Advanced Molecular Detection Clips || Public Health Genomics Knowledge Base (v1.2)

Public Health Genomics Knowledge Base (v1.2)

Advanced Molecular Detection Clips (AMD Clips) are selected weekly from a variety of sources, including PubMed, journal tables of contents, and online media. Special emphasis is given to the use of next-generation genetic sequencing in infectious disease public health surveillance, investigation, and development of new diagnostics and interventions. The collection is not comprehensive but aims to capture highlights, while surveying a wide range of topics. CDC-authored articles are flagged. Items marked I&E address aspects of implementation or evaluation in clinical or public health practice.

Current Edition (Published on Jan 5, 2017)

• News
• Events / Training / Web Resources
• Policy
• Concepts / Comments
• Methods / Tools
• Evolution / Ecology / Populations
• Pathogenicity / Antimicrobial Resistance
• Detection / Diagnosis
• Epidemiology / Outbreaks / Transmission
• Antimicrobials / Vaccines / Interventions
• Host-Microbe Interactions

NEWS

• A Gut Makeover for the New Year
   Rabin RC. New York Times, Dec 29, 2016.
• Genomic sequencing illuminates recent Shigella outbreaks in California 
  [UC Davis press release] EurekAlert, Dec 23, 2016.

EVENTS / TRAINING / WEB RESOURCES

• Lifemap: Exploring the Entire Tree of Life.
  de Vienne Damien M et al. PLoS biology 2016 Dec (12) e2001624

POLICY

• Zika Virus: 10 Public Health Achievements in 2016 and Future Priorities
  Oussayef NL, et al. MMWR, Dec 30, 2016. 

CONCEPTS / COMMENTS

• Applied epidemiology and public health: are we training the future generations appropriately?
  Brownson Ross C et al. Annals of epidemiology 2016 Dec 
• Integrating advanced molecular technologies into public health.
  Gwinn Marta et al. Journal of clinical microbiology 2016 Dec 
• Application of next generation sequencing in clinical microbiology and infection prevention.
  Deurenberg Ruud H et al. Journal of biotechnology 2016 Dec
• Introducing the Microbiome into Precision Medicine.
  Kuntz Thomas M et al. Trends in pharmacological sciences 2017 Jan (1) 81-91
• Implementation of Rapid Molecular Infectious Disease Diagnostics: The Role of Diagnostic and Antimicrobial Stewardship.
  Messacar Kevin et al. Journal of clinical microbiology 2016 Dec
• Clostridium difficile infection: Evolution, phylogeny and molecular epidemiology.
  Elliott Briony et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 Dec
• Human transmission of Ebola virus.
  Lawrence Philip et al. Current opinion in virology 2016 Dec 51-58
• Progress Towards Rapid Diagnosis of Measles Vaccine Strains - A Tool to Inform Public Health Interventions.
  Hacker Jill K et al. Journal of clinical microbiology 2016 Dec
• The mysterious Zika virus: Adding to the tropical flavivirus mayhem.
  Mishra B et al. Journal of postgraduate medicine (4) 249-254

METHODS / TOOLS

• Comparing genome versus proteome-based identification of clinical bacterial isolates.
  Galata Valentina et al. Briefings in bioinformatics 2016 Dec
• A Review of Analytical Techniques and Their Application in Disease Diagnosis in Breathomics and Salivaomics Research.
  Beale David J et al. International journal of molecular sciences 2016 Dec (1)
• Microfluidic-Based Bacteria Isolation from Whole Blood for Diagnostics of Blood Stream Infection.
  Zelenin Sergey et al. Methods in molecular biology (Clifton, N.J.) 2017 175-186
• Examining the potential use and long-term stability of guaiac faecal occult blood test cards for microbial DNA 16S rRNA sequencing.
  Taylor Morag et al. Journal of clinical pathology 2016 Dec
• BreathDx - molecular analysis of exhaled breath as a diagnostic test for ventilator-associated pneumonia: protocol for a European multicentre observational study.
  van Oort Pouline M P et al. BMC pulmonary medicine 2017 Jan (1) 1
• Error rates, PCR recombination, and sampling depth in HIV-1 Whole Genome Deep Sequencing.
  Zanini Fabio et al. Virus research 2016 Dec
• Measuring the diversity of the human microbiota with targeted next-generation sequencing.
  Finotello Francesca et al. Briefings in bioinformatics 2016 Dec
• A review on machine learning principles for multi-view biological data integration.
  Li Yifeng et al. Briefings in bioinformatics 2016 Dec
• AlmostSignificant: simplifying quality control of high-throughput sequencing data.
  Ward Joseph et al. Bioinformatics (Oxford, England) 2016 Dec (24) 3850-3851
• Using nearly full-genome HIV sequence data improves phylogeny reconstruction in a simulated epidemic.
  Yebra Gonzalo et al. Scientific reports 2016 Dec 39489
• Identifying Candidate Targets of Immune Responses in Zika Virus Based on Homology to Epitopes in Other Flavivirus Species.
  Xu Xiaojun et al. PLoS currents 2016 Nov
• From Genomes to Phenotypes: Traitar, the Microbial Trait Analyzer
  Weimann A, et al. mSystems, Nov/Dec 2016 1:e00101-16.
• Metavisitor, a Suite of Galaxy Tools for Simple and Rapid Detection and Discovery of Viruses in Deep Sequence Data.
  Carissimo Guillaume et al. PloS one 2017 (1) e0168397
• Construction of a Pan-Genome Allele Database of Salmonella enterica Serovar Enteritidis for Molecular Subtyping and Disease Cluster Identification.
  Liu Yen-Yi et al. Frontiers in microbiology 2016 2010
• Calypso: a user-friendly web-server for mining and visualizing microbiome-environment interactions.
  Zakrzewski Martha et al. Bioinformatics (Oxford, England) 2016 Dec

EVOLUTION / ECOLOGY / POPULATIONS

• Whole Genome Sequence and Comparative Genomics of the Novel Lyme Borreliosis Causing Pathogen, Borrelia mayonii.
  Kingry Luke C et al. PloS one 2016 (12) e0168994 
• Complete Genome Sequences of Four Bordetella pertussis Vaccine Reference Strains from Serum Institute of India.
  Weigand Michael R et al. Genome announcements 2016 Dec (6) 
• Comparative genome analysis and global phylogeny of the toxin variant Clostridium difficile PCR Ribotype 017 reveals the evolution of two independent sub-lineages.
  Cairns M D et al. Journal of clinical microbiology 2016 Dec
• Haemophilus ducreyi Cutaneous Ulcer Strains Diverged from Both Class I and Class II Genital Ulcer Strains: Implications for Epidemiological Studies.
  Gangaiah Dharanesh et al. PLoS neglected tropical diseases 2016 Dec (12) e0005259
• Evolution of a zoonotic pathogen: investigating prophage diversity in enterohaemorrhagic Escherichia coli O157 by long-read sequencing 
  Shaaban S, et al. Microb Genom, Dec 1, 2016.
• Identification of Escherichia coli and Shigella species from whole genome sequences.
  Chattaway Marie A et al. Journal of clinical microbiology 2016 Dec
• Spread of avian pathogenic Escherichia coli ST117 O78:H4 in Nordic broiler production.
  Ronco Troels et al. BMC genomics 2017 Jan (1) 13
• The First population structure and comparative genomics analysis of Mycobacterium africanum strains from Ghana reveals higher diversity of Lineage 5.
  Otchere Isaac D et al. International journal of mycobacteriology 2016 Dec S80-S81
• Comparative genome analyses of Mycobacterium avium reveal genomic features of its subspecies and strains that cause progression of pulmonary disease.
  Uchiya Kei-Ichi et al. Scientific reports 2017 Jan 39750
• Norovirus and Sapovirus Epidemiology and Strain Characteristics among Navajo and Apache Infants.
  Grant Lindsay R et al. PloS one 2017 (1) e0169491 
• Shifting clade distribution, reassortment, and emergence of new subtypes of highly pathogenic avian influenza A(H5) viruses collected in Vietnamese poultry from 2012 to 2015.
  Nguyen Diep T et al. Journal of virology 2016 Dec 
• The Global Phylogeography of Lyssaviruses - Challenging the 'Out of Africa' Hypothesis.
  Hayman David T S et al. PLoS neglected tropical diseases 2016 Dec (12) e0005266
• Evidence for Hepatitis A virus endemic circulation in Israel despite universal toddlers' vaccination since 1999 and low clinical incidence in all age groups.
  Manor Yosef et al. The Journal of infectious diseases 2016 Dec
• Molecular epidemiology and evolutionary analysis of dengue virus type 2, circulating in Delhi, India.
  Sharma Pankaj et al. Virusdisease 2016 Dec (4) 400-404
• Genomic variation in IbA10G2 and other patient derived Cryptosporidium hominis subtypes.
  Sikora Per et al. Journal of clinical microbiology 2016 Dec
• Genome-Wide Analyses of Individual Strongyloides stercoralis (Nematoda: Rhabditoidea) Provide Insights into Population Structure and Reproductive Life Cycles.
  Kikuchi Taisei et al. PLoS neglected tropical diseases 2016 Dec (12) e0005253

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Use of whole-genome sequencing data to analyze 23S rRNA-mediated azithromycin resistance.
  Johnson Steven R et al. International journal of antimicrobial agents 2016 Dec 
• Chromosomal Integration of the Klebsiella pneumoniae carbapenemase gene (blaKPC) in Klebsiella Species: Elusive but not Rare.
  Mathers Amy J et al. Antimicrobial agents and chemotherapy 2016 Dec
• Impact of genotypic and phenotypic resistance to second-line anti-tuberculosis drugs on treatment outcomes in multidrug-resistant tuberculosis in China.
  Hu Yi et al. International journal of mycobacteriology 2016 Dec S34-S35
• Increased expression of efflux pump genes in extensively drug-resistant isolates of Mycobacterium tuberculosis.
  Kanji Akbar et al. International journal of mycobacteriology 2016 Dec S150
• The molecular epidemiology and antimicrobial resistance phenotypes of Acinetobacter baumannii isolated from patients in three hospitals in southern Vietnam.
  Tuan Anh Nguyen et al. Journal of medical microbiology 2016 Dec
• Mechanisms of Evolution in High-Consequence Drug Resistance Plasmids.
  He Susu et al. mBio 2016 Dec (6)
• Sequential Acquisition of Virulence and Fluoroquinolone Resistance Has Shaped the Evolution of Escherichia coli ST131.
  Ben Zakour Nouri L et al. mBio 2016 Apr (2) e00347-16
• Single-Molecule Sequencing (PacBio) of the Staphylococcus capitis NRCS-A Clone Reveals the Basis of Multidrug Resistance and Adaptation to the Neonatal Intensive Care Unit Environment.
  Simões Patrícia Martins et al. Frontiers in microbiology 2016 1991
• Recent Outbreaks of Shigellosis in California Caused by Two Distinct Populations of Shigella sonnei with either Increased Virulence or Fluoroquinolone Resistance.
  Kozyreva Varvara K et al. mSphere (6)
• Detection of premature stop codons leading to truncated internalin A among food and clinical strains of Listeria monocytogenes.
  Ferreira da Silva Margarida et al. Food microbiology 2017 May 6-11
• Large scale genomic analysis shows no evidence for pathogen adaptation between the blood and cerebrospinal fluid niches during bacterial meningitis 
  Lees JA, et al. Microb Genom, Dec 19, 2016.

DETECTION / DIAGNOSIS

• Diagnostic testing methods for Clostridium difficile infection: A statewide survey of Ohio acute care hospitals.
  Wong Ken Koon et al. American journal of infection control 2016 Oct 
• Potential for Pharmacy-Public Health Collaborations Using Pharmacy-Based Point-of-Care Testing Services for Infectious Diseases.
  Gubbins Paul O et al. Journal of public health management and practice : JPHMP 2016 Dec 
• Detection and molecular characterisation of Livestock-Associated MRSA in raw meat on retail sale in North West England.
  Fox Andrew et al. Letters in applied microbiology 2016 Dec
• Next-generation sequencing-based user-friendly platforms for drug-resistant tuberculosis diagnosis: A promise for the near future.
  Dolinger David L et al. International journal of mycobacteriology 2016 Dec S27-S28
• The analysis of exosomal micro-RNAs in peripheral blood mononuclear cell-derived macrophages after infection with bacillus Calmette-Guérin by RNA sequencing.
  Mortaz Esmaeil et al. International journal of mycobacteriology 2016 Dec S184-S185
• MALDI-TOF for Combined Species Identification and Drug Sensitivity Testing in Mycobacteria.
  Ceyssens Pieter-Jan et al. Journal of clinical microbiology 2016 Dec
• HPV Genotyping of Modified General Primer-Amplicons Is More Analytically Sensitive and Specific by Sequencing than by Hybridization.
  Meisal Roger et al. PloS one 2017 (1) e0169074
• Issues in contemporary and potential future molecular diagnostics for dengue.
  Sekaran Shamala Devi et al. Expert review of molecular diagnostics 2016 Dec 1-7
• Application of next generation sequencing for the detection of human viral pathogens in clinical specimens.
  Parker Jayme et al. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2017 Jan 20-26
• Molecular diagnosis of Entamoeba spp. versus microscopy in the Great Cairo.
  Roshdy Mohamed H et al. Acta parasitologica 2017 Mar (1) 188-191
• Development of a rapid antibody test for point-of-care diagnosis of animal African trypanosomosis.
  Boulangé Alain et al. Veterinary parasitology 2017 Jan 32-38

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Laboratory Investigation of Salmonella enterica serovar Poona Outbreak in California: Comparison of Pulsed-Field Gel Electrophoresis (PFGE) and Whole Genome Sequencing (WGS) Results.
  Kozyreva Varvara K et al. PLoS currents 2016 Nov  
• Outbreak of Salmonella Oslo Infections Linked to Persian Cucumbers - United States, 2016.
  Bottichio Lyndsay et al. MMWR. Morbidity and mortality weekly report 2016 Dec (5051) 1430-1433 
• Case Series Description and Genomic Characterization of Invasive Group A Streptococcal Infections in Pediatric Patients.
  Bard Jennifer Dien et al. The Pediatric infectious disease journal 2016 Dec
• Whole genome sequencing to investigate a putative outbreak of the virulent community-associated methicillin-resistant Staphylococcus aureus ST93 clone in a remote Indigenous community 
  Meumann EM, et al. Microb Genom, Dec1, 2016.
• A brief primer on genomic epidemiology: lessons learned from Mycobacterium tuberculosis.
  Guthrie Jennifer L et al. Annals of the New York Academy of Sciences 2016 Dec
• Subtypes and risk behaviors among incident HIV cases in the Bangkok Men Who Have Sex with Men Cohort Study, Thailand, 2006-2015.
  Lam Caitlin R et al. AIDS research and human retroviruses 2016 Dec 
• HIV-1 Infection and Transmission Networks of Younger People in Chicago, Illinois, 2005-2011.
  Morgan Ethan et al. Public health reports (Washington, D.C. : 1974) (1) 48-55 
• Occupational HIV infection in a research laboratory with unknown mode of transmission: a case report.
  Soria Alessandro et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2016 Dec
• Molecular Virologic and Clinical Characteristics of a Chikungunya Fever Outbreak in La Romana, Dominican Republic, 2014.
  Langsjoen Rose M et al. PLoS neglected tropical diseases 2016 Dec (12) e0005189

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• Implementation of a Rapid Genotypic Assay to Promote Targeted Ciprofloxacin Therapy of Neisseria gonorrhoeae in a Large Health System.
  Allan-Blitz Lao-Tzu et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2016 Dec 
• Qualitative and quantitative HIV antibodies and viral reservoir size characterization in vertically infected children with virological suppression.
  Brice Josephine et al. The Journal of antimicrobial chemotherapy 2016 Dec
• Deep sequencing in the management of hepatitis virus infections.
  Quer Josep et al. Virus research 2016 Dec
• Genetic stability of genome-scale deoptimized RNA virus vaccine candidates under selective pressure.
  Le Nouën Cyril et al. Proceedings of the National Academy of Sciences of the United States of America 2017 Jan

HOST-MICROBE INTERACTIONS

• The gut microbiota in conventional and serrated precursors of colorectal cancer.
  Peters Brandilyn A et al. Microbiome 2016 Dec (1) 69 
• Gut microbiota as a source of a surrogate antigen that triggers autoimmunity in an immune privileged site.
  Zárate-Bladés Carlos R et al. Gut microbes 2017 Jan 0
• Temporal bacterial and metabolic development of the preterm gut reveals specific signatures in health and disease.
  Stewart Christopher J et al. Microbiome 2016 Dec (1) 67
• Nasal Airway Microbiota Profile and Severe Bronchiolitis in Infants: A Case-Control Study.
  Hasegawa Kohei et al. The Pediatric infectious disease journal 2016 Dec

Note:  indicates that at least one CDC-affiliated author;  indicates that the article addresses aspects of implementation or evaluation in clinical or public health practice.