Genome sequencing of an XDR Klebsiella pneumoniae ST101 strain isolated from a Brazilian Amazon river
Objective: : Herein, this study aimed to perform the genomic characterization of a blaKPC-2 positive Klebsiella pneumoniae (KP1.1JP) strain isolated from the surface water of river located the Brazilian Amazon region. Methods: : Antimicrobial susceptibility testing was performed following BrCAST/EUC...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2022-12-01
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| Series: | Journal of Global Antimicrobial Resistance |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2213716522002120 |
| _version_ | 1811196817126195200 |
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| author | Tiago Barcelos Valiatti Fernanda Fernandes Santos André Valêncio Rodrigo Cayô Tânia Aparecida Tardelli Gomes Ana Cristina Gales |
| author_facet | Tiago Barcelos Valiatti Fernanda Fernandes Santos André Valêncio Rodrigo Cayô Tânia Aparecida Tardelli Gomes Ana Cristina Gales |
| author_sort | Tiago Barcelos Valiatti |
| collection | DOAJ |
| description | Objective: : Herein, this study aimed to perform the genomic characterization of a blaKPC-2 positive Klebsiella pneumoniae (KP1.1JP) strain isolated from the surface water of river located the Brazilian Amazon region. Methods: : Antimicrobial susceptibility testing was performed following BrCAST/EUCAST recommendations. Genomic DNA was extracted and sequenced using the Illumina® NextSeq platform and the assembly of the generated reads was performed using the SPAdes software. Research on the sequence type, resistance and virulence encoding genes, and plasmid replicon typing was carried out. Results: : The KP1.1JP strain was resistant to all β-lactams, aminoglycosides, and fluoroquinolones tested. The genome size was 5 626 346 bp, distributed in 203 contigs and a guanine and cytosine content of 57.02%. The values of N50 and N75 were 285 583 bp and 173 927 bp, respectively. We verified that KP1.1JP belongs to ST101 and carries genes encoding resistance to β-lactams (blaCTX-M-15, blaTEM-1B, blaOXA-1, blaSVH-182, and blaKPC-2), aminoglycosides [aac(3′)-IIa, aph(3′)-Vla], fluoroquinolones [aac(6′)-Ib-cr], phenicol (catA1, catA2, catB3), tetracycline [tet(D)], trimethoprim (dfrA14), and fosfomycin (fosA). Additionally, the following virulence encoding genes were also detected: mrkABCDFHIJ (Fimbria type 3); fimABCDRFGHIK (Fimbria type 1); entABCDEFS and fepABCDG (siderophores); iroN, irp1, and irp2 (salmochelins); fyuA and ybtAEPQSTUX (yersiniabactin); and iutA (aerobactin). Conclusions: : We report the occurrence of a K. pneumoniae ST101 strain carrying blaKPC-2 gene in an Amazon river in Brazil. The genomic characteristics of this strain will contribute to a better understanding of the spread of pathogens of clinical importance in the environment based on a One Health perspective. |
| first_indexed | 2024-04-12T01:05:38Z |
| format | Article |
| id | doaj.art-6a386c3959dd4192bc76ed94728b230a |
| institution | Directory Open Access Journal |
| issn | 2213-7165 |
| language | English |
| last_indexed | 2024-04-12T01:05:38Z |
| publishDate | 2022-12-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Global Antimicrobial Resistance |
| spelling | doaj.art-6a386c3959dd4192bc76ed94728b230a2022-12-22T03:54:17ZengElsevierJournal of Global Antimicrobial Resistance2213-71652022-12-0131165166Genome sequencing of an XDR Klebsiella pneumoniae ST101 strain isolated from a Brazilian Amazon riverTiago Barcelos Valiatti0Fernanda Fernandes Santos1André Valêncio2Rodrigo Cayô3Tânia Aparecida Tardelli Gomes4Ana Cristina Gales5Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo, São Paulo, Brazil; Corresponding Authors. Mailing Address: Laboratório ALERTA, Universidade Federal de São Paulo - UNIFESP, Rua Pedro de Toledo, 781, 6th floor, Vila Clementino, 04039-032, São Paulo - SP, BrazilUniversidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo, São Paulo, BrazilUniversidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo, São Paulo, BrazilUniversidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo, São Paulo, Brazil; Universidade Federal de São Paulo (UNIFESP), Laboratório de Imunologia e Bacteriologia (LIB), Setor de Biologia Molecular, Microbiologia e Imunologia, Departamento de Ciências Biológicas (DCB), Instituto de Ciências Ambientais, Químicas e Farmaciêuticas (ICAQF), Diadema, São Paulo, BrazilUniversidade Federal de São Paulo (UNIFESP), Laboratório Experimental de Patogenicidade de Enterobactérias (LEPE), Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia (DMIP), São Paulo 04023-062, BrazilUniversidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo, São Paulo, BrazilObjective: : Herein, this study aimed to perform the genomic characterization of a blaKPC-2 positive Klebsiella pneumoniae (KP1.1JP) strain isolated from the surface water of river located the Brazilian Amazon region. Methods: : Antimicrobial susceptibility testing was performed following BrCAST/EUCAST recommendations. Genomic DNA was extracted and sequenced using the Illumina® NextSeq platform and the assembly of the generated reads was performed using the SPAdes software. Research on the sequence type, resistance and virulence encoding genes, and plasmid replicon typing was carried out. Results: : The KP1.1JP strain was resistant to all β-lactams, aminoglycosides, and fluoroquinolones tested. The genome size was 5 626 346 bp, distributed in 203 contigs and a guanine and cytosine content of 57.02%. The values of N50 and N75 were 285 583 bp and 173 927 bp, respectively. We verified that KP1.1JP belongs to ST101 and carries genes encoding resistance to β-lactams (blaCTX-M-15, blaTEM-1B, blaOXA-1, blaSVH-182, and blaKPC-2), aminoglycosides [aac(3′)-IIa, aph(3′)-Vla], fluoroquinolones [aac(6′)-Ib-cr], phenicol (catA1, catA2, catB3), tetracycline [tet(D)], trimethoprim (dfrA14), and fosfomycin (fosA). Additionally, the following virulence encoding genes were also detected: mrkABCDFHIJ (Fimbria type 3); fimABCDRFGHIK (Fimbria type 1); entABCDEFS and fepABCDG (siderophores); iroN, irp1, and irp2 (salmochelins); fyuA and ybtAEPQSTUX (yersiniabactin); and iutA (aerobactin). Conclusions: : We report the occurrence of a K. pneumoniae ST101 strain carrying blaKPC-2 gene in an Amazon river in Brazil. The genomic characteristics of this strain will contribute to a better understanding of the spread of pathogens of clinical importance in the environment based on a One Health perspective.http://www.sciencedirect.com/science/article/pii/S2213716522002120 |
| spellingShingle | Tiago Barcelos Valiatti Fernanda Fernandes Santos André Valêncio Rodrigo Cayô Tânia Aparecida Tardelli Gomes Ana Cristina Gales Genome sequencing of an XDR Klebsiella pneumoniae ST101 strain isolated from a Brazilian Amazon river Journal of Global Antimicrobial Resistance |
| title | Genome sequencing of an XDR Klebsiella pneumoniae ST101 strain isolated from a Brazilian Amazon river |
| title_full | Genome sequencing of an XDR Klebsiella pneumoniae ST101 strain isolated from a Brazilian Amazon river |
| title_fullStr | Genome sequencing of an XDR Klebsiella pneumoniae ST101 strain isolated from a Brazilian Amazon river |
| title_full_unstemmed | Genome sequencing of an XDR Klebsiella pneumoniae ST101 strain isolated from a Brazilian Amazon river |
| title_short | Genome sequencing of an XDR Klebsiella pneumoniae ST101 strain isolated from a Brazilian Amazon river |
| title_sort | genome sequencing of an xdr klebsiella pneumoniae st101 strain isolated from a brazilian amazon river |
| url | http://www.sciencedirect.com/science/article/pii/S2213716522002120 |
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