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
Policy
Concepts / Comments
Methods / Tools
Evolution / Ecology / Populations
Pathogenicity / Antimicrobial Resistance
Detection / Diagnosis
Epidemiology / Outbreaks / Transmission
Antimicrobials / Vaccines / Interventions
Host-Microbe Interactions
NEWS
WHO issues new guidance on HIV self-testing ahead of World AIDS Day
[news release] WHO, Nov 29, 2016.
Genomics Technique Could Accelerate Detection of Foodborne Bacterial Outbreaks
Georgia Tech Research Horizons, Nov 30, 2016.
The Ebola outbreak may have been bigger than believed, with ‘invisible’ infection
Cha AE. Washington Post, Nov 17, 2016.
River Blindness Parasite Genome Studies Provide Resources for Neglected Disease
GenomeWeb, Nov 21, 2016.
POLICY
FDA Delays Guidance on Lab-Developed Tests—Agency will wait until new administration is in place
Firth S. MedPage Today, Nov 21, 2016.
Microbiological Research Under the Nagoya Protocol: Facts and Fiction.
Overmann Jörg et al. Trends in microbiology 2016 Nov
CONCEPTS / COMMENTS
Combined harvest of knowledge
[editorial] Nat Genet, Nov 29, 2016.
Human host range of Mycobacterium tuberculosis
Hershberg R. Nat Genet, Nov 29, 2016.
Non-Cholera Vibrios: The Microbial Barometer of Climate Change.
Baker-Austin Craig et al. Trends in microbiology 2016 Nov
METHODS / TOOLS
Enrichment dynamics of Listeria monocytogenes and the associated microbiome from naturally contaminated ice cream linked to a listeriosis outbreak.
Ottesen Andrea et al. BMC microbiology 2016 Nov (1) 275
Generation and Screening of an Insertion Sequencing-Compatible Mutant Library of Campylobacter jejuni.
Johnson Jeremiah G et al. Methods in molecular biology (Clifton, N.J.) 2017 257-272
Large-scale benchmarking reveals false discoveries and count transformation sensitivity in 16S rRNA gene amplicon data analysis methods used in microbiome studies.
Thorsen Jonathan et al. Microbiome 2016 Nov (1) 62
Functional Metagenomics to Study Antibiotic Resistance.
Boolchandani Manish et al. Methods in molecular biology (Clifton, N.J.) 2017 307-329
Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary.
Brynildsrud Ola et al. Genome biology 2016 Nov (1) 238
Markov Networks of Collateral Resistance: National Antimicrobial Resistance Monitoring System Surveillance Results from Escherichia coli Isolates, 2004-2012.
Love William J et al. PLoS computational biology 2016 Nov (11) e1005160
EVOLUTION / ECOLOGY / POPULATIONS
Complete Genome Sequences for Three Chromosomes of the Burkholderia stabilis Type Strain (ATCC BAA-67).
Bugrysheva Julia V et al. Genome announcements 2016 Nov (6) 
MRSA and multidrug-resistant Staphylococcus aureus in U.S. retail meats, 2010-2011.
Ge Beilei et al. Food microbiology 2017 Apr 289-297
Serotype distribution, population structure and antimicrobial resistance of Group B Streptococcus strains recovered from colonized pregnant women.
Teatero Sarah et al. Journal of clinical microbiology 2016 Nov
Armed conflict and population displacement as drivers of the evolution and dispersal of Mycobacterium tuberculosis.
Eldholm Vegard et al. Proceedings of the National Academy of Sciences of the United States of America 2016 Nov
Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sublineages.
Stucki David et al. Nature genetics 2016 Dec (12) 1535-1543
Comparative genome analysis between Southeast Asian and South American Zika viruses.
Kochakarn Theerarat et al. Asian Pacific journal of tropical medicine 2016 Nov (11) 1048-1054
Phylogeography of Crimean Congo Hemorrhagic Fever Virus.
Lukashev Alexander N et al. PloS one 2016 (11) e0166744
Molecular Epidemiology of Agents of Human Chromoblastomycosis in Brazil with the Description of Two Novel Species.
Gomes Renata R et al. PLoS neglected tropical diseases 2016 Nov (11) e0005102
Selective sweep suggests transcriptional regulation may underlie Plasmodium vivax resilience to malaria control measures in Cambodia
Parobek CM, et al. Proc Natl Acad Sci, Nov 28, 2016.
Genomic diversity in Onchocerca volvulus and its Wolbachia endosymbiont.
Choi Young-Jun et al. Nature microbiology 2016 Nov 16207
Molecular epidemiology and multilocus sequence analysis of potentially zoonotic Giardia spp. from humans and dogs in Jamaica.
Lee Mellesia F et al. Parasitology research 2016 Nov
The genome of Onchocerca volvulus, agent of river blindness.
Cotton James A et al. Nature microbiology 2016 Nov 16216
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
Detection of an Escherichia coli ST167 strain with two tandem copies of blaNDM-1 encoded in the chromosome.
Shen Ping et al. Journal of clinical microbiology 2016 Nov
Genome-wide association of functional traits linked with Campylobacter jejuni survival from farm to fork.
Yahara Koji et al. Environmental microbiology 2016 Nov
Methods to Study Antimicrobial Resistance in Campylobacter jejuni.
Sahin Orhan et al. Methods in molecular biology (Clifton, N.J.) 2017 29-42
MCR: modern colistin resistance.
Caniaux I et al. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 2016 Nov
Whole-genome sequencing and comparative genomic analysis of Escherichia coli O91 strains isolated from symptomatic and asymptomatic human carriers.
Kwon Taesoo et al. Gut pathogens 2016 57
Molecular Characteristic and Virulence Gene Profiles of Community-Associated Methicillin-Resistant Staphylococcus aureus Isolates from Pediatric Patients in Shanghai, China.
Wang Xing et al. Frontiers in microbiology 2016 1818
Emergence of Multidrug-resistant Pneumococcal Serotype 35B among U.S. Children.
Olarte Liset et al. Journal of clinical microbiology 2016 Nov
Mutations Associated with Decreased Susceptibility to Seven Antimicrobial Families in Field and Laboratory-Derived Mycoplasma bovis Strains.
Sulyok Kinga M et al. Antimicrobial agents and chemotherapy 2016 Nov
HIV-1 drug resistance mutations emerging on darunavir therapy in PI-naive and -experienced patients in the UK.
El Bouzidi Kate et al. The Journal of antimicrobial chemotherapy 2016 Dec (12) 3487-3494
DETECTION / DIAGNOSIS
Relative prevalence and antimicrobial susceptibility of clinical isolates of Elizabethkingia species based on 16S rRNA gene sequencing.
Han Mi-Soon et al. Journal of clinical microbiology 2016 Nov
Informing Antibiotic Treatment Decisions: Evaluating Rapid Molecular Diagnostics (RMDs) to Identify Susceptibility and Resistance to Carbapenems against Acinetobacter spp. PRIMERS III.
Evans Scott R et al. Journal of clinical microbiology 2016 Oct
Host-based Peripheral Blood Gene Expression Analysis for the Diagnosis of Infectious Diseases.
Holcomb Zachary E et al. Journal of clinical microbiology 2016 Oct
A Retrospective Study of the Impact of Rapid Diagnostic Testing on Time to Pathogen Identification and Antibiotic Use for Children with Positive Blood Cultures.
Veesenmeyer Angela Fimbres et al. Infectious diseases and therapy 2016 Nov
The Role of Whole Genome Sequencing (WGS) in Antimicrobial Susceptibility Testing of Bacteria: Report from the EUCAST Subcommittee
Ellington MJ, et al. Clin Microbiol Infect, Nov 12, 2016.
Identification of IncA/C Plasmid Replication and Maintenance Genes and Development of a Plasmid Multi-Locus Sequence-Typing Scheme.
Hancock Steven J et al. Antimicrobial agents and chemotherapy 2016 Nov
Antimicrobial resistance surveillance in the genomic age.
McArthur Andrew G et al. Annals of the New York Academy of Sciences 2016 Nov
Metagenomics of two severe foodborne outbreaks provides diagnostic signatures and signs of co-infection not attainable by traditional methods.
Huang Andrew D et al. Applied and environmental microbiology 2016 Nov
Highly Multiplexed Proteomic Analysis of Quantiferon Supernatants to Identify Biomarkers of Latent Tuberculosis Infection.
De Groote Mary Ann et al. Journal of clinical microbiology 2016 Nov
Whole genome sequencing of Mycobacterium tuberculosis for detection of drug resistance: a systematic review.
Papaventsis D et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2016 Sep
Whole genome sequencing for M/XDR tuberculosis surveillance and for resistance testing.
Walker T M et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2016 Oct
Zika virus and diagnostics.
Gabaglia Claudia Raja et al. Current opinion in pediatrics 2016 Nov
Rapid Detection of Common HIV-1 Drug Resistance Mutations Using High Resolution Melting Analysis and Unlabelled Probes.
Sacks David et al. Journal of clinical microbiology 2016 Oct
Progress in Quantitative Viral Load Testing: Variability and Impact of the WHO Quantitative International Standards.
Hayden R T et al. Journal of clinical microbiology 2016 Nov
Rapid identification of measles virus vaccine genotypes by real time PCR.
Roy Felicia et al. Journal of clinical microbiology 2016 Nov
An isothermal, label-free, and rapid one-step RNA amplification/detection assay for diagnosis of respiratory viral infections.
Koo Bonhan et al. Biosensors & bioelectronics 2016 Nov 187-194
Superiority of digital RT-PCR over real-time RT-PCR for quantitation of highly divergent human rhinoviruses.
Hall Sedlak Ruth et al. Journal of clinical microbiology 2016 Nov
Identification of Molds by MALDI-TOF Mass Spectrometry.
Sanguinetti Maurizio et al. Journal of clinical microbiology 2016 Nov
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
Transmission of Staphylococcus aureus between health-care workers, the environment, and patients in an intensive care unit: a longitudinal cohort study based on whole-genome sequencing.
Price James R et al. The Lancet. Infectious diseases 2016 Nov
MALDI-TOF MS meets WGS in a VRE outbreak investigation.
Schlebusch S et al. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 2016 Nov
A polyclonal outbreak of bloodstream infections by Enterococcus faecium in patients with hematologic malignancies.
Alatorre-Fernández Pamela et al. American journal of infection control 2016 Nov
Molecular, Spatial, and Field Epidemiology Suggesting TB Transmission in Community, Not Hospital, Gaborone, Botswana.
Surie Diya et al. Emerging infectious diseases 2017 Mar (3)
Genomic epidemiology of Lineage 4 Mycobacterium tuberculosis subpopulations in New York city and New Jersey, 1999-2009.
Brown Tyler S et al. BMC genomics 2016 Nov (1) 947
Unusual Ebola Virus Chain of Transmission, Conakry, Guinea, 2014-2015.
Keita Mory et al. Emerging infectious diseases 2016 Dec (12) 2149-2152
Epidemiological and Molecular Analysis of an Outbreak of Highly Pathogenic Avian Influenza H5N8 clade 2.3.4.4 in a German Zoo: Effective Disease Control with Minimal Culling.
Globig A et al. Transboundary and emerging diseases 2016 Nov
The hepatitis C virus nonstructural protein 3 Q80K polymorphism is frequently detected and transmitted among HIV-infected MSM in the Netherlands.
Newsum Astrid M et al. AIDS (London, England) 2017 Jan (1) 105-112
ANTIMICROBIALS / VACCINES / INTERVENTIONS
Cost Analysis of Implementing MALDI-TOF plus Real-time Antimicrobial Stewardship Intervention for Bloodstream Infections.
Patel Twisha S et al. Journal of clinical microbiology 2016 Oct
Use of whole genome sequencing in the Dutch Acute HCV in HIV study. A focus on transmitted antiviral resistance.
Christiansen Mette T et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2016 Sep
HOST-MICROBE INTERACTIONS
Identification of the transcripts associated with spontaneous HCV clearance in individuals co-infected with HIV and HCV.
Chen Yue et al. BMC infectious diseases 2016 Nov (1) 693
Minimal immune determinants connect Zika virus, human Cytomegalovirus, and Toxoplasma gondii to microcephaly-related human proteins.
Lucchese Guglielmo et al. American journal of reproductive immunology (New York, N.Y. : 1989) 2016 Nov
ABO antigen and secretor statuses are not associated with gut microbiota composition in 1,500 twins.
Davenport Emily R et al. BMC genomics 2016 Nov (1) 941
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.
Disclaimer: Articles listed in the Advanced Molecular Detection Clips are selected by the CDC Office of Public Health Genomics to provide current awareness of the scientific literature and news. Inclusion in the clips 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 Clips, 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.