Getting the Complete Picture
Protecting global health is best accomplished through comprehensive surveillance, complete genomic information, and accurate tracking. Tremendous progress has been made since technology first enabled the routine sequencing of pathogenic microbes.
The advent of Single Molecule, Real-Time (SMRT) Sequencing has radically increased the understanding of microbial genomics, pathogenicity, and antimicrobial resistance. The PacBio Systems deliver the most comprehensive genetic information available, and with SMRT Sequencing, federal agencies, healthcare centers, and other public health organizations have the ability to:
- Generate complete genome assemblies and gain a deeper understanding of community-acquired and hospital associated infections and transmission.
- Use microbial epigenetics to further characterize global outbreaks, pandemics, and epidemics.
- Inform local and global preparedness and response to seasonal and annual infections by rapidly resolving viral populations.
- Characterize complex populations to support surveillance and tracking of foodborne pathogens.
Spotlight: Long-reads shed light on the genetics of antibiotic resistance
Scientists interrogated the mobilome of drug resistant bacteria to understand their capacity for adaptation. This research showed that replicative transposons and homologous recombination are driving forces in rearrangements and evolution of resistance plasmids. Explore this research further:
He, S. et al., 2016. Mechanisms of evolution in high-consequence drug resistance plasmids. mBio, 7(6), pp.e01987–16.
Spotlight: Exploring antifungal resistance in sequential human isolates
Long-read sequencing enabled scientists to uncover 100 adhesin-like genes in Candida glabrate isolated from an HIV-positive patient. A broader understanding of adhesin biology will aid in combating the increased virulence of this fungal pathogen. Explore this research further.
Vale-Silva, L.A. et al., 2017. Comparative genomics of two sequential Candida glabrata clinical isolates. bioRxiv, Preprint.
Selected Resources
- Liang, Quanhui et al. (2018) Sequencing and Genomic Diversity Analysis of IncHI5 Plasmids. Frontiers in microbiology
- Beaulaurier, John et al. (2018) Deciphering bacterial epigenomes using modern sequencing technologies Nature reviews. Genetics
- Fallon, Timothy R et al. (2018) Firefly genomes illuminate parallel origins of bioluminescence in beetles. eLife
- Yan, Bo et al. (2018) SMRT-Cappable-seq reveals complex operon variants in bacteria. Nature communications
- Callahan, Benjamin J et al. (2018) High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution BioRxiv
- Kumari, Romika et al. (2018) PausePred and Rfeet: webtools for inferring ribosome pauses and visualizing footprint density from ribosome profiling data. RNA
- Tai, Phillip WL et al. (2018) Adeno-associated virus genome population sequencing achieves full vector genome resolution and reveals human-vector chimeras Molecular therapy
- Xin, Tianyi et al. (2018) Biomonitoring for traditional herbal medicinal products using DNA metabarcoding and single molecule, real-time sequencing. Acta pharmaceutica Sinica. B
- Vincent, Antony T et al. (2018) Unexpected diversity in the mobilome of a Pseudomonas aeruginosa strain isolated from a dental unit waterline revealed by SMRT Sequencing. Genome
- Haig, Sarah-Jane et al. (2018) A high-throughput approach for identification of nontuberculous mycobacteria in drinking water reveals relationship between water age and Mycobacterium avium. mBio
- Weingarten, Rebecca A et al. (2018) Genomic analysis of hospital plumbing reveals diverse reservoir of bacterial plasmids conferring carbapenem resistance. mBio
- Phelan, Jody et al. (2018) Methylation in Mycobacterium tuberculosis is lineage specific with associated mutations present globally. Scientific reports
- Acuña-Amador, Luis et al. (2018) Genomic repeats, misassembly and reannotation: a case study with long-read resequencing of Porphyromonas gingivalis reference strains. BMC genomics
- Li, M et al. (2017) High frequency of mitochondrial DNA mutations in HIV-infected treatment-experienced individuals. HIV medicine
- Beaulaurier, John et al. (2018) Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation. Nature biotechnology
- Pfeiffer, Friedhelm et al. (2018) The complete and fully assembled genome sequence of Aeromonas salmonicida subsp. pectinolytica and its comparative analysis with other Aeromonas species: investigation of the mobilome in environmental and pathogenic strains. BMC genomics
- Revez, Joana et al. (2017) Survey on the use of whole-genome sequencing for infectious diseases surveillance: Rapid expansion of European national capacities, 2015-2016. Frontiers in public health
- Perraudeau, Fanny et al. (2017) Accurate determination of bacterial abundances in human metagenomes using full-length 16S sequencing reads BioRxiv
- Hazen, Tracy H et al. (2017) Characterization of a large antibiotic resistance plasmid found in enteropathogenic Escherichia coli strain B171 and its relatedness to plasmids of diverse E. coli and Shigella. Antimicrobial agents and chemotherapy
- Forde, Brian M. et al. (2017) SMRT Sequencing reveals differential patterns of methylation in two O111:H- Shiga toxigenic Escherichia coli isolates from a historic hemolytic uremic syndrome outbreak in Australia BioRxiv
- Vale-Silva, Luis et al. (2017) Comparative genomics of two sequential Candida glabrata clinical isolates. G3
- Zhao, J et al. (2017) Reduction in fecal microbiota diversity and short-chain fatty acid producers in Methicillin-resistant Staphylococcus aureus infected individuals as revealed by PacBio single molecule, real-time sequencing technology. European journal of clinical microbiology & infectious diseases
- Stoesser, N et al. (2017) Genomic epidemiology of global Klebsiella pneumoniae carbapenemase (KPC)-producing Escherichia coli. Scientific reports
- Zautner, Andreas E et al. (2017) Monitoring microevolution of OXA-48-producing Klebsiella pneumoniae ST147 in a hospital setting by SMRT Sequencing Journal of antimicrobial chemotherapy
- Nakano, Kazuma et al. (2017) Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area. Human Cell
- Pasini, Erica M et al. (2017) An improved Plasmodium cynomolgi genome assembly reveals an unexpected methyltransferase gene expansion. Wellcome open research
- Tate, Heather et al. (2017) Comparative analysis of extended-spectrum-ß-lactamase CTX-M-65-producing Salmonella enterica serovar Infantis isolates from humans, food animals, and retail chickens in the United States. Antimicrobial agents and chemotherapy
- van Boheemen, Sander et al. (2017) Quasispecies composition and evolution of a typical Zika virus clinical isolate from Suriname. Scientific reports
- Elghraoui, Afif et al. (2017) SMRT genome assembly corrects reference errors, resolving the genetic basis of virulence in Mycobacterium tuberculosis. BMC genomics
- Diaz, Maureen H et al. (2017) Comprehensive bioinformatics analysis of Mycoplasma pneumoniae genomes to investigate underlying population structure and type-specific determinants. PloS one
- Karl, Julie A et al. (2017) Major histocompatibility complex haplotyping and long-amplicon allele discovery in cynomolgus macaques from Chinese breeding facilities. Immunogenetics
- Weigand, Michael R et al. (2017) The history of Bordetella pertussis genome evolution includes structural rearrangement. Journal of bacteriology
- Bashir, Ali et al. (2017) Genomic confirmation of vancomycin-resistant Enterococcus transmission from deceased donor to liver transplant recipient. PloS one
- Mathers, Amy J et al. (2017) Chromosomal integration of the Klebsiella pneumoniae carbapenemase gene, blaKPC, in Klebsiella species is elusive but not rare. Antimicrobial agents and chemotherapy
- Ho, Cynthia K Y et al. (2017) Characterization of hepatitis C virus (HCV) envelope diversification from acute to chronic infection within a sexually transmitted HCV cluster by using single-molecule, real-time sequencing. Journal of virology
- Poster: Boitano, M. et al. (2018) Full-length cDNA sequencing of prokaryotic transcriptome and metatranscriptome samples
- Poster: Heiner, Cheryl et al. (2018) Multiplexed complete microbial genomes on the Sequel System
- Poster: Lambert, C. et al. (2017) Multiplexing strategies for microbial whole genome sequencing using the Sequel System
- Poster: Seetin, M. et al. (2016) Complete telomere-to-telomere de novo assembly of the Plasmodium falciparum genome using long-read sequencing
- Poster: Laird Smith, M. et al. (2016) An improved circular consensus algorithm with an application to detect HIV-1 Drug Resistance Associated Mutations (DRAMs)
- Poster: Oh, S. et al. (2016) Minimization of chimera formation and substitution errors in full-length 16S PCR amplification
- Poster: Heiner, C. et al. (2016) WGS SMRT Sequencing of patient samples from a fecal microbiota transplant trial
- Poster: Hall, R. et al. (2016) Workflow for processing high-throughput, Single Molecule, Real-Time Sequencing data for analyzing the microbiome of patients undergoing fecal microbiota transplantation
- Poster: Hepler, N. Lance et al. (2016) An improved circular consensus algorithm with an application to detection of HIV-1 Drug-Resistance Associated Mutations (DRAMs)
- Poster: Baybayan, Primo et al. (2016) Application specific barcoding strategies for SMRT Sequencing
- Poster: Seetin, Matthew et al. (2016) Long-read assembly of the Aedes aegypti Aag2 cell line genome resolves ancient endogenous viral elements
- Poster: Heiner, Cheryl et al. (2016) Low-input long-read sequencing for complete microbial genomes and metagenomic community analysis
- Poster: Hall, Richard et al. (2016) Profiling the microbiome in fecal microbiota transplantation using circular consensus and Single Molecule, Real-Time Sequencing
- (2017) Tutorial: Minor variant analysis [SMRT Link v5.0.0]
- Auvignen, Petra (2017) AGBT Virtual Poster: Interspecies interation amoung meat spoilage-related lactic acid bacteria
- Matthews, Ben (2017) PAG PacBio Workshop: Genome assembly and molecular genetics of the dengue, yellow fever, and zika vector Aedes aegypti
- Paxinos, Ellen (2016) AGBT Virtual Poster: An improved circular consensus algorithm with an application to detect HIV-1 Drug Resistance Associated Mutations (DRAMs)
- Seetin, Matthew (2016) AGBT Virtual Poster: Long-read assembly of the Aedes aegypti Aag2 cell line genome resolves ancient endogenous viral elements
- Heiner, Cheryl (2016) AGBT Virtual Poster: Low-input long-read sequencing for complete microbial genomes and metagenomic community analysis
- Heiner, Cheryl (2016) AGBT Virtual Poster: Minimization of chimera formation and substitution errors in full-length 16S PCR amplification
- Hall, Richard (2016) AGBT Virtual Poster: Profiling the microbiome in fecal microbiota transplantation using circular consensus and Single Molecule, Real-Time Sequencing
- PacBio Certified Service Providers (2018)
- Application Brochure: Microbial communities – Complex microbial populations simplified (2018)
- SMRT Sequencing Brochure: Revolutionize genomics with SMRT Sequencing (2018)
- Application Brief: Microbial whole genome sequencing – Best Practices (2018)
- Epigenetics Application Brochure: Characterize the epigenetic landscape of your genome (2016)