Publication Date: Feb 22, 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
Advanced Molecular Detection Clips Content
NEWS
- Senate bill would jump-start universal flu vaccine efforts
Schnirring L. CIDRAP, Feb 19, 2018. - New CRISPR-Based Tools Flag Genetic Sequences and Log Data
Kwon D. The Scientist, Feb 16, 2018. - XDR typhoid in Pakistan carries added resistance genes
Dall C. CIDRAP, Feb 20, 2018. - Scientists Develop A Way To Use A Smartphone To Prevent Food Poisoning
Brown K. NPR, Feb 19, 2018. - New C diff guidelines incorporate fecal transplant
Dall C. CIDRAP, Feb 16, 2018. - Did Pox Virus Research Put Potential Profits Ahead of Public Safety?
Greenfield-Boyce N. NPR, Feb 17, 2018. - Genomic Particularities Hint at Vampire Bat’s Ability to Live Off Blood
Grens K. The Scientist, Feb 19, 2018.
CONCEPTS / COMMENTS
- Twitter big data and infectious disease conferences.
Mackenzie Graham et al. The Lancet. Infectious diseases 2018 Feb (2) 154 - Deep learning for biology
Webb S. Nature, Feb 20, 2017. - TB diagnosis from the Dark Ages to fluorescence
Rubin EJ. Nat Microbiol 2018;3:268?269. - Influenza interaction with cocirculating pathogens and its impact on surveillance, pathogenesis, and epidemic profile: A key role for mathematical modelling.
Opatowski Lulla et al. PLoS pathogens 2018 Feb (2) e1006770 - The emerging influenza virus threat: status and new prospects for its therapy and control.
Kumar Binod et al. Archives of virology 2018 Jan - Pandemic preparedness and forecast
Shaman J. Nat Microbiol 2018;3:265?267 - Informed consent in field trials of gene-drive mosquitoes.
Kolopack Pamela A et al. Gates open research 2017 Dec 14 - Community Engagement and Field Trials of Genetically Modified Insects and Animals.
Neuhaus Carolyn P et al. The Hastings Center report 2018 Jan (1) 25-36 - Why should we care about genetic diversity in mosquitoes?
(blog post) Faust C. BugBitten (BioMed Central), Feb 16, 2018.
METHODS / TOOLS
- Rapid one-step extraction method for the identification of molds using MALDI-TOF MS.
Luethy Paul M et al. Diagnostic microbiology and infectious disease 2018 Feb - Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6.
Gootenberg Jonathan S et al. Science (New York, N.Y.) 2018 Feb - SEED 2: a user-friendly platform for amplicon high-throughput sequencing data analyses.
Vetrovský Tomáš et al. Bioinformatics (Oxford, England) 2018 Feb - Know Your Enemy: Successful Bioinformatic Approaches to Predict Functional RNA Structures in Viral RNAs.
Lim Chun Shen et al. Frontiers in microbiology 2017 2582 - PATRIC as a unique resource for studying antimicrobial resistance.
Antonopoulos Dionysios A et al. Briefings in bioinformatics 2017 Jul - Assembly, Annotation, and Comparative Genomics in PATRIC, the All Bacterial Bioinformatics Resource Center.
Wattam Alice R et al. Methods in molecular biology (Clifton, N.J.) 2018 79-101 - HIV-TRACE (Transmission Cluster Engine): a tool for large scale molecular epidemiology of HIV-1 and other rapidly evolving pathogens.
Kosakovsky Pond Sergei L et al. Molecular biology and evolution 2018 Jan - Bipartite network analysis of gene sharings in the microbial world.
Corel Eduardo et al. Molecular biology and evolution 2018 Jan - The state of software for evolutionary biology.
Darriba Diego et al. Molecular biology and evolution 2018 Jan
EVOLUTION / ECOLOGY / POPULATIONS
- Convergent amino acid signatures in polyphyletic Campylobacter jejuni sub-populations suggest human niche tropism.
Méric Guillaume et al. Genome biology and evolution 2018 Feb - Whole genome sequencing of multidrug-resistant Salmonella enterica serovar Typhimurium isolated from humans and poultry in Burkina Faso.
Kagambèga Assèta et al. Tropical medicine and health 2018 4 - Comparative genomics of pathogenic Leptospira interrogans serovar Canicola isolated from swine and human in Brazil.
Moreno Luisa Z et al. Memorias do Instituto Oswaldo Cruz 2018 Feb (2) 126-129 - Geogenomic Segregation and Temporal Trends of Human Pathogenic Escherichia coli O157:H7, Washington, USA, 2005-2014
Tarr Gillian A M et al. Emerging infectious diseases 2018 Jan (1) 32-39 - Genetic characterization of Listeria monocytogenes from ruminant listeriosis from different geographical regions in the U.S.
Steckler Abbey J et al. Veterinary microbiology 2018 Feb 93-97 - Comparative genomics of Vibrio cholerae El Tor strains isolated at epidemic complications in Siberia and at the Far East.
Mironova Liliya V et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2018 Feb - Ecology and evolution of Mycobacterium tuberculosis.
Gagneux Sebastien et al. Nature reviews. Microbiology 2018 Feb - Phylodynamics of Crimean Congo hemorrhagic fever virus in South Russia.
Lukashev A N et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2018 Jan 23-27 - Convergent Evolution of Human-Isolated H7N9 Avian Influenza A Viruses.
Xiang Dan et al. The Journal of infectious diseases 2018 Feb - Genetic diversity and cross-species transmission of kobuviruses in Vietnam.
Lu Lu et al. Virus evolution 2018 Jan (1) vey002 - Dynamics of Evolution of Poliovirus Neutralizing Antigenic Sites and Other Capsid Functional Domains during a Large and Prolonged Outbreak.
Shaw Jing et al. Journal of virology 2018 Feb
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
- Comparative genomic analysis of ten clinical Streptococcus pneumoniae collected from a Malaysian hospital reveal 31 new unique drug-resistant SNPs using whole genome sequencing.
Jindal Hassan Mahmood et al. Journal of biomedical science 2018 Feb (1) 15 - Emergence of an extensively drug-resistant Salmonella enterica serovar typhi clone harboring a promiscuous plasmid encoding resistance to fluoroquinolones and third-generation cephalosporins
Klemm EJ, et al. mBio, Feb 20, 2018. - Novel single-nucleotide variations associated with vancomycin resistance in vancomycin-intermediate Staphylococcus aureus.
Lin Lee-Chung et al. Infection and drug resistance 2018 113-123 - Genomic investigation of Staphylococcus aureus isolates from bulk tank milk and dairy cows with clinical mastitis.
Ronco Troels et al. Veterinary microbiology 2018 Feb 35-42 - Enriched whole genome sequencing identified compensatory mutations in the RNA polymerase gene of rifampicin-resistant Mycobacterium leprae strains.
Lavania Mallika et al. Infection and drug resistance 2018 169-175 - Quantifying the fitness cost of HIV-1 drug resistance mutations through phylodynamics.
Kühnert Denise et al. PLoS pathogens 2018 Feb (2) e1006895 - Identification and characterization of viral defective RNA genomes in influenza B virus.
Sheng Zizhang et al. The Journal of general virology 2018 Feb - West Nile and St. Louis encephalitis viral genetic determinants of avian host competence.
Maharaj Payal D et al. PLoS neglected tropical diseases 2018 Feb (2) e0006302 - Prevalence of molecular markers of artemisinin and lumefantrine resistance among patients with uncomplicated Plasmodium falciparum malaria in three provinces in Angola, 2015.
Ljolje Dragan et al. Malaria journal 2018 Feb (1) 84
DETECTION / DIAGNOSIS
- Examination of 16S-23S rRNA intergenic spacer region (ISR) heterogeneity in a population of clinical Streptococcus pneumoniae- a new laboratory epidemiological genotyping tool to aid outbreak analysis.
Moore J E et al. British journal of biomedical science 2018 Feb 1-3 - A multiplex serologic platform for diagnosis of tick-borne diseases.
Tokarz Rafal et al. Scientific reports 2018 Feb (1) 3158 - Detection and incidence of Bordetella holmesii in respiratory specimens from patients with pertussis-like symptoms in New South Wales, Australia.
Fong Winkie et al. Pathology 2018 Feb - PCR ribotyping and antimicrobial susceptibility testing of isolates of Clostridium difficile cultured from toxin-positive diarrheal stools of patients receiving medical care in Canadian hospitals: the Canadian Clostridium difficile Surveillance Study (CAN-DIFF) 2013-2015.
Karlowsky James A et al. Diagnostic microbiology and infectious disease 2018 Jan - Accuracy of high-throughput nanofluidic PCR-based pneumococcal serotyping and quantification assays using sputum samples for diagnosing vaccine serotype pneumococcal pneumonia: analyses by composite diagnostic standards and Bayesian latent class models.
Kakiuchi Satoshi et al. Journal of clinical microbiology 2018 Feb - Detection of Bartonella spp. in fleas by MALDI-TOF MS.
El Hamzaoui Basma et al. PLoS neglected tropical diseases 2018 Feb (2) e0006189 - A community approach to mortality prediction in sepsis via gene expression analysis.
Sweeney Timothy E et al. Nature communications 2018 Feb (1) 694 - Use of Genome Sequencing to Define Institutional Influenza Outbreaks, Toronto, Ontario, Canada, 2014-15.
MacFadden Derek R et al. Emerging infectious diseases 2018 Mar (3) 492-497 - TiO
Zhang Rutan et al. Analytical chemistry 2018 Feb - Absence of association between polymorphisms in the K13 gene and the presence of Plasmodium falciparum parasites at day 3 after treatment with artemisinin derivatives in Senegal.
Madamet Marylin et al. International journal of antimicrobial agents 2017 Jun (6) 754-756
- Results of the first international HIV-1 coreceptor proficiency panel test.
Heger Eva et al. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2017 Aug 53-56 - Sensitive and less invasive confirmatory diagnosis of visceral leishmaniasis in Sudan using loop-mediated isothermal amplification (LAMP).
Mukhtar Maowia et al. PLoS neglected tropical diseases 2018 Feb (2) e0006264 - Molecular diagnosis of protozoan parasites by Recombinase Polymerase Amplification.
Castellanos-Gonzalez A et al. Acta tropica 2018 Feb
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
- Transmission of ESBL-producing Enterobacteriaceae and their mobile genetic elements-identification of sources by whole genome sequencing: study protocol for an observational study in Switzerland.
Stadler Tanja et al. BMJ open 2018 Feb (2) e021823 - Whole-genome sequence analysis of Streptococcus pneumoniae strains that cause hospital-acquired pneumonia infections.
Chang Bin et al. Journal of clinical microbiology 2018 Feb - Molecular characteristics and successful management of a respiratory syncytial virus outbreak among pediatric patients with hemato-oncological disease.
Baier Claas et al. Antimicrobial resistance and infection control 2018 21 - Emergence of Vaccine-Derived Polioviruses during Ebola Virus Disease Outbreak, Guinea, 2014-2015.
Fernandez-Garcia Maria Dolores et al. Emerging infectious diseases 2018 Jan (1) 65-74
HOST-MICROBE INTERACTIONS
- A new piece in the microbiome puzzle.
Pike Lindsay J et al. Nature reviews. Microbiology 2018 Feb - Host genetic variation and its microbiome interactions within the Human Microbiome Project.
Kolde Raivo et al. Genome medicine 2018 Jan (1) 6 - Joint ancestry and association test indicate two distinct pathogenic pathways involved in classical dengue fever and dengue shock syndrome.
Oliveira Marisa et al. PLoS neglected tropical diseases 2018 Feb (2) e0006202 - Virome and bacteriome characterization of children with pneumonia and asthma in Mexico City during winter seasons 2014 and 2015.
Romero-Espinoza Jose A et al. PloS one 2018 (2) e0192878 - Strain Tracking Reveals the Determinants of Bacterial Engraftment in the Human Gut Following Fecal Microbiota Transplantation.
Smillie Christopher S et al. Cell host & microbe 2018 Feb (2) 229-240.e5 - Cervicovaginal Microbiota and Reproductive Health: The Virtue of Simplicity.
Anahtar Melis N et al. Cell host & microbe 2018 Feb (2) 159-168 - A microbiome case-control study of recurrent acute otitis media identified potentially protective bacterial genera.
Lappan Rachael et al. BMC microbiology 2018 Feb (1) 13 - The Impact of NOD2 Variants on Fecal Microbiota in Crohn's Disease and Controls Without Gastrointestinal Disease.
Kennedy Nicholas A et al. Inflammatory bowel diseases 2018 Feb (3) 583-592 - Maternal Microbiota, Prepregnancy Weight, and Mode of Delivery: Intergenerational Transmission of Risk for Childhood Overweight and Obesity
Paolella G, Vajro P. JAMA Pediatr, Feb 19, 2018. - Gut microbiota trajectory in early life may predict development of celiac disease.
Olivares Marta et al. Microbiome 2018 Feb (1) 36
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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