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Bitew A, Gelaw A, Wondimeneh Y, Ayenew Z, Getie M, Tafere W, Gebre-Eyesus T, Yimer M, Beyene GT, Bitew M, Abayneh T, Abebe M, Mihret A, Yeshitela B, Teferi M, Gelaw B. Prevalence and antimicrobial susceptibility pattern of Vibrio cholerae isolates from cholera outbreak sites in Ethiopia. BMC Public Health 2024; 24:2071. [PMID: 39085873 PMCID: PMC11292863 DOI: 10.1186/s12889-024-19621-4] [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: 01/23/2024] [Accepted: 07/29/2024] [Indexed: 08/02/2024] Open
Abstract
BACKGROUND Cholera is an acute infectious disease caused by ingestion of contaminated food or water with Vibrio cholerae. Cholera remains a global threat to public health and an indicator of inequity and lack of social development. The aim of this study was to assess the prevalence and antimicrobial susceptibility pattern of V. cholerae from cholera outbreak sites in Ethiopia. METHODS Across-sectional study was conducted from May 2022 to October 2023 across different regions in Ethiopia: Oromia National Regional State, Amhara National Regional State and Addis Ababa City Administration. A total of 415 fecal samples were collected from the three regions. Two milliliter fecal samples were collected from each study participants. The collected samples were cultured on Blood Agar, MacConkey Agar and Thiosulfate Citrate Bile Salt Sucrose Agar. A series of biochemical tests Oxidase test, String test, Motility, Indole, Citrate, Gas production, H2S production, Urease test were used to identify V. cholerae species. Both polyvalent and monovalent antisera were used for agglutination tests to identify and differentiate V. cholerae serogroup and serotypes. In addition, Kirby-Bauer Disk diffusion antibiotic susceptibility test method was done. Data were registered in epi-enfo version 7 and analyzed by Statistical Package for Social Science version 25. Descriptive statistics were used to determine the prevalence of Vibrio cholerae. Logistic regression model was fitted and p-value < 0.05 was considered as statically significant. RESULTS The prevalence of V. cholerae in the fecal samples was 30.1%. Majority of the isolates were from Oromia National Regional State 43.2% (n = 54) followed by Amhara National Regional State 31.2% (n = 39) and Addis Ababa City Administration 25.6% (n = 32). Most of the V. cholerae isolates were O1 serogroups 90.4% (n = 113) and Ogawa serotypes 86.4% (n = 108). Majority of the isolates were susceptible to ciprofloxacin 100% (n = 125), tetracycline 72% (n = 90) and gentamycin 68% (n = 85). More than half of the isolates were resistant to trimethoprim-sulfamethoxazole 62.4% (n = 78) and ampicillin 56.8% (n = 71). In this study, participants unable to read and write were about four times more at risk for V. cholerae infection (AOR: 3.8, 95% CI: 1.07-13.33). In addition, consumption of river water were about three times more at risk for V. cholerae infection (AOR: 2.8, 95% CI: 1.08-7.08). CONCLUSION our study revealed a high prevalence of V. cholerae from fecal samples. The predominant serogroups and serotypes were O1 and Ogawa, respectively. Fortunately, the isolates showed susceptible to most tested antibiotics. Drinking water from river were the identified associated risk factor for V. cholerae infection. Protecting the community from drinking of river water and provision of safe and treated water could reduce cholera outbreaks in the study areas.
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Affiliation(s)
- Abebaw Bitew
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia.
- Department of Medical Microbiology, College of Medicine and Health Sciences, Debre Markos University, Debre Markos, Ethiopia.
| | - Aschalew Gelaw
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Yitayih Wondimeneh
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Zeleke Ayenew
- Department of Bacteriology, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Michael Getie
- Department of Medical Microbiology, Amhara National Regional State Public Health Institute, Bahir Dar, Ethiopia
| | - Wudu Tafere
- Department of Medical Microbiology, Amhara National Regional State Public Health Institute, Bahir Dar, Ethiopia
| | - Tsehaynesh Gebre-Eyesus
- Department of Medical Microbiology, Amhara National Regional State Public Health Institute, Bahir Dar, Ethiopia
| | - Marechign Yimer
- Bacterial and Viral Disease Research Directorate, Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Getachew Tesfaye Beyene
- Bacterial and Viral Disease Research Directorate, Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Molalegne Bitew
- Bio and Emerging Technology Institute of Ethiopia, Addis Ababa, Ethiopia
| | | | - Markos Abebe
- Bacterial and Viral Disease Research Directorate, Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Adane Mihret
- Bacterial and Viral Disease Research Directorate, Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Biruk Yeshitela
- Bacterial and Viral Disease Research Directorate, Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Mekonnen Teferi
- Bacterial and Viral Disease Research Directorate, Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Baye Gelaw
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
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Moore S, Worku Demlie Y, Muluneh D, Dunoyer J, Hussen M, Wossen M, Edosa M, Sudre B. Spatiotemporal dynamics of cholera epidemics in Ethiopia: 2015-2021. Sci Rep 2024; 14:7170. [PMID: 38570534 PMCID: PMC10991303 DOI: 10.1038/s41598-024-51324-z] [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: 10/04/2023] [Accepted: 01/03/2024] [Indexed: 04/05/2024] Open
Abstract
Since the onset of the seventh cholera pandemic, Ethiopia has been affected by recurrent epidemics. However, the epidemiology of cholera in this country remains poorly understood. This study aimed to describe cholera outbreak characteristics in Ethiopia from 2015 to 2021. During this period, Ethiopia experienced four epidemic waves. The first wave involved nationwide outbreaks during the second half of 2016 followed by outbreaks predominantly affecting Somali Region in 2017. The second wave primarily affected Tigray and Afar Regions. During the third wave, multiple smaller-scale outbreaks occurred during 2019. The fourth wave was limited to Bale Zone (Oromia Region) in 2021. Overall, a north to south shift was observed over the course of the study period. Major cholera transmission factors included limited access to safe water and sanitation facilities. Severe weather events (drought and flooding) appear to aggravate cholera diffusion. Cholera transmission between Ethiopia and nearby countries (Kenya and Somalia), likely plays a major role in regional cholera dynamics. Overall, this study provides the first understanding of recent spatiotemporal cholera dynamics in Ethiopia to inform cholera control and elimination strategies.
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Affiliation(s)
- Sandra Moore
- Prospective and Cooperation, 1 Place Gabriel Péri, Vieux Port, 13001, Marseille, France
| | - Yeshambel Worku Demlie
- Public Health Emergency Management, Ethiopian Public Health Institute (EPHI), Addis Ababa, Ethiopia.
| | - Dereje Muluneh
- Health Section, UNICEF Ethiopia, UNECA Compound, Zambezi Building, Box 1169, Addis Ababa, Ethiopia
| | - Jessica Dunoyer
- Prospective and Cooperation, 1 Place Gabriel Péri, Vieux Port, 13001, Marseille, France
| | - Mukemil Hussen
- Public Health Emergency Management, Ethiopian Public Health Institute (EPHI), Addis Ababa, Ethiopia
| | - Mesfin Wossen
- Public Health Emergency Management, Ethiopian Public Health Institute (EPHI), Addis Ababa, Ethiopia
| | - Moti Edosa
- Public Health Emergency Management, Ethiopian Public Health Institute (EPHI), Addis Ababa, Ethiopia
| | - Bertrand Sudre
- Prospective and Cooperation, 1 Place Gabriel Péri, Vieux Port, 13001, Marseille, France
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Adera NG, Ketema B, Girma E. Effectiveness and quality of risk communication process in Ethiopia: The case of risk communication during cholera outbreak in Addis Ababa, Ethiopia. PLoS One 2022; 17:e0265203. [PMID: 35984824 PMCID: PMC9390904 DOI: 10.1371/journal.pone.0265203] [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: 02/25/2022] [Accepted: 07/27/2022] [Indexed: 11/18/2022] Open
Abstract
Background WHO states risk communication as the conversation of actual information, guidance, and thoughts between specialists and people fronting risks to their well-being, economic or social safety. As risk communication activities are complex and costly usually, evaluation assessment are the best approach to advance risk communication interventions. This study aims to evaluate the effectiveness of risk communication and the quality of health communication materials developed during the 2019 cholera outbreak at Addis Ababa, Ethiopia. Methods A community-based parallel mixed design was conducted from May to June 2020 at Addis Ababa. A total of 605 adults were selected randomly from Addis Ketema sub-city and ten purposely selected adults were interviewed for qualitative data. In addition eight health communication materials on cholera were randomly selected for evaluation. The quantitative data were analyzed using SPSS version 25. After audio recorded interviews transcribed verbatim and translated into English the qualitative data were entered into open code version 4.02 for analysis. And then the data were analyzed using thematic analysis. Result Respondents exposed for cholera related messages and outbreak information were 71.8% and 52.7% respectively. Respondents have moderate knowledge for cholera with (M = 14.72 and SD ±4.02) with (0–34) scale range. Both Television and radio spots were found as simple and easy to understand and printed health communication materials score low quality. Poor documentation, lack of data management system and less attention for risk communication activities were identified as a gaps in risk communication in the study settings. Conclusion this study revealed the positive effects of risk communication messages in increasing individuals’ knowledge. Even though the risk communication spots were found to be simple and easy to understand, the quality of printed materials was low and less attention was given for the risk-communication activities. Thus, strengthening the quality of risk communication and materials development process is very important to bring desired effects in disease prevention strategies and for effective emergency responses in the future.
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Affiliation(s)
- Nardos Gelana Adera
- Department of Preventive Medicine, School of Public Health, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
- * E-mail:
| | - Bezawit Ketema
- Department of Preventive Medicine, School of Public Health, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Eshetu Girma
- Department of Preventive Medicine, School of Public Health, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
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Epidemiology of Cholera Outbreak and Summary of the Preparedness and Response Activities in Addis Ababa, Ethiopia, 2016. JOURNAL OF ENVIRONMENTAL AND PUBLIC HEALTH 2022; 2022:4671719. [PMID: 35874895 PMCID: PMC9300272 DOI: 10.1155/2022/4671719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 06/21/2022] [Accepted: 06/28/2022] [Indexed: 11/18/2022]
Abstract
Background Cholera is a major public health problem in Ethiopia. This study aimed to generate evidence to better understand the epidemiology of cholera as well as chronicle the city administration's emergency management efforts during the Addis Ababa cholera outbreak in 2016. Method A descriptive analysis was performed using the cholera outbreak data collected from June 8 to October 31, 2016. A case was defined as a patient aged 5 years or older who develops acute watery diarrhea with or without vomiting. Administrative and laboratory finding reports were also used, as well as documented situational updates. Result A total of 8,083 cases (AR of 0.24 percent) with 15 deaths (CFR of 0.18 percent) were reported. Males in unskilled manual occupations and housewives accounted for 2,198 (27.2%) and 1,195 (14.8%), respectively, of the total. A total of 6,908 cases (85.46 percent) sought medical attention within two days of the onset of the condition. The presence of the Kolfie river as well as the relatively confined living conditions of the residents aided in the emergence and rapid spread of the disease. The increased in-and-out movement of people, combined with the city administration's deficient development infrastructure of water, hygiene, and sanitation, contributes to higher morbidity and a longer duration of the outbreak. Multiple command posts established in various locations as well as a lack of collaboration among relevant stakeholders resulted in inefficient information and resource management. Furthermore, there is a lack of risk factor surveillance for the early detection of cholera-causing agents. Conclusion and Recommendations. This outbreak caused significant morbidity and mortality. Prioritizing early risk detection, implementing preventive measures, and developing positive working relationships with relevant parties are all critical. A well-established community-based surveillance system and incident management system (IMS) will be required for future emergency management. It is recommended that the city administration make critical adjustments to its developmental infrastructures related to water, sanitation, and hygiene and implement risk factor surveillance from sewerage lines for the early detection of agents that cause cholera.
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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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Park SE, Jeon Y, Kang S, Gedefaw A, Hailu D, Yeshitela B, Edosa M, Getaneh MW, Teferi M. Infectious Disease Control and Management in Ethiopia: A Case Study of Cholera. Front Public Health 2022; 10:870276. [PMID: 35712321 PMCID: PMC9197421 DOI: 10.3389/fpubh.2022.870276] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 04/19/2022] [Indexed: 11/30/2022] Open
Abstract
Cholera remains a significant public health problem among the vulnerable populations living in many resource-limited settings with poor access to safe and clean water and hygiene practice. Around 2.86 million cholera cases and 95,000 deaths are estimated to occur in endemic countries. In Ethiopia, cholera has been one of the major epidemic diseases since 1634 when the first cholera outbreak was recorded in-country. Several cholera epidemics occurred with recent outbreaks in 2019–2021. Cholera has been often reported as acute watery diarrhea due to limited diagnostic capacity in remote areas in Ethiopia and sensitivities around cholera outbreaks. The government of Ethiopia has been executing several phases of multi-year health sector development plan in the past decades and has recently developed a national cholera control plan. Here, we aim to present the existing cholera control guidelines and health system in Ethiopia, including case detection and reporting, outbreak declaration, case management, and transmission control. Challenges and way forward on further research and public health interventions are also discussed to address the knowledge and health service gaps related to cholera control in Ethiopia.
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Affiliation(s)
- Se Eun Park
- Clinical, Assessment, Regulatory, Evaluation (CARE) Unit, International Vaccine Institute, Seoul, South Korea.,Yonsei University Graduate School of Public Health, Seoul, South Korea
| | - Yeonji Jeon
- Clinical, Assessment, Regulatory, Evaluation (CARE) Unit, International Vaccine Institute, Seoul, South Korea
| | - Sunjoo Kang
- Yonsei University Graduate School of Public Health, Seoul, South Korea
| | - Abel Gedefaw
- Clinical, Assessment, Regulatory, Evaluation (CARE) Unit, International Vaccine Institute, Seoul, South Korea.,College of Medicine and Health Sciences, Hawassa University, Hawassa, Ethiopia
| | - Dejene Hailu
- Clinical, Assessment, Regulatory, Evaluation (CARE) Unit, International Vaccine Institute, Seoul, South Korea.,School of Public Health, Hawassa University, Hawassa, Ethiopia
| | - Biruk Yeshitela
- Bacterial and Viral Disease Research Directorate, Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Moti Edosa
- Diseases Surveillance and Response Directorate, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Mesfin Wossen Getaneh
- Diseases Surveillance and Response Directorate, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Mekonnen Teferi
- Clinical Trials Directorate, Armauer Hansen Research Institute, Addis Ababa, Ethiopia
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7
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Endris AA, Tadesse M, Alemu E, Musa EO, Abayneh A, Assefa Z. A case-control study to assess risk factors related to cholera outbreak in Addis Ababa, Ethiopia, July 2016. Pan Afr Med J 2019; 34:128. [PMID: 33708297 PMCID: PMC7906546 DOI: 10.11604/pamj.2019.34.128.17997] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 09/24/2019] [Indexed: 11/29/2022] Open
Abstract
INTRODUCTION Suspected cholera cases were reported to the city administration health bureau in Addis-Ababa, Ethiopia on June 5, 2016 and it was laboratory confirmed by culture on 7 June 2016. The outbreak was declared by the government on June 8, 2016. The aim of this study was to rapidly investigate the outbreak epidemiologically and guide response activities in the affected Sub cities of Addis Ababa city administration. METHODS An unmatched 1:2 case-control study was conducted in six selected sub-cities of the city administration. Different laboratory tests were also done from suspected possible risk factors identified to support the epidemiological findings. A case was a patient greater than 5 years old, who developed acute watery diarrhea with or without Vomiting. Control was an individual greater than 5 years' old who stayed in the same township and did not suffer from cholera. A structured questionnaire was used to select cases and controls. Epi InfoTM statistical software was used to analyze the data. Results were presented in narratives, figures and tables. RESULTS The present study found that, the study participants who used street-vended water (Odds Ratio (OR)=10.4; 95% CI: 1.20-90.9), those who reported holy water sources use (OR=2.7, 95% CI: 1.45-5.04), eating raw meat (OR=7.75; 95% CI: 3.86-15.54) or roasted meat (OR=2.16; 95% CI: 1.19-3.93) and vegetable salad (OR=2.07; 95% CI: 1.14-3.76) were associated with contracting cholera infection. The likelihood of contracting cholera was significantly higher among those who ate food from street vendor sources (OR=5.32; 95% CI: 1.82-15.56) and those who practiced open defecation (OR=8.12; 95% CI (2.20-29.81). Having a latrine (OR=0.29; 95% CI: 0.12-0.69) and proper hand hygiene practice (OR=0.22; 95% CI: 0.14-0.38) were found to be protective against cholera infection. CONCLUSION Improving awareness of the community by intensifying social mobilization activities through community participation in proper hygienic practice, proper waste disposal and latrine facility construction and utilization. Provision of safe water for the community by strictly conducting end-point assessment of water points and conducting a KAP assessment among food handlers to explore their knowledge and practices regarding safe food/drink handling and water treatment as well as initiate appropriate PH actions based on the findings which will be necessary for prevention of similar cholera outbreaks in the future.
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Affiliation(s)
| | - Musse Tadesse
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Emana Alemu
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | | | | | - Zewdu Assefa
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
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8
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Smith AM. Review of molecular subtyping methodologies used to investigate outbreaks due to multidrug-resistant enteric bacterial pathogens in sub-Saharan Africa. Afr J Lab Med 2019; 8:760. [PMID: 31205868 PMCID: PMC6556818 DOI: 10.4102/ajlm.v8i1.760] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 09/25/2018] [Indexed: 01/05/2023] Open
Abstract
Background In sub-Saharan Africa, molecular epidemiological investigation of outbreaks caused by antimicrobial-resistant enteric bacterial pathogens have mostly been described for Salmonella species, Vibrio cholerae, Shigella species and Escherichia coli. For these organisms, I reviewed all publications describing the use of molecular subtyping methodologies to investigate outbreaks caused by multidrug-resistant (MDR) enteric bacterial infections. Objectives To describe the use of molecular subtyping methodologies to investigate outbreaks caused by MDR enteric bacterial pathogens in sub-Saharan Africa and to describe the current status of molecular subtyping capabilities in the region. Methods A PubMed database literature search (English language only) was performed using the search strings: ‘Africa outbreak MDR’, ‘Africa outbreak multi’, ‘Africa outbreak multidrug’, ‘Africa outbreak multi drug’, ‘Africa outbreak resistance’, ‘Africa outbreak resistant’, ‘Africa outbreak drug’, ‘Africa outbreak antibiotic’, ‘Africa outbreak antimicrobial’. These search strings were used in combination with genus and species names of the organisms listed above. All results were included in the review. Results The year 1991 saw one of the first reports describing the use of molecular subtyping methodologies in sub-Saharan Africa; this included the use of plasmid profiling to characterise Salmonella Enteritidis. To date, several methodologies have been used; pulsed-field gel electrophoresis analysis and multilocus sequence typing have been the most commonly used methodologies. Investigations have particularly highlighted the emergence and spread of MDR clones; these include Salmonella Typhi H58 and Salmonella Typhimurium ST313 clones. In recent times, whole-genome sequencing (WGS) analysis approaches have increasingly been used. Conclusion Traditional molecular subtyping methodologies are still commonly used and still have their place in investigations; however, WGS approaches have increasingly been used and are slowly gaining a stronghold. African laboratories need to start adapting their molecular surveillance methodologies to include WGS, as it is foreseen that WGS analysis will eventually replace all traditional methodologies.
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Affiliation(s)
- Anthony M Smith
- Centre for Enteric Diseases, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa.,Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Oliva M, Monno R, D'Addabbo P, Pesole G, Dionisi AM, Scrascia M, Chiara M, Horner DS, Manzari C, Luzzi I, Calia C, D'Erchia AM, Pazzani C. A novel group of IncQ1 plasmids conferring multidrug resistance. Plasmid 2016; 89:22-26. [PMID: 27916622 DOI: 10.1016/j.plasmid.2016.11.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/28/2016] [Accepted: 11/29/2016] [Indexed: 11/28/2022]
Abstract
The IncQ is a group of non-conjugative but mobilisable plasmids that are found and stably maintained in a wide range of bacteria contributing to the spread of antimicrobial resistance genes and to the insurgence of multidrug resistant bacteria. Here we report the identification, in clinical Salmonella Typhimurium strains, of an IncQ1 plasmid (pNUC) which confers resistance to sulfamethoxazole, streptomycin and tetracycline through the presence of sul2, strAB and tetA genes, respectively. pNUC was detected in five multidrug resistant S. Typhimurium strains collected in Southern Italy from various hospitals and years of isolation. Bioinformatics analyses highlighted the presence of pNUC-like plasmids in pathogenic bacteria of various Enterobacteriaceae genera or species. Taken as a whole, these plasmids constitute a novel group of IncQ1 plasmids that might have originated through recombination events between a tetR-tetA gene cluster (possibly derived from a Tn1721) and a recipient IncQ1 plasmid related to RSF1010. Our findings raise concerns regarding the possible contribution of the newly identified group of IncQ1 plasmids to the spread of tetracycline resistance.
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Affiliation(s)
- M Oliva
- Department of Biology, University of Bari, via Orabona, 4, 70125 Bari, Italy
| | - R Monno
- Department of Basic Medical Sciences Neurosciences and Sense Organs Medical Faculty, University of Bari Piazza G. Cesare Policlinico, 70124 Bari, Italy
| | - P D'Addabbo
- Department of Biology, University of Bari, via Orabona, 4, 70125 Bari, Italy
| | - G Pesole
- Institute of Biomembranes and Bioenergetics, National Research Council, via Amendola 165A, 70125 Bari, Italy; Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, via Orabona, 4, 70125 Bari, Italy
| | - A M Dionisi
- Department of Infectious, Parasitic and Immuno-Mediated Diseases, Istituto Superiore di Sanità, Rome 00161, Italy
| | - M Scrascia
- Department of Biology, University of Bari, via Orabona, 4, 70125 Bari, Italy
| | - M Chiara
- Department of Biosciences, University of Milano, via Celoria 26, 20131 Milano, Italy
| | - D S Horner
- Department of Biosciences, University of Milano, via Celoria 26, 20131 Milano, Italy
| | - C Manzari
- Institute of Biomembranes and Bioenergetics, National Research Council, via Amendola 165A, 70125 Bari, Italy
| | - I Luzzi
- Department of Infectious, Parasitic and Immuno-Mediated Diseases, Istituto Superiore di Sanità, Rome 00161, Italy
| | - C Calia
- Department of Basic Medical Sciences Neurosciences and Sense Organs Medical Faculty, University of Bari Piazza G. Cesare Policlinico, 70124 Bari, Italy
| | - A M D'Erchia
- Institute of Biomembranes and Bioenergetics, National Research Council, via Amendola 165A, 70125 Bari, Italy; Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, via Orabona, 4, 70125 Bari, Italy
| | - C Pazzani
- Department of Biology, University of Bari, via Orabona, 4, 70125 Bari, Italy.
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Chattaway MA, Aboderin AO, Fashae K, Okoro CK, Opintan JA, Okeke IN. Fluoroquinolone-Resistant Enteric Bacteria in Sub-Saharan Africa: Clones, Implications and Research Needs. Front Microbiol 2016; 7:558. [PMID: 27148238 PMCID: PMC4841292 DOI: 10.3389/fmicb.2016.00558] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 04/04/2016] [Indexed: 11/13/2022] Open
Abstract
Fluoroquinolones came into widespread use in African countries in the early 2000s, after patents for the first generation of these drugs expired. By that time, quinolone antibacterial agents had been used intensively worldwide and resistant lineages of many bacterial species had evolved. We sought to understand which Gram negative enteric pandemic lineages have been reported from Africa, as well as the nature and transmission of any indigenous resistant clones. A systematic review of articles indexed in the Medline and AJOL literature databases was conducted. We report on the findings of 43 eligible studies documenting local or pandemic fluoroquinolone-resistant enteric clones in sub-Sahara African countries. Most reports are of invasive non-typhoidal Salmonella and Escherichia coli lineages and there have been three reports of cholera outbreaks caused by fluoroquinolone-resistant Vibrio cholerae O1. Fluoroquinolone-resistant clones have also been reported from commensals and animal isolates but there are few data for non-Enterobacteriaceae and almost none for difficult-to-culture Campylobacter spp. Fluoroquinolone-resistant lineages identified in African countries were universally resistant to multiple other classes of antibacterial agents. Although as many as 972 non-duplicate articles refer to fluoroquinolone resistance in enteric bacteria from Africa, most do not report on subtypes and therefore information on the epidemiology of fluoroquinolone-resistant clones is available from only a handful of countries in the subcontinent. When resistance is reported, resistance mechanisms and lineage information is rarely investigated. Insufficient attention has been given to molecular and sequence-based methods necessary for identifying and tracking resistant clones in Africa and more research is needed in this area.
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Affiliation(s)
- Marie A Chattaway
- Gastrointestinal Bacteria Reference Unit, Public Health England London, UK
| | - Aaron O Aboderin
- Department of Medical Microbiology and Parasitology, College of Health Sciences, Obafemi Awolowo University Ile-Ife, Nigeria
| | - Kayode Fashae
- Department of Microbiology, University of Ibadan Ibadan, Nigeria
| | | | - Japheth A Opintan
- Department of Medical Microbiology, School of Biomedical and Allied Health Sciences, University of Ghana Accra, Ghana
| | - Iruka N Okeke
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan Ibadan, Nigeria
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A review of 40 years of enteric antimicrobial resistance research in Eastern Africa: what can be done better? Antimicrob Resist Infect Control 2015; 4:1. [PMID: 25717374 PMCID: PMC4339253 DOI: 10.1186/s13756-014-0041-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 12/16/2014] [Indexed: 01/08/2023] Open
Abstract
The emergence and persistence of antimicrobial resistance is driven by varied factors including the indiscriminate use of antibiotics and variable drug efficacy and presents a major threat to the control of infectious diseases. Despite the high burden of disease in sub-Saharan Africa and the potential health and economic consequences, the level of research on antimicrobial resistance in the region remains unknown. Little data exists to quantify the contribution of different factors to the current levels of antimicrobial resistance. To identify the factors that contribute most to the emergence, amplification, persistence and dissemination of antimicrobial resistance in humans and animals, we used the PRISMA 2009 guidelines to conduct a systematic review of studies on antibiotic-resistant enteric bacteria in Eastern Africa. We searched PubMed and Google Scholar databases and identified 2,155 probable articles, of which 89 studies on humans and 28 on animals remained after full-text review. These were articles from Kenya, Tanzania, Uganda, Ethiopia, Rwanda and Burundi, published between 1974 and 2013, that reported resistance in Salmonella, Shigella, Escherichia coli and Vibrio sp. The majority (98%) of human studies were based on hospital- (rather than community-wide) sampling and although they report high levels of antimicrobial resistance in the region, study design and methodological differences preclude conclusions about the magnitude and trends of antimicrobial resistance. To remedy this, we discuss and propose minimum reporting guidelines for the level of detail that should be explicitly provided for antimicrobial resistance study designs, testing of samples and reporting of results that would permit comparative inferences and enable meta-analyses. Further, we advocate for increased focus on community- rather than hospital-based sampling to provide a better indication of population-wide trends in antimicrobial resistance. This approach, together with the establishment of a robust regional surveillance network, should over time build a pool of evidence-based data useful for policy decisions and interventions aimed at controlling antimicrobial resistance.
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12
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Leopold SJ, van Leth F, Tarekegn H, Schultsz C. Antimicrobial drug resistance among clinically relevant bacterial isolates in sub-Saharan Africa: a systematic review. J Antimicrob Chemother 2014; 69:2337-53. [PMID: 24879668 DOI: 10.1093/jac/dku176] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Little is known about the prevalence of antimicrobial resistance (AMR) amongst bacterial pathogens in sub-Saharan Africa (sSA), despite calls for continent-wide surveillance to inform empirical treatment guidelines. METHODS We searched PubMed and additional databases for susceptibility data of key pathogens for surveillance, published between 1990 and 2013. Extracted data were standardized to a prevalence of resistance in populations of isolates and reported by clinical syndrome, microorganism, relevant antimicrobial drugs and region. RESULTS We identified 2005 publications, of which 190 were analysed. Studies predominantly originated from east sSA (61%), were hospital based (60%), were from an urban setting (73%) and reported on isolates from patients with a febrile illness (42%). Quality procedures for susceptibility testing were described in <50% of studies. Median prevalence (MP) of resistance to chloramphenicol in Enterobacteriaceae, isolated from patients with a febrile illness, ranged between 31.0% and 94.2%, whilst MP of resistance to third-generation cephalosporins ranged between 0.0% and 46.5%. MP of resistance to nalidixic acid in Salmonella enterica Typhi ranged between 15.4% and 43.2%. The limited number of studies providing prevalence data on AMR in Gram-positive pathogens or in pathogens isolated from patients with a respiratory tract infection, meningitis, urinary tract infection or hospital-acquired infection suggested high prevalence of resistance to chloramphenicol, trimethoprim/sulfamethoxazole and tetracycline and low prevalence to third-generation cephalosporins and fluoroquinolones. CONCLUSIONS Our results indicate high prevalence of AMR in clinical bacterial isolates to antimicrobial drugs commonly used in sSA. Enhanced approaches for AMR surveillance are needed to support empirical therapy in sSA.
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Affiliation(s)
- Stije J Leopold
- Department of Global Health, Amsterdam Institute for Global Health and Development, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Frank van Leth
- Department of Global Health, Amsterdam Institute for Global Health and Development, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Hayalnesh Tarekegn
- Department of Global Health, Amsterdam Institute for Global Health and Development, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Constance Schultsz
- Department of Global Health, Amsterdam Institute for Global Health and Development, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
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Rebaudet S, Sudre B, Faucher B, Piarroux R. Cholera in coastal Africa: a systematic review of its heterogeneous environmental determinants. J Infect Dis 2013; 208 Suppl 1:S98-106. [PMID: 24101653 DOI: 10.1093/infdis/jit202] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
According to the "cholera paradigm," epidemiology of this prototypical waterborne disease is considered to be driven directly by climate-induced variations in coastal aquatic reservoirs of Vibrio cholerae. This systematic review on environmental determinants of cholera in coastal Africa shows that instead coastal epidemics constitute a minor part of the continental cholera burden. Most of coastal cholera foci are located near estuaries, lagoons, mangrove forests, and on islands. Yet outbreaks often originate in coastal cities, where cholera is more likely to be imported from distant areas. Cholera outbreaks also may intensify in densely populated slum quarters before spreading to adjacent regions. Frequent seasonality of cholera incidence appears driven by the rainfall-induced contamination of unprotected water sources through latrine overflow and sewage, as well as by the periodicity of human activities like fishing or traveling. Lulls in transmission periods of several years are repeatedly recorded even in high-risk coastal areas. To date, environmental studies have failed to demonstrate a perennial aquatic reservoir of toxigenic V. cholerae around the continent. Finally, applicability of the cholera paradigm therefore appears questionable in Africa, although available data remain limited. Thorough surveys with microbiological analyses of water samples and prospective genotyping of environmental and clinical strains of V. cholerae are needed to understand determinants of cholera in coastal Africa and better target prevention and control measures.
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14
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Kiiru J, Mutreja A, Mohamed AA, Kimani RW, Mwituria J, Sanaya RO, Muyodi J, Revathi G, Parkhill J, Thomson N, Dougan G, Kariuki S. A study on the geophylogeny of clinical and environmental Vibrio cholerae in Kenya. PLoS One 2013; 8:e74829. [PMID: 24066154 PMCID: PMC3774669 DOI: 10.1371/journal.pone.0074829] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 08/06/2013] [Indexed: 12/13/2022] Open
Abstract
Cholera remains a significant public health challenge in many sub-Saharan countries including Kenya. We have performed a combination of phylogenetic and phenotypic analysis based on whole genome DNA sequences derived from 40 environmental and 57 clinical V. cholerae from different regions of Kenya isolated between 2005 and 2010. Some environmental and all clinical isolates mapped back onto wave three of the monophyletic seventh pandemic V. cholerae El Tor phylogeny but other environmental isolates were phylogenetically very distinct. Thus, the genomes of the Kenyan V. cholerae O1 El Tor isolates are clonally related to other El Tor V. cholerae isolated elsewhere in the world and similarly harbour antibiotic resistance-associated STX elements. Further, the Kenyan O1 El Tor isolates fall into two distinct clades that may have entered Kenya independently.
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Affiliation(s)
- John Kiiru
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Ankur Mutreja
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | | | - Racheal W. Kimani
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Joyce Mwituria
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Robert Onsare Sanaya
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Jane Muyodi
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Gunturu Revathi
- Division of Microbiology, Department of Pathology, Aga Khan University Hospital, Nairobi, Kenya
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Nicholas Thomson
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Gordon Dougan
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Samuel Kariuki
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
- * E-mail:
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15
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Mohamed AA, Oundo J, Kariuki SM, Boga HI, Sharif SK, Akhwale W, Omolo J, Amwayi AS, Mutonga D, Kareko D, Njeru M, Li S, Breiman RF, Stine OC. Molecular epidemiology of geographically dispersed Vibrio cholerae, Kenya, January 2009-May 2010. Emerg Infect Dis 2012; 18:925-31. [PMID: 22607971 PMCID: PMC3358164 DOI: 10.3201/eid1806.111774] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Isolates represent multiple genetic lineages, a finding consistent with multiple emergences from endemic reservoirs. Numerous outbreaks of cholera have occurred in Kenya since 1971. To more fully understand the epidemiology of cholera in Kenya, we analyzed the genetic relationships among 170 Vibrio cholerae O1 isolates at 5 loci containing variable tandem repeats. The isolates were collected during January 2009–May 2010 from various geographic areas throughout the country. The isolates grouped genetically into 5 clonal complexes, each comprising a series of genotypes that differed by an allelic change at a single locus. No obvious correlation between the geographic locations of the isolates and their genotypes was observed. Nevertheless, geographic differentiation of the clonal complexes occurred. Our analyses showed that multiple genetic lineages of V. cholerae were simultaneously infecting persons in Kenya. This finding is consistent with the simultaneous emergence of multiple distinct genetic lineages of V. cholerae from endemic environmental reservoirs rather than recent introduction and spread by travelers.
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Kiiru JN, Saidi SM, Goddeeris BM, Wamae NC, Butaye P, Kariuki SM. Molecular characterisation of Vibrio cholerae O1 strains carrying an SXT/R391-like element from cholera outbreaks in Kenya: 1994-2007. BMC Microbiol 2009; 9:275. [PMID: 20040104 PMCID: PMC2806261 DOI: 10.1186/1471-2180-9-275] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2009] [Accepted: 12/29/2009] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Over the last decade, cholera outbreaks in parts of Kenya have become common. Although a number of recent studies describe the epidemiology of cholera in Kenya, there is paucity of information concerning the diversity and occurrence of mobile genetic elements in Vibrio cholerae strains implicated in these outbreaks. A total of 65 Vibrio cholerae O1 El Tor serotype Inaba isolated between 1994 and 2007 from various outbreaks in Kenya were investigated for mobile genetic elements including integrons, transposons, the integrating conjugative elements (ICEs), conjugative plasmids and for their genotypic relatedness. RESULTS All the strains were haemolytic on 5% sheep blood and positive for the Vibrio cholerae El Tor-specific haemolysin toxin gene (hylA) by PCR. They all contained strB, sulII, floR and the dfrA1 genes encoding resistance to streptomycin, sulfamethoxazole, chloramphenicol and trimethoprim respectively. These genes, together with an ICE belonging to the SXT/R391 family were transferable to the rifampicin-resistant E. coli C600 en bloc. All the strains were negative for integron class 1, 2 and 3 and for transposase gene of transposon Tn7 but were positive for integron class 4 and the trpM gene of transposon Tn21. No plasmids were isolated from any of the 65 strains. All the strains were also positive for all V. cholera El Tor pathogenic genes except the NAG- specific heat-stable toxin (st) gene. None of the strains were positive for virulence genes associated with the V. cholerae classical biotype. All the strains were positive for El Tor-specific CTXphi bacteriophage rstrR repressor gene (CTXETPhi) but negative for the Classical, Calcutta, and the Environmental repressor types. Pulse Field Gel Electrophoresis (PFGE) showed that regardless of the year of isolation, all the strains bearing the SXT element were clonally related. CONCLUSIONS This study demonstrates that the V. cholerae O1 strains carrying an SXT/R391-like element implicated in recent cholera outbreaks in Kenya has not changed significantly between 1994 and 2007 and are clonally related.
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Affiliation(s)
- John N Kiiru
- Centre for Microbiology Research, Kenya Medical Research Institute, PO Box 43640, Nairobi, Kenya.
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