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

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.

Antimicrobial Resistance Genes in ESBL-Producing Escherichia coli Isolates from Animals in Greece

“…PMQR genes qnrS, qnrB, or both were identified in 5 out of the 11 fluoroquinolone resistant and in one fluoroquinolone susceptible ESBL-producing strains and were the gene family least frequently detected. Similarly, low PMQR detection rates have been reported in isolates obtained from cattle feces in Canada [61] and from lake water in Singapore [62]. The only study from Greece that has formerly identified concurrent presence of a qnr variant (qnrS1) with an ESBL gene (bla CTX-M-15 ) refers to a human E. coli isolate [63].…”

Arrangements of Mobile Genetic Elements among Virotype E Subpopulation of Escherichia coli Sequence Type 131 Strains with High Antimicrobial Resistance and Virulence Gene Content

“…Diverse bla CTX-M-15 genetic environments have been reported among E. coli isolated all over the world ( 20 ). Structures containing the intact IS Ecp1 , followed by bla CTX-M-15 and reversed WbuC cupin fold metalloprotein, have been identified in many different species ( 21 ).…”

“…First, it encodes a transposase that facilitates CTX-M-15 mobilization, and second, it promotes the weakly expression state of this ESBL gene by playing as a promoter ( 24 ). A histidine residue as a metal-binding ligand was identified in the WbuC family protein and has been reported to relate to O-antigen biosynthesis ( 20 ). The other RAST (Rapid Annotation using Subsystem Technology) annotation of the WbuC gene at this position was tryptophane synthase, due to the similar sequence protein that has been reported in Klebsiella spp.…”

“…The other RAST (Rapid Annotation using Subsystem Technology) annotation of the WbuC gene at this position was tryptophane synthase, due to the similar sequence protein that has been reported in Klebsiella spp. ( 20 ). Varied roles of WbuC have been attributed to this metalloprotein among different species; however, its specific function here with bla CTX-M-15 needs to be studied further.…”

The complete genome of carbapenem-resistant Escherichia coli ST410 harbored blaNDM-5 isolated from reservoir water in Singapore

“…Two integrases IntI leading gene cassette were detected on the upstream and downstream of bla TEM-1 , respectively. A partial converse gene cluster contains ISEcp1 , the bla CTX-M-15 , and WubC , which has been reported by our group to be located on the chromosome of other E. coli isolates, was also find on this plasmid[5]. But the first 1375 bp of ISEcp1 was replaced by a partial reverse transposase (Access: EIL37998.1), which may as a consequence of recombination during transfer.…”