crossmark
Draft Genome Sequences of Seven Multidrug-Resistant Acinetobacter baumannii Strains, Isolated from Respiratory Samples in Spain Gema Labrador-Herrera,a Rocío Álvarez,a Rafael López-Rojas,b Younes Smani,a Tania Cebrero-Cangueiro,a Antonio Rueda,c Javier Pérez Florido,c Jerónimo Pachón,a María Eugenia Pachón-Ibáñeza Unit of Infectious Diseases, Microbiology and Preventive Medicine and Biomedical Institute of Seville (IBiS), University Hospital Virgen del Rocio/CSIC/University of Seville, Seville, Spaina; Infectious Diseases and Clinical Microbiology Unit, University Hospital Virgen Macarena, Seville, Spainb; Medical Genome Project, Genomics and Bioinformatics Platform of Andalusia (GBPA), Seville, Spainc
The draft genome sequences of seven multidrug-resistant Acinetobacter baumannii clinical strains belonging to sequence types ST-208 and ST-218 are reported in this study. They were isolated from tracheobronchial aspirate of mechanically ventilated adult patients admitted to the intensive care unit of a Spanish tertiary hospital during 2010 to 2011. Received 21 January 2016 Accepted 12 February 2016 Published 31 March 2016 Citation Labrador-Herrera G, Álvarez R, López-Rojas R, Smani Y, Cebrero-Cangueiro T, Rueda A, Pérez Florido J, Pachón J, Pachón-Ibáñez ME. 2016. Draft genome sequences of seven multidrug-resistant Acinetobacter baumannii strains, isolated from respiratory samples in Spain. Genome Announc 4(2):e00083-16. doi:10.1128/genomeA.00083-16. Copyright © 2016 Labrador-Herrera et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Jerónimo Pachón, [email protected].
A
cinetobacter baumannii is among the leading etiologies of hospital-acquired infections, particularly in critically ill patients (1). The increasing prevalence of multidrug-resistance reduces available treatments and threatens public health (2). During 2010 to 2011, 207 multidrug-resistant (MDR) A. baumannii strains were isolated from 100 adult patients in the intensive care unit of a tertiary hospital in Seville, Spain. In this study, we present the draft genome sequences of 7 of these MDR A. baumannii clinical strains (including resistance to gentamicin, imipenem, meropenem, ceftazidime, cefepime, ticarcillin, trimethoprim-sulfamethoxazole, tetracycline, levofloxacin, and ciprofloxacin; and susceptibility to colistin) isolated from tracheobronchial aspirates. Whole-genome sequencing was performed using the Illumina MiSeq platform with 300 bp paired-end reads, resulting in mean genome coverage of 25.2 ⫾ 5.5-fold (mean ⫾ SD of the 7 strains). Reads were preprocessed with Trimmomatic v0.32 (http: //www.usadellab.org/cms/?page⫽trimmomatic) (3) and de novo assembled with ABySS assembler v1.5.2 (http://www.bcgsc.ca /platform/bioinfo/software/abyss) (4), resulting in 381 ⫾ 52 contigs. The assemblies were filtered for contigs larger than 500 bp, leaving 210 ⫾ 34 contigs with a total length of 4,036,456 ⫾ 123,611 bp and an N50 of 47,317 ⫾ 8,993 bp. The G⫹C content was 39.2 ⫾ 0.1%. Gene prediction and annotation were performed utilizing GeneMark v2.5 (http://exon.gatech.edu/Gene Mark/) and RAST server v1.0 (http://rast.nmpdr.org) (5), respectively, yielding a total of 3,876 ⫾ 134 coding sequences and 70 ⫾ 15 RNAs. Two different sequence types (ST) were found with MLST v1.8 using the Oxford database (https://cge.cbs.dtu.dk /services/MLST/) (6, 7). Most of the strains belong to ST-208, except AbMDR-GLH5 and AbMDR-GLH6 that belong to ST-218. With pulsed-field gel electrophoresis, 3 pulsotypes were found: pulsotype 1 (AbMDR-GLH2 and AbMDR-GLH4), pulsotype 2 (AbMDR-GLH1, AbMDR-GLH3, and AbMDR-GLH8), and pulsotype 3 (AbMDR-GLH5 and AbMDR-GLH6). To identify genes conferring antimicrobial resistance, the bioinformatic tool ResFinder v2.1 was used (https://cge.cbs.dtu.dk/services/ResFinder/)
March/April 2016 Volume 4 Issue 2 e00083-16
(8). The aminoglycoside resistance genes aac(6=)-II, strB, and strA, were detected in pulsotype 1 strains, while pulsotype 2 strains carry aac(3)-Ia, aadA1, strB, and strA genes, and pulsotype 3 strains carry aac(6=)-II, aac(3)-IIa, strB, and strA genes. Resistance genes blaOXA-58, blaOXA-66, and blaADC-25, which confer -lactam resistance, were found in strains from pulsotypes 1 and 2; nevertheless, pulsotype 3 strains carry blaOXA-109 and blaADC-25 genes. Referring to sulfonamide resistance, all the strains have sul1 gene, and strains from pulsotypes 1 and 2 also possess sul2 gene. The gene tet(B), related with tetracycline resistance, was found in all the strains. Furthermore, point mutations in genes associated with quinolone resistance were found in all the strains using BLAST (Basic Local Alignment Search Tool) (http://blast.ncbi.nlm.nih.gov/Blast .cgi) (9) comparing with genes from susceptible strains. Nucleotide sequence accession numbers. These wholegenome shotgun (WGS) projects have been deposited at DDBJ/ EMBL/GenBank under the accession numbers LIWE00000000 (AbMDR-GLH1), LIZZ00000000 (AbMDR-GLH2), LJAA00000000 (AbMDR-GLH3), LJAB00000000 (AbMDR-GLH4), LJAC00000000 (AbMDR-GLH5), LJAD00000000 (AbMDR-GLH6), and LJAF00000000 (AbMDR-GLH8). The versions described in this report are the first versions, LIWE01000000, LIZZ01000000, LJAA01000000, LJAB01000000, LJAC01000000, LJAD01000000, and LJAF01000000. ACKNOWLEDGMENT This study was supported by the Instituto de Salud Carlos III, Proyectos de Investigación en Salud (grant PI12/02553).
FUNDING INFORMATION This work, including the efforts of Jerónimo Pachón, was funded by MINECO | Instituto de Salud Carlos III (ISCIII) (PI12/02553).
REFERENCES 1. Peleg AY, Seifert H, Paterson DL. 2008. Acinetobacter baumannii: emergence of a successful pathogen. Clin Microbiol Rev 21:538 –582. http:// dx.doi.org/10.1128/CMR.00058-07.
Genome Announcements
genomea.asm.org 1
Labrador-Herrera et al.
2. 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. 3. Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114 –2120. http://dx.doi.org/ 10.1093/bioinformatics/btu170. 4. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I. 2009. ABySS: a parallel assembler for short read sequence data. Genome Res 19: 1117–1123. http://dx.doi.org/10.1101/gr.089532.108. 5. 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.
2 genomea.asm.org
6. Larsen MV, Cosentino S, Rasmussen S, Friis C, Hasman H, Marvig RL, Jelsbak L, Sicheritz-Pontén T, Ussery DW, Aarestrup FM, Lund O. 2012. Multilocus sequence typing of total-genome-sequenced bacteria. J Clin Microbiol 50:1355–1361. http://dx.doi.org/10.1128/JCM.06094-11. 7. Bartual SG, Seifert H, Hippler C, Luzon MA, Wisplinghoff H, Rodríguez-Valera F. 2005. Development of a multilocus sequence typing scheme for characterization of clinical isolates of Acinetobacter baumannii. J Clin Microbiol 43:4382– 4390. http://dx.doi.org/10.1128/JCM.43.9.4382 -4390.2005. 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. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol 215:403– 410. http://dx.doi.org/10.1016/ S0022-2836(05)80360-2.
Genome Announcements
March/April 2016 Volume 4 Issue 2 e00083-16
Draft Genome Sequences of Seven Multidrug-Resistant Acinetobacter baumannii Strains, Isolated from Respiratory Samples in Spain Gema Labrador-Herrera,a Rocío Álvarez,a Rafael López-Rojas,b Younes Smani,a Tania Cebrero-Cangueiro,a Antonio Rueda,c Javier Pérez Florido,c Jerónimo Pachón,a María Eugenia Pachón-Ibáñeza Unit of Infectious Diseases, Microbiology and Preventive Medicine and Biomedical Institute of Seville (IBiS), University Hospital Virgen del Rocio/CSIC/University of Seville, Seville, Spaina; Infectious Diseases and Clinical Microbiology Unit, University Hospital Virgen Macarena, Seville, Spainb; Medical Genome Project, Genomics and Bioinformatics Platform of Andalusia (GBPA), Seville, Spainc
The draft genome sequences of seven multidrug-resistant Acinetobacter baumannii clinical strains belonging to sequence types ST-208 and ST-218 are reported in this study. They were isolated from tracheobronchial aspirate of mechanically ventilated adult patients admitted to the intensive care unit of a Spanish tertiary hospital during 2010 to 2011. Received 21 January 2016 Accepted 12 February 2016 Published 31 March 2016 Citation Labrador-Herrera G, Álvarez R, López-Rojas R, Smani Y, Cebrero-Cangueiro T, Rueda A, Pérez Florido J, Pachón J, Pachón-Ibáñez ME. 2016. Draft genome sequences of seven multidrug-resistant Acinetobacter baumannii strains, isolated from respiratory samples in Spain. Genome Announc 4(2):e00083-16. doi:10.1128/genomeA.00083-16. Copyright © 2016 Labrador-Herrera et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Jerónimo Pachón, [email protected].
A
cinetobacter baumannii is among the leading etiologies of hospital-acquired infections, particularly in critically ill patients (1). The increasing prevalence of multidrug-resistance reduces available treatments and threatens public health (2). During 2010 to 2011, 207 multidrug-resistant (MDR) A. baumannii strains were isolated from 100 adult patients in the intensive care unit of a tertiary hospital in Seville, Spain. In this study, we present the draft genome sequences of 7 of these MDR A. baumannii clinical strains (including resistance to gentamicin, imipenem, meropenem, ceftazidime, cefepime, ticarcillin, trimethoprim-sulfamethoxazole, tetracycline, levofloxacin, and ciprofloxacin; and susceptibility to colistin) isolated from tracheobronchial aspirates. Whole-genome sequencing was performed using the Illumina MiSeq platform with 300 bp paired-end reads, resulting in mean genome coverage of 25.2 ⫾ 5.5-fold (mean ⫾ SD of the 7 strains). Reads were preprocessed with Trimmomatic v0.32 (http: //www.usadellab.org/cms/?page⫽trimmomatic) (3) and de novo assembled with ABySS assembler v1.5.2 (http://www.bcgsc.ca /platform/bioinfo/software/abyss) (4), resulting in 381 ⫾ 52 contigs. The assemblies were filtered for contigs larger than 500 bp, leaving 210 ⫾ 34 contigs with a total length of 4,036,456 ⫾ 123,611 bp and an N50 of 47,317 ⫾ 8,993 bp. The G⫹C content was 39.2 ⫾ 0.1%. Gene prediction and annotation were performed utilizing GeneMark v2.5 (http://exon.gatech.edu/Gene Mark/) and RAST server v1.0 (http://rast.nmpdr.org) (5), respectively, yielding a total of 3,876 ⫾ 134 coding sequences and 70 ⫾ 15 RNAs. Two different sequence types (ST) were found with MLST v1.8 using the Oxford database (https://cge.cbs.dtu.dk /services/MLST/) (6, 7). Most of the strains belong to ST-208, except AbMDR-GLH5 and AbMDR-GLH6 that belong to ST-218. With pulsed-field gel electrophoresis, 3 pulsotypes were found: pulsotype 1 (AbMDR-GLH2 and AbMDR-GLH4), pulsotype 2 (AbMDR-GLH1, AbMDR-GLH3, and AbMDR-GLH8), and pulsotype 3 (AbMDR-GLH5 and AbMDR-GLH6). To identify genes conferring antimicrobial resistance, the bioinformatic tool ResFinder v2.1 was used (https://cge.cbs.dtu.dk/services/ResFinder/)
March/April 2016 Volume 4 Issue 2 e00083-16
(8). The aminoglycoside resistance genes aac(6=)-II, strB, and strA, were detected in pulsotype 1 strains, while pulsotype 2 strains carry aac(3)-Ia, aadA1, strB, and strA genes, and pulsotype 3 strains carry aac(6=)-II, aac(3)-IIa, strB, and strA genes. Resistance genes blaOXA-58, blaOXA-66, and blaADC-25, which confer -lactam resistance, were found in strains from pulsotypes 1 and 2; nevertheless, pulsotype 3 strains carry blaOXA-109 and blaADC-25 genes. Referring to sulfonamide resistance, all the strains have sul1 gene, and strains from pulsotypes 1 and 2 also possess sul2 gene. The gene tet(B), related with tetracycline resistance, was found in all the strains. Furthermore, point mutations in genes associated with quinolone resistance were found in all the strains using BLAST (Basic Local Alignment Search Tool) (http://blast.ncbi.nlm.nih.gov/Blast .cgi) (9) comparing with genes from susceptible strains. Nucleotide sequence accession numbers. These wholegenome shotgun (WGS) projects have been deposited at DDBJ/ EMBL/GenBank under the accession numbers LIWE00000000 (AbMDR-GLH1), LIZZ00000000 (AbMDR-GLH2), LJAA00000000 (AbMDR-GLH3), LJAB00000000 (AbMDR-GLH4), LJAC00000000 (AbMDR-GLH5), LJAD00000000 (AbMDR-GLH6), and LJAF00000000 (AbMDR-GLH8). The versions described in this report are the first versions, LIWE01000000, LIZZ01000000, LJAA01000000, LJAB01000000, LJAC01000000, LJAD01000000, and LJAF01000000. ACKNOWLEDGMENT This study was supported by the Instituto de Salud Carlos III, Proyectos de Investigación en Salud (grant PI12/02553).
FUNDING INFORMATION This work, including the efforts of Jerónimo Pachón, was funded by MINECO | Instituto de Salud Carlos III (ISCIII) (PI12/02553).
REFERENCES 1. Peleg AY, Seifert H, Paterson DL. 2008. Acinetobacter baumannii: emergence of a successful pathogen. Clin Microbiol Rev 21:538 –582. http:// dx.doi.org/10.1128/CMR.00058-07.
Genome Announcements
genomea.asm.org 1
Labrador-Herrera et al.
2. 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. 3. Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114 –2120. http://dx.doi.org/ 10.1093/bioinformatics/btu170. 4. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I. 2009. ABySS: a parallel assembler for short read sequence data. Genome Res 19: 1117–1123. http://dx.doi.org/10.1101/gr.089532.108. 5. 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.
2 genomea.asm.org
6. Larsen MV, Cosentino S, Rasmussen S, Friis C, Hasman H, Marvig RL, Jelsbak L, Sicheritz-Pontén T, Ussery DW, Aarestrup FM, Lund O. 2012. Multilocus sequence typing of total-genome-sequenced bacteria. J Clin Microbiol 50:1355–1361. http://dx.doi.org/10.1128/JCM.06094-11. 7. Bartual SG, Seifert H, Hippler C, Luzon MA, Wisplinghoff H, Rodríguez-Valera F. 2005. Development of a multilocus sequence typing scheme for characterization of clinical isolates of Acinetobacter baumannii. J Clin Microbiol 43:4382– 4390. http://dx.doi.org/10.1128/JCM.43.9.4382 -4390.2005. 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. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol 215:403– 410. http://dx.doi.org/10.1016/ S0022-2836(05)80360-2.
Genome Announcements
March/April 2016 Volume 4 Issue 2 e00083-16
