Antimicrobial resistance analysis and whole-genome sequencing of Salmonella enterica serovar Indiana isolate from ducks

Abstract

Salmonella is one of the most important genera of enteric pathogenic bacteria that threaten duck farms. The aim of this study was to increase the understanding of antimicrobial resistance mechanisms in Salmonella enterica serovar Indiana isolates of duck origin. Salmonella were isolated from duck cloacal swabs collected from duck farms located in Zhejiang and Henan provinces of China. All of the isolates were identified after a series of confirmatory tests including selective culture method, biochemical tests, serotyping and PCR targeting the invA gene. Isolates were then subjected to antimicrobial susceptibility testing by the standard Kirby-Bauer disk diffusion method. Subsequently, whole-genome sequencing analysis of a representative multidrug-resistant Salmonella Indiana isolate (designated SAP) was performed using a combination of Nanopore and Illumina sequencing platforms. A total of 18 Salmonella isolates were identified. The predominant serotype was Salmonella Indiana (14 of 18 isolates). All 14 Salmonella Indiana isolates were multiresistant to ten antimicrobials with multidrug resistance to ampicillin, cefoperazone, gentamicin, kanamycin, neomycin, tetracycline, norfloxacin, ciprofloxacin, colistin B and trimethoprim/sulfamethoxazole. The genome of Salmonella Indiana isolate SAP carried 65 antimicrobial resistance genes (ARGs) belonging to different families, including genes encoding antibiotic efflux pumps, rpsL, kdpDE, aac(6'), general bacterial porin with reduced permeability to β-lactams, AmpC-type β-lactamase gene, mutant lpx gene conferring resistance to colistin, sulfonamide-resistant dihydropteroate synthase folP and trimethoprim-resistant dihydrofolate reductase dfr. The Salmonella Indiana strain isolated in this study carried multiple ARGs and exhibited resistance to multiple antibiotics.