Abstract
The sequence of methicillin-resistant Staphylococcus aureus strain B6 (sequence type 30 [ST30], spa type t433, staphylococcal chromosomal cassette mec element [SCCmec] type IVc, Panton-Valentine leukocidin [PVL] positive), isolated from a pediatric patient with a lung infection in Niterói, Rio de Janeiro, Brazil, is described here. The draft genome sequence includes a 2.8-Mb chromosome, accompanied by a 20-kb plasmid containing blaZ and two small cryptic plasmids.
GENOME ANNOUNCEMENT
The emergence of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has contributed significantly to an increase in the global staphylococcal disease burden (1, 2). We present here the genome sequence of an unusual CA-MRSA isolate from Niterói, Rio de Janeiro, Brazil. The source of the isolate was a 17-month-old boy diagnosed with pneumonia and pleural effusion of one lung. The S. aureus strain (designated B6) isolated from drainage fluid was resistant to methicillin and cefepime. The strain was characterized by multilocus sequence typing as sequence type 30 (ST30), by spa typing as t433, and as staphylococcal chromosomal cassette mec element (SCCmec) type IVc by PCR. The boy’s HIV-positive aunt, living in the same household, was asymptomatically colonized by a strain typed identically to B6 that may have been the source of the boy’s infection. ST30 strains are a major source of high-risk staphylococcal infection globally (3) but are rare in Brazil, where the ST239 Brazilian epidemic clone (SCCmec type III) is epidemiologically dominant (4). ST30 strains carrying Panton-Valentine leukocidin (PVL), as B6 does, are often associated with necrotizing pneumonia, which causes high morbidity and mortality rates in children (5, 6). Strain B6 is also unusual as a spa type t433 strain; most Brazilian ST30 isolates are t318, suggesting that this strain had a distinct origin. The genome sequence was therefore determined for use as a reference in the future.
DNA preparation for whole-genome sequencing was done with the Qiagen DNeasy kit (Qiagen, USA). Preparation of Illumina-compatible libraries (with index tags) for 300-bp paired-end reads were conducted according to a standard protocol (Wafergen Biosystems). Libraries were sequenced on a MiSeq instrument using V3 chemistry. Read trimming and contig assembly and analysis were performed using Geneious software (Biomatters Ltd.). Annotation of the draft genome employed RAST (7). Plasmids, resistance genes, and virulence factors were initially identified using Web-based tools from the Center for Genomic Epidemiology (http://www.genomicepidemiology.org), and prophages were identified using PHAST (8).
The S. aureus B6 draft genome sequence was assembled into 71 contigs >1 kb in length, with a mean contig length of 39,889 bp, maximum contig length of 222,661 bp, and an N50 of 72,253 bp. The mean read coverage of the assembled contigs was approximately 25-fold. The contigs comprise a 2,808,089-bp chromosome, a 20,335-bp circular plasmid, and two small circular plasmids of 1,990 and 1,503 bp. The SCCmec type IVc element containing mecA was 21,398 bp in length. The genome contained two prophages associated with virulence factors ϕPVL (37 kb), containing the PVL subunit genes lukF and lukS, and a prophage highly similar to ϕNM-3 (44 kb), which contains the enterotoxin A (sea) and staphylokinase genes, as well as other known virulence factors (9). The 20-kb plasmid, which closely resembled pMW2 from CA-MRSA strain MW2 (10), contained blaZ (β-lactamase) and genes for heavy metal resistance. The B6 genome encodes numerous additional virulence factors potentially relevant to pulmonary infection, including the ica operon (for the synthesis of extracellular poly-N-acetyl-glucosamine for biofilm formation); adhesins binding elastin (ebpS), fibronectin (fnbA), and collagen (cna); and multiple staphylococcal enterotoxins, exotoxins, and superantigens (11).
Nucleotide sequence accession numbers.
This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. LDIT00000000. The version described in this paper is version LDIT01000000.
ACKNOWLEDGMENTS
We thank the team of professionals from the pediatric unit of Antonio Pedro University Hospital at Fluminense Federal University for assistance with this study.
This research was supported by The Fulbright International Visiting Scholar Program, Fluminense Federal University, and FAPERJ (Rio de Janeiro, Brazil) grants FOPESQ-UFF and APQ1, Fogarty International Center/NIH Global Infectious Disease Research grant TW006563, and a training grant from the Fogarty International Center (TW009338). The Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley has been supported by NIH S10 Instrumentation grants S10RR029668 and S10RR027303.
Footnotes
Citation Stephens C, Cho PJ-Y, Afonso de Araujo V, Gomes IM, de Azevedo Sias SM, Araújo Cardoso CA, Riley LW, Aguiar-Alves F. 2015. Draft genome sequence of a community-associated methicillin-resistant Panton-Valentine leukocidin-positive Staphylococcus aureus sequence type 30 isolate from a pediatric patient with a lung infection in Brazil. Genome Announc 3(4):e00907-15. doi:10.1128/genomeA.00907-15.
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