Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Oct 18, 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

Archived Editions
Search AMD Clips database
Visit AMD website

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

• Vertical Flow Assay Being Developed to Detect Biological Threats at the Point of Need
  O'Connor L. 360dx, Oct 10, 2018.
• A Simpler Way to Get to the Bottom of Mysterious Illnesses in Poor Countries
  Yong E. Atlantic, Oct 15, 2018.
• Progress on antibiotic resistance
  (editorial) Nature, Oct 17, 2018.
• Antibiotic Resistance Monitoring Consortium Expands to Highlight Battle Against Superbugs
  Johnson M. 360dx, Oct 12, 2018.
• Researchers Uncover Three New Biomarkers of Active Tuberculosis
  GenomeWeb, Oct 12, 2018.
• Outbreaks of poliolike disease pose a puzzle
  Vogel G. Science, Oct 19, 2018.
• Real-Time Lassa Virus Genome Analysis Shows Increase in Cases Not Due to New Strain
  GenomeWeb, Oct 18, 2018.
• New York City Drinking Water Microbiome Study Reveals Variety of Bacterial Species
  Karow J. GenomeWeb, Oct 15, 2018.
• Researchers Tie Some Bloodstream Infections to the Gut Microbiome
  GenomeWeb, Oct 15, 2018.

CONCEPTS / COMMENTS

• Microbial forensics: new breakthroughs and future prospects.
  Oliveira Manuela et al. Applied microbiology and biotechnology 2018 Oct
• Why Surveillance of Antimicrobial Resistance needs to be Automated and Comprehensive.
  O'Brien Thomas F et al. Journal of global antimicrobial resistance 2018 Oct
• Extensively Drug-Resistant Typhoid - Are Conjugate Vaccines Arriving Just in Time?
  Andrews Jason R et al. The New England journal of medicine 2018 Oct (16) 1493-1495
• Is Microbiota Research Advancing Our Understanding of Infection?
  Paganelli Fernanda L et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2018 Oct

METHODS / TOOLS

• High-quality genome sequences of uncultured microbes by assembly of read clouds.
  Bishara Alex et al. Nature biotechnology 2018 Oct
• AIRR Community Standardized Representations for Annotated Immune Repertoires.
  Vander Heiden Jason Anthony et al. Frontiers in immunology 2018 2206
• Host switching pathogens, infectious outbreaks and zoonosis: A Marie Skłodowska-Curie innovative training network (HONOURs).
  van der Hoek Lia et al. Virus research 2018 Sep 120-124
• Pipeline for specific subtype amplification and drug resistance detection in hepatitis C virus.
  Soria María Eugenia et al. BMC infectious diseases 2018 Sep (1) 446

EVOLUTION / ECOLOGY / POPULATIONS

• Nonhuman primates across sub-Saharan Africa are infected with the yaws bacterium Treponema pallidum subsp. pertenue.
  Knauf Sascha et al. Emerging microbes & infections 2018 Sep (1) 157 
• Complete genome sequences of two strains of Treponema pallidum subsp. pertenue from Indonesia: Modular structure of several treponemal genes.
  Strouhal Michal et al. PLoS neglected tropical diseases 2018 Oct (10) e0006867
• Global expansion of Mycobacterium tuberculosis lineage 4 shaped by colonial migration and local adaptation
  Brynildsrud OB, et al. Science Adv, Oct 17, 2018.
• Spatial structuring of a Legionella pneumophila population within the water system of a large occupational building.
  David Sophia et al. Microbial genomics 2018 Oct
• Patterns of Mutation Within An Emerging Endemic Lineage of HEV-3a.
  Zhu Yuan O et al. Journal of viral hepatitis 2018 Oct
• Genome Sequences of Rhinovirus Genotype C56 Detected in Three Patients with Acute Respiratory Illness, California, 2016 to 2017.
  Pan Chao-Yang et al. Microbiology resource announcements 2018 (7) 
• Genetic characterization of chikungunya viruses isolated during the 2015-2017 outbreaks in different states of India, based on their E1 and E2 genes.
  Patil Jayashri et al. Archives of virology 2018 Nov (11) 3135-3140

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Discovery of mcr-1 -Mediated Colistin Resistance in a Highly Virulent Escherichia coli Lineage.
  Forde Brian M et al. mSphere 2018 Oct (5)
• Cross-sectional whole-genome sequencing and epidemiological study of multidrug-resistant Mycobacterium tuberculosis in China.
  Huang Hairong et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2018 Oct
• Multidrug-Resistant Aspergillus fumigatus Carrying Mutations Linked to Environmental Fungicide Exposure - Three States, 2010-2017.
  Beer Karlyn D et al. MMWR. Morbidity and mortality weekly report 2018 Sep (38) 1064-1067 

DETECTION / DIAGNOSIS

• A Metagenomic Approach to Evaluating Surface Water Quality in Haiti.
  Roy Monika A et al. International journal of environmental research and public health 2018 Oct (10)
• Rapid identification of pathogens from positive blood culture bottles with the MinION nanopore sequencer.
  Ashikawa Sae et al. Journal of medical microbiology 2018 Oct
• The use of broad-range bacterial PCR in the diagnosis of infectious diseases: a prospective cohort study.
  Tkadlec Jan et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2018 Oct
• Candidate Treponema pallidum biomarkers uncovered in urine from individuals with syphilis using mass spectrometry.
  Osbak Kara K et al. Future microbiology 2018 Oct
• Direct Diagnostic Tests for Lyme Disease.
  Schutzer Steven E et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2018 Oct
• Molecular point-of-care testing for chlamydia and gonorrhoea in Indigenous Australians attending remote primary health services (TTANGO): a cluster-randomised, controlled, crossover trial.
  Guy Rebecca J et al. The Lancet. Infectious diseases 2018 Oct (10) 1117-1126
• An Outbreak of Human Parvovirus B19 Hidden by Dengue Fever.
  Di Paola Nicholas et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2018 Oct
• Screening for Zika virus RNA in sera of suspected cases: a retrospective cross-sectional study.
  Sacchetto Lívia et al. Virology journal 2018 Oct (1) 155
• Characterization of real-time microarrays for simultaneous detection of HIV-1, HIV-2, and hepatitis viruses.
  Granade Timothy C et al. Journal of virological methods 2018 09 60-65 

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Reinfection with Streptococcus suis analysed by whole genome sequencing.
  Willemse Niels et al. Zoonoses and public health 2018 Oct
• Within-host Mycobacterium tuberculosis diversity and its utility for inferences of transmission.
  Martin Michael A et al. Microbial genomics 2018 Sep
• Pre Treatment HIV-1 Drug Resistance In Transmission Clusters Of The Cologne-Bonn Region, Germany.
  Stecher Melanie et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2018 Oct
• Surveillance of transmitted HIV-1 antiretroviral drug resistance in the context of decentralized HIV care in Senegal and the Ebola outbreak in Guinea.
  Mbange Aristid Ekollo et al. BMC research notes 2018 Oct (1) 723
• Genomic Analysis of Lassa Virus during an Increase in Cases in Nigeria in 2018.
  Siddle Katherine J et al. The New England journal of medicine 2018 Oct

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• Impact of next generation sequencing defined HIV pre-treatment drug resistance on virological outcomes in the ANRS 12249 treatment as prevention trial.
  Derache Anne et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2018 Oct

HOST-MICROBE INTERACTIONS

• Gut microbiome can be restored without adverse events after Helicobacter pylori eradication therapy in teenagers.
  Gotoda Takuji et al. Helicobacter 2018 Oct e12541
• Diversity of vaginal microbiota in sub-Saharan Africa and its effects on HIV transmission and prevention.
  Bayigga Lois et al. American journal of obstetrics and gynecology 2018 Oct
• Deconvolution of pro- and antiviral genomic responses in Zika virus-infected and bystander macrophages.
  Carlin Aaron F et al. Proceedings of the National Academy of Sciences of the United States of America 2018 09 (39) E9172-E9181

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.

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB