Volume 35 Number 4 July 23-30, 2015
News/ Reviews/ Commentaries
HHS partners on Ebola drug
Akst J. The Scientist, Jul 22, 2015.
Akst J. The Scientist, Jul 22, 2015.
Antibiotic Resistance can boost bacterial fitness
Azvolinsky A. The Scientist, Jul 22, 2015.
Azvolinsky A. The Scientist, Jul 22, 2015.
U of Melbourne launches genomics research center for infectious disease
GenomeWeb, Jul 22, 2015.
GenomeWeb, Jul 22, 2015.
Crossing the scale from within-host infection dynamics to between-host transmission fitness: a discussion of current assumptions and knowledge.
Handel A et al. Philos. Trans. R. Soc. Lond., B, Biol. Sci. 2015 Aug 19. (1675)
Handel A et al. Philos. Trans. R. Soc. Lond., B, Biol. Sci. 2015 Aug 19. (1675)
The role of surveillance systems in confronting the global crisis of antibiotic-resistant bacteria.
Perez F et al. Curr. Opin. Infect. Dis. 2015 Aug (4) 375-83
Perez F et al. Curr. Opin. Infect. Dis. 2015 Aug (4) 375-83
Beyond research: a primer for considerations on using viral metagenomics in the field and clinic.
Hall RJ et al. Front Microbiol 2015 224
Hall RJ et al. Front Microbiol 2015 224
Horizontal gene transfer: building the web of life.
Soucy SM et al. Nat. Rev. Genet. 2015 Jul 17. (8) 472-82
Soucy SM et al. Nat. Rev. Genet. 2015 Jul 17. (8) 472-82
Genomic Technologies speed pathogen detection
Stephenson J. JAMA 2015;314(3):212-214.
Stephenson J. JAMA 2015;314(3):212-214.
Methods/Tools
Sources of PCR-induced distortions in high-throughput sequencing data sets.
Kebschull JM et al. Nucleic Acids Res. 2015 Jul 17.
Kebschull JM et al. Nucleic Acids Res. 2015 Jul 17.
Methods for virus classification and the challenge of incorporating metagenomic sequence data.
Simmonds P et al. J. Gen. Virol. 2015 Jun (Pt 6) 1193-1206
Simmonds P et al. J. Gen. Virol. 2015 Jun (Pt 6) 1193-1206
VirSorter: mining viral signal from microbial genomic data.
Roux S et al. PeerJ 2015 e985
Roux S et al. PeerJ 2015 e985
Roary: Rapid large-scale prokaryote pan genome analysis.
Page AJ et al. Bioinformatics 2015 Jul 20.
Page AJ et al. Bioinformatics 2015 Jul 20.
Robust algorithm for systematic classification of malaria late treatment failures as recrudescence or reinfection using microsatellite genotyping.
Plucinski MM et al. Antimicrob. Agents Chemother. 2015 Jul 20.
Plucinski MM et al. Antimicrob. Agents Chemother. 2015 Jul 20.
Viral dark matter and virus-host interactions resolved from publicly available microbial genomes.
Roux S et al. Elife 2015 Jul 22.
Roux S et al. Elife 2015 Jul 22.
Evolution/ Ecology/ Populations
Newly-emergent highly pathogenic H5N9 subtype avian influenza A virus.
Yu Y et al. J. Virol. 2015 Jun 17.
Yu Y et al. J. Virol. 2015 Jun 17.
Complete genome sequence of Chikungunya virus isolated from an Aedes aegypti mosquito during an outbreak in Yemen, 2011.
Fahmy NT et al. Genome Announc 2015 (4)
Fahmy NT et al. Genome Announc 2015 (4)
Genetic similarities between Cyclospora cayetanensis and cecum-infecting avian Eimeria spp. in apicoplast and mitochondrial genomes.
Tang K et al. Parasit Vectors 2015 (1) 358
Tang K et al. Parasit Vectors 2015 (1) 358
The mitochondrial genome of the lone star tick (Amblyomma americanum).
Williams-Newkirk AJ et al. Ticks Tick Borne Dis 2015 Jul 8.
Williams-Newkirk AJ et al. Ticks Tick Borne Dis 2015 Jul 8.
Genomic Analysis of the emergence and rapid global dissemination of the clonal group 258 Klebsiella pneumoniae pandemic.
Bowers JR et al. PLoS ONE 2015 (7) e0133727
Bowers JR et al. PLoS ONE 2015 (7) e0133727
Ebolavirus comparative genomics.
Jun Se-Ran et al. FEMS Microbiol. Rev. 2015 Jul 14.
Jun Se-Ran et al. FEMS Microbiol. Rev. 2015 Jul 14.
Effective transfer of a 47 kb NDM-1-positive plasmid among Acinetobacter species.
Huang Tzu-W et al. J. Antimicrob. Chemother. 2015 Jul 14.
Huang Tzu-W et al. J. Antimicrob. Chemother. 2015 Jul 14.
Molecular epidemiology of Neisseria gonorrhoeae using multi-antigen sequence typing and pulse-field gel electrophoresis in highly endemic Western Australian populations.
O'Reilly LC et al. BMC Infect. Dis. 2015 272
O'Reilly LC et al. BMC Infect. Dis. 2015 272
Genetic diversity of Trypanosoma cruzi in bats, and multilocus phylogenetic and phylogeographical analyses supporting Tcbat as an independent DTU (discrete typing unit).
Lima L et al. Acta Trop. 2015 Jul 19.
Lima L et al. Acta Trop. 2015 Jul 19.
De novo whole-genome sequence and annotation of a leishmania strain isolated from a case of post-kala-azar dermal leishmaniasis.
Gupta AK et al. Genome Announc 2015 (4)
Gupta AK et al. Genome Announc 2015 (4)
Pathogenicity / Antimicrobial Resistance
Evolutionary consequences of drug resistance: shared principles across diverse targets and organisms.
Hughes D et al. Nat. Rev. Genet. 2015 Aug (8) 459-71
Hughes D et al. Nat. Rev. Genet. 2015 Aug (8) 459-71
The speciation and genotyping of Cronobacter isolates from hospitalised patients.
Alsonosi A et al. Eur. J. Clin. Microbiol. Infect. Dis. 2015 Jul 15.
Alsonosi A et al. Eur. J. Clin. Microbiol. Infect. Dis. 2015 Jul 15.
Fate and behavior of extended-spectrum ?-lactamase-producing genes in municipal sewage treatment plants.
Yi T et al. J Environ Sci Health A Tox Hazard Subst Environ Eng 2015 Sep 19. (11) 1160-1168
Yi T et al. J Environ Sci Health A Tox Hazard Subst Environ Eng 2015 Sep 19. (11) 1160-1168
Fitness cost of antibiotic susceptibility during bacterial infection
Roux D, et al. Sci Transl Med 2015; 7: 297ra114.
Roux D, et al. Sci Transl Med 2015; 7: 297ra114.
Mapping the evolution of hypervirulent Klebsiella pneumoniae.
Struve C et al. MBio 2015 (4)
Struve C et al. MBio 2015 (4)
In vitro antimicrobial susceptibility of Helcococcus kunzii and molecular analysis of macrolide and tetracycline resistance.
Vergne A et al. Eur. J. Clin. Microbiol. Infect. Dis. 2015 Jul 21.
Vergne A et al. Eur. J. Clin. Microbiol. Infect. Dis. 2015 Jul 21.
Characterization of fecal vancomycin-resistant enterococci with acquired and intrinsic resistance mechanisms in wild animals, Spain.
Lozano C et al. Microb. Ecol. 2015 Jul 21.
Lozano C et al. Microb. Ecol. 2015 Jul 21.
Escherichia coli of sequence type 3835 carrying blaNDM-1, blaCTX-M-15, blaCMY-42 and blaSHV-12.
Feng Y et al. Sci Rep 2015 12275
Feng Y et al. Sci Rep 2015 12275
A combinational approach of multilocus sequence typing and other molecular typing methods in unravelling the epidemiology of Erysipelothrix rhusiopathiae strains from poultry and mammals.
Janßen T et al. Vet. Res. 2015 (1) 84
Janßen T et al. Vet. Res. 2015 (1) 84
Genomic and functional portrait of a highly virulent, CTX-M-15-producing H30-Rx subclone of Escherichia coli sequence type (ST) 131.
Ranjan A et al. Antimicrob. Agents Chemother. 2015 Jul 20.
Ranjan A et al. Antimicrob. Agents Chemother. 2015 Jul 20.
Detection/ Diagnosis
Isothermal detection of Mycoplasma pneumoniae directly from respiratory clinical specimens.
Petrone BL et al. J. Clin. Microbiol. 2015 Jul 15.
Petrone BL et al. J. Clin. Microbiol. 2015 Jul 15.
Incidence of Echinococcus granulosus in domestic dogs in Palestine as revealed by Copro-PCR.
Al-Jawabreh A et al. PLoS Negl Trop Dis 2015 Jul (7) e0003934
Al-Jawabreh A et al. PLoS Negl Trop Dis 2015 Jul (7) e0003934
Development of recombinase polymerase amplification assays for detection of Orientia tsutsugamushi or Rickettsia typhi.
Chao Chien-Chung et al. PLoS Negl Trop Dis 2015 Jul (7) e0003884
Chao Chien-Chung et al. PLoS Negl Trop Dis 2015 Jul (7) e0003884
Design and application of a core genome multilocus sequence typing scheme for investigation of Legionnaires' disease incidents
Moran-Gilad J, et al. Euro Surveill 2015;20(28):pii=21186.
Moran-Gilad J, et al. Euro Surveill 2015;20(28):pii=21186.
Deletion of Plasmodium falciparum histidine-rich protein 2 (pfhrp2) and histidine-rich protein 3 (pfhrp3) genes in Colombian parasites.
Murillo SC et al. PLoS ONE 2015 (7) e0131576
Murillo SC et al. PLoS ONE 2015 (7) e0131576
A rapid field-deployable reverse transcription-insulated isothermal polymerase chain reaction assay for sensitive and specific detection of Bluetongue virus.
Ambagala A et al. Transbound Emerg Dis 2015 Jul 19.
Ambagala A et al. Transbound Emerg Dis 2015 Jul 19.
Application of a high-resolution melting technique for the rapid detection of partial replacement of HCV-1b by HCV-1a after PEG-IFN?/RBV therapy.
Holysz M et al. J. Appl. Genet. 2015 May (2) 271-5
Holysz M et al. J. Appl. Genet. 2015 May (2) 271-5
Randomized trial of rapid multiplex polymerase chain reaction-based blood culture identification and susceptibility testing.
Banerjee R et al. Clin. Infect. Dis. 2015 Jul 20.
Banerjee R et al. Clin. Infect. Dis. 2015 Jul 20.
A single-loop recombinant pseudotyped-virus-based assay to detect HIV-1 phenotypic resistance.
Wu S et al. Arch. Virol. 2015 Jun (6) 1385-95
Wu S et al. Arch. Virol. 2015 Jun (6) 1385-95
Real-time PCR detection of Campylobacter spp.: A comparison to classic culturing and enrichment.
de Boer P et al. Food Microbiol. 2015 Oct 96-100
de Boer P et al. Food Microbiol. 2015 Oct 96-100
Epidemiology/ Outbreaks/ Transmission
Asymptomatic transmission and the resurgence of Bordetella pertussis.
Althouse BM et al. BMC Med 2015 (1) 146
Althouse BM et al. BMC Med 2015 (1) 146
Whole genome sequencing shows a low proportion of tuberculosis disease Is attributable to known close contacts in rural Malawi.
Glynn JR et al. PLoS ONE 2015 (7) e0132840
Glynn JR et al. PLoS ONE 2015 (7) e0132840
Outbreak investigation identifies a single Listeria monocytogenes strain in sheep with different clinical manifestations, soil and water
Dreyer M, et al. Vet Microbiol 2015; 179: 69-75.
Dreyer M, et al. Vet Microbiol 2015; 179: 69-75.
A large-scale community-based outbreak of paratyphoid fever caused by hospital-derived transmission in Southern China.
Yan Meiying et al. PLoS Negl Trop Dis 2015 Jul (7) e0003859
Yan Meiying et al. PLoS Negl Trop Dis 2015 Jul (7) e0003859
Genomic epidemiology of a protracted hospital outbreak caused by a toxin A negative, Clostridium difficile sublineage PCR ribotype 017 strain in London, England.
Cairns MD et al. J. Clin. Microbiol. 2015 Jul 15.
Cairns MD et al. J. Clin. Microbiol. 2015 Jul 15.
Outbreak of vanB vancomycin-resistant Enterococcus faecium colonization in a neonatal service.
Lister DM et al. Am J Infect Control 2015 Jul 16.
Lister DM et al. Am J Infect Control 2015 Jul 16.
Molecular epidemiology of hospital outbreak of Middle East Respiratory syndrome, Riyadh, Saudi Arabia, 2014
Fagbo S, et al. Emerg Infect Dis, Nov 2015. ]. http://dx.doi.org/10.3201/eid2111.150944
Fagbo S, et al. Emerg Infect Dis, Nov 2015. ]. http://dx.doi.org/10.3201/eid2111.150944
Antimicrobials/ Vaccines/ Interventions
Improved virological and immunological efficacy of resistance-guided switch in antiretroviral therapy: a Frankfurt HIV cohort analysis.
Wolf T et al. Med. Microbiol. Immunol. 2014 Dec (6) 409-14
Wolf T et al. Med. Microbiol. Immunol. 2014 Dec (6) 409-14
Exploring the benefits of molecular testing for gonorrhoea antibiotic resistance surveillance in remote settings.
Hui BB et al. PLoS ONE 2015 (7) e0133202
Hui BB et al. PLoS ONE 2015 (7) e0133202
Vaccination drives changes in metabolic and virulence profiles of streptococcus pneumoniae.
Watkins ER et al. PLoS Pathog. 2015 Jul (7) e1005034
Watkins ER et al. PLoS Pathog. 2015 Jul (7) e1005034
Host-Microbe Interactions
Colonic bacterial composition in Parkinson's disease.
Keshavarzian A et al. Mov. Disord. 2015 Jul 16.
Keshavarzian A et al. Mov. Disord. 2015 Jul 16.
Association of anti-GT1a antibodies with an outbreak of Guillain-Barré syndrome and analysis of ganglioside mimicry in an associated Campylobacter jejuni strain.
Zhang M et al. PLoS ONE 2015 (7) e0131730
Zhang M et al. PLoS ONE 2015 (7) e0131730
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