[6] Increased availability of whole-genome and metagenomic next-generation sequencing techniques have revealed significant reservoirs of antibiotic resistant bacteria outside of clinical settings.
[4] In this study, they observed nearly 200 different resistance profiles among the bacteria sequenced, indicating a diverse and robust response to the antibiotics tested regardless of their bacterial target or natural or synthetic origin.
[4] Antibiotic resistant bacteria have observed through metagenomic surveys in non-clinical environments such as water treatment facilities[5][8] and human microbiomes like the mouth.
A major question surrounding the environmental resistome is: How do pathogenic bacteria acquire antibiotic resistance genes from the environment (and vice versa)?
To answer this, we need to consider the mechanisms of horizontal gene transfer (HGT) and the various opportunities for contact between environmental bacteria and human pathogens.
[12] Metagenomic sequencing and short-read based assembly have revealed the exchange of antibiotic resistance genes between non-pathogenic environmental soil bacteria and clinical pathogens.
[13] The portions in the soil bacteria perfectly match the identity of several diverse human pathogens and contain resistance cassettes against five classes of antibiotics.
[3] Comparing different mutations in the germline can be used to help define the size and position of the resistome, this set of genes conferring an inherited immune response.