Abstract
In recent decades, the emergence and spread of antibiotic resistance among bacterial pathogens has become a major threat to public health. Bacteria can acquire antibiotic resistance genes by the mobilization and transfer of resistance genes from a donor strain. The human gut contains a densely populated microbial ecosystem, termed the gut microbiota, which offers ample opportunities for the horizontal transfer of genetic material, including antibiotic resistance genes. Recent technological advances allow microbiota-wide studies into the diversity and dynamics of the antibiotic resistance genes that are harboured by the gut microbiota (‘the gut resistome’). Genes conferring resistance to antibiotics are ubiquitously present among the gut microbiota of humans and most resistance genes are harboured by strictly anaerobic gut commensals. The horizontal transfer of genetic material, including antibiotic resistance genes, through conjugation and transduction is a frequent event in the gut microbiota, but mostly involves non-pathogenic gut commensals as these dominate the microbiota of healthy individuals. Resistance gene transfer from commensals to gut-dwelling opportunistic pathogens appears to be a relatively rare event but may contribute to the emergence of multi-drug resistant strains, as is illustrated by the vancomycin resistance determinants that are shared by anaerobic gut commensals and the nosocomial pathogen Enterococcus faecium.
Highlights
In recent decades, the emergence and spread of antibiotic resistance among bacterial pathogens has become a major threat to public health
The horizontal transfer of genetic material, including antibiotic resistance genes, through conjugation and transduction is a frequent event in the gut microbiota, but mostly involves non-pathogenic gut commensals as these dominate the microbiota of healthy individuals
Antibiotic resistance genes are widely distributed in the environment and the studies that are discussed in this review have provided convincing evidence that the gut microbiota form a large reservoir for antibiotic resistance genes
Summary
Methodological approaches for the study of the resistome are outlined in figure 1 and are further discussed below. The resulting sequencing datasets can be analysed by assembly of the short reads into larger contiguous DNA fragments or by mapping the sequence reads to reference sequences This method allows the determination of the phylogenetic composition of the microbiota and can be used to simultaneously detect and quantify antibiotic resistance genes in the microbiota [35]. Functional metagenomic analyses of the gut resistome are considerably more labour-intensive the previously discussed methods but have the advantage that novel resistance genes (i.e. those that are currently not included in antibiotic resistance gene databases) are identified and that, in the case of large-insert fosmid libraries, information can be obtained about the genetic context of antibiotic resistance genes
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