Diagnostic Microbiology and Infectious Disease

Background: Pharmacogenomic point-of-care testing (PGx POCT) enables genotype-informed prescribing at the bedside, but implementation is limited by the lack of suitable reference materials and standardised external quality assessment (EQA). Methods: Fixed lymphoblastoid cell lines were formulated as swab-based materials at defined cellular inputs for MTRNR1 POCT. Materials were evaluated using Genedrive MTRNR1 assays, quantitative PCR, acceptance quality limit batch release, workflow perturbation testing and stability studies, then deployed in an international EQA programme. Results: Materials were homogeneous, workflow-compatible and reproducible, with 100% correct genotype calls at the lowest intended manufacturing cell load. Seven EQA surveys yielded 253 participant results, with full-mark rates between 87.5 and 100%, and six test failures. Most failures occurred with low cell-input materials near the assay limit of detection. The materials supported genotype concordance, performance monitoring and identification of workflow and sample-related variability. Conclusions: Workflow-compatible cell-based reference materials combined with EQA provide a scalable framework for quality-assured PGx POCT beyond specialist laboratories. International MT-RNR1 PGx POCT EQA programme deployment demonstrated feasibility in decentralised settings. The framework may provide a model for the implementation, verification and ongoing quality assessment of PGx POCT. Further evaluation across platforms, analytes, settings and participant groups is required to establish broader applicability.

Sepsis is a substantial contributor to neonatal mortality in Africa, with Klebsiella pneumoniae as the leading causative pathogen. Incorporating molecular tools such as whole genome sequencing (WGS) into routine surveillance of important bacterial pathogens, including those causing neonatal sepsis, can support targeted deployment of infection prevention and control measures and treatment interventions. This study aimed to understand the current practices and capacity for culture, identification and genomic analysis of bacterial pathogens in Africa, with a particular focus on K. pneumoniae, to support standardised genomic surveillance. A cross-sectional online survey was distributed to various clinician and scientist networks across Africa. All respondents completed a demographics section, while sections on laboratory test capacity, blood culture practices, WGS, and bioinformatics analysis were completed based on experience in these aspects. Responses were received from 52 institutions in 25 African countries. Among 51 institutions completing the laboratory test capacity section, 61% reported performing blood cultures, with the majority using manual commercial biochemical systems for species identification (71%) and manual disk diffusion for antibiotic susceptibility testing (82%). Participating institutions reported near-universal access to a -80{degrees}C freezer, centrifuge and thermocycler, but shaking incubators were less commonly available (67%). More than half of respondents (54%) indicated that they perform the entire WGS workflow (including DNA extraction, library preparation and WGS) internally, with most performing DNA extraction internally (88%) using column-based kits (70%). Outsourcing was progressively more common at later workflow stages. Infrastructure challenges that limit bioinformatics analysis capabilities were reported by all 23 respondents who completed this question, including limited access to high-performance computing and data storage space. This survey found sufficient capacity to support genomic surveillance of neonatal sepsis pathogens across participating African institutions. However, investments in blood culture, supply chains, sequencing, bioinformatics, and data dissemination capacity are needed to realise its full potential. These findings will support the development of standardised genomic surveillance protocols tailored to the diverse capacities of African laboratories.

Background: Rapid genome sequencing (rGS) is a first-tier test in the neonatal intensive care unit (NICU). Implementation strategies to scale rGS for clinical care may change clinician roles. We analyzed the NICU rGS workflow to understand challenges rGS poses for clinical roles and responsibilities. Methods: The study took a qualitative approach to understanding the rGS workflow in Level III and Level IV NICUs. The five workflow phases studied included: i) identification of a patient with a suspected genetic disorder, ii) subspecialist consultation, iii) test selection and ordering, iv) return of results, and v) disclosure. Data were collected via job task journals, interviews, and workflow diagram construction with clinicians involved in rGS. Analysis included participant-guided workflow diagram refinement, qualitative thematic analysis, and identification of rGS workflow challenges. Results: We documented issues related to decision-making authority and scope of responsibility for clinicians, with the majority relating to complexities of subspecialist consultations. Issues included differences in: criteria for triggering consultations, expectations of consulted subspecialists' roles, test selection preferences, and responsibility for documenting clinical interpretations and disclosure. Conclusion: Subspecialist consultations in clinical rGS involved significant role ambiguity and communication challenges, requiring intentional implementation efforts to ensure clear clinical roles and responsibilities.

Background Best practice alerts (BPAs) used in emergency departments (EDs) to identify patients with possible sepsis lack specificity and some ED patients with sepsis BPAs are discharged. We evaluated factors associated with ED discharge following a sepsis BPA and with subsequent 7-day return admissions with sepsis or infection. Methods We conducted a retrospective cohort study using an electronic health record data query from five hospitals (2022-2024). Using logistic regression, we evaluated the association of participant demographics and clinical characteristics with ED discharge and factors at the initial ED visit associated with return admission. Results Among 62,068 ED visits with a sepsis BPA, one third resulted in ED discharge. Discharged participants were younger and more often female, Black, multiracial, and/or Hispanic; they more often had an initially normal pulse, respiratory rate, blood pressure, and lactic acid than admitted participants. Discharged participants more often had a fever on arrival (adjusted odds ratio (aOR) 6.03; p<0.001) and a white blood cell (WBC) count 11,000-14,999 (aOR 4.57; p<0.001) or 15,000-19,999/uL (aOR 2.01; p<0.001). One percent of discharged participants experienced a 7-day return admission with a diagnosis of sepsis or infection, which was associated with older age, White or Asian race, diastolic hypotension, WBC count [&le;]15,000/uL or <4,000/uL, and an index visit BPA response indicating sepsis or non-response. Conclusions Return admissions among discharged ED patients with a sepsis BPA are rare. Several factors are associated both with hospital admission at the index visit and return admission, indicating a need for additional risk-stratification tools.

GeneCapture is developing a novel, point-of-care, rapid AST technique that, when fully automated, can accomplish AST within 2 hours directly from a raw sample, representing a significant advancement in diagnostic capabilities. For this study, a panel of uropathogen isolates was collected from clinical specimens positive for urinary tract infection from various laboratories in the southern US. A selection of these isolates were then spiked into fresh clean-catch urine samples to produce mock samples covering a variety of antibiotic responses. Testing was performed on 20 strains of Escherichia coli, the cause of over 80% of UTIs, and 6 strains each of Klebsiella pneumoniae and Proteus mirabilis, the next most common causes. Each strain was tested against the susceptible, intermediate and resistant (S-I-R) breakpoints of up to 5 appropriate antibiotics including Amoxicillin-Clavulanate, Cefpodoxime, Ciprofloxacin, Nitrofurantoin and Trimethoprim-Sulfamethoxazole. The new method uses a phenotypic assessment of bacterial growth, comparing responses from bacteria treated with antibiotics at S-I-R breakpoint concentrations to untreated controls as the metric for determining susceptibility. Exposure to the drugs for only 90 minutes gave a Categorical Agreement of 98% to gold standard culture results across the resulting 247 bacteria/antibiotic pairs. Testing on separate days of nine of these strains in triplicate gave a reproducibility of 97%. The sequential steps of this novel AST - sample processing, growth, labeling, and counting - can readily be performed on an automated cartridge that is currently under development. The presented work, which took place in a laboratory setting, demonstrates the efficacy of the assay.

Background: During emergency tracheal intubation, clinicians use waveform capnography or colorimetric carbon dioxide (CO2) detection to confirm exhaled CO2 from the endotracheal tube to determine its location. Both devices reliably yield a negative result when the tube is in the esophagus. However, in most emergency intubations the tube is correctly located in the trachea, and in this circumstance the relative diagnostic accuracy of the two devices is uncertain. If one device more often fails to detect exhaled CO2 despite correct tube placement (a false negative result), this could lead to unnecessary tube removal, repeated intubation attempts, and an increased risk of serious complications. Research Question: Among critically ill adults undergoing emergency tracheal intubation, is waveform capnography or colorimetric CO2 detection more sensitive for identifying an endotracheal tube correctly placed in the trachea? Study Design and Methods: The WAVE study is a pragmatic, prospective, paired diagnostic accuracy study conducted in emergency departments and intensive care units in the United States. The study compares waveform capnography and colorimetric CO2 detection (index tests) against a non-CO2-based reference standard for endotracheal tube location among 2,092 critically ill adults undergoing tracheal intubation. The primary outcome is the sensitivity of each index test for identifying a tube located in the trachea. The secondary outcome is specificity for identifying a tube located outside the trachea. Results: Enrollment began on April 21, 2025 and is ongoing, with completion anticipated in 2026. Interpretation: The WAVE study will provide prospective evidence comparing waveform capnography with colorimetric CO2 detection for determination of endotracheal tube location in critically ill adults. These findings may inform clinical practice and guideline recommendations regarding the optimal test of exhaled CO2 for use in the ED and ICU. Prespecifying the protocol and statistical analysis plan before completion of enrollment enhances the rigor, reproducibility, and transparency of the study.

Background: Surveillance tells laboratories which antimicrobial resistance genes are circulating now, but not which will change next. We built a model that forecasts, for each resistance gene and year, whether the following year brings a previously unseen allele (sequence variant), called emergence, or a change in the most common allele, called turnover. We tested it separately in Klebsiella pneumoniae and Acinetobacter baumannii. Results: We used genomes annotated with AMRFinderPlus: 2,385 gene-years across 331 genes for K.pneumoniae and 1,059 across 216 for A. baumannii. To remove the effect of sequencing effort, each gene-year was sampled to 10 records and the analysis repeated 25 times. Models were trained on earlier years and tested on later ones, and on genes held out of training. On later years every model ranked genes by risk better than simple baselines in both organisms, and results for held-out genes were close. In K.pneumoniae, turnover was predicted better than emergence (best area under the ROC curve, AUROC, 0.909 versus 0.819). In A. baumannii the order reversed (emergence 0.789, turnover 0.722). The two events also relied on different features. Emergence depended mainly on how many alleles a gene had already accumulated, in both organisms. Turnover in K. pneumoniae depended mainly on how dominant the leading allele already was, and a stability index added a small gain. In A. baumannii it was spread across many weaker features. There, 56% of changes in the leading allele involved only alleles already seen, against 23% in K. pneumoniae, which may make them harder to predict. Conclusions: Changes in resistance genes can be forecast a year ahead from routine genomic surveillance data, including for genes the model has not seen. How well it works, and what it depends on, differs between organisms, so models should be built and validated for each organism, not assumed to transfer. Such models could help laboratories decide which resistance genes to monitor most closely. Keywords: antimicrobial resistance; genomic surveillance; forecasting; machine learning; allele dynamics; Klebsiella pneumoniae; Acinetobacter baumannii

Context: Cytological specimens allow minimally invasive, repeated sampling for diagnosis and molecular testing. However, cytology biobanking protocols have primarily been optimized for morphology, and the effects of preanalytical handling and storage on intracellular proteins remain unclear. Objective: To assess how fixation, staining, storage temperature, and duration affect intracellular protein preservation in cytological specimens and to identify conditions suitable for in situ proximity ligation assay (isPLA). Design: Human cancer cell lines were processed under different preanalytical conditions. Intracellular proteins and protein protein interactions were assessed by isPLA, fluorescence microscopy, and quantitative image analysis. Slides were stored at room temperature or minus 20 Celsius, with or without MayGrunwaldGiemsa (MGG) staining. Results: Storage temperature had the greatest effect on protein signal. Unstained slides stored at minus 20 Celsius retained strong signals for up to 24 months, whereas room temperature storage reduced detectable protein interactions by approximately 95%. MGG staining further reduced signal intensity during prolonged storage. Nevertheless, stained slides remained suitable for isPLA when staining, microscopic evaluation, destaining, and antibody labeling were completed on the same day. Prolonged room temperature storage of stained slides caused loss of antigenicity, increased autofluorescence, and false negative findings. Conclusions: Low temperature storage and standardized preanalytical handling preserve intracellular protein signals in cytological specimens. These conditions support reliable single cell protein profiling of archived samples and their use in biomarker research and translational pathology.

BackgroundFebrile neutropenia requires rapid empirical antibiotic therapy, with regimen selection shaped by local prescribing practice and pathogen patterns. We described starting treatment, later drug changes, microbiological findings, and inpatient outcomes. MethodsThis ambispective cohort comprised 96 episodes from 90 patients admitted to a tertiary-level teaching hospital. Treatment and outcome analyses used each episode as the unit of observation. Recorded variables included the starting antibiotics, later regimen modification, microbiology, hospitalization length, invasive fungal infection (IFI) as captured in study records, and disposition. Comparisons based on escalation status were exploratory. ResultCefoperazone-sulbactam appeared in 62/96 initial regimens (64.6%), amikacin in 42 (43.8%), teicoplanin in 28 (29.2%), and meropenem in 14 (14.6%). Eighteen episodes (18.8%) required a change that broadened or substituted antibacterial therapy. Among 31 microbiologically documented infections, 22 (71.0%) yielded Gram-negative organisms and 9 (29.0%) were polymicrobial. Median length of admission was 18.5 days in the escalation group and 9 days in the remainder (p<0.001). Mortality was 27.8% (5/18) with escalation and 5.1% (4/78) without it (p=0.011), with nine inhospital deaths overall (9.4%). ConclusionAntibacterial management differed within this cohort, with treatment escalation required in 18 of 96 episodes. Gram-negative organisms comprised most microbiologically confirmed infections. Escalation marked a clinically complex course with prolonged hospitalization and greater observed mortality; the observational design does not establish comparative efficacy or causation.

Hybrid capture approaches can detect a broad range of pathogens directly from clinical samples with greater sensitivity than untargeted approaches. Clinical adoption has been limited by long turnaround times, complex workflows, and perceived high costs. We iteratively developed and validated a rapid hybrid capture workflow based on Illumina's RPIP protocol (standard workflow). Rapid-RPIP v1 reduced wet-lab time from ~11.4 to ~7.3 h, for a turnaround time (TAT) of <15 h. Rapid-RPIP v2 further reduced wet-lab time by ~0.7 h and used Illumina Turbo Sequencing shortening the sequencing time from ~5.5 to ~2.5 h thus achieving a TAT of <10 h without compromising sensitivity and yielding higher RPKMs for RNA viruses than the standard workflow. This approach could be readily adapted to a broad range of clinical and public health applications.

ObjectiveTo evaluate usability and workflow implications of Pheno+, an electronic health record- (EHR) embedded natural language processing tool that extracts patient phenotypes and maps them to Human Phenotype Ontology (HPO) terms. Materials and MethodsThis study performed a mixed-methods formative evaluation of Pheno+ in the context of rapid genome sequencing in the neonatal intensive care unit. Two rounds of think-aloud interviews and surveys were conducted with neonatologists, advanced practice providers, medical geneticists, genetic counselors, non-genetics pediatric subspecialists and laboratory molecular geneticists. Usability was assessed using the System Usability Scale (SUS). Structured data were analyzed descriptively. Qualitative data underwent hybrid deductive-inductive thematic analysis. ResultsTwenty-eight interviewees participated in two rounds of data collection. Users retained an average of 24.2 HPO terms from an average of 45.6 terms per patient. Mean time curating terms was 8:59 per patient. Final SUS score was 76 (above scale mean). Qualitative themes included: burden of curating terms; interpretation of phenotypes; adding information to phenotypes; role of genetics expertise; and tool uses beyond the original core use case for Pheno+. DiscussionPheno+ demonstrated positive usability but required curation effort to reduce erroneous terms. Participant responses indicate that effective use may depend on knowledge of HPO structure and laboratory workflows. Automated phenotyping seems likely to reduce net clinician workload, while also reshaping clinical responsibilities, expertise requirements, and communication in genetic testing. ConclusionTools like Pheno+ can support scalable genomic medicine. Design and implementation may benefit from addressing curation burden, phenotype contextualization, expertise requirements, and other workflow needs.

Neurologic autoantibody cell-based assay images are difficult to interpret when fluorescence is weak, focal or dominated by background signal. We developed a visual artificial intelligence overlay that transfers detected cell boundaries from the structural channel to the antibody-staining image and evaluated standalone model concordance and its association with reader classifications. The analysis used 2 763 records for model development and 499 held-out records spanning 14 antibody targets. Four readers assessed the held-out records first without assistance and then with the boundary overlay and model category available. The selected model agreed with the reader-derived three-class reference in 85.2% of records, but recall was lowest for weak-positive or equivocal records. Reader agreement increased in the assisted session, and almost all revised ratings moved towards the model category. The combined display may support consistent visual review while also creating a risk of model-directed anchoring; its role as a second-read aid requires independent validation.

Background: Short-read whole-genome sequencing (sWGS) has limitations in characterizing tandem-repeat expansions and variants in highly homologous or pseudogene-associated regions. Long-read sequencing can address some of these challenges but often benefits from high-molecular-weight DNA. TruPath Genome incorporates spatial proximity information into a short-read sequencing framework. This study evaluated its performance in characterizing selected complex genomic variants using archived clinical DNA specimens. Methods: Ten archived peripheral blood DNA specimens were analyzed, comprising seven cases with disease-associated short tandem repeat (STR) expansions and three cases involving homologous or pseudogene-associated loci (STRC, SMN1/SMN2, and CYP21A2). TruPath results were compared with previously available orthogonal assay results, including triplet repeat-primed PCR (TP-PCR), multiplex ligation-dependent probe amplification (MLPA), quantitative PCR (qPCR), and sWGS-based ExpansionHunter analysis. Results: TruPath generated repeat-length estimates across the evaluated STR loci. For two FMR1 full-mutation alleles, TruPath estimated 284 and 295 CGG repeats, respectively, while TP-PCR reported expansions exceeding 200 repeats. In a DMPK case, TruPath estimated an expanded allele of 1,203 CTG repeats, compared with a TP-PCR result exceeding 100 repeats. At the STRC and SMN1/SMN2 loci, TruPath findings were consistent with available orthogonal results for deletion and copy-number status. At the CYP21A2 locus, TruPath reconstructed the RCCX gene arrangement and assigned the I2G variant and a chimeric allele to different haplotypes. Conclusions: In this small series of archived clinical DNA specimens, TruPath Genome enabled characterization of selected repeat expansions and homologous or pseudogene-associated variants. The findings support further evaluation of proximity-mapped sequencing as a complementary approach for complex genomic regions, particularly when conventional short-read sequencing is limited.

Objective: To evaluate the specimen-level performance of a multichannel electronic nose (e-nose) sensor array in classifying stool specimens into relevant Clostridioides difficile categories. Design: Retrospective single-center validation study with reference to polymerase chain reaction (PCR) and C. difficile toxin testing. Participants: A convenience sample of 31 discarded stool specimens with PCR and confirmatory toxin testing. Categorized into PCR-positive (+)/toxin+, PCR+/toxin-negative (-), and PCR-. Methods: Specimens were sampled in controlled headspace by two e-nose sensor arrays in 10-minute sessions with 5-second sampling intervals. The primary endpoint was one-versus rest classification performance (sensitivity, specificity, positive predictive value, and accuracy) into three classes: PCR+/toxin+, PCR+/toxin-, and PCR-. Data were normalized and the region of interest was extracted for training and testing. Random forests were utilized for classification of normalized data with a test-train split at the specimen-level. Results: There were 457 unique 10-minute sampling events (147 PCR+/toxin+, 183 PCR+/toxin-, 127 PCR-). Sensors 1 and 2 captured 20,331 and 23,538 unique 5-second exposures within the region of interest, respectively. Testing data classification accuracy was 0.79 [0.78, 0.81] and 0.84 [0.83, 0.85] for Sensors 1 and 2. Sensitivity for PCR+/toxin+ exposures was 0.82 [0.79, 0.84] and 0.94 [0.92, 0.95], and specificity was 0.91[0.90, 0.93] and 0.93 [0.92, 0.94] for Sensors 1 and 2. Conclusion: An e-nose sensor array partially differentiated PCR-classified C. difficile specimen classes at the exposure level under headspace-controlled conditions. Performance was strongest for PCR+/toxin+ exposures. Findings support further prospective validation in the hospital room setting.

Abstract Background The Simplified Geneva Score (SGS) incorporates two heart-rate thresholds. Multiple heart-rate measurements are commonly recorded during emergency department (ED) assessment. While the original SGS specifies use of mean heart rate, real-world implementation is unlikely to reflect this, and the effect of alternative heart-rate selection methods on score performance is unknown. Methods SCORES was a retrospective within-subject study of consecutive ED patients at a single urban hospital undergoing computed tomography pulmonary angiography (CTPA) for suspected pulmonary embolism (PE). Four SGS variants were calculated using the first, highest, mean, and lowest recorded pre-CTPA heart rate. Outcomes included score output, risk classification, diagnostic performance, reclassification flow, and downstream imaging utilisation. Precision estimates and comparisons were derived using empirical resampling techniques. Results 590 episodes were reviewed with 581 included for analysis. PE was confirmed in 50 cases (8.6%). Mean SGS differed significantly across all heart-rate implementations (p<0.0001). The proportion classified as high risk varied from 15% using the lowest heart rate to 40% using the highest heart rate. Reclassification across the SGS threshold was common, with 25% of episodes changing risk category unidirectionally between lowest and highest heart rate implementations. SGS(lowest HR) compared with SGS(mean HR) and SGS(highest HR) demonstrated higher specificity (87.6% vs 73.4% vs 62.1%), improved AUROC (0.744 vs 0.704 vs 0.659), and reduced downstream CTPA utilisation (818 vs 876 vs 920 scans per 100 PEs diagnosed), with no additional pulmonary emboli missed within the complete diagnostic pathway. Conclusions Heart-rate selection materially influences SGS output, risk classification, diagnostic performance, and imaging utilisation. In this retrospective cohort, use of the lowest recorded heart rate produced the most favourable overall balance of discrimination and diagnostic efficiency, supporting prospective validation.

Broad-range RT-qPCR assays are essential for detecting highly diverse viruses within virus families, but designing suitable primers remains challenging because of extensive sequence diversity and biases in public sequence databases. Here, we present a semi-automated workflow that combines sequence clustering and varVAMP to streamline pan-RT-qPCR primer design. The workflow reduces sequence redundancy, improves the representation of viral diversity, and facilitates the identification of broadly reactive primer candidates. We demonstrate the workflow using the arboviral genera Orthoflavivirus and Alphavirus as proof-of-concept datasets, showing its applicability to large and genetically diverse viral sequence collections. The workflow provides a practical, scalable, and reproducible framework for developing broad-range primer candidates and may support surveillance, diagnostics, and preparedness for emerging or divergent viruses.

Background: Shotgun metagenomic pipelines routinely discard host-derived reads, which can exceed 90% of reads in low-biomass clinical samples. Whether these reads support mitochondrial heteroplasmy detection, and at what allele fraction, has not been established. Methods: Shotgun metagenomic data from 47 upper respiratory tract swabs from healthy adults in Nagpur, India, were analysed. Human Reads were recruited against the rCRS and realigned competitively to GRCh38 to remove nuclear mitochondrial segments (NUMTs). Kraken2 was used as a microbial control. Heteroplasmy was called against a pooled, substitution-specific beta-binomial error model and a leave-one-out panel of normals. The detection limit was evaluated from the substitution spectrum against gnomAD v3.1. Results: Complete mitochondrial genomes were recovered from all samples (mean depth 433X, range 9-3,029X). Competitive realignment relocated 3.22% of recruited reads to nuclear loci; microbial cross-mapping removed 0.045%. Error rates varied 12.8-fold across substitution classes, with T>A being the highest. The 134 calls had a Ti/Tv of 0.43, compared with 3.51 in gnomAD, and T>A accounted for 42.5% of calls. T>A allele fractions never exceeded 4.72%, whereas transitions reached 90.81%. At a 5% threshold, T>A calls disappeared, and Ti/Tv rose to 2.20 before plateauing; 16 calls exceeded this limit. Macrohaplogroups were assigned in 46 of 47 samples (M 22, R 23, N 1). Conclusions: Metagenomic host reads support complete mitochondrial recovery, haplogroup typing, and heteroplasmy detection for allele fractions > 5%. Below this, a T>A-dominated error process persists after NUMT removal that background-fitted models do not capture.

Objective Heme-dependent metronidazole (MTZ) resistance has emerged in Clostridioides difficile and is primarily mediated by a T-to-G single-nucleotide polymorphism (SNP) in the promoter of nimB (PnimBG). We aimed to develop a CRISPR-Cas12a-based assay for rapid detection of the PnimBG mutation associated with MTZ resistance. Methods A series of primers and CRISPR RNAs (crRNAs) were designed and optimized to identify the most effective combination for discriminating between PnimBG (MTZ-resistant) and PnimBT (MTZ-susceptible) alleles. Detection was evaluated by visual fluorescence using blue-light and UV imaging systems, as well as by quantitative fluorescence measurements. Results The CRISPR-Cas12a assay accurately differentiated PnimBG and PnimBT alleles in C. difficile. In a collection of clinical isolates, the assay correctly identified all 11 MTZ-susceptible isolates carrying the PnimBT allele and all 10 MTZ-resistant isolates carrying the PnimBG allele. Fluorescence signals were readily detected both visually and quantitatively. Furthermore, colony PCR using crude colony lysates yielded results comparable to those obtained with purified genomic DNA, enabling rapid colony-based detection without conventional DNA extraction. Conclusions The CRISPR-Cas12a assay enables rapid molecular detection of the PnimBG mutation associated with heme-dependent MTZ resistance in C. difficile. This approach could complement conventional susceptibility testing for MTZ resistance detection.

Macrolides remain the first-line antimicrobial treatment for pertussis, primarily caused by Bordetella pertussis. Emergence of macrolide-resistant B. pertussis in Australia and globally presents a growing concern for clinical management. As molecular diagnosis predominates for pertussis, limited numbers of cultures are available for antimicrobial susceptibility testing. The A2037G mutation in the 23S rRNA gene is most commonly associated with macrolide resistance in B. pertussis, yet no commercial molecular assay is available for its detection. In this study, we adapted and validated a previously published real-time PCR assay as a laboratory developed test (LDT) on the Panther Fusion(R) system using Open Access functionality to detect the macrolide resistance-associated mutation in B. pertussis from culture isolates and clinical specimens. Total turnaround time was ~2.5 h for the first result and 2-3 min for subsequent results in the same batch, with an estimated cost of AUD 18 per sample, excluding labour. A total of 30 samples were included in the validation panel to assess assay performance. All isolates and clinical specimens in the validation panel produced results concordant with the expected mutation status, demonstrating 100% accuracy, sensitivity and specificity. The assay demonstrated a limit of detection of 1.5 x 103 CFU/mL (22 CFU/reaction). This Panther Fusion(R) LDT provides a rapid and fully automated approach for molecular detection of the targeted mutation associated with macrolide resistance in B. pertussis. Its integration into routine molecular workflows as a reflex test following identification of B. pertussis may facilitate timely identification of resistant infections.

Background: Amplicon-based next-generation sequencing is a cornerstone of viral genomic surveillance, but it often produces datasets with highly uneven read coverage due to PCR amplification bias. This leads to excessive data generation and substantial computational overhead for downstream bioinformatic analysis. Results: We evaluated the efficacy of two data reduction strategies on 220 SARS-CoV-2 clinical specimens and 12 wastewater samples: random subsampling with SeqKit and read depth normalization with BBNorm. FASTQ files were reduced to target depths from 10X to 10,000X to compare genome coverage, lineage assignment concordance, and computational resource usage. Both strategies markedly reduced total processing time. For clinical isolates, read depth normalization corrected for amplification bias resulting in highly concordant lineage assignments at a target depth of just 200X. Random subsampling preserved inherent bias but produced reliable assignments at depths over 500X. Reducing target depths below 500X in complex wastewater mixtures severely degraded variant deconvolution accuracy and heavily skewed lineage abundance profiles for both methods. Conclusion: Both random subsampling and read depth normalization successfully reduce computational overhead while preserving key clinical sequencing metrics at appropriate reduction settings. The optimal method depends on the analytical goal, ranging from computationally lightweight random subsampling for rapid lineage assignment, to read depth normalization for generating high-quality consensus sequences. However, aggressive data reduction should be avoided in environmental surveillance, where maintaining a high baseline sequencing depth is critical for accurate mixed-variant deconvolution.