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Dorman MJ, Domman D, Poklepovich T, Tolley C, Zolezzi G, Kane L, Viñas MR, Panagópulo M, Moroni M, Binsztein N, Caffer MI, Clare S, Dougan G, Salmond GPC, Parkhill J, Campos J, Thomson NR. Genomics of the Argentinian cholera epidemic elucidate the contrasting dynamics of epidemic and endemic Vibrio cholerae. Nat Commun 2020; 11:4918. [PMID: 33004800 PMCID: PMC7530988 DOI: 10.1038/s41467-020-18647-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 09/03/2020] [Indexed: 12/19/2022] Open
Abstract
In order to control and eradicate epidemic cholera, we need to understand how epidemics begin, how they spread, and how they decline and eventually end. This requires extensive sampling of epidemic disease over time, alongside the background of endemic disease that may exist concurrently with the epidemic. The unique circumstances surrounding the Argentinian cholera epidemic of 1992-1998 presented an opportunity to do this. Here, we use 490 Argentinian V. cholerae genome sequences to characterise the variation within, and between, epidemic and endemic V. cholerae. We show that, during the 1992-1998 cholera epidemic, the invariant epidemic clone co-existed alongside highly diverse members of the Vibrio cholerae species in Argentina, and we contrast the clonality of epidemic V. cholerae with the background diversity of local endemic bacteria. Our findings refine and add nuance to our genomic definitions of epidemic and endemic cholera, and are of direct relevance to controlling current and future cholera epidemics.
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Affiliation(s)
- Matthew J Dorman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Daryl Domman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Department of Internal Medicine, Center for Global Health, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Tomás Poklepovich
- Instituto Nacional de Enfermedades Infecciosas, INEI-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Charlotte Tolley
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Gisella Zolezzi
- Instituto Nacional de Enfermedades Infecciosas, INEI-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Leanne Kane
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - María Rosa Viñas
- Instituto Nacional de Enfermedades Infecciosas, INEI-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Marcela Panagópulo
- Instituto Nacional de Enfermedades Infecciosas, INEI-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Miriam Moroni
- Instituto Nacional de Enfermedades Infecciosas, INEI-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Norma Binsztein
- Instituto Nacional de Enfermedades Infecciosas, INEI-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - María Inés Caffer
- Instituto Nacional de Enfermedades Infecciosas, INEI-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Simon Clare
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Gordon Dougan
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Department of Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge, CB2 0QW, UK
| | - George P C Salmond
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Julian Parkhill
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Josefina Campos
- Instituto Nacional de Enfermedades Infecciosas, INEI-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina.
| | - Nicholas R Thomson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK.
- London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK.
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2
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Zhan X, Zheng Q, Fu J, Xu J, Cao J. A Rapid Multiplex PCR-DHPLC Method of Detection and Identification of Pathogenic Bacteria in Aquatic Products. J Food Saf 2014. [DOI: 10.1111/jfs.12156] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Xiaowei Zhan
- College of Plant protection; Shenyang Agricultural University; Dongling Road No.120, Shenhe District Shenyang 110866 China
| | - Qiuyue Zheng
- Microbiology Laboratory; Liaoning entry-exit inspection and quarantine bureau; Changjiang East Road No.60 Zhongshan District Dalian 116001 China
| | - Junfan Fu
- College of Plant protection; Shenyang Agricultural University; Dongling Road No.120, Shenhe District Shenyang 110866 China
| | - Junyi Xu
- Microbiology Laboratory; Liaoning entry-exit inspection and quarantine bureau; Changjiang East Road No.60 Zhongshan District Dalian 116001 China
| | - Jijuan Cao
- Microbiology Laboratory; Liaoning entry-exit inspection and quarantine bureau; Changjiang East Road No.60 Zhongshan District Dalian 116001 China
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Kanungo S, Sen B, Ramamurthy T, Sur D, Manna B, Pazhani GP, Chowdhury G, Jhunjhunwala P, Nandy RK, Koley H, Bhattacharya MK, Gupta S, Goel G, Dey B, M T, Nair GB, Ghosh A, Mahalanabis D. Safety and immunogenicity of a live oral recombinant cholera vaccine VA1.4: a randomized, placebo controlled trial in healthy adults in a cholera endemic area in Kolkata, India. PLoS One 2014; 9:e99381. [PMID: 24983989 PMCID: PMC4077646 DOI: 10.1371/journal.pone.0099381] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 05/08/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND A live oral cholera vaccine VA 1.4 developed from a non-toxigenic Vibrio cholerae O1 El Tor strain using ctxB gene insertion was further developed into a clinical product following cGMP and was evaluated in a double-blind randomized placebo controlled parallel group two arm trial with allocation ratio of 1∶1 for safety and immunogenicity in men and women aged 18-60 years from Kolkata, India. METHOD A lyophilized dose of 1.9×109 CFU (n = 44) or a placebo (n = 43) reconstituted with a diluent was administered within 5 minutes of drinking 100 ml of a buffer solution made of sodium bicarbonate and ascorbic acid and a second dose on day 14. RESULT The vaccine did not elicit any diarrhea related adverse events. Other adverse events were rare, mild and similar in two groups. One subject in the vaccine group excreted the vaccine strain on the second day after first dose. The proportion of participants who seroconverted (i.e. had 4-folds or higher rise in reciprocal titre) in the vaccine group were 65.9% (95% CI: 50.1%-79.5%) at both 7 days (i.e. after 1st dose) and 21 days (i.e. after 2nd dose). None of the placebo recipients seroconverted. Anti-cholera toxin antibody was detected in very few recipients of the vaccine. CONCLUSION This study demonstrates that VA 1.4 at a single dose of 1.9×109 is safe and immunogenic in adults from a cholera endemic region. No additional benefit after two doses was seen. TRIAL REGISTRATION Clinical Trials Registry-India, National Institute of Medical Statistics (Indian Council of Medical Research) CTRI/2012/04/002582.
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Affiliation(s)
- Suman Kanungo
- Department of Epidemiology, National Institute of Cholera & Enteric Diseases, Kolkata, West Bengal, India
| | - Bandana Sen
- Society for Applied Studies, Kolkata, West Bengal, India
| | - Thandavarayan Ramamurthy
- Department of Microbiology, National Institute of Cholera & Enteric Diseases, Kolkata, West Bengal, India
| | - Dipika Sur
- Department of Epidemiology, National Institute of Cholera & Enteric Diseases, Kolkata, West Bengal, India
| | - Byomkesh Manna
- Department of Epidemiology, National Institute of Cholera & Enteric Diseases, Kolkata, West Bengal, India
| | - Gururaja P. Pazhani
- Department of Microbiology, National Institute of Cholera & Enteric Diseases, Kolkata, West Bengal, India
| | - Goutam Chowdhury
- Department of Microbiology, National Institute of Cholera & Enteric Diseases, Kolkata, West Bengal, India
| | - Puja Jhunjhunwala
- Department of Microbiology, National Institute of Cholera & Enteric Diseases, Kolkata, West Bengal, India
| | - Ranjan K. Nandy
- Department of Microbiology, National Institute of Cholera & Enteric Diseases, Kolkata, West Bengal, India
| | - Hemanta Koley
- Department of Microbiology, National Institute of Cholera & Enteric Diseases, Kolkata, West Bengal, India
| | - Mihir Kumar Bhattacharya
- Department of Epidemiology, National Institute of Cholera & Enteric Diseases, Kolkata, West Bengal, India
| | - Sanjay Gupta
- Catalyst Clinical Services Pvt. Ltd., Delhi, India
| | - Gaurav Goel
- Catalyst Clinical Services Pvt. Ltd., Delhi, India
| | - Bindu Dey
- Department of Biotechnology, Ministry of Science and Technology, New Delhi, India
| | - Thungapathra M
- Institute of Post Graduate Medicine and Research, Chandigarh, India
| | - G. Balakrish Nair
- Translational Health Science and Technology Institute, Gurgaon, Haryana, India
| | - Amit Ghosh
- Department of Microbiology, National Institute of Cholera & Enteric Diseases, Kolkata, West Bengal, India
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Mahalanabis D, Ramamurthy T, Nair G, Ghosh A, Shaikh S, Sen B, Thungapathra M, Ghosh R, Pazhani G, Nandy R, Jana S, Bhattacharya S. Randomized placebo controlled human volunteer trial of a live oral cholera vaccine VA1.3 for safety and immune response. Vaccine 2009; 27:4850-6. [DOI: 10.1016/j.vaccine.2009.05.065] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2009] [Revised: 05/11/2009] [Accepted: 05/21/2009] [Indexed: 11/24/2022]
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Theron J, Cilliers J, Du Preez M, Brözel VS, Venter SN. Detection of toxigenic Vibrio cholerae from environmental water samples by an enrichment broth cultivation-pit-stop semi-nested PCR procedure. J Appl Microbiol 2000; 89:539-46. [PMID: 11021588 DOI: 10.1046/j.1365-2672.2000.01140.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A pit-stop semi-nested PCR assay for the detection of toxigenic Vibrio cholerae in environmental water samples was developed and its performance evaluated. The PCR technique amplifies sequences within the cholera toxin operon specific for toxigenic V. cholerae. The PCR procedure coupled with an enrichment culture detected as few as four V. cholerae organisms in pure culture. Treated sewage, surface, ground and drinking water samples were seeded with V. cholerae and following enrichment, a detection limit of as few as 1 V. cholerae cfu ml(-1) was obtained with amplification reactions from crude bacterial lysates. The proposed method, which includes a combination of enrichment, rapid sample preparation and a pit-stop semi-nested PCR, could be applicable in the rapid detection of toxigenic V. cholerae in environmental water samples.
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Affiliation(s)
- J Theron
- Department of Microbiology and Plant Pathology, University of Pretoria, South Africa.
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Olsen JE, Aabo S, Hill W, Notermans S, Wernars K, Granum PE, Popovic T, Rasmussen HN, Olsvik O. Probes and polymerase chain reaction for detection of food-borne bacterial pathogens. Int J Food Microbiol 1995; 28:1-78. [PMID: 8751091 DOI: 10.1016/0168-1605(94)00159-4] [Citation(s) in RCA: 122] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
DNA-hybridization and the polymerase chain reaction (PCR) are techniques commonly used to detect pathogenic bacteria. In this paper, the use of these techniques for detection of Salmonella, E. coli, V. cholerae, non-O1 Vibrio, Yersinia enterocolitica, Campylobacter, Listeria monocytogenes, Staphylococcus aureus, Bacillus cereus, Clostridium perfringens, and C. botulinum is reviewed with emphasis on application in food microbiology. In food control, DNA-techniques have most often been used in a 'culture confirmation' fashion, i.e. bacteria are enriched and sometimes even purified by traditional culture procedures and thereafter identified by the use of DNA-based methods. The most desirable approach is, however, to detect organisms directly in the food, but major problems remain to be solved before this can be routinely performed.
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Affiliation(s)
- J E Olsen
- KVL - Centre for Food Research, Department of Veterinary Microbiology, The Royal Veterinary and Agricultural University, Frederiksberg C., Denmark
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7
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Shangkuan YH, Show YS, Wang TM. Multiplex polymerase chain reaction to detect toxigenic Vibrio cholerae and to biotype Vibrio cholerae O1. THE JOURNAL OF APPLIED BACTERIOLOGY 1995; 79:264-73. [PMID: 7592121 DOI: 10.1111/j.1365-2672.1995.tb03136.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A multiplex polymerase chain reaction (PCR) was developed to identify cholera toxin-producing Vibrio cholerae and to biotype V. cholerae O1. Enterotoxin-producing V. cholerae strains were identified with a primer pair that amplified a fragment of the ctxA2-B gene. Vibrio cholerae O1 strains were simultaneously differentiated into biotypes with three primers specified for the hylA gene in the same reaction. The hlyA amplicon in the multiplex PCR serves as an internal control when testing toxin-producing strains, as hlyA gene sequences exist in all tested V. cholerae strains. Enrichment of V. cholerae present on oysters for 6 h in alkaline peptone water before detection by a nested PCR with internal primers for ctxA2-B gene yielded a detection limit lower than 3 colony-forming units (cfu) per gram of food.
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Affiliation(s)
- Y H Shangkuan
- Division of Epidemiology, National Defense Medical Center, Sanhsia, Taipei, Taiwan, ROC
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8
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Abstract
Despite more than a century of study, cholera still presents challenges and surprises to us. Throughout most of the 20th century, cholera was caused by Vibrio cholerae of the O1 serogroup and the disease was largely confined to Asia and Africa. However, the last decade of the 20th century has witnessed two major developments in the history of this disease. In 1991, a massive outbreak of cholera started in South America, the one continent previously untouched by cholera in this century. In 1992, an apparently new pandemic caused by a previously unknown serogroup of V. cholerae (O139) began in India and Bangladesh. The O139 epidemic has been occurring in populations assumed to be largely immune to V. cholerae O1 and has rapidly spread to many countries including the United States. In this review, we discuss all aspects of cholera, including the clinical microbiology, epidemiology, pathogenesis, and clinical features of the disease. Special attention will be paid to the extraordinary advances that have been made in recent years in unravelling the molecular pathogenesis of this infection and in the development of new generations of vaccines to prevent it.
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Affiliation(s)
- J B Kaper
- Center for Vaccine Development, University of Maryland School of Medicine, Baltimore 21201
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9
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Makino S, Okada Y, Maruyama T, Ishikawa K, Takahashi T, Nakamura M, Ezaki T, Morita H. Direct and rapid detection of Erysipelothrix rhusiopathiae DNA in animals by PCR. J Clin Microbiol 1994; 32:1526-31. [PMID: 7521358 PMCID: PMC264031 DOI: 10.1128/jcm.32.6.1526-1531.1994] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Erysipelothrix rhusiopathiae is a gram-positive rod capable of causing erysipelas in swine. To establish a method for specifically detecting E. rhusiopathiae for practical applications, such as for the inspection of slaughterhouses, the feasibility of using primers derived from the DNA sequence coding for 16S rRNA in a PCR-specific detection system was investigated. Oligonucleotide primers were designed to amplify a 407-bp DNA fragment by PCR. The amplification was specific to the Erysipelothrix DNA but not to that of other bacterial genera tested. This PCR-based method efficiently and specifically detected the Erysipelothrix DNA sequence in joint and spleen samples from mice within 6 h, and application of the 407-bp DNA segment from samples containing very low numbers of bacteria (< 20 bacteria per spleen from mice) was possible. Although this PCR amplification is specific for the Erysipelothrix genus, which contains at least two species, E. rhusiopathiae and E. tonsillarum, it can be concluded that all Erysipelothrix strains detected by this PCR system in diseased pigs are E. rhusiopathiae because only E. rhusiopathiae is virulent for pigs. These results show that this PCR amplification system using the DNA sequence coding for 16S rRNA is very rapid and reliable and avoids cumbersome and lengthy cultivation steps, demonstrating that this system could be used for practical applications.
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Affiliation(s)
- S Makino
- Department of Veterinary Public Health, Institute of Public Health, Tokyo, Japan
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Varela P, Pollevick GD, Rivas M, Chinen I, Binsztein N, Frasch AC, Ugalde RA. Direct detection of Vibrio cholerae in stool samples. J Clin Microbiol 1994; 32:1246-8. [PMID: 8051251 PMCID: PMC263658 DOI: 10.1128/jcm.32.5.1246-1248.1994] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
A direct method to detect Vibrio cholerae in stool samples was developed by using a PCR procedure that did not require a DNA purification step. Dilution (1/100) of stool samples prevented inhibition of the reaction by contaminants, and two consecutive PCRs, the second one with a nested primer, achieved the desired sensitivity. Comparison of the results obtained from stool swab samples processed by the two-step PCR and by an enzyme-linked immunosorbent assay using GM1 as the capture molecule showed that the former is more sensitive and gave positive results even when V. cholerae was not culturable or dead.
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Affiliation(s)
- P Varela
- Instituto Nacional de Microbiología Carlos G Malbrán, Buenos Aires, Argentina
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