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Objectives:  Ongoing acquisition of antimicrobial resistance genes has made  Morganella morganii  a new clinical treatment challenge. Understanding the molecular epidemiology of  M. morganii  will contribute to clinical treatment and prevention.   Methods:  We undertook a 6-year clinical molecular epidemiological investigation of  M. morganii  from three tertiary hospitals in China since 2014. Antimicrobial susceptibility testing was performed using a VITEK-2 system. All isolates were screened for β-lactam and plasmid-mediated quinolone resistance genes by PCR. Isolates carrying carbapenem-resistant genes were subjected to whole-genome sequencing (WGS). The variation and evolution of these mobile genetic elements (MGEs) were then systematically analyzed.   Results:  Among all  M. morganii  isolates ( n  = 335), forty (11.9%) were recognized as multidrug resistant strains.  qnrD1 ,  aac(6′)-Ib-cr ,  bla  TEM–104 , and  bla  CTX–M–162  were the top four most prevalent resistance genes. Notably, phylogenomic and population structure analysis suggested clade 1 (rhierBAPS SC3 and SC5) associated with multiple resistance genes seemed to be widely spread. WGS showed a  bla  OXA–181 -carrying IncX3 plasmid and a  Proteus  genomic island 2 variant carrying  bla  CTX–M–3 ,  aac(6′)-Ib-cr  coexisted in the same multidrug resistant strain zy_m28. Additionally, a  bla  IMP–1 -carrying IncP-1β type plasmid was found in the strain nx_m63.   Conclusion:  This study indicates a clade of  M. morganii  is prone to acquire resistance genes, and multidrug resistant  M. morganii  are increasing by harboring a variety of MGEs including two newly discovered ones in the species. We should be vigilant that  M. morganii  may bring more extensive and challenging antimicrobial resistance issue.

Clinical Molecular and Genomic Epidemiology of Morganella morganii in China