192 research outputs found
Identifying Influenza Viruses with Resequencing Microarrays
Resequencing microarrays rapidly identify influenza viruses
Influenza A (H3N2) Outbreak, Nepal
Worldwide emergence of variant viruses has prompted a change in the 2005–2006 H3N2 influenza A vaccine strain
Improved detection by next-generation sequencing of pyrazinamide resistance in mycobacterium tuberculosis isolates
Technical limitations of common tests used for detecting pyrazinamide (PZA) resistance in
Mycobacterium tuberculosis (MTB) isolates pose challenges for comprehensive and accurate
descriptions of drug resistance in patients with multi-drug resistant tuberculosis (MDR-TB) . In
this study, a 606 base pair fragment (comprising the pncA coding region plus promoter) was
sequenced using Ion Torrent next generation sequencing (NGS) for detecting associated PZA
resistance mutations in 90 re-cultured, MDR-TB isolates from an archived series collected in
2001. These 90 isolates were previously Sanger sequenced, with 55 (62%) designated as carrying
wild type pncA gene and 33 (38%) showing mutations. Also earlier, PZA susceptibility of the isolates was determined using the Bactec 460 TB system and the Wayne test. In this study,
isolates were re-cultured and susceptibility testing performed in Bactec 960 MGIT. Concordance
between NGS and MGIT results was 87% (n = 90), and with the Bactec 460, Wayne test, and
pncA gene Sanger sequencing, 82% (n = 88), 83% (n = 88), and 89% (n = 88), respectively.
NGS confirmed the majority of pncA mutations detected by Sanger sequencing, but revealed
several new and mixed-strain mutations that resolved discordancy in other phenotypic results.
Importantly, in 53% (18/34) of these isolates, pncA mutations were located in the 151-360
region, and warrants further exploration. In these isolates, with known resistance to rifampicin,
NGS of pncA improved PZA resistance detection sensitivity to 97% and specificity to 94% using
NGS as the gold standard, and helped to resolve discordant results from conventional
methodologies.University of Pretoria, the South African Medical Research Council, and the National Research Foundation of South Africa.http://jcm.asm.org2016-06-30hb201
Next-generation sequencing for identifying pyrazinamide resistance in Mycobacterium tuberculosis
No abstract available.http://cid.oxfordjournals.orgam201
Opsonic monoclonal antibodies enhance phagocytic killing activity and clearance of Mycobacterium tuberculosis from blood in a quantitative qPCR mouse model
BACKGROUND : Patients with impaired immunity often have rapid progression of tuberculosis (TB) which can lead to
highly lethal Mycobacterium tuberculosis (MTB) sepsis. Opsonic monoclonal antibodies (MABs) directed against
MTB that enhance phagocytic killing activity and clearance of MTB from blood may be useful to enhance TB
immunity.
METHODS : BALB/c mice were immunized with ethanol-killed MTB (EK-MTB) and MABs were produced and
screened by ELISA for binding to killed and live Mycobacterium smegmatis (SMEG) and MTB. MAB opsonophagocytic
killing activity (OPKA) was examined using SMEG with HL60 and U-937 cells and MTB with U-937 cells.
Clearance of MTB from blood was evaluated in Institute of Cancer Research (ICR) mice given opsonic anti-MTB
MABs or saline (control) 24 h prior to intravenous infusion with 108 CFUs gamma-irradiated MTB (HN878). MTB
levels in murine blood collected 0.25, 4 and 24 h post-challenge were assessed by qPCR. MAB binding to
peptidoglycan (PGN) was examined by ELISA using PGN cell wall mixture and ultra-pure PGN.
RESULTS : Two MABs (GG9 and JG7) bound to killed and live SMEG and MTB (susceptible and resistant), and
promoted OPKA with live MTB. MAB JG7 significantly enhanced OPKA of MTB. Both MABs significantly
enhanced clearance of killed MTB from murine blood at 4 and 24 h as measured by qPCR. These opsonic MABs
bound to PGN, a major cell wall constituent.
CONCLUSIONS : Anti-MTB MABs that promote bactericidal phagocytic activity of MTB and enhance clearance of killed
MTB from the blood, may offer an immunotherapeutic approach for treatment of MTB bacteremia or sepsis, and
augment treatment of multi-drug resistant (MDR) or extensively drug resistant (XDR) TB.This work was supported by Longhorn Vaccines and Diagnostics, LLC.
Live MTB work was additionally supported from post-graduate student
bursaries to Bong-Akee Shey from the University of Pretoria and from
grant 105830 to PBF by the National Research Foundation of South Africa.Post-graduate student
bursaries to Bong-Akee Shey from the University of Pretoria and from
grant 105830 to PBF by the National Research Foundation of South Africa.https://www.heliyon.comam2020Medical Microbiolog
Multi- and extensively drug resistant mycobacterium tuberculosis in South Africa : a molecular analysis of historical isolates
Modern advances in genomics provide an opportunity to reinterpret historical bacterial culture collections. In this study, genotypic antibiotic resistance profiles of Mycobacterium tuberculosis isolates from a historical 20-year-old multidrug-resistant tuberculosis (MDR-TB) culture collection in South Africa are described. DNA samples extracted from the phenotypically MDR-TB isolates (n = 240) were assayed by Hain line probe assay (LPA) for the confirmation of MDR-TB and by Illumina Miseq whole-genome sequencing (WGS) for the characterization of mutations in eight genes (rpoB, katG, inhA, rpsL, pncA, embB, gyrA, and rrs) that are known to code for resistance to commonly used anti-TB agents. LPA identified 71.3% of the TB isolates as MDR-TB, 18.3% as rifampin (RIF) monoresistant, 2% as isoniazid (INH) monoresistant, and 8.3% as susceptible to both RIF and INH (RIF+INH). In a subset of 42 randomly selected isolates designated as RIF+INH resistant by Löwenstein-Jensen (LJ) culture in 1993, LPA and WGS results confirmed MDR-TB. In all five INH-monoresistant isolates by LPA and in all but one (the wild type) of the 34 successfully sequenced RIF-monoresistant isolates, WGS revealed matching mutations. Only 26% of isolates designated as susceptible by LPA, however, were found to be wild type by WGS. Novel mutations were found in the rpoB (Thr480Ala, Gln253Arg, Val249Met, Val251Tyr, Val251Phe), katG (Trp477STOP, Gln88STOP, Trp198STOP, Trp412STOP), embB (Thr11Xaa, Gln59Pro), and pncA (Thr100Ile, Thr159Ala, Ala134Arg, Val163Ala, Thr153Ile, DelGpos7, Phe106Ser) genes. Three MDR-TB isolates showed mutations in both the gyrA and rrs genes, suggesting that extensively drug-resistant tuberculosis existed in South Africa well before its formal recognition in 2006.The Global Infectious Diseases Research Training Fogarty Fellowship, the University of Pretoria; the South African Medical Research Council and the National Research Foundation of South Africa.http://jcm.asm.org2018-10-31hj2018Medical Microbiolog
Deep-Inelastic Inclusive ep Scattering at Low x and a Determination of alpha_s
A precise measurement of the inclusive deep-inelastic e^+p scattering cross
section is reported in the kinematic range 1.5<= Q^2 <=150 GeV^2 and
3*10^(-5)<= x <=0.2. The data were recorded with the H1 detector at HERA in
1996 and 1997, and correspond to an integrated luminosity of 20 pb^(-1). The
double differential cross section, from which the proton structure function
F_2(x,Q^2) and the longitudinal structure function F_L(x,Q^2) are extracted, is
measured with typically 1% statistical and 3% systematic uncertainties. The
measured partial derivative (dF_2(x,Q^2)/dln Q^2)_x is observed to rise
continuously towards small x for fixed Q^2. The cross section data are combined
with published H1 measurements at high Q^2 for a next-to-leading order DGLAP
QCD analysis.The H1 data determine the gluon momentum distribution in the range
3*10^(-4)<= x <=0.1 to within an experimental accuracy of about 3% for Q^2 =20
GeV^2. A fit of the H1 measurements and the mu p data of the BCDMS
collaboration allows the strong coupling constant alpha_s and the gluon
distribution to be simultaneously determined. A value of alpha
_s(M_Z^2)=0.1150+-0.0017 (exp) +0.0009-0.0005 (model) is obtained in NLO, with
an additional theoretical uncertainty of about +-0.005, mainly due to the
uncertainty of the renormalisation scale.Comment: 68 pages, 24 figures and 18 table
Searches at HERA for Squarks in R-Parity Violating Supersymmetry
A search for squarks in R-parity violating supersymmetry is performed in e^+p
collisions at HERA at a centre of mass energy of 300 GeV, using H1 data
corresponding to an integrated luminosity of 37 pb^(-1). The direct production
of single squarks of any generation in positron-quark fusion via a Yukawa
coupling lambda' is considered, taking into account R-parity violating and
conserving decays of the squarks. No significant deviation from the Standard
Model expectation is found. The results are interpreted in terms of constraints
within the Minimal Supersymmetric Standard Model (MSSM), the constrained MSSM
and the minimal Supergravity model, and their sensitivity to the model
parameters is studied in detail. For a Yukawa coupling of electromagnetic
strength, squark masses below 260 GeV are excluded at 95% confidence level in a
large part of the parameter space. For a 100 times smaller coupling strength
masses up to 182 GeV are excluded.Comment: 32 pages, 14 figures, 3 table
Multi-Jet Event Rates in Deep Inelastic Scattering and Determination of the Strong Coupling Constant
Jet event rates in deep inelastic ep scattering at HERA are investigated
applying the modified JADE jet algorithm. The analysis uses data taken with the
H1 detector in 1994 and 1995. The data are corrected for detector and
hadronization effects and then compared with perturbative QCD predictions using
next-to-leading order calculations. The strong coupling constant alpha_S(M_Z^2)
is determined evaluating the jet event rates. Values of alpha_S(Q^2) are
extracted in four different bins of the negative squared momentum
transfer~\qq in the range from 40 GeV2 to 4000 GeV2. A combined fit of the
renormalization group equation to these several alpha_S(Q^2) values results in
alpha_S(M_Z^2) = 0.117+-0.003(stat)+0.009-0.013(syst)+0.006(jet algorithm).Comment: 17 pages, 4 figures, 3 tables, this version to appear in Eur. Phys.
J.; it replaces first posted hep-ex/9807019 which had incorrect figure 4
Multiplicity Structure of the Hadronic Final State in Diffractive Deep-Inelastic Scattering at HERA
The multiplicity structure of the hadronic system X produced in
deep-inelastic processes at HERA of the type ep -> eXY, where Y is a hadronic
system with mass M_Y< 1.6 GeV and where the squared momentum transfer at the pY
vertex, t, is limited to |t|<1 GeV^2, is studied as a function of the invariant
mass M_X of the system X. Results are presented on multiplicity distributions
and multiplicity moments, rapidity spectra and forward-backward correlations in
the centre-of-mass system of X. The data are compared to results in e+e-
annihilation, fixed-target lepton-nucleon collisions, hadro-produced
diffractive final states and to non-diffractive hadron-hadron collisions. The
comparison suggests a production mechanism of virtual photon dissociation which
involves a mixture of partonic states and a significant gluon content. The data
are well described by a model, based on a QCD-Regge analysis of the diffractive
structure function, which assumes a large hard gluonic component of the
colourless exchange at low Q^2. A model with soft colour interactions is also
successful.Comment: 22 pages, 4 figures, submitted to Eur. Phys. J., error in first
submission - omitted bibliograph
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