High-throughput automated microfluidic sample preparation for accurate microbial genomics

Nature Communications

Volumn 8, Issue , 2017, Pages

  Kim, Soohong ^a,b   De Jonghe, Joachim ^a,c   Kulesa, Anthony B ^a,b   Feldman, David ^a,d   Vatanen, Tommi ^a,e   Bhattacharyya, Roby P ^a,f   Berdy, Brittany ^g   Gomez, James ^a   Nolan, Jill ^a   Epstein, Slava ^g   Blainey, Paul C ^a,b  

^a BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^b Massachusetts Institute of Technology Cambridge   (United States)

^c UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^d MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^e AALTO UNIVERSITY   (Finland)

^f MASSACHUSETTS GENERAL HOSPITAL   (United States)

^g NORTHEASTERN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AUTOMATION; BACTERIUM; CELLS AND CELL COMPONENTS; DATA QUALITY; DETECTION METHOD; DNA; GENOMICS; LIMITING FACTOR; MICROORGANISM; POLYMORPHISM; SAMPLE PREPARATION;

ANTIBIOTIC RESISTANCE; BASIC RESEARCH; GENE MUTATION; GENOME; GENOMICS; LIBRARY; MAJOR CLINICAL STUDY; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PSEUDOMONAS AERUGINOSA; SINGLE NUCLEOTIDE POLYMORPHISM; SOIL; WORKFLOW; BACTERIAL GENOME; BACTERIAL INFECTION; DEVICES; DNA MICROARRAY; ENVIRONMENTAL MONITORING; GENE LIBRARY; GENETICS; HIGH THROUGHPUT SCREENING; HIGH THROUGHPUT SEQUENCING; HUMAN; ISOLATION AND PURIFICATION; LAB ON A CHIP; MICROBIOLOGY; MICROFLUIDICS; PROCEDURES; WHOLE GENOME SEQUENCING;

MYCOBACTERIUM TUBERCULOSIS; PSEUDOMONAS AERUGINOSA;

BACTERIAL INFECTIONS; DRUG RESISTANCE, MICROBIAL; ENVIRONMENTAL MONITORING; GENE LIBRARY; GENOME, BACTERIAL; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HIGH-THROUGHPUT SCREENING ASSAYS; HUMANS; LAB-ON-A-CHIP DEVICES; MICROFLUIDICS; MYCOBACTERIUM TUBERCULOSIS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE; PSEUDOMONAS AERUGINOSA; SOIL MICROBIOLOGY; WHOLE GENOME SEQUENCING;

EID: 85010903349     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms13919     Document Type: Article

References (53)

1. Yatsunenko, T., et al. Human gut microbiome viewed across age, geography. Nature 486, 222-227 (2012).
2. Marvig, R. L., Sommer, L. M., Molin, S., Johansen, H. K. Convergent evolution, adaptation of Pseudomonas aeruginosa within patients with cystic fibrosis. Nat. Genet. 47, 57-64 (2014).
3. Dallman, T. J., et al. Whole-genome sequencing for national surveillance of shiga toxin-producing Escherichia coli O157. Clin. Infect. Dis. 61, 305-312 (2015).
4. Nasser, W., et al. Evolutionary pathway to increased virulence, epidemic group A Streptococcus disease derived from 3, 615 genome sequences. Proc. Natl Acad. Sci. USA 111, E1768-E1776 (2014).
5. Chewapreecha, C., et al. Dense genomic sampling identifies highways of pneumococcal recombination. Nat. Genet. 46, 305-309 (2014).
6. Smith, E. E., et al. Genetic adaptation by Pseudomonas aeruginosa to the airways of cystic fibrosis patients. Proc. Natl Acad. Sci. USA 103, 8487-8492 (2006).
7. Snitkin, E. S., et al. Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing. Sci. Transl. Med. 4, 148ra116 (2012).
8. Centers for Disease Control, Prevention Antibiotic-Resistant Gonorrhea-STD information from CDC. Available at https://www.cdc.gov/std/gonorrhea/arg/basic.htm.
9. Obama, B. Executive Order-Combating Antibiotic-Resistant Bacteria whitehouse.gov. the White house (2014). Available at https://www.whitehouse. gov/the-press-office/2014/09/18/executive-order-combating-antibiotic-resistantbacteria& gt;.
10. Newman, D. J., Cragg, G. M. Natural products as sources of new drugs over the 30 years from 1981 to 2010. J. Nat. Prod. 75, 311-335 (2012).
11. Weber, T., et al. antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Res. 43, W237-W243 (2015).
12. Kim, H., et al. A microfluidic DNA library preparation platform for next-generation sequencing. PLoS ONE 8, e68988 (2013).
13. de Bourcy, C. F. A., et al. A quantitative comparison of single-cell whole genome amplification methods. PLoS ONE 9, e105585 (2014).
14. Kram, K. E., Finkel, S. E. Rich medium composition affects Escherichia coli survival, glycation, mutation frequency during long-term batch culture. Appl. Environ. Microbiol. 81, 4442-4450 (2015).
15. Blainey, P. C. The future is now: single-cell genomics of bacteria, archaea. FEMS Microbiol. Rev. 37, 407-427 (2013).
16. Salter, S. J., et al. Reagent, laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol. 12, 87 (2014).
17. Jones, M. B., et al. Library preparation methodology can influence genomic, functional predictions in human microbiome research. Proc. Natl Acad. Sci. USA 112, 14024-14029 (2015).
18. Brooks, J. P., et al. The truth about metagenomics: quantifying, counteracting bias in 16S rRNA studies. BMC Microbiol. 15, 66 (2015).
19. Witney, A. A., et al. Clinical use of whole genome sequencing for Mycobacterium tuberculosis. BMC Med. 14, 46 (2016).
20. Wilson, M. R., et al. Actionable diagnosis of neuroleptospirosis by next-generation sequencing. N. Engl. J. Med. 370, 2408-2417 (2014).
21. Naccache, S. N., et al. A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples. Genome Res. 24, 1180-1192 (2014).
22. Nichols, D., et al. Use of ichip for high-throughput in situ cultivation of "uncultivable" microbial species. Appl. Environ. Microbiol. 76, 2445-2450 (2010).
23. Anderson, S. Shotgun DNA sequencing using cloned DNase I-generated fragments. Nucleic Acids Res. 9, 3015-3027 (1981).
24. Ramsköld, D., et al. Full-length mRNA-Seq from single-cell levels of RNA, individual circulating tumor cells. Nat. Biotechnol. 30, 777-782 (2012).
25. Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y., Greenleaf, W. J. Transposition of native chromatin for fast, sensitive epigenomic profiling of open chromatin, DNA-binding proteins, nucleosome position. Nat. Methods 10, 1213-1218 (2013).
26. Robertson, G., et al. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation, massively parallel sequencing. Nat. Methods 4, 651-657 (2007).
27. Melin, J., Quake, S. R. Microfluidic large-scale integration: the evolution of design rules for biological automation. Annu. Rev. Biophys. Biomol. Struct. 36, 213-231 (2007).
28. Morinishi, L. S., Blainey, P. Simple bulk readout of digital nucleic acid quantification assays. J. Vis. Exp. e52925 (2015).
29. Caruccio, N. Preparation of next-generation sequencing libraries using Nextera technology: simultaneous DNA fragmentation, adaptor tagging by in vitro transposition. Methods Mol. Biol. 733, 241-255 (2011).
30. DeAngelis, M. M., Wang, D. G., Hawkins, T. L. Solid-phase reversible immobilization for the isolation of PCR products. Nucleic Acids Res. 23, 4742-4743 (1995).
31. Kim, S., et al. High-throughput single-molecule optofluidic analysis. Nat. Methods 8, 242-245 (2011).
32. Bhattacharyya, A., Klapperich, C. M. Thermoplastic microfluidic device for on-chip purification of nucleic acids for disposable diagnostics. Anal. Chem. 78, 788-792 (2006).
33. Tan, S. J., et al. A microfluidic device for preparing next generation DNA sequencing libraries, for automating other laboratory protocols that require one or more column chromatography steps. PLoS ONE 8, e64084 (2013).
34. Balagaddé, F. K., You, L., Hansen, C. L., Arnold, F. H., Quake, S. R. Long-term monitoring of bacteria undergoing programmed population control in a microchemostat. Science 309, 137-140 (2005).
35. Parkinson, N. J., et al. Preparation of high-quality next-generation sequencing libraries from picogram quantities of target DNA. Genome Res. 22, 125-133 (2012).
36. Li, H. Mathematical Notes on SAMtools Algorithms. (2010). Available at https://www.broadinstitute.org/gatk/media/docs/Samtools.pdf.
37. Kelley, D. R., Schatz, M. C., Salzberg, S. L. Quake: quality-aware detection, correction of sequencing errors. Genome Biol. 11, R116 (2010).
38. Robasky, K., Lewis, N. E., Church, G. M. The role of replicates for error mitigation in next-generation sequencing. Nat. Rev. Genet. 15, 56-62 (2014).
39. Walker, B. J., et al. Pilon: an integrated tool for comprehensive microbial variant detection, genome assembly improvement. PLoS ONE 9, e112963 (2014).
40. Lieberman, T. D., et al. Genetic variation of a bacterial pathogen within individuals with cystic fibrosis provides a record of selective pressures. Nat. Genet. 46, 82-87 (2014).
41. Schmitt, M. W., et al. Detection of ultra-rare mutations by next-generation sequencing. Proc. Natl Acad. Sci. USA 109, 14508-14513 (2012).
42. Pai, H., Kim, J., Lee, J. H., Choe, K. W., Gotoh, N. Carbapenem resistance mechanisms in Pseudomonas aeruginosa clinical isolates. Antimicrob. Agents Chemother. 45, 480-484 (2001).
43. Lomholt, J. A., Kilian, M. Ciprofloxacin susceptibility of Pseudomonas aeruginosa isolates from keratitis. Br. J. Ophthalmol. 87, 1238-1240 (2003).
44. Bruchmann, S., Dötsch, A., Nouri, B., Chaberny, I. F., Haüssler, S. Quantitative contributions of target alteration, decreased drug accumulation to Pseudomonas aeruginosa fluoroquinolone resistance. Antimicrob. Agents Chemother. 57, 1361-1368 (2013).
45. Bauer, A. W., Kirby, W. M., Sherris, J. C., Turck, M. Antibiotic susceptibility testing by a standardized single disk method. Am. J. Clin. Pathol. 45, 493-496 (1966).
46. Darling, A. E., et al. PhyloSift: phylogenetic analysis of genomes, metagenomes. PeerJ 2, e243 (2014).
47. Winsor, G. L., et al. Enhanced annotations, features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database. Nucleic Acids Res. 44, D646-D653 (2015).
48. Ling, L. L., et al. A new antibiotic kills pathogens without detectable resistance. Nature 517, 455-459 (2015).
49. Skurnik, D., et al. Is exposure to mercury a driving force for the carriage of antibiotic resistance genes J. Med. Microbiol. 59, 804-807 (2010).
50. Rowland, I. R., Robinson, R. D., Doherty, R. A. Effects of diet on mercury metabolism, excretion in mice given methylmercury: role of gut flora. Arch. Environ. Health 39, 401-408 (1984).
51. Smanski, M. J., et al. Synthetic biology to access, expand nature's chemical diversity. Nat. Rev. Microbiol. 14, 135-149 (2016).
52. Baltz, R. H. Antimicrobials from actinomycetes: back to the future. Microbe Am. Soc. Microbiol. 2, 125 (2007).
53. Fitzsimons, M. S., et al. Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome. Genome Res. 23, 878-888 (2013).