AUTHOR=Li Shuangshuang , Jiang Xiaoyuan , Li Cuidan , Ju Yingjiao , Yue Liya , Chen Fangzhou , Hu Lingfei , Wang Jing , Hu Xin , Tuohetaerbaike Bahetibieke , Wen Hao , Zhang Wenbao , Zhou Dongsheng , Yin Zhe , Chen Fei 

TITLE=A blaSIM-1 and mcr-9.2 harboring Klebsiella michiganensis strain reported and genomic characteristics of Klebsiella michiganensis

JOURNAL=Frontiers in Cellular and Infection Microbiology

VOLUME=12

YEAR=2022

URL=https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2022.973901

DOI=10.3389/fcimb.2022.973901

ISSN=2235-2988

ABSTRACT=<p>As a newly emerging <italic>Klebsiella</italic> pathogen, more and more <italic>Klebsiella michiganensis</italic> drug resistant strains have been reported in recent years, which posed serious threats to public health. Here we first reported a multidrug-resistant <italic>K. michiganensis</italic> strain 12084 with two <italic>bla</italic><sub>SIM-1</sub> and one <italic>mcr-9.2</italic> genes isolated from the sputum specimen of a patient in the Second Affiliated Hospital of Zhejiang University School of Medicine and analyzed its genetic basis and drug-resistance phenotypes. Genetic analysis showed that this strain harbored three different incompatibility groups (IncHI2, IncHI5, and IncFII<sub>pKPHS2</sub>:IncFIB-4.1) of plasmids (p12084-HI2, p12084-HI5, and p12084-FII). A total of 26 drug-resistance genes belonging to 12 classes of antibiotics were identified, most of which (24) were located on two plasmids (p12084-HI2 and p12084-HI5). Interestingly, two <italic>bla</italic><sub>SIM-1</sub> genes were identified to locate on p12084-HI2 and p12084-HI5, respectively, both of which were embedded in In630, indicating their genetic homogeny. It was noting that one <italic>bla</italic><sub>SIM-1</sub> gene was situated in a novel unit transposon (referred to as Tn<italic>6733</italic>) on the p12084-HI5 plasmid. We also discovered an <italic>mcr-9.2</italic> gene on the p12084-HI2 plasmid. To the best of our knowledge, this is the first report of a <italic>bla</italic><sub>SIM-1</sub> and <italic>mcr-9.2</italic> harboring <italic>K. michiganensis</italic> strain. We then investigated the population structure/classification, and antibiotic resistance for all 275 availably global <italic>K. michiganensis</italic> genomes. Population structure revealed that <italic>K. michiganensis</italic> could be divided into two main clades (Clade 1 and Clade 2); the most popular ST29 was located in Clade 1, while other common STs (such as ST50, ST27, and ST43) were located in Clade 2. Drug-resistance analysis showed 25.5% of the <italic>K. michiganensis</italic> strains (70/275) harboring at least one carbapenemase gene, indicating severe drug resistance of <italic>K. michiganensis</italic> beyond our imagination; this is a dangerous trend and should be closely monitored, especially for ST27 <italic>K. michiganensis</italic> with the most drug-resistant genes among all the STs. Overall, we reported a <italic>bla</italic><sub>SIM-1</sub> and <italic>mcr-9.2</italic> harboring <italic>K. michiganensis</italic> strain, and further revealed the population structure/classification, and drug-resistance of <italic>K. michiganensis</italic>, which provided an important framework, reference, and improved understanding of <italic>K. michiganensis</italic>.</p>