Detection and Genomic Characterization of a Morganella morganii Isolate From China That Produces NDM-5

Abstract

The increasing prevalence and transmission of the carbapenem resistance gene bla _NDM-5 has led to a severe threat to public health. So far, bla _NDM-5 has been widely detected in various species of Enterobacterales and different hosts across various cities. However, there is no report on the bla _NDM-5- harboring Morganella morganii. In January 2016, the first NDM-5-producing Morganella morganii L241 was found in a stool sample of a patient diagnosed as recurrence of liver cancer in China. Identification of the species was performed using 16S rRNA gene sequencing. Carbapenemase genes were identified through both PCR and sequencing. To investigate the characteristics and complete genome sequence of the bla _NDM-5-harboring clinical isolate, antimicrobial susceptibility testing, S1 nuclease pulsed field gel electrophoresis, Southern blotting, transconjugation experiment, complete genome sequencing, and comparative genomic analysis were performed. M. morganii L241 was found to be resistant to broad-spectrum cephalosporins and carbapenems. The complete genome of L241 is made up from both a 3,850,444 bp circular chromosome and a 46,161 bp self-transmissible IncX3 plasmid encoding bla _NDM-5, which shared a conserved genetic context of bla _NDM-5 (ΔIS3000-ΔISAba125-IS5-bla _NDM-5-ble-trpF-dsbC-IS26). BLASTn analysis showed that IncX3 plasmids harboring bla _NDM genes have been found in 15 species among Enterobacterales from 13 different countries around the world thus far. In addition, comparative genomic analysis showed that M. morganii L241 exhibits a close relationship to M. morganii subsp. morganii KT with 107 SNPs. Our research demonstrated that IncX3 is a key element in the worldwide dissemination of bla _NDM-₅ among various species. Further research will be necessary to control and prevent the spread of such plasmids.

Keywords: IncX3; Morganella morganii; blaNDM–5; comparative genomic analysis; complete genome sequence.

FIGURE 1

A comparative genome analysis of NDM-5-producing Morganella morganii L241 and other M. morganii isolates based on SNPs. The plasmid replication types, β-lactamases resistance genes, catA genes, collection dates, locations, isolation sources, and hosts of isolates are shown. The annotation denotes the presence of plasmid replication types, β-lactamases resistance genes and catA genes as determined by online tools (http://www.genomicepidemiology.org/). The M. morganii L241 is indicated by red. Regions with bla_DHA gene among isolates are shown by gray shading. The detail information of isolates included in this study is summarized in Supplementary Table S1.

FIGURE 2

Plasmid profiles of M. morganii L241. (A) Plasmid size determination by S1-PFGE, with Salmonella enterica serotype Braenderup H9812 as the size marker. (B) Southern blotting hybridization with a bla_NDM-specific probe.

FIGURE 3

The genomic analysis of pNDM5-L241 plasmid. (A) Comparison of the pNDM5-L241 plasmid with the closely related plasmid based on BLASTn analyses (GenBank accession numbers from inside to outside are CP024820, MH105050, KX214669, MG833406, KY296103, and CP021759). (B) Genetic context of bla_NDM–5 on pNDM5-L241, pTB203 (CP029245) and pNDM_MGR194 (KF220657). Open reading frames (ORFs) are represented by arrows and colored in accordance with their putative functions: red arrows indicate antimicrobial resistance genes, green arrows represent mobile genetic elements, while genes encoding hypothetical proteins and proteins for plasmid stability are colored as gray and brown, respectively. Regions with a high degree of homology between plasmids are shown by gray shading.