Genomic characterization of Pseudomonas spp. on food: implications for spoilage, antimicrobial resistance and human infection

Abstract

Background: Pseudomonas species are common on food, but their contribution to the antimicrobial resistance gene (ARG) burden within food or as a source of clinical infection is unknown. Pseudomonas aeruginosa is an opportunistic pathogen responsible for a wide range of infections and is often hard to treat due to intrinsic and acquired ARGs commonly carried by this species. This study aimed to understand the potential role of Pseudomonas on food as a reservoir of ARGs and to assess the presence of potentially clinically significant Pseudomonas aeruginosa strains on food. To achieve this, we assessed the genetic relatedness (using whole genome sequencing) and virulence of food-derived isolates to those collected from humans.

Results: A non-specific culturing approach for Pseudomonas recovered the bacterial genus from 28 of 32 (87.5%) retail food samples, although no P. aeruginosa was identified. The Pseudomonas species recovered were not clinically relevant, contained no ARGs and are likely associated with food spoilage. A specific culture method for P. aeruginosa resulted in the recovery of P. aeruginosa from 14 of 128 (11%) retail food samples; isolates contained between four and seven ARGs each and belonged to 16 sequence types (STs), four of which have been isolated from human infections. Food P. aeruginosa isolates from these STs demonstrated high similarity to human-derived isolates, differing by 41-312 single nucleotide polymorphisms (SNPs). There were diverse P. aeruginosa collected from the same food sample with distinct STs present on some samples and isolates belonging to the same ST differing by 19-67 SNPs. The Galleria mellonella infection model showed that 15 of 16 STs isolated from food displayed virulence between a low-virulence (PAO1) and a high virulence (PA14) control.

Conclusion: The most frequent Pseudomonas recovered from food examined in this study carried no ARGs and are more likely to play a role in food spoilage rather than infection. P. aeruginosa isolates likely to be able to cause human infections and with multidrug resistant genotypes are present on a relatively small but still substantial proportions of retail foods examined. Given the frequency of exposure, the potential contribution of food to the burden of P. aeruginosa infections in humans should be evaluated more closely.

Keywords: Antimicrobial resistance; Food; Pseudomonas aeruginosa; Pseudomonas spp.; Spoilage; Whole genome sequencing.

Fig. 1

Pseudomonas species isolated from different food commodities. Number of Pseudomonas isolates analyzed from each food commodity, colored by species

Fig. 2

Prevalence of Pseudomonas aeruginosa found on different food commodities. Number of food samples belonging to each commodity that were cultured for and tested positive for P. aeruginosa

Fig. 3

Phylogenetic relationship between P. aeruginosa isolates collected from retail food samples. Maximum likelihood tree of the 56 P. aeruginosa isolates collected from food samples, colored by sample, food type (commodity) and sequence type (ST), along with a presence-absence matrix of the antimicrobial resistance genes (ARGs) they contained. The phylogenetic branch lengths are given in nucleotide substitutions per site, therefore a branch of length 0.0007 (as represented by the scale bar) equates to 3,356 substitutions, given that the core gene alignment consisted of 4,794,505 bp

Fig. 4

Phylogenetic relationship between Pseudomonas aeruginosa isolates collected from retail food samples and publicly available genomes. Maximum likelihood tree of 662 P. aeruginosa isolates, colored by source and continent of origin. The phylogenetic branch lengths are given in nucleotide substitutions per site, therefore a branch of length 0.009 (as represented by the scale bar) equates to 26,141 substitutions, given that the core gene alignment consisted of 2,904,504 bp