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Background   Shigella  spp., facultative anaerobic bacilli of the family  Enterobacteriaceae , are one of the most common causes of diarrheal diseases in human worldwide which have become a significant public health burden. So, we aimed to analyze the antimicrobial phenotypes and to elucidate the molecular mechanisms underlying resistance to cephalosporins and fluoroquinolones in  Shigella  isolates from patients with diarrhea in Shanxi Province.    Results  During 2006–2016, we isolated a total of 474  Shigella  strains (including 337  S. flexneri  and 137  S. sonnei ). The isolates showed high rates of resistance to traditional antimicrobials, and 26, 18.1 and 3.0% of them exhibited resistance to cephalosporins, fluoroquinolones and co-resistance to cephalosporins and fluoroquinolones, respectively. Notably, 91.1% of these isolates, including 22 isolates that showed an ACTSuT profile, exhibited multidrug resistance (MDR). The resistance rates to cephalosporins in  S. sonnei  isolates were higher than those in  S. flexneri.  Conversely, the resistance rates to fluoroquinolones were considerably higher in  S. flexneri  isolates. Among the 123 cephalosporins-resistant isolates, the most common extended-spectrum beta-lactamase gene was  bla  TEM-1 , followed by  bla  CTX-M ,  bla  OXA-1 , and  bla  SHV-12 . Six subtypes of  bla  CTX-M  were identified,  bla  CTX-M-14  ( n  = 36) and  bla  CTX-M-55  ( n  = 26) were found to be dominant. Of all the 86 isolates with resistance to fluoroquinolones and having at least one mutation (Ser83Leu, His211Tyr, or Asp87Gly) in the the quinolone resistance-determining regions of  gyr A, 79 also had mutation of  par C (Ser80Ile), whereas 7 contained plasmid-mediated quinolone resistance genes including  qnr A,  qnr B,  qnr S, and  aac(60)-Ib-cr.  Furthermore, pulsed-field gel electrophoresis analysis (PFGE) showed a considerable genetic diversity in  S. flexneri  isolates. However, the  S. sonnei  isolates had a high genetic similarity.    Conclusions  Coexistence of diverse resistance genes causing the emergence and transmission of MDR might render the treatment of shigellosis difficult. Therefore, continuous surveillance might be needed to understand the actual disease burden and provide guidance for shigellosis.    Electronic supplementary material  The online version of this article (10.1186/s12866-019-1495-6) contains supplementary material, which is available to authorized users.

Antimicrobial resistance and genetic characterization of Shigella spp. in Shanxi Province, China, during 2006–2016