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...
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MDPI AG
2023-11-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/11/12/2836 |
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| 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 |
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