Transmission dynamics of carbapenemase-producing bacteria and mobile genetic elements between hospital and household settings in Benin

Background Patients can acquire resistance to critical carbapenemase-producing bacteria during hospitalization and may transmit them to household contacts after discharge. The present study aimed to assess the transmission of carbapenemase-producing bacteria from hospitals to households through patients and their caregivers. Methods A total of 248 participants were included in this study across 5 hospitals, comprising 81 index patients, 81 caregivers, 58 healthcare workers, and 28 household members. Rectal swabs samples were collected from the participants from admission to discharge and during follow-up at home. Samples were plated on mSuperCARBA™, and obtained isolates were tested for carbapenem resistance. A subset of 41 carbapenem resistant isolates were selected and subjected to Whole Genome Sequencing (WGS) and hybrid assembly analysis to determine genetic relatedness and resistance determinants across sampling networks. Results A total of 412 isolates were recovered from hospital and household settings. Among these, 141 isolates were resistant to carbapenem, predominantly E. coli (40.42%), K. pneumoniae (19.14%), and A. baumannii (10.63%). For those enrolled at hospital, the prevalence of carbapenem-resistant bacterial colonization increased from 7.3% (16/220) at admission to 22.7% (10/44) by day 8 of hospitalization. Among patients or caregivers that were still positive at discharge, the prevalence at home rose from 8.0% (7/87) on day 0 of discharge to 57.1% (8/14) by day 14 of follow-up. Long- and short-read sequencing identified the carbapenem resistance genes blaNDM-5 and blaNDM-1 as the main determinants found in Escherichia coli ST410 and Klebsiella pneumoniae ST147, respectively. Several strains, including Klebsiella pneumoniae (ST147) and Escherichia coli (ST410), showed genetic relatedness and potential transmission within households and between healthcare and home settings. Inc FII and Inc FI conjugative plasmids carried most carbapenemase genes in healthcare and community settings representing another layer of resistance spread via horizontal gene transfer. Conclusion This study reveals, for the first time in Benin, the role of patients and their caregivers in facilitating the spread of antimicrobial resistance between hospitals and the community.