AUTHOR=Mazumder Razib , Hussain Arif , Phelan Jody E. , Campino Susana , Haider S. M. Arefeen , Mahmud Araf , Ahmed Dilruba , Asadulghani Md , Clark Taane G. , Mondal Dinesh 

TITLE=Non-lactose fermenting Escherichia coli: Following in the footsteps of lactose fermenting E. coli high-risk clones

JOURNAL=Frontiers in Microbiology

VOLUME=13

YEAR=2022

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2022.1027494

DOI=10.3389/fmicb.2022.1027494

ISSN=1664-302X

ABSTRACT=<p>Multi-resistant pathogenic strains of non-lactose fermenting <italic>Escherichia coli</italic> (NLF <italic>E. coli</italic>) are responsible for various intestinal and extraintestinal infections. Although several studies have characterised such strains using conventional methods, they have not been comprehensively studied at the genomic level. To address this gap, we used whole-genome sequencing (WGS) coupled with detailed microbiological and biochemical testing to investigate 17 NLF <italic>E. coli</italic> from a diagnostic centre (icddr,b) in Dhaka, Bangladesh. The prevalence of NLF <italic>E. coli</italic> was 10%, of which 47% (8/17) exhibited multi-drug resistant (MDR) phenotypes. All isolates (17/17) were confirmed as <italic>E. coli</italic> and could not ferment lactose sugar. WGS data analysis revealed international high-risk clonal lineages. The most prevalent sequence types (STs) were ST131 (23%), ST1193 (18%), ST12 (18%), ST501 (12%), ST167 (6%), ST73 (6%) and ST12 (6%). Phylogenetic analysis corroborated a striking clonal population amongst the studied NLF <italic>E. coli</italic> isolates. The predominant phylogroup detected was B2 (65%). The <italic>bla</italic><sub>CTX-M-15</sub> extended-spectrum beta-lactamase gene was present in 53% of isolates (9/17), whilst 64.7% (11/17) isolates were affiliated with pathogenic pathotypes. All extraintestinal pathogenic <italic>E. coli</italic> pathotypes demonstrated β-hemolysis. Our study underscores the presence of critical pathogens and MDR clones amongst non-lactose fermenting <italic>E. coli.</italic> We suggest that non-lactose fermenting <italic>E. coli</italic> be considered equally capable as lactose fermenting forms in causing intestinal and extraintestinal infections. Further, there is a need to undertake systematic, unbiased monitoring of predominant lineages amongst non-lactose fermenting <italic>E. coli</italic> that would help in better treatment and prevention strategies.</p>