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Shackleton D, Memon FA, Nichols G, Phalkey R, Chen AS. Mechanisms of cholera transmission via environment in India and Bangladesh: state of the science review. REVIEWS ON ENVIRONMENTAL HEALTH 2024; 39:313-329. [PMID: 36639850 DOI: 10.1515/reveh-2022-0201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 12/10/2022] [Indexed: 06/17/2023]
Abstract
OBJECTIVES Cholera has a long history in India and Bangladesh, the region where six out of the past seven global pandemics have been seeded. The changing climate and growing population have led to global cholera cases remaining high despite a consistent improvement in the access to clean water and sanitation. We aim to provide a holistic overview of variables influencing environmental cholera transmission within the context of India and Bangladesh, with a focus on the mechanisms by which they act. CONTENT We identified 56 relevant texts (Bangladesh n = 40, India n = 7, Other n = 5). The results of the review found that cholera transmission is associated with several socio-economic and environmental factors, each associated variable is suggested to have at least one mediating mechanism. Increases in ambient temperature and coastal sea surface temperature support cholera transmission via increases in plankton and a preference of Vibrio cholerae for warmer waters. Increased rainfall can potentially support or reduce transmission via several mechanisms. SUMMARY AND OUTLOOK Common issues in the literature are co-variance of seasonal factors, limited access to high quality cholera data, high research bias towards research in Dhaka and Matlab (Bangladesh). A specific and detailed understanding of the relationship between SST and cholera incidence remains unclear.
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Affiliation(s)
- Debbie Shackleton
- College of Engineering, Mathematics, and Physical Sciences, University of Exeter, Exeter, EX4 4QF, UK
| | - Fayyaz A Memon
- College of Engineering, Mathematics, and Physical Sciences, University of Exeter, Exeter, EX4 4QF, UK
| | - Gordon Nichols
- European Centre for Environment and Human Health, University of Exeter Medical School, Knowledge Spa, Royal Cornwall Hospital, Truro, Cornwall, UK
- University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Revati Phalkey
- Climate Change and Health Group, UK Health Security Agency, London, UK
- Heidelberg Institute of Global Health, University of Heidelberg, Heidelberg, Germany
- Division of Epidemiology and Public Health, School of Medicine, University of Nottingham, Nottingham, UK
| | - Albert S Chen
- College of Engineering, Mathematics, and Physical Sciences, University of Exeter, Exeter, EX4 4QF, UK
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2
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Rothstein AP, Jesser KJ, Feistel DJ, Konstantinidis KT, Trueba G, Levy K. Population genomics of diarrheagenic Escherichia coli uncovers high connectivity between urban and rural communities in Ecuador. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 113:105476. [PMID: 37392822 PMCID: PMC10599324 DOI: 10.1016/j.meegid.2023.105476] [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: 05/07/2023] [Revised: 05/11/2023] [Accepted: 06/28/2023] [Indexed: 07/03/2023]
Abstract
Human movement may be an important driver of transmission dynamics for enteric pathogens but has largely been underappreciated except for international 'travelers' diarrhea or cholera. Phylodynamic methods, which combine genomic and epidemiological data, are used to examine rates and dynamics of disease matching underlying evolutionary history and biogeographic distributions, but these methods often are not applied to enteric bacterial pathogens. We used phylodynamics to explore the phylogeographic and evolutionary patterns of diarrheagenic E. coli in northern Ecuador to investigate the role of human travel in the geographic distribution of strains across the country. Using whole genome sequences of diarrheagenic E. coli isolates, we built a core genome phylogeny, reconstructed discrete ancestral states across urban and rural sites, and estimated migration rates between E. coli populations. We found minimal structuring based on site locations, urban vs. rural locality, pathotype, or clinical status. Ancestral states of phylogenomic nodes and tips were inferred to have 51% urban ancestry and 49% rural ancestry. Lack of structuring by location or pathotype E. coli isolates imply highly connected communities and extensive sharing of genomic characteristics across isolates. Using an approximate structured coalescent model, we estimated rates of migration among circulating isolates were 6.7 times larger for urban towards rural populations compared to rural towards urban populations. This suggests increased inferred migration rates of diarrheagenic E. coli from urban populations towards rural populations. Our results indicate that investments in water and sanitation prevention in urban areas could limit the spread of enteric bacterial pathogens among rural populations.
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Affiliation(s)
- Andrew P. Rothstein
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, USA
| | - Kelsey J. Jesser
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, USA
| | - Dorian J. Feistel
- School of a Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Konstantinos T. Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
- School of a Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Gabriel Trueba
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Pichincha, Ecuador
| | - Karen Levy
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, USA
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3
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Clutter CH, Klarman MB, Cajusma Y, Cato ET, Abu Sayeed M, Brinkley L, Jensen O, Baril C, De Rochars VMB, Azman AS, Long MT, Cummings D, Leung DT, Nelson EJ. Population-Based Serologic Survey of Vibrio cholerae Antibody Titers before Cholera Outbreak, Haiti, 2022. Emerg Infect Dis 2023; 29:1864-1867. [PMID: 37487168 PMCID: PMC10461687 DOI: 10.3201/eid2909.230174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023] Open
Abstract
A Vibrio cholerae O1 outbreak emerged in Haiti in October 2022 after years of cholera absence. In samples from a 2021 serosurvey, we found lower circulating antibodies against V. cholerae lipopolysaccharide in children <5 years of age and no vibriocidal antibodies, suggesting high susceptibility to cholera, especially among young children.
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Affiliation(s)
| | | | - Youseline Cajusma
- University of Utah, Salt Lake City, Utah, USA (C.H. Clutter, O. Jensen, D.T. Leung)
- University of Florida, Gainesville, Florida, USA (M.B. Klarman, Y. Cajusma, E.T. Cato, M.A. Sayeed, L. Brinkley, V.M. Beau De Rochars, M.T. Long, D. Cummings, E.J. Nelson)
- Université d'État d'Haïti, Port au Prince, Haiti (C. Baril)
- Johns Hopkins University, Baltimore, Maryland, USA (A.S. Azman)
| | - Emilee T. Cato
- University of Utah, Salt Lake City, Utah, USA (C.H. Clutter, O. Jensen, D.T. Leung)
- University of Florida, Gainesville, Florida, USA (M.B. Klarman, Y. Cajusma, E.T. Cato, M.A. Sayeed, L. Brinkley, V.M. Beau De Rochars, M.T. Long, D. Cummings, E.J. Nelson)
- Université d'État d'Haïti, Port au Prince, Haiti (C. Baril)
- Johns Hopkins University, Baltimore, Maryland, USA (A.S. Azman)
| | - Md. Abu Sayeed
- University of Utah, Salt Lake City, Utah, USA (C.H. Clutter, O. Jensen, D.T. Leung)
- University of Florida, Gainesville, Florida, USA (M.B. Klarman, Y. Cajusma, E.T. Cato, M.A. Sayeed, L. Brinkley, V.M. Beau De Rochars, M.T. Long, D. Cummings, E.J. Nelson)
- Université d'État d'Haïti, Port au Prince, Haiti (C. Baril)
- Johns Hopkins University, Baltimore, Maryland, USA (A.S. Azman)
| | - Lindsey Brinkley
- University of Utah, Salt Lake City, Utah, USA (C.H. Clutter, O. Jensen, D.T. Leung)
- University of Florida, Gainesville, Florida, USA (M.B. Klarman, Y. Cajusma, E.T. Cato, M.A. Sayeed, L. Brinkley, V.M. Beau De Rochars, M.T. Long, D. Cummings, E.J. Nelson)
- Université d'État d'Haïti, Port au Prince, Haiti (C. Baril)
- Johns Hopkins University, Baltimore, Maryland, USA (A.S. Azman)
| | - Owen Jensen
- University of Utah, Salt Lake City, Utah, USA (C.H. Clutter, O. Jensen, D.T. Leung)
- University of Florida, Gainesville, Florida, USA (M.B. Klarman, Y. Cajusma, E.T. Cato, M.A. Sayeed, L. Brinkley, V.M. Beau De Rochars, M.T. Long, D. Cummings, E.J. Nelson)
- Université d'État d'Haïti, Port au Prince, Haiti (C. Baril)
- Johns Hopkins University, Baltimore, Maryland, USA (A.S. Azman)
| | - Chantale Baril
- University of Utah, Salt Lake City, Utah, USA (C.H. Clutter, O. Jensen, D.T. Leung)
- University of Florida, Gainesville, Florida, USA (M.B. Klarman, Y. Cajusma, E.T. Cato, M.A. Sayeed, L. Brinkley, V.M. Beau De Rochars, M.T. Long, D. Cummings, E.J. Nelson)
- Université d'État d'Haïti, Port au Prince, Haiti (C. Baril)
- Johns Hopkins University, Baltimore, Maryland, USA (A.S. Azman)
| | - V. Madsen Beau De Rochars
- University of Utah, Salt Lake City, Utah, USA (C.H. Clutter, O. Jensen, D.T. Leung)
- University of Florida, Gainesville, Florida, USA (M.B. Klarman, Y. Cajusma, E.T. Cato, M.A. Sayeed, L. Brinkley, V.M. Beau De Rochars, M.T. Long, D. Cummings, E.J. Nelson)
- Université d'État d'Haïti, Port au Prince, Haiti (C. Baril)
- Johns Hopkins University, Baltimore, Maryland, USA (A.S. Azman)
| | - Andrew S. Azman
- University of Utah, Salt Lake City, Utah, USA (C.H. Clutter, O. Jensen, D.T. Leung)
- University of Florida, Gainesville, Florida, USA (M.B. Klarman, Y. Cajusma, E.T. Cato, M.A. Sayeed, L. Brinkley, V.M. Beau De Rochars, M.T. Long, D. Cummings, E.J. Nelson)
- Université d'État d'Haïti, Port au Prince, Haiti (C. Baril)
- Johns Hopkins University, Baltimore, Maryland, USA (A.S. Azman)
| | - Maureen T. Long
- University of Utah, Salt Lake City, Utah, USA (C.H. Clutter, O. Jensen, D.T. Leung)
- University of Florida, Gainesville, Florida, USA (M.B. Klarman, Y. Cajusma, E.T. Cato, M.A. Sayeed, L. Brinkley, V.M. Beau De Rochars, M.T. Long, D. Cummings, E.J. Nelson)
- Université d'État d'Haïti, Port au Prince, Haiti (C. Baril)
- Johns Hopkins University, Baltimore, Maryland, USA (A.S. Azman)
| | - Derek Cummings
- University of Utah, Salt Lake City, Utah, USA (C.H. Clutter, O. Jensen, D.T. Leung)
- University of Florida, Gainesville, Florida, USA (M.B. Klarman, Y. Cajusma, E.T. Cato, M.A. Sayeed, L. Brinkley, V.M. Beau De Rochars, M.T. Long, D. Cummings, E.J. Nelson)
- Université d'État d'Haïti, Port au Prince, Haiti (C. Baril)
- Johns Hopkins University, Baltimore, Maryland, USA (A.S. Azman)
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Walton MG, Cubillejo I, Nag D, Withey JH. Advances in cholera research: from molecular biology to public health initiatives. Front Microbiol 2023; 14:1178538. [PMID: 37283925 PMCID: PMC10239892 DOI: 10.3389/fmicb.2023.1178538] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 04/14/2023] [Indexed: 06/08/2023] Open
Abstract
The aquatic bacterium Vibrio cholerae is the etiological agent of the diarrheal disease cholera, which has plagued the world for centuries. This pathogen has been the subject of studies in a vast array of fields, from molecular biology to animal models for virulence activity to epidemiological disease transmission modeling. V. cholerae genetics and the activity of virulence genes determine the pathogenic potential of different strains, as well as provide a model for genomic evolution in the natural environment. While animal models for V. cholerae infection have been used for decades, recent advances in this area provide a well-rounded picture of nearly all aspects of V. cholerae interaction with both mammalian and non-mammalian hosts, encompassing colonization dynamics, pathogenesis, immunological responses, and transmission to naïve populations. Microbiome studies have become increasingly common as access and affordability of sequencing has improved, and these studies have revealed key factors in V. cholerae communication and competition with members of the gut microbiota. Despite a wealth of knowledge surrounding V. cholerae, the pathogen remains endemic in numerous countries and causes sporadic outbreaks elsewhere. Public health initiatives aim to prevent cholera outbreaks and provide prompt, effective relief in cases where prevention is not feasible. In this review, we describe recent advancements in cholera research in these areas to provide a more complete illustration of V. cholerae evolution as a microbe and significant global health threat, as well as how researchers are working to improve understanding and minimize impact of this pathogen on vulnerable populations.
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Affiliation(s)
| | | | | | - Jeffrey H. Withey
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI, United States
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Environmental Reservoirs of Pathogenic Vibrio spp. and Their Role in Disease: The List Keeps Expanding. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1404:99-126. [PMID: 36792873 DOI: 10.1007/978-3-031-22997-8_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Vibrio species are natural inhabitants of aquatic environments and have complex interactions with the environment that drive the evolution of traits contributing to their survival. These traits may also contribute to their ability to invade or colonize animal and human hosts. In this review, we attempt to summarize the relationships of Vibrio spp. with other organisms in the aquatic environment and discuss how these interactions could potentially impact colonization of animal and human hosts.
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6
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Clutter CH, Klarman MB, Cajusma Y, Cato ET, Sayeed A, Brinkley L, Jensen O, Baril C, De Rochars VMB, Azman AS, Long MT, Cummings D, Leung DT, Nelson EJ. A population-based serological survey of Vibrio cholerae antibody titers in Ouest Department, Haiti in the year prior to the 2022 cholera outbreak. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.02.06.23285537. [PMID: 36798289 PMCID: PMC9934795 DOI: 10.1101/2023.02.06.23285537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
After three years with no confirmed cholera cases in Haiti, an outbreak of Vibrio cholerae O1 emerged in October 2022. Levels of pre-existing antibodies provide an estimate of prior immunologic exposure, reveal potentially relevant immune responses, and set a baseline for future serosurveillance. We analyzed dried blood spots collected in 2021 from a population-weighted representative cross-sectional serosurvey in two communes in the Ouest Department of Haiti. We found lower levels of circulating IgG and IgA antibodies against V. cholerae lipopolysaccharide (LPS, IgG and IgA p<0.0001) in those below 5 years of age compared to those five years and older. Among a subset of patients with higher titers of antibodies, we were unable to detect any functional (vibriocidal) antibodies. In conclusion, the lack of detectable functional antibodies, and age-discordant levels of V. cholerae LPS IgG, suggest that populations in Haiti may be highly susceptible to cholera disease, especially among young children.
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Affiliation(s)
- Christy H. Clutter
- Division of Infectious Disease, University of Utah, Salt Lake City, Utah, USA
- Division of Microbiology & Immunology, University of Utah, Salt Lake City, Utah, USA
| | - Molly B. Klarman
- University of Florida, Departments of Pediatrics and Environmental and Global Health, Gainesville, Florida, USA
| | - Youseline Cajusma
- University of Florida, Departments of Pediatrics and Environmental and Global Health, Gainesville, Florida, USA
| | - Emilie T. Cato
- University of Florida, Departments of Pediatrics and Environmental and Global Health, Gainesville, Florida, USA
| | - Abu Sayeed
- University of Florida, Departments of Pediatrics and Environmental and Global Health, Gainesville, Florida, USA
| | - Lindsey Brinkley
- University of Florida, Departments of Pediatrics and Environmental and Global Health, Gainesville, Florida, USA
| | - Owen Jensen
- Division of Microbiology & Immunology, University of Utah, Salt Lake City, Utah, USA
| | | | - V. Madsen Beau De Rochars
- Department of Health Services Research, Management and Policy, School of Public Health and Health Professions, University of Florida, Gainesville, Florida, USA
| | - Andrew S. Azman
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Maureen T. Long
- Department of Comparative Diagnostic and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
- University of Florida, Emerging Pathogens Institute, Gainesville, Florida, USA
| | - Derek Cummings
- Department of Comparative Diagnostic and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
- University of Florida, Emerging Pathogens Institute, Gainesville, Florida, USA
| | - Daniel T. Leung
- Division of Infectious Disease, University of Utah, Salt Lake City, Utah, USA
- Division of Microbiology & Immunology, University of Utah, Salt Lake City, Utah, USA
| | - Eric J. Nelson
- Department of Comparative Diagnostic and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
- University of Florida, Emerging Pathogens Institute, Gainesville, Florida, USA
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7
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Abstract
Natural and human-made disasters can cause tremendous physical damage, societal change, and suffering. In addition to their effects on people, disasters have been shown to alter the microbial population in the area affected. Alterations for microbial populations can lead to new ecological interactions, with additional potentially adverse consequences for many species, including humans. Disaster-related stressors can be powerful forces for microbial selection. Studying microbial adaptation in disaster sites can reveal new biological processes, including mechanisms by which some microbes could become pathogenic and others could become beneficial (e.g., used for bioremediation). Here we survey examples of how disasters have affected microbiology and suggest that the topic of "disaster microbiology" is itself a new field of study. Given the accelerating pace of human-caused climate change and the increasing encroachment of the natural word by human activities, it is likely that this area of research will become increasingly relevant to the broader field of microbiology. Since disaster microbiology is a broad term open to interpretation, we propose criteria for what phenomena fall under its scope. The basic premise is that there must be a disaster that causes a change in the environment, which then causes an alteration to microbes (either a physical or biological adaptation), and that this adaptation must have additional ramifications.
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8
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Markwalter CF, Menya D, Wesolowski A, Esimit D, Lokoel G, Kipkoech J, Freedman E, Sumner KM, Abel L, Ambani G, Meredith HR, Taylor SM, Obala AA, O'Meara WP. Plasmodium falciparum importation does not sustain malaria transmission in a semi-arid region of Kenya. PLOS GLOBAL PUBLIC HEALTH 2022; 2:e0000807. [PMID: 36962553 PMCID: PMC10021402 DOI: 10.1371/journal.pgph.0000807] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 07/17/2022] [Indexed: 11/19/2022]
Abstract
Human movement impacts the spread and transmission of infectious diseases. Recently, a large reservoir of Plasmodium falciparum malaria was identified in a semi-arid region of northwestern Kenya historically considered unsuitable for malaria transmission. Understanding the sources and patterns of transmission attributable to human movement would aid in designing and targeting interventions to decrease the unexpectedly high malaria burden in the region. Toward this goal, polymorphic parasite genes (ama1, csp) in residents and passengers traveling to Central Turkana were genotyped by amplicon deep sequencing. Genotyping and epidemiological data were combined to assess parasite importation. The contribution of travel to malaria transmission was estimated by modelling case reproductive numbers inclusive and exclusive of travelers. P. falciparum was detected in 6.7% (127/1891) of inbound passengers, including new haplotypes which were later detected in locally-transmitted infections. Case reproductive numbers approximated 1 and did not change when travelers were removed from transmission networks, suggesting that transmission is not fueled by travel to the region but locally endemic. Thus, malaria is not only prevalent in Central Turkana but also sustained by local transmission. As such, interrupting importation is unlikely to be an effective malaria control strategy on its own, but targeting interventions locally has the potential to drive down transmission.
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Affiliation(s)
| | - Diana Menya
- School of Public Health, Moi University College of Health Sciences, Eldoret, Kenya
| | - Amy Wesolowski
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Daniel Esimit
- Department of Health Services and Sanitation, Turkana County, Kenya
| | - Gilchrist Lokoel
- Department of Health Services and Sanitation, Turkana County, Kenya
| | - Joseph Kipkoech
- Academic Model Providing Access to Healthcare, Eldoret, Kenya
| | - Elizabeth Freedman
- Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Kelsey M Sumner
- Duke University School of Medicine, Durham, North Carolina, United States of America
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Lucy Abel
- Academic Model Providing Access to Healthcare, Eldoret, Kenya
| | - George Ambani
- Academic Model Providing Access to Healthcare, Eldoret, Kenya
| | - Hannah R Meredith
- Duke Global Health Institute, Durham, North Carolina, United States of America
| | - Steve M Taylor
- Duke Global Health Institute, Durham, North Carolina, United States of America
- Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Andrew A Obala
- School of Medicine, Moi University College of Health Sciences, Eldoret, Kenya
| | - Wendy P O'Meara
- Duke Global Health Institute, Durham, North Carolina, United States of America
- Duke University School of Medicine, Durham, North Carolina, United States of America
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9
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Chaufan C, Dutescu IA, Fekre H, Marzabadi S, Noh KJ. The military as a neglected pathogen transmitter, from the nineteenth century to COVID-19: a systematic review. Glob Health Res Policy 2021; 6:48. [PMID: 34893071 PMCID: PMC8661370 DOI: 10.1186/s41256-021-00232-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 11/17/2021] [Indexed: 12/02/2022] Open
Abstract
Background The risk of outbreaks escalating into pandemics has soared with globalization. Therefore, understanding transmission mechanisms of infectious diseases has become critical to formulating global public health policy. This systematic review assessed evidence in the medical and public health literature for the military as a disease vector. Methods We searched 3 electronic databases without temporal restrictions. Two researchers independently extracted study data using a standardized form. Through team discussions, studies were grouped according to their type of transmission mechanism and direct quotes were extracted to generate themes and sub-themes. A content analysis was later performed and frequency distributions for each theme were generated. Results Of 6477 studies, 210 met our inclusion criteria and provided evidence, spanning over two centuries (1810–2020), for the military as a pathogen transmitter, within itself or between it and civilians. Biological mechanisms driving transmission included person-to-person transmission, contaminated food and water, vector-borne, and airborne routes. Contaminated food and/or water were the most common biological transmission route. Social mechanisms facilitating transmission included crowded living spaces, unhygienic conditions, strenuous working, training conditions, absent or inadequate vaccination programs, pressure from military leadership, poor compliance with public health advice, contractor mismanagement, high-risk behaviours, and occupation-specific freedom of movement. Living conditions were the most common social transmission mechanism, with young, low ranking military personnel repeatedly reported as the most affected group. Selected social mechanisms, such as employment-related freedom of movement, were unique to the military as a social institution. While few studies explicitly studied civilian populations, considerably more contained information that implied that civilians were likely impacted by outbreaks described in the military. Conclusions This study identified features of the military that pose a significant threat to global health, especially to civilian health in countries with substantial military presence or underdeveloped health systems. While biological transmission mechanisms are shared by other social groups, selected social transmission mechanisms are unique to the military. As an increasingly interconnected world faces the challenges of COVID-19 and future infectious diseases, the identified features of the military may exacerbate current and similar challenges and impair attempts to implement successful and equitable global public health policies. Supplementary Information The online version contains supplementary material available at 10.1186/s41256-021-00232-0.
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Affiliation(s)
| | | | - Hanah Fekre
- Faculty of Health, York University, Toronto, Canada.
| | | | - K J Noh
- Independent Scholar, Oakland, USA
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Ogisma L, Li T, Xiao H, O'Donnell F, Molnar J. Analysis of community-level factors contributing to cholera infection and water testing access in the Northern Corridor of Haiti. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2021; 93:1819-1828. [PMID: 34036666 DOI: 10.1002/wer.1591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/14/2021] [Accepted: 05/13/2021] [Indexed: 06/12/2023]
Abstract
Vibrio cholera, the bacteria that cause cholera, is endemic in Haiti with a presence in both cities and remote areas. Improved access to drinking water testing and treatment in remote areas may reduce the impact of the disease. This case study uses correlation and regression analysis to identify the main factors that hinder access to water testing and that lead to high cholera infection rates among communities in the Northern Corridor of Haiti. Poor road conditions, mountainous terrain, and limited transportation options lead to high travel times up to 5.7 min/km between remote communities and drinking water testing facilities. The presence of springs in a community has a significant positive correlation with cholera infection rates in the Northern Corridor. However, socioeconomic factors had no significant correlation with cholera infection rate. The results of this study will be used to plan the implementation of a new drinking water testing laboratory near the city of Cap-Haitian and other programs for vulnerable remote areas. PRACTITIONER POINTS: Topography and road conditions may be more important than distance in determining the accessibility of water testing facilities for rural communities. A lack of access to private vehicles is a substantial challenge for many rural communities in accessing water testing. The presence of springs in a community had a significant positive correlation with cholera infection rate.
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Affiliation(s)
- Lonege Ogisma
- Department of Civil and Environmental Engineering, Auburn University, Auburn, AL, USA
| | - Tonghui Li
- Department of Civil and Environmental Engineering, Auburn University, Auburn, AL, USA
| | - Han Xiao
- Department of Civil and Environmental Engineering, Auburn University, Auburn, AL, USA
| | - Frances O'Donnell
- Department of Civil and Environmental Engineering, Auburn University, Auburn, AL, USA
| | - Joseph Molnar
- Department of Agricultural Economics and Rural Sociology, Auburn University, Auburn, AL, USA
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11
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Arima Y, Kanou K, Arashiro T, K Ko Y, Otani K, Tsuchihashi Y, Takahashi T, Miyahara R, Sunagawa T, Suzuki M. Epidemiology of Coronavirus Disease 2019 in Japan: Descriptive Findings and Lessons Learned through Surveillance during the First Three Waves. JMA J 2021; 4:198-206. [PMID: 34414313 PMCID: PMC8355718 DOI: 10.31662/jmaj.2021-0043] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 03/22/2021] [Indexed: 11/09/2022] Open
Abstract
Introduction Coronavirus disease 2019 (COVID-19) has caused unprecedented global morbidity and mortality. Japan has faced three epidemic "waves" of COVID-19 from early 2020 through early 2021. Here we narratively review the three waves in Japan, describe the key epidemiologic features of COVID-19, and discuss lessons learned. Methods We assessed publicly available surveillance data, routine surveillance reports, and other relevant sources-multiple indicators were monitored to improve interpretation of surveillance data. Weekly trends for each wave were described based on the number of case notifications; number of tests performed; proportion of those tests that were positive for the novel coronavirus; the prevalent number of COVID-19 hospitalizations (total hospitalizations and those categorized as severe); and number of COVID-19 deaths. For each indicator and wave, we recorded the first calendar week to show an increase over two consecutive previous weeks, along with the peak week. Results The spring wave was characterized by detection of cases imported from China, followed by notifications of sporadic cases without travel history, clusters, and mild/asymptomatic cases. The summer wave saw a large increase in notifications and a younger age distribution, but in the context of increased testing with lower test positivity. The winter wave brought considerable morbidity and mortality, surpassing the cumulative case counts and fatalities from the earlier waves, with high peak values. Overall, relative to the first wave, the burden of severe outcomes was lower in the second and higher in the third wave, but varied by prefecture. In all three waves, severe outcomes peaked after notification counts and test positivity peaked; severe outcomes were also consistently skewed toward the elderly. Conclusions Important lessons were learned from each wave and across waves-some aspects remained constant, while others changed over time. In order to rapidly detect an increase in incidence, continuous, timely, and sensitive surveillance-using multiple information sources with careful interpretations-will be key in COVID-19 control.
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Affiliation(s)
- Yuzo Arima
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kazuhiko Kanou
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takeshi Arashiro
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yura K Ko
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kanako Otani
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yuuki Tsuchihashi
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takuri Takahashi
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Reiko Miyahara
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tomimasa Sunagawa
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Motoi Suzuki
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
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12
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Efthimiou G, Tucker NP. Microbes Against Humanity, a workshop game for horrible students: using a creative card game in higher education microbiology teaching. Access Microbiol 2021; 3:000186. [PMID: 34151143 PMCID: PMC8209641 DOI: 10.1099/acmi.0.000186] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 11/16/2020] [Indexed: 01/15/2023] Open
Abstract
Introducing creative workshops in higher education curricula, in addition to formal lectures, is an excellent way of reinforcing knowledge and encouraging creative thinking. In particular, the use of card games as a tool for inducing student engagement and enthusiasm has been reported to be a very effective approach. Here, we report an innovative card game-based workshop for use at the intermediate undergraduate level. The name of the game is Microbes Against Humanity and has been adapted from the widely known party game Cards Against Humanity, which is freely available under a creative commons licence. Overall, 64 students and two academics participated in this 2 h workshop. Our students found the workshop to be very enjoyable, considered it to be helpful for their learning and suggested interesting ideas for further improvement. In conclusion, it was shown that such exciting workshops can trigger students’ enthusiasm for microbiology and enhance their learning potential.
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Affiliation(s)
- Georgios Efthimiou
- Department of Biomedical and Forensic Sciences, Hardy Building, University of Hull, Cottingham Road, Hull HU6 7RX, UK
| | - Nicholas P Tucker
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK
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13
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Forshey BM, Woodward A, Sanchez JL, Petzing SR. Military Participation in Health Security: Analysis of Joint External Evaluation Reports and National Action Plans for Health Security. Health Secur 2021; 19:173-182. [PMID: 33719585 DOI: 10.1089/hs.2020.0030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Militaries around the world play an important but at times poorly defined and underappreciated role in global health security. They are often called upon to support civilian authorities in humanitarian crises and to provide routine healthcare for civilians. Military personnel are a unique population in a health security context, as they are highly mobile and often deploy to austere settings domestically and internationally, which may increase exposure to endemic and emerging infectious diseases. Despite the role of militaries, few studies have systematically evaluated their involvement in global health security activities including the Global Health Security Agenda. We analyzed Joint External Evaluation (JEE) mission reports (n = 94) and National Action Plan for Health Security plans (n = 12), published as of July 2020, to determine the extent to which military organizations were involved in the evaluation process, military involvement in health security activities were described, and specific recommendations were provided for the country's military. For JEE reports, descriptions of military involvement were highest in 3 of the 4 core areas: Respond (76%), Prevent (39%), and Detect (32%). Similarly, National Action Plan for Health Security plans mentioned military involvement in the same 3 core areas: Respond (58%), Prevent (33%), and Detect (33%). Only 28% of JEE reports provided recommendations for the military in any of the core areas. Our results indicate that military roles and contributions are incorporated into some aspects of country-level health security activities, but that more extensive involvement may be warranted to improve national capabilities to prevent, detect, and respond to infectious disease threats.
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Affiliation(s)
- Brett M Forshey
- Brett M. Forshey, PhD, is a US Public Health Service Officer and an Epidemiologist and Alexandra Woodward, MPH, is a Senior Biosurveillance Specialist, Global Emerging Infections Surveillance; and Jose L. Sanchez, MD, is Deputy Chief; all with the Armed Forces Health Surveillance Division, Silver Spring, MD. Alexandra Woodward is also a Senior Biosurveillance Specialist, Cherokee Nation Strategic Programs, Tulsa, OK; and a DrPH Health Security Student, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD. Stephanie R. Petzing, PhD, is Senior Global Health Security Advisor, Henry M. Jackson Foundation, Center for Global Health Engagement, Bethesda, MD. The views expressed in this article are those of the authors and do not reflect the official policy or position of the US Department of Defense or of the US government
| | - Alexandra Woodward
- Brett M. Forshey, PhD, is a US Public Health Service Officer and an Epidemiologist and Alexandra Woodward, MPH, is a Senior Biosurveillance Specialist, Global Emerging Infections Surveillance; and Jose L. Sanchez, MD, is Deputy Chief; all with the Armed Forces Health Surveillance Division, Silver Spring, MD. Alexandra Woodward is also a Senior Biosurveillance Specialist, Cherokee Nation Strategic Programs, Tulsa, OK; and a DrPH Health Security Student, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD. Stephanie R. Petzing, PhD, is Senior Global Health Security Advisor, Henry M. Jackson Foundation, Center for Global Health Engagement, Bethesda, MD. The views expressed in this article are those of the authors and do not reflect the official policy or position of the US Department of Defense or of the US government
| | - Jose L Sanchez
- Brett M. Forshey, PhD, is a US Public Health Service Officer and an Epidemiologist and Alexandra Woodward, MPH, is a Senior Biosurveillance Specialist, Global Emerging Infections Surveillance; and Jose L. Sanchez, MD, is Deputy Chief; all with the Armed Forces Health Surveillance Division, Silver Spring, MD. Alexandra Woodward is also a Senior Biosurveillance Specialist, Cherokee Nation Strategic Programs, Tulsa, OK; and a DrPH Health Security Student, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD. Stephanie R. Petzing, PhD, is Senior Global Health Security Advisor, Henry M. Jackson Foundation, Center for Global Health Engagement, Bethesda, MD. The views expressed in this article are those of the authors and do not reflect the official policy or position of the US Department of Defense or of the US government
| | - Stephanie R Petzing
- Brett M. Forshey, PhD, is a US Public Health Service Officer and an Epidemiologist and Alexandra Woodward, MPH, is a Senior Biosurveillance Specialist, Global Emerging Infections Surveillance; and Jose L. Sanchez, MD, is Deputy Chief; all with the Armed Forces Health Surveillance Division, Silver Spring, MD. Alexandra Woodward is also a Senior Biosurveillance Specialist, Cherokee Nation Strategic Programs, Tulsa, OK; and a DrPH Health Security Student, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD. Stephanie R. Petzing, PhD, is Senior Global Health Security Advisor, Henry M. Jackson Foundation, Center for Global Health Engagement, Bethesda, MD. The views expressed in this article are those of the authors and do not reflect the official policy or position of the US Department of Defense or of the US government
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Fraulin G, Lee S, Bartels SA. 'They came with cholera when they were tired of killing us with bullets': Community perceptions of the 2010 origin of Haiti's cholera epidemic. Glob Public Health 2021; 17:738-752. [PMID: 33600731 DOI: 10.1080/17441692.2021.1887315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
In 2010 following a catastrophic earthquake, Haiti saw the beginning of what would become the world's largest cholera epidemic. Nepalese United Nations peacekeepers were later implicated as the source of cholera. Our research examines Haitian community beliefs and perceptions, six-and-a-half years after the outbreak began, regarding the origin of Haiti's cholera outbreak. A narrative capture tool was used to record micronarratives of Haitian participants surrounding ten United Nations bases across Haiti. Seventy-seven micronarratives focused on cholera were selected for qualitative analysis from a larger dataset. Three themes emerged: who introduced cholera to Haiti, how cholera was introduced to Haiti, and preventative measures against cholera. With varying levels of confidence, the origins of the epidemic were conceptualised as directly resulting from the actions of the United Nations and Nepalese peacekeepers, exhibiting a distrust of foreign intervention in Haiti and frustration with inadequate water and sanitation infrastructure that facilitated widespread transmission of cholera. This study reinforces the need for additional transparent communication from the UN to address ongoing misconceptions surrounding the cholera outbreak, action to clean water and sanitation practices in Haiti, and for the voices of Haitian citizens to be heard and included in reforming foreign aid delivery in the country.
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Affiliation(s)
- Georgia Fraulin
- Faculty of Arts and Science, Queen's University, Kingston, Canada
| | - Sabine Lee
- Department of History, University of Birmingham, Birmingham, UK
| | - Susan A Bartels
- Department of Emergency Medicine, Queen's University, Kingston, Canada.,Department of Public Health Sciences, Queen's University, Kingston, Canada
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15
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López-Vélez R, Presotto D. Cholera in travellers: improving vaccination guidance in Europe. J Travel Med 2021; 28:6032632. [PMID: 33313739 DOI: 10.1093/jtm/taaa209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 10/28/2020] [Accepted: 10/30/2020] [Indexed: 11/13/2022]
Abstract
BACKGROUND Cholera is endemic in ~50 countries worldwide and remains a disease associated with poverty, causing illness and death in the poorest and most vulnerable people. In travellers, cholera is considered a low-incidence disease, but the true impact on travellers is difficult to assess. Cholera vaccination may improve safety for certain European travellers at risk. Effective vaccines are available; however, vaccination recommendations in Europe vary considerably between countries. METHODS In this review, a comparison of cholera vaccination recommendations from 29 advice reference bodies across key European countries (United Kingdom, Germany, Spain, Italy, Portugal, Switzerland, Sweden, Finland, Norway, France and Denmark) is presented. The differences in perceived cholera risk are highlighted, and a comparison with the United States Centers for Disease Control and Prevention (CDC) recommendations is included. RESULTS In general terms, the recommendations from European organizations are ambiguous and differ widely. This contrasts with the situation in the United States, where the CDC publishes a consistent set of guidelines. CONCLUSION With the ease of intra-European travel, it would seem sensible to harmonize the recommendations for cholera vaccination and risk perception across Europe, providing pre-travel health advisers with a trusted source of information that allows them to provide consistent recommendations.
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Affiliation(s)
- Rogelio López-Vélez
- National Referral Unit for Tropical Diseases, Infectious Diseases Department, Ramon y Cajal University Hospital, Madrid, Spain
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16
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Invisible epidemics: ethics and asymptomatic infection. Monash Bioeth Rev 2020; 38:1-16. [PMID: 33326062 PMCID: PMC7738616 DOI: 10.1007/s40592-020-00123-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/18/2020] [Indexed: 11/08/2022]
Abstract
Interactions between microbes and human hosts can lead to a wide variety of possible outcomes including benefits to the host, asymptomatic infection, disease (which can be more or less severe), and/or death. Whether or not they themselves eventually develop disease, asymptomatic carriers can often transmit disease-causing pathogens to others. This phenomenon has a range of ethical implications for clinical medicine, public health, and infectious disease research. The implications of asymptomatic infection are especially significant in situations where, and/or to the extent that, the microbe in question is transmissible, potentially harmful, and/or untreatable. This article reviews the history and concept of asymptomatic infection, and relevant ethical issues associated with this phenomenon. It illustrates the role and ethical significance of asymptomatic infection in outbreaks, epidemics, and pandemics–including recent crises involving drug resistance, Zika, and Covid19. Serving as the Introduction to this Special Issue of Monash Bioethics Review, it also provides brief summaries of the other articles comprising this collection.
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Abstract
Vibrio is a large and diverse genus of bacteria, of which most are nonpathogenic species found in the aquatic environment. However, a subset of the Vibrio genus includes several species that are highly pathogenic, either to humans or to aquatic animals. In recent years, Danio rerio, commonly known as the zebrafish, has emerged as a major animal model used for studying nearly every aspect of biology, including infectious diseases. Zebrafish are especially useful because the embryos are transparent, larvae are small and facilitate imaging studies, and numerous transgenic fish strains have been constructed. Zebrafish models for several pathogenic Vibrio species have been described, and indeed a fish model is highly relevant for the study of aquatic bacterial pathogens. Here, we summarize the zebrafish models that have been used to study pathogenic Vibrio species to date.
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Affiliation(s)
- Dhrubajyoti Nag
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Dustin A Farr
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Madison G Walton
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Jeffrey H Withey
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, Michigan, USA
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18
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Liang KYH, Orata FD, Islam MT, Nasreen T, Alam M, Tarr CL, Boucher YF. A Vibrio cholerae Core Genome Multilocus Sequence Typing Scheme To Facilitate the Epidemiological Study of Cholera. J Bacteriol 2020; 202:e00086-20. [PMID: 32540931 PMCID: PMC7685551 DOI: 10.1128/jb.00086-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 06/07/2020] [Indexed: 12/11/2022] Open
Abstract
Core genome multilocus sequence typing (cgMLST) has gained popularity in recent years in epidemiological research and subspecies-level classification. cgMLST retains the intuitive nature of traditional MLST but offers much greater resolution by utilizing significantly larger portions of the genome. Here, we introduce a cgMLST scheme for Vibrio cholerae, a bacterium abundant in marine and freshwater environments and the etiologic agent of cholera. A set of 2,443 core genes ubiquitous in V. cholerae were used to analyze a comprehensive data set of 1,262 clinical and environmental strains collected from 52 countries, including 65 newly sequenced genomes in this study. We established a sublineage threshold based on 133 allelic differences that creates clusters nearly identical to traditional MLST types, providing backwards compatibility to new cgMLST classifications. We also defined an outbreak threshold based on seven allelic differences that is capable of identifying strains from the same outbreak and closely related isolates that could give clues on outbreak origin. Using cgMLST, we confirmed the South Asian origin of modern epidemics and identified clustering affinity among sublineages of environmental isolates from the same geographic origin. Advantages of this method are highlighted by direct comparison with existing classification methods, such as MLST and single-nucleotide polymorphism-based methods. cgMLST outperforms all existing methods in terms of resolution, standardization, and ease of use. We anticipate this scheme will serve as a basis for a universally applicable and standardized classification system for V. cholerae research and epidemiological surveillance in the future. This cgMLST scheme is publicly available on PubMLST (https://pubmlst.org/vcholerae/).IMPORTANCE Toxigenic Vibrio cholerae isolates of the O1 and O139 serogroups are the causative agents of cholera, an acute diarrheal disease that plagued the world for centuries, if not millennia. Here, we introduce a core genome multilocus sequence typing scheme for V. cholerae Using this scheme, we have standardized the definition for subspecies-level classification, facilitating global collaboration in the surveillance of V. cholerae In addition, this typing scheme allows for quick identification of outbreak-related isolates that can guide subsequent analyses, serving as an important first step in epidemiological research. This scheme is also easily scalable to analyze thousands of isolates at various levels of resolution, making it an invaluable tool for large-scale ecological and evolutionary analyses.
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Affiliation(s)
- Kevin Y H Liang
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Fabini D Orata
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | | | - Tania Nasreen
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Munirul Alam
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Cheryl L Tarr
- Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Yann F Boucher
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- Singapore Center for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
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19
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The evolution of bacterial pathogens in the Anthropocene. INFECTION GENETICS AND EVOLUTION 2020; 86:104611. [PMID: 33130070 DOI: 10.1016/j.meegid.2020.104611] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 10/23/2020] [Accepted: 10/27/2020] [Indexed: 12/18/2022]
Abstract
Humankind has become a primary driver of global environmental and climate change. The extent of planetary change is such that it has been proposed to classify the current geological age as the 'Anthropocene'. Anthropogenic environmental degradation presents numerous threats to human health and wellbeing, including an increased risk of infectious disease. This review focuses on how processes such as pollution, climate change and human-mediated dispersal could affect the evolution of bacterial pathogens. Effects of environmental change on the 'big five' of evolution: mutation rate, recombination (horizontal gene transfer), migration, selection and drift are discussed. Microplastic pollution is used as a case study to highlight the combined effects of some of these processes on the evolutionary diversification of human pathogens. Although the evidence is still incomplete, a picture is emerging that environmental pathogens could evolve at increased rates in the Anthropocene, with potential consequences for human infection.
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20
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Lee EC, Chao DL, Lemaitre JC, Matrajt L, Pasetto D, Perez-Saez J, Finger F, Rinaldo A, Sugimoto JD, Halloran ME, Longini IM, Ternier R, Vissieres K, Azman AS, Lessler J, Ivers LC. Achieving coordinated national immunity and cholera elimination in Haiti through vaccination: a modelling study. Lancet Glob Health 2020; 8:e1081-e1089. [PMID: 32710864 PMCID: PMC7738665 DOI: 10.1016/s2214-109x(20)30310-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 02/17/2020] [Accepted: 05/06/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Cholera was introduced into Haiti in 2010. Since then, more than 820 000 cases and nearly 10 000 deaths have been reported. Oral cholera vaccine (OCV) is safe and effective, but has not been seen as a primary tool for cholera elimination due to a limited period of protection and constrained supplies. Regionally, epidemic cholera is contained to the island of Hispaniola, and the lowest numbers of cases since the epidemic began were reported in 2019. Hence, Haiti may represent a unique opportunity to eliminate cholera with OCV. METHODS In this modelling study, we assessed the probability of elimination, time to elimination, and percentage of cases averted with OCV campaign scenarios in Haiti through simulations from four modelling teams. For a 10-year period from January 19, 2019, to Jan 13, 2029, we compared a no vaccination scenario with five OCV campaign scenarios that differed in geographical scope, coverage, and rollout duration. Teams used weekly department-level reports of suspected cholera cases from the Haiti Ministry of Public Health and Population to calibrate the models and used common vaccine-related assumptions, but other model features were determined independently. FINDINGS Among campaigns with the same vaccination coverage (70% fully vaccinated), the median probability of elimination after 5 years was 0-18% for no vaccination, 0-33% for 2-year campaigns focused in the two departments with the highest historical incidence, 0-72% for three-department campaigns, and 35-100% for nationwide campaigns. Two-department campaigns averted a median of 12-58% of infections, three-department campaigns averted 29-80% of infections, and national campaigns averted 58-95% of infections. Extending the national campaign to a 5-year rollout (compared to a 2-year rollout), reduced the probability of elimination to 0-95% and the proportion of cases averted to 37-86%. INTERPRETATION Models suggest that the probability of achieving zero transmission of Vibrio cholerae in Haiti with current methods of control is low, and that bolder action is needed to promote elimination of cholera from the region. Large-scale cholera vaccination campaigns in Haiti would offer the opportunity to synchronise nationwide immunity, providing near-term population protection while improvements to water and sanitation promote long-term cholera elimination. FUNDING Bill & Melinda Gates Foundation, Global Good Fund, Institute for Disease Modeling, Swiss National Science Foundation, and US National Institutes of Health.
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Affiliation(s)
- Elizabeth C Lee
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Joseph C Lemaitre
- Laboratory of Ecohydrology, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Laura Matrajt
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Damiano Pasetto
- Laboratory of Ecohydrology, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University of Venice, Venice, Italy
| | - Javier Perez-Saez
- Laboratory of Ecohydrology, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Flavio Finger
- Centre for Mathematical Modelling of Infectious Diseases and Department for Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Andrea Rinaldo
- Laboratory of Ecohydrology, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Jonathan D Sugimoto
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - M Elizabeth Halloran
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Ira M Longini
- Department of Biostatistics, College of Public Health and Health Professions, and Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Ralph Ternier
- Partners In Health/Zanmi Lasante, Port-au-Prince, Haiti
| | | | - Andrew S Azman
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Justin Lessler
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Louise C Ivers
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA; Center for Global Health, Massachusetts General Hospital, Boston, MA, USA.
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21
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Deen J, Mengel MA, Clemens JD. Epidemiology of cholera. Vaccine 2020; 38 Suppl 1:A31-A40. [DOI: 10.1016/j.vaccine.2019.07.078] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 07/06/2019] [Accepted: 07/24/2019] [Indexed: 12/12/2022]
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22
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Bastaraud A, Cecchi P, Handschumacher P, Altmann M, Jambou R. Urbanization and Waterborne Pathogen Emergence in Low-Income Countries: Where and How to Conduct Surveys? INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17020480. [PMID: 31940838 PMCID: PMC7013806 DOI: 10.3390/ijerph17020480] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 12/16/2019] [Accepted: 12/20/2019] [Indexed: 11/29/2022]
Abstract
A major forthcoming sanitary issue concerns the apparition and spreading of drug-resistant microorganisms, potentially threatening millions of humans. In low-income countries, polluted urban runoff and open sewage channels are major sources of microbes. These microbes join natural microbial communities in aquatic ecosystems already impacted by various chemicals, including antibiotics. These composite microbial communities must adapt to survive in such hostile conditions, sometimes promoting the selection of antibiotic-resistant microbial strains by gene transfer. The low probability of exchanges between planktonic microorganisms within the water column may be significantly improved if their contact was facilitated by particular meeting places. This could be specifically the case within biofilms that develop on the surface of the myriads of floating macroplastics increasingly polluting urban tropical surface waters. Moreover, as uncultivable bacterial strains could be involved, analyses of the microbial communities in their whole have to be performed. This means that new-omic technologies must be routinely implemented in low- and middle-income countries to detect the appearance of resistance genes in microbial ecosystems, especially when considering the new ‘plastic context.’ We summarize the related current knowledge in this short review paper to anticipate new strategies for monitoring and surveying microbial communities.
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Affiliation(s)
- Alexandra Bastaraud
- Laboratoire d’Hygiène des Aliments et de l’Environnement, Institut Pasteur de Madagascar, BP 1274, Antananarivo 101, Madagascar;
| | - Philippe Cecchi
- MARBEC (IRD, IFREMER, UM2 and CNRS), University Montpellier, 34095 Montpellier, France;
- Centre de Recherche Océanologique (CRO), Abidjan BPV 18, Ivory Coast
| | - Pascal Handschumacher
- IRD UMR 912 SESSTIM, INSERM-IRD-Université de Marseille II, 13000 Marseille, France;
| | - Mathias Altmann
- ISPED Université Victor Segalen Bordeaux II, 146 rue Leo Saignat, 33076 Bordeaux cedex, France;
| | - Ronan Jambou
- Département de Parasitologie et des insectes vecteurs, Institut Pasteur Paris, 75015 Paris, France
- Correspondence: ; Tel.: +33-622-10-72-96
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Guillaume Y, Raymond M, Jerome GJ, Ternier R, Ivers LC. 'It was a ravage!': lived experiences of epidemic cholera in rural Haiti. BMJ Glob Health 2019; 4:e001834. [PMID: 31798994 PMCID: PMC6861088 DOI: 10.1136/bmjgh-2019-001834] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/11/2019] [Accepted: 09/21/2019] [Indexed: 11/03/2022] Open
Abstract
Introduction A cholera epidemic began in Haiti over 8 years ago, prompting numerous, largely quantitative research studies. Assessments of local 'knowledge, attitudes and practices' relevant for cholera control have relied primarily on cross-sectional surveys. The voices of affected Haitians have rarely been elevated in the scientific literature on the topic. Methods We undertook focus groups with stakeholders in the Artibonite region of Haiti in 2011, as part of planning for a public health intervention to control cholera at the height of the epidemic. In this study, we coded and analysed themes from 55 community members in five focus groups, focusing on local experiences of cholera and responses to the prevention messages. Results The majority of participants had a personal experience with cholera and described its spread in militaristic terms, as a disease that 'attacked' individuals, 'ravaged' communities and induced fear. Pre-existing structural deficiencies were identified as increasing the risk of illness and death. Knowledge of public health messages coincided with some improvements in water treatment and handwashing, but not changes in open defecation in their community, and was sometimes associated with self-blame or shame. Most participants cited constrained resources, and a minority listed individual neglect, for inconsistent or unimproved practices. Conclusion The experience of epidemic cholera in a rural Haitian community at the beginning of a major outbreak included a high burden and was exacerbated by poverty, which increased risk while hindering practice of known prevention messages. To interrupt cholera transmission, public health education must be paired with investments in structural improvements that expand access to prevention and healthcare services.
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Affiliation(s)
- Yodeline Guillaume
- Center for Global Health, Massachusetts General Hospital, Boston, Massachusetts, USA
| | | | | | | | - Louise C Ivers
- Center for Global Health, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, USA
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Phelps MD, Simonsen L, Jensen PKM. Individual and household exposures associated with cholera transmission in case–control studies: a systematic review. Trop Med Int Health 2019; 24:1151-1168. [DOI: 10.1111/tmi.13293] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Matthew D. Phelps
- Copenhagen Center for Disaster Research, Department of Public Health, Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark
| | - Lone Simonsen
- Department of Science and Environment Roskilde University Roskilde Denmark
| | - Peter K. M. Jensen
- Copenhagen Center for Disaster Research, Department of Public Health, Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark
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25
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Rao MC. Physiology of Electrolyte Transport in the Gut: Implications for Disease. Compr Physiol 2019; 9:947-1023. [PMID: 31187895 DOI: 10.1002/cphy.c180011] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We now have an increased understanding of the genetics, cell biology, and physiology of electrolyte transport processes in the mammalian intestine, due to the availability of sophisticated methodologies ranging from genome wide association studies to CRISPR-CAS technology, stem cell-derived organoids, 3D microscopy, electron cryomicroscopy, single cell RNA sequencing, transgenic methodologies, and tools to manipulate cellular processes at a molecular level. This knowledge has simultaneously underscored the complexity of biological systems and the interdependence of multiple regulatory systems. In addition to the plethora of mammalian neurohumoral factors and their cross talk, advances in pyrosequencing and metagenomic analyses have highlighted the relevance of the microbiome to intestinal regulation. This article provides an overview of our current understanding of electrolyte transport processes in the small and large intestine, their regulation in health and how dysregulation at multiple levels can result in disease. Intestinal electrolyte transport is a balance of ion secretory and ion absorptive processes, all exquisitely dependent on the basolateral Na+ /K+ ATPase; when this balance goes awry, it can result in diarrhea or in constipation. The key transporters involved in secretion are the apical membrane Cl- channels and the basolateral Na+ -K+ -2Cl- cotransporter, NKCC1 and K+ channels. Absorption chiefly involves apical membrane Na+ /H+ exchangers and Cl- /HCO3 - exchangers in the small intestine and proximal colon and Na+ channels in the distal colon. Key examples of our current understanding of infectious, inflammatory, and genetic diarrheal diseases and of constipation are provided. © 2019 American Physiological Society. Compr Physiol 9:947-1023, 2019.
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Affiliation(s)
- Mrinalini C Rao
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, Illinois, USA
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26
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Mari L, Casagrandi R, Bertuzzo E, Rinaldo A, Gatto M. Conditions for transient epidemics of waterborne disease in spatially explicit systems. ROYAL SOCIETY OPEN SCIENCE 2019; 6:181517. [PMID: 31218018 PMCID: PMC6549988 DOI: 10.1098/rsos.181517] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 03/12/2019] [Indexed: 05/06/2023]
Abstract
Waterborne diseases are a diverse family of infections transmitted through ingestion of-or contact with-water infested with pathogens. Outbreaks of waterborne infections often show well-defined spatial signatures that are typically linked to local eco-epidemiological conditions, water-mediated pathogen transport and human mobility. In this work, we apply a spatially explicit network model describing the transmission cycle of waterborne pathogens to determine invasion conditions in metacommunities endowed with a realistic spatial structure. Specifically, we aim to define conditions under which pathogens can temporarily colonize a set of human communities, thus triggering a transient epidemic outbreak. To that end, we apply generalized reactivity analysis, a recently developed methodological framework for the study of transient dynamics in ecological systems subject to external perturbations. The study of pathogen invasion is complemented by the detection of the spatial signatures associated with the perturbations to a disease-free system that are expected to be amplified the most over different time scales. Understanding the drivers of waterborne disease dynamics over time scales that are relevant to epidemic and/or endemic transmission is a crucial, cross-disciplinary challenge, as large portions of the developing world still struggle to cope with the burden of these infections.
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Affiliation(s)
- Lorenzo Mari
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, 20133 Milano, Italy
- Author for correspondence: Lorenzo Mari e-mail:
| | - Renato Casagrandi
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, 20133 Milano, Italy
| | - Enrico Bertuzzo
- Dipartimento di Scienze Ambientali, Informatica e Statistica, Università Ca’ Foscari Venezia, 30170 Venezia Mestre, Italy
| | - Andrea Rinaldo
- Laboratory of Ecohydrology, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
- Dipartimento ICEA, Università di Padova, 35131 Padova, Italy
| | - Marino Gatto
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, 20133 Milano, Italy
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Implications of converging conflicts, emergencies, and mass gatherings for global health security. LANCET GLOBAL HEALTH 2019; 6:e834-e835. [PMID: 30012261 DOI: 10.1016/s2214-109x(18)30256-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Accepted: 05/04/2018] [Indexed: 01/19/2023]
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Lemaitre J, Pasetto D, Perez-Saez J, Sciarra C, Wamala JF, Rinaldo A. Rainfall as a driver of epidemic cholera: Comparative model assessments of the effect of intra-seasonal precipitation events. Acta Trop 2019; 190:235-243. [PMID: 30465744 DOI: 10.1016/j.actatropica.2018.11.013] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 11/04/2018] [Accepted: 11/14/2018] [Indexed: 01/18/2023]
Abstract
The correlation between cholera epidemics and climatic drivers, in particular seasonal tropical rainfall, has been studied in a variety of contexts owing to its documented relevance. Several mechanistic models of cholera transmission have included rainfall as a driver by focusing on two possible transmission pathways: either by increasing exposure to contaminated water (e.g. due to worsening sanitary conditions during water excess), or water contamination by freshly excreted bacteria (e.g. due to washout of open-air defecation sites or overflows). Our study assesses the explanatory power of these different modeling structures by formal model comparison using deterministic and stochastic models of the type susceptible-infected-recovered-bacteria (SIRB). The incorporation of rainfall effects is generalized using a nonlinear function that can increase or decrease the relative importance of the large precipitation events. Our modelling framework is tested against the daily epidemiological data collected during the 2015 cholera outbreak within the urban context of Juba, South Sudan. This epidemic is characterized by a particular intra-seasonal double peak on the incidence in apparent relation with particularly strong rainfall events. Our results show that rainfall-based models in both their deterministic and stochastic formulations outperform models that do not account for rainfall. In fact, classical SIRB models are not able to reproduce the second epidemiological peak, thus suggesting that it was rainfall-driven. Moreover we found stronger support across model types for rainfall acting on increased exposure rather than on exacerbated water contamination. Although these results are context-specific, they stress the importance of a systematic and comprehensive appraisal of transmission pathways and their environmental forcings when embarking in the modelling of epidemic cholera.
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Affiliation(s)
- Joseph Lemaitre
- Laboratory of Ecohydrology, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Damiano Pasetto
- Laboratory of Ecohydrology, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Javier Perez-Saez
- Laboratory of Ecohydrology, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Carla Sciarra
- Dipartimento di Ingegneria dell'Ambiente, del Territorio e delle Infrastrutture, Politecnico di Torino, Corso Duca degli Abruzzi, 24, 10129 Torino, Italy.
| | | | - Andrea Rinaldo
- Laboratory of Ecohydrology, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland; Dipartimento ICEA, Università di Padova, 35100 Padova, Italy.
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Pierson L, Millum J. Health Research Priority Setting: The Duties of Individual Funders. THE AMERICAN JOURNAL OF BIOETHICS : AJOB 2018; 18:6-17. [PMID: 30475176 DOI: 10.1080/15265161.2018.1523490] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The vast majority of health research resources are used to study conditions that affect a small, advantaged portion of the global population. This distribution has been widely criticized as inequitable and threatens to exacerbate health disparities. However, there has been little systematic work on what individual health research funders ought to do in response. In this article, we analyze the general and special duties of research funders to the different populations that might benefit from health research. We assess how these duties apply to governmental, multilateral, nonprofit, and for-profit organizations. We thereby derive a framework for how different types of funders should take the beneficiaries of research into account when they allocate scarce research resources.
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Pérez-Losada M, Arenas M, Castro-Nallar E. Microbial sequence typing in the genomic era. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2018; 63:346-359. [PMID: 28943406 PMCID: PMC5908768 DOI: 10.1016/j.meegid.2017.09.022] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 09/18/2017] [Accepted: 09/19/2017] [Indexed: 12/18/2022]
Abstract
Next-generation sequencing (NGS), also known as high-throughput sequencing, is changing the field of microbial genomics research. NGS allows for a more comprehensive analysis of the diversity, structure and composition of microbial genes and genomes compared to the traditional automated Sanger capillary sequencing at a lower cost. NGS strategies have expanded the versatility of standard and widely used typing approaches based on nucleotide variation in several hundred DNA sequences and a few gene fragments (MLST, MLVA, rMLST and cgMLST). NGS can now accommodate variation in thousands or millions of sequences from selected amplicons to full genomes (WGS, NGMLST and HiMLST). To extract signals from high-dimensional NGS data and make valid statistical inferences, novel analytic and statistical techniques are needed. In this review, we describe standard and new approaches for microbial sequence typing at gene and genome levels and guidelines for subsequent analysis, including methods and computational frameworks. We also present several applications of these approaches to some disciplines, namely genotyping, phylogenetics and molecular epidemiology.
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Affiliation(s)
- Marcos Pérez-Losada
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Ashburn, VA 20147, USA; CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão 4485-661, Portugal; Children's National Medical Center, Washington, DC 20010, USA.
| | - Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain
| | - Eduardo Castro-Nallar
- Universidad Andrés Bello, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biológicas, Santiago 8370146, Chile
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31
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Polio priority countries and the 2018 Hajj: Leveraging an opportunity. Travel Med Infect Dis 2018; 25:3-5. [PMID: 30096355 DOI: 10.1016/j.tmaid.2018.08.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 08/06/2018] [Indexed: 11/20/2022]
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Abstract
Vibrio is a genus of ubiquitous bacteria found in a wide variety of aquatic and marine habitats; of the >100 described Vibrio spp., ~12 cause infections in humans. Vibrio cholerae can cause cholera, a severe diarrhoeal disease that can be quickly fatal if untreated and is typically transmitted via contaminated water and person-to-person contact. Non-cholera Vibrio spp. (for example, Vibrio parahaemolyticus, Vibrio alginolyticus and Vibrio vulnificus) cause vibriosis - infections normally acquired through exposure to sea water or through consumption of raw or undercooked contaminated seafood. Non-cholera bacteria can lead to several clinical manifestations, most commonly mild, self-limiting gastroenteritis, with the exception of V. vulnificus, an opportunistic pathogen with a high mortality that causes wound infections that can rapidly lead to septicaemia. Treatment for Vibrio spp. infection largely depends on the causative pathogen: for example, rehydration therapy for V. cholerae infection and debridement of infected tissues for V. vulnificus-associated wound infections, with antibiotic therapy for severe cholera and systemic infections. Although cholera is preventable and effective oral cholera vaccines are available, outbreaks can be triggered by natural or man-made events that contaminate drinking water or compromise access to safe water and sanitation. The incidence of vibriosis is rising, perhaps owing in part to the spread of Vibrio spp. favoured by climate change and rising sea water temperature.
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Jutla A, Khan R, Colwell R. Natural Disasters and Cholera Outbreaks: Current Understanding and Future Outlook. Curr Environ Health Rep 2018; 4:99-107. [PMID: 28130661 DOI: 10.1007/s40572-017-0132-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
PURPOSE OF REVIEW Diarrheal diseases remain a serious global public health threat, especially for those populations lacking access to safe water and sanitation infrastructure. Although association of several diarrheal diseases, e.g., cholera, shigellosis, etc., with climatic processes has been documented, the global human population remains at heightened risk of outbreak of diseases after natural disasters, such as earthquakes, floods, or droughts. In this review, cholera was selected as a signature diarrheal disease and the role of natural disasters in triggering and transmitting cholera was analyzed. RECENT FINDINGS Key observations include identification of an inherent feedback loop that includes societal structure, prevailing climatic processes, and spatio-temporal seasonal variability of natural disasters. Data obtained from satellite-based remote sensing are concluded to have application, although limited, in predicting risks of a cholera outbreak(s). We argue that with the advent of new high spectral and spatial resolution data, earth observation systems should be seamlessly integrated in a decision support mechanism to be mobilize resources when a region suffers a natural disaster. A framework is proposed that can be used to assess the impact of natural disasters with response to outbreak of cholera, providing assessment of short- and long-term influence of climatic processes on disease outbreaks.
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Affiliation(s)
- Antarpreet Jutla
- Human Health and Hydro-environmental Sustainability Simulation Laboratory, Department of Civil and Environmental Engineering, West Virginia University, Morgantown, WV, 26505, USA.
| | - Rakibul Khan
- Human Health and Hydro-environmental Sustainability Simulation Laboratory, Department of Civil and Environmental Engineering, West Virginia University, Morgantown, WV, 26505, USA
| | - Rita Colwell
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742, USA.,Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, 20742, USA
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Abstract
Cholera was a major global scourge in the 19th century, with frequent large-scale epidemics in European cities primarily originating in the Indian subcontinent. John Snow conducted pioneering investigations on cholera epidemics in England and particularly in London in 1854 in which he demonstrated that contaminated water was the key source of the epidemics. His thorough investigation of an epidemic in the Soho district of London led to his conclusion that contaminated water from the Broad Street pump was the source of the disease and, consequently, the removal of the handle led to cessation of the epidemic. He further studied cholera in London homes that were receiving water from two water supply systems; one from the sewage contaminated portion of the Thames River and the other that drew its water upstream from an uncontaminated part of the river. Rates of infection among clients of the distribution system drawing contaminated water far exceeded the, rates among those served by the company whose water intake was from above the contaminated section of the river. This demonstration reinforced the goals of the sanitation movement, which developed sewage drainage systems and water purification systems in cities and towns in the following decades, therewith vastly reducing the threats of cholera, typhoid and many other waterborne diseases. Despite progress being made globally, the public health problems of waterborne disease, including cholera, are by no means gone today, even in high-income countries. The tragic introduction of cholera after the earthquake devastation in Haiti in 2010 resulted in many thousands of cases and deaths from cholera indicating the still-present dangers of diseases spread into disaster situations. Cholera and other waterborne diseases remain some of the heaviest burdens of disease and death in low-income countries, especially after natural disasters or warfare as in Yemen in 2017 and are continuing challenges for global health.
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Phelps MD, Azman AS, Lewnard JA, Antillón M, Simonsen L, Andreasen V, Jensen PKM, Pitzer VE. The importance of thinking beyond the water-supply in cholera epidemics: A historical urban case-study. PLoS Negl Trop Dis 2017; 11:e0006103. [PMID: 29176791 PMCID: PMC5720805 DOI: 10.1371/journal.pntd.0006103] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 12/07/2017] [Accepted: 11/07/2017] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Planning interventions to respond to cholera epidemics requires an understanding of the major transmission routes. Interrupting short-cycle (household, foodborne) transmission may require different approaches as compared long-cycle (environmentally-mediated/waterborne) transmission. However, differentiating the relative contribution of short- and long-cycle routes has remained difficult, and most cholera outbreak control efforts focus on interrupting long-cycle transmission. Here we use high-resolution epidemiological and municipal infrastructure data from a cholera outbreak in 1853 Copenhagen to explore the relative contribution of short- and long-cycle transmission routes during a major urban epidemic. METHODOLOGY/PRINCIPAL FINDINGS We fit a spatially explicit time-series meta-population model to 6,552 physician-reported cholera cases from Copenhagen in 1853. We estimated the contribution of long-cycle waterborne transmission between neighborhoods using historical municipal water infrastructure data, fitting the force of infection from hydraulic flow, then comparing model performance. We found the epidemic was characterized by considerable transmission heterogeneity. Some neighborhoods acted as localized transmission hotspots, while other neighborhoods were less affected or important in driving the epidemic. We found little evidence to support long-cycle transmission between hydrologically-connected neighborhoods. Collectively, these findings suggest short-cycle transmission was significant. CONCLUSIONS/SIGNIFICANCE Spatially targeted cholera interventions, such as reactive vaccination or sanitation/hygiene campaigns in hotspot neighborhoods, would likely have been more effective in this epidemic than control measures aimed at interrupting long-cycle transmission, such as improving municipal water quality. We recommend public health planners consider programs aimed at interrupting short-cycle transmission as essential tools in the cholera control arsenal.
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Affiliation(s)
- Matthew D. Phelps
- Copenhagen Center for Disaster Research (COPE), Department of Public Health, Faculty of Health and Medical Sciences, Copenhagen, Denmark
| | - Andrew S. Azman
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Joseph A. Lewnard
- Center for Communicable Disease Dynamics, Harvard TH Chan School of Public Health, Boston, MA, United States of America
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Marina Antillón
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Lone Simonsen
- Copenhagen Center for Disaster Research (COPE), Department of Public Health, Faculty of Health and Medical Sciences, Copenhagen, Denmark
| | - Viggo Andreasen
- Department of Science and the Environment, Roskilde University, Roskilde, Denmark
| | - Peter K. M. Jensen
- Copenhagen Center for Disaster Research (COPE), Department of Public Health, Faculty of Health and Medical Sciences, Copenhagen, Denmark
| | - 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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Khan R, Anwar R, Akanda S, McDonald MD, Huq A, Jutla A, Colwell R. Assessment of Risk of Cholera in Haiti following Hurricane Matthew. Am J Trop Med Hyg 2017; 97:896-903. [PMID: 28749774 DOI: 10.4269/ajtmh.17-0048] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Damage to the inferior and fragile water and sanitation infrastructure of Haiti after Hurricane Matthew has created an urgent public health emergency in terms of likelihood of cholera occurring in the human population. Using satellite-derived data on precipitation, gridded air temperature, and hurricane path and with information on water and sanitation (WASH) infrastructure, we tracked changing environmental conditions conducive for growth of pathogenic vibrios. Based on these data, we predicted and validated the likelihood of cholera cases occurring past hurricane. The risk of cholera in the southwestern part of Haiti remained relatively high since November 2016 to the present. Findings of this study provide a contemporary process for monitoring ground conditions that can guide public health intervention to control cholera in human population by providing access to vaccines, safe WASH facilities. Assuming current social and behavioral patterns remain constant, it is recommended that WASH infrastructure should be improved and considered a priority especially before 2017 rainy season.
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Affiliation(s)
- Rakib Khan
- Department of Civil and Environmental Engineering, West Virginia University, Morgantown, West Virginia
| | - Rifat Anwar
- Department of Civil and Environmental Engineering, West Virginia University, Morgantown, West Virginia
| | - Shafqat Akanda
- Department of Civil and Environmental Engineering, University of Rhode Island, Kingston, Rhode Island
| | - Michael D McDonald
- Global Health Response and Resilience Alliance, Washington, District of Columbia; Health Initiatives Foundation, Inc., Washington, District of Columbia
| | - Anwar Huq
- Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland
| | - Antarpreet Jutla
- Department of Civil and Environmental Engineering, West Virginia University, Morgantown, West Virginia
| | - Rita Colwell
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland.,Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland.,Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland
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Petkau A, Mabon P, Sieffert C, Knox NC, Cabral J, Iskander M, Iskander M, Weedmark K, Zaheer R, Katz LS, Nadon C, Reimer A, Taboada E, Beiko RG, Hsiao W, Brinkman F, Graham M, Van Domselaar G. SNVPhyl: a single nucleotide variant phylogenomics pipeline for microbial genomic epidemiology. Microb Genom 2017; 3:e000116. [PMID: 29026651 PMCID: PMC5628696 DOI: 10.1099/mgen.0.000116] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 04/12/2017] [Indexed: 11/18/2022] Open
Abstract
The recent widespread application of whole-genome sequencing (WGS) for microbial disease investigations has spurred the development of new bioinformatics tools, including a notable proliferation of phylogenomics pipelines designed for infectious disease surveillance and outbreak investigation. Transitioning the use of WGS data out of the research laboratory and into the front lines of surveillance and outbreak response requires user-friendly, reproducible and scalable pipelines that have been well validated. Single Nucleotide Variant Phylogenomics (SNVPhyl) is a bioinformatics pipeline for identifying high-quality single-nucleotide variants (SNVs) and constructing a whole-genome phylogeny from a collection of WGS reads and a reference genome. Individual pipeline components are integrated into the Galaxy bioinformatics framework, enabling data analysis in a user-friendly, reproducible and scalable environment. We show that SNVPhyl can detect SNVs with high sensitivity and specificity, and identify and remove regions of high SNV density (indicative of recombination). SNVPhyl is able to correctly distinguish outbreak from non-outbreak isolates across a range of variant-calling settings, sequencing-coverage thresholds or in the presence of contamination. SNVPhyl is available as a Galaxy workflow, Docker and virtual machine images, and a Unix-based command-line application. SNVPhyl is released under the Apache 2.0 license and available at http://snvphyl.readthedocs.io/ or at https://github.com/phac-nml/snvphyl-galaxy.
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Affiliation(s)
- Aaron Petkau
- 1National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada
| | - Philip Mabon
- 1National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada
| | - Cameron Sieffert
- 1National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada
| | - Natalie C Knox
- 1National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada
| | - Jennifer Cabral
- 1National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada
| | | | - Mark Iskander
- 2University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Kelly Weedmark
- 3Health Canada - Bureau of Microbial Hazards, Ottawa, ON K1A 0K9, Canada
| | - Rahat Zaheer
- 4Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, Canada
| | - Lee S Katz
- 5Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Celine Nadon
- 1National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada
| | - Aleisha Reimer
- 1National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada
| | - Eduardo Taboada
- 1National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada
| | | | - William Hsiao
- 7BC Public Health Microbiology and Reference Laboratory, Vancouver, BC V5Z 4R4, Canada
| | | | - Morag Graham
- 1National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada
| | - Gary Van Domselaar
- 1National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada
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Frerichs RR. Disease Maps, History, and More. Am J Public Health 2017; 107:633-635. [DOI: 10.2105/ajph.2017.303734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Ralph R. Frerichs
- Ralph R. Frerichs is professor emeritus with the Department of Epidemiology, University of California, Los Angeles Fielding School of Public Health
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Ronholm J, Nasheri N, Petronella N, Pagotto F. Navigating Microbiological Food Safety in the Era of Whole-Genome Sequencing. Clin Microbiol Rev 2016; 29:837-57. [PMID: 27559074 PMCID: PMC5010751 DOI: 10.1128/cmr.00056-16] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The epidemiological investigation of a foodborne outbreak, including identification of related cases, source attribution, and development of intervention strategies, relies heavily on the ability to subtype the etiological agent at a high enough resolution to differentiate related from nonrelated cases. Historically, several different molecular subtyping methods have been used for this purpose; however, emerging techniques, such as single nucleotide polymorphism (SNP)-based techniques, that use whole-genome sequencing (WGS) offer a resolution that was previously not possible. With WGS, unlike traditional subtyping methods that lack complete information, data can be used to elucidate phylogenetic relationships and disease-causing lineages can be tracked and monitored over time. The subtyping resolution and evolutionary context provided by WGS data allow investigators to connect related illnesses that would be missed by traditional techniques. The added advantage of data generated by WGS is that these data can also be used for secondary analyses, such as virulence gene detection, antibiotic resistance gene profiling, synteny comparisons, mobile genetic element identification, and geographic attribution. In addition, several software packages are now available to generate in silico results for traditional molecular subtyping methods from the whole-genome sequence, allowing for efficient comparison with historical databases. Metagenomic approaches using next-generation sequencing have also been successful in the detection of nonculturable foodborne pathogens. This review addresses state-of-the-art techniques in microbial WGS and analysis and then discusses how this technology can be used to help support food safety investigations. Retrospective outbreak investigations using WGS are presented to provide organism-specific examples of the benefits, and challenges, associated with WGS in comparison to traditional molecular subtyping techniques.
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Affiliation(s)
- J Ronholm
- Bureau of Microbial Hazards, Food Directorate, Health Canada, Ottawa, ON, Canada
| | - Neda Nasheri
- Bureau of Microbial Hazards, Food Directorate, Health Canada, Ottawa, ON, Canada
| | - Nicholas Petronella
- Biostatistics and Modelling Division, Bureau of Food Surveillance and Science Integration, Food Directorate, Health Canada, Ottawa, ON, Canada
| | - Franco Pagotto
- Bureau of Microbial Hazards, Food Directorate, Health Canada, Ottawa, ON, Canada Listeriosis Reference Centre, Bureau of Microbial Hazards, Food Directorate, Health Canada, Ottawa, ON, Canada
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Abstract
The number of large-scale genomics projects is increasing due to the availability of affordable high-throughput sequencing (HTS) technologies. The use of HTS for bacterial infectious disease research is attractive because one whole-genome sequencing (WGS) run can replace multiple assays for bacterial typing, molecular epidemiology investigations, and more in-depth pathogenomic studies. The computational resources and bioinformatics expertise required to accommodate and analyze the large amounts of data pose new challenges for researchers embarking on genomics projects for the first time. Here, we present a comprehensive overview of a bacterial genomics projects from beginning to end, with a particular focus on the planning and computational requirements for HTS data, and provide a general understanding of the analytical concepts to develop a workflow that will meet the objectives and goals of HTS projects.
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Did point-of-use drinking water strategies for children change in the Dominican Republic during a cholera epidemic? Public Health 2016; 138:57-62. [PMID: 27080584 DOI: 10.1016/j.puhe.2016.03.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 03/03/2016] [Accepted: 03/07/2016] [Indexed: 11/22/2022]
Abstract
OBJECTIVE Point-of-use (POU) strategies to improve drinking water, particularly chlorination, are promoted within cholera epidemics when centrally delivered safe drinking water is lacking. Most studies examining POU practices during cholera epidemics have relied on single cross-sectional studies which are limited for assessing behavioural changes. This study examined POU practices in a community over time during a cholera outbreak. STUDY DESIGN Secondary data analysis of existing dataset. METHODS During attendance at well-baby clinics serving a low-income peri-urban community in the Dominican Republic, mothers had been routinely asked, using a structured questionnaire, about POU strategies used for drinking water for their children. Frequency distribution of reported practices was determined over a 21 month period during the cholera outbreak on the island of Hispaniola. RESULTS An estimated 27.8% of children were reported to have had some exposure to untreated tap water. Unsustained reductions in exposure to untreated tap water were noted early in the epidemic. POU chlorination was infrequent and showed no significant or sustained increases over the study time period. CONCLUSION High reliance on bottled water, consistent with national household patterns prior to the cholera outbreak, may have reduced the perceived need for POU chlorination. Examination of the safety of relying on bottled water during cholera outbreaks is needed. Additionally, further inquiries are needed to understand variation in POU practices both during and beyond cholera outbreaks.
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Abstract
Big Data has increasingly been promoted as a revolutionary development in the future of science, including epidemiology. However, the definition and implications of Big Data for epidemiology remain unclear. We here provide a working definition of Big Data predicated on the so-called "three V's": variety, volume, and velocity. From this definition, we argue that Big Data has evolutionary and revolutionary implications for identifying and intervening on the determinants of population health. We suggest that as more sources of diverse data become publicly available, the ability to combine and refine these data to yield valid answers to epidemiologic questions will be invaluable. We conclude that while epidemiology as practiced today will continue to be practiced in the Big Data future, a component of our field's future value lies in integrating subject matter knowledge with increased technical savvy. Our training programs and our visions for future public health interventions should reflect this future.
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Bentley SD, Parkhill J. Genomic perspectives on the evolution and spread of bacterial pathogens. Proc Biol Sci 2015; 282:20150488. [PMID: 26702036 PMCID: PMC4707741 DOI: 10.1098/rspb.2015.0488] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 05/19/2015] [Indexed: 12/22/2022] Open
Abstract
Since the first complete sequencing of a free-living organism, Haemophilus influenzae, genomics has been used to probe both the biology of bacterial pathogens and their evolution. Single-genome approaches provided information on the repertoire of virulence determinants and host-interaction factors, and, along with comparative analyses, allowed the proposal of hypotheses to explain the evolution of many of these traits. These analyses suggested many bacterial pathogens to be of relatively recent origin and identified genome degradation as a key aspect of host adaptation. The advent of very-high-throughput sequencing has allowed for detailed phylogenetic analysis of many important pathogens, revealing patterns of global and local spread, and recent evolution in response to pressure from therapeutics and the human immune system. Such analyses have shown that bacteria can evolve and transmit very rapidly, with emerging clones showing adaptation and global spread over years or decades. The resolution achieved with whole-genome sequencing has shown considerable benefits in clinical microbiology, enabling accurate outbreak tracking within hospitals and across continents. Continued large-scale sequencing promises many further insights into genetic determinants of drug resistance, virulence and transmission in bacterial pathogens.
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Affiliation(s)
- Stephen D Bentley
- The Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Julian Parkhill
- The Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
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Cholera and blame in Haiti. THE LANCET. INFECTIOUS DISEASES 2015; 15:1380-1. [DOI: 10.1016/s1473-3099(15)00411-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 10/21/2015] [Indexed: 11/17/2022]
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Allan M, Grandesso F, Pierre R, Magloire R, Coldiron M, Martinez-Pino I, Goffeau T, Gitenet R, François G, Olson D, Porten K, Luquero FJ. High-resolution spatial analysis of cholera patients reported in Artibonite department, Haiti in 2010-2011. Epidemics 2015; 14:1-10. [PMID: 26972509 DOI: 10.1016/j.epidem.2015.08.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 08/25/2015] [Accepted: 08/26/2015] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Cholera is caused by Vibrio cholerae, and is transmitted through fecal-oral contact. Infection occurs after the ingestion of the bacteria and is usually asymptomatic. In a minority of cases, it causes acute diarrhea and vomiting, which can lead to potentially fatal severe dehydration, especially in the absence of appropriate medical care. Immunity occurs after infection and typically lasts 6-36 months. Cholera is responsible for outbreaks in many African and Asian developing countries, and caused localised and episodic epidemics in South America until the early 1990s. Haiti, despite its low socioeconomic status and poor sanitation, had never reported cholera before the recent outbreak that started in October 2010, with over 720,000 cases and over 8700 deaths (Case fatality rate: 1.2%) through 8 december 2014. So far, this outbreak has seen 3 epidemic peaks, and it is expected that cholera will remain in Haiti for some time. METHODOLOGY/FINDINGS To trace the path of the early epidemic and to identify hot spots and potential transmission hubs during peaks, we examined the spatial distribution of cholera patients during the first two peaks in Artibonite, the second-most populous department of Haiti. We extracted the geographic origin of 84,000 patients treated in local health facilities between October 2010 and December 2011 and mapped these addresses to 63 rural communal sections and 9 urban cities. Spatial and cluster analysis showed that during the first peak, cholera spread along the Artibonite River and the main roads, and sub-communal attack rates ranged from 0.1% to 10.7%. During the second peak, remote mountain areas were most affected, although sometimes to very different degrees even in closely neighboring locations. Sub-communal attack rates during the second peak ranged from 0.2% to 13.7%. The relative risks at the sub-communal level during the second phase showed an inverse pattern compared to the first phase. CONCLUSION/SIGNIFICANCE These findings demonstrate the value of high-resolution mapping for pinpointing locations most affected by cholera, and in the future could help prioritize the places in need of interventions such as improvement of sanitation and vaccination. The findings also describe spatio-temporal transmission patterns of the epidemic in a cholera-naïve country such as Haiti. By identifying transmission hubs, it is possible to target prevention strategies that, over time, could reduce transmission of the disease and eventually eliminate cholera in Haiti.
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Affiliation(s)
| | | | - Ronald Pierre
- Artibonite Surveillance Department, MSPP, Gonaïves, Haiti.
| | - Roc Magloire
- Surveillance Department, DELR, Port-au-Prince, Haiti.
| | | | - Isabel Martinez-Pino
- Epicentre, Paris, France; European Programme for Intervention Epidemiology Training (EPIET), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden.
| | | | | | | | - David Olson
- Médecins Sans Frontières, New York, NY, USA.
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Bengtsson L, Gaudart J, Lu X, Moore S, Wetter E, Sallah K, Rebaudet S, Piarroux R. Using mobile phone data to predict the spatial spread of cholera. Sci Rep 2015; 5:8923. [PMID: 25747871 PMCID: PMC4352843 DOI: 10.1038/srep08923] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 02/10/2015] [Indexed: 02/08/2023] Open
Abstract
Effective response to infectious disease epidemics requires focused control measures in areas predicted to be at high risk of new outbreaks. We aimed to test whether mobile operator data could predict the early spatial evolution of the 2010 Haiti cholera epidemic. Daily case data were analysed for 78 study areas from October 16 to December 16, 2010. Movements of 2.9 million anonymous mobile phone SIM cards were used to create a national mobility network. Two gravity models of population mobility were implemented for comparison. Both were optimized based on the complete retrospective epidemic data, available only after the end of the epidemic spread. Risk of an area experiencing an outbreak within seven days showed strong dose-response relationship with the mobile phone-based infectious pressure estimates. The mobile phone-based model performed better (AUC 0.79) than the retrospectively optimized gravity models (AUC 0.66 and 0.74, respectively). Infectious pressure at outbreak onset was significantly correlated with reported cholera cases during the first ten days of the epidemic (p < 0.05). Mobile operator data is a highly promising data source for improving preparedness and response efforts during cholera outbreaks. Findings may be particularly important for containment efforts of emerging infectious diseases, including high-mortality influenza strains.
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Affiliation(s)
- Linus Bengtsson
- 1] Department of Public Health Sciences. Karolinska Institutet, Stockholm, Sweden [2] Flowminder Foundation, Stockholm, Sweden
| | - Jean Gaudart
- Aix-Marseille University, UMR 912 SESSTIM (INSERM-IRD-AMU), Marseille, France
| | - Xin Lu
- 1] College of Information System and Management, National University of Defence Technology, Changsha, China [2] Department of Public Health Sciences. Karolinska Institutet, Stockholm, Sweden [3] Flowminder Foundation, Stockholm, Sweden
| | - Sandra Moore
- Aix-Marseille University, UMR MD 3, Marseille, France
| | - Erik Wetter
- 1] Flowminder Foundation, Stockholm, Sweden [2] Stockholm School of Economics, Stockholm, Sweden
| | - Kankoe Sallah
- Aix-Marseille University, UMR 912 SESSTIM (INSERM-IRD-AMU), Marseille, France
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Mari L, Bertuzzo E, Finger F, Casagrandi R, Gatto M, Rinaldo A. On the predictive ability of mechanistic models for the Haitian cholera epidemic. J R Soc Interface 2015; 12:20140840. [PMID: 25631563 PMCID: PMC4345467 DOI: 10.1098/rsif.2014.0840] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 01/02/2015] [Indexed: 12/17/2022] Open
Abstract
Predictive models of epidemic cholera need to resolve at suitable aggregation levels spatial data pertaining to local communities, epidemiological records, hydrologic drivers, waterways, patterns of human mobility and proxies of exposure rates. We address the above issue in a formal model comparison framework and provide a quantitative assessment of the explanatory and predictive abilities of various model settings with different spatial aggregation levels and coupling mechanisms. Reference is made to records of the recent Haiti cholera epidemics. Our intensive computations and objective model comparisons show that spatially explicit models accounting for spatial connections have better explanatory power than spatially disconnected ones for short-to-intermediate calibration windows, while parsimonious, spatially disconnected models perform better with long training sets. On average, spatially connected models show better predictive ability than disconnected ones. We suggest limits and validity of the various approaches and discuss the pathway towards the development of case-specific predictive tools in the context of emergency management.
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Affiliation(s)
- Lorenzo Mari
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, 20133 Milano, Italy Laboratory of Ecohydrology ECHO/IIE/ENAC, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Enrico Bertuzzo
- Laboratory of Ecohydrology ECHO/IIE/ENAC, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Flavio Finger
- Laboratory of Ecohydrology ECHO/IIE/ENAC, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Renato Casagrandi
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, 20133 Milano, Italy
| | - Marino Gatto
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, 20133 Milano, Italy
| | - Andrea Rinaldo
- Laboratory of Ecohydrology ECHO/IIE/ENAC, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland Dipartimento di Ingegneria Civile, Edile ed Ambientale, Università di Padova, 35131 Padova, Italy
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Phylodynamic analysis of clinical and environmental Vibrio cholerae isolates from Haiti reveals diversification driven by positive selection. mBio 2014; 5:mBio.01824-14. [PMID: 25538191 PMCID: PMC4278535 DOI: 10.1128/mbio.01824-14] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
UNLABELLED Phylodynamic analysis of genome-wide single-nucleotide polymorphism (SNP) data is a powerful tool to investigate underlying evolutionary processes of bacterial epidemics. The method was applied to investigate a collection of 65 clinical and environmental isolates of Vibrio cholerae from Haiti collected between 2010 and 2012. Characterization of isolates recovered from environmental samples identified a total of four toxigenic V. cholerae O1 isolates, four non-O1/O139 isolates, and a novel nontoxigenic V. cholerae O1 isolate with the classical tcpA gene. Phylogenies of strains were inferred from genome-wide SNPs using coalescent-based demographic models within a Bayesian framework. A close phylogenetic relationship between clinical and environmental toxigenic V. cholerae O1 strains was observed. As cholera spread throughout Haiti between October 2010 and August 2012, the population size initially increased and then fluctuated over time. Selection analysis along internal branches of the phylogeny showed a steady accumulation of synonymous substitutions and a progressive increase of nonsynonymous substitutions over time, suggesting diversification likely was driven by positive selection. Short-term accumulation of nonsynonymous substitutions driven by selection may have significant implications for virulence, transmission dynamics, and even vaccine efficacy. IMPORTANCE Cholera, a dehydrating diarrheal disease caused by toxigenic strains of the bacterium Vibrio cholerae, emerged in 2010 in Haiti, a country where there were no available records on cholera over the past 100 years. While devastating in terms of morbidity and mortality, the outbreak provided a unique opportunity to study the evolutionary dynamics of V. cholerae and its environmental presence. The present study expands on previous work and provides an in-depth phylodynamic analysis inferred from genome-wide single nucleotide polymorphisms of clinical and environmental strains from dispersed geographic settings in Haiti over a 2-year period. Our results indicate that even during such a short time scale, V. cholerae in Haiti has undergone evolution and diversification driven by positive selection, which may have implications for understanding the global clinical and epidemiological patterns of the disease. Furthermore, the continued presence of the epidemic strain in Haitian aquatic environments has implications for transmission.
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Weppelmann TA, Alam MT, Widmer J, Morrissey D, Rashid MH, Beau De Rochars VM, Morris JG, Ali A, Johnson JA. Feasibility of the hydrogen sulfide test for the assessment of drinking water quality in post-earthquake Haiti. ENVIRONMENTAL MONITORING AND ASSESSMENT 2014; 186:8509-8516. [PMID: 25182685 PMCID: PMC4213301 DOI: 10.1007/s10661-014-4020-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 08/21/2014] [Indexed: 05/30/2023]
Abstract
In 2010, a magnitude 7.0 earthquake struck Haiti, severely damaging the drinking and wastewater infrastructure and leaving millions homeless. Compounding this problem, the introduction of Vibrio cholerae resulted in a massive cholera outbreak that infected over 700,000 people and threatened the safety of Haiti's drinking water. To mitigate this public health crisis, non-government organizations installed thousands of wells to provide communities with safe drinking water. However, despite increased access, Haiti currently lacks the monitoring capacity to assure the microbial safety of any of its water resources. For these reasons, this study was designed to assess the feasibility of using a simple, low-cost method to detect indicators of fecal contamination of drinking water that could be implemented at the community level. Water samples from 358 sources of drinking water in the Léogâne flood basin were screened with a commercially available hydrogen sulfide test and a standard membrane method for the enumeration of thermotolerant coliforms. When compared with the gold standard method, the hydrogen sulfide test had a sensitivity of 65 % and a specificity of 93 %. While the sensitivity of the assay increased at higher fecal coliform concentrations, it never exceeded 88 %, even with fecal coliform concentrations greater than 100 colony-forming units per 100 ml. While its simplicity makes the hydrogen sulfide test attractive for assessing water quality in low-resource settings, the low sensitivity raises concerns about its use as the sole indicator of the presence or absence of fecal coliforms in individual or community water sources.
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Affiliation(s)
- Thomas A. Weppelmann
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, PO Box 100188, Gainesville, FL 32610, USA
- Emerging Pathogens Institute, University of Florida, 2055 Mowry Rd, P.O. Box 100009, Gainesville, FL 32610, USA
| | - Meer T. Alam
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, PO Box 100188, Gainesville, FL 32610, USA
- Emerging Pathogens Institute, University of Florida, 2055 Mowry Rd, P.O. Box 100009, Gainesville, FL 32610, USA
- Laboratwa Sante Piblik Christianville, Haiti
| | - Jocelyn Widmer
- Urban Affairs and Planning, School of Public and International Affairs, Virginia Tech University, 140 Otey Street, Blacksburg, VA 24061, USA
| | | | - Mohammed H. Rashid
- Emerging Pathogens Institute, University of Florida, 2055 Mowry Rd, P.O. Box 100009, Gainesville, FL 32610, USA
| | - Valery M. Beau De Rochars
- Emerging Pathogens Institute, University of Florida, 2055 Mowry Rd, P.O. Box 100009, Gainesville, FL 32610, USA
- Laboratwa Sante Piblik Christianville, Haiti
- Department of Health Services Research, Management and Policy, College of Public Health and Health Professions, University of Florida, Gainesville, FL 32610, USA
| | - J. Glenn Morris
- Emerging Pathogens Institute, University of Florida, 2055 Mowry Rd, P.O. Box 100009, Gainesville, FL 32610, USA
| | - Afsar Ali
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, PO Box 100188, Gainesville, FL 32610, USA
- Emerging Pathogens Institute, University of Florida, 2055 Mowry Rd, P.O. Box 100009, Gainesville, FL 32610, USA
| | - Judith A. Johnson
- Emerging Pathogens Institute, University of Florida, 2055 Mowry Rd, P.O. Box 100009, Gainesville, FL 32610, USA
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL 32610, USA
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Genomic epidemiology of the Haitian cholera outbreak: a single introduction followed by rapid, extensive, and continued spread characterized the onset of the epidemic. mBio 2014; 5:e01721. [PMID: 25370488 PMCID: PMC4222100 DOI: 10.1128/mbio.01721-14] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
For centuries, cholera has been one of the most feared diseases. The causative agent Vibrio cholerae is a waterborne Gram-negative enteric pathogen eliciting a severe watery diarrheal disease. In October 2010, the seventh pandemic reached Haiti, a country that had not experienced cholera for more than a century. By using whole-genome sequence typing and mapping strategies of 116 serotype O1 strains from global sources, including 44 Haitian genomes, we present a detailed reconstructed evolutionary history of the seventh pandemic with a focus on the Haitian outbreak. We catalogued subtle genomic alterations at the nucleotide level in the genome core and architectural rearrangements from whole-genome map comparisons. Isolates closely related to the Haitian isolates caused several recent outbreaks in southern Asia. This study provides evidence for a single-source introduction of cholera from Nepal into Haiti followed by rapid, extensive, and continued clonal expansion. The phylogeographic patterns in both southern Asia and Haiti argue for the rapid dissemination of V. cholerae across the landscape necessitating real-time surveillance efforts to complement the whole-genome epidemiological analysis. As eradication efforts move forward, phylogeographic knowledge will be important for identifying persistent sources and monitoring success at regional levels. The results of molecular and epidemiological analyses of this outbreak suggest that an indigenous Haitian source of V. cholerae is unlikely and that an indigenous source has not contributed to the genomic evolution of this clade. In this genomic epidemiology study, we have applied high-resolution whole-genome-based sequence typing methodologies on a comprehensive set of genome sequences that have become available in the aftermath of the Haitian cholera epidemic. These sequence resources enabled us to reassess the degree of genomic heterogeneity within the Vibrio cholerae O1 serotype and to refine boundaries and evolutionary relationships. The established phylogenomic framework showed how outbreak isolates fit into the global phylogeographic patterns compared to a comprehensive globally and temporally diverse strain collection and provides strong molecular evidence that points to a nonindigenous source of the 2010 Haitian cholera outbreak and refines epidemiological standards used in outbreak investigations for outbreak inclusion/exclusion following the concept of genomic epidemiology. The generated phylogenomic data have major public health relevance in translating sequence-based information to assist in future diagnostic, epidemiological, surveillance, and forensic studies of cholera.
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