Characterization of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli Isolates from Jurong Lake, Singapore with Whole-Genome-Sequencing.

Siyao Guo,Yang Zhong,Joergen Schlundt,Kelyn Lee Ghee Seow,Glendon Ong Hong Ming

doi:10.3390/ijerph18030937

Abstract

Background: The fast-spreading of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli (ESBL-producing E. coli) and ESBL genes has become a big challenge to public health. The risk of spreading ESBL genes and pathogens in the environment and community has raised public health concern. The characterizing and whole-genome sequencing studies of ESBL-producing bacteria from reservoir water in Singapore is still limited. Materials and methods: The reservoir water sample was taken from two randomly selected sampling points of the Chinese Garden (Jurong river reservoir), which is a popular reservoir park in Singapore. The bacteria of the water sample were collected with 0.45 µm filter membranes and enriched before processing with ESBL-producing E. coli screening. The collected ESBL positive isolates were further characterized by both phenotypic tests including disc diffusion and microdilution Minimum Inhibitory Concentration (MIC) test, and also genotypic test as whole-genome sequencing analysis. Besides, to investigate the transferability of the resistance gene, a conjugation test was performed with the J53 E. coli strain as the gene receptor. Result: Nine ESBL-producing E. coli isolates were collected and confirmed as ESBL-producing with both phenotypic and genotypic tests. A potential pathogen as ST131 clade A isolate was identified, and all isolates were determined to harbor a blaCTX-M gene. Among them, strain J1E4 was resistant to polymyxin E and confirmed to harboring a conjugatable mcr-1 gene. Further genetic environment analysis has reflected a conversed gene cluster formed by insert sequence (IS), blaCTX-M-15, and WbuC family cupin-fold metalloprotein, which may potentially jump from the plasmids to the chromosome. Conclusion: The first time we reported the whole genome sequencing (WGS) data of ESBL-producing E. coli including potential pathogen (ST131) present in reservoir water in Singapore. The ESBL-producing E. coli from reservoir water also carrying conjugatable colistin resistance genes which may become a risk to human health.

Highlights

Extended-Spectrum Beta-Lactamase (ESBL)-producing Enterobacteriaceae has become a big challenge to infection control due to their resistance to most of the betalactams
ESBL-producing bacteria are frequently reported to carry multi-drug resistance (MDR), which limits the options of antimicrobials to treat infections caused by them [2]
This study aims towards a genetic characterization of ESBLproducing E. coli from reservoir water, further, investigate their phylogenetic relationship with isolates from humans, report the acquired ESBL genes as well as other resistance genes harbored by the isolates, predict the transferability of the Antimicrobial Resistance (AMR) genes with sequencing data

Summary

Introduction

Extended-Spectrum Beta-Lactamase (ESBL)-producing Enterobacteriaceae has become a big challenge to infection control due to their resistance to most of the betalactams. The ESBL can hydrolyze the most commonly used penicillin, monobactam, and cephalosporin including the 3rd generation [1]. ESBL-producing bacteria are frequently reported to carry multi-drug resistance (MDR), which limits the options of antimicrobials to treat infections caused by them [2]. The prevalence of ESBL-E. coli is increasing fast worldwide, especially some prevalent sequencing types like ST131. A study from Europe in 2018 has reported a fraction of 20.5% of ST131 among the ESBL-producing. E. coli from four European hospitals [3]. As the situation gains importance, a higher requirement of sequencing information for deeper genetic alignment of the ESBL-producing

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