Genomics|Update|Infectious Diseases: Advanced Molecular Detection in Action

Genomics|Update|Infectious Diseases

Advanced Molecular Detection in Action

• Methods
• Evolution, Ecology, Pathogenicity, Populations
• Detection & Diagnosis
• Epidemiology, Outbreaks, Transmission

• Antimicrobials, Vaccines, Interventions
• Host-Pathogen Interactions
• Reviews, News & Commentaries
• Tools, Databases

Methods

Inter-laboratory comparison of multi-locus variable-number tandem repeat analysis (MLVA) for verocytotoxin-producing Escherichia coli O157 to facilitate data sharing 
Holmes A, et al. 104-107. Epidemiol Infect 2015; 143(01): 104-107.

Proteomic differences between Listeria monocytogenes isolates from food and clinical environments 
Huang G, et al. Pathogens 2014; 3(4): 920-933.

The influence of incubation time, sample preparation and exposure to oxygen on the quality of the MALDI-TOF MS spectrum of anaerobic bacteria
Veloo ACM, et al. Clin Microbiol Infect, Dec 13, 2014.

Preliminary evaluation of next-generation sequencing performance relative to qPCR and in vitro cell culture tests for human cytomegalovirus
Ng SHS, et al. PDA J Pharm Sci Technol 2014; 68(6):563-571.

Comment:

Study shows promise of NGS, qPCR to detect vaccine contaminants 
Han AP. GenomeWeb, Dec 15, 2014.

Genome-scale RNAi screens for high-throughput phenotyping in bloodstream-form African trypanosomes
Glover L, et al. Nat Protoc  2015; 10: 106–133.

Sources of blood meals of sylvatic Triatoma guasayana near Zurima, Bolivia, Assayed with qPCR and 12S cloning
Lucero DE, et al. PLoS Negl Trop Dis 2014; 8(12): e3365.

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Evolution, Ecology, Pathogenicity, Populations

Global phylogenomic analysis of nonencapsulated Streptococcus pneumoniae reveals a deep-branching classic lineage that is distinct from multiple sporadic lineages
Hilty M, et al. Genome Biol Evol, 2014 Dec 4.

Identification and characterization of regions of difference between the Salmonella Gallinarum biovar Gallinarum and the Salmonella Gallinarum biovar Pullorum genomes
Batista DFA, et al. Infect Genet Evol, Dec 9, 2014.

Genomic sequences of six botulinum neurotoxin-producing strains representing three clostridial species illustrate the mobility and diversity of botulinum neurotoxin genes
Smith TJ, et al. Infect Genet Evol, Dec 6, 2014.

Reassortant highly pathogenic influenza A(H5N6) virus in Laos
Wong FYK, et al. Emerg Infect Dis, Mar 2015.

Two different genotypes of H1N2 swine influenza virus isolated in northern China and their pathogenicity in animals
Yang H, et al. Vet Microbiol, Dec 9, 2014.

A decade of norovirus genetic diversity in Belgium
Wollants E, et al. Infect Genet Evol, Dec 10, 2014.

Full genome sequence of a reassortant human G9P[4] rotavirus strain
Lewis J, et al. Genome Announc 2014 Dec 11;2(6). pii: e01284-14.

Genetic and antigenic analysis of foot-and-mouth disease virus serotype O responsible for outbreaks in India during 2013
Subramaniam S, et al. Infect Genet Evol, Dec 13, 2014.

Comparison of porcine epidemic diarrhea viruses from Germany and the United States, 2014
Hanke D, et al. Emerg Infect Dis, Mar 2015.

Molecular characterization of a new mosaic simian immunodeficiency virus in a naturally infected tantalus monkey (Chlorocebus tantalus) from Cameroon: a challenge to the virus–host co-evolution of SIVagm in African green monkeys
Ayouba A, et al. Infect Genet Evol, Dec 11, 2014.

Plasmodium falciparum field isolates from areas of repeated emergence of drug resistant malaria show no evidence of hypermutator phenotype
Brown TS, et al. Infect Genet Evol, Dec 13, 2014.

Genome update of the dimorphic human pathogenic fungi causing Paracoccidioidomycosis
Munoz JF, et al. PLoS Negl Trop Dis 2014; 8(12): e3348.

Population genetics of two key mosquito vectors of Rift Valley fever virus reveals new insights into the changing disease outbreak patterns in Kenya
Tchouassi DP, et al. PLoS Negl Trop Dis 2014; 8(12): e3364.

Thirty years of tick population genetics: a comprehensive review
Anaya-Anchetta A, et al. Infect Genet Evol 2015; 29: 164–179.

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Detection and Diagnosis

Phylogenetic analysis of environmental Legionella pneumophila isolates from an endemic area (Alcoy, Spain)
Sanchez-Buso L, et al. Infect Genet Evol, Dec 11, 2014.

Real-world performance of a microarray-based rapid diagnostic for Gram-positive bloodstream infections and potential utility for antimicrobial stewardship
Aitken SL, et al. Diag Microbiol Infect Dis 2015; 81(1): 4–8.

A simple, robust and rapid approach to detect carbapenemases in Gram-negative isolates by MALDI-TOF mass spectrometry: validation with triple quadripole tandem mass spectrometry, microarray and PCR
Vogne C, et al. Clin Microbiol Infect, Dec 12, 2014.

Evaluation of Vitek MS for rapid classification of clinical isolates belonging to Mycobacterium avium complex
Boyle DP, et al. Diag Microbiol Infect Dis 2015; 81(1): 41-43.

Protocol for metagenomic virus detection in clinical specimens
Kohl C, et al. Emerg Infect Dis, Jan 2015.

Nanomicroarray and multiplex next-generation sequencing for simultaneous identification and characterization of influenza viruses
Zhao J, et al. Emerg Infect Dis, Mar 2015.

Rapid diagnostic tests for identifying avian influenza A(H7N9) virus in clinical samples
Chen Y, et al. Emerg Infect Dis, Jan 2015.

Evaluation of novel second-generation RSV and influenza rapid tests at the point-of-care
Tuttle RC, et al. Diag Microbiol Infect Dis, Dec 3, 2014.

Evaluation of 2 multiplex real-time PCR assays for the detection of HSV-1/2 and Varicella zoster virus directly from clinical samples 
Heaton PR, et al. Clin Microbiol Infect, Dec 3, 2014.

Systematic detection and association of Entamoeba species in stool samples from selected sites in India
Nath J, et al. Epidemiol Infect 2015; 143(01): 108-119.

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry: revolutionizing clinical laboratory diagnosis of mold infections
Gautier M, et al. Clin Microbiol Infect, Dec 12, 2014.

Rapid identification of black grain eumycetoma causative agents using rolling circle amplification
Ahmed SAA, et al. PLoS Negl Trop Dis 2014; 8(12): e3368.

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Epidemiology, Outbreaks, Transmission

Genome sequencing defines phylogeny and spread of methicillin-resistant Staphylococcus aureus in a high transmission setting 
Tong SY, et al. Genome Res, 2014 Dec 9.

Whole genome sequencing and epidemiological analysis does not provide evidence for cross-transmission of Mycobacterium abscessus in a cohort of paediatric cystic fibrosis patients
Harris KA, et al. Clin Infect Dis, Dec 1, 2014.

Multidrug-resistant tuberculosis outbreak in gaming centers, Singapore, 2012
Chee CBE, et al. Emerg Infect Dis, Jan 2015.

Epidemiological and viral genomic sequence analysis of the 2014 Ebola outbreak reveals clustered transmission
Scarpino SV, et al. Clin Infect Dis, Dec 15, 2014.

Molecular epidemiology of enterovirus B77 isolated from non polio acute flaccid paralytic patients in Pakistan during 2013
Angez M, et al. Infect Genet Evol 2015; 29: 189–195.

Nucleotide correlations between rotavirus C isolates in clinical samples from outbreaks and in sewage samples
Kumazaki M, Usuku S. Food Environ Virol 2014 Dec 5.

Identification of new sub-genotypes of virulent Newcastle disease virus with potential panzootic features
Miller PJ, et al. Infect Genet Evol  2015; 29: 216–229.

Multicenter outbreak of infections by Saprochaete clavata, an unrecognized opportunistic fungal pathogen
Vaux S, et al. mBio 2014; 5(6): e02309-14.

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Antimicrobials, Vaccines, Interventions

Molecular mechanisms of antibiotic resistance
Blair JMA, et al. Nat Rev Microbiol 2015; 14:32-51.

Genomic analysis of isolates from the UK 2012 pertussis outbreak reveals that vaccine antigen genes are unusually fast evolving
Sealey KL, et al. J Infect Dis, 2014 Dec 8.

Characterization of a multidrug-resistant, novel Bacteroides genomospecies
Salipante SJ, et al. Emerg Infect Dis, Jan 2015.

Glucose- but not rice-based oral rehydration therapy enhances the production of virulence determinants in the human pathogen Vibrio cholerae
Kuhn J, et al. PLoS Negl Trop Dis 2014; 8(12): e3347.

Use of highly pathogenic avian influenza A(H5N1) gain-of-function studies for molecular-based surveillance and pandemic preparedness
Davis CT, et al. mBio 2014; 5(6): e02431-14.

Influenza gain-of-function experiments: their role in vaccine virus recommendation and pandemic preparedness
Schultz-Cherry S, et al. mBio 2014; 5(6): e02430-14.

Comment:

mBio addresses the pause in gain-of-function (GOF) experiments involving pathogens with pandemic potential (PPP)
Casadevall A, Schenk T. mBio 2014; 5(6): e02434-14.

Special issue on ‘Genetic diversity and evolution of rotavirus strains: Possible impact of global immunization programs’
Banyai K, Gentsch J. Infect Genet Evol 2014; 28: 375–376.

Population transcriptomics of human malaria parasites reveals the mechanism of artemisinin resistance
Mok S, et al. Science, Dec 11, 2014.

Comment:

The genetics of resistant malaria
Vogel G.  Science, Dec 12, 2014.

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Host-Pathogen Interactions

Host genetics: deciphering the variability in susceptibility to infections 
Antonelli G, Roilides E. Clin Microbiol Infect, Dec 12, 2014.

High A. vaginae and G. vaginalis vaginal loads are associated with preterm birth
Bretelle F, et al. Clin Infect Dis, Dec 1, 2014.

Noma affected children from Niger have distinct oral microbial communities based on high-throughput sequencing of 16S rRNA gene fragments
Whiteson KL, et al. PLoS Negl Trop Dis 2014; 8(12): e3240.

A novel psittacine adenovirus identified during an outbreak of avian chlamydiosis and human psittacosis: zoonosis associated with virus-bacterium coinfection in birds
To KKW, et al. PLoS Negl Trop Dis 2014; 8(12): e3318.

Genetic tuning of avian influenza A (H7N9) virus promotes viral fitness within different species
Zhu W, Shu Y. Microbes Infect, Dec 11, 2014.

IL-28B is a key regulator of B- and T-cell vaccine responses against influenza 
Egli A, et al. PLoS Pathog 2014; 10(12): e1004556.

Association of interleukin-10 polymorphisms with chronic hepatitis C virus infection in a case-control study and its effect on the response to combined pegylated interferon/ribavirin therapy 
Khan AJ, et al. Epidemiol Infect 2015; 143(01): 71-80.

Influence of IL10 gene polymorphisms on the severity of liver fibrosis and susceptibility to liver cirrhosis in HBV/HCV-infected patients 
Guo PF, et al. Infect Genet Evol, Dec 13, 2014.

Host genetics and parasitic infections 
Mangano VD, Modiano D. Clin Microbiol Infect, Dec 14, 2014.

Gut microbiota elicits a protective immune response against malaria transmission 
Yilmaz B, et al. Cell 2014; 159(6): 1277–1289.
Comment:
Gut microbes trigger malaria-fighting antibodies 
Sharlach M. The Scientist, Dec 4, 2014.

Gut microbiota as an epigenetic regulator: pilot study based on whole-genome methylation analysis 
Kumar H, et al. mBio 2014; 5(6): e02113-14.

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Reviews, News and Commentaries

US budget deal gives small increases to research
Reardon S, et al. Nature, Dec 14, 2014.

Critical path receives $3M Gates Foundation award for TB genome database 
Han AP. GenomeWeb, Dec 15, 2014.

Ebola experts seek to expand testing: rapid local diagnosis is essential for curbing spread
Butler D. Nature, Dec 9, 2014.

Hospital pauses test of an Ebola vaccine licensed to Merck 
Pollack A. New York Times, Dec 11, 2014.

How DNA sequencing in sewers could detect disease outbreaks 
Herper M. Forbes.com, Dec 11, 2014.

F.D.A. approves system that may make blood transfusions safer
Pollack A. New York Times, Dec 16, 2014.

PATH team completes prototype electricity-free reusable MDx platform; eyes disposable version
Butkus B. GenomeWeb, Dec 11, 2014.

Immunosequencing comes of age as researchers demo clinical utility, aim for FDA-cleared products 
Heger M. GenomeWeb, Dec 9, 2014.

Study shows promise of NGS, qPCR to detect vaccine contaminants 
Han AP. GenomeWeb, Dec 15, 2014.

Building a worldwide genetic library BRIC-by-BRIC 
Hubscher B. Phys.org, Dec 12, 2014.

The 20% who spread most disease: why some people are more contagious than others
Reddy S. Wall Street Journal, Dec 15, 2014.

Superbugs could eventually kill more people than cancer
Millman J. Washington Post (blog), Dec 12, 2014.

GenomeWeb updates on molecular diagnostics:

Abbott pathogen detection platform obtains CE mark

NIH awards $640K grant to Rutgers researcher for rapid Ebola Dx

Great Basin Scientific begins trial for Staph assay; updates MDx pipeline

FDA, HHS awards Diatherix contract for PCR-based pathogen detection methods

FDA clears Quidel's MDx for Bordetella pertussis

FDA clears additional flu strains for Focus' MDx assay

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Tools, Databases

SRST2: a new tool for genomic epidemiology, by Andreia Cunha BioMed Central, Dec 18