Molecular Characterization of Stenotrophomonas maltophilia in Nosocomial Infections: Challenges and Way Forward

Introduction: Stenotrophomonas maltophilia (S. maltophilia), is an important rapidly emerging, opportunistic, non-fermenting Gram negative bacillus with high intrinsic resistance to drugs. It is one of the leading causative agents of nosocomial infections especially in the immunocompromised patients. Molecular typing of pathogens provides an important tool in epidemiological investigations involving nosocomial infections. Due to high geno-diversity, typing of S. maltophilia is challenging. Aim: The study was aimed to evaluate the best epidemiological tool to investigate clonal relatedness of S. maltophilia. Materials and Methods: A prospective study was conducted at a 2400 bedded tertiary care centre in southern India over a period of six months. Twenty-six isolates of S. maltophilia were obtained during the study period. Of these, 18 isolates from blood and Endotracheal Aspirates (ETA) cultures were included in the study since they were incriminated in causing nosocomial infection clinically for which appropriate treatment was initiated. These 18 clinical isolates of S. maltophilia were characterised to identify the clonality using Conventional Multi Locus Sequence Typing (MLST). A subset of 9 S. maltophilia isolates were sequenced using IonTorrent PGM platform. Further phylogenetic analysis was inferred from core genome Single Nucleotide Polymorphisms (SNPs). Results: Using conventional MLST, one isolate (S04384), was identified as belonging to sequence type 13 (ST13) whereas sequencing of the remaining 17 isolates could not be successfully done using MLST PCR even after several attempts. A subset of nine isolates from these 17 were subjected to sequencing using Ion Torrent PGM platform. Using MLST Finder tool on this platform, one isolate was found to belong to sequence type 15 (ST15). The remaining eight isolates were observed to have novel sequence types; four of which were assigned sequence types ST283, ST284, ST285 and ST286. The remaining four had <50% similarity for mutM gene. Further phylogenetic analysis was studied using core genome SNPs. They revealed bifurcating and multifurcating groups among all these nine S. maltophilia isolates. None of them belonged to the same clonal group according to SNP based phylogeny. Conclusion: Frequent recombination events in S. maltophilia genome make it difficult to identify the clonality based on MLST. From this study, SNPs based whole genome phylogeny was observed as better methodology to identify clonal relatedness among S. maltophilia.