AUTHOR=Alzahrani Khaloud O. , AL-Reshoodi Fahad M. , Alshdokhi Elaf A. , Alhamed Ashwaq S. , Al Hadlaq Meshari A. , Mujallad Mohammed I. , Mukhtar Lenah E. , Alsufyani Amani T. , Alajlan Abdullah A. , Al Rashidy Malfi S. , Al Dawsari Mashan J. , Al-Akeel Saleh I. , AL-Harthi Meshari H. , Al Manee Abdulaziz M. , Alghoribi Majed F. , Alajel Suliman M. 

TITLE=Antimicrobial resistance and genomic characterization of Salmonella enterica isolates from chicken meat

JOURNAL=Frontiers in Microbiology

VOLUME=14

YEAR=2023

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1104164

DOI=10.3389/fmicb.2023.1104164

ISSN=1664-302X

ABSTRACT=<p>This study investigated genotypic and phenotypic antimicrobial resistance profiles, phylogenic relatedness, plasmid and virulence composition of 39 <italic>Salmonella enterica</italic> strains isolated from chicken meat samples using whole genome sequencing (WGS) technology. Four distinct serotypes were identified; <italic>Salmonella</italic> Minnesota (16/39, 41%), <italic>Salmonella</italic> Infantis (13/39, 33.3%), <italic>Salmonella</italic> Enteritidis (9/39, 23.1%), and one isolate was detected for <italic>Salmonella</italic> Kentucky (1/39, 2.6%), with sequence types (STs) as followed: ST548, ST32, ST11, and ST198, respectively. Phenotypic resistance to tetracycline (91.2%), ampicillin (82.4%), sulfisoxazole (64.7%), and nalidixic acid (61.6%) was the most observed. Resistome analysis revealed the presence of resistance genes to aminoglycosides, β-lactamase, sulfonamides, trimethoprim, phenicol, lincosamide, macrolides, and tetracyclines. Plasmidome showed the presence of eight incompatibility groups, including IncA/C2, IncFIB(K)_1_Kpn3, Col440I_1, IncR, IncX1, IncI1_1_Alpha, IncFIB(S)/IncFII(S), IncHI2/IncHI2A, IncX2 and ColpVC plasmids across the 39 genomes. Three resistance genes, <italic>sul2, tetA</italic> and <italic>bla<sub>CMY-2,</sub></italic> were predicted to be located on IncA/C2 plasmid in <italic>S.</italic> Minnesota isolates, whereas all <italic>S.</italic> Infantis isolates were positive to IncFIB(K)_1_Kpn3 plasmid that carries <italic>bla</italic><sub>CTX-M-65</sub> gene. Eleven <italic>Salmonella</italic> pathogenicity islands and up to 131 stress and/or virulence genes were identified in the evaluated genomes. Phylogenetic analysis showed four phylogroups that were consistent with the identified ST profiles with a high level of inter-diversity between isolates. This is the first genomic characterization of <italic>Salmonella</italic> isolates from retail chicken meat in Saudi Arabia using WGS technology. The availability of <italic>Salmonella</italic> genomes from multiple geographic locations, including Saudi Arabia, would be highly beneficial in future source-tracking, especially during epidemiological surveillance and outbreak investigations.</p>