Molecular Detection and Antimicrobial Resistance Profiling of Salmonella spp. in Commercial Poultry Farms

Abstract

Salmonella spp., particularly nontyphoidal serovars, remain a leading cause of zoonotic foodborne illness globally, with commercial poultry serving as a primary reservoir and contributing to an estimated 153 million human cases and over 155,000 deaths annually. This review synthesizes recent advances in molecular detection and antimicrobial resistance (AMR) profiling of Salmonella in poultry production systems. Conventional culture-based methods are increasingly supplemented or replaced by rapid, sensitive techniques including PCR (targeting invA, ttr, hilA), real-time qPCR, loop-mediated isothermal amplification (LAMP), digital PCR, and CRISPR-based serotyping (CRISPR-SeroSeq), enabling high-throughput identification and serovar discrimination even in complex matrices (cloacal swabs, litter, embryonated eggs). Prevalence varies widely (pooled estimates 12–14% in meta-analyses from Ethiopia, Bangladesh, and Nepal), with S. Typhimurium, S. Enteritidis, and S. Kentucky frequently dominant. AMR profiling reveals alarming trends of multidrug resistance (MDR), including resistance to critically important classes (fluoroquinolones, third-generation cephalosporins, colistin), driven by extended-spectrum β-lactamases (ESBLs), plasmid-mediated quinolone resistance (PMQR), and integrons. Horizontal gene transfer and biofilm formation further complicate control. Integrated strategies—stringent biosecurity, vaccination, competitive exclusion, and prudent antimicrobial stewardship—are emphasized to mitigate transmission and preserve treatment efficacy in the face of rising AMR threats.