AUTHOR=Mazumder Razib , Hussain Arif , Abdullah Ahmed , Islam Md. Nazrul , Sadique Md. Tuhin , Muniruzzaman S. M. , Tabassum Anika , Halim Farhana , Akter Nasrin , Ahmed Dilruba , Mondal Dinesh 

TITLE=International High-Risk Clones Among Extended-Spectrum β-Lactamase–Producing Escherichia coli in Dhaka, Bangladesh

JOURNAL=Frontiers in Microbiology

VOLUME=12

YEAR=2021

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2021.736464

DOI=10.3389/fmicb.2021.736464

ISSN=1664-302X

ABSTRACT=<p><bold>Background:</bold><italic>Escherichia coli</italic> is a major extended-spectrum β-lactamase (ESBL)–producing organism responsible for the rapid spread of antimicrobial resistance (AMR) that has compromised our ability to treat infections. Baseline data on population structure, virulence, and resistance mechanisms in <italic>E. coli</italic> lineages from developing countries such as Bangladesh are lacking.</p><p><bold>Methods:</bold> Whole-genome sequencing was performed for 46 ESBL–<italic>E. coli</italic> isolates cultured from patient samples at the International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b)-Dhaka. Sequence data were analyzed to glean details of AMR, virulence, and phylogenetic and molecular markers of <italic>E. coli</italic> lineages.</p><p><bold>Results:</bold> Genome comparison revealed presence of all major high-risk clones including sequence type 131 (ST131) (46%), ST405 (13%), ST648 (7%), ST410 (4.3%), ST38 (2%), ST73 (2%), and ST1193 (2%). The predominant ESBL gene and plasmid combination were <italic>bla</italic><sub>CTX</sub><sub>–</sub><sub>M</sub><sub>–</sub><sub>15</sub> and FII-FIA-FIB detected in diverse <italic>E. coli</italic> phylogroups and STs. The <italic>bla</italic><sub>NDM</sub><sub>–</sub><sub>5</sub> (9%) gene was present in prominent <italic>E. coli</italic> STs. One (2%) <italic>mcr-1–</italic>positive ST1011 <italic>E. coli</italic>, coharboring <italic>bla</italic><sub>CTXM</sub><sub>–</sub><sub>55</sub> gene, was detected. The extraintestinal pathogenic <italic>E. coli</italic> genotype was associated with specific <italic>E. coli</italic> lineages. The single nucleotide polymorphism (SNP)-based genome phylogeny largely showed correlation with phylogroups, serogroups, and <italic>fimH</italic> types. Majority of these isolates were susceptible to amikacin (93%), imipenem (93%), and nitrofurantoin (83%).</p><p><bold>Conclusion:</bold> Our study reveals a high diversity of <italic>E. coli</italic> lineages among ESBL-producing <italic>E. coli</italic> from Dhaka. This study suggests ongoing circulation of ST131 and all major non-ST131 high-risk clones that are strongly associated with cephalosporin resistance and virulence genes. These findings warrant prospective monitoring of high-risk clones, which would otherwise worsen the AMR crises.</p>