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. 2016 Apr 21;4(2):e00302-16. doi: 10.1128/genomeA.00302-16

Complete Genome Sequences of Aerococcus christensenii CCUG 28831T, Aerococcus sanguinicola CCUG 43001T, Aerococcus urinae CCUG 36881T, Aerococcus urinaeequi CCUG 28094T, Aerococcus urinaehominis CCUG 42038 BT, and Aerococcus viridans CCUG 4311T

Derya Carkaci a,b,c, Rimtas Dargis a, Xiaohui Chen Nielsen a,✉, Ole Skovgaard b, Kurt Fuursted c, Jens Jørgen Christensen a,d,✉
PMCID: PMC4841142  PMID: 27103727

Abstract

Strains belonging to the genus Aerococcus are causative agents of human and animal infections, including urogenital infections, bacteremia/septicemia, and infective endocarditis. This study reports the first fully closed and complete genome sequences of six type strains belonging to the genus Aerococcus using a combination of Illumina HiSeq and PacBio sequencing technologies.

GENOME ANNOUNCEMENT

The genus Aerococcus encompasses eight species, which are Gram-positive cocci. For a long time, Aerococcus viridans (1953) (1) was the only known species. An additional seven species were described: A. urinae (1992) (2), A. christensenii (1999) (3), A. urinaehominis (2001) (4), A. sanguinicola (2001) (5), A. urinaeequi (2005) (6), A. suis (2007) (7), and A. vaginalis (2014) (8). Aerococcus spp. have been reported as human pathogens and associated with urogenital infections, bacteremia/septicemia, and infective endocarditis (1–5, 7–9). A. suis (from pig farms), A. urinaeequi (from horses and cattle), and A. vaginalis (from cow) have only been described as pathogens in animals (6–8).

In fact, little is known about Aerococcus pathogenicity and virulence mechanisms for causing infections in human and animals (10–13). One explanation for this has been stated as underestimated incidence in clinical settings, partly due to misidentification with closely related Gram-positive cocci (10, 14–16).

To date, six Aerococcus strains (A. christensenii, A. urinae, two A. urinaeequi, and two A. viridans) have been whole-genome sequenced and published in NCBI (National Center for Biotechnology Information), but these strains were either nontype strains or incomplete genome sequences.

Here, we announce the complete genome sequences of six Aerococcus type strains: A. christensenii CCUG 28831T, A. sanguinicola CCUG 43001T, A. urinae CCUG 36881T, A. urinaeequi CCUG 28094T, A. urinaehominis CCUG 42038 BT, and A. viridans CCUG 4311T.

The type strains were cultivated at 35 to 37°C for 9 to 10 h in Todd-Hewitt media with shaking in 5% CO2 atmosphere. Isolation and purification of high-quality genomic DNA was achieved using the Qiagen Genomic-tip 500/G system and the corresponding Genomic DNA buffer set with additional lysozyme and mutanolysin to improve bacterial cell lysis.

Illumina HiSeq (Illumina, USA) and PacBio (Pacific Biosciences, USA) sequence reads were generated at BGI (BGI, Shenzhen, China) and used in combination to obtain complete genome sequences. The HiSeq library sizes of 500-bp and 2-kb (500-bp and 6-kb for A. urinaehominis CCUG 42038 BT) were prepared using a BGI in-house method and were sequenced using the Illumina HiSeq2000 platform. The 20-kb PacBio Template Prep Kit was used to generate the PacBio libraries, followed by PacBio RS II sequencing. SOAPdenovo version 2.04 (17) was used to assemble preprosedded HiSeq sequence reads, whereas PacBio sequence reads were assembled using the Celera Assembler version 8.1 from the SMRT Analysis version 2.3.0 (http://www.pacb.com/products-and-services/analytical-software/smrt-analysis/). The combined HiSeq and PacBio assemblies generated one single contig of 1.6 to 2.2 Mb with 100% HiSeq coverages of the PacBio assemblies (Table 1). The NCBI Prokaryotic Genome Annotation pipeline version 3.1 (18) was used to annotate 1,428 to 1,914 coding genes, and plasmids were not detected in any of the genomes.

TABLE 1 .

Aerococcus type strain information, genome sequence data, and GenBank accession numbers

Type strain Sequence depth
 PacBio sequence statistic
 NCBI prokaryotic genome annotation pipeline
 General strain information
 Accession no.a
PacBio HiSeq No. of contigs Genome size (bp) and N50 (bp) G+C content (%) No. of coding genes No. of 5S, 16S, and 23S rRNAs No. of tRNAs Yr of strain announcement Source of isolation Host disease
A. christensenii CCUG 28831T 467× 290× 1 1,634,920 39.2 1,428 4, 4, 4 60 1988/1999b Human vagina Vaginosis CP014159
A. sanguinicola CCUG 43001T 515× 210× 1 2,033,849 47.6 1,733 4, 4, 4 62 2001 Human blood Septicemia CP014160
A. urinae CCUG 36881T 594× 190× 1 1,974,262 42.6 1,712 4, 4, 4 60 1989/1992c Human urine Urinary tract infection CP014161
A. urinaeequi CCUG 28094T 348× 220× 1 2,013,339 39.4 1,761 5, 5, 5 54 1934/1988/2005d Horse urine NDe CP014162
A. urinaehominis CCUG 42038 BT 592× 170× 1 1,831,400 42.8 1,605 4, 4, 4 57 2001 Human urine Urinary tract infection CP014163
A. viridans CCUG 4311T 486× 250× 1 2,199,877 39.4 1,914 7, 7, 7 55 1953 Air sample ND CP014164
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a

Bioproject accession number PRJNA308559.

b

Reclassification of Streptococcus acidominimus (1988) as Aerococcus christensenii in 1999.

c

Characterization of Aerococcus-like organisms (1989) as Aerococcus urinae in 1992.

d

Reclassification of Pediococcus urinaeequi ([ex Mees 1934] Garvie 1988) as Aerococcus urinaeequi in 2005.

e

ND, not defined.

Genome sequences were in silico NCBI BLAST (19) confirmed by rRNAmmer version 1.2 (20) predicted 16S rRNA gene sequences achieving 99 to 100% sequence identities with corresponding NCBI deposited 16S rRNA gene sequences. Additional analysis of 16S-23S rRNA gene sequences distinguished A. viridans from A. urinaeequi.

The availability of these six Aerococcus type strain complete genome sequences will provide important information concerning the genetic content of the genus Aerococcus. These genomes will act as reference strains in terms of comparative genomics in relation to pathogenicity, which will improve the understanding of Aerococcus-associated infections in the future.

Nucleotide sequence accession numbers.

The complete genome sequences of the six Aerococcus type strains were deposited in GenBank under the accession numbers stated in Table 1.

ACKNOWLEDGMENTS

We thank the staff of BGI, Shenzhen, China, for providing expert technical assistance and bioinformatic knowledge during the sequencing process.

Funding Statement

This study was supported by the Research Foundation at Region Zealand (Denmark), the Common Funds for Research between Roskilde University (Denmark) and Region Zealand (Denmark), and The Danish Heart Foundation (Denmark).

Footnotes

Citation Carkaci D, Dargis R, Nielsen XC, Skovgaard O, Fuursted K, Christensen JJ. 2016. Complete genome sequences of Aerococcus christensenii CCUG 28831T, Aerococcus sanguinicola CCUG 43001T, Aerococcus urinae CCUG 36881T, Aerococcus urinaeequi CCUG 28094T, Aerococcus urinaehominis CCUG 42038 BT, and Aerococcus viridans CCUG 4311T. Genome Announc 4(2):e00302-16. doi:10.1128/genomeA.00302-16.

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