Advanced Molecular Detection Clips Content

Public Health Genomics Knowledge Base (v1.2)

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

NEWS

• Health officials find first cases of new superbug in US
  Begley S. STAT, Nov 4, 2016.
• Scientists seek a way to predict antibiotic resistance
  Love S. STAT, Nov 7, 2016.
• What’s the next global disease threat? Some predictions
  Branswell H. STAT, Nov 7, 2016.
• Malaria Parasite Drug Resistance Linked to Copy Number Variant in Cambodian Studies
  GenomeWeb, Nov 4, 2016.
• Fungal Genome Assembled With Only Nanopore-Generated Reads
  GenomeWeb, Nov 3, 2016.
• Ebola Evolved Into Deadlier Enemy During the African Epidemic
  Zimmer C. New York Times, Nov 3, 2016.

CONCEPTS / COMMENTS

• Translational metagenomics and the human resistome: confronting the menace of the new millennium.
  Willmann Matthias et al. Journal of molecular medicine (Berlin, Germany) 2016 Oct
• Viruses of the Human Body
  Delwart E. The Scientist, Nov 1, 2016.
• Whole-genome sequencing-new tools for gonorrhoea control.
  Allen Vanessa G et al. The Lancet. Infectious diseases 2016 Nov (11) 1214-1215
• The gut microbiome-an emerging complex trait.
  Benson Andrew K et al. Nature genetics 2016 Oct (11) 1301-1302
• Rapid Diagnostic Tests for Neglected Infectious Diseases: Case Study Highlights Need for Customer Awareness and Postmarket Surveillance.
  Barbé Barbara et al. PLoS neglected tropical diseases 2016 Nov (11) e0004655

METHODS / TOOLS

• Exploring Viral Infection using Single-Cell Sequencing.
  Rato Sylvie et al. Virus research 2016 Nov
• Community-Wide Evaluation of Computational Function Prediction.
  Friedberg Iddo et al. Methods in molecular biology (Clifton, N.J.) 2017 133-146
• Metagenomic Investigation of Plasma in Individuals with ME/CFS Highlights the Importance of Technical Controls to Elucidate Contamination and Batch Effects.
  Miller Ruth R et al. PloS one 2016 (11) e0165691
• Rapid SNP Detection and Genotyping of Bacterial Pathogens by Pyrosequencing.
  Amoako Kingsley K et al. Methods in molecular biology (Clifton, N.J.) 2017 203-220
• PGAdb-builder: A web service tool for creating pan-genome allele database for molecular fine typing.
  Liu Yen-Yi et al. Scientific reports 2016 Nov 36213
• Feature selection and validated predictive performance in the domain of Legionella pneumophila: a comparative study.
  van der Ploeg Tjeerd et al. BMC research notes 2016 Mar 147
• The effect of phylogenetic signal reduction on genotyping of hepatitis E viruses of the species Orthohepevirus A.
  Purdy Michael A et al. Archives of virology 2016 Nov 
• Development and Characterization of Recombinant Virus Generated from a New World Zika Virus Infectious Clone.
  Weger-Lucarelli James et al. Journal of virology 2016 Oct 
• ZikaVR: An Integrated Zika Virus Resource for Genomics, Proteomics, Phylogenetic and Therapeutic Analysis.
  Gupta Amit Kumar et al. Scientific reports 2016 Sep 32713
• The European Classical Swine Fever Virus Database: Blueprint for a Pathogen-Specific Sequence Database with Integrated Sequence Analysis Tools.
  Postel Alexander et al. Viruses 2016 Nov (11)

EVOLUTION / ECOLOGY / POPULATIONS

• Complete, Closed Genome Sequences of 10 Salmonella enterica subsp. enterica Serovar Typhimurium Strains Isolated from Human and Bovine Sources.
  Nguyen Scott V et al. Genome announcements 2016 Nov (6) 
• Complete Genome Sequences of Four Different Bordetella sp. Isolates Causing Human Respiratory Infections.
  Weigand Michael R et al. Genome announcements 2016 Oct (5) 
• High-throughput sequencing highlights the significant influence of seasonal housing and teat preparation on the raw milk microbiota.
  Doyle Conor J et al. Applied and environmental microbiology 2016 Nov
• The endotracheal tube microbiome associated with Pseudomonas aeruginosa or Staphylococcus epidermidis.
  Hotterbeekx An et al. Scientific reports 2016 Nov 36507
• Genomic Comparisons and Zoonotic Potential of Campylobacter Between Birds, Primates, and Livestock.
  Weis Allison M et al. Applied and environmental microbiology 2016 Oct
• Distribution of two distinct rotavirus B (RVB) strains in the north-central Bangladesh and evidence for reassortment event among human RVB revealed by whole genomic analysis.
  Aung Meiji Soe et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 Nov
• Molecular Evolution of Human Coronavirus Genomes.
  Forni Diego et al. Trends in microbiology 2016 Oct
• Novel Viruses Isolated from Mosquitoes in Pantanal, Brazil.
  Pauvolid-Corrêa Alex et al. Genome announcements 2016 Nov (6) 
• Complete Genome Sequence of Human Norovirus Strain GII.P7-GII.6 Detected in a Patient in the United States in 2014.
  Yang Zhihui et al. Genome announcements 2016 Oct (5) 
• Evidence of the presence of the Zika virus in Mexico since early 2015.
  Díaz-Quiñonez José Alberto et al. Virus genes 2016 Dec (6) 855-857
• Assessment of fungal diversity in a water-damaged office building.
  Green Brett J et al. Journal of occupational and environmental hygiene 2016 Oct 0 
• The queenslandensis and the type Form of the Dengue Fever Mosquito (Aedes aegypti L.) Are Genomically Indistinguishable.
  Rašic Gordana et al. PLoS neglected tropical diseases 2016 Nov (11) e0005096
• Identification of Blood Meals from Potential Arbovirus Mosquito Vectors in the Peruvian Amazon Basin.
  Palermo Pedro M et al. The American journal of tropical medicine and hygiene 2016 Nov (5) 1026-1030 

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Corrected Genome Annotations Reveal Gene Loss and Antibiotic Resistance as Drivers in the Fitness Evolution of Salmonella enterica Serovar Typhimurium.
  Paul Sandip et al. Journal of bacteriology 2016 Dec (23) 3152-3161
• Understanding pneumococcal serotype 1 biology through population genomic analysis.
  Chaguza Chrispin et al. BMC infectious diseases 2016 Nov (1) 649 
• The emerging threat of pre-extensively drug-resistant tuberculosis in West Africa: preparing for large-scale tuberculosis research and drug resistance surveillance.
  Gehre Florian et al. BMC medicine 2016 Nov (1) 160 
• Analysis of worldwide sequence mutations in Zika virus proteins E, NS1, NS3 and NS5 from a structural point of view.
  Baez C F et al. Molecular bioSystems 2016 Nov
• Human Adaptation of Ebola Virus during the West African Outbreak.
  Urbanowicz Richard A et al. Cell 2016 Nov (4) 1079-1087.e5
• Ebola Virus Glycoprotein with Increased Infectivity Dominated the 2013-2016 Epidemic.
  Diehl William E et al. Cell 2016 Nov (4) 1088-1098.e6
• Screening and characterization of the non-cyp51A mutation Afcox10 conferring azole resistance in Aspergillus fumigatus.
  Wei Xiaolei et al. Antimicrobial agents and chemotherapy 2016 Oct
• Analysis of anti-malarial resistance markers in pfmdr1 and pfcrt across Southeast Asia in the Tracking Resistance to Artemisinin Collaboration.
  Srimuang Krongkan et al. Malaria journal 2016 Nov (1) 541
• Genetic markers associated with dihydroartemisinin-piperaquine failure in Plasmodium falciparum malaria in Cambodia: a genotype-phenotype association study.
  Amato Roberto et al. The Lancet. Infectious diseases 2016 Nov
• A surrogate marker of piperaquine-resistant Plasmodium falciparum malaria: a phenotype-genotype association study.
  Witkowski Benoit et al. The Lancet. Infectious diseases 2016 Nov
• Sodium Channel Mutations and Pyrethroid Resistance in Aedes aegypti.
  Du Yuzhe et al. Insects 2016 Oct (4)
• Genome Investigations of Vector Competence in Aedes aegypti to Inform Novel Arbovirus Disease Control Approaches.
  Severson David W et al. Insects 2016 Oct (4)

DETECTION / DIAGNOSIS

• Evaluation and validity of a polymerase chain reaction-based open reading frame typing method to dissect the molecular epidemiology for Acinetobacter baumannii in an epidemiologic study of a hospital outbreak.
  Fujikura Yuji et al. American journal of infection control 2016 Nov (11) e275-e278
• Identification, antimicrobial resistance and molecular characterization of the human emerging pathogen Streptococcus gallolyticus subsp. pasteurianus.
  Gherardi Giovanni et al. Diagnostic microbiology and infectious disease 2016 Dec (4) 329-335
• Molecular Epidemiology and Antimicrobial Susceptibility of Clostridium difficile Isolates from a University Teaching Hospital in China.
  Cheng Jing-Wei et al. Frontiers in microbiology 2016 1621
• The contribution of genomics to the study of Q fever.
  D'Amato Felicetta et al. Future microbiology 2016 (2) 253-72
• Highly multiplexed, ten-color detection of isoniazid, fluoroquinolone, amikacin and kanamycin resistant tuberculosis in an automated assay suitable for point-of-care use.
  Chakravorty Soumitesh et al. Journal of clinical microbiology 2016 Nov
• Detection of transrenal DNA for the diagnosis of pulmonary tuberculosis and treatment monitoring.
  Labugger Ines et al. Infection 2016 Oct
• A Pyrosequencing-Based Approach to High-Throughput Identification of Influenza A(H3N2) Virus Clades Harboring Antigenic Drift Variants.
  Mishin Vasiliy P et al. Journal of clinical microbiology 2016 Oct 
• Rapid and sensitive detection of Zika virus by reverse transcription loop-mediated isothermal amplification.
  Wang Xuan et al. Journal of virological methods 2016 Oct
• Viral Metagenomics on Blood-Feeding Arthropods as a Tool for Human Disease Surveillance.
  Brinkmann Annika et al. International journal of molecular sciences 2016 Oct (10)
• Affordable HIV drug-resistance testing for monitoring of antiretroviral therapy in sub-Saharan Africa.
  Inzaule Seth C et al. The Lancet. Infectious diseases 2016 Nov (11) e267-e275 
• Molecular detection of human parechovirus in under-Five-Year-Old Children with gastroenteritis.
  Bergallo Massimiliano et al. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2016 Oct 17-21
• Lymphatic Filariasis Elimination in American Samoa: Evaluation of Molecular Xenomonitoring as a Surveillance Tool in the Endgame.
  Lau Colleen L et al. PLoS neglected tropical diseases 2016 Nov (11) e0005108  
• Use of DNA barcoding to distinguish the malaria vector Anopheles neivai in Colombia.
  López-Rubio Andrés et al. Zootaxa 2016 Oct (4) 377-389 

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Viral respiratory infections in a nursing home: a six-month prospective study.
  Uršic Tina et al. BMC infectious diseases 2016 Nov (1) 637
• Series of Norovirus Outbreaks Caused by Consumption of Green Coral Lettuce, Denmark, April 2016.
  Müller Luise et al. PLoS currents 2016 Oct
• Rapid metagenomic next-generation sequencing during an investigation of hospital-acquired human parainfluenza virus 3 infections.
  Greninger Alexander L et al. Journal of clinical microbiology 2016 Oct 
• Investigation of the First Seven Reported Cases of Candida auris, a Globally Emerging Invasive, Multidrug-Resistant Fungus — United States, May 2013–August 2016
  Vallabhaneni S, et al. MMWR, Nov 4, 2016. 

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• From ZikV genome to vaccine: in silico approach for the epitope-based peptide vaccine against Zika virus envelope glycoprotein.
  Alam Aftab et al. Immunology 2016 Dec (4) 386-399
• Prevalence and effect of pre-treatment drug resistance on the virological response to antiretroviral treatment initiated in HIV-infected children - a EuroCoord-CHAIN-EPPICC joint project.
  Ngo-Giang-Huong Nicole et al. BMC infectious diseases 2016 Nov (1) 654 

HOST-MICROBE INTERACTIONS

• Novel tuberculosis susceptibility candidate genes revealed by the reconstruction and analysis of associative networks.
  Bragina Elena Yu et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 Oct
• Influenza Virus-Associated Fatal Acute Necrotizing Encephalopathy: Role of Nonpermissive Viral Infection?
  Mungaomklang Anek et al. Clinical medicine insights. Case reports 2016 99-102
• Molecular-level analysis of the serum antibody repertoire in young adults before and after seasonal influenza vaccination.
  Lee Jiwon et al. Nature medicine 2016 Nov
• Qualitative Parameters of the Colonic Flora in Patients with HNF1A-MODY Are Different from Those Observed in Type 2 Diabetes Mellitus.
  Mrozinska Sandra et al. Journal of diabetes research 2016 3876764
• Association of nasopharyngeal microbiota profiles with bronchiolitis severity in infants hospitalised for bronchiolitis.
  Hasegawa Kohei et al. The European respiratory journal 2016 Nov (5) 1329-1339
• Characterization of the Gastric Microbiota in a Pediatric Population According to Helicobacter pylori Status.
  Llorca Laura et al. The Pediatric infectious disease journal 2016 Nov

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.