1
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Lassalle F, Al-Shalali S, Al-Hakimi M, Njamkepo E, Bashir IM, Dorman MJ, Rauzier J, Blackwell GA, Taylor-Brown A, Beale MA, Cazares A, Al-Somainy AA, Al-Mahbashi A, Almoayed K, Aldawla M, Al-Harazi A, Quilici ML, Weill FX, Dhabaan G, Thomson NR. Genomic epidemiology reveals multidrug resistant plasmid spread between Vibrio cholerae lineages in Yemen. Nat Microbiol 2023; 8:1787-1798. [PMID: 37770747 PMCID: PMC10539172 DOI: 10.1038/s41564-023-01472-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/11/2023] [Indexed: 09/30/2023]
Abstract
Since 2016, Yemen has been experiencing the largest cholera outbreak in modern history. Multidrug resistance (MDR) emerged among Vibrio cholerae isolates from cholera patients in 2018. Here, to characterize circulating genotypes, we analysed 260 isolates sampled in Yemen between 2018 and 2019. Eighty-four percent of V. cholerae isolates were serogroup O1 belonging to the seventh pandemic El Tor (7PET) lineage, sub-lineage T13, whereas 16% were non-toxigenic, from divergent non-7PET lineages. Treatment of severe cholera with macrolides between 2016 and 2019 coincided with the emergence and dominance of T13 subclones carrying an incompatibility type C (IncC) plasmid harbouring an MDR pseudo-compound transposon. MDR plasmid detection also in endemic non-7PET V. cholerae lineages suggested genetic exchange with 7PET epidemic strains. Stable co-occurrence of the IncC plasmid with the SXT family of integrative and conjugative element in the 7PET background has major implications for cholera control, highlighting the importance of genomic epidemiological surveillance to limit MDR spread.
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Affiliation(s)
- Florent Lassalle
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK.
| | | | | | - Elisabeth Njamkepo
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Paris, France
| | | | - Matthew J Dorman
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK
- Churchill College, Cambridge, UK
| | - Jean Rauzier
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Paris, France
| | - Grace A Blackwell
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK
- EMBL-EBI, Hinxton, UK
| | - Alyce Taylor-Brown
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Mathew A Beale
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Adrián Cazares
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK
| | | | | | - Khaled Almoayed
- National Centre of Public Health Laboratories, Sana'a, Yemen
| | - Mohammed Aldawla
- Ministry of Public Health, Infection Control Unit, Sana'a, Yemen
| | | | - Marie-Laure Quilici
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Paris, France
| | - François-Xavier Weill
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Paris, France
| | - Ghulam Dhabaan
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.
| | - Nicholas R Thomson
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK.
- London School of Hygiene and Tropical Medicine, London, UK.
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2
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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.
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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.
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3
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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.
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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.
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4
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Santoriello FJ, Kirchberger PC, Boucher Y, Pukatzki S. Pandemic Vibrio cholerae acquired competitive traits from an environmental Vibrio species. Life Sci Alliance 2023; 6:6/2/e202201437. [PMID: 36446527 PMCID: PMC9711863 DOI: 10.26508/lsa.202201437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 11/05/2022] [Accepted: 11/07/2022] [Indexed: 11/30/2022] Open
Abstract
Vibrio cholerae is a human pathogen that thrives in estuarine environments. Within the environment and human host, V. cholerae uses the type VI secretion system (T6SS) to inject toxic effectors into neighboring microbes and to establish its replicative niche. V. cholerae strains encode a wide variety of horizontally shared effectors, but pandemic isolates encode an identical set of distinct effectors. Effector set retention in pandemic strains despite mobility between disparate strains suggests that horizontal acquisition of these effectors was crucial for evolving pandemic V. cholerae We attempted to locate the donor of the pandemic effectors to V. cholerae To this end, we identified potential gene transfer events of the pandemic-associated T6SS clusters between a fish pathogen, Vibrio anguillarum, and V. cholerae We supported the likelihood of interaction between these species by demonstrating that homologous effector-immunity pairs from V. cholerae and V. anguillarum can cross-neutralize one another. Thus, V. anguillarum constitutes an environmental reservoir of pandemic-associated V. cholerae T6SS effectors that may have initially facilitated competition between pre-pandemic V. cholerae and V. anguillarum for an environmental niche.
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Affiliation(s)
- Francis J Santoriello
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,Department of Biology, The City College of New York, New York, NY, USA
| | - Paul C Kirchberger
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Yann Boucher
- Saw Swee Hock School of Public Health and National University Hospital System, National University of Singapore, Singapore, Singapore.,Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore.,Infectious Diseases Translational Research Program, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore and National University Hospital System, Singapore, Singapore
| | - Stefan Pukatzki
- Department of Biology, The City College of New York, New York, NY, USA
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5
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O’Hara BJ, Alam M, Ng WL. The Vibrio cholerae Seventh Pandemic Islands act in tandem to defend against a circulating phage. PLoS Genet 2022; 18:e1010250. [PMID: 36026491 PMCID: PMC9455884 DOI: 10.1371/journal.pgen.1010250] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 09/08/2022] [Accepted: 08/02/2022] [Indexed: 11/19/2022] Open
Abstract
The current circulating pandemic El Tor biotype of Vibrio cholerae has persisted for over sixty years and is characterized by its acquisition of two unique genomic islands called the Vibrio Seventh Pandemic Islands 1 and 2 (VSP-I and VSP-II). However, the functions of most of the genes on VSP-I and VSP-II are unknown and the advantages realized by El Tor through these two islands are not clear. Recent studies have broadly implicated these two mobile genetic elements with phage defense. Still, protection against phage infection through these islands has not been observed directly in any V. cholerae El Tor biotype. Here we report the isolation of a circulating phage from a cholera patient stool sample and demonstrate that propagation of this phage in its native host is inhibited by elements in both VSP-I and VSP-II, providing direct evidence for the role of these genomic islands in phage defense. Moreover, we show that these defense systems are regulated by quorum sensing and active only at certain cell densities. Finally, we have isolated a naturally occurring phage variant that is resistant to the defense conferred by the VSP islands, illustrating the countermeasures used by phages to evade these defense mechanisms. Together, this work demonstrates a functional role for the VSPs in V. cholerae and highlights the key regulatory and mechanistic insights that can be gained by studying anti-phage systems in their native contexts. The current pandemic strain of Vibrio cholerae carries two unique genomic islands. How these two islands confer evolutionary advantage to the pathogen is unknown. We show here the identification of a circulating phage that is sensitive to the defense systems present on these two islands and demonstrate how phage variants can evade these defenses. Our studies provide the first direct evidence showing the importance of these genomic islands in defending against phage in their native environments; and in doing so provide novel insight into the mechanisms of these highly conserved defense elements.
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Affiliation(s)
- Brendan J. O’Hara
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- Program of Molecular Microbiology, Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Munirul Alam
- Infectious Diseases Division, International Center for Diarrheal Disease Research, Dhaka, Bangladesh
| | - Wai-Leung Ng
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- Program of Molecular Microbiology, Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- * E-mail:
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6
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Shaw S, Samanta P, Chowdhury G, Ghosh D, Dey TK, Deb AK, Ramamurthy T, Miyoshi SI, Ghosh A, Dutta S, Mukhopadhyay AK. Altered Molecular Attributes and Antimicrobial Resistance Patterns of Vibrio cholerae O1 El Tor Strains Isolated from the Cholera Endemic Regions of India. J Appl Microbiol 2022; 133:3605-3616. [PMID: 36000378 DOI: 10.1111/jam.15794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 07/18/2022] [Accepted: 08/20/2022] [Indexed: 11/28/2022]
Abstract
AIMS The present study aimed to document the comparative analysis of differential hyper-virulent features of Vibrio cholerae O1 strains isolated during 2018 from cholera endemic regions in Gujarat and Maharashtra (Western India) and West Bengal (Eastern India). METHODS AND RESULTS A total of 87 V. cholerae O1 clinical strains from Western India and 48 from Eastern India were analyzed for a number of biotypic and genotypic features followed by antimicrobial resistance (AMR) profile. A novel PCR was designed to detect a large fragment deletion in the Vibrio seventh pandemic island II (VSP-II) genomic region, which is a significant genetic feature of the V. cholerae strains that has caused Yemen cholera outbreak. All the strains from Western India were belong to the Ogawa serotype, polymyxin B-sensitive, hemolytic, had a deletion in VSP-II (VSP-IIC) region and carried Haitian genetic alleles of ctxB, tcpA and rtxA. Conversely, 14.6% (7/48) of the strains from Eastern India belonged to the Inaba serotype, polymyxin B-resistant, non-hemolytic, harbored VSP-II other than VSP-IIC type, classical ctxB, Haitian tcpA and El Tor rtxA alleles. Resistance to tetracycline and chloramphenicol has been observed in strains from both the regions. CONCLUSIONS This study showed hyper-virulent, polymyxin B-sensitive epidemic causing strains in India along with the strains with polymyxin B-resistant and non-hemolytic traits that may spread and cause serious disease outcome in future. SIGNIFICANCE AND IMPACT OF THE STUDY The outcomes of this study can help to improve the understanding of the hyper-pathogenic property of recently circulating pandemic V. cholerae strains in India. A special attention is also needed on the monitoring of AMR surveillance because V. cholerae strains are losing susceptibility to many antibiotics used as a second line of defense in the treatment of cholera.
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Affiliation(s)
- Sreeja Shaw
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Prosenjit Samanta
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Goutam Chowdhury
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Debjani Ghosh
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Tanmoy Kumar Dey
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Alok Kumar Deb
- Division of Epidemiology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Thandavarayan Ramamurthy
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Shin-Ichi Miyoshi
- Collaborative Research Centre of Okayama University for Infectious Diseases at ICMR-NICED, Kolkata, India.,Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Amit Ghosh
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Shanta Dutta
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Asish Kumar Mukhopadhyay
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
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7
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Liu T, Kang L, Xu J, Wang J, Gao S, Li Y, Li J, Yuan Y, Yuan B, Wang J, Zhao B, Xin W. PVBase: A MALDI-TOF MS Database for Fast Identification and Characterization of Potentially Pathogenic Vibrio Species From Multiple Regions of China. Front Microbiol 2022; 13:872825. [PMID: 35656002 PMCID: PMC9152771 DOI: 10.3389/fmicb.2022.872825] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 03/16/2022] [Indexed: 11/13/2022] Open
Abstract
The potentially pathogenic species of the genus Vibrio pose a threat to both humans and animals, creating medical burdens and economic losses to the mariculture industry. Improvements in surveillance and diagnosis are needed to successfully manage vibriosis outbreaks. Matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) can provide rapid diagnosis and has been widely used in the identification of Vibrio spp. The main weakness of this technology is the limited number of strains and species of Vibrio in the existing commercial database. Here, we develop a new in-house database named PVBase containing 790 main spectra projections (MSP) of ten Vibrio species that come from various regions of China and include abundant clinical and environmental strains. PVBase was validated through a blind test of 65 Vibrio strains. The identification accuracy and scoring of Vibrio strains was greatly improved through the addition of PVBase. Identification accuracy increased from 73.4 to 100%. The number of strains with identification scores above 2.2 increased from 53.1% to 96.9% and 53.1% of strains had an identification score above 2.59. Moreover, perfect discrimination was obtained when using all of the MSPs created for the Vibrio species, even for very closely related species such as V. cholerae, V. albensis, and V. mimicus or V. alginolyticus, V. parahaemolyticus, and V. harveyi. In addition, we used phyloproteomic analysis to study whether there are differences in protein fingerprints of different regions or pathogenic strains. We found that MSP characteristics of Vibrio species were not related to their region or source. With the construction of PVBase, the identification efficiency of potentially pathogenic Vibrio species has been greatly improved, which is an important advance for epidemic prevention and control, and aquaculture disease detection.
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Affiliation(s)
- Tingting Liu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Lin Kang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Jinglin Xu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Jing Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Shan Gao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Yanwei Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Jiaxin Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Yuan Yuan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Bing Yuan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Jinglin Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Baohua Zhao
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Wenwen Xin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
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8
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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.
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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
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