crossmark
Draft Genome Sequence of Colistin-Resistant Acinetobacter baumannii Strain VB22595 Isolated from a Central Line-Associated Bloodstream Infection Balaji Veeraraghavan,a Shalini Anandan,a Naveen Kumar Devanga Ragupathi,a Saranya Vijayakumar,a Dhiviya Prabaa Muthuirulandi Sethuvel,a Indranil Biswasa,b Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, Indiaa; Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, Kansas, USAb
Acinetobacter baumannii is an important emerging pathogen that causes health care-associated infections. In this study, we determined the genome of a multidrug-resistant clinical strain, VB22595, isolated from a hospital in Southern India. The draft genome indicates that strain VB22595 encodes a genome of ~3.92 Mb in size and does not contain plasmid derived MCR-1 for colistin resistance. Received 19 June 2016 Accepted 21 June 2016 Published 11 August 2016 Citation Veeraraghavan B, Anandan S, Ragupathi NKD, Vijayakumar S, Sethuvel DPM, Biswas I. 2016. Draft genome sequence of colistin-resistant Acinetobacter baumannii strain VB22595 isolated from a central line-associated bloodstream infection. Genome Announc 4(4):e00835-16. doi:10.1128/genomeA.00835-16. Copyright © 2016 Veeraraghavan et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Indranil Biswas, [email protected].
A
cinetobacter baumannii, an opportunistic pathogen, is responsible for causing a wide range of infections including bacteremia, meningitis, ventilator-associated pneumonia, skin and soft tissue infections, and urinary tract infections (1). A. baumannii is intrinsically resistant to many antibiotics and it has the ability to acquire resistance determinants from the environment (2). Carbapenems are one of the drugs chosen to treat infections caused by multidrug-resistant A. baumannii. However, resistance to these agents is being increasingly reported worldwide (3). In this report, we present the draft genome sequence of A. baumannii strain VB22595, isolated from a central line-associated bloodstream infection in a 12-year old male patient from Christian Medical College, India. Strain VB22592 was resistant to cefepime, piperacillin-tazobactam, imipenem, meropenem, aztreonam, amikacin, netilmicin, tobramycin, and colistin. When strain VB22595 was subjected to broth microdilution to determine the MIC for colistin, it was found to be ⬎256 g/ml. Since strain VB22595 was resistant to colistin, we decided to determine its whole-genome sequence (WGS). WGS was performed on the Ion Torrent PGM platform using 400-bp read chemistry. Sequencing was done following the protocol recommended by Life Technologies. Raw reads were assembled de novo using AssemblerSPAdes software v4.4.0.1 in Torrent suite server version 4.4.3. Sequencing generated 228,653,931 bp sequences with 72 contigs (ⱖ500 bp) of 57⫻ coverage. The genome was annotated using the RAST (http://rast.nmpdr.org/rast.cgi) (4–6) and PATRIC (https://www .patricbrc.org) databases (7). The annotation revealed 3,860 CDS with eight ARDB and 54 CARD antimicrobial resistance genes. In addition, four and seven virulence factors have been identified by the VFDB and Victors databases, respectively (https://www.patricbrc.org). The sequence type (ST) was found to be ST1305 (http: //pubmlst.org/abaumannii/) based on the analysis of seven house-
July/August 2016 Volume 4 Issue 4 e00835-16
keeping genes included in the pubMLST database (cpn60-2, gdhB-3, gltA-1, gpi-96, gyrB-12, recA-2, and rpoD-3). Further analysis of antimicrobial resistance genes with Res Finder found different classes of resistance genes (8). These include betalactams [blaOXA-23, blaOXA-66, and blaADC-25]; aminoglycosides [strB, strA and armA], sulfonamide [sul2], tetracycline [tet (B)], and macrolide [mphE and msrE]. WGS indicates that VB22595 does not carry a plasmid-encoded MCR-1 gene (9). Further transcriptomics analysis is needed to understand the mechanism behind the antibiotic resistance. Accession number(s). The WGS of A. baumannii VB22595 was submitted to NCBI under the accession no. LTAJ00000000. The version described in this manuscript is version LTAJ01000000. ACKNOWLEDGMENTS This work was supported in part by Indian Council of Medical Research (fund AMR/TF/54/13ECDHII dated 23 October 2013). This work was also supported in part by a KUMC start-up fund and a Fulbright-Nehru grant awarded to I.B.
FUNDING INFORMATION This work, including the efforts of Indranil Biswas, was funded by Fulbright Nehru. This work, including the efforts of Balaji Veeraraghavan, Shalini Anandan, Naveen Ragupathi, and Saranya Vijayakumar, was funded by Indian Council of Medical Research (ICMR) (AMR/TF/54/13ECDHII).
REFERENCES 1. Abbott I, Cerqueira GM, Bhuiyan S, Peleg AY. 2013. Carbapenem resistance in Acinetobacter baumannii: laboratory challenges, mechanistic insights and therapeutic strategies. Expert Rev Anti Infect Ther 11:395– 409. http://dx.doi.org/10.1586/eri.13.21. 2. Poirel L, Nordmann P. 2006. Carbapenem resistance in Acinetobacter baumannii: mechanisms and epidemiology. Clin Microbiol Infect 12: 826 – 836. http://dx.doi.org/10.1111/j.1469-0691.2006.01456.x.
Genome Announcements
genomea.asm.org 1
Veeraraghavan et al.
3. Dijkshoorn L, Nemec A, Seifert H. 2007. An increasing threat in hospitals: multidrug-resistant Acinetobacter baumannii. Nat Rev Microbiol 5:939 –951. http://dx.doi.org/10.1038/nrmicro1789. 4. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. 2008. The RAST server: Rapid Annotations using Subsystems Technology. BMC Genomics 9:75. http://dx.doi.org/10.1186/ 1471-2164-9-75. 5. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards RA, Gerdes S, Parrello B, Shukla M, Vonstein V, Wattam AR, Xia F, Stevens R. 2014. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res 42: D206 –D214. http://dx.doi.org/10.1093/nar/gkt1226. 6. Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S, Olsen GJ, Olson R, Overbeek R, Parrello B, Pusch GD, Shukla M, Thomason JA III, Stevens R, Vonstein V, Wattam AR, Xia F. 2015. RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annota-
2 genomea.asm.org
tion pipelines and annotating batches of genomes. Sci Rep 5:8365. http:// dx.doi.org/10.1038/srep08365. 7. Wattam AR, Abraham D, Dalay O, Disz TL, Driscoll T, Gabbard JL, Gillespie JJ, Gough R, Hix D, Kenyon R, Machi D, Mao C, Nordberg EK, Olson R, Overbeek R, Pusch GD, Shukla M, Schulman J, Stevens RL, Sullivan DE, Vonstein V, Warren A, Will R, Wilson MJ, Yoo HS, Zhang C, Zhang Y, Sobral BW. 2014. PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Res 42:D581–D591. http:// dx.doi.org/10.1093/nar/gkt1099. 8. Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S, Lund O, Aarestrup FM, Larsen MV. 2012. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother 67:2640 –2644. http:// dx.doi.org/10.1093/jac/dks261. 9. Liu YY, Wang Y, Walsh TR, Yi LX, Zhang R, Spencer J, Doi Y, Tian G, Dong B, Huang X, Yu LF, Gu D, Ren H, Chen X, Lv L, He D, Zhou H, Liang Z, Liu JH, Shen J. 2016. Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study. Lancet Infect Dis 16: 161–168. http://dx.doi.org/10.1016/S1473-3099(15)00424-7.
Genome Announcements
July/August 2016 Volume 4 Issue 4 e00835-16
Draft Genome Sequence of Colistin-Resistant Acinetobacter baumannii Strain VB22595 Isolated from a Central Line-Associated Bloodstream Infection Balaji Veeraraghavan,a Shalini Anandan,a Naveen Kumar Devanga Ragupathi,a Saranya Vijayakumar,a Dhiviya Prabaa Muthuirulandi Sethuvel,a Indranil Biswasa,b Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, Indiaa; Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, Kansas, USAb
Acinetobacter baumannii is an important emerging pathogen that causes health care-associated infections. In this study, we determined the genome of a multidrug-resistant clinical strain, VB22595, isolated from a hospital in Southern India. The draft genome indicates that strain VB22595 encodes a genome of ~3.92 Mb in size and does not contain plasmid derived MCR-1 for colistin resistance. Received 19 June 2016 Accepted 21 June 2016 Published 11 August 2016 Citation Veeraraghavan B, Anandan S, Ragupathi NKD, Vijayakumar S, Sethuvel DPM, Biswas I. 2016. Draft genome sequence of colistin-resistant Acinetobacter baumannii strain VB22595 isolated from a central line-associated bloodstream infection. Genome Announc 4(4):e00835-16. doi:10.1128/genomeA.00835-16. Copyright © 2016 Veeraraghavan et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Indranil Biswas, [email protected].
A
cinetobacter baumannii, an opportunistic pathogen, is responsible for causing a wide range of infections including bacteremia, meningitis, ventilator-associated pneumonia, skin and soft tissue infections, and urinary tract infections (1). A. baumannii is intrinsically resistant to many antibiotics and it has the ability to acquire resistance determinants from the environment (2). Carbapenems are one of the drugs chosen to treat infections caused by multidrug-resistant A. baumannii. However, resistance to these agents is being increasingly reported worldwide (3). In this report, we present the draft genome sequence of A. baumannii strain VB22595, isolated from a central line-associated bloodstream infection in a 12-year old male patient from Christian Medical College, India. Strain VB22592 was resistant to cefepime, piperacillin-tazobactam, imipenem, meropenem, aztreonam, amikacin, netilmicin, tobramycin, and colistin. When strain VB22595 was subjected to broth microdilution to determine the MIC for colistin, it was found to be ⬎256 g/ml. Since strain VB22595 was resistant to colistin, we decided to determine its whole-genome sequence (WGS). WGS was performed on the Ion Torrent PGM platform using 400-bp read chemistry. Sequencing was done following the protocol recommended by Life Technologies. Raw reads were assembled de novo using AssemblerSPAdes software v4.4.0.1 in Torrent suite server version 4.4.3. Sequencing generated 228,653,931 bp sequences with 72 contigs (ⱖ500 bp) of 57⫻ coverage. The genome was annotated using the RAST (http://rast.nmpdr.org/rast.cgi) (4–6) and PATRIC (https://www .patricbrc.org) databases (7). The annotation revealed 3,860 CDS with eight ARDB and 54 CARD antimicrobial resistance genes. In addition, four and seven virulence factors have been identified by the VFDB and Victors databases, respectively (https://www.patricbrc.org). The sequence type (ST) was found to be ST1305 (http: //pubmlst.org/abaumannii/) based on the analysis of seven house-
July/August 2016 Volume 4 Issue 4 e00835-16
keeping genes included in the pubMLST database (cpn60-2, gdhB-3, gltA-1, gpi-96, gyrB-12, recA-2, and rpoD-3). Further analysis of antimicrobial resistance genes with Res Finder found different classes of resistance genes (8). These include betalactams [blaOXA-23, blaOXA-66, and blaADC-25]; aminoglycosides [strB, strA and armA], sulfonamide [sul2], tetracycline [tet (B)], and macrolide [mphE and msrE]. WGS indicates that VB22595 does not carry a plasmid-encoded MCR-1 gene (9). Further transcriptomics analysis is needed to understand the mechanism behind the antibiotic resistance. Accession number(s). The WGS of A. baumannii VB22595 was submitted to NCBI under the accession no. LTAJ00000000. The version described in this manuscript is version LTAJ01000000. ACKNOWLEDGMENTS This work was supported in part by Indian Council of Medical Research (fund AMR/TF/54/13ECDHII dated 23 October 2013). This work was also supported in part by a KUMC start-up fund and a Fulbright-Nehru grant awarded to I.B.
FUNDING INFORMATION This work, including the efforts of Indranil Biswas, was funded by Fulbright Nehru. This work, including the efforts of Balaji Veeraraghavan, Shalini Anandan, Naveen Ragupathi, and Saranya Vijayakumar, was funded by Indian Council of Medical Research (ICMR) (AMR/TF/54/13ECDHII).
REFERENCES 1. Abbott I, Cerqueira GM, Bhuiyan S, Peleg AY. 2013. Carbapenem resistance in Acinetobacter baumannii: laboratory challenges, mechanistic insights and therapeutic strategies. Expert Rev Anti Infect Ther 11:395– 409. http://dx.doi.org/10.1586/eri.13.21. 2. Poirel L, Nordmann P. 2006. Carbapenem resistance in Acinetobacter baumannii: mechanisms and epidemiology. Clin Microbiol Infect 12: 826 – 836. http://dx.doi.org/10.1111/j.1469-0691.2006.01456.x.
Genome Announcements
genomea.asm.org 1
Veeraraghavan et al.
3. Dijkshoorn L, Nemec A, Seifert H. 2007. An increasing threat in hospitals: multidrug-resistant Acinetobacter baumannii. Nat Rev Microbiol 5:939 –951. http://dx.doi.org/10.1038/nrmicro1789. 4. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. 2008. The RAST server: Rapid Annotations using Subsystems Technology. BMC Genomics 9:75. http://dx.doi.org/10.1186/ 1471-2164-9-75. 5. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards RA, Gerdes S, Parrello B, Shukla M, Vonstein V, Wattam AR, Xia F, Stevens R. 2014. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res 42: D206 –D214. http://dx.doi.org/10.1093/nar/gkt1226. 6. Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S, Olsen GJ, Olson R, Overbeek R, Parrello B, Pusch GD, Shukla M, Thomason JA III, Stevens R, Vonstein V, Wattam AR, Xia F. 2015. RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annota-
2 genomea.asm.org
tion pipelines and annotating batches of genomes. Sci Rep 5:8365. http:// dx.doi.org/10.1038/srep08365. 7. Wattam AR, Abraham D, Dalay O, Disz TL, Driscoll T, Gabbard JL, Gillespie JJ, Gough R, Hix D, Kenyon R, Machi D, Mao C, Nordberg EK, Olson R, Overbeek R, Pusch GD, Shukla M, Schulman J, Stevens RL, Sullivan DE, Vonstein V, Warren A, Will R, Wilson MJ, Yoo HS, Zhang C, Zhang Y, Sobral BW. 2014. PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Res 42:D581–D591. http:// dx.doi.org/10.1093/nar/gkt1099. 8. Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S, Lund O, Aarestrup FM, Larsen MV. 2012. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother 67:2640 –2644. http:// dx.doi.org/10.1093/jac/dks261. 9. Liu YY, Wang Y, Walsh TR, Yi LX, Zhang R, Spencer J, Doi Y, Tian G, Dong B, Huang X, Yu LF, Gu D, Ren H, Chen X, Lv L, He D, Zhou H, Liang Z, Liu JH, Shen J. 2016. Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study. Lancet Infect Dis 16: 161–168. http://dx.doi.org/10.1016/S1473-3099(15)00424-7.
Genome Announcements
July/August 2016 Volume 4 Issue 4 e00835-16
