Abstract
Pseudomonas aeruginosa is a highly versatile, antibiotic-resistant Gram-negative bacterium known for causing opportunistic infections and contamination of industrial products. Despite extensive genomic analysis of clinical P. aeruginosa strains, no genomes exist for preservative-tolerant industrial strains. A unique collection of 69 industrial isolates was assembled and compared to clinical and environmental strains; 16 genetically distinct industrial strains were subjected to array tube genotyping, multilocus sequence typing and whole-genome sequencing. The industrial strains possessed high preservative tolerance and were dispersed widely across P. aeruginosa as a species, but recurrence of strains from the same lineage within specific industrial products and locations was identified. The industrial P. aeruginosa genomes (mean=7.0 Mb) were significantly larger than those of previously sequenced environmental (mean=6.5 Mb; n=19) and clinical (mean=6.6 Mb; n=66) strains. Complete sequencing of the P. aeruginosa industrial strain RW109, which encoded the largest genome (7.75 Mb), revealed a multireplicon structure including a megaplasmid (555 265 bp) and large plasmid (151 612 bp). The RW109 megaplasmid represented an emerging plasmid family conserved in seven industrial and two clinical P. aeruginosa strains, and associated with extremely stress-resilient phenotypes, including antimicrobial resistance and solvent tolerance. Here, by defining the detailed phylogenomics of P. aeruginosa industrial strains, we show that they uniquely possess multireplicon, megaplasmid-bearing genomes, and significantly greater genomic content worthy of further study.
Highlights
Pseudomonas aeruginosa is a widespread human opportunistic pathogen and has been highlighted as a key global threat in relation to antimicrobial resistance, as one of the ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, P. aeruginosa and Enterobacter cloacae) pathogens [1]
By establishing a unique collection of P. aeruginosa isolates from industrial sources spanning a decade, different global locations and multiple product types, we have shown that they possess multireplicon genomes encoding 300 kb of extra DNA compared to strains from other sources
P. aeruginosa is a common contaminant in xenobiotic settings and we identified problematic strains with high preservative tolerance that were capable of causing recurrent industrial incidents
Summary
Pseudomonas aeruginosa is a widespread human opportunistic pathogen and has been highlighted as a key global threat in relation to antimicrobial resistance, as one of the ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, P. aeruginosa and Enterobacter cloacae) pathogens [1]. Within the home and personal care industry, microbial contamination is a major cause of product recalls and may represent a threat to consumer health [6]. Industrial manufacturers work to a number of guidelines and International Organization for Standardization (ISO) recommendations to prevent contaminated products from reaching the market place. Preservatives such as parabens, isothiazolinones, formaldehyde releasers, alcohols and organic acids are widely used to maintain product stability and prevent microbial proliferation [10]. Global recall databases show that P. aeruginosa is a major cause of contamination, with, for example, >33 % of cosmetic product incidents involving the bacterium [11]
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