Related Experiment Video
Updated: Nov 6, 2025
Automated Analysis of Intracellular Phenotypes of Salmonella Using ImageJ
Published on: August 9, 2022
Genomic Identification of Multidrug-Resistant Salmonella Virchow Monophasic Variant Causing Human Septic Arthritis
Zhenyu Wang1,2,3, Haiyan Xu4, Chao Chu1,2,3
1Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-Food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Wenhui East Road 48, Yangzhou 225009, China.
Abstract:
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.
Insights
A novel multidrug-resistant Salmonella Virchow monophasic variant was identified in a child with septic arthritis. Whole-genome sequencing revealed genetic changes causing its unique characteristics and antimicrobial resistance, highlighting its importance for surveillance.
Area of Science:
- Microbiology and Infectious Diseases
- Genomics and Molecular Epidemiology
- Antimicrobial Resistance Surveillance
Background:
- The monophasic variant of *Salmonella* Typhimurium has globally increased, characterized by loss of second-phase flagella and multidrug resistance.
- Emergence of novel *Salmonella* serovariants poses challenges to traditional identification methods and public health surveillance.
Purpose of the Study:
- To characterize two *Salmonella* strains isolated from a pediatric septic arthritis case presenting with fever and knee effusion.
- To identify the genomic basis for the non-expression of phase-2 flagellar antigens and multidrug resistance in the isolated strains.
Main Methods:
- Classical slide agglutination test for initial serovar identification.
- Whole-genome sequencing (WGS) for detailed genomic analysis.
- Core-genome multi-locus sequence typing (cgMLST) and CRISPR typing for phylogenetic analysis and comparison with existing *S. Virchow* genomes.
Main Results:
- The isolated strains were identified as a novel *Salmonella* Virchow monophasic variant (6,7,14:r:-) due to replacement of the *fljAB* operon by an *E. coli*-derived cassette.
- cgMLST and CRISPR typing revealed a close genetic relationship to other *S. Virchow* strains and identified a unique CRISPR type (VCT12).
- Acquisition of *Salmonella* genomic island 2 (SGI2) conferred multidrug resistance to chloramphenicol, tetracycline, trimethoprim, and sulfamethoxazole.
Conclusions:
- The emergence of this multidrug-resistant *S. Virchow* monophasic variant underscores the need for advanced genomic surveillance.
- WGS and CRISPR typing are effective tools for identifying *Salmonella enterica* serovariants and tracking their spread within surveillance systems.
