Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Jan 2, 2020

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

• Rumours fly about changes to US government open-access policy
  Subbaraman N. Nature, Dec 20, 2020.
• Study pushes emergence of measles back to antiquity
  Kupferschmidt K. Science, Jan 3, 2020
• Drilling down in the fight against bacterial superbugs
  McCain ML. Sci Transl Med, Jan 1, 2020.
• Malaria-carrying mosquitoes get a leg up on insecticides
  Catteruccia F. Nature, Dec 25, 2020.
• NIH Awards $102.5M for Antibacterial Resistance Research, Dx Development
  Han AP. 360dx, Dec 13, 2019.
• Blood-Based Sequencing Test Identifies Pediatric Cancer Infections Before Symptoms
  360dx, Dec 19, 2019.
• Nanopore Sequencing Shows Promise for Rapid Diagnosis of Gut Condition in Preterm Infants
  Karow J. 360dx, Dec 16, 2019.
• No answers yet in China's pneumonia outbreak
  Schnirring L. CIDRAP, Jan 2, 2020.

EVENTS / TRAINING / WEB RESOURCES

• U.S. Investments in Medical and Health Research and Development, 2013 - 2018
  Research!America, Fall 2019.

CONCEPTS / COMMENTS

• Pathogen Genomics in Public Health.
  Armstrong Gregory L et al. The New England journal of medicine 2019 Dec (26) 2569-2580  
• The power and limitations of genomic surveillance of bacteria.
  González-Candelas Fernando et al. Future microbiology 2019 Nov 1345-1348
• Contaminations in (meta)genome data: An open issue for the scientific community.
  De Simone Giovanna et al. IUBMB life 2019 Dec
• Molecular Imaging of Infection: The First 50 Years.
  Palestro Christopher J et al. Seminars in nuclear medicine 2020 Jan (1) 23-34
• The Joint Mobile Emerging Disease Clinical Capability (JMEDICC) laboratory approach: Capabilities for high-consequence pathogen clinical research.
  Naluyima Prossy et al. PLoS neglected tropical diseases 2019 Dec (12) e0007787
• Uncovering the ART of antimalarial resistance
  Marapana D, Cowman AF. Science, Jan 3, 2020.

METHODS / TOOLS

• Benchmarking immunoinformatic tools for the analysis of antibody repertoire sequences.
  Smakaj Erand et al. Bioinformatics (Oxford, England) 2019 Dec
• Optimizing DNA extraction methods for Nanopore sequencing of Neisseria gonorrhoeae direct from urine samples.
  Street Teresa L et al. Journal of clinical microbiology 2019 Dec
• Infectious Disease Metagenomics: Error Mitigation and Best Practices for the Clinical Routine Use of Metagenomic Sequencing.
  Hasan Nur A et al. Journal of biomolecular techniques : JBT 2019 Dec (Suppl) S22-S23 
• Cost effective, experimentally robust differential-expression analysis for human/mammalian, pathogen and dual-species transcriptomics.
  Shetty Amol C et al. Microbial genomics 2019 Dec
• BacPipe: A Rapid, User-Friendly Whole-Genome Sequencing Pipeline for Clinical Diagnostic Bacteriology.
  Xavier Basil B et al. iScience 2019 Dec (1) 100769
• Retrospective Validation of a Metagenomic Sequencing Protocol for Combined Detection of RNA and DNA Viruses Using Respiratory Samples from Pediatric Patients.
  van Boheemen Sander et al. The Journal of molecular diagnostics : JMD 2019 Dec
• Molecular sampling at logarithmic rates for next-generation sequencing.
  Horn Caroline et al. PLoS computational biology 2019 Dec (12) e1007537
• FDA-ARGOS is a database with public quality-controlled reference genomes for diagnostic use and regulatory science.
  Sichtig Heike et al. Nature communications 2019 07 (1) 3313 
• The COMPARE Data Hubs.
  Amid Clara et al. Database : the journal of biological databases and curation 2019 Jan 
• The ability of single genes vs full genomes to resolve time and space in outbreak analysis.
  Dudas Gytis et al. BMC evolutionary biology 2019 Dec (1) 232

EVOLUTION / ECOLOGY / POPULATIONS

• Phylogenomic structure of Bacillus anthracis isolates in the Northern Cape Province, South Africa revealed novel single nucleotide polymorphisms.
  Lekota Kgaugelo Edward et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2019 Dec 104146
• Genomic insights into Vibrio cholerae O1 responsible for cholera epidemics in Tanzania between 1993 and 2017.
  Hounmanou Yaovi Mahuton Gildas et al. PLoS neglected tropical diseases 2019 Dec (12) e0007934
• Pan-genome diversification and recombination in Cronobacter sakazakii, an opportunistic pathogen in neonates, and insights to its xerotolerant lifestyle.
  Lee Isaiah Paolo A et al. BMC microbiology 2019 Dec (1) 306
• Francisella opportunistica sp. nov., isolated from human blood and cerebrospinal fluid.
  Dietrich Elizabeth A et al. International journal of systematic and evolutionary microbiology 2019 Dec 
• Invasive Nontypeable Haemophilus influenzae Infection Among Adults With HIV in Metropolitan Atlanta, Georgia, 2008-2018.
  Collins Lauren F et al. JAMA 2019 12 (24) 2399-2410 
• Genomic Features of Rickettsia heilongjiangensis Revealed by Intraspecies Comparison and Detailed Comparison With Rickettsia japonica .
  Kasama Kentaro et al. Frontiers in microbiology 2019 2787
• Zika Virus Surveillance at the Human-Animal Interface in West-Central Brazil, 2017-2018.
  Pauvolid-Corrêa Alex et al. Viruses 2019 Dec (12)  
• Re-evaluation of the evolution of influenza H1 viruses using direct PCA.
  Konishi Tomokazu et al. Scientific reports 2019 Dec (1) 19287
• The history of measles: from a 1912 genome to an antique origin
  Dux A, et al. bioRxiv, Dec 30, 2019.
• Divergent evolutionary trajectories of influenza B viruses underlie their contemporaneous epidemic activity.
  Virk Ramandeep K et al. Proceedings of the National Academy of Sciences of the United States of America 2019 Dec
• Molecular evidence of Babesia in pet cats in mainland China.
  Zhang Xue-Lian et al. BMC veterinary research 2019 Dec (1) 476
• Genetic diversity of laboratory strains and implications for research: The case of Aedes aegypti.
  Gloria-Soria Andrea et al. PLoS neglected tropical diseases 2019 Dec (12) e0007930 
• Host dispersal shapes the population structure of a tick-borne bacterial pathogen.
  Norte Ana Cláudia et al. Molecular ecology 2019 Dec

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Genomic analysis of carbapenemase-producing Enterobacteriaceae in Queensland reveals widespread transmission of bla IMP-4 on an IncHI2 plasmid.
  Roberts Leah W et al. Microbial genomics 2019 Dec
• Emergence and Evolution of High-Level Cephalosporin-Resistant Salmonella Goldcoast in Northern Taiwan.
  Feng Ye et al. Open forum infectious diseases 2019 Dec (12) ofz447
• Identification and Characterization of Shigella with Decreased Susceptibility to Azithromycin in the United States, 2005 to 2014.
  Campbell Davina et al. Journal of global antimicrobial resistance 2019 Dec 
• Molecular surveillance of carbapenemase-producing Pseudomonas aeruginosa at three medical centres in Cologne, Germany.
  Schäfer Elena et al. Antimicrobial resistance and infection control 2019 208
• Biochemistry and computer generated graph comparison of the structural and nonstructural proteins of spanish-1918 Influenza, pandemic-2009, and bird flu viruses.
  Mahardika Gusti Ngurah et al. Acta biochimica Polonica 2019 Jul (3) 329-336
• Deep-sequencing reveals broad subtype-specific HCV resistance mutations associated with treatment failure.
  Chen Qian et al. Antiviral research 2019 Dec 104694
• Comparative Genomics for the Elucidation of Multidrug Resistance in Candida lusitaniae.
  Kannan Abhilash et al. mBio 2019 Dec (6)
• Cotrimoxazole prophylaxis increases resistance gene prevalence and α-diversity but decreases β-diversity in the gut microbiome of HIV-exposed, uninfected infants.
  D'Souza Alaric W et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2019 Dec

DETECTION / DIAGNOSIS

• Molecular Detection of Biological Agents in the Field: Then and Now.
  Yeh Kenneth B et al. mSphere 2019 Dec (6) 
• Accurate Detection of the Four Most Prevalent Carbapenemases in E. coli and K. pneumoniae by High-Resolution Mass Spectrometry.
  Foudraine Dimard E et al. Frontiers in microbiology 2019 2760
• One System for All: Is Mass Spectrometry a Future Alternative for Conventional Antibiotic Susceptibility Testing?
  Welker Martin et al. Frontiers in microbiology 2019 2711
• Antimicrobial resistance genetic factor identification from whole-genome sequence data using deep feature selection.
  Shi Jinhong et al. BMC bioinformatics 2019 Dec (Suppl 15) 535
• Detection of Antimicrobial Resistance Using Proteomics and the Comprehensive Antibiotic Resistance Database: a Case Study.
  Chen Chih-Yu et al. Proteomics. Clinical applications 2019 Dec e1800182
• Molecular typing of Campylobacter jejuni strains: comparison among four different techniques.
  Frazão Miliane Rodrigues et al. Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] 2019 Dec
• Equations to predict antimicrobial minimum inhibitory concentrations in Neisseria gonorrhoeae using molecular antimicrobial resistance determinants.
  Demczuk Walter et al. Antimicrobial agents and chemotherapy 2019 Dec
• Evaluation of the Results of Group B Streptococcus Screening by MALDI-TOF MS among Pregnant Women in a Hungarian Hospital.
  Ábrók Marianna et al. Pathogens (Basel, Switzerland) 2019 Dec (1) 
• Comparative assessment of the performance and accuracy of four open-source tools for in silico serotyping of Salmonella spp. based on whole-genome short read sequencing data.
  Uelze Laura et al. Applied and environmental microbiology 2019 Dec 
• Introduction of NGS in Environmental Surveillance for Healthcare-Associated Infection Control.
  Comar Manola et al. Microorganisms 2019 Dec (12)
• An improved simple method for the identification of Mycobacteria by MALDI-TOF MS (Matrix-Assisted Laser Desorption- Ionization mass spectrometry).
  Alcolea-Medina Adela et al. Scientific reports 2019 Dec (1) 20216
• An optimized genomic VCF workflow for precise identification of Mycobacterium tuberculosis cluster from cross-platform whole genome sequencing data.
  Disratthakit Areeya et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2019 Dec 104152
• Assessment of a metabarcoding approach for the characterisation of vector-borne bacteria in canines from Bangkok, Thailand.
  Huggins Lucas G et al. Parasites & vectors 2019 Aug (1) 394
• Unbiased Metagenomic Sequencing for Pediatric Meningitis in Bangladesh Reveals Neuroinvasive Chikungunya Virus Outbreak and Other Unrealized Pathogens.
  Saha Senjuti et al. mBio 2019 12 (6)
• Toscana, West Nile, Usutu and tick-borne encephalitis viruses: external quality assessment for molecular detection of emerging neurotropic viruses in Europe, 2017.
  Reusken Chantal et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2019 Dec (50) 
• A rapid and label-free platform for virus capture and identification from clinical samples.
  Yeh Yin-Ting et al. Proceedings of the National Academy of Sciences of the United States of America 2019 Dec
• Loop-Mediated Isothermal Amplification (LAMP) for the Diagnosis of Zika Virus: A Review.
  Silva Severino Jefferson Ribeiro da et al. Viruses 2019 Dec (1)
• Use of TaqMan Array card for the detection of respiratory viral pathogens in children under 5 years old hospitalised with acute medical illness in Ballabgarh, Haryana, India.
  Gaur Bharti et al. Indian journal of medical microbiology (1) 105-108 
• A European multi-centre evaluation of detection and typing methods for human enteroviruses and parechoviruses using RNA transcripts.
  Hayes A et al. Journal of medical virology 2019 Dec 
• Laboratory Analysis of an Outbreak of Candida auris in New York from 2016 to 2018-Impact and Lessons Learned.
  Zhu YanChun et al. Journal of clinical microbiology 2019 Dec  
• Molecular Surveillance for Polymorphisms Associated with artemisinin-based combination therapie Resistance in Plasmodium falciparum Isolates Collected in the State of Roraima, Brazil.
  Lucchi Naomi W et al. The American journal of tropical medicine and hygiene 2019 Dec  
• Sero-identification of the aetiologies of human malaria exposure (Plasmodium spp.) in the Limu Kossa District of Jimma Zone, South western Ethiopia.
  Feleke Sindew Mekasha et al. Malaria journal 2019 Aug (1) 292  
• Genomes of Leishmania parasites directly sequenced from patients with visceral leishmaniasis in the Indian subcontinent.
  Domagalska Malgorzata A et al. PLoS neglected tropical diseases 2019 Dec (12) e0007900

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Serratia marcescens in the neonatal intensive care unit: A cluster investigation using molecular methods.
  Yeo Kee T et al. Journal of infection and public health 2019 Dec 
• Case report: whole genome sequencing based investigation of maternal-neonatal listeriosis in Sichuan, China.
  Luo Lijuan et al. BMC infectious diseases 2019 Oct (1) 893
• Transmission Network of Deer-Borne Mycobacterium bovis Infection Revealed by a WGS Approach.
  Michelet Lorraine et al. Microorganisms 2019 Dec (12)
• Bloodstream Infections with a Novel Nontuberculous Mycobacterium Involving 52 Outpatient Oncology Clinic Patients - Arkansas, 2018.
  Labuda Sarah M et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2019 Nov  
• Combining genomics and epidemiology to analyse bi-directional transmission of Mycobacterium bovis in a multi-host system.
  Crispell Joseph et al. eLife 2019 12
• Genomic epidemiology supports multiple introductions and cryptic transmission of Zika virus in Colombia.
  Black Allison et al. BMC infectious diseases 2019 Nov (1) 963
• Ebola Virus Disease Outbreak - Democratic Republic of the Congo, August 2018-November 2019.
  Aruna Aaron et al. MMWR. Morbidity and mortality weekly report 2019 Dec (50) 1162-1165  
• Natural selection favoring more transmissible HIV detected in United States molecular transmission network.
  Wertheim Joel O et al. Nature communications 2019 Dec (1) 5788 
• Prevalence of Non-B HIV-1 Subtypes in North Italy and Analysis of Transmission Clusters Based on Sequence Data Analysis.
  Lorenzin Giovanni et al. Microorganisms 2019 Dec (1)
• An outbreak of candidemia due to Candida parapsilosis in an adult intensive care unit.
  Haciseyitoglu Demet et al. Le infezioni in medicina 2019 Dec (4) 403-409
• Applying next-generation sequencing to track falciparum malaria in sub-Saharan Africa.
  Tessema Sofonias K et al. Malaria journal 2019 Sep (1) 268 

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• Toward insights on determining factors for high activity in antimicrobial peptides via machine learning.
  Li Hao et al. PeerJ 2019 e8265
• Effect of Treating Parents Colonized With Staphylococcus aureus on Transmission to Neonates in the Intensive Care Unit: A Randomized Clinical Trial.
  Milstone Aaron M et al. JAMA 2019 Dec
• Japanese encephalitis vaccine-specific envelope protein E138K mutation does not attenuate virulence of West Nile virus.
  Kaiser Jaclyn A et al. NPJ vaccines 2019 50 
• Gene drives for schistosomiasis transmission control.
  Maier Theresa et al. PLoS neglected tropical diseases 2019 Dec (12) e0007833

HOST-MICROBE INTERACTIONS

• Characterization of vaginal microbiota in women with preterm labor with intra-amniotic inflammation.
  Cobo Teresa et al. Scientific reports 2019 Dec (1) 18963
• Rapid MinION profiling of preterm microbiota and antimicrobial-resistant pathogens.
  Leggett Richard M et al. Nature microbiology 2019 Dec
• Temporal development of the oral microbiome and prediction of early childhood caries.
  Dashper S G et al. Scientific reports 2019 Dec (1) 19732
• Manipulating the Human Microbiome to Manage Disease.
  Harkins Catriona P et al. JAMA 2019 Dec
• Polymorphisms in Interferon Pathway Genes and Risk of Mycobacterium tuberculosis Infection in Contacts of Tuberculosis Cases in Brazil.
  Cubillos-Angulo Juan Manuel et al. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2019 Dec
• Association between the IL-10-1082G/A, IL-10-819T/C and IL-10-592A/C polymorphisms and Brucellosis susceptibility: a meta-analysis.
  Jin Xiaochun et al. Epidemiology and infection 2019 Dec e316
• Genetic diversity and virulence characteristics of Helicobacter pylori isolates in different human ethnic groups.
  Hanafiah Alfizah et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2019 Dec 104135
• Deep sequence analysis of HIV adaptation following vertical transmission reveals the impact of immune pressure on the evolution of HIV.
  Currenti Jennifer et al. PLoS pathogens 2019 Dec (12) e1008177
• Genetic Variants in the Promoter Region of the Macrophage Migration Inhibitory Factor are Associated with the Severity of Hepatitis C Virus-Induced Liver Fibrosis.
  Wirtz Theresa Hildegard et al. International journal of molecular sciences 2019 Jul (15)
• First genome-wide association study of non-severe malaria in two birth cohorts in Benin.
  Milet Jacqueline et al. Human genetics 2019 Dec (11-12) 1341-1357
• Insights into malaria susceptibility using genome-wide data on 17,000 individuals from Africa, Asia and Oceania.
  et al. Nature communications 2019 Dec (1) 5732

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.