Molecular typing and drug resistance gene carriage of non-typhoidal Salmonella in Xi'an, Shaanxi, 2021−2023

Objective To analyze the molecular typing and drug resistance gene carriage of non-typhoidal Salmonella in Xi'an, Shaanxi province, from 2021 to 2023, explore its population structure and distribution of drug resistance genes, and provide evidence for the development of targeted Salmonella infection prevention and control strategies.

Methods The whole genome of 96 non-typhoid Salmonella strains was sequenced by using the MGISEQ-200 sequencing platform. After the assembly was completed, the minimum spanning tree of the whole genome alleles was constructed based on the core genome multilocus sequence typing (cgMLST) scheme provided by EntroBase, and software ResFinder 4.2.0 was used to identify drug-resistant genes.

Results The 96 strains of non-typhoidal Salmonella were divided into 17 HCC50 types, with HCC50_1 to HCC50_4 being the main prevalent types. The 9 strains of Salmonella HCC50_3 were all isolated in 2021, and the number of allele differences was less than 10. According to epidemiological data, they might have a common source. In HCC50_1 type, two single clone subtypes, HCC5_1 and HCC5_2, were detected in both 2022 and 2023, indicating the spread of two monoclonal strains in Xi'an. HCC50_2 and HCC50_4 could be further divided into 25 HCC5 subtypes, exhibiting sporadic distribution. β-lactam resistant gene bla_TEM-1 was carried by 80.21% (77/96) of the 96 non-typhoidal Salmonella isolates, and aminoglycoside resistant genes aph(3'')-Ib and aph(6)-Id were also carried by 80.21% (77/96) of the isolates, tetracycline resistant genes tet(A), tet(B), and tet(M) were carried by 69.79% (67/96) of the isolates, and sulfonamide resistant gene sul2 was carried by 73.96% (71/96) of the isolates.

Conclusion Whole genome cgMLST typing has high resolution to describe the population structure of Salmonella at multiple levels and identify sporadic outbreak clones. It is an important tool for epidemiological tracing. Predominant epidemic clones of non-typhoidal Salmonella exist in Xi'an, and most of them carry multiple drug-resistant genes, showing a trend of multidrug resistance. Drug-resistance surveillance and management should be strengthened.