1
|
Sajeevan A, Ramamurthy T, Solomon AP. Vibrio cholerae virulence and its suppression through the quorum-sensing system. Crit Rev Microbiol 2024:1-22. [PMID: 38441045 DOI: 10.1080/1040841x.2024.2320823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 02/10/2024] [Indexed: 03/06/2024]
Abstract
Vibrio cholerae is a cholera-causing pathogen known to instigate severe contagious diarrhea that affects millions globally. Survival of vibrios depend on a combination of multicellular responses and adapt to changes that prevail in the environment. This process is achieved through a strong communication at the cellular level, the process has been recognized as quorum sensing (QS). The severity of infection is highly dependent on the QS of vibrios in the gut milieu. The quorum may exist in a low/high cell density (LCD/HCD) state to exert a positive or negative response to control the regulatory pathogenic networks. The impact of this regulation reflects on the transition of pathogenic V. cholerae from the environment to infect humans and cause outbreaks or epidemics of cholera. In this context, the review portrays various regulatory processes and associated virulent pathways, which maneuver and control LCD and HCD states for their survival in the host. Although several treatment options are existing, promotion of therapeutics by exploiting the virulence network may potentiate ineffective antibiotics to manage cholera. In addition, this approach is also useful in resource-limited settings, where the accessibility to antibiotics or conventional therapeutic options is limited.
Collapse
Affiliation(s)
- Anusree Sajeevan
- Quorum Sensing Laboratory, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Thandavarayan Ramamurthy
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Disease, Kolkata, India
| | - Adline Princy Solomon
- Quorum Sensing Laboratory, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| |
Collapse
|
2
|
Lee D, Choi H, Son S, Bae J, Joo J, Kim DW, Kim EJ. Expression of Cholera Toxin (CT) and the Toxin Co-Regulated Pilus (TCP) by Variants of ToxT in Vibrio cholerae Strains. Toxins (Basel) 2023; 15:507. [PMID: 37624264 PMCID: PMC10467113 DOI: 10.3390/toxins15080507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/11/2023] [Accepted: 08/15/2023] [Indexed: 08/26/2023] Open
Abstract
The expression of the two major virulence genes of Vibrio cholerae-tcpA (the major subunit of the toxin co-regulated pilus) and ctxAB (cholera toxin)-is regulated by the ToxR regulon, which is triggered by environmental stimuli during infection within the human small intestine. Special culture methods are required to induce the expression of virulence genes in V. cholerae in the laboratory setting. In the present study, induction of the expression of virulence genes by two point mutations (65th and 139th amino acids) in toxT, which is produced by the ToxR regulon and activates the transcription of the virulence genes in V. cholerae, under laboratory culture conditions has been investigated. Each of the four toxT alleles assessed displayed different transcriptional activator functions in a given V. cholerae strain. Although the ToxR regulon has been known to not be expressed by El Tor biotype V. cholerae strains cultured under standard laboratory conditions, the variant toxT alleles that we assessed in this study enabled the expression virulence genes in El Tor biotype strains grown under simple culture conditions comprising shake culture in LB medium, suggesting that the regulation of virulence gene expression may be regulated more complexly than previously thought and may involve additional factors beyond the production of ToxT by the ToxR regulon.
Collapse
Affiliation(s)
- Donghyun Lee
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan 15588, Republic of Korea
- Institute of Pharmacological Research, Hanyang University, Ansan 15588, Republic of Korea
| | - Hunseok Choi
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan 15588, Republic of Korea
- Institute of Pharmacological Research, Hanyang University, Ansan 15588, Republic of Korea
| | - Seonghyeon Son
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan 15588, Republic of Korea
- Institute of Pharmacological Research, Hanyang University, Ansan 15588, Republic of Korea
| | - Jonghyun Bae
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan 15588, Republic of Korea
- Institute of Pharmacological Research, Hanyang University, Ansan 15588, Republic of Korea
| | - Jayun Joo
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan 15588, Republic of Korea
- Institute of Pharmacological Research, Hanyang University, Ansan 15588, Republic of Korea
| | - Dong Wook Kim
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan 15588, Republic of Korea
- Institute of Pharmacological Research, Hanyang University, Ansan 15588, Republic of Korea
| | - Eun Jin Kim
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan 15588, Republic of Korea
- Institute of Pharmacological Research, Hanyang University, Ansan 15588, Republic of Korea
| |
Collapse
|
3
|
Matimba HH, Joachim A, Mizinduko MM, Maseke IA, Nyanga SK, Kelly ME, Nyanga AS, Mghamba JM, Majigo MV, Mohamed AA. Genetic relatedness, virulence factors and antibiotics susceptibility pattern of Vibrio cholerae isolates from various regions during cholera outbreak in Tanzania. PLoS One 2022; 17:e0265868. [PMID: 35333909 PMCID: PMC8956160 DOI: 10.1371/journal.pone.0265868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 03/09/2022] [Indexed: 11/29/2022] Open
Abstract
Background Cholera continues to cause morbidity and mortality in developing countries, including Tanzania. Since August 2015, Tanzania Mainland has experienced cholera outbreaks affecting 26 regions and a 1.6% case fatality rate. The current study determined the virulence factors, genetic relatedness and antimicrobial susceptibility patterns of the Vibrio cholerae isolated from different regions in Tanzania. Methods A cross-sectional study that involved the genetic characterization of V. cholerae isolates from eleven regions in Tanzania was carried out. There were 99 V. cholerae isolates collected between January 2016 and December 2017. The study perfomed a Multi-locus Variable-number tandem-repeat analysis for genetic relatedness and Mismatch Amplification Mutation Analysis polymerase chain reaction for analyzing toxin genes. All the isolates were tested for antimicrobial susceptibility using the Kirby Bauer disk diffusion method. Data were generally analyzed using Microsoft excel, where genetic relatedness was analyzed using eBurst software v3. Results All isolates were V. cholerae O1. Ogawa was the most predominant 97(98%) serotype. Isolates were genetically related with a small genetic diversity and were positive for ctxA, tcpA El Tor virulence genes. All isolates (100%) were sensitive to doxycycline, trimethoprim-sulphamethoxazole, tetracycline, ceftriaxone, and chloramphenicol, while 87.8% were sensitive to ciprofloxacin. A high resistance rate (100%) was detected towards erythromycin, nalidixic acid, amoxicillin, and ampicillin. Conclusion The V.cholerae O1 serotypes Ogawa, El Tor variant predominantly caused cholera outbreaks in Tanzania with strains clonally related regardless of the place and time of the outbreak. Most of the isolates were susceptible to the antibiotic regimen currently used in Tanzania. The high resistance rate detected for the other common antibiotics calls for continuous antimicrobial susceptibility testing during outbreaks.
Collapse
Affiliation(s)
- Hamza Hamad Matimba
- Department of Epidemiology and Biostatistics, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Tanzania Field Epidemiology and Laboratory Training Program, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- * E-mail: (HHM); (AJ)
| | - Agricola Joachim
- Department Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- * E-mail: (HHM); (AJ)
| | - Mucho Michael Mizinduko
- Department of Epidemiology and Biostatistics, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Irene Anthony Maseke
- National Health Laboratory, Quality Assurance, and Training Centre, Dar es Salaam, Tanzania
| | - Salum Kassim Nyanga
- National Health Laboratory, Quality Assurance, and Training Centre, Dar es Salaam, Tanzania
| | - Maria Ezekiely Kelly
- National Health Laboratory, Quality Assurance, and Training Centre, Dar es Salaam, Tanzania
| | - Ali Said Nyanga
- Ministry of Health, Community Development, Gender, Elderly and Children, Dar es Salaam, Tanzania
| | - Janneth Maridadi Mghamba
- Tanzania Field Epidemiology and Laboratory Training Program, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Ministry of Health, Community Development, Gender, Elderly and Children, Dar es Salaam, Tanzania
| | - Mtebe Venance Majigo
- Department Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Ahmed Abade Mohamed
- Tanzania Field Epidemiology and Laboratory Training Program, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| |
Collapse
|
4
|
OUP accepted manuscript. FEMS Microbiol Lett 2022; 369:6570571. [DOI: 10.1093/femsle/fnac041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 03/21/2022] [Accepted: 04/15/2022] [Indexed: 11/14/2022] Open
|
5
|
Narendrakumar L, Jaikumar VS, Chandrika SK, Thomas S. Epidemiological and pathogenic characteristics of Haitian variant V. cholerae circulating in India over a decade (2000-2018). Microb Pathog 2020; 149:104538. [PMID: 32987116 DOI: 10.1016/j.micpath.2020.104538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 09/19/2020] [Accepted: 09/21/2020] [Indexed: 10/23/2022]
Abstract
Vibrio cholerae, causative agent of the water-borne disease cholera still threatens a large proportion of world's population. The major biotypes of the pathogen are classical and El Tor. There have been recent reports of variant V. cholerae strains circulating around the world. In the present study, the epidemiological status of V. cholerae strains circulating in the country over a decade was assessed. Also, a comprehensive analysis of the difference in pathogenicity between the different biotypes of V. cholerae strains was evaluated both in-vitro and in-vivo. The amount of CT produced by different biotypes of V. cholerae strains were analyzed by GM1 ELISA and the probable reasons for the difference in toxin production was discussed. MLST analysis grouped the isolates into a single Sequence Type (ST 69) whereas PFGE analysis clustered the isolates into ten different pulsotypes revealing molecular diversity. The circulating strains were identified to produce cholera toxin and CT mRNA intermediate to the classical and prototype El Tor strains. Also, the circulating strains were identified to possess four ToxR binding sequences. In-vivo pathogenicity analysis by rabbit ileal loop fluid accumulation assay revealed the Haitian variant strains to be more hyperemic than the prototype strains.
Collapse
Affiliation(s)
- Lekshmi Narendrakumar
- Cholera and Biofilm Research Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695 014, Kerala, India
| | - Vishnu S Jaikumar
- Animal Research Facility, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695 014, Kerala, India
| | - Sivakumar K Chandrika
- Distributed Information Sub-Centre, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695 014, Kerala, India
| | - Sabu Thomas
- Cholera and Biofilm Research Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695 014, Kerala, India.
| |
Collapse
|
6
|
Irenge LM, Ambroise J, Mitangala PN, Bearzatto B, Kabangwa RKS, Durant JF, Gala JL. Genomic analysis of pathogenic isolates of Vibrio cholerae from eastern Democratic Republic of the Congo (2014-2017). PLoS Negl Trop Dis 2020; 14:e0007642. [PMID: 32310947 PMCID: PMC7192507 DOI: 10.1371/journal.pntd.0007642] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 04/30/2020] [Accepted: 03/12/2020] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Over the past recent years, Vibrio cholerae has been associated with outbreaks in sub-Saharan Africa, notably in Democratic Republic of the Congo (DRC). This study aimed to determine the genetic relatedness of isolates responsible for cholera outbreaks in eastern DRC between 2014 and 2017, and their potential spread to bordering countries. METHODS/PRINCIPAL FINDINGS Phenotypic analysis and whole genome sequencing (WGS) were carried out on 78 clinical isolates of V. cholerae associated with cholera in eastern provinces of DRC between 2014 and 2017. SNP-based phylogenomic data show that most isolates (73/78) were V. cholerae O1 biotype El Tor with CTX-3 type prophage. They fell within the third transmission wave of the current seventh pandemic El Tor (7PET) lineage and were contained in the introduction event (T)10 in East Africa. These isolates clustered in two sub-clades corresponding to Multiple Locus Sequence Types (MLST) profiles ST69 and the newly assigned ST515, the latter displaying a higher genetic diversity. Both sub-clades showed a distinct geographic clustering, with ST69 isolates mostly restricted to Lake Tanganyika basin and phylogenetically related to V. cholerae isolates associated with cholera outbreaks in western Tanzania, whereas ST515 isolates were disseminated along the Albertine Rift and closely related to isolates in South Sudan, Uganda, Tanzania and Zambia. Other V. cholerae isolates (5/78) were non-O1/non-O139 without any CTX prophage and no phylogenetic relationship with already characterized non-O1/non-O139 isolates. CONCLUSIONS/SIGNIFICANCE Current data confirm the association of both DRC O1 7PET (T)10 sub-clades ST69 and ST515 with recurrent outbreaks in eastern DRC and at regional level over the past 10 years. Interestingly, while ST69 is predominantly a locally endemic sequence type, ST515 became adaptable enough to expand across DRC neighboring countries.
Collapse
Affiliation(s)
- Leonid M. Irenge
- Center for Applied Molecular Technologies, Institute of Clinical and Experimental Research, Université catholique de Louvain, Brussels, Belgium
- Defence Laboratories Department, ACOS Ops&Trg, Belgian Armed Forces, Peutie, Belgium
| | - Jérôme Ambroise
- Center for Applied Molecular Technologies, Institute of Clinical and Experimental Research, Université catholique de Louvain, Brussels, Belgium
| | | | - Bertrand Bearzatto
- Center for Applied Molecular Technologies, Institute of Clinical and Experimental Research, Université catholique de Louvain, Brussels, Belgium
| | | | - Jean-François Durant
- Center for Applied Molecular Technologies, Institute of Clinical and Experimental Research, Université catholique de Louvain, Brussels, Belgium
| | - Jean-Luc Gala
- Center for Applied Molecular Technologies, Institute of Clinical and Experimental Research, Université catholique de Louvain, Brussels, Belgium
- * E-mail:
| |
Collapse
|
7
|
Naha A, Mandal RS, Samanta P, Saha RN, Shaw S, Ghosh A, Chatterjee NS, Dutta P, Okamoto K, Dutta S, Mukhopadhyay AK. Deciphering the possible role of ctxB7 allele on higher production of cholera toxin by Haitian variant Vibrio cholerae O1. PLoS Negl Trop Dis 2020; 14:e0008128. [PMID: 32236098 PMCID: PMC7112172 DOI: 10.1371/journal.pntd.0008128] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 02/10/2020] [Indexed: 12/16/2022] Open
Abstract
Cholera continues to be an important public health concern in developing countries where proper hygiene and sanitation are compromised. This severe diarrheal disease is caused by the Gram-negative pathogen Vibrio cholerae belonging to serogroups O1 and O139. Cholera toxin (CT) is the prime virulence factor and is directly responsible for the disease manifestation. The ctxB gene encodes cholera toxin B subunit (CTB) whereas the A subunit (CTA) is the product of ctxA gene. Enzymatic action of CT depends on binding of B pentamers to the lipid-based receptor ganglioside GM1. In recent years, emergence of V. cholerae Haitian variant strains with ctxB7 allele and their rapid spread throughout the globe has been linked to various cholera outbreaks in Africa and Asia. These strains produce classical type (WT) CTB except for an additional mutation in the signal sequence region where an asparagine (N) residue replaces a histidine (H) at the 20th amino acid position (H20N) of CTB precursor (pre-CTB). Here we report that Haitian variant V. cholerae O1 strains isolated in Kolkata produced higher amount of CT compared to contemporary O1 El Tor variant strains under in vitro virulence inducing conditions. We observed that the ctxB7 allele, itself plays a pivotal role in higher CT production. Based on our in silico analysis, we hypothesized that higher accumulation of toxin subunits from ctxB7 allele might be attributed to the structural alteration at the CTB signal peptide region of pre-H20N CTB. Overall, this study provides plausible explanation regarding the hypertoxigenic phenotype of the Haitian variant strains which have spread globally, possibly through positive selection for increased pathogenic traits.
Collapse
Affiliation(s)
- Arindam Naha
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Rahul Shubhra Mandal
- Biomedical Informatics Center, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Prosenjit Samanta
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Rudra Narayan Saha
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Sreeja Shaw
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Amit Ghosh
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | | | - Pujarini Dutta
- Division of Clinical Medicine, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Keinosuke Okamoto
- Collaborative Research Center of Okayama University for Infectious Diseases at NICED, Kolkata, India
| | - Shanta Dutta
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Asish Kumar Mukhopadhyay
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
- * E-mail:
| |
Collapse
|
8
|
Mohanraj RS, Samanta P, Mukhopadhyay AK, Mandal J. Haitian-like genetic traits with creeping MIC of Azithromycin in Vibrio cholerae O1 isolates from Puducherry, India. J Med Microbiol 2020; 69:372-378. [PMID: 31961790 DOI: 10.1099/jmm.0.001131] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction. The emergence of novel strains of Vibrio cholerae O1 El Tor biotype has gained attention due to causing several epidemics around the world. Variant strains have evolved as a result of the acquisition of genes that confer extended virulence and pathogenicity.Aim. This study aimed to determine the presence of the most recently emerging Haitian-like genetic traits among the isolates from Jawaharlal Institute of Postgraduate Medical Education and Research, Pondicherry, Southern India. We also wanted to detect the prevalence of the sulfamethoxazole and trimethoprim (SXT) element, which is an integrating conjugative element (ICE) and the antimicrobial resistance genes present in our isolates.Methodology. Identification of Haitian-specific alleles was done by mismatched amplification mutation assay PCR (MAMA-PCR). The presence of SXT elements was carried out by PCR by detecting int, eex, att-prfC and setR genes. Detection of antibiotic resistance determinant, sul(1,2,3); dfr(A1,18,5) for trimethoprim resistance, tet(A,B,C,D,E,Y,G,M), tet34 for tetracycline resistance and erm(A,B,C), mph(A,B), ere(A,B), msr(A,D) for azithromycin resistance were targeted by PCR. The MIC of tetracycline, ciprofloxacin and azithromycin was determined by the E-test method.Results. Of the 95 isolates, 60 % of the isolates were found to carry Haitian-specific alleles of ctxB, tcpA and rtxA gene, 100 % of the isolates were found to carry SXT elements. All the isolates harboured the four conserved genes of the SXT element, except one which had only eex, att-prfC, setR genes. About 99 % harboured sul2 and dfrA1 genes. No tet and macrolide genes were detected. We observed a progressive increase in the MIC of azithromycin ranging from 0.75 µg ml-1 to 2 µg ml-1.Conclusion. None of the isolates were the prototype El Tor biotype. All the isolates were a Haitian variant. The presence of SXT elements across all our isolates and their creeping MIC of azithromycin is a matter of concern. Further testing for other genetic determinants of resistance will be carried out in our future studies.
Collapse
Affiliation(s)
| | | | | | - Jharna Mandal
- Department of Microbiology, JIPMER, Puducherry, India
| |
Collapse
|
9
|
Machine Learning Model for Imbalanced Cholera Dataset in Tanzania. ScientificWorldJournal 2019; 2019:9397578. [PMID: 31427903 PMCID: PMC6683776 DOI: 10.1155/2019/9397578] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Revised: 05/15/2019] [Accepted: 06/09/2019] [Indexed: 11/28/2022] Open
Abstract
Cholera epidemic remains a public threat throughout history, affecting vulnerable population living with unreliable water and substandard sanitary conditions. Various studies have observed that the occurrence of cholera has strong linkage with environmental factors such as climate change and geographical location. Climate change has been strongly linked to the seasonal occurrence and widespread of cholera through the creation of weather patterns that favor the disease's transmission, infection, and the growth of Vibrio cholerae, which cause the disease. Over the past decades, there have been great achievements in developing epidemic models for the proper prediction of cholera. However, the integration of weather variables and use of machine learning techniques have not been explicitly deployed in modeling cholera epidemics in Tanzania due to the challenges that come with its datasets such as imbalanced data and missing information. This paper explores the use of machine learning techniques to model cholera epidemics with linkage to seasonal weather changes while overcoming the data imbalance problem. Adaptive Synthetic Sampling Approach (ADASYN) and Principal Component Analysis (PCA) were used to the restore sampling balance and dimensional of the dataset. In addition, sensitivity, specificity, and balanced-accuracy metrics were used to evaluate the performance of the seven models. Based on the results of the Wilcoxon sign-rank test and features of the models, XGBoost classifier was selected to be the best model for the study. Overall results improved our understanding of the significant roles of machine learning strategies in health-care data. However, the study could not be treated as a time series problem due to the data collection bias. The study recommends a review of health-care systems in order to facilitate quality data collection and deployment of machine learning techniques.
Collapse
|
10
|
Recurrent cholera epidemics in Africa: which way forward? A literature review. Infection 2018; 47:341-349. [DOI: 10.1007/s15010-018-1186-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 07/27/2018] [Indexed: 02/03/2023]
|
11
|
Samanta P, Saha RN, Chowdhury G, Naha A, Sarkar S, Dutta S, Nandy RK, Okamoto K, Mukhopadhyay AK. Dissemination of newly emerged polymyxin B sensitive Vibrio cholerae O1 containing Haitian-like genetic traits in different parts of India. J Med Microbiol 2018; 67:1326-1333. [PMID: 29927375 DOI: 10.1099/jmm.0.000783] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
PURPOSE Two natural epidemic biotypes of Vibrio cholerae O1, classical and El Tor, exhibit different patterns of sensitivity against the antimicrobial peptide polymyxin B. This difference in sensitivity has been one of the major markers in biotype classification system for several decades. A recent report regarding the emergence of polymyxin B-sensitive El Tor V. cholerae O1 in Kolkata has motivated us to track the spread of the strains containing this important trait, along with Haitian-like genetic content, in different parts of India. METHODOLOGY We have collected 260 clinical V. cholerae O1 strains from 12 states in India and screened them for polymyxin B susceptibility. Genetic characterization was also performed to study the tcpA, ctxB and rtxA genotypes by allele-specific polymerase chain reaction (PCR) and nucleotide sequencing. RESULTS Interestingly, 88.85 % of the isolates were found to be sensitive to polymyxin B. All of the states, with the exception of Assam, had polymyxin B-sensitive V. cholerae strains and complete replacement with this strain was found in eight of the states. However, from 2016 onwards, all the strains tested showed sensitivity to polymyxin B. Allele-specific PCR and sequencing confirmed that all strains possessed Haitian-like genetic traits. CONCLUSION Polymyxin B-sensitive strains have begun to spread throughout India and may lead to the revision of the biotype classification. The dissemination of these new variant strains needs to be carefully monitored in different endemic populations through active holistic surveillance to understand their clinical and epidemiological consequences.
Collapse
Affiliation(s)
- Prosenjit Samanta
- 1Division of Bacteriology, National Institute of Cholera and Enteric Diseases, Kolkata 700010, India
| | - Rudra Narayan Saha
- 1Division of Bacteriology, National Institute of Cholera and Enteric Diseases, Kolkata 700010, India
| | - Goutam Chowdhury
- 1Division of Bacteriology, National Institute of Cholera and Enteric Diseases, Kolkata 700010, India
| | - Arindam Naha
- 1Division of Bacteriology, National Institute of Cholera and Enteric Diseases, Kolkata 700010, India
| | - Sounak Sarkar
- 1Division of Bacteriology, National Institute of Cholera and Enteric Diseases, Kolkata 700010, India
| | - Shanta Dutta
- 1Division of Bacteriology, National Institute of Cholera and Enteric Diseases, Kolkata 700010, India
| | - Ranjan Kumar Nandy
- 1Division of Bacteriology, National Institute of Cholera and Enteric Diseases, Kolkata 700010, India
| | - Keinosuke Okamoto
- 2Collaborative Research Center of Okayama University for Infectious Diseases in India, Kolkata 700010, India
| | - Asish Kumar Mukhopadhyay
- 1Division of Bacteriology, National Institute of Cholera and Enteric Diseases, Kolkata 700010, India
| |
Collapse
|
12
|
Zaw MT, Emran NA, Ibrahim MY, Suleiman M, Awang Mohd TA, Yusuff AS, Naing KS, Myint T, Jikal M, Salleh MA, Lin Z. Genetic diversity of toxigenic Vibrio cholerae O1 from Sabah, Malaysia 2015. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2018; 52:563-570. [PMID: 29428381 DOI: 10.1016/j.jmii.2018.01.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 08/01/2017] [Accepted: 01/09/2018] [Indexed: 10/18/2022]
Abstract
BACKGROUND Cholera is an important health problem in Sabah, a Malaysian state in northern Borneo; however, Vibrio cholerae in Sabah have never been characterized. Since 2002, serogroup O1 strains having the traits of both classical and El Tor biotype, designated as atypical El Tor biotype, have been increasingly reported as the cause of cholera worldwide. These variants are believed to produce clinically more severe disease like classical strains. PURPOSE The purpose of this study is to investigate the genetic diversity of V.cholerae in Sabah and whether V.cholerae in Sabah belong to atypical El Tor biotype. METHODS ERIC-PCR, a DNA fingerprinting method for bacterial pathogens based on the enterobacterial repetitive intergenic consensus sequence, was used to study the genetic diversity of 65 clinical V.cholerae O1 isolates from 3 districts (Kudat, Beluran, Sandakan) in Sabah and one environmental isolate from coastal sea water in Kudat district. In addition, we studied the biotype-specific genetic traits in these isolates to establish their biotype. RESULTS Different fingerprint patterns were seen in isolates from these three districts but one of the patterns was seen in more than one district. Clinical isolates and environmental isolate have different patterns. In addition, Sabah isolates harbor genetic traits specific to both classical biotype (ctxB-1, rstRCla) and El Tor biotype (rstRET, rstC, tcpAET, rtxC, VC2346). CONCLUSION This study revealed that V.cholerae in Sabah were genetically diverse and were atypical El Tor strains. Fingerprint patterns of these isolates will be useful in tracing the origin of this pathogen in the future.
Collapse
Affiliation(s)
- Myo Thura Zaw
- Pathobiological and Medical Diagnostics Department, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Jalan UMS, 88400 Kota Kinabalu, Sabah, Malaysia
| | - Nor Amalina Emran
- Pathobiological and Medical Diagnostics Department, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Jalan UMS, 88400 Kota Kinabalu, Sabah, Malaysia
| | - Mohd Yusof Ibrahim
- Department of Community Medicine, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Jalan UMS, 88400 Kota Kinabalu, Sabah, Malaysia
| | - Maria Suleiman
- Sabah State Health Department, Jalan Tunku Abdul Rahman, Bandaran, 88000 Kota Kinabalu, Sabah, Malaysia
| | - Tajul Ariffin Awang Mohd
- Kota Kinabalu Public Health Laboratory, Bukit Padang, Jalan Kolam, 88850 Kota Kinabalu, Sabah, Malaysia
| | - Aza Sherin Yusuff
- Department of Community Medicine, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Jalan UMS, 88400 Kota Kinabalu, Sabah, Malaysia
| | - Khin Saw Naing
- Department of Community Medicine, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Jalan UMS, 88400 Kota Kinabalu, Sabah, Malaysia
| | - Than Myint
- Department of Community Medicine, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Jalan UMS, 88400 Kota Kinabalu, Sabah, Malaysia
| | | | - Mohd Azmi Salleh
- Pathology Department, Hospital Duchess of Kent, KM3.2 Jalan Utara, 9000 Sandakan, Sabah, Malaysia
| | - Zaw Lin
- Pathobiological and Medical Diagnostics Department, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Jalan UMS, 88400 Kota Kinabalu, Sabah, Malaysia.
| |
Collapse
|
13
|
Mukhopadhyay AK, Al Benwan K, Samanta P, Chowdhury G, Albert MJ. Vibrio cholerae O1 Imported from Iraq to Kuwait, 2015. Emerg Infect Dis 2018; 22:1693-4. [PMID: 27532267 PMCID: PMC4994364 DOI: 10.3201/eid2209.160811] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
|
14
|
Characterization of Vibrio cholerae O1 strains that trace the origin of Haitian-like genetic traits. INFECTION GENETICS AND EVOLUTION 2017. [PMID: 28625543 DOI: 10.1016/j.meegid.2017.06.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Vibrio cholerae O1 is the etiological agent of the severe diarrheal disease cholera. The bacterium has recently been causing outbreaks in Haiti with catastrophic effects. Numerous mutations have been reported in V. cholerae O1 strains associated with the Haitian outbreak. These mutations encompass among other the genes encoding virulence factors such as the pilin subunit of the toxin-co-regulated pilus (tcpA), cholera toxin B subunit (ctxB), repeat in toxins (rtxA), and other genes such as the quinolone resistance-determining region (QRDR) of gyrase A (gyrA), rstB of RS element along with the alteration in the number of repeat sequences at the promoter region of ctxAB. Given the numerous genetic changes in those Haitian isolates, we decided to investigate the possible origins of those variations in the Indian subcontinent. Thus, we determined the genetic traits among V. cholerae O1 strains in Delhi, India. A total of 175 strains isolated from cholera patients during 2004 to 2012 were analysed in the present study. Our results showed that all the tested strains carried Haitian type tcpA (tcpACIRS) and variant gyrA indicating their first appearance before 2004 in Delhi. The Haitian variant rtxA and ctxB7 were first detected in Delhi during 2004 and 2006, respectively. Interestingly, not a single strain with the combination of El Tor rtxA and ctxB7 was detected in this study. The Delhi strains carried four heptad repeats (TTTTGAT) in the CT promoter region whereas Haitian strains carried 5 such repeats. Delhi strains did not have any deletion mutations in the rstB like Haitian strains. Overall, our study demonstrates the sequential accumulation of Haitian-like genetic traits among V. cholerae O1 strains in Delhi at different time points prior to the Haitian cholera outbreak.
Collapse
|
15
|
Vezzulli L, Grande C, Tassistro G, Brettar I, Höfle MG, Pereira RPA, Mushi D, Pallavicini A, Vassallo P, Pruzzo C. Whole-Genome Enrichment Provides Deep Insights into Vibrio cholerae Metagenome from an African River. MICROBIAL ECOLOGY 2017; 73:734-738. [PMID: 27888291 DOI: 10.1007/s00248-016-0902-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 11/16/2016] [Indexed: 06/06/2023]
Abstract
The detection and typing of Vibrio cholerae in natural aquatic environments encounter major methodological challenges related to the fact that the bacterium is often present in environmental matrices at very low abundance in nonculturable state. This study applied, for the first time to our knowledge, a whole-genome enrichment (WGE) and next-generation sequencing (NGS) approach for direct genotyping and metagenomic analysis of low abundant V. cholerae DNA (<50 genome unit/L) from natural water collected in the Morogoro river (Tanzania). The protocol is based on the use of biotinylated RNA baits for target enrichment of V. cholerae metagenomic DNA via hybridization. An enriched V. cholerae metagenome library was generated and sequenced on an Illumina MiSeq platform. Up to 1.8 × 107 bp (4.5× mean read depth) were found to map against V. cholerae reference genome sequences representing an increase of about 2500 times in target DNA coverage compared to theoretical calculations of performance for shotgun metagenomics. Analysis of metagenomic data revealed the presence of several V. cholerae virulence and virulence associated genes in river water including major virulence regions (e.g. CTX prophage and Vibrio pathogenicity island-1) and genetic markers of epidemic strains (e.g. O1-antigen biosynthesis gene cluster) that were not detectable by standard culture and molecular techniques. Overall, besides providing a powerful tool for direct genotyping of V. cholerae in complex environmental matrices, this study provides a 'proof of concept' on the methodological gap that might currently preclude a more comprehensive understanding of toxigenic V. cholerae emergence from natural aquatic environments.
Collapse
Affiliation(s)
- L Vezzulli
- Department of Earth, Environmental and Life Sciences (DISTAV), University of Genoa, Genoa, Italy.
| | - C Grande
- Department of Earth, Environmental and Life Sciences (DISTAV), University of Genoa, Genoa, Italy
| | - G Tassistro
- Department of Earth, Environmental and Life Sciences (DISTAV), University of Genoa, Genoa, Italy
| | - I Brettar
- Department of Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - M G Höfle
- Department of Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - R P A Pereira
- Department of Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - D Mushi
- Department of Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - A Pallavicini
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - P Vassallo
- Department of Earth, Environmental and Life Sciences (DISTAV), University of Genoa, Genoa, Italy
| | - C Pruzzo
- Department of Earth, Environmental and Life Sciences (DISTAV), University of Genoa, Genoa, Italy
| |
Collapse
|
16
|
Oladokun MO, Okoh IA. Vibrio cholerae: A historical perspective and current trend. ASIAN PACIFIC JOURNAL OF TROPICAL DISEASE 2016. [DOI: 10.1016/s2222-1808(16)61154-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
17
|
Mukhopadhyay AK. Mapping of cholera cases using satellite based recording systems to investigate the outbreak. Indian J Med Res 2016; 142:509-11. [PMID: 26658582 PMCID: PMC4743334 DOI: 10.4103/0971-5916.171269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Affiliation(s)
- Ashish K Mukhopadhyay
- Division of Bacteriology, National Institute of Cholera & Enteric Diseases (ICMR), P33, CIT Road, Scheme XM, Beliaghata, Kolkata 700 010, West Bengal, India
| |
Collapse
|
18
|
Shinoda S, Imamura D, Mizuno T, Miyoshi SI, Ramamurthy T. International collaborative research on infectious diseases by Japanese universities and institutes in Asia and Africa, with a special emphasis on J-GRID. Biocontrol Sci 2016; 20:77-89. [PMID: 26133505 DOI: 10.4265/bio.20.77] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
In developed countries including Japan, malignant tumor (cancer), heart disease and cerebral apoplexy are major causes of death, but infectious diseases are still responsible for a high number of deaths in developing countries, especially among children aged less than 5 years. World Health Statistics published by WHO reports a high percentage of mortality from infectious diseases in children, and many of these diseases may be subject to transmission across borders and could possibly invade Japan. Given this situation, the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan initiated Phase I of the Program of Founding Research Centers for Emerging and Reemerging Infectious Disease, which ran from FY 2005 to 2009, and involved 8 Japanese universities and 2 research centers. The program was established for the following purposes: 1) creation of a domestic research structure to promote the accumulation of fundamental knowledge about infectious diseases, 2) establishment of 13 overseas research collaboration centers in 8 countries at high risk of emerging and reemerging infections and at which Japanese researchers are stationed and conduct research in partnership with overseas instructors, 3) development of a network among domestic and overseas research centers, and 4) development of human resources. The program was controlled under MEXT and managed by the RIKEN Center of Research Network for Infectious Diseases (Riken CRNID). Phase II of the program was set up as the Japan Initiative for Global Research Network on Infectious Diseases (J-GRID), and has been running in FY 2010-2014. Phase III will start in April 2015, and will be organized by the newly established Japanese governmental organization "Japan Agency for Medical Research and Development (AMED)", the so-called Japanese style NIH. The Collaborative Research Center of Okayama University for Infectious Diseases in India (CRCOUI) was started up in 2007 at the National Institute of Cholera and Enteric Disease, Kolkata, India. Major projects of CRCOUI are concerned with diarrheal diseases such as, 1) active surveillance of diarrheal patients, 2) development of dysentery vaccines, 3) viable but nonculturable (VBNC) Vibrio cholerae, and 4) pathogenic mechanisms of various diarrhogenic microorganisms. This review article outlines project of J-GRID and CRCOUI which the authors carried out collaboratively with NICED staff members.
Collapse
Affiliation(s)
- Sumio Shinoda
- Collaborative Research Center of Okayama University for Infectious Disease in India
| | | | | | | | | |
Collapse
|
19
|
Kim EJ, Lee CH, Nair GB, Kim DW. Whole-genome sequence comparisons reveal the evolution of Vibrio cholerae O1. Trends Microbiol 2015; 23:479-89. [DOI: 10.1016/j.tim.2015.03.010] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 03/23/2015] [Accepted: 03/31/2015] [Indexed: 12/20/2022]
|
20
|
Moore S, Miwanda B, Sadji AY, Thefenne H, Jeddi F, Rebaudet S, de Boeck H, Bidjada B, Depina JJ, Bompangue D, Abedi AA, Koivogui L, Keita S, Garnotel E, Plisnier PD, Ruimy R, Thomson N, Muyembe JJ, Piarroux R. Relationship between Distinct African Cholera Epidemics Revealed via MLVA Haplotyping of 337 Vibrio cholerae Isolates. PLoS Negl Trop Dis 2015; 9:e0003817. [PMID: 26110870 PMCID: PMC4482140 DOI: 10.1371/journal.pntd.0003817] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 05/06/2015] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Since cholera appeared in Africa during the 1970s, cases have been reported on the continent every year. In Sub-Saharan Africa, cholera outbreaks primarily cluster at certain hotspots including the African Great Lakes Region and West Africa. METHODOLOGY/PRINCIPAL FINDINGS In this study, we applied MLVA (Multi-Locus Variable Number Tandem Repeat Analysis) typing of 337 Vibrio cholerae isolates from recent cholera epidemics in the Democratic Republic of the Congo (DRC), Zambia, Guinea and Togo. We aimed to assess the relationship between outbreaks. Applying this method, we identified 89 unique MLVA haplotypes across our isolate collection. MLVA typing revealed the short-term divergence and microevolution of these Vibrio cholerae populations to provide insight into the dynamics of cholera outbreaks in each country. Our analyses also revealed strong geographical clustering. Isolates from the African Great Lakes Region (DRC and Zambia) formed a closely related group, while West African isolates (Togo and Guinea) constituted a separate cluster. At a country-level scale our analyses revealed several distinct MLVA groups, most notably DRC 2011/2012, DRC 2009, Zambia 2012 and Guinea 2012. We also found that certain MLVA types collected in the DRC persisted in the country for several years, occasionally giving rise to expansive epidemics. Finally, we found that the six environmental isolates in our panel were unrelated to the epidemic isolates. CONCLUSIONS/SIGNIFICANCE To effectively combat the disease, it is critical to understand the mechanisms of cholera emergence and diffusion in a region-specific manner. Overall, these findings demonstrate the relationship between distinct epidemics in West Africa and the African Great Lakes Region. This study also highlights the importance of monitoring and analyzing Vibrio cholerae isolates.
Collapse
Affiliation(s)
- Sandra Moore
- Department of Parasitology and Mycology, Assistance Publique—Hôpitaux de Marseille/Aix-Marseille University, UMR MD3, Marseille, France
| | - Berthe Miwanda
- Institut National de Recherche Biomédicale, Ministry of Public Health, Kinshasa, Democratic Republic of the Congo
| | - Adodo Yao Sadji
- Department of Bacteriology, National Institute of Hygiene, Lomé, Togo
| | | | - Fakhri Jeddi
- Department of Parasitology and Mycology, Assistance Publique—Hôpitaux de Marseille/Aix-Marseille University, UMR MD3, Marseille, France
| | - Stanislas Rebaudet
- Department of Parasitology and Mycology, Assistance Publique—Hôpitaux de Marseille/Aix-Marseille University, UMR MD3, Marseille, France
| | - Hilde de Boeck
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Bawimodom Bidjada
- Department of Bacteriology, National Institute of Hygiene, Lomé, Togo
| | | | - Didier Bompangue
- Institut National de Recherche Biomédicale, Ministry of Public Health, Kinshasa, Democratic Republic of the Congo
- Department of Microbiology, Faculty of Medicine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
- Laboratoire Chrono-Environnement, UMR 6249, CNRS, University of Franche-Comte, Besançon, France
| | | | - Lamine Koivogui
- Institut National de Santé Publique, Conakry, Republic of Guinea
| | - Sakoba Keita
- Division Prévention et Lutte contre la Maladie, Ministère de la Santé Publique et de l’Hygiène Publique, Conakry, Republic of Guinea
| | - Eric Garnotel
- Hôpital d'Instruction des Armées Laveran, Marseille, France
| | | | - Raymond Ruimy
- Clinical Research Department, Nice University Hospital, Nice, France
| | - Nicholas Thomson
- Pathogen Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
- London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Jean-Jacques Muyembe
- Institut National de Recherche Biomédicale, Ministry of Public Health, Kinshasa, Democratic Republic of the Congo
- Department of Microbiology, Faculty of Medicine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Renaud Piarroux
- Department of Parasitology and Mycology, Assistance Publique—Hôpitaux de Marseille/Aix-Marseille University, UMR MD3, Marseille, France
| |
Collapse
|
21
|
Ramazanzadeh R, Rouhi S, Shakib P, Shahbazi B, Bidarpour F, Karimi M. Molecular Characterization of Vibrio cholerae Isolated From Clinical Samples in Kurdistan Province, Iran. Jundishapur J Microbiol 2015; 8:e18119. [PMID: 26060565 PMCID: PMC4458358 DOI: 10.5812/jjm.8(5)2015.18119] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Revised: 04/12/2014] [Accepted: 04/23/2014] [Indexed: 11/16/2022] Open
Abstract
Background: Vibrio cholerae causes diarrhoeal disease that afflicts thousands of people annually. V. cholerae is classified on the basis of somatic antigens into serovars or serogroups and there are at least 200 known serogroup. Two serogroups, O1 and O139 have been associated with epidemic diseases. Virulence genes of these bacteria are OmpW, ctxA and tcpA. Objectives: Due to the importance of V. cholerae infection and developing molecular diagnostics of this organism in medical and microbiology sciences, this study aimed to describe molecular characterization of V. cholerae isolated from clinical samples using a molecular method. Materials and Methods: In this study, 48 samples were provided during summer 2013 (late August and early September) by reference laboratory. Samples were assessed using biochemical tests initially. The primer of OmpW, ctxA and tcpA genes was used in Polymerase Chain Reaction (PCR) protocols. Enterobacterial Repetitive Intergenic Consensus (ERIC)-PCR and Repetitive Extragenic Palindromic (REP)-PCR methods were used to subtype V. cholerae. Results: In this study, from a total of 48 clinical stool samples 39 (81.2 %) were positive for V. cholerae in biochemical tests and bacteria culture tests. The PCR results showed that of 39 positive isolates 35 (89.7%), 34 (87.1%) and 37 (94.8%) were positive for ctxA, tcpA and OmpW gene, respectively. Also, in the REP-PCR method with ERIC primer strains were divided into 10 groups. In the REP-PCR method with REP primer, strains were divided into 13 groups. Conclusions: Polymerase chain reaction has specificity and accuracy for identification of the organism and is able to differentiate biotypes. Enterobacterial repetitive intergenic consensus sequence is one of the informative and discriminative methods for the analysis of V. cholerae diversity. The REP-PCR is a less informative and discriminative method compared to other methods for the analysis of V. cholerae diversity.
Collapse
Affiliation(s)
- Rashid Ramazanzadeh
- Cellular and Molecular Research Center, Kurdistan University of Medical Sciences, Sanandaj, IR Iran
- Department of Microbiology, Faculty of Medicine, Kurdistan University of Medical Sciences, Sanandaj, IR Iran
| | - Samaneh Rouhi
- Student Research Committee, Kurdistan University of Medical Sciences, Sanandaj, IR Iran
| | - Pegah Shakib
- Student Research Committee, Kurdistan University of Medical Sciences, Sanandaj, IR Iran
| | - Babak Shahbazi
- Department of Microbiology, Faculty of Medicine, Kurdistan University of Medical Sciences, Sanandaj, IR Iran
- Corresponding author: Babak Shahbazi, Department of Microbiology, Faculty of Medicine, Kurdistan University of Medical Sciences, Sanandaj, IR Iran. Tel: +98-9353929575, E-mail:
| | - Farzam Bidarpour
- Deputy of Public Health Affairs, Kurdistan University of Medical Sciences, Sanandaj, IR Iran
| | - Mohammad Karimi
- Deputy of Public Health Affairs, Kurdistan University of Medical Sciences, Sanandaj, IR Iran
| |
Collapse
|
22
|
Samadi N, Pakzad I, Monadi Sefidan A, Hosainzadegan H, Tanomand A. Study of aminoglycoside resistance genes in enterococcus and salmonella strains isolated from ilam and milad hospitals, iran. Jundishapur J Microbiol 2015; 8:e18102. [PMID: 26034551 PMCID: PMC4449854 DOI: 10.5812/jjm.8(4)2015.18102] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Revised: 04/26/2014] [Accepted: 05/11/2014] [Indexed: 01/07/2023] Open
Abstract
Background: Aminoglycosides are a group of antibiotics that have been widely used in the treatment of life-threatening infections of Gram-negative bacteria. Objectives: This study aimed to evaluate the frequency of aminoglycoside resistance genes in Enterococcus and Salmonella strains isolated from clinical samples by PCR. Materials and Methods: In this study, 140 and 79 isolates of Enterococcus and Salmonella were collected, respectively. After phenotypic biochemical confirmation, 117 and 77 isolates were identified as Enterococcus and Salmonella, respectively. After the biochemical identification of the isolates, antibiotic susceptibility for screening of resistance was done using the Kirby-Bauer method for gentamicin, amikacin, kanamycin, tobramycin and netilmycin. DNA was extracted from resistant strains and the presence of acc (3)-Ia, aac (3′)-Ib, acc (6)-IIa ,16SrRNA methylase genes (armA and rat) was detected by PCR amplification using special primers and positive controls. Results: Enterococcus isolates have the highest prevalence of resistance to both kanamycin and amikacin (68.4%), and Salmonella isolates have the highest prevalence of resistance against kanamycin (6.9%). Ninety-three and 26 isolates of Enterococcus and Salmonella at least were resistant against one of the aminoglycosides, respectively. Moreover, 72.04%, 66.7%, and 36.6% of the resistant strains of Enterococcus had the aac (3′)-Ia, aac (3′)-IIa, and acc (6′)-Ib genes, respectively. None of the Salmonella isolates have the studied aminoglycoside genes. Conclusions: Our results indicate that acetylation genes have an important role in aminoglycoside resistance of the Enterococcus isolates from clinical samples. Moreover, Salmonella strains indicate very low level of aminoglycoside resistance, and aminoglycoside resistance genes were not found in Salmonella isolates. These results indicate that other resistance mechanisms, including efflux pumps have an important role in aminoglycoside resistance of Salmonella.
Collapse
Affiliation(s)
- Nasser Samadi
- Department of Microbiology, Faculty of Medicine, Ilam University of Medical Sciences, Ilam, IR Iran
| | - Iraj Pakzad
- Department of Microbiology, Faculty of Medicine, Ilam University of Medical Sciences, Ilam, IR Iran
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, IR Iran
| | | | - Hasan Hosainzadegan
- Department of Basic Sciences, Faculty Of Medicine, Maragheh University of Medical Science, Maragheh , IR Iran
- Corresponding author: Hasan Hosainzadegan, Department of Basic Sciences, Faculty Of Medicine, Maragheh University of Medical Science, Maragheh , IR Iran. Tel: +98-4137276364, Fax: +98-4137276363, E-mail:
| | - Asghar Tanomand
- Department of Basic Sciences, Faculty Of Medicine, Maragheh University of Medical Science, Maragheh , IR Iran
| |
Collapse
|
23
|
Dalusi L, Lyimo TJ, Lugomela C, Hosea KMM, Sjöling S. Toxigenic Vibrio cholerae identified in estuaries of Tanzania using PCR techniques. FEMS Microbiol Lett 2015; 362:fnv009. [PMID: 25743072 DOI: 10.1093/femsle/fnv009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The current study assessed the occurrence of the Vibrio cholerae serogroups O1 and O139 in environmental samples along salinity gradients in three selected estuaries of Tanzania both through culture independent methods and by cultured bacteria. Occurrence of V. cholerae was determined by PCR targeting the V. cholerae outer membrane protein gene ompW. Furthermore, the presence of toxigenic strains and serogroups O1 and O139 was determined using multiplex PCR with specific primers targeting the cholera toxin gene subunit A, ctxA, and serotype specific primers, O1-rfb and O139-rfb, respectively. Results showed that V. cholerae occurred in approximately 10% (n = 185) of both the environmental samples and isolated bacteria. Eight of the bacteria isolates (n = 43) were confirmed as serogroup O1 while one belonged to serogroup O139, the first reported identification of this epidemic strain in East African coastal waters. All samples identified as serogroup O1 or O139 and a number of non-O1/O139 strains were ctxA positive. This study provides in situ evidence of the presence of pathogenic V. cholerae O1 and O139 and a number of V. cholerae non-O1/O139 that carry the cholera toxin gene in estuaries along the coast of Tanzania.
Collapse
Affiliation(s)
- Lucy Dalusi
- Amana Regional Referral Hospital, P.O. Box 25411, Dar es Salaam, Tanzania Department of Molecular Biology and Biotechnology, University of Dar es Salaam, P.O. Box 35179, Dar es Salaam, Tanzania
| | - Thomas J Lyimo
- Department of Molecular Biology and Biotechnology, University of Dar es Salaam, P.O. Box 35179, Dar es Salaam, Tanzania
| | - Charles Lugomela
- Department of Aquatic Sciences and Fisheries, University of Dar es Salaam, P.O. Box 35064, Dar es Salaam, Tanzania
| | - Ken M M Hosea
- Department of Molecular Biology and Biotechnology, University of Dar es Salaam, P.O. Box 35179, Dar es Salaam, Tanzania
| | - Sara Sjöling
- Department of Natural Sciences, Technology and Environmental Studies, Sodertorn University, 141 89 Huddinge, Sweden
| |
Collapse
|
24
|
Genetic traits of Vibrio cholerae O1 Haitian isolates that are absent in contemporary strains from Kolkata, India. PLoS One 2014; 9:e112973. [PMID: 25415339 PMCID: PMC4240540 DOI: 10.1371/journal.pone.0112973] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 10/17/2014] [Indexed: 11/19/2022] Open
Abstract
The world's worst cholera epidemic in Haiti (2010) coerced to trace the origin and dissemination of the causative agent Vibrio cholerae O1 for proper management of cholera. Sequence analysis of the Haitian strain showed several variations in the genes encoding cholera toxin B subunit (ctxB); toxin-co-regulated pilus (tcpA), repeat in toxins (rtxA), quinolone resistance-determining region (QRDR) of gyrase A (gyrA), rstB of RS element along with the change in the number of repeat sequences at the promoter region of ctxAB. Our earlier studies showed that variant tcpA (tcpA CIRS) and ctxB (ctxB7) first appeared in Kolkata during 2003 and 2006, respectively. The present study revealed that a variant rtxA was first isolated in Kolkata during 2004 and probably formed the genetic background for the emergence of the ctxB7 allele as we were unable to detect a single strain with the combination of El Tor rtxA and ctxB7. The variant gyrA was first time detected in Kolkata during 1994. The Kolkata strains contained four heptad repeats (TTTTGAT) in their CT promoter regions whereas Haitian strains carried 5 heptad repeats. Haitian strains had 3 nucleotide deletions at the rstB gene, which is a unique feature of the classical biotype strains. But the Kolkata strains did not have such deletion mutations in the rstB. Our study demonstrated the existence of some Haitian genetic traits in Kolkata isolates along with the dissimilarities in genomic content with respect to rstB and ctxAB promoter region. Finally, we conclude that Haitian variant strain may be evolved due to sequential event in the Indian subcontinent strain with some cryptic modification in the genome.
Collapse
|
25
|
Mukhopadhyay AK, Takeda Y, Balakrish Nair G. Cholera outbreaks in the El Tor biotype era and the impact of the new El Tor variants. Curr Top Microbiol Immunol 2014; 379:17-47. [PMID: 24710767 DOI: 10.1007/82_2014_363] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
Vibrio cholerae O1, the causative agent of the disease cholera, has two biotypes namely the classical and El Tor. Biotype is a subspecific taxonomic classification of V. cholerae O1. Differentiation of V. cholerae strains into biotype does not alter the clinical management of cholera but is of immense public health and epidemiological importance in identifying the source and spread of infection, particularly when V. cholerae is first isolated in a country or geographic area. From recorded history, till date, the world has experienced seven pandemics of cholera. Among these, the first six pandemics are believed to have been caused by the classical biotype whereas the ongoing seventh pandemic is caused by the El Tor biotype. In recent years, new pathogenic variants of V. cholerae have emerged and spread throughout many Asian and African countries with corresponding cryptic changes in the epidemiology of cholera. In this chapter, we describe the outbreaks during the seventh pandemic El Tor biotype era spanning more than five decades along with the recent advances in our understanding of the development, evolution, spread, and impact of the new variants of El Tor strains.
Collapse
Affiliation(s)
- Asish K Mukhopadhyay
- National Institute of Cholera and Enteric Diseases, P 33, CIT Road, Scheme XM, Beliaghata, Kolkata, 700010, India,
| | | | | |
Collapse
|
26
|
A molecular surveillance reveals the prevalence of Vibrio cholerae O139 isolates in China from 1993 to 2012. J Clin Microbiol 2014; 52:1146-52. [PMID: 24452176 DOI: 10.1128/jcm.03354-13] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Vibrio cholerae serogroup O139 was first identified in 1992 in India and Bangladesh, in association with major epidemics of cholera in both countries; cases were noted shortly thereafter in China. We characterized 211 V. cholerae O139 isolates that were isolated at multiple sites in China between 1993 and 2012 from patients (n = 92) and the environment (n = 119). Among clinical isolates, 88 (95.7%) of 92 were toxigenic, compared with 47 (39.5%) of 119 environmental isolates. Toxigenic isolates carried the El Tor CTX prophage and toxin-coregulated pilus A gene (tcpA), as well as the Vibrio seventh pandemic island I (VSP-I) and VSP-II. Among a subset of 42 toxigenic isolates screened by multilocus sequence typing (MLST), all were in the same sequence type as a clinical isolate (MO45) from the original Indian outbreak. Nontoxigenic isolates, in contrast, generally lacked VSP-I and -II, and fell within 13 additional sequence types in two clonal complexes distinct from the toxigenic isolates. In further pulsed-field gel electrophoresis (PFGE) (with NotI digestion) studies, toxigenic isolates formed 60 pulsotypes clustered in one group, while the nontoxigenic isolates formed 43 pulsotypes which clustered into 3 different groups. Our data suggest that toxigenic O139 isolates from widely divergent geographic locations, while showing some diversity, have maintained a relatively tight clonal structure across a 20-year time span. Nontoxigenic isolates, in contrast, exhibited greater diversity, with multiple clonal lineages, than did their toxigenic counterparts.
Collapse
|
27
|
Saidi SM, Chowdhury N, Awasthi SP, Asakura M, Hinenoya A, Iijima Y, Yamasaki S. Prevalence of Vibrio cholerae O1 El Tor variant in a cholera-endemic zone of Kenya. J Med Microbiol 2014; 63:415-420. [PMID: 24396087 DOI: 10.1099/jmm.0.068999-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Since 2007, Kenya has experienced an increase in cholera outbreaks characterized by a high fatality rate. In this study, we characterized 81 Vibrio cholerae isolates from diarrhoeal stool samples in Nyanza, a cholera-endemic lake region of Kenya, for virulence properties, clonality and antibiotic susceptibility. Eighty of these isolates were V. cholerae O1 El Tor variants carrying the classical ctxB gene sequence, while one isolate was V. cholerae non-O1/O139. All of the El Tor variants were of clonal origin, as revealed by PFGE, and were susceptible to ampicillin, tetracycline, ciprofloxacin, fosfomycin, kanamycin and norfloxacin. However, the isolates showed resistance to sulfamethoxazole/trimethoprim and streptomycin, and intermediate resistance to nalidixic acid, chloramphenicol and imipenem. The non-O1/O139 isolate carried the cholix toxin II gene (chxA II) and was susceptible to all antimicrobials tested except ampicillin. We propose that an El Tor variant clone caused the Nyanza cholera outbreak of 2007-2008.
Collapse
Affiliation(s)
- Suleiman M Saidi
- Medical Sciences Department, Technical University of Mombasa, Mombasa, Kenya.,International Prevention of Epidemics, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, Japan
| | - Nityananda Chowdhury
- International Prevention of Epidemics, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, Japan
| | - Sharda P Awasthi
- International Prevention of Epidemics, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, Japan
| | - Masahiro Asakura
- International Prevention of Epidemics, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, Japan
| | - Atsushi Hinenoya
- International Prevention of Epidemics, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, Japan
| | | | - Shinji Yamasaki
- International Prevention of Epidemics, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, Japan
| |
Collapse
|
28
|
The seventh pandemic Vibrio cholerae O1 El Tor isolate in China has undergone genetic shifts. J Clin Microbiol 2013; 52:964-7. [PMID: 24353005 DOI: 10.1128/jcm.03121-13] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A total of 330 clinical Vibrio cholerae O1 serogroups from China dating between 1961 and 2010 were investigated. By phenotypic biotyping and genetic analysis, during the seventh pandemic of V. cholerae O1 in China, the isolates of hybrid biotype (mixed classical phenotypes) were present during the entire1961-2010 period, while El Tor genetic shifts appeared in 1992 and replaced the prototype El Tor from 2002 to 2010.
Collapse
|
29
|
Zhang P, Zhou H, Kan B, Wang D. Novel ctxB variants of Vibrio cholerae O1 isolates, China. INFECTION GENETICS AND EVOLUTION 2013; 20:48-53. [DOI: 10.1016/j.meegid.2013.08.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2013] [Revised: 07/17/2013] [Accepted: 08/05/2013] [Indexed: 02/03/2023]
|