Advanced Molecular Detection Clips || AMD Clips

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.

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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.

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Site Citation

• Yu W, Gwinn M, Dotson WD, Green RF, Clyne M, Wulf A, Bowen S, Kolor K, Khoury MJ. A knowledge base for tracking the impact of genomics on population health Genet Med. 2016 Jun 9. doi: 10.1038/gim.2016.63. [Epub ahead of print]

Disclaimer: Articles listed in the Public Health Knowledge Base are selected by the CDC Office of Public Health Genomics to provide current awareness of the literature and news. Inclusion in the update does not necessarily represent the views of the Centers for Disease Control and Prevention nor does it imply endorsement of the article's methods or findings. CDC and DHHS assume no responsibility for the factual accuracy of the items presented. The selection, omission, or content of items does not imply any endorsement or other position taken by CDC or DHHS. Opinion, findings and conclusions expressed by the original authors of items included in the update, or persons quoted therein, are strictly their own and are in no way meant to represent the opinion or views of CDC or DHHS. References to publications, news sources, and non-CDC Websites are provided solely for informational purposes and do not imply endorsement by CDC or DHHS.