Volume 34 Number 2 January 15-22, 2015
Antimicrobials, Vaccines, Interventions
The resistome of Pseudomonas aeruginosa in relationship to phenotypic susceptibility
Kos VM, et al. Antimicrob Agents Chemother 2015; 59(1): 427-436.
Kos VM, et al. Antimicrob Agents Chemother 2015; 59(1): 427-436.
Genomic and transcriptomic analyses of colistin-resistant clinical isolates of Klebsiella pneumoniae reveal multiple pathways of resistance
Wright MS, et al. Antimicrob Agents Chemother 2015; 59(1): 536-543.
Wright MS, et al. Antimicrob Agents Chemother 2015; 59(1): 536-543.
Chromosome-mediated multidrug resistance in Salmonella enterica serovar typhi
Chiou CS, et al. Antimicrob Agents Chemother 2015; 59(1): 721-723.
Chiou CS, et al. Antimicrob Agents Chemother 2015; 59(1): 721-723.
Complete nucleotide sequence of cfr-carrying IncX4 plasmid pSD11 from Escherichia coli
Sun J, et al. Antimicrob Agents Chemother 2015; 59(1): 738-741.
Sun J, et al. Antimicrob Agents Chemother 2015; 59(1): 738-741.
Characterization of a multidrug-resistant, novel Bacteroides genomospecies
Salipante SJ, et al. Emerg Infect Dis, Jan 2015.
Salipante SJ, et al. Emerg Infect Dis, Jan 2015.
Bacterial resistance to leucyl-tRNA synthetase inhibitor GSK2251052 develops during treatment of complicated urinary tract infections
O’Dwyer K, et al. Antimicrob Agents Chemother 2015; 59(1): 289-298.
O’Dwyer K, et al. Antimicrob Agents Chemother 2015; 59(1): 289-298.
Genomic analysis of reduced susceptibility to tigecycline in Enterococcus faecium
Cattoir V, et al. Antimicrob Agents Chemother 2015; 59(1): 239-244.
Cattoir V, et al. Antimicrob Agents Chemother 2015; 59(1): 239-244.
Clostridium difficile isolates with high linezolid MICs harbor the multiresistance gene cfr
Marin M, et al. Antimicrob Agents Chemother 2015; 59(1): 586-589.
Marin M, et al. Antimicrob Agents Chemother 2015; 59(1): 586-589.
Molecular characterization of fluoroquinolone resistance in nontypeable Haemophilus influenzae clinical isolates
Puig C, et al. Antimicrob Agents Chemother 2015; 59(1): 461-466.
Puig C, et al. Antimicrob Agents Chemother 2015; 59(1): 461-466.
Antimicrobial susceptibility among clinical Nocardia species identified by multilocus sequence analysis
McTaggart LR, et al. Antimicrob Agents Chemother 2015; 59(1): 269-275.
McTaggart LR, et al. Antimicrob Agents Chemother 2015; 59(1): 269-275.
Radioiodinated DPA-713 imaging correlates with bactericidal activity of tuberculosis treatments in mice
Ordonez AA, et al. Antimicrob Agents Chemother 2015; 59(1): 642-649.
Ordonez AA, et al. Antimicrob Agents Chemother 2015; 59(1): 642-649.
Human cytomegalovirus resistance to deoxyribosylindole nucleosides maps to a transversion mutation in the terminase subunit-encoding gene UL89
Gentry BG, et al. Antimicrob Agents Chemother 2015; 59(1): 226-232.
Gentry BG, et al. Antimicrob Agents Chemother 2015; 59(1): 226-232.
Detection and Diagnosis
Rapid identification of major Escherichia coli sequence types causing urinary tract and bloodstream infections
Doumith M, et al. J Clin Microbiol 2015; 53(1): 160-166.
Doumith M, et al. J Clin Microbiol 2015; 53(1): 160-166.
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. Epidemiol Infect 2015; 143(1): 104-107.
Holmes A, et al. Epidemiol Infect 2015; 143(1): 104-107.
Evaluation of matrix-assisted laser desorption ionization–time of flight mass spectrometry for identification of Vibrio cholerae
Rychert J, et al. J Clin Microbiol 2015; 53(1): 329-331.
Rychert J, et al. J Clin Microbiol 2015; 53(1): 329-331.
Harmonization of Bordetella pertussis real-time PCR diagnostics in the United States in 2012
Williams MM, et al. J Clin Microbiol 2015; 53(1): 118-123.
Williams MM, et al. J Clin Microbiol 2015; 53(1): 118-123.
A multicenter prospective trial to asses a new real-time polymerase chain reaction for detection of Treponema pallidum, herpes simplex-1/2 and Haemophilus ducreyi in genital, anal and oropharyngeal ulcers
Glatz M, et al. Clin Microbiol Infect 2014; 20(12): O1020–O1027.
Glatz M, et al. Clin Microbiol Infect 2014; 20(12): O1020–O1027.
Identification of Brucella spp. isolated from human brucellosis in Malaysia using high-resolution melt (HRM) analysis
Zahidi JM, et al. Diag Microbiol Infect Dis, Jan 7, 2015.
Zahidi JM, et al. Diag Microbiol Infect Dis, Jan 7, 2015.
Polymerase-chain reaction/electrospray ionization-mass spectrometry for the detection of bacteria and fungi in bronchoalveolar lavage fluids: a prospective observational study
Huttner A, et al. Clin Microbiol Infect 2014; 20(12): O1059–O1066.
Huttner A, et al. Clin Microbiol Infect 2014; 20(12): O1059–O1066.
Genotypic susceptibility testing of Mycobacterium tuberculosis isolates for amikacin and kanamycin resistance by use of a rapid sloppy molecular beacon-based assay identifies more cases of low-level drug resistance than phenotypic Lowenstein-Jensen Testing
Chakravorty S, et al. J Clin Microbiol 2015; 53(1): 43-51.
Chakravorty S, et al. J Clin Microbiol 2015; 53(1): 43-51.
Optimization of a nucleic acid-based reporter system to detect Mycobacterium tuberculosis antibiotic sensitivity
Mulvey MC, et al. Antimicrob Agents Chemother 2015; 59(1): 407-413.
Mulvey MC, et al. Antimicrob Agents Chemother 2015; 59(1): 407-413.
Detection of small amounts of human adenoviruses in stools: comparison of a new immuno real-time PCR assay with classical tools
Bonot S, et al. Clin Microbiol Infect 2014; 20(12): O1010–O1016.
Bonot S, et al. Clin Microbiol Infect 2014; 20(12): O1010–O1016.
Development of an efficient entire-capsid-coding-region amplification method for direct detection of poliovirus from stool extracts
Arita M, et al. J Clin Microbiol 2015; 53(1): 73-78.
Arita M, et al. J Clin Microbiol 2015; 53(1): 73-78.
DNA microarray for detection of gastrointestinal viruses
Martinez MA, et al. J Clin Microbiol 2015; 53(1): 136-145.
Martinez MA, et al. J Clin Microbiol 2015; 53(1): 136-145.
High-resolution hepatitis C virus subtyping using NS5B deep sequencing and phylogeny, an alternative to current methods
Quer J, et al. J Clin Microbiol 2015; 53(1): 219-226.
Quer J, et al. J Clin Microbiol 2015; 53(1): 219-226.
Early detection of the dengue virus using reverse transcription-recombinase polymerase amplification
Teoh BT, et al. J Clin Microbiol, Jan 7, 2015.
Teoh BT, et al. J Clin Microbiol, Jan 7, 2015.
Diagnosis of neuroinvasive astrovirus infection in an immunocompromised adult with encephalitis by unbiased next-generation sequencing
Naccache SN, et al. Clin Infect Dis, Jan 7, 2015.
Naccache SN, et al. Clin Infect Dis, Jan 7, 2015.
Astrovirus VA1/HMO-C: an increasingly recognized neurotropic pathogen in immunocompromised patients
Brown JR, et al. Clin Infect Dis, Jan 7, 2015.
Brown JR, et al. Clin Infect Dis, Jan 7, 2015.
Comment:
Unbiased next-generation sequencing and new pathogen discovery: undeniable advantages and still-existing drawbacks
Calistri A, Palu G. Clin Infect Dis, Jan 7, 2015.
Unbiased next-generation sequencing and new pathogen discovery: undeniable advantages and still-existing drawbacks
Calistri A, Palu G. Clin Infect Dis, Jan 7, 2015.
T2 Magnetic resonance assay for the rapid diagnosis of candidemia in whole blood: a clinical trial
Mylonakis E, et al. Clin Infect Dis, Jan 12, 2015.
Mylonakis E, et al. Clin Infect Dis, Jan 12, 2015.
Evaluation of the loop mediated isothermal DNA amplification (LAMP) kit for malaria diagnosis in P. vivax endemic settings of Colombia
Vallejo AF, et al. PLoS Negl Trop Dis 2015; 9(1): e3453.
Vallejo AF, et al. PLoS Negl Trop Dis 2015; 9(1): e3453.
Detection of single-nucleotide polymorphisms in Plasmodium falciparum by PCR primer extension and lateral flow immunoassay
Moers AP, et al. Antimicrob Agents Chemother 2015; 59(1): 365-371.
Moers AP, et al. Antimicrob Agents Chemother 2015; 59(1): 365-371.
Novel recombinant multiepitope proteins for the diagnosis of asymptomatic Leishmania infantum-infected dogs
Faria AR, et al. PLoS Negl Trop Dis 2015; 9(1): e3429.
Faria AR, et al. PLoS Negl Trop Dis 2015; 9(1): e3429.
Development of an immunochromatographic assay kit using fluorescent silica nanoparticles for rapid diagnosis of Acanthamoeba keratitis
Toriyama K, et al. J Clin Microbiol 2015; 53(1): 273-277.
Toriyama K, et al. J Clin Microbiol 2015; 53(1): 273-277.
Noninvasive detection of Echinococcus multilocularis tapeworm in urban area, Estonia
Laurimaa L, et al. Emerg Infect Dis, Jan 2015.
Laurimaa L, et al. Emerg Infect Dis, Jan 2015.
Epidemiology, Outbreaks, Transmission
Genomic signature of multidrug-resistant Salmonella enterica serovar typhi isolates related to a massive outbreak in Zambia between 2010 and 2012
Hendriksen RS, et al. J Clin Microbiol 2015; 53(1): 262-272.
Hendriksen RS, et al. J Clin Microbiol 2015; 53(1): 262-272.
Contaminated handwashing sinks as the source of a clonal outbreak of KPC-2-producing Klebsiella oxytoca on a hematology ward
Leitner E, et al. Antimicrob Agents Chemother 2015; 59(1): 714-716.
Leitner E, et al. Antimicrob Agents Chemother 2015; 59(1): 714-716.
Methicillin-resistant Staphylococcus aureus and extended-spectrum and AmpC β-lactamase-producing Escherichia coli in broilers and in people living and/or working on organic broiler farms
Huijbers PM, et al. Vet Microbiol, Dec 19, 2014.
Huijbers PM, et al. Vet Microbiol, Dec 19, 2014.
An outbreak of Burkholderia stabilis colonization in a nasal ward
Wang L, et al. Int J Infect Dis, Jan 8, 2015.
Wang L, et al. Int J Infect Dis, Jan 8, 2015.
Metagenomic analysis of viruses in feces from unsolved outbreaks of gastroenteritis in humans
Moore NE, et al. J Clin Microbiol 2015; 53(1): 15-21.
Moore NE, et al. J Clin Microbiol 2015; 53(1): 15-21.
HIV reverse-transcriptase drug resistance mutations during early infection reveal greater transmission diversity than in envelope sequences
Lipscomb JT, et al. J Infect Dis 2014;210(11):1827-37.
Lipscomb JT, et al. J Infect Dis 2014;210(11):1827-37.
Origin of HTLV-1 in hunters of nonhuman primates in Central Africa
Kazanji M, et al. J Infect Dis 2015; 211(3): 361-365.
Kazanji M, et al. J Infect Dis 2015; 211(3): 361-365.
Evolution, Ecology, Pathogenicity, Populations
Large-scale genomic sequencing of extraintestinal pathogenic Escherichia coli strains
Salipante SJ, et al. Genome Res 2015; 25: 119-128.
Salipante SJ, et al. Genome Res 2015; 25: 119-128.
Molecular epidemiology of OXA-48-producing Klebsiella pneumoniae in France
Liapis E, et al. Clin Microbiol Infect 2014; 20(12): O1121–O1123.
Liapis E, et al. Clin Microbiol Infect 2014; 20(12): O1121–O1123.
Genomic epidemiology of Klebsiella pneumoniae in Italy and novel insights into the origin and global evolution of its resistance to carbapenem antibiotics
Gaiarsa S, et al. Antimicrob Agents Chemother 2015; 59(1): 389-396.
Gaiarsa S, et al. Antimicrob Agents Chemother 2015; 59(1): 389-396.
Comparative analysis of subtyping methods against a whole-genome-sequencing standard for Salmonella enterica serotype enteritidis
Deng X, et al. J Clin Microbiol 2015; 53(1): 212-218.
Deng X, et al. J Clin Microbiol 2015; 53(1): 212-218.
Trends in serotype distribution and antimicrobial susceptibility in Salmonella enterica Isolates from humans in Belgium, 2009 to 2013
Ceyssens PJ, et al. Antimicrob Agents Chemother 2015; 59(1): 544-552.
Ceyssens PJ, et al. Antimicrob Agents Chemother 2015; 59(1): 544-552.
Epidemiological analysis of the dynamic and diversity of Salmonella spp. in five German pig production clusters using pheno- and genotyping methods: An exploratory study
Niemann J, et al. Vet Microbiol, Dec 23, 2014.
Niemann J, et al. Vet Microbiol, Dec 23, 2014.
Clinical and molecular epidemiology of Staphylococcus argenteus infections in Thailand
Thaipadungpanit J, et al. J Clin Microbiol, Jan 7, 2015.
Thaipadungpanit J, et al. J Clin Microbiol, Jan 7, 2015.
Draft genome sequence of Legionella pneumophila D-5864, a serogroup 6 strain
Morrison SS, et al. Genome Announc 2015; 3(1): e01379-14.
Morrison SS, et al. Genome Announc 2015; 3(1): e01379-14.
Investigations of Mycoplasma pneumoniae infections in the United States: trends in molecular typing and macrolide resistance from 2006 to 2013
Diaz MH, et al. J Clin Microbiol 2015; 53(1): 124-130.
Diaz MH, et al. J Clin Microbiol 2015; 53(1): 124-130.
Whole-genome phylogenomic heterogeneity of Neisseria gonorrhoeae isolates with decreased cephalosporin susceptibility collected in Canada between 1989 and 2013
Demczuk W, et al. J Clin Microbiol 2015; 53(1): 191-200.
Demczuk W, et al. J Clin Microbiol 2015; 53(1): 191-200.
Whole-genome sequencing confirms that Burkholderia pseudomallei multilocus sequence types common to both Cambodia and Australia are due to homoplasy
De Smet B, et al. J Clin Microbiol 2015; 53(1): 323-326.
De Smet B, et al. J Clin Microbiol 2015; 53(1): 323-326.
Whole-genome sequencing of Burkholderia pseudomallei Isolates from an unusual melioidosis case identifies a polyclonal infection with the same multilocus sequence type
Price EP, et al. J Clin Microbiol 2015; 53(1): 282-286.
Price EP, et al. J Clin Microbiol 2015; 53(1): 282-286.
Orientia tsutsugamushi, agent of scrub typhus, displays a single metapopulation with maintenance of ancestral haplotypes throughout continental South East Asia
Wongprompitak P, et al. Infect Genet Evol, Jan 8, 2015.
Wongprompitak P, et al. Infect Genet Evol, Jan 8, 2015.
Genome sequence of enterovirus D68 from St. Louis, Missouri, USA
Wylie KM, et al. Emerg Infect Dis, Jan 2015.
Wylie KM, et al. Emerg Infect Dis, Jan 2015.
Genetic diversity of Enterovirus A71, India
Saxena VK, et al. Emerg Infect Dis, Jan 2015.
Saxena VK, et al. Emerg Infect Dis, Jan 2015.
Host-Pathogen Interactions
Host genetics: deciphering the variability in susceptibility to infections
Antonelli G, Roilides E. Clin Microbiol Infect 2014; 20(12): 1235-1236.
Antonelli G, Roilides E. Clin Microbiol Infect 2014; 20(12): 1235-1236.
Hepatitis C virus and interferon type III (interferon-λ3/interleukin-28B and interferon-λ4): genetic basis of susceptibility to infection and response to antiviral treatment
Riva E, et al. Clin Microbiol Infect 2014; 20(12): 1237-1245.
Riva E, et al. Clin Microbiol Infect 2014; 20(12): 1237-1245.
Host factors and genetic susceptibility to infections due to intracellular bacteria and fastidious organisms
Asner AS, et al. Clin Microbiol Infect 2014; 20(12): 1246-1253.
Asner AS, et al. Clin Microbiol Infect 2014; 20(12): 1246-1253.
Host genetics and opportunistic fungal infections
Pana ZD, et al. Clin Microbiol Infect 2014; 20(12): 1254-1264.
Pana ZD, et al. Clin Microbiol Infect 2014; 20(12): 1254-1264.
Host genetics and parasitic infections
Mangano VD, Modiani D. Clin Microbiol Infect 2014; 20(12): 1265-1275.
Mangano VD, Modiani D. Clin Microbiol Infect 2014; 20(12): 1265-1275.
Community behavior and spatial regulation within a bacterial microcolony in deep tissue sites serves to protect against host attack
Davis KM, et al. Cell Host Microbe 2015; 17(1): 21–31.
Davis KM, et al. Cell Host Microbe 2015; 17(1): 21–31.
Comment:
Heterogeneous host-pathogen encounters: act locally, think globally
Bumann D. Cell Host Microbe 2015; 17(1): 13-19.
Heterogeneous host-pathogen encounters: act locally, think globally
Bumann D. Cell Host Microbe 2015; 17(1): 13-19.
Diet dominates host genotype in shaping the murine gut microbiota
Carmody RM, et al. Cell Host Microbe 2015; 17(1): 72–84.
Carmody RM, et al. Cell Host Microbe 2015; 17(1): 72–84.
Analysis of changes in diversity and abundance of the microbial community in a cystic fibrosis patient over a multiyear period
Stokell JR, et al. J Clin Microbiol 2015; 53(1): 237-247.
Stokell JR, et al. J Clin Microbiol 2015; 53(1): 237-247.
The BER necessities: the repair of DNA damage in human-adapted bacterial pathogens
van der Veen S, et al. Nat Rev Microbiol, Jan 12, 2015.
van der Veen S, et al. Nat Rev Microbiol, Jan 12, 2015.
Single nucleotide polymorphisms in immune response genes in acute Q fever cases with differences in self-reported symptoms
Wielders CC, et al. Eur J Clin Microbiol Infect Dis, Jan 11, 2015.
Wielders CC, et al. Eur J Clin Microbiol Infect Dis, Jan 11, 2015.
Mycobacterium africanum Is associated with patient ethnicity in Ghana
Asante-Poku A, et al. PLoS Negl Trop Dis 9(1): e3370.
Asante-Poku A, et al. PLoS Negl Trop Dis 9(1): e3370.
HIV infection en route to endogenization: two cases
Colson P, et al. Clin Microbiol Infect 2014; 20(12): 1280–1288.
Colson P, et al. Clin Microbiol Infect 2014; 20(12): 1280–1288.
Comment:
From ‘purging’ to ‘endogenization’ of the HIV genome: a new approach to HIV eradication?
Antonelli G. Clin Microbiol Infect 2014; 20(12): 1278-1279.
From ‘purging’ to ‘endogenization’ of the HIV genome: a new approach to HIV eradication?
Antonelli G. Clin Microbiol Infect 2014; 20(12): 1278-1279.
A study of genotyping for management of human papillomavirus-positive, cytology-negative cervical screening results
Schiffman M, et al. J Clin Microbiol 2015; 53(1): 52-59.
Schiffman M, et al. J Clin Microbiol 2015; 53(1): 52-59.
Methods
A method for de novo nucleic acid diagnostic target discovery
Zhang Y, Sun Y. Bioinformatics 2014;30(22):3174-80.
Zhang Y, Sun Y. Bioinformatics 2014;30(22):3174-80.
Identification of human semiochemicals attractive to the major vectors of onchocerciasis
Young YM, et al. PLoS Negl Trop Dis 2015; 9(1): e3450.
Young YM, et al. PLoS Negl Trop Dis 2015; 9(1): e3450.
Oxford Nanopore sequencing and de novo assembly of a eukaryotic genome
Goodwin S, et al. bioRxiv, Jan 6, 2015.
Goodwin S, et al. bioRxiv, Jan 6, 2015.
Comment:
CSHL scientists sequence yeast genome with Oxford Nanopore MinIon
Anderson A. GenomeWeb, Jan 14, 2015.
CSHL scientists sequence yeast genome with Oxford Nanopore MinIon
Anderson A. GenomeWeb, Jan 14, 2015.
Protocol for metagenomic virus detection in clinical specimens
Kohl C, et al. Emerg Infect Dis, Jan 2015.
Kohl C, et al. Emerg Infect Dis, Jan 2015.
Probing of a human proteome microarray with a recombinant pathogen protein reveals a novel mechanism by which hookworms suppress B-cell receptor signaling
Tribolet L, et al. J Infect Dis 2015; 211(3): 416-425.
Tribolet L, et al. J Infect Dis 2015; 211(3): 416-425.
Use of whole-genus genome sequence data to develop a multilocus sequence typing tool that accurately identifies Yersinia isolates to the species and subspecies levels
Hall M, et al. J Clin Microbiol 2015; 53(1): 35-42.
Hall M, et al. J Clin Microbiol 2015; 53(1): 35-42.
Policy
The anatomy of medical research: US and international comparisons
Moses H III, et al. JAMA 2015;313(2):174-189.
Moses H III, et al. JAMA 2015;313(2):174-189.
Funding research in Africa
Park P. The Scientist, Jan 1, 2015.
Park P. The Scientist, Jan 1, 2015.
Reviews, News and Commentaries
Emergency Ebola response: a new approach to the rapid design and development of vaccines against emerging diseases
Tully CM, et al. Lancet Infect Dis, Jan 14, 2015.
Tully CM, et al. Lancet Infect Dis, Jan 14, 2015.
2014's Turning points in genomics
Krol A. BioIT World, Jan 7, 2015.
Krol A. BioIT World, Jan 7, 2015.
Proposed regulation of lab tests draws mixed reviews at workshop
Lee J. Modern Healthcare, Jan 9, 2015.
Lee J. Modern Healthcare, Jan 9, 2015.
Antibiotics: US discovery labelled 'game-changer' for medicine
Gallagher J, BBC News, Jan 7, 2015.
Gallagher J, BBC News, Jan 7, 2015.
Food can be tracked with sugar-based barcode that is safe to eat
Lewis M. Inside Science, Jan 15, 2015.
Lewis M. Inside Science, Jan 15, 2015.
Glaxo, Merck Ebola vaccine trials to start in West Africa
Bennett S. Bloomberg News, Jan 9, 2015.
Bennett S. Bloomberg News, Jan 9, 2015.
Taming bushmeat
Madhusoodanan J. The Scientist, Jan 1, 2015.
Madhusoodanan J. The Scientist, Jan 1, 2015.
Picturing infection
Chi KR. The Scientist, Jan 1, 2015.
Chi KR. The Scientist, Jan 1, 2015.
Fat to the rescue
Rood J. The Scientist, Jan 5, 2015.
Rood J. The Scientist, Jan 5, 2015.
Google named as partner in bid For DOD's EHR Contract
Tahir D. Modern Healthcare, Jan 15, 2014.
Tahir D. Modern Healthcare, Jan 15, 2014.
Deals for genetic data raise issues of privacy, sharing
Lauerman J, Kitamura M. Bloomberg News, Jan 14, 2015.
Lauerman J, Kitamura M. Bloomberg News, Jan 14, 2015.
Bats as ‘special’ reservoirs for emerging zoonotic pathogens
Brook CE, Dobson AP. Trends Microbiol, Jan 5, 2015.
Brook CE, Dobson AP. Trends Microbiol, Jan 5, 2015.
After Enterovirus 68 outbreak, a paralysis mystery, The New York Times, Jan 12
The New York Times, Jan 12GenomeWeb updates on molecular diagnostics [by free subscription only]:
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