Public Health Genomics Knowledge Base (v1.0)
Advanced Molecular Detection Clips
Spotlight
The utility of multiple molecular methods including whole genome sequencing as tools to differentiate Escherichia coli O157:H7 outbreaks. A standardised method for determining Escherichia coli O157:H7 strain relatedness using whole genome sequencing or virulence gene profiling is not yet established. We sought to assess the capacity of either high-throughput polymerase chain reaction (PCR) of 49 virulence genes, core-genome single nt variants (SNVs) or k-mer clustering to discriminate between outbreak-associated and sporadic E. coli O157:H7 isolates. Three outbreaks and multiple sporadic isolates from the province of Alberta, Canada were included in the study. Two of the outbreaks occurred concurrently in 2014 and one occurred in 2012. Pulsed-field gel electrophoresis (PFGE) and multilocus variable-number tandem repeat analysis (MLVA) were employed as comparator typing methods. The virulence gene profiles of isolates from the 2012 and 2014 Alberta outbreak events and contemporary sporadic isolates were mostly identical; therefore the set of virulence genes chosen in this study were not discriminatory enough to distinguish between outbreak clusters. Concordant with PFGE and MLVA results, core genome SNV and k-mer phylogenies clustered isolates from the 2012 and 2014 outbreaks as distinct events. k-mer phylogenies demonstrated increased discriminatory power compared with core SNV phylogenies. Prior to the widespread implementation of whole genome sequencing for routine public health use, issues surrounding cost, technical expertise, software standardisation, and data sharing/comparisons must be addressed.
Advanced Molecular Detection Clips Content
News
Events / Training / Web Resources
Concepts / Comments
Methods / Tools
Evolution / Ecology / Populations
Pathogenicity / Antimicrobial Resistance
Detection / Diagnosis
Epidemiology / Outbreaks / Transmission
Antimicrobials / Vaccines / Interventions
Host-Microbe Interactions
NEWS
Microbiome Startup uBiome Will Sequence Poop for the CDC
Zhang S. Wired, Nov 30, 2015.
SCIENCE AND SOCIETY. Gene drive turns mosquitoes into malaria fighters.
Pennisi Elizabeth et al. Science (New York, N.Y.) 2015 Nov (6264) 1014
NIH Earmarks $2M for Pediatric TB Biomarker Research
GenomeWeb, Dec 2, 2015.
Amid PAMA Implementation, Stakeholders Contemplate Coding to Facilitate Market-Based MDx Pricing
Ray T. GenomeWeb, Dec 2, 2015.
Bay Area Synthetic Biologist Looks to Establish CRISPR as DIY Science
Han AP. GenomeWeb, Nov 20, 2015.
EVENTS / TRAINING / WEB RESOURCES
Short Course 22: NGS for Infectious Disease Diagnostics
(conference) Charles Chiu. Molecular Med Tri-Con, San Francisco, March 7, 2016,
Translating the microbiome: health and disease
(call for papers) Genome Medicine, deadline Jan 16, 2015.
CONCEPTS / COMMENTS
Nosocomial transmission of avian influenza virus A (H7N9).
van der Sande Marianne A B et al. BMJ (Clinical research ed.) h5980
Accelerating tuberculosis elimination in low-incidence settings: the role of genomics.
Guthrie Jennifer L et al. The European respiratory journal 2015 Dec (6) 1840-1
Collaborating to deliver pathogen genomics - share the risks and reap the rewards
Raza S. PHGF, Nov 11, 2015.
Understanding the incremental value of novel diagnostic tests for tuberculosis
Arinaminpathy N, Dowdy D. Nature, Dec 2, 2015.
Genome editing: 4 big questions
Tauxe W. Nature, Dec 2, 2015.
Infectious disease control and elimination: Modelling the impact of improved diagnostics
Nature (Supplement), Dec 3, 2015.
Assessing the impact of next-generation rapid diagnostic tests on Plasmodium falciparum malaria elimination strategies
Slater HC, et al. Nature 2015; 528: S94?S101.
METHODS / TOOLS
Reads2Type: a web application for rapid microbial taxonomy identification.
Saputra Dhany et al. BMC bioinformatics 2015 (1) 398
Web Resources for Metagenomics Studies.
Dudhagara Pravin et al. Genomics, proteomics & bioinformatics 2015 Nov
An ultra-dense library resource for rapid deconvolution of mutations that cause phenotypes in Escherichia coli.
Nehring Ralf B et al. Nucleic acids research 2015 Nov
Computing Workflows for Biologists: A Roadmap.
Shade Ashley et al. PLoS biology 2015 Nov (11) e1002303
A Systematic Bayesian Integration of Epidemiological and Genetic Data.
Lau Max S Y et al. PLoS computational biology 2015 Nov (11) e1004633
Database resources of the National Center for Biotechnology Information.
et al. Nucleic acids research 2015 Nov
EVOLUTION / ECOLOGY / POPULATIONS
Whole genome investigation of a divergent clade of the pathogen Streptococcus suis.
Baig Abiyad et al. Frontiers in microbiology 1191
Genetic analysis of human clinical isolates of Lactococcus garvieae: relatedness with isolates from foods.
Reguera-Brito Mercedes et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2015 Nov
Coexistence of Bartonella henselae and B. clarridgeiae in populations of cats and their fleas in Guatemala.
Bai Ying et al. Journal of vector ecology : journal of the Society for Vector Ecology 2015 Dec (2) 327-32 (CDC Author)
Genomic Epidemiology of Hypervirulent Serogroup W, ST-11 Neisseria meningitidis.
Mustapha Mustapha M et al. EBioMedicine 2015 Oct (10) 1447-55 (CDC Author)
Molecular, serological and in vitro culture-based characterization of Bourbon virus, a newly described human pathogen of the genus Thogotovirus.
Lambert Amy J et al. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2015 Oct 127-132 (CDC Author)
Natural co-infection of influenza A/H3N2 and A/H1N1pdm09 viruses resulting in a reassortant A/H3N2 virus.
Rith Sareth et al. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2015 Nov 108-111 (CDC Author)
An Insight into Recombination with Enterovirus Species C and Nucleotide G-480 Reversion from the Viewpoint of Neurovirulence of Vaccine-Derived Polioviruses.
Zhang Yong et al. Scientific reports 2015 17291 (CDC Author)
Genetic and molecular characterization of H9N2 and H5 avian influenza viruses from live poultry markets in Zhejiang Province, eastern China.
Wu Haibo et al. Scientific reports 2015 17508
Analysis of Enterovirus 68 Strains from the 2014 North American Outbreak Reveals a New Clade, Indicating Viral Evolution.
Du Juan et al. PloS one (12) e0144208
The Molecular Epidemiology and Evolution of Murray Valley Encephalitis Virus: Recent Emergence of Distinct Sub-lineages of the Dominant Genotype 1.
Williams David T et al. PLoS neglected tropical diseases 2015 Nov (11) e0004240
Molecular and epidemiological studies of Porcine rubulavirus infection - an overview.
Cuevas-Romero Julieta Sandra et al. Infection ecology & epidemiology 29602
Non-Human Primates Harbor Diverse Mammalian and Avian Astroviruses Including Those Associated with Human Infections.
Karlsson Erik A et al. PLoS pathogens 2015 Nov (11) e1005225
Cryptococcus gattii in the Age of Whole-Genome Sequencing.
Meyer Wieland et al. mBio 2015 (6)
Draft Genome Sequences from Cyclospora cayetanensis Oocysts Purified from a Human Stool Sample.
Qvarnstrom Yvonne et al. Genome announcements (6) (CDC Author)
Genetic deviation in geographically close populations of the dengue vector Aedes aegypti (Diptera: Culicidae): influence of environmental barriers in South India.
Vadivalagan Chithravel et al. Parasitology research 2015 Dec
Genome of Rhodnius prolixus, an insect vector of Chagas disease, reveals unique adaptations to hematophagy and parasite infection.
Mesquita Rafael D et al. Proceedings of the National Academy of Sciences of the United States of America 2015 Dec (48) 14936-14941 (CDC Author)
Presence of the knockdown resistance mutation, Vgsc-1014F in Anopheles gambiae and An. arabiensis in western Kenya.
Ochomo Eric et al. Parasites & vectors 2015 (1) 616 (CDC Author)
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
Epidemiologic and Genotypic Review of Carbapenemase-Producing Organisms in British Columbia between 2008 and 2014.
Sekirov Inna et al. Journal of clinical microbiology 2015 Nov
Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study.
Liu Yi-Yun et al. The Lancet. Infectious diseases 2015 Nov
First identification of an IMI-1 carbapenemase-producing colistin-resistant Enterobacter cloacae in China.
Huang Liang et al. Annals of clinical microbiology and antimicrobials 2015 (1) 51
Quantifying the Determinants of Evolutionary Dynamics Leading to Drug Resistance.
Chevereau Guillaume et al. PLoS biology 2015 Nov (11) e1002299
Study on Prevalence, Antibiotic Susceptibility, and tuf Gene Sequence-Based Genotyping of Species-Level of Coagulase-Negative Staphylococcus Isolated From Keratitis Caused by Using Soft Contact Lenses.
Faghri Jamshid et al. Eye & contact lens 2015 Dec
Molecular Characterization, Antimicrobial Resistance and Caco-2 Cell Invasion Potential of Campylobacter Jejuni/Coli from Young Children with Diarrhea.
Pan Haijian et al. The Pediatric infectious disease journal 2015 Nov
Comparative Genomics of Field Isolates of Mycobacterium bovis and M. caprae Provides Evidence for Possible Correlates with Bacterial Viability and Virulence.
de la Fuente José et al. PLoS neglected tropical diseases 2015 Nov (11) e0004232
Within patient microevolution of Mycobacterium tuberculosis correlates with heterogeneous responses to treatment.
Liu Qingyun et al. Scientific reports 2015 17507
Correlation of phylogenetic clade diversification and in vitro infectivity differences among Cosmopolitan genotype strains of Chikungunya virus.
Abraham Rachy et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2015 Nov 174-184
Identification of minority resistance mutations in the HIV-1 integrase coding region using next generation sequencing.
Fonager Jannik et al. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2015 Nov 95-100
Acute chagas outbreaks: molecular and biological features of Trypanosoma cruzi isolates, and clinical aspects of acute cases in Santander, Colombia.
Díaz Martha Lucía et al. Parasites & vectors 2015 608
DETECTION / DIAGNOSIS
Development and evaluation of double locus sequence typing for molecular epidemiological investigations of Clostridium difficile.
Stojanov M et al. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 2015 Nov
Synthetic biology devices for in vitro and in vivo diagnostics.
Slomovic Shimyn et al. Proceedings of the National Academy of Sciences of the United States of America 2015 Nov (47) 14429-35
Effectiveness of Practices To Increase Timeliness of Providing Targeted Therapy for Inpatients with Bloodstream Infections: a Laboratory Medicine Best Practices Systematic Review and Meta-analysis.
Buehler Stephanie S et al. Clinical microbiology reviews 2016 Jan (1) 59-103 (CDC Author)
An integrated microfluidic system for diagnosis of the resistance of Helicobacter pylori to quinolone-based antibiotics.
Chao Chih-Yu et al. Biosensors & bioelectronics 2015 Nov 281-289
Identification of low abundance microbiome in clinical samples using whole genome sequencing.
Zhang Chao et al. Genome biology 2015 (1) 265
Presence of Mycobacterium leprae DNA and PGL-1 antigen in household contacts of leprosy patients from a hyperendemic area in Brazil.
Pinho J D et al. Genetics and molecular research : GMR 2015 (4) 14479-87
Molecular identification of Histoplasma capsulatum using rolling circle amplification.
Furuie Jason L et al. Mycoses 2015 Nov
Rapid detection of rifampicin resistance in Mycobacterium tuberculosis by high-resolution melting curve analysis.
Malhotra B et al. The international journal of tuberculosis and lung disease : the official journal of the International Union against Tuberculosis and Lung Disease 2015 Dec (12) 1536-41
Multilocus Enzyme Electrophoresis Analysis of Rapidly-Growing Mycobacteria: an Alternative Tool for Identification and Typing.
Caierão Juliana et al. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2015 Nov
Rapid genome sequencing and characterization of novel avian-origin influenza A H7N9 virus directly from clinical sample by semiconductor sequencing.
Hu Yongfeng et al. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2015 Oct 84-88
Accurate genetic detection of hepatitis C virus transmissions in outbreak settings.
Campo D S et al. The Journal of infectious diseases 2015 Nov (CDC Author)
Molecular Diagnosis of Pathogenic Sporothrix Species.
Rodrigues Anderson Messias et al. PLoS neglected tropical diseases 2015 Dec (12) e0004190
Loop-Mediated Isothermal Amplification for Laboratory Confirmation of Buruli Ulcer Disease-Towards a Point-of-Care Test.
Beissner Marcus et al. PLoS neglected tropical diseases 2015 Nov (11) e0004219
A Genomic Approach to Resolving Relapse versus Reinfection among Four Cases of Buruli Ulcer.
Eddyani Miriam et al. PLoS neglected tropical diseases 2015 Nov (11) e0004158
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
The utility of multiple molecular methods including whole genome sequencing as tools to differentiate Escherichia coli O157:H7 outbreaks.
Berenger Byron M et al. Euro surveillance : bulletin Europe´en sur les maladies transmissibles = European communicable disease bulletin 2015 Nov (47)
Characterization of a CTX-M-15 Producing Klebsiella Pneumoniae Outbreak Strain Assigned to a Novel Sequence Type (1427).
Zhou Kai et al. Frontiers in microbiology 1250
Whole genome sequencing provides possible explanations for the difference in phage susceptibility among two Salmonella Typhimurium phage types (DT8 and DT30) associated with a single foodborne outbreak.
Mohammed Manal et al. BMC research notes 2015 728
Investigation of a staphylococcal food poisoning outbreak combining case-control, traditional typing and whole genome sequencing methods, Luxembourg, June 2014.
Mossong Joël et al. Euro surveillance : bulletin Europe´en sur les maladies transmissibles = European communicable disease bulletin 2015 Nov (45)
Prospective whole genome sequencing enhances national surveillance of Listeria monocytogenes.
Kwong Jason C et al. Journal of clinical microbiology 2015 Nov
An outbreak of high-level azithromycin resistant Neisseria gonorrhoeae in England.
Chisholm Stephanie A et al. Sexually transmitted infections 2015 Nov
Evolutionary Relationships of Outbreak-associated Listeria monocytogenes Strains of Serotypes 1/2a and 1/2b Determined by Whole Genome Sequencing.
Bergholz Teresa M et al. Applied and environmental microbiology 2015 Nov (CDC Author)
Porcine Epidemic Diarrhea Virus among Farmed Pigs, Ukraine.
Dastjerdi Akbar et al. Emerging infectious diseases 2015 Dec (12) 2235-7
Outbreak of KPC-3 Producing Carbapenem-Resistant Klebsiella pneumoniae in a US Pediatric Hospital.
Stillwell Terri et al. Journal of the Pediatric Infectious Diseases Society 2015 Dec (4) 330-8
Usefulness of hqSNV analysis for subtyping the highly clonal and the most prevalent Salmonella Heidelberg clone in the context of outbreak investigations.
Bekal S et al. Journal of clinical microbiology 2015 Nov
Enhanced tracking of the nosocomial transmission of endemic ST22-MRSA-IV among patients and environmental sites using whole-genome sequencing.
Kinnevey Peter M et al. Journal of clinical microbiology 2015 Nov
Characterization of H5N1 influenza A virus that caused the first highly pathogenic avian influenza outbreak in Saudi Arabia.
Al-Qahtani Ahmed Ali et al. Journal of infection in developing countries 2015 (11) 1210-9
The distinct distribution and phylogenetic characteristics of dengue virus serotypes/genotypes during the 2013 outbreak in Yunnan, China: Phylogenetic characteristics of 2013 dengue outbreak in Yunnan, China.
Wang Binghui et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2015 Oct 1-7
Multiple Sources of Infection and Potential Endemic Characteristics of the Large Outbreak of Dengue in Guangdong in 2014.
Shen Shu-Qun et al. Scientific reports 2015 16913
First report of an astrovirus type 5 gastroenteritis outbreak in a residential elderly care home identified by sequencing.
Jarchow-Macdonald Anna A et al. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2015 Nov 115-119
A report on the outbreak of Zika virus on Easter Island, South Pacific, 2014.
Tognarelli J et al. Archives of virology 2015 Nov
ANTIMICROBIALS / VACCINES / INTERVENTIONS
Engineering Enhanced Vaccine Cell Lines to Eradicate Vaccine-Preventable Diseases: The Polio Endgame.
van der Sanden Sabine M G et al. Journal of virology 2015 Nov (CDC Author)
Composition and Interactions of Hepatitis B Virus Quasispecies Defined the Virological Response During Telbivudine Therapy.
Zhou Bin et al. Scientific reports 2015 17123
Highly efficient Cas9-mediated gene drive for population modification of the malaria vector mosquito Anopheles stephensi.
Gantz Valentino M et al. Proceedings of the National Academy of Sciences of the United States of America 2015 Nov
Assessment of Inhibitors of Pathogenic Crimean-Congo Hemorrhagic Fever Virus Strains Using Virus-Like Particles.
Zivcec Marko et al. PLoS neglected tropical diseases 2015 Dec (12) e0004259 (CDC Author)
HOST-MICROBE INTERACTIONS
Human genetic basis of interindividual variability in the course of infection. <a class="external" href="http://www.cdc.gov/spanish/CDC/