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Infectious Diseases
What's New
Last Posted: Nov 12, 2018
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The promise and peril of gene drives- A new genetic-engineering technology should be used with care
The Economist, November 8, 2018 -
An outbreak of Shigella boydii serotype 20 in January 2015 amongst United Kingdom healthcare workers involved in the Ebola response in Sierra Leone.
Todkill Daniel et al. Journal of medical microbiology 2018 Nov (11) 1596-1600 -
Estimating effects of HIV sequencing data completeness on transmission network patterns and detection of growing HIV transmission clusters.
Dasgupta Sharoda et al. AIDS research and human retroviruses 2018 Nov -
Genomic Surveillance of Enterococcus faecium Reveals Limited Sharing of Strains and Resistance Genes between Livestock and Humans in the United Kingdom.
Gouliouris Theodore et al. mBio 2018 Nov (6) -
The Microbiome and Tuberculosis: Early Evidence for Cross Talk.
Namasivayam Sivaranjani et al. mBio 2018 Sep (5) -
Circulation of Distinct Treponema pallidum Strains in Individuals with Heterosexual Orientation and Men Who Have Sex with Men (MSM).
Kojima Yoko et al. Journal of clinical microbiology 2018 Oct -
Comparison of Six Sample-to-Answer Influenza A/B and Respiratory Syncytial Virus Nucleic Acid Amplification Assays Using Respiratory Specimens from Children.
Banerjee Dithi et al. Journal of clinical microbiology 2018 Nov (11) -
Designing Studies Acceptable for Abstraction and Inclusion in Evidence-Based Laboratory Practice Guidelines.
Saubolle Michael A et al. Journal of clinical microbiology 2018 Oct -
Distinct microbes, metabolites, and ecologies define the microbiome in deficient and proficient mismatch repair colorectal cancers.
Hale Vanessa L et al. Genome medicine 2018 Oct (1) 78 -
Evaluation of Whole-Genome Sequencing for Identification and Typing of Vibrio cholerae.
Greig David R et al. Journal of clinical microbiology 2018 Nov (11)
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 Nov 8, 2018
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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Sequencing Method Screens for All Known Bacterial Pathogens, Resistance Markers
Johnson M. 360dx, Oct 24, 2018. -
Machine learning helps to identify the animals that deadly viruses call home
Callaway E. Nature, Nov 1, 2018. -
Researchers Analyze Genomes of 81 Parasitic Worm Species
Taylor AP. The Scientist, Nov 5, 2018. -
Negative HPV DNA Test Result Could Lessen Need for Cervical Cancer Screening
GenomeWeb, Nov 2, 2018. -
Just Months of American Life Change the Microbiome
Khazan O. Atlantic, Nov 1, 2018.
CONCEPTS / COMMENTS
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The Spanish Flu, Epidemics, and the Turn to Biomedical Responses.
Schwartz Jason L et al. American journal of public health 2018 Nov (11) 1455-1458 -
Neisseria gonorrhoeae Rising Infection Rates, Dwindling Treatment Options
Blank S, Daskalakis DC. New Engl J Med, Nov 8, 2018.
METHODS / TOOLS
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A computational framework to integrate high-throughput '-omics' datasets for the identification of potential mechanistic links.
Pedersen Helle Krogh et al. Nature protocols 2018 Oct -
mlplasmids: a user-friendly tool to predict plasmid- and chromosome-derived sequences for single species.
Arredondo-Alonso Sergio et al. Microbial genomics 2018 Nov -
CLIMB (the Cloud Infrastructure for Microbial Bioinformatics): an online resource for the medical microbiology community.
Connor Thomas R et al. Microbial genomics 2016 09 (9) e000086 -
Real-Time Analysis and Visualization of Pathogen Sequence Data.
Neher Richard A et al. Journal of clinical microbiology 2018 Nov (11) -
Two methods for mapping and visualizing associated data on phylogeny using ggtree.
Yu Guangchuang et al. Molecular biology and evolution 2018 Oct -
Whole-Genome Sequencing and Bioinformatic Analysis of Isolates from Foodborne Illness Outbreaks of Campylobacter jejuni and Salmonella enterica.
Oakeson Kelly F et al. Journal of clinical microbiology 2018 Nov (11) -
Designing Studies Acceptable for Abstraction and Inclusion in Evidence-Based Laboratory Practice Guidelines.
Saubolle Michael A et al. Journal of clinical microbiology 2018 Oct
EVOLUTION / ECOLOGY / POPULATIONS
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Genomic Surveillance of Enterococcus faecium Reveals Limited Sharing of Strains and Resistance Genes between Livestock and Humans in the United Kingdom.
Gouliouris Theodore et al. mBio 2018 Nov (6) -
Niche adaptation and viral transmission of human papillomaviruses from archaic hominins to modern humans.
Chen Zigui et al. PLoS pathogens 2018 Nov (11) e1007352 -
Metagenomic sequencing of HIV-1 in the blood and female genital tract reveals little quasispecies diversity during acute infection.
Piantadosi Anne et al. Journal of virology 2018 Oct -
Survey of Ebola Viruses in Frugivorous and Insectivorous Bats in Guinea, Cameroon, and the Democratic Republic of the Congo, 2015-2017.
De Nys Helene M et al. Emerging infectious diseases 2018 Dec (12) -
Comparative genomics of the major parasitic worms
International Helminth Genomes Consortium, Nat Genet, Nov 5, 2018.
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
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PacBio Genome Sequences of Escherichia coli Serotype O157:H7, Diffusely Adherent E. coli , and Salmonella enterica Strains, All Carrying Plasmids with an mcr-1 Resistance Gene.
Lindsey Rebecca L et al. Microbiology resource announcements 2018 (14)
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Tracking microevolution events among ST11 carbapenemase-producing hypervirulent Klebsiella pneumoniae outbreak strains.
Dong Ning et al. Emerging microbes & infections 2018 Aug (1) 146 -
A new mechanism of resistance of HIV-2 to integrase inhibitors: a 5 amino-acids insertion in the integrase C-terminal domain.
Le Hingrat Quentin et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2018 Nov -
Emerging implications of policies on malaria treatment: genetic changes in the Pfmdr-1 gene affecting susceptibility to artemether-lumefantrine and artesunate-amodiaquine in Africa.
Okell Lucy C et al. BMJ global health 2018 (5) e000999
DETECTION / DIAGNOSIS
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Laboratory Methods in Molecular Epidemiology: Bacterial Infections.
Riley Lee W et al. Microbiology spectrum 2018 Nov (6) -
Transmission Surveillance for Antimicrobial-Resistant Organisms in the Health System.
Pitout Johann D D et al. Microbiology spectrum 2018 Sep (5) -
Genome-based prediction of bacterial antibiotic resistance.
Su Michelle et al. Journal of clinical microbiology 2018 Oct -
Genotyping and Quantifying Lyme Pathogen Strains by Deep Sequencing of the Outer Surface Protein C ( ospC ) Locus.
Di Lia et al. Journal of clinical microbiology 2018 Nov (11) -
Evaluation of Whole-Genome Sequencing for Identification and Typing of Vibrio cholerae.
Greig David R et al. Journal of clinical microbiology 2018 Nov (11) -
PCR detection of respiratory pathogens in asymptomatic and symptomatic adults.
Sundell Nicklas et al. Journal of clinical microbiology 2018 Oct -
Identifying Mixed Mycobacterium tuberculosis Infection and Laboratory Cross-Contamination during Mycobacterial Sequencing Programs.
Wyllie David H et al. Journal of clinical microbiology 2018 Nov (11) -
Evaluation of the impact of a sequencing assay for detection of drug resistance on the clinical management of tuberculosis.
Lowenthal Phil et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2018 Nov
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Serotyping of foot-and-mouth disease virus using oxford nanopore sequencing.
Hansen Sören et al. Journal of virological methods 2018 Oct 50-53 -
Laboratory Methods in Molecular Epidemiology: Viral Infections.
Parreira Ricardo et al. Microbiology spectrum 2018 Nov (6) -
Zika Virus and the Safety of Blood Supply in Brazil: A Retrospective Epidemiological Evaluation.
Benites Bruno Deltreggia et al. The American journal of tropical medicine and hygiene 2018 Nov
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Survey of diagnostic testing for respiratory syncytial virus (RSV) in adults: Infectious disease physician practices and implications for burden estimates.
Allen Kristen E et al. Diagnostic microbiology and infectious disease 2018 Nov (3) 206-209
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Comparison of Six Sample-to-Answer Influenza A/B and Respiratory Syncytial Virus Nucleic Acid Amplification Assays Using Respiratory Specimens from Children.
Banerjee Dithi et al. Journal of clinical microbiology 2018 Nov (11) -
Development of a Digital Droplet Polymerase Chain Reaction (ddPCR) assay to detect Leishmania DNA in samples from Cutaneous Leishmaniasis patients.
Ramírez Juan David et al. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2018 Nov -
Multiplex TaqMan qPCR assay for specific identification of encapsulated Trichinella species prevalent in North America.
Almeida Marcos de et al. Memorias do Instituto Oswaldo Cruz 2018 Oct (11) e180305
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
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Circulation of Distinct Treponema pallidum Strains in Individuals with Heterosexual Orientation and Men Who Have Sex with Men (MSM).
Kojima Yoko et al. Journal of clinical microbiology 2018 Oct -
An outbreak of Shigella boydii serotype 20 in January 2015 amongst United Kingdom healthcare workers involved in the Ebola response in Sierra Leone.
Todkill Daniel et al. Journal of medical microbiology 2018 Nov (11) 1596-1600
-
Estimating effects of HIV sequencing data completeness on transmission network patterns and detection of growing HIV transmission clusters.
Dasgupta Sharoda et al. AIDS research and human retroviruses 2018 Nov
ANTIMICROBIALS / VACCINES / INTERVENTIONS
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Metanetwork Transmission Model for Predicting a Malaria-Control Strategy.
Li Bo et al. Frontiers in genetics 2018 446
HOST-MICROBE INTERACTIONS
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Mendelian susceptibility to mycobacterial disease: 2014-2018 update.
Rosain Jérémie et al. Immunology and cell biology 2018 Sep -
The Microbiome and Tuberculosis: Early Evidence for Cross Talk.
Namasivayam Sivaranjani et al. mBio 2018 Sep (5) -
Distinct microbes, metabolites, and ecologies define the microbiome in deficient and proficient mismatch repair colorectal cancers.
Hale Vanessa L et al. Genome medicine 2018 Oct (1) 78 -
The complex association of virus- and host-related factors with HCC rate following HCV clearance.
Akuta Norio et al. Journal of clinical microbiology 2018 Oct -
Gastrointestinal microbiota disruption and risk of colonization with carbapenem-resistant Pseudomonas aeruginosa in ICU patients.
Pettigrew Melinda M et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2018 Nov
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Preterm infants have distinct microbiomes not explained by mode of delivery, breastfeeding duration or antibiotic exposure.
Dahl Cecilie et al. International journal of epidemiology 2018 Oct (5) 1658-1669 -
Gut Microbiota in the First 2 Years of Life and the Association with Body Mass Index at Age 12 in a Norwegian Birth Cohort.
Stanislawski Maggie A et al. mBio 2018 Oct (5) -
Forensic human identification with targeted microbiome markers using nearest neighbor classification.
Woerner August E et al. Forensic science international. Genetics 2018 Oct 130-139
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.