1
|
Belman S, Pesonen H, Croucher NJ, Bentley SD, Corander J. Estimating between-country migration in pneumococcal populations. G3 (BETHESDA, MD.) 2024; 14:jkae058. [PMID: 38507601 PMCID: PMC11152062 DOI: 10.1093/g3journal/jkae058] [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: 11/22/2023] [Revised: 02/29/2024] [Accepted: 03/11/2024] [Indexed: 03/22/2024]
Abstract
Streptococcus pneumoniae (the pneumococcus) is a globally distributed, human obligate opportunistic bacterial pathogen which, although often carried commensally, is also a significant cause of invasive disease. Apart from multi-drug resistant and virulent clones, the rate and direction of pneumococcal dissemination between different countries remains largely unknown. The ability for the pneumococcus to take a foothold in a country depends on existing population configuration, the extent of vaccine implementation, as well as human mobility since it is a human obligate bacterium. To shed light on its international movement, we used extensive genome data from the Global Pneumococcal Sequencing project and estimated migration parameters between multiple countries in Africa. Data on allele frequencies of polymorphisms at housekeeping-like loci for multiple different lineages circulating in the populations of South Africa, Malawi, Kenya, and The Gambia were used to calculate the fixation index (Fst) between countries. We then further used these summaries to fit migration coalescent models with the likelihood-free inference algorithms available in the ELFI software package. Synthetic datawere additionally used to validate the inference approach. Our results demonstrate country-pair specific migration patterns and heterogeneity in the extent of migration between different lineages. Our approach demonstrates that coalescent models can be effectively used for inferring migration rates for bacterial species and lineages provided sufficiently granular population genomics surveillance data. Further, it can demonstrate the connectivity of respiratory disease agents between countries to inform intervention policy in the longer term.
Collapse
Affiliation(s)
- Sophie Belman
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Henri Pesonen
- Oslo Centre for Biostatistics and Epidemiology, Oslo University Hospital, Oslo, 0372, Norway
| | - Nicholas J Croucher
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, White City Campus, Imperial College London, London W12 0BZ, UK
| | - Stephen D Bentley
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Jukka Corander
- Department of Biostatistics, University of Oslo, Oslo, 0372, Norway
- Helsinki Institute for Information Technology HIIT, Department of Mathematics and Statistics, University of Helsinki, Espoo, Helsinki, 02150, Finland
| |
Collapse
|
2
|
Okada K, Roobthaisong A, Hamada S. Flagella-related gene mutations in Vibrio cholerae during extended cultivation in nutrient-limited media impair cell motility and prolong culturability. mSystems 2023; 8:e0010923. [PMID: 37642466 PMCID: PMC10654082 DOI: 10.1128/msystems.00109-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 04/19/2023] [Indexed: 08/31/2023] Open
Abstract
IMPORTANCE Vibrio cholerae undergoes a transition to a viable but non-culturable (VNC) state when subjected to various environmental stresses. We showed here that flagellar motility was involved in the development of the VNC state of V. cholerae. In this study, motility-defective isolates with mutations in various flagella-related genes, but not motile isolates, were predominantly obtained under the stress of long-term batch culture. Other genomic regions were highly conserved, suggesting that the mutations were selective. During the stationary phase of long-term culture, V. cholerae isolates with mutations in the acetate kinase and flagella-related genes were predominant. This study suggests that genes involved in specific functions in V. cholerae undergo mutations under certain environmental conditions.
Collapse
Affiliation(s)
- Kazuhisa Okada
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
- Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections, National Institute of Health, Nonthaburi, Thailand
| | - Amonrattana Roobthaisong
- Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections, National Institute of Health, Nonthaburi, Thailand
| | - Shigeyuki Hamada
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| |
Collapse
|
3
|
Mavian CN, Tagliamonte MS, Alam MT, Sakib SN, Cash MN, Moir M, Jimenez JP, Riva A, Nelson EJ, Cato ET, Ajayakumar J, Louis R, Curtis A, De Rochars VMB, Rouzier V, Pape JW, de Oliveira T, Morris JG, Salemi M, Ali A. Ancestral Origin and Dissemination Dynamics of Reemerging Toxigenic Vibrio cholerae, Haiti. Emerg Infect Dis 2023; 29:2072-2082. [PMID: 37735743 PMCID: PMC10521621 DOI: 10.3201/eid2910.230554] [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: 09/23/2023] Open
Abstract
The 2010 cholera epidemic in Haiti was thought to have ended in 2019, and the Prime Minister of Haiti declared the country cholera-free in February 2022. On September 25, 2022, cholera cases were again identified in Port-au-Prince. We compared genomic data from 42 clinical Vibrio cholerae strains from 2022 with data from 327 other strains from Haiti and 1,824 strains collected worldwide. The 2022 isolates were homogeneous and closely related to clinical and environmental strains circulating in Haiti during 2012-2019. Bayesian hypothesis testing indicated that the 2022 clinical isolates shared their most recent common ancestor with an environmental lineage circulating in Haiti in July 2018. Our findings strongly suggest that toxigenic V. cholerae O1 can persist for years in aquatic environmental reservoirs and ignite new outbreaks. These results highlight the urgent need for improved public health infrastructure and possible periodic vaccination campaigns to maintain population immunity against V. cholerae.
Collapse
Affiliation(s)
- Carla N. Mavian
- University of Florida, Gainesville, Florida, USA (C.N. Mavian, M.S. Tagliamonte, M.T. Alam, S.N. Sakib, M.N. Cash, J.P. Jimenez, A. Riva, E.J. Nelson, E.T. Cato, R. Louis, V.M. Beau De Rochars, J.G. Morris Jr., M. Salemi, A. Ali)
- Stellenbosch University, Stellenbosch, South Africa (M. Moir, T. de Oliveira)
- Case Western Reserve University School of Medicine, Cleveland, Ohio, USA (J. Ajayakumar, A. Curtis)
- Les Centres GHESKIO, Port-au-Prince, Haiti (V. Rouzier, J.W. Pape)
- Weill Cornell Medical College, New York, New York, USA (V. Rouzier, J.W. Pape)
- University of KwaZulu-Natal, Durban, South Africa (T. de Oliveira)
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa (T. de Oliveira)
- University of Washington, Seattle, Washington, USA (T. de Oliveira)
| | - Massimiliano S. Tagliamonte
- University of Florida, Gainesville, Florida, USA (C.N. Mavian, M.S. Tagliamonte, M.T. Alam, S.N. Sakib, M.N. Cash, J.P. Jimenez, A. Riva, E.J. Nelson, E.T. Cato, R. Louis, V.M. Beau De Rochars, J.G. Morris Jr., M. Salemi, A. Ali)
- Stellenbosch University, Stellenbosch, South Africa (M. Moir, T. de Oliveira)
- Case Western Reserve University School of Medicine, Cleveland, Ohio, USA (J. Ajayakumar, A. Curtis)
- Les Centres GHESKIO, Port-au-Prince, Haiti (V. Rouzier, J.W. Pape)
- Weill Cornell Medical College, New York, New York, USA (V. Rouzier, J.W. Pape)
- University of KwaZulu-Natal, Durban, South Africa (T. de Oliveira)
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa (T. de Oliveira)
- University of Washington, Seattle, Washington, USA (T. de Oliveira)
| | - Meer T. Alam
- University of Florida, Gainesville, Florida, USA (C.N. Mavian, M.S. Tagliamonte, M.T. Alam, S.N. Sakib, M.N. Cash, J.P. Jimenez, A. Riva, E.J. Nelson, E.T. Cato, R. Louis, V.M. Beau De Rochars, J.G. Morris Jr., M. Salemi, A. Ali)
- Stellenbosch University, Stellenbosch, South Africa (M. Moir, T. de Oliveira)
- Case Western Reserve University School of Medicine, Cleveland, Ohio, USA (J. Ajayakumar, A. Curtis)
- Les Centres GHESKIO, Port-au-Prince, Haiti (V. Rouzier, J.W. Pape)
- Weill Cornell Medical College, New York, New York, USA (V. Rouzier, J.W. Pape)
- University of KwaZulu-Natal, Durban, South Africa (T. de Oliveira)
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa (T. de Oliveira)
- University of Washington, Seattle, Washington, USA (T. de Oliveira)
| | - S. Nazmus Sakib
- University of Florida, Gainesville, Florida, USA (C.N. Mavian, M.S. Tagliamonte, M.T. Alam, S.N. Sakib, M.N. Cash, J.P. Jimenez, A. Riva, E.J. Nelson, E.T. Cato, R. Louis, V.M. Beau De Rochars, J.G. Morris Jr., M. Salemi, A. Ali)
- Stellenbosch University, Stellenbosch, South Africa (M. Moir, T. de Oliveira)
- Case Western Reserve University School of Medicine, Cleveland, Ohio, USA (J. Ajayakumar, A. Curtis)
- Les Centres GHESKIO, Port-au-Prince, Haiti (V. Rouzier, J.W. Pape)
- Weill Cornell Medical College, New York, New York, USA (V. Rouzier, J.W. Pape)
- University of KwaZulu-Natal, Durban, South Africa (T. de Oliveira)
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa (T. de Oliveira)
- University of Washington, Seattle, Washington, USA (T. de Oliveira)
| | - Melanie N. Cash
- University of Florida, Gainesville, Florida, USA (C.N. Mavian, M.S. Tagliamonte, M.T. Alam, S.N. Sakib, M.N. Cash, J.P. Jimenez, A. Riva, E.J. Nelson, E.T. Cato, R. Louis, V.M. Beau De Rochars, J.G. Morris Jr., M. Salemi, A. Ali)
- Stellenbosch University, Stellenbosch, South Africa (M. Moir, T. de Oliveira)
- Case Western Reserve University School of Medicine, Cleveland, Ohio, USA (J. Ajayakumar, A. Curtis)
- Les Centres GHESKIO, Port-au-Prince, Haiti (V. Rouzier, J.W. Pape)
- Weill Cornell Medical College, New York, New York, USA (V. Rouzier, J.W. Pape)
- University of KwaZulu-Natal, Durban, South Africa (T. de Oliveira)
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa (T. de Oliveira)
- University of Washington, Seattle, Washington, USA (T. de Oliveira)
| | - Monika Moir
- University of Florida, Gainesville, Florida, USA (C.N. Mavian, M.S. Tagliamonte, M.T. Alam, S.N. Sakib, M.N. Cash, J.P. Jimenez, A. Riva, E.J. Nelson, E.T. Cato, R. Louis, V.M. Beau De Rochars, J.G. Morris Jr., M. Salemi, A. Ali)
- Stellenbosch University, Stellenbosch, South Africa (M. Moir, T. de Oliveira)
- Case Western Reserve University School of Medicine, Cleveland, Ohio, USA (J. Ajayakumar, A. Curtis)
- Les Centres GHESKIO, Port-au-Prince, Haiti (V. Rouzier, J.W. Pape)
- Weill Cornell Medical College, New York, New York, USA (V. Rouzier, J.W. Pape)
- University of KwaZulu-Natal, Durban, South Africa (T. de Oliveira)
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa (T. de Oliveira)
- University of Washington, Seattle, Washington, USA (T. de Oliveira)
| | - Juan Perez Jimenez
- University of Florida, Gainesville, Florida, USA (C.N. Mavian, M.S. Tagliamonte, M.T. Alam, S.N. Sakib, M.N. Cash, J.P. Jimenez, A. Riva, E.J. Nelson, E.T. Cato, R. Louis, V.M. Beau De Rochars, J.G. Morris Jr., M. Salemi, A. Ali)
- Stellenbosch University, Stellenbosch, South Africa (M. Moir, T. de Oliveira)
- Case Western Reserve University School of Medicine, Cleveland, Ohio, USA (J. Ajayakumar, A. Curtis)
- Les Centres GHESKIO, Port-au-Prince, Haiti (V. Rouzier, J.W. Pape)
- Weill Cornell Medical College, New York, New York, USA (V. Rouzier, J.W. Pape)
- University of KwaZulu-Natal, Durban, South Africa (T. de Oliveira)
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa (T. de Oliveira)
- University of Washington, Seattle, Washington, USA (T. de Oliveira)
| | - Alberto Riva
- University of Florida, Gainesville, Florida, USA (C.N. Mavian, M.S. Tagliamonte, M.T. Alam, S.N. Sakib, M.N. Cash, J.P. Jimenez, A. Riva, E.J. Nelson, E.T. Cato, R. Louis, V.M. Beau De Rochars, J.G. Morris Jr., M. Salemi, A. Ali)
- Stellenbosch University, Stellenbosch, South Africa (M. Moir, T. de Oliveira)
- Case Western Reserve University School of Medicine, Cleveland, Ohio, USA (J. Ajayakumar, A. Curtis)
- Les Centres GHESKIO, Port-au-Prince, Haiti (V. Rouzier, J.W. Pape)
- Weill Cornell Medical College, New York, New York, USA (V. Rouzier, J.W. Pape)
- University of KwaZulu-Natal, Durban, South Africa (T. de Oliveira)
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa (T. de Oliveira)
- University of Washington, Seattle, Washington, USA (T. de Oliveira)
| | - Eric J. Nelson
- University of Florida, Gainesville, Florida, USA (C.N. Mavian, M.S. Tagliamonte, M.T. Alam, S.N. Sakib, M.N. Cash, J.P. Jimenez, A. Riva, E.J. Nelson, E.T. Cato, R. Louis, V.M. Beau De Rochars, J.G. Morris Jr., M. Salemi, A. Ali)
- Stellenbosch University, Stellenbosch, South Africa (M. Moir, T. de Oliveira)
- Case Western Reserve University School of Medicine, Cleveland, Ohio, USA (J. Ajayakumar, A. Curtis)
- Les Centres GHESKIO, Port-au-Prince, Haiti (V. Rouzier, J.W. Pape)
- Weill Cornell Medical College, New York, New York, USA (V. Rouzier, J.W. Pape)
- University of KwaZulu-Natal, Durban, South Africa (T. de Oliveira)
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa (T. de Oliveira)
- University of Washington, Seattle, Washington, USA (T. de Oliveira)
| | - Emilie T. Cato
- University of Florida, Gainesville, Florida, USA (C.N. Mavian, M.S. Tagliamonte, M.T. Alam, S.N. Sakib, M.N. Cash, J.P. Jimenez, A. Riva, E.J. Nelson, E.T. Cato, R. Louis, V.M. Beau De Rochars, J.G. Morris Jr., M. Salemi, A. Ali)
- Stellenbosch University, Stellenbosch, South Africa (M. Moir, T. de Oliveira)
- Case Western Reserve University School of Medicine, Cleveland, Ohio, USA (J. Ajayakumar, A. Curtis)
- Les Centres GHESKIO, Port-au-Prince, Haiti (V. Rouzier, J.W. Pape)
- Weill Cornell Medical College, New York, New York, USA (V. Rouzier, J.W. Pape)
- University of KwaZulu-Natal, Durban, South Africa (T. de Oliveira)
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa (T. de Oliveira)
- University of Washington, Seattle, Washington, USA (T. de Oliveira)
| | - Jayakrishnan Ajayakumar
- University of Florida, Gainesville, Florida, USA (C.N. Mavian, M.S. Tagliamonte, M.T. Alam, S.N. Sakib, M.N. Cash, J.P. Jimenez, A. Riva, E.J. Nelson, E.T. Cato, R. Louis, V.M. Beau De Rochars, J.G. Morris Jr., M. Salemi, A. Ali)
- Stellenbosch University, Stellenbosch, South Africa (M. Moir, T. de Oliveira)
- Case Western Reserve University School of Medicine, Cleveland, Ohio, USA (J. Ajayakumar, A. Curtis)
- Les Centres GHESKIO, Port-au-Prince, Haiti (V. Rouzier, J.W. Pape)
- Weill Cornell Medical College, New York, New York, USA (V. Rouzier, J.W. Pape)
- University of KwaZulu-Natal, Durban, South Africa (T. de Oliveira)
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa (T. de Oliveira)
- University of Washington, Seattle, Washington, USA (T. de Oliveira)
| | - Rigan Louis
- University of Florida, Gainesville, Florida, USA (C.N. Mavian, M.S. Tagliamonte, M.T. Alam, S.N. Sakib, M.N. Cash, J.P. Jimenez, A. Riva, E.J. Nelson, E.T. Cato, R. Louis, V.M. Beau De Rochars, J.G. Morris Jr., M. Salemi, A. Ali)
- Stellenbosch University, Stellenbosch, South Africa (M. Moir, T. de Oliveira)
- Case Western Reserve University School of Medicine, Cleveland, Ohio, USA (J. Ajayakumar, A. Curtis)
- Les Centres GHESKIO, Port-au-Prince, Haiti (V. Rouzier, J.W. Pape)
- Weill Cornell Medical College, New York, New York, USA (V. Rouzier, J.W. Pape)
- University of KwaZulu-Natal, Durban, South Africa (T. de Oliveira)
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa (T. de Oliveira)
- University of Washington, Seattle, Washington, USA (T. de Oliveira)
| | - Andrew Curtis
- University of Florida, Gainesville, Florida, USA (C.N. Mavian, M.S. Tagliamonte, M.T. Alam, S.N. Sakib, M.N. Cash, J.P. Jimenez, A. Riva, E.J. Nelson, E.T. Cato, R. Louis, V.M. Beau De Rochars, J.G. Morris Jr., M. Salemi, A. Ali)
- Stellenbosch University, Stellenbosch, South Africa (M. Moir, T. de Oliveira)
- Case Western Reserve University School of Medicine, Cleveland, Ohio, USA (J. Ajayakumar, A. Curtis)
- Les Centres GHESKIO, Port-au-Prince, Haiti (V. Rouzier, J.W. Pape)
- Weill Cornell Medical College, New York, New York, USA (V. Rouzier, J.W. Pape)
- University of KwaZulu-Natal, Durban, South Africa (T. de Oliveira)
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa (T. de Oliveira)
- University of Washington, Seattle, Washington, USA (T. de Oliveira)
| | - V. Madsen Beau De Rochars
- University of Florida, Gainesville, Florida, USA (C.N. Mavian, M.S. Tagliamonte, M.T. Alam, S.N. Sakib, M.N. Cash, J.P. Jimenez, A. Riva, E.J. Nelson, E.T. Cato, R. Louis, V.M. Beau De Rochars, J.G. Morris Jr., M. Salemi, A. Ali)
- Stellenbosch University, Stellenbosch, South Africa (M. Moir, T. de Oliveira)
- Case Western Reserve University School of Medicine, Cleveland, Ohio, USA (J. Ajayakumar, A. Curtis)
- Les Centres GHESKIO, Port-au-Prince, Haiti (V. Rouzier, J.W. Pape)
- Weill Cornell Medical College, New York, New York, USA (V. Rouzier, J.W. Pape)
- University of KwaZulu-Natal, Durban, South Africa (T. de Oliveira)
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa (T. de Oliveira)
- University of Washington, Seattle, Washington, USA (T. de Oliveira)
| | - Vanessa Rouzier
- University of Florida, Gainesville, Florida, USA (C.N. Mavian, M.S. Tagliamonte, M.T. Alam, S.N. Sakib, M.N. Cash, J.P. Jimenez, A. Riva, E.J. Nelson, E.T. Cato, R. Louis, V.M. Beau De Rochars, J.G. Morris Jr., M. Salemi, A. Ali)
- Stellenbosch University, Stellenbosch, South Africa (M. Moir, T. de Oliveira)
- Case Western Reserve University School of Medicine, Cleveland, Ohio, USA (J. Ajayakumar, A. Curtis)
- Les Centres GHESKIO, Port-au-Prince, Haiti (V. Rouzier, J.W. Pape)
- Weill Cornell Medical College, New York, New York, USA (V. Rouzier, J.W. Pape)
- University of KwaZulu-Natal, Durban, South Africa (T. de Oliveira)
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa (T. de Oliveira)
- University of Washington, Seattle, Washington, USA (T. de Oliveira)
| | - Jean William Pape
- University of Florida, Gainesville, Florida, USA (C.N. Mavian, M.S. Tagliamonte, M.T. Alam, S.N. Sakib, M.N. Cash, J.P. Jimenez, A. Riva, E.J. Nelson, E.T. Cato, R. Louis, V.M. Beau De Rochars, J.G. Morris Jr., M. Salemi, A. Ali)
- Stellenbosch University, Stellenbosch, South Africa (M. Moir, T. de Oliveira)
- Case Western Reserve University School of Medicine, Cleveland, Ohio, USA (J. Ajayakumar, A. Curtis)
- Les Centres GHESKIO, Port-au-Prince, Haiti (V. Rouzier, J.W. Pape)
- Weill Cornell Medical College, New York, New York, USA (V. Rouzier, J.W. Pape)
- University of KwaZulu-Natal, Durban, South Africa (T. de Oliveira)
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa (T. de Oliveira)
- University of Washington, Seattle, Washington, USA (T. de Oliveira)
| | - Tulio de Oliveira
- University of Florida, Gainesville, Florida, USA (C.N. Mavian, M.S. Tagliamonte, M.T. Alam, S.N. Sakib, M.N. Cash, J.P. Jimenez, A. Riva, E.J. Nelson, E.T. Cato, R. Louis, V.M. Beau De Rochars, J.G. Morris Jr., M. Salemi, A. Ali)
- Stellenbosch University, Stellenbosch, South Africa (M. Moir, T. de Oliveira)
- Case Western Reserve University School of Medicine, Cleveland, Ohio, USA (J. Ajayakumar, A. Curtis)
- Les Centres GHESKIO, Port-au-Prince, Haiti (V. Rouzier, J.W. Pape)
- Weill Cornell Medical College, New York, New York, USA (V. Rouzier, J.W. Pape)
- University of KwaZulu-Natal, Durban, South Africa (T. de Oliveira)
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa (T. de Oliveira)
- University of Washington, Seattle, Washington, USA (T. de Oliveira)
| | | | | | | |
Collapse
|
4
|
Taylor-Brown A, Afrad MH, Khan AI, Lassalle F, Islam MT, Tanvir NA, Thomson NR, Qadri F. Genomic epidemiology of Vibrio cholerae during a mass vaccination campaign of displaced communities in Bangladesh. Nat Commun 2023; 14:3773. [PMID: 37355673 PMCID: PMC10290697 DOI: 10.1038/s41467-023-39415-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 06/12/2023] [Indexed: 06/26/2023] Open
Abstract
Ongoing diarrheal disease surveillance throughout Bangladesh over the last decade has revealed seasonal localised cholera outbreaks in Cox's Bazar, where both Bangladeshi Nationals and Forcibly Displaced Myanmar Nationals (FDMNs) reside in densely populated settlements. FDMNs were recently targeted for the largest cholera vaccination campaign in decades. We aimed to infer the epidemic risk of circulating Vibrio cholerae strains by determining if isolates linked to the ongoing global cholera pandemic ("7PET" lineage) were responsible for outbreaks in Cox's Bazar. We found two sublineages of 7PET in this setting during the study period; one with global distribution, and a second lineage restricted to Asia and the Middle East. These subclades were associated with different disease patterns that could be partially explained by genomic differences. Here we show that as the pandemic V. cholerae lineage circulates in this vulnerable population, without a vaccine intervention, the risk of an epidemic was very high.
Collapse
Affiliation(s)
- Alyce Taylor-Brown
- Parasites & Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
| | - Mokibul Hassan Afrad
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Ashraful Islam Khan
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Florent Lassalle
- Parasites & Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Md Taufiqul Islam
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
- School of Medical Science, Griffith University, Gold Coast, QLD, Australia
| | - Nabid Anjum Tanvir
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Nicholas R Thomson
- Parasites & Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
- London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK.
| | - Firdausi Qadri
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh.
| |
Collapse
|
5
|
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.
Collapse
Affiliation(s)
| | | | | | - Jeffrey H. Withey
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI, United States
| |
Collapse
|
6
|
Hao T, Zheng W, Wu Y, Yu H, Qian X, Yang C, Zheng Z, Zhang X, Guo Y, Cui M, Wang H, Pan J, Cui Y. Population genomics implies potential public health risk of two non-toxigenic Vibrio cholerae lineages. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 112:105441. [PMID: 37146742 DOI: 10.1016/j.meegid.2023.105441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 04/28/2023] [Accepted: 04/29/2023] [Indexed: 05/07/2023]
Abstract
Diarrheal cases caused by non-toxigenic Vibrio cholerae have been reported globally. Lineages L3b and L9, characterized as ctxAB-negative and tcpA-positive (CNTP), pose the highest risk and have caused long-term epidemics in different regions worldwide. From 2001 to 2018, two waves (2001-2012 and 2013-2018) of epidemic caused by non-toxigenic V. cholerae occurred in the developed city of Hangzhou, China. In this study, through the integrated analysis of 207 genomes of Hangzhou isolates from these two waves (119 and 88) and 1573 publicly available genomes, we showed that L3b and L9 lineages together caused the second wave as had happened in the first wave, but the dominant lineage shifted from L3b (first wave: 69%) to L9 (second wave: 50%). We further found that the genotype of a key virulence gene, tcpF, in the L9 lineage during the second wave shifted to type I, which may have enhanced bacterial colonization in humans and potentially promoted the pathogenic lineage shift. Moreover, we found that 21% of L3b and L9 isolates had changed to predicted cholera toxin producers, providing evidence that gain of complete CTXφ-carrying ctxAB genes, rather than ctxAB gain in pre-CTXφ-carrying isolates, led to the transition. Taken together, our findings highlight the possible public health risk associated with L3b and L9 lineages due to their potential to cause long-term epidemics and turn into high-virulent cholera toxin producers, which necessitates a more comprehensive and unbiased sampling in further disease control efforts.
Collapse
Affiliation(s)
- Tongyu Hao
- School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui Province, China; Microbiology Laboratory, Hangzhou Center for Disease Control and Prevention, Hangzhou, Zhejiang Province, China; State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Wei Zheng
- Microbiology Laboratory, Hangzhou Center for Disease Control and Prevention, Hangzhou, Zhejiang Province, China
| | - Yarong Wu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Hua Yu
- Microbiology Laboratory, Hangzhou Center for Disease Control and Prevention, Hangzhou, Zhejiang Province, China
| | - Xiuwei Qian
- School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui Province, China; State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Chao Yang
- The Center for Microbes, Development and Health, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, China
| | - Zhibei Zheng
- Microbiology Laboratory, Hangzhou Center for Disease Control and Prevention, Hangzhou, Zhejiang Province, China
| | - Xianglilan Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yan Guo
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Mengnan Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Haoqiu Wang
- Microbiology Laboratory, Hangzhou Center for Disease Control and Prevention, Hangzhou, Zhejiang Province, China.
| | - Jingcao Pan
- Microbiology Laboratory, Hangzhou Center for Disease Control and Prevention, Hangzhou, Zhejiang Province, China.
| | - Yujun Cui
- School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui Province, China; State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.
| |
Collapse
|
7
|
Monir MM, Islam MT, Mazumder R, Mondal D, Nahar KS, Sultana M, Morita M, Ohnishi M, Huq A, Watanabe H, Qadri F, Rahman M, Thomson N, Seed K, Colwell RR, Ahmed T, Alam M. Genomic attributes of Vibrio cholerae O1 responsible for 2022 massive cholera outbreak in Bangladesh. Nat Commun 2023; 14:1154. [PMID: 36859426 PMCID: PMC9977884 DOI: 10.1038/s41467-023-36687-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 02/09/2023] [Indexed: 03/03/2023] Open
Abstract
In 2022, one of its worst cholera outbreaks began in Bangladesh and the icddr,b Dhaka hospital treated more than 1300 patients and ca. 42,000 diarrheal cases from March-1 to April-10, 20221. Here, we present genomic attributes of V. cholerae O1 responsible for the 2022 Dhaka outbreak and 960 7th pandemic El Tor (7PET) strains from 88 countries. Results show strains isolated during the Dhaka outbreak cluster with 7PET wave-3 global clade strains, but comprise subclade BD-1.2, for which the most recent common ancestor appears to be that responsible for recent endemic cholera in India. BD-1.2 strains are present in Bangladesh since 2016, but not establishing dominance over BD-2 lineage strains2 until 2018 and predominantly associated with endemic cholera. In conclusion, the recent shift in lineage and genetic attributes, including serotype switching of BD-1.2 from Ogawa to Inaba, may explain the increasing number of cholera cases in Bangladesh.
Collapse
Affiliation(s)
- Md Mamun Monir
- Infectious diseases division, icddr,b (International Centre for Diarrhoeal Disease Research, Bangladesh), Dhaka, Bangladesh
| | - Mohammad Tarequl Islam
- Infectious diseases division, icddr,b (International Centre for Diarrhoeal Disease Research, Bangladesh), Dhaka, Bangladesh
| | - Razib Mazumder
- Laboratory Sciences and Services Division, icddr,b (International Centre for Diarrhoeal Disease Research, Bangladesh), Dhaka, Bangladesh
| | - Dinesh Mondal
- Laboratory Sciences and Services Division, icddr,b (International Centre for Diarrhoeal Disease Research, Bangladesh), Dhaka, Bangladesh
| | - Kazi Sumaita Nahar
- Infectious diseases division, icddr,b (International Centre for Diarrhoeal Disease Research, Bangladesh), Dhaka, Bangladesh
| | - Marzia Sultana
- Infectious diseases division, icddr,b (International Centre for Diarrhoeal Disease Research, Bangladesh), Dhaka, Bangladesh
| | - Masatomo Morita
- Department of Bacteriology, National Institute of Infectious Diseases (NIID), Tokyo, Japan
| | - Makoto Ohnishi
- Department of Bacteriology, National Institute of Infectious Diseases (NIID), Tokyo, Japan
| | - Anwar Huq
- Maryland Pathogen Research Institute, University of Maryland, College Park, MD, USA
| | - Haruo Watanabe
- Department of Bacteriology, National Institute of Infectious Diseases (NIID), Tokyo, Japan
| | - Firdausi Qadri
- Infectious diseases division, icddr,b (International Centre for Diarrhoeal Disease Research, Bangladesh), Dhaka, Bangladesh
| | - Mustafizur Rahman
- Infectious diseases division, icddr,b (International Centre for Diarrhoeal Disease Research, Bangladesh), Dhaka, Bangladesh
| | - Nicholas Thomson
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- London School of Hygiene and Tropical Medicine, London, WC1E 7HT, United Kingdom
| | - Kimberley Seed
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Rita R Colwell
- Maryland Pathogen Research Institute, University of Maryland, College Park, MD, USA
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Tahmeed Ahmed
- Nutrition and Clinical Services Division, icddr,b (International Centre for Diarrhoeal Disease Research, Bangladesh), Dhaka, Bangladesh
| | - Munirul Alam
- Infectious diseases division, icddr,b (International Centre for Diarrhoeal Disease Research, Bangladesh), Dhaka, Bangladesh.
| |
Collapse
|
8
|
Lau DYL, Aguirre Sánchez JR, Baker-Austin C, Martinez-Urtaza J. What Whole Genome Sequencing Has Told Us About Pathogenic Vibrios. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1404:337-352. [PMID: 36792883 DOI: 10.1007/978-3-031-22997-8_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
When the first microbial genome sequences were published just 20 years ago, our understanding regarding the microbial world changed dramatically. The genomes of the first pathogenic vibrios sequenced, including Vibrio cholerae, Vibrio parahaemolyticus, and Vibrio vulnificus revealed a functional and phylogenetic diversity previously unimagined as well as a genome structure indelibly shaped by horizontal gene transfer. The initial glimpses into these organisms also revealed a genomic plasticity that allowed these bacteria to thrive in challenging and varied aquatic and marine environments, but critically also a suite of pathogenicity attributes. In this review we outline how our understanding of vibrios has changed over the last two decades with the advent of genomics and advances in bioinformatic and data analysis techniques, it has become possible to provide a more cohesive understanding regarding these bacteria: how these pathogens have evolved and emerged from environmental sources, their evolutionary routes through time and space, how they interact with other bacteria and the human host, as well as initiate disease. We outline novel approaches to the use of whole genome sequencing for this important group of bacteria and how new sequencing technologies may be applied to study these organisms in future studies.
Collapse
Affiliation(s)
- Dawn Yan Lam Lau
- Centre for Environment, Fisheries and Aquaculture (CEFAS), Weymouth, Dorset, UK
| | - Jose Roberto Aguirre Sánchez
- Centre for Environment, Fisheries and Aquaculture (CEFAS), Weymouth, Dorset, UK.,Centro de Investigación en Alimentación y Desarrollo (CIAD), Culiacán, Sinaloa, Mexico
| | - Craig Baker-Austin
- Centre for Environment, Fisheries and Aquaculture (CEFAS), Weymouth, Dorset, UK
| | - Jaime Martinez-Urtaza
- Centre for Environment, Fisheries and Aquaculture (CEFAS), Weymouth, Dorset, UK. .,Department of Genetics and Microbiology, Facultat de Biociències, Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona, Spain.
| |
Collapse
|
9
|
Balasubramanian D, López-Pérez M, Almagro-Moreno S. Cholera Dynamics and the Emergence of Pandemic Vibrio cholerae. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1404:127-147. [PMID: 36792874 DOI: 10.1007/978-3-031-22997-8_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Cholera is a severe diarrheal disease caused by the aquatic bacterium Vibrio cholerae. Interestingly, to date, only one major clade has emerged to cause pandemic disease in humans: the clade that encompasses the strains from the O1 and O139 serogroups. In this chapter, we provide a comprehensive perspective on the virulence factors and mobile genetic elements (MGEs) associated with the emergence of pandemic V. cholerae strains and highlight novel findings such as specific genomic background or interactions between MGEs that explain their confined distribution. Finally, we discuss pandemic cholera dynamics contextualizing them within the evolution of the bacterium.
Collapse
Affiliation(s)
- Deepak Balasubramanian
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA
- National Center for Integrated Coastal Research, University of Central Florida, Orlando, FL, USA
| | - Mario López-Pérez
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA
- National Center for Integrated Coastal Research, University of Central Florida, Orlando, FL, USA
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Salvador Almagro-Moreno
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA.
- National Center for Integrated Coastal Research, University of Central Florida, Orlando, FL, USA.
| |
Collapse
|
10
|
Walker LM, Haycocks JR, van Kessel JC, Dalia TN, Dalia AB, Grainger DC. A simple mechanism for integration of quorum sensing and cAMP signalling in V. cholerae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.08.527633. [PMID: 36798193 PMCID: PMC9934648 DOI: 10.1101/2023.02.08.527633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Many bacteria use quorum sensing to control changes in lifestyle. The process is regulated by microbially derived "autoinducer" signalling molecules, that accumulate in the local environment. Individual cells sense autoinducer abundance, to infer population density, and alter their behaviour accordingly. In Vibrio cholerae , quorum sensing signals are transduced by phosphorelay to the transcription factor LuxO. Unphosphorylated LuxO permits expression of HapR, which alters global gene expression patterns. In this work, we have mapped the genome-wide distribution of LuxO and HapR in V. cholerae . Whilst LuxO has a small regulon, HapR targets 32 loci. Many HapR targets coincide with sites for the cAMP receptor protein (CRP) that regulates the transcriptional response to carbon starvation. This overlap, also evident in other Vibrio species, results from similarities in the DNA sequence bound by each factor. At shared sites, HapR and CRP simultaneously contact the double helix and binding is stabilised by direct interaction of the two factors. Importantly, this involves a CRP surface that usually contacts RNA polymerase to stimulate transcription. As a result, HapR can block transcription activation by CRP. Thus, by interacting at shared sites, HapR and CRP integrate information from quorum sensing and cAMP signalling to control gene expression.
Collapse
Affiliation(s)
- Lucas M. Walker
- School of Biosciences, University of Birmingham, Edgbaston B15 2TT, UK
| | | | | | - Triana N. Dalia
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Ankur B. Dalia
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - David C. Grainger
- School of Biosciences, University of Birmingham, Edgbaston B15 2TT, UK,for correspondence: , Tel: +44 (0)121 414 5437
| |
Collapse
|
11
|
Johura FT, Biswas SR, Rashed SM, Islam MT, Islam S, Sultana M, Watanabe H, Huq A, Thomson NR, Colwell RR, Alam M. Vibrio cholerae O1 El Tor strains linked to global cholera show region-specific patterns by pulsed-field gel electrophoresis. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 105:105363. [PMID: 36087684 PMCID: PMC10695325 DOI: 10.1016/j.meegid.2022.105363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 06/28/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
Vibrio cholerae O1 El Tor, causative agent of the ongoing seventh cholera pandemic, is native to the aquatic environment of the Ganges Delta, Bay of Bengal (GDBB). Recent studies traced pandemic strains to the GDBB and proposed global spread of cholera had occurred via intercontinental transmission. In the research presented here, NotI-digested genomic DNA extracted from V. cholerae O1 clinical and environmental strains isolated in Bangladesh during 20042014 was analyzed by pulsed-field gel electrophoresis (PFGE). Results of cluster analysis showed 94.67% of the V. cholerae strains belonged to clade A and included the majority of clinical strains of spatio-temporal origin and representing different cholera endemic foci. The rest of the strains were estuarine, all environmental strains from Mathbaria, Bangladesh, and occurred as singletons, clustered in clades B and C, or in the small clades D and E. Cluster analysis of the Bangladeshi strains and including 157 El Tor strains from thirteen countries in Asia, Africa, and the Americas revealed 85% of the total set of strains belonged to clade A, indicating all were related, yet did not form an homogeneous cluster. Overall, 15% of the global strains comprised multiple small clades or segregated as singletons. Three sub-clades could be discerned within the major clade A, reflecting distinct lineages of V. cholerae O1 El Tor associated with cholera in Asia, Africa, and the Americas. The presence in Asia and the Americas of non-pandemic V. cholerae O1 El Tor populations differing by PFGE and from strains associated with cholera globally suggests different ecotypes are resident in distant geographies.
Collapse
Affiliation(s)
- Fatema-Tuz Johura
- icddr, b (International Centre for Diarrhoeal Disease Research, Bangladesh), Dhaka, Bangladesh
| | - Sahitya Ranjan Biswas
- icddr, b (International Centre for Diarrhoeal Disease Research, Bangladesh), Dhaka, Bangladesh
| | - Shah M Rashed
- icddr, b (International Centre for Diarrhoeal Disease Research, Bangladesh), Dhaka, Bangladesh
| | - Mohammad Tarequl Islam
- icddr, b (International Centre for Diarrhoeal Disease Research, Bangladesh), Dhaka, Bangladesh
| | - Saiful Islam
- icddr, b (International Centre for Diarrhoeal Disease Research, Bangladesh), Dhaka, Bangladesh
| | - Marzia Sultana
- icddr, b (International Centre for Diarrhoeal Disease Research, Bangladesh), Dhaka, Bangladesh
| | - Haruo Watanabe
- National Institutes of Infectious Diseases (NIID), Tokyo, Japan
| | - Anwar Huq
- Maryland Pathogen Research Institute, University of Maryland, College Park, MD, USA
| | - Nicholas R Thomson
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Rita R Colwell
- Maryland Pathogen Research Institute, University of Maryland, College Park, MD, USA; Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Center for Bioinformatics and Computational Biology, University of Maryland Institute of Advanced Computer Studies, University of Maryland, College Park, MD 20742, USA
| | - Munirul Alam
- icddr, b (International Centre for Diarrhoeal Disease Research, Bangladesh), Dhaka, Bangladesh.
| |
Collapse
|
12
|
Adade NE, Aniweh Y, Mosi L, Valvano MA, Duodu S, Ahator SD. Comparative analysis of Vibrio cholerae isolates from Ghana reveals variations in genome architecture and adaptation of outbreak and environmental strains. Front Microbiol 2022; 13:998182. [PMID: 36312941 PMCID: PMC9608740 DOI: 10.3389/fmicb.2022.998182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 09/20/2022] [Indexed: 12/01/2022] Open
Abstract
Recurrent epidemics of cholera denote robust adaptive mechanisms of Vibrio cholerae for ecological shifting and persistence despite variable stress conditions. Tracking the evolution of pathobiological traits requires comparative genomic studies of isolates from endemic areas. Here, we investigated the genetic differentiation among V. cholerae clinical and environmental isolates by highlighting the genomic divergence associated with gene decay, genome plasticity, and the acquisition of virulence and adaptive traits. The clinical isolates showed high phylogenetic relatedness due to a higher frequency of shared orthologs and fewer gene variants in contrast to the evolutionarily divergent environmental strains. Divergence of the environmental isolates is linked to extensive genomic rearrangements in regions containing mobile genetic elements resulting in numerous breakpoints, relocations, and insertions coupled with the loss of virulence determinants acf, zot, tcp, and ctx in the genomic islands. Also, four isolates possessed the CRISPR-Cas systems with spacers specific for Vibrio phages and plasmids. Genome synteny and homology analysis of the CRISPR-Cas systems suggest horizontal acquisition. The marked differences in the distribution of other phage and plasmid defense systems such as Zorya, DdmABC, DdmDE, and type-I Restriction Modification systems among the isolates indicated a higher propensity for plasmid or phage disseminated traits in the environmental isolates. Our results reveal that V. cholerae strains undergo extensive genomic rearrangements coupled with gene acquisition, reflecting their adaptation during ecological shifts and pathogenicity.
Collapse
Affiliation(s)
- Nana Eghele Adade
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- Department of Biochemistry, Cell, and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast, United Kingdom
- Department of Microbiology, Korle-Bu Teaching Hospital, Accra, Ghana
| | - Yaw Aniweh
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Lydia Mosi
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- Department of Biochemistry, Cell, and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Miguel A. Valvano
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast, United Kingdom
| | - Samuel Duodu
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- Department of Biochemistry, Cell, and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- Samuel Duodu,
| | - Stephen Dela Ahator
- Centre for New Antibacterial Strategies (CANS) and Research Group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT- The Arctic University of Norway, Tromsø, Norway
- *Correspondence: Stephen Dela Ahator,
| |
Collapse
|
13
|
Chen D, Wang H. Redclaw crayfish (Cherax quadricarinatus) responds to Vibrio parahaemolyticus infection by activating toll and immune deficiency signaling pathways and transcription of associated immune response genes. FISH & SHELLFISH IMMUNOLOGY 2022; 127:611-622. [PMID: 35809883 DOI: 10.1016/j.fsi.2022.06.069] [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: 02/14/2022] [Revised: 06/28/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
In invertebrates, several genes controlled by the Toll and immunodeficiency (IMD) signaling cascade are altered during microbial infection. However, little is known about the expression patterns of innate immune response genes in red-clawed crayfish (Cherax quadricarinatus). In the present study, the transcription of five genes was assessed in C. quadricarinatus challenged with Vibrio parahaemolyticus (V. parahaemolyticus). The expression of Relish, Toll-like receptor (TLR), tumor necrosis factor receptor-related factor 6 (TRAF6), Akirin, and IMD in different tissues and at different time points after infection were assessed. In addition, the Relish gene was amplified, the protein conformation of the Relish gene was predicted, and gene expression changes associated with antimicrobial peptide production in C. quadricarinatus were analyzed using RNA interference (RNAi). During V. parahaemolyticus infection, the transcripts of the above five genes were significantly increased in the hepatopancreas of C. quadricarinatus (P < 0.05). In contrast, TLR was significantly downregulated in muscle tissue at the initial stage of infection (P < 0.05); TRAF6 and IMD were significantly down-regulated throughout infection (P < 0.05); Akirin transcripts had the lowest abundance at 24 h post-infection; Relish, IMD and Akirin genes were significantly up-regulated in gill tissue at the early stage of infection (P < 0.05); only TRAF6 was significantly up-regulated at 6, 24 and 48 h after infection. The Relish gene of C. quadricarinatus is closely related to the Exopalaemon carinicauda. When the Relish gene was knocked down by RNAi, the V. parahaemolyticus challenge showed that the mortality rate of the RANi group was significantly higher than that of the NC group; pathological sections showed that the hepatopancreatic tissue damage was the most severe 12 h after the interference; and the interference significantly inhibited IRF4, NF-κB, ALF, laccase, SOD1, and lectin genes. Therefore, it can be hypothesized that the Toll and IMD pathways are activated in C. quadricarinatus in response to bacterial infection and that genes associated with these pathways are differentially transcribed in different tissues. This study provides insights into the Toll and IMD signaling pathways and the spatiotemporal expression of key genes regulating bacterial infection resistance in C. quadricarinatus.
Collapse
Affiliation(s)
- Duanduan Chen
- College of Agronomy Liaocheng University, Liaochen, 252000, China; Aquaculture Research Lab, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian, 271018, China.
| | - Hui Wang
- Aquaculture Research Lab, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian, 271018, China.
| |
Collapse
|
14
|
Sit B, Fakoya B, Waldor MK. Emerging Concepts in Cholera Vaccine Design. Annu Rev Microbiol 2022; 76:681-702. [PMID: 35759873 DOI: 10.1146/annurev-micro-041320-033201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cholera is a severe diarrheal disease caused by the bacterium Vibrio cholerae and constitutes a significant public health threat in many areas of the world. V. cholerae infection elicits potent and long-lasting immunity, and efforts to develop cholera vaccines have been ongoing for more than a century. Currently available inactivated two-dose oral cholera vaccines are increasingly deployed to both prevent and actively curb cholera outbreaks, and they are key components of the global effort to eradicate cholera. However, these killed whole-cell vaccines have several limitations, and a variety of new oral and nonoral cholera vaccine platforms have recently been developed. Here, we review emerging concepts in cholera vaccine design and implementation that have been driven by insights from human and animal studies. As a prototypical vaccine-preventable disease, cholera continues to be an excellent target for the development and application of cutting-edge technologies and platforms that may transform vaccinology. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Brandon Sit
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA; .,Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Bolutife Fakoya
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA; .,Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Matthew K Waldor
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA; .,Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Massachusetts, USA.,Howard Hughes Medical Institute, Bethesda, Maryland, USA
| |
Collapse
|
15
|
Piarroux R, Moore S, Rebaudet S. Cholera in Haiti. Presse Med 2022; 51:104136. [PMID: 35705115 DOI: 10.1016/j.lpm.2022.104136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/31/2022] [Indexed: 10/18/2022] Open
Abstract
The cholera epidemic that hit Haiti from October 2010 to February 2019 was the world's deadliest of the last 25 years. Officially, the successive waves caused 9789 deaths, although numerous additional casualties could not be recorded. The origin of this epidemic has been the subject of a controversy involving two opposing theories. The first hypothesis, put forward by renowned American academics, was that the cholera epidemic originated from the environment, due to the proliferation and transmission of aquatic Vibrio cholerae bacteria driven by a confluence of circumstances, i.e., the earthquake followed by a hot summer and, ultimately, heavy rainfall and flooding. The alternative hypothesis, which was subsequently confirmed by epidemiological and genomic studies, attributed the epidemic to the recent importation of cholera by UN peacekeepers having recently arriving from Nepal, and to a river polluted with sewage. In late 2016, the Secretary General of the United Nations finally begged the Haitian people for forgiveness. This implicit recognition of the role of the UN in the cholera epidemic helped to fund the ongoing fight against it. Case-area targeted interventions aimed at interrupting cholera transmission were reinforced, which resulted in the extinction of the epidemic within two years. In the meantime, several phylogenetic studies on Vibrio cholerae during the seventh cholera pandemic demonstrated that local environmental and global epidemic Vibrio populations were distinct. These studies also showed that epidemics arose when the bacterium had diversified and that it had spread during transmission events associated with human travel.
Collapse
Affiliation(s)
- Renaud Piarroux
- Sorbonne Université, INSERM, Institut Pierre-Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpital Pitié-Salpêtrière, Paris, France.
| | | | - Stanislas Rebaudet
- Hôpital Européen, Aix Marseille Univ, INSERM, IRD, SESTIM, ISSPAM, Marseille, France
| |
Collapse
|
16
|
Miele S, Provan JI, Vergne J, Possoz C, Ochsenbein F, Barre FX. The Xer activation factor of TLCΦ expands the possibilities for Xer recombination. Nucleic Acids Res 2022; 50:6368-6383. [PMID: 35657090 PMCID: PMC9226527 DOI: 10.1093/nar/gkac429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 05/03/2022] [Accepted: 06/01/2022] [Indexed: 11/13/2022] Open
Abstract
The chromosome dimer resolution machinery of bacteria is generally composed of two tyrosine recombinases, XerC and XerD. They resolve chromosome dimers by adding a crossover between sister copies of a specific site, dif. The reaction depends on a cell division protein, FtsK, which activates XerD by protein-protein interactions. The toxin-linked cryptic satellite phage (TLCΦ) of Vibrio cholerae, which participates in the emergence of cholera epidemic strains, carries a dif-like attachment site (attP). TLCΦ exploits the Xer machinery to integrate into the dif site of its host chromosomes. The TLCΦ integration reaction escapes the control of FtsK because TLCΦ encodes for its own XerD-activation factor, XafT. Additionally, TLCΦ attP is a poor substrate for XerD binding, in apparent contradiction with the high integration efficiency of the phage. Here, we present a sequencing-based methodology to analyse the integration and excision efficiency of thousands of synthetic mini-TLCΦ plasmids with differing attP sites in vivo. This methodology is applicable to the fine-grained analyses of DNA transactions on a wider scale. In addition, we compared the efficiency with which XafT and the XerD-activation domain of FtsK drive recombination reactions in vitro. Our results suggest that XafT not only activates XerD-catalysis but also helps form and/or stabilize synaptic complexes between imperfect Xer recombination sites.
Collapse
Affiliation(s)
- Solange Miele
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - James Iain Provan
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Justine Vergne
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Christophe Possoz
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Françoise Ochsenbein
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - François-Xavier Barre
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| |
Collapse
|
17
|
Benamrouche N, Belkader C, Njamkepo E, Zemam SS, Sadat S, Saighi K, Boutabba DT, Mechouet F, Benhadj-Slimani R, Zmit FZ, Rauzier J, Kias F, Zouagui S, Ruckly C, Yousfi M, Zertal A, Chouikrat R, Quilici ML, Weill FX. Outbreak of Imported Seventh Pandemic Vibrio cholerae O1 El Tor, Algeria, 2018. Emerg Infect Dis 2022; 28:1241-1245. [PMID: 35608654 PMCID: PMC9155889 DOI: 10.3201/eid2806.212451] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
After a lull of >20 years, Algeria experienced a cholera outbreak in 2018 that included 291 suspected cases. We found that outbreak isolates were Vibrio cholerae O1 serotype Ogawa from seventh pandemic El Tor sublineage AFR14, which corresponds to a new introduction of cholera into Africa from South Asia.
Collapse
|
18
|
GSDMEa-mediated pyroptosis is bi-directionally regulated by caspase and required for effective bacterial clearance in teleost. Cell Death Dis 2022; 13:491. [PMID: 35610210 PMCID: PMC9130220 DOI: 10.1038/s41419-022-04896-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 04/25/2022] [Accepted: 04/28/2022] [Indexed: 12/14/2022]
Abstract
Gasdermin (GSDM) is a family of pore-forming proteins that, after cleavage by caspase (CASP), induce a type of programmed necrotic cell death called pyroptosis. Gasdermin E (GSDME) is the only pyroptosis-inducing member of the GSDM family existing in teleost. To date, the regulation and function of teleost GSDME in response to bacterial infection remain elusive. In this study, we observed activation of GSDME, as well as multiple CASPs, in turbot Scophthalmus maximus during the infection of the bacterial pathogen Vibrio harveyi. Turbot has two GSDME orthologs named SmGSDMEa and SmGSDMEb. We found that SmGSDMEa was specifically cleaved by turbot CASP (SmCASP) 3/7 and SmCASP6, which produced two different N-terminal (NT) fragments. Only the NT fragment produced by SmCASP3/7 cleavage was able to induce pyroptosis. Ectopically expressed SmCASP3/7 activated SmGSDMEa, resulting in pyroptotic cell death. In contrast, SmCASP6 inactivated SmGSDMEa by destructive cleavage of the NT domain, thus nullifying the activation effect of SmCASP3/7. Unlike SmGSDMEa, SmGSDMEb was cleaved by SmCASP8 and unable to induce cell death. V. harveyi infection dramatically promoted the production and activation of SmGSDMEa, but not SmGSDMEb, and caused pyroptosis in turbot. Interference with SmCASP3/7 activity significantly enhanced the invasiveness and lethality of V. harveyi in a turbot infection model. Together, these results revealed a previously unrecognized bi-directional regulation mode of GSDME-mediated pyroptosis, and a functional difference between teleost GSDMEa and GSDMEb in the immune defense against bacterial infection.
Collapse
|
19
|
Rouard C, Njamkepo E, Quilici ML, Weill FX. Contribution of microbial genomics to cholera epidemiology. C R Biol 2022; 345:37-56. [DOI: 10.5802/crbiol.77] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 03/28/2022] [Indexed: 11/24/2022]
|
20
|
Monir MM, Hossain T, Morita M, Ohnishi M, Johura FT, Sultana M, Monira S, Ahmed T, Thomson N, Watanabe H, Huq A, Colwell RR, Seed K, Alam M. Genomic Characteristics of Recently Recognized Vibrio cholerae El Tor Lineages Associated with Cholera in Bangladesh, 1991 to 2017. Microbiol Spectr 2022; 10:e0039122. [PMID: 35315699 PMCID: PMC9045249 DOI: 10.1128/spectrum.00391-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 03/02/2022] [Indexed: 11/20/2022] Open
Abstract
Comparative genomic analysis of Vibrio cholerae El Tor associated with endemic cholera in Asia revealed two distinct lineages, one dominant in Bangladesh and the other in India. An in-depth whole-genome study of V. cholerae El Tor strains isolated during endemic cholera in Bangladesh (1991 to 2017) included reference genome sequence data obtained online. Core genome phylogeny established using single nucleotide polymorphisms (SNPs) showed V. cholerae El Tor strains comprised two lineages, BD-1 and BD-2, which, according to Bayesian phylodynamic analysis, originated from paraphyletic group BD-0 around 1981. BD-1 and BD-2 lineages overlapped temporally but were negatively associated as causative agents of cholera during 2004 to 2017. Genome-wide association study (GWAS) revealed 140 SNPs and 31 indels, resulting in gene alleles unique to BD-1 and BD-2. Regression analysis of root to tip distance and year of isolation indicated early BD-0 strains at the base, whereas BD-1 and BD-2 subsequently emerged and progressed by accumulating SNPs. Pangenome analysis provided evidence of gene acquisition by both BD-1 and BD-2, of which six crucial proteins of known function were predominant in BD-2. BD-1 and BD-2 diverged and have distinctively different genomic traits, namely, heterogeneity in VSP-2, VPI-1, mobile elements, toxin encoding elements, and total gene abundance. In addition, the observed phage-inducible chromosomal island-like element (PLE1), and SXT ICE elements (ICETET) in BD-2 presumably provided a fitness advantage for the lineage to outcompete BD-1 as the etiological agent of endemic cholera in Bangladesh, with implications for global cholera epidemiology. IMPORTANCE Cholera is a global disease with specific reference to the Bay of Bengal Ganges Delta where Vibrio cholerae O1 El Tor, the causative agent of the disease showed two circulating lineages, one dominant in Bangladesh and the other in India. Results of an in-depth genomic study of V. cholerae associated with endemic cholera during the past 27 years (1991 to 2017) indicate emergence and succession of the two lineages, BD-1 and BD-2, arising from a common ancestral paraphyletic group, BD-0, comprising the early strains and short-term evolution of the bacterium in Bangladesh. Among the two V. cholerae lineages, BD-2 supersedes BD-1 and is predominant in the most recent endemic cholera in Bangladesh. The BD-2 lineage contained significantly more SNPs and indels, and showed richness in gene abundance, including antimicrobial resistance genes, gene cassettes, and PLE to fight against bacteriophage infection, acquired over time. These findings have important epidemic implications on a global scale.
Collapse
Affiliation(s)
- Md Mamun Monir
- icddr, b, Formerly International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Talal Hossain
- icddr, b, Formerly International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Masatomo Morita
- National Institutes of Infectious Diseases (NIID), Tokyo, Japan
| | - Makoto Ohnishi
- National Institutes of Infectious Diseases (NIID), Tokyo, Japan
| | - Fatema-Tuz Johura
- icddr, b, Formerly International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Marzia Sultana
- icddr, b, Formerly International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Shirajum Monira
- icddr, b, Formerly International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Tahmeed Ahmed
- icddr, b, Formerly International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | | | - Haruo Watanabe
- National Institutes of Infectious Diseases (NIID), Tokyo, Japan
| | - Anwar Huq
- Maryland Pathogen Research Institute, University of Maryland, Baltimore, Maryland, USA
| | - Rita R. Colwell
- Maryland Pathogen Research Institute, University of Maryland, Baltimore, Maryland, USA
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | | | - Munirul Alam
- icddr, b, Formerly International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| |
Collapse
|
21
|
Yan H, Pang B, Lu X, Gao Z, Lu P, Zhang X, Wang M, Shen L, Zhao W, Zhao J, Liang W, Jia L, Zhou H, Cui Z, Du X, Kan B, Wang Q. Cholera Caused by a New Clone of Serogroup O1 Vibrio cholerae — Beijing Municipality, China, June 2021. China CDC Wkly 2022; 4:31-32. [PMID: 35586521 PMCID: PMC8796729 DOI: 10.46234/ccdcw2021.279] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/14/2021] [Indexed: 11/14/2022] Open
Affiliation(s)
- Hanqiu Yan
- Beijing Center for Disease Prevention and Control, Beijing Research Center for Preventive Medicine, Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing, China
| | - Bo Pang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xin Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhiyong Gao
- Beijing Center for Disease Prevention and Control, Beijing Research Center for Preventive Medicine, Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing, China
| | - Pan Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xin Zhang
- Beijing Center for Disease Prevention and Control, Beijing Research Center for Preventive Medicine, Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing, China
| | - Mengyu Wang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Lingyu Shen
- Beijing Center for Disease Prevention and Control, Beijing Research Center for Preventive Medicine, Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing, China
| | - Wenxuan Zhao
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jianhong Zhao
- Beijing Chaoyang Center for Disease Prevention and Control, Beijing, China
| | - Weili Liang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Lei Jia
- Beijing Center for Disease Prevention and Control, Beijing Research Center for Preventive Medicine, Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing, China
| | - Haijian Zhou
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhigang Cui
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiaoli Du
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Biao Kan
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Biao Kan,
| | - Quanyi Wang
- Beijing Center for Disease Prevention and Control, Beijing Research Center for Preventive Medicine, Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing, China
- Quanyi Wang,
| |
Collapse
|
22
|
Guest T, Haycocks JRJ, Warren GZL, Grainger DC. Genome-wide mapping of Vibrio cholerae VpsT binding identifies a mechanism for c-di-GMP homeostasis. Nucleic Acids Res 2021; 50:149-159. [PMID: 34908143 PMCID: PMC8754643 DOI: 10.1093/nar/gkab1194] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/16/2021] [Accepted: 11/18/2021] [Indexed: 11/13/2022] Open
Abstract
Many bacteria use cyclic dimeric guanosine monophosphate (c-di-GMP) to control changes in lifestyle. The molecule, synthesized by proteins having diguanylate cyclase activity, is often a signal to transition from motile to sedentary behaviour. In Vibrio cholerae, c-di-GMP can exert its effects via the transcription factors VpsT and VpsR. Together, these proteins activate genes needed for V. cholerae to form biofilms. In this work, we have mapped the genome-wide distribution of VpsT in a search for further regulatory roles. We show that VpsT binds 23 loci and recognises a degenerate DNA palindrome having the consensus 5'-W-5R-4[CG]-3Y-2W-1W+1R+2[GC]+3Y+4W+5-3'. Most genes targeted by VpsT encode functions related to motility, biofilm formation, or c-di-GMP metabolism. Most notably, VpsT activates expression of the vpvABC operon that encodes a diguanylate cyclase. This creates a positive feedback loop needed to maintain intracellular levels of c-di-GMP. Mutation of the key VpsT binding site, upstream of vpvABC, severs the loop and c-di-GMP levels fall accordingly. Hence, as well as relaying the c-di-GMP signal, VpsT impacts c-di-GMP homeostasis.
Collapse
Affiliation(s)
- Thomas Guest
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - James R J Haycocks
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Gemma Z L Warren
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - David C Grainger
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| |
Collapse
|
23
|
Pal BB, Behera DR, Nayak SR, Nayak AK. Origin and Dissemination of Altered El Tor Vibrio cholerae O1 Causing Cholera in Odisha, India: Two and Half Decade's View. Front Microbiol 2021; 12:757986. [PMID: 34867883 PMCID: PMC8637270 DOI: 10.3389/fmicb.2021.757986] [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] [Received: 08/13/2021] [Accepted: 10/08/2021] [Indexed: 11/13/2022] Open
Abstract
The origin, spread and molecular epidemiology of altered El Tor Vibrio cholerae O1 strains isolated from cholera outbreaks/surveillance studies between 1995 and 2019 from different district of Odisha were analyzed. The stock cultures of V. cholerae O1 strains from 1995 to 2019 were analyzed through molecular analysis using different PCR assays and pulse field gel electrophoresis (PFGE) analysis. The spread map (month, year and place) was constructed to locate the dissemination of altered El Tor variants of V. cholerae O1 in this region. A total of 13 cholera outbreaks were caused by V. cholerae O1 Ogawa biotype El Tor carrying ctxB1 and ctxB7 genotypes. The ctxB1 alleles of V. cholerae O1 mostly confined to the coastal areas, whereas the ctxB7 genotypes, though originating in the coastal region of Odisha, concentrated more in the tribal areas. The positive correlation between virulence-associated genes (VAGs) was found through Pearson’s correlation model, indicative of a stronger association between the VAGs. The clonal relationship through PFGE between ctxB1 and ctxB7 genotypes of V. cholerae O1 strains exhibited 80% similarity indicating single- or multi-clonal evolution. It is evident from this study that the spread of multidrug-resistant V. cholerae O1-altered El Tor was dominant over the prototype El Tor strains in this region. The origin of altered El Tor variants of V. cholerae O1 occurred in the East Coast of Odisha established that the origin of cholera happened in the Gangetic belts of Bay of Bengal where all new variants of V. cholerae O1 might have originated from the Asian countries.
Collapse
Affiliation(s)
- Bibhuti Bhusan Pal
- Microbiology Division, ICMR-Regional Medical Research Centre, Bhubaneswar, India
| | - Dipti Ranjan Behera
- Microbiology Division, ICMR-Regional Medical Research Centre, Bhubaneswar, India
| | - Smruti Ranjan Nayak
- Microbiology Division, ICMR-Regional Medical Research Centre, Bhubaneswar, India
| | - Ashish Kumar Nayak
- Microbiology Division, ICMR-Regional Medical Research Centre, Bhubaneswar, India
| |
Collapse
|
24
|
Bugayong MP, Izumiya H, Bilar JM, Morita M, Arakawa E, Saito-Obata M, Oshitani H, Ohnishi M. Molecular characterization of Vibrio cholerae O1 isolates obtained from outbreaks in the Philippines, 2015-2016. J Med Microbiol 2021; 70. [PMID: 34817317 DOI: 10.1099/jmm.0.001443] [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: 11/18/2022] Open
Abstract
Introduction. The Philippines, comprising three island groups, namely, Luzon, Visayas and Mindanao, experienced an increase in cholera outbreaks in 2016. Previous studies have shown that Vibrio cholerae isolates obtained from the Philippines are novel hybrid El Tor strains that have evolved in the country and are clearly distinct from those found in Mozambique and Cameroon.Gap statement. The characterization of the strains isolated from outbreaks has been limited to phenotypic characteristics, such as biochemical and serological characteristics, in most previous studies.Aim. We performed multilocus variable-number tandem repeat (VNTR) analysis (MLVA) for V. cholerae isolates obtained from 2015 to 2016 to further characterize and understand the emergence and dissemination of the strains in the Philippines.Methodology. A total of 139 V. cholerae O1 Ogawa biotype El Tor isolates were obtained from the Philippines during diarrhoeal outbreaks in 18 provinces between 2015 and 2016. VNTR data were analysed to classify the MLVA profiles where the large-chromosome types (LCTs) were applied for grouping.Results. We identified 50 MLVA types among 139 isolates originating from 18 provinces, and 14 LCTs. The distribution of the LCTs was variable, and a few were located in specific areas or even in specific provinces. Based on eBURST analysis, 99 isolates with 7 LCTs and 32 MLVA types belonged to 1 group, suggesting that they were related to each other. LCT A was predominant (n=67) and was isolated from Luzon and Visayas. LCT A had 14 MLVA types; however, it mostly emerged during a single quarter of a year. Eight clusters were identified, each of which involved specific MLVA type(s). The largest cluster involved 23 isolates showing 3 MLVA types, 21 of which were MLVA type A-14 isolated from Negros Occidental during quarter 4 of 2016. Comparative analysis showed that almost all isolates from the Philippines were distinct from those in other countries.Conclusions. The genotypic relationship of the V. cholerae isolates obtained during outbreaks in the Philippines was studied, and their emergence and dissemination were elucidated. MLVA revealed the short-term dynamics of V. cholerae genotypes in the Philippines.
Collapse
Affiliation(s)
- Mark Philip Bugayong
- Department of Microbiology, Research Institute for Tropical Medicine, Muntinlupa, Philippines
| | - Hidemasa Izumiya
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Josie M Bilar
- Department of Microbiology, Research Institute for Tropical Medicine, Muntinlupa, Philippines
| | - Masatomo Morita
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Eiji Arakawa
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Mariko Saito-Obata
- Department of Virology, Tohoku University Graduate School of Medicine, Miyagi, Japan.,RITM-Tohoku Collaborating Research Center for Emerging and Re-emerging Infectious Diseases, Muntinlupa, Philippines
| | - Hitoshi Oshitani
- Department of Virology, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Makoto Ohnishi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| |
Collapse
|
25
|
Smith AM, Weill FX, Njamkepo E, Ngomane HM, Ramalwa N, Sekwadi P, Thomas J. Emergence of Vibrio cholerae O1 Sequence Type 75, South Africa, 2018-2020. Emerg Infect Dis 2021; 27:2927-2931. [PMID: 34670657 PMCID: PMC8544974 DOI: 10.3201/eid2711.211144] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We describe the molecular epidemiology of cholera in South Africa during 2018-2020. Vibrio cholerae O1 sequence type (ST) 75 recently emerged and became more prevalent than the V. cholerae O1 biotype El Tor pandemic clone. ST75 isolates were found across large spatial and temporal distances, suggesting local ST75 spread.
Collapse
|
26
|
Climate Precursors of Satellite Water Marker Index for Spring Cholera Outbreak in Northern Bay of Bengal Coastal Regions. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph181910201. [PMID: 34639500 PMCID: PMC8507903 DOI: 10.3390/ijerph181910201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/19/2021] [Accepted: 09/22/2021] [Indexed: 11/16/2022]
Abstract
Cholera is a water-borne infectious disease that affects 1.3 to 4 million people, with 21,000 to 143,000 reported fatalities each year worldwide. Outbreaks are devastating to affected communities and their prospects for development. The key to support preparedness and public health response is the ability to forecast cholera outbreaks with sufficient lead time. How Vibrio cholerae survives in the environment outside a human host is an important route of disease transmission. Thus, identifying the environmental and climate drivers of these pathogens is highly desirable. Here, we elucidate for the first time a mechanistic link between climate variability and cholera (Satellite Water Marker; SWM) index in the Bengal Delta, which allows us to predict cholera outbreaks up to two seasons earlier. High values of the SWM index in fall were associated with above-normal summer monsoon rainfalls over northern India. In turn, these correlated with the La Niña climate pattern that was traced back to the summer monsoon and previous spring seasons. We present a new multi-linear regression model that can explain 50% of the SWM variability over the Bengal Delta based on the relationship with climatic indices of the El Niño Southern Oscillation, Indian Ocean Dipole, and summer monsoon rainfall during the decades 1997–2016. Interestingly, we further found that these relationships were non-stationary over the multi-decadal period 1948–2018. These results bear novel implications for developing outbreak-risk forecasts, demonstrating a crucial need to account for multi-decadal variations in climate interactions and underscoring to better understand how the south Asian summer monsoon responds to climate variability.
Collapse
|
27
|
Abstract
Since 1817, cholera, caused by Vibrio cholerae, has been characterized by seven distinct pandemics. The ongoing seventh pandemic (7P) began in 1961. In this study, we developed a Multilevel Genome Typing (MGT) tool for classifying the V. cholerae species with a focus on the 7P. MGT is based on multilocus sequence typing (MLST), but the concept has been expanded to include a series of MLST schemes that compare population structure from broad to fine resolutions. The V. cholerae MGT consists of eight levels, with the lowest, MGT1, composed of 7 loci and the highest, MGT8, consisting of the 7P core genome (3,759 loci). We used MGT to analyze 5,771 V. cholerae genomes. The genetic relationships revealed by lower MGT levels recapitulated previous findings of large-scale 7P transmission across the globe. Furthermore, the higher MGT levels provided an increased discriminatory power to differentiate subgroups within a national outbreak. Additionally, we demonstrated the usefulness of MGT for non-7P classification. In a large non-7P MGT1 type, MGT2 and MGT3 described continental and regional distributions, respectively. Finally, MGT described trends of 7P in virulence, and MGT2 to MGT3 sequence types (STs) grouped isolates of the same ctxB, tcpA, and ctxB-tcpA genotypes and characterized their trends over the pandemic. MGT offers a range of resolutions for typing V. cholerae. The MGT nomenclature is stable, transferable, and directly comparable between investigations. The MGT database (https://mgtdb.unsw.edu.au/) can accept and process newly submitted samples. MGT allows tracking of existing and new isolates and will be useful for understanding future spread of cholera. IMPORTANCE In 2017, the World Health Organization launched the “Ending Cholera” initiative to reduce cholera-related deaths by 90% by 2030. This strategy emphasized the importance of the speed and accessibility of newer technologies to contain outbreaks. Here, we present a new tool named Multilevel Genome Typing (MGT), which classifies isolates of the cholera-causing agent, Vibrio cholerae. MGT is a freely available online database that groups genetically similar V. cholerae isolates to quickly indicate the origins of outbreaks. We validated the MGT database retrospectively in an outbreak setting, showcasing rapid confirmation of the Nepalese origins for the 2010 Haiti outbreak. In the past 5 years, thousands of V. cholerae genomes have been submitted to the NCBI database, which underscores the importance of and need for proper genome data classification for cholera epidemiology. The V. cholerae MGT database can assist in early decision making that directly impacts controlling both the local and global spread of cholera.
Collapse
|
28
|
Dissecting serotype-specific contributions to live oral cholera vaccine efficacy. Proc Natl Acad Sci U S A 2021; 118:2018032118. [PMID: 33558237 DOI: 10.1073/pnas.2018032118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The O1 serogroup of Vibrio cholerae causes pandemic cholera and is divided into the Ogawa and Inaba serotypes. The O-antigen is V. cholerae's immunodominant antigen, and the two serotypes, which differ by the presence or absence of a terminally methylated O-antigen, likely influence development of immunity to cholera and oral cholera vaccines (OCVs). However, there is no consensus regarding the relative immunological potency of each serotype, in part because previous studies relied on genetically heterogeneous strains. Here, we engineered matched serotype variants of a live OCV candidate, HaitiV, and used a germfree mouse model to evaluate the immunogenicity and protective efficacy of each vaccine serotype. By combining vibriocidal antibody quantification with single- and mixed-strain infection assays, we found that all three HaitiV variants-InabaV, OgawaV, and HikoV (bivalent Inaba/Ogawa)-were immunogenic and protective. None of the vaccine serotypes were superior across both of these vaccine metrics, suggesting that the impact of O1-serotype variation in OCV design, although detectable, is subtle. However, all three live vaccines significantly outperformed formalin-killed HikoV, supporting the idea that live OCV usage will bolster current cholera control practices. The potency of OCVs was found to be challenge strain-dependent, emphasizing the importance of appropriate strain selection for cholera challenge studies. Our findings and experimental approaches will be valuable for guiding the development of live OCVs and oral vaccines for additional pathogens.
Collapse
|
29
|
Breurec S, Franck T, Njamkepo E, Mbecko JR, Rauzier J, Sanke-Waïgana H, Kamwiziku G, Piarroux R, Quilici ML, Weill FX. Seventh Pandemic Vibrio cholerae O1 Sublineages, Central African Republic. Emerg Infect Dis 2021; 27:262-266. [PMID: 33350910 PMCID: PMC7774542 DOI: 10.3201/eid2701.200375] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Four cholera outbreaks were reported in the Central African Republic during 1997–2016. We show that the outbreak isolates were Vibrio cholerae O1 serotype Inaba from 3 seventh pandemic El Tor sublineages originating from West Africa (sublineages T7 and T9) or the African Great Lakes Region (T10).
Collapse
|
30
|
Ekeng E, Tchatchouang S, Akenji B, Issaka BB, Akintayo I, Chukwu C, Dano ID, Melingui S, Ousmane S, Popoola MO, Nzouankeu A, Boum Y, Luquero F, Ahumibe A, Naidoo D, Azman A, Lessler J, Wohl S. Regional sequencing collaboration reveals persistence of the T12 Vibrio cholerae O1 lineage in West Africa. eLife 2021; 10:e65159. [PMID: 34143732 PMCID: PMC8213408 DOI: 10.7554/elife.65159] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 06/05/2021] [Indexed: 11/23/2022] Open
Abstract
Background Despite recent insights into cholera transmission patterns in Africa, regional and local dynamics in West Africa-where cholera outbreaks occur every few years-are still poorly understood. Coordinated genomic surveillance of Vibrio cholerae in the areas most affected may reveal transmission patterns important for cholera control. Methods During a regional sequencing workshop in Nigeria, we sequenced 46 recent V. cholerae isolates from Cameroon, Niger, and Nigeria (37 from 2018 to 2019) to better understand the relationship between the V. cholerae bacterium circulating in these three countries. Results From these isolates, we generated 44 whole Vibrio cholerae O1 sequences and analyzed them in the context of 1280 published V. cholerae O1 genomes. All sequences belonged to the T12 V. cholerae seventh pandemic lineage. Conclusions Phylogenetic analysis of newly generated and previously published V. cholerae genomes suggested that the T12 lineage has been continuously transmitted within West Africa since it was first observed in the region in 2009, despite lack of reported cholera in the intervening years. The results from this regional sequencing effort provide a model for future regionally coordinated surveillance efforts. Funding Funding for this project was provided by Bill and Melinda Gates Foundation OPP1195157.
Collapse
Affiliation(s)
- Eme Ekeng
- Nigeria Centre for Disease ControlAbujaNigeria
| | | | | | | | - Ifeoluwa Akintayo
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of IbadanIbadanNigeria
| | | | | | | | - Sani Ousmane
- Centre de Recherche Médicale et SanitaireNiameyNiger
| | | | | | | | | | | | | | - Andrew Azman
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public HealthBaltimoreUnited States
| | - Justin Lessler
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public HealthBaltimoreUnited States
| | - Shirlee Wohl
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public HealthBaltimoreUnited States
| |
Collapse
|
31
|
Dorman MJ, Thomson NR, Campos J. Genomic contextualisation of ancient DNA molecular data from an Argentinian fifth pandemic Vibrio cholerae infection. Microb Genom 2021; 7. [PMID: 34128784 PMCID: PMC8461468 DOI: 10.1099/mgen.0.000580] [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] [Indexed: 11/18/2022] Open
Abstract
Specific lineages of serogroup O1
Vibrio cholerae
are notorious for causing cholera pandemics, of which there have been seven since the 1800s. Much is known about the sixth pandemic (1899–1923) and the ongoing seventh pandemic (1961–present), but we know very little about the bacteriology of pandemics 1 to 5. Moreover, although we are learning about the contribution of non-O1 non-pandemic
V. cholerae
to cholera dynamics during the current pandemic, we know almost nothing about their role in the past. A recent ancient DNA study has presented what may be the first molecular evidence of a
V. cholerae
infection from the fifth cholera pandemic period (1886–1887 AD) in Argentina. Here, we place the molecular evidence from that study into the genomic context of non-pandemic
V. cholerae
from Latin America and elsewhere, and show that a gene fragment amplified from ancient DNA is most similar to that of
V. cholerae
from the Americas, and from Argentina. Our results corroborate and reinforce the findings of the original study, and collectively suggest that even in the 1880s, non-pandemic
V. cholerae
local to the Americas may have caused sporadic infections in Argentina, just as we know this to have happened during the seventh pandemic in Latin America.
Collapse
Affiliation(s)
- Matthew J Dorman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK.,Churchill College, Storey's Way, Cambridge, CB3 0DS, UK
| | - Nicholas R Thomson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK.,London School of Hygiene and Tropical Medicine, Keppel St., Bloomsbury, London, WC1E 7HT, UK
| | - Josefina Campos
- Instituto Nacional de Enfermedades Infecciosas, INEI-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| |
Collapse
|
32
|
Fennell TG, Blackwell GA, Thomson NR, Dorman MJ. gbpA and chiA genes are not uniformly distributed amongst diverse Vibrio cholerae. Microb Genom 2021; 7:000594. [PMID: 34100695 PMCID: PMC8461464 DOI: 10.1099/mgen.0.000594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 04/26/2021] [Indexed: 11/18/2022] Open
Abstract
Members of the bacterial genus Vibrio utilize chitin both as a metabolic substrate and a signal to activate natural competence. Vibrio cholerae is a bacterial enteric pathogen, sub-lineages of which can cause pandemic cholera. However, the chitin metabolic pathway in V. cholerae has been dissected using only a limited number of laboratory strains of this species. Here, we survey the complement of key chitin metabolism genes amongst 195 diverse V. cholerae. We show that the gene encoding GbpA, known to be an important colonization and virulence factor in pandemic isolates, is not ubiquitous amongst V. cholerae. We also identify a putatively novel chitinase, and present experimental evidence in support of its functionality. Our data indicate that the chitin metabolic pathway within V. cholerae is more complex than previously thought, and emphasize the importance of considering genes and functions in the context of a species in its entirety, rather than simply relying on traditional reference strains.
Collapse
Affiliation(s)
- Thea G. Fennell
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Churchill College, Storey’s Way, Cambridge, CB3 0DS, UK
- Present address: Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge, UK
| | - Grace A. Blackwell
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- EMBL-EBI, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Nicholas R. Thomson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- London School of Hygiene and Tropical Medicine, Keppel St., Bloomsbury, London, WC1E 7HT, UK
| | - Matthew J. Dorman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Churchill College, Storey’s Way, Cambridge, CB3 0DS, UK
| |
Collapse
|
33
|
Balasubramanian D, Murcia S, Ogbunugafor CB, Gavilan R, Almagro-Moreno S. Cholera dynamics: lessons from an epidemic. J Med Microbiol 2021; 70. [PMID: 33416465 DOI: 10.1099/jmm.0.001298] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cholera is a severe diarrhoeal disease that spreads rapidly and affects millions of people each year, resulting in tens of thousands of deaths. The disease is caused by Vibrio cholerae O1 and is characterized by watery diarrhoea that can be lethal if not properly treated. Cholera had not been reported in South America from the late 1800s until 1991, when it was introduced in Peru, wreaking havoc in one of the biggest epidemics reported to date. Within a year, the disease had spread to most of the Latin American region, resulting in millions of cases and thousands of deaths in all affected countries. Despite its aggressive entry, cholera virtually disappeared from the continent after 1999. The progression of the entire epidemic was well documented, making it an ideal model to understand cholera dynamics. In this review, we highlight how the synergy of socioeconomic, political and ecological factors led to the emergence, rapid spread and eventual disappearance of cholera in Latin America. We discuss how measures implemented during the cholera epidemic drastically changed its course and continental dynamics. Finally, we synthesize our findings and highlight potential lessons that can be learned for efficient and standardized cholera management programmes during future outbreaks in non-endemic areas.
Collapse
Affiliation(s)
- Deepak Balasubramanian
- National Center for Integrated Coastal Research, University of Central Florida, Orlando FL 32816, USA.,Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando FL 32816, USA
| | - Sebastian Murcia
- National Center for Integrated Coastal Research, University of Central Florida, Orlando FL 32816, USA.,Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando FL 32816, USA
| | - C Brandon Ogbunugafor
- Department of Ecology and Evolutionary Biology, Yale University, New Haven CT 06511, USA
| | - Ronnie Gavilan
- Escuela Profesional de Medicina Humana, Universidad Privada San Juan Bautista, Lima, Peru.,Centro Nacional de Salud Publica, Instituto Nacional de Salud-Peru, Jesus Maria, Lima, Peru
| | - Salvador Almagro-Moreno
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando FL 32816, USA.,National Center for Integrated Coastal Research, University of Central Florida, Orlando FL 32816, USA
| |
Collapse
|
34
|
L-arabinose induces the formation of viable non-proliferating spheroplasts in Vibrio cholerae. Appl Environ Microbiol 2021; 87:AEM.02305-20. [PMID: 33355111 PMCID: PMC8090878 DOI: 10.1128/aem.02305-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Vibrio cholerae, the agent of the deadly human disease cholera, propagates as a curved rod-shaped bacterium in warm waters. It is sensitive to cold, but persists in cold waters under the form of viable but non-dividing coccoidal shaped cells. Additionally, V. cholerae is able to form non-proliferating spherical cells in response to cell wall damage. It was recently reported that L-arabinose, a component of the hemicellulose and pectin of terrestrial plants, stops the growth of V. cholerae. Here, we show that L-arabinose induces the formation of spheroplasts that lose the ability to divide and stop growing in volume over time. However, they remain viable and upon removal of L-arabinose they start expanding in volume, form branched structures and give rise to cells with a normal morphology after a few divisions. We further show that WigKR, a histidine kinase/response regulator pair implicated in the induction of a high expression of cell wall synthetic genes, prevents the lysis of the spheroplasts during growth restart. Finally, we show that the physiological perturbations result from the import and catabolic processing of L-arabinose by the V. cholerae homolog of the E. coli galactose transport and catabolic system. Taken together, our results suggest that the formation of non-growing spherical cells is a common response of Vibrios exposed to detrimental conditions. They also permit to define conditions preventing any physiological perturbation of V. cholerae when using L-arabinose to induce gene expression from the tightly regulated promoter of the Escherichia coli araBAD operon.Importance Vibrios among other bacteria form transient cell wall deficient forms as a response to different stresses and revert to proliferating rods when permissive conditions have been restored. Such cellular forms have been associated to antimicrobial tolerance, chronic infections and environmental dispersion.The effect of L-Ara on V. cholerae could provide an easily tractable model to study the ability of Vibrios to form viable reversible spheroplasts. Indeed, the quick transition to spheroplasts and reversion to proliferating rods by addition or removal of L-Ara is ideal to understand the genetic program governing this physiological state and the spatial rearrangements of the cellular machineries during cell shape transitions.
Collapse
|
35
|
Bhandari M, Jennison AV, Rathnayake IU, Huygens F. Evolution, distribution and genetics of atypical Vibrio cholerae - A review. INFECTION GENETICS AND EVOLUTION 2021; 89:104726. [PMID: 33482361 DOI: 10.1016/j.meegid.2021.104726] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 01/07/2021] [Accepted: 01/15/2021] [Indexed: 12/21/2022]
Abstract
Vibrio cholerae is the etiological agent of cholera, a severe diarrheal disease, which can occur as either an epidemic or sporadic disease. Cholera pandemic-causing V. cholerae O1 and O139 serogroups originated from the Indian subcontinent and spread globally and millions of lives are lost each year, mainly in developing and underdeveloped countries due to this disease. V. cholerae O1 is further classified as classical and El Tor biotype which can produce biotype specific cholera toxin (CT). Since 1961, the current seventh pandemic El Tor strains replaced the sixth pandemic strains resulting in the classical biotype strain that produces classical CT. The ongoing evolution of Atypical El Tor V. cholerae srains encoding classical CT is of global concern. The severity in the pathophysiology of these Atypical El Tor strains is significantly higher than El Tor or classical strains. Pathogenesis of V. cholerae is a complex process that involves coordinated expression of different sets of virulence-associated genes to cause disease. We are yet to understand the complete virulence profile of V. cholerae, including direct and indirect expression of genes involved in its survival and stress adaptation in the host. In recent years, whole genome sequencing has paved the way for better understanding of the evolution and strain distribution, outbreak identification and pathogen surveillance for the implementation of direct infection control measures in the clinic against many infectious pathogens including V. cholerae. This review provides a synopsis of recent studies that have contributed to the understanding of the evolution, distribution and genetics of the seventh pandemic Atypical El Tor V. cholerae strains.
Collapse
Affiliation(s)
- Murari Bhandari
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia; Public Health Microbiology, Forensic and Scientific Services, Queensland Department of Health, Brisbane, QLD, Australia
| | - Amy V Jennison
- Public Health Microbiology, Forensic and Scientific Services, Queensland Department of Health, Brisbane, QLD, Australia
| | - Irani U Rathnayake
- Public Health Microbiology, Forensic and Scientific Services, Queensland Department of Health, Brisbane, QLD, Australia
| | - Flavia Huygens
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia.
| |
Collapse
|
36
|
Santoriello FJ, Michel L, Unterweger D, Pukatzki S. Pandemic Vibrio cholerae shuts down site-specific recombination to retain an interbacterial defence mechanism. Nat Commun 2020; 11:6246. [PMID: 33288753 PMCID: PMC7721734 DOI: 10.1038/s41467-020-20012-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 11/06/2020] [Indexed: 12/18/2022] Open
Abstract
Vibrio cholerae is an aquatic microbe that can be divided into three subtypes: harmless environmental strains, localised pathogenic strains, and pandemic strains causing global cholera outbreaks. Each type has a contact-dependent type VI secretion system (T6SS) that kills neighbouring competitors by translocating unique toxic effector proteins. Pandemic isolates possess identical effectors, indicating that T6SS effectors may affect pandemicity. Here, we show that one of the T6SS gene clusters (Aux3) exists in two states: a mobile, prophage-like element in a small subset of environmental strains, and a truncated Aux3 unique to and conserved in pandemic isolates. Environmental Aux3 can be readily excised from and integrated into the genome via site-specific recombination, whereas pandemic Aux3 recombination is reduced. Our data suggest that environmental Aux3 acquisition conferred increased competitive fitness to pre-pandemic V. cholerae, leading to grounding of the element in the chromosome and propagation throughout the pandemic clade. Vibrio cholerae uses a type VI secretion system (T6SS) to kill neighbouring competitors. Here, Santoriello et al. show that a T6SS gene cluster (Aux3) exists as a mobile, prophage-like element in some environmental strains, and as a stable truncated form in pandemic isolates. They propose that Aux3 acquisition increased competitive fitness of pre-pandemic V. cholerae.
Collapse
Affiliation(s)
- Francis J Santoriello
- Department of Immunology and Microbiology, University of Colorado Denver Anschutz Medical Campus, 13001 E 17th Pl, Aurora, CO, 80045, USA.,Department of Biology, The City College of New York, 160 Convent Ave, New York, NY, 10031, USA
| | - Lina Michel
- Department of Immunology and Microbiology, University of Colorado Denver Anschutz Medical Campus, 13001 E 17th Pl, Aurora, CO, 80045, USA.,Heidelberg University, Grabengasse 1, 69117, Heidelberg, Germany
| | - Daniel Unterweger
- Institute for Experimental Medicine, Kiel University, Michaelisstraße 5, 24105, Kiel, Germany.,Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, 24306, Plön, Germany
| | - Stefan Pukatzki
- Department of Immunology and Microbiology, University of Colorado Denver Anschutz Medical Campus, 13001 E 17th Pl, Aurora, CO, 80045, USA. .,Department of Biology, The City College of New York, 160 Convent Ave, New York, NY, 10031, USA.
| |
Collapse
|
37
|
Rebaudet S, Gaudart J, Piarroux R. Cholera in Haiti. THE LANCET GLOBAL HEALTH 2020; 8:e1468. [DOI: 10.1016/s2214-109x(20)30430-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 09/23/2020] [Indexed: 11/26/2022] Open
|
38
|
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.
Collapse
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
| |
Collapse
|
39
|
Whole-Genome Analysis of Clinical Vibrio cholerae O1 in Kolkata, India, and Dhaka, Bangladesh, Reveals Two Lineages of Circulating Strains, Indicating Variation in Genomic Attributes. mBio 2020; 11:mBio.01227-20. [PMID: 33172996 PMCID: PMC7667034 DOI: 10.1128/mbio.01227-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Cholera continues to be a global concern, as large epidemics have occurred recently in Haiti, Yemen, and countries of sub-Saharan Africa. A single lineage of Vibrio cholerae O1 has been considered to be introduced into these regions from South Asia and to cause the spread of cholera. Using genomic epidemiology, we showed that two distinct lineages exist in Bengal, one of which is linked to the global lineage. The other lineage was found only in Iran, Iraq, and countries in Asia and differed from the global lineage regarding cholera toxin variant and drug resistance profile. Therefore, the potential transmission of this lineage to other regions would likely cause worldwide cholera spread and may result in this lineage replacing the current global lineage. Vibrio cholerae serogroup O1 is responsible for epidemic and pandemic cholera and remains a global public health threat. This organism has been well established as a resident flora of the aquatic environment that alters its phenotypic and genotypic attributes for better adaptation to the environment. To reveal the diversity of clinical isolates of V. cholerae O1 in the Bay of Bengal, we performed whole-genome sequencing of isolates from Kolkata, India, and Dhaka, Bangladesh, collected between 2009 and 2016. Comparison with global isolates by phylogenetic analysis placed the current isolates in two Asian lineages, with lineages 1 and 2 predominant in Dhaka and Kolkata, respectively. Each lineage possessed different genetic traits in the cholera toxin B subunit gene, Vibrio seventh pandemic island II, integrative and conjugative element, and antibiotic-resistant genes. Thus, although recent global transmission of V. cholerae O1 from South Asia has been attributed only to isolates of lineage 2, another distinct lineage exists in Bengal.
Collapse
|
40
|
Sharma T, Joshi N, Kumar Mandyal A, Nordqvist SL, Lebens M, Kanchan V, Löfstrand M, Jeverstam F, Mainul Ahasan M, Khan I, Karim M, Muktadir H, Muktadir A, Gill D, Holmgren J. Development of Hillchol®, a low-cost inactivated single strain Hikojima oral cholera vaccine. Vaccine 2020; 38:7998-8009. [DOI: 10.1016/j.vaccine.2020.10.043] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 08/30/2020] [Accepted: 10/12/2020] [Indexed: 01/21/2023]
|
41
|
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.
Collapse
|
42
|
Harris JB, Larocque RC. Hiding in Plain View: Cholera in Bangladesh. Clin Infect Dis 2020; 71:1643-1644. [DOI: 10.1093/cid/ciz1079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 10/25/2019] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jason B Harris
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Regina C Larocque
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| |
Collapse
|
43
|
Oprea M, Njamkepo E, Cristea D, Zhukova A, Clark CG, Kravetz AN, Monakhova E, Ciontea AS, Cojocaru R, Rauzier J, Damian M, Gascuel O, Quilici ML, Weill FX. The seventh pandemic of cholera in Europe revisited by microbial genomics. Nat Commun 2020; 11:5347. [PMID: 33093464 PMCID: PMC7582136 DOI: 10.1038/s41467-020-19185-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/30/2020] [Indexed: 01/09/2023] Open
Abstract
In 1970, the seventh pandemic of cholera (7 P) reached both Africa and Europe. Between 1970 and 2011, several European countries reported cholera outbreaks of a few to more than 2,000 cases. We report here a whole-genome analysis of 1,324 7 P V. cholerae El Tor (7 PET) isolates, including 172 from autochthonous sporadic or outbreak cholera cases occurring between 1970 and 2011 in Europe, providing insight into the spatial and temporal spread of this pathogen across Europe. In this work, we show that the 7 PET lineage was introduced at least eight times into two main regions: Eastern and Southern Europe. Greater recurrence of the disease was observed in Eastern Europe, where it persisted until 2011. It was introduced into this region from Southern Asia, often circulating regionally in the countries bordering the Black Sea, and in the Middle East before reaching Eastern Africa on several occasions. In Southern Europe, the disease was mostly seen in individual countries during the 1970s and was imported from North and West Africa, except in 1994, when cholera was imported into Albania and Italy from the Black Sea region. These results shed light on the geographic course of cholera during the seventh pandemic and highlight the role of humans in its global dissemination.
Collapse
Affiliation(s)
- Mihaela Oprea
- Cantacuzino National Medico-Military Institute for Research and Development, 050096, Bucharest, Romania
| | - Elisabeth Njamkepo
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Paris, 75015, France
| | - Daniela Cristea
- Cantacuzino National Medico-Military Institute for Research and Development, 050096, Bucharest, Romania
| | - Anna Zhukova
- Unité Bioinformatique Evolutive, USR3756 (C3BI/DBC), Institut Pasteur & CNRS, Paris, France
- Hub Bioinformatique et Biostatistique, USR3756 (C3BI/DBC), Institut Pasteur, Paris, France
| | - Clifford G Clark
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MN, Canada
| | - Anatoly N Kravetz
- Kiev Research Institute of Epidemiology and Infectious Diseases, Protasiv Yar Uzuiz, Ukraine
| | - Elena Monakhova
- Rostov-on-Don Research Anti-Plague Institute, Rostov-on-Don, Russia, 344002
| | - Adriana S Ciontea
- Cantacuzino National Medico-Military Institute for Research and Development, 050096, Bucharest, Romania
| | - Radu Cojocaru
- National Centre for Public Health, Chisinau, Republic of Moldova
| | - Jean Rauzier
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Paris, 75015, France
| | - Maria Damian
- Cantacuzino National Medico-Military Institute for Research and Development, 050096, Bucharest, Romania
| | - Olivier Gascuel
- Unité Bioinformatique Evolutive, USR3756 (C3BI/DBC), Institut Pasteur & CNRS, Paris, France
| | - Marie-Laure Quilici
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Paris, 75015, France
| | | |
Collapse
|
44
|
Baker KS. Microbe hunting in the modern era: reflecting on a decade of microbial genomic epidemiology. Curr Biol 2020; 30:R1124-R1130. [PMID: 33022254 PMCID: PMC7534602 DOI: 10.1016/j.cub.2020.06.097] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Since the first recognition that infectious microbes serve as the causes of many human diseases, physicians and scientists have sought to understand and control their spread. For the past 150+ years, these ‘microbe hunters’ have learned to combine epidemiological information with knowledge of the infectious agent(s). In this essay, I reflect on the evolution of microbe hunting, beginning with the history of pre-germ theory epidemiological studies, through the microbiological and molecular eras. Now in the genomic age, modern-day microbe hunters are combining pathogen whole-genome sequencing with epidemiological data to enhance epidemiological investigations, advance our understanding of the natural history of pathogens and drivers of disease, and ultimately reshape our plans and priorities for global disease control and eradication. Indeed, as we have seen during the ongoing Covid-19 pandemic, the role of microbe hunters is now more important than ever. Despite the advances already made by microbial genomic epidemiology, the field is still maturing, with many more exciting developments on the horizon.
Collapse
Affiliation(s)
- Kate S Baker
- University of Liverpool, Institute for Infection, Ecology and Veterinary Sciences, Department of Clinical Infection, Microbiology, and Immunology, Liverpool L69 7ZB, UK.
| |
Collapse
|
45
|
David S, Cohen V, Reuter S, Sheppard AE, Giani T, Parkhill J, Rossolini GM, Feil EJ, Grundmann H, Aanensen DM. Integrated chromosomal and plasmid sequence analyses reveal diverse modes of carbapenemase gene spread among Klebsiella pneumoniae. Proc Natl Acad Sci U S A 2020; 117:25043-25054. [PMID: 32968015 PMCID: PMC7587227 DOI: 10.1073/pnas.2003407117] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Molecular and genomic surveillance systems for bacterial pathogens currently rely on tracking clonally evolving lineages. By contrast, plasmids are usually excluded or analyzed with low-resolution techniques, despite being the primary vectors of antibiotic resistance genes across many key pathogens. Here, we used a combination of long- and short-read sequence data of Klebsiella pneumoniae isolates (n = 1,717) from a European survey to perform an integrated, continent-wide study of chromosomal and plasmid diversity. This revealed three contrasting modes of dissemination used by carbapenemase genes, which confer resistance to last-line carbapenems. First, blaOXA-48-like genes have spread primarily via the single epidemic pOXA-48-like plasmid, which emerged recently in clinical settings and spread rapidly to numerous lineages. Second, blaVIM and blaNDM genes have spread via transient associations of many diverse plasmids with numerous lineages. Third, blaKPC genes have transmitted predominantly by stable association with one successful clonal lineage (ST258/512) yet have been mobilized among diverse plasmids within this lineage. We show that these plasmids, which include pKpQIL-like and IncX3 plasmids, have a long association (and are coevolving) with the lineage, although frequent recombination and rearrangement events between them have led to a complex array of mosaic plasmids carrying blaKPC Taken altogether, these results reveal the diverse trajectories of antibiotic resistance genes in clinical settings, summarized as using one plasmid/multiple lineages, multiple plasmids/multiple lineages, and multiple plasmids/one lineage. Our study provides a framework for the much needed incorporation of plasmid data into genomic surveillance systems, an essential step toward a more comprehensive understanding of resistance spread.
Collapse
Affiliation(s)
- Sophia David
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, CB10 1SA Cambridge, United Kingdom;
| | - Victoria Cohen
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, CB10 1SA Cambridge, United Kingdom
| | - Sandra Reuter
- Institute for Infection Prevention and Hospital Epidemiology, Medical Centre, University of Freiburg, 79106 Freiburg, Germany
- Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Anna E Sheppard
- Modernizing Medical Microbiology Consortium, Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford University, Oxford OX3 9DU, United Kingdom
| | - Tommaso Giani
- Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy
- Clinical Microbiology and Virology Unit, Florence Careggi University Hospital, 50134 Florence, Italy
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, CB3 0ES Cambridge, United Kingdom
| | | | | | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy
- Clinical Microbiology and Virology Unit, Florence Careggi University Hospital, 50134 Florence, Italy
| | - Edward J Feil
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom
| | - Hajo Grundmann
- Institute for Infection Prevention and Hospital Epidemiology, Medical Centre, University of Freiburg, 79106 Freiburg, Germany
- Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, CB10 1SA Cambridge, United Kingdom;
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, Oxford University, Oxford OX3 7LF, United Kingdom
| |
Collapse
|
46
|
Kumar A, Das B, Kumar N. Vibrio Pathogenicity Island-1: The Master Determinant of Cholera Pathogenesis. Front Cell Infect Microbiol 2020; 10:561296. [PMID: 33123494 PMCID: PMC7574455 DOI: 10.3389/fcimb.2020.561296] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 09/11/2020] [Indexed: 11/13/2022] Open
Abstract
Cholera is an acute secretory diarrhoeal disease caused by the bacterium Vibrio cholerae. The key determinants of cholera pathogenicity, cholera toxin (CT), and toxin co-regulated pilus (TCP) are part of the genome of two horizontally acquired Mobile Genetic Elements (MGEs), CTXΦ, and Vibrio pathogenicity island 1 (VPI-1), respectively. Besides, V. cholerae genome harbors several others MGEs that provide antimicrobial resistance, metabolic functions, and other fitness traits. VPI-1, one of the most well characterized genomic island (GI), deserved a special attention, because (i) it encodes many of the virulence factors that facilitate development of cholera (ii) it is essential for the acquisition of CTXΦ and production of CT, and (iii) it is crucial for colonization of V. cholerae in the host intestine. Nevertheless, VPI-1 is ubiquitously present in all the epidemic V. cholerae strains. Therefore, to understand the role of MGEs in the evolution of cholera pathogen from a natural aquatic habitat, it is important to understand the VPI-1 encoded functions, their acquisition and possible mode of dissemination. In this review, we have therefore discussed our present understanding of the different functions of VPI-1 those are associated with virulence, important for toxin production and essential for the disease development.
Collapse
Affiliation(s)
- Ashok Kumar
- Translational Health Science and Technology Institute, Faridabad, India.,Centre for Doctoral Studies, Advanced Research Centre, Manipal Academy of Higher Education, Manipal, India
| | - Bhabatosh Das
- Translational Health Science and Technology Institute, Faridabad, India.,Centre for Doctoral Studies, Advanced Research Centre, Manipal Academy of Higher Education, Manipal, India
| | - Niraj Kumar
- Translational Health Science and Technology Institute, Faridabad, India.,Centre for Doctoral Studies, Advanced Research Centre, Manipal Academy of Higher Education, Manipal, India
| |
Collapse
|
47
|
Drebes Dörr NC, Blokesch M. Interbacterial competition and anti-predatory behaviour of environmental Vibrio cholerae strains. Environ Microbiol 2020; 22:4485-4504. [PMID: 32885535 PMCID: PMC7702109 DOI: 10.1111/1462-2920.15224] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 12/21/2022]
Abstract
Vibrio cholerae isolates responsible for cholera pandemics represent only a small portion of the diverse strains belonging to this species. Indeed, most V. cholerae are encountered in aquatic environments. To better understand the emergence of pandemic lineages, it is crucial to discern what differentiates pandemic strains from their environmental relatives. Here, we studied the interaction of environmental V. cholerae with eukaryotic predators or competing bacteria and tested the contributions of the haemolysin and the type VI secretion system (T6SS) to those interactions. Both of these molecular weapons are constitutively active in environmental isolates but subject to tight regulation in the pandemic clade. We showed that several environmental isolates resist amoebal grazing and that this anti‐grazing defense relies on the strains' T6SS and its actincross‐linking domain (ACD)‐containing tip protein. Strains lacking the ACD were unable to defend themselves against grazing amoebae but maintained high levels of T6SS‐dependent interbacterial killing. We explored the latter phenotype through whole‐genome sequencing of 14 isolates, which unveiled a wide array of novel T6SS effector and (orphan) immunity proteins. By combining these in silico predictions with experimental validations, we showed that highly similar but non‐identical immunity proteins were insufficient to provide cross‐immunity among those wild strains.
Collapse
Affiliation(s)
- Natália C Drebes Dörr
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland
| | - Melanie Blokesch
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland
| |
Collapse
|
48
|
Dorman MJ, Domman D, Poklepovich T, Tolley C, Zolezzi G, Kane L, Viñas MR, Panagópulo M, Moroni M, Binsztein N, Caffer MI, Clare S, Dougan G, Salmond GPC, Parkhill J, Campos J, Thomson NR. Genomics of the Argentinian cholera epidemic elucidate the contrasting dynamics of epidemic and endemic Vibrio cholerae. Nat Commun 2020; 11:4918. [PMID: 33004800 PMCID: PMC7530988 DOI: 10.1038/s41467-020-18647-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 09/03/2020] [Indexed: 12/19/2022] Open
Abstract
In order to control and eradicate epidemic cholera, we need to understand how epidemics begin, how they spread, and how they decline and eventually end. This requires extensive sampling of epidemic disease over time, alongside the background of endemic disease that may exist concurrently with the epidemic. The unique circumstances surrounding the Argentinian cholera epidemic of 1992-1998 presented an opportunity to do this. Here, we use 490 Argentinian V. cholerae genome sequences to characterise the variation within, and between, epidemic and endemic V. cholerae. We show that, during the 1992-1998 cholera epidemic, the invariant epidemic clone co-existed alongside highly diverse members of the Vibrio cholerae species in Argentina, and we contrast the clonality of epidemic V. cholerae with the background diversity of local endemic bacteria. Our findings refine and add nuance to our genomic definitions of epidemic and endemic cholera, and are of direct relevance to controlling current and future cholera epidemics.
Collapse
Affiliation(s)
- Matthew J Dorman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Daryl Domman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Department of Internal Medicine, Center for Global Health, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Tomás Poklepovich
- Instituto Nacional de Enfermedades Infecciosas, INEI-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Charlotte Tolley
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Gisella Zolezzi
- Instituto Nacional de Enfermedades Infecciosas, INEI-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Leanne Kane
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - María Rosa Viñas
- Instituto Nacional de Enfermedades Infecciosas, INEI-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Marcela Panagópulo
- Instituto Nacional de Enfermedades Infecciosas, INEI-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Miriam Moroni
- Instituto Nacional de Enfermedades Infecciosas, INEI-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Norma Binsztein
- Instituto Nacional de Enfermedades Infecciosas, INEI-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - María Inés Caffer
- Instituto Nacional de Enfermedades Infecciosas, INEI-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Simon Clare
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Gordon Dougan
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Department of Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge, CB2 0QW, UK
| | - George P C Salmond
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Julian Parkhill
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Josefina Campos
- Instituto Nacional de Enfermedades Infecciosas, INEI-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina.
| | - Nicholas R Thomson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK.
- London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK.
| |
Collapse
|
49
|
Tümmler B. Molecular epidemiology in current times. Environ Microbiol 2020; 22:4909-4918. [PMID: 32945108 DOI: 10.1111/1462-2920.15238] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/10/2020] [Accepted: 09/15/2020] [Indexed: 01/04/2023]
Abstract
Motivated to find options for prevention or intervention, molecular epidemiology aims to identify the host and microbial factors that determine the transmission, manifestation and progression of infectious disease. The genotyping of cultivatable bacterial strains is performed by either anonymous fingerprinting techniques or sequence-based exploration of variable genomic sites. Multilocus sequence typing of housekeeping genes and allele profiling of the core genome have become standard techniques of bacterial strain typing that may be supplemented by whole genome sequencing to explore all single nucleotide variants and/or the composition of the accessory genome. Next, novel protocols to investigate host and microbiome based upon smart third generation sequencing technologies are being developed for an effective surveillance, rapid diagnosis and real-time tracking of infectious diseases.
Collapse
Affiliation(s)
- Burkhard Tümmler
- Clinical Research Group, Clinic for Paediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| |
Collapse
|
50
|
Stutzmann S, Blokesch M. Comparison of chitin-induced natural transformation in pandemic Vibrio cholerae O1 El Tor strains. Environ Microbiol 2020; 22:4149-4166. [PMID: 32860313 PMCID: PMC7693049 DOI: 10.1111/1462-2920.15214] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 08/23/2020] [Accepted: 08/25/2020] [Indexed: 12/23/2022]
Abstract
The human pathogen Vibrio cholerae serves as a model organism for many important processes ranging from pathogenesis to natural transformation, which has been extensively studied in this bacterium. Previous work has deciphered important regulatory circuits involved in natural competence induction as well as mechanistic details related to its DNA acquisition and uptake potential. However, since competence was first reported for V. cholerae in 2005, many researchers have struggled with reproducibility in certain strains. In this study, we therefore compare prominent seventh pandemic V. cholerae isolates, namely strains A1552, N16961, C6706, C6709, E7946, P27459, and the close relative MO10, for their natural transformability and decipher underlying defects that mask the high degree of competence conservation. Through a combination of experimental approaches and comparative genomics based on new whole‐genome sequences and de novo assemblies, we identify several strain‐specific defects, mostly in genes that encode key players in quorum sensing. Moreover, we provide evidence that most of these deficiencies might have recently occurred through laboratory domestication events or through the acquisition of mobile genetic elements. Lastly, we highlight that differing experimental approaches between research groups might explain more of the variations than strain‐specific alterations.
Collapse
Affiliation(s)
- Sandrine Stutzmann
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland
| | - Melanie Blokesch
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland
| |
Collapse
|