Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Oct 10, 2019

Advanced Molecular Detection Clips Content

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

NEWS

• Lab-made primordial soup yields RNA bases
  Castelvecchi D. Nature, Oct 4, 2019.
• Papers highlight challenges, solutions in developing antibiotics
  Dall C. CIDRAP, Oct 8, 2019.
• C. auris outbreak spreads in 9 California health facilities after single introduction
  Healio, Oct 5, 2019.
• In the Pancreas, Common Fungi May Drive Cancer
  Sheikh K. New York Times, Oct 3, 2019.

METHODS / TOOLS

• BELLA: Berkeley Efficient Long-Read to Long-Read Aligner and Overlapper
  Guidi G, et al. bioRxiv, Oct 10, 2019.
• The Mobilome: Metagenomic Analysis of Circular Plasmids, Viruses, and Other Extrachromosomal Elements.
  Browne Patrick Denis et al. Methods in molecular biology (Clifton, N.J.) 2020 253-264
• Plasmid Reconstruction from Next-Gen Data: A Detailed Protocol for the Use of PLACNETw for the Reconstruction of Plasmids from WGS Datasets.
  de Toro María et al. Methods in molecular biology (Clifton, N.J.) 2020 323-339
• WASPS: Web-Assisted Symbolic Plasmid Synteny Server.
  Badel Catherine et al. Bioinformatics (Oxford, England) 2019 Oct
• A systematic review and evaluation of Zika virus forecasting and prediction research during a public health emergency of international concern.
  Kobres Pei-Ying et al. PLoS neglected tropical diseases 2019 Oct (10) e0007451  

EVOLUTION / ECOLOGY / POPULATIONS

• Invasive disease potential of Streptococcus pneumoniae serotypes before and after 10-valent pneumococcal conjugate vaccine introduction in a rural area, southern Mozambique.
  Massora Sérgio et al. Vaccine 2019 Sep  
• Co-existence of multiple distinct lineages in Vibrio parahaemolyticus serotype O4:K12.
  Zhao Lin et al. Microbial genomics 2019 Oct
• Strain diversity of Treponema pallidum subsp. pertenue suggests rare interspecies transmission in African nonhuman primates.
  Chuma Idrissa S et al. Scientific reports 2019 Oct (1) 14243
• Molecular Surveillance of EHV-1 Strains Circulating in France during and after the Major 2009 Outbreak in Normandy Involving Respiratory Infection, Neurological Disorder, and Abortion.
  Sutton Gabrielle et al. Viruses 2019 Oct (10)
• Lassa virus circulating in Liberia: a retrospective genomic characterisation.
  Wiley Michael R et al. The Lancet. Infectious diseases 2019 Oct 
• Bloodmeal, Host Selection, and Genetic Admixture Analyses of Culex pipiens Complex (Diptera: Culicidae) Mosquitoes in Chicago, IL.
  Kothera Linda et al. Journal of medical entomology 2019 Oct 

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Evolution of the β-lactam-resistant Streptococcus pneumoniae PMEN3 clone over a 30 year period in Barcelona, Spain.
  Càmara Jordi et al. The Journal of antimicrobial chemotherapy 2018 11 (11) 2941-2951
• Six penA codons accurately and reliably predict cefixime-decreased susceptibility in Neisseria gonorrhoeae.
  Deng Xiaomeng et al. The Journal of infectious diseases 2019 Oct
• Molecular epidemiology of isolates with multiple mcr plasmids from a pig farm in Great Britain: the effects of colistin withdrawal in the short and long term.
  Duggett Nicholas A et al. The Journal of antimicrobial chemotherapy 2018 11 (11) 3025-3033 
• Genome-wide assessment of antimicrobial tolerance in Yersinia pseudotuberculosis under ciprofloxacin stress.
  Willcocks Samuel et al. Microbial genomics 2019 Oct
• Long-term Persistence of an Extensively Drug Resistant Subclade of Globally Distributed Pseudomonas aeruginosa Clonal Complex 446 in an Academic Medical Center.
  Pincus Nathan B et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2019 Oct
• Identification and characterization of " Haemophilus quentini" strains causing invasive disease in Ontario, Canada (2016-2018).
  Kus Julianne V et al. Journal of clinical microbiology 2019 Oct
• PacBio Amplicon Sequencing Method To Measure Pilin Antigenic Variation Frequencies of Neisseria gonorrhoeae.
  Ozer Egon A et al. mSphere 2019 Oct (5)
• Plasmid Dissemination and Selection of a Multidrug-Resistant Klebsiella pneumoniae Strain during Transplant-Associated Antibiotic Therapy.
  Conlan Sean et al. mBio 2019 Oct (5)
• Isolation and growth characterization of novel full length and deletion mutant human MERS-CoV strains from clinical specimens collected during 2015.
  Tamin Azaibi et al. The Journal of general virology 2019 Oct 
• Molecular epidemiology and clinical characteristics of norovirus gastroenteritis with seizures in children in Taiwan, 2006-2015.
  Chen Ying Fang Elaine et al. Medicine 2019 Oct (40) e17269
• Analysis of Plasmodium falciparum Pfcrt and Pfmdr1 genes in parasite isolates from asymptomatic individuals in Southeast Nigeria 11 years after withdrawal of chloroquine.
  Ikegbunam Moses N et al. Malaria journal 2019 Oct (1) 343

DETECTION / DIAGNOSIS

• Optimization of the MALDIxin test for the rapid identification of colistin resistance in Klebsiella pneumoniae using MALDI-TOF MS.
  Dortet Laurent et al. The Journal of antimicrobial chemotherapy 2019 Oct
• Implications of mobile genetic elements for Salmonella enterica single nucleotide polymorphism subtyping and source tracking investigations.
  Li Shaoting et al. Applied and environmental microbiology 2019 Oct 
• Genus-wide Yersinia core-genome multilocus sequence typing for species identification and strain characterization.
  Savin Cyril et al. Microbial genomics 2019 Oct
• Janibacter species with evidence of genomic polymorphism isolated from resected heart valve in a patient with aortic stenosis.
  Malania Lile et al. Infectious disease reports 2019 Sep (2) 8132 
• Metagenomic signatures of gut infection caused by different Escherichia coli pathotypes.
  Peña-Gonzalez Angela et al. Applied and environmental microbiology 2019 Oct
• Bacteria and fungi in acute cholecystitis. A prospective study comparing next generation sequencing to culture.
  Dyrhovden Ruben et al. The Journal of infection 2019 Oct
• Nanotechnology: a reality for diagnosis of HCV infectious disease.
  Arca-Lafuente Sonia et al. The Journal of infection 2019 Sep
• Application of metagenomic shotgun sequencing to detect vector-borne pathogens in clinical blood samples.
  Vijayvargiya Prakhar et al. PloS one 2019 (10) e0222915
• Standardising surveillance of hepatitis E virus infection in the EU/EEA: A review of national practices and suggestions for the way forward.
  Adlhoch Cornelia et al. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2019 Sep 63-67 
• Multiplex PCR assay for simultaneous detection and differentiation of Entamoeba histolytica, Giardia lamblia , and Salmonella spp. in the municipality-supplied drinking water.
  Shankar Prem et al. Journal of laboratory physicians (3) 275-280

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Onsite investigation at a mail-order hatchery following a multistate Salmonella illness outbreak linked to live poultry-United States, 2018.
  Robertson Scott A et al. Poultry science 2019 Oct  
• A complete genome screening program of clinical methicillin-resistant Staphylococcus aureus isolates identifies the origin and progression of a neonatal intensive care unit outbreak.
  Sullivan Mitchell J et al. Journal of clinical microbiology 2019 Oct 
• Sequence-based epidemiology of an OXA-48 plasmid during a hospital outbreak.
  Hidalgo Laura et al. Antimicrobial agents and chemotherapy 2019 Oct
• Improved characterisation of MRSA transmission using within-host bacterial sequence diversity.
  Hall Matthew D et al. eLife 2019 Oct
• Resolution by deep sequencing of a dual hepatitis E virus infection transmitted via blood components.
  Ledesma Juan et al. The Journal of general virology 2019 Oct
• High-resolution micro-epidemiology of parasite spatial and temporal dynamics in a high malaria transmission setting in Kenya
  Nelson CS, et al. bioRxiv, Oct 9, 2019.

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• Integrated evolutionary analysis reveals antimicrobial peptides with limited resistance.
  Spohn Réka et al. Nature communications 2019 Oct (1) 4538
• Polyclonal and convergent antibody response to Ebola virus vaccine rVSV-ZEBOV.
  Ehrhardt Stefanie A et al. Nature medicine 2019 Oct

HOST-MICROBE INTERACTIONS

• Early progression to active tuberculosis is a highly heritable trait driven by 3q23 in Peruvians.
  Luo Yang et al. Nature communications 2019 Aug (1) 3765
• Genetic associations of vitamin D receptor polymorphisms with advanced liver fibrosis and response to pegylated interferon-based therapy in chronic hepatitis C.
  Thanapirom Kessarin et al. PeerJ 2019 e7666
• The influence of interleukin 28B polymorphisms on the risk of hepatocellular carcinoma among patients with HBV or HCV infection: An updated meta-analysis.
  Qin Shaoyou et al. Medicine 2019 Sep (38) e17275 
• Four Weeks of Treatment With Rifaximin Fails to Significantly Alter Microbial Diversity in Rectal Samples of HIV-Infected Immune Non-Responders (ACTG A5286) Which May be Attributed to Rectal Swab Use.
  Williams Brett B et al. Pathogens & immunity 2019 (2) 235-250 
• Longitudinal antibody responses in people who inject drugs infected with similar HIV strains.
  Redd Andrew D et al. The Journal of infectious diseases 2019 Oct
• Synthetic ecology of the human gut microbiota.
  Vrancken Gino et al. Nature reviews. Microbiology 2019 Oct
• Transmission and clearance of potential procarcinogenic bacteria during fecal microbiota transplantation for recurrent Clostridioides difficile.
  Drewes Julia L et al. JCI insight 2019 Oct (19)
• Diversity of vaginal microbiome and metabolome during genital infections.
  Ceccarani Camilla et al. Scientific reports 2019 Oct (1) 14095
• Isolates from Colonic Spirochetosis in Humans Show High Genomic Divergence and Potential Pathogenic Features but Are Not Detected Using Standard Primers for the Human Microbiota.
  Thorell Kaisa et al. Journal of bacteriology 2019 Nov (21)

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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