebeck, Germany
| | - Timothy J. Dallman
- National Infections Service, Public Health England, Colindale, United Kingdom
| | - Daniel Eibach
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
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23
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Albert MJ, Bulach D, Alfouzan W, Izumiya H, Carter G, Alobaid K, Alatar F, Sheikh AR, Poirel L. Non-typhoidal Salmonella blood stream infection in Kuwait: Clinical and microbiological characteristics. PLoS Negl Trop Dis 2019; 13:e0007293. [PMID: 30986214 PMCID: PMC6483562 DOI: 10.1371/journal.pntd.0007293] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 04/25/2019] [Accepted: 03/12/2019] [Indexed: 12/12/2022] Open
Abstract
Non-typhoidal Salmonella (NTS) bacteremia is a significant cause of morbidity and mortality worldwide. It is considered to be an emerging and neglected tropical disease in Africa. We studied this in two tertiary hospitals–Al Farwaniya and Al Amiri–in Kuwait, a subtropical country, from April 2013-May 2016. NTS bacteremia was present in 30 of 53,860 (0.75%) and 31 of 290,36 (1.33%) blood cultures in the two hospitals respectively. In Al Farwaniya hospital, one-third of the patients were from some tropical developing countries of Asia. About 66% of all patients (40/61) had diarrhea, and of these, 65% had the corresponding blood serovar isolated from stool culture. A few patients had Salmonella cultured from urine. Patients were either young or old. Most of the patients had co-morbidities affecting the immune system. Two patients each died in both hospitals. The number of different serovars cultured in each hospital was 13, and most infections were due to S. Enteritidis (all sequence type [ST]) 11) and S. Typhimurium (all ST19) except in a subgroup of expatriate patients from tropical developing countries in Al Farwaniya hospital. About a quarter of the isolates were multidrug-resistant. Most patients were treated with a cephalosporin with or without other antibiotics. S. Enteritidis and S. Typhimurium isolates were typed by pulsed field-gel electrophoresis (PFGE) and a selected number of isolates were whole-genome sequenced. Up to four different clades were present by PFGE in either species. Whole-genome sequenced isolates showed antibiotic-resistance genes that showed phenotypic correlation, and in some cases, phenotypes showed absence of specific genes. Whole-genome sequenced isolates showed presence of genes that contributed to blood-stream infection. Phylogeny by core genome analysis showed a close relationship with S. Typhimurium and S. Enteritidis from other parts of the world. The uniqueness of our study included the finding of a low prevalence of infection, mortality and multidrug-resistance, a relatively high prevalence of gastrointestinal infection in patients, and the characterization of selected isolates of S. Typhimurium and S. Enteritidis serovars by whole-genome sequencing that shed light on phylogeny, virulence and resistance. Similarities with studies from developing countries especially Africa included infection in patients with co-morbidities affecting the immune system, predominance of S. Typhimurium and S. Enteritidis serovars and presence of drug-resistance in isolates. Salmonella organisms are classified into typhoidal Salmonella (causing enteric fever) and non-typhoidal Salmonella (NTS) (causing infections other than enteric fever). Apart from causing other infections, NTS causes blood-stream infection (bacteremia and septicemia). NTS blood stream infection (NTS-BI) is considered to be an emerging and neglected tropical disease in Africa. It causes a very high morbidity and mortality in Africa. The individuals affected in Africa are children, malnourished people, patients with malaria or HIV etc. These conditions affect the immune system and make them vulnerable to infection with NTS. In these patients, diarrheal disease due to NTS is rare. The majority of infections are due to two types of NTS: Typhimurium and Enteritidis. There is a very high prevalence of multidrug-resistance in NTS making the infection difficult to treat. NTS-BI is also present in other parts of the world including developed countries albeit at a lower prevalence. Kuwait is a high-income, subtropical country in transition (from a developing to developed country), located in the Middle East. We studied NTS-BI in Al Farwaniya and Al Amiri hospitals in Kuwait during April 2013 to May 2016. Out of nearly 30,000 to more than 50,000 blood cultures done in these hospitals, NTS was present in 0. 75 to 1.33% of blood cultures, representing a very small proportion of blood cultures, unlike in Africa. This showed that 31 patients in Al Farwaniya hospital and 30 patients in Al Amari hospital had NTS-BI. Most of these patients had underlying illnesses such as diabetes, lung infection, cancer etc. that affect the immune system, as in Africa. Many patients also had diarrheal disease caused by the same NTS that caused blood stream infection, unlike in Africa. Only two patients in each hospital died, a low mortality, unlike in Africa. The majority of the isolates belonged to Typhimurium and Enteritidis as in Africa. Even though resistance to drugs was a problem, about quarter of the isolates only were multidrug-resistant, a lower prevalence compared to in Africa. In Kuwait, we performed a detailed genetic study of a selected number of Typhimurium and Enteritidis isolates by a modern technique called whole genome sequencing. This revealed genetic determinants encoding drug-resistance and virulence causing blood-stream infection. This type of study was not performed in African isolates. Thus, our study revealed similarities and differences with studies of NTS-BI in Africa.
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Affiliation(s)
- M. John Albert
- Department of Microbiology, Faculty of Medicine, Kuwait University, Jabriya, Kuwait
- * E-mail:
| | - Dieter Bulach
- Microbiological Diagnostic Unit, Public Health Laboratory, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Victoria, Australia
| | - Wadha Alfouzan
- Department of Microbiology, Faculty of Medicine, Kuwait University, Jabriya, Kuwait
- Microbiology Unit, Department of Laboratories, Al Farwaniya Hospital, Sabah Al-Nasser, Kuwait
| | | | - Glen Carter
- Microbiological Diagnostic Unit, Public Health Laboratory, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Victoria, Australia
| | - Khaled Alobaid
- Department of Microbiology, Al Amiri Hospital, Sharq, Kuwait
| | - Fatemah Alatar
- Microbiology Unit, Muabarak Al Kabeer Hospital, Jabriya, Kuwait, and
| | | | - Laurent Poirel
- Department of Medicine, University of Fribourg, Switzerland
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