From isolate to answer: how whole genome sequencing is helping us rapidly characterise nosocomial bacterial outbreaks
Leah Roberts
+ Author Affiliations
- Author Affiliations
School of Chemistry and Molecular Biosciences (SCMB), University of Queensland, St Lucia, Qld, Australia
Tel: +61 7 3365 8549
Email: l.roberts3@uq.edu.au
Microbiology Australia 38(3) 127-130 https://doi.org/10.1071/MA17047
Published: 18 August 2017
Abstract
The occurrence of highly resistant bacterial pathogens has risen in recent years, causing immense strain on the healthcare industry. Hospital-acquired infections are arguably of most concern, as bacterial outbreaks in clinical settings provide an ideal environment for proliferation among vulnerable populations. Understanding these outbreaks beyond what can be determined with traditional clinical diagnostics and implementing these new techniques routinely in the hospital environment has now become a major focus. This brief review will discuss the three main whole genome sequence techniques available today, and how they are being used to further discriminate bacterial outbreaks in nosocomial settings.
References
[1] WHO (2016) World Health Organization Antimicrobial resistance facts sheet. http://www.who.int/mediacentre/factsheets/fs194/en/ (accessed 15 June 2017).[2] Kaye, K.S. et al. (2014) Effect of nosocomial bloodstream infections on mortality, length of stay, and hospital costs in older adults. J. Am. Geriatr. Soc. 62, 306–311.
| Effect of nosocomial bloodstream infections on mortality, length of stay, and hospital costs in older adults.Crossref | GoogleScholarGoogle Scholar |
[3] Kollef, M.H. (2000) Inadequate antimicrobial treatment: an important determinant of outcome for hospitalized patients. Clin. Infect. Dis. 31, S131–S138.
| Inadequate antimicrobial treatment: an important determinant of outcome for hospitalized patients.Crossref | GoogleScholarGoogle Scholar |
[4] Sydnor, E.R. and Perl, T.M. (2011) Hospital epidemiology and infection control in acute-care settings. Clin. Microbiol. Rev. 24, 141–173.
| Hospital epidemiology and infection control in acute-care settings.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3MXjtFSgu7Y%3D&md5=7b7e48a9b0c88ee37e7e68f136acfeccCAS |
[5] Ben Zakour, N.L. et al. (2012) Analysis of a Streptococcus pyogenes puerperal sepsis cluster by use of whole-genome sequencing. J. Clin. Microbiol. 50, 2224–2228.
| Analysis of a Streptococcus pyogenes puerperal sepsis cluster by use of whole-genome sequencing.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC38XhtFCmsL7O&md5=b50ba83f7d5e3fe5dabee03799888b0eCAS |
[6] Köser, C.U. et al. (2012) Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak. N. Engl. J. Med. 366, 2267–2275.
| Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak.Crossref | GoogleScholarGoogle Scholar |
[7] Lewis, T. et al. (2010) High-throughput whole-genome sequencing to dissect the epidemiology of Acinetobacter baumannii isolates from a hospital outbreak. J. Hosp. Infect. 75, 37–41.
| High-throughput whole-genome sequencing to dissect the epidemiology of Acinetobacter baumannii isolates from a hospital outbreak.Crossref | GoogleScholarGoogle Scholar | 1:STN:280:DC%2BC3c3lsVGgtg%3D%3D&md5=a4b03d0512dba57ad8943e145ee8f9a2CAS |
[8] Babouee Flury, B. et al. (2016) Association of novel nonsynonymous single nucleotide polymorphisms in ampD with cephalosporin resistance and phylogenetic variations in ampC, ampR, ompF, and ompC in Enterobacter cloacae isolates that are highly resistant to carbapenems. Antimicrob. Agents Chemother. 60, 2383–2390.
| Association of novel nonsynonymous single nucleotide polymorphisms in ampD with cephalosporin resistance and phylogenetic variations in ampC, ampR, ompF, and ompC in Enterobacter cloacae isolates that are highly resistant to carbapenems.Crossref | GoogleScholarGoogle Scholar |
[9] Ocampo-Sosa, A.A. et al. (2012) Alterations of OprD in carbapenem-intermediate and -susceptible strains of Pseudomonas aeruginosa isolated from patients with bacteremia in a Spanish multicenter study. Antimicrob. Agents Chemother. 56, 1703–1713.
| Alterations of OprD in carbapenem-intermediate and -susceptible strains of Pseudomonas aeruginosa isolated from patients with bacteremia in a Spanish multicenter study.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC38XltV2rurg%3D&md5=e930eb91d5bb0c7bace31893e0cc600cCAS |
[10] uz Zaman, T. et al. (2014) Multi-drug carbapenem-resistant Klebsiella pneumoniae infection carrying the OXA-48 gene and showing variations in outer membrane protein 36 causing an outbreak in a tertiary care hospital in Riyadh, Saudi Arabia. Int. J. Infect. Dis. 28, 186–192.
| Multi-drug carbapenem-resistant Klebsiella pneumoniae infection carrying the OXA-48 gene and showing variations in outer membrane protein 36 causing an outbreak in a tertiary care hospital in Riyadh, Saudi Arabia.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC2cXhs1KgtrvE&md5=78f93f116213591b5accdfab6c6f6367CAS |
[11] CDC (2017) Antibiotic/antimicrobial resistance. https://http://www.cdc.gov/drugresistance/biggest_threats.html (accessed 23 June 2017).
[12] Snitkin, E.S. et al. (2012) Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing. Sci. Transl. Med. 4, 148ra116.
| Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing.Crossref | GoogleScholarGoogle Scholar |
[13] Roberts, L.W. et al. (2017) Genomic investigation of an outbreak of carbapenemase-producing Enterobacter cloacae: long-read sequencing reveals the context of blaIMP4 on a widely distributed IncHI2 plasmid. BioRxiv. , .
| Genomic investigation of an outbreak of carbapenemase-producing Enterobacter cloacae: long-read sequencing reveals the context of blaIMP4 on a widely distributed IncHI2 plasmid.Crossref | GoogleScholarGoogle Scholar |
[14] Brown-Jaque, M. et al. (2015) Transfer of antibiotic-resistance genes via phage-related mobile elements. Plasmid 79, 1–7.
| Transfer of antibiotic-resistance genes via phage-related mobile elements.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC2MXhtVGgurk%3D&md5=9c2d28db8455df111e7161c008beb458CAS |
[15] Liu, Y.Y. et al. (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.
| Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study.Crossref | GoogleScholarGoogle Scholar |
[16] Wellington, E.M. et al. (2013) The role of the natural environment in the emergence of antibiotic resistance in gram-negative bacteria. Lancet Infect. Dis. 13, 155–165.
| The role of the natural environment in the emergence of antibiotic resistance in gram-negative bacteria.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3sXht1Ghsb0%3D&md5=92a212e456cd1706ab0c065fb7a0ee8bCAS |
[17] Siguier, P. et al. (2014) Bacterial insertion sequences: their genomic impact and diversity. FEMS Microbiol. Rev. 38, 865–891.
| Bacterial insertion sequences: their genomic impact and diversity.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC2cXhsFOgu7vP&md5=de76a93e07958f822ef6df52599426d9CAS |
[18] Kingsford, C. et al. (2010) Assembly complexity of prokaryotic genomes using short reads. BMC Bioinformatics 11, 21.
| Assembly complexity of prokaryotic genomes using short reads.Crossref | GoogleScholarGoogle Scholar |
[19] Ricker, N. et al. (2012) The limitations of draft assemblies for understanding prokaryotic adaptation and evolution. Genomics 100, 167–175.
| The limitations of draft assemblies for understanding prokaryotic adaptation and evolution.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC38XhtVKntbnE&md5=12b6c3e6a68904eae6d45137b7e292bbCAS |
[20] Toussaint, A. and Chandler, M. (2012) Prokaryote genome fluidity: toward a system approach of the mobilome. Methods Mol. Biol. 804, 57–80.
| Prokaryote genome fluidity: toward a system approach of the mobilome.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC38XhslaitL3P&md5=353e77b99febf8b606f392e00cb9cd76CAS |
[21] Wick, R.R. et al. (2015) Bandage: interactive visualization of de novo genome assemblies. Bioinformatics 31, 3350–3352.
| Bandage: interactive visualization of de novo genome assemblies.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC28Xhs1Git7%2FJ&md5=361f32e83a52d5aeefc661a595e0ceb5CAS |
[22] Koren, S. and Phillippy, A.M. (2015) One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly. Curr. Opin. Microbiol. 23, 110–120.
| One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC2cXhvF2hu7jF&md5=909e8064d6e4826b6f4ce45bddfb5c54CAS |
[23] Stoesser, N. et al. (2016) Complete sequencing of plasmids containing bla OXA-163 and bla OXA-48 in Escherichia coli sequence type 131. Antimicrob. Agents Chemother. 60, 6948–6951.
| Complete sequencing of plasmids containing bla OXA-163 and bla OXA-48 in Escherichia coli sequence type 131.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC2sXitlSqsrc%3D&md5=98cd199d3f2865525631d9eec60148e8CAS |
[24] Rasko, D.A. et al. (2011) Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany. N. Engl. J. Med. 365, 709–717.
| Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3MXhtV2lu7jJ&md5=1e7c2af1a19520b4354e32a1f4a7f685CAS |
[25] Sullivan, M. et al. (2016) Continuous surveillance by whole-genome sequencing to identify and manage methicillin-resistant Staphylococcus aureus outbreaks. Open Forum Infectious Diseases 3, 942.
[26] Abraham, S. et al. (2016) Isolation and plasmid characterization of carbapenemase (IMP-4) producing Salmonella enterica Typhimurium from cats. Sci. Rep. 6, 35527.
| Isolation and plasmid characterization of carbapenemase (IMP-4) producing Salmonella enterica Typhimurium from cats.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC28XhslGrtr%2FF&md5=ed77178a0603a34c1de3c37a6c3449caCAS |
[27] Sheppard, A.E. et al. (2016) Nested Russian Doll-like genetic mobility drives rapid dissemination of the carbapenem resistance gene blaKPC. Antimicrob. Agents Chemother. 60, 3767–3778.
| Nested Russian Doll-like genetic mobility drives rapid dissemination of the carbapenem resistance gene blaKPC.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC28XhslKrsLvF&md5=3d8145847e5d5ddbdc736928eb662439CAS |
[28] Goodwin, S. et al. (2016) Coming of age: ten years of next-generation sequencing technologies. Nat. Rev. Genet. 17, 333–351.
| Coming of age: ten years of next-generation sequencing technologies.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC28XnvFOksL8%3D&md5=bad76d9c276dbc8f2ea01cc4042626f4CAS |
[29] Faria, N.R. et al. (2017) Establishment and cryptic transmission of Zika virus in Brazil and the Americas. Nature 546, 406–410.
| Establishment and cryptic transmission of Zika virus in Brazil and the Americas.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC2sXosVagt7s%3D&md5=4b8f107f4fee23f95bebbb72d5d3bc50CAS |
[30] Quick, J. et al. (2015) Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella. Genome Biol. 16, 114.
| Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella.Crossref | GoogleScholarGoogle Scholar |
[31] Greninger, A.L. et al. (2015) Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis. Genome Med. 7, 99.
| Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis.Crossref | GoogleScholarGoogle Scholar |
[32] Lu, H. et al. (2016) Oxford Nanopore MinION Sequencing and Genome Assembly. Genomics Proteomics Bioinformatics 14, 265–279.
| Oxford Nanopore MinION Sequencing and Genome Assembly.Crossref | GoogleScholarGoogle Scholar |
[33] Mardis, E.R. (2011) A decade’s perspective on DNA sequencing technology. Nature 470, 198–203.
| A decade’s perspective on DNA sequencing technology.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3MXhslWktbk%3D&md5=9361ed7363868580e4c5721e03a1863dCAS |
[34] Muir, P. et al. (2016) The real cost of sequencing: scaling computation to keep pace with data generation. Genome Biol. 17, 53.
| The real cost of sequencing: scaling computation to keep pace with data generation.Crossref | GoogleScholarGoogle Scholar |
[35] Wetterstrand, K.A. DNA Sequencing Costs: Data from the NHGRI Genome Sequencing Program (GSP) 2016. http://www.genome.gov/sequencingcostsdata/ (accessed 15 June 2017).
