A novel characterised multidrug-resistant Pseudocitrobacter isolated from a patient colonised while admitted to a tertiary teaching hospital

S. A. Kelly, N. H. O'Connell, T. P. Thompson, L. Dillon, J. Wu, C. Creevey, J. Powell, B. F. Gilmore, C. P. Dunne*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

1 Citation (Scopus)
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Abstract

Background: Reports of nosocomial infections typically describe recognised microorganisms. Here, a novel bacterial species was isolated, based on rectal swab screening for carbapenemases post-admission, then phenotypically and genetically characterized. 

Methods: Sensititre, Vitek and API kits, MALDI and Illumina MiSeq were employed before profiles and phylogeny were compared with other related species.

 Findings: Determined to be a possible Enterobacterales, the isolate was found to have 99.7% 16s rRNA identity to Pseudocitrobacter corydidari; an Asian cockroach-associated species. Given the highly conserved/low variability of 16S rRNA genes in Enterobacterales, average nucleotide identity (ANI) analysis compared the new isolate's genome with those of 18 Enterobacteriaceae species, including confirmed species of Pseudocitrobacter and unnamed Pseudocitrobacter species in the SILVA database. Of these, Pseudocitrobacter corydidari had the highest ANI at 0.9562. The published genome of the only known isolate of P. corydidari does not include Antimicrobial Resistance Genes (ARGs), with exception of potential drug efflux transporters. In contrast, our clinical isolate bears recognised antimicrobial resistance genes, including Klebsiella pneumoniae carbapenemase. The associated genome suggests resistance to carbapenems, β-lactams, sulfonamides, fluoroquinolones, macrolides, aminoglycosides and cephalosporins. Phenotypic antimicrobial resistance was confirmed. 

Conclusion: Evident variations in ARG profiles, human colonization and origin in a clinically relevant niche that is geographically, physically and chemically disparate lend credibility for divergent evolution or, less likely, parallel evolution with P. corydidari. Genome data for this new species have been submitted to GENBANK using the proposed nomenclature Pseudocitrobacter limerickensis. The patient was colonized, rather than infected, and did not require antimicrobial treatment.

Original languageEnglish
Pages (from-to)193-202
Number of pages10
JournalJournal of Hospital Infection
Volume145
Early online date13 Feb 2024
DOIs
Publication statusPublished - Mar 2024

Bibliographical note

Funding Information:
The authors wish to thank the medical scientists and Larry Murphy at University Hospital Limerick, and technician staff at the University of Limerick School of Medicine (Dr Miranda Kiernan, Dr Margaret Toomey and Hilda Fogarty) and Keith McCracken for their aid in this work. In addition, the authors wish to thank the Irish CPE National Reference Laboratory for their cooperation in this work, and Professor Emeritus Aharon Oren (The Hebrew University of Jerusalem, Israel) for expert guidance on nomenclature.

Publisher Copyright:
© 2024 The Author(s)

Keywords

  • Hospital
  • Hospital-acquired infection
  • Novel species
  • Pseudocitrobacter spp.
  • Resistance
  • Wastewater

ASJC Scopus subject areas

  • Microbiology (medical)
  • Infectious Diseases

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