Publication Date: Nov 14, 2019
Advanced Molecular Detection Clips Content
NEWS
- Make code accessible with these cloud services
Perkel JM. Nature, Nov 5, 2019. - Deadly superbugs pose greater threat than previously estimated
Sun LH. Washington Post, Nov 13, 2019. - Scientists discover first new HIV strain in nearly two decades
Christensen J. CNN, Nov 8, 2019. - Gene Screen Leads to Potential Malaria Targets in Liver-Stage Plasmodium Parasites
GenomeWeb, Nov 14, 2019. - Bacterial toxin linked to severe alcoholic liver disease
Frederick E. Science, Nov 15, 2019.
EVENTS / TRAINING / WEB RESOURCES
- CSELS Science Seminar: Visual Abstracts
(announcement) Wed, November 20, 2019, 11:30am- 12:2pm, Century Center 2400 or online - The Next Generation Sequencing Quality Initiative
(website) CDC, Nov 5, 2019. - A five-year strategy for infectious diseases
(blog post) PHG Foundation, Sep 12, 2019. - Ten quick tips for delivering programming lessons.
Wilson Greg et al. PLoS computational biology 2019 Oct (10) e1007433
POLICY
- Implementation of the US Department of Health and Human Services Zika Specimen Repository and Its Effect on Zika Diagnostic Test Development, 2016.
Petway Marla et al. Public health reports (Washington, D.C. : 1974) (2_suppl) 53S-57S
CONCEPTS / COMMENTS
- RNA sequencing: the teenage years.
Stark Rory et al. Nature reviews. Genetics 2019 Nov (11) 631-656 - A new twenty-first century science for effective epidemic response.
Bedford Juliet et al. Nature 2019 Nov (7781) 130-136 - Is Mycobacterium tuberculosis infection life long?
Behr Marcel A et al. BMJ (Clinical research ed.) 2019 10 l5770 - Tuberculosis Vaccine Development: Progress in Clinical Evaluation.
Sable Suraj B et al. Clinical microbiology reviews 2019 Dec (1) - An open challenge to advance probabilistic forecasting for dengue epidemics.
Johansson Michael A et al. Proceedings of the National Academy of Sciences of the United States of America 2019 Nov - The pan-immune system of bacteria: antiviral defence as a community resource.
Bernheim Aude et al. Nature reviews. Microbiology 2019 Nov - A sequence of unfortunate events
York A. Nat Rev Microbiol, Nov 12, 2019. - Human Genetics Influence the Susceptibility to Cutaneous Leishmanisis Caused by Leishmania guyanensis.
Petersen Eskild et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2019 Nov - Hype or hope?
(editorial) Nat Rev Microbiol, Nov 12, 2019. - The future of faecal transplants.
Giles Edward M et al. Nature reviews. Microbiology 2019 Dec (12) 719
METHODS / TOOLS
- Reliable variant calling during runtime of Illumina sequencing.
Loka Tobias P et al. Scientific reports 2019 Nov (1) 16502 - Digital PCR-An Emerging Technology with Broad Applications in Microbiology.
Salipante Stephen J et al. Clinical chemistry 2019 Nov - Entirely Off-Grid and Solar-Powered DNA Sequencing of Microbial Communities during an Ice Cap Traverse Expedition.
Gowers Glen-Oliver F et al. Genes 2019 Nov (11) - Selective culture enrichment and sequencing of feces to enhance detection of antimicrobial resistance genes in third-generation cephalosporin resistant Enterobacteriaceae.
Peto Leon et al. PloS one 2019 (11) e0222831 - Application of different DNA extraction procedures, library preparation protocols and sequencing platforms: impact on sequencing results.
Pasquali F et al. Heliyon 2019 Oct (10) e02745 - Comparison of four DNA extraction and three preservation protocols for the molecular detection and quantification of soil-transmitted helminths in stool.
Ayana Mio et al. PLoS neglected tropical diseases 2019 Oct (10) e0007778 - MERCAT: Visualising molecular epidemiology data combining genetic markers and drug resistance profiles.
Aandahl R Zach et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2019 Nov 104043 - MEGARes 2.0: a database for classification of antimicrobial drug, biocide and metal resistance determinants in metagenomic sequence data.
Doster Enrique et al. Nucleic acids research 2019 Nov - Reintroducing mothur: 10 years later.
Schloss Patrick D et al. Applied and environmental microbiology 2019 Nov
EVOLUTION / ECOLOGY / POPULATIONS
- Genome Sequence of a Salmonella enterica subsp. enterica Serovar Corvallis Strain Isolated from Human Blood.
McCutchen Emily L et al. Microbiology resource announcements 2019 Oct (44) - Epidemiology of Bacterial Meningitis in the Nine Years Since Meningococcal Serogroup A Conjugate Vaccine Introduction, Niger, 2010-2018.
Sidikou Fati et al. The Journal of infectious diseases 2019 Oct (Supplement_4) S206-S215 - US immigration is associated with rapid and persistent acquisition of antibiotic resistance genes in the gut.
Le Bastard Quentin et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2019 Nov - Twenty years of West Nile virus spread and evolution in the Americas visualized by Nextstrain.
Hadfield James et al. PLoS pathogens 2019 Oct (10) e1008042 - Complete genome sequence of CG-0018a-01 establishes HIV-1 subtype L.
Yamaguchi Julie et al. Journal of acquired immune deficiency syndromes (1999) 2019 Nov - Identification and complete-genome phylogenetic analysis of an epizootic hemorrhagic disease virus serotype 7 strain isolated in China.
Qi Yinglin et al. Archives of virology 2019 Dec (12) 3121-3126 - An Evolutionary Insight into Emerging Ebolavirus Strains Isolated in Africa.
Pereira-Gomez Marianoel et al. Journal of medical virology 2019 Nov - Antigenic variations of recent street rabies virus.
Wang Wenbo et al. Emerging microbes & infections 2019 (1) 1584-1592 - Recurrent herpes zoster in the Shingles Prevention Study: Are second episodes caused by the same varicella-zoster virus strain?
Harbecke Ruth et al. Vaccine 2019 Oct - Nearly Complete Genome Sequence of an Echovirus 30 Strain from a Cluster of Aseptic Meningitis Cases in California, September 2017.
Pan Chao-Yang et al. Microbiology resource announcements 2019 Oct (44) - Resurrection of the ancestral RH5 invasion ligand provides a molecular explanation for the origin of P. falciparum malaria in humans.
Galaway Francis et al. PLoS biology 2019 Oct (10) e3000490
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
- Genomic Epidemiology of Major Extraintestinal Pathogenic Escherichia coli Lineages Causing Urinary Tract Infections in Young Women Across Canada.
Fibke Chad D et al. Open forum infectious diseases 2019 Nov (11) ofz431 - An Emerging Clone, KPC-2-Producing Klebsiella pneumoniae ST16, Associated with High Mortality Rates in a CC258 Endemic Setting.
Andrey Diego O et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2019 Nov - Complete genome analysis of clinical Shigella strains reveals plasmid pSS1653 with resistance determinants: a triumph of hybrid approach.
Muthuirulandi Sethuvel Dhiviya Prabaa et al. Gut pathogens 2019 55 - Neisseria meningitidis: using genomics to understand diversity, evolution and pathogenesis.
Caugant Dominique A et al. Nature reviews. Microbiology 2019 Nov - Chlamydia trachomatis : when the virulence-associated genome backbone imports a prevalence-associated major antigen signature.
Borges Vítor et al. Microbial genomics 2019 Nov - Human bocavirus infection in Belgian children with respiratory tract disease.
Verbeke Vanessa et al. Archives of virology 2019 Dec (12) 2919-2930
DETECTION / DIAGNOSIS
- Temporal trends of inpatient C. difficile infections within the Veterans Health Administration hospitals: An analysis of the effect of molecular testing, time to testing, and mandatory reporting.
Sumon Zarchi E et al. Infection control and hospital epidemiology 2019 Nov 1-8 - PulseNet and the Changing Paradigm of Laboratory-Based Surveillance for Foodborne Diseases.
Kubota Kristy A et al. Public health reports (Washington, D.C. : 1974) (2_suppl) 22S-28S - Enhancing genomics-based outbreak detection of endemic Salmonella enterica serovar Typhimurium using dynamic thresholds.
Payne Michael et al. Microbial genomics 2019 Nov - Toward a Global Genomic Epidemiology of Meningococcal Disease.
Retchless Adam C et al. The Journal of infectious diseases 2019 Oct (Supplement_4) S266-S273 - A New Sequence Type of Neisseria meningitidis Serogroup C Associated With a 2016 Meningitis Outbreak in Mali.
Sanogo Yibayiri Osee et al. The Journal of infectious diseases 2019 Oct (Supplement_4) S190-S197 - Rapid sequencing-based diagnosis of infectious bacterial species from meningitis patients in Zambia.
Nakagawa So et al. Clinical & translational immunology 2019 (11) e01087 - Development and Implementation of Whole Genome Sequencing-Based Typing Schemes for Clostridioides difficile .
Janezic Sandra et al. Frontiers in public health 2019 309 - BCG strains with defined resistance mutations: a new tool for TB lab quality control.
Danchuk Sarah N et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2019 Nov - Genotyping of Mycobacterium tuberculosis spreading in Hanoi, Vietnam using conventional and whole genome sequencing methods.
Maeda Shinji et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2019 Nov 104107 - Development of a universal and lineage-specific primer sets for Zika virus (ZIKV) rapid detection in blood and urine samples by using one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP).
Bui Thu Thuy et al. Japanese journal of infectious diseases 2019 Oct - Evaluation of PCR to monitor Plasmodium falciparum treatment efficacy in a non-endemic setting.
Kamaliddin Claire et al. Journal of clinical microbiology 2019 Oct - Genetic diversity and drug resistance surveillance of Plasmodium falciparum for malaria elimination: is there an ideal tool for resource-limited sub-Saharan Africa?
Apinjoh Tobias O et al. Malaria journal 2019 Jun (1) 217 - Development of a recombinase polymerase amplification (RPA) fluorescence assay for the detection of Schistosoma haematobium.
Rostron Penelope et al. Parasites & vectors 2019 Nov (1) 514 - Parasite-derived microRNAs in plasma as novel promising biomarkers for the early detection of hydatid cyst infection and post-surgery follow-up.
Alizadeh Zahra et al. Acta tropica 2019 Nov 105255
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
- Agrobacterium spp. nosocomial outbreak assessment using rapid MALDI-TOF MS based typing, confirmed by whole genome sequencing.
Casanova Carlo et al. Antimicrobial resistance and infection control 2019 171 - An outbreak of ST307 extended-spectrum beta-lactamase (ESBL)-producing Klebsiella pneumoniae in a rehabilitation center: An unusual source and route of transmission.
Boonstra Marrit B et al. Infection control and hospital epidemiology 2019 Nov 1-6 - The relevance of molecular genotyping to allocate cases in a suspected outbreak of Legionella pneumonia in patients with prolonged immunosuppressive therapy.
Borella Paola et al. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2019 Nov - High-resolution mapping of tuberculosis transmission: Whole genome sequencing and phylogenetic modelling of a cohort from Valencia Region, Spain.
Xu Yuanwei et al. PLoS medicine 2019 Oct (10) e1002961 - Genomic Epidemiology as a Public Health Tool to Combat Mosquito-Borne Virus Outbreaks.
Pollett S et al. The Journal of infectious diseases 2019 Nov - Temporal and Genotypic Associations of Sporadic Norovirus Gastroenteritis and Reported Norovirus Outbreaks in Middle Tennessee, 2012-2016.
Parikh Meghana P et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2019 Nov
HOST-MICROBE INTERACTIONS
- Diet-microbiome-disease: Investigating diet's influence on infectious disease resistance through alteration of the gut microbiome.
Harris Erica V et al. PLoS pathogens 2019 Oct (10) e1007891 - Host genetic variability and pneumococcal disease: a systematic review and meta-analysis.
Kloek Anne T et al. BMC medical genomics 2019 09 (1) 130 - MAL adaptor (TIRAP) S180L polymorphism and tuberculosis disease severity among TB patients.
Saranathan Rajagopalan et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2019 Oct 104093 - Longitudinal profiling of gut microbiome among tuberculosis patients under anti-tuberculosis treatment in China: protocol of a prospective cohort study.
Shi Wenpei et al. BMC pulmonary medicine 2019 Nov (1) 211 - Using compositional principal component analysis to describe children's gut microbiota in relation to diet and body composition.
Leong Claudia et al. The American journal of clinical nutrition 2019 Nov - Interplay between host-microbe and microbe-microbe interactions in cystic fibrosis.
Armbruster Catherine R et al. Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society 2019 Nov - Chlamydia trachomatis and human herpesvirus 6 infections in ovarian cancer-Casual or causal?
Gulve Nitish et al. PLoS pathogens 2019 Nov (11) e1008055 - A Single Haplotype of IFNG Correlating With Low Circulating Levels of Interferon-γ Is Associated With Susceptibility to Cutaneous Leishmaniasis Caused by Leishmania guyanensis.
da Silva George A V et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2019 Nov
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.
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