CRISPR Typing of Salmonella Isolates from Different Resources

Prevalence and genetic characteristics of Salmonella enterica serovar Meleagridis from animals and humans

Salmonella enterica serovar Meleagridis (S. Meleagridis) is a non-typhoidal Salmonella serotype commonly found in food and humans. In this study, we investigated 61 Chinese S. Meleagridis isolates from various sources, predominantly from pigs and pig products. Additionally, the serotype was also identified in samples from human infections. Whole-genome sequencing analysis of these isolates, combined with 10 isolates from other countries, demonstrated that the Chinese isolates formed a distinct Cluster C, further divided into two subclusters (Cluster C-1 and Cluster C-2) based on cgMLST analysis. CRISPR typing divided the 61 isolates into three CRISPR types (MCT1, MCT2, MCT3), belonging to Cluster I (96.7%, 59/61) and Cluster II (3.3%, 2/61), which corresponded to Cluster C-2 and Cluster C-1, respectively. Among the 48 identified spacers, the spacer SoeB5 was the only target differentiating MCT1 and MCT2 isolates of Cluster I. MelB12 and MelB13, identified in US and Denmark isolates, were not found among the 61 Chinese isolates. Examination of antimicrobial resistance gene profiles and their genetic contexts uncovered the presence of IncR plasmids in 43 (70.5%, 43/61) isolates within Cluster C, conferring resistance to tetracycline and trimethoprim/sulfamethoxazole. Homology analysis of spacers showed that 12 spacers exhibited similarity to sequences in phages or plasmids. Additionally, five spacers showed homology to sequences in plasmids from other Salmonella serotypes, suggesting their potential role in helping S. Meleagridis resist against Salmonella isolates carrying similar plasmids. The comprehensive analysis of CRISPR, cgMLST, and antimicrobial resistance in S. Meleagridis highlights the pig reservoir as a crucial factor in the evolution and transmission of this serotype to humans.

Genomic Identification of Multidrug-Resistant Salmonella Virchow Monophasic Variant Causing Human Septic Arthritis

The monophasic variant of Salmonella Typhimurium has emerged and increased rapidly worldwide during the past two decades. The loss of genes encoding the second-phase flagella and the acquirement of the multi-drug resistance cassette are the main genomic characteristics of the S. Typhimurium monophasic variant. In this study, two Salmonella strains were isolated from the knee effusion and feces of a 4-year-old girl who presented with a case of septic arthritis and fever, respectively. Primary serovar identification did not detect the second-phase flagellar antigens of the strains using the classical slide agglutination test. Whole-genome sequencing analysis was performed to reveal that the replacement of the fljAB operon by a 4.8-kb cassette from E. coli caused the non-expression of phase-2 flagellar antigens of the strains, which were confirmed to be a novel S. Virchow monophasic variant (Salmonella 6,7,14:r:-) by core-genome multi-locus sequence typing (cgMLST). Compared to the 16 published S. Virchow genomes, the two strains shared a unique CRISPR type of VCT12, and showed a close genetic relationship to S. Virchow BCW_2814 and BCW_2815 strains, isolated from Denmark and China, respectively, based on cgMLST and CRISPR typing. Additionally, the acquisition of Salmonella genomic island 2 (SGI2) with an antimicrobial resistance gene cassette enabled the strains to be multidrug-resistant to chloramphenicol, tetracycline, trimethoprim, and sulfamethoxazole. The emergence of the multidrug-resistant S. Virchow monophasic variant revealed that whole-genome sequencing and CRISPR typing could be applied to identify the serovaraints of Salmonella enterica strains in the national Salmonella surveillance system.