Community and clinical resistomes and mobilomes: a correlation.

Abstract

Bacteria acquire antibiotic resistance genes (ARGs) through horizontal gene transfer or mutations. Colonization of healthy individuals with multidrug-resistant (MDR) bacteria therefore poses a public health concern, as these individuals may serve as reservoirs of antimicrobial resistance (AMR). This study compared the resistomes, mobilomes, and phylogenetic relationships of Escherichia coli and Klebsiella pneumoniae isolates from a regional hospital and nearby healthy community dwellers in uMgungundlovu District, using whole genome sequencing (WGS) and bioinformatics to assess AMR transmission directionality. Stool and clinical samples were collected, and presumptively identified isolates underwent antimicrobial susceptibility testing, extended-spectrum β-lactamase (ESBL) screening, and WGS. Bioinformatic analyses were conducted using RAST, ResFinder, CARD, PlasmidFinder, INTEGRALL, ISFinder, PGAP, MLST, BV-BRC, and iTOL. This study reports on 32 E. coli isolates (15 clinical and 17 community) and 14 K. pneumoniae isolates (6 clinical and 8 community) confirmed by WGS. Seven E. coli isolates (3 clinical and 4 community) and one community K. pneumoniae isolate were identified as ESBL producers, with E. coli from both settings sharing multiple resistance genes, including blaCTX-M-15, blaTEM-1B, dfrA17, sul1, sul2, aph(3'')-Ib, aph(6)- Id, qnrS1, mph(A), catA1, and tet(A), while K. pneumoniae isolates commonly carried blaSHV-1, blaTEM- 1B, sul1, sul2, aph(3'')-Ib, aph(6)-Id, qnrS1, and fosA5. Most of these ARGs were associated with insertion sequences and transposons in both settings. Among E. coli, the most common sequence types (STs) in both clinical and community isolates were ST131, ST10, and ST1193, while ST17 was shared among K. pneumoniae isolates. Phylogenetic analysis revealed clustering between clinical and community isolates, although clustering was less pronounced for K. pneumoniae. In conclusion, this study revealed the possibility of bidirectional AMR transmission between clinical and community settings. These findings highlight healthy individuals as potential reservoirs of resistance and strengthen the need to include community settings in AMR mitigation strategies.