Community carriage of ESBL-producingEscherichia coliandKlebsiella pneumoniae: A cross-sectional study of risk factors and comparative genomics of carriage and clinical isolates

Abstract

The global prevalence of infections caused by ESBL-producing Enterobacterales (ESBL-E) is increasing and for Escherichia coli observations indicate that this is partly driven by community-onset cases. The ESBL-E population structure in the community is scarcely described and data on risk factors for carriage are conflicting. Here, we report the prevalence and population structure of fecal ESBL-producing E. coli and Klebsiella pneumoniae (ESBL-Ec/Kp) in a general adult population, examine risk factors, and compare carriage isolates with contemporary clinical isolates. Fecal samples obtained from 4999 participants (54% women) ≥40 years in the seventh survey of the population-based Tromsø Study, Norway (2015-2016) were screened for ESBL-Ec/Kp. In addition, we included 118 ESBL-Ec clinical isolates from the Norwegian surveillance program in 2014. All ESBL-producing isolates were whole-genome sequenced. Risk factors associated with carriage were analyzed using multivariable logistic regression. ESBL-Ec gastrointestinal carriage prevalence was 3.3% (95%CI 2.8-3.9%, no sex difference) and 0.08% (0.02-0.20%) for ESBL-Kp. For ESBL-Ec, travel to Asia was the only independent risk factor (AOR 3.47, 95%CI 2.18-5.51). E. coli ST131 was most prevalent in both collections. However, the ST131 proportion was significantly lower in carriage (24%) vs. clinical isolates (58%, p<0.001). Carriage isolates were genetically more diverse with a higher proportion of phylogroup A (26% vs. 5%, p<0.001), indicating that ESBL gene acquisition occurs in a variety of E. coli lineages colonizing the gut. STs commonly related to extra-intestinal infections were more frequent in the clinical isolates also carrying a higher prevalence of antimicrobial resistance, which could indicate clone associated pathogenicity.

Modeling the transmission of antibiotic-resistant Enterobacterales in the community: a systematic review

“…25,30 From epidemiological studies, it has been shown that travel to high-prevalence areas, including certain countries in Africa and Asia, was an important risk factor for resistant Enterobacterales acquisition. 20,46 However, despite this high acquisition risk, both model and epidemiological studies suggested that returning travelers might be associated with a low subsequent transmission risk in households, 37 possibly due to a short carriage duration. 37,47,48 Future research should further investigate the traveler's role in spreading resistant Enterobacterales locally: while the rapid global spread of high-risk multidrug-resistant clones is clearly linked to travel, 49 it is unclear to what extent population movement contributes to community transmission dynamics once a clone has become established in a given region.…”

“…13,14 The biological and epidemiological mechanisms that drive antibiotic-resistant Enterobacterales selection and transmission in the community remain relatively poorly characterized and little quantified. [15][16][17] For instance, the contribution of horizontal gene transfer (HGT) within or between different reservoirs in driving the population-level epidemiology of antibiotic resistance is still poorly understood, 18 as is the role of asymptomatic carriage in driving transmission and infection 19,20 (note: we use the terms carriage and colonization interchangeably). It is also unclear how bacterial persistence in the environment contributes to maintain community transmission.…”

Deep sequencing of Escherichia coli exposes colonisation diversity and impact of antibiotics in Punjab, Pakistan

“…While the prevalence of these genes was not particularly high, usage of carbapenems is relatively rare in this region due to their cost (WHO GLASS: https://www.who.int/publications/i/item/ 9789240062702), which suggests that generalist lineages such as ST10 are capable of acquiring and maintaining these genes without an excessive fitness cost. Given its ability to effectively colonise the human gut asymptomatically, ST10 has the potential to act as a global dissemination vehicle of AMR genes without becoming notified as a prevalent source, since beyond some exceptions considering community carriage 31 , surveillance is nearly exclusively performed from clinical samples, in particular for critical AMR such as ESBLs and carbapenemases 16,32 . Neither the global population structure of ST10, nor the molecular mechanisms behind its general success in colonising humans are currently well understood, which calls for in-depth studies of this generalist E. coli to aid future efforts in mitigating the public health burden across the wide spectrum of extra-intestinal pathogenic E. coli genetic variation.…”

Monitoring ESBL-Escherichia coliin Swiss wastewater between November 2021 and November 2022: insights into population carriage

“…There are other potential causes for higher percentages of ESBL- E. coli than population density alone. Zurich and Geneva are also home of to large international airports, associated with increased international travel and food import, which are known risk factors for the spread of resistant bacterial strains across borders [27,28]. Furthermore, the cities of Zurich and Geneva contain multiple healthcare clinics and hospitals, known to have higher carriage rates compared to community settings [24].…”