Purpose: A detailed genomic comparison of Peruvian clinical Salmonella enterica serovar Infantis strains bearing a blaCTX-M 65 (cefotaximase) gene in relation to similar strains from environmental and food sources is presented.
Methods: Three hundred twenty-two clinical S. Infantis strains were obtained from patients with diarrhea from 1997-2014, representing a network of 13 Peruvian hospitals. These strains were characterized using PCR; microarray; whole genome sequencing (WGS); whole genome core gene (wgCGA) with 2700+ Salmonella core gene loci; kSNP3; in-house R; and ResFinder analyses for blaCTX-M-65 genes. Serotype was confirmed with SeqSero, Premitest, and microarray.
Results: Results showed that 206 (64%) of the strains associated with 6 different hospitals were PCR-positive for blaCTX-M-65 which was confirmed by WGS in 26 strains. Other antibiotic resistance genes: blaCTX-M- 15; blaSHV-129; blaOXA-2; blaTEM-1B; and blaCTX-M-2 were also noteworthy. Genomic reconstruction revealed a highly conserved, previously reported 320 kb plasmid in all blaCTX-M-65-positive strains. For comparison, other S. Infantis genomes (100+) of environmental, animal, and human origin were obtained from NCBI; intra-serovar differences were seen with these strains compared to Peruvian clinical strains. Microarray, wgCGA and kSNP3 separated the S. Infantis strains into distinct clusters. Microarray analysis, which included the mobilome region, provided a higher resolution of blaCTX-M-65 S. Infantis strains. Genomic characterization showed that the blaCTX-M 65 genes among these Peruvian clinical S. Infantis strains were comparable to resistant strains from environmental and animal origin.
Significance: High similarity between blaCTX-M-65 positive S. Infantis strains from hospitals, and other sources, is a matter of concern for public health. The results of the study demonstrate a need to expand genomic targets to detect blaCTX-M-65-resistant strains including those associated with the food supply.