Whole-Genome Based Molecular Characterization of Stenotrophomonas maltophilia

Abstract

Stenotrophomonas maltophilia is a rod-shaped Gram-negative emerging opportunistic pathogen. It causes community and nosocomial infections and is most often recovered from respiratory infections. The organism infects severely ill or immunocompromised individuals and is intrinsically resistant to multiple antibiotics along with the development of acquired resistance through horizontal gene transfer. In this study, we used whole-genome sequencing (WGS), for the in depth molecular characterization of six clinical S. maltophilia isolates collected from hospitals in Lebanon during 2018-2019. Disk diffusion assay was used to determine resistance patterns which were confirmed through in silico detection of relevant genes. All the isolates were resistant to tetracycline, ticarcillin, and imipenem. The β-lactamase blaL1, and the aminoglycoside aac(6’)-Iz and aph(3’)-IIc resistance determinants were detected in the studied isolates. Nucleotide sequences for virulence determinants were downloaded from NCBI and blasted against the isolates whole-genomes. Results showed the presence of a number of extracellular enzymes and other virulence factors (VFs) such as hemolysins and siderophores. The IslandViewer database was used to detect the number of genomic islands (GIs) and the gene pool. Isolates were found to harbor between 20 and 29 GIs each. The GIs were highly diverse and carried multiple VFs. The relatedness between the isolates was investigated through multi-locus sequence typing (MLST), whole genome SNP-based analysis, and pulse field gel electrophoresis (PFGE). We reported three novel STs (ST639, ST640, and ST641). Two quorum sensing rpfF gene variants were detected and which were found to control biofilm formation. Our study is the first of its type in Lebanon and it helped in characterizing and identifying at the molecular level resistance and virulence patterns of an important globally emerging human pathogen. Prevention of related infections depends on establishing and developing infection-control strategies while controlling antibiotic use and environmental reservoirs.