Community carriage of ESBL-producing Escherichia coli and Klebsiella pneumoniae: A cross-sectional study of risk factors and comparative genomics of carriage and clinical isolates

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 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 clinical isolates also carrying a higher prevalence of antimicrobial resistance, which could indicate clone associated pathogenicity. Importance ESBL-producing E. coli (ESBL-Ec) and K. pneumoniae (ESBL-Kp) are major pathogens in the global burden of antimicrobial resistance. However, there is a gap in knowledge concerning the bacterial population structure of human ESBL-Ec/Kp carriage isolates in the community. We have examined ESBL-Ec/Kp isolates from a population-based study and compared these to contemporary clinical isolates. The large genetic diversity of carriage isolates indicates frequent ESBL gene acquisition, while those causing invasive infections are more clone dependent and associated with a higher prevalence of antibiotic resistance. The knowledge of factors associated with ESBL carriage helps to identify patients at risk to combat the spread of resistant bacteria within the healthcare system. Particularly, previous travel to Asia stands out as a major risk factor for carriage and should be considered in selecting empirical antibiotic treatment in critically ill patients. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This study was supported by grants from the Northern Norway Regional Health Authority (HNF1415-18) and the Trond Mohn Foundation (TMF2019TMT03). The funders of the study played no role in study design, data collection, data analysis, data interpretation, or writing of the report. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The study was approved by the Regional Committee for Medical and Health Research Ethics, North Norway (REC North reference: 2016/1788 and 2014/940) and the Data Protection Officer at University Hospital of North Norway (reference: 2019/4264). The study complied with the Declaration of Helsinki. All participants in Tromsø7 signed an informed consent form prior to participation. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes Bacterial genome data (raw Illumina reads) are publicly available in NCBI under BioProject PRJEB53319 (NORM 2014 collection) and PRJEB57251 (Tromsø7 collection). This study is based on data owned by a third party (The Tromsø Study, Department of Community Medicine, UiT The Arctic University of Norway). Confidentiality requirements according to Norwegian law prevents sharing of individual patient level data in public repositories. Application of legal basis and exemption from professional secrecy requirements for the use of personal health data in research may be sent to a regional committee for medical and health research ethics (). The authors gained access to the data through the Tromsø Study application process. Guidelines on how to access the data are available at the website . All enquiries about the Tromsø Study should be sent by e-mail to tromsous{at}ism.uit.no. All the questionnaire variables are published in the NESSTAR program system and results can be viewed online: .