Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: May 23, 2019

Advanced Molecular Detection Clips Content

• News
• Events / Training / Web Resources
• Concepts / Comments
• Methods / Tools
• Evolution / Ecology / Populations
• Pathogenicity / Antimicrobial Resistance
• Detection / Diagnosis
• Epidemiology / Outbreaks / Transmission
• Antimicrobials / Vaccines / Interventions
• Host-Microbe Interactions

NEWS

• New Graph-Based Assemblers Promise Speedier, Cheaper Computing for Long-Read Sequencing
  GenomeWeb, May 21, 2019.
• Scientists Created Bacteria With a Synthetic Genome. Is This Artificial Life? 
  Zimmer C. New York Times, May 15, 2019.
• Scientists Modify Viruses With CRISPR To Create New Weapon Against Superbugs
  Stein R. NPR, May 22, 2019.
• Host, Bacterial Genes Influence Meningitis Infection Susceptibility, Severity
  GenomeWeb, May 17, 2019.
• Long-term studies will track indelible marks of first flu
  Butler D. Nature, May 14, 2019.
• Bedbugs Predated T. rex and Triceratops, New Family Tree Shows
  Yeager A. The Scientist, May 17, 2019.

EVENTS / TRAINING / WEB RESOURCES

• Antibiotic resistant pathogen outbreak investigation: an interdisciplinary module to teach fundamentals of evolutionary biology.
  Pierce Amanda A et al. Journal of biological education 2019 (2) 150-156
• A genomic approach to microbiology
  (editorial, special issue)Nat Rev Genet, May 17, 2019.

CONCEPTS / COMMENTS

• Achieving Health Security and Threat Reduction through Sharing Sequence Data.
  Yeh Kenneth et al. Tropical medicine and infectious disease 2019 May (2)
• How microbes "jeopardize" the modern synthesis.
  Novick Aaron et al. PLoS genetics 2019 May (5) e1008166
• On the evolutionary ecology of multidrug resistance in bacteria.
  Lehtinen Sonja et al. PLoS pathogens 2019 May (5) e1007763
• PulseNet Latin America and the Caribbean Network: Present and Future.
  Chinen Isabel et al. Foodborne pathogens and disease 2019 May
• Looking backwards to move forward: the utility of sequencing historical bacterial genomes.
  Bennett Rebecca J et al. Journal of clinical microbiology 2019 May
• Emerging Challenges and Opportunities in Infectious Disease Epidemiology.
  Lewnard Joseph A et al. American journal of epidemiology 2019 May (5) 873-882

METHODS / TOOLS

• Ultra-deep, long-read nanopore sequencing of mock microbial community standards.
  Nicholls Samuel M et al. GigaScience 2019 May (5)
• Estimating epidemic incidence and prevalence from genomic data.
  Vaughan Timothy G et al. Molecular biology and evolution 2019 May
• M1CR0B1AL1Z3R-a user-friendly web server for the analysis of large-scale microbial genomics data.
  Avram Oren et al. Nucleic acids research 2019 May
• Whole-genome SNP analysis applied directly to stool for genotyping Shiga toxin-producing Escherichia coli : An advanced molecular detection method for foodborne surveillance and outbreak tracking.
  Singh Navjot et al. Journal of clinical microbiology 2019 May
• Evaluation of SNP calling methods for closely related bacterial isolates and a novel high-accuracy pipeline: BactSNP.
  Yoshimura Dai et al. Microbial genomics 2019 May
• Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands.
  Warwick-Dugdale Joanna et al. PeerJ 2019 e6800
• Illumina and Nanopore methods for whole genome sequencing of hepatitis B virus (HBV).
  McNaughton Anna L et al. Scientific reports 2019 May (1) 7081

EVOLUTION / ECOLOGY / POPULATIONS

• Emergence and divergence of major lineages of Shiga-toxin-producing Escherichia coli in Australia.
  Ingle Danielle J et al. Microbial genomics 2019 May
• Early signals of vaccine driven perturbation seen in pneumococcal carriage population genomic data.
  Chaguza Chrispin et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2019 May 
• Dengue viruses circulating in Indonesia: A systematic review and phylogenetic analysis of data from five decades.
  Harapan Harapan et al. Reviews in medical virology 2019 May e2037
• Gradual replacement of all previously circulating respiratory syncytial virus A strain with the novel ON1 genotype in Lanzhou from 2010 to 2017.
  Liang Xuan et al. Medicine 2019 May (19) e15542
• Re-emergence of chikungunya in the Republic of the Congo in 2019 associated with a possible vector-host switch.
  Matthieu Fritz et al. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2019 May
• Genome sequencing reveals coinfection by multiple chikungunya virus genotypes in a recent outbreak in Brazil.
  Machado Lais Ceschini et al. PLoS neglected tropical diseases 2019 May (5) e0007332
• Human Migration and the Spread of the Nematode Parasite Wuchereria bancrofti.
  Small Scott T et al. Molecular biology and evolution 2019 May
• Draft Genome Sequences of Leishmania ( Leishmania ) amazonensis , Leishmania ( Leishmania ) mexicana , and Leishmania ( Leishmania ) aethiopica , Potential Etiological Agents of Diffuse Cutaneous Leishmaniasis.
  Batra Dhwani et al. Microbiology resource announcements 2019 May (20) 
• Unbiased Assessment of Abundance of Rhipicephalus sanguineus sensu lato Ticks, Canine Exposure to Spotted Fever Group Rickettsia , and Risk Factors in Mexicali, México.
  Foley Janet et al. The American journal of tropical medicine and hygiene 2019 May  

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Lack of correlation of virulence gene profiles of Staphylococcus aureus bacteremia isolates with mortality.
  Park Kyung-Hwa et al. Microbial pathogenesis 2019 May 103543
• Integrating Culture-based Antibiotic Resistance Profiles with Whole-genome Sequencing Data for 11,087 Clinical Isolates.
  Galata Valentina et al. Genomics, proteomics & bioinformatics 2019 May
• Pathogenicity Factors in Group C and G Streptococci.
  Turner Claire E et al. Microbiology spectrum 2019 May (3)
• Stealth MRSA: Emergence of resistance in oxacillin-susceptible MRSA due to mec A sequence instability.
  Goering Richard V et al. Antimicrobial agents and chemotherapy 2019 May
• Complete Assembly of Escherichia coli Sequence Type 131 Genomes Using Long Reads Demonstrates Antibiotic Resistance Gene Variation within Diverse Plasmid and Chromosomal Contexts.
  Decano Arun Gonzales et al. mSphere 2019 May (3)
• Global phylogenomics of multidrug-resistant Salmonella enterica serotype Kentucky ST198.
  Hawkey Jane et al. Microbial genomics 2019 May
• Network Integrative Genomic and Transcriptomic Analysis of Carbapenem-Resistant Klebsiella pneumoniae Strains Identifies Genes for Antibiotic Resistance and Virulence.
  Lee Muyoung et al. mSystems 2019 May (4)
• An evolutionary-based approach to quantify the genetic barrier to drug resistance in fast-evolving viruses: an application to HIV-1 subtypes and integrase inhibitors.
  Theys Kristof et al. Antimicrobial agents and chemotherapy 2019 May
• Evolution and genetic diversity of the k13 gene associated with artemisinin delayed parasite clearance in Plasmodium falciparum .
  Pacheco M Andreína et al. Antimicrobial agents and chemotherapy 2019 May
• Antibiotic resistomes of healthy pig faecal metagenomes.
  Joyce Aoife et al. Microbial genomics 2019 May

DETECTION / DIAGNOSIS

• In silico Identification of Serovar-Specific Genes for Salmonella Serotyping.
  Zhang Xiaomei et al. Frontiers in microbiology 2019 835
• Genomic surveillance of Escherichia coli in municipal wastewater treatment plants as an indicator of clinically relevant pathogens and their resistance genes.
  Raven Kathy E et al. Microbial genomics 2019 May
• Use of whole genome sequencing in surveillance for antimicrobial-resistant Shigella sonnei infections acquired from domestic and international sources.
  Abelman Rebecca L et al. Microbial genomics 2019 May
• Resistance diagnostics as a public health tool to combat antibiotic resistance: A model-based evaluation.
  McAdams David et al. PLoS biology 2019 May (5) e3000250
• FLASH: a next-generation CRISPR diagnostic for multiplexed detection of antimicrobial resistance sequences.
  Quan Jenai et al. Nucleic acids research 2019 May
• Parachlamydia acanthamoebae Detected during a Pneumonia Outbreak in Southeastern Finland, in 2017⁻2018.
  Hokynar Kati et al. Microorganisms 2019 May (5)
• Progress Toward Polio Eradication — Worldwide, January 2017–March 2019
  Greene SA, et al. MMWR, May 24, 2019.  
• Expanded Molecular Testing on Patients with Suspected West Nile Virus Disease.
  Lindsey Nicole P et al. Vector borne and zoonotic diseases (Larchmont, N.Y.) 2019 May 
• In silico Selection of Amplification Targets for Rapid Polymorphism Screening in Ebola Virus Outbreaks.
  Wassenaar Trudy M et al. Frontiers in microbiology 2019 857
• Piloting a surveillance system for HIV drug resistance in the European Union.
  van de Laar Marita Jw et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2019 May (19) 
• A novel multilocus sequence typing scheme identifying genetic diversity amongst Leishmania donovani isolates from a genetically homogeneous population in the Indian subcontinent.
  Banu Sultana Shahana et al. International journal for parasitology 2019 May
• Clinical metagenomics.
  Chiu Charles Y et al. Nature reviews. Genetics 2019 Jun (6) 341-355

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Polyclonal spread of multiple genotypes of Mycoplasma pneumoniae in semi-closed settings in Yamagata, Japan.
  Suzuki Yu et al. Journal of medical microbiology 2019 May (5) 785-790
• Whole genome sequencing for improved understanding of Mycobacterium tuberculosis transmission in a remote circumpolar region
  Guthrie J, et al. Epidemiol Infect, May 9, 2019.
• A hospital cluster combined with a family cluster of avian influenza H7N9 infection in Anhui Province, China.
  Zhang Wenyan et al. The Journal of infection 2019 May
• Prevalence, concordance and transmission of human papillomavirus infection among heterosexual couples in Liuzhou, China: an observational perspective study.
  Su Yingying et al. The Journal of infectious diseases 2019 May
• Injection of cocaine is associated with a recent HIV outbreak in people who inject drugs in Luxembourg.
  Arendt Vic et al. PloS one 2019 (5) e0215570

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• Use of whole genome sequencing for the molecular comparison of Neisseria gonorrhoeae isolates with decreased susceptibility to extended spectrum cephalosporins from two geographically different regions in America.
  Gianecini Ricardo A et al. Sexually transmitted diseases 2019 Apr

HOST-MICROBE INTERACTIONS

• Joint sequencing of human and pathogen genomes reveals the genetics of pneumococcal meningitis.
  Lees John A et al. Nature communications 2019 May (1) 2176
• Early nasal microbiota and acute respiratory infections during the first years of life.
  Toivonen Laura et al. Thorax 2019 Jun (6) 592-599
• Host contact dynamics shapes richness and dominance of pathogen strains.
  Pinotti Francesco et al. PLoS computational biology 2019 May (5) e1006530
• Influence of a Serratia marcescens outbreak on the gut microbiota establishment process in low-weight preterm neonates.
  Escribano Esperanza et al. PloS one 2019 (5) e0216581
• The ancestral and industrialized gut microbiota and implications for human health.
  Sonnenburg Erica D et al. Nature reviews. Microbiology 2019 Jun (6) 383-390
• Genome-wide patterns of gene expression in a wild primate indicate species-specific mechanisms associated with tolerance to natural simian immunodeficiency virus infection.
  Simons Noah D et al. Genome biology and evolution 2019 May 

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.