Antimicrobial resistance

SRST2¹, ARIBA², and KmerResistance (web service, code)³ are three widely used pieces of standalone software for read-based detection of target genes in bacterial genomes. Published in 2014, SRST2 is recognised as the pioneer amongst these three tools^{2, 3}. In this post, I compare methodologies underlying these tools in a concise manner to shed light on the selection of appropriate software for gene detection. Particularly, I herein presume that detecting antimicrobial resistance determinants is the only use case. Whenever unspecified, software versions referred to in this post are: SRST2 v0.2.0, ARIBA 2.14.4, and KmerResistance v2.2.

Reliable and up-to-date databases play a pivotal role in reference-based detection of antimicrobial resistance genes (ARGs) in bacteria. Nonetheless, these databases differ in their content and quality, making it challenging to decide an appropriate reference database for a particular research project. In order to address this challenge, this post offers a review of several ARG databases that are publicly available and widely used in bacterial genomics. Particularly, I focus on databases that are still undergoing regular maintenance, and I do not discuss any program released with these databases for sequence search or statistical analysis.