Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Aug 1, 2019

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

• NIH-funded project aims to build a "Google" for biomedical data
  Hailu R. STAT, Jul 31, 2019.
• MIT Researchers Developing Amplification-Free 'Massively Parallel' Microfluidic Testing Platform
  O'Connor L. GenomeWeb, Jul 31, 2019.
• UK Researchers Developing Blood-Based TB DNA Test, Eyeing Broader Screening
  O'Connor L. GenomeWeb, Jul 25, 2019.
• Alarming surge in drug-resistant HIV uncovered
  Mega ER. Nature, Jul 30, 2019.
• "Mosaic" HIV vaccine to be tested in thousands of people across the world
  Mega ER. Nature, Jul 31, 2019.
• Alarming surge in drug-resistant HIV uncovered
  Mega ER. Nature, Jul 30, 2019.
• Placental microbiome's existence challenged
  Olena A. The Scientist, Jul 31, 2019.

CONCEPTS / COMMENTS

• Julia: come for the syntax, stay for the speed
  Perkel JM. Nature, Jul 30, 2019.
• Three pitfalls to avoid in machine learning
  Riley P. Nature, Jul 30, 2019.
• The 1918 influenza pandemic: 100 years of questions answered and unanswered.
  Taubenberger Jeffery K et al. Science translational medicine 2019 Jul (502)
• Considerations in the deployment of novel universal vaccines against epidemic and pandemic influenza
  Arinaminpathy N, et al. medRxiv, Jul 29, 2019.

METHODS / TOOLS

• Benchmarking of alignment-free sequence comparison methods.
  Zielezinski Andrzej et al. Genome biology 2019 Jul (1) 144
• Universal amplification-free molecular diagnostics by billion-fold hierarchical nanofluidic concentration.
  Ouyang Wei et al. Proceedings of the National Academy of Sciences of the United States of America 2019 Jul
• Targeted metagenomic sequencing enhances the identification of pathogens associated with acute infection 
  Goh C, et al. bioRxiv, Jul 28, 2019.
• Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks.
  Rule Adam et al. PLoS computational biology 2019 Jul (7) e1007007

EVOLUTION / ECOLOGY / POPULATIONS

• Molecular epidemiology and intercontinental spread of cholera.
  Mutreja Ankur et al. Vaccine 2019 Jul
• Draft Genome Sequences of Antimicrobial-Resistant Shigella Clinical Isolates from Pakistan.
  Lomonaco Sara et al. Microbiology resource announcements 2019 Jul (30) 
• The speciation and hybridization history of the genus Salmonella.
  Criscuolo Alexis et al. Microbial genomics 2019 Jul
• Phylogenetic measures of indel rate variation among the HIV-1 group M subtypes.
  Palmer John et al. Virus evolution 2019 Jul (2) vez022
• Inter- and intra-lineage genetic diversity of wild-type Zika viruses reveals both common and distinctive nucleotide variants and clusters of genomic diversity.
  Collins Natalie D et al. Emerging microbes & infections 2019 (1) 1126-1138
• Near full genome characterization of HIV-1 unique recombinant forms in Cameroon reveals dominant CRF02_AG and F2 recombination patterns.
  Banin Andrew N et al. Journal of the International AIDS Society 2019 Jul (7) e25362
• Multiple introductions of dengue virus strains contribute to dengue outbreaks in East Kalimantan, Indonesia, in 2015-2016.
  Sasmono R Tedjo et al. Virology journal 2019 Jul (1) 93
• Introduction and Dispersal of Sindbis Virus from Central Africa to Europe.
  Ling Jiaxin et al. Journal of virology 2019 Aug (16)
• Reconstruction of the spatial and temporal dynamics of hepatitis B virus genotype D in the Americas.
  Spitz Natália et al. PloS one 2019 (7) e0220342
• Potential Fifth Clade of Candida auris, Iran, 2018.
  Chow Nancy A et al. Emerging infectious diseases 2019 Sep (9) 
• Diverse origin of Plasmodium falciparum in northwest Ecuador.
  Vera-Arias Claudia A et al. Malaria journal 2019 Jul (1) 251
• Genetic diversity and population structure of Glossina morsitans morsitans in the active foci of human African trypanosomiasis in Zambia and Malawi.
  Nakamura Yukiko et al. PLoS neglected tropical diseases 2019 Jul (7) e0007568

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Helicobacter pylori Mutations Conferring Resistance to Fluoroquinolones and Clarithromycin among Dyspeptic Patients Attending a Tertiary Hospital, Tanzania.
  Jaka Hyasinta et al. Canadian journal of gastroenterology & hepatology 2019 8481375
• Investigating colistin drug resistance: The role of high-throughput sequencing and bioinformatics.
  Aruhomukama Dickson et al. F1000Research 2019 150
• Genotypic and Phenotypic Characterization of Antimicrobial Resistance in Neisseria gonorrhoeae: a Cross-Sectional Study of Isolates Recovered from Routine Urine Cultures in a High-Incidence Setting.
  Bailey Adam L et al. mSphere 2019 Jul (4)
• The impact of antimicrobials on gonococcal evolution.
  Sánchez-Busó Leonor et al. Nature microbiology 2019 Jul
• Withdraw of prophylactic antimicrobials does not change the pigs' resistome
  Fernanda LV, et al. bioRxiv, Jul 26, 2019. 
• Deciphering drug resistance in Mycobacterium tuberculosis using whole-genome sequencing: progress, promise, and challenges.
  Cohen Keira A et al. Genome medicine 2019 Jul (1) 45
• Determinants of dihydroartemisinin-piperaquine treatment failure in Plasmodium falciparum malaria in Cambodia, Thailand, and Vietnam: a prospective clinical, pharmacological, and genetic study.
  van der Pluijm Rob W et al. The Lancet. Infectious diseases 2019 Jul
• Evolution and expansion of multidrug-resistant malaria in southeast Asia: a genomic epidemiology study.
  Hamilton William L et al. The Lancet. Infectious diseases 2019 Jul
• Whole-genome sequencing reveals high complexity of copy number variation at insecticide resistance loci in malaria mosquitoes.
  Lucas Eric R et al. Genome research 2019 Jul

DETECTION / DIAGNOSIS

• Evaluation of empiric beta-lactam susceptibility prediction among Enterobacteriaceae by molecular beta-lactamase gene testing.
  Spafford Kyle et al. Journal of clinical microbiology 2019 Jul 
• Tracking carbapenemase-producing bacteria by molecular typing: Population diversity and sampling pitfall.
  Baranovsky Sophie et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2018 11 104-106
• Application of high-throughput 16S rRNA sequencing to identify fecal contamination sources and to complement the detection of fecal indicator bacteria in rural groundwater.
  Naphtali Paul et al. Journal of water and health 2019 Jun (3) 393-403
• Matrix-Assisted Laser Desorption-Ionization Time-of-Flight mass spectrometry using a custom-made database, biomarker assignment or mathematical classifiers does not differentiate Shigella spp. and Escherichia coli
  van den Beld MJ. bioRxiv, Jul 25, 2019.
• Molecular identification and phylogenetic relationships of clinical Nocardia isolates.
  Wei Ming et al. Antonie van Leeuwenhoek 2019 Jul
• Missed detections of influenza A(H1)pdm09 by real-time RT-PCR assay due to haemagglutinin sequence mutation, December 2017 to March 2018, northern Viet Nam.
  Hoang Vu Mai Phuong et al. Western Pacific surveillance and response journal : WPSAR (1) 32-38
• No evidence of Zika, dengue, or chikungunya virus infection in field-caught mosquitoes from the Recife Metropolitan Region, Brazil, 2015.
  Ramesh Anita et al. Wellcome open research 2019 93
• Candida auris in a U.S. Patient with Carbapenemase-Producing Organisms and Recent Hospitalization in Kenya
  Brooks RB, et al. MMWR, Aug 2, 2019.  
• Proof of concept: used malaria rapid diagnostic tests applied for parallel sequencing for surveillance of molecular markers of anti-malarial resistance in Bissau, Guinea-Bissau during 2014-2017.
  Nag Sidsel et al. Malaria journal 2019 Jul (1) 252 

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Epidemic of carbapenem-resistant Klebsiella pneumoniae in Europe is driven by nosocomial spread.
  David Sophia et al. Nature microbiology 2019 Jul
• Multistate Outbreak of Listeriosis Associated with Packaged Leafy Green Salads, United States and Canada, 2015-2016.
  Self Julie L et al. Emerging infectious diseases 2019 08 (8) 1461-1468  
• Social mixing and clinical features linked with transmission in a network of extensively drug-resistant (XDR) tuberculosis cases in KwaZulu-Natal, South Africa.
  Nelson Kristin N et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2019 Jul 
• Whole genome sequencing for improved understanding of Mycobacterium tuberculosis transmission in a remote circumpolar region.
  Guthrie J L et al. Epidemiology and infection 2019 Jan e188
• Molecular Epidemiology of an Outbreak of Human Parainfluenza Virus 3 Among Oncology Patients.
  Bailey Emily S et al. The Journal of hospital infection 2019 Jul 
• Transmission Dynamics of HIV Subtype A in Tel Aviv, Israel: Implications for HIV Spread and Eradication.
  Grossman Zehava et al. Open forum infectious diseases 2019 Jul (7)

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• Viral gene drive in herpesviruses
  Walter M, Verdin E. bioRxiv, Jul 30, 2019.

HOST-MICROBE INTERACTIONS

• Repertoire of human breast and milk microbiota: a systematic review.
  Togo Amadou et al. Future microbiology 2019 05 623-641
• Human placenta has no microbiome but can contain potential pathogens
  de Goffau MC, et al. Nature, Jul 31, 2019.
• Microbiome evolution during host aging.
  Aleman Francisco Daniel Davila et al. PLoS pathogens 2019 Jul (7) e1007727
• No Evidence for Role of Cutavirus in Malignant Melanoma.
  Wieland Ulrike et al. Emerging infectious diseases 2019 08 (8) 1600-16002
• Genetic mutations in NF-κB pathway genes were associated with the protection from hepatitis C virus infection among Chinese Han population.
  Yue Ming et al. Scientific reports 2019 Jul (1) 10830
• RWHMDA: Random Walk on Hypergraph for Microbe-Disease Association Prediction.
  Niu Ya-Wei et al. Frontiers in microbiology 2019 1578

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.