In situ, in vivo, and in vitro approaches for studying AMR plasmid conjugation in the gut microbiome

Abstract

Antimicrobial resistance (AMR) is a global threat, with evolution and spread of resistance to frontline antibiotics outpacing the development of novel treatments. The spread of AMR is perpetuated by transfer of antimicrobial resistance genes (ARGs) between bacteria, notably those encoded by conjugative plasmids. The human gut microbiome is a known ‘melting pot’ for plasmid conjugation, with ARG transfer in this environment widely documented. There is a need to better understand the factors affecting the incidence of these transfer events, and to investigate methods of potentially counteracting the spread of ARGs. This review describes the use and potential of three approaches to studying conjugation in the human gut: observation of in situ events in hospitalized patients, modelling of the microbiome in vivo predominantly in rodent models, and the use of in vitro models of various complexities. Each has brought unique insights to our understanding of conjugation in the gut. The use and development of these systems, and combinations thereof, will be pivotal in better understanding the significance, prevalence and manipulability of horizontal gene transfer in the gut microbiome.

Factors and Mechanisms Influencing Conjugation In Vivo in the Gastrointestinal Tract Environment: A Review

“…In vivo, the gastrointestinal tract contains the highest number and diversity of microorganisms. Studies have clearly shown that the density of donor and recipient bacteria is a key factor affecting the CF in vivo ( Figure 2 ) [ 36 ]. Enterobacteriaceae are usually a minority in the normal gut, but plasmid conjugation between members of Enterobacteriales is particularly frequent.…”

“…The density of donor and recipient bacteria, both intergeneric or intrageneric, is a key variable in the CF in vivo, especially in the gastrointestinal tract [ 36 ]. Therefore, any factor that causes disturbance in the conjugation environment may lead to changes in the density of the donor or recipient bacteria, thereby affecting the conjugation transfer.…”