Abstract:
:Global HIV treatment programs need sensitive and affordable tests to monitor HIV drug resistance. We compared mutant detection by the oligonucleotide ligation assay (OLA), an economical and simple test, to massively parallel sequencing. Nonnucleoside reverse transcriptase inhibitor (K103N, V106M, Y181C, and G190A) and lamivudine (M184V) resistance mutations were quantified in blood-derived plasma RNA and cell DNA specimens by OLA and 454 pyrosequencing. A median of 1,000 HIV DNA or RNA templates (range, 163 to 1,874 templates) from blood specimens collected in Mozambique (n = 60) and Kenya (n = 51) were analyzed at 4 codons in each sample (n = 441 codons assessed). Mutations were detected at 75 (17%) codons by OLA sensitive to 2.0%, at 71 codons (16%; P = 0.78) by pyrosequencing using a cutoff value of ≥ 2.0%, and at 125 codons (28%; P < 0.0001) by pyrosequencing sensitive to 0.1%. Discrepancies between the assays included 15 codons with mutant concentrations of ∼2%, one at 8.8% by pyrosequencing and not detected by OLA, and one at 69% by OLA and not detected by pyrosequencing. The latter two cases were associated with genetic polymorphisms in the regions critical for ligation of the OLA probes and pyrosequencing primers, respectively. Overall, mutant concentrations quantified by the two methods correlated well across the codons tested (R(2) > 0.8). Repeat pyrosequencing of 13 specimens showed reproducible detection of 5/24 mutations at <2% and 6/6 at ≥ 2%. In conclusion, the OLA and pyrosequencing performed similarly in the quantification of nonnucleoside reverse transcriptase inhibitor and lamivudine mutations present at >2% of the viral population in clinical specimens. While pyrosequencing was more sensitive, detection of mutants below 2% was not reproducible.
journal_name
J Clin Microbioljournal_title
Journal of clinical microbiologyauthors
Beck IA,Deng W,Payant R,Hall R,Bumgarner RE,Mullins JI,Frenkel LMdoi
10.1128/JCM.00306-14subject
Has Abstractpub_date
2014-07-01 00:00:00pages
2320-7issue
7eissn
0095-1137issn
1098-660Xpii
JCM.00306-14journal_volume
52pub_type
杂志文章abstract::Murine monoclonal antibodies (MAbs) against herpes simplex virus type 1 and 2 (HSV-1 and -2, respectively) nuclear antigens were used to identify cells infected with HSV-1 or -2 by indirect immunofluorescence in conjunction with flow cytometry after virus amplification of MRC-5 cell monolayers. The results indicate th...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.28.8.1864-1866.1990
更新日期:1990-08-01 00:00:00
abstract::Lysis and filtration of blood culture specimens were combined with impedance detection of bacterial growth to facilitate the diagnosis of bacteremia. A blood lysis-filtration technique (Zierdt et al., 1976) was coupled to a simple, inexpensive automated detection system. The practical and technical aspects of the impe...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:
更新日期:1977-01-01 00:00:00
abstract::We report a novel IS711 chromosomal location that is specific for the Brucella genotype ST27 previously associated with Pacific marine mammals and human zoonotic infection in New Zealand and Peru. Our data support the previous observation that this peculiar genotype is distinct from those commonly isolated from the At...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.05238-11
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journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/jcm.40.4.1381-1386.2002
更新日期:2002-04-01 00:00:00
abstract::Syrian hamsters were shown to be susceptible to infection by the Lyme disease spirochete Borrelia burgdorferi. Although these spirochetes did not cause any outward signs of illness in these animals, they did cause a generalized infection. Spirochetemia was present during the first 6 days of infection. At 14 days posti...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.20.6.1099-1101.1984
更新日期:1984-12-01 00:00:00
abstract::Metagenomic next-generation sequencing (mNGS) of samples from 15 patients with documented Zika virus (ZIKV) infection in Bahia, Brazil, from April 2015 to January 2016 identified coinfections with chikungunya virus (CHIKV) in 2 of 15 ZIKV-positive cases by PCR (13.3%). While generally nonspecific, the clinical present...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.00877-16
更新日期:2016-09-01 00:00:00
abstract::Monoclonal antibodies to K88ac and K88ab were used in enzyme-linked immunosorbent assays on Escherichia coli cultures known to produce K88 pili. A total of 415 K88-positive E. coli isolates from nine states were all found to be the K88ac variant. The cultures tested were isolated during the years 1976 to 1985. ...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.26.1.149-150.1988
更新日期:1988-01-01 00:00:00
abstract::Previously, we designed an internally controlled quantitative nested real-time (QNRT) PCR assay for Mycobacterium tuberculosis DNA in order to rapidly diagnose tuberculous meningitis. This technique combined the high sensitivity of nested PCR with the accurate quantification of real-time PCR. In this study, we attempt...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.01200-07
更新日期:2008-05-01 00:00:00
abstract::We systematically evaluated 5 methods for testing daptomycin versus 48 Enterococcus faecalis, 51 Enterococcus faecium, and 50 Staphylococcus aureus isolates using (i and ii) broth microdilution (BMD) with 50-mg/liter calcium medium supplementation (reference method) and 30-mg/liter calcium medium supplementation (BMD3...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.03439-13
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journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.05255-11
更新日期:2011-10-01 00:00:00
abstract::An 840-bp fragment of the 18S rRNA gene was used to identify Cryptosporidium spp. recovered from human immunodeficiency virus (HIV)-infected and -uninfected patients from Kenya, Malawi, Brazil, the United Kingdom, and Vietnam. Initial identification was by Ziehl-Neelsen acid-fast staining. Confirmation was by nested P...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/jcm.41.4.1458-1462.2003
更新日期:2003-04-01 00:00:00
abstract::The aims of this study were to evaluate the use of molecular fingerprinting for assessment of bacterial diversity in canine duodenal juice and to evaluate the variation in the small intestinal microflora at repeated sampling. Two groups of dogs were used. Duodenal juice was collected from eight dogs euthanized for an ...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.42.10.4702-4708.2004
更新日期:2004-10-01 00:00:00
abstract::Ninety-five isolates of Haemophilus paragallinarum were classified serologically by a hemagglutinin serotyping scheme, and the results were compared with results from agglutinin serotyping of the same isolates. Of the isolates, 65 were from Australia, 5 were from Japan, 6 were from the Federal Republic of Germany, 7 w...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.27.7.1510-1513.1989
更新日期:1989-07-01 00:00:00
abstract::The BACTEC MGIT 960 system, a fully automated, nonradiometric, noninvasive system for detection and drug susceptibility testing of mycobacteria, was evaluated for the ability to test susceptibilities to second-line drugs. In this study, which was carried out in three phases (phase I, mostly susceptible strains; phase ...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章,多中心研究
doi:10.1128/JCM.44.3.688-692.2006
更新日期:2006-03-01 00:00:00
abstract::A premarket trial of the Becton Dickinson Directigen respiratory syncytial virus membrane-based enzyme immunoassay compared the test with virus isolation for the detection of respiratory syncytial virus in 583 nasopharyngeal aspirates. After modification, the Directigen test showed a sensitivity of 83% and a specifici...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.28.6.1458-1459.1990
更新日期:1990-06-01 00:00:00
abstract::bla(OXA-51-like) was sought in clinical isolates of Acinetobacter species in a multiplex PCR, which also detects bla(OXA-23-like) and class 1 integrase genes. All isolates that gave a band for bla(OXA-51-like) identified as A. baumannii. This gene was detected in each of 141 isolates of A. baumannii but not in those o...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.01021-06
更新日期:2006-08-01 00:00:00
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journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.35.3.764-766.1997
更新日期:1997-03-01 00:00:00
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journal_title:Journal of clinical microbiology
pub_type: 临床试验,杂志文章
doi:
更新日期:2000-06-01 00:00:00
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journal_title:Journal of clinical microbiology
pub_type: 杂志文章
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journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.01781-06
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journal_title:Journal of clinical microbiology
pub_type: 杂志文章
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更新日期:2011-09-01 00:00:00
abstract::The incidence of vancomycin resistance among enterococci is increasing in the United States and elsewhere in the world, but automated susceptibility testing methods have difficulty detecting resistance expressed by certain strains. The agar screening method described by Willey et al. (B. M. Willey, B. N. Kreiswirth, A...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.32.7.1700-1704.1994
更新日期:1994-07-01 00:00:00
abstract::A molecular hybridization technique with radiolabeled, strand-specific RNA probes was developed to detect dengue virus type 2 RNA in pools of infected Aedes albopictus mosquitoes. One infected mosquito in a pool of 25 could be detected, corresponding to a dengue virus type 2 titer of 2.75 log10 50% tissue culture infe...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.26.3.579-581.1988
更新日期:1988-03-01 00:00:00
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journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.01921-15
更新日期:2015-12-01 00:00:00
abstract::A quantitative modification of the shell vial assay was used to investigate cytomegalovirus viremia in solid-organ transplant recipients. The level of viremia detected in 109 of 407 specimens ranged from 0.02 to 28 infectious foci per 100,000 leukocytes. By using a Poisson model, a technique was developed to determine...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.30.10.2620-2624.1992
更新日期:1992-10-01 00:00:00
abstract::Urinary tract infections caused by staphylococci are usually attributed to Staphylococcus epidermidis or S. saprophyticus. The case study reported here describes a persistent urinary tract infection caused by S. haemolyticus in a 38-year-old male whose infection was ultimately resolved through the use of the antibioti...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.26.5.1055-1057.1988
更新日期:1988-05-01 00:00:00
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journal_title:Journal of clinical microbiology
pub_type: 杂志文章
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更新日期:2007-02-01 00:00:00
abstract::Family members of hepatitis C virus (HCV)-infected hemodialysis patients had a high rate (8.1%) of HCV infection and were often infected by the same genotype of HCV as the renal patients. Renal patients who had a longer history of hemodialysis or more frequent arteriovenous shunt replacement posed a higher risk to the...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.32.11.2824-2826.1994
更新日期:1994-11-01 00:00:00
abstract::Salmonella enterica subsp. enterica serovar Agona was not frequently encountered in Finland until an increase in rates of isolation among animal and feed was seen in 1994. A small outbreak among cattle farms in the regions of Oulu and Vaasa in northwestern Finland in 1994-1995 included eight farms. After the outbreak,...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/jcm.40.10.3648-3653.2002
更新日期:2002-10-01 00:00:00
abstract::We have investigated 677 Shiga toxin-producing Escherichia coli (STEC) strains from humans to determine their serotypes, virulence genes, and clinical signs in patients. Six different Shiga toxin types (1, 1c, 2, 2c, 2d, and 2e) were distributed in the STEC strains. Intimin (eae) genes were present in 62.6% of the str...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章,多中心研究
doi:10.1128/jcm.42.3.1099-1108.2004
更新日期:2004-03-01 00:00:00