Antibiotic Resistance and Phylogeny of Pseudomonas spp. Isolated over Three Decades from Chicken Meat in the Norwegian Food Chain

Abstract

Pseudomonas is ubiquitous in nature and a predominant genus in many foods and food processing environments, where it primarily represents major food spoilage organisms. The food chain has also been reported to be a potential reservoir of antibiotic-resistant Pseudomonas. The purpose of the current study was to determine the occurrence of antibiotic resistance in psychrotrophic Pseudomonas spp. collected over a time span of 26 years from retail chicken in Norway and characterize their genetic diversity, phylogenetic distribution and resistance genes through whole-genome sequence analyses. Among the 325 confirmed Pseudomonas spp. isolates by 16S rRNA gene sequencing, antibiotic susceptibility profiles of 175 isolates to 12 antibiotics were determined. A subset of 31 isolates being resistant to ≥3 antibiotics were whole-genome sequenced. The isolates were dominated by species of the P. fluorescens lineage. Isolates susceptible to all antibiotics or resistant to ≥3 antibiotics comprised 20.6% and 24.1%, respectively. The most common resistance was to aztreonam (72.6%), colistin (30.2%), imipenem (25.6%) and meropenem (12.6%). Resistance properties appeared relatively stable over the 26-year study period but with taxa-specific differences. Whole-genome sequencing showed high genome variability, where isolates resistant to ≥3 antibiotics belonged to seven species. A single metallo-betalactmase gene (cphA) was detected, though intrinsic resistance determinants dominated, including resistance-nodulation (RND), ATP-binding cassette (ABC) and small multidrug resistance (Smr) efflux pumps. This study provides further knowledge on the distribution of psychrotrophic Pseudomonas spp. in chicken meat and their antibiotic resistance properties. Further monitoring should be encouraged to determine food as a source of antibiotic resistance and maintain the overall favorable situation with regard to antibiotic resistance in the Norwegian food chain.

Keywords: Pseudomonas; antibiotic resistance; phylogeny; poultry; whole-genome sequencing.

Figure 1

Phylogenetic distribution of Pseudomonas spp. isolates (n = 325) based on partial 16S rRNA gene (288 bp) sequencing. Assignment of the isolates to presumptive species and to the strain collections is indicated. The subsets of isolates subjected to MIC (n = 175) and WGS (n = 31) analyses are shown. Isolates with resistance to the specific antibiotics are indicated in red. Antibiotic abbreviations: MERO (meropenem), IMI (imipenem), TAZ (ceftazidime), CZA (ceftazidime/avibactam), C/T (ceftolozane/tazobactam), CIP (ciprofloxacin), AZT (aztreonam), P/T4 (piperacillin/tazobactam), COL (colistin). Antibiotics for which all isolates were sensitive (amikacin, gentamicin, tobramycin; according to Table 2) were not included.

Figure 2

Proportion of antibiotic-susceptible and resistant isolates (total numbers n = 175) for all collections. See Table 2 for the 12 antibiotics tested.

Figure 3

Core gene alignment tree. The presence or absence of 42,492 aggregated pan-genome genes in 31 isolates is shown. Blue denotes that a gene is present in the corresponding isolate (identified by isolate name to the right). The isolate names are colored according to the collection number (see Figure 1). Species assignment is shown according to rMLST for isolates with 100% match (except for P. brenneri).