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Infectious Diseases
What's New
Last Posted: Sep 19, 2019
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C-section babies are missing key microbes-
E Callaway, Nature, September 18, 2019 -
Maternal microbiota in pregnancy and early life
B McDonald et al, Sci Trans Medicine, September 2019 -
Real-time flu tracking- By monitoring social media, scientists can monitor outbreaks as they happen.
C Schmidt, Nature Outlook, September 18, 2019 -
Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth
Y Shao et al, Nature, September 18, 2019 -
Multidrug-Resistant Malaria Expands its Reach
B Kuehn, JAMA, September 17, 2019 -
Evaluation of parameters affecting performance and reliability of machine learning-based antibiotic susceptibility testing from whole genome sequencing data.
Hicks Allison L et al. PLoS computational biology 2019 Sep (9) e1007349 -
Modified CRISPR cuts and splices whole genomes.
Service Robert F et al. Science (New York, N.Y.) 2019 08 (6456) 849 -
Redondoviridae, a Family of Small, Circular DNA Viruses of the Human Oro-Respiratory Tract Associated with Periodontitis and Critical Illness.
Abbas Arwa A et al. Cell host & microbe 2019 08 (2) 297 -
Ten simple rules for helping newcomers become contributors to open projects.
Sholler Dan et al. PLoS computational biology 2019 Sep (9) e1007296 -
The cat is out of the bag: How parasites know their hosts.
English Elizabeth D et al. PLoS biology 2019 Sep (9) e3000446
About Infectious Diseases PHGKB
The Infectious Diseases Public Health Genomics Knowledge Base (PHGKB) is an online, continuously updated, searchable database of published scientific literature, CDC resources, and other materials that address the translation of genomic discoveries into improved
Advanced Molecular Detection Clips (current edition) Published on Sep 18, 2019
Advanced Molecular Detection Clips (AMD 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.
NEWS
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New Strep A Strain Linked to Scarlet Fever Surge in U.K.
Boyles S. MedPage Today, Sep 11, 2019. -
MRSA Susceptibility Study Uncovers Protective Variant in Methyltransferase
GenomeWeb, Sept 16, 2019. -
Unreported Zika Outbreak in Cuba Uncovered With Genomics, Travel Surveillance
GenomeWeb, Aug 22, 2019. -
Researchers Discover New Family of Viruses
Offord C. The Scientist, Sep 1, 2019. -
Scientists use gene-edited stem cells to treat HIV--with mixed success
Lambert J. Nature, Sep 11, 2019. -
Gut Microbes Boost Flu Vaccine's Success: Clinical Trial
Olena A. The Scientist, Sep 5, 2019. -
Genetically Modified Mosquitoes Are Breeding in Brazil, Despite Biotech Firm's Assurances to the Contrary
Dvorsky G. Gizmodo, Sep 15, 2019.
CONCEPTS / COMMENTS
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Bacterial Persisters and Infection: Past, Present, and Progressing.
Gollan Bridget et al. Annual review of microbiology 2019 Sep 359-385 -
The evolution of antibiotic resistance
MacLean RC, San Millan A. Science, Sep 13, 2019. -
The cat is out of the bag: How parasites know their hosts.
English Elizabeth D et al. PLoS biology 2019 Sep (9) e3000446 -
Rock-paper-scissors: Engineered population dynamics increase genetic stability.
Liao Michael J et al. Science (New York, N.Y.) 2019 09 (6457) 1045-1049 -
Engineering microbial peer pressure.
Johnston Chad W et al. Science (New York, N.Y.) 2019 09 (6457) 986-987 -
Modified CRISPR cuts and splices whole genomes.
Service Robert F et al. Science (New York, N.Y.) 2019 08 (6456) 849 -
Ten simple rules for helping newcomers become contributors to open projects.
Sholler Dan et al. PLoS computational biology 2019 Sep (9) e1007296
METHODS / TOOLS
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Evaluation of Rapid Library Preparation Protocols for Whole Genome Sequencing Based Outbreak Investigation.
Seth-Smith Helena M B et al. Frontiers in public health 2019 241 -
A New Solid Matrix for Preservation of Viral Nucleic Acid from Clinical Specimens at Ambient Temperature.
Cromeans Theresa et al. Journal of virological methods 2019 Sep 113732
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Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes.
De Maio Nicola et al. Microbial genomics 2019 09
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Is reliance on an inaccurate genome sequence sabotaging your experiments?
Baptista Rodrigo P et al. PLoS pathogens 2019 Sep (9) e1007901
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ZIKAVID-Zika virus infection database: a new platform to analyze the molecular impact of Zika virus infection.
Rosa Rafael L et al. Journal of neurovirology 2019 Sep -
Introducing SPeDE: High-Throughput Dereplication and Accurate Determination of Microbial Diversity from Matrix-Assisted Laser Desorption-Ionization Time of Flight Mass Spectrometry Data.
Dumolin Charles et al. mSystems 2019 Sep (5) -
OutbreakFinder: a visualization tool for rapid detection of bacterial strain clusters based on optimized multidimensional scaling.
Tsai Ming-Hsin et al. PeerJ 2019 e7600 -
Evaluation of parameters affecting performance and reliability of machine learning-based antibiotic susceptibility testing from whole genome sequencing data.
Hicks Allison L et al. PLoS computational biology 2019 Sep (9) e1007349 -
Consistent and correctable bias in metagenomic sequencing experiments.
McLaren Michael R et al. eLife 2019 Sep -
CCMP: software-as-a-service approach for fully-automated microbiome profiling.
Park Sung Yong et al. Journal of biomedical informatics: X 2019 Jun -
Baseline human gut microbiota profile in healthy people and standard reporting template.
King Charles H et al. PloS one 2019 (9) e0206484
EVOLUTION / ECOLOGY / POPULATIONS
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Burkholderia pseudomallei, the causative agent of melioidosis, is rare but ecologically established and widely dispersed in the environment in Puerto Rico.
Hall Carina M et al. PLoS neglected tropical diseases 2019 Sep (9) e0007727
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Multiple introductions of methicillin-resistant Staphylococcus aureus ST612 into Western Australia associated with both human and equine reservoirs.
Murphy Riley Jt et al. International journal of antimicrobial agents 2019 Aug -
The molecular clock of Mycobacterium tuberculosis.
Menardo Fabrizio et al. PLoS pathogens 2019 Sep (9) e1008067 -
Hand-Foot-and-Mouth Disease in Uruguay: Coxsackievirus A6 Identified as Causative of an Outbreak in a Rural Childcare Center.
Lizasoain A et al. Journal of medical virology 2019 Sep -
Updated classification of norovirus genogroups and genotypes.
Chhabra Preeti et al. The Journal of general virology 2019 Sep
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Outbreak of diarrhoea in piglets caused by novel rotavirus genotype G4P[49] in north-western district of Bangladesh, February 2014.
Sarkar Shamim et al. Transboundary and emerging diseases 2019 Aug
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Origins of the arctic fox variant rabies viruses responsible for recent cases of the disease in southern Ontario.
Nadin-Davis Susan A et al. PLoS neglected tropical diseases 2019 Sep (9) e0007699
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Molecular typing of Cryptosporidium in Israel.
Grossman Tamar et al. PloS one 2019 (9) e0219977
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A global genotyping survey of Strongyloides stercoralis and Strongyloides fuelleborni using deep amplicon sequencing.
Barratt Joel L N et al. PLoS neglected tropical diseases 2019 Sep (9) e0007609
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
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Emergence of dominant toxigenic M1T1 Streptococcus pyogenes clone during increased scarlet fever activity in England: a population-based molecular epidemiological study.
Lynskey Nicola N et al. The Lancet. Infectious diseases 2019 Sep -
Contrasting patterns of longitudinal population dynamics and antimicrobial resistance mechanisms in two priority bacterial pathogens over 7 years in a single center.
Ellington Matthew J et al. Genome biology 2019 09 (1) 184 -
Evolution of Outbreak-Causing Carbapenem-Resistant Klebsiella pneumoniae ST258 at a Tertiary Care Hospital over 8 Years.
Marsh Jane W et al. mBio 2019 Sep (5) -
"The recent emergence of a highly related virulent Clostridium difficile clade with unique characteristics".
Shaw Helen Alexandra et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2019 Sep -
Dramatic rise in the proportion of ESBL-producing Escherichia coli and Klebsiella pneumoniae among clinical isolates identified in Canadian hospital laboratories from 2007 to 2016.
Denisuik Andrew J et al. The Journal of antimicrobial chemotherapy 2019 Aug (Supplement_4) iv64-iv71 -
Pasteurella multocida: Genotypes and Genomics.
Peng Zhong et al. Microbiology and molecular biology reviews : MMBR 2019 Nov (4) -
Influence of agricultural antibiotic use on chicken meat-associated enterococci and their connection to the clinic.
Manson Abigail L et al. Applied and environmental microbiology 2019 Aug -
Colistin resistance emerges in pandrug-resistant Klebsiella pneumoniae epidemic clones in Rio de Janeiro, Brazil.
Longo Luís G A et al. International journal of antimicrobial agents 2019 Aug -
Redondoviridae, a Family of Small, Circular DNA Viruses of the Human Oro-Respiratory Tract Associated with Periodontitis and Critical Illness.
Abbas Arwa A et al. Cell host & microbe 2019 08 (2) 297 -
Understanding Enterovirus D68-Induced Neurologic Disease: A Basic Science Review.
Hixon Alison M et al. Viruses 2019 Sep (9) -
A unique multidrug-resistant clonal Trichophyton population distinct from Trichophytonmentagrophytes / Trichophytoninterdigitale complex causing an ongoing alarming dermatophytosis outbreak in India: genomic insights and resistance profile.
Singh Ashutosh et al. Fungal genetics and biology : FG & B 2019 Sep 103266 -
Epidemiological distribution of genotypes of Giardia duodenalis in humans in Spain.
Wang Yuanfei et al. Parasites & vectors 2019 Sep (1) 432
DETECTION / DIAGNOSIS
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Pilot evaluation of a fully automated bioinformatics system for the analysis of MRSA genomes and detection of outbreaks.
Brown Nicholas M et al. Journal of clinical microbiology 2019 Aug -
Informal genomic surveillance of regional distribution of Salmonella Typhi genotypes and antimicrobial resistance via returning travellers.
Ingle Danielle J et al. PLoS neglected tropical diseases 2019 Sep (9) e0007620 -
Quality assurance for genotyping and resistance testing of Clostridium (Clostridioides) difficile isolates - experiences from the first inter-laboratory ring trial in four German speaking countries.
Berger Fabian K et al. Anaerobe 2019 Sep 102093
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Molecular imaging of bacterial infections: Overcoming the barriers to clinical translation.
Ordonez Alvaro A et al. Science translational medicine 2019 Sep (508) -
A multilocus sequence typing scheme for Mycobacterium abscessus complex (MAB-multilocus sequence typing) using whole-genome sequencing data.
Wuzinski Michelle et al. International journal of mycobacteriology (3) 273-280 -
Comparing QuantiFERON-TB Gold Plus with other tests to diagnose Mycobacterium tuberculosis infection.
Venkatappa Thara K et al. Journal of clinical microbiology 2019 Aug
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A Deep-Sequencing Workflow for the Fast and Efficient Generation of High-Quality African Swine Fever Virus Whole-Genome Sequences.
Forth Jan H et al. Viruses 2019 Sep (9) -
Development and validation of a pen side test for Rift Valley fever.
Cêtre-Sossah Catherine et al. PLoS neglected tropical diseases 2019 Sep (9) e0007700 -
The detection of Coccidioides from ambient air in Phoenix, Arizona: Evidence of uneven distribution and seasonality.
Gade Lalitha et al. Medical mycology 2019 Sep
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Real-time PCR for diagnosis of imported schistosomiasis.
Guegan Hélène et al. PLoS neglected tropical diseases 2019 Sep (9) e0007711 -
A novel MALDI-TOF MS-based method for blood meal identification in insect vectors: A proof of concept study on phlebotomine sand flies.
Hlavackova Kristyna et al. PLoS neglected tropical diseases 2019 Sep (9) e0007669
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
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An investigation of Salmonella Fluntern illnesses linked to leopard geckos-United States, 2018.
Koski Lia et al. Zoonoses and public health 2019 Sep
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Multistate outbreak of Salmonella Poona infections associated with imported cucumbers, 2015-2016.
Laughlin M et al. Epidemiology and infection 2019 Sep e270
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Comparative Genomic Analysis of the 2016 Vibrio cholerae Outbreak in South Korea.
Ha Sung-Min et al. Frontiers in public health 2019 228
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Molecular characterization of carbapenem-resistant Acinetobacter baumannii using WGS revealed missed transmission events in Germany from 2012-15.
Eigenbrod Tatjana et al. The Journal of antimicrobial chemotherapy 2019 Aug
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Whole Genome Sequencing for Surveillance of Diphtheria in Low Incidence Settings.
Seth-Smith Helena M B et al. Frontiers in public health 2019 235 -
Population structure and transmission modes of indigenous typhoid in Taiwan.
Wang Kai-Yu et al. BMC medical genomics 2019 09 (1) 126 -
Salmonellosis outbreak with novel Salmonella enterica subspecies enterica serotype (11:z41:e,n,z15) attributable to sesame products in five European countries, 2016 to 2017.
Meinen Anika et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2019 Sep (36)
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MYCOBACTERIUM CHIMAERA INFECTIONS AFTER CARDIOVASCULAR SURGERY: LESSONS FROM A GLOBAL OUTBREAK.
Diekema Daniel J et al. Transactions of the American Clinical and Climatological Association 2019 136-144
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Evaluating the use of whole genome sequencing for the investigation of a large mumps outbreak in Ontario, Canada.
Stapleton P J et al. Scientific reports 2019 Aug (1) 12615 -
Bridging of Neisseria gonorrhoeae lineages across sexual networks in the HIV pre-exposure prophylaxis era.
Williamson Deborah A et al. Nature communications 2019 Sep (1) 3988 -
The use of genome sequencing to investigate an outbreak of hospital-acquired mucormycosis in transplant patients.
Marek Caitlyn et al. Transplant infectious disease : an official journal of the Transplantation Society 2019 Aug e13163
ANTIMICROBIALS / VACCINES / INTERVENTIONS
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Altering Antibiotic Regimen as Additional Control Measure in Suspected Multi-Drug-Resistant Enterobacter cloacae Outbreak in a Neonatal Intensive Care Unit.
Eichel Vanessa et al. The Journal of hospital infection 2019 Sep
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Genetic stability of live-attenuated Zika vaccine candidates.
Muruato Antonio E et al. Antiviral research 2019 Sep 104596 -
Deployment and utilization of next-generation sequencing of Plasmodium falciparum to guide anti-malarial drug policy decisions in sub-Saharan Africa: opportunities and challenges.
Ishengoma Deus S et al. Malaria journal 2019 Sep (1) 267 -
Transgenic Aedes aegypti Mosquitoes Transfer Genes into a Natural Population.
Evans Benjamin R et al. Scientific reports 2019 Sep (1) 13047
HOST-MICROBE INTERACTIONS
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The impact of KIR/HLA genes on the risk of developing multibacillary leprosy.
Alves Hugo Vicentin et al. PLoS neglected tropical diseases 2019 Sep (9) e0007696 -
HIV Rebound Is Predominantly Fueled by Genetically Identical Viral Expansions from Diverse Reservoirs.
De Scheerder Marie-Angélique et al. Cell host & microbe 2019 Sep (3) 347-358.e7 -
The ferroportin Q248H mutation protects from anemia, but not malaria or bacteremia.
Muriuki John Muthii et al. Science advances 2019 Sep (9) eaaw0109
indicates that at least one CDC-affiliated author; indicates that the article addresses aspects of implementation or evaluation in clinical or public health practice. 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.
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Disclaimer: Articles listed in the Public Health Knowledge Base are selected by the CDC Office of Public Health Genomics to provide current awareness of the literature and news. Inclusion in the update 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 update, 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.