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Ayyappan MV, Kishore P, Panda SK, Kumar A, Uchoi D, Nadella RK, Priyadarshi H, Obaiah MC, George D, Hamza M, Ramannathan SK, Ravishankar CN. Emergence of multidrug resistant, ctx negative seventh pandemic Vibrio cholerae O1 El Tor sequence type (ST) 69 in coastal water of Kerala, India. Sci Rep 2024; 14:2031. [PMID: 38263228 PMCID: PMC10805778 DOI: 10.1038/s41598-023-50536-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 12/21/2023] [Indexed: 01/25/2024] Open
Abstract
Seventh pandemic Vibrio choleare O1 El Tor strain is responsible for the on-going pandemic outbreak of cholera globally. This strain evolved from non-pathogenic V. cholerae by acquiring seventh pandemic gene (VC 2346), pandemic Islands (VSP1 and VSP2), pathogenicity islands (VP1 and VP2) and CTX prophage region. The cholera toxin production is mainly attributed to the presence of ctx gene in these strains. However, several variants of this strain emerged as hybrid strains or atypical strains. The present study aimed to assess the aquatic environment of Cochin, India, over a period of 5 years for the emergence of multidrug resistant V. cholerae and its similarity with seventh pandemic strain. The continuous surveillance and monitoring resulted in the isolation of ctx negative, O1 positive V. cholerae isolate (VC6) from coastal water, Cochin, Kerala. The isolate possessed the biotype specific O1 El Tor tcpA gene and lacked other biotype specific ctx, zot, ace and rst genes. Whole genome analysis revealed the isolate belongs to pandemic sequence type (ST) 69 with the possession of pandemic VC2346 gene, pathogenic island VPI1, VPI2, and pandemic island VSP1 and VSP2. The isolate possessed several insertion sequences and the SXT/R391 family related Integrative Conjugative Elements (ICEs). In addition to this, the isolate genome carried virulence genes such as VgrG, mshA, ompT, toxR, ompU, rtxA, als, VasX, makA, and hlyA and antimicrobial resistance genes such as gyrA, dfrA1, strB, parE, sul2, parC, strA, VC1786ICE9-floR, and catB9. Moreover, the phylogenetic analysis suggests that the isolate genome is more closely related to seventh pandemic V. cholerae O1 N16961 strain. This study reports the first incidence of environmental ctx negative seventh pandemic V. choleare O1 El Tor isolate, globally and its presence in the aquatic system likely to induce toxicity in terms of public health point of view. The presence of this isolate in the aquatic environment warns the strict implementation of the epidemiological surveillance on the occurrence of emerging strains and the execution of flagship program for the judicious use of antibiotics in the aquatic ecosystem.
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Affiliation(s)
| | - Pankaj Kishore
- ICAR-Central Institute of Fisheries Technology, Kochi, India.
| | | | - Anuj Kumar
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
| | - Devananda Uchoi
- ICAR-Central Institute of Fisheries Technology, Kochi, India
| | | | | | | | - Dybin George
- Kerala University of Fisheries and Ocean Studies, Kochi, India
| | - Muneeb Hamza
- Cochin University of Science and Technology, Kochi, India
| | | | - C N Ravishankar
- ICAR-Central Institute of Fisheries Education, Mumbai, India
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Luo Y, Payne M, Kaur S, Octavia S, Jiang J, Lan R. Emergence and genomic insights of non-pandemic O1 Vibrio cholerae in Zhejiang, China. Microbiol Spectr 2023; 11:e0261523. [PMID: 37819129 PMCID: PMC10871787 DOI: 10.1128/spectrum.02615-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 09/06/2023] [Indexed: 10/13/2023] Open
Abstract
IMPORTANCE It is well recognized that only Vibrio cholerae O1 causes cholera pandemics. However, not all O1 strains cause pandemic-level disease. In this study, we analyzed non-pandemic O1 V. cholerae isolates from the 1960s to the 1990s from China and found that they fell into three lineages, one of which shared the most recent common ancestor with pandemic O1 strains. Each of these non-pandemic O1 lineages has unique properties that contribute to their capacity to cause cholera. The findings of this study enhanced our understanding of the emergence and evolution of both pandemic and non-pandemic O1 V. cholerae.
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Affiliation(s)
- Yun Luo
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Michael Payne
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Sandeep Kaur
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Sophie Octavia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Jianmin Jiang
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang, China
- Key Lab of Vaccine, Prevention and Control of Infectious Disease of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
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3
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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.
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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)
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4
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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.
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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.
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5
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Molecular Basis of the Toxigenic Vibrio cholerae O1 Serotype Switch from Ogawa to Inaba in Haiti. Microbiol Spectr 2023; 11:e0362422. [PMID: 36537825 PMCID: PMC9927444 DOI: 10.1128/spectrum.03624-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023] Open
Abstract
Toxigenic Vibrio cholerae O1 serotype Ogawa was introduced involuntarily into Haiti in October 2010, and virtually all of the clinical strains isolated during the first 5 years of the epidemic were Ogawa. Inaba strains were identified intermittently prior to 2015, with diverse mutations resulting in a common phenotype. In 2015, the percentage of clinical infections due to the Inaba serotype began to rapidly increase, with Inaba supplanting Ogawa as the dominant serotype during the subsequent 4 years. We investigated the molecular basis of the serotype switch and confirmed that all Inaba strains had the same level of mRNA expression of the wbeT genes, as well as the same translation levels for the truncated WbeT proteins in the V. cholerae Inaba isolates. Neither wbeT gene expression levels, differential mutations, or truncation size of the WbeT proteins appeared to be responsible for the successful Inaba switch in 2015. Our phylodynamic analysis demonstrated that the V. cholerae Inaba strains in Haiti evolved directly from Ogawa strains and that a significant increase of diversifying selection at the population level occurred at the time of the Ogawa-Inaba switch. We conclude that the emergence of the Inaba serotype was driven by diversifying selection, independent of the mutational pattern in the wbeT gene. IMPORTANCE Our phylodynamic analysis demonstrated that Vibrio cholerae Inaba strains in Haiti evolved directly from Ogawa strains. Our results support the hypothesis that after an initial Ogawa-dominated epidemic wave, V. cholerae Inaba was able to become the dominant strain thanks to a selective advantage driven by ongoing diversifying selection, independently from the mutational pattern in the wbeT gene.
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6
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Brumfield KD, Usmani M, Chen KM, Gangwar M, Jutla AS, Huq A, Colwell RR. Environmental parameters associated with incidence and transmission of pathogenic Vibrio spp. Environ Microbiol 2021; 23:7314-7340. [PMID: 34390611 DOI: 10.1111/1462-2920.15716] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 07/27/2021] [Accepted: 08/10/2021] [Indexed: 12/17/2022]
Abstract
Vibrio spp. thrive in warm water and moderate salinity, and they are associated with aquatic invertebrates, notably crustaceans and zooplankton. At least 12 Vibrio spp. are known to cause infection in humans, and Vibrio cholerae is well documented as the etiological agent of pandemic cholera. Pathogenic non-cholera Vibrio spp., e.g., Vibrio parahaemolyticus and Vibrio vulnificus, cause gastroenteritis, septicemia, and other extra-intestinal infections. Incidence of vibriosis is rising globally, with evidence that anthropogenic factors, primarily emissions of carbon dioxide associated with atmospheric warming and more frequent and intense heatwaves, significantly influence environmental parameters, e.g., temperature, salinity, and nutrients, all of which can enhance growth of Vibrio spp. in aquatic ecosystems. It is not possible to eliminate Vibrio spp., as they are autochthonous to the aquatic environment and many play a critical role in carbon and nitrogen cycling. Risk prediction models provide an early warning that is essential for safeguarding public health. This is especially important for regions of the world vulnerable to infrastructure instability, including lack of 'water, sanitation, and hygiene' (WASH), and a less resilient infrastructure that is vulnerable to natural calamity, e.g., hurricanes, floods, and earthquakes, and/or social disruption and civil unrest, arising from war, coups, political crisis, and economic recession. Incorporating environmental, social, and behavioural parameters into such models allows improved prediction, particularly of cholera epidemics. We have reported that damage to WASH infrastructure, coupled with elevated air temperatures and followed by above average rainfall, promotes exposure of a population to contaminated water and increases the risk of an outbreak of cholera. Interestingly, global predictive risk models successful for cholera have the potential, with modification, to predict diseases caused by other clinically relevant Vibrio spp. In the research reported here, the focus was on environmental parameters associated with incidence and distribution of clinically relevant Vibrio spp. and their role in disease transmission. In addition, molecular methods designed for detection and enumeration proved useful for predictive modelling and are described, namely in the context of prediction of environmental conditions favourable to Vibrio spp., hence human health risk.
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Affiliation(s)
- Kyle D Brumfield
- Maryland Pathogen Research Institute, University of Maryland, College Park, MD, USA.,University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, MD, USA
| | - Moiz Usmani
- Geohealth and Hydrology Laboratory, Department of Environmental Engineering Sciences, University of Florida, Gainesville, FL, USA
| | - Kristine M Chen
- Geohealth and Hydrology Laboratory, Department of Environmental Engineering Sciences, University of Florida, Gainesville, FL, USA
| | - Mayank Gangwar
- Geohealth and Hydrology Laboratory, Department of Environmental Engineering Sciences, University of Florida, Gainesville, FL, USA
| | - Antarpreet S Jutla
- Geohealth and Hydrology Laboratory, Department of Environmental Engineering Sciences, University of Florida, Gainesville, FL, USA
| | - Anwar Huq
- Maryland Pathogen Research Institute, University of Maryland, College Park, MD, USA
| | - Rita R Colwell
- Maryland Pathogen Research Institute, University of Maryland, College Park, MD, USA.,University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, MD, USA
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7
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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.
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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
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8
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Anani H, Zgheib R, Hasni I, Raoult D, Fournier PE. Interest of bacterial pangenome analyses in clinical microbiology. Microb Pathog 2020; 149:104275. [PMID: 32562810 DOI: 10.1016/j.micpath.2020.104275] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/22/2020] [Accepted: 05/25/2020] [Indexed: 12/12/2022]
Abstract
Thanks to the progress and decreasing costs in genome sequencing technologies, more than 250,000 bacterial genomes are currently available in public databases, covering most, if not all, of the major human-associated phylogenetic groups of these microorganisms, pathogenic or not. In addition, for many of them, sequences from several strains of a given species are available, thus enabling to evaluate their genetic diversity and study their evolution. In addition, the significant cost reduction of bacterial whole genome sequencing as well as the rapid increase in the number of available bacterial genomes have prompted the development of pangenomic software tools. The study of bacterial pangenome has many applications in clinical microbiology. It can unveil the pathogenic potential and ability of bacteria to resist antimicrobials as well identify specific sequences and predict antigenic epitopes that allow molecular or serologic assays and vaccines to be designed. Bacterial pangenome constitutes a powerful method for understanding the history of human bacteria and relating these findings to diagnosis in clinical microbiology laboratories in order to optimize patient management.
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Affiliation(s)
- Hussein Anani
- Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, AP-HM, UMR Vecteurs Infections Tropicales et Méditerranéennes (VITROME), Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France; Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Rita Zgheib
- Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, AP-HM, UMR Vecteurs Infections Tropicales et Méditerranéennes (VITROME), Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France; Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Issam Hasni
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France; Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Didier Raoult
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France; Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France; Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Pierre-Edouard Fournier
- Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, AP-HM, UMR Vecteurs Infections Tropicales et Méditerranéennes (VITROME), Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France; Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France.
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9
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Wang H, Yang C, Sun Z, Zheng W, Zhang W, Yu H, Wu Y, Didelot X, Yang R, Pan J, Cui Y. Genomic epidemiology of Vibrio cholerae reveals the regional and global spread of two epidemic non-toxigenic lineages. PLoS Negl Trop Dis 2020; 14:e0008046. [PMID: 32069325 PMCID: PMC7048298 DOI: 10.1371/journal.pntd.0008046] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 02/28/2020] [Accepted: 01/09/2020] [Indexed: 12/14/2022] Open
Abstract
Non-toxigenic Vibrio cholerae isolates have been found associated with diarrheal disease globally, however, the global picture of non-toxigenic infections is largely unknown. Among non-toxigenic V. cholerae, ctxAB negative, tcpA positive (CNTP) isolates have the highest risk of disease. From 2001 to 2012, 71 infectious diarrhea cases were reported in Hangzhou, China, caused by CNTP serogroup O1 isolates. We sequenced 119 V. cholerae genomes isolated from patients, carriers and the environment in Hangzhou between 2001 and 2012, and compared them with 850 publicly available global isolates. We found that CNTP isolates from Hangzhou belonged to two distinctive lineages, named L3b and L9. Both lineages caused disease over a long time period with usually mild or moderate clinical symptoms. Within Hangzhou, the spread route of the L3b lineage was apparently from rural to urban areas, with aquatic food products being the most likely medium. Both lineages had been previously reported as causing local endemic disease in Latin America, but here we show that global spread of them has occurred, with the most likely origin of L3b lineage being in Central Asia. The L3b lineage has spread to China on at least three occasions. Other spread events, including from China to Thailand and to Latin America were also observed. We fill the missing links in the global spread of the two non-toxigenic serogroup O1 V. cholerae lineages that can cause human infection. The results are important for the design of future disease control strategies: surveillance of V. cholerae should not be limited to ctxAB positive strains.
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Affiliation(s)
- Haoqiu Wang
- Microbiology Laboratory, Hangzhou Center for Disease Control and Prevention, Hangzhou, Zhejiang Province, China
| | - Chao Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zhou Sun
- Institution of Infectious Disease Control, Hangzhou Center for Disease Control and Prevention, Hangzhou, Zhejiang Province, China
| | - Wei Zheng
- Microbiology Laboratory, Hangzhou Center for Disease Control and Prevention, Hangzhou, Zhejiang Province, China
| | - Wei Zhang
- Microbiology Laboratory, Hangzhou Center for Disease Control and Prevention, Hangzhou, Zhejiang Province, China
| | - Hua Yu
- 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
| | - Xavier Didelot
- School of Life Sciences, University of Warwick, Gibbet Hill Campus, Coventry, United Kingdom
- Department of Statistics, University of Warwick, Coventry, United Kingdom
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jingcao Pan
- Microbiology Laboratory, Hangzhou Center for Disease Control and Prevention, Hangzhou, Zhejiang Province, China
| | - Yujun Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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10
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Environmental Reservoirs of Vibrio cholerae: Challenges and Opportunities for Ocean-Color Remote Sensing. REMOTE SENSING 2019. [DOI: 10.3390/rs11232763] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The World Health Organization has estimated the burden of the on-going pandemic of cholera at 1.3 to 4 million cases per year worldwide in 2016, and a doubling of case-fatality-rate to 1.8% in 2016 from 0.8% in 2015. The disease cholera is caused by the bacterium Vibrio cholerae that can be found in environmental reservoirs, living either in free planktonic form or in association with host organisms, non-living particulate matter or in the sediment, and participating in various biogeochemical cycles. An increasing number of epidemiological studies are using land- and water-based remote-sensing observations for monitoring, surveillance, or risk mapping of Vibrio pathogens and cholera outbreaks. Although the Vibrio pathogens cannot be sensed directly by satellite sensors, remotely-sensed data can be used to infer their presence. Here, we review the use of ocean-color remote-sensing data, in conjunction with information on the ecology of the pathogen, to map its distribution and forecast risk of disease occurrence. Finally, we assess how satellite-based information on cholera may help support the Sustainable Development Goals and targets on Health (Goal 3), Water Quality (Goal 6), Climate (Goal 13), and Life Below Water (Goal 14).
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11
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Sinha-Ray S, Alam MT, Bag S, Morris JG, Ali A. Conversion of a recA-Mediated Non-toxigenic Vibrio cholerae O1 Strain to a Toxigenic Strain Using Chitin-Induced Transformation. Front Microbiol 2019; 10:2562. [PMID: 31787954 PMCID: PMC6854035 DOI: 10.3389/fmicb.2019.02562] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 10/23/2019] [Indexed: 01/08/2023] Open
Abstract
Toxigenic Vibrio cholerae strains, including strains in serogroups O1 and O139 associated with the clinical disease cholera, are ubiquitous in aquatic reservoirs, including fresh, estuarine, and marine environments. Humans acquire cholera by consuming water and/or food contaminated with the microorganism. The genome of toxigenic V. cholerae harbors a cholera-toxin producing prophage (CT-prophage) encoding genes that promote expression of cholera toxin. The CT-prophage in V. cholerae is flanked by two satellite prophages, RS1 and TLC. Using cell surface appendages (TCP and/or MSHA pili), V. cholerae can sequentially acquire TLC, RS1, and CTX phages by transduction; the genome of each of these phages ultimately integrates into V. cholerae's genome in a site-specific manner. Here, we showed that a non-toxigenic V. cholerae O1 biotype El Tor strain, lacking the entire RS1-CTX-TLC prophage complex (designated as RCT: R for RS1, C for CTX and T for TLC prophage, respectively), was able to acquire RCT from donor genomic DNA (gDNA) of a wild-type V. cholerae strain (E7946) via chitin-induced transformation. Moreover, we demonstrated that a chitin-induced transformant (designated as AAS111) harboring RCT was capable of producing cholera toxin. We also showed that recA, rather than xerC and xerD recombinases, promoted the acquisition of RCT from donor gDNA by the recipient non-toxigenic V. cholerae strain. Our data document the existence of an alternative pathway by which a non-toxigenic V. cholerae O1 strain can transform to a toxigenic strain by using chitin induction. As chitin is an abundant natural carbon source in aquatic reservoirs where V. cholerae is present, chitin-induced transformation may be an important driver in the emergence of new toxigenic V. cholerae strains.
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Affiliation(s)
- Shrestha Sinha-Ray
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States.,Department of Microbiology and Cell Science, College of Agricultural and Life Sciences, University of Florida, Gainesville, FL, United States
| | - Meer T Alam
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States.,Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, FL, United States
| | - Satyabrata Bag
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States.,Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, FL, United States
| | - J Glenn Morris
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States.,Department of Medicine, School of Medicine, University of Florida, Gainesville, FL, United States
| | - Afsar Ali
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States.,Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, FL, United States
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12
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Hounmanou YMG, Leekitcharoenphon P, Hendriksen RS, Dougnon TV, Mdegela RH, Olsen JE, Dalsgaard A. Surveillance and Genomics of Toxigenic Vibrio cholerae O1 From Fish, Phytoplankton and Water in Lake Victoria, Tanzania. Front Microbiol 2019; 10:901. [PMID: 31114556 PMCID: PMC6503148 DOI: 10.3389/fmicb.2019.00901] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 04/09/2019] [Indexed: 12/29/2022] Open
Abstract
The occurrence of toxigenic Vibrio cholerae O1 during a non- outbreak period in Lake Victoria was studied and genetic characteristics for environmental persistence and relatedness to pandemic strains were assessed. We analyzed 360 samples of carps, phytoplankton and water collected in 2017 during dry and rainy seasons in the Tanzanian basin of Lake Victoria. Samples were tested using PCR (ompW and ctxA) with DNA extracted from bacterial isolates and samples enriched in alkaline peptone water. Isolates were screened with polyvalent antiserum O1 followed by antimicrobial susceptibility testing. Whole genome sequencing and bioinformatics tools were employed to investigate the genomic characteristics of the isolates. More V. cholerae positive samples were recovered by PCR when DNA was obtained from enriched samples than from isolates (69.0% vs. 21.3%, p < 0.05), irrespectively of season. We identified ten V. cholerae O1 among 22 ctxA-positive isolates. Further studies are needed to serotype the remaining ctxA-positive non-O1 strains. Sequenced strains belonged to El Tor atypical biotype of V. cholerae O1 of MLST ST69 harboring the seventh pandemic gene. Major virulence genes, ctxA, ctxB, zot, ace, tcpA, hlyA, rtxA, ompU, toxR, T6SS, alsD, makA and pathogenicity islands VPI-1, VPI-2, VSP-1, and VSP-2 were found in all strains. The strains contained Vibrio polysaccharide biosynthesis enzymes, the mshA gene and two-component response regulator proteins involved in stress response and autoinducers for quorum sensing and biofilm formation. They carried the SXT integrative conjugative element with phenotypic and genotypic resistance to aminoglycoside, sulfamethoxazole, trimethoprim, phenicol, and quinolones. Strains contained a multidrug efflux pump component and were resistant to toxic compounds with copper homeostasis and cobalt-zinc-cadmium resistance proteins. The environmental strains belonged to the third wave of the seventh pandemic and most are genetically closely related to recent outbreak strains from Tanzania, Kenya, and Uganda with as low as three SNPs difference. Some strains have persisted longer in the environment and were more related to older outbreak strains in the region. V. cholerae O1 of outbreak potential seem to persist in Lake Victoria through interactions with fish and phytoplankton supported by the optimum water parameters and intrinsic genetic features enhancing survival in the aquatic environment.
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Affiliation(s)
- Yaovi M Gildas Hounmanou
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Pimlapas Leekitcharoenphon
- National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Food Borne Pathogens and Genomics and European Union Reference Laboratory for Antimicrobial Resistance, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Rene S Hendriksen
- National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Food Borne Pathogens and Genomics and European Union Reference Laboratory for Antimicrobial Resistance, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Tamegnon V Dougnon
- Research Unit in Applied Microbiology and Pharmacology of Natural Substances, Laboratory of Research in Applied Biology, Polytechnic School of Abomey-Calavi, University of Abomey-Calavi, Cotonou, Benin
| | - Robinson H Mdegela
- Department of Veterinary Medicine and Public Health, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania
| | - John E Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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13
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Willner MR, Vikesland PJ. Nanomaterial enabled sensors for environmental contaminants. J Nanobiotechnology 2018; 16:95. [PMID: 30466465 PMCID: PMC6249933 DOI: 10.1186/s12951-018-0419-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 11/07/2018] [Indexed: 12/19/2022] Open
Abstract
The need and desire to understand the environment, especially the quality of one's local water and air, has continued to expand with the emergence of the digital age. The bottleneck in understanding the environment has switched from being able to store all of the data collected to collecting enough data on a broad range of contaminants of environmental concern. Nanomaterial enabled sensors represent a suite of technologies developed over the last 15 years for the highly specific and sensitive detection of environmental contaminants. With the promise of facile, low cost, field-deployable technology, the ability to quantitatively understand nature in a systematic way will soon be a reality. In this review, we first introduce nanosensor design before exploring the application of nanosensors for the detection of three classes of environmental contaminants: pesticides, heavy metals, and pathogens.
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Affiliation(s)
- Marjorie R. Willner
- Department of Civil and Environmental Engineering and the Institute for Critical Technology and Applied Science, Center for Sustainable Nanotechnology (VTSuN), Virginia Tech, Blacksburg, USA
| | - Peter J. Vikesland
- Department of Civil and Environmental Engineering and the Institute for Critical Technology and Applied Science, Center for Sustainable Nanotechnology (VTSuN), Virginia Tech, Blacksburg, USA
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14
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Guardiola-Avila I, Martínez-Vázquez V, Requena-Castro R, Juárez-Rendón K, Aguilera-Arreola M, Rivera G, Bocanegra-García V. Isolation and identification ofVibriospecies in the Rio Bravo/Grande and water bodies from Reynosa, Tamaulipas. Lett Appl Microbiol 2018; 67:190-196. [DOI: 10.1111/lam.13009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 05/11/2018] [Accepted: 05/12/2018] [Indexed: 02/02/2023]
Affiliation(s)
- I. Guardiola-Avila
- CONACyT Research Fellow; Centro de Biotecnología Genómica; Instituto Politécnico Nacional; Reynosa Tamaulipas México
| | - V. Martínez-Vázquez
- Centro de Biotecnología Genómica; Instituto Politécnico Nacional; Reynosa Tamaulipas México
| | - R. Requena-Castro
- Centro de Biotecnología Genómica; Instituto Politécnico Nacional; Reynosa Tamaulipas México
| | - K. Juárez-Rendón
- CONACyT Research Fellow; Centro de Biotecnología Genómica; Instituto Politécnico Nacional; Reynosa Tamaulipas México
| | - M.G. Aguilera-Arreola
- Escuela Nacional de Ciencias Biológicas; Instituto Politécnico Nacional; Ciudad de México; Mexico City México
| | - G. Rivera
- Centro de Biotecnología Genómica; Instituto Politécnico Nacional; Reynosa Tamaulipas México
| | - V. Bocanegra-García
- Centro de Biotecnología Genómica; Instituto Politécnico Nacional; Reynosa Tamaulipas México
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15
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Hossain ZZ, Farhana I, Tulsiani SM, Begum A, Jensen PKM. Transmission and Toxigenic Potential of Vibrio cholerae in Hilsha Fish ( Tenualosa ilisha) for Human Consumption in Bangladesh. Front Microbiol 2018. [PMID: 29515532 PMCID: PMC5826273 DOI: 10.3389/fmicb.2018.00222] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Fish have been considered natural reservoirs of Vibrio cholerae, the deadly diarrheal pathogen. However, little is known about the role of fish in the transmission of V. cholerae from the Bay of Bengal to the households of rural and urban Bangladesh. This study analyzes the incidence and pathogenic potential of V. cholerae in Hilsha (Tenualosa ilisha), a commonly caught and consumed fish that exhibits a life cycle in both freshwater and marine environments in Bangladesh. During the period from October 2014 to October 2015, samples from the gills, recta, intestines, and scale swabs of a total of 48 fish were analyzed. The fish were collected both at local markets in the capital city Dhaka and directly from fishermen at the river. PCR analysis by targeting V. cholerae species-specific ompW gene revealed that 39 of 48 (81%) fish were positive in at least one of the sample types. Real-time PCR analysis demonstrated that the cholera-causing ctxA gene was detected in 20% (8 of 39) of V. cholerae-positive fish. A total of 158 V. cholerae isolates were obtained which were categorized into 35 genotypic groups. Altogether, 25 O1 and 133 non-O1/O139 strains were isolated, which were negative for the cholera toxin gene. Other pathogenic genes such as stn/sto, hlyA, chxA, SXT, rtxC, and HA-P were detected. The type three secretion system gene cluster (TTSS) was present in 18% (24 of 133) of non-O1/O139 isolates. The antibiotic susceptibility test revealed that the isolates conferred high resistance to sulfamethoxazole-trimethoprim and kanamycin. Both O1 and non-O1/O139 strains were able to accumulate fluid in rabbit ileal loops and caused distinctive cell death in HeLa cell. Multilocus sequence typing (MLST) showed clonal diversity among fish isolates with pandemic clones. Our data suggest a high prevalence of V. cholerae in Hilsha fish, which indicates that this fish could serve as a potential vehicle for V. cholerae transmission. Moreover, the indigenous V. cholerae strains isolated from Hilsha fish possess considerable virulence potential despite being quite diverse from current epidemic strains. This represents the first study of the population structure of V. cholerae associated with fish in Bangladesh.
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Affiliation(s)
- Zenat Z Hossain
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh.,Institute of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Israt Farhana
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - Suhella M Tulsiani
- Institute of Public Health, University of Copenhagen, Copenhagen, Denmark.,Copenhagen Centre for Disaster Research, University of Copenhagen, Copenhagen, Denmark
| | - Anowara Begum
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - Peter K M Jensen
- Institute of Public Health, University of Copenhagen, Copenhagen, Denmark.,Copenhagen Centre for Disaster Research, University of Copenhagen, Copenhagen, Denmark
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16
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Mironova LV, Gladkikh AS, Ponomareva AS, Feranchuk SI, Bochalgin NО, Basov EA, Yu Khunkheeva Z, Balakhonov SV. Comparative genomics of Vibrio cholerae El Tor strains isolated at epidemic complications in Siberia and at the Far East. INFECTION GENETICS AND EVOLUTION 2018; 60:80-88. [PMID: 29462719 DOI: 10.1016/j.meegid.2018.02.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 02/13/2018] [Accepted: 02/16/2018] [Indexed: 11/30/2022]
Abstract
The territory of Siberia and the Far East of Russia is classified as epidemically safe for cholera; however, in the 1970s and 1990s a number of infection importation cases and acute outbreaks associated with the cholera importation were reported. Here, we analyze genomes of four Vibrio cholerae El Tor strains isolated from humans during epidemic complications (imported cases, an outbreak) in the 1990s. The analyzed strains harbor the classical allele of the cholera toxin subunit B gene (ctxB1); thus, belong to genetically altered variants of the El Tor biotype. Analysis of the genomes revealed their high homology with the V. cholerae N16961 reference strain: 85-93 SNPs were identified in the core genome as compared to the reference. The determined features of SNPs in the CTX prophage made it possible to propose the presence of a new subtype - CTX-2a in two strains; the other two strains carried the prophage of CTX-3 type. Results of phylogenetic analysis based on SNP-typing demonstrated that two strains belonged to the second wave, and two - to the early third wave of cholera dissemination in the world. Phylogenetic reconstruction in combination with epidemiological data permitted to trace the origin of the strains and the way of their importation to the Russian Federation directly or through temporary cholera foci.
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Affiliation(s)
- Liliya V Mironova
- Irkutsk Antiplague Research Institute of Rospotrebnadzor, 78, Trillisser str., Irkutsk 664047, Russia
| | - Anna S Gladkikh
- Irkutsk Antiplague Research Institute of Rospotrebnadzor, 78, Trillisser str., Irkutsk 664047, Russia.
| | - Anna S Ponomareva
- Irkutsk Antiplague Research Institute of Rospotrebnadzor, 78, Trillisser str., Irkutsk 664047, Russia
| | - Sergey I Feranchuk
- Irkutsk Antiplague Research Institute of Rospotrebnadzor, 78, Trillisser str., Irkutsk 664047, Russia; Limnological Institute of Siberian Branch of Russian Academy of Sciences, 3, Ulan-Batorskaya str., Irkutsk 664033, Russia
| | - Nikita О Bochalgin
- Irkutsk Antiplague Research Institute of Rospotrebnadzor, 78, Trillisser str., Irkutsk 664047, Russia
| | - Evgenii A Basov
- Irkutsk Antiplague Research Institute of Rospotrebnadzor, 78, Trillisser str., Irkutsk 664047, Russia
| | - Zhanna Yu Khunkheeva
- Irkutsk Antiplague Research Institute of Rospotrebnadzor, 78, Trillisser str., Irkutsk 664047, Russia
| | - Sergey V Balakhonov
- Irkutsk Antiplague Research Institute of Rospotrebnadzor, 78, Trillisser str., Irkutsk 664047, Russia
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17
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Domman D, Quilici ML, Dorman MJ, Njamkepo E, Mutreja A, Mather AE, Delgado G, Morales-Espinosa R, Grimont PAD, Lizárraga-Partida ML, Bouchier C, Aanensen DM, Kuri-Morales P, Tarr CL, Dougan G, Parkhill J, Campos J, Cravioto A, Weill FX, Thomson NR. Integrated view of Vibrio cholerae in the Americas. Science 2017; 358:789-793. [DOI: 10.1126/science.aao2136] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 10/10/2017] [Indexed: 01/24/2023]
Abstract
Latin America has experienced two of the largest cholera epidemics in modern history; one in 1991 and the other in 2010. However, confusion still surrounds the relationships between globally circulating pandemic Vibrio cholerae clones and local bacterial populations. We used whole-genome sequencing to characterize cholera across the Americas over a 40-year time span. We found that both epidemics were the result of intercontinental introductions of seventh pandemic El Tor V. cholerae and that at least seven lineages local to the Americas are associated with disease that differs epidemiologically from epidemic cholera. Our results consolidate historical accounts of pandemic cholera with data to show the importance of local lineages, presenting an integrated view of cholera that is important to the design of future disease control strategies.
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Affiliation(s)
- Daryl Domman
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Marie-Laure Quilici
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Paris, 75015, France
| | - Matthew J. Dorman
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Elisabeth Njamkepo
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Paris, 75015, France
| | - Ankur Mutreja
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0SP, UK
| | - Alison E. Mather
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK
| | - Gabriella Delgado
- Department of Microbiology and Parasitology, Faculty of Medicine, Universidad Nacional Autónoma de México, Mexico, D.F., Mexico
| | - Rosario Morales-Espinosa
- Department of Microbiology and Parasitology, Faculty of Medicine, Universidad Nacional Autónoma de México, Mexico, D.F., Mexico
| | - Patrick A. D. Grimont
- Institut Pasteur, Unité Biodiversité des Bactéries Pathogènes Emergentes, Paris, 75015, France
| | | | | | - David M. Aanensen
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Pablo Kuri-Morales
- Subsecretaría de Prevención y Promoción de la Salud, Secretaría de Salud, Ciudad de México, Mexico
| | - Cheryl L. Tarr
- Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Gordon Dougan
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0SP, UK
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Josefina Campos
- Instituto Nacional de Enfermedades Infecciosas, ANLIS, Buenos Aires, Argentina
| | - Alejandro Cravioto
- Faculty of Medicine, Universidad Nacional Autónoma de México, Mexico, D.F., Mexico
| | - François-Xavier Weill
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Paris, 75015, France
| | - Nicholas R. Thomson
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
- London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
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