Virulence and antimicrobial resistance genes profiling of Salmonella isolated from dead-in-shell eggs and hatchery environments with emphasis on class 1 integron gene cassette sequencing in XDR strains.

BACKGROUND: Dead-in-shell embryos may result from bacterial contamination of eggs, particularly infections caused by Salmonella spp. This study was conducted to investigate Salmonella prevalence in chicken farms in Ismailia Governorate, Egypt, characterization of serogroups, antimicrobial resistance profiles, biofilm-forming ability, virulence determinants (fimA, fimH, invA, stn, pefA, sopB, sopE1, and hilA), antimicrobial resistance genes (qnrS, qnrA, blaTEM, blaSHV, blaCTX-M, floR, tetA, and mcr-1), integrase genes (intI1 and intI3) and sequence analysis of gene cassettes associated with class 1 integrons.

METHODS: A total of 350 samples were collected, including dead-in-shell embryos (n = 285), egg nests (n = 33), and hatchery environments (n = 32). Bacteriological analysis, serogrouping, antimicrobial sensitivity testing, biofilm formation was performed as well as screening of virulence, antimicrobial resistance and integrase genes using PCR. Adding, sequencing of class 1 integron-associated gene cassettes.

RESULTS: The overall prevalence of Salmonella was 9.71%. Salmonella Enteritidis was the predominant serovar (29.41%). Among the recovered isolates, 23.53% were classified as extensively drug-resistant (XDR), while 76.47% exhibited multidrug resistance (MDR), with a notably high resistance to colistin (88.24%). Biofilm was detected in 79.41% of the isolates at varying degrees. All tested isolates (100%) harbored the examined virulence genes (fimA, fimH, invA, stn, pefA, sopB, sopE1, and hilA) as well as the antimicrobial resistance genes qnrS, blaTEM, and blaSHV, with a high prevalence of the mcr-1 gene (87.5%). The class 1 integron integrase gene (intI1) was detected in 87.5% of the tested isolates, whereas all isolates were negative for the class 3 integron gene (intI3). Sequencing of the integron-associated gene cassettes revealed the presence of estX, aadA alleles, purL, dfrA, and lnuF genes. Given the critical role of hatcheries in poultry production chain, the emergence of XDR and MDR Salmonella strains facilitates early colonization of hatched chicks, promoting persistence and dissemination throughout the poultry production system.

CONCLUSION: The emergence of highly virulent XDR and MDR Salmonella strains represents a significant public health threat, underscoring the urgent need for a One Health approach that integrates human, animal, and environmental health strategies to mitigate the spread of antimicrobial resistance and prevent further escalation of this alarming phenomenon.