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Infectious Diseases
What's New
Last Posted: Jul 18, 2019
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How the Microbiome Influences Drug Action
S Williams, The Scientist, July 15, 2019 -
A 5-year study of human parechoviruses in children living in bad sanitation conditions and non-polio acute flaccid paralysis children from Greece.
Ioulia Karageorgou et al. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 2019 Jul -
Added diagnostic value of 16S rRNA gene pan-mycobacterial PCR for nontuberculous mycobacterial infections: a 10-year retrospective study.
Simon Andenmatten et al. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 2019 Jul -
Changing pattern of the genetic diversities of Plasmodium falciparum merozoite surface protein-1 and merozoite surface protein-2 in Myanmar isolates.
Lê Huong Giang et al. Malaria journal 2019 Jul (1) 241 -
Crypt- and Mucosa-Associated Core Microbiotas in Humans and Their Alteration in Colon Cancer Patients.
Saffarian Azadeh et al. mBio 2019 Jul (4) -
Detection of nosocomial outbreaks: Genomic surveillance takes the lead.
Hayden Mary K et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2019 Jul -
Genome and plasmid diversity of Extended-Spectrum β-Lactamase-producing Escherichia coli ST131 - tracking phylogenetic trajectories with Bayesian inference.
Ny Sofia et al. Scientific reports 2019 Jul (1) 10291 -
High-throughput sequencing for the aetiologic identification of viral encephalitis, meningoencephalitis, and meningitis. A narrative review and clinical appraisal.
Zanella M-C et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2019 Apr (4) 422-430 -
Identification of a Novel Plasmid Lineage Associated With the Dissemination of Metallo-β-Lactamase Genes Among Pseudomonads.
Di Pilato Vincenzo et al. Frontiers in microbiology 2019 1504 -
Identification of Pathogen Genomic Differences That Impact Human Immune Response and Disease during Cryptococcus neoformans Infection.
Gerstein Aleeza C et al. mBio 2019 Jul (4)
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 Jul 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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Digital DNA Detection: A CRISPR-based electronic sensor flags target DNA sequences at high speed
Williams R. The Scientist, Jul 15, 2019. -
HIVs genetic code, extracted from a nub of tissue, adds to evidence of virus emergence in humans a century ago
Branswell H. STAT, Jul 16, 2019. -
Investigation into fungal infection reveals genetic vulnerability in Hmong
Tyrrell KA. Univ of Wisconsin-Madison, Jul 15, 2019. -
Worlds most invasive mosquito nearly eradicated from two islands in China
Guglielmi G. Nature, Jul 17, 2019.
CONCEPTS / COMMENTS
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Detection of nosocomial outbreaks: Genomic surveillance takes the lead.
Hayden Mary K et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2019 Jul -
Responsible stewardship for communicating microbiome research to the press and public.
Shan Yue et al. Nature medicine 2019 06 (6) 872-874
METHODS / TOOLS
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Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps.
Dilthey Alexander T et al. Nature communications 2019 Jul (1) 3066 -
OMMA enables population-scale analysis of complex genomic features and phylogenomic relationships from nanochannel-based optical maps.
Leung Alden King-Yung et al. GigaScience 2019 Jul (7) -
A binning tool to reconstruct viral haplotypes from assembled contigs
Chen J, et al. bioRxiv, Jul 16, 2019. -
Adaptive Estimation for Epidemic Renewal and Phylogenetic Skyline Models
Parag KV, Donnelly CA. bioRxiv, Jul 16, 2019. -
Quantifying the surveillance required to sustain genetic marker-based antibiotic resistance diagnostics
Hicks AL, et al. bioRxiv, Jul 11, 2019. -
A likelihood ratio-based approach for improved source attribution in microbiological forensic investigations.
Lindgren Petter et al. Forensic science international 2019 Jul 109869
EVOLUTION / ECOLOGY / POPULATIONS
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Whole genome analysis reveals new insights into the molecular characteristics of Clostridioides difficile NAP1/BI/027/ST1 clinical isolates in the People's Republic of China.
Lv Tao et al. Infection and drug resistance 2019 1783-1794 -
Domestication of Campylobacter jejuni NCTC 11168.
Pascoe Ben et al. Microbial genomics 2019 Jul -
Genomic surveillance of invasive meningococcal disease in the Czech Republic, 2015-2017.
Krizova Pavla et al. PloS one 2019 (7) e0219477 -
Complete Genome Sequence of a Severe Acute Respiratory Syndrome-Related Coronavirus from Kenyan Bats.
Tao Ying et al. Microbiology resource announcements 2019 Jul (28)
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A near-full-length HIV-1 genome from 1966 recovered from formalin-fixed paraffin-embedded tissue
Gryseels S, et al. bioRxiv, Jul 1, 2019. -
A 5-year study of human parechoviruses in children living in bad sanitation conditions and non-polio acute flaccid paralysis children from Greece.
Ioulia Karageorgou et al. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 2019 Jul -
Changing pattern of the genetic diversities of Plasmodium falciparum merozoite surface protein-1 and merozoite surface protein-2 in Myanmar isolates.
Lê Huong Giang et al. Malaria journal 2019 Jul (1) 241
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
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Molecular characterization of Campylobacter causing human clinical infection using whole-genome sequencing: Virulence, antimicrobial resistance and phylogeny in Ireland.
Redondo Natalia et al. PloS one 2019 (7) e0219088 -
Genome sequencing and analysis of Salmonella enterica subsp. enterica serovar Stanley UPM 517: Insights on its virulence-associated elements and their potentials as vaccine candidates.
Ashari Khalidah Syahirah et al. PeerJ 2019 e6948 -
Use of Whole Genome Sequencing for the Molecular Comparison of Neisseria gonorrhoeae Isolates With Decreased Susceptibility to Extended Spectrum Cephalosporins From 2 Geographically Different Regions in America.
Gianecini Ricardo A et al. Sexually transmitted diseases 2019 Aug (8) 548-555 -
Identification of a Novel Plasmid Lineage Associated With the Dissemination of Metallo-β-Lactamase Genes Among Pseudomonads.
Di Pilato Vincenzo et al. Frontiers in microbiology 2019 1504 -
Genome and plasmid diversity of Extended-Spectrum β-Lactamase-producing Escherichia coli ST131 - tracking phylogenetic trajectories with Bayesian inference.
Ny Sofia et al. Scientific reports 2019 Jul (1) 10291 -
Evaluating the clinical significance of nontuberculous mycobacteria isolated from respiratory samples in Iran: an often overlooked disease.
Mortazavi Zahra et al. Infection and drug resistance 2019 1917-1927 -
Identification of Pathogen Genomic Differences That Impact Human Immune Response and Disease during Cryptococcus neoformans Infection.
Gerstein Aleeza C et al. mBio 2019 Jul (4) -
Analysis-ready datasets for insecticide resistance phenotype and genotype frequency in African malaria vectors.
Moyes Catherine L et al. Scientific data 2019 Jul (1) 121
DETECTION / DIAGNOSIS
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Rapid screening and early precautions for carbapenem-resistant Acinetobacter baumannii carriers decreased nosocomial transmission in hospital settings: a quasi-experimental study.
Yamamoto Norihisa et al. Antimicrobial resistance and infection control 2019 110
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Optical DNA Mapping Combined with Cas9-Targeted Resistance Gene Identification for Rapid Tracking of Resistance Plasmids in a Neonatal Intensive Care Unit Outbreak.
Bikkarolla Santosh K et al. mBio 2019 Jul (4) -
Detection of respiratory pathogens in clinical samples using metagenomic shotgun sequencing.
Qi Chao et al. Journal of medical microbiology 2019 Jul (7) 996-1002 -
Added diagnostic value of 16S rRNA gene pan-mycobacterial PCR for nontuberculous mycobacterial infections: a 10-year retrospective study.
Simon Andenmatten et al. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 2019 Jul -
High-throughput sequencing for the aetiologic identification of viral encephalitis, meningoencephalitis, and meningitis. A narrative review and clinical appraisal.
Zanella M-C et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2019 Apr (4) 422-430
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Improving preparedness to respond to cross-border hepatitis A outbreaks in the European Union/European Economic Area: towards comparable sequencing of hepatitis A virus.
Enkirch Theresa et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2019 Jul (28)
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Ultra-rapid, sensitive and specific digital diagnosis of HIV with a dual-channel SAW biosensor in a pilot clinical study.
Gray Eleanor R et al. NPJ digital medicine 2018 35
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
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Outbreak strain characterisation and pharyngeal carriage detection following a protracted group B meningococcal outbreak in adolescents in South-West England.
Clark Stephen A et al. Scientific reports 2019 Jul (1) 9990
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Outbreak of Vancomycin-resistant Enterococcus faecium in Interventional Radiology: Detection Through Whole Genome Sequencing-Based Surveillance.
Sundermann Alexander J et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2019 Jul
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Rabies Outbreak in Captive Big Brown Bats ( Eptesicus fuscus ) Used in a White-nose Syndrome Vaccine Trial.
Abbott Rachel C et al. Journal of wildlife diseases 2019 Jul
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Genomic analysis of respiratory syncytial virus infections in households and utility in inferring who infects the infant.
Agoti Charles N et al. Scientific reports 2019 Jul (1) 10076 -
Outbreak of human monkeypox in Nigeria in 2017-18: a clinical and epidemiological report.
Yinka-Ogunleye Adesola et al. The Lancet. Infectious diseases 2019 Jul
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Molecular Genotyping of Hepatitis A Virus, California, USA, 2017-2018.
Probert William S et al. Emerging infectious diseases 2019 Aug (8) 1594-1596
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An outbreak of epidemic keratoconjunctivitis caused by human adenovirus type 8 in primary school, southwest China.
Li Duo et al. BMC infectious diseases 2019 Jul (1) 624
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The origins and relatedness structure of mixed infections vary with local prevalence of P. falciparum malaria.
Zhu Sha Joe et al. eLife 2019 Jul
HOST-MICROBE INTERACTIONS
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Dietary quality and the colonic mucosa-associated gut microbiome in humans.
Liu Yanhong et al. The American journal of clinical nutrition 2019 Jul -
Metagenomics and transcriptomics data from human colorectal cancer.
Visnovska Tina et al. Scientific data 2019 Jul (1) 116 -
Crypt- and Mucosa-Associated Core Microbiotas in Humans and Their Alteration in Colon Cancer Patients.
Saffarian Azadeh et al. mBio 2019 Jul (4) -
Unfolding the Human Milk Microbiome Landscape in the Omics Era.
Ruiz Lorena et al. Frontiers in microbiology 2019 1378 -
Next generation microbiology and cystic fibrosis diagnostics: are we there yet?
Moser Claus et al. Current opinion in pulmonary medicine 2018 11 (6) 599-605
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.
Archived Editions
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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.