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Kanje LE, Kumburu H, Kuchaka D, Shayo M, Juma MA, Kimu P, Beti M, van Zwetselaar M, Wadugu B, Mmbaga BT, Mkumbaye SI, Sonda T. Short reads-based characterization of pathotype diversity and drug resistance among Escherichia coli isolated from patients attending regional referral hospitals in Tanzania. BMC Med Genomics 2024; 17:110. [PMID: 38671498 PMCID: PMC11055328 DOI: 10.1186/s12920-024-01882-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Escherichia coli is known to cause about 2 million deaths annually of which diarrhea infection is leading and typically occurs in children under 5 years old. Although Africa is the most affected region there is little information on their pathotypes diversity and their antimicrobial resistance. OBJECTIVE To determine the pathotype diversity and antimicrobial resistance among E. coli from patients attending regional referral hospitals in Tanzania. MATERIALS AND METHODS A retrospective cross-section laboratory-based study where a total of 138 archived E. coli isolates collected from 2020 to 2021 from selected regional referral hospitals in Tanzania were sequenced using the Illumina Nextseq550 sequencer platform. Analysis of the sequences was done in the CGE tool for the identification of resistance genes and virulence genes. SPSS version 20 was used to summarize data using frequency and proportion. RESULTS Among all 138 sequenced E. coli isolates, the most prevalent observed pathotype virulence genes were of extraintestinal E. coli UPEC fyuA gene 82.6% (114/138) and NMEC irp gene 81.9% (113/138). Most of the E. coli pathotypes observed exist as a hybrid due to gene overlapping, the most prevalent pathotypes observed were NMEC/UPEC hybrid 29.7% (41/138), NMEC/UPEC/EAEC hybrid 26.1% (36/138), NMEC/UPEC/DAEC hybrid 18.1% (25/138) and EAEC 15.2% (21/138). Overall most E. coli carried resistance gene to ampicillin 90.6% (125/138), trimethoprim 85.5% (118/138), tetracycline 79.9% (110/138), ciprofloxacin 76.1% (105/138) and 72.5% (100/138) Nalidixic acid. Hybrid pathotypes were more resistant than non-hybrid pathotypes. CONCLUSION Whole genome sequencing reveals the presence of hybrid pathotypes with increased drug resistance among E. coli isolated from regional referral hospitals in Tanzania.
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Affiliation(s)
- Livin E Kanje
- Department of Microbiology and Immunology, Kilimanjaro Christian Medical University College, Kilimanjaro, Tanzania.
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania.
| | - Happiness Kumburu
- Department of Microbiology and Immunology, Kilimanjaro Christian Medical University College, Kilimanjaro, Tanzania
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
- Clinical Laboratory, Kilimanjaro Christian Medical Center, Kilimanjaro, Tanzania
| | - Davis Kuchaka
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
| | - Mariana Shayo
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
| | - Masoud A Juma
- Department of Microbiology and Immunology, Kilimanjaro Christian Medical University College, Kilimanjaro, Tanzania
- State University of Zanzibar, Zanzibar, Tanzania
| | - Patrick Kimu
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
| | - Melkiory Beti
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
| | | | - Boaz Wadugu
- Department of Microbiology and Immunology, Kilimanjaro Christian Medical University College, Kilimanjaro, Tanzania
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
| | - Blandina T Mmbaga
- Department of Microbiology and Immunology, Kilimanjaro Christian Medical University College, Kilimanjaro, Tanzania
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
- Clinical Laboratory, Kilimanjaro Christian Medical Center, Kilimanjaro, Tanzania
| | - Sixbert Isdory Mkumbaye
- Department of Microbiology and Immunology, Kilimanjaro Christian Medical University College, Kilimanjaro, Tanzania
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
- Clinical Laboratory, Kilimanjaro Christian Medical Center, Kilimanjaro, Tanzania
| | - Tolbert Sonda
- Department of Microbiology and Immunology, Kilimanjaro Christian Medical University College, Kilimanjaro, Tanzania
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
- Clinical Laboratory, Kilimanjaro Christian Medical Center, Kilimanjaro, Tanzania
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Sarenje KL, van Zwetselaar M, Kumburu H, Sonda T, Mmbaga B, Ngalamika O, Maimbolwa MC, Siame A, Munsaka S, Kwenda G. Antimicrobial resistance and heterogeneity of Neisseria gonorrhoeae isolated from patients attending sexually transmitted infection clinics in Lusaka, Zambia. BMC Genomics 2024; 25:290. [PMID: 38500064 PMCID: PMC10949682 DOI: 10.1186/s12864-024-10155-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 02/22/2024] [Indexed: 03/20/2024] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR) of Neisseria gonorrhoeae is a threat to public health as strains have developed resistance to antimicrobials available for the treatment of gonorrhea. Whole genome sequencing (WGS) can detect and predict antimicrobial resistance to enhance the control and prevention of gonorrhea. Data on the molecular epidemiology of N. gonorrhoeae is sparse in Zambia. This study aimed to determine the genetic diversity of N. gonorrhoeae isolated from patients attending sexually transmitted infection (STI) clinics in Lusaka, Zambia. METHODS A cross-sectional study that sequenced 38 N. gonorrhoeae isolated from 122 patients with gonorrhea from 2019 to 2020 was conducted. The AMR profiles were determined by the E-test, and the DNA was extracted using the NucliSens easyMaG magnetic device. Whole genome sequencing was performed on the Illumina NextSeq550 platform. The Bacterial analysis pipeline (BAP) that is readily available at: https://cge.cbs.dtu.dk/services/CGEpipeline-1.1 was used for the identification of the species, assembling the genome, multi-locus sequence typing (MLST), detection of plasmids and AMR genes. Phylogeny by single nucleotide polymorphisms (SNPs) was determined with the CCphylo dataset. RESULTS The most frequent STs with 18.4% of isolates each were ST7363, ST1921 and ST1582, followed by ST1583 (13%), novel ST17026 (7.9%), ST1588 (7.9%), ST1596 (5.3%), ST11181 (5.3%), ST11750 (2.6/%) and ST11241 (2.6%) among the 38 genotyped isolates. The blaTeM-1B and tetM (55%) was the most prevalent combination of AMR genes, followed by blaTeM-1B (18.4%), tetM (15.8%), and the combination of blaTeM-1B, ermT, and tetL was 2.6% of the isolates. The AMR phenotypes were predicted in ciprofloxacin, penicillin, tetracycline, azithromycin, and cefixime. The combination of mutations 23.7% was gryA (S91F), parC (E91G), ponA (L421) and rpsJ (V57M), followed by 18.4% in gyrA (S91F), ponA (L421P), rpsJ (V57M), and 18.4% in gyrA (D95G, S91F), ponA (L421P), and rpsJ (V57M). The combinations in gyrA (D95G, S91F) and rpsJ (V57M), and gyrA (D95G, S91F), parC (E91F), ponA (L421P) and rpsJ (V57M) were 13.2% each of the isolates. Plasmid TEM-1 (84.2%), tetM (15.8%), and gonococcal genetic island (GGI) was detected in all isolates. CONCLUSION This study revealed remarkable heterogeneity of N. gonorrhoeae with blaTEM-1, tetM, ponA, gyrA, and parC genes associated with high resistance to penicillin, tetracycline, and ciprofloxacin demanding revision of the standard treatment guidelines and improved antimicrobial stewardship in Zambia.
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Affiliation(s)
- Kelvin Lutambo Sarenje
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka, P.O. Box 50110, Zambia.
- Department of Dermato-venereology, University Teaching Hospital, Lusaka, Zambia.
| | | | - Happiness Kumburu
- Kilimanjaro Clinical Research Institute, Moshi, Kilimanjaro, Tanzania
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Tolbert Sonda
- Kilimanjaro Clinical Research Institute, Moshi, Kilimanjaro, Tanzania
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Blandina Mmbaga
- Kilimanjaro Clinical Research Institute, Moshi, Kilimanjaro, Tanzania
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Owen Ngalamika
- Department of Dermato-venereology, University Teaching Hospital, Lusaka, Zambia
| | - Margaret C Maimbolwa
- Department of Midwifery Child, and Women's Health, School of Nursing Sciences, University of Zambia, Lusaka, Zambia
| | - Amon Siame
- Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
| | - Sody Munsaka
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka, P.O. Box 50110, Zambia
| | - Geoffrey Kwenda
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka, P.O. Box 50110, Zambia
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Mbwambo GA, van Zwetselaar M, Sonda T, Lukambagire AS, Njau JS, Wadugu B, Ignass IP, Amani NB, Hugho EA, Rubach MP, Sakasaka P, Oisso RS, Mkenda N, Shirima G, Ashford RT, Haydon DT, Maro VP, Kazwala RR, Kumburu HH, Mmbaga BT, Halliday JEB. Complete genome sequence of Brucella abortus isolated from a human blood culture sample in Tanzania. Microbiol Resour Announc 2024; 13:e0093023. [PMID: 38289053 PMCID: PMC10871059 DOI: 10.1128/mra.00930-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/07/2024] [Indexed: 02/16/2024] Open
Abstract
Brucella abortus causes infections in humans and livestock. Bacterial isolates are challenging to obtain, and very little is known about the genomic epidemiology of this species in Africa. Here, we report the complete genome sequence of a Brucella abortus isolate cultured from a febrile human in northern Tanzania.
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Affiliation(s)
| | | | - Tolbert Sonda
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
| | | | - Judith S. Njau
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
| | - Boaz Wadugu
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
| | | | | | - Ephrasia A. Hugho
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
- Institute of Public Health, Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Matthew P. Rubach
- Department of Medicine, Division of Infectious Disease and International Health, Duke Global Health Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | | | - Rose S. Oisso
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
| | | | - Gabriel Shirima
- Nelson Mandela Africa Institute of Science and Technology, Arusha, Tanzania
| | - Roland T. Ashford
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Daniel T. Haydon
- School of Biodiversity, One Health & Veterinary Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Venance P. Maro
- Department of Internal Medicine, Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Rudovick R. Kazwala
- Department of Veterinary Medicine and Public Health, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Happiness H. Kumburu
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Blandina T. Mmbaga
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Jo E. B. Halliday
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
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Vasudevan L, Ostermann J, Thielman N, Baumgartner JN, Solomon D, Mosses A, Hobbie A, Hair NL, Liang C, van Zwetselaar M, Mfinanga S, Ngadaya E. Leveraging Community Health Workers and a Responsive Digital Health System to Improve Vaccination Coverage and Timeliness in Resource-Limited Settings: Protocol for a Cluster Randomized Type 1 Effectiveness-Implementation Hybrid Study. JMIR Res Protoc 2024; 13:e52523. [PMID: 38214956 PMCID: PMC10818232 DOI: 10.2196/52523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 10/26/2023] [Indexed: 01/13/2024] Open
Abstract
BACKGROUND Tanzania is 1 of 20 countries where the majority of unvaccinated and undervaccinated children reside. Prior research identified substantial rural-urban disparities in the coverage and timeliness of childhood vaccinations in Tanzania, with children in rural settings being more likely to receive delayed or no vaccinations. Further research is necessary to identify effective and scalable interventions that can bridge rural-urban gaps in childhood vaccination while accounting for multifaceted barriers to vaccination. OBJECTIVE This protocol describes a type 1 effectiveness-implementation hybrid study to evaluate Chanjo Kwa Wakati (timely vaccination in Kiswahili), a community-based digital health intervention to improve vaccination timeliness. The intervention combines human resources (community health workers), low-cost digital strategies (electronic communication, digital case management, and task automation), a vaccination knowledge intervention, and insights from behavioral economics (reminders and incentives) to promote timely childhood vaccinations. METHODS The study will be conducted in 2 predominantly rural regions in Tanzania with large numbers of unvaccinated or undervaccinated children: Shinyanga and Mwanza. Forty rural health facilities and their catchment areas (clusters) will be randomized to an early or delayed onset study arm. From each cluster, 3 cohorts of mother-child dyads (1 retrospective cohort and 2 prospective cohorts) will be enrolled in the study. The timeliness and coverage of all vaccinations recommended during the first year of life will be observed for 1200 children (n=600, 50% intervention group children and n=600, 50% nonintervention group children). The primary effectiveness outcome will be the timeliness of the third dose of the pentavalent vaccine (Penta3). Quantitative surveys, vaccination records, study logs, fidelity checklists, and qualitative interviews with mothers and key informants will inform the 5 constructs of the reach, effectiveness, adoption, implementation, and maintenance (RE-AIM) framework. The results will be used to develop an implementation blueprint to guide future adaptations and scale-up of Chanjo Kwa Wakati. RESULTS The study was funded in August 2022. Data collection is expected to last from February 2024 to July 2027. CONCLUSIONS This study will address the lack of rigorous evidence on the effectiveness of community-based digital health interventions for promoting vaccination coverage and timeliness among children from sub-Saharan Africa and identify potential implementation strategies to facilitate the deployment of vaccination promotion interventions in low- and middle-income countries. TRIAL REGISTRATION ClinicalTrials.gov NCT06024317; https://www.clinicaltrials.gov/study/NCT06024317. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID) PRR1-10.2196/52523.
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Affiliation(s)
- Lavanya Vasudevan
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, United States
- Duke Global Health Institute, Duke University, Durham, NC, United States
| | - Jan Ostermann
- Duke Global Health Institute, Duke University, Durham, NC, United States
- Department of Health Services Policy & Management, Arnold School of Public Health, University of South Carolina, Columbia, SC, United States
| | - Nathan Thielman
- Duke Global Health Institute, Duke University, Durham, NC, United States
- Department of Medicine, Duke University, Durham, NC, United States
| | - Joy Noel Baumgartner
- School of Social Work, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - David Solomon
- National Institute for Medical Research, Muhimbili Research Centre, Dar es Salaam, United Republic of Tanzania
| | - Anna Mosses
- National Institute for Medical Research, Muhimbili Research Centre, Dar es Salaam, United Republic of Tanzania
| | - Amy Hobbie
- Duke Global Health Institute, Duke University, Durham, NC, United States
| | - Nicole L Hair
- Department of Health Services Policy & Management, Arnold School of Public Health, University of South Carolina, Columbia, SC, United States
| | - Chen Liang
- Department of Health Services Policy & Management, Arnold School of Public Health, University of South Carolina, Columbia, SC, United States
| | | | - Sayoki Mfinanga
- National Institute for Medical Research, Muhimbili Research Centre, Dar es Salaam, United Republic of Tanzania
| | - Esther Ngadaya
- National Institute for Medical Research, Muhimbili Research Centre, Dar es Salaam, United Republic of Tanzania
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Mzee T, Kumburu H, Kazimoto T, Leekitcharoenphon P, van Zwetselaar M, Masalu R, Mlaganile T, Sonda T, Wadugu B, Mushi I, Aarestrup FM, Matee M. Molecular Characterization of Staphylococcus aureus Isolated from Raw Milk and Humans in Eastern Tanzania: Genetic Diversity and Inter-Host Transmission. Microorganisms 2023; 11:1505. [PMID: 37375007 DOI: 10.3390/microorganisms11061505] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/22/2023] [Accepted: 04/23/2023] [Indexed: 06/29/2023] Open
Abstract
Staphylococcus aureus is a common cause of infection in humans and animals, including bovine mastitis, globally. The objective of this study was to genetically characterize a collection of S. aureus isolates recovered from milk and nasal swabs from humans with and without animal contact (bovine = 43, human = 12). Using whole genome sequencing (NextSeq550), isolates were sequence typed, screened for antimicrobial resistance and virulence genes and examined for possible inter-species host transmission. Multi locus sequence typing (MLST) and single nucleotide polymorphism (SNP)-based phylogeny revealed 14 different sequence types, including the following six novel sequence types: ST7840, 7841, 7845, 7846, 7847, and 7848. The SNP tree confirmed that MLST clustering occurred most commonly within CC97, CC5477, and CC152. ResFinder analysis revealed five common antibiotic resistance genes, namely tet(K), blaZ, dfrG, erm©, and str, encoding for different antibiotics. mecA was discovered in one human isolate only. Multidrug resistance was observed in 25% of the isolates, predominantly in CC152 (7/8) and CC121 (3/4). Known bovine S. aureus (CC97) were collected in humans and known human S. aureus lineages (CC152) were collected in cattle; additionally, when these were compared to bovine-isolated CC97 and human-isolated CC152, respectively, no genetic distinction could be observed. This is suggestive of inter-host transmission and supports the need for surveillance of the human-animal interface.
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Affiliation(s)
- Tutu Mzee
- Ifakara Health Institute, Bagamoyo Branch, Bagamoyo P.O. Box 74, Tanzania
- Department of Molecular Biology and Biotechnology, University of Dar es Salaam, Dar es Salaam P.O. Box 35179, Tanzania
| | - Happiness Kumburu
- Kilimanjaro Clinical Research Institute, Moshi P.O. Box 2236, Tanzania
| | - Theckla Kazimoto
- Ifakara Health Institute, Bagamoyo Branch, Bagamoyo P.O. Box 74, Tanzania
| | - Pimlapas Leekitcharoenphon
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kemitorvet, DK 2800 Kgs. Lyngby, Denmark
| | | | - Rose Masalu
- Department of Molecular Biology and Biotechnology, University of Dar es Salaam, Dar es Salaam P.O. Box 35179, Tanzania
| | - Tarsis Mlaganile
- Ifakara Health Institute, Bagamoyo Branch, Bagamoyo P.O. Box 74, Tanzania
| | - Tolbert Sonda
- Kilimanjaro Clinical Research Institute, Moshi P.O. Box 2236, Tanzania
| | - Boaz Wadugu
- Kilimanjaro Clinical Research Institute, Moshi P.O. Box 2236, Tanzania
| | - Ignass Mushi
- Kilimanjaro Clinical Research Institute, Moshi P.O. Box 2236, Tanzania
| | - Frank M Aarestrup
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kemitorvet, DK 2800 Kgs. Lyngby, Denmark
| | - Mecky Matee
- Department of Microbiology and Immunology, School of Medicine, Muhimbili University of Health and Allied Sciences, Dar es Salaam P.O. Box 65001, Tanzania
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Mziray SR, van Zwetselaar M, Kayuki CC, Mbelele PM, Makubi AN, Magesa AS, Kisonga RM, Sonda TB, Kibiki GS, Githinji G, Heysell SK, Chilongola JO, Mpagama SG. Whole-genome sequencing of SARS-CoV-2 isolates from symptomatic and asymptomatic individuals in Tanzania. Front Med (Lausanne) 2023; 9:1034682. [PMID: 36687433 PMCID: PMC9846855 DOI: 10.3389/fmed.2022.1034682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/05/2022] [Indexed: 01/06/2023] Open
Abstract
Background Coronavirus Disease-2019 (COVID-19), caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) accounts for considerable morbidity and mortality globally. Paucity of SARS-CoV-2 genetic data from Tanzania challenges in-country tracking of the pandemic. We sequenced SARS-CoV-2 isolated in the country to determine circulating strains, mutations and phylogenies and finally enrich international genetic databases especially with sequences from Africa. Methods This cross-sectional study utilized nasopharyngeal swabs of symptomatic and asymptomatic adults with positive polymerase chain reaction tests for COVID-19 from January to May 2021. Viral genomic libraries were prepared using ARTIC nCoV-2019 sequencing protocol version three. Whole-genome sequencing (WGS) was performed using Oxford Nanopore Technologies MinION device. In silico genomic data analysis was done on ARTIC pipeline version 1.2.1 using ARTIC nCoV-2019 bioinformatics protocol version 1.1.0. Results Twenty-nine (42%) out of 69 samples qualified for sequencing based on gel electrophoretic band intensity of multiplex PCR amplicons. Out of 29 isolates, 26 were variants of concern [Beta (n = 22); and Delta (n = 4)]. Other variants included Eta (n = 2) and B.1.530 (n = 1). We found combination of mutations (S: D80A, S: D215G, S: K417N, ORF3a: Q57H, E: P71L) in all Beta variants and absent in other lineages. The B.1.530 lineage carried mutations with very low cumulative global prevalence, these were nsp13:M233I, nsp14:S434G, ORF3a:A99S, S: T22I and S: N164H. The B.1.530 lineage clustered phylogenetically with isolates first reported in south-east Kenya, suggesting regional evolution of SARS-CoV-2. Conclusion We provide evidence of existence of Beta, Delta, Eta variants and a locally evolving lineage (B.1.530) from samples collected in early 2021 in Tanzania. This work provides a model for ongoing WGS surveillance that will be required to inform on emerging and circulating SARS-CoV-2 diversity in Tanzania and East Africa.
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Affiliation(s)
- Shabani Ramadhani Mziray
- Department of Biochemistry and Molecular Biology, Kilimanjaro Christian Medical University College, Moshi, Tanzania
- Kibong’oto Infectious Diseases Hospital, Sanya Juu, Tanzania
| | | | | | | | | | | | | | | | - Gibson S. Kibiki
- The Africa Research Excellence Fund (AREF), London, United Kingdom
| | - George Githinji
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
| | - Scott K. Heysell
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, United States
| | - Jaffu O. Chilongola
- Department of Biochemistry and Molecular Biology, Kilimanjaro Christian Medical University College, Moshi, Tanzania
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
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Sengeruan LP, van Zwetselaar M, Kumburu H, Aarestrup FM, Kreppel K, Sauli E, Sonda T. Plasmid characterization in bacterial isolates of public health relevance in a tertiary healthcare facility in Kilimanjaro, Tanzania. J Glob Antimicrob Resist 2022; 30:384-389. [DOI: 10.1016/j.jgar.2022.06.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/15/2022] [Accepted: 06/27/2022] [Indexed: 10/17/2022] Open
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Sadiq AM, Mariki DE, Gundah CM, Assey EV, van Zwetselaar M, Howlett WP, Dekker MCJ. Feeling the price tag of magnetic resonance imaging claustrophobia. J Magn Reson Imaging 2021; 54:328. [PMID: 33491271 DOI: 10.1002/jmri.27512] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/31/2020] [Accepted: 01/04/2021] [Indexed: 11/07/2022] Open
Affiliation(s)
- Adnan M Sadiq
- MRI Unit, Department of Radiology, Kilimanjaro Christian Medical Centre, Moshi, United Republic of Tanzania
| | - Daniel E Mariki
- MRI Unit, Department of Radiology, Kilimanjaro Christian Medical Centre, Moshi, United Republic of Tanzania
| | - Cleopah M Gundah
- MRI Unit, Department of Radiology, Kilimanjaro Christian Medical Centre, Moshi, United Republic of Tanzania
| | - Emmanuel V Assey
- Neurology Clinic, Department of Internal Medicine, Kilimanjaro Christian Medical Centre, Moshi, United Republic of Tanzania
| | - Marco van Zwetselaar
- Bioinformatics Unit, Kilimanjaro Clinical Research Institute, Moshi, United Republic of Tanzania
| | - William P Howlett
- Neurology Clinic, Department of Internal Medicine, Kilimanjaro Christian Medical Centre, Moshi, United Republic of Tanzania
| | - Marieke C J Dekker
- Neurology Clinic, Department of Internal Medicine, Kilimanjaro Christian Medical Centre, Moshi, United Republic of Tanzania
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Ostermann J, Njau B, Hobbie A, Mtuy T, Masaki ML, Shayo A, van Zwetselaar M, Masnick M, Flaherty B, Brown DS, Mühlbacher AC, Thielman NM. Using discrete choice experiments to design interventions for heterogeneous preferences: protocol for a pragmatic randomised controlled trial of a preference-informed, heterogeneity-focused, HIV testing offer for high-risk populations. BMJ Open 2020; 10:e039313. [PMID: 33158826 PMCID: PMC7651730 DOI: 10.1136/bmjopen-2020-039313] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
INTRODUCTION Approximately one million undiagnosed persons living with HIV in Southern and Eastern Africa need to test for HIV. Novel approaches are necessary to identify HIV testing options that match the heterogeneous testing preferences of high-risk populations. This pragmatic randomised controlled trial (PRCT) will evaluate the efficacy of a preference-informed, heterogeneity-focused HIV counselling and testing (HCT) offer, for improving rates of HIV testing in two high-risk populations. METHODS AND ANALYSIS The study will be conducted in Moshi, Tanzania. The PRCT will randomise 600 female barworkers and 600 male Kilimanjaro mountain porters across three study arms. All participants will receive an HIV testing offer comprised of four preference-informed testing options, including one 'common' option-comprising features that are commonly available in the area and, on average, most preferred among study participants-and three options that are specific to the study arm. Options will be identified using mixed logit and latent class analyses of data from a discrete choice experiment (DCE). Participants in Arm 1 will be offered the common option and three 'targeted' options that are predicted to be more preferred than the common option and combine features widely available in the study area. Participants in Arm 2 will be offered the common option and three 'enhanced' options, which also include HCT features that are not yet widely available in the study area. Participants in Arm 3, an active control arm, will be offered the common option and three predicted 'less preferred' options. The primary outcome will be uptake of HIV testing. ETHICS AND DISSEMINATION Ethical approval was obtained from the Duke University Health System IRB, the University of South Carolina IRB, the Ethics Review Committee at Kilimanjaro Christian Medical University College, Tanzania's National Institute for Medical Research, and the Tanzania Food & Drugs Authority (now Tanzania Medicines & Medical Devices Authority). Findings will be published in peer-reviewed journals. The use of rigorous DCE methods for the preference-based design and tailoring of interventions could lead to novel policy options and implementation science approaches. TRIAL REGISTRATION NUMBER NCT02714140.
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Affiliation(s)
- Jan Ostermann
- Department of Health Services Policy & Management, University of South Carolina, Columbia, South Carolina, USA
- South Carolina Smart State Center for Healthcare Quality, University of South Carolina, Carolina, South Carolina, USA
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA
- Center for Health Policy & Inequalities Research, Duke University, Durham, North Carolina, USA
| | - Bernard Njau
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Amy Hobbie
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA
- Center for Health Policy & Inequalities Research, Duke University, Durham, North Carolina, USA
| | - Tara Mtuy
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
- Department of Global Health and Development, London School of Hygiene and Tropical Medicine, London, UK
| | | | - Aisa Shayo
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | | | - Max Masnick
- Selway Labs, LLC, Barrington, Rhode Island, USA
| | - Brian Flaherty
- Department of Psychology, University of Washington, Seattle, Washington, USA
| | - Derek S Brown
- Brown School, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Axel C Mühlbacher
- Center for Health Policy & Inequalities Research, Duke University, Durham, North Carolina, USA
- Institut Gesundheitsökonomie und Medizinmanagement, Hochschule Neubrandenburg, Neubrandenburg, Germany
- Department of Population Health Sciences, Duke University, Durham, North Carolina, USA
| | - Nathan M Thielman
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA
- Center for Health Policy & Inequalities Research, Duke University, Durham, North Carolina, USA
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10
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Kumburu HH, Sonda T, van Zwetselaar M, Leekitcharoenphon P, Lukjancenko O, Mmbaga BT, Alifrangis M, Lund O, Aarestrup FM, Kibiki GS. Using WGS to identify antibiotic resistance genes and predict antimicrobial resistance phenotypes in MDR Acinetobacter baumannii in Tanzania. J Antimicrob Chemother 2020; 74:1484-1493. [PMID: 30843063 PMCID: PMC6524488 DOI: 10.1093/jac/dkz055] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 12/11/2018] [Accepted: 01/16/2019] [Indexed: 11/25/2022] Open
Abstract
Background Reliable phenotypic antimicrobial susceptibility testing can be a challenge in clinical settings in low- and middle-income countries. WGS is a promising approach to enhance current capabilities. Aim To study diversity and resistance determinants and to predict and compare resistance patterns from WGS data of Acinetobacter baumannii with phenotypic results from classical microbiological testing at a tertiary care hospital in Tanzania. Methods and results MLST using Pasteur/Oxford schemes yielded eight different STs from each scheme. Of the eight, two STs were identified to be global clones 1 (n = 4) and 2 (n = 1) as per the Pasteur scheme. Resistance testing using classical microbiology determined between 50% and 92.9% resistance across all drugs. Percentage agreement between phenotypic and genotypic prediction of resistance ranged between 57.1% and 100%, with coefficient of agreement (κ) between 0.05 and 1. Seven isolates harboured mutations at significant loci (S81L in gyrA and S84L in parC). A number of novel plasmids were detected, including pKCRI-309C-1 (219000 bp) carrying 10 resistance genes, pKCRI-43-1 (34935 bp) carrying two resistance genes and pKCRI-49-1 (11681 bp) and pKCRI-28-1 (29606 bp), each carrying three resistance genes. New ampC alleles detected included ampC-69, ampC-70 and ampC-71. Global clone 1 and 2 isolates were found to harbour ISAba1 directly upstream of the ampC gene. Finally, SNP-based phylogenetic analysis of the A. baumannii isolates revealed closely related isolates in three clusters. Conclusions The validity of the use of WGS in the prediction of phenotypic resistance can be appreciated, but at this stage is not sufficient for it to replace conventional antimicrobial susceptibility testing in our setting.
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Affiliation(s)
- Happiness H Kumburu
- Kilimanjaro Christian Medical University College, Moshi, Tanzania.,Kilimanjaro Clinical Research Institute, Moshi, Tanzania.,Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Tolbert Sonda
- Kilimanjaro Christian Medical University College, Moshi, Tanzania.,Kilimanjaro Clinical Research Institute, Moshi, Tanzania.,Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | | | | | | | - Blandina T Mmbaga
- Kilimanjaro Christian Medical University College, Moshi, Tanzania.,Kilimanjaro Clinical Research Institute, Moshi, Tanzania.,Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Michael Alifrangis
- Centre for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen and Department of Infectious Diseases, Copenhagen University Hospital, Copenhagen, Denmark
| | - Ole Lund
- DTU-Bioinformatics, Technical University of Denmark, Copenhagen, Denmark
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11
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Nkya S, Mwita L, Mgaya J, Kumburu H, van Zwetselaar M, Menzel S, Mazandu GK, Sangeda R, Chimusa E, Makani J. Identifying genetic variants and pathways associated with extreme levels of fetal hemoglobin in sickle cell disease in Tanzania. BMC Med Genet 2020; 21:125. [PMID: 32503527 PMCID: PMC7275552 DOI: 10.1186/s12881-020-01059-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 05/24/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND Sickle cell disease (SCD) is a blood disorder caused by a point mutation on the beta globin gene resulting in the synthesis of abnormal hemoglobin. Fetal hemoglobin (HbF) reduces disease severity, but the levels vary from one individual to another. Most research has focused on common genetic variants which differ across populations and hence do not fully account for HbF variation. METHODS We investigated rare and common genetic variants that influence HbF levels in 14 SCD patients to elucidate variants and pathways in SCD patients with extreme HbF levels (≥7.7% for high HbF) and (≤2.5% for low HbF) in Tanzania. We performed targeted next generation sequencing (Illumina_Miseq) covering exonic and other significant fetal hemoglobin-associated loci, including BCL11A, MYB, HOXA9, HBB, HBG1, HBG2, CHD4, KLF1, MBD3, ZBTB7A and PGLYRP1. RESULTS Results revealed a range of genetic variants, including bi-allelic and multi-allelic SNPs, frameshift insertions and deletions, some of which have functional importance. Notably, there were significantly more deletions in individuals with high HbF levels (11% vs 0.9%). We identified frameshift deletions in individuals with high HbF levels and frameshift insertions in individuals with low HbF. CHD4 and MBD3 genes, interacting in the same sub-network, were identified to have a significant number of pathogenic or non-synonymous mutations in individuals with low HbF levels, suggesting an important role of epigenetic pathways in the regulation of HbF synthesis. CONCLUSIONS This study provides new insights in selecting essential variants and identifying potential biological pathways associated with extreme HbF levels in SCD interrogating multiple genomic variants associated with HbF in SCD.
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Affiliation(s)
- Siana Nkya
- Department of Biological Sciences, Dar es Salaam University College of Education, Dar es Salaam, Tanzania. .,Sickle Cell Program, Department of Hematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania.
| | - Liberata Mwita
- Sickle Cell Program, Department of Hematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Josephine Mgaya
- Sickle Cell Program, Department of Hematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Happiness Kumburu
- Department of Biotechnology Laboratory, Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
| | - Marco van Zwetselaar
- Department of Biotechnology Laboratory, Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
| | - Stephan Menzel
- Department of Molecular Hematology, King's College of London, London, UK
| | - Gaston Kuzamunu Mazandu
- Department of Pathology, Division of Human Genetics, University of Cape Town, IDM, Cape Town, South Africa. .,Department of Integrative Biomedical Sciences, Computational Biology Division, University of Cape Town, Observatory, 7925, South Africa. .,African Institute for Mathematical Sciences, Muizenberg, Cape Town, 7945, South Africa.
| | - Raphael Sangeda
- Sickle Cell Program, Department of Hematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania.,Department of Pharmaceutical Microbiology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Emile Chimusa
- Department of Pathology, Division of Human Genetics, University of Cape Town, IDM, Cape Town, South Africa
| | - Julie Makani
- Sickle Cell Program, Department of Hematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
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12
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Sonda TB, Horumpende PG, Kumburu HH, van Zwetselaar M, Mshana SE, Alifrangis M, Lund O, Aarestrup FM, Chilongola JO, Mmbaga BT, Kibiki GS. Ceftriaxone use in a tertiary care hospital in Kilimanjaro, Tanzania: A need for a hospital antibiotic stewardship programme. PLoS One 2019; 14:e0220261. [PMID: 31381579 PMCID: PMC6681960 DOI: 10.1371/journal.pone.0220261] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 07/11/2019] [Indexed: 12/12/2022] Open
Abstract
Excessive use of antibiotics, especially watch group antibiotics such as ceftriaxone leads to emergence and spread of antimicrobial resistance (AMR). In low and middle-income countries (LMICs), antibiotics are overused but data on consumption is scarcely available. We aimed at determining the extent and predictors of ceftriaxone use in a tertiary care university teaching hospital in Kilimanjaro, Tanzania. A hospital-based cross-sectional study was conducted from August 2013 through August 2015. Patients admitted in the medical, surgical wards and their respective intensive care units, receiving antimicrobials and other medications for various ailments were enrolled. Socio-demographic and clinical data were recorded in a structured questionnaire from patients' files and logistic regression was performed to determine the predictors for ceftriaxone use. Out of the 630 patients included in this study, 322 (51.1%) patients were on ceftriaxone during their time of hospitalization. Twenty-two patients out of 320 (6.9%) had been on ceftriaxone treatment without evidence of infection. Ceftriaxone use for surgical prophylaxis was 44 (40.7%), of which 32 (72.7%) and 9 (20.5%) received ceftriaxone prophylaxis before and after surgery, respectively. Three (6.8%) received ceftriaxone prophylaxis during surgery. Predicting factors for that the health facility administered ceftriaxone were identified as history of any medication use before referral to hospital [OR = 3.4, 95% CI (1.0-11.4), p = 0.047], bacterial infection [OR = 18.0, 95% CI (1.4-225.7, p = 0.025)], surgical ward [OR = 2.9, 95% CI (0.9-9.4), p = 0.078] and medical wards [OR = 5.0, 95% CI (0.9-28.3), p = 0.070]. Overall, a high ceftriaxone use at KCMC hospital was observed. Antimicrobial stewardship programs are highly needed to monitor and regulate hospital antimicrobial consumption, which in turn could help in halting the rising crisis of antimicrobial resistance.
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Affiliation(s)
- Tolbert B. Sonda
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Pius G. Horumpende
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania
- Department of Biochemistry and Molecular Biology, Kilimanjaro Christian Medical University College, Moshi, Tanzania
- Lugalo General Military Hospital, Military College of Medical Sciences, Dar es Salaam, Tanzania
| | - Happiness H. Kumburu
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Marco van Zwetselaar
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | | | - Michael Alifrangis
- Centre for Medical Parasitology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Ole Lund
- Centre for Biological Sequence Analysis, Technical University of Denmark; Copenhagen, Denmark
| | - Frank M. Aarestrup
- Centre for Genomic Epidemiology, Technical University of Denmark; Copenhagen, Denmark
| | - Jaffu O. Chilongola
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania
- Department of Biochemistry and Molecular Biology, Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Blandina T. Mmbaga
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania
- Department of Biochemistry and Molecular Biology, Kilimanjaro Christian Medical University College, Moshi, Tanzania
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13
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Horumpende PG, Sonda TB, van Zwetselaar M, Antony ML, Tenu FF, Mwanziva CE, Shao ER, Mshana SE, Mmbaga BT, Chilongola JO. Prescription and non-prescription antibiotic dispensing practices in part I and part II pharmacies in Moshi Municipality, Kilimanjaro Region in Tanzania: A simulated clients approach. PLoS One 2018; 13:e0207465. [PMID: 30462700 PMCID: PMC6248976 DOI: 10.1371/journal.pone.0207465] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 10/31/2018] [Indexed: 11/18/2022] Open
Abstract
Antibiotic dispensing without a prescription poses a threat to public health as it leads to excessive antibiotic consumption. Inappropriate antibiotic availability to the community has been documented to be amongst drivers of antimicrobial resistance emergence. Community pharmacies are a source of antibiotics in low and middle-income countries (LMICs). We aimed at assessing antibiotic dispensing practices by community pharmacy retailers in Moshi urban, Kilimanjaro, Tanzania and recommend interventions to improve practice. Using a Simulated Client (SC) Method, an observational cross-sectional survey of antibiotic dispensing practices was conducted from 10th June to 10th July 2017. Data analysis was done using Stata 13 (StataCorp, College Station, TX, USA). A total of 82 pharmacies were visited. Part I pharmacies were 26 (31.71%) and 56 (68.29%) were part II. Overall 92.3% (95% CI 77.8-97.6) of retailers dispensed antibiotics without prescriptions. The antibiotics most commonly dispensed without a prescription were ampiclox for cough (3 encounters) and azithromycin for painful urination (3 encounters). An oral third generation cephalosporin (cefixime) was dispensed once for painful urination without prescription by a part I pharmacy retailer. Out of 21, 15(71.43%) prescriptions with incomplete doses were accepted and had antibiotics dispensed. Out of 68, 4(5.9%) retailers gave instructions for medicine use voluntarily. None of the retailers voluntarily explained drug side-effects. In Moshi pharmacies, a high proportion of antibiotics are sold and dispensed without prescriptions. Instructions for medicine use are rarely given and none of the retailers explain side effects. These findings support the need for a legislative enforcement of prescription-only antibiotic dispensing rules and regulations. Initiation of clinician and community antibiotic stewardship and educational programs on proper antibiotic use to both pharmacists and public by the regulatory bodies are highly needed.
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Affiliation(s)
- Pius G. Horumpende
- Department of Biochemistry and Molecular Biology, Kilimanjaro Christian Medical University College, Moshi, Tanzania
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
- Department of Preventive Medicine and Research, Lugalo General Military Hospital and Military College of Medical Sciences (MCMS), Dar es Salaam, Tanzania
| | - Tolbert B. Sonda
- Department of Biochemistry and Molecular Biology, Kilimanjaro Christian Medical University College, Moshi, Tanzania
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
| | | | - Magreth L. Antony
- Section of HIV Viral Load and Early Infant Diagnostics, National Health Laboratory Quality Assurance and Training Centre, Dar es Salaam, Tanzania
| | - Filemon F. Tenu
- Department of Biochemistry and Molecular Biology, Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Charles E. Mwanziva
- Department of Preventive Medicine and Research, Lugalo General Military Hospital and Military College of Medical Sciences (MCMS), Dar es Salaam, Tanzania
| | - Elichilia R. Shao
- Department of Biochemistry and Molecular Biology, Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Stephen E. Mshana
- Department of Microbiology and Immunology, Catholic University of Health and Allied Sciences, Mwanza, Tanzania
| | | | - Jaffu O. Chilongola
- Department of Biochemistry and Molecular Biology, Kilimanjaro Christian Medical University College, Moshi, Tanzania
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
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Sonda T, Kumburu H, van Zwetselaar M, Alifrangis M, Mmbaga BT, Lund O, Kibiki GS, Aarestrup FM. Molecular epidemiology of virulence and antimicrobial resistance determinants in Klebsiella pneumoniae from hospitalised patients in Kilimanjaro, Tanzania. Eur J Clin Microbiol Infect Dis 2018; 37:1901-1914. [PMID: 30030694 DOI: 10.1007/s10096-018-3324-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 07/09/2018] [Indexed: 11/30/2022]
Abstract
This study aimed to use whole-genome sequencing to determine virulence and antimicrobial resistance genes in K. pneumoniae isolated from patients in a tertiary care hospital in Kilimanjaro. K. pneumoniae isolates from patients attending Kilimanjaro Christian Medical Centre between August 2013 and August 2015 were fully genome-sequenced and analysed locally. Sequence analysis was done for identification of virulence and AMR genes. Plasmid and multi-locus sequence typing and capsular or capsular (K) typing were performed and phylogeny was done to ascertain K. pneumoniae relatedness. Stata 13 (College Station, TX, 77845, USA) was used to determine Cohen's kappa coefficient of agreement between the phenotypically tested and sequence-predicted resistance. A total of 16 (47.1%) sequence types (STs) and 10 (29.4%) K types were identified in 30 (88.2%) and 17 (50.0%) of all analysed isolates, respectively. K. pneumoniae ST17 were 6 (17.6%). The commonest determinants were blaCTX-M-15 in 16 (47.1%) isolates, blaSHV in 30 (88.2%), blaOXA-1 in 8 (23.5%) and blaTEM-1 in 18 (52.9%) isolates. Resistance genes for aminoglycosides were detected in 21 (61.8%) isolates, fluoroquinolones in 13 (38.2%) and quinolones 34 (100%). Ceftazidime and ceftriaxone showed the strongest agreement between phenotype- and sequence-based resistance results: 93.8%, kappa = 0.87 and p = 0.0002. Yersiniabactin determinant was detected in 12 (35.3%) of K. pneumoniae. The proportion of AMR and virulence determinants detected in K. pneumoniae is alarming. WGS-based diagnostic approach has showed promising potentials in clinical microbiology, hospital outbreak source tracing virulence and AMR detection at KCMC.
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Affiliation(s)
- Tolbert Sonda
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania. .,Kilimanjaro Christian Medical University College, Moshi, Tanzania.
| | - Happiness Kumburu
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania.,Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Marco van Zwetselaar
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Michael Alifrangis
- Centre for Medical Parasitology, Department of Immunology and Microbiology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Blandina T Mmbaga
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania.,Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Ole Lund
- Centre for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
| | - Gibson S Kibiki
- Kilimanjaro Christian Medical University College, Moshi, Tanzania.,East African Health Research Commission, Bujumbura, Burundi
| | - Frank M Aarestrup
- DTU-Food, Centre for Genomic Epidemiology, Technical University of Denmark, Lyngby, Denmark
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15
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Sonda T, Kumburu H, van Zwetselaar M, Alifrangis M, Mmbaga BT, Aarestrup FM, Kibiki G, Lund O. Whole genome sequencing reveals high clonal diversity of Escherichia coli isolated from patients in a tertiary care hospital in Moshi, Tanzania. Antimicrob Resist Infect Control 2018; 7:72. [PMID: 29977533 PMCID: PMC5992844 DOI: 10.1186/s13756-018-0361-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 05/22/2018] [Indexed: 01/06/2023] Open
Abstract
Background Limited information regarding the clonality of circulating E. coli strains in tertiary care hospitals in low and middle-income countries is available. The purpose of this study was to determine the serotypes, antimicrobial resistance and virulence genes. Further, we carried out a phylogenetic tree reconstruction to determine relatedness of E. coli isolated from patients in a tertiary care hospital in Tanzania. Methods E. coli isolates from inpatients admitted at Kilimanjaro Christian Medical Centre between August 2013 and August 2015 were fully genome-sequenced at KCMC hospital. Sequence analysis was done for identification of resistance genes, Multi-Locus Sequence Typing, serotyping, and virulence genes. Phylogeny reconstruction using CSI Phylogeny was done to ascertain E. coli relatedness. Stata 13 (College Station, Texas 77,845 USA) was used to determine Cohen's kappa coefficient of agreement between the phenotypically tested and whole genome sequence predicted antimicrobial resistance. Results Out of 38 E. coli isolates, 21 different sequence types (ST) were observed. Eight (21.1%) isolates belonged to ST131; of which 7 (87.5.%) were serotype O25:H4. Ten (18.4%) isolates belonged to ST10 clonal complex; of these, four (40.0%) were ST617 with serotype O89:H10. Twenty-eight (73.7%) isolates carried genes encoding beta-lactam resistance enzymes. On average, agreement across all drugs tested was 83.9%. Trimethoprim/sulphamethoxazole (co-trimoxazole) showed moderate agreement: 45.8%, kappa =15% and p = 0.08. Amoxicillin-clavulanate showed strongest agreement: 87.5%, kappa = 74% and p = 0.0001. Twenty-two (57.9%) isolates carried virulence factors for host cells adherence and 25 (65.7%) for factors that promote E. coli immune evasion by increasing survival in serum. The phylogeny analysis showed that ST131 clustering close together whereas ST10 clonal complex had a very clear segregation of the ST617 and a mix of the rest STs. Conclusion There is a high diversity of E. coli isolated from patients admitted to a tertiary care hospital in Tanzania. This underscores the necessity to routinely screen all bacterial isolates of clinical importance in tertiary health care facilities. WGS use for laboratory-based surveillance can be an effective early warning system for emerging pathogens and resistance mechanisms in LMICs.
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Affiliation(s)
- Tolbert Sonda
- 1Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania.,2Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Happiness Kumburu
- 1Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania.,2Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Marco van Zwetselaar
- 1Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Michael Alifrangis
- Centre for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen and Department of Infectious Diseases, Copenhagen University Hospital, Copenhagen, Denmark
| | - Blandina T Mmbaga
- 1Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania.,2Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | | | - Gibson Kibiki
- 2Kilimanjaro Christian Medical University College, Moshi, Tanzania.,East African Health Research Commission, Bujumbura, Burundi
| | - Ole Lund
- 5Centre for Biological Sequence Analysis, Technical University of Denmark, Copenhagen, Denmark
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van Zwetselaar M, Nyombi B, Sonda T, Kumburu H, Chamba N, Dekker MCJ, Kilonzo KG, Urasa SJ, Mmbaga BT. Aeromonas caviae mimicking Vibrio cholerae infectious enteropathy in a cholera-endemic region with possible public health consequences: two case reports. J Med Case Rep 2018; 12:71. [PMID: 29548295 PMCID: PMC5857081 DOI: 10.1186/s13256-018-1603-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 02/02/2018] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Aeromonas species have been documented to yield false positive results in microbiological tests for Vibrio cholerae. They share many biochemical properties with Vibrio species, with which they were jointly classified in the family Vibrionaceae until genotypic information provided new insights. Aeromonas species are increasingly associated with gastrointestinal infections, albeit with great apparent variation in pathogenicity and virulence both between and within species of the genus. We report two cases with clinically mild cholera-like symptoms, at a time when a cholera outbreak was unfolding in other regions of the country (Tanzania). These are the first cases to be reported with Aeromonas mimicking cholera in our area. CASE PRESENTATION Two patients were admitted at the isolation unit designated by the Kilimanjaro Christian Medical Centre for emerging infectious diseases and provided informed consent about regular stool analysis and culture under the provisional diagnosis of gastroenteritis. The first patient was a 23-year-old black African woman with a 2-day history of watery diarrhea and vomiting associated with a temperature of 39.7 °C. The second patient was a 47-year-old black African woman with a 2-day history of diarrhea and vomiting with a temperature of 37.7 °C, and she was hemodynamically stable. Both patients were isolated in a specific area for infection control and treated with fluids and orally administered rehydration solution, ciprofloxacin, metronidazole, and paracetamol. Stool culture was done. The isolated colonies were reported as V. cholerae and transferred to the research laboratory of Kilimanjaro Clinical Research Institute for confirmation using whole genome sequencing. Microbiological testing determined colonies isolated from stool to be V. cholerae, and warranted the conclusion "presumptive cholera." Whole genome sequencing, however, established the presence of Aeromonas caviae rather than V. cholerae. CONCLUSIONS The co-existence of Aeromonas species with V. cholerae in cholera-endemic regions suggests the possibility that a proportion of suspected cholera cases may be Aeromonas infections. However, with close to no epidemiological data available on Aeromonas infection in cases of diarrhea and dysentery in Sub-Saharan Africa, it is not currently possible to establish the extent of misdiagnosis to any degree of certainty. Whole genome sequencing was shown to readily exclude V. cholerae as the etiological agent and establish the presence of Aeromonas species.
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Affiliation(s)
- Marco van Zwetselaar
- Kilimanjaro Clinical Research Institute, Moshi, Kilimanjaro United Republic of Tanzania
| | - Balthazar Nyombi
- 0000 0004 0648 072Xgrid.415218.bKilimanjaro Christian Medical Centre, Moshi, Kilimanjaro United Republic of Tanzania ,0000 0004 0648 0439grid.412898.eKilimanjaro Christian Medical University College, Moshi, United Republic of Tanzania
| | - Tolbert Sonda
- Kilimanjaro Clinical Research Institute, Moshi, Kilimanjaro United Republic of Tanzania ,0000 0004 0648 0439grid.412898.eKilimanjaro Christian Medical University College, Moshi, United Republic of Tanzania
| | - Happiness Kumburu
- Kilimanjaro Clinical Research Institute, Moshi, Kilimanjaro United Republic of Tanzania ,0000 0004 0648 0439grid.412898.eKilimanjaro Christian Medical University College, Moshi, United Republic of Tanzania
| | - Nyasatu Chamba
- 0000 0004 0648 072Xgrid.415218.bKilimanjaro Christian Medical Centre, Moshi, Kilimanjaro United Republic of Tanzania
| | - Marieke C. J. Dekker
- 0000 0004 0648 072Xgrid.415218.bKilimanjaro Christian Medical Centre, Moshi, Kilimanjaro United Republic of Tanzania
| | - Kajiru G. Kilonzo
- 0000 0004 0648 072Xgrid.415218.bKilimanjaro Christian Medical Centre, Moshi, Kilimanjaro United Republic of Tanzania ,0000 0004 0648 0439grid.412898.eKilimanjaro Christian Medical University College, Moshi, United Republic of Tanzania
| | - Sarah J. Urasa
- 0000 0004 0648 072Xgrid.415218.bKilimanjaro Christian Medical Centre, Moshi, Kilimanjaro United Republic of Tanzania ,0000 0004 0648 0439grid.412898.eKilimanjaro Christian Medical University College, Moshi, United Republic of Tanzania
| | - Blandina T. Mmbaga
- Kilimanjaro Clinical Research Institute, Moshi, Kilimanjaro United Republic of Tanzania ,0000 0004 0648 072Xgrid.415218.bKilimanjaro Christian Medical Centre, Moshi, Kilimanjaro United Republic of Tanzania ,0000 0004 0648 0439grid.412898.eKilimanjaro Christian Medical University College, Moshi, United Republic of Tanzania
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17
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Sonda T, Kumburu H, van Zwetselaar M, Alifrangis M, Mmbaga BT, Lund O, Aarestrup FM, Kibiki G. Prevalence and risk factors for CTX-M gram-negative bacteria in hospitalized patients at a tertiary care hospital in Kilimanjaro, Tanzania. Eur J Clin Microbiol Infect Dis 2018; 37:897-906. [PMID: 29464424 PMCID: PMC5917002 DOI: 10.1007/s10096-018-3196-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 01/18/2018] [Indexed: 12/19/2022]
Abstract
Emergence and spread of extended spectrum beta-lactamase (ESBL)-producing gram-negative bacteria, mainly due to CTX-M, is a major global public health problem. Patients infected with ESBL-producing gram-negative bacteria have an increased risk of treatment failure and death. We investigated the prevalence and risk factors for CTX-M gram-negative bacteria isolated from clinical specimens of patients hospitalized at a tertiary care hospital in Kilimanjaro, Tanzania. Isolated gram-negative bacteria from inpatients admitted at Kilimanjaro Christian Medical Centre (KCMC) between August 2013 and August 2015 were fully genome sequenced. The prevalence of ESBL-producing gram-negative bacteria was determined based on the presence of blaCTX-M. The odds ratio (OR) and risk factors for ESBL-producing gram-negative bacteria due to CTX-M were assessed using logistic regression models. The overall CTX-M prevalence (95% CI) was 13.6% (10.1–18.1). Adjusted for other factors, the OR of CTX-M gram-negative bacteria for patients previously hospitalized was 0.26 (0.08–0.88), p = 0.031; the OR for patients currently on antibiotics was 4.02 (1.29–12.58), p = 0.017; the OR for patients currently on ceftriaxone was 0.14 (0.04–0.46), p = 0.001; and the OR for patients with wound infections was 0.24 (0.09–0.61), p = 0.003. The prevalence of ESBL-producing gram-negative bacteria due to CTX-M in this setting is relatively low compared to other previous reports in similar settings. However, to properly stop further spread in the hospital, we recommend setting up a hospital surveillance system that takes full advantage of the available next-generation sequencing facility to routinely screen for all types of bacterial resistance genes.
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Affiliation(s)
- Tolbert Sonda
- Kilimanjaro Christian Medical Centre, Kilimanjaro Clinical Research Institute, Moshi, Tanzania. .,Kilimanjaro Christian Medical University College, Moshi, Tanzania.
| | - Happiness Kumburu
- Kilimanjaro Christian Medical Centre, Kilimanjaro Clinical Research Institute, Moshi, Tanzania.,Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Marco van Zwetselaar
- Kilimanjaro Christian Medical Centre, Kilimanjaro Clinical Research Institute, Moshi, Tanzania
| | - Michael Alifrangis
- Centre for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark.,Department of Infectious Diseases, Copenhagen University Hospital, Copenhagen, Denmark
| | - Blandina T Mmbaga
- Kilimanjaro Christian Medical Centre, Kilimanjaro Clinical Research Institute, Moshi, Tanzania.,Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Ole Lund
- Centre for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
| | - Frank M Aarestrup
- DTU-Food, Centre for Genomic Epidemiology, Technical University of Denmark, Lyngby, Denmark
| | - Gibson Kibiki
- Kilimanjaro Christian Medical University College, Moshi, Tanzania.,East African Health Research Commission, Bujumbura, Burundi
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18
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Sonda T, Kumburu H, van Zwetselaar M, Alifrangis M, Lund O, Kibiki G, Aarestrup FM. Meta-analysis of proportion estimates of Extended-Spectrum-Beta-Lactamase-producing Enterobacteriaceae in East Africa hospitals. Antimicrob Resist Infect Control 2016; 5:18. [PMID: 27186369 PMCID: PMC4868002 DOI: 10.1186/s13756-016-0117-4] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 05/09/2016] [Indexed: 01/16/2023] Open
Abstract
Background A high proportion of Extended-Spectrum-Beta-Lactamase (ESBL) producing Enterobacteriaceae is causing common infections in all regions of the world. The burden of antibiotic resistance due to ESBL in East Africa is large but information is scarce and thus it is unclear how big the problem really is. To gain insight into the magnitude and molecular epidemiology of ESBL-producing Enterobacteriaceae in East Africa a literature search was performed in PubMed on 31 July 2015 to retrieve articles with relevant information on ESBL. Methods and results Meta-analysis was performed to determine overall proportion estimate of ESBL-producing Enterobacteriaceae. A total of 4076 bacterial isolates were included in the analysis. The overall pooled proportion of ESBL-producing Enterobacteriaceae among included surveys done in East African hospitals was found to be 0.42 (95 % CI: 0.34–0.50). Heterogeneity (I2) between countries’ proportions in ESBL was significantly high (96.95 % and p < 0.001). The frequently detected genes encoding ESBL were CTX-M, TEM, SHV and OXA while the most infrequent reported genes were KPC and NDM. Conclusion The available studies show a very wide variation in resistance due to ESBL between countries. This highlights a need for active surveillance systems which can help understand the actual epidemiology of ESBL, aid in formulating national or regional guidelines for proper screening of ESBL, and support developing standardized approaches for managing patients colonized with ESBL. Electronic supplementary material The online version of this article (doi:10.1186/s13756-016-0117-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tolbert Sonda
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania ; Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Happiness Kumburu
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania ; Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Marco van Zwetselaar
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Michael Alifrangis
- Centre for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark ; Department of Infectious Diseases, Copenhagen University Hospital, Copenhagen, Denmark
| | - Ole Lund
- Centre for Biological Sequence Analysis, Technical University of Denmark, Copenhagen, Denmark
| | - Gibson Kibiki
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania ; Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Frank M Aarestrup
- Centre for Genomic Epidemiology, Technical University of Denmark, Copenhagen, Denmark
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19
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Kavishe RA, Paulo P, Kaaya RD, Kalinga A, van Zwetselaar M, Chilongola J, Roper C, Alifrangis M. Surveillance of artemether-lumefantrine associated Plasmodium falciparum multidrug resistance protein-1 gene polymorphisms in Tanzania. Malar J 2014; 13:264. [PMID: 25007802 PMCID: PMC4099215 DOI: 10.1186/1475-2875-13-264] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 07/07/2014] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Resistance to anti-malarials is a major public health problem worldwide. After deployment of artemisinin-based combination therapy (ACT) there have been reports of reduced sensitivity to ACT by malaria parasites in South-East Asia. In Tanzania, artemether-lumefantrine (ALu) is the recommended first-line drug in treatment of uncomplicated malaria. This study surveyed the distribution of the Plasmodium falciparum multidrug resistance protein-1 single nucleotide polymorphisms (SNPs) associated with increased parasite tolerance to ALu, in Tanzania. METHODS A total of 687 Plasmodium falciparum positive dried blood spots on filter paper and rapid diagnostic test strips collected by finger pricks from patients attending health facilities in six regions of Tanzania mainland between June 2010 and August 2011 were used. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique was used to detect Pfmdr1 SNPs N86Y, Y184F and D1246Y. RESULTS There were variations in the distribution of Pfmdr1 polymorphisms among regions. Tanga region had exceptionally high prevalence of mutant alleles, while Mbeya had the highest prevalence of wild type alleles. The haplotype YFY was exclusively most prevalent in Tanga (29.6%) whereas the NYD haplotype was the most prevalent in all other regions. Excluding Tanga and Mbeya, four, most common Pfmdr1 haplotypes did not vary between the remaining four regions (χ² = 2.3, p = 0.512). The NFD haplotype was the second most prevalent haplotype in all regions, ranging from 17% - 26%. CONCLUSION This is the first country-wide survey on Pfmdr1 mutations associated with ACT resistance. Distribution of individual Pfmdr1 mutations at codons 86, 184 and 1246 varies throughout Tanzanian regions. There is a general homogeneity in distribution of common Pfmdr1 haplotypes reflecting strict implementation of ALu policy in Tanzania with overall prevalence of NFD haplotype ranging from 17 to 26% among other haplotypes. With continuation of ALu as first-line drug this haplotype is expected to keep rising, thus there is need for continued pharmacovigilance studies to monitor any delayed parasite clearance by the drug.
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Affiliation(s)
- Reginald A Kavishe
- Kilimanjaro Christian Medical University College and Kilimanjaro Clinical Research Institute, Moshi, Tanzania.
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20
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Mohammed A, Ndaro A, Kalinga A, Manjurano A, Mosha JF, Mosha DF, van Zwetselaar M, Koenderink JB, Mosha FW, Alifrangis M, Reyburn H, Roper C, Kavishe RA. Trends in chloroquine resistance marker, Pfcrt-K76T mutation ten years after chloroquine withdrawal in Tanzania. Malar J 2013; 12:415. [PMID: 24225406 PMCID: PMC3830541 DOI: 10.1186/1475-2875-12-415] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 11/11/2013] [Indexed: 12/22/2022] Open
Abstract
Background Plasmodium falciparum resistance to anti-malarial drugs remains a major obstacle to the control of malaria. In 2001 Tanzania replaced chloroquine (CQ) with sulphadoxine-pyrimethamine (SP) as first-line drug, which in turn was replaced by artemisinin combination therapy in 2006. SP has however, continued to be used in intermittent preventive treatment of malaria in pregnancy (IPTp) despite reports of high levels of resistance to SP due to the lack of alternatives to SP for IPTp. Recent reports have indicated recovery of CQ-susceptibility in Malawi, Kenya, Mozambique, and Tanzania based on the prevalence of wild types at codon 76 of the Pfcrt gene in indigenous P. falciparum populations. The current prevalence of this Pfcrt-76 CQ resistance marker from six regions of Tanzania mainland is hereby reported. Methods DNA extracted from filter-paper dried blood spots and rapid diagnostics kit strips collected from finger-prick blood were used to genotype the Pfcrt-76 resistance marker using PCR-RFLP. Data from previously published studies were used to generate CQ susceptibility recovery trends using logistic regression model. Results Seven hundred and forty one (741) samples were genotyped. The current frequency of the CQ-susceptible Pfcrt-K76 was above 92% and did not differ between regions in Tanzania (χ2 = 2.37; p = 0.795). The K76 allelic prevalence was between 85.7 and 93% in regions (χ2 = 7.88, p = 0.163). The CQ resistance recovery trends showed regional variability that may be caused by differences in malaria transmission intensity, but overall the trends converge as the susceptibility levels in all regions approach >90%. Conclusions CQ withdrawal in Tanzania has resulted into >90% recovery of susceptibility in ten years of withdrawal. These findings are in support of the search for CQ-based combination drugs as a possible future alternative to SP for IPTp in places where full recovery of CQ-susceptibility will be evident.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Reginald A Kavishe
- Kilimanjaro Christian Medical University College and Kilimanjaro Clinical Research Institute, Moshi, Tanzania.
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