Short reads-based characterization of pathotype diversity and drug resistance among Escherichia coli isolated from patients attending regional referral hospitals in Tanzania

Author:

Kanje Livin E.,Kumburu Happiness,Kuchaka Davis,Shayo Mariana,Juma Masoud A.,Kimu Patrick,Beti Melkiory,van Zwetselaar Marco,Wadugu Boaz,Mmbaga Blandina T.,Mkumbaye Sixbert Isdory,Sonda Tolbert

Abstract

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.

Funder

SeqAfrica project under the Department of Health and Social Care’s Fleming Fund using UK aid.

Publisher

Springer Science and Business Media LLC

Reference42 articles.

1. Robbens J, Devriese L, Verstraete K, Heyndrickx M. Escherichia coli. Encycl Toxicol. Third Edit. Elsevier; 2014. pp. 459–61.

2. Kotloff KL, Nataro JP, Blackwelder WC, Nasrin D, Farag TH, Panchalingam S et al. Burden and aetiology of diarrhoeal disease in infants and young children in developing countries (the Global Enteric Multicenter Study, GEMS): a prospective, case-control study. Lancet [Internet]. 2013;382:209–22. https://doi.org/10.1016/S0140-6736(13)60844-2.

3. Moyo SJ, Aboud S, Kasubi M, Lyamuya EF, Maselle SY. Antimicrobial resistance among producers and non-producers of extended spectrum beta-lactamases in urinary isolates at a tertiary Hospital in Tanzania. BMC Res Notes [Internet]. 2010;3:348. https://bmcresnotes.biomedcentral.com/articles/https://doi.org/10.1186/1756-0500-3-348.

4. Gidabayda J, Philemon R, Abdallah M, Saajan A, Temu T, Kunjumu I et al. Prevalence, Aetiology, and Antimicrobial Susceptibility Patterns of Urinary Tract Infection Amongst Children Admitted at Kilimanjaro Christian Medical Centre, Moshi, Tanzania. East African Heal Res J. 2017;1:53–61. http://www.eac.int/sites/default/files/docs/eahrj_i1v1_0.pdf.

5. Ngowi BN, Sunguya B, Herman A, Chacha A, Maro E, Rugarabamu LF et al. Prevalence of Multidrug Resistant UTI Among People Living with HIV in Northern Tanzania. Infect Drug Resist [Internet]. 2021;Volume 14:1623–33. https://www.dovepress.com/prevalence-of-multidrug-resistant-uti-among-people-living-with-hiv-in--peer-reviewed-fulltext-article-IDR.

Cited by 2 articles. 订阅此论文施引文献 订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献

同舟云学术

1.学者识别学者识别

2.学术分析学术分析

3.人才评估人才评估

"同舟云学术"是以全球学者为主线,采集、加工和组织学术论文而形成的新型学术文献查询和分析系统,可以对全球学者进行文献检索和人才价值评估。用户可以通过关注某些学科领域的顶尖人物而持续追踪该领域的学科进展和研究前沿。经过近期的数据扩容,当前同舟云学术共收录了国内外主流学术期刊6万余种,收集的期刊论文及会议论文总量共计约1.5亿篇,并以每天添加12000余篇中外论文的速度递增。我们也可以为用户提供个性化、定制化的学者数据。欢迎来电咨询!咨询电话:010-8811{复制后删除}0370

www.globalauthorid.com

TOP

Copyright © 2019-2024 北京同舟云网络信息技术有限公司
京公网安备11010802033243号  京ICP备18003416号-3