Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Jan 17, 2019

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

NEWS

• DNA Extraction Remains Bottleneck for Long-Read Techs But Solutions Begin to Emerge
  Karow J. GenomeWeb, Jan 14, 2019.
• How elusive can a malaria vaccine be?
  Pance A. Nat Rev Microbiol, Jan 9, 2019.
• The bacteria in your gut may reveal your true age
  Mullin E. Science, Jan 11, 2019.

EVENTS / TRAINING / WEB RESOURCES

• Fundamentals of Data Visualization
  (online book) Wilke CO. 2018.
• Applied Bioinformatics and Public Health Microbiology
  (course) Wellcome Genome Campus, UK, June 5-7, 2019.

POLICY

• Science with borders: A debate over genetic sequences and national rights threatens to inhibit research
  Branswell H. STAT, Jan 14, 2019.

CONCEPTS / COMMENTS

• Integration of microbiology, molecular pathology, and epidemiology: a new paradigm to explore the pathogenesis of microbiome-driven neoplasms.
  Hamada Tsuyoshi et al. The Journal of pathology 2019 Jan
• Invited Commentary: Improving accessibility of the Human Microbiome Project data through integration with R/Bioconductor.
  Griffith Jocelyn C et al. American journal of epidemiology 2019 Jan

METHODS / TOOLS

• Improved DNA extraction technique from clot for the diagnosis of Chagas disease.
  Mayta Holger et al. PLoS neglected tropical diseases 2019 Jan (1) e0007024
• Impact of inter- and intra-individual variation, sample storage and sampling fraction on human stool microbial community profiles.
  Yeoh Yun Kit et al. PeerJ 2019 e6172
• Identifying accurate metagenome and amplicon software via a meta-analysis of sequence to taxonomy benchmarking studies.
  Gardner Paul P et al. PeerJ 2019 e6160
• HMP16SData: Efficient Access to the Human Microbiome Project through Bioconductor.
  Schiffer Lucas et al. American journal of epidemiology 2019 Jan
• Shared genome analyses of notable listeriosis outbreaks, highlighting the critical importance of epidemiological evidence, input datasets and interpretation criteria.
  Reimer Aleisha et al. Microbial genomics 2019 Jan
• Tracking the popularity and outcomes of all bioRxiv preprints
  Abdill RJ, Blekhman R. bioRxiv, Jan 13, 2019.

EVOLUTION / ECOLOGY / POPULATIONS

• Limited contribution of non-intensive chicken farming to ESBL-producing Escherichia coli colonization in humans in Vietnam: an epidemiological and genomic analysis.
  Nguyen Vinh Trung et al. The Journal of antimicrobial chemotherapy 2019 Jan
• Where the plasmids roam: large-scale sequence analysis reveals plasmids with large host ranges.
  Brooks Lauren Elisabeth et al. Microbial genomics 2019 Jan
• Whole genome sequencing reveals Trans-European spread of an epidemic Neisseria meningitidis serogroup W clone.
  Taha Muhamed-Kheir et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2019 Jan
• Complete Genome Sequences of Four Salmonella enterica Strains (Including Those of Serotypes Montevideo, Mbandaka, and Lubbock) Isolated from Peripheral Lymph Nodes of Healthy Cattle.
  Bugarel Marie et al. Microbiology resource announcements 2019 Jan (2) 
• Genome Sequences of Penicillin-Resistant Bacillus anthracis Strains.
  Gargis Amy S et al. Microbiology resource announcements 2019 Jan (2) 
• Molecular Detection and Phylogenetic Analysis of Anaplasma phagocytophilum in Horses in Korea.
  Seo Min-Goo et al. The Korean journal of parasitology 2018 Dec (6) 559-565
• A cross-sectional screening by next-generation sequencing reveals Rickettsia, Coxiella, Francisella, Borrelia, Babesia, Theileria and Hemolivia species in ticks from Anatolia.
  Brinkmann Annika et al. Parasites & vectors 2019 Jan (1) 26
• Longitudinal study for enterovirus A71 and coxsackievirus A16 genotype/subgenotype replacements in hand, foot and mouth disease patients in Thailand, 2000-2017.
  Noisumdaeng Pirom et al. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2019 Jan
• Emergence of new genotypes and lineages of dengue viruses during the 2012-15 epidemics in southern India.
  Ahamed Syed Fazil et al. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2019 Jan
• Occurrence of noroviruses in recycled water and sewage sludge: emergence of recombinant norovirus strains.
  Kittigul L et al. Journal of applied microbiology 2019 Jan
• Phylogeographic analysis of human influenza A and B viruses in Myanmar, 2010-2015.
  Htwe Khin Thu Zar et al. PloS one 2019 (1) e0210550
• Monkeypox virus phylogenetic similarities between a human case detected in Cameroon in 2018 and the 2017-2018 outbreak in Nigeria.
  Sadeuh-Mba Serge Alain et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2019 Jan
• New strains of Japanese encephalitis virus circulating in Shanghai, China after a ten-year hiatus in local mosquito surveillance.
  Fang Yuan et al. Parasites & vectors 2019 Jan (1) 22
• The reemergence of human rabies and emergence of an Indian subcontinent lineage in Tibet, China.
  Tao Xiao-Yan et al. PLoS neglected tropical diseases 2019 Jan (1) e0007036

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Sequential evolution of virulence and resistance during clonal spread of community-acquired methicillin-resistant Staphylococcus aureus .
  Copin Richard et al. Proceedings of the National Academy of Sciences of the United States of America 2019 Jan
• Regional outbreak of community-associated methicillin-resistant Staphylococcus aureus ST834 in Japanese children.
  Uehara Yuki et al. BMC infectious diseases 2019 Jan (1) 35
• Development of New Tools to Detect Colistin-Resistance among Enterobacteriaceae Strains.
  Bardet Lucie et al. The Canadian journal of infectious diseases & medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale 2018 3095249
• Dissemination and characterization of extended spectrum β-lactamase, AmpC β-lactamase and metallo β-lactamase producing Escherichia coli from livestock and poultry in Northeastern India: A molecular surveillance approach.
  Tewari Rituparna et al. Journal of global antimicrobial resistance 2019 Jan
• Adding function to the genome of African Salmonella Typhimurium ST313 strain D23580.
  Canals Rocío et al. PLoS biology 2019 Jan (1) e3000059
• Molecular epidemiology and expression of capsular polysaccharides in Staphylococcus aureus clinical isolates in the United States.
  Mohamed Naglaa et al. PloS one 2019 (1) e0208356
• Genome-wide association analyses of invasive pneumococcal isolates identify a missense bacterial mutation associated with meningitis.
  Li Yuan et al. Nature communications 2019 Jan (1) 178 
• Analysis of antifungal resistance genes in Candida albicans and Candida glabrata using next generation sequencing.
  Spettel Kathrin et al. PloS one 2019 (1) e0210397

DETECTION / DIAGNOSIS

• Determining the Cause of Death Among Children Hospitalized With Respiratory Illness in Kenya: Protocol for Pediatric Respiratory Etiology Surveillance Study (PRESS).
  Njuguna Henry N et al. JMIR research protocols 2019 Jan (1) e10854  
• Metagenomic analysis of viruses in toilet waste from long distance flights-A new procedure for global infectious disease surveillance.
  Hjelmsø Mathis Hjort et al. PloS one 2019 (1) e0210368
• Analysis of serum hepatitis B virus RNA levels in a multiethnic cohort of pregnant chronic hepatitis B carriers.
  Patel Nishi H et al. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2019 Jan 42-47
• Emergence of Madariaga virus as a cause of acute febrile illness in children, Haiti, 2015-2016.
  Lednicky John A et al. PLoS neglected tropical diseases 2019 Jan (1) e0006972

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Nosocomial outbreak of esbl-producing enterobacter cloacae among cardio-thoracic surgical patients: causes and consequences.
  Noël A et al. The Journal of hospital infection 2019 Jan
• Multi-step genomic dissection of a suspected intra-hospital Helicobacter cinaedi outbreak.
  Gotoh Yasuhiro et al. Microbial genomics 2018 Dec (12)
• An outbreak of vanA vancomycin-resistant Enterococcus faecium in a hospital with endemic vanB VRE.
  Hughes Angus et al. Infection, disease & health 2019 Jan
• Genomic approaches used to investigate an atypical outbreak of Salmonella Adjame.
  Chattaway Marie Anne et al. Microbial genomics 2019 Jan
• Whole genome sequencing suggests transmission of Corynebacterium diphtheriae -caused cutaneous diphtheria in two siblings, Germany, 2018.
  Berger Anja et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2019 Jan (2)
• Unmasking leading to a healthcare worker Mycobacterium tuberculosis transmission.
  Holden K L et al. The Journal of hospital infection 2018 Dec (4) e226-e232
• Modeling suggests that microliter volumes of contaminated blood caused an outbreak of hepatitis C during computerized tomography.
  Shteyer Eyal et al. PloS one 2019 (1) e0210173
• Epidemiological aspects of the persistent transmission of rabies during an outbreak (2010 - 2017) in Harare, Zimbabwe.
  Coetzer Andre et al. PloS one 2019 (1) e0210018

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• Impact of single room contact precautions on hospital-acquisition and transmission of multidrug-resistant Escherichia coli: a prospective multicentre cohort-study in haematological and oncological wards.
  Biehl Lena M et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2019 Jan 

HOST-MICROBE INTERACTIONS

• The effect of antimicrobial drug use on the composition of the genitourinary microbiota in an elderly population.
  Mulder M et al. BMC microbiology 2019 Jan (1) 9
• Intestinal parasitic infection alters bacterial gut microbiota in children.
  Toro-Londono Miguel A et al. PeerJ 2019 e6200
• Comparison of the salivary and dentinal microbiome of children with severe-early childhood caries to the salivary microbiome of caries-free children.
  Hurley Eimear et al. BMC oral health 2019 Jan (1) 13
• Role of colonic microbiota in the pathogenesis of ulcerative colitis.
  Pei Ling-Yan et al. BMC gastroenterology 2019 Jan (1) 10
• Genetic variation/evolution and differential host responses resulting from in-patient adaptation of Mycobacterium avium .
  Kannan N et al. Infection and immunity 2019 Jan
• Association study between CCR2-CCR5 genes polymorphisms and chronic Chagas heart disease in Wichi and in admixed populations from Argentina.
  Juiz Natalia Anahí et al. PLoS neglected tropical diseases 2019 Jan (1) e0007033

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.