Whole-Genomic Analysis of NDM-5-Producing Enterobacteriaceae Recovered from an Urban River in China
Ying Li,1,2,* Min Tang,3,* Xiaoyi Dai,4,5 Yingshun Zhou,4,5 Zhikun Zhang,4,5 Yichuan Qiu,4,5 Chengwen Li,1,2 Luhua Zhang4,5 1Department of Immunology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan, People’s Republic of China; 2Immunological Technolog...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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Dove Medical Press
2021-10-01
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| Series: | Infection and Drug Resistance |
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| Online Access: | https://www.dovepress.com/whole-genomic-analysis-of-ndm-5-producing-enterobacteriaceae-recovered-peer-reviewed-fulltext-article-IDR |
| _version_ | 1818896602947911680 |
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| author | Li Y Tang M Dai X Zhou Y Zhang Z Qiu Y Li C Zhang L |
| author_facet | Li Y Tang M Dai X Zhou Y Zhang Z Qiu Y Li C Zhang L |
| author_sort | Li Y |
| collection | DOAJ |
| description | Ying Li,1,2,* Min Tang,3,* Xiaoyi Dai,4,5 Yingshun Zhou,4,5 Zhikun Zhang,4,5 Yichuan Qiu,4,5 Chengwen Li,1,2 Luhua Zhang4,5 1Department of Immunology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan, People’s Republic of China; 2Immunological Technology Platform, Southwest Medical University, Luzhou, Sichuan, People’s Republic of China; 3Department of Laboratory Medicine, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, People’s Republic of China; 4Department of Pathogenic Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan, People’s Republic of China; 5Pathogen Biology Platform, Southwest Medical University, Luzhou, Sichuan, People’s Republic of China*These authors contributed equally to this workCorrespondence: Luhua Zhang; Chengwen Li Xiang Lin Road, Longmatan District, Luzhou City, Sichuan Province, 646000, People’s Republic of ChinaTel/Fax +86-0830-3160073Email zhluhua@swmu.edu.cn; Lichw110119@163.comPurpose: Three NDM-5-producing Enterobacteriaceae (Escherichia coli, Klebsiella pneumoniae, and Citrobacter braakii, one each) were isolated during a screening study for the presence of carbapenemase-producing Enterobacteriaceae (CPE) strains in urban rivers in China. The aim of the present study was to characterize these NDM-5-producing isolates by using whole-genome analysis.Methods: In vitro susceptibility testing was performed using the broth microdilution method. Conjugation assay was carried out to investigate the transferability of blaNDM-5-harboring plasmids. Whole-genome sequencing was performed using an Illumina HiSeq combined with the PacBio RSII system. The genetic characteristics of the blaNDM-5-harboring plasmids were analyzed. Antimicrobial resistance genes and virulence genes were identified from the genome sequences. Phylogenetic analysis was performed based on core genome.Results: Antimicrobial susceptibility testing showed that all three isolates were resistant to carbapenems, cephalosporins, quinolones, and aminoglycosides, and susceptible to colistin. Whole-genome sequencing showed that each isolate carried multiple antibiotic resistance genes mediating multidrug resistance, and harbored numerous virulence genes, some of which were located on plasmids. In these isolates, blaNDM-5 was carried by an IncX3 plasmid in K. pneumoniae and C. braakii, and on an IncR/IncX1 plasmid in E. coli. Conjugation experiments showed that these blaNDM-5-haboring plasmids were successfully transferred to E. coli J53. Phylogenetic analysis revealed that E. coli SCLZR49 was present in a cluster with isolates of different origin, K. pneumoniae SCLZR50 was mainly clustered with clinical isolates, and C. braakii SCLZR53 had closely genetic relationship with environmental isolates.Conclusion: This study revealed contamination of the urban river ecosystems by clinically significant carbapenemase gene blaNDM-5, raising the possibility of plasmid transmission into the environmental from humans and highlighting the need for a constant surveillance of CPE in the environment under the “One-Health” perspective.Keywords: carbapenemase, antimicrobial resistance, aquatic environment, river water |
| first_indexed | 2024-12-19T19:02:54Z |
| format | Article |
| id | doaj.art-84a4682f709640a4878f0240336429f1 |
| institution | Directory Open Access Journal |
| issn | 1178-6973 |
| language | English |
| last_indexed | 2024-12-19T19:02:54Z |
| publishDate | 2021-10-01 |
| publisher | Dove Medical Press |
| record_format | Article |
| series | Infection and Drug Resistance |
| spelling | doaj.art-84a4682f709640a4878f0240336429f12022-12-21T20:09:31ZengDove Medical PressInfection and Drug Resistance1178-69732021-10-01Volume 144427444070019Whole-Genomic Analysis of NDM-5-Producing Enterobacteriaceae Recovered from an Urban River in ChinaLi YTang MDai XZhou YZhang ZQiu YLi CZhang LYing Li,1,2,* Min Tang,3,* Xiaoyi Dai,4,5 Yingshun Zhou,4,5 Zhikun Zhang,4,5 Yichuan Qiu,4,5 Chengwen Li,1,2 Luhua Zhang4,5 1Department of Immunology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan, People’s Republic of China; 2Immunological Technology Platform, Southwest Medical University, Luzhou, Sichuan, People’s Republic of China; 3Department of Laboratory Medicine, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, People’s Republic of China; 4Department of Pathogenic Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan, People’s Republic of China; 5Pathogen Biology Platform, Southwest Medical University, Luzhou, Sichuan, People’s Republic of China*These authors contributed equally to this workCorrespondence: Luhua Zhang; Chengwen Li Xiang Lin Road, Longmatan District, Luzhou City, Sichuan Province, 646000, People’s Republic of ChinaTel/Fax +86-0830-3160073Email zhluhua@swmu.edu.cn; Lichw110119@163.comPurpose: Three NDM-5-producing Enterobacteriaceae (Escherichia coli, Klebsiella pneumoniae, and Citrobacter braakii, one each) were isolated during a screening study for the presence of carbapenemase-producing Enterobacteriaceae (CPE) strains in urban rivers in China. The aim of the present study was to characterize these NDM-5-producing isolates by using whole-genome analysis.Methods: In vitro susceptibility testing was performed using the broth microdilution method. Conjugation assay was carried out to investigate the transferability of blaNDM-5-harboring plasmids. Whole-genome sequencing was performed using an Illumina HiSeq combined with the PacBio RSII system. The genetic characteristics of the blaNDM-5-harboring plasmids were analyzed. Antimicrobial resistance genes and virulence genes were identified from the genome sequences. Phylogenetic analysis was performed based on core genome.Results: Antimicrobial susceptibility testing showed that all three isolates were resistant to carbapenems, cephalosporins, quinolones, and aminoglycosides, and susceptible to colistin. Whole-genome sequencing showed that each isolate carried multiple antibiotic resistance genes mediating multidrug resistance, and harbored numerous virulence genes, some of which were located on plasmids. In these isolates, blaNDM-5 was carried by an IncX3 plasmid in K. pneumoniae and C. braakii, and on an IncR/IncX1 plasmid in E. coli. Conjugation experiments showed that these blaNDM-5-haboring plasmids were successfully transferred to E. coli J53. Phylogenetic analysis revealed that E. coli SCLZR49 was present in a cluster with isolates of different origin, K. pneumoniae SCLZR50 was mainly clustered with clinical isolates, and C. braakii SCLZR53 had closely genetic relationship with environmental isolates.Conclusion: This study revealed contamination of the urban river ecosystems by clinically significant carbapenemase gene blaNDM-5, raising the possibility of plasmid transmission into the environmental from humans and highlighting the need for a constant surveillance of CPE in the environment under the “One-Health” perspective.Keywords: carbapenemase, antimicrobial resistance, aquatic environment, river waterhttps://www.dovepress.com/whole-genomic-analysis-of-ndm-5-producing-enterobacteriaceae-recovered-peer-reviewed-fulltext-article-IDRcarbapenemaseantimicrobial resistanceaquatic environmentriver water |
| spellingShingle | Li Y Tang M Dai X Zhou Y Zhang Z Qiu Y Li C Zhang L Whole-Genomic Analysis of NDM-5-Producing Enterobacteriaceae Recovered from an Urban River in China Infection and Drug Resistance carbapenemase antimicrobial resistance aquatic environment river water |
| title | Whole-Genomic Analysis of NDM-5-Producing Enterobacteriaceae Recovered from an Urban River in China |
| title_full | Whole-Genomic Analysis of NDM-5-Producing Enterobacteriaceae Recovered from an Urban River in China |
| title_fullStr | Whole-Genomic Analysis of NDM-5-Producing Enterobacteriaceae Recovered from an Urban River in China |
| title_full_unstemmed | Whole-Genomic Analysis of NDM-5-Producing Enterobacteriaceae Recovered from an Urban River in China |
| title_short | Whole-Genomic Analysis of NDM-5-Producing Enterobacteriaceae Recovered from an Urban River in China |
| title_sort | whole genomic analysis of ndm 5 producing enterobacteriaceae recovered from an urban river in china |
| topic | carbapenemase antimicrobial resistance aquatic environment river water |
| url | https://www.dovepress.com/whole-genomic-analysis-of-ndm-5-producing-enterobacteriaceae-recovered-peer-reviewed-fulltext-article-IDR |
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