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Draft Genome Sequence of a Metronidazole-Susceptible Atopobium vaginae Isolate Jessica A. Schuyler, Eli Mordechai, Martin E. Adelson, Scott E. Gygax, David W. Hilbert Femeris Women’s Health Research Center, Medical Diagnostic Laboratories, A Member of Genesis Biotechnology Group, Hamilton, New Jersey, USA
We report the draft genome sequence of a vaginal isolate of Atopobium vaginae vaginae (strain 44061), an organism linked to bacterial vaginosis (BV), the most common gynecological infection in the United States. This species is often highly resistant to metronidazole, which is a front-line therapy for BV. Strain 44061 is a metronidazole-susceptible isolate (MIC, 16 g/ml), and its genome sequence will be useful for comparative studies to elucidate the molecular basis of metronidazole resistance in this species. Received 20 July 2015 Accepted 24 July 2015 Published 3 September 2015 Citation Schuyler JA, Mordechai E, Adelson ME, Gygax SE, Hilbert DW. 2015. Draft genome sequence of a metronidazole-susceptible Atopobium vaginae isolate. Genome Announc 3(5):e00991-15. doi:10.1128/genomeA.00991-15. Copyright © 2015 Schuyler et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license. Address correspondence to David W. Hilbert, [email protected].
A
topobium vaginae is strongly associated with bacterial vaginosis (BV) (1), the most common cause of vaginal discharge in the United States (2). The antibiotic metronidazole is recommended by the Centers for Disease Control and Prevention as a front-line therapy for BV (3), but treatment failure is common (4), generating interest in evaluating metronidazole susceptibility of BV-associated organisms. A. vaginae is often highly resistant to metronidazole (5), including the sequenced strain DSM 15829 (GenBank accession number NZ_ACGK02000000), which has a MIC of ⬎256 g/ml when 32 g/ml is considered a standard breakpoint for metronidazole resistance (6). For comparative studies, we sequenced the genome of 44061, an isolate we found to be susceptible to metronidazole (MIC, 16 g/ml). Isolate 44061 was obtained from the Culture Collection of the University of Goteborg. It was originally isolated from the fornix of the vagina from a woman with bacterial vaginosis. We determined the metronidaozle MIC using a metronidazole Etest strip (bioMérieux). Genomic DNA was isolated using a Gentra PureGene kit (Qiagen). Genomic DNA was sequenced using the 454-GS Junior System (Roche) following the manufacturer’s instructions, and genome assembly was performed using the GS De Novo Assembler (version 3.0). The NCBI Prokaryotic Genome Annotation Pipeline (http://www.ncbi.nlm.nih.gov /genome/annotation_prok/) was used for genome annotation. We generated 91,698 reads totaling 41,189,768 nucleotides. These reads were assembled into a draft genome of 1,483,295 nucleotides with 26-fold coverage. The genome encodes 1,267 genes, 3 rRNA operons, 45 tRNA genes, 109 pseudogenes, 1 noncoding RNA (ncRNA), and 1 clustered regularly interspaced short palindromic repeat (CRISPR) array. We compared the genome sequence to that of DSM 15829 using GS Reference Mapper (version 3.0) and found 25,419 high confidence differences (i.e., nucleotide polymorphisms). In addition, we found structural variations in-
September/October 2015 Volume 3 Issue 5 e00991-15
cluding 10 deletions, 15 duplications, 16 insertions, 44 substitutions, one inversion, and one translocation. Further analysis of this genome in comparison to genome sequences of metronidazole-resistant A. vaginae isolates may help identify molecular determinants of metronidazole resistance in this species. Nucleotide sequence accession numbers. The whole-genome shotgun project has been deposited in GenBank under the accession number LFWE00000000. The version described in this paper is version LFWE00000000.1. ACKNOWLEDGMENT All research support was provided by the Genesis Biotechnology Group.
REFERENCES 1. Ferris MJ, Masztal A, Aldridge KE, Fortenberry JD, Fidel PL, Jr, Martin DH. 2004. Association of Atopobium vaginae, a recently described metronidazole resistant anaerobe, with bacterial vaginosis. BMC Infect Dis 4:5. http://dx.doi.org/10.1186/1471-2334-4-5. 2. Koumans EH, Sternberg M, Bruce C, McQuillan G, Kendrick J, Sutton M, Markowitz LE. 2007. The prevalence of bacterial vaginosis in the United States, 2001–2004; associations with symptoms, sexual behaviors, and reproductive health. Sex Transm Dis 34:864 – 869. http://dx.doi.org/10.1097/ OLQ.0b013e318074e565. 3. Workowski KA, Berman S, Centers for Disease Control and Prevention. 2010. Sexually transmitted diseases treatment guidelines, 2010. MMWR Recomm Rep 17:1–110. 4. Koumans EH, Markowitz LE, Hogan V, Group CBW. 2002. Indications for therapy and treatment recommendations for bacterial vaginosis in nonpregnant and pregnant women: a synthesis of data. Clin Infect Dis 35: S152–S172. 5. De Backer E, Verhelst R, Verstraelen H, Claeys G, Verschraegen G, Temmerman M, Vaneechoutte M. 2006. Antibiotic susceptibility of Atopobium vaginae. BMC Infect Dis 6:51. http://dx.doi.org/10.1186/1471 -2334-6-51. 6. Löfmark S, Edlund C, Nord CE. 2010. Metronidazole is still the drug of choice for treatment of anaerobic infections. Clin Infect Dis 50:S16 –S23. http://dx.doi.org/10.1086/647939.
Genome Announcements
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Draft Genome Sequence of a Metronidazole-Susceptible Atopobium vaginae Isolate Jessica A. Schuyler, Eli Mordechai, Martin E. Adelson, Scott E. Gygax, David W. Hilbert Femeris Women’s Health Research Center, Medical Diagnostic Laboratories, A Member of Genesis Biotechnology Group, Hamilton, New Jersey, USA
We report the draft genome sequence of a vaginal isolate of Atopobium vaginae vaginae (strain 44061), an organism linked to bacterial vaginosis (BV), the most common gynecological infection in the United States. This species is often highly resistant to metronidazole, which is a front-line therapy for BV. Strain 44061 is a metronidazole-susceptible isolate (MIC, 16 g/ml), and its genome sequence will be useful for comparative studies to elucidate the molecular basis of metronidazole resistance in this species. Received 20 July 2015 Accepted 24 July 2015 Published 3 September 2015 Citation Schuyler JA, Mordechai E, Adelson ME, Gygax SE, Hilbert DW. 2015. Draft genome sequence of a metronidazole-susceptible Atopobium vaginae isolate. Genome Announc 3(5):e00991-15. doi:10.1128/genomeA.00991-15. Copyright © 2015 Schuyler et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license. Address correspondence to David W. Hilbert, [email protected].
A
topobium vaginae is strongly associated with bacterial vaginosis (BV) (1), the most common cause of vaginal discharge in the United States (2). The antibiotic metronidazole is recommended by the Centers for Disease Control and Prevention as a front-line therapy for BV (3), but treatment failure is common (4), generating interest in evaluating metronidazole susceptibility of BV-associated organisms. A. vaginae is often highly resistant to metronidazole (5), including the sequenced strain DSM 15829 (GenBank accession number NZ_ACGK02000000), which has a MIC of ⬎256 g/ml when 32 g/ml is considered a standard breakpoint for metronidazole resistance (6). For comparative studies, we sequenced the genome of 44061, an isolate we found to be susceptible to metronidazole (MIC, 16 g/ml). Isolate 44061 was obtained from the Culture Collection of the University of Goteborg. It was originally isolated from the fornix of the vagina from a woman with bacterial vaginosis. We determined the metronidaozle MIC using a metronidazole Etest strip (bioMérieux). Genomic DNA was isolated using a Gentra PureGene kit (Qiagen). Genomic DNA was sequenced using the 454-GS Junior System (Roche) following the manufacturer’s instructions, and genome assembly was performed using the GS De Novo Assembler (version 3.0). The NCBI Prokaryotic Genome Annotation Pipeline (http://www.ncbi.nlm.nih.gov /genome/annotation_prok/) was used for genome annotation. We generated 91,698 reads totaling 41,189,768 nucleotides. These reads were assembled into a draft genome of 1,483,295 nucleotides with 26-fold coverage. The genome encodes 1,267 genes, 3 rRNA operons, 45 tRNA genes, 109 pseudogenes, 1 noncoding RNA (ncRNA), and 1 clustered regularly interspaced short palindromic repeat (CRISPR) array. We compared the genome sequence to that of DSM 15829 using GS Reference Mapper (version 3.0) and found 25,419 high confidence differences (i.e., nucleotide polymorphisms). In addition, we found structural variations in-
September/October 2015 Volume 3 Issue 5 e00991-15
cluding 10 deletions, 15 duplications, 16 insertions, 44 substitutions, one inversion, and one translocation. Further analysis of this genome in comparison to genome sequences of metronidazole-resistant A. vaginae isolates may help identify molecular determinants of metronidazole resistance in this species. Nucleotide sequence accession numbers. The whole-genome shotgun project has been deposited in GenBank under the accession number LFWE00000000. The version described in this paper is version LFWE00000000.1. ACKNOWLEDGMENT All research support was provided by the Genesis Biotechnology Group.
REFERENCES 1. Ferris MJ, Masztal A, Aldridge KE, Fortenberry JD, Fidel PL, Jr, Martin DH. 2004. Association of Atopobium vaginae, a recently described metronidazole resistant anaerobe, with bacterial vaginosis. BMC Infect Dis 4:5. http://dx.doi.org/10.1186/1471-2334-4-5. 2. Koumans EH, Sternberg M, Bruce C, McQuillan G, Kendrick J, Sutton M, Markowitz LE. 2007. The prevalence of bacterial vaginosis in the United States, 2001–2004; associations with symptoms, sexual behaviors, and reproductive health. Sex Transm Dis 34:864 – 869. http://dx.doi.org/10.1097/ OLQ.0b013e318074e565. 3. Workowski KA, Berman S, Centers for Disease Control and Prevention. 2010. Sexually transmitted diseases treatment guidelines, 2010. MMWR Recomm Rep 17:1–110. 4. Koumans EH, Markowitz LE, Hogan V, Group CBW. 2002. Indications for therapy and treatment recommendations for bacterial vaginosis in nonpregnant and pregnant women: a synthesis of data. Clin Infect Dis 35: S152–S172. 5. De Backer E, Verhelst R, Verstraelen H, Claeys G, Verschraegen G, Temmerman M, Vaneechoutte M. 2006. Antibiotic susceptibility of Atopobium vaginae. BMC Infect Dis 6:51. http://dx.doi.org/10.1186/1471 -2334-6-51. 6. Löfmark S, Edlund C, Nord CE. 2010. Metronidazole is still the drug of choice for treatment of anaerobic infections. Clin Infect Dis 50:S16 –S23. http://dx.doi.org/10.1086/647939.
Genome Announcements
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