Epidemiology, Risk Factors, Hidden Gut Resistome and Characterization of Multidrug-Resistant Enterobacterales Colonizing the Intestinal Tract of Swiss Expatriates

Abstract: A study following long-term residents from countries with low prevalence of multidrug-resistant Enterobacterales residing in countries with high prevalence has never been done before at this scale. In this ongoing work, we analyzed the epidemiology and risk factors for colonization with multidrug-resistant Enterobacterales in 57 Swiss embassy employees and expatriates stationed worldwide by administering a questionnaire to establish facets of participants' diet, lifestyle, and medical history. From stool samples sent by these participants, we found 33% were colonized with extended-spectrum β-lactamase and/or AmpC-β-lactamase producing Escherichia coli at the intestinal level. We then characterized the molecular features of these strains using whole-genome sequencing. Various strains carried blaCTX-M-15, blaDHA-1, qnr, and other resistance genes. Four strains also belonged to the pandemic clone of sequence type 131. We characterized the hidden gut resistome using a shotgun metagenomics approach and found that the hidden gut resistome is a reservoir for many antibiotic resistance genes. Surprisingly, we found no clear difference in the hidden gut resistome between participants colonized by multidrug-resistant Enterobacterales and non-colonized participants, and we were unable to reliably identify multidrug-resistant Enterobacterales using this method. Lastly, we identified the most significant risk factors for colonization with multidrug-resistant Enterobacterales were: use of antibiotics in the last 2 years, diarrhea in the last 3 months, individuals aged 36-50, being stationed in an embassy in Africa or Asia, and international travel to Africa or Asia. This study provides preliminary results for a previously unexplored population and will aid in ameliorating the problem of antibiotic resistance worldwide.