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Growing antimicrobial resistance (AMR) in Salmonella spp. is an evolving crisis exacerbated by antibiotic misuse. The present study was undertaken to delineate the temporal trends in the emergence of AMR among Salmonella enterica strains from India. Genome sequences and metadata of Salmonella enterica isolates were obtained from NCBI and were analyzed by the Resistance Gene Identifier tool (Comprehensive Antimicrobial Resistance Database), ABRicate (PlasmidFinderDB), BacAnt (IntegronDB, TransposonDB). Core-genome phylogeny was constructed with Roary and IQ-TREE. Antibiotics approval data were collected from the Central Drug Control Standards Organisation website and were analyzed with SPSS. Overall, AMR genes against 23 antibiotic classes were detected with cephalosporins and fluoroquinolones being at the top (17 genes each). For many antibiotics (monobactams, glycylcyclines, fosfomycins, elfamycins, edeine) occurrences of AMR genes preceded approval of the antibiotic for use. A statistically significant difference (p<0.05) was observed for resistance mechanisms, gene families, and SNP patterns, though no difference was noted for AMR gene carriage among salmonellae at decadal intervals. Our results deciphered the trends of AMR in Indian isolates of Salmonella enterica, highlighting occurrences of AMR genes and mechanisms before antibiotic approval and the usefulness of WGS-based AMR analysis for guiding future policy. [ABSTRACT FROM AUTHOR]

Salmonella enterica serovar Kentucky is a frequent cause for clinical infections in human patients. They are isolated and reported with multidrug resistance from the foods of animal origin from various countries. However, studies inferring the colistin resistance are limited. Hence, the current study reports the genetic factors and genomic analysis of the colistin-resistant Salmonella enterica serovar Kentucky strain COL-R for better understanding of its pathogenic potential and phylogenetic relatedness. The S. Kentucky strain COL-R was successfully isolated from chicken meat during ongoing surveillance of food of animal origin. Antimicrobial susceptibility testing revealed resistance to cefoxitin, erythromycin, gentamicin, tetracycline, and most disturbingly to ciprofloxacin and colistin (broth microdilution method). Whole-genome sequence of the COL-R strain was subjected to various in silico analysis to identify the virulence factors, antimicrobial resistance genes, pathogenicity islands and sequence type. The S. Kentucky COL-R strain belonged to sequence type (ST) 198 with a high probability (0.943) of being a human pathogen. Besides presence of integrated phage in the S. Kentucky COL-R genome, 38 genes conferring resistance to various antimicrobials and disinfectants were also identified. Nucleotide Polymorphism analysis indicated triple mutations in gyrA and parC genes conferring fluoroquinolone resistance. Phylogenomic analysis with 31 other S. Kentucky genomes revealed discernible clusters with S. Kentucky COL-R strain latching onto a cluster of high diversity (geographic location and isolation sources). Taken together, our results document the first occurrence of colistin resistance in a fluoroquinolone resistant S. Kentucky COL-R strain isolated from retail chicken and provide crucial information on the genomic features of the strain. [ABSTRACT FROM AUTHOR]

Introduction: Escherichia fergusonii is regarded as an emerging pathogen with zoonotic potential. In the current study, we undertook source-wise comparative genomic analyses (resistome, virulome, mobilome and pangenome) to understand the antimicrobial resistance, virulence, mobile genetic elements and phylogenetic diversity of E. fergusonii. Methods: Six E. fergusonii strains (5 multidrug resistant strains and 1 biofilm former) were isolated from poultry (duck faeces and retail chicken samples). Following confirmation by phenotypic and molecular methods, the isolates were further characterized and their genomes were sequenced. Comparative resisto-virulomobilome analyses and pangenomics were performed for E. fergusonii genomes, while including 125 other E. fergusonii genomes available from NCBI database. Results and discussion: Avian and porcine strains of E. fergusonii were found to carry significantly higher number of antimicrobial resistance genes (p < 0.05) and mobile genetic elements (plasmids, transposons and integrons) (p < 0.05), while the pathogenic potential of bovine strains was significantly higher compared to other strains (p < 0.05). Pan-genome development trends indicated open pan-genome for all strains (0 < γ < 1). Genomic diversity of avian strains was found to be greater than that from other sources. Phylogenetic analysis revealed close clustering among isolates of similar isolation source and geographical location. Indian isolates of E. fergusonii clustered closely with those from Chinese and a singleton Australian isolate. Overall, being the first pangenomic study on E. fergusonii, our analysis provided important cues on genomic features of the emerging pathogen E. fergusonii while highlighting the potential role of avian strains in dissemination of AMR. [ABSTRACT FROM AUTHOR]

This study reports faecal prevalence of Clostridium perfringens in free range ducks in North East India for the first time. We also report C. perfringens type A carrying cpb2 and cpe and type C carrying cpb2 and cpe strains in these ducks. Notably, a high prevalence (17.5%) of enterotoxin carrying C. perfringens strains and low antimicrobial resistance were observed. • Prevalence of C. perfringens in free-range ducks was 33.33% with lower antimicrobial resistance rate. • For the first time, C. perfringens type A cpb 2+ cpe +, type A cpe + and type C cpb2 + cpe + positive strains in free range ducks were detected. • 17.5% of C. perfringens isolates were positive for CP enterotoxin. [ABSTRACT FROM AUTHOR]