Draft Genome Sequences of Staphylococcus aureus Sequence Type 34 (ST34) and ST42 Hybrids

Abstract

Staphylococcus aureus is a major cause of antimicrobial-resistant infections of humans. Hybrids of S. aureus, which originate from large-scale chromosomal recombinations between parents of distinct genetic backgrounds, are of interest from clinical and evolutionary perspectives. We present draft genome sequences of two S. aureus hybrids of sequence type 34 (ST34) and ST42.

GENOME ANNOUNCEMENT

Staphylococcus aureus, a premier human pathogen, possesses an arsenal of virulence and antimicrobial resistance genes that are subject to horizontal genetic transfer and recombination (2, 8). Some entire S. aureus genetic backgrounds are hybrids that originated from recombinations of large, contiguous portions of the chromosomes of genetically distinct parent backgrounds (14). The first described bacterial hybrid of this sort from nature was the S. aureus sequence type 239 (ST239). ST239 strains are resistant to multiple antimicrobials and cause epidemics of hospital-associated infections (5, 16). Genome sequencing has confirmed the ST239 hybrid genome structure (7). S. aureus ST34 and ST42 backgrounds have also been suggested to be of hybrid origin based on multilocus sequencing (14), but these two backgrounds have not been studied previously through genome sequencing. ST42 is relatively rare, whereas ST34 has spread to multiple continents and can cause community-associated skin and soft tissue infections (1, 4, 18).

Genome sequences were determined for ST34 (strain C160) and ST42 (strain C427), using 454 FLX pyrosequencing (Roche). Sequencing, assembly, and annotation were performed as described previously (17). The ST34 genome was assembled into 26 scaffolds and 63 contigs, whereas the ST42 genome was assembled into 18 scaffolds and 54 contigs; >50% of each genome was assembled into contigs of >95.66 kb and scaffolds of >974.96 kb. The average coverage was >25×. The ST34 and ST42 genomes were 2.82 and 2.86 Mb in length, with 32.69 and 32.70% G+C ratios, and comprised 2,750 and 2,781 open reading frames (ORFs), respectively, with 56 tRNAs each, but only 10 and 4 rRNAs, respectively, were detected.

The genomes of the two putative hybrids and the previously sequenced parent-like backgrounds ST145 (strain D139), ST10 (strain H19), ST36 (strain MRSA252), and ST30 (strain WW2703/97) (6, 17) were aligned using the progressiveMauve algorithm of Mauve v2.3.1 (3) with default parameters. Putative recombination events were detected using the Chimaera (13), Geneconv (15), MaxChi (12), and RDP (10) methods, implemented by RDP v.3.44 (11). Statistical significance was based at a P value of < 0.05, and a Bonferroni correction for multiple tests was applied. Events detected by three of the four methods were further examined by manual inspection and confirmed using the genetic algorithm for recombination detection (GARD) method (9).

The previously identified breakpoints of the two recombination events that resulted in ST34 and ST42 (14), including a common breakpoint 3′ of the origin of replication in ORFs SFAG_00636/SASG_01570 and unique breakpoints 5′ of the origin in ORFs SFAG_00460 and SASG_01367, respectively, were confirmed. For ST34 and ST42, respectively, at least 199,596 and 230,662 bp of contiguous sequence was inherited from their ST10/ST145-like parent, and at least 2,623,050 and 2,631,028 bp of contiguous sequence was inherited from their ST30/ST36-like parent. One additional recombination event of at least 164 bp was identified in ORF SASG_01774 for ST42. Four other potential recombination events were rejected as analysis artifacts that occurred in repeat regions and other regions of poor alignment quality. Further analyses of these two genome sequences, in addition to those of other S. aureus hybrids, may provide insight into the mechanisms by which bacterial hybrids form and diversify.

Nucleotide sequence accession numbers.

Draft genome sequences of S. aureus strains C160 and C427 were deposited in GenBank under accession numbers ACUV00000000 and ACSQ00000000, respectively.