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Background  The natural hosts of  Shigella  are typically humans and other primates, but it has been shown that the host range of  Shigella  has expanded to many animals. Although  Shigella  is becoming a major threat to animals, there is limited information on the genetic background of local strains. The purpose of this study was to assess the presence of virulence factors and the molecular characteristics of  S. flexneri  isolated from calves with diarrhea.    Results  Fifty-four  S. flexneri  isolates from Gansun, Shanxi, Qinghai, Xinjiang and Tibet obtained during 2014 to 2016 possessed four typical biochemical characteristics of  Shigella . The prevalences of  ipaH ,  virA ,  ipaBCD ,  ial ,  sen ,  set1A ,  set1B  and  stx  were 100 %, 100 %, 77.78 %, 79.63 %, 48.15 %, 48.15 and 0 %, respectively. Multilocus variable number tandem repeat analysis (MLVA) based on 8 variable number of tandem repeat (VNTR) loci discriminated the isolates into 39 different MLVA types (MTs), pulsed field gel electrophoresis (PFGE) based on  Not I digestion divided the 54 isolates into 31 PFGE types (PTs), and multilocus sequence typing (MLST) based on 15 housekeeping genes differentiated the isolates into 7 MLST sequence types (STs).    Conclusions  The findings from this study enrich our knowledge of the molecular characteristics of  S. flexneri  collected from calves with diarrhea, which will be important for addressing clinical and epidemiological issues regarding shigellosis.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12866-021-02277-0.

Virulence factors and molecular characteristics of Shigella flexneri isolated from calves with diarrhea