In this study, a 4-year-old girl presented with a case of septic arthritis and fever. Salmonella was isolated from her knee effusion and feces; isolates were confirmed to be a novel S. Virchow monophasic variant (Salmonella 6,7,14:r:-) based on core genome MLST (cgMLST), CRISPR typing combined with analysis of the fljAB operon. Whole-genome sequencing analysis revealed that replacement of the fljAB operon by a 4.8 kb cassette from E. coli caused the nonexpression of phase-2 flagellar antigen in S. Virchow monophasic variant. Additionally, the acquisition of Salmonella genomic island 2 (SGI2) with an antimicrobial resistance gene cassette enabled the isolates to be multidrug-resistant (MDR) to chloramphenicol, tetracycline, trimethoprim, and sulfamethoxazole. The emerging of MDR S. Virchow monophasic variant causing human infection should be concerned in the national Salmonella surveillance system.

Background: Swine influenza is not only an economically important respiratory disease in swine, but also constantly poses a threat to human health. Hence, developing a rapid, sensitive and efficient detection method of swine influenza virus (SIV) is highly essential. Method: By aligning the HA gene sequences of SIV circulating in China in recent 10 years, a H1 primer-probe set targeting both Eurasian avian-like H1N1 (EA H1N1) and Pandemic 2009 H1N1 (Pdm09 H1N1) lineages plus a H3 prime-probe set targeting the prevalent human-like H3N2 (HL H3N2) subtype were designed, respectively. Further, a TaqMan-MGB based duplex one-step real time RT-PCR (RRT-PCR) assay was established, and the sensitivity, specificity and repeatability were evaluated. Results: The duplex RRT-PCR exhibited good sensitivity with the detection limit of 5 copies/μL HA plasmid for each of the EA H1N1, Pdm09 H1N1 and HL H3N2 subtype SIVs, and matched a detection accuracy of 94.4% (17/18) with traditional virus isolation through chicken embryo inoculation using experimentally infected mice lung samples. Besides, the method showed high repeatability both within-run and between-runs, and no cross-reactivity against some commonly circulated porcine viruses in China. Furthermore, the duplex RRT-PCR method revealed a relatively higher prevalent rate of H1 than H3 subtype SIV in 166 nasal swabs from pigs in some slaughterhouse during October~December, 2019. Conclusions: This developed assay could be very helpful for rapid differential detection and routine surveillance of EA H1N1, Pdm H1N1 and HL H3N2 subtype SIVs in China.