ArticleBMC medical genomics2024
Short reads-based characterization of pathotype diversity and drug resistance among Escherichia coli isolated from patients attending regional referral hospitals in Tanzania.
Article in BMC medical genomics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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8 citing papers in PubMed, 9 citations in OpenAlex.
- One health analysis of antimicrobial resistance inBioinformatics advances · 2026Article
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- Genomic insight into the high-risk hypervirulent multidrug resistant enteroaggregative-hemorrhagicGene reports · 2025Article
- Genomic epidemiology of extended-spectrum beta-lactamase-producingMicrobial genomics · 2025Article
- Article
- Quantitative real-time PCR analysis of gut microbiota in rheumatoid arthritis patients compared to healthy controls.AMB Express · 2024Article
- Developing the PIP-eco: An integrated genomic pipeline for identification and characterization ofComputational and structural biotechnology journal · 2024Article
- Population structure and antibiotic resistance of swine extraintestinal pathogenic Escherichia coli from China.Nature communications · 2024Article
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Authors and funding
12 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundEscherichia 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.
objectiveTo determine the pathotype diversity and antimicrobial resistance among E. coli from patients attending regional referral hospitals in Tanzania. MATERIALS AND
methodsA 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.
resultsAmong 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.
conclusionWhole 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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