Towards global multi-host bacterial genomic epidemiology

Abstract

Whole Genome Sequencing (WGS) is the desirable option for conducting molecular epidemiology of bacteria. There is an assortment of approaches to analyse WGS data, from genome phylogenies or core genome MLST schemes, to Average Nucleotide Identity analysis, and even to molecular dating analysis. These approaches have advanced the genomic epidemiology of bacterial pathogens successfully. Yet, a few important sampling challenges remain. First, the strong bias towards clinical surveillance, yet many of the so-called “human pathogens” are also found in other hosts. Secondly, the very patchy distribution of countries with WGS available, with many countries having hardly any isolates sequenced. Finally, many studies just focus on antibiotic-resistant isolates, overlooking the diversity hosted by the antibiotic-susceptible isolates. Thus, ideally, future studies should conduct global multi-host bacterial genomic epidemiology despite the antibiotic phenotype of the isolates.