When partial information is not enough
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:
- Gain a deeper understanding of community-acquired illness
- Accurately characterize global outbreaks, pandemics, and epidemics
- Inform local and global preparedness and response to seasonal and annual infections
- Recognize nosocomial illnesses, transmission, and sources
- Perform surveillance and tracking of foodborne pathogens
Applications of SMRT Sequencing to public health
Featured research: characterization of an opportunistic fungal pathogen using next generation multilocus sequence typing (NGMLST)
Cryptococcus neoformans is a well-characterized, opportunistic human fungal pathogen, and is responsible for > 500,000 annual deaths worldwide. Isolates were genotyped using a cost-effective, well-characterized new MLST method that uses SMRT Sequencing, a multiplexing protocol, and appropriate analytical software that provides accurate, rapid, and economical genotyping of 96 or more isolates in single assay. A phylogeny of the SOD1 locus among isolates with different molecular types and both alleles of six hybrids are visualized by the neighbor-joining dendrogram1.
Explore this research further.
Reference
Selected Resources
- Chavda, Kalyan D et al. (2016) Comprehensive genome analysis of carbapenemase- producing Enterobacter spp.: new insights into phylogeny, population structure and resistance mechanisms. mBio
- He, Susu et al. (2016) Mechanisms of evolution in high-consequence drug resistance plasmids. mBio
- Zheng, Yi et al. (2016) Using PacBio long-read high-throughput microbial gene amplicon sequencing to evaluate infant formula safety. Journal of Agricultural and Food Chemistry
- Betz-Stablein, B D et al. (2016) Single-molecule sequencing reveals complex genomic variation of hepatitis B virus during 15 years of chronic infection following liver transplantation. Journal of Virology
- Laird Smith, Melissa et al. (2016) Rapid sequencing of complete env genes from primary HIV-1 samples Virus Evolution
- Li, M et al. (2017) High frequency of mitochondrial DNA mutations in HIV-infected treatment-experienced individuals. HIV Medicine
- Weigele, Peter et al. (2016) Biosynthesis and function of modified bases in bacteria and their viruses. Chemical Reviews
- Sheppard, Anna E et al. (2016) Nested Russian doll-like genetic mobility drives rapid dissemination of the Carbapenem resistance gene blaKPC Antimicrobial Agents and Chemotherapy
- Rutledge, Gavin G et al. (2016) Elusive Plasmodium species complete the human malaria genome set bioRxiv
- Bowden, Katherine E. et al. (2016) Genome structural diversity among 31 Bordetella pertussis isolates from two recent U.S. whooping cough statewide epidemics mSphere
- Rojas, Laura J et al. (2016) Initial assessment of the molecular epidemiology of blaNDM-1 in Colombia. Antimicrobial Agents and Chemotherapy
- Hughes, Heather Y et al. (2016) Detection and whole genome sequencing of carbapenemase-producing Aeromonas hydrophila isolated from routine perirectal surveillance culture. Journal of Clinical Microbiology
- Cohen, Nadia R et al. (2016) A role for the bacterial GATC methylome in antibiotic stress survival. Nature Genetics
- Bull, Rowena A et al. (2016) A method for near full-length amplification and sequencing for six hepatitis C virus genotypes. BMC Genomics
- Tsai, Yu-Chih et al. (2016) Resolving the complexity of human skin metagenomes using single-molecule sequencing. mBio
- Poon, Leo L M et al. (2016) Quantifying influenza virus diversity and transmission in humans. Nature Genetics
- Broecker, Felix et al. (2016) Long-term changes of bacterial and viral compositions in the intestine of a recovered Clostridium difficile patient after fecal microbiota transplantation Molecular Case Studies
- Huang, Da Wei et al. (2016) Towards better precision medicine: PacBio single-molecule long reads resolve the interpretation of HIV drug resistant mutation profiles at explicit quasispecies (haplotype) level. Journal of Data Mining in Genomics & Proteomics
- Poster: Boitano, M. et al. (2017) Full-length cDNA sequencing of prokaryotic transcriptome and metatranscriptome samples
- 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
- 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
- Application Brief: Microbial Whole Genome Sequencing – Best Practices (2017)
- Application Brochure Microbial Communities: Complex microbial populations simplified (2017)
- PacBio Certified Service Providers (2017)
- SMRT Sequencing Brochure: Revolutionize genomics with SMRT Sequencing (2017)
- Case Study: Scientists advance understanding of microbial genomes, epigenomes and communities with SMRT Sequencing (2016)
- Epigenetics Application Brochure: Characterize the epigenetic landscape of your genome (2016)