PMCCPMCCPMCC

Search tips
Search criteria 

Advanced

 
Logo of genannJournal InfoAuthorsPermissionsJournals.ASM.orggenomeA ArticleGenome Announcements
 
Genome Announc. 2017 August; 5(31): e00693-17.
Published online 2017 August 3. doi:  10.1128/genomeA.00693-17
PMCID: PMC5543635

Complete Genome Sequence of Mycobacterium chimaera Strain CDC2015-22-71

ABSTRACT

Mycobacterium chimaera is a nontuberculous mycobacterium species commonly found in the environment. Here, we report the first complete genome sequence of a strain from the investigation of invasive infections following open-heart surgeries that used contaminated LivaNova Sorin Stockert 3T heater-cooler devices.

GENOME ANNOUNCEMENT

Mycobacterium chimaera is a nontuberculous mycobacterium (NTM) species within the Mycobacterium avium complex (MAC). M. chimaera is an emerging cause of infection, in particular due to increasing awareness of infections linked with exposure to contaminated LivaNova Sorin Stockert 3T heater-cooler unit (HCU) devices (1,12). Despite the public health relevance of M. chimaera, no publicly available genome is representative of genotypes implicated in HCU contamination (13, 14). We present this here, using CDC2015-22-71, a clinical isolate from a Pennsylvania patient epidemiologically linked to a cluster of M. chimaera infections following exposure to an HCU.

Genomic DNA was extracted from CDC2015-22-71 grown in 7H9 broth (BD, Franklin Lakes, NJ, USA) at 36°C for approximately 1 week. The genome was sequenced using the Pacific Biosciences RSII (PacBio, Menlo Park, CA, USA) and Illumina MiSeq (San Diego, CA, USA) platforms. A 10-kb library was generated with the SMRTbell template prep kit 1. The library was then bound to polymerase using the DNA/polymerase binding kit P6v2. The bound library was loaded on two SMRTcells and sequenced with C4v2 chemistry for 360-min movies on the RSII instrument. Sequence reads were filtered and assembled de novo utilizing the PacBio HGAP version 3 (15). The PacBio assembly was corrected with Illumina reads using Pilon version 1.20 (16). The resulting assembly was compared to other M. chimaera genomes using Mauve version 2.3.1 (17). Genomic features were identified and annotated using the NCBI Prokaryotic Genome Annotation Pipeline.

The genome of M. chimaera CDC2015-22-71 consists of four scaffolds, equaling 6,247,640 bp (6,078,351-bp chromosome; 97,267-bp plasmid; 39,887-bp plasmid; 32,135-bp plasmid) and a G+C content of 67.6%. A total of 5,795 coding sequences were predicted, including 5,627 protein-coding genes and 168 pseudogenes. Our genome assembly contains 47 tRNAs, 3 noncoding RNAs, and 1 rRNA cistron consisting of the 16S, 23S, and 5S rRNA genes.

Whole-genome alignments of M. chimaera CDC2015-22-71, Hawaiian respiratory strain AH16 (GenBank accession number CP012885 [13]), and Irish respiratory strains MCIMRL6, MCIMRL4, and MCIMRL2 (GenBank accession numbers LJHN00000000, LJHM00000000, and LJHL00000000 [14]) revealed 15,077 single-nucleotide polymorphisms (SNPs) compared to AH16; 8,870 SNPs compared to MCIMRL2; 2,229 SNPs compared to MCIMRL4; and 8,098 SNPs compared to MCIMRL6. Comparison of gene content between the five M. chimaera genomes revealed a core gene set of 4,726 genes (83.9% of the 2015-22-71 genome [18]). The comparison of CDC2015-22-71 against all previously identified M. chimaera genomes resulted in average nucleotide identity values greater than or equal to 98.70%, which are greater than the 95 to 96% cutoff for species boundaries (19).

This M. chimaera genome assembly is the first complete NTM genome associated with an outbreak and will serve as a reference for epidemiological investigations of North American-based HCU contamination and postsurgical M. chimaera infections.

Accession number(s).

The genome sequence of M. chimaera CDC2015-22-71 has been deposited in NCBI GenBank under accession numbers CP019221 through CP019224. PacBio and Illumina reads have been deposited in NCBI under BioProject number PRJNA344472 and BioSample number SAMN05824346.

ACKNOWLEDGMENTS

N.A.H. and M.S. acknowledge support from the Cystic Fibrosis Foundation. A.L., K.A.P., D.B., and A.L.H. acknowledge support from U.S. government funds. The findings and conclusions in this report are those of the Centers for Disease Control and Prevention (CDC) authors and do not necessarily represent the views of the CDC.

Footnotes

Citation Hasan NA, Lawsin A, Perry KA, Alyanak E, Toney NC, Malecha A, Rowe LA, Batra D, Moulton-Meissner H, Miller JR, Strong M, Laufer Halpin A. 2017. Complete genome sequence of Mycobacterium chimaera strain CDC2015-22-71. Genome Announc 5:e00693-17. https://doi.org/10.1128/genomeA.00693-17.

REFERENCES

1. Svensson E, Jensen ET, Rasmussen EM, Folkvardsen DB, Norman A, Lillebaek T 2017. Mycobacterium chimaera in heater-cooler units in Denmark related to isolates from the United States and United Kingdom. Emerg Infect Dis J 23:507–509. doi:.10.3201/eid2303.161941 [PMC free article] [PubMed] [Cross Ref]
2. Sommerstein R, Schreiber PW, Diekema DJ, Edmond MB, Hasse B, Marschall J, Sax H 2017. Mycobacterium chimaera outbreak associated with heater-cooler devices: piecing the puzzle together. Infect Control Hosp Epidemiol 38:103–108. doi:.10.1017/ice.2016.283 [PubMed] [Cross Ref]
3. Chand M, Lamagni T, Kranzer K, Hedge J, Moore G, Parks S, Collins S, del Ojo Elias C, Ahmed N, Brown T, Smith EG, Hoffman P, Kirwan P, Mason B, Smith-Palmer A, Veal P, Lalor MK, Bennett A, Walker J, Yeap A, Isidro Carrion Martin A, Dolan G, Bhatt S, Skingsley A, Charlett A, Pearce D, Russell K, Kendall S, Klein AA, Robins S, Schelenz S, Newsholme W, Thomas S, Collyns T, Davies E, McMenamin J, Doherty L, Peto TE, Crook D, Zambon M, Phin N 2017. Insidious risk of severe Mycobacterium chimaera infection in cardiac surgery patients. Clin Infect Dis 64:335–342. doi:.10.1093/cid/ciw754 [PubMed] [Cross Ref]
4. Haller S, Höller C, Jacobshagen A, Hamouda O, Abu Sin M, Monnet D, Plachouras D, Eckmanns T 2016. Contamination during production of heater-cooler units by Mycobacterium chimaera potential cause for invasive cardiovascular infections: results of an outbreak investigation in Germany, April 2015 to February 2016. Euro Surveill 21:pii=30215 http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId=22461. [PubMed]
5. Honda JR, Hasan NA, Davidson RM, Williams MD, Epperson LE, Reynolds PR, Smith T, Iakhiaeva E, Bankowski MJ, Wallace RJ Jr, Chan ED, Falkinham JO III, Strong M 2016. Environmental nontuberculous mycobacteria in the Hawaiian Islands. PLoS Negl Trop Dis 10:e0005068. doi:.10.1371/journal.pntd.0005068 [PMC free article] [PubMed] [Cross Ref]
6. Perkins KM, Lawsin A, Hasan NA, Strong M, Halpin AL, Rodger RR, Moulton-Meissner H, Crist MB, Schwartz S, Marders J, Daley CL, Salfinger M, Perz JF 2016. Mycobacterium chimaera contamination of heater-cooler devices used in cardiac surgery—United States. Morb Mortal Wkly Rep 65:1117–1118. doi:.10.15585/mmwr.mm6540a6 [PubMed] [Cross Ref]
7. Robinson JO, Coombs GW, Speers DJ, Keehner T, Keil AD, D’Abrera V, Boan P, Pang S 2016. Mycobacterium chimaera colonisation of heater-cooler units (HCU) in Western Australia, 2015: investigation of possible iatrogenic infection using whole-genome sequencing. Euro Surveill 21:30396 http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId=22640. [PMC free article] [PubMed]
8. Struelens MJ, Plachouras D 2016. Mycobacterium chimaera infections associated with heater-cooler units (HCU): closing another loophole in patient safety. Euro Surveill 21:pii=30397 http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId=22645. [PMC free article] [PubMed]
9. Kohler P, Kuster SP, Bloemberg G, Schulthess B, Frank M, Tanner FC, Rössle M, Böni C, Falk V, Wilhelm MJ, Sommerstein R, Achermann Y, ten Oever J, Debast SB, Wolfhagen MJHM, Brandon Bravo Bruinsma GJ, Vos MC, Bogers A, Serr A, Beyersdorf F, Sax H, Böttger EC, Weber R, van Ingen J, Wagner D, Hasse B 2015. Healthcare-associated prosthetic heart valve, aortic vascular graft, and disseminated Mycobacterium chimaera infections subsequent to open heart surgery. Eur Heart J 36:2745–2753. doi:.10.1093/eurheartj/ehv342 [PubMed] [Cross Ref]
10. Sax H, Bloemberg G, Hasse B, Sommerstein R, Kohler P, Achermann Y, Rössle M, Falk V, Kuster SP, Böttger EC, Weber R 2015. Prolonged outbreak of Mycobacterium chimaera infection after open-chest heart surgery. Clin Infect Dis 61:67–75. doi:.10.1093/cid/civ198 [PubMed] [Cross Ref]
11. Wallace RJ, Iakhiaeva E, Williams MD, Brown-Elliott BA, Vasireddy S, Vasireddy R, Lande L, Peterson DD, Sawicki J, Kwait R, Tichenor WS, Turenne C, Falkinham JO 2013. Absence of Mycobacterium intracellulare and presence of Mycobacterium chimaera in household water and biofilm samples of patients in the United States with Mycobacterium avium complex respiratory disease. J Clin Microbiol 51:1747–1752. doi:.10.1128/JCM.00186-13 [PMC free article] [PubMed] [Cross Ref]
12. Schweickert B, Goldenberg O, Richter E, Göbel UB, Petrich A, Buchholz P, Moter A 2008. Occurrence and clinical relevance of Mycobacterium chimaera sp. nov., Germany. Emerg Infect Dis 14:1443–1446. doi:.10.3201/eid1409.071032 [PMC free article] [PubMed] [Cross Ref]
13. Hasan NA, Honda JR, Davidson RM, Epperson LE, Bankowski MJ, Chan ED, Strong M 2016. Complete genome sequence of Mycobacterium chimaera strain AH16. Genome Announc 4(6):e01276-01216. doi:.10.1128/genomeA.01276-16 [PMC free article] [PubMed] [Cross Ref]
14. Mac Aogáin M, Roycroft E, Raftery P, Mok S, Fitzgibbon M, Rogers TR 2015. Draft genome sequences of three Mycobacterium chimaera respiratory isolates. Genome Announc 3(6):e01409-15. doi:.10.1128/genomeA.01409-15 [PMC free article] [PubMed] [Cross Ref]
15. Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, Turner SW, Korlach J 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 10:563–569. doi:.10.1038/nmeth.2474 [PubMed] [Cross Ref]
16. Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, Young SK, Earl AM 2014. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 9:e112963. doi:.10.1371/journal.pone.0112963 [PMC free article] [PubMed] [Cross Ref]
17. Darling AE, Mau B, Perna NT 2010. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One 5:e11147. doi:.10.1371/journal.pone.0011147 [PMC free article] [PubMed] [Cross Ref]
18. Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S, Holden MT, Fookes M, Falush D, Keane JA, Parkhill J 2015. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 31:3691–3693. doi:.10.1093/bioinformatics/btv421 [PMC free article] [PubMed] [Cross Ref]
19. Richter M, Rosselló-Móra R 2009. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 106:19126–19131. doi:.10.1073/pnas.0906412106 [PubMed] [Cross Ref]

Articles from Genome Announcements are provided here courtesy of American Society for Microbiology (ASM)