Whole-genome characterisation of TEM-1 and CMY-2 β-lactamase-producing Salmonella Kentucky ST198 in Lebanese broiler chain. (December 2020) - El Hage, Rima
Highlights: First study confirming the emergence of ciprofloxacin-resistant (CIP R ) Salmonella Kentucky ST198 in Lebanese broilers. First evidence of cephamycinase-producing strains in Lebanon. High relatedness between seven CIP R Salmonella Kentucky ST198 clones. Involvement of IS 10 -mediated transposition in IS Ecp1 – bla CMY-2 mobilisation. Findings of an arsenal of virulence genes in Salmonella Kentucky ST198 isolates. Abstract: Objectives: Salmonella enterica subsp. enterica serovar Kentucky has been associated with the worldwide ciprofloxacin-resistant (CIP R ) Salmonella Kentucky sequence type 198 (ST198) epidemic clone, mostly recovered from poultry farms and products. The aim of this study was to examine whether this expanding clone exists in the Lebanese broiler chain. Methods: Eight CIP R and extended-spectrum cephalosporin-resistant Salmonella Kentucky isolates previously recovered from Lebanese broilers were genetically characterised by whole-genome sequencing. Results: Seven of the eight isolates belonged to ST198 and were phylogenetically closely related. They all harboured mutations in the chromosomal quinolone resistance genes gyrA and parC with double and single substitutions, respectively. The bla TEM-1B and bla CMY-2 genes were both detected in six isolates. Insertion sequence IS Ecp1 was located upstream of bla CMY-2, harboured by IncI1 plasmids in four strains. An IS 10 transposition coupled to homologous recombination at transposition sites mediated CMY-2 plasmid integration into the chromosome of one strain. Resistance genes to aminoglycosides [ aadA7 and aac(3)-Id ], tetracyclines [ tet(A) ] and sulfonamides ( sul1 ) were detected in five strains, among which four were positive for the presence of Salmonella genomic island 1 (SGI1) variant SGI1-K. All studied isolates harboured a variety of Salmonella pathogenicity islands (SPIs) as well as common regulatory and virulence genes. Conclusion: Here we report for the first time in Lebanon the detection and dissemination of the emerging highly drug-resistant Salmonella Kentucky ST198. Our findings shed new light on this clone as a potential public-health threat.