Campylobacter

Whole genome sequencing and metagenomics for outbreak investigation, source attribution and risk assessment of food‐borne microorganisms

“…Standardisation or harmonisation would increase the possibilities for assessing the dissemination of AMR in a ‘one‐health’ approach and would lead to an increased support of an effective AMR management based on AMR monitoring data of strains from different sources. WGS‐AMR offers the opportunity to link for a group of strains the presence of AMR genes with information from strain evolution deduced from the general genome structure. This allows for increased understanding of the generation, spread and loss of AMR over time which was illustrated for Campylobacter isolates (McCarthy, ). WGS‐AMR can contribute to an increased insight into the recognition and function of genetic elements able to mobilise resistance genes. Recently, it was recognised that several carbapenemases are mobilised by integrative conjugative elements (Botelho et al., 2018b) and that transposases can play a role in inducing AMR genes as has been reported for K. pneumoniae, where an insertion in mgrB led to colistin resistance (Poirel et al., ), and for E. coli, where an increased expression of an efflux system contributed to fluoroquinolone resistance (Jellen‐Ritter and Kern, ). An increasing availability of WGS data from clinical samples will allow to determine the public health relevance of different AMR determinants.…”