Genomic characterization of a multidrug-resistant Salmonella Rissen ST469 carrying blaCTX-M-55 gene and Tn6777 isolated from a paediatric patient in China
ABSTRACT: Objectives: Here we report a complete genome sequence of a multidrug-resistant Salmonella Rissen, carrying blaCTX-M-55 and Tn6777, isolated from a Chinese paediatric patient. Methods: Whole genome of S. Rissen S1905 was sequenced using the Oxford Nanopore MinION and Illumina NovaSeq 6000...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2023-06-01
|
| Series: | Journal of Global Antimicrobial Resistance |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2213716523000383 |
| _version_ | 1797802220838715392 |
|---|---|
| author | Meina Yue Xinfeng Zhao Xue Hu Di Liu Xiaoyu Li Yidong Wu |
| author_facet | Meina Yue Xinfeng Zhao Xue Hu Di Liu Xiaoyu Li Yidong Wu |
| author_sort | Meina Yue |
| collection | DOAJ |
| description | ABSTRACT: Objectives: Here we report a complete genome sequence of a multidrug-resistant Salmonella Rissen, carrying blaCTX-M-55 and Tn6777, isolated from a Chinese paediatric patient. Methods: Whole genome of S. Rissen S1905 was sequenced using the Oxford Nanopore MinION and Illumina NovaSeq 6000 platforms. Unicycler was used to perform a de novo assembly of Illumina and Nanopore reads. The genome sequence was annotated using the NCBI Prokaryotic Genome Annotation Pipeline. In silico multilocus sequence typing, plasmid replicons, antimicrobial resistance genes and virulence factors were identified from the genome sequence by multiple bioinformatics tools. Core genome multilocus sequence typing analysis between S. Rissen S1905 and all retrieved from the NCBI GenBank database was performed using BacWGSTdb 2.0 server. Results: Six contigs totaling 5 056 896 bp make up the complete genome sequence of S. Rissen S1905, which includes 1 chromosome and 5 plasmids. The blaCTX-M-55 was embedded in the ISEcp1-blaCTX-M-55-wbuC transposition unit located in an 85 991-bp IncI1 plasmid. However, the pco-sil operon and other eight antimicrobial resistance genes were carried by Tn6777 in the chromosome. There are 162 virulence genes in S1905. S. Rissen S1905 belongs to ST469; the closest relative was another isolate originating from a human faecal specimen in Shanghai, China, which differed by 60 core genome multilocus sequence type alleles. Conclusion: These data on the multidrug-resistant S. Rissen carrying blaCTX-M-55 and Tn6777 can provide a foundation for further studies on the molecular epidemiological characteristics, pathogenicity, antimicrobial resistance mechanisms, and dissemination mechanism of Salmonella. |
| first_indexed | 2024-03-13T05:02:50Z |
| format | Article |
| id | doaj.art-19443ec4dd8e4865b1fa3ef98b4e6346 |
| institution | Directory Open Access Journal |
| issn | 2213-7165 |
| language | English |
| last_indexed | 2024-03-13T05:02:50Z |
| publishDate | 2023-06-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Global Antimicrobial Resistance |
| spelling | doaj.art-19443ec4dd8e4865b1fa3ef98b4e63462023-06-17T05:18:27ZengElsevierJournal of Global Antimicrobial Resistance2213-71652023-06-0133238241Genomic characterization of a multidrug-resistant Salmonella Rissen ST469 carrying blaCTX-M-55 gene and Tn6777 isolated from a paediatric patient in ChinaMeina Yue0Xinfeng Zhao1Xue Hu2Di Liu3Xiaoyu Li4Yidong Wu5Department of Clinical Laboratory, Hangzhou Children's Hospital, Hangzhou, Zhejiang, ChinaDepartment of Clinical Laboratory, Hangzhou Children's Hospital, Hangzhou, Zhejiang, ChinaDepartment of Clinical Laboratory, Hangzhou Children's Hospital, Hangzhou, Zhejiang, ChinaDepartment of Clinical Laboratory, Hangzhou Children's Hospital, Hangzhou, Zhejiang, ChinaDepartment of Clinical Laboratory, Hangzhou Children's Hospital, Hangzhou, Zhejiang, ChinaDepartment of Clinical Laboratory, Hangzhou Children's Hospital, Hangzhou, Zhejiang, China; Department of Clinical Laboratory, Hangzhou Ninth People's Hospital, Hangzhou, Zhejiang, China; Corresponding author. Department of Clinical Laboratory, Hangzhou Children's Hospital, 195 Wenhui Road, Hangzhou, Zhejiang, ChinaABSTRACT: Objectives: Here we report a complete genome sequence of a multidrug-resistant Salmonella Rissen, carrying blaCTX-M-55 and Tn6777, isolated from a Chinese paediatric patient. Methods: Whole genome of S. Rissen S1905 was sequenced using the Oxford Nanopore MinION and Illumina NovaSeq 6000 platforms. Unicycler was used to perform a de novo assembly of Illumina and Nanopore reads. The genome sequence was annotated using the NCBI Prokaryotic Genome Annotation Pipeline. In silico multilocus sequence typing, plasmid replicons, antimicrobial resistance genes and virulence factors were identified from the genome sequence by multiple bioinformatics tools. Core genome multilocus sequence typing analysis between S. Rissen S1905 and all retrieved from the NCBI GenBank database was performed using BacWGSTdb 2.0 server. Results: Six contigs totaling 5 056 896 bp make up the complete genome sequence of S. Rissen S1905, which includes 1 chromosome and 5 plasmids. The blaCTX-M-55 was embedded in the ISEcp1-blaCTX-M-55-wbuC transposition unit located in an 85 991-bp IncI1 plasmid. However, the pco-sil operon and other eight antimicrobial resistance genes were carried by Tn6777 in the chromosome. There are 162 virulence genes in S1905. S. Rissen S1905 belongs to ST469; the closest relative was another isolate originating from a human faecal specimen in Shanghai, China, which differed by 60 core genome multilocus sequence type alleles. Conclusion: These data on the multidrug-resistant S. Rissen carrying blaCTX-M-55 and Tn6777 can provide a foundation for further studies on the molecular epidemiological characteristics, pathogenicity, antimicrobial resistance mechanisms, and dissemination mechanism of Salmonella.http://www.sciencedirect.com/science/article/pii/S2213716523000383Whole-genome sequencingSalmonella RissenVirulence factorsblaCTX-M-55Tn6777Paediatric |
| spellingShingle | Meina Yue Xinfeng Zhao Xue Hu Di Liu Xiaoyu Li Yidong Wu Genomic characterization of a multidrug-resistant Salmonella Rissen ST469 carrying blaCTX-M-55 gene and Tn6777 isolated from a paediatric patient in China Journal of Global Antimicrobial Resistance Whole-genome sequencing Salmonella Rissen Virulence factors blaCTX-M-55 Tn6777 Paediatric |
| title | Genomic characterization of a multidrug-resistant Salmonella Rissen ST469 carrying blaCTX-M-55 gene and Tn6777 isolated from a paediatric patient in China |
| title_full | Genomic characterization of a multidrug-resistant Salmonella Rissen ST469 carrying blaCTX-M-55 gene and Tn6777 isolated from a paediatric patient in China |
| title_fullStr | Genomic characterization of a multidrug-resistant Salmonella Rissen ST469 carrying blaCTX-M-55 gene and Tn6777 isolated from a paediatric patient in China |
| title_full_unstemmed | Genomic characterization of a multidrug-resistant Salmonella Rissen ST469 carrying blaCTX-M-55 gene and Tn6777 isolated from a paediatric patient in China |
| title_short | Genomic characterization of a multidrug-resistant Salmonella Rissen ST469 carrying blaCTX-M-55 gene and Tn6777 isolated from a paediatric patient in China |
| title_sort | genomic characterization of a multidrug resistant salmonella rissen st469 carrying blactx m 55 gene and tn6777 isolated from a paediatric patient in china |
| topic | Whole-genome sequencing Salmonella Rissen Virulence factors blaCTX-M-55 Tn6777 Paediatric |
| url | http://www.sciencedirect.com/science/article/pii/S2213716523000383 |
| work_keys_str_mv | AT meinayue genomiccharacterizationofamultidrugresistantsalmonellarissenst469carryingblactxm55geneandtn6777isolatedfromapaediatricpatientinchina AT xinfengzhao genomiccharacterizationofamultidrugresistantsalmonellarissenst469carryingblactxm55geneandtn6777isolatedfromapaediatricpatientinchina AT xuehu genomiccharacterizationofamultidrugresistantsalmonellarissenst469carryingblactxm55geneandtn6777isolatedfromapaediatricpatientinchina AT diliu genomiccharacterizationofamultidrugresistantsalmonellarissenst469carryingblactxm55geneandtn6777isolatedfromapaediatricpatientinchina AT xiaoyuli genomiccharacterizationofamultidrugresistantsalmonellarissenst469carryingblactxm55geneandtn6777isolatedfromapaediatricpatientinchina AT yidongwu genomiccharacterizationofamultidrugresistantsalmonellarissenst469carryingblactxm55geneandtn6777isolatedfromapaediatricpatientinchina |