Genome sequence of a multidrug-resistant Corynebacterium striatum isolated from bloodstream infection from a nosocomial outbreak in Rio de Janeiro, Brazil

Multidrug-resistant (MDR) Corynebacterium striatum has been cited with increased frequency as pathogen of nosocomial infections. In this study, we report the draft genome of a C. striatum isolated from a patient with bloodstream infection in a hospital of Rio de Janeiro, Brazil. The isolate presented susceptibility only to tetracycline, vancomycin and linezolid. The detection of various antibiotic resistance genes is fully consistent with previously observed multidrug-resistant pattern in Corynebacterium spp. A large part of the pTP10 plasmid of MDR C. striatum M82B is present in the genome of our isolate. A SpaDEF cluster and seven arrays of CRISPR-Cas were found.

Key words:
multidrug-resistant; Corynebacterium striatum; bloodstream infection; CRISPR-Cas; spaDEF cluster

Authorship

Juliana Nunes Ramos

Fundação Oswaldo Cruz-Fiocruz, Instituto Nacional de Controle de Qualidade em Saúde, Rio de Janeiro, RJ, BrasilFundação Oswaldo Cruz-FiocruzBrazilRio de Janeiro, RJ, BrazilFundação Oswaldo Cruz-Fiocruz, Instituto Nacional de Controle de Qualidade em Saúde, Rio de Janeiro, RJ, Brasil

Universidade do Estado do Rio de Janeiro, Faculdade de Ciências Médicas, Laboratório de Difteria e Corinebactérias de Importância Clínica, Rio de Janeiro, RJ, BrasilUniversidade do Estado do Rio de JaneiroBrazilRio de Janeiro, RJ, BrazilUniversidade do Estado do Rio de Janeiro, Faculdade de Ciências Médicas, Laboratório de Difteria e Corinebactérias de Importância Clínica, Rio de Janeiro, RJ, Brasil

Izabel dos Santos Rodrigues

Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório Interdisciplinar de Pesquisas Médicas, Rio de Janeiro, RJ, BrasilFundação Oswaldo Cruz-FiocruzBrazilRio de Janeiro, RJ, BrazilFundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório Interdisciplinar de Pesquisas Médicas, Rio de Janeiro, RJ, Brasil

Paulo Victor Pereira Baio

João Flávio Carneiro Veras

Rommel Thiago Jucá Ramos

Universidade Federal do Pará, Centro de Genômica e Biologia de Sistemas, Belém, PA, BrasilUniversidade Federal do ParáBrazilBelém, PA, BrazilUniversidade Federal do Pará, Centro de Genômica e Biologia de Sistemas, Belém, PA, Brasil

Luis GC Pacheco

Universidade Federal da Bahia, Instituto de Ciências da Saúde, Salvador, BA, BrasilUniversidade Federal da BahiaBrazilSalvador, BA, BrazilUniversidade Federal da Bahia, Instituto de Ciências da Saúde, Salvador, BA, Brasil

Vasco Ariston Azevedo

Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Belo Horizonte, MG, BrasilUniversidade Federal de Minas GeraisBrazilBelo Horizonte, MG, BrazilUniversidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Belo Horizonte, MG, Brasil

Raphael Hirata Júnior

Michel Abanto Marín

University of La Frontera, Scientific and Technological Bioresource Nucleus, Temuco, ChileUniversity of La FronteraChileTemuco, ChileUniversity of La Frontera, Scientific and Technological Bioresource Nucleus, Temuco, Chile

Ana Luiza de Mattos-Guaraldi

Verônica Viana Vieira ⁺+ Corresponding author: vieira@ioc.fiocruz.br

+ Corresponding author: vieira@ioc.fiocruz.br

JNR, MAM, ALMG and VVV conceived and designed the study; JNR, ISR and RHJ selected and collected the strains; PVPB and JFCV prepared the genomic DNA; MAM and JFCV sequenced the genome; JNR, ISR and PVPB conducted the experiments of PFGE, antimicrobial assays and PCR; RTJR, LGCP and VAA performed the assemble and curation of genome; JNR, PVPB, JFCV, RTJR, LGCP, VAA, RHJ, MAM, ALMG and VVV analysed the data; JNR, PVPB, MAM and VVV wrote the manuscript with input from all others authors. All authors reviewed and approved the final manuscript.

SCIMAGO INSTITUTIONS RANKINGS

Figures

Figures (2)

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Fig. 1:
comparison generated by BRIG program using the MDR pTP10 of Corynebacterium striatum M82B (Genbank accession number: AF024666) as reference on the inner black circle. Absence of colour in the red ring that represents the genome of MDR C. striatum 2308 indicates absence of this region. The strA-strB genes are currently called aph(3”)-Ib-aph(6)-Id. The gene aphA1-IAB gene is currently named aph(3’)-Ia.

Thumbnail

Fig. 2:
scheme generated by EasyFig program showing the high nucleotide similarity between the spaDEF cluster of Corynebacterium striatum 2308 isolate and C. diphtheriae HC01 (GenBank accession: CP003212) and HC02 (GenBank accession: CP003213). The C. diphtheriae HC03 (Genbank accession: CP003214) e HC04 (GenBank accession: CP003215) isolates also were included in the analysis. The spaDEF cluster of C. diphtheriae HC03 and HC04 is not very similar to C. diphtheriae HC01 and HC02 isolates.

Fig. 1: comparison generated by BRIG program using the MDR pTP10 of Corynebacterium striatum M82B (Genbank accession number: AF024666) as reference on the inner black circle. Absence of colour in the red ring that represents the genome of MDR C. striatum 2308 indicates absence of this region. The strA-strB genes are currently called aph(3”)-Ib-aph(6)-Id. The gene aphA1-IAB gene is currently named aph(3’)-Ia.

Fig. 2: scheme generated by EasyFig program showing the high nucleotide similarity between the spaDEF cluster of Corynebacterium striatum 2308 isolate and C. diphtheriae HC01 (GenBank accession: CP003212) and HC02 (GenBank accession: CP003213). The C. diphtheriae HC03 (Genbank accession: CP003214) e HC04 (GenBank accession: CP003215) isolates also were included in the analysis. The spaDEF cluster of C. diphtheriae HC03 and HC04 is not very similar to C. diphtheriae HC01 and HC02 isolates.

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Instituto Oswaldo Cruz, Ministério da Saúde Av. Brasil, 4365 - Pavilhão Mourisco, Manguinhos, 21040-900 Rio de Janeiro RJ Brazil, Tel.: (55 21) 2562-1222, Fax: (55 21) 2562 1220 - Rio de Janeiro - RJ - Brazil
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Genome sequence of a multidrug-resistant Corynebacterium striatum isolated from bloodstream infection from a nosocomial outbreak in Rio de Janeiro, Brazil

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[1] + Corresponding author: vieira@ioc.fiocruz.br