Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Aug 2, 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

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Advanced Molecular Detection Clips Content

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

NEWS

• Foodborne Parasite Tied to Eating Raw Centipedes
  Walker M. MedPage Today, Jul 31, 2018.
• New Ebola species is reported for first time in a decade
  Branswell H. STAT, Jul 27, 2018.
• New Ebola outbreak declared in DRC a week after earlier one declared over
  Branswell H. STAT, Aug 1, 2018.

EVENTS / TRAINING / WEB RESOURCES

• Applications of Clinical Microbial Next-Generation Sequencing: Report on an American Academy of Microbiology Colloquium held in Washington, DC, in April 2015
  (online book) Am Soc Microbiol, 2017.
• Shotgun Metagenomic Detection of Pathogens: a Micro-Comic Strip
  (slide) McAdam AJ. J Clin Microbiol, Aug 2018.

CONCEPTS / COMMENTS

• A one-health approach to antimicrobial resistance.
  Walsh Timothy R et al. Nature microbiology 2018 Aug (8) 854-855
• Gaps in the Clinical Management of Influenza- A Century Since the 1918 Pandemic
  Uyeki TM, et al. JAMA, Jul 30, 2018.  
• Beyond the myths: Novel findings for old paradigms in the history of the smallpox vaccine.
  Esparza José et al. PLoS pathogens 2018 Jul (7) e1007082
• Genetically engineered mosquitoes, Zika and other arboviruses, community engagement, costs, and patents: Ethical issues.
  Meghani Zahra et al. PLoS neglected tropical diseases 2018 Jul (7) e0006501 

METHODS / TOOLS

• Nanopore-based DNA sequencing in clinical microbiology: preliminary assessment of basic requirements
  Harstad H, et al. bioRxiv, Aug 1, 2018.
• NanoPack: visualizing and processing long-read sequencing data.
  De Coster Wouter et al. Bioinformatics (Oxford, England) 2018 Aug (15) 2666-2669
• Resolving the complex Bordetella pertussis genome using barcoded nanopore sequencing
  Ring N, et al. bioRxiv, Jul 31, 2018.
• MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies.
  Robertson James et al. Microbial genomics 2018 Jul
• Geographically-stratified HIV-1 group M pol subtype and circulating recombinant form sequences.
  Rhee Soo-Yon et al. Scientific data 2018 Jul 180148
• Selection analyses of paired HIV-1 gag and gp41 sequences obtained before and after antiretroviral therapy.
  Tzou Philip L et al. Scientific data 2018 Jul 180147
• Detecting within-host interactions using genotype combination prevalence data
  Alizon S, et al. bioRxiv, Jul 30, 2018.
• Characterizing Microbiome Dynamics - Flow Cytometry Based Workflows from Pure Cultures to Natural Communities.
  Lambrecht Johannes et al. Journal of visualized experiments : JoVE 2018 07 (137)
• Recognizing the reagent microbiome.
  de Goffau Marcus C et al. Nature microbiology 2018 Aug (8) 851-853
• Digital open science-Teaching digital tools for reproducible and transparent research.
  Toelch Ulf et al. PLoS biology 2018 Jul (7) e2006022

EVOLUTION / ECOLOGY / POPULATIONS

• Characterization of the clonal subpopulation Fiocruz L1-130 of Leptospira interrogans in rats and dogs from Brazil.
  Jaeger Lauren Hubert et al. Journal of medical microbiology 2018 Jul
• Comparative genomics of Salmonella enterica serovar Montevideo reveals lineage-specific gene differences that may influence ecological niche association.
  Nguyen Scott V et al. Microbial genomics 2018 Jul 
• Loss of genomic diversity in a Neisseria meningitidis clone through a colonization bottleneck.
  Lamelas Araceli et al. Genome biology and evolution 2018 Jul
• Comparative genomics of Mycobacterium africanum Lineage 5 and Lineage 6 from Ghana suggests distinct ecological niches.
  Otchere Isaac Darko et al. Scientific reports 2018 Jul (1) 11269
• Re-emergence of H3N8 Equine Influenza A virus in Chile, 2018.
  Mena Juan et al. Transboundary and emerging diseases 2018 Jul
• Genetic evidence supports sporadic and independent introductions of subtype H5 low pathogenic avian influenza A viruses from wild birds to domestic poultry in North America.
  Li Lei et al. Journal of virology 2018 Jul
• Genetic diversity of noroviruses circulating in a pediatric cohort in Bangladesh.
  Nelson Martha I et al. The Journal of infectious diseases 2018 Jul 
• Discovery of Novel Bat Coronaviruses in South China That Use the Same Receptor as Middle East Respiratory Syndrome Coronavirus.
  Luo Chu-Ming et al. Journal of virology 2018 07 (13)
• Differing epidemiological dynamics of Chikungunya virus in the Americas during the 2014-2015 epidemic.
  Tan Yi et al. PLoS neglected tropical diseases 2018 Jul (7) e0006670
• Responses of the Human Gut Escherichia coli Population to Pathogen and Antibiotic Disturbances.
  Richter Taylor K S et al. mSystems (4)

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Occurrence of colistin-resistant hypervirulent Klebsiella variicola.
  Lu Yang et al. The Journal of antimicrobial chemotherapy 2018 Jul
• FRI-4 carbapenemase-producing Enterobacter cloacae complex isolated in Tokyo, Japan.
  Kubota Hiroaki et al. The Journal of antimicrobial chemotherapy 2018 Jul
• Linking toxin-antitoxin systems with phenotypes: A Staphylococcus aureus viewpoint.
  Sierra Roberto et al. Biochimica et biophysica acta 2018 Jul
• Antibiotic resistance plasmids and mobile genetic elements of Clostridium perfringens.
  Adams Vicki et al. Plasmid 2018 Jul
• Genomic characterization of extensively drug-resistant Acinetobacter baumannii strain, KAB03 belonging to ST451 from Korea.
  Lee Sang-Yeop et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2018 Jul
• Increasing tolerance of hospital Enterococcus faecium to handwash alcohols
  Pidot SJ, et al. Sci Transl Med, Aug 1, 2018.
• The 2011 German Enterohemorrhagic Escherichia Coli O104:H4 Outbreak-The Danger Is Still Out There.
  Kampmeier Stefanie et al. Current topics in microbiology and immunology 2018 Jul
• Alterations of Salmonella Typhimurium Antibiotic Resistance under Environmental Pressure.
  Peng Mengfei et al. Applied and environmental microbiology 2018 Jul
• Proposal for assignment of allele numbers for mobile colistin resistance (mcr) genes.
  Partridge Sally R et al. The Journal of antimicrobial chemotherapy 2018 Jul
• The S Genome Segment Is Sufficient to Maintain Pathogenicity in Intra-Clade Lassa Virus Reassortants in a Guinea Pig Model.
  Welch Stephen R et al. Frontiers in cellular and infection microbiology 2018 240 
• A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses.
  Bae Joon-Yong et al. Journal of virology 2018 07 (13)
• Evolution of protease inhibitor resistance in HIV-1-infected patients failing protease inhibitor monotherapy as second-line therapy in low-income countries: an observational analysis within the EARNEST randomised trial.
  Thompson Jennifer A et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2018 Jul

DETECTION / DIAGNOSIS

• Emerging needs and opportunities in foodborne disease detection and prevention: From tools to people.
  Hoelzer Karin et al. Food microbiology 2018 Oct 65-71
• Serotype to genotype: The changing landscape of listeriosis outbreak investigations.
  Datta Atin R et al. Food microbiology 2018 Oct 18-27
• Changing the paradigm for hospital outbreak detection by leading with genomic surveillance of nosocomial pathogens.
  Peacock Sharon J et al. Microbiology (Reading, England) 2018 Jul
• Bacterial DNA patterns identified using paired-end Illumina sequencing of 16S rRNA genes from whole blood samples of septic patients in the emergency room and intensive care unit.
  Faria Monica Martins Pereira et al. BMC microbiology 2018 Jul (1) 79
• Clinical Impact of a Rapid Streptococcal Antigen Test on Antibiotic Use in Adult Patients.
  Dodd Monique et al. Diagnostic microbiology and infectious disease 2018 Aug (4) 339-344 
• Point-Counterpoint: Active Surveillance for Carriers of Toxigenic Clostridium difficile Should Be Performed To Guide Prevention Efforts.
  McDonald L Clifford et al. Journal of clinical microbiology 2018 Aug (8)  
• Molecular characterization of Treponema pallidum subsp. pallidum in Switzerland and France with a new multilocus sequence typing scheme.
  Grillová Linda et al. PloS one 2018 (7) e0200773
• Human Immunodeficiency Virus Drug Resistance: 2018 Recommendations of the International Antiviral Society-USA Panel.
  Günthard Huldrych F et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2018 Jul
• Duration of Infectious Zika Virus in Semen and Serum.
  Medina Freddy A et al. The Journal of infectious diseases 2018 Jul 
• First case of confirmed congenital Zika syndrome in continental Africa.
  Sassetti Madalena et al. Transactions of the Royal Society of Tropical Medicine and Hygiene 2018 Jul
• Impact of a multiplex PCR point-of-care test for influenza A/B and respiratory syncytial virus on an acute pediatric hospital ward.
  Vecino-Ortiz Andres I et al. Diagnostic microbiology and infectious disease 2018 Aug (4) 331-335 
• Molecular identification and antifungal susceptibility profiles of clinical strains of Fonsecaea spp. isolated from patients with chromoblastomycosis in Rio de Janeiro, Brazil.
  Coelho Rowena Alves et al. PLoS neglected tropical diseases 2018 Jul (7) e0006675
• Malaria Surveillance - United States, 2015.
  Mace Kimberly E et al. Morbidity and mortality weekly report. Surveillance summaries (Washington, D.C. : 2002) 2018 05 (7) 1-28 
• Operational Performance of a Plasmodium falciparum Ultrasensitive Rapid Diagnostic Test for Detection of Asymptomatic Infections in Eastern Myanmar.
  Landier Jordi et al. Journal of clinical microbiology 2018 Aug (8)
• A case of Naegleria fowleri related primary amoebic meningoencephalitis in China diagnosed by next-generation sequencing.
  Wang Qiang et al. BMC infectious diseases 2018 Jul (1) 349
• Molecular xenomonitoring for Wuchereria bancrofti in Culex quinquefasciatus in two districts in Bangladesh supports transmission assessment survey findings.
  Irish Seth R et al. PLoS neglected tropical diseases 2018 Jul (7) e0006574  

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Retrospective use of whole genome sequencing to better understand an outbreak of Salmonella enterica serovar Mbandaka in New South Wales, Australia.
  Lindsay Cassia et al. Western Pacific surveillance and response journal : WPSAR (2) 20-25
• Phylogenetic patterns recover known HIV epidemiological relationships and reveal common transmission of multiple variants
  Leitner T, Romero-Severson E. Nat Microbiol, Jul 30, 2018.

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• Genome sequence analysis of a novel Bacillus thuringiensis strain BLB406 active against Aedes aegypti larvae, a novel potential bioinsecticide.
  Zribi Zghal Raida et al. International journal of biological macromolecules 2018 Sep 1153-1162

HOST-MICROBE INTERACTIONS

• Systematic detection of positive selection in the human-pathogen interactome and lasting effects on infectious disease susceptibility.
  Corona Erik et al. PloS one 2018 (5) e0196676
• The nasopharyngeal microbiota in patients with viral respiratory tract infections is enriched in bacterial pathogens.
  Edouard Sophie et al. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 2018 Jul
• Human genetic variants and age are the strongest predictors of humoral immune responses to common pathogens and vaccines.
  Scepanovic Petar et al. Genome medicine 2018 Jul (1) 59
• Sputum Detection of Predisposing Genetic Mutations in Women with Pulmonary Nontuberculous Mycobacterial Disease.
  Philley Julie V et al. Scientific reports 2018 Jul (1) 11336
• Decreased microbiome diversity in the HIV small airway epithelium.
  Xu Stella et al. Respiratory research 2018 Jul (1) 140

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.