Journal of Clinical Microbiology

BackgroundMatrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is pivotal in clinical microbiology. The VITEK MS Research Use Only (RUO) database offers broader species coverage, yet its clinical adoption is hindered by insufficient performance validation against the approved in vitro diagnostic (IVD) database and inefficient manual operational workflows. ObjectiveThis two-phase study first aimed to develop and evaluate an automated integrated workflow to enhance laboratory efficiency and diagnostic capability. MethodsThe RUO databases two-tier identification architecture was utilized and in-house automated relay software was developed to parse IVD results and fully automate RUO reanalysis. Phase 1 (Mar 2021-Jun 2022) involved parallel manual testing of 2,432 isolates with both databases to analyze concordance and supplementary performance. Phase 2 (Jul-Nov 2022) prospectively incorporated 3,954 isolates to implement and assess the "IVD screening - automated RUO reanalysis" workflow. ResultsPhase 1 demonstrated high RUO-IVD concordance (95.7% species/genus agreement). The RUO database correctly identified 98.9% of isolates and provided valid supplementary identification for 84.4% (108/128) of IVD-failed cases, with Tier 2 contributing 28.9%. Phase 2 revealed that the integrated workflow increased the overall identification rate from 95.5% to 98.7%, with Tier 2 contributing an additional 14.5%. The automated software reduced reanalysis turnaround time by > 75%, saving consumables and labor. ConclusionThe VITEK MS RUO database is a reliable and complementary tool to the IVD database. Integration with automated software creates an efficient, compliant clinical workflow, providing a practical model to enhance pathogen identification for infectious disease management. IMPORTANCEThe present study bridges the validation-to-application gap for the VITEK MS RUO database. We confirm its high concordance (95.7%) and complementary value to the IVD database, quantify the impact of manual workflow inefficiency and introduce an automated software solution. The strategy highlights the key role of Reference Spectra (Tier 2) in expanding coverage and simultaneously improves diagnostic efficacy ([~]99% ID rate), operational efficiency (> 75% time saved) and cost-effectiveness, offering a practical model to accelerate pathogen reporting and to guide therapy.

BackgroundDiagnosis of Neisseria (N.) gonorrhoeae is dependent on nucleic acid amplification testing (NAAT), which is not available in resource-limited settings where the prevalence of infection is highest. Recent advances in molecular diagnostics leveraging the high specificity of CRISPR enzymes can permit field-deployable, point-of-care lateral flow assays. We previously reported on the development and in vitro performance of a lateral flow assay for detecting N. gonorrhoeae. Here we aimed to pair that assay with point-of-care DNA extraction techniques and assess the performance on clinical urine specimens. MethodsWe collected an additional urine specimen among individuals enrolling in an ongoing clinical trial at the Massachusetts General Hospital Sexual Health Clinic who presented with symptoms of urethritis or cervicitis (urethral or vaginal discharge, dysuria, or dyspareunia). We then assessed thermal, detergent, and combination DNA extraction conditions, varying the duration of heat at 95{degrees}C and concentration of Triton X. We assessed the efficacy of the various DNA extraction methods by quantitative polymerase chain reaction (qPCR). Once an extraction method was selected, we incubated samples for 90 minutes to permit isothermal recombinase polymerase amplification. We then assessed the performance of lateral flow Cas13a-based detection using our previously designed porA probe and primer system for N. gonorrhoeae detection, comparing lateral flow results with NAAT results from clinical care. ResultsWe assessed DNA extraction conditions on 3 clinical urine specimens. There was no consistent significant difference in copies per microliter of DNA obtained using more or less heat. On average, we noted that 0.02% triton combined with 5 minutes of heating to 95{degrees}C resulted in the highest DNA yield, however, 0.02% triton alone resulted in a quantity of DNA that was above the previously determined analytic sensitivity of the assay. Given that detergent-based extraction is more easily deployable, we selected that as our method for extraction. We treated 23 clinical specimens with 0.02% triton, which we added to the Cas13a detection system. We ran all lateral flow detections in duplicate. The Cas13a-based assay detected 8 of 8 (100%) positive specimens, and 0 of 15 negative specimens. ConclusionUsing point-of-care DNA extraction, isothermal amplification, and Cas13a-based detection, our point-of-care lateral flow N. gonorrhoeae assay correctly identified 23 clinical urine specimens as either positive or negative. Further evaluation of this assay among larger samples and more diverse sample types is warranted.

In wound specimens, co-detection of mecA and Staphylococcus aureus by PCR does not necessarily indicate MRSA because coagulase-negative staphylococci (CoNS) frequently harbor mecA. We evaluated a {Delta}Ct-informed, biologically gated, calibrated logistic regression to attribute mecA to S. aureus versus CoNS. Using paired culture/AST and multiplex real-time PCR Ct values (internal n=93; external n=47), we trained 5-fold cross-validated models in the culture-positive S. aureus subset (n=36) and applied an S. aureus PCR gate (no attribution when S. aureus PCR is negative). The primary model achieved sensitivity 90.9% and specificity 92.0% for MRSA attribution with AUC 0.931 (out-of-fold). Decision curve analysis showed positive net benefit across clinically relevant thresholds; at the prespecified 50% cutoff, the model achieved a net benefit of 0.222 compared with negative benefit for a treat-all strategy. In an external cohort, S. aureus detection by PCR versus culture showed 92.3% sensitivity and 97.1% specificity; within S. aureus PCR-positives (n=12), MRSA attribution reached 100% sensitivity and 87.5% specificity (accuracy = 91.7%). This framework improves mecA interpretability in polymicrobial specimens and can reduce unnecessary MRSA-directed antibiotics.

Introduction: Rapid pathogen identification, resistance detection, and susceptibility profiling improve antimicrobial prescribing and associated outcomes, but fragmented workflows lead to inefficiencies and are costly. We evaluated a research-use-only (RUO) approach using ASTar(R) remnant bacterial suspension from routine AST for MALDI-TOF MS pathogen identification and Lateral Flow Assay (LFA)-based detection of targeted resistance mechanisms. Methods: Gram-negative (GN) bacterial strains from reference and curated resistance collections (CDC1, ARLG2, ATCC3) [n=119] were contrived into blood culture bottles and processed in the ASTar 16 System using the ASTar BC G- Kit (Q-linea AB, Sweden). Under RUO conditions, remnant bacterial suspensions were collected ~1-2 h after ASTar run initiation and analyzed using NG Test CTX-M Multi, NG Test CARBA-5, NG Test Acineto-5 RUO, and MALDI-TOF MS. Results: Mean ({+/-} SD) remnant suspension volume was 2722 L ({+/-} 300 L). All samples yielded high confidence MALDI-TOF MS scores (>2.0), with five initially scoring <2.0 and resolving on repeat testing. LFA results showed full agreement with reference isolates for blaCTX-M positive/negative (30/30) and with 60 or 61 target carbapenemase-positive/negative isolates. Testing of a subset of samples to mimic reflex workflows with ASTar phenotypic results did not affect LFA performance 24 (n=26; 23 Enterobacterales, 3 P. aeruginosa and 9 A. baumannii). Cost savings can be realised versus commercial multiplex PCR. Conclusion: This integrated approach of ~6 h rapid phenotypic AST with same-run identification and resistance detection (1-2 h from instrument start) or reflex testing upon availability of ASTar results may support earlier susceptibility results and offer cost savings to current workflows.

In March 2019 the outbreak of SARS-CoV 2 was officially defined as a pandemic by the World Health Organization and shortly after, the United States Food and Drug Administration (FDA) granted Emergency Use Authorization (EUA) to the Centers for Disease Control (CDC) for reverse transcription polymerase chain reaction (rtPCR) molecular testing for the detection of the SARS-CoV-2 virus from NP swabs. Since then, EUA with relaxed regulations were granted to numerous manufacturers and clinical microbiology laboratories to implement in-house testing assays with nasopharyngeal swabs (NP) and subsequently additional specimen types. Because of supply chain shortages leading to competition for reagents, sustaining any significant volume of testing soon became problematic. As a countermeasure, within several weeks the Henry Ford Microbiology Laboratory validated 4 different rtPCR assays and multiple specimen types using NeuMoDX, Diasorin Simplexa, Cepheid and Roche platforms. The purpose of this study was to analyze the analytic sensitivity of these rtPCR assays with NP/nasal swabs and sputum/tracheal aspirates. Qualitative analytic agreement between the 4 platforms for NP/nasal swabs ranged 95% - 100% overall with no statistically significant difference in threshold cT values. Similar results were obtained with the sputum/tracheal aspirates. These data demonstrate the high accuracy and reproducibility in detection of SARS-CoV 2 between the rtPCR assays performed on 4 different platforms with numerous specimen types.

Three enzyme immunoassays (EIAs) were evaluated on two platforms each for detecting Cryptosporidium, Giardia, and Campylobacter in stool samples compared to gold standard methods. The Cryptosporidium EIAs run on stool specimens in three preservative media showed 100% agreement with direct fluorescent antibody (DFA) testing and high correlation with the microscopic method. The Giardia EIAs demonstrated 100% sensitivity but only moderate correlation with the microscopic method. The Campylobacter EIAs had 93.5% sensitivity (out of 65 positives) and 100% specificity compared to the culture method. Automation on a DS2 system for these three EIAs, along with five others, yielded acceptable performance (92.5-100% accuracy) compared to manual methods. The automation saved labor time and improved operational efficiency but may not be cost-effective for low-volume runs due to the labor required for automation not scaling proportionally with sample numbers. In conclusion, EIAs are preferred for detecting protozoan parasites in stool, with the Cryptosporidium EIA showing potential as a semi-quantitative assay and a reference method. Automation benefits high-throughput laboratories but may not be as advantageous for low-volume laboratories. IMPORTANCEEnzyme immunoassay (EIA) is a widely used method in clinical laboratories to detect pathogens in stool samples related to diarrhea diseases. This study evaluated the performance of three EIAs for detecting Cryptosporidium, Giardia, and Campylobacter antigens compared to their gold standard methods. The Cryptosporidium EIAs matched the direct fluorescent antibody (DFA) testing and had a high correlation with microscopic findings (99.7%). The Giardia EIAs showed 100% sensitivity but lower specificity (58%) and moderate correlation with microscopic results (87.4%). The Campylobacter EIA had 93.5% sensitivity (n=65 positive samples) with few discrepancies. Automating these three and five other EIAs using a DS2 system (Dynex) yielded good accuracy (92.5-100%) and 100% precision compared to manual methods. While automation saved hands-on time for high-volume assays, it may not be cost-effective for low-volume laboratories.

We identify a mutation in the N gene of SARS-CoV-2 that adversely affects annealing of a commonly used RT-PCR primer; epidemiologic evidence suggests the virus retains pathogenicity and competence for spread. This reinforces the importance of using multiple targets, preferably in at least 2 genes, for robust SARS-CoV-2 detection. Article Summary LineA SARS-CoV-2 variant that occurs worldwide and has spread in California significantly affects diagnostic sensitivity of an N gene assay, highlighting the need to employ multiple viral targets for detection.

Traditional nucleic acid extraction methods are costly, lengthy, and highly variable depending on the complexity of the sample matrix or the organism of interest. Workflows may exceed twenty steps, require separate kits for RNA and DNA, and demand expensive instrumentation, creating barriers to both speed and scalability. The AutolabTM HBH system addresses these limitations by using hyperbaric heating (HBH) to achieve temperatures above 100 {degrees}C in a sealed, pressurized environment through induction heating, enabling rapid lysis of diverse organisms and neutralization of macromolecular PCR inhibitors within minutes. The combination of extreme heat and HBH-optimized lyophilized reagents rapidly inactivates nucleases while preserving free nucleic acids. The workflow is streamlined to two steps: heating up to 1 mL of sample in the proprietary HBH bullet, followed by a brief centrifugation to pellet additives. The resulting supernatant is immediately compatible with real-time reverse transcription polymerase chain reaction (RT-PCR) and other downstream molecular assays. Here, we evaluate the systems broad compatibility with diverse sample buffers, matrices, and organisms. Comparative testing was conducted alongside Qiagen extraction methods to benchmark performance.

Enteric fever caused by Salmonella enterica serovars Typhi and Paratyphi A, B and C remains a major public health burden in endemic regions. Existing molecular assays frequently demonstrate limited specificity due to cross-reactivity with non-typhoidal Salmonella (NTS). In this study, we developed and validated a genomics-informed multiplex PCR assay capable of simultaneously differentiating all four typhoidal Salmonella serovars. A curated dataset of 3,239 Salmonella genomes, including S. Typhi (n=361), S. Paratyphi A (n=453), S. Paratyphi B (n=511), S. Paratyphi C (n=62), and NTS genomes (n=1,853), was used for comparative genomic analysis. Thirty published PCR targets were evaluated in silico, followed by pangenome and SNP analyses to identify discriminatory loci for mismatch amplification mutation assay (MAMA)-based primer design. Candidate primers were validated using in silico PCR, BLASTn analysis, and laboratory testing against a panel of typhoidal Salmonella, clinical NTS isolates, and non-Salmonella bacterial pathogens. In silico evaluation demonstrated substantial cross-reactivity among many published targets, whereas SNP-informed primer design targeting staG (S. Typhi), SPA0152 (S. Paratyphi A), SPAB_03490 (S. Paratyphi B), and SPC_0571 (S. Paratyphi C) achieved predicted specificities of 98-100% while retaining high analytical sensitivity (>97%) across target genomes. Combined with a pan-Salmonella invA target, the multiplex assay precisely identified all target serovars in vitro with minimal cross-reactivity. These findings demonstrate that genomics-informed SNP-based primer design enables reliable multiplex differentiation of typhoidal Salmonella serovars and provides a scalable framework for improving enteric fever diagnosis and surveillance in endemic settings. ImportanceTyphoidal Salmonella serovars remain major causes of enteric fever in endemic regions, yet molecular differentiation from non-typhoidal Salmonella (NTS) remains challenging because of extensive genomic conservation and cross-reactivity of commonly used diagnostic targets. In this study, we combined large-scale comparative genomics of 3,239 Salmonella genomes with SNP-informed primer design to develop a multiplex PCR assay capable of simultaneously differentiating all four typhoidal serovars (S. Typhi, S. Paratyphi A, B, and C) from NTS and other non-Salmonella pathogens. Unlike conventional gene-content-based assays, this approach incorporated lineage-specific SNPs and mismatch amplification strategies to improve specificity while maintaining high analytical sensitivity. In silico evaluation demonstrated high diagnostic performance across diverse global lineages, while in vitro testing confirmed accurate serovar-level discrimination with minimal cross-reactivity. These findings demonstrate the value of population-scale genomics for molecular assay development and provide a scalable framework for improving diagnosis and surveillance of enteric fever in endemic settings.

Direct sputum whole genome sequencing (dsWGS) can revolutionize Mycobacterium tuberculosis (Mtb) diagnosis by enabling rapid detection of drug resistance and strain diversity without the biohazard of culture. We searched PubMed, Web of Science and Google scholar, and identified 8 studies that met inclusion criteria for testing protocols for dsWGS. Utilising meta-regression we identify several key factors positively associated with dsWGS success, including higher Mtb bacillary load, mechanical disruption, and enzymatic/chemical lysis. Specifically, smear grades of 3+ (OR = 14.7, 95% CI: 3.5, 62.1; p = 0.0005) were strongly associated with improved outcomes, whereas decontamination with sodium hydroxide (NaOH) was negatively associated (OR = 0.005, 95% CI: 0.001, 0.03; p = 7e-06), likely due to its harsh effects on Mtb cells. Furthermore, mechanical lysis (OR = 193.3, 95% CI: 11.7, 3197.8; p = 0.008) and enzymatic/chemical lysis (OR = 18.5, 95% CI: 1.9, 183.1; p = 0.02) were also strongly associated with improved dsWGS. Across the studies, we observed a high degree of variability in approaches to sputum pre-processing prior to dsWGS highlighting the need for standardized best practices. In particular we conclude that optimizing pre-processing steps including decontamination with the exploration of alternatives to NaOH to better preserve Mtb cells and DNA, and best practices for cell lysis during DNA extraction as priorities. Further and considering the strong association between Mtb load and successful dsWGS, protocol improvements for optimal sputum sample collection, handling, and storage could also further enhance the success rate of dsWGS.

BackgroundThe detection of pathogens causing infections by conventional diagnostic methods can be challenging and next-generation sequencing (NGS) technology offers a promising alternative method. In this study, we evaluated the performance of real-time metagenomic next-generation sequencing (rt-mNGS) for the detection of pathogens in respiratory samples. MethodWe used rt-mNGS, using the Seqstant LiveGene Analysis platform, on 335 respiratory samples in comparison to conventional culture results. ResultsWe observed an overall good concordance in 71.64% (240/335) of the methods. The rt-mNGS outperformed the gold standard culture in 16.12% (54/335) of the samples, while the culture was superior in detecting the clinically relevant pathogen in 12.24% (41/335) of the samples. The non-inferiority of rt-mNGS was statistically significant ({delta} = 10, = 0.05, 1 - {beta}= 0.8). We also observed that the real-time analysis of NGS data is beneficial in obtaining reliable timely results as the initial report at cycle 46 exhibits a Positive Predictive Value (PPV) of 93.75% at the species-level with a sensitivity of 32.09%. ConclusionOverall, our study showed the non-inferiority of rt-mNGS compared to the standard-of-care microbiology for respiratory samples with statistical significance. Moreover, the rt-mNGS method exhibited superior sensitivity and superior overall performance. It also uniquely detected certain organisms that are typically hard to culture. However, rt-mNGS reported a higher number of false positives and faced limitations in detecting Aspergillus spp. In conclusion, the study highlights the potential of rt-mNGS as a powerful tool in clinical diagnostics of respiratory infections and beyond.

Illumina sequencing of primary MGIT cultures is an established workflow in several reference mycobacteriology laboratories. Oxford Nanopore Technologies (ONT) provides real-time genetic sequencing yielding long reads which help resolve repetitive genomes and is being explored for in-house implementation within diagnostic laboratories. However, low DNA yields from primary MGIT cultures frequently limit the application of ONT workflows, due to high minimum DNA input requirements for library preparation. We evaluated a modified ONT workflow combining rapid, semi-automated DNA extraction from MGIT cultures with PCR-based whole-genome amplification, and compared its performance with Illumina sequencing for species identification and Mycobacterium tuberculosis complex (MTBC) single-nucleotide polymorphism (SNP) detection. A platformagnostic analysis pipeline enabled consistent human read removal, taxonomic assignment, and MTBC genomic characterisation. ONT sequencing data was subsampled at 1 h, 6 h, and 72 h to determine the earliest time point for reliable species identification. The concordance between sequencing platforms of species classification and MTBC lineage assignment was 95%. SNP agreement was high, with a mean of 1.0 and a median of 0 SNP differences between sequencing platforms after masking. These findings demonstrate the feasibility of PCR-amplified ONT sequencing as a reliable alternative for routine genomic characterisation of MGIT cultures. IMPORTANCERapid genomic characterisation of mycobacteria from primary MGIT cultures is valuable for timely and accurate clinical diagnosis. Although Illumina sequencing provides high sequence accuracy, its longer turnaround time and workflow complexity limit the rapid delivery of actionable results. Oxford Nanopore Technologies (ONT) sequencing enables continuous data generation and analysis, allowing real-time species identification and genomic characterisation. However, low DNA yield from primary MGIT cultures has limited the reliable application of ONT sequencing using standard extraction and PCR-free rapid library preparation methods. This study shows that combining semi-automated DNA extraction with PCR-based wholegenome amplification substantially improves ONT sequencing performance from primary MGIT cultures. The resulting increase in data yield enables more samples to be multiplexed and shorter sequencing run times while retaining comprehensive diagnostic information from a single whole-genome sequencing assay. Together, these improvements enable the practical implementation of ONT sequencing for routine mycobacterial diagnostics and may reduce both turnaround time and sequencing costs in clinical laboratories.

Mycobacterium tuberculosis (MTB) disease is a major global health threat with most tuberculosis (TB) cases occurring in low-and middle-income countries (LMIC) with limited healthcare infrastructure. Near-point-of-care testing which can be deployed at peripheral clinical settings is needed to start treatment earlier and thereby improve treatment outcomes. Here we report the development and preliminary characterization of an MTB detection assay that utilizes tongue swab or sputum specimens for The DASH(R) Rapid PCR System which employs cartridge-based automated sequence specific capture sample prep combined with dual target qPCR multicopy MTB insertion sequences IS6110 and IS1081 amplification and detection. MTB is resistant to conventional bacterial lysis techniques; therefore, we evaluated two pre-cartridge lysing techniques, mechanical lysis and sonication, and selected sonication for all subsequent studies. The DASH MTB assay demonstrated a limit of detection of 2.5 MTB cells/swab with no detection of 10 non-tuberculosis Mycobacterium strains. Clinical testing of 100 (49 positive and 51 negative) de-identified blinded sputa from South African symptomatic clinic attendees yielded an overall test sensitivity of 96% (100% for smear positive samples and 88% for smear negative samples) and specificity of 88% when compared to sputum culture. In a separate study of 110 tongue swab specimens (70 positive and 40 negative) from South African symptomatic clinic attendees, the sensitivity was 93% and the specificity was 100%. We further demonstrated that the test is compatible with peripheral LMIC settings via external battery operation and cartridge stability at 45{degrees}C for up to one year. ImportanceTuberculosis (TB) is the single most deadly infectious disease with 1.23 million deaths in 2024. Near-point-of-care testing which can be deployed at peripheral settings that lack laboratory infrastructure to deliver prompt and accurate diagnosis is needed to start treatment earlier and thereby improve treatment outcomes. In this study, we have developed an automated test to detect Mycobacterium tuberculosis (MTB), the cause of TB, from sputum and tongue swab specimens. Its high sensitivity and specificity, rapid time to result, and compatibility with environments that lack air conditioning and consistent electricity make this assay suitable for diverse clinical settings.

Enterococcus faecium is one of the leading pathogens in the world. In this study, we proposed a strategy to rapidly and accurately distinguish vancomycin-resistant Enterococcus faecium (VREfm) and vancomycin-susceptible E. faecium (VSEfm) to help doctors correctly determine the use of vancomycin by a machine learning (ML)-based algorithm. A predictive model was developed and validated to distinguish VREfm and VSEfm by analyzing MALDI-TOF MS spectra of unique E. faecium isolates from different specimen types. Firstly, 5717 mass spectra, including 2795 VREfm and 2922 VSEfm, were used to develop the algorithm. And 2280 mass spectra of isolates, namely 1222 VREfm and 1058 VSEfm, were used to externally validate the algorithm. The random forest-based algorithm demonstrated good classification performances for overall specimens, whose mean AUROC in 5-fold cross validation, time-wise validation, and external validation was all greater than 0.84. For the detection of VREfm in blood, sterile body fluid, urinary tract, and wound, the AUROC in external validation was also greater than 0.84. The predictions with algorithms were significantly more accurate than empirical antibiotic use. The accuracy of antibiotics administration could be improved by 30%. And the algorithm could provide rapid antibiotic susceptibility results at least 24 hours ahead of routine laboratory tests. The turn-around-time of antibiotic susceptibility could be reduced by 50%. In conclusion, a ML algorithm using MALDI-TOF MS spectra obtained in routine workflow accurately differentiated VREfm from VSEfm, especially in blood and sterile body fluid, which can be applied to facilitate the clinical testing process due to its accuracy, generalizability, and rapidness.

Laboratory confirmation of infection is an essential component of measles surveillance. Detection of measles specific IgM in serum by enzyme linked immunosorbent assay (ELISA) is the most used method for confirming measles infection. ELISA formats vary as does the sensitivity and specificity of each assay. Specimens collected within 3 days of rash onset can yield a false negative result, which can delay confirmation of measles cases. Interfering substances can yield a false positive result, leading to unnecessary public health interventions. The IgM capture assay developed at the Centers for Disease Control (CDC) was compared against 5 commercially available ELISA kits for the ability to detect measles virus-specific IgM in a panel of 90 well-characterized specimens. Serum samples were tested in triplicate using each commercial kit as recommended by the manufacturer. Using the CDC measles IgM capture assay as the reference test; sensitivity and specificity for the commercial kits ranged from 50 to 83% and 86.9 to 98%, respectively. Discrepant results were observed for samples tested with all five commercial kits and ranged from 13.8 to 28.8% of the specimens tested. False positive results occurred in 2.0 to 13.1% of sera while negative results were observed in 16.7 to 50% of sera that were positive by the CDC measles IgM capture assay. Evaluation and interpretation of measles IgM serologic results can be complex, particularly in measles elimination settings. The performance characteristics of a measles IgM assay should be carefully considered when selecting an assay to achieve high quality measles surveillance.

Rapid point-of-care (POC) diagnostics are essential tools for improving timely treatment and reducing the transmission of sexually transmitted infections (STIs). The STI NG Plus Assay is a rapid multiplex LAMP (loop-mediated isothermal amplification) NAAT (nucleic acid amplification test) capable of simultaneously detecting Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG), Trichomonas vaginalis (TV), and fluoroquinolone resistance-associated mutations in NG (gyrA S91F). In this study, we assessed the STI NG Plus assay primer design and analytical sensitivity. Using a bioinformatically optimized primer design pipeline and empirical screening, the assay demonstrated high inclusivity and specificity, with no cross-reactivity to 48 urogenital organisms or the human genome. Analytical sensitivity testing showed reliable detection of all targets in both lysis buffer and clinical matrix. Limits of detection were lower than those of an existing FDA-cleared test. The assays robustness, speed, and sensitivity support its potential for decentralized STI testing with integrated antimicrobial resistance profiling.

BackgroundAztreonam-avibactam (AZA) is a recently approved agent active against metallo-{beta}-lactamase-producing Enterobacterales. However, independent evaluations of commercially available antimicrobial susceptibility testing (AST) products remain limited. MethodsWe evaluated 56 carbapenem-resistant Enterobacterales isolates using four newly available AZA AST products, including two gradient diffusion (bioMerieux Etest; Liofilchem MIC Test Strip) and two disk diffusion (Hardy, Liofilchem) tests across three Mueller-Hinton agar manufacturers at two independent clinical laboratories. A diverse isolate collection enriched for nonsusceptible and breakpoint-adjacent MICs was used to rigorously assess categorical agreement. Broth microdilution (BMD) was used as the reference method. Essential agreement (EA), categorical agreement (CA), error rates, and reproducibility were analyzed. ResultsAll four commercial AST products demonstrated acceptable analytical performance compared with reference BMD. Gradient diffusion demonstrated high EA (bioMerieux 94.3%, Liofilchem 90.5%), whereas CA ranged from 83.3% to 89.0% across all four products. Minor errors accounted for all categorical discrepancies, and occurred almost exclusively among breakpoint-adjacent isolates. Media-related variability was modest, and quality control performance was generally high, with strong within-site precision and consistent performance across laboratories. ConclusionsThis study provides the first comprehensive head-to-head comparison of commercial AZA susceptibility testing products and supports their implementation in clinical microbiology laboratories.

Whole-genome sequencing (WGS) of microbial pathogens recovered from patients with infectious disease facilitates high-resolution strain characterization and molecular epidemiology. However, increasing reliance on culture-independent methods to diagnose infectious diseases has resulted in few isolates available for WGS. Here we report a novel culture-independent approach to genome characterization of Bordetella pertussis, the causative agent of pertussis and a paradigm for insufficient genomic surveillance due to limited culture of clinical isolates. Sequencing libraries constructed directly from residual pertussis-positive diagnostic nasopharyngeal specimens were hybridized with biotinylated RNA "baits" targeting B. pertussis fragments within complex mixtures that contained high concentrations of host and microbial background DNA. Recovery of B. pertussis genome sequence data was evaluated with mock and pooled negative clinical specimens spiked with reducing concentrations of either purified DNA or inactivated cells. Targeted enrichment increased yield of B. pertussis sequencing reads up to 90% while simultaneously decreasing host reads to less than 10%. Filtered sequencing reads provided sufficient genome coverage to perform characterization via whole-genome single nucleotide polymorphisms (wgSNP) and whole-genome multilocus sequencing typing (wgMLST). Moreover, these data were concordant with sequenced isolates recovered from the same specimens such that phylogenetic reconstructions from either consistently clustered the same putatively linked cases. The optimized protocol is suitable for nasopharyngeal specimens with IS481 Ct < 35 and > 10 ng DNA. Routine implementation of these methods could strengthen surveillance and study of pertussis resurgence by capturing additional cases with genomic characterization.

Mycobacterium tuberculosis (MTB) is the leading cause of death from bacterial infection. Improved rapid diagnosis and antimicrobial resistance determination, such as by whole genome sequencing, are required. Our aim was to develop a simple, low-cost method of preparing DNA for Oxford Nanopore Technologies (ONT) sequencing direct from MTB positive clinical samples (without culture). Simultaneous sputum liquefaction, bacteria heat-inactivation (99{degrees}C/30min) and enrichment for Mycobacteria DNA was achieved using an equal volume of thermo-protection buffer (4M KCl, 0.05M HEPES buffer pH7.5, 0.1% DTT). The buffer emulated intracellular conditions found in hyperthermophiles, thus protecting DNA from rapid thermo-degradation, which renders it a poor template for sequencing. Initial validation employed Mycobacteria DNA (extracted or intracellular). Next, mock clinical samples (infection-negative human sputum spiked 0-105 BCG cells/ml) underwent liquefaction in thermo-protection buffer and heat-inactivation. DNA was extracted and sequenced. Human DNA degraded faster than Mycobacteria DNA, resulting in target enrichment. Four replicate experiments each demonstrated detection at 101 BCG cells/ml, with 31-59 MTB complex reads. Maximal genome coverage (>97% at 5x-depth) was achieved at 104 BCG cells/ml; >91% coverage (1x depth) at 103 BCG cells/ml. Final validation employed MTB positive clinical samples (n=20), revealed initial sample volumes [&ge;]1ml typically yielded higher mean depth of MTB genome coverage, the overall range 0.55-81.02. A mean depth of 3 gave >96% one-fold TB genome coverage (in 15/20 clinical samples). A mean depth of 15 achieved >99% five-fold genome coverage (in 9/20 clinical samples). In summary, direct-from-sample sequencing of MTB genomes was facilitated by a low cost thermo-protection buffer.

Clostridioides difficile (C. diff) is a leading cause of hospital-acquired infections with severity ranging from mild diarrhea to fulminant colitis and death. Current antigen tests lack adequate sensitivity and DNA-based nucleic acid amplification tests (DNA-NAATs) exhibit limited specificity for active infection, leading to either underdiagnosis or inappropriate treatment of colonized individuals. Unlike DNA, mRNA is expressed only by metabolically active bacteria and is rapidly hydrolyzed, providing natural advantages to distinguish active infection from colonization. In this study, we developed and evaluated a novel multiplexed reverse-transcriptase PCR assay (RNA-NAAT) targeting C. diff-specific sequences. No cross-reactivity was observed with other gastrointestinal pathogens, commensal enteric flora, or closely-related Clostridioides or Clostridium species. Toxin gene RNA expression was detected only in samples spiked with metabolically active C. diff at a limit of detection 30-to-50-fold less than current diagnostic methods. Sequential clinical samples (n=260) were collected in proprietary RNA-preservative solution from patients receiving standard of care C. diff diagnostic testing. All samples were evaluated with RNA-NAAT, Alere GDH/toxin EIA, Solana DNA-NAAT, and both forward- and reverse-2-Step Algorithms (2-SA). Samples yielding valid results on all platforms (n=239) with discordant test results (n=14) were adjudicated via toxigenic culture and blinded chart review by infectious disease physicians. RNA-NAAT outperformed all comparator test strategies, simultaneously exhibiting higher sensitivity and specificity, including a higher specificity for active infection than the specific toxin EIA (99.5% vs 98.2%) and a higher sensitivity for organism identification than the sensitive DNA-NAAT (100% vs 88.2%), with significantly reduced false positive test results (1 vs 7). One Sentence SummaryA novel RNA diagnostic distinguishes clinically-relevant C. difficile infection from toxigenic carrier states, improving sensitivity and specificity.