Integrated MALDI‑TOF MS and WGS in a Prolonged ICU Pseudomonas Outbreak

In a prolonged intensive care unit (ICU) outbreak investigation of Pseudomonas aeruginosa, authors report using an integrated laboratory approach that combined phenotypic antimicrobial testing, MALDI‑TOF MS proteomic clustering, and whole genome sequencing to describe relatedness and resistance features over time. The outbreak set included 38 clinical isolates and one environmental isolate recovered from an ICU sink. Within this defined set, the report focuses on how antimicrobial resistance, biofilm phenotypes, environmental linkage, and method-to-method clustering agreement were described across the investigation.

Across the 38 clinical isolates, the authors describe phenotypic susceptibility results as showing high resistance rates to several commonly tested agents, with most isolates classified as multidrug resistant. They report that 32/38 clinical isolates were meropenem-resistant and were categorized as carbapenem-resistant P. aeruginosa (CRPA) based on that phenotype. For carbapenemase detection, the authors report identifying blaVIM in 22 isolates and note that the sink isolate was among the VIM-positive strains. In the report’s framing, meropenem resistance and blaVIM distribution are presented as co-occurring features observed within the outbreak isolates.

Biofilm formation was assessed for clinical and environmental isolates using the biofilm formation index (BFI), and the authors report that all 39 isolates were categorized as moderate or strong biofilm formers. Within that distribution, they report that 11 isolates met the study’s threshold for strong biofilm production and highlight examples including the sink isolate (PA_35) and a central venous catheter isolate (PA_34). By including the environmental isolate in the same assay series, the authors describe biofilm phenotyping as a characteristic assessed across sources rather than a clinical-only observation. Overall, biofilm-forming capacity was reported as consistently present across the outbreak isolate collection.

For genomic characterization, the authors report performing WGS on 12 representative isolates selected to reflect diversity over time, proteomic clustering patterns, resistance profiles, and inclusion of the environmental strain. Among the sequenced isolates, they report that ST111 and ST253 were predominant sequence types (ST111, n=4; ST253, n=4). They also describe WGS resistome findings as confirming blaVIM where previously detected and identifying oprD alterations in a subset as an additional reported feature compatible with carbapenem resistance mechanisms. In the report’s presentation, sequencing added strain-typing and resistance-feature detail alongside the phenotypic and targeted molecular findings.

When the authors compared MALDI‑TOF MS spectral clustering with whole genome sequencing (WGS) phylogeny for the sequenced isolates, they report predominant concordance with 9/12 clustering matches, while noting that subclusters were largely preserved even when higher-level cluster assignments differed. They identify PA_32, PA_28, and PA_23 as isolates that were discordant between methods in the comparison. For the environmental linkage described by sequencing, the authors report that the sink isolate clustered closely with a clinical subcluster and provide pairwise core-genome SNP distances to PA_23, PA_22, and PA_27 of 455, 791, and 933, respectively. They describe using routine AST alongside MALDI‑TOF MS spectral clustering as a rapid way to screen related isolates and prioritize representative samples for subsequent genomic analysis, including WGS for higher-resolution mapping.

Key Takeaways:

• The authors report an ICU outbreak investigation characterized with integrated phenotypic testing, proteomic clustering, and genomic analysis.
• Carbapenem resistance and blaVIM carriage were reported among outbreak isolates, with additional resistance-associated genomic features (including oprD alterations) described in sequenced representatives.
• MALDI‑TOF MS clustering was reported as largely concordant with WGS at the subcluster level in the sequenced set, with specific discordant isolates noted.