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He Y, Liu L, Wang Q, Dong X, Huang J, Jia X, Peng X. Bio-degraded of sulfamethoxazole by microbial consortia without addition nutrients: Mineralization, nitrogen removal, and proteomic characterization. JOURNAL OF HAZARDOUS MATERIALS 2024; 466:133558. [PMID: 38262313 DOI: 10.1016/j.jhazmat.2024.133558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 01/25/2024]
Abstract
Sulfamethoxazole (SMX) is widely employed as an antibiotic, while its residue in environment has become a common public concern. Using 100 mg/L SMX as the sole nutrient source, the acclimated sludge obtained by this study displayed an excellent SMX degradation performance. The addition of SMX resulted in significant microbiological differentiation within the acclimated sludge. Microbacterium (6.6%) was identified as the relatively dominant genera in metabolism group that used SMX as sole carbon source. Highly expressed proteins from this strain strongly suggested its essential role in SMX degradation, while the degradation of SMX by other strains (Thaurea 78%) in co-metabolism group appeared to also rely on this strain. The interactions of differentially expressed proteins were primarily involved in metabolic pathways including TCA cycle and nitrogen metabolism. It is concluded that the sulfonamides might serve not only as the carbon source but also as the nitrogen source in the reactor. A total of 24 intermediates were identified, 13 intermediates were newly reported. The constructed pathway suggested the mineralizing and nitrogen conversion ability towards SMX. Batch experiments also proved that the acclimated sludge displayed ability to biodegrade other sulfonamides, including SM2 and SDZ and SMX-N could be removed completely.
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Affiliation(s)
- Yuzhe He
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China
| | - Lei Liu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China
| | - Qi Wang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China
| | - Xiaoqi Dong
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China
| | - Jingfei Huang
- College of Plant Protection, Fujian Agriculture and Forestry University, 15 Shangxiadian Road, Fuzhou 350002, China.
| | - Xiaoshan Jia
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China
| | - Xingxing Peng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China.
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Taylor-Brown A, Afrad MH, Khan AI, Lassalle F, Islam MT, Tanvir NA, Thomson NR, Qadri F. Genomic epidemiology of Vibrio cholerae during a mass vaccination campaign of displaced communities in Bangladesh. Nat Commun 2023; 14:3773. [PMID: 37355673 PMCID: PMC10290697 DOI: 10.1038/s41467-023-39415-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 06/12/2023] [Indexed: 06/26/2023] Open
Abstract
Ongoing diarrheal disease surveillance throughout Bangladesh over the last decade has revealed seasonal localised cholera outbreaks in Cox's Bazar, where both Bangladeshi Nationals and Forcibly Displaced Myanmar Nationals (FDMNs) reside in densely populated settlements. FDMNs were recently targeted for the largest cholera vaccination campaign in decades. We aimed to infer the epidemic risk of circulating Vibrio cholerae strains by determining if isolates linked to the ongoing global cholera pandemic ("7PET" lineage) were responsible for outbreaks in Cox's Bazar. We found two sublineages of 7PET in this setting during the study period; one with global distribution, and a second lineage restricted to Asia and the Middle East. These subclades were associated with different disease patterns that could be partially explained by genomic differences. Here we show that as the pandemic V. cholerae lineage circulates in this vulnerable population, without a vaccine intervention, the risk of an epidemic was very high.
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Affiliation(s)
- Alyce Taylor-Brown
- Parasites & Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
| | - Mokibul Hassan Afrad
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Ashraful Islam Khan
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Florent Lassalle
- Parasites & Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Md Taufiqul Islam
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
- School of Medical Science, Griffith University, Gold Coast, QLD, Australia
| | - Nabid Anjum Tanvir
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Nicholas R Thomson
- Parasites & Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
- London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK.
| | - Firdausi Qadri
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh.
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3
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Walton MG, Cubillejo I, Nag D, Withey JH. Advances in cholera research: from molecular biology to public health initiatives. Front Microbiol 2023; 14:1178538. [PMID: 37283925 PMCID: PMC10239892 DOI: 10.3389/fmicb.2023.1178538] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 04/14/2023] [Indexed: 06/08/2023] Open
Abstract
The aquatic bacterium Vibrio cholerae is the etiological agent of the diarrheal disease cholera, which has plagued the world for centuries. This pathogen has been the subject of studies in a vast array of fields, from molecular biology to animal models for virulence activity to epidemiological disease transmission modeling. V. cholerae genetics and the activity of virulence genes determine the pathogenic potential of different strains, as well as provide a model for genomic evolution in the natural environment. While animal models for V. cholerae infection have been used for decades, recent advances in this area provide a well-rounded picture of nearly all aspects of V. cholerae interaction with both mammalian and non-mammalian hosts, encompassing colonization dynamics, pathogenesis, immunological responses, and transmission to naïve populations. Microbiome studies have become increasingly common as access and affordability of sequencing has improved, and these studies have revealed key factors in V. cholerae communication and competition with members of the gut microbiota. Despite a wealth of knowledge surrounding V. cholerae, the pathogen remains endemic in numerous countries and causes sporadic outbreaks elsewhere. Public health initiatives aim to prevent cholera outbreaks and provide prompt, effective relief in cases where prevention is not feasible. In this review, we describe recent advancements in cholera research in these areas to provide a more complete illustration of V. cholerae evolution as a microbe and significant global health threat, as well as how researchers are working to improve understanding and minimize impact of this pathogen on vulnerable populations.
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Affiliation(s)
| | | | | | - Jeffrey H. Withey
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI, United States
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Nateghizad H, Sajadi R, Shivaee A, Shirazi O, Sharifian M, Tadi DA, Amini K. Resistance of Vibrio cholera to antibiotics that inhibit cell wall synthesis: A systematic review and meta-analysis. Front Pharmacol 2023; 14:1027277. [PMID: 37021056 PMCID: PMC10069679 DOI: 10.3389/fphar.2023.1027277] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 01/10/2023] [Indexed: 04/07/2023] Open
Abstract
Objective: Cholera is a challenging ancient disease caused by Vibrio cholera (V. cholera). Antibiotics that prevent cell wall synthesis are among the first known antibiotic groups. Due to its high consumption, V. cholera has developed resistance to the majority of antibiotics in this class. Resistance to recommended antibiotics for the treatment of V. cholera has also increased. In light of the decrease in consumption of certain antibiotics in this group that inhibit cell wall synthesis and the implementation of new antibiotics, it is necessary to determine the antibiotic resistance pattern of V. cholera and to employ the most effective treatment antibiotic. Method: An comprehensive systematic search for relevant articles was conducted in PubMed, Web of Science, Scopus, and EMBASE through October 2020. Stata version 17.1 utilized the Metaprop package to execute a Freeman-Tukey double arcsine transformation in order to estimate weighted pooled proportions. Results: A total of 131 articles were included in the meta-analysis. Ampicillin was the most investigated antibiotic. The prevalence of antibiotic resistance was in order aztreonam (0%), cefepime (0%), imipenem (0%), meropenem (3%), fosfomycin (4%), ceftazidime (5%), cephalothin (7%), augmentin (8%), cefalexin (8%), ceftriaxone (9%), cefuroxime (9%), cefotaxime (15%), cefixime (37%), amoxicillin (42%), penicillin (44%), ampicillin (48%), cefoxitin (50%), cefamandole (56%), polymyxin-B (77%), carbenicillin (95%) respectively. Discussion: Aztreonam, cefepime, and imipenem are the most efficient V. cholera cell wall synthesis inhibitors. There has been an increase in resistance to antibiotics such as cephalothin, ceftriaxone, amoxicillin, and meropenem. Over the years, resistance to penicillin, ceftazidime, and cefotaxime, has decreased.
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Affiliation(s)
- Hossein Nateghizad
- Department of Biology, Faculty of Basic Sciences, East of Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Rojina Sajadi
- Department of Biology, Faculty of Basic Sciences, East of Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Ali Shivaee
- Department of Microbiology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Omid Shirazi
- Department of Veterinary medicine, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Mohadeseh Sharifian
- Department of Veterinary medicine, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Danyal Abbasi Tadi
- Department Of Veterinary, Azad University Of Shahr-E Kord, Shahrekord, Iran
| | - Kumarss Amini
- Department of Microbiology, Saveh Branch, Islamic Azad University, Saveh, Iran
- *Correspondence: Kumarss Amini,
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Liu C, Wang Y, Azizian K, Omidi N, Kaviar VH, Kouhsari E, Maleki A. Antimicrobial resistance in Vibrio cholerae O1/O139 clinical isolates: a systematic review and meta-analysis. Expert Rev Anti Infect Ther 2022; 20:1217-1231. [PMID: 35790112 DOI: 10.1080/14787210.2022.2098114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
OBJECTIVES Vibrio cholerae O1/O139 is responsible for cholera epidemics; that remains a huge public health menace across the globe. Furthermore, an increasing resistance rate among V. cholerae strains has been reported around the world. Therefore, the objective of this meta-analysis was to evaluate the weighted pooled resistance (WPR) rates in clinical V. cholerae O1/O139 isolates based on different years, areas, antimicrobial susceptibility testing, and resistance rates. RESEARCH DESIGN AND METHODS : We searched the studies in PubMed, Scopus, Embase, and Web of Science (until January 2020). Statistical analyses were conducted using STATA software (ver. 14.0). RESULTS : A total of 139 studies investigating 24062 V. cholerae O1/O139 isolates were analyzed. The majority of the studies originated in Asia (n=102). The WPR rates were as follows: azithromycin 1%, erythromycin 36%, ciprofloxacin 3%, cotrimoxazole 79%, doxycycline 7%, tetracycline 20%. There was increased resistance to cotrimoxazole, ciprofloxacin, and tetracycline during the 1980 to 2020 years. CONCLUSIONS : Temporal changes in antibiotic resistance rate found in this study demonstrated the critical continuous surveillance of antibiotic resistance. Also, ciprofloxacin, azithromycin, gentamicin, cephalexin, imipenem, ofloxacin, and norfloxacin were found to be the best antibiotics against V. cholera, with the highest and the lowest effectiveness resistance rate.
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Affiliation(s)
- Chaoying Liu
- Zhumadian Academy of Industry Innovation and Development, Huanghuai University, Zhumadian 463000, China
| | - Ye Wang
- School of Biological and Food Processing Engineering, Huanghuai University, Zhumadian 463000, China
| | - Khalil Azizian
- Department of Microbiology, Faculty of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Nazanin Omidi
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Vahab Hassan Kaviar
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Ebrahim Kouhsari
- Laboratory Sciences Research Center, Golestan University of Medical Sciences, Gorgan, Iran.,Department of Laboratory Sciences, Faculty of Paramedicine, Golestan University of Medical Sciences, Iran
| | - Abbas Maleki
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
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6
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Globally Vibrio cholera antibiotics resistance to RNA and DNA effective antibiotics: A systematic review and meta-analysis. Microb Pathog 2022; 172:105514. [DOI: 10.1016/j.micpath.2022.105514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 11/19/2022]
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7
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Monir MM, Hossain T, Morita M, Ohnishi M, Johura FT, Sultana M, Monira S, Ahmed T, Thomson N, Watanabe H, Huq A, Colwell RR, Seed K, Alam M. Genomic Characteristics of Recently Recognized Vibrio cholerae El Tor Lineages Associated with Cholera in Bangladesh, 1991 to 2017. Microbiol Spectr 2022; 10:e0039122. [PMID: 35315699 PMCID: PMC9045249 DOI: 10.1128/spectrum.00391-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 03/02/2022] [Indexed: 11/20/2022] Open
Abstract
Comparative genomic analysis of Vibrio cholerae El Tor associated with endemic cholera in Asia revealed two distinct lineages, one dominant in Bangladesh and the other in India. An in-depth whole-genome study of V. cholerae El Tor strains isolated during endemic cholera in Bangladesh (1991 to 2017) included reference genome sequence data obtained online. Core genome phylogeny established using single nucleotide polymorphisms (SNPs) showed V. cholerae El Tor strains comprised two lineages, BD-1 and BD-2, which, according to Bayesian phylodynamic analysis, originated from paraphyletic group BD-0 around 1981. BD-1 and BD-2 lineages overlapped temporally but were negatively associated as causative agents of cholera during 2004 to 2017. Genome-wide association study (GWAS) revealed 140 SNPs and 31 indels, resulting in gene alleles unique to BD-1 and BD-2. Regression analysis of root to tip distance and year of isolation indicated early BD-0 strains at the base, whereas BD-1 and BD-2 subsequently emerged and progressed by accumulating SNPs. Pangenome analysis provided evidence of gene acquisition by both BD-1 and BD-2, of which six crucial proteins of known function were predominant in BD-2. BD-1 and BD-2 diverged and have distinctively different genomic traits, namely, heterogeneity in VSP-2, VPI-1, mobile elements, toxin encoding elements, and total gene abundance. In addition, the observed phage-inducible chromosomal island-like element (PLE1), and SXT ICE elements (ICETET) in BD-2 presumably provided a fitness advantage for the lineage to outcompete BD-1 as the etiological agent of endemic cholera in Bangladesh, with implications for global cholera epidemiology. IMPORTANCE Cholera is a global disease with specific reference to the Bay of Bengal Ganges Delta where Vibrio cholerae O1 El Tor, the causative agent of the disease showed two circulating lineages, one dominant in Bangladesh and the other in India. Results of an in-depth genomic study of V. cholerae associated with endemic cholera during the past 27 years (1991 to 2017) indicate emergence and succession of the two lineages, BD-1 and BD-2, arising from a common ancestral paraphyletic group, BD-0, comprising the early strains and short-term evolution of the bacterium in Bangladesh. Among the two V. cholerae lineages, BD-2 supersedes BD-1 and is predominant in the most recent endemic cholera in Bangladesh. The BD-2 lineage contained significantly more SNPs and indels, and showed richness in gene abundance, including antimicrobial resistance genes, gene cassettes, and PLE to fight against bacteriophage infection, acquired over time. These findings have important epidemic implications on a global scale.
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Affiliation(s)
- Md Mamun Monir
- icddr, b, Formerly International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Talal Hossain
- icddr, b, Formerly International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Masatomo Morita
- National Institutes of Infectious Diseases (NIID), Tokyo, Japan
| | - Makoto Ohnishi
- National Institutes of Infectious Diseases (NIID), Tokyo, Japan
| | - Fatema-Tuz Johura
- icddr, b, Formerly International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Marzia Sultana
- icddr, b, Formerly International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Shirajum Monira
- icddr, b, Formerly International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Tahmeed Ahmed
- icddr, b, Formerly International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | | | - Haruo Watanabe
- National Institutes of Infectious Diseases (NIID), Tokyo, Japan
| | - Anwar Huq
- Maryland Pathogen Research Institute, University of Maryland, Baltimore, Maryland, USA
| | - Rita R. Colwell
- Maryland Pathogen Research Institute, University of Maryland, Baltimore, Maryland, USA
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | | | - Munirul Alam
- icddr, b, Formerly International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
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Guan J, Bao C, Wang P, Jing Y, Wang L, Li X, Mu X, Li B, Zhou D, Guo X, Yin Z. Genetic Characterization of Four Groups of Chromosome-Borne Accessory Genetic Elements Carrying Drug Resistance Genes in Providencia. Infect Drug Resist 2022; 15:2253-2270. [PMID: 35510160 PMCID: PMC9058013 DOI: 10.2147/idr.s354934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/20/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose The aim of this study was to gain a deeper genomics and bioinformatics understanding of diversification of accessory genetic elements (AGEs) in Providencia. Methods Herein, the complete genome sequences of five Providencia isolates from China were determined, and seven AGEs were identified from the chromosomes. Detailed genetic dissection and sequence comparison were applied to these seven AGEs, together with additional 10 chromosomal ones from GenBank (nine of them came from Providencia). Results These 17 AGEs were divided into four groups: Tn6512 and its six derivatives, Tn6872 and its two derivatives, Tn6875 and its one derivative, and Tn7 and its four derivatives. These AGEs display high-level diversification in modular structures that had complex mosaic natures, and particularly different multidrug resistance (MDR) regions were presented in these AGEs. At least 52 drug resistance genes, involved in resistance to 15 different categories of antimicrobials and heavy metal, were found in 15 of these 17 AGEs. Conclusion Integration of these AGEs into the Providencia chromosomes would contribute to the accumulation and distribution of drug resistance genes and enhance the ability of Providencia isolates to survive under drug selection pressure.
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Affiliation(s)
- Jiayao Guan
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin, 130122, People’s Republic of China
| | - Chunmei Bao
- Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100039, People’s Republic of China
| | - Peng Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People’s Republic of China
| | - Ying Jing
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People’s Republic of China
| | - Lingling Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People’s Republic of China
| | - Xinyue Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People’s Republic of China
| | - Xiaofei Mu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People’s Republic of China
| | - Boan Li
- Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100039, People’s Republic of China
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People’s Republic of China
| | - Xuejun Guo
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin, 130122, People’s Republic of China
- Xuejun Guo, Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin, 130122, People’s Republic of China, Tel +86-431-86985931, Email
| | - Zhe Yin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People’s Republic of China
- Correspondence: Zhe Yin, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People’s Republic of China, Tel +86-10-66948557, Email
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Azithromycin can induce SOS response and horizontal gene transfer of SXT element in Vibrio cholerae. Mol Biol Rep 2022; 49:4737-4748. [DOI: 10.1007/s11033-022-07323-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 03/02/2022] [Indexed: 10/18/2022]
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10
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Kim H, Burkinshaw BJ, Lam LG, Manera K, Dong TG. Identification of Small Molecule Inhibitors of the Pathogen Box against Vibrio cholerae. Microbiol Spectr 2021; 9:e0073921. [PMID: 34937180 PMCID: PMC8694189 DOI: 10.1128/spectrum.00739-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 11/18/2021] [Indexed: 11/20/2022] Open
Abstract
Antimicrobial resistance (AMR) has become a serious public and economic threat. The rate of bacteria acquiring AMR surpasses the rate of new antibiotics discovery, projecting more deadly AMR infections in the future. The Pathogen Box is an open-source library of drug-like compounds that can be screened for antibiotic activity. We have screened molecules of the Pathogen Box against Vibrio cholerae, the cholera-causing pathogen, and successfully identified two compounds, MMV687807 and MMV675968, that inhibit growth. RNA-seq analyses of V. cholerae after incubation with each compound revealed that both compounds affect cellular functions on multiple levels including carbon metabolism, iron homeostasis, and biofilm formation. In addition, whole-genome sequencing analysis of spontaneous resistance mutants identified an efflux system that confers resistance to MMV687807. We also identified that the dihydrofolate reductase is the likely target of MMV675968 suggesting it acts as an analog of trimethoprim but with a MIC 14-fold lower than trimethoprim in molar concentration. In summary, these two compounds that effectively inhibit V. cholerae and other bacteria may lead to the development of new antibiotics for better treatment of the cholera disease. IMPORTANCE Cholera is a serious infectious disease in tropical regions causing millions of infections annually. Vibrio cholerae, the causative agent of cholera, has gained multi-antibiotic resistance over the years, posing greater threat to public health and current treatment strategies. Here we report two compounds that effectively target the growth of V. cholerae and have the potential to control cholera infection.
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Affiliation(s)
- Haeun Kim
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
- Biochemistry and Molecular Biology, Cumming School of Medicine, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Brianne J. Burkinshaw
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
- Biochemistry and Molecular Biology, Cumming School of Medicine, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Linh G. Lam
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
- Biochemistry and Molecular Biology, Cumming School of Medicine, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Kevin Manera
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
- Biochemistry and Molecular Biology, Cumming School of Medicine, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Tao G. Dong
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
- Biochemistry and Molecular Biology, Cumming School of Medicine, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
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11
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Comparative Genomics of Clinical and Environmental Isolates of Vibrio spp. of Colombia: Implications of Traits Associated with Virulence and Resistance. Pathogens 2021; 10:pathogens10121605. [PMID: 34959560 PMCID: PMC8706872 DOI: 10.3390/pathogens10121605] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/06/2021] [Accepted: 11/09/2021] [Indexed: 01/22/2023] Open
Abstract
There is widespread concern about the increase in cases of human and animal infections caused by pathogenic Vibrio species due to the emergence of epidemic lineages. In Colombia, active surveillance by the National Institute of Health (INS) has confirmed the presence of Vibrio; however, in routine surveillance, these isolates are not genomically characterized. This study focused on the pangenome analysis of six Vibrio species: V. parahaemolyticus, V. vulnificus, V. alginolyticus, V. fluvialis, V. diabolicus and V. furnissii to determine the genetic architectures of potentially virulent and antimicrobial resistance traits. Isolates from environmental and clinical samples were genome sequenced, assembled and annotated. The most important species in public health were further characterized by multilocus sequence typing and phylogenomics. For V. parahaemolyticus, we found the virulent ST3 and ST120 genotypes. For V. vulnificus, we identified isolates belonging to lineages 1 and 2. Virulence gene homologues between species were found even in non-pathogenic species such as V. diabolicus. Annotations related to the mobilome, integrative mobile and conjugative elements and resistance genes were obtained from environmental and clinical isolates. This study contributes genomic information to the intensified surveillance program implemented by the INS to establish potential sources of vibriosis in Colombia.
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12
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LeGault KN, Hays SG, Angermeyer A, McKitterick AC, Johura FT, Sultana M, Ahmed T, Alam M, Seed KD. Temporal shifts in antibiotic resistance elements govern phage-pathogen conflicts. Science 2021; 373:373/6554/eabg2166. [PMID: 34326207 PMCID: PMC9064180 DOI: 10.1126/science.abg2166] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 06/06/2021] [Indexed: 12/23/2022]
Abstract
Bacteriophage predation selects for diverse antiphage systems that frequently cluster on mobilizable defense islands in bacterial genomes. However, molecular insight into the reciprocal dynamics of phage-bacterial adaptations in nature is lacking, particularly in clinical contexts where there is need to inform phage therapy efforts and to understand how phages drive pathogen evolution. Using time-shift experiments, we uncovered fluctuations in Vibrio cholerae's resistance to phages in clinical samples. We mapped phage resistance determinants to SXT integrative and conjugative elements (ICEs), which notoriously also confer antibiotic resistance. We found that SXT ICEs, which are widespread in γ-proteobacteria, invariably encode phage defense systems localized to a single hotspot of genetic exchange. We identified mechanisms that allow phage to counter SXT-mediated defense in clinical samples, and document the selection of a novel phage-encoded defense inhibitor. Phage infection stimulates high-frequency SXT ICE conjugation, leading to the concurrent dissemination of phage and antibiotic resistances.
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Affiliation(s)
- Kristen N LeGault
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Stephanie G Hays
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Angus Angermeyer
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Amelia C McKitterick
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Fatema-Tuz Johura
- icddr,b, formerly International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Marzia Sultana
- icddr,b, formerly International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Tahmeed Ahmed
- icddr,b, formerly International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Munirul Alam
- icddr,b, formerly International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Kimberley D Seed
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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De R. Mobile Genetic Elements of Vibrio cholerae and the Evolution of Its Antimicrobial Resistance. FRONTIERS IN TROPICAL DISEASES 2021. [DOI: 10.3389/fitd.2021.691604] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Vibrio cholerae (VC) is the causative agent of the severe dehydrating diarrheal disease cholera. The primary treatment for cholera is oral rehydration therapy (ORT). However, in case of moderate to severe dehydration, antibiotics are administered to reduce morbidity. Due to the emergence of multidrug resistant (MDR) strains of VC routinely used antibiotics fail to be effective in cholera patients. Antimicrobial resistance (AMR) is encoded in the genome of bacteria and is usually acquired from other organisms cohabiting in the environment or in the gut with which it interacts in the gut or environmental niche. The antimicrobial resistance genes (ARGs) are usually borne on mobile genetic elements (MGEs) like plasmids, transposons, integrons and SXT constin. Horizontal gene transfer (HGT) helps in the exchange of ARGs among bacteria leading to dissemination of AMR. In VC the acquisition and loss of AMR to many antibiotics have been found to be a dynamic process. This review describes the different AMR determinants and mechanisms of resistance that have been discovered in VC. These ARGs borne usually on MGEs have been recovered from isolates associated with past and present epidemics worldwide. These are responsible for resistance of VC to common antibiotics and are periodically lost and gained contributing to its genetic evolution. These resistance markers can be routinely used for AMR surveillance in VC. The review also presents a precise perspective on the importance of the gut microbiome in the emergence of MDR VC and concludes that the gut microbiome is a potential source of molecular markers and networks which can be manipulated for the interception of AMR in the future.
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Abstract
Cholera, an acute diarrheal disease, is caused by pathogenic strains of Vibrio cholerae generated by the lysogenization of the filamentous cholera toxin phage CTXΦ. Although CTXΦ phage in the classical biotype are usually integrated solitarily or with a truncated copy, those in El Tor biotypes are generally found in tandem and/or with related genetic elements. Due to this structural difference in the CTXΦ prophage array, the prophage in the classical biotype strains does not yield extrachromosomal CTXΦ DNA and does not produce virions, whereas the El Tor biotype strains can replicate the CTXΦ genome and secrete infectious CTXΦ phage particles. However, information on the CTXΦ prophage array structure of pathogenic V. cholerae is limited. Therefore, we investigated the complete genomic sequences of five clinical V. cholerae isolates obtained in Kolkata (India) during 2007 to 2011. The analysis revealed that recent isolates possessed an altered CTXΦ prophage array of the prototype El Tor strain. These strains were defective in replicating the CTXΦ genome. All recent isolates possessed identical rstA and intergenic sequence 1 (Ig-1) sequences and comparable rstA expression in the prototype El Tor strain, suggesting that the altered CTXΦ array was responsible for the defective replication of the prophage. Therefore, CTXΦ structures available in the database and literatures can be classified as replicative and nonreplicative. Furthermore, V. cholerae epidemic strains became capable of producing CTXΦ phage particles since the 1970s. However, V. cholerae epidemic strains again lost the capacity for CTXΦ production around the year 2010, suggesting that a significant change in the dissemination pattern of the current cholera pandemic occurred. IMPORTANCE Cholera is an acute diarrheal disease caused by pathogenic strains of V. cholerae generated by lysogenization of the filamentous cholera toxin phage CTXΦ. The analysis revealed that recent isolates possessed altered CTXΦ prophage array of prototype El Tor strain and were defective in replicating the CTXΦ genome. Classification of CTXΦ structures in isolated years suggested that V. cholerae epidemic strains became capable of producing CTXΦ phage particles since the 1970s. However, V. cholerae epidemic strains again lost the capacity for CTXΦ production around the year 2010, suggesting that a critical change had occurred in the dissemination pattern of the current cholera pandemic.
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Nayak AK, Nayak SR, Behera DR, Pal BB. Dissemination of Vibrio cholerae O1 isolated from Odisha, India. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:355-363. [PMID: 33660421 DOI: 10.1111/1758-2229.12940] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/20/2021] [Indexed: 06/12/2023]
Abstract
The present study reported the antimicrobial susceptibility trends, virulence genes, and drug resistance genes of Vibrio cholerae O1 strains isolated from outbreaks and epidemics over two and half decades (1995-2019) from Odisha, India. Antimicrobial susceptibility testing was performed by disc diffusion method. Virulence and drug resistance genes were detected by multiplex PCR assays. All V. cholerae O1 strains were sensitive to gentamicin, chloramphenicol, norfloxacin and ciprofloxacin while resistant to one or more antibiotics used. About 90% of the isolates of V. cholerae O1 carried antibiotic drug resistant genes (SulII, dfrA1 and strB) and SXT elements and the results correlated with the phenotypic antibiotic data obtained through disc diffusion assay. The tcpA Haitian variant V. cholerae O1 first appeared in 1999, gradually showing its increasing number upto 2019. TcpA El Tor strains only prevailed from 1995 to 2006; whereas the tcpA classical strains of V.choleraeO1 were found in less number from 1995 to 2016. Two multiplex PCR assays confirmed the presence of various toxigenic and virulence genes (toxR, ompU, ace, rtxC, ctxA, tcpA, rfbO1 and ompW) in all isolate of V. cholerae O1 strains. The present findings demonstrated the origin and spread of Haitian variants tcpA in V. cholerae O1 strains over two and half decades.
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Affiliation(s)
- Ashish Kumar Nayak
- Microbiology Division, ICMR-Regional Medical Research Centre, Chandrasekharpur, Bhubaneswar, Orissa, 751023, India
| | - Smruti Ranjan Nayak
- Microbiology Division, ICMR-Regional Medical Research Centre, Chandrasekharpur, Bhubaneswar, Orissa, 751023, India
| | - Dipti Ranjan Behera
- Microbiology Division, ICMR-Regional Medical Research Centre, Chandrasekharpur, Bhubaneswar, Orissa, 751023, India
| | - Bibhuti Bhusan Pal
- Microbiology Division, ICMR-Regional Medical Research Centre, Chandrasekharpur, Bhubaneswar, Orissa, 751023, India
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Assessment and Antibiotic Resistance Profiling in Vibrio Species Isolated from Wild Birds Captured in Danube Delta Biosphere Reserve, Romania. Antibiotics (Basel) 2021; 10:antibiotics10030333. [PMID: 33809945 PMCID: PMC8004222 DOI: 10.3390/antibiotics10030333] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/16/2021] [Accepted: 03/17/2021] [Indexed: 12/13/2022] Open
Abstract
Antimicrobial and multidrug-resistant bacteria are a major problem worldwide and, consequently, the surveillance of antibiotic-resistant bacteria and assessment of the dissemination routes are essential. We hypothesized that migratory birds, coming from various environments, would carry more numerous Vibrio strains than sedentary species, with increased risk to be passed to their contacts or environment in habitats they transit or nest in. Similarly, we presumed that strains from migratory birds will show multidrug resistance. A total of 170 oral and rectal swabs were collected from wild birds captured in different locations of the Danube Delta (Malic, Sfantu-Gheorghe, Letea Forest) and processed using standardized selective media. V. cholerae strains were confirmed by serology and molecular methods and, subsequently, their susceptibility was evaluated. The prevalence of Vibrio species by host species, habitat type, and location was interpreted. The isolated Vibrio species were identified as Vibrio cholerae 14.33%, V. fluvialis 13.33%, V. alginolyticus 12%, V. mimicus 17.33%, V. vulnificus 10.88%, with V. parahaemolyticus and V. metschnikovii (16%) also being prevalent. Of the 76 Vibrio spp. isolates, 18.42% were resistant towards at least three antimicrobials, and 81.57% demonstrated a multidrug resistance phenotype, including mainly penicillins, aminoglycosides, and macrolides. The results of the present study indicate higher numbers of Vibrio strains in migratory (74.66%) than in sedentary birds (25.33%), confirming our hypothesis. Furthermore, the increased pathogenicity of Vibrio spp. strains, isolated from wild migratory and sedentary birds, was confirmed by their increased multiple antibiotic resistance (MAR) index (0.09–0.81).
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Bhandari M, Jennison AV, Rathnayake IU, Huygens F. Evolution, distribution and genetics of atypical Vibrio cholerae - A review. INFECTION GENETICS AND EVOLUTION 2021; 89:104726. [PMID: 33482361 DOI: 10.1016/j.meegid.2021.104726] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 01/07/2021] [Accepted: 01/15/2021] [Indexed: 12/21/2022]
Abstract
Vibrio cholerae is the etiological agent of cholera, a severe diarrheal disease, which can occur as either an epidemic or sporadic disease. Cholera pandemic-causing V. cholerae O1 and O139 serogroups originated from the Indian subcontinent and spread globally and millions of lives are lost each year, mainly in developing and underdeveloped countries due to this disease. V. cholerae O1 is further classified as classical and El Tor biotype which can produce biotype specific cholera toxin (CT). Since 1961, the current seventh pandemic El Tor strains replaced the sixth pandemic strains resulting in the classical biotype strain that produces classical CT. The ongoing evolution of Atypical El Tor V. cholerae srains encoding classical CT is of global concern. The severity in the pathophysiology of these Atypical El Tor strains is significantly higher than El Tor or classical strains. Pathogenesis of V. cholerae is a complex process that involves coordinated expression of different sets of virulence-associated genes to cause disease. We are yet to understand the complete virulence profile of V. cholerae, including direct and indirect expression of genes involved in its survival and stress adaptation in the host. In recent years, whole genome sequencing has paved the way for better understanding of the evolution and strain distribution, outbreak identification and pathogen surveillance for the implementation of direct infection control measures in the clinic against many infectious pathogens including V. cholerae. This review provides a synopsis of recent studies that have contributed to the understanding of the evolution, distribution and genetics of the seventh pandemic Atypical El Tor V. cholerae strains.
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Affiliation(s)
- Murari Bhandari
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia; Public Health Microbiology, Forensic and Scientific Services, Queensland Department of Health, Brisbane, QLD, Australia
| | - Amy V Jennison
- Public Health Microbiology, Forensic and Scientific Services, Queensland Department of Health, Brisbane, QLD, Australia
| | - Irani U Rathnayake
- Public Health Microbiology, Forensic and Scientific Services, Queensland Department of Health, Brisbane, QLD, Australia
| | - Flavia Huygens
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia.
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Chakrabarti AK, Biswas A, Tewari DN, Mondal PP, Dutta S. Phage Types of Vibrio cholerae 01 Biotype ElTor Strains Isolated from India during 2012-2017. J Glob Infect Dis 2020; 12:94-100. [PMID: 32773997 PMCID: PMC7384690 DOI: 10.4103/jgid.jgid_42_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 04/17/2019] [Accepted: 12/07/2019] [Indexed: 11/04/2022] Open
Abstract
Background Cholera is a primordial disease caused by Vibrio cholerae which existed from centuries in different parts of the world and still shows its periodic, endemic and epidemic presence. Thousands of cholera cases are reported from different parts of India and the disease remains endemic throughout the year. At present, we do not have enough knowledge about the phenotypic nature of the circulating V. cholerae strains in this part of the world. Objectives This study was carried out over a period of 6 years with the aim defer with the changes in the prevalence and distribution of biotypes, serotypes and phage types of V. cholerae clinical isolates from various endemic regions of the country to determine phenotypic characteristics of the circulating strains and also to predict the attributes of cholera strains responsible for causing significant outbreaks in future. Materials and Methods A total of 1882 V.cholerae O1 isolates from different cholera endemic areas of India were included in this study. V.cholerae strains which were identified as O1 biotype ElTor further analyzed for serotype and phage types using the standard methodologies. Polyvalent O1 and monospecific Inaba and Ogawa antisera were used for serotyping. A panel of five phages of Basu and Mukherjee phage typing scheme and five phages from the new phage typing scheme were used for phage typing analysis following standard methodology. Results Maximum numbers of strains were isolated from cholera-endemic states like Gujarat and Maharashtra. All the isolates were confirmed as V. cholerae O1 biotype ElTor and majority of them were serotype Ogawa (93.2%). New phage typing scheme resulted in almost 100% typeable V. cholerae O1 strains included in this study and phage type 27 was the predominant type. Although 80% of the strains used in this study were sensitive to all the vibrio phages, S5 phage was found most efficient in lysing cholera strains indicating its broader host range. Conclusion The current study identified phage type 27 as the most dominant type and serotype Ogawa was found continuous in circulation throughout the year which has caused recent cholera outbreaks in India during the past years. Phage sensitivity data propose an alternative cost-effective approach to prevent cholera outbreak by therapeutic uses of typing phages irrespective of origin or clonality of the strains.
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Affiliation(s)
- Alok Kumar Chakrabarti
- Division of Virology, ICMR - National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
| | - Asim Biswas
- Division of Virology, ICMR - National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
| | - Devendra Nath Tewari
- Division of Virology, ICMR - National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
| | - Partha Pratim Mondal
- Division of Virology, ICMR - National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
| | - Shanta Dutta
- Division of Bacteriology, ICMR - National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
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