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Accurate and rapid diagnosis of sexually transmitted infections (STIs) is essential for timely administration of appropriate treatment and reducing the spread of the disease. We examined the performance of the new Alinity m STI assay, a qualitative real-time multiplex PCR test for simultaneous identification of Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG), Mycoplasma genitalium (MG), and Trichomonas vaginalis (TV) run on the fully automated Alinity m platform.

Automated molecular analyzers have accelerated diagnosis, allowing earlier intervention and better patient follow-up. A recently developed completely automated molecular analyzer, Alinity™ m (Abbott), offers consolidated, continuous, and random-access testing that may improve molecular laboratory workflow.

Background. Interpreting human immunodeficiency virus type 1 (HIV-1) genotypic drug-resistance test results is challenging for clinicians treating HIV-1-infected patients. Multiple drug-resistance interpretation algorithms have been developed, but their predictive value has rarely been evaluated using contemporary clinical data sets. Methods. We examined the predictive value of 4 algorithms at predicting virologic response (VR) during 734 treatment-change episodes (TCEs). VR was defined as attaining plasma HIV-1 RNA levels below the limit of quantification. Drug-specific genotypic susceptibility scores (GSSs) were calculated by applying each algorithm to the baseline genotype. Weighted GSSs were calculated by multiplying drug-specific GSSs by antiretroviral (ARV) potency factors. Regimen-specific GSSs (rGSSs) were calculated by adding unweighted or weighted drug-specific GSSs for each salvage therapy ARV. The predictive value of rGSSs were estimated by use of multivariate logistic regression. Results. Of 734 TCEs, 475 (65%) were associated with VR. The rGSSs for the 4 algorithms were the variables most strongly predictive of VR. The adjusted rGSS odds ratios ranged from 1.6 to 2.2 (P < .001). Using 10-fold cross-validation, the averaged area under the receiver operating characteristic curve for all algorithms increased from 0.76 with unweighted rGSSs to 0.80 with weighted rGSSs. Conclusions. Unweighted and weighted rGSSs of 4 genotypic resistance algorithms were the strongest independent predictors of VR. Optimizing ARV weighting may further improve VR predictions. [ABSTRACT FROM AUTHOR]

Aim The aim of this study was to evaluate the workflow and performance of a NGS-based high resolution HLA typing prototype assay developed by GenDx. Methods 48 UCLA reference panel samples were amplified at 11 loci (HLA-A, B, C, DRB1, DRB3/4/5, DQB1, DQA1, DPB, DPA) using NGS-go® primers with Long-Range (LR) PCR and sequenced on the Illumina MiSeq platform. A full gene (5’ UTR to 3’ UTR) amplification strategy was applied with the exception of DRB1 which amplified from exon 2 to exon 4. Individual amplicons were generated for each sample using 100 ng of gDNA per LR-PCR reaction. Intrapatient amplicons were pooled, enzymatically fragmented, and purified. Purified fragmented dsDNA was brought through library preparation using NEBNext (New England Biolabs) for MiSeq sequencing. Due to the limited number of indices (24) in NEBNext, two 2 × 150 paired-end sequencing runs were completed with each run containing 24 samples. Demultiplexed reads were aligned and typed using GenDx NGSengine® v1.4.0 (IMGT v 3.15.0) and Omixon Target v1.8.0 (IMGT v 3.10.0) software. Results 47/48 UCLA samples successfully amplified; a single sample failed potentially due to gDNA integrity. For HLA-A, B, C, DRB1, DQB1, DQA1, DPB and DPA an average of 5 μ g of dsDNA was produced per amplicon, and 99.7% agreed with the reference SBT allele assignments. In one sample DRB1 04:05/15:02 were mistyped by both software packages. SBT reference typing was not available for DRB3/4/5, however when both software packages called a loci, there was 100% agreement at 4 digit allele typing level. Average sequencing output was 3.65 Gb of sequence (12 million paired sequence reads) per run and a mean of 459,573 (median: 433,292) paired-end reads per sample. Conclusion We have demonstrated that GenDx’s NGS HLA typing assay has high accuracy, throughput, and provided unambiguous high resolution results for 47/48 UCLA reference panel samples. This assay delivered full genomic sequences for all targeted HLA loci except DRB1 exon 1 and had the capacity to analyze 11 loci for 24 samples per MiSeq run. [ABSTRACT FROM AUTHOR]