WGS-Based Lineage and Antimicrobial Resistance Pattern of Salmonella Typhimurium Isolated during 2000–2017 in Peru

Abstract

Salmonella Typhimurium is associated with foodborne diseases worldwide, including in Peru, and its emerging antibiotic resistance (AMR) is now a global public health problem. Therefore, country-specific monitoring of the AMR emergence is vital to control this pathogen, and in these aspects, whole genome sequence (WGS)—based approaches are better than gene-based analyses. Here, we performed the antimicrobial susceptibility test for ten widely used antibiotics and WGS-based various analyses of 90 S. Typhimurium isolates (human, animal, and environment) from 14 cities of Peru isolated from 2000 to 2017 to understand the lineage and antimicrobial resistance pattern of this pathogen in Peru. Our results suggest that the Peruvian isolates are of Typhimurium serovar and predominantly belong to sequence type ST19. Genomic diversity analyses indicate an open pan-genome, and at least ten lineages are circulating in Peru. A total of 48.8% and 31.0% of isolates are phenotypically and genotypically resistant to at least one antibiotic, while 12.0% are multi-drug resistant (MDR). Genotype–phenotype correlations for ten tested drugs show >80% accuracy, and >90% specificity. Sensitivity above 90% was only achieved for ciprofloxacin and ceftazidime. Two lineages exhibit the majority of the MDR isolates. A total of 63 different AMR genes are detected, of which 30 are found in 17 different plasmids. Transmissible plasmids such as lncI-gamma/k, IncI1-I(Alpha), Col(pHAD28), IncFIB, IncHI2, and lncI2 that carry AMR genes associated with third-generation antibiotics are also identified. Finally, three new non-synonymous single nucleotide variations (SNVs) for nalidixic acid and eight new SNVs for nitrofurantoin resistance are predicted using genome-wide association studies, comparative genomics, and functional annotation. Our analysis provides for the first time the WGS-based details of the circulating S. Typhimurium lineages and their antimicrobial resistance pattern in Peru.

Genomic Characterization and Genetic Profiles of Salmonella Gallinarum Strains Isolated from Layers with Fowl Typhoid in Colombia

“…We found 26 chromosomal genes in all the SG strains, with most encoding efflux pumps, associated with resistance to 16 classes of antimicrobial agents as well as antiseptics and disinfectants. These results are similar to previous WGS-based studies of chromosome-encoded genes [ 49 , 50 , 51 ]. The bacterial chromosome-encoded systems involved in AMR typically confer a low level of resistance, but they are important as possible ‘stepping stones’ to higher levels of resistance [ 52 ].…”

Genetic diversity of Salmonella enterica isolated over 13 years from raw California almonds and from an almond orchard

“…One gene, aac(6')-Iaa, which confers resistance to aminoglycosides, was detected in the chromosome of all Salmonella subspecies diarizonae (3) and enterica (165) but not in arizonae (3) (Fig 1). The frequency of Salmonella enterica subspecies enterica isolates that carried an aminoglycoside acetyltransferase aac(6')-Iaa has been reported to be high (>95%) in multiple WGS analysis [55][56][57]. However, in a surveillance study of non-typhoidal Salmonella enterica, 11 isolates out of 3,491 (0.3%) showed phenotypic resistance to an aminoglycoside antimicrobial [55].…”

Antimicrobial Resistance Genes in Respiratory Bacteria from Weaned Dairy Heifers

“…In a similar study on Salmonella from small ruminants in Peru, partial concordance between the genotype and phenotype was identified. However, investigators also found some AMR was not predicted by the genotype [ 31 ]. A global study of AMR in Salmonella typhoid also found a similar result [ 28 ], suggesting that phenotype determined by MIC is not only conferred by known genes and may include yet-to-be-discovered regulatory methods.…”

“…The use of AMR gene presence to predict resistance phenotype has not been widely validated in multiple bacteria and within a genus [ 28 ]. Genotype predictions of phenotype are emerging with variable results; even within a single organism, the concordance of AMR genotype with phenotypic is variable [ 31 , 32 , 33 ]. Studies in Salmonella spp.…”

“…Studies in Salmonella spp. and Staphylococcus aureus reported some agreement between AMR genotypic and phenotype [ 31 , 34 , 35 ]. Substantial discrepancies were identified between AMR phenotype and genotype in Mannheimia haemolytica respiratory isolates from beef cattle, depending on what drug was being analyzed [ 36 ].…”