Draft Genomes Sequences of KPC-2, OXA-1, OXA-9, SHV-28, TEM-1 and CTX-M-15 Producing Klebsiella pneumoniae ST15 and KPC-2, OXA-1, TEM-1 and LEN-2 Producing Klebsiella variicola ST32 from Clinical Samples in Rio de Janeiro, Brazil

Author's: Cristiane Rodrigues Silva1,3*, Rafael Monção Miller2,3, Victor Hugo Lima de Medeiros Macedo2,3, Mara Adriana Oliveira da Silva4, Karla Regina Oliveira de Moura Ronchini4,5, Victor Augustus Marin1,2,3
Authors' Affiliations
1Graduate Program in Food and Nutrition (PPGAN), Nutrition School, 2Nutrition School, 3Microbiological Control Laboratory of Nutrition School (LACOMEN), Department of Food Science (DCA), Nutrition School, Federal University of the State of Rio de Janeiro (UNIRIO), Pasteur Avenue, 296, Urca - Rio de Janeiro/RJ - Brazil, 22290-240.4Gafrée and Guinle University Hospital, Federal University of the State of Rio de Janeiro (UNIRIO), Mariz e Barros Street Rua Mariz E Barros, 775, Praça da Bandeira, Rio de Janeiro/RJ - Brazil, 20270-004.5Internal Medicine Department, School of Medicine, Infectious Disease, Fluminense Federal University, (UFF), Marques do Paraná Avenue, 303, Centro, Niterói/RJ - Brazil, 24033-900.*Corresponding Author: Cristiane Rodrigues Silva;Email:cristiane.silva@unirio.br
Article Type: Research Article     Published: Oct. 27, 2020 Pages: Online first
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Abstract:

KPC-producing bacteria are considered one of the most worrisome multidrug-resistant micro-organisms in nosocomial infections. Here we report the draft genomes sequences of two KPC-2 and CTX-M-15 producing Klebsiella pneumoniae sequence type 15 (ST15) and Klebsiella variicola sequence type 32 (ST32) isolates obtained from clinical samples of patients in Rio de Janeiro. A genomic library was constructed using a Nextera XT Kit. An Illumina platform was used to perform whole-genome sequencing (WGS). WGS of isolates K. pneumoniae and K. variicola resulted in estimated genome sizes of 5 662 554 and 5 868 756 bp, respectively. Resistome analysis of the clinical strains revealed the presence of resistance genes to the following antimicrobials in K. pneumoniae: aminoglycosides [aadA1], [aph (3’)-Ia], [aph(3”)-Ib], [aac(6′)-Ib3], [aadA2] and [aph(6)-Id]; β-lactams (blaOXA-1, blaoxa-9, blaCTX-M-15, blaTEM-1, andblaSHV-28); carbapenem  (blaKPC-2); fluoroquinolones [aac(60)-Ib-cr], [oqxA]and [oqxB]; fosfomycin [fosA]; macrolides [mph(A)] and [erm(B)]; phenicols [catB3]; sulfonamides [sul1]; trimethoprim [dfrA12] and tetracycline [tetA] and to K. variicola:  aminoglycosides [aadA1], [aph (3)-IIa], [aac(6′)-Ib-cr] and [aph(6)-Id]; β-lactams (blaOXA-1blaCTX-M-15, blaTEM-1B andblaLEN-2); carbapenem (blaKPC-2); fluoroquinolones [aac(60)-Ib-cr], [qnrB1], [oqxA]and [oqxB]; fosfomycin [fosA]; phenicols [catB3]; sulfonamides [sul2]; trimethoprim [dfrA14] and tetracycline [tetA]. The resistome revealed by this study might be a useful tool to elucidate the dissemination of nosocomial resistance genes in Rio de Janeiro.

Keywords:

Genome, antibiotic resistance, infection, Klebsiella pneumonia, Klebsiella variicola.

Citation:

Silva, C.R., Miller, R.M., Macedo, V.H.L.M., da Silva, M.A.O., Ronchini, K.R.O.M., Marin, V.A., 2020. Draft Genomes Sequences of KPC-2, OXA-1, OXA-9, SHV-28, TEM-1 and CTX-M-15 Producing Klebsiella pneumoniae ST15 and KPC-2, OXA-1, TEM-1 and LEN-2 Producing Klebsiella variicola ST32 from Clinical Samples in Rio de Janeiro, Brazil. PSM Microbiol., 5(4): MB-2020-025.