Inter-species geographic signatures for tracing horizontal gene transfer and long-term persistence of carbapenem resistance

Abstract

Background Carbapenem-resistant Enterobacterales (CRE) are an urgent global health threat. Inferring the dynamics of local CRE dissemination is currently limited by our inability to confidently trace the spread of resistance determinants to unrelated bacterial hosts. Whole-genome sequence comparison is useful for identifying CRE clonal transmission and outbreaks, but high-frequency horizontal gene transfer (HGT) of carbapenem resistance genes and subsequent genome rearrangement complicate tracing the local persistence and mobilization of these genes across organisms. Methods To overcome this limitation, we developed a new approach to identify recent HGT of large, near-identical plasmid segments across species boundaries, which also allowed us to overcome technical challenges with genome assembly. We applied this to complete and near-complete genome assemblies to examine the local spread of CRE in a systematic, prospective collection of all CRE, as well as time- and species-matched carbapenem-susceptible Enterobacterales, isolated from patients from four US hospitals over nearly 5 years. Results Our CRE collection comprised a diverse range of species, lineages, and carbapenem resistance mechanisms, many of which were encoded on a variety of promiscuous plasmid types. We found and quantified rearrangement, persistence, and repeated transfer of plasmid segments, including those harboring carbapenemases, between organisms over multiple years. Some plasmid segments were found to be strongly associated with specific locales, thus representing geographic signatures that make it possible to trace recent and localized HGT events. Functional analysis of these signatures revealed genes commonly found in plasmids of nosocomial pathogens, such as functions required for plasmid retention and spread, as well survival against a variety of antibiotic and antiseptics common to the hospital environment. Conclusions Collectively, the framework we developed provides a clearer, high-resolution picture of the epidemiology of antibiotic resistance importation, spread, and persistence in patients and healthcare networks.

Genomic population structures of microbial pathogens

“…However, downstream inferences of plasmid transfer between strains, and of the transfer of plasmid-encoded AMR genes, were quite robust to methodological choices. These findings are encouraging for the burgeoning field of plasmid genomics and transmission tracking [ 13 ], the importance of which is increasingly recognized in public health genomics and infection control.…”

Empirical genomic methods for tracking plasmid spread among healthcare-associated bacteria

“…8,9,35 Applying these refined, plasmid-focused approaches in healthcare settings could help infection prevention teams better understand signs and risk factors for the dissemination of drug resistance, allowing them to improve their approaches to reduce the risk of severe infections among patients. 5,7,35…”

“…8,9,35 Applying these refined, plasmid-focused approaches in healthcare settings could help infection prevention teams better understand signs and risk factors for the dissemination of drug resistance, allowing them to improve their approaches to reduce the risk of severe infections among patients. 5,7,35 Future work in this area should focus on refining similarity thresholds and surveillance methods, further examining patterns of mutation and genetic plasticity among circulating plasmids, and implementing these methods in real-time to control the spread of plasmid-borne antimicrobial resistance and virulence factors that exacerbate nosocomial infections.…”

“…Developing metrics to establish plasmid transmission can aid infection prevention personnel in the spread of multidrug-resistant bacteria in hospitals, helping to intervene directly against the dissemination of antimicrobial resistance and virulence. 2,5,7…”

“…Developing metrics to establish plasmid transmission can aid infection prevention personnel in the spread of multidrug-resistant bacteria in hospitals, helping to intervene directly against the dissemination of antimicrobial resistance and virulence. 2,5,7 Our study had two objectives. The first was to establish sequence similarity thresholds to infer horizontal transfer of plasmids among bacteria collected from a single hospital.…”