Publication Date: Mar 16, 2017
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.
Advanced Molecular Detection Clips Content
NEWS
- Tennessee bird flu shares name, not genetics, of feared China strain: USDA
Polansek T. Reuters, Mar 7, 2017. - Feds warn of Zika threat to sperm donations in 3 Florida counties
Schnirring L. CIDRAP News, Mar 13, 2017. - Genomics Reveal Surprises About Florida Zika Outbreak
McNamara D. Healio, Mar 4, 2017. - Transmitted drug resistance mutations increase in HIV
Healio, Mar 3, 2017. - Protein signature in mucus reveals infection status
Healio, Mar 6, 2017. - Scientists get closer to lab-made genome
Begley S. STAT, Mar 9, 2017. - In a remote West African village, a revolutionary genetic experiment is on its way — if residents agree to it
Swetlitz I. STAT, Mar 14, 2017. - The 'Dark Matter' of the Microbial World
Zhang S. The Atlantic, Mar 7, 2017.
EVENTS / TRAINING / WEB RESOURCES
- Attacking Legionnaires’ Disease: Rapid molecular detection of Legionella for outbreak response
(web page) OAMD, Mar 1, 2017. - Silencing the 100-day Cough: Using AMD technologies to understand changes in virulence of Bordetella pertussis and find effective vaccine components and diagnostic markers
(web page) OAMD, Mar 1, 2017. - How CDC Is Using Advanced Molecular Detection Technology To Better Fight Flu!
(blog post) Barnes J. CDC Public Health Matters, Mar 6, 2017. - Infectious Disease Genomic Epidemiology
(workshop) Bioinformatics Canada, Vancouver BC, May 1-3, 2017.
CONCEPTS / COMMENTS
- Whole Genome Sequencing-Implications for Infection Prevention and Outbreak Investigations.
Popovich Kyle J et al. Current infectious disease reports 2017 Apr (4) 15 - Metagenomic Sequencing for Surveillance of Food- and Waterborne Viral Diseases.
Nieuwenhuijse David F et al. Frontiers in microbiology 2017 230 - Preprinting Microbiology
Schloss PD. bioRxiv, Feb 23, 2017. - All biology is computational biology.
Markowetz Florian et al. PLoS biology 2017 Mar (3) e2002050 - Bringing Treponema into the spotlight
Everall I, Sanchez-Buso L. Nat Microbiol, Mar 13, 2017. - CRE surveillance: Is tracking of 'nightmare' bacteria adequate?
Dall C. CIDRAP, Mar 13, 2017. - West African Ebola Virus Strains: Unstable and Ready to Invade?
Basler Christopher F et al. Cell host & microbe 2017 Mar (3) 316-318 - A Feast of Malaria Parasite Genomes.
Carlton Jane M et al. Cell host & microbe 2017 Mar (3) 310-312 - The shape of the microbiome in early life.
von Mutius Erika et al. Nature medicine 2017 Mar (3) 274-275
METHODS / TOOLS
- Foodborne Illness Outbreak Investigation Training Needs: A Survey Among State Public Health Staff in the Northeast and Mid-Atlantic United States.
Ho Alphina et al. Journal of public health management and practice : JPHMP 2017 Mar - Unmet Needs for Analyzing Biological Big Data: A Survey of 704 NSF Principal Investigators
Barone L, et al. bioRxiv, Feb 27, 2017. - Phylodynamic inference across epidemic scales.
Volz Erik M et al. Molecular biology and evolution 2017 Feb - Dissecting malaria biology and epidemiology using population genetics and genomics.
Auburn Sarah et al. International journal for parasitology 2017 Feb (2-3) 77-85 - A Reverse Genetics Platform That Spans the Zika Virus Family Tree.
Widman Douglas G et al. mBio 2017 Mar (2) - SAG-QC: quality control of single amplified genome information by subtracting non-target sequences based on sequence compositions.
Maruyama Toru et al. BMC bioinformatics 2017 Mar (1) 152 - Fungal ITS1 Deep-Sequencing Strategies to Reconstruct the Composition of a 26-Species Community and Evaluation of the Gut Mycobiota of Healthy Japanese Individuals.
Motooka Daisuke et al. Frontiers in microbiology 2017 238 - PBHMDA: Path-Based Human Microbe-Disease Association Prediction.
Huang Zhi-An et al. Frontiers in microbiology 2017 233
EVOLUTION / ECOLOGY / POPULATIONS
- Genomic heterogeneity of Salmonella enterica serovar Typhimurium bacteriuria from chronic infection.
Octavia Sophie et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2017 Mar - Genome Surfing As Driver of Microbial Genomic Diversity.
Choudoir Mallory J et al. Trends in microbiology 2017 Mar - Molecular identification of Mycobacterium tuberculosis in cattle.
Sweetline Anne N et al. Veterinary microbiology 2017 Jan 81-87 - Emergence of a novel subclade of influenza A(H3N2) virus in London, December 2016 to January 2017.
Harvala Heli et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2017 Feb (8) - First Report of the East-Central South African Genotype of Chikungunya Virus in Rio de Janeiro, Brazil.
Souza Thiara Manuele Alves et al. PLoS currents 2017 Feb - Genome Hotspots for Nucleotide Substitutions and the Evolution of Influenza A (H1N1) Human Strains.
Civetta Alberto et al. Genome biology and evolution 2016 Apr (4) 986-93 - Diversification of Orientia tsutsugamushi genotypes by intragenic recombination and their potential expansion in endemic areas.
Kim Gwanghun et al. PLoS neglected tropical diseases 2017 Mar (3) e0005408
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
- Characterisation of invasive clinical Haemophilus influenzae isolates in Queensland, Australia using whole-genome sequencing.
Staples M et al. Epidemiology and infection 2017 Mar 1-10 - Members of a new subgroup of Streptococcus anginosus harbor virulence related genes previously observed in Streptococcus pyogenes.
Babbar Anshu et al. International journal of medical microbiology : IJMM 2017 Feb - Short-read whole genome sequencing for determination of antimicrobial resistance mechanisms and capsular serotypes of current invasive Streptococcus agalactiae recovered in the United States.
Metcalf Benjamin J et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2017 Feb - Molecular prevalence of putative virulence-associated genes in Brucella melitensis and Brucella abortus isolates from human and livestock specimens in Iran.
Hashemifar Iman et al. Microbial pathogenesis 2017 Mar - Molecular mechanisms of polymyxin resistance: knowns and unknowns.
Baron Sophie et al. International journal of antimicrobial agents 2016 Dec (6) 583-591 - Genome analysis following a national increase in Scarlet Fever in England 2014.
Chalker Victoria et al. BMC genomics 2017 Mar (1) 224 - Increase in Human Infections with Avian Influenza A(H7N9) Virus During the Fifth Epidemic - China, October 2016-February 2017.
Iuliano A Danielle et al. MMWR. Morbidity and mortality weekly report 2017 Mar (9) 254-255
- Associations of Adenovirus Genotypes in Korean Acute Gastroenteritis Patients with Respiratory Symptoms and Intussusception.
Kim Jae-Seok et al. BioMed research international 2017 1602054 - Microevolution of Serial Clinical Isolates of Cryptococcus neoformans var. grubii and C. gattii.
Chen Yuan et al. mBio 2017 Mar (2)
DETECTION / DIAGNOSIS
- Whole-genome sequencing in the epidemiology of Campylobacter jejuni infections.
Llarena Ann-Katrin et al. Journal of clinical microbiology 2017 Mar - Multilocus sequence type profiles of Bacillus cereus isolates from infant formula in China.
Yang Yong et al. Food microbiology 2017 Apr 46-50 - Evaluating next-generation sequencing for direct clinical diagnostics in diarrhoeal disease.
Joensen K G et al. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 2017 Mar - Clonal distribution and associated characteristics of Escherichia coli clinical and surveillance isolates from a military medical center.
Manges Amee R et al. Diagnostic microbiology and infectious disease 2017 Apr (4) 382-385 - Same-day diagnostic and surveillance data for tuberculosis via whole genome sequencing of direct respiratory samples.
Votintseva Antonina A et al. Journal of clinical microbiology 2017 Mar - Variable-number tandem repeat markers for Mycobacterium intracellulare genotyping: comparison to the 16S rRNA gene sequencing.
Chen Kaisen et al. Journal of infection in developing countries 2017 Feb (2) 158-165 - Zika Virus Infection and Prolonged Viremia in Whole-Blood Specimens.
Mansuy Jean Michel et al. Emerging infectious diseases 2017 May (5) - Implications of hepatitis C virus subtype 1a migration patterns for virus genetic sequencing policies in Italy.
Cuypers Lize et al. BMC evolutionary biology 2017 Mar (1) 70 - Molecular tests potentially improving HPV screening and genotyping for cervical cancer prevention.
Gradíssimo Ana et al. Expert review of molecular diagnostics 2017 Feb 1-13 - Ebola Virus RNA in Semen from an HIV-Positive Survivor of Ebola.
Purpura Lawrence J et al. Emerging infectious diseases 2017 Apr (4) - Using record linkage to examine testing patterns for respiratory viruses among children born in Western Australia.
Lim F J et al. Epidemiology and infection 2017 Mar 1-11
- Evaluating novel diagnostics in an outbreak setting: lessons learned from Ebola.
Pollock Nira R et al. Journal of clinical microbiology 2017 Mar - Nasopharyngeal Protein Biomarkers of Acute Respiratory Virus Infection.
Burke Thomas W et al. EBioMedicine 2017 Feb - Usefulness of molecular markers in the diagnosis of occupational and recreational histoplasmosis outbreaks.
Frías-De-León María Guadalupe et al. Folia microbiologica 2017 Mar (2) 111-116 - Single locus genotyping to track Leishmania donovani in the Indian subcontinent: Application in Nepal.
Rai Keshav et al. PLoS neglected tropical diseases 2017 Mar (3) e0005420 - Evaluation of four molecular methods to detect Leishmania infection in dogs.
Albuquerque Andreia et al. Parasites & vectors 2017 Mar (1) 57
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
- Outbreak of KPC-2-producing Enterobacteriaceae caused by clonal dissemination of Klebsiella pneumoniae ST307 carrying an IncX3-type plasmid harboring a truncated Tn4401a.
Kim Jung Ok et al. Diagnostic microbiology and infectious disease 2017 Apr (4) 343-348 - Utility of Combining Whole Genome Sequencing with Traditional Investigational Methods To Solve Foodborne Outbreaks of Salmonella Infections Associated with Chicken: A New Tool for Tackling This Challenging Food Vehicle.
Crowe Samuel J et al. Journal of food protection 2017 Mar 654-660 - Hepatitis A outbreak among men who have sex with men (MSM) predominantly linked with the EuroPride, the Netherlands, July 2016 to February 2017.
Freidl Gudrun S et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2017 Feb (8) - Molecular Fingerprinting Studies Do Not Support Intrahospital Transmission of Candida albicans among Candidemia Patients in Kuwait.
Asadzadeh Mohammad et al. Frontiers in microbiology 2017 247
ANTIMICROBIALS / VACCINES / INTERVENTIONS
- Generation of a Live Attenuated Influenza Vaccine that Elicits Broad Protection in Mice and Ferrets.
Wang Lulan et al. Cell host & microbe 2017 Mar (3) 334-343 - Time for Genome Editing: Next-Generation Attenuated Malaria Parasites.
Singer Mirko et al. Trends in parasitology 2017 Mar (3) 202-213
HOST-MICROBE INTERACTIONS
- The role of the microbiome in human health and disease: an introduction for clinicians
Young VB. BMJ, March 15, 2017. - Longitudinal sampling of the lung microbiota in individuals with cystic fibrosis.
Whelan Fiona J et al. PloS one 2017 (3) e0172811 - Vaginal Microbiome and Its Relationship to Behavior, Sexual Health, and Sexually Transmitted Diseases.
Lewis Felicia M T et al. Obstetrics and gynecology 2017 Mar - Intestinal dysbiosis in preterm infants preceding necrotizing enterocolitis: a systematic review and meta-analysis.
Pammi Mohan et al. Microbiome 2017 Mar (1) 31 - Transcriptome Remodeling of Acinetobacter baumannii during Infection and Treatment.
Wright Meredith S et al. mBio 2017 Mar (2) - High-risk and low-risk human papilloma virus in association to spontaneous preterm labor: a case-control study in a tertiary center, Egypt.
Mosbah Alaa et al. The journal of maternal-fetal & neonatal medicine : the official journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians 2017 Mar 1-6 - Partial dysfunction of STAT1 profoundly reduces host resistance to flaviviral infection.
Larena Maximilian et al. Virology 2017 Mar 1-6 - Increased susceptibility of blood type O individuals to develop anemia in Plasmodium vivax infection.
Resende Sarah Stela et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2017 Mar 87-92
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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