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

Genomics|Update|Infectious Diseases

Volume 35  Number 10  September 3-17, 2015

Advanced Molecular Detection in Action

• News/ Reviews/ Commentaries
• Policy
• Methods/ Tools
• Evolution/ Ecology/ Populations
• Pathogenicity / Antimicrobial Resistance

• Detection/ Diagnosis
• Epidemiology/ Outbreaks/ Transmission
• Antimicrobials/ Vaccines/ Interventions
• Host-Microbe Interactions

News/ Reviews/ Commentaries

Web-based phylogenetic rools offer insights into viral evolution, geographic spread
Thomas UG. GenomeWeb, Aug 27, 2015.

New ring can diagnose sexually transmitted diseases in a single test
Medical News Today, Aug 24, 2015.

New Zealand 'virus hunter' team explores MinION for influenza genome, metagenomic sequencing
Karow J. GenomeWeb, Aug 20, 2015.

With new law passed, NYC will consider testing options for Legionnaire's disease
Johnson M. GenomeWeb, Aug 19, 2015.

FDA wants food companies to hand over their pathogens
Steenhuysen J. Reuters, Aug 27, 2015.

NIH funds effort to develop PCR test to diagnose infections in infants
GenomeWeb, Aug 25, 2015.

UC San Diego teams up with Illumina to launch bioinformatics specialization on Coursera
Thomas UG. GenomeWeb, Aug 28, 2015.

Hope for universal flu vax?
Akst J. The Scientist, Aug 26, 2015.

How DNA detectives are helping solve the rise of superbugs
Marks L. The Conversation, Aug 18, 2015.

The great big clean-up
Grens K. The Scientist, Sep 1, 2015.

PrecisionFDA to test accuracy of genomic analysis tools
Krol A. Bio-IT World, Aug 27, 2015.

The detection of and response to a foodborne disease outbreak: A cautionary tale.
Osterholm MT et al. Clin. Infect. Dis. 2015 Jun 10.

Emergence of whooping cough: notes from three early epidemics in Persia.
Aslanabadi A et al. Lancet Infect Dis 2015 Aug 19.

Multiplex molecular panels for the diagnosis of gastrointestinal infection: performance, result interpretation and cost-effectiveness.
Binnicker MJ et al. J. Clin. Microbiol. 2015 Aug 26.

Towards host-directed therapies for tuberculosis.
Zumla A et al. Nat Rev Drug Discov 2015 Aug (8) 511-2

Evolving resistance among gram-positive pathogens.
Munita JM et al. Clin. Infect. Dis. 2015 Sep 15. S48-57

The need for evolutionarily rational disease interventions: Vaccination can select for higher virulence.
Boots M et al. PLoS Biol. 2015 Aug (8) e1002236

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Policy

Sharing research data and intellectual property law: A primer.
Carroll MW et al. PLoS Biol. 2015 Aug (8) e1002235

U.S. to finalize new human subject protections
Servick K. Science, Sep 2, 2015. 

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Methods/Tools

MinION nanopore sequencing of an influenza genome
Wang J, et al. Front Microbiol, Aug 18, 2015.

Phylesystem: a git-based data store for community-curated phylogenetic estimates.
McTavish EJ et al. Bioinformatics 2015 Sep 1. (17) 2794-800

IonGAP: integrative bacterial genome analysis for Ion Torrent sequence data.
Baez-Ortega A et al. Bioinformatics 2015 Sep 1. (17) 2870-3

phylogeo: an R package for geographic analysis and visualization of microbiome data.
Charlop-Powers Z et al. Bioinformatics 2015 Sep 1. (17) 2909-11

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Evolution/ Ecology/ Populations

A Comparison between transcriptome sequencing and 16S metagenomics for detection of bacterial pathogens in wildlife.
Razzauti M et al. PLoS Negl Trop Dis 2015 Aug (8) e0003929

Bacillus anthracis diversity and geographic potential across Nigeria, Cameroon and Chad: Further support of a novel West African lineage.
Blackburn JK et al. PLoS Negl Trop Dis 2015 Aug (8) e0003931

The ecology of microscopic life in household dust.
BarberÃA et al. Proc. Biol. Sci. 2015 Sep 7. (1814) 

Exploring genomic, geographic and virulence interactions among epidemic and non-epidemic St. Louis encephalitis virus (flavivirus) strains.
Diaz LA et al. PLoS ONE 2015 (8) e0136316

An integrative analysis of foot-and-mouth disease virus carriers in Vietnam achieved through targeted surveillance and molecular epidemiology.
de Carvalho FHC et al. Transbound Emerg Dis 2015 Aug 24.

Ebolavirus is evolving but not changing: No evidence for functional change in EBOV from 1976 to the 2014 outbreak.
Olabode AS et al. Virology 2015 Aug 202-7

Molecular epidemiological analysis of Saffold cardiovirus genotype 3 from upper respiratory infection patients in Taiwan.
Lin Tsuey-Li et al. J. Clin. Virol. 2015 Sep 7-13

Multiple-locus variable-number tandem repeat analysis of Leptospira interrogans and Leptospira borgpetersenii isolated from small feral and wild mammals in East Asia.
Koizumi N et al. Infect. Genet. Evol. 2015 Aug 18.

Enteropathogenic and enteroaggregative E. coli in stools of children with acute gastroenteritis in Davidson County, Tennessee.
Foster MA et al. Diagn. Microbiol. Infect. Dis. 2015 Jul 26. (CDC Author)

Fourteen types of co-circulating recombinant enterovirus were associated with hand, foot, and mouth disease in children from Wenzhou, China.
Guo Wen-Ping et al. J. Clin. Virol. 2015 Sep 29-38

Haemophilus influenzae: using comparative genomics to accurately identify a highly recombinogenic human pathogen.
Price EP et al. BMC Genomics 2015 641

Swine and rabbits are the main reservoirs of hepatitis E virus in China: detection of HEV RNA in feces of farmed and wild animals.
Xia Junke et al. Arch. Virol. 2015 Aug 26.

Identification of bufavirus-1 and bufavirus-3 in feces of patients with acute diarrhea, China.
Huang Dou-Dou et al. Sci Rep 2015 13272

Spatio-temporal genetic structuring of Leishmania major in Tunisia by microsatellite analysis.
Harrabi M et al. PLoS Negl Trop Dis 2015 Aug (8) e0004017

Phylogenetic and geographic relationships of severe fever with thrombocytopenia syndrome virus in China, South Korea, and Japan.
Yoshikawa T et al. J. Infect. Dis. 2015 Sep 15. (6) 889-98

The rural-urban effect on spatial genetic structure of type II Toxoplasma gondii strains involved in human congenital toxoplasmosis, France, 2002-2009.
Ajzenberg D et al. Infect. Genet. Evol. 2015 Aug 22.

Complete genome sequences of two Bordetella hinzii strains isolated from humans.
Weigand MR et al. Genome Announc 2015 (4) (CDC Author)

Molecular epidemiology of oyster-related human noroviruses: Global genetic diversity and temporal-geographical distribution from 1983 to 2014.
Yu Y et al. Appl. Environ. Microbiol. 2015 Aug 28.

Isolation and molecular characterization of Acanthamoeba genotypes in recreational and domestic water sources from Jamaica, West Indies.
Todd CD et al. J Water Health 2015 Sep (3) 909-919

The diversity and geographical structure of Orientia tsutsugamushi strains from scrub typhus patients in Laos.
Phetsouvanh R et al. PLoS Negl Trop Dis 2015 Aug (8) e0004024

A new trend of genotype distribution of hepatitis B virus infection in southeast China (Fujian), 2006-2013.
Wei DH et al. Epidemiol. Infect. 2015 Oct (13) 2822-6

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Pathogenicity / Antimicrobial Resistance

Systematic analysis of viral genes responsible for differential virulence between American and Australian West Nile virus strains.
Setoh YX et al. J. Gen. Virol. 2015 Jun (Pt 6) 1297-308

Mycobacterium tuberculosis pncA polymorphisms that do not confer pyrazinamide resistance at a breakpoint concentration of 100 ug/ml in MGIT.
Whitfield MG et al. J. Clin. Microbiol. 2015 Aug 19. (CDC Author)

Emergence of a hypervirulent carbapenem-resistant Klebsiella pneumoniae isolate from clinical infections in China.
Zhang Yawei et al. J. Infect. 2015 Aug 21. 

Molecular characterization of extended-spectrum beta-lactamases (ESBLs) produced by clinical isolates of Acinetobacter baumannii in Saudi Arabia.
Alyamani EJ et al. Ann. Clin. Microbiol. Antimicrob. 2015 (1) 38

Are Shiga toxin negative Escherichia coli O157:H7 enteropathogenic or enterohaemorrhagic Escherichia coli? A comprehensive molecular analysis using whole genome sequencing.
Ferdous M et al. J. Clin. Microbiol. 2015 Aug 26. 

Whole genome sequence typing and microarray profiling of nasal and blood stream methicillin-resistant Staphylococcus aureus isolates: Clues to phylogeny and invasiveness.
Hamed M et al. Infect. Genet. Evol. 2015 Aug 20. 

Transcriptional adaptation of drug-tolerant Mycobacterium tuberculosis During treatment of human tuberculosis.
Walter ND et al. J. Infect. Dis. 2015 Sep 15. (6) 990-8

Genetic diversity of blaTEM alleles, antimicrobial susceptibility and molecular epidemiological characteristics of penicillinase-producing Neisseria gonorrhoeae from England and Wales.
Cole MJ et al. J. Antimicrob. Chemother. 2015 Aug 27.

Phylogenetic lineages, clones and beta-lactamases in an international collection of Klebsiella oxytoca isolates non-susceptible to expanded-spectrum cephalosporins.
Izdebski R et al. J. Antimicrob. Chemother. 2015 Aug 27.

Molecular epidemiology of VIM-1 producing Escherichia coli from Germany referred to the National Reference Laboratory.
Kaase M et al. Int. J. Med. Microbiol. 2015 Aug 22. 

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Detection/ Diagnosis

Deep sequencing of HIV-1 in cerebrospinal fluid.
Tong Cheuk YW et al. Clin. Infect. Dis. 2015 May 28.

Re-analysis of metagenomic sequences from acute flaccid myelitis patients reveals alternatives to enterovirus D68 infection.
Breitwieser FP et al. F1000Res 2015 180

Genotyping of classical swine fever virus using high-resolution melt analysis.
Titov I et al. J. Virol. Methods 2015 Aug 20.

Subtyping of the Legionella pneumophila "Ulm" outbreak strain using the CRISPR-Cas system.
Lück C et al. Int. J. Med. Microbiol. 2015 Aug 7.

Comparison of phenotypic and genotypic approaches to capsule typing neisseria meningitidis using invasive and carriage isolate collections.
Jones CH et al. J. Clin. Microbiol. 2015 Aug 26.

Fast technology analysis (FTA) enables identification of species and genotypes of latent microsporidia infections in healthy native cameroonians.
Ndzi ES et al. J. Eukaryot. Microbiol. 2015 Aug 25.

Diagnosing balamuthia mandrillaris encephalitis with metagenomic deep sequencing.
Wilson MR et al. Ann. Neurol. 2015 Aug 20.

NMR-based metabolomic urinalysis: a rapid screening test for urinary tract infection.
Lam Ching-Wan et al. Clin. Chim. Acta 2014 Sep 25. 217-23

Assessment of a molecular diagnostic platform for integrated isolation and quantification of mRNA in whole blood.
van den Kieboom CH et al. Eur. J. Clin. Microbiol. Infect. Dis. 2015 Aug 23.

Fast, sensitive, and specific diagnosis of infections with Leishmania species by Cytochrome b PCR in formalin-fixed, paraffin-embedded skin biopsies.
Gebhardt M et al. Br. J. Dermatol. 2015 Aug 19.

Mass spectrometry-based PhyloProteomics (MSPP): A novel microbial typing method.
Erich Zautner A et al. Sci Rep 2015 13431

Genetic and resistance phenotypic subtyping of salmonella saintpaul isolates from various food sources and humans: Phylogenetic concordance in combinatory analyses.
Hayford AE et al. Infect. Genet. Evol. 2015 Aug 20.

Comparative evaluation of matrix-assisted laser desorption ionisation-time of flight mass spectrometry and conventional phenotypic-based methods for identification of clinically important yeasts in a UK-based medical microbiology laboratory.
Fatania N et al. J. Clin. Pathol. 2015 Aug 25.

Characterization of the bacterial community naturally present on commercially grown basil leaves: Evaluation of sample preparation prior to culture-independent techniques.
Ceuppens S et al. Int J Environ Res Public Health 2015 (8) 10171-10197

Using amplicon deep sequencing to detect genetic signatures of plasmodium vivax relapse.
Lin JT et al. J. Infect. Dis. 2015 Sep 15. (6) 999-1008

Detection of streptococcus pyogenes using rapid visual molecular assay.
Zhao X et al. FEMS Microbiol. Lett. 2015 Aug 27.

H1N1 viral proteome peptide microarray predicts individuals at risk for H1N1 infection and segregates infection versus Pandemrix(®) vaccination.
Ambati A et al. Immunology 2015 Jul (3) 357-66

Generation of whole genome sequences of new Cryptosporidium hominis and Cryptosporidium parvum isolates directly from stool samples.
Hadfield SJ et al. BMC Genomics 2015 650

Direct identification and discernment of Mycobacterium avium and Mycobacterium intracellulare using a real-time RNA isothermal amplification and detection method.
Cui Z et al. Tuberculosis (Edinb) 2015 Aug 12.

H1N1 viral proteome peptide microarray predicts individuals at risk for H1N1 infection and segregates infection versus Pandemrix(®) vaccination.
Ambati A et al. Immunology 2015 Jul (3) 357-66

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Epidemiology/ Outbreaks/ Transmission

Epidemiologic investigation of a cluster of neuroinvasive bacillus cereus infections in 5 patients with acute myelogenous leukemia.
Rhee C et al. Open Forum Infect Dis 2015 Sep (3) ofv096 (CDC Author)

Partial failure of milk pasteurization as a risk for the transmission of campylobacter from cattle to humans.
Fernandes AM et al. Clin. Infect. Dis. 2015 Jun 10.

Genomic epidemiology of clostridium botulinum isolates from temporally related cases of infant botulism in New South Wales, Australia.
McCallum N et al. J. Clin. Microbiol. 2015 Sep (9) 2846-53

It is not all about SNPs: comparison of mobile genetic elements and deletions in Listeria monocytogenes genomes links cases of hospital-acquired listeriosis to the environmental source.
Wang Q et al. J. Clin. Microbiol. 2015 Aug 26. 

Living poultry markets in rural area: Human infection with H7N9 virus re-emerges in Zhejiang Province, China, in winter 2014.
Sun Yi et al. J. Clin. Virol. 2015 Sep 16-22

Using molecular HIV surveillance data to understand transmission between subpopulations in the United States.
Oster AM et al. J. Acquir. Immune Defic. Syndr. 2015 Aug 21. (CDC Author)

Ultra-deep sequencing provides insights into the virology of hepatitis C super-infections in a case of three sequential infections with different genotypes.
Chung E et al. J. Clin. Virol. 2015 Sep 63-6

Molecular typing of toxic shock syndrome toxin-1- and Enterotoxin A-producing methicillin-sensitive Staphylococcus aureus isolates from an outbreak in a neonatal intensive care unit.
Layer F et al. Int. J. Med. Microbiol. 2015 Aug 22. 

Polyclonal outbreak of bacteremia caused by Burkholderia cepacia complex and the presumptive role of ultrasound gel.
Nannini EC et al. Braz J Infect Dis 2015 Aug 28.

Stool screening of Syrian refugees and asylum seekers in Germany, 2013/2014: Identification of Sabin like polioviruses.
Boettcher S et al. Int. J. Med. Microbiol. 2015 Aug 21.

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Antimicrobials/ Vaccines/ Interventions

A synthetic consensus anti-spike protein DNA vaccine induces protective immunity against Middle East respiratory syndrome coronavirus in nonhuman primates.
Muthumani K et al. Sci Transl Med 2015 Aug 19. (301) 301ra132

Virological failure and development of new resistance mutations according to CD4 count at combination antiretroviral therapy initiation.
Jose S et al. HIV Med. 2015 Aug 25.

Twenty-eight years of poliovirus replication in an immunodeficient individual: Impact on the global polio eradication initiative.
Dunn G et al. PLoS Pathog. 2015 Aug (8) e1005114

Identification of agents effective against multiple toxins and viruses by host-oriented cell targeting.
Zilbermintz L et al. Sci Rep 2015 13476

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Host-Microbe Interactions

The fecal virome of children with hand, foot, and mouth disease that tested PCR negative for pathogenic enteroviruses.
Linsuwanon P et al. PLoS ONE 2015 (8) e0135573

Toll-like receptor-3 gene polymorphism in patients with Japanese encephalitis.
Biyani S et al. J. Neuroimmunol. 2015 Sep 15. 71-6

Structure and function of the healthy pre-adolescent pediatric gut microbiome.
Hollister EB et al. Microbiome 2015 36

HLA class I supertype associations with clinical outcome of secondary dengue virus infections in ethnic Thais.
Vejbaesya S et al. J. Infect. Dis. 2015 Sep 15. (6) 939-47

Stool microbiota composition is associated with the prospective risk of Plasmodium falciparum infection.
Yooseph Shibu et al. BMC Genomics 2015 (1) 631

HLA class-II associated HIV polymorphisms predict escape from CD4+ T cell responses.
Erdmann N et al. PLoS Pathog. 2015 Aug (8) e1005111

Genetic determinants of anti-malarial acquired immunity in a large multi-centre study.
Shelton JMG et al. Malar. J. 2015 (1) 333

Beijing clades of Mycobacterium tuberculosis are associated with differential survival in HIV-negative Russian patients.
Balabanova Y et al. Infect. Genet. Evol. 2015 Aug 28.

Tracking dengue virus intra-host genetic diversity during human-to-mosquito transmission.
Sim S et al. PLoS Negl Trop Dis 2015 Sep (9) e0004052

Analysis of dengue virus genetic diversity during human and mosquito infection reveals genetic constraints
Sessions OM, et al. PLoS Negl Trop Dis, Sep 1, 2015.