Publication Date: Jan 4, 2018
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. View Data Selection Criteria
Advanced Molecular Detection Clips Content
- State-mandated MRSA surveillance fails to reduce prevalence in ICUs
Healio, Dec 19, 2017.
- Fast, Cheap Testing for Tuberculosis? Soon It May Be Possible
McNeil Jr, DG. New York Times, Jan 1, 2018.
- Preliminary study hints that genetically modified T cells might fight HIV
Begley S. STAT, Jan 2, 2018.
- Why Has Science Only Cured One Person of HIV?
Brown KV. Gizmodo, Dec 28, 2017.
- Yale Researchers Find Host mRNA, Protein Biomarkers Predictive of Viral Infections
Gilmore J. GenomeWeb, Jan 3, 2018.
- Researchers Reconstruct Hepatitis B Virus Genome from 16th Century Mummy
GenomeWeb, Jan 4, 2018.
- How the Chan Zuckerberg Science Initiative plans to solve disease by 2100
Bergmann C. Nature, Jan 3, 2018.
- Exercise Alters Our Microbiome. Is That One Reason Its So Good for Us?
G Reynolds, NY Times, Jan 3, 2017
CONCEPTS / COMMENTS
- Sex in microbial pathogens.
Bernstein Harris et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2018 Jan 8-25
- The Colombian peace deal and its impact on the evolution of tropical diseases agents.
Higuera Adriana et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2018 Jan 145-150
- One Step Forward in the Road Toward a Universal Influenza Vaccine.
Ramilo Octavio et al. The Journal of infectious diseases 2017 Dec (1) 1-2
- Implications of segment mismatch for influenza A virus evolution.
White Maria C et al. The Journal of general virology 2018 Jan (1) 3-16
- Arbovirus Diagnostics: From Bad to Worse due to Expanding Dengue Virus Vaccination and Zika Virus Epidemics
Simmons G, et al. Clin Infect Dis, Dec 30, 2017.
- Through the Scope Darkly: The Gut Mycobiome Comes into Focus.
Hernández-Santos Nydiaris et al. Cell host & microbe 2017 Dec (6) 728-729
METHODS / TOOLS
- Surfaceome Analysis Protocol for the Identification of Novel Bordetella pertussis Antigens.
Williamson Yulanda M et al. Methods in molecular biology (Clifton, N.J.) 2018 3-20
- Flow cytometric fingerprinting for microbial strain discrimination and physiological characterization.
Buysschaert Benjamin et al. Cytometry. Part A : the journal of the International Society for Analytical Cytology 2017 Dec
- Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes.
Chun Jongsik et al. International journal of systematic and evolutionary microbiology 2018 Jan (1) 461-466
- QSdpR: Viral Quasispecies Reconstruction via Correlation Clustering.
Barik Somsubhra et al. Genomics 2017 Dec
- 16SPIP: a comprehensive analysis pipeline for rapid pathogen detection in clinical samples based on 16S metagenomic sequencing.
Miao Jiaojiao et al. BMC bioinformatics 2017 Dec (Suppl 16) 568
- Bioinformatic Approaches for Comparative Analysis of Viruses.
Amgarten Deyvid et al. Methods in molecular biology (Clifton, N.J.) 2018 401-417
- MPLasso: Inferring microbial association networks using prior microbial knowledge.
Lo Chieh et al. PLoS computational biology 2017 Dec (12) e1005915
- Phandango: an interactive viewer for bacterial population genomics.
Hadfield James et al. Bioinformatics (Oxford, England) 2017 Sep
EVOLUTION / ECOLOGY / POPULATIONS
- Within-host evolution of Enterococcus faecium during longitudinal carriage and transition to bloodstream infection in immunocompromised patients.
Moradigaravand Danesh et al. Genome medicine 2017 Dec (1) 119
- Genome-based analysis of Enterococcus faecium bacteremia associated with recurrent and mixed strain infection.
Raven Kathy E et al. Journal of clinical microbiology 2017 Dec
- Phylogenetic inference of Coxiella burnetii by 16S rRNA gene sequencing.
McLaughlin Heather P et al. PloS one 2017 (12) e0189910
- Comparison of Zoonotic Bacterial Agents in Fleas Collected from Small Mammals or Host-Seeking Fleas from a Ugandan Region Where Plague Is Endemic.
Bai Ying et al. mSphere (6)
- Range Expansion and the Origin of USA300 North American Epidemic Methicillin-Resistant Staphylococcus aureus.
Challagundla Lavanya et al. mBio 2018 Jan (1)
- Clonal diversity and geographic distribution of methicillin-resistant Staphylococcus pseudintermedius from Australian animals: Discovery of novel sequence types.
Worthing Kate A et al. Veterinary microbiology 2018 Jan 58-65
- Mycoplasma genitalium: whole genome sequence analysis, recombination and population structure.
Fookes Maria C et al. BMC genomics 2017 Dec (1) 993
- An epidemic surge of influenza A(H3N2) virus at the end of the 2016-2017 season in Taiwan with an increased viral genetic heterogeneity.
Yang Ji-Rong et al. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2017 Dec 15-21
- Genome-wide evolutionary dynamics of influenza B viruses on a global scale.
Langat Pinky et al. PLoS pathogens 2017 Dec (12) e1006749
- Early Epstein-Barr Virus Genomic Diversity and Convergence toward the B95.8 Genome in Primary Infection.
Weiss Eric R et al. Journal of virology 2018 Jan (2)
- Whole-genome analyses of human adenovirus type 55 emerged in Tibet, Sichuan and Yunnan in China, in 2016.
Wang Wenbo et al. PloS one 2017 (12) e0189625
- Understanding orthopoxvirus host range and evolution: from the enigmatic to the usual suspects.
Reynolds Mary G et al. Current opinion in virology 2017 Dec 108-115
- Molecular characterization of hepatitis B virus in Bangladesh reveals a highly recombinant population.
Munshi Saif Ullah et al. PloS one 2017 (12) e0188944
- Are Circulating Type 2 Vaccine-derived Polioviruses (VDPVs) Genetically Distinguishable from Immunodeficiency-associated VDPVs?
Zhao Kun et al. Computational and structural biotechnology journal 2017 456-462
- Population genetic characterization of Cyclospora cayetanensis from discrete geographical regions.
Guo Yaqiong et al. Experimental parasitology 2017 Dec
- Genetic diversity and distribution differ between long-established and recently introduced populations in the invasive mosquito Aedes albopictus.
Sherpa Stéphanie et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2017 Dec 145-156
- Analysis of over 1500 triatomine vectors from across the US, predominantly Texas, for Trypanosoma cruzi infection and discrete typing units.
Curtis-Robles Rachel et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2017 Dec 171-180
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
- Genomic, Transcriptomic, and Phenotypic Analyses of Neisseria meningitidis Isolates from Disease Patients and Their Household Contacts.
Ren Xiaoyun et al. mSystems (6)
- Comparison of genomes and proteomes of four whole genome-sequenced Campylobacter jejuni from different phylogenetic backgrounds.
Clark Clifford G et al. PloS one 2018 (1) e0190836
- Multilocus sequence types of clinical Burkholderia pseudomallei isolates from peninsular Malaysia and their associations with disease outcomes.
Zueter Abdel Rahman et al. BMC infectious diseases 2018 Jan (1) 5
- A standardised method for interpreting the association between mutations and phenotypic drug resistance in Mycobacterium tuberculosis.
Miotto Paolo et al. The European respiratory journal 2017 Dec (6)
- Convergent evolution and topologically disruptive polymorphisms among multidrug-resistant tuberculosis in Peru.
Grandjean Louis et al. PloS one 2017 (12) e0189838
- Evolution and Virulence of Influenza A Virus Protein PB1-F2.
Kamal Ram P et al. International journal of molecular sciences 2017 Dec (1)
- HIV-1 Subtypes and 5'LTR-Leader Sequence Variants Correlate with Seroconversion Status in Pumwani Sex Worker Cohort.
Sampathkumar Raghavan et al. Viruses 2017 Dec (1)
DETECTION / DIAGNOSIS
- Rapid identification of pathogens responsible for necrotizing fasciitis on an integrated microfluidic system.
Yu Ju-Ching et al. Biomicrofluidics 2017 Nov (6) 064108
- A Combined Syndromic Approach to Examine Viral, Bacterial, and Parasitic Agents among Febrile Patients: A Pilot Study in Kilombero, Tanzania.
Hercik Christine et al. The American journal of tropical medicine and hygiene 2017 Dec
- Surveillance for and Discovery of Borrelia Species in US Patients Suspected of Tickborne Illness.
Kingry Luke C et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2017 Dec
- Molecular characterization and phylogenetic analysis of Clostridium perfringens from animals and their environments by cpn60 UT sequencing analysis.
Das Shreya et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2017 Dec
- A real-time multiplex PCR for the identification and typing of Vibrio cholerae.
Greig David R et al. Diagnostic microbiology and infectious disease 2017 Dec
- Development of a Multilocus Sequence Typing (MLST) scheme for Treponema pallidum subsp. pertenue: Application to yaws in Lihir Island, Papua New Guinea.
Godornes Charmie et al. PLoS neglected tropical diseases 2017 Dec (12) e0006113
- Rapid discrimination of Staphylococcus epidermidis genotypes in a routine clinical microbiological laboratory using single nucleotide polymorphisms in housekeeping genes.
Larssen Kjersti Wik et al. Journal of medical microbiology 2018 Jan
- Impact of Culture-Independent Diagnostic Testing on Recovery of Enteric Bacterial Infections.
Imdad Aamer et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2017 Dec
- Evaluation of a Urine-Based Rapid Molecular Diagnostic Test with Potential to be used at Point-of-Care for Pulmonary Tuberculosis: Cape Town Cohort.
Patel Krutarth et al. The Journal of molecular diagnostics : JMD 2017 Dec
- Direct detection of Mycobacterium tuberculosis rifampin resistance in bio-safe stained sputum smears.
Lavania Surabhi et al. PloS one 2017 (12) e0189149
- Pathogen genomic surveillance elucidates the origins, transmission and evolution of emerging viral agents in China.
Shi Weifeng et al. Science China. Life sciences 2017 Nov
- Identifying the Genotypes of Hepatitis B Virus (HBV) with DNA Origami Label.
Liu Ke et al. Small (Weinheim an der Bergstrasse, Germany) 2017 Dec
- Utility of high-throughput DNA sequencing in the study of the human papillomaviruses.
Escobar-Escamilla Noé et al. Virus genes 2017 Dec
- Antiviral response in the nasopharynx identifies patients with respiratory virus infection.
Landry Marie L et al. The Journal of infectious diseases 2017 Dec
- Standardization and validation of real time PCR assays for the diagnosis of histoplasmosis using three molecular targets in an animal model.
López Luisa F et al. PloS one 2017 (12) e0190311
- Assessment of MALDI-TOF mass spectrometry for filariae detection in Aedes aegypti mosquitoes.
Tahir Djamel et al. PLoS neglected tropical diseases 2017 Dec (12) e0006093
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
- Cross-border outbreak of listeriosis caused by cold-smoked salmon, revealed by integrated surveillance and whole genome sequencing (WGS), Denmark and France, 2015 to 2017.
Schjørring Susanne et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2017 Dec (50)
- Complex patterns of Hepatitis-C virus longitudinal clustering in a high-risk population.
Rose Rebecca et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2017 Dec 77-82
- Hepatitis C virus spread from HIV-positive to HIV-negative men who have sex with men.
Charre Caroline et al. PloS one 2018 (1) e0190340
- Prevalence of genital human papillomavirus among sexually experienced males and females aged 14-59 years, United States, 2013-2014.
Lewis Rayleen M et al. The Journal of infectious diseases 2017 Dec
- Investigating cross-contamination by yeast strains from dental solid waste to waste-handling workers by DNA sequencing.
Vieira Cristina Dutra et al. MicrobiologyOpen 2017 Dec
ANTIMICROBIALS / VACCINES / INTERVENTIONS
- Sex differences shape the response to infectious diseases.
Ingersoll Molly A et al. PLoS pathogens 2017 Dec (12) e1006688
- Gut microbiome in gestational diabetes: a cross-sectional study of mothers and offspring 5 years postpartum.
Hasan Sayyid et al. Acta obstetricia et gynecologica Scandinavica 2018 Jan (1) 38-46
- Women and Their Microbes: The Unexpected Friendship.
Younes Jessica A et al. Trends in microbiology 2018 Jan (1) 16-32
- Weaker HLA Footprints on HIV in the Unique and Highly Genetically Admixed Host Population of Mexico.
Soto-Nava Maribel et al. Journal of virology 2018 Jan (2)
- The role of microbial amyloid in neurodegeneration.
Friedland Robert P et al. PLoS pathogens 2017 12 (12) e1006654
- Analysis of Epstein-Barr Virus Genomes and Expression Profiles in Gastric Adenocarcinoma.
Borozan Ivan et al. Journal of virology 2018 Jan (2)
- KIR3DL1 alleles and their Epistatic Interactions with HLA Class I Influence Resistance and Susceptibility to HIV-1 acquisition in the Pumwani Sex Worker cohort.
Luo Ma et al. AIDS (London, England) 2017 Dec
- Zika virus infection modulates the bacterial diversity associated with Aedes aegypti as revealed by metagenomic analysis.
Villegas Luis E M et al. PloS one 2018 (1) e0190352
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.
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