Long-term gut colonization with ESBL-producingEscherichia coliin participants without known risk factors from the southeastern United States

Abstract

We evaluated gut carriage of extended spectrum beta lactamase producingEnterobacteriaceae(ESBL-E) in southeastern U.S. residents without recent in-patient healthcare exposure. Study enrollment was January 2021-February 2022 in Athens, Georgia, U.S. and included a diverse population of 505 adults plus 50 child participants (age 0-5). Based on culture-based screening of stool samples, 4.5% of 555 participants carried ESBL-Es. This is slightly higher than reported in studies conducted 2012-2015, which found carriage rates of 2.5-3.9% in healthy U.S. residents. All ESBL-E confirmed isolates (n=25) were identified asEscherichia coli.Isolates belonged to 11 sequence types, with 48% classified as ST131. Ninety six percent of ESBL-E isolates carried a blaCTX-Mgene. Isolated ESBL-Es frequently carried virulence genes as well as multiple classes of antibiotic resistance genes. Long-term colonization was common, with 64% of ESBL-positive participants testing positive when rescreened three months later. One participant yielded isolates belonging to two differentE. colisequence types that carried blaCTX-M-1genes on near-identical plasmids, suggesting intra-gut plasmid transfer. Isolation ofE. colion media without antibiotics revealed that ESBL-E. colitypically made up a minor fraction of the overall gutE. colipopulation, although in some cases they were the dominant strain. ESBL-E carriage was not associated with a significantly different stool microbiome composition. However, some microbial taxa were differentially abundant in ESBL-E carriers. Together, these results suggest that a small subpopulation of US residents are long-term, asymptomatic carriers of ESBL-Es, and may serve as an important reservoir for community spread of these ESBL genes.