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Getahun Strobel A, Hayes AJ, Wirth W, Mua M, Saumalua T, Cabenatabua O, Soqo V, Rosa V, Wang N, Lacey JA, Hocking D, Valcanis M, Jenney A, Howden BP, Duchene S, Mulholland K, Strugnell RA, Davies MR. Genetic heterogeneity in the Salmonella Typhi Vi capsule locus: a population genomic study from Fiji. Microb Genom 2024; 10. [PMID: 39254668 PMCID: PMC11385387 DOI: 10.1099/mgen.0.001288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/11/2024] Open
Abstract
Typhoid fever is endemic in many parts of the world and remains a major public health concern in tropical and sub-tropical developing nations, including Fiji. To address high rates of typhoid fever, the Northern Division of Fiji implemented a mass vaccination with typhoid conjugate vaccine (Vi-polysaccharide conjugated to tetanus toxoid) as a public health control measure in 2023. In this study we define the genomic epidemiology of Salmonella Typhi in the Northern Division prior to island-wide vaccination, sequencing 85% (n=419) of the total cases from the Northern and Central Divisions of Fiji that occurred in the period 2017-2019. We found elevated rates of nucleotide polymorphisms in the tviD and tviE genes (responsible for Vi-polysaccharide synthesis) relative to core genome levels within the Fiji endemic S. Typhi genotype 4.2. Expansion of these findings within a globally representative database of 12 382 S. Typhi (86 genotyphi clusters) showed evidence of convergent evolution of the same tviE mutations across the S. Typhi population, indicating that tvi selection has occurred both independently and globally. The functional impact of tvi mutations on the Vi-capsular structure and other phenotypic characteristics are not fully elucidated, yet commonly occurring tviE polymorphisms localize adjacent to predicted active site residues when overlayed against the predicted TviE protein structure. Given the central role of the Vi-polysaccharide in S. Typhi biology and vaccination, further integrated epidemiological, genomic and phenotypic surveillance is required to determine the spread and functional implications of these mutations.
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Affiliation(s)
- Aneley Getahun Strobel
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- College of Medicine and Health Sciences, Fiji National University, Suva, Fiji
| | - Andrew J Hayes
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Wytamma Wirth
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Mikaele Mua
- Labasa Divisional Hospital, Fiji Ministry of Health, and Medical Services, Labasa, Fiji
| | - Tiko Saumalua
- Northern Health, Fiji Ministry of Health, and Medical Services, Labasa, Fiji
| | - Orisi Cabenatabua
- Labasa Divisional Hospital, Fiji Ministry of Health, and Medical Services, Labasa, Fiji
| | - Vika Soqo
- Labasa Divisional Hospital, Fiji Ministry of Health, and Medical Services, Labasa, Fiji
| | - Varanisese Rosa
- New Vaccines Group, Murdoch Childrens Research Institute, Melbourne, Victoria, Australia
| | - Nancy Wang
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Jake A Lacey
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Dianna Hocking
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Adam Jenney
- College of Medicine and Health Sciences, Fiji National University, Suva, Fiji
- New Vaccines Group, Murdoch Childrens Research Institute, Melbourne, Victoria, Australia
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Centre for Pathogen Genomics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Sebastian Duchene
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- London School of Hygiene and Tropical Medicine, London, UK
| | - Kim Mulholland
- Department of Computational Biology, Institut Pasteur, Paris, France
- New Vaccines Group, Murdoch Childrens Research Institute, Melbourne, Victoria, Australia
| | - Richard A Strugnell
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Mark R Davies
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
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Adhikari S, Anthony S, Baleinamau P, Coriakula J, Daurewa T, Devi R, Gavidi S, Horwitz P, Hunter EC, Jenkins A, Jupiter S, Lalamacuata M, Mailautoka K, Mangubhai S, Naivalu K, Naivalulevu T, Naivalulevu V, Nasim N, Naucunivanua S, Negin J, van Nimwegen P, Ratu A, Ravoka M, Tukana A, van de Vossenberg J, Wilson D, Thomas J. An assessment of latrine front-end characteristics and associated surface E. coli indicated faecal contamination in rural Fiji. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:52948-52962. [PMID: 39164561 PMCID: PMC11379791 DOI: 10.1007/s11356-024-34668-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 08/05/2024] [Indexed: 08/22/2024]
Abstract
In Fiji, 90% of the population has access to basic sanitation; however, there are still persistent health risks from endemic faecal-oral diseases such as typhoid fever. There is a need to assess the contribution of existing sanitation facilities in the faecal pathogen transmission pathway. This study was conducted as part of a larger planetary health study across 29 rural communities within five river catchments. This specific research aimed to characterise latrine front-ends, both infrastructure and usage behaviour, and to assess the faecal contamination levels on various frequently contacted latrine surfaces in rural Fiji. A sanitation survey, along with observation and latrine swab sampling, was conducted in households over three phases: baseline (n = 311) (Aug-Dec 2019), endline (n = 262) (Jun-Sep 2022) and an in-depth front-end study (n = 12) (Oct-Nov 2022). Of 311 households, almost all had pedestal-type latrines, predominately cistern-flush (83%), followed by pour-flush (13%), and then hole-type (pit) latrines (4%). Washable latrine floors had significantly higher E. coli densities (6.7 × 102 CFU/25 cm2) compared to non-washable floors (1.3 × 102 CFU/25 cm2) (p = 0.05), despite washable floors indicating improved latrines. The in-depth front-end analysis found that moist latrine surfaces had significantly elevated E. coli densities (1.2 × 103 CFU/25 cm2) compared to the dry ones (14.3 CFU/25 cm2) (p < 0.001), highlighting the importance of maintaining dry latrine surfaces. Latrine floors and mid-walls were the most frequently contaminated surfaces, emphasising the need to clean and disinfect these surfaces. Only 46% of the households reported always using soap for handwashing after defecation, exacerbating the risk of transmitting faecal pathogens. This study highlights that latrine cleanliness and hygiene are as crucial as latrine infrastructures for the effective disruption of faecal pathogens transmission during latrine use.
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Affiliation(s)
- Sabita Adhikari
- School of Civil Engineering, The University of Sydney, Darlington, NSW, 2006, Australia.
| | - Shylett Anthony
- Fiji Institute of Pacific Health Research, College of Medicine, Nursing & Health Sciences, Fiji National University, Hoodless House, Suva, Fiji
| | - Ponipate Baleinamau
- Fiji Institute of Pacific Health Research, College of Medicine, Nursing & Health Sciences, Fiji National University, Hoodless House, Suva, Fiji
| | - Jeremaia Coriakula
- Fiji Institute of Pacific Health Research, College of Medicine, Nursing & Health Sciences, Fiji National University, Hoodless House, Suva, Fiji
| | - Thompson Daurewa
- Fiji Institute of Pacific Health Research, College of Medicine, Nursing & Health Sciences, Fiji National University, Hoodless House, Suva, Fiji
| | - Rachel Devi
- Fiji Institute of Pacific Health Research, College of Medicine, Nursing & Health Sciences, Fiji National University, Hoodless House, Suva, Fiji
| | - Sikeli Gavidi
- Fiji Institute of Pacific Health Research, College of Medicine, Nursing & Health Sciences, Fiji National University, Hoodless House, Suva, Fiji
| | - Pierre Horwitz
- Centre for People, Place, and Planet, Edith Cowan University, Joondalup, WA, Australia
| | - Erin C Hunter
- Department of Public Health Sciences, College of Behavioural, Social and Health Sciences, Clemson University, Clemson, USA
| | - Aaron Jenkins
- Centre for People, Place, and Planet, Edith Cowan University, Joondalup, WA, Australia
- School of Public Health, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Stacy Jupiter
- Wildlife Conservation Society, Melanesia Program, Suva, Fiji
| | - Maria Lalamacuata
- Fiji Institute of Pacific Health Research, College of Medicine, Nursing & Health Sciences, Fiji National University, Hoodless House, Suva, Fiji
| | - Kinikoto Mailautoka
- Fiji Institute of Pacific Health Research, College of Medicine, Nursing & Health Sciences, Fiji National University, Hoodless House, Suva, Fiji
| | - Sangeeta Mangubhai
- Wildlife Conservation Society, Fiji Program, Suva, Fiji
- Talanoa Consulting, 42 Knollys Street, Suva, Fiji
| | - Kelera Naivalu
- Fiji Institute of Pacific Health Research, College of Medicine, Nursing & Health Sciences, Fiji National University, Hoodless House, Suva, Fiji
| | - Timoci Naivalulevu
- Fiji Institute of Pacific Health Research, College of Medicine, Nursing & Health Sciences, Fiji National University, Hoodless House, Suva, Fiji
| | - Vilisi Naivalulevu
- Fiji Institute of Pacific Health Research, College of Medicine, Nursing & Health Sciences, Fiji National University, Hoodless House, Suva, Fiji
| | - Nabeela Nasim
- School of Civil Engineering, The University of Sydney, Darlington, NSW, 2006, Australia
| | | | - Joel Negin
- School of Public Health, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
| | | | - Anaseini Ratu
- School of Public Health, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Mereia Ravoka
- Wildlife Conservation Society, Fiji Program, Suva, Fiji
| | - Andrew Tukana
- Wildlife Conservation Society, Fiji Program, Suva, Fiji
| | - Jack van de Vossenberg
- Water Supply, Sanitation and Environmental Engineering Department, IHE Delft Institute of Water Education, Delft, The Netherlands
| | - Donald Wilson
- Fiji Institute of Pacific Health Research, College of Medicine, Nursing & Health Sciences, Fiji National University, Hoodless House, Suva, Fiji
| | - Jacqueline Thomas
- School of Civil Engineering, The University of Sydney, Darlington, NSW, 2006, Australia
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Davies MR, Duchene S, Valcanis M, Jenkins AP, Jenney A, Rosa V, Hayes AJ, Strobel AG, McIntyre L, Lacey JA, Klemm EJ, Wong VK, Sahukhan A, Thomson H, Page A, Hocking D, Wang N, Tudravu L, Rafai E, Dougan G, Howden BP, Crump JA, Mulholland K, Strugnell RA. Genomic epidemiology of Salmonella Typhi in Central Division, Fiji, 2012 to 2016. THE LANCET REGIONAL HEALTH. WESTERN PACIFIC 2022; 24:100488. [PMID: 35769175 PMCID: PMC9234096 DOI: 10.1016/j.lanwpc.2022.100488] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
BACKGROUND Typhoid fever is endemic in some Pacific Island Countries including Fiji and Samoa yet genomic surveillance is not routine in such settings. Previous studies suggested imports of the global H58 clade of Salmonella enterica var Typhi (Salmonella Typhi) contribute to disease in these countries which, given the MDR potential of H58, does not auger well for treatment. The objective of the study was to define the genomic epidemiology of Salmonella Typhi in Fiji. METHODS Genomic sequencing approaches were implemented to study the distribution of 255 Salmonella Typhi isolates from the Central Division of Fiji. We augmented epidemiological surveillance and Bayesian phylogenomic approaches with a multi-year typhoid case-control study to define geospatial patterns among typhoid cases. FINDINGS Genomic analyses showed Salmonella Typhi from Fiji resolved into 2 non-H58 genotypes with isolates from the two dominant ethnic groups, the Indigenous (iTaukei) and non-iTaukei genetically indistinguishable. Low rates of international importation of clones was observed and overall, there were very low levels an antibiotic resistance within the endemic Fijian typhoid genotypes. Genomic epidemiological investigations were able to identify previously unlinked case clusters. Bayesian phylodynamic analyses suggested that genomic variation within the larger endemic Salmonella Typhi genotype expanded at discreet times, then contracted. INTERPRETATION Cyclones and flooding drove 'waves' of typhoid outbreaks in Fiji which, through population aggregation, poor sanitation and water safety, and then mobility of the population, spread clones more widely. Minimal international importations of new typhoid clones suggest that targeted local intervention strategies may be useful in controlling endemic typhoid infection. These findings add to our understanding of typhoid transmission networks in an endemic island country with broad implications, particularly across Pacific Island Countries. FUNDING This work was supported by the Coalition Against Typhoid through the Bill and Melinda Gates Foundation [grant number OPP1017518], the Victorian Government, the National Health and Medical Research Council Australia, the Australian Research Council, and the Fiji Ministry of Health and Medical Services.
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Affiliation(s)
- Mark R. Davies
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | - Sebastian Duchene
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Aaron P. Jenkins
- Centre for Ecosystem Management, Edith Cowan University, Western Australia
- School of Public Health, University of Sydney, Sydney, NSW, Australia
| | - Adam Jenney
- New Vaccines Group, Murdoch Children's Research Institute, Victoria, Australia
- College of Medicine, Nursing and Health Sciences, Fiji National University, Suva, Fiji
| | - Varanisese Rosa
- Fiji Centre for Disease Control, Fiji Ministry of Health, Suva, Fiji
| | - Andrew J. Hayes
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | - Aneley Getahun Strobel
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | - Liam McIntyre
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | - Jake A. Lacey
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute of Infection and Immunity, Victoria, Australia
| | - Elizabeth J. Klemm
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Vanessa K. Wong
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Aalisha Sahukhan
- Fiji Centre for Disease Control, Fiji Ministry of Health, Suva, Fiji
| | - Helen Thomson
- New Vaccines Group, Murdoch Children's Research Institute, Victoria, Australia
| | - Andrew Page
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Quadram Institute Bioscience, Norwich Research Park, Norfolk, United Kingdom
| | - Dianna Hocking
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | - Nancy Wang
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | | | - Eric Rafai
- Fiji Ministry of Health and Medical Services, Suva, Fiji
| | - Gordon Dougan
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Benjamin P. Howden
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - John A. Crump
- Centre for International Health, Otago Medical School, University of Otago, Dunedin, New Zealand
| | - Kim Mulholland
- New Vaccines Group, Murdoch Children's Research Institute, Victoria, Australia
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Richard A. Strugnell
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
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Batool R, Qureshi S, Yousafzai MT, Kazi M, Ali M, Qamar FN. Risk Factors Associated with Extensively Drug-Resistant Typhoid in an Outbreak Setting of Lyari Town Karachi, Pakistan. Am J Trop Med Hyg 2022; 106:tpmd211323. [PMID: 35344928 PMCID: PMC9128702 DOI: 10.4269/ajtmh.21-1323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 01/18/2022] [Indexed: 11/23/2022] Open
Abstract
Typhoid fever is endemic in Pakistan, with high annual incidence rates. An outbreak of extensively drug-resistant typhoid fever that first started in the Hyderabad District, Sindh Province, in November 2016 immediately spread to the entire province. We conducted an age-matched case-control study to assess the risk factors of typhoid fever in an outbreak setting of Lyari Town, Karachi. We enrolled 82 patients with blood culture-confirmed Salmonella typhi between August 2019 to December 2019, and 82 age-matched hospital and 164 age-matched community control subjects. In a matched conditional logistic regression model, consumption of meals outside the home more than once per month was associated significantly with developing culture-confirmed typhoid fever compared with no consumption of food outside the home (odds ratio, 4.11). Hygiene of the environment in which food is prepared, practices of adult food handlers, access to clean water, and food legislation play significant roles in the spread of typhoid fever.
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Affiliation(s)
- Rabab Batool
- Department of Pediatrics and Child Health, Aga Khan University Hospital, Karachi City, Sindh, Pakistan
- Center for Child, Adolescent, and Maternal Health, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Sonia Qureshi
- Department of Pediatrics and Child Health, Aga Khan University Hospital, Karachi City, Sindh, Pakistan
| | - Mohammad Tahir Yousafzai
- Department of Pediatrics and Child Health, Aga Khan University Hospital, Karachi City, Sindh, Pakistan
| | - Momin Kazi
- Department of Pediatrics and Child Health, Aga Khan University Hospital, Karachi City, Sindh, Pakistan
| | - Miqdad Ali
- Department of Pediatrics and Child Health, Aga Khan University Hospital, Karachi City, Sindh, Pakistan
| | - Farah Naz Qamar
- Department of Pediatrics and Child Health, Aga Khan University Hospital, Karachi City, Sindh, Pakistan
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Forster DP, Leder K. Typhoid fever in travellers: estimating the risk of acquisition by country. J Travel Med 2021; 28:6383558. [PMID: 34619766 PMCID: PMC8715417 DOI: 10.1093/jtm/taab150] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/15/2021] [Accepted: 09/16/2021] [Indexed: 11/13/2022]
Abstract
BACKGROUND Typhoid fever is a notifiable disease within Australia. Although studies in endemic regions give an indication of acquisition risk, many countries lack reliable data, and little is known of the absolute or relative risk in Australian travellers. By combining notified case data with travel statistics provided by the Australian Bureau of Statistics, the aim of this study was to give an indication of risk for typhoid acquisition among Australian travellers. METHODS Australian typhoid notifications between 1st January 2010 and 30th June 2017 were grouped by country of acquisition and age category (<15 or ≥15 years). Australian travel data were used to inform time at risk and incidence rate of Australian typhoid notifications pertaining to country and region of acquisition. Salmonella Paratyphi infections, though notifiable, were excluded as the focus was vaccine preventable illness. Data from New South Wales and Victoria were used to examine the incidence in those acquiring infection in their country of birth (COB) against travellers who did not. RESULTS Nine hundred twenty-three cases of typhoid were notified over the period of review, 96% of which were acquired overseas. The greatest determinant of risk was travel destination, with countries in south Asia associated with highest crude incidence rate (252 per 100 000 person-years), particularly Bangladesh. Younger age and immigrants returning to their COB were generally associated with higher risk of acquisition. CONCLUSIONS The risk of typhoid fever in Australian travellers to endemic regions is considerable. Immigrants returning to their COB appear to be at higher risk and it is likely that this risk extends to their traveling dependents. These findings help clinicians and public health officials to plan and advise pre-travel vaccination strategies with at-risk individuals and groups. Additional sociodemographic data collection with Australian typhoid notifications would enhance the surveillance of differing international travel risk groups leaving Australia.
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Affiliation(s)
- Daniel P Forster
- Public Events, COVID-19 Response, Engagement & Delivery, Department of Health, VIC, Melbourne, Australia.,Victorian Infectious Diseases Service, Royal Melbourne Hospital at the Doherty Institute for Infection and Immunity, VIC, Melbourne, Australia
| | - Karin Leder
- Victorian Infectious Diseases Service, Royal Melbourne Hospital at the Doherty Institute for Infection and Immunity, VIC, Melbourne, Australia.,School of Public Health and Preventive Medicine, Monash University, VIC, Melbourne, Australia
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6
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Marchello CS, Carr SD, Crump JA. A Systematic Review on Antimicrobial Resistance among Salmonella Typhi Worldwide. Am J Trop Med Hyg 2020; 103:2518-2527. [PMID: 32996447 PMCID: PMC7695120 DOI: 10.4269/ajtmh.20-0258] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Understanding patterns and trends of antimicrobial resistance (AMR) in Salmonella Typhi can guide empiric treatment recommendations and contribute to country decisions about typhoid conjugate vaccine (TCV) introduction. We systematically reviewed PubMed and Web of Science for articles reporting the proportion of Salmonella Typhi isolates resistant to individual antimicrobials worldwide from any time period. Isolates resistant to chloramphenicol, ampicillin, and trimethoprim–sulfamethoxazole were classified as multidrug resistant (MDR), and isolates that were MDR plus resistant to a fluoroquinolone and a third-generation cephalosporin were extensively drug resistant (XDR). Among the 198 articles eligible for analysis, a total of 55,459 Salmonella Typhi isolates were tested for AMR (median 80; range 2–5,191 per study). Of isolates from 2015 through 2018 in Asia, 1,638 (32.6%) of 5,032 were MDR, 167 (5.7%) of 2,914 were resistant to third-generation cephalosporins, and 148 (8.3%) of 1,777 were resistant to azithromycin. Two studies from Pakistan reported 14 (2.6%) of 546 isolates were XDR. In Africa, the median proportion of Salmonella Typhi isolates that were MDR increased each consecutive decade from 1990 to 1999 through 2010 to 2018. Salmonella Typhi has developed resistance to an increasing number of antimicrobial classes in Asia, where XDR Salmonella Typhi is now a major threat, whereas MDR has expanded in Africa. We suggest continued and increased surveillance is warranted to inform empiric treatment decisions and that AMR data be incorporated into country decisions on TCV introduction.
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Affiliation(s)
| | - Samuel D Carr
- Centre for International Health, University of Otago, Dunedin, New Zealand
| | - John A Crump
- Centre for International Health, University of Otago, Dunedin, New Zealand
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7
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Getahun Strobel A, Parry CM, Crump JA, Rosa V, Jenney A, Naidu R, Mulholland K, Strugnell RA. A retrospective study of patients with blood culture-confirmed typhoid fever in Fiji during 2014-2015: epidemiology, clinical features, treatment and outcome. Trans R Soc Trop Med Hyg 2020; 113:764-770. [PMID: 31638153 PMCID: PMC6907003 DOI: 10.1093/trstmh/trz075] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 06/25/2019] [Accepted: 07/15/2019] [Indexed: 01/22/2023] Open
Abstract
Background Typhoid fever is endemic in Fiji. We sought to describe the epidemiology, clinical features and case fatality risk of blood culture-confirmed typhoid fever from January 2014 through December 2015. Methods Blood culture-positive patients were identified from a typhoid surveillance line list. A standardised case investigation form was used to record data from patients’ medical records. Results Of 542 patients, 518 (95.6%) were indigenous Fijians (iTaukei) and 285 (52.6%) were male. The median (IQR) age was 25 (16–38) y. Mean (SD) time from the onset of illness to admission was 11.1 (6.9) d. Of 365 patients with clinical information, 346 (96.9%) had fever, 239 (66.9%) diarrhoea, 113 (33.5%) vomiting, and 72 (30.2%) abdominal pain. There were 40 (11.0%) patients with complications, including 17 (4.7%) with shock, and 11 (3.0%) with hepatitis. Nine patients died for a case fatality risk of 1.7%. Of the 544 Salmonella Typhi isolates tested, none were resistant to first line antimicrobials; 3(0.8%) were resistant to ciprofloxacin and 5(1.4%) to nalidixic acid. Conclusions In Fiji, most blood culture-confirmed typhoid fever cases were in young adults. Common clinical manifestations were fever and gastrointestinal symptoms. Further studies are required to elucidate the factors associated with complications and death.
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Affiliation(s)
- Aneley Getahun Strobel
- School of Public Health and Primary Care, College of Medicine, Nursing and Health Sciences, Fiji National University, Private mail bag, Suva, Fiji.,Doherty Institute for Infection and Immunity, University of Melbourne, 792 Elizabeth Street, Melbourne VIC 3000, Australia
| | - Christopher M Parry
- Institute of Infection and Global Health, University of Liverpool, The Ronald Ross Building, 8 West Derby Street, Liverpool, L69 7BE UK.,School of Tropical Medicine and Global Health, University of Nagasaki, 12, Nagasaki, 852-8102, Japan
| | - John A Crump
- Centre for International Health, University of Otago, 55 Hanover Street, Dunedin 9016, New Zealand
| | - Varanisese Rosa
- Fiji Centre for Communicable Diseases Control, Fiji Ministry of Health and Medical Services, Tamavua, Suva, Fiji
| | - Adam Jenney
- School of Medical Science, College of Medicine, Nursing and Health Sciences, Fiji National University, Private mail bag, Suva, Fiji
| | - Ravi Naidu
- Colonial War Memorial Hospital, Fiji Ministry of Health and Medical Services, Waimanu Road, Suva, Fiji
| | - Kim Mulholland
- Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Melbourne VIC 3052, Australia.,London School of Hygiene and Tropical Medicine, Keppel St, Bloomsbury, London WC1E 7HT UK
| | - Richard A Strugnell
- Doherty Institute for Infection and Immunity, University of Melbourne, 792 Elizabeth Street, Melbourne VIC 3000, Australia
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8
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Sikorski MJ, Desai SN, Tupua S, Thomsen RE, Han J, Rambocus S, Nimarota-Brown S, Punimata L, Tusitala S, Sialeipata M, Hoffman SA, Tracy JK, Higginson EE, Tennant SM, Gauld JS, Klein DJ, Ballard SA, Robins-Browne RM, Dougan G, Nilles EJ, Howden BP, Crump JA, Naseri TK, Levine MM. Tenacious Endemic Typhoid Fever in Samoa. Clin Infect Dis 2020; 71:S120-S126. [PMID: 32725232 PMCID: PMC7388710 DOI: 10.1093/cid/ciaa314] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background Typhoid fever has been endemic on the island nation of Samoa (2016 population, 195 979) since the 1960s and has persisted through 2019, despite economic development and improvements in water supply and sanitation. Methods Salmonella enterica serovar Typhi isolates from the 2 hospitals with blood culture capability and matched patient demographic and clinical data from January 2008 through December 2019 were analyzed. Denominators to calculate incidence by island, region, and district came from 2011 and 2016 censuses and from 2017–2019 projections from Samoa’s Bureau of Statistics. Data were analyzed to describe typhoid case burden and incidence from 2008 to 2019 by time, place, and person. Results In sum, 53–193 blood culture-confirmed typhoid cases occurred annually from 2008 to 2019, without apparent seasonality. Typhoid incidence was low among children age < 48 months (17.6–27.8/105), rose progressively in ages 5–9 years (54.0/105), 10–19 years (60.7–63.4/105), and 20–34 years (61.0–79.3/105), and then tapered off; 93.6% of cases occurred among Samoans < 50 years of age. Most typhoid cases and the highest incidence occurred in Northwest Upolu, but Apia Urban Area (served by treated water supplies) also exhibited moderate incidence. The proportion of cases from short-cycle versus long-cycle transmission is unknown. Samoan S. Typhi are pansusceptible to traditional first-line antibiotics. Nevertheless, enhanced surveillance in 2019 detected 4 (2.9%) deaths among 140 cases. Conclusions Typhoid has been endemic in Samoa in the period 2008–2019. Interventions, including mass vaccination with a Vi-conjugate vaccine coadministered with measles vaccine are planned.
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Affiliation(s)
- Michael J Sikorski
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Ministry of Health, Government of Samoa, Apia, Samoa
| | - Sachin N Desai
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Ministry of Health, Government of Samoa, Apia, Samoa
| | - Siaosi Tupua
- Ministry of Health, Government of Samoa, Apia, Samoa
| | | | - Jane Han
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Ministry of Health, Government of Samoa, Apia, Samoa
| | - Savitra Rambocus
- Ministry of Health, Government of Samoa, Apia, Samoa.,Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | | | | | | | | | - Seth A Hoffman
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - J Kathleen Tracy
- Clinical Translational Research and Informatics Center, Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Ellen E Higginson
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Sharon M Tennant
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | | | - Daniel J Klein
- Institute for Disease Modeling, Bellevue, Washington, USA
| | - Susan A Ballard
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Roy M Robins-Browne
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Gordon Dougan
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Eric J Nilles
- World Health Organization, Division of Pacific Technical Support, Suva, Fiji
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - John A Crump
- Centre for International Health, University of Otago, Dunedin, New Zealand
| | - Take K Naseri
- Ministry of Health, Government of Samoa, Apia, Samoa
| | - Myron M Levine
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
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Potential of Black Soldier Fly Production for Pacific Small Island Developing States. Animals (Basel) 2020; 10:ani10061038. [PMID: 32560146 PMCID: PMC7341329 DOI: 10.3390/ani10061038] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 06/02/2020] [Accepted: 06/12/2020] [Indexed: 12/24/2022] Open
Abstract
Organic waste such as food waste and livestock manure is a serious concern in the Pacific Islands, where landfills are overflowing and illegal dumping of waste threatens the fragile ecosystems. Organic waste also attracts filth flies, some of which are vectors for pathogens that cause human disease. The black soldier fly, Hermetia illucens, has tremendous potential for the Pacific Islands. Capable of digesting almost any organic matter and converting it into insect biomass, black soldier flies are already being used around the world to process organic waste into larvae. The system can be adapted to large-scale municipal composting as well as small sizes for individual livestock farms or even urban households. The larvae can be fed live to fish or poultry, processed into feed comparable to fishmeal or soy meal, or even used to generate biofuel. Thus, the fly not only eliminates waste, but also can improve the sustainability of livestock production. The Pacific Small Island Developing States stand to benefit immensely from black soldier fly bioconversion facilities, used primarily as a means to compost organic waste; however, several knowledge gaps must first be addressed. We reviewed the state of black soldier flies in the Pacific and identified where their use shows the most promise. Research priorities for the field include fly surveys and bioconversion assays using Pacific crop waste.
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10
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Pitzer VE, Meiring J, Martineau FP, Watson CH, Kang G, Basnyat B, Baker S. The Invisible Burden: Diagnosing and Combatting Typhoid Fever in Asia and Africa. Clin Infect Dis 2019; 69:S395-S401. [PMID: 31612938 PMCID: PMC6792124 DOI: 10.1093/cid/ciz611] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Measuring the burden of typhoid fever and developing effective strategies to reduce it require a surveillance infrastructure that is currently lacking in many endemic countries. Recent efforts and partnerships between local and international researchers have helped to provide new data on the incidence and control of typhoid in parts of Asia and Africa. Here, we highlight examples from India, Nepal, Vietnam, Fiji, Sierra Leone, and Malawi that summarize past and present experiences with the diagnosis, treatment, and prevention of typhoid fever in different locations with endemic disease. While there is no validated road map for the elimination of typhoid, the lessons learned in studying the epidemiology and control of typhoid in these settings can provide insights to guide future disease control efforts.
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Affiliation(s)
- Virginia E Pitzer
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, Connecticut
| | - James Meiring
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the National Institute for Health Research Oxford Biomedical Research Centre, United Kingdom
| | | | - Conall H Watson
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, United Kingdom
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, United Kingdom
| | - Gagandeep Kang
- Translational Health Sciences Technology Institute, Faridabad, Haryana, India
| | - Buddha Basnyat
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, United Kingdom
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - Stephen Baker
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Department of Medicine, University of Cambridge, United Kingdom
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11
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Getahun S A, Limaono J, Ligaitukana R, Cabenatabua O, Soqo V, Diege R, Mua M. Ovarian abscess caused by Salmonella enterica serovar Typhi: a case report. J Med Case Rep 2019; 13:303. [PMID: 31551082 PMCID: PMC6760102 DOI: 10.1186/s13256-019-2229-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 08/13/2019] [Indexed: 11/10/2022] Open
Abstract
Background Typhoid fever is a human-specific disease caused by a bacterium, Salmonella enterica subspecies enterica serovar Typhi. It is transmitted through ingestion of contaminated food or water. It is mostly diagnosed by blood culture. Salmonella Typhi usually manifests as a febrile illness with bacteremia after initial entry through the gastrointestinal route, but it can occasionally cause significant disease in extraintestinal sites. We report a case of a girl in Fiji with a right ovarian abscess infected by Salmonella Typhi. Case presentation A 14-year-old iTaukei (indigenous Fijian) girl presented to our hospital with abdominal pain of 1 month’s duration. Two days prior to her admission, she developed high-grade fever and nausea and had one episode of vomiting. On presentation, she appeared unwell; she was tachycardic (116 beats per minute) and febrile (38.8 °C). Her abdominal examination revealed generalized tenderness. Other examination findings were normal. The provisional diagnosis of abdominal sepsis led to an emergency laparotomy during which an enlarged right ovary was found to be spontaneously discharging pus. The ovary was incised and drained, and the patient was commenced on intravenous ceftriaxone 1 g twice daily, cloxacillin 1 g four times daily, and metronidazole 500 mg three times daily. She recovered promptly and was discharged to home on the sixth postoperative day. The purulent material from the ovary grew Salmonella Typhi. Conclusion Extraintestinal infections caused by Salmonella Typhi are rare but can cause severe and life-threatening disease. Our patient had a prolonged history of abdominal pain and was found to have a ruptured right ovarian abscess due to Salmonella Typhi. Ovarian abscesses in girls who are not sexually active are not associated with pelvic inflammatory disease and suggest local or hematogenous spread. This case report may increase health workers awareness to include common and endemic infections in the differential diagnosis of unusual clinical presentations to help the initiation of appropriate investigation and management as quickly as possible.
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Affiliation(s)
- Aneley Getahun S
- School of Public Health, College of Medicine Nursing and Health Science, Fiji National University, Suva, Fiji. .,The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia.
| | - Josese Limaono
- Labasa Hospital, Ministry of Health and Medical Services, Labasa, Fiji
| | - Raween Ligaitukana
- Northern Health Services, Ministry of Health and Medical Services, Labasa, Fiji
| | - Orisi Cabenatabua
- Labasa Hospital, Ministry of Health and Medical Services, Labasa, Fiji
| | - Vika Soqo
- Labasa Hospital, Ministry of Health and Medical Services, Labasa, Fiji
| | - Raape Diege
- Labasa Hospital, Ministry of Health and Medical Services, Labasa, Fiji
| | - Mikaele Mua
- Labasa Hospital, Ministry of Health and Medical Services, Labasa, Fiji
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12
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Environmental Foundations of Typhoid Fever in the Fijian Residential Setting. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16132407. [PMID: 31284613 PMCID: PMC6651141 DOI: 10.3390/ijerph16132407] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/28/2019] [Accepted: 06/29/2019] [Indexed: 11/16/2022]
Abstract
Proximal characteristics and conditions in the residential setting deserve greater attention for their potential to influence typhoid transmission. Using a case-control design in Central Division, Republic of Fiji, we examined bacterial (coliform and Escherichia coli) contamination and chemical composition of water and soil as potential vehicles of exposure to Salmonella Typhi, combining observational analysis of residential living conditions, geospatial analysis of household locations, and factor analysis to explore multivariate associations with the risk of developing typhoid fever. Factors positively associated with typhoid infection related to drainage [phosphate (OR 4.235, p = 0.042) and E. coli concentrations (OR 2.248, p = 0.029) in toilet drainage soil, housing [external condition (OR 3.712, p < 0.001)], drinking water contamination (OR 2.732, p = 0.003) and sanitary condition (OR 1.973, p = 0.031). These five factors explained 42.5% of the cumulative variance and were significant in predicting typhoid infection. Our results support the hypothesis that a combination of spatial and biophysical attributes of the residential setting influence the probability of typhoid transmission; in this study, factors associated with poor drainage, flooding, and sanitary condition increase local exposure to contaminated water and soil, and thereby infection. These findings extend testing of causal assumptions beyond the immediate domestic domain, enhance the scope of traditional case control epidemiology and allow greater specificity of interventions at the scale of the residential setting.
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13
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Antibiotic Resistance in Pacific Island Countries and Territories: A Systematic Scoping Review. Antibiotics (Basel) 2019; 8:antibiotics8010029. [PMID: 30893880 PMCID: PMC6466536 DOI: 10.3390/antibiotics8010029] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 03/13/2019] [Accepted: 03/14/2019] [Indexed: 11/16/2022] Open
Abstract
Several studies have investigated antimicrobial resistance in low- and middle-income countries, but to date little attention has been paid to the Pacific Islands Countries and Territories (PICTs). This study aims to review the literature on antibiotic resistance (ABR) in healthcare settings in PICTs to inform further research and future policy development for the region. Following the PRISMA-ScR checklist health databases and grey literature sources were searched. Three reviewers independently screened the literature for inclusion, data was extracted using a charting tool and the results were described and synthesised. Sixty-five studies about ABR in PICTs were identified and these are primarily about New Caledonia, Fiji and Papua New Guinea. Ten PICTs contributed the remaining 21 studies and nine PICTs were not represented. The predominant gram-positive pathogen reported was community-acquired methicillin resistant S. aureus and the rates of resistance ranged widely (>50% to <20%). Resistance reported in gram-negative pathogens was mainly associated with healthcare-associated infections (HCAIs). Extended spectrum beta-lactamase (ESBL) producing K. pneumoniae isolates were reported in New Caledonia (3.4%) and Fiji (22%) and carbapenem resistant A. baumannii (CR-ab) isolates in the French Territories (24.8%). ABR is a problem in the PICTs, but the epidemiology requires further characterisation. Action on strengthening surveillance in PICTs needs to be prioritised so strategies to contain ABR can be fully realised.
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14
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de Alwis R, Watson C, Nikolay B, Lowry JH, Thieu NTV, Van TT, Ngoc DTT, Rawalai K, Taufa M, Coriakula J, Lau CL, Nilles EJ, Edmunds WJ, Kama M, Baker S, Cano J. Role of Environmental Factors in Shaping Spatial Distribution of Salmonella enterica Serovar Typhi, Fiji. Emerg Infect Dis 2019; 24:284-293. [PMID: 29350150 PMCID: PMC5782885 DOI: 10.3201/eid2402.170704] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Fiji recently experienced a sharp increase in reported typhoid fever cases. To investigate geographic distribution and environmental risk factors associated with Salmonella enterica serovar Typhi infection, we conducted a cross-sectional cluster survey with associated serologic testing for Vi capsular antigen–specific antibodies (a marker for exposure to Salmonella Typhi in Fiji in 2013. Hotspots with high seroprevalence of Vi-specific antibodies were identified in northeastern mainland Fiji. Risk for Vi seropositivity increased with increased annual rainfall (odds ratio [OR] 1.26/quintile increase, 95% CI 1.12–1.42), and decreased with increased distance from major rivers and creeks (OR 0.89/km increase, 95% CI 0.80–0.99) and distance to modeled flood-risk areas (OR 0.80/quintile increase, 95% CI 0.69–0.92) after being adjusted for age, typhoid fever vaccination, and home toilet type. Risk for exposure to Salmonella Typhi and its spatial distribution in Fiji are driven by environmental factors. Our findings can directly affect typhoid fever control efforts in Fiji.
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15
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Prasad N, Jenkins AP, Naucukidi L, Rosa V, Sahu-Khan A, Kama M, Jenkins KM, Jenney AWJ, Jack SJ, Saha D, Horwitz P, Jupiter SD, Strugnell RA, Mulholland EK, Crump JA. Epidemiology and risk factors for typhoid fever in Central Division, Fiji, 2014-2017: A case-control study. PLoS Negl Trop Dis 2018; 12:e0006571. [PMID: 29883448 PMCID: PMC6010302 DOI: 10.1371/journal.pntd.0006571] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 06/20/2018] [Accepted: 05/29/2018] [Indexed: 11/26/2022] Open
Abstract
Background Typhoid fever is endemic in Fiji, with high reported annual incidence. We sought to identify the sources and modes of transmission of typhoid fever in Fiji with the aim to inform disease control. Methodology/Principal findings We identified and surveyed patients with blood culture-confirmed typhoid fever from January 2014 through January 2017. For each typhoid fever case we matched two controls by age interval, gender, ethnicity, and residential area. Univariable and multivariable analysis were used to evaluate associations between exposures and risk for typhoid fever. We enrolled 175 patients with typhoid fever and 349 controls. Of the cases, the median (range) age was 29 (2–67) years, 86 (49%) were male, and 84 (48%) lived in a rural area. On multivariable analysis, interrupted water availability (odds ratio [OR] = 2.17; 95% confidence interval [CI] 1.18–4.00), drinking surface water in the last 2 weeks (OR = 3.61; 95% CI 1.44–9.06), eating unwashed produce (OR = 2.69; 95% CI 1.48–4.91), and having an unimproved or damaged sanitation facility (OR = 4.30; 95% CI 1.14–16.21) were significantly associated with typhoid fever. Frequent handwashing after defecating (OR = 0.57; 95% CI 0.35–0.93) and using soap for handwashing (OR = 0.61; 95% CI 0.37–0.95) were independently associated with a lower odds of typhoid fever. Conclusions Poor sanitation facilities appear to be a major source of Salmonella Typhi in Fiji, with transmission by drinking contaminated surface water and consuming unwashed produce. Improved sanitation facilities and protection of surface water sources and produce from contamination by human feces are likely to contribute to typhoid control in Fiji. Modeling suggests that Oceania has surpassed Asia and sub-Saharan Africa as the region with the highest typhoid fever incidence. While Pacific Islands are often neglected due to small population sizes, there is an urgent need to understand the epidemiology of typhoid fever in the region. Fiji, an upper-middle income country in Oceania, has reported an increase in typhoid fever notifications over the last decade. However, the epidemiology of typhoid fever in Fiji is incompletely understood due to gaps in surveillance and lack of epidemiological research on local risk factors. We conducted a case-control study in the Central Division of Fiji to help inform prevention and control strategies. We found unimproved sanitation facilities to be major source of typhoid fever in Fiji, with transmission by drinking contaminated surface water and consumption of unwashed produce. We also found an association between poor water availability and poor hygiene with typhoid fever. Improvements in sanitation facilities to protect surface water and produce from contamination are likely to contribute to improved typhoid control in Fiji. Because of the distinct socio-demographic and environmental conditions found in Oceania, our findings may reflect sources and modes of transmission predominant elsewhere in the region.
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Affiliation(s)
- Namrata Prasad
- Centre for International Health, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
- * E-mail: (NP); (JAC)
| | - Aaron P. Jenkins
- School of Science, Edith Cowan University, Joondalup, Australia
- School of Public Health, University of Sydney, Sydney, Australia
| | - Lanieta Naucukidi
- Fiji Centre for Communicable Disease Control, Fiji Ministry of Health, Suva, Fiji
| | - Varanisese Rosa
- Fiji Centre for Communicable Disease Control, Fiji Ministry of Health, Suva, Fiji
| | - Aalisha Sahu-Khan
- Fiji Centre for Communicable Disease Control, Fiji Ministry of Health, Suva, Fiji
| | - Mike Kama
- Fiji Centre for Communicable Disease Control, Fiji Ministry of Health, Suva, Fiji
| | - Kylie M. Jenkins
- Fiji Health Sector Support Program, Suva, Fiji
- Telethon Kids Institute, Perth, Western Australia
| | - Adam W. J. Jenney
- Murdoch Childrens Research Institute, Melbourne, Victoria, Australia
- College of Medicine, Nursing and Health Sciences, Fiji National University, Suva, Fiji
| | - Susan J. Jack
- Centre for International Health, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Debasish Saha
- Centre for International Health, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Pierre Horwitz
- School of Science, Edith Cowan University, Joondalup, Australia
| | - Stacy D. Jupiter
- Wildlife Conservation Society, Melanesia Regional Program, Suva, Fiji
| | - Richard A. Strugnell
- Department of Microbiology and Immunology, University of Melbourne, Victoria, Australia
| | - E. Kim Mulholland
- Murdoch Childrens Research Institute, Melbourne, Victoria, Australia
| | - John A. Crump
- Centre for International Health, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
- * E-mail: (NP); (JAC)
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16
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Meiring JE, Gibani M. The Typhoid Vaccine Acceleration Consortium (TyVAC): Vaccine effectiveness study designs: Accelerating the introduction of typhoid conjugate vaccines and reducing the global burden of enteric fever. Report from a meeting held on 26-27 October 2016, Oxford, UK. Vaccine 2017; 35:5081-5088. [PMID: 28802757 DOI: 10.1016/j.vaccine.2017.08.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 07/31/2017] [Accepted: 08/01/2017] [Indexed: 11/26/2022]
Abstract
Typhoid fever is estimated to cause between 11.9-26.9 million infections globally each year with 129,000-216,510 deaths. Access to improved water sources have reduced disease incidence in parts of the world but the use of efficacious vaccines is seen as an important public health tool for countries with a high disease burden. A new generation of Vi typhoid conjugate vaccines (TCVs), licensed for use in young children and expected to provide longer lasting protection than previous vaccines, are now available. The WHO Strategic Advisory Group of Experts on Immunization (SAGE) has convened a working group to review the evidence on TCVs and produce an updated WHO position paper for all typhoid vaccines in 2018 that will inform Gavi, the Vaccine Alliance's future vaccine investment strategies for TCVs. The Typhoid Vaccine Acceleration Consortium (TyVAC) has been formed through a $36.9 million funding program from the Bill & Melinda Gates Foundation to accelerate the introduction of TCVs into Gavi-eligible countries. In October 2016, a meeting was held to initiate planning of TCV effectiveness studies that will provide the data required by policy makers and stakeholders to support decisions on TCV use in countries with a high typhoid burden. Discussion topics included (1) the latest evidence and data gaps in typhoid epidemiology; (2) WHO and Gavi methods and data requirements; (3) data on TCV efficacy; (4) cost effectiveness analysis for TCVs from mathematical models; (5) TCV delivery and effectiveness study design. Specifically, participants were asked to comment on study design in 3 sites for which population-based typhoid surveillance is underway. The conclusion of the meeting was that country-level decision making would best be informed by the respective selected sites in Africa and Asia vaccinating children aged from 9-months to 15-years-old, employing either an individual or cluster randomized design with design influenced by population characteristics, transmission dynamics, and statistical considerations.
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Affiliation(s)
- James E Meiring
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom.
| | - Malick Gibani
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
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A cross-sectional seroepidemiological survey of typhoid fever in Fiji. PLoS Negl Trop Dis 2017; 11:e0005786. [PMID: 28727726 PMCID: PMC5549756 DOI: 10.1371/journal.pntd.0005786] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 08/08/2017] [Accepted: 07/06/2017] [Indexed: 12/26/2022] Open
Abstract
Fiji, an upper-middle income state in the Pacific Ocean, has experienced an increase in confirmed case notifications of enteric fever caused by Salmonella enterica serovar Typhi (S. Typhi). To characterize the epidemiology of typhoid exposure, we conducted a cross-sectional sero-epidemiological survey measuring IgG against the Vi antigen of S. Typhi to estimate the effect of age, ethnicity, and other variables on seroprevalence. Epidemiologically relevant cut-off titres were established using a mixed model analysis of data from recovering culture-confirmed typhoid cases. We enrolled and assayed plasma of 1787 participants for anti-Vi IgG; 1,531 of these were resident in mainland areas that had not been previously vaccinated against S. Typhi (seropositivity 32.3% (95%CI 28.2 to 36.3%)), 256 were resident on Taveuni island, which had been previously vaccinated (seropositivity 71.5% (95%CI 62.1 to 80.9%)). The seroprevalence on the Fijian mainland is one to two orders of magnitude higher than expected from confirmed case surveillance incidence, suggesting substantial subclinical or otherwise unreported typhoid. We found no significant differences in seropositivity prevalences by ethnicity, which is in contrast to disease surveillance data in which the indigenous iTaukei Fijian population are disproportionately affected. Using multivariable logistic regression, seropositivity was associated with increased age (odds ratio 1.3 (95% CI 1.2 to 1.4) per 10 years), the presence of a pit latrine (OR 1.6, 95%CI 1.1 to 2.3) as opposed to a septic tank or piped sewer, and residence in settlements rather than residential housing or villages (OR 1.6, 95% CI 1.0 to 2.7). Increasing seropositivity with age is suggestive of low-level endemic transmission in Fiji. Improved sanitation where pit latrines are used and addressing potential transmission routes in settlements may reduce exposure to S. Typhi. Widespread unreported infection suggests there may be a role for typhoid vaccination in Fiji, in addition to public health management of cases and outbreaks. Fiji has experienced a decade-long increase in typhoid fever cases, a potentially life-threatening systemic bacterial disease caused by Salmonella Typhi. We undertook a representative blood-serum community survey to measure antibodies (IgG) against the Vi antigen of Salmonella Typhi using a rigorous survey design. We found one in three residents of mainland, unvaccinated Fiji had detectable antibody against Vi. This was higher than would be expected from confirmed case notifications received by the national surveillance system. Additionally, similar antibody responses were detected in Fijians of all ethnicities, which contrasts to surveillance cases in which indigenous iTaukei Fijians were disproportionately affected. Serology on a Fijian island where a significant proportion of the population has been vaccinated found that three-quarters of residents were seropositive three years after the Vi-polysaccharide typhoid vaccination campaign. Importantly, in mainland participants, seroprevalence increased with age, suggesting long-standing, low-level, endemic transmission. Pit latrines were associated with seropositivity when compared with septic tanks, and settlements compared with residential housing. Very high antibody titres in a small percentage of participants may suggest carriage of Salmonella Typhi. The seroprevalence findings suggest eliminating typhoid from Fiji by focussing on cases and outbreaks alone will be challenging. Our results support typhoid vaccination and further development of water, sanitation and hygiene infrastructure in Fiji.
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18
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Dyson ZA, Thanh DP, Bodhidatta L, Mason CJ, Srijan A, Rabaa MA, Vinh PV, Thanh TH, Thwaites GE, Baker S, Holt KE. Whole Genome Sequence Analysis of Salmonella Typhi Isolated in Thailand before and after the Introduction of a National Immunization Program. PLoS Negl Trop Dis 2017; 11:e0005274. [PMID: 28060810 PMCID: PMC5245908 DOI: 10.1371/journal.pntd.0005274] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 01/19/2017] [Accepted: 12/20/2016] [Indexed: 12/31/2022] Open
Abstract
Vaccines against Salmonella Typhi, the causative agent of typhoid fever, are commonly used by travellers, however, there are few examples of national immunization programs in endemic areas. There is therefore a paucity of data on the impact of typhoid immunization programs on localised populations of S. Typhi. Here we have used whole genome sequencing (WGS) to characterise 44 historical bacterial isolates collected before and after a national typhoid immunization program that was implemented in Thailand in 1977 in response to a large outbreak; the program was highly effective in reducing typhoid case numbers. Thai isolates were highly diverse, including 10 distinct phylogenetic lineages or genotypes. Novel prophage and plasmids were also detected, including examples that were previously only reported in Shigella sonnei and Escherichia coli. The majority of S. Typhi genotypes observed prior to the immunization program were not observed following it. Post-vaccine era isolates were more closely related to S. Typhi isolated from neighbouring countries than to earlier Thai isolates, providing no evidence for the local persistence of endemic S. Typhi following the national immunization program. Rather, later cases of typhoid appeared to be caused by the occasional importation of common genotypes from neighbouring Vietnam, Laos, and Cambodia. These data show the value of WGS in understanding the impacts of vaccination on pathogen populations and provide support for the proposal that large-scale typhoid immunization programs in endemic areas could result in lasting local disease elimination, although larger prospective studies are needed to test this directly. Typhoid fever is a systemic infection caused by the bacterium Salmonella Typhi. Typhoid fever is associated with inadequate hygiene in low-income settings and a lack of sanitation infrastructure. A sustained outbreak of typhoid fever occurred in Thailand in the 1970s, which peaked in 1975–1976. In response to this typhoid fever outbreak the government of Thailand initiated an immunization program, which resulted in a dramatic reduction in the number of typhoid cases in Thailand. To better understand the population of S. Typhi circulating in Thailand at this time, as well as the impact of the immunization program on the pathogen population, we sequenced the genomes of 44 S. Typhi obtained from hospitals in Thailand before and after the immunization program. The genome sequences showed that isolates of S. Typhi bacteria isolated from post-immunization era typhoid cases were likely imported from neighbouring countries, rather than strains that have persisted in Thailand throughout the immunization period. Our work provides the first historical insights into S. Typhi in Thailand during the 1970s, and provides a model for the impact of immunization on S. Typhi populations.
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Affiliation(s)
- Zoe A. Dyson
- Centre for Systems Genomics, University of Melbourne, Parkville, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
- * E-mail: (KEH); (ZAD)
| | - Duy Pham Thanh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Ladaporn Bodhidatta
- Department of Enteric Diseases, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Carl Jeffries Mason
- Department of Enteric Diseases, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Apichai Srijan
- Department of Enteric Diseases, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Maia A. Rabaa
- 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, Oxford University, Oxford, United Kingdom
| | - Phat Voong Vinh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Tuyen Ha Thanh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Guy E. Thwaites
- 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, Oxford University, Oxford, United Kingdom
| | - Stephen Baker
- 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, Oxford University, Oxford, United Kingdom
- The London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Kathryn E. Holt
- Centre for Systems Genomics, University of Melbourne, Parkville, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
- * E-mail: (KEH); (ZAD)
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19
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Watson CH, Coriakula J, Ngoc DTT, Flasche S, Kucharski AJ, Lau CL, Thieu NTV, le Polain de Waroux O, Rawalai K, Van TT, Taufa M, Baker S, Nilles EJ, Kama M, Edmunds WJ. Social mixing in Fiji: Who-eats-with-whom contact patterns and the implications of age and ethnic heterogeneity for disease dynamics in the Pacific Islands. PLoS One 2017; 12:e0186911. [PMID: 29211731 PMCID: PMC5718486 DOI: 10.1371/journal.pone.0186911] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 10/10/2017] [Indexed: 11/17/2022] Open
Abstract
Empirical data on contact patterns can inform dynamic models of infectious disease transmission. Such information has not been widely reported from Pacific islands, nor strongly multi-ethnic settings, and few attempts have been made to quantify contact patterns relevant for the spread of gastrointestinal infections. As part of enteric fever investigations, we conducted a cross-sectional survey of the general public in Fiji, finding that within the 9,650 mealtime contacts reported by 1,814 participants, there was strong like-with-like mixing by age and ethnicity, with higher contact rates amongst iTaukei than non-iTaukei Fijians. Extra-domiciliary lunchtime contacts follow these mixing patterns, indicating the overall data do not simply reflect household structures. Inter-ethnic mixing was most common amongst school-age children. Serological responses indicative of recent Salmonella Typhi infection were found to be associated, after adjusting for age, with increased contact rates between meal-sharing iTaukei, with no association observed for other contact groups. Animal ownership and travel within the geographical division were common. These are novel data that identify ethnicity as an important social mixing variable, and use retrospective mealtime contacts as a socially acceptable metric of relevance to enteric, contact and respiratory diseases that can be collected in a single visit to participants. Application of these data to other island settings will enable communicable disease models to incorporate locally relevant mixing patterns in parameterisation.
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Affiliation(s)
- Conall H Watson
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | | | - Dung Tran Thi Ngoc
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit-Vietnam, Ho Chi Minh City, Vietnam
| | - Stefan Flasche
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Adam J Kucharski
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Colleen L Lau
- Department of Global Health, Research School of Population Health, The Australian National University, Canberra, Australia
| | - Nga Tran Vu Thieu
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit-Vietnam, Ho Chi Minh City, Vietnam
| | - Olivier le Polain de Waroux
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | | | - Tan Trinh Van
- School of Medicine, Fiji National University, Suva, Fiji
| | - Mere Taufa
- Fiji Centre for Communicable Disease Control, Ministry of Health and Medical Services, Suva, Fiji
| | - Stephen Baker
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit-Vietnam, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Oxford University, Oxford, United Kingdom.,Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Eric J Nilles
- Division of Pacific Technical Support, World Health Organization-Western Pacific Region, Suva, Fiji
| | - Mike Kama
- Fiji Centre for Communicable Disease Control, Ministry of Health and Medical Services, Suva, Fiji
| | - W John Edmunds
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
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20
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Jenkins AP, Jupiter S, Mueller U, Jenney A, Vosaki G, Rosa V, Naucukidi A, Mulholland K, Strugnell R, Kama M, Horwitz P. Health at the Sub-catchment Scale: Typhoid and Its Environmental Determinants in Central Division, Fiji. ECOHEALTH 2016; 13:633-651. [PMID: 27557784 DOI: 10.1007/s10393-016-1152-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 07/11/2016] [Accepted: 07/22/2016] [Indexed: 06/06/2023]
Abstract
The impact of environmental change on transmission patterns of waterborne enteric diseases is a major public health concern. This study concerns the burden and spatial nature of enteric fever, attributable to Salmonella Typhi infection in the Central Division, Republic of Fiji at a sub-catchment scale over 30-months (2013-2015). Quantitative spatial analysis suggested relationships between environmental conditions of sub-catchments and incidence and recurrence of typhoid fever. Average incidence per inhabited sub-catchment for the Central Division was high at 205.9/100,000, with cases recurring in each calendar year in 26% of sub-catchments. Although the numbers of cases were highest within dense, urban coastal sub-catchments, the incidence was highest in low-density mountainous rural areas. Significant environmental determinants at this scale suggest increased risk of exposure where sediment yields increase following runoff. The study suggests that populations living on large systems that broaden into meandering mid-reaches and floodplains with alluvial deposition are at a greater risk compared to small populations living near small, erosional, high-energy headwaters and small streams unconnected to large hydrological networks. This study suggests that anthropogenic alteration of land cover and hydrology (particularly via fragmentation of riparian forest and connectivity between road and river networks) facilitates increased transmission of typhoid fever and that environmental transmission of typhoid fever is important in Fiji.
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Affiliation(s)
- Aaron Peter Jenkins
- Edith Cowan University, 270 Joondalup Drive, Joondalup, WA, 6027, Australia.
| | | | - Ute Mueller
- Edith Cowan University, 270 Joondalup Drive, Joondalup, WA, 6027, Australia
| | - Adam Jenney
- Fiji National University, Suva, Fiji
- Murdoch Childrens Research Institute, Parkville, Australia
| | | | | | | | - Kim Mulholland
- Murdoch Childrens Research Institute, Parkville, Australia
- London School of Hygiene and Tropical Medicine, London, England
| | | | - Mike Kama
- Fiji Ministry of Health and Medical Services, Suva, Fiji
| | - Pierre Horwitz
- Edith Cowan University, 270 Joondalup Drive, Joondalup, WA, 6027, Australia
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21
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Abstract
INTRODUCTION Typhoid fever (TF), caused by Salmonella enterica serovar Typhi, is the most common cause of enteric fever, responsible for an estimated 129,000 deaths and more than 11 million cases annually. Although several reviews have provided global and regional TF disease burden estimates, major gaps in our understanding of TF epidemiology remain. Areas covered: We provide an overview of the gaps in current estimates of TF disease burden and offer suggestions for addressing them, so that affected communities can receive the full potential of disease prevention offered by vaccination and water, sanitation, and hygiene interventions. Expert commentary: Current disease burden estimates for TF do not capture cases from certain host populations, nor those with atypical presentations of TF, which may lead to substantial underestimation of TF cases and deaths. These knowledge gaps pose major obstacles to the informed use of current and new generation typhoid vaccines.
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Affiliation(s)
- Stephen K Obaro
- a Department of Pediatrics , University of Nebraska Medical Center , Omaha , NE , USA
| | - Pui-Ying Iroh Tam
- b Department of Pediatrics , University of Minnesota Masonic Children's Hospital , Minneapolis , MN , USA
| | - Eric Daniel Mintz
- c Division of Foodborne, Waterborne and Environmental Diseases , Centers for Disease Control and Prevention , Atlanta , GA , USA
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22
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Mobile genes in the human microbiome are structured from global to individual scales. Nature 2016; 535:435-439. [PMID: 27409808 PMCID: PMC4983458 DOI: 10.1038/nature18927] [Citation(s) in RCA: 173] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 06/15/2016] [Indexed: 12/11/2022]
Abstract
Recent work has underscored the importance of the microbiome in human health, largely attributing differences in phenotype to differences in the species present across individuals1,2,3,4,5. But mobile genes can confer profoundly different phenotypes on different strains of the same species. Little is known about the function and distribution of mobile genes in the human microbiome, and in particular whether the gene pool is globally homogenous or constrained by human population structure. Here, we investigate this question by comparing the mobile genes found in the microbiomes of 81 metropolitan North Americans with that of 172 agrarian Fiji islanders using a combination of single-cell genomics and metagenomics. We find large differences in mobile gene content between the Fijian and North American microbiomes, with functional variation that mirrors known dietary differences such as the excess of plant-based starch degradation genes. Remarkably, differences are also observed between the mobile gene pools of proximal Fijian villages, even though microbiome composition across villages is similar. Finally, we observe high rates of recombination leading to individual-specific mobile elements, suggesting that the abundance of some genes may reflect environmental selection rather than dispersal limitation. Together, these data support the hypothesis that human activities and behaviors provide selective pressures that shape mobile gene pools, and that acquisition of mobile genes is important to colonizing specific human populations.
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23
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Abstract
A brief history of vaccination is presented since the Jenner's observation, through the first golden age of vaccinology (from Pasteur's era to 1938), the second golden age (from 1940 to 1970), until the current period. In the first golden age, live, such as Bacille Calmette Guérin (BCG), and yellow fever, inactivated, such as typhoid, cholera, plague, and influenza, and subunit vaccines, such as tetanus and diphtheria toxoids, have been developed. In the second golden age, the cell culture technology enabled polio, measles, mumps, and rubella vaccines be developed. In the era of modern vaccines, in addition to the conjugate polysaccharide, hepatitis A, oral typhoid, and varicella vaccines, the advent of molecular biology enabled to develop hepatitis B, acellular pertussis, papillomavirus, and rotavirus recombinant vaccines. Great successes have been achieved in the fight against infectious diseases, including the smallpox global eradication, the nearly disappearance of polio, the control of tetanus, diphtheria, measles, rubella, yellow fever, and rabies. However, much work should still be done for improving old vaccines, such as BCG, anthrax, smallpox, plague, or for developing effective vaccines against old or emerging infectious threats, such as human-immunodeficiency-virus, malaria, hepatitis C, dengue, respiratory-syncytial-virus, cytomegalovirus, multiresistant bacteria, Clostridium difficile, Ebola virus. In addition to search for innovative and effective vaccines and global infant coverage, even risk categories should adequately be protected. Despite patients under immunosuppressive therapy are globally increasing, their vaccine coverage is lower than recommended, even in developed and affluent countries.
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Affiliation(s)
| | - Simonetta Salemi
- c S. Andrea University Hospital , Via di Grottarossa Rome, Italy
| | - Raffaele D'Amelio
- b Sapienza University of Rome , Department of Clinical and Molecular Medicine , Via di Grottarossa Rome, Italy.,c S. Andrea University Hospital , Via di Grottarossa Rome, Italy
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24
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Watson CH, Edmunds WJ. A review of typhoid fever transmission dynamic models and economic evaluations of vaccination. Vaccine 2015; 33 Suppl 3:C42-54. [PMID: 25921288 PMCID: PMC4504000 DOI: 10.1016/j.vaccine.2015.04.013] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 03/31/2015] [Accepted: 04/01/2015] [Indexed: 01/22/2023]
Abstract
There are relatively few dynamic models or economic analyses of typhoid vaccination. The relative contribution of carriage to transmission is a key uncertainty. Published economic analyses use static models that omit indirect protection of vaccines. Nevertheless, vaccines appear highly cost-effective against WHO criteria in high-incidence settings. No economic model was found to compare vaccine and sanitation.
Despite a recommendation by the World Health Organization (WHO) that typhoid vaccines be considered for the control of endemic disease and outbreaks, programmatic use remains limited. Transmission models and economic evaluation may be informative in decision making about vaccine programme introductions and their role alongside other control measures. A literature search found few typhoid transmission models or economic evaluations relative to analyses of other infectious diseases of similar or lower health burden. Modelling suggests vaccines alone are unlikely to eliminate endemic disease in the short to medium term without measures to reduce transmission from asymptomatic carriage. The single identified data-fitted transmission model of typhoid vaccination suggests vaccines can reduce disease burden substantially when introduced programmatically but that indirect protection depends on the relative contribution of carriage to transmission in a given setting. This is an important source of epidemiological uncertainty, alongside the extent and nature of natural immunity. Economic evaluations suggest that typhoid vaccination can be cost-saving to health services if incidence is extremely high and cost-effective in other high-incidence situations, when compared to WHO norms. Targeting vaccination to the highest incidence age-groups is likely to improve cost-effectiveness substantially. Economic perspective and vaccine costs substantially affect estimates, with disease incidence, case-fatality rates, and vaccine efficacy over time also important determinants of cost-effectiveness and sources of uncertainty. Static economic models may under-estimate benefits of typhoid vaccination by omitting indirect protection. Typhoid fever transmission models currently require per-setting epidemiological parameterisation to inform their use in economic evaluation, which may limit their generalisability. We found no economic evaluation based on transmission dynamic modelling, and no economic evaluation of typhoid vaccination against interventions such as improvements in sanitation or hygiene.
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Affiliation(s)
- Conall H Watson
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, United Kingdom.
| | - W John Edmunds
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, United Kingdom
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