Advanced Molecular Detection Clips Content || Current|Update|Genomics|CDC

Public Health Genomics Knowledge Base (v1.0)

Advanced Molecular Detection Clips

About Advanced Molecular Detection Clips

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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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

• Building Off NYC Subway Study, Consortium to Profile Metagenomes of Transit Systems in 45 Cities 
  Heger M. GenomeWeb, Mar 2, 2016.
• Spoiler Alert: How to store microbiome samples without losing or altering diversity 
  Yan W. The Scientist, Mar 1, 2016.
• MALDI-Based Fatty Acid Profiling Offers Infectious Disease Dx Potential 
  Han AP. GenomeWeb, Feb 25, 2016.
• Texas hospitals announce first quick test for Zika that could help identify when the virus reaches U.S. 
  Cha AE. Washington Post, Feb 24, 2016.
• Genome Sequences Suggest Diminishing Virulence During Korean MERS Outbreak 
  GenomeWeb, Mar 1, 2016.
• Direct Transmission Seems to Drive XDR TB 
  Susman E. MedPage Today, Feb 28, 2016.
• Researchers Develop MALDI-TOF Method for Detecting Vancomycin-Resistant MRSA 
  Bonislawski A. GenomeWeb, Mar 2, 2016.
• FDA proposes greater oversight of stool banks distributing FMT for C. difficile infection 
  Healio, Mar 1, 2016.

EVENTS / TRAINING / WEB RESOURCES

• Zika virus resource page provides access to nucleotide, protein sequences from latest outbreak 
  (web resource) NCBI, Feb 23, 2016.
• The 2015 Bioinformatics Open Source Conference (BOSC 2015). 
  Harris Nomi L et al. PLoS computational biology 2016 Feb (2) e1004691

CONCEPTS / COMMENTS

• Lessons from the Ebola Outbreak: Action Items for Emerging Infectious Disease Preparedness and Response. 
  Jacobsen Kathryn H et al. EcoHealth 2016 Feb
• Role of Clinicogenomics in Infectious Disease Diagnostics and Public Health Microbiology. 
  Westblade Lars F et al. Journal of clinical microbiology 2016 Feb

METHODS / TOOLS

• Genome-wide Annotation, Identification, and Global Transcriptomic Analysis of Regulatory or Small RNA Gene Expression in Staphylococcus aureus.
  Carroll Ronan K et al. mBio 2015 (1)
• ViromeScan: a new tool for metagenomic viral community profiling 
  Rampelli S, et al. BMC Genomics, Mar 1, 2016.
• A Toolbox for Herpesvirus miRNA Research: Construction of a Complete Set of KSHV miRNA Deletion Mutants. 
  Jain Vaibhav et al. Viruses 2016 (2)

EVOLUTION / ECOLOGY / POPULATIONS

• Whole-genome sequencing reveals the origin and rapid evolution of an emerging outbreak strain of Streptococcus pneumoniae 12F. 
  Deng Xianding et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2016 Feb
• Nocardia donostiensis sp. nov., isolated from human respiratory specimens. 
  Ercibengoa Maria et al. Antonie van Leeuwenhoek 2016 Feb 
• Biochemical and full genome sequence analyses of clinical Vibrio cholerae isolates in Mexico reveals the presence of novel V. cholerae strains. 
  Díaz-Quiñonez José Alberto et al. Microbes and infection / Institut Pasteur 2016 Jan
• Identification of a Latin American-specific BabA adhesin variant through whole genome sequencing of Helicobacter pylori patient isolates from Nicaragua. 
  Thorell Kaisa et al. BMC evolutionary biology (1) 53
• The Widespread Presence of a Multidrug-Resistant Escherichia coli ST131 Clade among Community-Associated and Hospitalized Patients. 
  den Reijer P Martijn et al. PloS one (3) e0150420
• Chlamydia trachomatis from Australian Aboriginal people with trachoma are polyphyletic composed of multiple distinctive lineages. 
  Andersson Patiyan et al. Nature communications 2016 10688
• Genetic characterization of measles virus in the Philippines, 2008-2011. 
  Centeno Rex et al. BMC research notes 2015 211
• Coexistence of multiple coronaviruses in several bat colonies in an abandoned mineshaft. 
  Ge Xing-Yi et al. Virologica Sinica 2016 Feb (1) 31-40
• Re-emergence of dengue virus serotype 2 strains in the 2013 outbreak in Nepal. 
  Gupta Birendra Prasad et al. The Indian journal of medical research 2015 Dec S1-6

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Predictability of phenotype in relation to common β-lactam resistance mechanisms in Escherichia coli and Klebsiella pneumoniae. 
  Agyekum Alex et al. Journal of clinical microbiology 2016 Feb
• Virulence-associated genes, antimicrobial resistance and molecular typing of Salmonella Typhimurium strains isolated from swine from 2000-2012 in Brazil. 
  Almeida Fernanda et al. Journal of applied microbiology 2016 Feb
• Mechanobiology of Antimicrobial Resistant Escherichia coli and Listeria innocua. 
  Tajkarimi Mehrdad et al. PloS one 2016 (2) e0149769
• Analysis of Multilocus Sequence Typing and Virulence Characterization of Listeria monocytogenes Isolates from Chinese Retail Ready-to-Eat Food.
  Wu Shi et al. Frontiers in microbiology 2016 168
• Correlation between antimicrobial resistance and virulence in Klebsiella pneumoniae. 
  Hennequin C et al. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 2016 Mar (3) 333-41
• Identification of low-level vancomycin resistance in Staphylococcus aureus in the era of informatics. 
  Ford Bradley A et al. Journal of clinical microbiology 2016 Feb
• Genetic Determinants of Drug Resistance in Mycobacterium tuberculosis and Their Diagnostic Value. 
  Farhat Maha R et al. American journal of respiratory and critical care medicine 2016 Feb 
• Genetic features of Mycobacterium tuberculosis modern Beijing sublineage. 
  Liu Qingyun et al. Emerging microbes & infections 2016 e14
• Whole genome sequencing to complement tuberculosis drug resistance surveys in Uganda. 
  Ssengooba Willy et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 Feb
• Exploiting HIV-1 protease and reverse transcriptase cross-resistance information for improved drug resistance prediction by means of multi-label classification 
  Riemenschneider M, et al. BioData Mining, Feb 29, 2016.

DETECTION / DIAGNOSIS

• Intestinal microbiome disruption in patients in a long-term acute care hospital: A case for development of microbiome disruption indices to improve infection prevention. 
  Halpin Alison Laufer et al. American journal of infection control 2016 Feb 
• Development of a Flow Cytometry-Based Method for Rapid Detection of Escherichia coli and Shigella Spp. Using an Oligonucleotide Probe. 
  Xue Yong et al. PloS one 2016 (2) e0150038
• Development of Real-Time PCR Methods for the Detection of Bacterial Meningitis Pathogens without DNA Extraction. 
  Vuong Jeni et al. PloS one 2016 (2) e0147765 
• DNA aptamers for the detection of Haemophilus influenzae type b by cell SELEX. 
  Bitaraf F S et al. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 2016 Mar (3) 503-10
• Diagnosis of Bacterial Bloodstream Infections: A 16S Metagenomics Approach. 
  Decuypere Saskia et al. PLoS neglected tropical diseases 2016 Feb (2) e0004470
• Rapid Detection of Vancomycin Intermediate Staphylococcus aureus (VISA) by Matrix Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS). 
  Mather Cheryl A et al. Journal of clinical microbiology 2016 Jan
• Impact of a Rapid Blood Culture Assay for Gram-Positive Identification and Detection of Resistance Markers in a Pediatric Hospital. 
  Felsenstein Susanna et al. Archives of pathology & laboratory medicine 2016 Mar (3) 267-75 
• Methodological and Clinical Aspects of the Molecular Epidemiology of Mycobacterium tuberculosis and Other Mycobacteria. 
  Jagielski Tomasz et al. Clinical microbiology reviews 2016 Apr (2) 239-90
• Xpert MTB/RIF Results in Patients With Previous Tuberculosis: Can We Distinguish True From False Positive Results? 
  Theron Grant et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2016 Feb
• Korean Society for Laboratory Medicine Practice Guidelines for the Molecular Diagnosis of Middle East Respiratory Syndrome During an Outbreak in Korea in 2015. 
  Ki Chang Seok et al. Annals of laboratory medicine 2016 May (3) 203-8
• Human Papillomavirus Laboratory Testing: the Changing Paradigm. 
  Burd Eileen M et al. Clinical microbiology reviews 2016 Apr (2) 291-319
• Optimizing Virus Identification in Critically Ill Children Suspected of Having an Acute Severe Viral Infection. 
  Randolph Adrienne G et al. Pediatric critical care medicine : a journal of the Society of Critical Care Medicine and the World Federation of Pediatric Intensive and Critical Care Societies 2016 Feb  
• Identification and Validation of Loa loa Microfilaria-Specific Biomarkers: a Rational Design Approach Using Proteomics and Novel Immunoassays. 
  Drame Papa M et al. mBio 2015 (1)
• Use of a Chagas Urine Nanoparticle Test (Chunap) to Correlate with Parasitemia Levels in T. cruzi/HIV Co-infected Patients. 
  Castro-Sesquen Yagahira E et al. PLoS neglected tropical diseases 2016 Feb (2) e0004407
• High Resolution Melting Analysis Targeting hsp70 as a Fast and Efficient Method for the Discrimination of Leishmania Species. 
  Zampieri Ricardo Andrade et al. PLoS neglected tropical diseases 2016 Feb (2) e0004485

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• US Gulf-like toxigenic O1 Vibrio cholerae causing sporadic cholera outbreaks in China. 
  Luo Yun et al. The Journal of infection 2016 Feb
• The Transmission and Antibiotic Resistance Variation in a Multiple Drug Resistance Clade of Vibrio cholerae Circulating in Multiple Countries in Asia.
  Pang Bo et al. PloS one (3) e0149742
• Genotyping Influenza Virus by Next-Generation Deep Sequencing in Clinical Specimens. 
  Seong Moon Woo et al. Annals of laboratory medicine 2016 May (3) 255-8
• Transmission dynamics of HIV-1 subtype B in the Basque country, Spain. 
  Patiño-Galindo J A et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 Feb
• Maternal Neutralization-Resistant Virus Variants Do Not Predict Infant HIV Infection Risk. 
  Milligan Caitlin et al. mBio 2016 (1)

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• Immunomics: a 21st century approach to vaccine development for complex pathogens. 
  DE Sousa Karina P et al. Parasitology 2016 Feb (2) 236-44
• Increased Prevalence of Controlled Viremia and Decreased Rates of HIV Drug Resistance Among HIV-Positive People Who Use Illicit Drugs During a Community-wide Treatment-as-Prevention Initiative. 
  Milloy M-J et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2016 Mar (5) 640-7 
• Initiating a watch list for Ebola virus antibody escape mutations. 
  Miller Craig R et al. PeerJ 2016 e1674

HOST-MICROBE INTERACTIONS

• Helicobacter pylori CagL Hypervariable Motif: a Global Analysis of Geographical Diversity and Association with Gastric Cancer. 
  Gorrell Rebecca J et al. The Journal of infectious diseases 2016 Feb
• Metabolomics-Based Discovery of Small Molecule Biomarkers in Serum Associated with Dengue Virus Infections and Disease Outcomes. 
  Voge Natalia V et al. PLoS neglected tropical diseases 2016 Feb (2) e0004449
• Assessment of Point-of-Care Diagnostics for G6PD Deficiency in Malaria Endemic Rural Eastern Indonesia. 
  Satyagraha Ari W et al. PLoS neglected tropical diseases 2016 Feb (2) e0004457
• Changes in Proteome Profile of Peripheral Blood Mononuclear Cells in Chronic Chagas Disease. 
  Garg Nisha Jain et al. PLoS neglected tropical diseases 2016 Feb (2) e0004490
• Epidemiologic Association Between FUT2 Secretor Status and Severe Rotavirus Gastroenteritis in Children in the United States. 
  Payne Daniel C et al. JAMA pediatrics 2015 Nov (11) 1040-5 
• Unraveling the Molecular Mechanisms Underlying the Nasopharyngeal Bacterial Community Structure. 
  de Steenhuijsen Piters Wouter A A et al. mBio 2016 (1)

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. 

Current|Update|Genomics|CDC

Current|Update|Genomics|CDC