The phylogenetic landscape and nosocomial spread of the multidrug-resistant opportunist Stenotrophomonas maltophilia

Abstract

Recent studies portend a rising global spread and adaptation of human-or healthcareassociated pathogens. Here, we analyse an international collection of the emerging, multidrug-resistant, opportunistic pathogen Stenotrophomonas maltophilia from 22 countries to infer population structure and clonality at a global level. We show that the S. maltophilia complex is divided into 23 monophyletic lineages, most of which harbour strains of all degrees of human virulence. Lineage Sm6 comprises the highest rate of human-associated strains, linked to key virulence and resistance genes. Transmission analysis identifies potential outbreak events of genetically closely related strains isolated within days or weeks in the same hospitals.

Genetic Variants of the DSF Quorum Sensing System in Stenotrophomonas maltophilia Influence Virulence and Resistance Phenotypes Among Genotypically Diverse Clinical Isolates

“…In agreement with previous studies (Corlouer et al, 2017;Mercier-Darty et al, 2020), genogroup #2 represents the most genetically diverse group in our collection. As proposed by Gröschel et al (2020) and shown in Supplementary Table S1, the strains could be further classified into the monophyletic lineages named Sm1-Sm18 (termed S. maltophilia sensu lato) or the more distantly related lineages Sgn1-Sgn4 according to Vinuesa et al (2018). All our strains, except the phylogenetically distant strain OU111 (genogroup A), belong to the S. maltophilia sensu lato cluster.…”

“…Annotated genome sequences of the unique isolates studied here were generated in the study by Gröschel et al (2020) and are available from NCBI repository under the accession numbers RASX00000000-RAVB00000000. Genome sequences from S. maltophilia strains K279a, D457, and ATCC13637 were obtained from the NCBI genome database 1 .…”

“…Due to these large genetic divergences, and because previously proposed species are recognized to be closely related to S. maltophilia, it is increasingly accepted to present it as the S. maltophilia complex (Svensson-Stadler et al, 2012;Patil et al, 2018;Vinuesa et al, 2018). PCRbased multilocus sequence typing (MLST) and whole-genome sequencing (WGS) have clearly shown the existence of several genomic or phylogenetic groups in the S. maltophilia complex, and have helped to clarify the taxonomic status of the species (Hauben et al, 1999;Kaiser et al, 2009;Ochoa-Sánchez and Vinuesa, 2017;Steinmann et al, 2018;Gröschel et al, 2020;Mercier-Darty et al, 2020). Even strains isolated from the same patient (Pompilio et al, 2016;Chung et al, 2017) or patients within the same hospital (Valdezate et al, 2004) can belong to distant phylogenetic groups with different phenotypes, probably due to the emergence of adaptive mutations as a result of selective pressure in the clinical environment or inside the host.…”

Overcoming Challenges to Make Bacteriophage Therapy Standard Clinical Treatment Practice for Cystic Fibrosis

“…Phage therapy has also been applied for compassionate use at various sites other than the lung (non-CF associated) suggesting that a number of other CF-associated pathogens including S. aureus , A. baumanii , and Klebsiella pneumoniae may also be clinically targeted using phage therapy ( Figure 1 ). Emerging CF pathogens such as Stenotrophomonas maltophilia , are also of concern due to their increasing incidence of isolation ( Millar et al, 2009 ; Razvi et al, 2009 ; Emerson et al, 2010 ) and multidrug resistance ( Gajdács and Urbán, 2019 ; Gröschel et al, 2020 ). Since their infectivity and transmission mechanisms are still to be elucidated ( Stanojevic et al, 2013 ; Gröschel et al, 2020 ) which would typically direct targeted treatment regimens, phage therapy has been postulated as a potential therapeutic option currently ( Chang et al, 2005 ; Peters et al, 2015 , 2017 ).…”

Complete Genome Sequence of Stenotrophomonas maltophilia Strain CF13, Recovered from Sputum from an Australian Cystic Fibrosis Patient

“…1 ). The population structure of S. maltophilia consists of 23 monophyletic lineages, with the largest lineage, Sm6, known as S. maltophilia sensu stricto , containing most strains characterized to date, including K279a ( 18 ). Hence, CF13 also belongs to Sm6.…”