Abstract
Recent studies portend a rising global spread and adaptation of human- or healthcare-associated 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.
Highlights
Recent studies portend a rising global spread and adaptation of human- or healthcareassociated pathogens
Local transmission and global spread of hospitalacquired pathogens such as Mycobacterium abscessus and Mycobacterium chimaera were revealed by whole-genome sequencing (WGS), thereby challenging the prevailing concepts of disease acquisition and transmission of these pathogens in the hospital setting[1,2,3]
Using 171 publicly available assembled genomes of the S. maltophilia complex that represent its currently known diversity (Supplementary Data 1), we constructed a whole-genome multilocus sequence typing (wgMLST) scheme consisting of 17,603 loci (Supplementary Data 2)
Summary
Recent studies portend a rising global spread and adaptation of human- or healthcareassociated pathogens. Previous work indicated the presence of at least 13 lineages or species-like lineages in the S. maltophilia complex, defined as S. maltophilia strains with 16S rRNA gene sequence similarities >99.0%, with nine of these potentially human-associated[14,15,16,17,18] These S. maltophilia complex lineages are further divided into four more distantly related lineages (Sgn1-4) and several S. maltophilia sensu lato and sensu stricto lineages[14,19]. To understand the global population structure of the S. maltophilia complex and the potential for global and local spread of strains, in particular of human-associated lineages, we performed a large-scale genome-based phylogenetic and cluster analysis of a global collection of newly sequenced S. maltophilia strains together with publicly available whole-genome data
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