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

Abstract

Multi-resistant pathogenic strains of non-lactose fermenting Escherichia coli (NLF E. coli) 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 E. coli from a diagnostic centre (icddr,b) in Dhaka, Bangladesh. The prevalence of NLF E. coli was 10%, of which 47% (8/17) exhibited multi-drug resistant (MDR) phenotypes. All isolates (17/17) were confirmed as E. coli 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 E. coli isolates. The predominant phylogroup detected was B2 (65%). The blaCTX-M-15 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 E. coli pathotypes demonstrated β-hemolysis. Our study underscores the presence of critical pathogens and MDR clones amongst non-lactose fermenting E. coli. We suggest that non-lactose fermenting E. coli 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 E. coli that would help in better treatment and prevention strategies.

Evaluation of phenotypic and genotypic methods for the identification and characterisation of bacterial isolates recovered from catheter-associated urinary tract infections

“…However, non-lactose fermenting and slow lactose fermenting E. coli have been shown to account for 10-20% of E. coli isolates [43,44], which are often more sensitive to cephalosporins, agreeing with antibiotic sensitivity testing (Table 2). Non-lactose fermenting E. coli strains are more likely to be community strains but this feature cannot be used as a predictive factor for infection as it does not affect the capability to cause disease compared with strains that are lactose fermenters [43,44].…”

“…However, non-lactose fermenting and slow lactose fermenting E. coli have been shown to account for 10-20% of E. coli isolates [43,44], which are often more sensitive to cephalosporins, agreeing with antibiotic sensitivity testing (Table 2). Non-lactose fermenting E. coli strains are more likely to be community strains but this feature cannot be used as a predictive factor for infection as it does not affect the capability to cause disease compared with strains that are lactose fermenters [43,44]. This phenotype suggests that E. coli 20Y000092 is an opportunistic urinary pathogen, with WGS confirming the presence of numerous virulence factors but a lack of those that would be present in different pathovars of E. coli such as enteroaggregative or enteroinvasive (Table S3).…”

Unveiling multi-drug resistant (MDR) gram negative pathogenic bacteria from poultry chickens in the Noakhali region of Bangladesh

“…To our best known, Lactose negative E. coli, M. morganii, E. hormaechei and W. chitiniclastica were identified for the first time in Bangladeshi poultry chicken gut sample. MDR Lactose negative E. coli isolates found from human gut can cause different types of intestinal and non-intestinal infections as reported by one study conducted in Bangladesh (68).…”

“…To our best known, Lactose negative E. coli, M. morganii, E. hormaechei and W. chitiniclastica were identified for the first time in Bangladeshi poultry chicken gut sample. MDR Lactose negative E. coli isolates found from human gut can cause different types of intestinal and non-intestinal infections as reported by one study conducted in Bangladesh(68).After identifying the isolates, we conducted a phenotypic analysis of antibiotic resistance in the bacterial samples obtained from both broiler and layer chickens. Our findings revealed the presence of antibiotic-resistant bacterial isolates in both groups.…”

Antimicrobial Resistance Patterns and Risk Factors Associated with ESBL-Producing and MDR Escherichia coli in Hospital and Environmental Settings in Lusaka, Zambia: Implications for One Health, Antimicrobial Stewardship and Surveillance Systems

“…E. coli , a gram-negative rod belonging to the Enterobacterales order, is a lactose and non-lactose fermenting microbe [ 22 , 23 , 24 ]. It is among the microorganisms that have developed considerable levels of resistance to most antimicrobials used in humans, animals, and agriculture, and has the potential to spread effectively in the environment [ 1 , 25 , 26 , 27 , 28 , 29 , 30 , 31 ].…”