Genome analysis of NDM-1 producing Morganella morganii clinical isolate

Abstract

Objective: To analyze the resistome and virulence genes of Morganella morganii F675, a multidrug-resistant clinical isolate using whole genome sequencing (WGS). Methods: M. morganii F675 was isolated from a patient from Jerusalem, Israel. WGS was performed using both 454 and SOLiD sequencing technologies. Analyses of the bacterial resistome and other virulence genes were performed in addition to comparison with other available M. morganii genomes. Results: The assembled sequence had a genome size of 4,127,528 bp with G+C content of 51%. The resistome consisted of 13 antibiotic resistance genes including bla_NDM-1 located in a plasmid likely acquired from Acinetobacter spp. Moreover, we characterized for the first time the whole lipid A biosynthesis pathway in this species along with the O-antigen gene cluster, the urease gene cluster and several other virulence genes. Conclusion: The WGS analysis of this pathogen further provides insight into its pathogenicity and resistance to antibiotics.

Keywords::

• intrinsic colistin resistance
• multidrug-resistant bacteria
• NDM-1
• O-antigen
• resistome
• virulence genes

Acknowledgement

We thank Linda Hadjadj for technical assistance.

Financial & competing interests disclosure

This work was funded by the French Centre National de la Recherche Scientifique (CNRS) and Infectiopole Sud Foundation. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.

Key issues

• Whole-genome sequencing technology is a promising technology that could be implemented in clinical microbiology for studying pathogens and for antimicrobial resistance surveillance in real time.

• Morganella morganii F675 is a multidrug-resistant clinical isolate, harboring a total of 13 antibiotic resistance genes and showing susceptibility to only two antibiotics.

• The bla_NDM-1 of M. morganii F675 is likely to have been acquired from Acinetobacter spp. harboring such gene.

• M. morganii F675, though noncapsulated, possesses numerous virulence genes including urease-, hemolysin- and flagellar-encoding genes that have contributed to its distinctive infections.

• The putative O-antigen gene cluster of M. morganii is likely located within yibK-cpxA locus, similar to that of Providencia spp., and could be the same among the Proteeae bacteria.

• The presence, distinct clustering and gene duplications of genes known to be involved in lipid A modifications observed herein among intrinsically colistin-resistant bacteria (including M. morganii) could indicate that these bacteria have a unique lipid A structure different from that of naturally colistin-susceptible bacteria.

Notes