Growth kinetics of <i>P. aeruginosa</i> and <i>S. aureus</i> from blood cultures with and without antibiotics.

<p>AMX, amoxicillin; OXA, oxacillin; VAN, vancomycin; CIP, ciprofloxacin; GEN, gentamicin; AMC, amoxicillin/clavulanic acid; PIP, piperacillin; TZP, piperacillin/tazobactam; CAZ, ceftazidim.</p

Agreement and errors in the tested population, per antibiotic.

<p>Agreement and errors in the tested population, per antibiotic.</p

Pathogen identification of the 122 growth-positive urine specimens.

a<p>None of the species- or genus-specific probes generated a signal, only the universal 16S rDNA probe was positive, indicating the presence of another pathogen, not included in the bacterial panel of the real-time PCR assay.</p>b<p>The isolate was identified as <i>P. aeruginosa</i>, and this was shown by positive signals from both the <i>Pseudomonas</i> spp. and the <i>P. aeruginosa</i> probe.</p

Comparison of performance characteristics of the diagnostic test (real-time PCR assay, universal probe) using different PCR Ct cut-off values (25–30).

<p>Ct 25 was used as definitive cut-off value.</p

Receiver Operator Characteristic (ROC) decision plot.

<p>ROC curve analysis obtained by using the real-time PCR Ct values (universal probe) versus urine culture results (Cut-off value of ≥10⁵ CFU/ml).</p

Boxplot showing the correlation of PCR Ct values with bacterial load determined in culture.

<p>Culture results were grouped into three categories: <10³ CFU/ml, 10³–10⁴ CFU/ml and ≥10⁵ CFU/ml. Statistical significance was determined performing Kruskal-Wallis Test.</p

Evaluation of clinical samples by viability-PCR.

<p>(A) Δlog CT/ml of the clinical samples are presented as scatter dot plots displaying the median with the interquartile ranges. (B) Clinical samples categorized according to the amount of DNA originating from viable CT.</p

Effect of PMA treatment on defined viability ratios of CT.

<p>representing a untreated viable CT culture proportion of 0%, 0.1%, 1%, 10%, 50%, and 100%, respectively. qPCR was performed using primers specific for the chlamydial single-copy <i>ompA</i> gene. Error bars represent standard deviations from three independent replicates. (A) Log CT/ml obtained for each viability ratio treated with (w PMA; white bars) and without (w/o PMA; grey bars) PMA. (B) Bars present the change in log CT/ml observed as a result of treatment with PMA prior to DNA purification.</p

Factors associated with test of cure and retest results among general practices in the Netherlands, based on the first positive <i>Neisseria gonorrhoeae</i> screening test between January 2011 and July 2015.

<p>Factors associated with test of cure and retest results among general practices in the Netherlands, based on the first positive <i>Neisseria gonorrhoeae</i> screening test between January 2011 and July 2015.</p

Development and Validation of a Single-Tube Multiple-Locus Variable Number Tandem Repeat Analysis for <i>Klebsiella pneumoniae</i>

<div><p>Genotyping of <i>Klebsiella pneumoniae</i> is indispensable for management of nosocomial infections, monitoring of emerging strains –including extended-spectrum beta-lactamase (ESBL) producers-, and general epidemiology. Such objectives require a high-resolution genotyping method with a fixed scheme that allows (1) long-term retrospective and prospective assessment, (2) objective result readout and (3) library storage for database development and exchangeable results. We have developed a multiple-locus variable number tandem repeat analysis (MLVA) using a single-tube fluorescently primed multiplex PCR for 8 Variable Number Tandem Repeats (VNTRs) and automated fragment size analysis. The type allocation scheme was optimized using 224 <i>K. pneumoniae</i> clinical isolates, which yielded 101 MLVA types. The method was compared to the gold standard multilocus sequence typing (MLST) using a subset of these clinical isolates (n = 95) and found to be highly concordant, with at least as high a resolution but with considerably less hands-on time. Our results position this MLVA scheme as an appropriate, high-throughput and relatively low-cost tool for <i>K. pneumoniae</i> epidemiology.</p></div