Genomic Epidemiology of MBL-Producing Pseudomonas putida Group Isolates in Poland

• Published in: Infectious diseases and therapy 2022-08, Vol.11 (4), p.1725-1740
• Main Authors: Urbanowicz, Paweł, Izdebski, Radosław, Biedrzycka, Marta, Literacka, Elżbieta, Hryniewicz, Waleria, Gniadkowski, Marek
• Format: Article
• Language: English
• Subjects: Analysis; Antibiotics; Brief Report; DNA sequencing; Drug resistance in microorganisms; Epidemiology; Genomes; Genomics; Genotypes; Infectious Diseases; Internal Medicine; Medicine; Medicine & Public Health; Nucleotide sequencing; Single nucleotide polymorphisms
• ISSN: 2193-8229; 2193-6382
• DOI: 10.1007/s40121-022-00659-z

Introduction Pseudomonas putida group are described as low-incidence opportunistic pathogens, but also as a significant reservoir of antimicrobial resistance (AMR) genes, including those of metallo-β-lactamases (MBLs). Our objective was the molecular and genomic characterization of MBL-producing P. putida (MPPP) group isolates from Poland, focusing on population structures, successful genotypes and MBL-encoding integrons. Methods During a country-wide MBL surveillance in Pseudomonas spp., 59 non-duplicate MPPP isolates were collected from 36 hospitals in 23 towns from 2003 to 2016. All of the isolates were subjected to whole-genome sequencing (WGS), followed by species identification, multi-locus sequence typing (MLST), single-nucleotide polymorphism (SNP)-based phylogenetic/clonality analysis, resistome determination, and susceptibility testing. Results The study collection comprised 12 species, of which P. alloputida ( n  = 19) , P. monteilii ( n  = 15), and P. asiatica ( n  = 11) prevailed, while the others were P. kurunegalensis, P. putida, P. soli, P. mosselii, P. juntendi , and four potentially new species. MLST classified the isolates into 23 sequence types (STs) of which 21 were new, with three main clones, namely P. alloputida ST69, P.monteilii ST95 and P. asiatica ST15. The isolates produced VIM-like MBLs only, largely VIM-2 ( n  = 40), encoded by 24 different class 1 integrons (ten new), a number of which occurred also in P. aeruginosa and/or Enterobacterales in Poland. The plasmid pool was dominated by IncP-9, IncP-2, and pMOS94-like types. Multiple isolates were extensively drug-resistant. Conclusions This study, being one of the most comprehensive analyses of MPPP so far, has shown high diversity of the isolates in general, with three apparently international lineages, each internally diversified by MBL-encoding structures.