Genomic insights into six clinical isolates of Stenotrophomonas maltophilia from Northern India

Stenotrophomonas maltophilia is a gram-negative opportunistic pathogen that causes respiratory, urinary and bloodstream infections. Due to rising prevalence of difficult to treat S. maltophilia infections, it is considered as one of the important pathogens in many regions, including India. Despite its importance in public health, very few studies provide detailed characterization of the genomes of clinical isolates of S. maltophilia. In this study, we sequence six isolates of S. maltophilia from a tertiary healthcare centre in the Northern India. Along with the culture sensitivity, we report the genomic underpinnings of resistance and virulence in these isolates. In three out of six isolates, we identify a rare beta-lactamase gene kbl-1 that can confer resistance to variety of beta-lactam antibiotics. Though truncated in two isolates, an intact copy of kbl-1 is present in the third isolate. This intact copy of kbl-1 is flanked by insertion elements that are commonly found in several pathogenic species indicating high potential for horizontal gene transfer. To the best of our knowledge, this is a first report of kbl-1 in S. maltophilia from India. ImportanceAntimicrobial resistance (AMR) is one of the biggest global public health challenges. Tackling AMR gets complicated as diverse pathogenic species are involved and resistance is manifested against several different kinds of antibiotics. Genomic surveillance of the resistant pathogens is a key to fight this global threat and needs to extend to important emerging pathogens as well. Here we report genomic sequences and associated characteristics of six Stenotrophomonas maltophilia isolates from Northern India. Along with several resistance and virulence genes we also discover a rare beta-lactamase, blaKBL-1, gene with a high potential of transfer to other species. blaKBL-1 beta-lactamase confers resistance to several beta-lactam antibiotics like ampicillin, amoxicillin, penicillin G, piperacillin, ceftazidime and cefozopran. This is the first report of the presences of this beta-lactamase from India.