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Meiring JE, Khanam F, Basnyat B, Charles RC, Crump JA, Debellut F, Holt KE, Kariuki S, Mugisha E, Neuzil KM, Parry CM, Pitzer VE, Pollard AJ, Qadri F, Gordon MA. Typhoid fever. Nat Rev Dis Primers 2023; 9:71. [PMID: 38097589 DOI: 10.1038/s41572-023-00480-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/06/2023] [Indexed: 12/18/2023]
Abstract
Typhoid fever is an invasive bacterial disease associated with bloodstream infection that causes a high burden of disease in Africa and Asia. Typhoid primarily affects individuals ranging from infants through to young adults. The causative organism, Salmonella enterica subsp. enterica serovar Typhi is transmitted via the faecal-oral route, crossing the intestinal epithelium and disseminating to systemic and intracellular sites, causing an undifferentiated febrile illness. Blood culture remains the practical reference standard for diagnosis of typhoid fever, where culture testing is available, but novel diagnostic modalities are an important priority under investigation. Since 2017, remarkable progress has been made in defining the global burden of both typhoid fever and antimicrobial resistance; in understanding disease pathogenesis and immunological protection through the use of controlled human infection; and in advancing effective vaccination programmes through strategic multipartner collaboration and targeted clinical trials in multiple high-incidence priority settings. This Primer thus offers a timely update of progress and perspective on future priorities for the global scientific community.
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Affiliation(s)
- James E Meiring
- Division of Clinical Medicine, School of Medicine and Population Health, University of Sheffield, Sheffield, UK
- Malawi-Liverpool-Wellcome Programme, Blantyre, Malawi
| | - Farhana Khanam
- International Centre for Diarrhoel Disease Research, Dhaka, Bangladesh
| | - Buddha Basnyat
- Oxford University Clinical Research Unit, Kathmandu, Nepal
| | - Richelle C Charles
- Massachusetts General Hospital, Harvard Medical School, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - John A Crump
- Centre for International Health, University of Otago, Dunedin, New Zealand
| | | | - Kathryn E Holt
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Samuel Kariuki
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Emmanuel Mugisha
- Center for Vaccine Innovation and Access, PATH, Seattle, WA, USA
| | - Kathleen M Neuzil
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Christopher M Parry
- Department of Clinical Sciences and Education, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Virginia E Pitzer
- Department of Epidemiology of Microbial Diseases and Public Health Modelling Unit, Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Firdausi Qadri
- International Centre for Diarrhoel Disease Research, Dhaka, Bangladesh
| | - Melita A Gordon
- Malawi-Liverpool-Wellcome Programme, Blantyre, Malawi.
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.
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Hoffman SA, Sikorski MJ, Levine MM. Chronic Salmonella Typhi carriage at sites other than the gallbladder. PLoS Negl Trop Dis 2023; 17:e0011168. [PMID: 36952437 PMCID: PMC10035749 DOI: 10.1371/journal.pntd.0011168] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023] Open
Abstract
Typhoid fever caused by infection with Salmonella enterica subspecies enterica serotype Typhi (S. Typhi), an important public health problem in many low- and middle-income countries, is transmitted by ingestion of water or food contaminated by feces or urine from individuals with acute or chronic S. Typhi infection. Most chronic S. Typhi carriers (shedding for ≥12 months) harbor infection in their gallbladder wherein preexisting pathologies, particularly cholelithiasis, provide an environment that fosters persistence. Much less appreciated is the existence of non-gallbladder hepatobiliary chronic S. Typhi carriers and urinary carriers. The former includes parasitic liver flukes as a chronic carriage risk factor. Chronic urinary carriers typically have pathology of their urinary tract, with or without renal or bladder stones. Even as the prevalence of multidrug-resistant and extensively drug-resistant S. Typhi strains is rising, global implementation of highly effective typhoid vaccines is increasing. There is also renewed interest in identifying, monitoring, and (where possible) treating chronic carriers who comprise the long-term reservoir of S. Typhi.
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Affiliation(s)
- Seth A Hoffman
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Michael J Sikorski
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Myron M Levine
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
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3
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Burrows H, Antillón M, Gauld JS, Kim JH, Mogasale V, Ryckman T, Andrews JR, Lo NC, Pitzer VE. Comparison of model predictions of typhoid conjugate vaccine public health impact and cost-effectiveness. Vaccine 2023; 41:965-975. [PMID: 36586741 PMCID: PMC9880559 DOI: 10.1016/j.vaccine.2022.12.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/31/2022]
Abstract
Models are useful to inform policy decisions on typhoid conjugate vaccine (TCV) deployment in endemic settings. However, methodological choices can influence model-predicted outcomes. To provide robust estimates for the potential public health impact of TCVs that account for structural model differences, we compared four dynamic and one static mathematical model of typhoid transmission and vaccine impact. All models were fitted to a common dataset of age-specific typhoid fever cases in Kolkata, India. We evaluated three TCV strategies: no vaccination, routine vaccination at 9 months of age, and routine vaccination at 9 months with a one-time catch-up campaign (ages 9 months to 15 years). The primary outcome was the predicted percent reduction in symptomatic typhoid cases over 10 years after vaccine introduction. For three models with economic analyses (Models A-C), we also compared the incremental cost-effectiveness ratios (ICERs), calculated as the incremental cost (US$) per disability-adjusted life-year (DALY) averted. Routine vaccination was predicted to reduce symptomatic cases by 10-46 % over a 10-year time horizon under an optimistic scenario (95 % initial vaccine efficacy and 19-year mean duration of protection), and by 2-16 % under a pessimistic scenario (82 % initial efficacy and 6-year mean protection). Adding a catch-up campaign predicted a reduction in incidence of 36-90 % and 6-35 % in the optimistic and pessimistic scenarios, respectively. Vaccine impact was predicted to decrease as the relative contribution of chronic carriers to transmission increased. Models A-C all predicted routine vaccination with or without a catch-up campaign to be cost-effective compared to no vaccination, with ICERs varying from $95-789 per DALY averted; two models predicted the ICER of routine vaccination alone to be greater than with the addition of catch-up campaign. Despite differences in model-predicted vaccine impact and cost-effectiveness, routine vaccination plus a catch-up campaign is likely to be impactful and cost-effective in high incidence settings such as Kolkata.
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Affiliation(s)
- Holly Burrows
- Yale School of Public Health, Yale University, New Haven, CT, USA.
| | - Marina Antillón
- Yale School of Public Health, Yale University, New Haven, CT, USA; Swiss Tropical and Public Health Institute, Allschwil, Switzerland; University of Basel, Basel, Switzerland
| | - Jillian S Gauld
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle, WA, USA
| | - Jong-Hoon Kim
- Public Health, Access, and Vaccine Epidemiology (PAVE) Unit, International Vaccine Institute, Seoul, Republic of Korea
| | - Vittal Mogasale
- Policy and Economic Research Department, International Vaccine Institute, Seoul 08826, Republic of Korea
| | - Theresa Ryckman
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Jason R Andrews
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Nathan C Lo
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
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Halla FF, Massawa SM, Joseph EK, Acharya K, Sabai SM, Mgana SM, Werner D. Attenuation of bacterial hazard indicators in the subsurface of an informal settlement and their application in quantitative microbial risk assessment. ENVIRONMENT INTERNATIONAL 2022; 167:107429. [PMID: 35914337 DOI: 10.1016/j.envint.2022.107429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
Pit latrines provide essential onsite sanitation services to over a billion people, but there are concerns about their role in infectious disease transmission, and impacts on groundwater resources. We conducted fieldwork in an informal settlement in Dar es Salaam, where cholera is endemic. We combined plate counting with portable MinION sequencing and quantitative polymerase chain reaction (qPCR) methods for characterization of bacteria in pit latrine sludge, leachate, shallow and deep groundwater resources. Pit latrine sludge was characterized by log10 marker gene concentrations per 100 mL of 11.2 ± 0.2, 9.9 ± 0.9, 6.0 ± 0.3, and 4.4 ± 0.8, for total bacteria (16S rRNA), E. coli (rodA), human-host-associated Bacteroides (HF183), and Vibrio cholerae (ompW), respectively. The ompW gene observations suggested 5 % asymptomatic Vibrio cholerae carriers amongst pit latrine users. Pit leachate percolation through one-meter-thick sand beds attenuated bacterial hazard indicators by 1 to 4 log10 units. But first-order removal rates derived from these data substantially overestimated the longer-range hazard attenuation in the sand aquifers. Cooccurrence of human sewage marker gene HF183 in all shallow groundwater samples testing positive for ompW genes demonstrated the human origin of Vibrio cholerae hazards in the subsurface. All borehole water samples tested negative for ompW and HF183 genes, but 16S rRNA gene sequencing data suggested ingress of faecal pollution into boreholes at the peak of the "long rainy season". Quantitative microbial risk assessment (QMRA) predicted a gastrointestinal disease burden of 0.05 DALY per person per year for the community, well above WHO targets of 10-4-10-6 DALY for disease related to drinking water.
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Affiliation(s)
- Franella Francos Halla
- Department of Environmental Engineering, School of Environmental Science and Technology, Ardhi University, Dar es Salaam, Tanzania
| | - Said Maneno Massawa
- Department of Environmental Engineering, School of Environmental Science and Technology, Ardhi University, Dar es Salaam, Tanzania
| | - Elihaika Kengalo Joseph
- Department of Environmental Engineering, School of Environmental Science and Technology, Ardhi University, Dar es Salaam, Tanzania
| | - Kishor Acharya
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Shadrack Mwita Sabai
- Department of Environmental Engineering, School of Environmental Science and Technology, Ardhi University, Dar es Salaam, Tanzania
| | - Shaaban Mrisho Mgana
- Department of Environmental Engineering, School of Environmental Science and Technology, Ardhi University, Dar es Salaam, Tanzania.
| | - David Werner
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK.
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Mathematical Models for Typhoid Disease Transmission: A Systematic Literature Review. MATHEMATICS 2022. [DOI: 10.3390/math10142506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Explaining all published articles on the typhoid disease transmission model was carried out. It has been conducted to understand how Salmonella is transmitted among humans and vectors with variation interventions to control the spread of the typhoid disease. Specific objectives were to (1) identify the model developed, (2) describe the studies, and (3) identify the interventions of the model. It systemically searched and reviewed Dimension, Scopus, and ScienceDirect databases from 2013 through to 2022 for articles that studied the spread of typhoid fever through a compartmental mathematical model. This study obtained 111 unique articles from three databases, resulting in 23 articles corresponding to the created terms. All the articles were elaborated on to identify their identities for more explanation. Various interventions were considered in the model of each article, are identified, and then summarized to find out the opportunities for model development in future works. The whole article’s content was identified and outlined regarding how mathematics plays a role in model analysis and study of typhoid disease spread with various interventions. The study of mathematical modeling for typhoid disease transmission can be developed on analysis and creating the model with direct and indirect interventions to the human population for further work.
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Maes M, Sikorski MJ, Carey ME, Higginson EE, Dyson ZA, Fernandez A, Araya P, Tennant SM, Baker S, Lagos R, Hormazábal JC, Levine MM, Dougan G. Whole genome sequence analysis of Salmonella Typhi provides evidence of phylogenetic linkage between cases of typhoid fever in Santiago, Chile in the 1980s and 2010-2016. PLoS Negl Trop Dis 2022; 16:e0010178. [PMID: 35767580 PMCID: PMC9275700 DOI: 10.1371/journal.pntd.0010178] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 07/12/2022] [Accepted: 06/08/2022] [Indexed: 11/25/2022] Open
Abstract
Typhoid fever epidemiology was investigated rigorously in Santiago, Chile during the 1980s, when Salmonella enterica serovar Typhi (S. Typhi) caused seasonal, hyperendemic disease. Targeted interventions reduced the annual typhoid incidence rates from 128–220 cases/105 population occurring between 1977–1984 to <8 cases/105 from 1992 onwards. As such, Santiago represents a contemporary example of the epidemiologic transition of an industrialized city from amplified hyperendemic typhoid fever to a period when typhoid is no longer endemic. We used whole genome sequencing (WGS) and phylogenetic analysis to compare the genotypes of S. Typhi cultured from acute cases of typhoid fever occurring in Santiago during the hyperendemic period of the 1980s (n = 74) versus the nonendemic 2010s (n = 80) when typhoid fever was rare. The genotype distribution between “historical” (1980s) isolates and “modern” (2011–2016) isolates was similar, with genotypes 3.5 and 2 comprising the majority of isolations, and 73/80 (91.3%) of modern isolates matching a genotype detected in the 1980s. Additionally, phylogenomically ‘ancient’ genotypes 1.1 and 1.2.1, uncommon in the global collections, were also detected in both eras, with a notable rise amongst the modern isolates. Thus, genotypes of S. Typhi causing acute illness in the modern nonendemic era match the genotypes circulating during the hyperendemic 1980s. The persistence of historical genotypes may be explained by chronic typhoid carriers originally infected during or before the 1980s. Studies of Salmonella Typhi (the cause of typhoid fever) rarely include isolates collected both before and after the interruption of hyperendemic transmission because this typically occurred decades before modern bacteria preservation methods. After substantial reduction in disease, it was assumed that sporadic cases and infrequent outbreaks were due to either chronic biliary carriers or importations, but this was difficult to characterize with low resolution bacterial typing methods. In Santiago, Chile, typhoid fever persisted at hyperendemic levels through the 1980s until organized control efforts in the 1980s and changes to wastewater policy in 1991 caused annual typhoid incidence to plummet. In this study, we used whole genome sequencing (WGS) to investigate whether recent sporadic cases occurring in Santiago in the 2010s were genomically similar to S. Typhi circulating in the 1980s, or dissimilar, possibly representing importations of S. Typhi from outside of Chile. We found concordance amongst S. Typhi genotypes between the 1980s and 2010s, and differences from genotypes circulating in Southeast Asia and Africa where typhoid remains hyperendemic. Our findings suggest that a proportion of modern, rare typhoid cases in Santiago are autochthonous, and that chronic carriers or another unknown reservoir likely contribute. Broadly, our findings corroborate the epidemiologic importance of long-term reservoirs of typhoid fever decades after typhoid elimination.
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Affiliation(s)
- Mailis Maes
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
| | - Michael J. Sikorski
- Center for Vaccine Development and Global Health (CVD), University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Megan E. Carey
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Ellen E. Higginson
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Zoe A. Dyson
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Department of Infectious Diseases, Monash University, Melbourne, Australia
- London School of Hygiene & Tropical Medicine, London, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Alda Fernandez
- Bacteriologia, Subdepartamento de Enfermedades Infecciosas, Departamento de Laboratorio Biomédico, Instituto de Salud Pública de Chile (ISP), Santiago, Chile
| | - Pamela Araya
- Bacteriologia, Subdepartamento de Enfermedades Infecciosas, Departamento de Laboratorio Biomédico, Instituto de Salud Pública de Chile (ISP), Santiago, Chile
| | - Sharon M. Tennant
- Center for Vaccine Development and Global Health (CVD), University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Rosanna Lagos
- Centro para Vacunas en Desarollo-Chile (CVD-Chile), Hospital de Niños Roberto del Rio, Santiago, Chile
| | - Juan Carlos Hormazábal
- Bacteriologia, Subdepartamento de Enfermedades Infecciosas, Departamento de Laboratorio Biomédico, Instituto de Salud Pública de Chile (ISP), Santiago, Chile
| | - Myron M. Levine
- Center for Vaccine Development and Global Health (CVD), University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Gordon Dougan
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
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Kariuki S, Dyson ZA, Mbae C, Ngetich R, Kavai SM, Wairimu C, Anyona S, Gitau N, Onsare RS, Ongandi B, Duchene S, Ali M, Clemens JD, Holt KE, Dougan G. Multiple introductions of multidrug-resistant typhoid associated with acute infection and asymptomatic carriage, Kenya. eLife 2021; 10:67852. [PMID: 34515028 PMCID: PMC8494480 DOI: 10.7554/elife.67852] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 09/08/2021] [Indexed: 02/02/2023] Open
Abstract
Background: Understanding the dynamics of infection and carriage of typhoid in endemic settings is critical to finding solutions to prevention and control. Methods: In a 3-year case-control study, we investigated typhoid among children aged <16 years (4670 febrile cases and 8549 age matched controls) living in an informal settlement, Nairobi, Kenya. Results: 148 S. Typhi isolates from cases and 95 from controls (stool culture) were identified; a carriage frequency of 1 %. Whole-genome sequencing showed 97% of cases and 88% of controls were genotype 4.3.1 (Haplotype 58), with the majority of each (76% and 88%) being multidrug-resistant strains in three sublineages of the H58 genotype (East Africa 1 (EA1), EA2, and EA3), with sequences from cases and carriers intermingled. Conclusions: The high rate of multidrug-resistant H58 S. Typhi, and the close phylogenetic relationships between cases and controls, provides evidence for the role of carriers as a reservoir for the community spread of typhoid in this setting. Funding: National Institutes of Health (R01AI099525); Wellcome Trust (106158/Z/14/Z); European Commission (TyphiNET No 845681); National Institute for Health Research (NIHR); Bill and Melinda Gates Foundation (OPP1175797).
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Affiliation(s)
- Samuel Kariuki
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya.,Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Zoe A Dyson
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom.,Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom.,London School of Hygiene & Tropical Medicine, London, United Kingdom.,Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Australia
| | - Cecilia Mbae
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Ronald Ngetich
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Susan M Kavai
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Celestine Wairimu
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Stephen Anyona
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Naomi Gitau
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Robert Sanaya Onsare
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Beatrice Ongandi
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Sebastian Duchene
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Mohamed Ali
- Department of International Health, John's Hopkins University, Baltimore, United States
| | | | - Kathryn E Holt
- London School of Hygiene & Tropical Medicine, London, United Kingdom.,Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Australia
| | - Gordon Dougan
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom
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Rigby J, Elmerhebi E, Diness Y, Mkwanda C, Tonthola K, Galloway H, Miles R, Henrion MYR, Edwards T, Gauld J, Msefula C, Johnston R, Nair S, Feasey N, Elviss NC. Optimized methods for detecting Salmonella Typhi in the environment using validated field sampling, culture and confirmatory molecular approaches. J Appl Microbiol 2021; 132:1503-1517. [PMID: 34324765 DOI: 10.1111/jam.15237] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 07/07/2021] [Accepted: 07/08/2021] [Indexed: 11/30/2022]
Abstract
AIMS This study evaluated detection methods for Salmonella Typhi (S. Typhi) in the environment, to establish a novel pathway from field sampling to isolation of viable organisms and molecular confirmation from complex environmental samples, thus enabling environmental surveillance of typhoid. METHODS AND RESULTS Multiple media were assessed using clinical isolates from the Public Health England's (PHE) Culture collection. The culture pathway selected consisted of a primary 2% bile broth and secondary Selenite F broth, followed by modified Chromogenic Agar for Salmonella Esterase (mCASE). A qPCR assay was adapted from a validated S. Typhi PCR panel for confirmation of isolates, with comparison to biochemical and serological tests showing good specificity. Sampling locations in Blantyre, Malawi were used to compare sampling methods. Viable S. Typhi were isolated from a mixture of trap and grab river water samples on six occasions. CONCLUSIONS Culture of viable S. Typhi from environmental samples was possible using effective capture and culture techniques. SIGNIFICANCE AND IMPACT OF STUDY Whilst several studies have attempted to detect S. Typhi from the environment, this is the first successful attempt to isolate the organism from river water since the 1980s. Supplementing clinical data with environmental screening offers the potential for enhanced surveillance, which might inform interventions and assess vaccination programmes.
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Affiliation(s)
- Jonathan Rigby
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK.,Malawi-Liverpool-Wellcome Research Programme, The College of Medicine, Blantyre, Malawi
| | | | - Yohane Diness
- Malawi-Liverpool-Wellcome Research Programme, The College of Medicine, Blantyre, Malawi
| | - Charity Mkwanda
- Malawi-Liverpool-Wellcome Research Programme, The College of Medicine, Blantyre, Malawi
| | - Katalina Tonthola
- Malawi-Liverpool-Wellcome Research Programme, The College of Medicine, Blantyre, Malawi
| | - Heather Galloway
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK.,Malawi-Liverpool-Wellcome Research Programme, The College of Medicine, Blantyre, Malawi
| | - Rory Miles
- Centre for Enzyme Innovation, University of Portsmouth, Portsmouth, UK
| | - Marc Y R Henrion
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK.,Malawi-Liverpool-Wellcome Research Programme, The College of Medicine, Blantyre, Malawi
| | - Thomas Edwards
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Jillian Gauld
- Faculty of Health and Medicine, University of Lancaster, Lancaster, UK
| | - Chisomo Msefula
- Department of Microbiology, The College of Medicine, University of Malawi, Blantyre, Malawi
| | - Rob Johnston
- National Infection Service, Public Health England, London, UK
| | - Satheesh Nair
- National Infection Service, Public Health England, London, UK
| | - Nicholas Feasey
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK.,Malawi-Liverpool-Wellcome Research Programme, The College of Medicine, Blantyre, Malawi.,Department of Microbiology, The College of Medicine, University of Malawi, Blantyre, Malawi
| | - Nicola C Elviss
- National Infection Service, Public Health England, London, UK
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Foster T, Falletta J, Amin N, Rahman M, Liu P, Raj S, Mills F, Petterson S, Norman G, Moe C, Willetts J. Modelling faecal pathogen flows and health risks in urban Bangladesh: Implications for sanitation decision making. Int J Hyg Environ Health 2021; 233:113669. [PMID: 33578186 DOI: 10.1016/j.ijheh.2020.113669] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 11/19/2020] [Accepted: 11/24/2020] [Indexed: 12/29/2022]
Abstract
Faecal-oral infections are a major component of the disease burden in low-income contexts, with inadequate sanitation seen as a contributing factor. However, demonstrating health effects of sanitation interventions - particularly in urban areas - has proved challenging and there is limited empirical evidence to support sanitation decisions that maximise health gains. This study aimed to develop, apply and validate a systems modelling approach to inform sanitation infrastructure and service decision-making in urban environments by examining enteric pathogen inputs, transport and reduction by various sanitation systems, and estimating corresponding exposure and public health impacts. The health effects of eight sanitation options were assessed in a low-income area in Dhaka, Bangladesh, with a focus on five target pathogens (Shigella, Vibrio cholerae, Salmonella Typhi, norovirus GII and Giardia). Relative to the sanitation base case in the study site (24% septic tanks, 5% holding tanks and 71% toilets discharging directly to open drains), comprehensive coverage of septic tanks was estimated to reduce the disease burden in disability-adjusted life years (DALYs) by 48-72%, while complete coverage of communal scale anaerobic baffled reactors was estimated to reduce DALYs by 67-81%. Despite these improvements, a concerning health risk persists with these systems as a result of effluent discharge to open drains, particularly when the systems are poorly managed. Other sanitation options, including use of constructed wetlands and small bore sewerage, demonstrated further reductions in local health risk, though several still exported pathogens into neighbouring areas, simply transferring risk to downstream communities. The study revealed sensitivity to and a requirement for further evidence on log reduction values for different sanitation systems under varying performance conditions, pathogen flows under flooding conditions as well as pathogen shedding and human exposure in typical low-income urban settings. Notwithstanding variability and uncertainties in input parameters, systems modelling can be a feasible and customisable approach to consider the relative health impact of different sanitation options across various contexts, and stands as a valuable tool to guide urban sanitation decision-making.
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Affiliation(s)
- Tim Foster
- Institute for Sustainable Futures, University of Technology Sydney, 235 Jones St, Ultimo, NSW, 2007, Australia.
| | - Jay Falletta
- Institute for Sustainable Futures, University of Technology Sydney, 235 Jones St, Ultimo, NSW, 2007, Australia.
| | - Nuhu Amin
- Environmental Interventions Unit, Infectious Disease Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh.
| | - Mahbubur Rahman
- Environmental Interventions Unit, Infectious Disease Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh.
| | - Pengbo Liu
- Center for Global Safe Water, Sanitation, and Hygiene, Rollins School of Public Health, Emory University, Atlanta, GA, USA.
| | - Suraja Raj
- Center for Global Safe Water, Sanitation, and Hygiene, Rollins School of Public Health, Emory University, Atlanta, GA, USA.
| | - Freya Mills
- Institute for Sustainable Futures, University of Technology Sydney, 235 Jones St, Ultimo, NSW, 2007, Australia.
| | - Susan Petterson
- Water & Health Pty Ltd., 13 Lord St, North Sydney, NSW, 2060, Australia; School of Medicine, Griffith University, Parklands Drive, Southport, QLD, 4222, Australia.
| | - Guy Norman
- Water and Sanitation for the Urban Poor, 10 Queen Street Place, London, EC4R 1BE, UK.
| | - Christine Moe
- Center for Global Safe Water, Sanitation, and Hygiene, Rollins School of Public Health, Emory University, Atlanta, GA, USA.
| | - Juliet Willetts
- Institute for Sustainable Futures, University of Technology Sydney, 235 Jones St, Ultimo, NSW, 2007, Australia.
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10
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Maes M, Dyson ZA, Higginson EE, Fernandez A, Araya P, Tennant SM, Baker S, Lagos R, Levine MM, Hormazabal JC, Dougan G. Multiple Introductions of Salmonella enterica Serovar Typhi H58 with Reduced Fluoroquinolone Susceptibility into Chile. Emerg Infect Dis 2020; 26:2736-2740. [PMID: 33079054 PMCID: PMC7588544 DOI: 10.3201/eid2611.201676] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Salmonella enterica serovar Typhi H58, an antimicrobial-resistant lineage, is globally disseminated but has not been reported in Latin America. Genomic analysis revealed 3 independent introductions of Salmonella Typhi H58 with reduced fluoroquinolone susceptibility into Chile. Our findings highlight the utility of enhanced genomic surveillance for typhoid fever in this region.
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11
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Pre-existing Helicobacter pylori serum IgG enhances the vibriocidal antibody response to CVD 103-HgR live oral cholera vaccine in Malian adults. Sci Rep 2020; 10:16871. [PMID: 33037244 PMCID: PMC7547695 DOI: 10.1038/s41598-020-71754-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 08/17/2020] [Indexed: 02/07/2023] Open
Abstract
Accumulating evidence indicates that persistent Helicobacter pylori gastric infection influences immune responses to oral enteric vaccines. We studied the association between pre-existing H. pylori serum IgG and serum pepsinogens levels (PGs) as markers of gastric inflammation and the immune response to single-dose live oral cholera vaccine CVD 103-HgR in Malian adults. Baseline sera obtained during a phase 2 safety/immunogenicity clinical trial of cholera vaccine CVD 103-HgR among 93 healthy Malian adults were tested for H. pylori IgG antibodies and PGI and PGII levels using enzyme linked immunosorbent assays. Overall 74/93 (80%) vaccine recipients were H. pylori IgG seropositive at baseline. Vibriocidal antibody seroconversion (≥ fourfold increase 14 days following administration of CVD 103-HgR compared to baseline) among vaccine recipients was 56%. However, vibriocidal antibody seroconversion was markedly higher among H. pylori seropositives than seronegatives 64% vs. 26% (p = 0.004); adjusted relative risk: 2.20 (95% confidence intervals 1.00–4.80; p = 0.049). Among H. pylori seropositive vaccine recipients, there were no significant associations between PGI, PGII and PGI:PGII levels and vibriocidal seroconversion. The enhanced seroconversion to oral cholera vaccine CVD 103-HgR among H. pylori seropositive African adults provides further evidence of the immunomodulating impact of H. pylori on oral vaccine immunogenicity.
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12
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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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13
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Reviving the "Moore Swab": a Classic Environmental Surveillance Tool Involving Filtration of Flowing Surface Water and Sewage Water To Recover Typhoidal Salmonella Bacteria. Appl Environ Microbiol 2020; 86:AEM.00060-20. [PMID: 32332133 PMCID: PMC7301852 DOI: 10.1128/aem.00060-20] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The “Moore swab” is a classic environmental surveillance tool whereby a gauze pad tied with string is suspended in flowing water or wastewater contaminated with human feces and harboring enteric pathogens that pose a human health threat. In contrast to single volume “grab” samples, Moore swabs act as continuous filters to “trap” microorganisms, which are subsequently isolated and confirmed using appropriate laboratory methods. Continuous filtration is valuable for the isolation of transiently present pathogens such as human-restricted Salmonella enterica serovars Typhi and Paratyphi A and B. The “Moore swab” is a classic environmental surveillance tool whereby a gauze pad tied with string is suspended in flowing water or wastewater contaminated with human feces and harboring enteric pathogens that pose a human health threat. In contrast to single volume “grab” samples, Moore swabs act as continuous filters to “trap” microorganisms, which are subsequently isolated and confirmed using appropriate laboratory methods. Continuous filtration is valuable for the isolation of transiently present pathogens such as human-restricted Salmonella enterica serovars Typhi and Paratyphi A and B. The technique was first proposed (1948) to trace Salmonella Paratyphi B systematically through sewers to pinpoint the residence of a chronic carrier responsible for sporadic outbreaks of paratyphoid fever. From 1948 to 1986, Moore swabs proved instrumental to identify long-term human reservoirs (chronic carriers) and long-cycle environmental transmission pathways of S. Typhi and Paratyphi, for example, to decipher endemic transmission in Santiago, Chile, during the 1980s. Despite limitations such as intermittent shedding of typhoidal Salmonella by humans and the effects of dilution, S. Typhi and S. Paratyphi have been recovered from sewers, surface waters, irrigation canals, storm drains, flush toilets, and septic tanks by using Moore swabs. Driven by the emergence of multiple antibiotic-resistant S. Typhi and S. Paratyphi A strains that limit treatment options, several countries are embarking on accelerated typhoid control programs using vaccines and environmental interventions. Moore swabs, which are regaining appreciation as important components of the public health/environmental microbiology toolbox, can enhance environmental surveillance for typhoidal Salmonella, thereby contributing to the control of typhoid fever.
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14
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Phillips MT, Owers KA, Grenfell BT, Pitzer VE. Changes in historical typhoid transmission across 16 U.S. cities, 1889-1931: Quantifying the impact of investments in water and sewer infrastructures. PLoS Negl Trop Dis 2020; 14:e0008048. [PMID: 32187188 PMCID: PMC7105137 DOI: 10.1371/journal.pntd.0008048] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 03/30/2020] [Accepted: 01/10/2020] [Indexed: 12/25/2022] Open
Abstract
Investments in water and sanitation systems are believed to have led to the decline in typhoid fever in developed countries, such that most cases now occur in regions lacking adequate clean water and sanitation. Exploring seasonal and long-term patterns in historical typhoid mortality in the United States can offer deeper understanding of disease drivers. We fit modified Time-series Susceptible-Infectious-Recovered models to city-level weekly mortality counts to estimate seasonal and long-term typhoid transmission. We examined seasonal transmission separately by city and aggregated by water source. Typhoid transmission peaked in late summer/early fall. Seasonality varied by water source, with the greatest variation occurring in cities with reservoirs. We then fit hierarchical regression models to measure associations between long-term transmission and annual financial investments in water and sewer systems. Overall historical $1 per capita ($16.13 in 2017) investments in the water supply were associated with approximately 5% (95% confidence interval: 3-6%) decreases in typhoid transmission, while $1 increases in the overall sewer system investments were associated with estimated 6% (95% confidence interval: 4-9%) decreases. Our findings aid in the understanding of typhoid transmission dynamics and potential impacts of water and sanitation improvements, and can inform cost-effectiveness analyses of interventions to reduce the typhoid burden.
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Affiliation(s)
- Maile T. Phillips
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Katharine A. Owers
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Bryan T. Grenfell
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Virginia E. Pitzer
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
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15
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Cost-effectiveness of using environmental surveillance to target the roll-out typhoid conjugate vaccine. Vaccine 2020; 38:1661-1670. [PMID: 31917040 DOI: 10.1016/j.vaccine.2019.12.061] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 12/26/2019] [Accepted: 12/27/2019] [Indexed: 01/15/2023]
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16
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Abstract
We combine methodology from history and genetics to reconstruct the biosocial history of antimicrobial resistance (AMR) in the bacterium Salmonella enterica serovar Typhi (S. Typhi). We show how evolutionary divergence in S. Typhi was driven by rising global antibiotic use and by the neglect of typhoid outside of high-income countries. Although high-income countries pioneered 1960s precautionary antibiotic regulations to prevent selection for multidrug resistance, new antibiotic classes, typhoid's cultural status as a supposedly ancient disease of "undeveloped" countries, limited international funding, and narrow biosecurity agendas helped fragment effective global collective action for typhoid control. Antibiotic-intensive compensation for weak water and healthcare systems subsequently fueled AMR selection in low- and middle-income countries but often remained invisible due to lacking surveillance capabilities. The recent rise of extensively drug-resistant typhoid bears the biosocial footprint of more than half a century of antibiotic-intensive international neglect.
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Affiliation(s)
- Claas Kirchhelle
- Wellcome Unit for the History of Medicine/Oxford Martin School, University of Oxford, Addenbrooke’s Hospital, United Kingdom
| | - Zoe Anne Dyson
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, United Kingdom
| | - Gordon Dougan
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, United Kingdom
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17
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Kerr CC. Is epidemiology ready for Big Software? Pathog Dis 2019; 77:5304613. [PMID: 30715264 DOI: 10.1093/femspd/ftz006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 01/29/2019] [Indexed: 01/18/2023] Open
Abstract
Large-scale, open-source software projects like EMOD offer a new approach to epidemiological modeling. Built by a team of professional software developers, EMOD offers significant advantages over 'single-use' models designed by individual research teams, including comprehensive documentation, automated testing and extensive support. In addition, as an individual-based model, it allows much greater complexity and flexibility than the compartmental models that are most commonly used in epidemiology. Adopting modern software development practices, as embodied by EMOD, is essential for ensuring that the best models are available to the greatest number of people.
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Affiliation(s)
- Cliff C Kerr
- A28 Physics Rd, Camperdown, Complex Systems Group, School of Physics, University of Sydney, NSW 2006, Australia
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