Genomic Characteristion of Opportunistic Pathogen <i>Kluyvera</i> Reveals a Novel CTX-M Subgroup

A rising incidence of clinical infections has been caused by <i>Kluyvera</i>, a significant opportunistic pathogen. Meanwhile, <i>Kluyvera</i> acts as an important reservoir of <i>bla</i><sub>CTX-Ms</sub>, which are the dominant genes of class A extend...

Full description

Bibliographic Details
Main Authors: Keyi Yu, Zhenzhou Huang, Ruiting Lan, J. Glenn Morris, Yue Xiao, Songzhe Fu, He Gao, Xuemei Bai, Kun Li, Duochun Wang
Format: Article
Language:English
Published: MDPI AG 2023-11-01
Series:Microorganisms
Subjects:
Online Access:https://www.mdpi.com/2076-2607/11/12/2836
_version_ 1827574066419073024
author Keyi Yu
Zhenzhou Huang
Ruiting Lan
J. Glenn Morris
Yue Xiao
Songzhe Fu
He Gao
Xuemei Bai
Kun Li
Duochun Wang
author_facet Keyi Yu
Zhenzhou Huang
Ruiting Lan
J. Glenn Morris
Yue Xiao
Songzhe Fu
He Gao
Xuemei Bai
Kun Li
Duochun Wang
author_sort Keyi Yu
collection DOAJ
description A rising incidence of clinical infections has been caused by <i>Kluyvera</i>, a significant opportunistic pathogen. Meanwhile, <i>Kluyvera</i> acts as an important reservoir of <i>bla</i><sub>CTX-Ms</sub>, which are the dominant genes of class A extended-spectrum β-lactamases (ESBLs). In this work, 60 strains of <i>Kluyvera</i> were subjected to phylogenetic relationship reconstruction, antimicrobial susceptibility testing, and antibiotic resistance genes prediction. All mature <i>bla</i><sub>CTX-Ms</sub> were gathered to perform subgroup reclassification. The findings demonstrate that <i>Kluyvera</i> has a large gene pool with significant genetic flexibility. Notably, 25% of strains showed simultaneous detection of ESBLs and carbapenem resistance genes. The genotypes of fourteen novel <i>bla</i><sub>CTX-Ms</sub> were identified. A new subgroup classification approach for <i>bla</i><sub>CTX-Ms</sub> was defined by using 20 amino acid site variants, which could split <i>bla</i><sub>CTX-Ms</sub> into 10 subgroups. The results of the subgroup division were consistent with the phylogenetic clustering. More significantly, we proposed a novel <i>bla</i><sub>CTX-M</sub> subgroup, KLUS, that is chromosomally encoded in <i>K. sichuanensis</i> and the new species put forward in this study, showing amino acid differences from the currently known sequences. Cloning and transformation tests demonstrated that the recipient bacteria had a robust phenotype of cefotaxime resistance. Closely related <i>Kluyvera</i> species had <i>bla</i><sub>CTX-Ms</sub> in the same subgroup. Our research lays the groundwork for a deeper comprehension of <i>Kluyvera</i> and emphasizes how important a <i>bla</i><sub>CTX-M</sub> reservoir it is. We provide an update on <i>bla</i><sub>CTX-M</sub> subgroups reclassification from the aspects of phylogenetic relationship, amino acid differences, and the new subgroup KLUS, which needs to be strengthen monitored due to its strong resistance phenotype to cefotaxime.
first_indexed 2024-03-08T20:31:39Z
format Article
id doaj.art-23cf3141009a445c8b2da1fc47e94a95
institution Directory Open Access Journal
issn 2076-2607
language English
last_indexed 2024-03-08T20:31:39Z
publishDate 2023-11-01
publisher MDPI AG
record_format Article
series Microorganisms
spelling doaj.art-23cf3141009a445c8b2da1fc47e94a952023-12-22T14:25:38ZengMDPI AGMicroorganisms2076-26072023-11-011112283610.3390/microorganisms11122836Genomic Characteristion of Opportunistic Pathogen <i>Kluyvera</i> Reveals a Novel CTX-M SubgroupKeyi Yu0Zhenzhou Huang1Ruiting Lan2J. Glenn Morris3Yue Xiao4Songzhe Fu5He Gao6Xuemei Bai7Kun Li8Duochun Wang9National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), State Key Laboratory of Infectious Disease Prevention and Control, Beijing 102206, ChinaHangzhou Center for Disease Control and Prevention, Hangzhou 310021, ChinaSchool of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, AustraliaEmerging Pathogens Institute, University of Florida, Gainesville, FL 32610, USANational Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), State Key Laboratory of Infectious Disease Prevention and Control, Beijing 102206, ChinaCollege of Marine Science and Environment, Dalian Ocean University, Dalian 116023, ChinaNational Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), State Key Laboratory of Infectious Disease Prevention and Control, Beijing 102206, ChinaNational Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), State Key Laboratory of Infectious Disease Prevention and Control, Beijing 102206, ChinaNational Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), State Key Laboratory of Infectious Disease Prevention and Control, Beijing 102206, ChinaNational Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), State Key Laboratory of Infectious Disease Prevention and Control, Beijing 102206, ChinaA rising incidence of clinical infections has been caused by <i>Kluyvera</i>, a significant opportunistic pathogen. Meanwhile, <i>Kluyvera</i> acts as an important reservoir of <i>bla</i><sub>CTX-Ms</sub>, which are the dominant genes of class A extended-spectrum β-lactamases (ESBLs). In this work, 60 strains of <i>Kluyvera</i> were subjected to phylogenetic relationship reconstruction, antimicrobial susceptibility testing, and antibiotic resistance genes prediction. All mature <i>bla</i><sub>CTX-Ms</sub> were gathered to perform subgroup reclassification. The findings demonstrate that <i>Kluyvera</i> has a large gene pool with significant genetic flexibility. Notably, 25% of strains showed simultaneous detection of ESBLs and carbapenem resistance genes. The genotypes of fourteen novel <i>bla</i><sub>CTX-Ms</sub> were identified. A new subgroup classification approach for <i>bla</i><sub>CTX-Ms</sub> was defined by using 20 amino acid site variants, which could split <i>bla</i><sub>CTX-Ms</sub> into 10 subgroups. The results of the subgroup division were consistent with the phylogenetic clustering. More significantly, we proposed a novel <i>bla</i><sub>CTX-M</sub> subgroup, KLUS, that is chromosomally encoded in <i>K. sichuanensis</i> and the new species put forward in this study, showing amino acid differences from the currently known sequences. Cloning and transformation tests demonstrated that the recipient bacteria had a robust phenotype of cefotaxime resistance. Closely related <i>Kluyvera</i> species had <i>bla</i><sub>CTX-Ms</sub> in the same subgroup. Our research lays the groundwork for a deeper comprehension of <i>Kluyvera</i> and emphasizes how important a <i>bla</i><sub>CTX-M</sub> reservoir it is. We provide an update on <i>bla</i><sub>CTX-M</sub> subgroups reclassification from the aspects of phylogenetic relationship, amino acid differences, and the new subgroup KLUS, which needs to be strengthen monitored due to its strong resistance phenotype to cefotaxime.https://www.mdpi.com/2076-2607/11/12/2836<i>Kluyvera</i>drug resistanceESBLs<i>bla</i><sub>CTX-Ms</sub>
spellingShingle Keyi Yu
Zhenzhou Huang
Ruiting Lan
J. Glenn Morris
Yue Xiao
Songzhe Fu
He Gao
Xuemei Bai
Kun Li
Duochun Wang
Genomic Characteristion of Opportunistic Pathogen <i>Kluyvera</i> Reveals a Novel CTX-M Subgroup
Microorganisms
<i>Kluyvera</i>
drug resistance
ESBLs
<i>bla</i><sub>CTX-Ms</sub>
title Genomic Characteristion of Opportunistic Pathogen <i>Kluyvera</i> Reveals a Novel CTX-M Subgroup
title_full Genomic Characteristion of Opportunistic Pathogen <i>Kluyvera</i> Reveals a Novel CTX-M Subgroup
title_fullStr Genomic Characteristion of Opportunistic Pathogen <i>Kluyvera</i> Reveals a Novel CTX-M Subgroup
title_full_unstemmed Genomic Characteristion of Opportunistic Pathogen <i>Kluyvera</i> Reveals a Novel CTX-M Subgroup
title_short Genomic Characteristion of Opportunistic Pathogen <i>Kluyvera</i> Reveals a Novel CTX-M Subgroup
title_sort genomic characteristion of opportunistic pathogen i kluyvera i reveals a novel ctx m subgroup
topic <i>Kluyvera</i>
drug resistance
ESBLs
<i>bla</i><sub>CTX-Ms</sub>
url https://www.mdpi.com/2076-2607/11/12/2836
work_keys_str_mv AT keyiyu genomiccharacteristionofopportunisticpathogenikluyverairevealsanovelctxmsubgroup
AT zhenzhouhuang genomiccharacteristionofopportunisticpathogenikluyverairevealsanovelctxmsubgroup
AT ruitinglan genomiccharacteristionofopportunisticpathogenikluyverairevealsanovelctxmsubgroup
AT jglennmorris genomiccharacteristionofopportunisticpathogenikluyverairevealsanovelctxmsubgroup
AT yuexiao genomiccharacteristionofopportunisticpathogenikluyverairevealsanovelctxmsubgroup
AT songzhefu genomiccharacteristionofopportunisticpathogenikluyverairevealsanovelctxmsubgroup
AT hegao genomiccharacteristionofopportunisticpathogenikluyverairevealsanovelctxmsubgroup
AT xuemeibai genomiccharacteristionofopportunisticpathogenikluyverairevealsanovelctxmsubgroup
AT kunli genomiccharacteristionofopportunisticpathogenikluyverairevealsanovelctxmsubgroup
AT duochunwang genomiccharacteristionofopportunisticpathogenikluyverairevealsanovelctxmsubgroup