Abstract
A global outbreak of infections due to Mycobacterium chimaera has been linked to the LivaNova (formerly Sorin) 3 T heater-cooler units (HCUs). We performed a study to investigate M. chimaera from HCUs in China. Water samples were collected from all 3 T HCUs (n = 5) at our hospital in May 2017. Mycobacteria isolates were subjected to genome sequencing using the HiSeq X10 Sequencer. Species were identified based on average nucleotide identity with M. chimaera type strain DSM 44623T. Paired-end reads of all M. chimaera genomes were retrieved from the SRA database and, together with our isolates, were mapped against the chromosome of M. chimaera reference strain ZUERICH-1 to call SNPs. Mycobacteria grew from three HCUs manufactured in 2009 but not from the two in 2016. The three isolates were identified as M. chimaera and differed from each other by 4 to 6 SNPs, and from ZUERICH-1 by 7 to 10 SNPs. The three isolates belonged to the subgroup 1.1 and were most closely related to strains of the subgroup 1.1 from HCUs or patients in Europe, Australia/New Zealand and USA, suggesting the same common source. This is the first report of M. chimaera from HCUs in China.
Similar content being viewed by others
Introduction
Mycobacterium chimaera, a species of the Mycobacterium avium complex, is ubiquitous in the environment and is an opportunistic pathogen capable of causing human infections. In 2015, the infection control team at University Hospital Zurich reported that multiple patients had infections due to M. chimaera following open-heart surgey, with the outbreak linked to LivaNova (formerly Sorin) 3 T heater-cooler units (HCUs)1. Since then, outbreaks of infections due to M. chimaera among patients who received open-heart surgeries and were exposed to 3 T HCUs have also been reported in several European countries (Germany, the Netherland and UK), USA and Australia2,3,4. Infections due to M. chimaera are extremely difficult to treat and patients with such infections have a mortality rate of approximately 50%4,5,6. HCU-associated outbreaks of infections due to M. chimaera have been linked to the manufacturing site7,8. Although 3 T HCUs are also used in China, no such HCU-associated outbreaks have been reported. Here we report a study looking for the presence of M. chimaera in HCUs in a university hospital in China, with a hypothesis that the absence of such outbreaks is due to the absence of the organism in HCUs used in our hospital.
Materials and Methods
Settings
West China Hospital of Sichuan University, Chengdu, China, is a 5,000-bed tertiary hospital and serves as one of the major referral medical centers in western China. Around 2,600 patients received HCU-required open-heart surgeries in 2016 in the hospital. There are five 3 T HCUs, which are the only type of HCU, in the hospital. Three HCUs were manufactured in July 2009 and were introduced into the hospital in 2010 (n = 1) and 2012 (n = 2), while the remaining two were manufactured and were introduced into the hospital in August 2016. The HCUs were cleaned and disinfected every two to three months using the manufacturer’s protocol.
Sampling and culture
We sampled 1 liter of water from each of the five 3 T HCUs at West China Hospital before they underwent disinfection in May 2017. The protocol developed by the European Center for Disease Prevention and Control (ECDC)9 was used for our study. Water samples were concentrated by filtration and were subjected to culture on M7H11 plates (Haibo, Qingdao, China) for up to eight weeks9.
Whole genome sequencing
Mycobacteria isolates were subjected to whole genome sequencing with 300× coverage using the HiSeq X10 Sequencer (Illumina, San Diego, CA). The coverage was calculated based on the estimated genome size and the average output of the sequencer. Reads were trimmed using Trimmomatic10 and were then de novo assembled to contigs using the SPAdes program11 with careful mode turned on. Species identification of mycobacteria isolates was established based on average nucleotide identity (ANI) with the genome of strain DSM 44623T, the type strain of M. chimaera (GenBank accession no. LQOO00000000), using the JSpecies web program (http://imedea.uib-csic.es/jspecies/).
Phylogenetic analysis
To determine the group and the subgroup of our three isolates, the paired-end reads of the isolates were mapped against the chromosome of the reference strain ZUERICH-1 of group 1 (Accession no. NZ_CP015272) using Bowtie 212 and SAMtools13. Raw variants were called using Freebayes (https://github.com/ekg/freebayes). INDELs were discarded, and SNPs were filtered keeping only those with a minimum coverage, quality score and allele frequency of 10-fold, 30 and 0.75, respectively using vcflib (https://github.com/vcflib/vcflib). SNPs due to recombination were filtered using Gubbins14.
Illumina paired-end reads of all M. chimaera genomes available in the NCBI SRA database with a minimum of 200 Mbp (approximately 30× genome coverage) were retrieved (n = 508; for strains with multiple genome sequencing, only the first SRA record was retrieved). Ninety-eight of these genomes of 98 were discarded due to unresolvable problems (e.g. unequal length of sequence and the presence of invalid characters) of format and quality of their reads, resulting in a collection of 410 genome sequences. The raw sequence reads of these 410 strains were mapped against ZUERICH-1 and SNPs were called as described above. A phylogenetic tree of isolates belonging to subgroup 1.1 was constructed using RAxML15 with the GTRGAMMA model and a 1,000-bootstrap test.
Nucleotide sequence accession numbers
Draft whole-genome sequences of the three strains have been deposited into GenBank under the accession no. NTFV00000000, NTFW00000000 and NTFX00000000.
Results
Mycobacteria grew from three HCUs manufactured in 2009 but did not grow from the two manufactured in 2016. One isolate from each of the three culture-positive HCUs, designated WCHMC000001, WCHMC000030 and WCHMC000032, was subjected to whole genome sequencing.
A total of 1.99 to 2.13 Gb clean bases and 6,618,824 to 7,116,445 clean reads were generated for the three isolates, which were then assembled to 6.1 to 6.6 Mb draft genomes with 84 to 112 contigs (77 to 104 were ≥1,000 bp in length) with a 67.46 to 67.64% GC content, respectively. The genome sequences of the three isolates had a 99.14 to 99.52% ANI with the genome of strain DSM 44623T. The three isolates were therefore identified as M. chimaera.
A recent study of the genomic sequence of 250 isolates revealed two major groups of M. chimaera and isolates of the HCU-related outbreaks belonged to group 17. Using 10 single nucleotide polymorphisms (SNPs) for subgroup attribution, group 1 has been further classified into 11 distinct subgroups. Most isolates from water systems of 3 T HCUs in clinical use (Australia, Denmark, Germany, the Netherlands, New Zealand, UK, USA) and some from patients (Australia, Germany, the Netherlands, UK, USA) plus one from HCUs sampled at the LivaNova production site were clustered in the subgroup 1.17. There were a maximum of 6 SNPs difference between our three isolates (Table 1), suggesting that they originated from a very recent common ancestor. WCHMC000001, WCHMC000030 and WCHMC000032 differed from ZUERICH-1 by only 7, 9 and 10 SNPs, respectively, suggesting that the three isolates belonged to group 1. Substitutions of guanine (G) by adenine (A) at positions 113,518 and 209,278 of the DSM 44623T genome (GenBank accession no. LQOO00000000) were specific to subgroup 1.17, both of which were found in our three isolates. This suggests that the three isolates belong to the subgroup 1.1.
Among the 410 strains from the SRA database, 169 were found to harbour either or both of the subgroup 1.1-specific SNPs. A total of 295 SNP sites were identified from these 169 strains. As revealed by the phylogenetic tree of isolates belonging to the subgroup 1.1 (Fig. 1), our three isolates were most closely related to strains recovered from HCUs or patients in several European countries, Australia, New Zealand and USA with a maximum of just 5 SNPs difference between them (Table 1). The high clonality of isolates of the subgroup 1.1 from different geographical regions suggests a common source, which is most likely from contamination at the manufacturer site.
Discussion
We recovered M. chimaera from water tanks of three LivaNova 3 T HCUs at a university hospital. To be the best of our knowledge, this is the first report of M. chimaera from HCUs in China. Genome sequencing and phylogenetic analysis revealed that the three isolates were clonal and were placed within strains from multiple countries, suggesting the same common source.
It has been reported that brand new 3 T HCUs direct from the manufacturer can be quickly contaminated by M. chimaera1,8. However, no M. chimaera was recovered from the two recent HCUs manufactured in August 2016. There are several possible reasons. First, brand new 3 T HCUs have been shown to be contaminated after 158 to 358 days16. The two HCUs in our hospital had been in use for 8 months and it may be that sufficient time has not yet passed for them to be colonized to detectable levels by the organism. Second, the manufacturer has modified the post-production process in response to the findings of M. chimaera contamination8, which may reduce the risk of contamination in all new units. Third, the M7H11 media that we used has a higher detection limitation than the Mycobacterial Growth Indicator Tubes and may therefore be suboptimal17.
Unfortunately, there is no facility for blood culture of mycobacteria available in the hospital and there is no follow-up system for patients who received heart surgeries in the region. We are therefore unable to identify any clinical case of M. chimaera infection at present. Nonetheless, information of the global 3 T HCU-associated outbreak of infections due to M. chimaera and the local discovery of such M. chimaera strains has been disseminated to the cardiac surgeons and infectious disease physicians in the hospital. The facility for blood culture of mycobacteria will be established soon in the hospital to allow thorough future investigation of potential cardiac related M. chimaera infections.
Several measures have been proposed to minimize the risksof M. chimaera infections including strict separation of HCUs from the air volume of critical medical areas such as operating rooms, ensuring traceability of HCD use and following the updated manufacturer’s disinfection recommendations5,18. Unfortunately, it is not practical to place 3 T HCUs outside operating rooms in our hospital at present. The devices have been placed further away from patients, guided by smoking tests as described previously19. This practice could reduce patient risk but as patients are still exposed to HCUs in the room they need to be monitored for M. chimaera infections18. Strict separation of HCUs from operating rooms will be considered at the time of renovation. In addition, HCUs have been subjected to cleaning and disinfection using the updated protocol provided by the manufacturer (http://www.livanova.sorin.com/products/cardiac-surgery/perfusion/hlm/3t) since June 2017.
References
Sax, H. et al. Prolonged Outbreak of Mycobacterium chimaera Infection After Open-Chest Heart Surgery. Clin Infect Dis 61, 67–75 (2015).
Achermann, Y. et al. Prosthetic valve endocarditis and bloodstream infection due to Mycobacterium chimaera. J Clin Microbiol 51, 1769–73 (2013).
Williamson, D., Howden, B. & Stinear, T. Mycobacterium chimaera Spread from Heating and Cooling Units in Heart Surgery. N Engl J Med 376, 600–2 (2017).
Kohler, P. et al. Healthcare-associated prosthetic heart valve, aortic vascular graft, and disseminated Mycobacterium chimaera infections subsequent to open heart surgery. Eur Heart J 36, 2745–53 (2015).
Marra, A. R., Diekema, D. J. & Edmond, M. B. Mycobacterium chimaera infections associated with contaminated heater-cooler devices for cardiac surgery: Outbreak Management. Clin Infect Dis 65, 669–74 (2017).
Chand, M. et al. Insidious Risk of Severe Mycobacterium chimaera Infection in Cardiac Surgery Patients. Clin Infect Dis 64, 335–42 (2017).
van Ingen, J. et al. Global outbreak of severe Mycobacterium chimaera disease after cardiac surgery: a molecular epidemiological study. Lancet Infect Dis 17, 1033–41 (2017).
Haller, S. et al. 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, 30215 (2016).
European Center for Disease Prevention and Control. EU protocol for case detection, laboratory diagnosis and environmental testing of Mycobacterium chimaera infections potentially associated with heater-cooler units: case definition and environmental testing methodology. Stockholm, Sweden (2015).
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–20 (2014).
Bankevich, A. et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19, 455–77 (2012).
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat Methods 9, 357–9 (2012).
Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–9 (2009).
Croucher, N. J. et al. Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. Nucleic Acids Res 43, e15 (2015).
Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–3 (2014).
Schreiber, P. W. et al. Reemergence of Mycobacterium chimaera in heater-cooler units despite intensified cleaning and disinfection protocol. Emerg Infect Dis 22, 1830–3 (2016).
Schreiber P. W. et al. Detection limit of Mycobacterium chimaera in water samples for monitoring medical device safety: insights from a pilot experimental series. J Hosp Infect In press: S0195-6701(17)30633-3 (2017).
Sommerstein, R. et al. Mycobacterium chimaera outbreak associated with heater-cooler devices: piecing the puzzle together. Infect Control Hosp Epidemiol 38, 103–8 (2017).
Sommerstein, R. et al. Transmission of Mycobacterium chimaera from heater-cooler units during cardiac surgery despite an ultraclean air ventilation system. Emerg Infect Dis 22, 1008–13 (2016).
Acknowledgements
The work was supported by grants from the National Natural Science Foundation of China (project no. 81572030 and 81772233 to ZZ) and a joint grant from the National Natural Science Foundation of China (project no. 81661130159 to ZZ) and the Newton Advanced Fellowship, Royal Society (NA015363), UK (to AM and ZZ). The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Author information
Authors and Affiliations
Contributions
Z.Z. designed the experiments, analyzed the data and wrote the manuscript. X.Z., J.L., Y.F. performed the experiments and analyzed the data. X.W., A.M. contributed to analyzing the data and co-wrote the manuscript.
Corresponding author
Ethics declarations
Competing Interests
The authors declare no competing interests.
Additional information
Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
About this article
Cite this article
Zhang, X., Lin, J., Feng, Y. et al. Identification of Mycobacterium chimaera in heater-cooler units in China. Sci Rep 8, 7843 (2018). https://doi.org/10.1038/s41598-018-26289-5
Received:
Accepted:
Published:
DOI: https://doi.org/10.1038/s41598-018-26289-5
Comments
By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.