1. Analysis of Escherichia coli STs and resistance mechanisms in sewage from Islamabad, Pakistan indicates a difference in E. coli carriage types between South Asia and Europe.
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Zahra, Rabaab, Javeed, Saba, Malala, Bibi, Babenko, Dmitriy, and Toleman, Mark A.
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MICROBIAL virulence , *URINARY tract infections , *DRUG resistance in microorganisms , *PATHOGENIC microorganisms , *BETA lactamases , *BACTERIAL proteins , *BACTERIOPHAGE typing , *COMPARATIVE studies , *ESCHERICHIA coli , *GENES , *GENOMES , *HYDROLASES , *RESEARCH methodology , *MEDICAL cooperation , *MICROBIAL sensitivity tests , *PULSED-field gel electrophoresis , *RESEARCH , *SEWAGE , *TOXINS , *EVALUATION research , *SEQUENCE analysis - Abstract
Objectives: To discover the Escherichia coli STs and associated resistance mechanisms in the community in Islamabad, Pakistan by analysis of E. coli isolates in sewage.Methods: One hundred and ten E. coli were isolated from sewage across the city of Islamabad without antibiotic bias and confirmed as E. coli by MALDI-TOF MS. Isolates were characterized by fumC/fimH (CH) typing and core-genome MLST. Resistance mechanisms, virulence genes, phylotypes and plasmid incompatibility types were determined in a subset of isolates by in silico analysis. The genomic position of blaCTX-M-15 was determined using S1-PFGE, probing and Nanopore MinION sequencing.Results and conclusions: The most prevalent STs were ST394, ST10 and ST648, accounting for 39% of all isolates collected and were found at many sites across Islamabad. Carbapenemase genes were absent and only a single isolate of ST131 was found. The most prevalent resistance mechanisms were qnrS1 and blaCTX-M-15, with blaCTX-M-15 penetrating many STs and found in 31% of all collected isolates. However, the majority of the successful STs were blaCTX-M-15 negative indicating that resistance is not the main driver of prevalence. Twenty-three percent of blaCTX-M-15 genes were chromosomally encoded and large ISEcp1-mediated insertions included qnrS1 and several plasmid genes. In all chromosomally encoded isolates no plasmid copies of blaCTX-M-15 were found. The most prevalent ST (ST394) contained many enteroaggregative E. coli virulence genes and the fimH30 variant allele previously linked to the success of ST131. [ABSTRACT FROM AUTHOR]- Published
- 2018
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