1
|
Mavian CN, Tagliamonte MS, Alam MT, Sakib SN, Cash MN, Moir M, Jimenez JP, Riva A, Nelson EJ, Cato ET, Ajayakumar J, Louis R, Curtis A, De Rochars VMB, Rouzier V, Pape JW, de Oliveira T, Morris JG, Salemi M, Ali A. Ancestral Origin and Dissemination Dynamics of Reemerging Toxigenic Vibrio cholerae, Haiti. Emerg Infect Dis 2023; 29:2072-2082. [PMID: 37735743 PMCID: PMC10521621 DOI: 10.3201/eid2910.230554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023] Open
Abstract
The 2010 cholera epidemic in Haiti was thought to have ended in 2019, and the Prime Minister of Haiti declared the country cholera-free in February 2022. On September 25, 2022, cholera cases were again identified in Port-au-Prince. We compared genomic data from 42 clinical Vibrio cholerae strains from 2022 with data from 327 other strains from Haiti and 1,824 strains collected worldwide. The 2022 isolates were homogeneous and closely related to clinical and environmental strains circulating in Haiti during 2012-2019. Bayesian hypothesis testing indicated that the 2022 clinical isolates shared their most recent common ancestor with an environmental lineage circulating in Haiti in July 2018. Our findings strongly suggest that toxigenic V. cholerae O1 can persist for years in aquatic environmental reservoirs and ignite new outbreaks. These results highlight the urgent need for improved public health infrastructure and possible periodic vaccination campaigns to maintain population immunity against V. cholerae.
Collapse
Affiliation(s)
- Carla N. Mavian
- University of Florida, Gainesville, Florida, USA (C.N. Mavian, M.S. Tagliamonte, M.T. Alam, S.N. Sakib, M.N. Cash, J.P. Jimenez, A. Riva, E.J. Nelson, E.T. Cato, R. Louis, V.M. Beau De Rochars, J.G. Morris Jr., M. Salemi, A. Ali)
- Stellenbosch University, Stellenbosch, South Africa (M. Moir, T. de Oliveira)
- Case Western Reserve University School of Medicine, Cleveland, Ohio, USA (J. Ajayakumar, A. Curtis)
- Les Centres GHESKIO, Port-au-Prince, Haiti (V. Rouzier, J.W. Pape)
- Weill Cornell Medical College, New York, New York, USA (V. Rouzier, J.W. Pape)
- University of KwaZulu-Natal, Durban, South Africa (T. de Oliveira)
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa (T. de Oliveira)
- University of Washington, Seattle, Washington, USA (T. de Oliveira)
| | - Massimiliano S. Tagliamonte
- University of Florida, Gainesville, Florida, USA (C.N. Mavian, M.S. Tagliamonte, M.T. Alam, S.N. Sakib, M.N. Cash, J.P. Jimenez, A. Riva, E.J. Nelson, E.T. Cato, R. Louis, V.M. Beau De Rochars, J.G. Morris Jr., M. Salemi, A. Ali)
- Stellenbosch University, Stellenbosch, South Africa (M. Moir, T. de Oliveira)
- Case Western Reserve University School of Medicine, Cleveland, Ohio, USA (J. Ajayakumar, A. Curtis)
- Les Centres GHESKIO, Port-au-Prince, Haiti (V. Rouzier, J.W. Pape)
- Weill Cornell Medical College, New York, New York, USA (V. Rouzier, J.W. Pape)
- University of KwaZulu-Natal, Durban, South Africa (T. de Oliveira)
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa (T. de Oliveira)
- University of Washington, Seattle, Washington, USA (T. de Oliveira)
| | - Meer T. Alam
- University of Florida, Gainesville, Florida, USA (C.N. Mavian, M.S. Tagliamonte, M.T. Alam, S.N. Sakib, M.N. Cash, J.P. Jimenez, A. Riva, E.J. Nelson, E.T. Cato, R. Louis, V.M. Beau De Rochars, J.G. Morris Jr., M. Salemi, A. Ali)
- Stellenbosch University, Stellenbosch, South Africa (M. Moir, T. de Oliveira)
- Case Western Reserve University School of Medicine, Cleveland, Ohio, USA (J. Ajayakumar, A. Curtis)
- Les Centres GHESKIO, Port-au-Prince, Haiti (V. Rouzier, J.W. Pape)
- Weill Cornell Medical College, New York, New York, USA (V. Rouzier, J.W. Pape)
- University of KwaZulu-Natal, Durban, South Africa (T. de Oliveira)
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa (T. de Oliveira)
- University of Washington, Seattle, Washington, USA (T. de Oliveira)
| | - S. Nazmus Sakib
- University of Florida, Gainesville, Florida, USA (C.N. Mavian, M.S. Tagliamonte, M.T. Alam, S.N. Sakib, M.N. Cash, J.P. Jimenez, A. Riva, E.J. Nelson, E.T. Cato, R. Louis, V.M. Beau De Rochars, J.G. Morris Jr., M. Salemi, A. Ali)
- Stellenbosch University, Stellenbosch, South Africa (M. Moir, T. de Oliveira)
- Case Western Reserve University School of Medicine, Cleveland, Ohio, USA (J. Ajayakumar, A. Curtis)
- Les Centres GHESKIO, Port-au-Prince, Haiti (V. Rouzier, J.W. Pape)
- Weill Cornell Medical College, New York, New York, USA (V. Rouzier, J.W. Pape)
- University of KwaZulu-Natal, Durban, South Africa (T. de Oliveira)
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa (T. de Oliveira)
- University of Washington, Seattle, Washington, USA (T. de Oliveira)
| | - Melanie N. Cash
- University of Florida, Gainesville, Florida, USA (C.N. Mavian, M.S. Tagliamonte, M.T. Alam, S.N. Sakib, M.N. Cash, J.P. Jimenez, A. Riva, E.J. Nelson, E.T. Cato, R. Louis, V.M. Beau De Rochars, J.G. Morris Jr., M. Salemi, A. Ali)
- Stellenbosch University, Stellenbosch, South Africa (M. Moir, T. de Oliveira)
- Case Western Reserve University School of Medicine, Cleveland, Ohio, USA (J. Ajayakumar, A. Curtis)
- Les Centres GHESKIO, Port-au-Prince, Haiti (V. Rouzier, J.W. Pape)
- Weill Cornell Medical College, New York, New York, USA (V. Rouzier, J.W. Pape)
- University of KwaZulu-Natal, Durban, South Africa (T. de Oliveira)
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa (T. de Oliveira)
- University of Washington, Seattle, Washington, USA (T. de Oliveira)
| | - Monika Moir
- University of Florida, Gainesville, Florida, USA (C.N. Mavian, M.S. Tagliamonte, M.T. Alam, S.N. Sakib, M.N. Cash, J.P. Jimenez, A. Riva, E.J. Nelson, E.T. Cato, R. Louis, V.M. Beau De Rochars, J.G. Morris Jr., M. Salemi, A. Ali)
- Stellenbosch University, Stellenbosch, South Africa (M. Moir, T. de Oliveira)
- Case Western Reserve University School of Medicine, Cleveland, Ohio, USA (J. Ajayakumar, A. Curtis)
- Les Centres GHESKIO, Port-au-Prince, Haiti (V. Rouzier, J.W. Pape)
- Weill Cornell Medical College, New York, New York, USA (V. Rouzier, J.W. Pape)
- University of KwaZulu-Natal, Durban, South Africa (T. de Oliveira)
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa (T. de Oliveira)
- University of Washington, Seattle, Washington, USA (T. de Oliveira)
| | - Juan Perez Jimenez
- University of Florida, Gainesville, Florida, USA (C.N. Mavian, M.S. Tagliamonte, M.T. Alam, S.N. Sakib, M.N. Cash, J.P. Jimenez, A. Riva, E.J. Nelson, E.T. Cato, R. Louis, V.M. Beau De Rochars, J.G. Morris Jr., M. Salemi, A. Ali)
- Stellenbosch University, Stellenbosch, South Africa (M. Moir, T. de Oliveira)
- Case Western Reserve University School of Medicine, Cleveland, Ohio, USA (J. Ajayakumar, A. Curtis)
- Les Centres GHESKIO, Port-au-Prince, Haiti (V. Rouzier, J.W. Pape)
- Weill Cornell Medical College, New York, New York, USA (V. Rouzier, J.W. Pape)
- University of KwaZulu-Natal, Durban, South Africa (T. de Oliveira)
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa (T. de Oliveira)
- University of Washington, Seattle, Washington, USA (T. de Oliveira)
| | - Alberto Riva
- University of Florida, Gainesville, Florida, USA (C.N. Mavian, M.S. Tagliamonte, M.T. Alam, S.N. Sakib, M.N. Cash, J.P. Jimenez, A. Riva, E.J. Nelson, E.T. Cato, R. Louis, V.M. Beau De Rochars, J.G. Morris Jr., M. Salemi, A. Ali)
- Stellenbosch University, Stellenbosch, South Africa (M. Moir, T. de Oliveira)
- Case Western Reserve University School of Medicine, Cleveland, Ohio, USA (J. Ajayakumar, A. Curtis)
- Les Centres GHESKIO, Port-au-Prince, Haiti (V. Rouzier, J.W. Pape)
- Weill Cornell Medical College, New York, New York, USA (V. Rouzier, J.W. Pape)
- University of KwaZulu-Natal, Durban, South Africa (T. de Oliveira)
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa (T. de Oliveira)
- University of Washington, Seattle, Washington, USA (T. de Oliveira)
| | - Eric J. Nelson
- University of Florida, Gainesville, Florida, USA (C.N. Mavian, M.S. Tagliamonte, M.T. Alam, S.N. Sakib, M.N. Cash, J.P. Jimenez, A. Riva, E.J. Nelson, E.T. Cato, R. Louis, V.M. Beau De Rochars, J.G. Morris Jr., M. Salemi, A. Ali)
- Stellenbosch University, Stellenbosch, South Africa (M. Moir, T. de Oliveira)
- Case Western Reserve University School of Medicine, Cleveland, Ohio, USA (J. Ajayakumar, A. Curtis)
- Les Centres GHESKIO, Port-au-Prince, Haiti (V. Rouzier, J.W. Pape)
- Weill Cornell Medical College, New York, New York, USA (V. Rouzier, J.W. Pape)
- University of KwaZulu-Natal, Durban, South Africa (T. de Oliveira)
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa (T. de Oliveira)
- University of Washington, Seattle, Washington, USA (T. de Oliveira)
| | - Emilie T. Cato
- University of Florida, Gainesville, Florida, USA (C.N. Mavian, M.S. Tagliamonte, M.T. Alam, S.N. Sakib, M.N. Cash, J.P. Jimenez, A. Riva, E.J. Nelson, E.T. Cato, R. Louis, V.M. Beau De Rochars, J.G. Morris Jr., M. Salemi, A. Ali)
- Stellenbosch University, Stellenbosch, South Africa (M. Moir, T. de Oliveira)
- Case Western Reserve University School of Medicine, Cleveland, Ohio, USA (J. Ajayakumar, A. Curtis)
- Les Centres GHESKIO, Port-au-Prince, Haiti (V. Rouzier, J.W. Pape)
- Weill Cornell Medical College, New York, New York, USA (V. Rouzier, J.W. Pape)
- University of KwaZulu-Natal, Durban, South Africa (T. de Oliveira)
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa (T. de Oliveira)
- University of Washington, Seattle, Washington, USA (T. de Oliveira)
| | - Jayakrishnan Ajayakumar
- University of Florida, Gainesville, Florida, USA (C.N. Mavian, M.S. Tagliamonte, M.T. Alam, S.N. Sakib, M.N. Cash, J.P. Jimenez, A. Riva, E.J. Nelson, E.T. Cato, R. Louis, V.M. Beau De Rochars, J.G. Morris Jr., M. Salemi, A. Ali)
- Stellenbosch University, Stellenbosch, South Africa (M. Moir, T. de Oliveira)
- Case Western Reserve University School of Medicine, Cleveland, Ohio, USA (J. Ajayakumar, A. Curtis)
- Les Centres GHESKIO, Port-au-Prince, Haiti (V. Rouzier, J.W. Pape)
- Weill Cornell Medical College, New York, New York, USA (V. Rouzier, J.W. Pape)
- University of KwaZulu-Natal, Durban, South Africa (T. de Oliveira)
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa (T. de Oliveira)
- University of Washington, Seattle, Washington, USA (T. de Oliveira)
| | - Rigan Louis
- University of Florida, Gainesville, Florida, USA (C.N. Mavian, M.S. Tagliamonte, M.T. Alam, S.N. Sakib, M.N. Cash, J.P. Jimenez, A. Riva, E.J. Nelson, E.T. Cato, R. Louis, V.M. Beau De Rochars, J.G. Morris Jr., M. Salemi, A. Ali)
- Stellenbosch University, Stellenbosch, South Africa (M. Moir, T. de Oliveira)
- Case Western Reserve University School of Medicine, Cleveland, Ohio, USA (J. Ajayakumar, A. Curtis)
- Les Centres GHESKIO, Port-au-Prince, Haiti (V. Rouzier, J.W. Pape)
- Weill Cornell Medical College, New York, New York, USA (V. Rouzier, J.W. Pape)
- University of KwaZulu-Natal, Durban, South Africa (T. de Oliveira)
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa (T. de Oliveira)
- University of Washington, Seattle, Washington, USA (T. de Oliveira)
| | - Andrew Curtis
- University of Florida, Gainesville, Florida, USA (C.N. Mavian, M.S. Tagliamonte, M.T. Alam, S.N. Sakib, M.N. Cash, J.P. Jimenez, A. Riva, E.J. Nelson, E.T. Cato, R. Louis, V.M. Beau De Rochars, J.G. Morris Jr., M. Salemi, A. Ali)
- Stellenbosch University, Stellenbosch, South Africa (M. Moir, T. de Oliveira)
- Case Western Reserve University School of Medicine, Cleveland, Ohio, USA (J. Ajayakumar, A. Curtis)
- Les Centres GHESKIO, Port-au-Prince, Haiti (V. Rouzier, J.W. Pape)
- Weill Cornell Medical College, New York, New York, USA (V. Rouzier, J.W. Pape)
- University of KwaZulu-Natal, Durban, South Africa (T. de Oliveira)
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa (T. de Oliveira)
- University of Washington, Seattle, Washington, USA (T. de Oliveira)
| | - V. Madsen Beau De Rochars
- University of Florida, Gainesville, Florida, USA (C.N. Mavian, M.S. Tagliamonte, M.T. Alam, S.N. Sakib, M.N. Cash, J.P. Jimenez, A. Riva, E.J. Nelson, E.T. Cato, R. Louis, V.M. Beau De Rochars, J.G. Morris Jr., M. Salemi, A. Ali)
- Stellenbosch University, Stellenbosch, South Africa (M. Moir, T. de Oliveira)
- Case Western Reserve University School of Medicine, Cleveland, Ohio, USA (J. Ajayakumar, A. Curtis)
- Les Centres GHESKIO, Port-au-Prince, Haiti (V. Rouzier, J.W. Pape)
- Weill Cornell Medical College, New York, New York, USA (V. Rouzier, J.W. Pape)
- University of KwaZulu-Natal, Durban, South Africa (T. de Oliveira)
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa (T. de Oliveira)
- University of Washington, Seattle, Washington, USA (T. de Oliveira)
| | - Vanessa Rouzier
- University of Florida, Gainesville, Florida, USA (C.N. Mavian, M.S. Tagliamonte, M.T. Alam, S.N. Sakib, M.N. Cash, J.P. Jimenez, A. Riva, E.J. Nelson, E.T. Cato, R. Louis, V.M. Beau De Rochars, J.G. Morris Jr., M. Salemi, A. Ali)
- Stellenbosch University, Stellenbosch, South Africa (M. Moir, T. de Oliveira)
- Case Western Reserve University School of Medicine, Cleveland, Ohio, USA (J. Ajayakumar, A. Curtis)
- Les Centres GHESKIO, Port-au-Prince, Haiti (V. Rouzier, J.W. Pape)
- Weill Cornell Medical College, New York, New York, USA (V. Rouzier, J.W. Pape)
- University of KwaZulu-Natal, Durban, South Africa (T. de Oliveira)
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa (T. de Oliveira)
- University of Washington, Seattle, Washington, USA (T. de Oliveira)
| | - Jean William Pape
- University of Florida, Gainesville, Florida, USA (C.N. Mavian, M.S. Tagliamonte, M.T. Alam, S.N. Sakib, M.N. Cash, J.P. Jimenez, A. Riva, E.J. Nelson, E.T. Cato, R. Louis, V.M. Beau De Rochars, J.G. Morris Jr., M. Salemi, A. Ali)
- Stellenbosch University, Stellenbosch, South Africa (M. Moir, T. de Oliveira)
- Case Western Reserve University School of Medicine, Cleveland, Ohio, USA (J. Ajayakumar, A. Curtis)
- Les Centres GHESKIO, Port-au-Prince, Haiti (V. Rouzier, J.W. Pape)
- Weill Cornell Medical College, New York, New York, USA (V. Rouzier, J.W. Pape)
- University of KwaZulu-Natal, Durban, South Africa (T. de Oliveira)
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa (T. de Oliveira)
- University of Washington, Seattle, Washington, USA (T. de Oliveira)
| | - Tulio de Oliveira
- University of Florida, Gainesville, Florida, USA (C.N. Mavian, M.S. Tagliamonte, M.T. Alam, S.N. Sakib, M.N. Cash, J.P. Jimenez, A. Riva, E.J. Nelson, E.T. Cato, R. Louis, V.M. Beau De Rochars, J.G. Morris Jr., M. Salemi, A. Ali)
- Stellenbosch University, Stellenbosch, South Africa (M. Moir, T. de Oliveira)
- Case Western Reserve University School of Medicine, Cleveland, Ohio, USA (J. Ajayakumar, A. Curtis)
- Les Centres GHESKIO, Port-au-Prince, Haiti (V. Rouzier, J.W. Pape)
- Weill Cornell Medical College, New York, New York, USA (V. Rouzier, J.W. Pape)
- University of KwaZulu-Natal, Durban, South Africa (T. de Oliveira)
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa (T. de Oliveira)
- University of Washington, Seattle, Washington, USA (T. de Oliveira)
| | | | | | | |
Collapse
|
2
|
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.
Collapse
|
3
|
Jugder BE, Batista JH, Gibson JA, Cunningham PM, Asara JM, Watnick PI. Vibrio cholerae high cell density quorum sensing activates the host intestinal innate immune response. Cell Rep 2022; 40:111368. [PMID: 36130487 PMCID: PMC9534793 DOI: 10.1016/j.celrep.2022.111368] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 07/17/2022] [Accepted: 08/26/2022] [Indexed: 12/03/2022] Open
Abstract
Quorum sensing fundamentally alters the interaction of Vibrio cholerae with aquatic environments, environmental hosts, and the human intestine. At high cell density, the quorum-sensing regulator HapR represses not only expression of cholera toxin and the toxin co-regulated pilus, virulence factors essential in human infection, but also synthesis of the Vibrio polysaccharide (VPS) exopolysaccharide-based matrix required for abiotic and biotic surface attachment. Here, we describe a feature of V. cholerae quorum sensing that shifts the host-pathogen interaction toward commensalism. By repressing pathogen consumptive anabolic metabolism and, in particular, tryptophan uptake, V. cholerae HapR stimulates host intestinal serotonin production. This, in turn, activates host intestinal innate immune signaling to promote host survival.
Collapse
Affiliation(s)
- Bat-Erdene Jugder
- Division of Infectious Diseases, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, 25 Shattuck St., Boston, MA 02115, USA
| | - Juliana H Batista
- Division of Infectious Diseases, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, 25 Shattuck St., Boston, MA 02115, USA
| | - Jacob A Gibson
- Division of Infectious Diseases, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, USA; Biological and Biomedical Sciences Program, Harvard Medical School, 25 Shattuck St., Boston, MA 02115, USA
| | - Paul M Cunningham
- Division of Infectious Diseases, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, USA
| | - John M Asara
- Division of Signal Transduction/Mass Spectrometry Core, Beth Israel Deaconess Medical Center, Blackfan Circle, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Paula I Watnick
- Division of Infectious Diseases, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, 25 Shattuck St., Boston, MA 02115, USA.
| |
Collapse
|
4
|
Outbreak dynamics of foodborne pathogen Vibrio parahaemolyticus over a seventeen year period implies hidden reservoirs. Nat Microbiol 2022; 7:1221-1229. [PMID: 35918422 DOI: 10.1038/s41564-022-01182-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 06/22/2022] [Indexed: 12/31/2022]
Abstract
Controlling foodborne diseases requires robust outbreak detection and a comprehensive understanding of outbreak dynamics. Here, by integrating large-scale phylogenomic analysis of 3,642 isolates and epidemiological data, we performed 'data-driven' outbreak detection and described the long-term outbreak dynamics of the leading seafood-associated pathogen, Vibrio parahaemolyticus, in Shenzhen, China, over a 17-year period. Contradictory to the widely accepted notion that sporadic patients and independent point-source outbreaks dominated foodborne infections, we found that 71% of isolates from patients grouped into within-1-month clusters that differed by ≤6 single nucleotide polymorphisms, indicating putative outbreaks. Furthermore, we showed that despite the long time spans between clusters, 70% of them were genomically closely related and were inferred to arise from a small number of common sources, which provides evidence that hidden persistent reservoirs generated most of the outbreaks rather than independent point-sources. Phylogeographical analysis further revealed the geographical heterogeneity of outbreaks and identified a coastal district as the potential hotspot of outbreaks and as the hub and major source of cross-district spread events. Our findings provide a comprehensive picture of the long-term spatiotemporal dynamics of foodborne outbreaks and present a different perspective on the major source of foodborne infections, which will inform the design of future disease control strategies.
Collapse
|
5
|
Kawai M, Ota A, Takemura T, Nakai T, Maruyama F. Continuation and replacement of Vibrio cholerae non-O1 clonal genomic groups isolated from Plecoglossus altivelis fish in freshwaters. Environ Microbiol 2020; 22:4473-4484. [PMID: 33448654 DOI: 10.1111/1462-2920.15199] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 08/11/2020] [Accepted: 08/13/2020] [Indexed: 01/14/2023]
Abstract
The dissemination and abundances of Vibrio species in aquatic environments are of interest, as some species cause emerging diseases in humans and in aquatic organisms like fish. It is suggested that Vibrio cholerae non-O1 infections of Plecoglossus altivelis ('ayu') were spread to various parts of Japan through the annual transplantation of juvenile fish. To investigate this, we used genome-aided tracing of 17 V. cholerae strains isolated from ayu between the 1970s and 1990s in different Japanese freshwater systems. The strains formed a genomic clade distinct from all known clades, which we designate as the Ayu clade. Two clonal genomic groups identified within the clade, Ayu-1 and Ayu-2, persisted for a few years (between 1977 to 1979 and 1987 to 1990, respectively), and clonal replacement of Ayu-1 by Ayu-2 took place over an 8-year period. Despite the high similarity between Ayu-1 and Ayu-2 (> 99.9% identity and > 97% fraction of genomes shared), differences in their gene repertoires were found, raising the possibility that they are phenotypically distinct. These results highlight the importance of genome-based studies for understanding the long-term dynamics of populations over the timescale of years.
Collapse
Affiliation(s)
- Mikihiko Kawai
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Atsushi Ota
- Office of Industry-Academia-Government and Community Collaboration, Hiroshima University, Higashihiroshima, Japan
| | - Taichiro Takemura
- Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Toshihiro Nakai
- Graduate School of Biosphere Science, Hiroshima University, Higashihiroshima, Japan
| | - Fumito Maruyama
- Office of Industry-Academia-Government and Community Collaboration, Hiroshima University, Higashihiroshima, Japan
| |
Collapse
|
6
|
Moshiri N, Ragonnet-Cronin M, Wertheim JO, Mirarab S. FAVITES: simultaneous simulation of transmission networks, phylogenetic trees and sequences. Bioinformatics 2020; 35:1852-1861. [PMID: 30395173 DOI: 10.1093/bioinformatics/bty921] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 10/29/2018] [Accepted: 11/01/2018] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION The ability to simulate epidemics as a function of model parameters allows insights that are unobtainable from real datasets. Further, reconstructing transmission networks for fast-evolving viruses like Human Immunodeficiency Virus (HIV) may have the potential to greatly enhance epidemic intervention, but transmission network reconstruction methods have been inadequately studied, largely because it is difficult to obtain 'truth' sets on which to test them and properly measure their performance. RESULTS We introduce FrAmework for VIral Transmission and Evolution Simulation (FAVITES), a robust framework for simulating realistic datasets for epidemics that are caused by fast-evolving pathogens like HIV. FAVITES creates a generative model to produce contact networks, transmission networks, phylogenetic trees and sequence datasets, and to add error to the data. FAVITES is designed to be extensible by dividing the generative model into modules, each of which is expressed as a fixed API that can be implemented using various models. We use FAVITES to simulate HIV datasets and study the realism of the simulated datasets. We then use the simulated data to study the impact of the increased treatment efforts on epidemiological outcomes. We also study two transmission network reconstruction methods and their effectiveness in detecting fast-growing clusters. AVAILABILITY AND IMPLEMENTATION FAVITES is available at https://github.com/niemasd/FAVITES, and a Docker image can be found on DockerHub (https://hub.docker.com/r/niemasd/favites). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Niema Moshiri
- Bioinformatics and Systems Biology Graduate Program, UC San Diego, La Jolla, USA
| | | | | | - Siavash Mirarab
- Department of Electrical and Computer Engineering, UC San Diego, La Jolla, USA
| |
Collapse
|
7
|
Comparative core/pan genome analysis of Vibrio cholerae isolates from Pakistan. INFECTION GENETICS AND EVOLUTION 2020; 82:104316. [PMID: 32278144 DOI: 10.1016/j.meegid.2020.104316] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 03/31/2020] [Accepted: 04/03/2020] [Indexed: 01/23/2023]
Abstract
Cholera is an endemic disease in many regions of Asia including, Pakistan. Vibrio cholerae, the causative agent of cholera, is considered as one of the best adapted bacteria due to its ability to withstand severe environmental stresses. The V. cholerae genome is very plastic with many gene additions and deletions. In this study, we sought to understand the diversity of V. cholerae genes in two Pakistani subclades [e.g. Pakistani subclade I (PSC I) and Pakistani subclade II (PSC II)]. We have analyzed 44 PSC I and 56 PSC II strains, respectively. By analyzing our data, it was concluded that subclade group 2 (PSC II) has 2967 core genes repositories, while the PSC 1 group has just 1062 core genes. It was observed that the pangenome in the PSC II group is open while the pan-genome in PSC I are closed. It was also noted that the number of accessory genes (n = 2500) is higher in the PSC I group compared to the PSC II group (n = 550). Furthermore, analysis extended to the study of unique gene profiles suggested that all strains of the PSC II group have unique genes. One strain among the PSC II group had a high number of unique genes (n = 2612). However, in the PSC I group, only a few strains had unique genes with a maximum of 86 unique genes being found in a single strain. Core phylogeny of PSC I indicated that just three groups initially arose from a single common ancestor. At the same time, a complex pattern of evolution was found in the PSC II phylogenetic tree based on core gene information. This comparative genomic analysis has revealed 'waves' of V. cholerae evolution and information on its transmission and ability to modify its genetic content to survive in different environmental conditions. Here, we have investigated how the versatility of V. cholerae, a bacterium that persists across different habitats, is reflected in its genome. The data generated during the study should be extremely beneficial in defining the evolutionary relationship as well as diversity between V. cholerae subclades. It will also benefit epidemiological studies and the design of better treatment strategies for controlling epidemics.
Collapse
|
8
|
Toxigenic Vibrio cholerae evolution and establishment of reservoirs in aquatic ecosystems. Proc Natl Acad Sci U S A 2020; 117:7897-7904. [PMID: 32229557 PMCID: PMC7149412 DOI: 10.1073/pnas.1918763117] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The spread of cholera in the midst of an epidemic is largely driven by direct transmission from person to person, although it is well-recognized that Vibrio cholerae is also capable of growth and long-term survival in aquatic ecosystems. While prior studies have shown that aquatic reservoirs are important in the persistence of the disease on the Indian subcontinent, an epidemiological view postulating that locally evolving environmental V. cholerae contributes to outbreaks outside Asia remains debated. The single-source introduction of toxigenic V. cholerae O1 in Haiti, one of the largest outbreaks occurring this century, with 812,586 suspected cases and 9,606 deaths reported through July 2018, provided a unique opportunity to evaluate the role of aquatic reservoirs and assess bacterial transmission dynamics across environmental boundaries. To this end, we investigated the phylogeography of both clinical and aquatic toxigenic V. cholerae O1 isolates and show robust evidence of the establishment of aquatic reservoirs as well as ongoing evolution of V. cholerae isolates from aquatic sites. Novel environmental lineages emerged from sequential population bottlenecks, carrying mutations potentially involved in adaptation to the aquatic ecosystem. Based on such empirical data, we developed a mixed-transmission dynamic model of V. cholerae, where aquatic reservoirs actively contribute to genetic diversification and epidemic emergence, which underscores the complexity of transmission pathways in epidemics and endemic settings and the need for long-term investments in cholera control at both human and environmental levels.
Collapse
|
9
|
Fontana C, Angeletti S, Mirandola W, Cella E, Alessia L, Zehender G, Favaro M, Leoni D, Rose DD, Gherardi G, Florio LD, Salemi M, Andreoni M, Sarmati L, Ciccozzi M. Whole genome sequencing of carbapenem-resistant Klebsiella pneumoniae: evolutionary analysis for outbreak investigation. Future Microbiol 2020; 15:203-212. [PMID: 32056447 DOI: 10.2217/fmb-2019-0074] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Aim: Carbapenemase-resistant Enterobacteriaceae represents a major concern in hospital setting. Materials & methods: The evolutionary history of carbapenem-resistant Klebsiella pneumonia strains was analyzed by core genome multilocus sequence typing and Bayesian phylogenesis by whole genomes sequencing. Results: A great increase carbapenem-resistant K. pneumoniae causing blood stream infection was observed in the years 2015-2016. At multilocus sequence typing (MLST), they were prevalently ST512 and ST101. ST512 were core genome (cg)MLST 53, while ST101 mainly cgMLST453. The minimum-spanning tree, based on cgMLST, showed strains clustering based on the different STs. By Bayesian phylogenetic analysis, maximum clade credibility tree showed that strains were introduced in the year 2005 with the most probable location in the ICU ward. Two outbreaks by ST101 and ST512 strains with Tower T8 as the probable location were evidenced. Conclusion: Molecular epidemiology is a powerful tool to track the way of transmission of resistant bacteria within the hospital setting.
Collapse
Affiliation(s)
- Carla Fontana
- Clinical Microbiology Laboratories, Polyclinic of Tor Vergata, Rome, Italy.,Department of Experimental Medicine & Biochemical Sciences, University of Rome "Tor Vergata", Rome, Italy
| | - Silvia Angeletti
- Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome, Rome, Italy
| | - Walter Mirandola
- Clinical Microbiology Laboratories, Polyclinic of Tor Vergata, Rome, Italy
| | - Eleonora Cella
- Unit of Medical Statistics & Molecular Epidemiology, University Campus Bio-Medico of Rome, Italy
| | - Lai Alessia
- Department of Biomedical & Clinical Sciences "L. Sacco", University of Milan, Milan, Italy
| | - Gianguglielmo Zehender
- Department of Biomedical & Clinical Sciences "L. Sacco", University of Milan, Milan, Italy
| | - Marco Favaro
- Department of Experimental Medicine & Biochemical Sciences, University of Rome "Tor Vergata", Rome, Italy
| | - Davide Leoni
- Clinical of Infectious Diseases, Department of System Medicine, Tor Vergata University, Rome, Italy
| | - Diego Delle Rose
- Clinical of Infectious Diseases, Department of System Medicine, Tor Vergata University, Rome, Italy
| | - Giovanni Gherardi
- Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome, Rome, Italy
| | - Lucia De Florio
- Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome, Rome, Italy
| | - Marco Salemi
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610, USA.,Department of Pathology, Immunology & Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Massimo Andreoni
- Clinical of Infectious Diseases, Department of System Medicine, Tor Vergata University, Rome, Italy
| | - Loredana Sarmati
- Clinical of Infectious Diseases, Department of System Medicine, Tor Vergata University, Rome, Italy
| | - Massimo Ciccozzi
- Unit of Medical Statistics & Molecular Epidemiology, University Campus Bio-Medico of Rome, Italy
| |
Collapse
|
10
|
Ryan MP, Slattery S, Pembroke JT. A Novel Arsenate-Resistant Determinant Associated with ICEpMERPH, a Member of the SXT/R391 Group of Mobile Genetic Elements. Genes (Basel) 2019; 10:genes10121048. [PMID: 31888308 PMCID: PMC6947025 DOI: 10.3390/genes10121048] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 12/09/2019] [Accepted: 12/10/2019] [Indexed: 12/17/2022] Open
Abstract
ICEpMERPH, the first integrative conjugative element (ICE) of the SXT/R391 family isolated in the United Kingdom and Europe, was analyzed to determine the nature of its adaptive functions, its genetic structure, and its homology to related elements normally found in pathogenic Vibrio or Proteus species. Whole genome sequencing of Escherichia coli (E. coli) isolate K802 (which contains the ICEpMERPH) was carried out using Illumina sequencing technology. ICEpMERPH has a size of 110 Kb and 112 putative open reading frames (ORFs). The “hotspot regions” of the element were found to contain putative restriction digestion systems, insertion sequences, and heavy metal resistance genes that encoded resistance to mercury, as previously reported, but also surprisingly to arsenate. A novel arsenate resistance system was identified in hotspot 4 of the element, unrelated to other SXT/R391 elements. This arsenate resistance system was potentially linked to two genes: orf69, encoding an organoarsenical efflux major facilitator superfamily (MFS) transporter-like protein related to ArsJ, and orf70, encoding nicotinamide adenine dinucleotide (NAD)-dependent glyceraldehyde-3-phosphate dehydrogenase. Phenotypic analysis using isogenic strains of Escherichia coli strain AB1157 with and without the ICEpMERPH revealed resistance to low levels of arsenate in the range of 1–5 mM. This novel, low-level resistance may have an important adaptive function in polluted environments, which often contain low levels of arsenate contamination. A bioinformatic analysis on the novel determinant and the phylogeny of ICEpMERPH was presented.
Collapse
|
11
|
Gestal MC, Johnson HM, Harvill ET. Immunomodulation as a Novel Strategy for Prevention and Treatment of Bordetella spp. Infections. Front Immunol 2019; 10:2869. [PMID: 31921136 PMCID: PMC6923730 DOI: 10.3389/fimmu.2019.02869] [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: 09/16/2019] [Accepted: 11/22/2019] [Indexed: 12/13/2022] Open
Abstract
Well-adapted pathogens have evolved to survive the many challenges of a robust immune response. Defending against all host antimicrobials simultaneously would be exceedingly difficult, if not impossible, so many co-evolved organisms utilize immunomodulatory tools to subvert, distract, and/or evade the host immune response. Bordetella spp. present many examples of the diversity of immunomodulators and an exceptional experimental system in which to study them. Recent advances in this experimental system suggest strategies for interventions that tweak immunity to disrupt bacterial immunomodulation, engaging more effective host immunity to better prevent and treat infections. Here we review advances in the understanding of respiratory pathogens, with special focus on Bordetella spp., and prospects for the use of immune-stimulatory interventions in the prevention and treatment of infection.
Collapse
Affiliation(s)
- Monica C Gestal
- Department of Infectious Diseases, College of Veterinary Sciences, University of Georgia, Athens, GA, United States
| | - Hannah M Johnson
- Department of Infectious Diseases, College of Veterinary Sciences, University of Georgia, Athens, GA, United States
| | - Eric T Harvill
- Department of Infectious Diseases, College of Veterinary Sciences, University of Georgia, Athens, GA, United States
| |
Collapse
|
12
|
Li Z, Pang B, Wang D, Li J, Xu J, Fang Y, Lu X, Kan B. Expanding dynamics of the virulence-related gene variations in the toxigenic Vibrio cholerae serogroup O1. BMC Genomics 2019; 20:360. [PMID: 31072300 PMCID: PMC6509779 DOI: 10.1186/s12864-019-5725-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 04/23/2019] [Indexed: 01/16/2023] Open
Abstract
Background Toxigenic Vibrio cholerae serogroup O1 is the causative pathogen in the sixth and seventh cholera pandemics. Cholera toxin is the major virulent factor but other virulence and virulence-related factors play certain roles in the pathogenesis and survival in the host. Along with the evolution of the epidemic strains, the virulence-related genes also experience variation, gain and loss, and lead to genetic divergence in different strains. Results In this study, we analyzed the virulence-related gene profiles in the toxigenic serogroup O1 strains isolated from 1923 to 2015, the genomes of which were publicly available. The virulence-related genes of the V. cholerae O1 strains were annotated based on the Virulence Factors Database (VFDB). An average of 230.1 virulence-related genes per strain were identified; significant differences in the average numbers were found between the classical and El Tor biotypes, and increasing trends in the number of virulence-related genes along with the isolation years were observed in the El Tor biotype strains. A total of 176 homologs of virulence-related genes were found from these strains, of which 25 belonged to the core genes, suggesting their conservative and necessary roles in V. cholerae pathogenesis. We described the diversities of the homologs by defining gene sequence type, and illustrated its association with gene duplication; we found that gene duplication clearly increased the complexity of the gene sequence types in the core virulence-related genes. In addition, we provided virulence-related gene profiles whose genetic characteristic depend on the isolation years from the view of gene gain and loss, variation, gene duplication and gene sequence type number. Conclusions Our study reveals the comprehensive variation dynamics of the virulence-related genes in toxigenic V. cholerae serogroup O1 during epidemics. The increasing trend for the virulence-related genes may suggest the evolutional advantage of strains by gaining virulence-related genes with diverse functional categories. Electronic supplementary material The online version of this article (10.1186/s12864-019-5725-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Zhenpeng Li
- State Key Laboratory for Infectious Disease Prevention and Control. National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310003, China
| | - Bo Pang
- State Key Laboratory for Infectious Disease Prevention and Control. National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310003, China
| | - Duochun Wang
- State Key Laboratory for Infectious Disease Prevention and Control. National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310003, China
| | - Jie Li
- State Key Laboratory for Infectious Disease Prevention and Control. National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310003, China
| | - Jialiang Xu
- Key Laboratory of Cleaner Production and Integrated Resource Utilization of China National Light Industry, School of Food and Chemical Engeering, Beijing Technology and Business University, Beijing, 100048, China
| | - Yujie Fang
- State Key Laboratory for Infectious Disease Prevention and Control. National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310003, China
| | - Xin Lu
- State Key Laboratory for Infectious Disease Prevention and Control. National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China. .,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310003, China.
| | - Biao Kan
- State Key Laboratory for Infectious Disease Prevention and Control. National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China. .,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310003, China.
| |
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
Genomic comparison of serogroups O159 and O170 with other Vibrio cholerae serogroups. BMC Genomics 2019; 20:241. [PMID: 30909880 PMCID: PMC6434791 DOI: 10.1186/s12864-019-5603-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 03/13/2019] [Indexed: 12/04/2022] Open
Abstract
Background Of the hundreds of Vibrio cholerae serogroups, O1 and O139 are the main epidemic-causing ones. Although non-O1/non-O139 serogroups rarely cause epidemics, the possibility exists for strains within them to have pathogenic potential. Results We selected 25 representative strains within 16 V. cholerae serogroups and examined their genomic and functional characteristics. We tentatively constructed a gene pool containing 405 homologous gene clusters, which is well organized and functions in O-antigen polysaccharide (O-PS) synthesis. Our network analysis indicate that great diversity exists in O-PS among the serogroups, and several serogroup pairs share a high number of homologous genes (e.g., O115 and O37; O170 and O139; O12 and O39). The phylogenetic analysis results suggest that a close relationship exists between serogroups O170, O89 and O144, based on neighbor-joining (NJ) and gene trees, although serogroup O159 showed an inconsistent phylogenetic relationship between the NJ tree and the gene tree, indicating that it may have undergone extensive recombination and horizontal gene transfer. Different phylogenetic structures were observed between the core genes, pan genes, and O-PS genes. The virulence gene analysis indicated that the virulence genes from all the representative strains may have their sources from four particular bacteria (Pseudomonas aeruginosa, V. vulnificus, Haemophilus somnus and H. influenzae), which suggests that V. cholerae may have exchanged virulence genes with other bacterial genera or species in certain environments. The mobile genetic element analysis indicated that O159 carries nearly complete VSP-II and partial VPI-1 and VPI-2, O170 carries partial VPI-1 and VPI-2, and several non-O1/non-O139 strains contain full or partial VPI-1 and VPI-2. Several genes showing evidence of positive selection are involved in chemotaxis, Na + resistance, or cell wall synthesis, suggestive of environmental adaptation. Conclusions This study reports on the newly sequenced O159 and O170 genomes and their comparisons with other V. cholerae serogroups. The complicated O-PS network of constituent genes highlights the detailed recombination mechanisms that have acted on the serogroups’ genomes. The serogroups have different virulence-related gene profiles, and there is evidence of positive selection acting on other genes, possibly during adaptation to different environments and hosts. Electronic supplementary material The online version of this article (10.1186/s12864-019-5603-7) contains supplementary material, which is available to authorized users.
Collapse
|
15
|
Rebaudet S, Moore S, Rossignol E, Bogreau H, Gaudart J, Normand AC, Laraque MJ, Adrien P, Boncy J, Piarroux R. Epidemiological and molecular forensics of cholera recurrence in Haiti. Sci Rep 2019; 9:1164. [PMID: 30718586 PMCID: PMC6361935 DOI: 10.1038/s41598-018-37706-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 12/05/2018] [Indexed: 01/01/2023] Open
Abstract
Cholera has affected Haiti with damping waves of outbreaks since October 2010. However, mechanisms behind disease persistence during lull periods remain poorly understood. By mid 2014, cholera transmission seemed to only persist in the northern part of Haiti. Meanwhile, cholera appeared nearly extinct in the capital, Port-au-Prince, where it eventually exploded in September 2014. This study aimed to determine whether this outbreak was caused by local undetected cases or by re-importation of the disease from the north. Applying an integrated approach between November 2013 and November 2014, we assessed the temporal and spatial dynamics of cholera using routine surveillance data and performed population genetics analyses of 178 Vibrio cholerae O1 clinical isolates. The results suggest that the northern part of the country exhibited a persisting metapopulation pattern with roaming oligoclonal outbreaks that could not be effectively controlled. Conversely, undetected and unaddressed autochthonous low-grade transmission persisted in the Port-au-Prince area, which may have been the source of the acute outbreak in late-2014. Cholera genotyping is a simple but powerful tool to adapt control strategies based on epidemic specificities. In Haiti, these data have already yielded significant progress in cholera surveillance, which is a key component of the strategy to eventually eliminate cholera.
Collapse
Affiliation(s)
- Stanislas Rebaudet
- Assistance Publique - Hôpitaux de Marseille, DRCI, Marseille, France. .,Hôpital Européen Marseille, Marseille, France.
| | | | - Emmanuel Rossignol
- Ministry of Public Health and Population, National Public Health Laboratory, Delmas, Haiti
| | - Hervé Bogreau
- Institut de Recherche Biomédicale des Armées, Département des Maladies Infectieuses, Unité de Parasitologie et d'Entomologie, Marseille, France.,Aix Marseille Univ, Institut Hospitalo-Universitaire Méditerranée Infection, VITROME, Marseille, France
| | - Jean Gaudart
- Aix Marseille Univ, APHM, IRD, INSERM, SESSTIM, BioSTIC, Marseille, France
| | - Anne-Cécile Normand
- Sorbonne Université, INSERM, Institut Pierre-Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpital Pitié-Salpêtrière, F-, 75013, Paris, France
| | - Marie-José Laraque
- Ministry of Public Health and Population, National Public Health Laboratory, Delmas, Haiti
| | - Paul Adrien
- Ministry of Public Health and Population, Directorate of Epidemiology Laboratory and Research, Delmas, Haiti
| | - Jacques Boncy
- Ministry of Public Health and Population, National Public Health Laboratory, Delmas, Haiti
| | - Renaud Piarroux
- Sorbonne Université, INSERM, Institut Pierre-Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpital Pitié-Salpêtrière, F-, 75013, Paris, France
| |
Collapse
|
16
|
Levade I, Terrat Y, Leducq JB, Weil AA, Mayo-Smith LM, Chowdhury F, Khan AI, Boncy J, Buteau J, Ivers LC, Ryan ET, Charles RC, Calderwood SB, Qadri F, Harris JB, LaRocque RC, Shapiro BJ. Vibrio cholerae genomic diversity within and between patients. Microb Genom 2019; 3. [PMID: 29306353 PMCID: PMC5761273 DOI: 10.1099/mgen.0.000142] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Cholera is a severe, water-borne diarrhoeal disease caused by toxin-producing strains of the bacterium Vibrio cholerae. Comparative genomics has revealed 'waves' of cholera transmission and evolution, in which clones are successively replaced over decades and centuries. However, the extent of V. cholerae genetic diversity within an epidemic or even within an individual patient is poorly understood. Here, we characterized V. cholerae genomic diversity at a micro-epidemiological level within and between individual patients from Bangladesh and Haiti. To capture within-patient diversity, we isolated multiple (8 to 20) V. cholerae colonies from each of eight patients, sequenced their genomes and identified point mutations and gene gain/loss events. We found limited but detectable diversity at the level of point mutations within hosts (zero to three single nucleotide variants within each patient), and comparatively higher gene content variation within hosts (at least one gain/loss event per patient, and up to 103 events in one patient). Much of the gene content variation appeared to be due to gain and loss of phage and plasmids within the V. cholerae population, with occasional exchanges between V. cholerae and other members of the gut microbiota. We also show that certain intra-host variants have phenotypic consequences. For example, the acquisition of a Bacteroides plasmid and non-synonymous mutations in a sensor histidine kinase gene both reduced biofilm formation, an important trait for environmental survival. Together, our results show that V. cholerae is measurably evolving within patients, with possible implications for disease outcomes and transmission dynamics.
Collapse
Affiliation(s)
- Inès Levade
- 1Department of Biological Sciences, University of Montreal, Montreal, Quebec, Canada
| | - Yves Terrat
- 1Department of Biological Sciences, University of Montreal, Montreal, Quebec, Canada
| | - Jean-Baptiste Leducq
- 1Department of Biological Sciences, University of Montreal, Montreal, Quebec, Canada
| | - Ana A Weil
- 2Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.,3Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Leslie M Mayo-Smith
- 2Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Fahima Chowdhury
- 4Center for Vaccine Sciences, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Ashraful I Khan
- 4Center for Vaccine Sciences, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Jacques Boncy
- 5National Public Health Laboratory, Ministry of Public Health and Population, Port-au-Prince, Haiti
| | - Josiane Buteau
- 5National Public Health Laboratory, Ministry of Public Health and Population, Port-au-Prince, Haiti
| | - Louise C Ivers
- 3Department of Medicine, Harvard Medical School, Boston, MA, USA.,6Division of Global Health Equity, Brigham and Women's Hospital, Boston, MA, USA.,7Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA
| | - Edward T Ryan
- 2Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.,3Department of Medicine, Harvard Medical School, Boston, MA, USA.,8Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, USA
| | - Richelle C Charles
- 2Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.,3Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Stephen B Calderwood
- 2Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.,3Department of Medicine, Harvard Medical School, Boston, MA, USA.,9Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Firdausi Qadri
- 4Center for Vaccine Sciences, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Jason B Harris
- 2Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.,10Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Regina C LaRocque
- 2Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.,3Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - B Jesse Shapiro
- 1Department of Biological Sciences, University of Montreal, Montreal, Quebec, Canada
| |
Collapse
|
17
|
Hossain ZZ, Leekitcharoenphon P, Dalsgaard A, Sultana R, Begum A, Jensen PKM, Hendriksen RS. Comparative genomics of Vibrio cholerae O1 isolated from cholera patients in Bangladesh. Lett Appl Microbiol 2018; 67:329-336. [PMID: 29981154 DOI: 10.1111/lam.13046] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Revised: 06/23/2018] [Accepted: 07/04/2018] [Indexed: 01/08/2023]
Abstract
Whole genome sequencing was utilized to investigate the genomic profile of Vibrio cholerae O1 strains, isolated from symptomatic patients in a low-income urban area of Dhaka, Bangladesh. Comparative genomics using bioinformatics tools were applied to identify major virulence factors, biotype and antimicrobial resistance genes in three V. cholerae O1 strains (VC-1, 2 and 3) isolated from two case patients. A phylogenetic SNP (single nucleotide polymorphism)-based analysis was conducted to infer the relatedness to V. cholerae O1 strains isolated elsewhere. The V. cholerae strains were the El Tor variant carrying ctxB1 (standard classical genotype). SNP-based global phylogeny revealed that the three isolates were strictly clonal and the closest neighbouring genomes were epidemic clones of V. cholerae O1 isolated in 2010 from cholera patients in Pakistan. All strains harboured the integrase gene of the SXT element (intSXT ), antimicrobial resistance genes for aminoglycosides, phenicol, sulphonamide and trimethoprim except VC-1 that lacked sulphonamide resistance genes. The multilocus sequence typing (MLST) revealed that the strains belonged to sequence type, ST69. The study provides knowledge on current genetic traits of clinical V. cholerae O1 circulating in urban household clusters of Bangladesh which may help in predicting emergence of new pandemic strains in Bangladesh. SIGNIFICANCE AND IMPACT OF THE STUDY Vibrio cholerae has frequently experienced genetic changes with rapid evolution of pandemic clones in the Ganges Delta region. Whole genome sequencing can reveal genetic information of current pathogenic V. cholerae in Bangladesh which includes cefotaxime genotypes, virulence factors, altered antimicrobial resistance pattern as well as mobile genetic element compared to global pandemic strains. This study data could be used in planning future surveillance strategies in Ganges Delta region by informing new epidemiology of current outbreak strains.
Collapse
Affiliation(s)
- Z Z Hossain
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh.,Institute of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - P Leekitcharoenphon
- National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Food borne Pathogens & Genomics and European Union Reference Laboratory for Antimicrobial Resistance, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - A Dalsgaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - R Sultana
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - A Begum
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - P K M Jensen
- Institute of Public Health, University of Copenhagen, Copenhagen, Denmark.,Copenhagen Centre for Disaster Research, University of Copenhagen, Copenhagen, Denmark
| | - R S Hendriksen
- National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Food borne Pathogens & Genomics and European Union Reference Laboratory for Antimicrobial Resistance, Technical University of Denmark, Kgs. Lyngby, Denmark
| |
Collapse
|
18
|
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.
Collapse
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
| |
Collapse
|
19
|
Kamareddine L, Wong ACN, Vanhove AS, Hang S, Purdy AE, Kierek-Pearson K, Asara JM, Ali A, Morris JG, Watnick PI. Activation of Vibrio cholerae quorum sensing promotes survival of an arthropod host. Nat Microbiol 2018; 3:243-252. [PMID: 29180725 PMCID: PMC6260827 DOI: 10.1038/s41564-017-0065-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 10/19/2017] [Indexed: 12/30/2022]
Abstract
Vibrio cholerae colonizes the human terminal ileum to cause cholera, and the arthropod intestine and exoskeleton to persist in the aquatic environment. Attachment to these surfaces is regulated by the bacterial quorum-sensing signal transduction cascade, which allows bacteria to assess the density of microbial neighbours. Intestinal colonization with V. cholerae results in expenditure of host lipid stores in the model arthropod Drosophila melanogaster. Here we report that activation of quorum sensing in the Drosophila intestine retards this process by repressing V. cholerae succinate uptake. Increased host access to intestinal succinate mitigates infection-induced lipid wasting to extend survival of V. cholerae-infected flies. Therefore, quorum sensing promotes a more favourable interaction between V. cholerae and an arthropod host by reducing the nutritional burden of intestinal colonization.
Collapse
Affiliation(s)
- Layla Kamareddine
- Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Adam C N Wong
- Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, USA
| | - Audrey S Vanhove
- Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Saiyu Hang
- Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- University of Massachusetts Medical School, Worcester, MA, USA
| | - Alexandra E Purdy
- Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Biology, AC #2237, Amherst College, Amherst, MA, USA
| | - Katharine Kierek-Pearson
- Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - John M Asara
- Division of Signal Transduction/Mass Spectrometry Core, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Afsar Ali
- Emerging Pathogens Institute University of Florida, Gainesville, FL, USA
- Department of Environmental & Global Health, School of Public Health and Health Profession, University of Florida, Gainesville, FL, USA
| | - J Glenn Morris
- Emerging Pathogens Institute University of Florida, Gainesville, FL, USA
| | - Paula I Watnick
- Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Microbiology and Immunobiology, Harvard Medical Schoolm, Boston, MA, USA.
| |
Collapse
|
20
|
Multi-drug resistant Klebsiella pneumoniae strains circulating in hospital setting: whole-genome sequencing and Bayesian phylogenetic analysis for outbreak investigations. Sci Rep 2017; 7:3534. [PMID: 28615687 PMCID: PMC5471223 DOI: 10.1038/s41598-017-03581-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 05/09/2017] [Indexed: 01/12/2023] Open
Abstract
Carbapenems resistant Enterobacteriaceae infections are increasing worldwide representing an emerging public health problem. The application of phylogenetic and phylodynamic analyses to bacterial whole genome sequencing (WGS) data have become essential in the epidemiological surveillance of multi-drug resistant nosocomial pathogens. Between January 2012 and February 2013, twenty-one multi-drug resistant K. pneumoniae strains, were collected from patients hospitalized among different wards of the University Hospital Campus Bio-Medico. Epidemiological contact tracing of patients and Bayesian phylogenetic analysis of bacterial WGS data were used to investigate the evolution and spatial dispersion of K. pneumoniae in support of hospital infection control. The epidemic curve of incident K. pneumoniae cases showed a bimodal distribution of cases with two peaks separated by 46 days between November 2012 and January 2013. The time-scaled phylogeny suggested that K. pneumoniae strains isolated during the study period may have been introduced into the hospital setting as early as 2007. Moreover, the phylogeny showed two different epidemic introductions in 2008 and 2009. Bayesian genomic epidemiology is a powerful tool that promises to improve the surveillance and control of multi-drug resistant pathogens in an effort to develop effective infection prevention in healthcare settings or constant strains reintroduction.
Collapse
|
21
|
Garrine M, Mandomando I, Vubil D, Nhampossa T, Acacio S, Li S, Paulson JN, Almeida M, Domman D, Thomson NR, Alonso P, Stine OC. Minimal genetic change in Vibrio cholerae in Mozambique over time: Multilocus variable number tandem repeat analysis and whole genome sequencing. PLoS Negl Trop Dis 2017; 11:e0005671. [PMID: 28622368 PMCID: PMC5489214 DOI: 10.1371/journal.pntd.0005671] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 06/28/2017] [Accepted: 05/30/2017] [Indexed: 01/05/2023] Open
Abstract
Although cholera is a major public health concern in Mozambique, its transmission patterns remain unknown. We surveyed the genetic relatedness of 75 Vibrio cholerae isolates from patients at Manhiça District Hospital between 2002-2012 and 3 isolates from river using multilocus variable-number tandem-repeat analysis (MLVA) and whole genome sequencing (WGS). MLVA revealed 22 genotypes in two clonal complexes and four unrelated genotypes. WGS revealed i) the presence of recombination, ii) 67 isolates descended monophyletically from a single source connected to Wave 3 of the Seventh Pandemic, and iii) four clinical isolates lacking the cholera toxin gene. This Wave 3 strain persisted for at least eight years in either an environmental reservoir or circulating within the human population. Our data raises important questions related to where these isolates persist and how identical isolates can be collected years apart despite our understanding of high change rate of MLVA loci and the V. cholerae molecular clock.
Collapse
Affiliation(s)
- Marcelino Garrine
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Inácio Mandomando
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
- Instituto Nacional de Saúde (INS), Ministério da Saúde, Maputo, Mozambique
| | - Delfino Vubil
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Tacilta Nhampossa
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
- Instituto Nacional de Saúde (INS), Ministério da Saúde, Maputo, Mozambique
| | - Sozinho Acacio
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
- Instituto Nacional de Saúde (INS), Ministério da Saúde, Maputo, Mozambique
| | - Shan Li
- Department of Epidemiology and Public Health, University of Maryland Baltimore, Baltimore, Maryland, United States of America
| | - Joseph N. Paulson
- Institute for Applied Computer Sciences, University of Maryland, College Park, Maryland, United States of America
- Department of Biostatistics, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Mathieu Almeida
- Institute for Applied Computer Sciences, University of Maryland, College Park, Maryland, United States of America
| | - Daryl Domman
- Infection Genomics, Wellcome Trust Sanger Instititue, Hinxton, England, United Kingdom
| | - Nicholas R. Thomson
- Infection Genomics, Wellcome Trust Sanger Instititue, Hinxton, England, United Kingdom
| | - Pedro Alonso
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
- ISGlobal Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic / Universitat de Barcelona, Barcelona, Spain
| | - Oscar Colin Stine
- Department of Epidemiology and Public Health, University of Maryland Baltimore, Baltimore, Maryland, United States of America
| |
Collapse
|
22
|
CRISPR-Cas and Contact-Dependent Secretion Systems Present on Excisable Pathogenicity Islands with Conserved Recombination Modules. J Bacteriol 2017; 199:JB.00842-16. [PMID: 28264992 DOI: 10.1128/jb.00842-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 02/27/2017] [Indexed: 12/29/2022] Open
Abstract
Pathogenicity islands (PAIs) are mobile integrated genetic elements that contain a diverse range of virulence factors. PAIs integrate into the host chromosome at a tRNA locus that contains their specific bacterial attachment site, attB, via integrase-mediated site-specific recombination generating attL and attR sites. We identified conserved recombination modules (integrases and att sites) previously described in choleragenic Vibrio cholerae PAIs but with novel cargo genes. Clustered regularly interspaced short palindromic repeat (CRISPR)-associated proteins (Cas proteins) and a type VI secretion system (T6SS) gene cluster were identified at the Vibrio pathogenicity island 1 (VPI-1) insertion site in 19 V. cholerae strains and contained the same recombination module. Two divergent type I-F CRISPR-Cas systems were identified, which differed in Cas protein homology and content. The CRISPR repeat sequence was identical among all V. cholerae strains, but the CRISPR spacer sequences and the number of spacers varied. In silico analysis suggests that the CRISPR-Cas systems were active against phages and plasmids. A type III secretion system (T3SS) was present in 12 V. cholerae strains on a 68-kb island inserted at the same tRNA-serine insertion site as VPI-2 and contained the same recombination module. Bioinformatics analysis showed that two divergent T3SSs exist among the strains examined. Both the CRISPR and T3SS islands excised site specifically from the bacterial chromosome as complete units, and the cognate integrases were essential for this excision. These data demonstrated that identical recombination modules that catalyze integration and excision from the chromosome can acquire diverse cargo genes, signifying a novel method of acquisition for both CRISPR-Cas systems and T3SSs.IMPORTANCE This work demonstrated the presence of CRISPR-Cas systems and T3SSs on PAIs. Our work showed that similar recombination modules can associate with different cargo genes and catalyze their incorporation into bacterial chromosomes, which could convert a strain into a pathogen with very different disease pathologies. Each island had the ability to excise from the chromosome as distinct, complete units for possible transfer. Evolutionary analysis of these regions indicates that they were acquired by horizontal transfer and that PAIs are the units of transfer. Similar to the case for phage evolution, PAIs have a modular structure where different functional regions are acquired by identical recombination modules.
Collapse
|
23
|
Azarian T, Ali A, Johnson JA, Jubair M, Cella E, Ciccozzi M, Nolan DJ, Farmerie W, Rashid MH, Sinha-Ray S, Alam MT, Morris JG, Salemi M. Non-toxigenic environmental Vibrio cholerae O1 strain from Haiti provides evidence of pre-pandemic cholera in Hispaniola. Sci Rep 2016; 6:36115. [PMID: 27786291 PMCID: PMC5081557 DOI: 10.1038/srep36115] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 10/11/2016] [Indexed: 12/31/2022] Open
Abstract
Vibrio cholerae is ubiquitous in aquatic environments, with environmental toxigenic V. cholerae O1 strains serving as a source for recurrent cholera epidemics and pandemic disease. However, a number of questions remain about long-term survival and evolution of V. cholerae strains within these aquatic environmental reservoirs. Through monitoring of the Haitian aquatic environment following the 2010 cholera epidemic, we isolated two novel non-toxigenic (ctxA/B-negative) Vibrio cholerae O1. These two isolates underwent whole-genome sequencing and were investigated through comparative genomics and Bayesian coalescent analysis. These isolates cluster in the evolutionary tree with strains responsible for clinical cholera, possessing genomic components of 6th and 7th pandemic lineages, and diverge from "modern" cholera strains around 1548 C.E. [95% HPD: 1532-1555]. Vibrio Pathogenicity Island (VPI)-1 was present; however, SXT/R391-family ICE and VPI-2 were absent. Rugose phenotype conversion and vibriophage resistance evidenced adaption for persistence in aquatic environments. The identification of V. cholerae O1 strains in the Haitian environment, which predate the first reported cholera pandemic in 1817, broadens our understanding of the history of pandemics. It also raises the possibility that these and similar environmental strains could acquire virulence genes from the 2010 Haitian epidemic clone, including the cholera toxin producing CTXϕ.
Collapse
Affiliation(s)
- Taj Azarian
- Emerging Pathogens Institute, University of Florida, Gainesville, USA
| | - Afsar Ali
- Emerging Pathogens Institute, University of Florida, Gainesville, USA.,Department of Environmental and Global Health, College of Public Health and Health Profession, University of Florida, Gainesville, Florida, USA
| | - Judith A Johnson
- Emerging Pathogens Institute, University of Florida, Gainesville, USA.,Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, USA
| | - Mohammad Jubair
- Emerging Pathogens Institute, University of Florida, Gainesville, USA.,Department of Environmental and Global Health, College of Public Health and Health Profession, University of Florida, Gainesville, Florida, USA
| | - Eleonora Cella
- Emerging Pathogens Institute, University of Florida, Gainesville, USA.,Department of Infectious, Parasitic and Immunomediated Diseases, Istituto Superiore di Sanità, Rome, Italy.,Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Massimo Ciccozzi
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy.,University Hospital Campus Bio-Medico, Italy
| | - David J Nolan
- Emerging Pathogens Institute, University of Florida, Gainesville, USA.,Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, USA
| | - William Farmerie
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, USA
| | - Mohammad H Rashid
- Emerging Pathogens Institute, University of Florida, Gainesville, USA
| | | | - Meer T Alam
- Emerging Pathogens Institute, University of Florida, Gainesville, USA.,Department of Environmental and Global Health, College of Public Health and Health Profession, University of Florida, Gainesville, Florida, USA
| | - J Glenn Morris
- Emerging Pathogens Institute, University of Florida, Gainesville, USA.,Department of Medicine, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Marco Salemi
- Emerging Pathogens Institute, University of Florida, Gainesville, USA.,Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, USA
| |
Collapse
|
24
|
Azarian T, Maraqa NF, Cook RL, Johnson JA, Bailey C, Wheeler S, Nolan D, Rathore MH, Morris JG, Salemi M. Genomic Epidemiology of Methicillin-Resistant Staphylococcus aureus in a Neonatal Intensive Care Unit. PLoS One 2016; 11:e0164397. [PMID: 27732618 PMCID: PMC5061378 DOI: 10.1371/journal.pone.0164397] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 09/23/2016] [Indexed: 11/19/2022] Open
Abstract
Despite infection prevention efforts, neonatal intensive care unit (NICU) patients remain at risk of Methicillin-resistant Staphylococcus aureus (MRSA) infection. Modes of transmission for healthcare-associated (HA) and community-associated (CA) MRSA remain poorly understood and may vary by genotype, hindering the development of effective prevention and control strategies. From 2008–2010, all patients admitted to a level III NICU were screened for MRSA colonization, and all available isolates were spa-typed. Spa-type t008, the most prevalent CA- genotype in the United States, spa-type t045, a HA- related genotype, and a convenience sample of strains isolated from 2003–2011, underwent whole-genome sequencing and phylodynamic analysis. Patient risk factors were compared between colonized and noncolonized infants, and virulence and resistance genes compared between spa-type t008 and non-t008 strains. Epidemiological and genomic data were used to estimate MRSA importations and acquisitions through transmission reconstruction. MRSA colonization was identified in 9.1% (177/1940) of hospitalized infants and associated with low gestational age and birth weight. Among colonized infants, low gestational age was more common among those colonized with t008 strains. Our data suggest that approximately 70% of colonizations were the result of transmission events within the NICU, with the remainder likely to reflect importations of “outside” strains. While risk of transmission within the NICU was not affected by spa-type, patterns of acquisition and importation differed between t008 and t045 strains. Phylodynamic analysis showed the effective population size of spa-type t008 has been exponentially increasing in both community and hospital, with spa-type t008 strains possessed virulence genes not found among t045 strains; t045 strains, in contrast, appeared to be of more recent origin, with a possible hospital source. Our data highlight the importance of both intra-NICU transmission and recurrent introductions in maintenance of MRSA colonization within the NICU environment, as well as spa-type-specific differences in epidemiology.
Collapse
Affiliation(s)
- Taj Azarian
- College of Public Health and Health Professions and College of Medicine, Department of Epidemiology, University of Florida, Gainesville, FL, United States of America
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States of America
- * E-mail:
| | - Nizar F. Maraqa
- Infectious Diseases and Immunology, Wolfson Children’s Hospital, Jacksonville, FL, United States of America
- University of Florida Center for HIV/AIDS Research, Education and Service, University of Florida, College of Medicine, Jacksonville, FL, United States of America
| | - Robert L. Cook
- College of Public Health and Health Professions and College of Medicine, Department of Epidemiology, University of Florida, Gainesville, FL, United States of America
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States of America
| | - Judith A. Johnson
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States of America
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, United States of America
| | - Christine Bailey
- Infectious Diseases and Immunology, Wolfson Children’s Hospital, Jacksonville, FL, United States of America
| | - Sarah Wheeler
- Infectious Diseases and Immunology, Wolfson Children’s Hospital, Jacksonville, FL, United States of America
| | - David Nolan
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States of America
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, United States of America
| | - Mobeen H. Rathore
- Infectious Diseases and Immunology, Wolfson Children’s Hospital, Jacksonville, FL, United States of America
- University of Florida Center for HIV/AIDS Research, Education and Service, University of Florida, College of Medicine, Jacksonville, FL, United States of America
| | - J. Glenn Morris
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States of America
- Division of Infectious Diseases, Department of Medicine, College of Medicine, University of Florida, Gainesville, FL, United States of America
| | - Marco Salemi
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States of America
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, United States of America
| |
Collapse
|
25
|
Major Shift of Toxigenic V. cholerae O1 from Ogawa to Inaba Serotype Isolated from Clinical and Environmental Samples in Haiti. PLoS Negl Trop Dis 2016; 10:e0005045. [PMID: 27716803 PMCID: PMC5055329 DOI: 10.1371/journal.pntd.0005045] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 09/15/2016] [Indexed: 02/04/2023] Open
Abstract
In October of 2010, an outbreak of cholera was confirmed in Haiti for the first time in more than a century. A single clone of toxigenic Vibrio cholerae O1 biotype El Tor serotype Ogawa strain was implicated as the cause. Five years after the onset of cholera, in October, 2015, we have discovered a major switch (ranging from 7 to 100%) from Ogawa serotype to Inaba serotype. Furthermore, using wbeT gene sequencing and comparative sequence analysis, we now demonstrate that, among 2013 and 2015 Inaba isolates, the wbeT gene, responsible for switching Ogawa to Inaba serotype, sustained a unique nucleotide mutation not found in isolates obtained from Haiti in 2012. Moreover, we show that, environmental Inaba isolates collected in 2015 have the identical mutations found in the 2015 clinical isolates. Our data indicate that toxigenic V. cholerae O1 serotype Ogawa can rapidly change its serotype to Inaba, and has the potential to cause disease in individuals who have acquired immunity against Ogawa serotype. Our findings highlight the importance of monitoring of toxigenic V. cholerae O1 and cholera in countries with established endemic disease. For the first time in 100 years, in October 2010, cholera caused by toxigenic strains of V. cholerae was introduced in Haiti. Conventional and genetic analysis revealed that a single clone of V. cholerae O1 biotype El Tor, serotype Ogawa strain was brought to Haiti by Nepalese Peace-Keeping troops. These troops arrived in January of that year to provide humanitarian assistance following Haiti’s deadliest earthquake. Subsequently our team has monitored the cholera epidemic by acquiring clinical and environmental samples to assess whether or not the pathogen was able to establish its environmental reservoirs within the country, and whether V. cholerae could undergo evolutionary changes in order to adapt to the stressors imparted by human gastrointestinal tract and environmental aquatic reservoirs. In this study we show that over the past 5 years the initially-introduced and circulating V. cholerae Ogawa serotype has significantly shifted to Inaba serotype by sustaining multiple mutations in wbeT gene, the gene known to mediate serotype shift. Our findings suggest that the new Inaba serotype may be replacing the Ogawa serotype in order to evade Ogawa-induced host immunity and thereby causing cholera potentially among individuals who may previously have suffered from cholera. Our study highlights the importance of ongoing monitoring of cholera in Haiti.
Collapse
|
26
|
Phenotypic Analysis Reveals that the 2010 Haiti Cholera Epidemic Is Linked to a Hypervirulent Strain. Infect Immun 2016; 84:2473-81. [PMID: 27297393 PMCID: PMC4995894 DOI: 10.1128/iai.00189-16] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 06/08/2016] [Indexed: 02/05/2023] Open
Abstract
Vibrio cholerae O1 El Tor strains have been responsible for pandemic cholera since 1961. These strains have evolved over time, spreading globally in three separate waves. Wave 3 is caused by altered El Tor (AET) variant strains, which include the strain with the signature ctxB7 allele that was introduced in 2010 into Haiti, where it caused a devastating epidemic. In this study, we used phenotypic analysis to compare an early isolate from the Haiti epidemic to wave 1 El Tor isolates commonly used for research. It is demonstrated that the Haiti isolate has increased production of cholera toxin (CT) and hemolysin, increased motility, and a reduced ability to form biofilms. This strain also outcompetes common wave 1 El Tor isolates for colonization of infant mice, indicating that it has increased virulence. Monitoring of CT production and motility in additional wave 3 isolates revealed that this phenotypic variation likely evolved over time rather than in a single genetic event. Analysis of available whole-genome sequences and phylogenetic analyses suggested that increased virulence arose from positive selection for mutations found in known and putative regulatory genes, including hns and vieA, diguanylate cyclase genes, and genes belonging to the lysR and gntR regulatory families. Overall, the studies presented here revealed that V. cholerae virulence potential can evolve and that the currently prevalent wave 3 AET strains are both phenotypically distinct from and more virulent than many El Tor isolates.
Collapse
|
27
|
Ngwa MC, Masalla T, Esemu S, Fumoloh FF, Kracalik I, Cella E, Alam MT, Akoachere JF, Liang S, Salemi M, Morris JG, Ali A, Ndip LM. Genetic Studies of Vibrio cholerae in South West Cameroon-A Phylogenetic Analysis of Isolates from the 2010-2011 Epidemic. PLOS CURRENTS 2016; 8:ecurrents.outbreaks.13b4e5e36a5c0831a1663fbdb5713fe9. [PMID: 27617169 PMCID: PMC5001702 DOI: 10.1371/currents.outbreaks.13b4e5e36a5c0831a1663fbdb5713fe9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
INTRODUCTION During the cholera outbreak from 2010 to 2011 in Cameroon, 33,192 cases with 1,440 deaths (case fatality ratio 4.34%) were reported to the World Health Organization. Of these, the South West Region reported 3,120 clinical cases. This region is in the Equatorial Monsoon climatic subzone of Cameroon, close to the coast, raising questions as to whether cases were linked with development of environmental reservoirs. METHODS In an investigation conducted by the Laboratory for Emerging Infectious Diseases, University of Buea, toxigenic V. cholerae O1 were isolated from diarrheal stool samples from 18 patients, with ages ranging from <3 to 70 years. Coordinates for clinical centers at which cases were identified were obtained using a handheld GPS, and were mapped using ArcGIS. Antibiotic susceptibility testing was performed using the Kirby 'Bauer agar disc diffusion method. The full genomes of these strains were sequenced with the Illumina MiSeq platform. De novo assembly of cholera genomes and multiple sequence alignment were carried out using the bioinformatics pipeline developed in the Emerging Pathogens Institute laboratory at the University of Florida. RESULTS/DISCUSSION Genetic comparisons showed that isolates were closely related, with pairwise p-distances ranging from 2.25 to 14.52 10-5 nt substitutions per site, and no statistically significant correlation between the pairwise genetic distances and the geographic distances among sampling locations. Indeed, the phylogeny of the Cameroonian strains displays the typical star-like topology and intermixing of strains from different locations that are characteristic of an exponential outbreak localized around a relatively restricted area with occasional spillover to other parts of the country, likely mediated by direct human contact and human movement. Findings highlight the utility of whole genome sequencing and phylogenetic analysis in understanding transmission patterns at the local level.
Collapse
Affiliation(s)
- Moise C Ngwa
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA; Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, USA
| | - Thomas Masalla
- Laboratory for Emerging Infectious Diseases, University of Buea, Buea, South West Region, Cameroon
| | - Seraphine Esemu
- Laboratory for Emerging Infectious Diseases, University of Buea, Buea, South West Region, Cameroon
| | - Foche Francis Fumoloh
- Laboratory for Emerging Infectious Diseases, University of Buea, Buea, South West Region, Cameroon
| | | | - Eleonora Cella
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - Meer Taifur Alam
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - Jane-Francis Akoachere
- Laboratory for Emerging Infectious Diseases, University of Buea, Buea, South West Region, Cameroon
| | - Song Liang
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA; Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, USA
| | - Marco Salemi
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - J Glenn Morris
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA; Department of Medicine, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Afsar Ali
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA; Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, USA
| | - Lucy M Ndip
- Laboratory for Emerging Infectious Diseases, University of Buea, Buea, South West Region, Cameroon; Department of Microbiology, University of Buea, Buea, South West Region, Cameroon
| |
Collapse
|
28
|
Rashid MU, Rashed SM, Islam T, Johura FT, Watanabe H, Ohnishi M, Alam M. CtxB1 outcompetes CtxB7 in Vibrio cholerae O1, Bangladesh. J Med Microbiol 2016; 65:101-103. [PMID: 26487638 DOI: 10.1099/jmm.0.000190] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Mahamud-Ur Rashid
- International Center for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Shah M Rashed
- International Center for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Tarequl Islam
- International Center for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Fatema-Tuz Johura
- International Center for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Haruo Watanabe
- National Institute of Infectious Diseases (NIID), Tokyo, Japan
| | - Makoto Ohnishi
- National Institute of Infectious Diseases (NIID), Tokyo, Japan
| | - Munirul Alam
- International Center for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| |
Collapse
|
29
|
Abstract
Although the current cholera pandemic can trace its origin to a specific time and place, many variants of Vibrio cholerae have caused this disease over the last 50 years. The relative clinical importance and geographical distribution of these variants have changed with time, but most remain in circulation. Some countries, such as Mexico and Haiti, had escaped the current pandemic, until large epidemics struck them in 1991 and 2010, respectively. Cholera has been endemic in these countries ever since. A recent retrospective study in mBio presents the results of more than 3 decades of V. cholerae monitoring from environmental and clinical sources in Mexico (S. Y. Choi et al., mBio 7:e02160-15, 2016, http://dx.doi.org/10.1128/mBio.02160-15). It reveals that multiple V. cholerae variants, including classical strains from the previous pandemic, as well as completely novel biotypes, have been circulating in Mexico. This discovery has important implications for the epidemiology and evolution of V. cholerae.
Collapse
|
30
|
Siboni N, Balaraju V, Carney R, Labbate M, Seymour JR. Spatiotemporal Dynamics of Vibrio spp. within the Sydney Harbour Estuary. Front Microbiol 2016; 7:460. [PMID: 27148171 PMCID: PMC4829023 DOI: 10.3389/fmicb.2016.00460] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Accepted: 03/21/2016] [Indexed: 01/22/2023] Open
Abstract
Vibrio are a genus of marine bacteria that have substantial environmental and human health importance, and there is evidence that their impact may be increasing as a consequence of changing environmental conditions. We investigated the abundance and composition of the Vibrio community within the Sydney Harbour estuary, one of the most densely populated coastal areas in Australia, and a region currently experiencing rapidly changing environmental conditions. Using quantitative PCR (qPCR) and Vibrio-specific 16S rRNA amplicon sequencing approaches we observed significant spatial and seasonal variation in the abundance and composition of the Vibrio community. Total Vibrio spp. abundance, derived from qPCR analysis, was higher during the late summer than winter and within locations with mid-range salinity (5-26 ppt). In addition we targeted three clinically important pathogens: Vibrio cholerae, V. Vulnificus, and V. parahaemolyticus. While toxigenic strains of V. cholerae were not detected in any samples, non-toxigenic strains were detected in 71% of samples, spanning a salinity range of 0-37 ppt and were observed during both late summer and winter. In contrast, pathogenic V. vulnificus was only detected in 14% of samples, with its occurrence restricted to the late summer and a salinity range of 5-26 ppt. V. parahaemolyticus was not observed at any site or time point. A Vibrio-specific 16S rRNA amplicon sequencing approach revealed clear shifts in Vibrio community composition across sites and between seasons, with several Vibrio operational taxonomic units (OTUs) displaying marked spatial patterns and seasonal trends. Shifts in the composition of the Vibrio community between seasons were primarily driven by changes in temperature, salinity and NO2, while a range of factors including pH, salinity, dissolved oxygen (DO) and NOx (Nitrogen Oxides) explained the observed spatial variation. Our evidence for the presence of a spatiotemporally dynamic Vibrio community within Sydney Harbour is notable given the high levels of human use of this waterway, and the significant increases in seawater temperature predicted for this region.
Collapse
Affiliation(s)
- Nachshon Siboni
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, UltimoNSW, Australia
| | - Varunan Balaraju
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, UltimoNSW, Australia
- School of Life Sciences, The ithree institute, University of Technology Sydney, UltimoNSW, Australia
| | - Richard Carney
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, UltimoNSW, Australia
| | - Maurizio Labbate
- School of Life Sciences, The ithree institute, University of Technology Sydney, UltimoNSW, Australia
| | - Justin R. Seymour
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, UltimoNSW, Australia
| |
Collapse
|
31
|
Lapierre M, Blin C, Lambert A, Achaz G, Rocha EPC. The Impact of Selection, Gene Conversion, and Biased Sampling on the Assessment of Microbial Demography. Mol Biol Evol 2016; 33:1711-25. [PMID: 26931140 PMCID: PMC4915353 DOI: 10.1093/molbev/msw048] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Recent studies have linked demographic changes and epidemiological patterns in bacterial populations using coalescent-based approaches. We identified 26 studies using skyline plots and found that 21 inferred overall population expansion. This surprising result led us to analyze the impact of natural selection, recombination (gene conversion), and sampling biases on demographic inference using skyline plots and site frequency spectra (SFS). Forward simulations based on biologically relevant parameters from Escherichia coli populations showed that theoretical arguments on the detrimental impact of recombination and especially natural selection on the reconstructed genealogies cannot be ignored in practice. In fact, both processes systematically lead to spurious interpretations of population expansion in skyline plots (and in SFS for selection). Weak purifying selection, and especially positive selection, had important effects on skyline plots, showing patterns akin to those of population expansions. State-of-the-art techniques to remove recombination further amplified these biases. We simulated three common sampling biases in microbiological research: uniform, clustered, and mixed sampling. Alone, or together with recombination and selection, they further mislead demographic inferences producing almost any possible skyline shape or SFS. Interestingly, sampling sub-populations also affected skyline plots and SFS, because the coalescent rates of populations and their sub-populations had different distributions. This study suggests that extreme caution is needed to infer demographic changes solely based on reconstructed genealogies. We suggest that the development of novel sampling strategies and the joint analyzes of diverse population genetic methods are strictly necessary to estimate demographic changes in populations where selection, recombination, and biased sampling are present.
Collapse
Affiliation(s)
- Marguerite Lapierre
- Atelier de Bioinformatique, UMR7205 ISYEB, MNHN-UPMC-CNRS-EPHE, Muséum National d'Histoire Naturelle, Paris, France Collège de France, Center for Interdisciplinary Research in Biology (CIRB), CNRS UMR 7241, Paris, France
| | - Camille Blin
- Sorbonne Universités, UPMC Univ Paris06, IFD, 4 Place Jussieu, Paris Cedex05, France Institut Pasteur, Microbial Evolutionary Genomics, Paris, France CNRS, UMR3525, Paris, France
| | - Amaury Lambert
- Collège de France, Center for Interdisciplinary Research in Biology (CIRB), CNRS UMR 7241, Paris, France UPMC Univ Paris 06, Laboratoire de Probabilités et Modèles Aléatoires (LPMA), CNRS UMR 7599, Paris, France
| | - Guillaume Achaz
- Atelier de Bioinformatique, UMR7205 ISYEB, MNHN-UPMC-CNRS-EPHE, Muséum National d'Histoire Naturelle, Paris, France Collège de France, Center for Interdisciplinary Research in Biology (CIRB), CNRS UMR 7241, Paris, France
| | - Eduardo P C Rocha
- Institut Pasteur, Microbial Evolutionary Genomics, Paris, France CNRS, UMR3525, Paris, France
| |
Collapse
|
32
|
Abstract
Microbial genome evolution is shaped by a variety of selective pressures. Understanding how these processes occur can help to address important problems in microbiology by explaining observed differences in phenotypes, including virulence and resistance to antibiotics. Greater access to whole-genome sequencing provides microbiologists with the opportunity to perform large-scale analyses of selection in novel settings, such as within individual hosts. This tutorial aims to guide researchers through the fundamentals underpinning popular methods for measuring selection in pathogens. These methods are transferable to a wide variety of organisms, and the exercises provided are designed for researchers with any level of programming experience.
Collapse
Affiliation(s)
- Jessica Hedge
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Daniel J. Wilson
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| |
Collapse
|
33
|
Evaluation in Cameroon of a Novel, Simplified Methodology to Assist Molecular Microbiological Analysis of V. cholerae in Resource-Limited Settings. PLoS Negl Trop Dis 2016; 10:e0004307. [PMID: 26735969 PMCID: PMC4703203 DOI: 10.1371/journal.pntd.0004307] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 11/25/2015] [Indexed: 12/28/2022] Open
Abstract
Background Vibrio cholerae is endemic in South Asia and Africa where outbreaks of cholera occur widely and are particularly associated with poverty and poor sanitation. Knowledge of the genetic diversity of toxigenic V. cholerae isolates, particularly in Africa, remains scarce. The constraints in improving this understanding is not only the lack of regular cholera disease surveillance, but also the lack of laboratory capabilities in endemic countries to preserve, store and ship isolates in a timely manner. We evaluated the use of simplified sample preservation methods for molecular characterization using multi-locus variable-number tandem-repeat analysis (MLVA) for differentiation of Vibrio cholerae genotypes. Methods and Findings Forty-seven V. cholerae isolates and 18 enriched clinical specimens (e.g. stool specimens after enrichment in broth) from cholera outbreaks in Cameroon were preserved on Whatman filter paper for DNA extraction. The samples were collected from two geographically distinct outbreaks in the Far North of Cameroon (FNC) in June 2014 and October 2014. In addition, a convenience sample of 14 isolates from the Philippines and 8 from Mozambique were analyzed. All 87 DNAs were successfully analyzed including 16 paired samples, one a cultured isolate and the other the enriched specimen from which the isolate was collected. Genotypic results were identical between 15 enriched specimens and their culture isolates and the other pair differed at single locus. Two closely related, but distinct clonal complexes were identified among the Cameroonian specimens from 2014. Conclusions Collecting V. cholerae using simplified laboratory methods in remote and low-resource settings allows for subsequent advanced molecular characterization of V. cholerae O1. These simplified DNA preservation methods identify V. cholerae and make possible timely information regarding the genetic diversity of V. cholerae; our results set the stage for continued molecular epidemiological research to better understand the transmission and dissemination of V. cholerae in Africa and elsewhere worldwide. Cholera, caused by the bacterium Vibrio cholerae, causes an estimated 3–5 million cases every year and more than 100,000 deaths. The highest disease burden is reported from Africa, however, the epidemic potential and transmission patterns among circulating strains is scarcely understood. The challenges of disease surveillance are constrained by the costs associated with laboratory confirmation and sample preservation. To improve the ability to identify the cholera disease burden, to subsequently understand the molecular epidemiology of circulating cholera strains, and to elucidate transmission patterns, we applied simplified collection methodologies to facilitate timely molecular characterization of V. cholerae isolates from Cameroon, Mozambique and the Philippines. Enriched specimens as well as cultured isolates were examined, demonstrating that enriched specimens provide sufficient material for genetic analysis. The results of the genetic analyses did not suggest significant genetic diversity within two distinct outbreaks in Cameroon. The study detected a possible relationship between isolates present in Cameroon and two isolates from Mozambique, two geographically distant nations in Africa. Whole genome sequencing can test whether this hypothesis is correct. Our findings set the stage for surveillance and molecular characterization in these areas to elucidate more fully the relationship and disease transmission patterns.
Collapse
|
34
|
Bentley SD, Parkhill J. Genomic perspectives on the evolution and spread of bacterial pathogens. Proc Biol Sci 2015; 282:20150488. [PMID: 26702036 PMCID: PMC4707741 DOI: 10.1098/rspb.2015.0488] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 05/19/2015] [Indexed: 12/22/2022] Open
Abstract
Since the first complete sequencing of a free-living organism, Haemophilus influenzae, genomics has been used to probe both the biology of bacterial pathogens and their evolution. Single-genome approaches provided information on the repertoire of virulence determinants and host-interaction factors, and, along with comparative analyses, allowed the proposal of hypotheses to explain the evolution of many of these traits. These analyses suggested many bacterial pathogens to be of relatively recent origin and identified genome degradation as a key aspect of host adaptation. The advent of very-high-throughput sequencing has allowed for detailed phylogenetic analysis of many important pathogens, revealing patterns of global and local spread, and recent evolution in response to pressure from therapeutics and the human immune system. Such analyses have shown that bacteria can evolve and transmit very rapidly, with emerging clones showing adaptation and global spread over years or decades. The resolution achieved with whole-genome sequencing has shown considerable benefits in clinical microbiology, enabling accurate outbreak tracking within hospitals and across continents. Continued large-scale sequencing promises many further insights into genetic determinants of drug resistance, virulence and transmission in bacterial pathogens.
Collapse
Affiliation(s)
- Stephen D Bentley
- The Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Julian Parkhill
- The Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| |
Collapse
|
35
|
A globally distributed mobile genetic element inhibits natural transformation of Vibrio cholerae. Proc Natl Acad Sci U S A 2015; 112:10485-90. [PMID: 26240317 DOI: 10.1073/pnas.1509097112] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Natural transformation is one mechanism of horizontal gene transfer (HGT) in Vibrio cholerae, the causative agent of cholera. Recently, it was found that V. cholerae isolates from the Haiti outbreak were poorly transformed by this mechanism. Here, we show that an integrating conjugative element (ICE)-encoded DNase, which we name IdeA, is necessary and sufficient for inhibiting natural transformation of Haiti outbreak strains. We demonstrate that IdeA inhibits this mechanism of HGT in cis via DNA endonuclease activity that is localized to the periplasm. Furthermore, we show that natural transformation between cholera strains in a relevant environmental context is inhibited by IdeA. The ICE encoding IdeA is globally distributed. Therefore, we analyzed the prevalence and role for this ICE in limiting natural transformation of isolates from Bangladesh collected between 2001 and 2011. We found that IdeA(+) ICEs were nearly ubiquitous in isolates from 2001 to 2005; however, their prevalence decreased to ∼40% from 2006 to 2011. Thus, IdeA(+) ICEs may have limited the role of natural transformation in V. cholerae. However, the rise in prevalence of strains lacking IdeA may now increase the role of this conserved mechanism of HGT in the evolution of this pathogen.
Collapse
|