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

doi:10.1016/j.jhin.2023.12.010

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 journal › Article › peer-review

2 Citations (Scopus)

88 Downloads (Pure)

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 language	English
Pages (from-to)	193-202
Number of pages	10
Journal	Journal of Hospital Infection
Volume	145
Early online date	13 Feb 2024
DOIs	https://doi.org/10.1016/j.jhin.2023.12.010
Publication status	Published - 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

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.1016/j.jhin.2023.12.010Licence: CC BY

A novel characterized multi-drug-resistant Pseudocitrobacter sp. isolated from a patient colonized while admitted to a tertiary teaching hospital
Copyright 2024 the authors. This is an open access article published under a Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium, provided the author and source are cited.
Final published version, 1.13 MBLicence: CC BY

Deciphering the relationship between AMR phenotype and genotype utilising machine learning models.
Dillon, L. (Author), Creevey, C. (Supervisor) & Huws, S. (Supervisor), Dec 2024
Student thesis: Doctoral Thesis › Doctor of Philosophy

File

Cite this

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

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.",

keywords = "Hospital, Hospital-acquired infection, Novel species, Pseudocitrobacter spp., Resistance, Wastewater",

author = "Kelly, {S. A.} and O'Connell, {N. H.} and Thompson, {T. P.} and L. Dillon and J. Wu and C. Creevey and J. Powell and Gilmore, {B. F.} and Dunne, {C. P.}",

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: {\textcopyright} 2024 The Author(s)",

year = "2024",

month = mar,

doi = "10.1016/j.jhin.2023.12.010",

language = "English",

volume = "145",

pages = "193--202",

journal = "Journal of Hospital Infection",

issn = "0195-6701",

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T1 - A novel characterised multidrug-resistant Pseudocitrobacter isolated from a patient colonised while admitted to a tertiary teaching hospital

AU - Kelly, S. A.

AU - O'Connell, N. H.

AU - Thompson, T. P.

AU - Dillon, L.

AU - Wu, J.

AU - Creevey, C.

AU - Powell, J.

AU - Gilmore, B. F.

AU - Dunne, C. P.

N1 - 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)

PY - 2024/3

Y1 - 2024/3

N2 - 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.

AB - 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.

KW - Hospital

KW - Hospital-acquired infection

KW - Novel species

KW - Pseudocitrobacter spp.

KW - Resistance

KW - Wastewater

U2 - 10.1016/j.jhin.2023.12.010

DO - 10.1016/j.jhin.2023.12.010

M3 - Article

C2 - 38215945

AN - SCOPUS:85185401206

SN - 0195-6701

VL - 145

SP - 193

EP - 202

JO - Journal of Hospital Infection

JF - Journal of Hospital Infection

ER -

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

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

UN SDGs

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Student theses

Deciphering the relationship between AMR phenotype and genotype utilising machine learning models.

Cite this