Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Jun 20, 2019

Advanced Molecular Detection Clips Content

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

NEWS

• Colistin-resistance gene MCR-3.1 makes US appearance
  Roos R. CIDRAP, Jun 14, 2019.
• New evidence points to possible cause of puzzling paralysis in kids
  Fox M. STAT, Jun 14, 2019.
• The secret social lives of viruses
  Dolgin E. Nature, Jun 18, 2019.
• Rotavirus Vaccine May Help Protect Against Type 1 Diabetes
  Bakalar N. New York Times, Jun 19, 2019.
• Why some people don’t respond to childhood vaccines -- and how our DNA could fix it
  Akpan N. PBS, Jun 17, 2019.
• FDA Suspends Clinical Trials Involving Fecal Transplants
  Hou CY. The Scientist, Jun 14, 2019.

CONCEPTS / COMMENTS

• Top 10 Statistics Mistakes Made by Data Scientists
  (blog post) Niemer N. Towards Data Science, Jun 17, 2019.
• Selective killing of antibiotic-resistant bacteria from within
  Sanna Koskiniemi & Koskiniemi S, Virtanen P. Nature, Jun 17, 2019.
• Sepsis in the era of data-driven medicine: personalizing risks, diagnoses, treatments and prognoses.
  Liu Andrew C et al. Briefings in bioinformatics 2019 Jun
• Harness microbes for humanity's future
  (editorial) Nature, Jun 18, 2019.

METHODS / TOOLS

• Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues.
  Meehan Conor J et al. Nature reviews. Microbiology 2019 Jun
• HumanMycobiomeScan: a new bioinformatics tool for the characterization of the fungal fraction in metagenomic samples.
  Soverini Matteo et al. BMC genomics 2019 Jun (1) 496
• Natural history, dynamics, and ecology of human papillomaviruses in genital infections of young women: protocol of the PAPCLEAR cohort study.
  Murall Carmen Lía et al. BMJ open 2019 Jun (6) e025129

EVOLUTION / ECOLOGY / POPULATIONS

• Global Extraintestinal Pathogenic Escherichia coli (ExPEC) Lineages.
  Manges Amee R et al. Clinical microbiology reviews 2019 Jun (3)
• Emergent Invasive Group A Streptococcus dysgalactiae subsp. Equisimilis, United States, 2015-2018.
  Chochua Sopio et al. Emerging infectious diseases 2019 Aug (8) 
• Identification of positively selected genes in human pathogenic treponemes: Syphilis-, yaws-, and bejel-causing strains differ in sets of genes showing adaptive evolution.
  Maderánková Denisa et al. PLoS neglected tropical diseases 2019 Jun (6) e0007463
• Molecular Identification of Transmitted/Founder Hepatitis C Viruses and Their Progeny by Single Genome Sequencing.
  Li Hui et al. Methods in molecular biology (Clifton, N.J.) 2019 139-155
• Population Genomics of GII.4 Noroviruses Reveal Complex Diversification and New Antigenic Sites Involved in the Emergence of Pandemic Strains
  Tohma K, et al. bioRxiv, Jun 12, 2019.
• Re-introduction of dengue virus serotype 2 in the State of Rio de Janeiro after almost a decade of epidemiological silence
  Torres MC, et al. bioRxiv, Jun 5, 2019.
• Characterization of New Recombinant Forms of HIV-1 From the Comunitat Valenciana (Spain) by Phylogenetic Incongruence.
  Beamud Beatriz et al. Frontiers in microbiology 2019 1006
• HIV diversity and genetic compartmentalization in blood and testes during suppressive antiretroviral therapy.
  Miller Rachel L et al. Journal of virology 2019 Jun
• Phylogeography, phylodynamics, and the recent outbreak of lineage 3 porcine reproductive and respiratory syndrome (PRRS) viruses in China.
  Sun Yan-Kuo et al. Transboundary and emerging diseases 2019 Jun
• Three phylogenetic groups have driven the recent population expansion of Cryptococcus neoformans.
  Ashton P M et al. Nature communications 2019 05 (1) 2035

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Phylogenomic analysis of Clostridium perfringens identifies isogenic strains in gastroenteritis outbreaks, and novel virulence-related features
  Kiu R, et al. bioRxiv, Jun 13, 2019.
• Comparative genomic analyses reveal diverse virulence factors and antimicrobial resistance mechanisms in clinical Elizabethkingia meningoseptica strains
  Chen S, et al. bioRxiv, Jun 13, 2019.
• Genomic and phenotypic comparison of environmental and patient-derived isolates of Pseudomonas aeruginosa suggest that antimicrobial resistance is rare within the environment
  Ramsay KA, et al. bioRxiv, Jun 7, 2019.
• Nationwide Stepwise Emergence and Evolution of Multidrug-Resistant Campylobacter jejuni Sequence Type 5136, United Kingdom 
  Lopes BS, et al. Emerg Infect Dis, Jul 2019.
• Microbiome and Antimicrobial Resistance Gene Dynamics in International Travelers 
  Langelier C, et al. Emerg Infect Dis, Jul 2019.
• Detection of VIM-1-Producing Enterobacter cloacae and Salmonella enterica Serovars Infantis and Goldcoast at a Breeding Pig Farm in Germany in 2017 and Their Molecular Relationship to Former VIM-1-Producing S. Infantis Isolates in German Livestock Production.
  Roschanski Nicole et al. mSphere 2019 Jun (3)
• Systematic analysis of supervised machine learning as an effective approach to predicate β-lactam resistance phenotype in Streptococcus pneumoniae.
  Zhang Chaodong et al. Briefings in bioinformatics 2019 Jun
• Overview of Direct-Acting Antiviral Drugs and Drug Resistance of Hepatitis C Virus.
  Li Darrick K et al. Methods in molecular biology (Clifton, N.J.) 2019 3-32
• A barcode of multilocus nuclear DNA identifies genetic relatedness in pre- and post-Artemether/Lumefantrine treated Plasmodium falciparum in Nigeria.
  Oyebola Kolapo Muyiwa et al. BMC infectious diseases 2018 08 (1) 392 
• African isolates show a high proportion of multiple copies of the Plasmodium falciparum plasmepsin-2 gene, a piperaquine resistance marker.
  Leroy Didier et al. Malaria journal 2019 Apr (1) 126

DETECTION / DIAGNOSIS

• Review of molecular subtyping methodologies used to investigate outbreaks due to multidrug-resistant enteric bacterial pathogens in sub-Saharan Africa.
  Smith Anthony M et al. African journal of laboratory medicine 2019 (1) 760 
• Rapid identification of unknown pathogens in environmental samples using a high-throughput sequencing-based approach.
  Israeli Ofir et al. Heliyon 2019 May (5) e01793
• Development of a loop-mediated isothermal amplification assay for rapid Helicobacter pylori detection.
  Horiuchi Saori et al. Journal of microbiological methods 2019 Jun 105653
• Use of Whole-Genome Sequencing for Food Safety and Public Health in the United States.
  Brown Eric et al. Foodborne pathogens and disease 2019 Jun  
• Evaluation of 16S next-generation sequencing of hypervariable region 4 in wastewater samples: An unsuitable approach for bacterial enteric pathogen identification.
  Greay Telleasha L et al. The Science of the total environment 2019 Jun 1111-1124
• Concise whole blood transcriptional signatures for incipient tuberculosis: A systematic review and patient-level pooled meta-analysis
  Gupta RK, et al. bioRxiv, Jun 13, 2019. 
• Serological and metagenomic interrogation of cerebrospinal fluid implicates enteroviruses in pediatric acute flaccid myelitis
  Schubert RD, et al. bioRxiv, Jun 10, 2019.
• A nanoelectronics-blood-based diagnostic biomarker for myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS).
  Esfandyarpour R et al. Proceedings of the National Academy of Sciences of the United States of America 2019 May (21) 10250-10257
• A PCR-based NGS protocol for whole genome sequencing of West Nile virus lineage 2 directly from biological specimens.
  Chaintoutis Serafeim C et al. Molecular and cellular probes 2019 Jun
• Improving care for pregnant women with suspected influenza: A retrospective study before and after introduction of a rapid molecular assay.
  Anselem Olivia et al. PloS one 2019 (6) e0217651 
• Development of a Direct-Reverse Transcription-Quantitative PCR (dirRT-qPCR) assay for Clinical Zika Diagnosis.
  Li Lang et al. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2019 Jun
• Detection of norovirus epidemic genotypes in raw sewage using next generation sequencing.
  Fumian Tulio M et al. Environment international 2019 02 282-291 
• Giardia lamblia miRNAs as a new diagnostic tool for human giardiasis.
  Meningher Tal et al. PLoS neglected tropical diseases 2019 Jun (6) e0007398
• Mitochondrial Junction Region as Genotyping Marker for Cyclospora cayetanensis.
  Nascimento Fernanda S et al. Emerging infectious diseases 2019 Jul (7) 1314-1319 
• Genotyping Genetically Heterogeneous Cyclospora cayetanensis Infections to Complement Epidemiological Case Linkage.
  Barratt Joel L N et al. Parasitology 2019 May 1-33 
• The Advances in Molecular and New Point-of-Care (POC) Diagnosis of Schistosomiasis Pre- and Post-praziquantel Use: In the Pursuit of More Reliable Approaches for Low Endemic and Non-endemic Areas.
  Cavalcanti Marta G et al. Frontiers in immunology 2019 858 

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Sepsis Attributed to Bacterial Contamination of Platelets Associated with a Potential Common Source - Multiple States, 2018.
  Jones Sydney A et al. MMWR. Morbidity and mortality weekly report 2019 Jun (23) 519-523  
• Whole Genome Sequencing Based Surveillance of L. monocytogenes for Early Detection and Investigations of Listeriosis Outbreaks.
  Pietzka Ariane et al. Frontiers in public health 2019 139
• Cross-border outbreak of Yersinia enterocolitica O3 associated with imported fresh spinach, Sweden and Denmark, March 2019.
  Espenhain Laura et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2019 Jun (24)
• Hepatitis A outbreak affecting men who have sex with men (MSM) in central Argentina, occurred in July 2017-April 2018, later than the European outbreak.
  Mariojoules Jorge et al. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2019 May 49-53 
• Epidemiology of Human Parechovirus Type 3 Upsurge in 2 Hospitals, Freiburg, Germany, 2018.
  Elling Roland et al. Emerging infectious diseases 2019 Jul (7) 1384-1388

HOST-MICROBE INTERACTIONS

• Long-term impact of fecal transplantation in healthy volunteers
  Goloshchapov OV, et al. bioRxiv, Jun 14, 2019.
• Common Genetic Variations Associated with the Persistence of Immunity following Childhood Immunization.
  O'Connor Daniel et al. Cell reports 2019 Jun (11) 3241-3253.e4
• Genome sequencing analysis identifies Epstein-Barr virus subtypes associated with high risk of nasopharyngeal carcinoma.
  Xu Miao et al. Nature genetics 2019 Jun
• Farm-like indoor microbiota in non-farm homes protects children from asthma development.
  Kirjavainen Pirkka V et al. Nature medicine 2019 Jun

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.