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Background  Members of the genus  Shigella  are intestinal pathogens and a major cause of seasonal outbreaks of bacterial diarrhea worldwide. Although humans are the conventional hosts of  Shigella  species, expansion of the  Shigella  host range to certain animals was recently reported. To investigate the prevalence of  Shigella sonnei  ( S. sonnei ) in yaks and perform molecular characterization, we analyzed 1132 fresh yak diarrheal stool samples and collected a total of 44 S. sonnei isolates.    Results  We performed multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) with  Xba I-digested DNA to study genetic relatedness among the 44 isolates, which were differentiated into 4 sequence types (STs) and 32 PFGE types (PTs). All isolates harbored virulence genes, and 87.36% tested positive for invasion plasmid antigen H ( ipaH ), invasion associated locus ( ial ) and the  Shigella  enterotoxin gene  sen . According to the results of antimicrobial susceptibility tests, 45.45% (20/44) were resistant to fluoroquinolones and/or cephalosporin. By sequencing the quinolone resistance determining region (QRDR) genes, we identified double mutations in  gyrA  (Ser83-Leu and Asp87-Asn) and a single mutation in  parC  (Ser80-Ile). All 12 fluoroquinolone-resistant  S. sonnei  isolates tested positive for the  aac(6′)-Ib-cr  gene but negative for  qepA . Three isolates harbored  qnr  genes, including two with  qnrS  and one with  qnrB.  In addition, three types of β-lactamase genes,  bla   TEM-1  ,  bla   OXA-1   and  bla   CTX-M-14/79  , were detected in cephalosporin-resistant isolates.    Conclusions  The findings of this study have enriched our knowledge of fluoroquinolone- and/or cephalosporin-resistant  S. sonnei  isolates from yaks, which has important public health significance.    Electronic supplementary material  The online version of this article (10.1186/s12917-018-1500-6) contains supplementary material, which is available to authorized users.

Molecular characterization of fluoroquinolone and/or cephalosporin resistance in Shigella sonnei isolates from yaks