Multidrug-resistant pathogen analyzed

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A genome analysis reveals insights into the global spread of S. maltophilia strains – multidrug-resistant pathogens causing hospital-acquired infections.

28.04.2020 · Life Sciences · Research Center Borstel - Leibniz Lung Center · News · Research result

An international consortium led by the Research Center Borstel describes for the first time the population structure and spread at scale of opportunistic multidrug-resistant pathogens of the Stenotrophomonas maltophilia complex. The study, now published in Nature Communications, provides a systematic understanding of the global phylogeny of S. maltophilia strains and enables efficient surveillance based on a standardized genomic classification system.

Bacteria of the S. maltophilia complex can be found ubiquitously in diverse natural and human-associated ecosystems. Recently, they emerged as opportunistic pathogens causing hospital-acquired drug-resistant infections, mainly in patients with immunosuppression or pre-existing inflammatory lung diseases such as cystic fibrosis. While almost any organ can be affected, respiratory tract infections, bacteraemia, or catheter-related bloodstream infections are most common. Alarmingly, treatment options are very limited by an inherent resistance of S. maltophilia strains to a large number of antibiotics. Considering the increasing importance and severe clinical outcomes caused by this emerging pathogen, insights into S. maltophilia virulence factors, and local and global spread are urgently needed.

"Recent reports indicate the worldwide spread of clearly defined and very successful subgroups of different pathogens in the hospital setting. However, little information is available for S. maltophilia, as infections are not routinely reported and systematically analyzed" says Prof. Stefan Niemann from the Research Center Borstel, who led the consortium.

The researchers from a large bioinformatics company and research institutions from eight countries first established a standardized genotyping approach that enables the comprehensive analysis of the diverse genomes of S. maltophilia strains by translating the genome sequences into a unique and strain-specific barcode (whole-genome Multilocus Sequence Types). In the next step, they performed a large-scale genome-based analysis of a worldwide collection of 1305 S. maltophilia isolates from 22 countries to define the worldwide population structure and detect the global and local spread of particular subtypes.

One major finding was that the S. maltophilia complex is divided into 23 lineages with distinct occurrences e.g. in the environment or human-associated. Strains of one particular lineage termed “Sm6” occurred globally, had the highest rate of human-associated strains and featured higher proportions of key virulence and resistance genes. “This suggests that a dedicated gene repertoire can fuel the spread of particular S. maltophilia subtypes in the hospital setting, i.e. under antimicrobial treatment” says Matthias Gröschel, first author of the study from the Harvard Medical School.

Strikingly, transmission analysis was able to identify several potential outbreak events of genetically closely related strains isolated within days or weeks in the same hospitals.

“In line with similar reports for other bacterial diseases, our results point towards systematic prospective molecular surveillance of S. maltophilia and other pathogens in the hospital setting as critical tool to define transmission pathways and improve infection control” adds Thomas Kohl from the Research Center Borstel (senior author).

To address these questions, the researchers are currently initiating larger research initiatives using genome-based tools to deepen our understanding of this emerging pathogen, in particular with regard to potential modes of pathogen transmission in the hospital setting.

Original publication

Gröschel, M.I., Meehan, C.J., Barilar, I. et al. The phylogenetic landscape and nosocomial spread of the multidrug-resistant opportunist Stenotrophomonas maltophilia. Nat Commun 11, 2044 (2020). https://doi.org/10.1038/s41467-020-15123-0

Further information and contact

www.fz-borstel.de