Candida auris is an emerging fungal pathogen linked to healthcare-associated infections, necessitating rapid and accurate detection for effective infection control. This study evaluated the analytical and clinical performance of the Diasorin Simplexa C. auris Direct IVD assay compared to traditional culture as the reference standard and also to two lab-developed tests (LDTs) already validated in our laboratory: one using DSQ Alert primers/probes on the Roche Cobas 5800 and another on the DiaSorin LIAISON MDX platform. Clinical accuracy was assessed using deidentified residual axillary/groin surveillance specimens from 20 culture-positive and 20 culture-negative patients. Analytical specificity was tested against 14 microbial species commonly found in the axilla/groin. Analytical sensitivity was determined using ZeptoMetrix C. auris strain Z485. Specimen stability was examined at various temperatures. Environmental swabbing was also conducted before and after sample handling. The Diasorin Simplexa C. auris IVD assay demonstrated 100% sensitivity and 90% specificity relative to culture and showed 100% positive agreement with both LDTs and 100% negative percent agreement with the DSQ Alert LDT. The assay also achieved 100% analytical specificity, with no cross-reactivity observed, and an analytical sensitivity of 702 CFU/mL. Specimen integrity remained stable for up to 30 days under all storage conditions. No environmental contamination was detected. The DiaSorin Simplexa C. auris IVD assay demonstrated strong analytical and clinical performance while offering advantages in speed, ease of use, and flexible batch size. It may serve as a practical solution for institutions seeking timely C. auris screening in support of infection prevention protocols. IMPORTANCE:Candida auris is an important yeast notable for its ability to easily colonize people as well as its drug resistance. Colonized patients who become immunocompromised may ultimately become infected with C. auris, without many options for treatment. Many health care facilities mandate screening patients for colonization with this yeast to help prevent transmission. This work evaluates the recently FDA approved Diasorin Simplexa C. auris PCR based screening assay and compares its performance to cultures, as well as two existing lab-developed assays. It is the first assay performance evaluation outside of the FDA submission.

Bacteriophage therapy is a promising strategy for treating multidrug-resistant bacteria, such as Escherichia coli, involved in urinary tract infections (UTIs), and Shigella spp., the main culprit in diarrheal diseases in children. Given these pathogens’ propensity for antibiotic resistance, phages offer a viable alternative, though challenges remain. A collection of 327 E. coli and 26 Shigella clinical isolates was tested for prophage induction with mitomycin C to exclude inducible phages prior to host range assessment. Six lytic bacteriophages were evaluated for their ability to lyse pathogenic isolates through double-layer plaque assays and bacterial growth kinetics at different multiplicities of infection (MOIs). Phage morphology was analysed by transmission electron microscopy (TEM), and genomes were sequenced and annotated. Most bacterial isolates were susceptible to at least one phage, with only 2.7

Bacteriophages are an increasingly attractive option for the treatment of antibiotic-resistant infections, but their efficacy is difficult to discern due to the confounding effects of antibiotics. Phages are generally delivered in conjunction with antibiotics, and thus, when patients improve, it is unclear whether the phages, antibiotics, or both are responsible. This question is particularly relevant for enterococcus infections, as limited data suggest phages might restore antibiotic efficacy against resistant strains. Enterococci can develop high-level resistance to vancomycin, a primary treatment. We assessed clinical and laboratory isolates of Enterococcus faecium and Enterococcus faecalis to determine whether we could observe synergistic interactions between phages and antibiotics. We identified synergy between multiple phages and antibiotics including linezolid, ampicillin, and vancomycin. Notably, antibiotic susceptibility did not predict synergistic interactions with phages. Vancomycin-resistant isolates (n = 6) were eradicated by the vancomycin-phage combination as effectively as vancomycin-susceptible isolates (n = 2). Transcriptome analysis revealed significant gene expression changes under antibiotic-phage conditions, especially for linezolid and vancomycin, with upregulated genes involved in nucleotide and protein biosynthesis and downregulated stress response and prophage-related genes. While our results do not conclusively determine the mechanism of the observed synergistic interactions between antibiotics and phages, they do confirm and build upon previous research that observed these synergistic interactions. Our work highlights how using phages can restore the effectiveness of vancomycin against resistant isolates. This finding provides a promising, although unexpected, strategy for moving forward with phage treatments for vancomycin-resistant Enterococcus infections.

Mycoplasma genitalium as a cause of genitourinary sexually transmitted disease symptoms often goes underdiagnosed in many patient populations. We investigated a patient population in Southern California at high risk for Chlamydia trachomatis (CT) and Neisseria gonorrhea (NG) infections to determine whether they also may be at high risk for Mycoplasma genitalium (MG) sexually transmitted infections that may be going untreated. We found that there was a relatively high prevalence of CT (13.9 %) and NG (9.0 %) in our population, but there was also a relatively high prevalence of undiagnosed MG infections (8.7 %). In this same patient population, there were few (0.5 %) subjects diagnosed with Trichomonas vaginalis (TV) infections; however, there were high numbers of coinfections identified for MG with CT and NG. We found high numbers of positive results in both symptomatic and asymptomatic individuals. We also identified that there were high numbers of subjects with genetic markers associated with resistance to macrolide antibiotics in the MG positive specimens. These data altogether strongly suggest that MG testing should be a routine part of screening for patient populations whether they are high- or normal-risk for sexually acquired infections.

The resurgence of phage therapy in Western societies has been in direct response to recent increases in antimicrobial resistance (AMR) that have ravaged many societies. While phage therapy as a concept has been around for over 100 years, it has largely been replaced by antibiotics due to their relative ease of use and their predictability in spectrum of activity. Now that antibiotics have become less reliable due to greater antibiotic resistance and microbiome disruption, phage therapy has once again become a viable and promising alternative, but it is not without its challenges. Much like the development of antibiotics, with deployment of phage therapeutics there will be a simultaneous need for diagnostics in the clinical laboratory. This review provides an overview of current challenges to widespread adoption of phage therapy with a focus on adoption in the clinical diagnostic laboratory. Current barriers include a lack of standard methodology and quality controls for phage susceptibility testing and selection, the absence of phage-antibiotic synergy testing, and the absence of standard methods to assay phage activity on biofilms. Additionally, there are a number of lab-specific administrative and regulatory barriers to widespread phage therapy adoption including the need for pharmacokinetic (PK) and pharmacodynamic (PD) assays, methods to account for changes in phages after passaging, an absence of regulatory guidance on what will be required for agency approvals of phages and how broad that approval will apply, and the increased need for lab personnel or automation to account for the work of testing large phage libraries against bacteria isolates.

Stenotrophomonas maltophilia is an understudied, gram-negative, aerobic bacterium that is widespread in the environment and increasingly a cause of opportunistic infections. Treating S. maltophilia remains difficult, leading to an increase in disease severity and higher hospitalization rates in people with cystic fibrosis, cancer, and other immunocompromised health conditions. The lack of effective antibiotics has led to renewed interest in phage therapy; however, there remains a great need for well-characterized phages, especially against S. maltophilia. In response to an oncology patient with a sepsis infection, we collected 18 phages from Southern California wastewater influent that exhibit different plaque morphology against S. maltophilia host strain B28B. We hypothesized that, when combined into a cocktail, genetically diverse phages would give rise to distinct lytic infection kinetics that would enhance bacterial killing when compared to the individual phages alone. We identified three genetically distinct clusters of phages, and a representative from each group was further investigated and screened for potential therapeutic use. The results demonstrated that the three-phage cocktail significantly suppressed bacterial growth compared with individual phages when observed for 48 h. We also assessed the lytic impacts of our three-phage cocktail against a collection of 46 S. maltophilia strains to determine if a multi-phage cocktail has an expanded host range. Our phages remained strain-specific and infected >50% of tested strains. In six clinically relevant S. maltophilia strains, the multi-phage cocktail has enhanced suppression of bacterial growth. These findings suggest that specialized phage cocktails may be an effective avenue of treatment for recalcitrant S. maltophilia infections resistant to current antibiotics.

A key issue hindering discoverability, attribution and reusability of open research software is that its existence often remains hidden within the manuscript of research papers. For these resources to become first-class bibliographic records, they first need to be identified and subsequently registered with persistent identifiers (PIDs) to be made FAIR (Findable, Accessible, Interoperable and Reusable). To this day, much open research software fails to meet FAIR principles and software resources are mostly not explicitly linked from the manuscripts that introduced them or used them. SoFAIR is a 2-year international project (2024-2025) which proposes a solution to the above problem realised over the content available through the global network of open repositories. SoFAIR will extend the capabilities of widely used open scholarly infrastructures (CORE, Software Heritage, HAL) and tools (GROBID) operated by the consortium partners, delivering and deploying an effective solution for the management of the research software lifecycle, including: 1) ML-assisted identification of research software assets from within the manuscripts of scholarly papers, 2) validation of the identified assets by authors, 3) registration of software assets with PIDs and their archival.

Bacteria showcase remarkable metabolic diversity and traits, even among strains of the same species. In recent years, a large number of bacterial genomes have been sequenced, leading to the elucidation and documentation of genomic differences and commonalities across and within species. Genome-scale metabolic reconstructions, which are often defined and curated using data from phenotype microarrays, elucidate the differences in metabolic traits resulting from genomic diversity. These microarrays measure cellular respiration on a variety of carbon, nitrogen, phosphorus, and sulfur sources and various stressors and inhibitors over a period of time to determine the metabolic activity of a given strain. Despite their popularity in measuring bacterial metabolic activity and traits, no public databases that allow researchers to warehouse, access, and analyze this information currently exist. Additionally, there are no publicly available tools that allow researchers to view the variance of these metabolic traits across bacterial strains. To address this need, we present Phenotype Microarray Knowledgebase (PMkbase [version 1.0], https://pmkbase.com/), an interactive database that acts as a repository of phenotype microarray (PM) data with integrated sequence information. Binarized activity calls, along with associated kinetic parameters, are made for all metabolic substrates and inhibitors. Users can upload their own data for analysis and visualization and to perform quality checks on their experiments. PMkbase will address an unmet need to track and view bacterial metabolic traits and provide researchers with valuable information to develop metabolic models, enrich pangenomic analyses, and design new experiments.IMPORTANCEBacterial species can be differentiated by their metabolic profiles or the type of nutrients they consume. Interestingly, strains within the same species also display differences in nutrient consumption. Phenotype microarrays are a high-throughput, widely used technology to measure which substrates can be metabolized by various microbial strains and the extent to which inhibitors can affect it. Despite their widespread use, public databases to parse and access this data type at scale do not exist. PMkbase, which contains 9,024 data points for nitrogen substrate utilization, 41,664 data points for carbon substrate utilization, 8,448 data points for phosphorus/sulfur substrate utilization, and 27,264 data points on various antibiotics across three species (Escherichia coli, Pseudomonas putida, and Staphylococcus aureus), has been developed to allow researchers to freely access PM data, along with enriching the data with sequence information.

Resistance to antibiotics is approaching crisis levels for organisms such as the ESKAPEE pathogens (includes Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp., and Escherichia coli) that often are acquired in hospitals. These organisms sometimes have acquired plasmids that confer resistance to most if not all beta-lactam antibiotics. We have been developing alternative means for dealing with antibiotic resistant microbes that cause infections in humans by developing viruses (bacteriophages) that attack and kill them. One of these pathogens, K. pneumoniae, has one of the highest propensities for antimicrobial resistance. We identified many phages that have lytic capacity against limited numbers of clinical isolates, and through experimental evolution over the course of 30 days, were able to vastly expand the host ranges of these phages to kill a broader range of clinical K. pneumoniae isolates including MDR (multi-drug resistant) and XDR (extensively-drug resistant) isolates. Most interestingly, they were capable of inhibiting growth of clinical isolates both on solid and in liquid medium over extended periods. That we were able to extend the host ranges of multiple naïve antibiotic resistant K. pneumoniae through experimental phage evolution suggests that such a technique may be applicable to other antibiotic-resistant organisms to help stem the tide of antibiotic resistance and offer further options for medical treatments.

BACKGROUND:Infection prevention (IP) measures are designed to mitigate the transmission of pathogens in healthcare. Using large-scale viral genomic and social network analyses, we determined if IP measures used during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic were adequate in protecting healthcare workers (HCWs) and patients from acquiring SARS-CoV-2. METHODS:We performed retrospective cross-sectional analyses of viral genomics from all available SARS-CoV-2 viral samples collected at UC San Diego Health and social network analysis using the electronic medical record to derive temporospatial overlap of infections among related viromes and supplemented with contact tracing data. The outcome measure was any instance of healthcare transmission, defined as cases with closely related viral genomes and epidemiological connection within the healthcare setting during the infection window. Between November 2020 through January 2022, 12 933 viral genomes were obtained from 35 666 patients and HCWs. RESULTS:Among 5112 SARS-CoV-2 viral samples sequenced from the second and third waves of SARS-CoV-2 (pre-Omicron), 291 pairs were derived from persons with a plausible healthcare overlap. Of these, 34 pairs (12%) were phylogenetically linked: 19 attributable to household and 14 to healthcare transmission. During the Omicron wave, 2106 contact pairs among 7821 sequences resulted in 120 (6%) related pairs among 32 clusters, of which 10 were consistent with healthcare transmission. Transmission was more likely to occur in shared spaces in the older hospital compared with the newer hospital (2.54 vs 0.63 transmission events per 1000 admissions, P < .001). CONCLUSIONS:IP strategies were effective at identifying and preventing healthcare SARS-CoV-2 transmission.

ESKAPE pathogens cause most hospital-acquired infections globally and often carry antibiotic resistance. Many of them have been the target of bacteriophage therapies. Enterobacter is an ESKAPE pathogen but is less frequently a target for phage therapy due to a relative lack of available phages. We isolated eight jumbo phages with genomes ranging from 223 to 366 kbp targeting Enterobacter spp. and found that they belonged to separate phage clades. Six of them formed nucleus-like structures confirmed by DAPI-staining, and were phylogenetically related to Chimalliviridae. Two jumbo phages did not form nucleus-like structures and did not cluster with Chimalliviridae. Although these jumbo phages were found on Enterobacter, many were closely related to phages with non-Enterobacter hosts. To test whether these phages may have had expanded host ranges, we examined 14 pathogenic Gammaproteobacteria and found that these phages were capable of creating plaques on 8 of them. These species included Escherichia coli, Klebsiella aerogenes, Serratia marcescens, Salmonella spp., Shigella spp., Providencia spp., Citrobacter spp., and Cronobacter sakazakii. We verified that there was phage amplification in these microbes rather than lysis from without by performing qPCR to confirm DNA replication in each species. Phages typically have narrow host ranges, a benefit for microbiome-sparing compared to antibiotics. However, the broad host ranges of these Gammaproteobacteria jumbo phages suggests that not all phages have the same risk/benefit ratios. While this broad range could aid their development as antibiotic alternatives, further study is needed to assess potential microbiome disruption. ### Competing Interest Statement The authors have declared no competing interest.

ABSTRACT Bacteroides fragilis is a Gram-negative commensal bacterium commonly found in the human colon, which differentiates into two genomospecies termed divisions I and II. Through a comprehensive collection of 694 B. fragilis whole genome sequences, we identify novel features distinguishing these divisions. Our study reveals a distinct geographic distribution with division I strains predominantly found in North America and division II strains in Asia. Additionally, division II strains are more frequently associated with bloodstream infections, suggesting a distinct pathogenic potential. We report differences between the two divisions in gene abundance related to metabolism, virulence, stress response, and colonization strategies. Notably, division II strains harbor more antimicrobial resistance (AMR) genes than division I strains. These findings offer new insights into the functional roles of division I and II strains, indicating specialized niches within the intestine and potential pathogenic roles in extraintestinal sites. IMPORTANCE Understanding the distinct functions of microbial species in the gut microbiome is crucial for deciphering their impact on human health. Classifying division II strains as Bacteroides fragilis can lead to erroneous associations, as researchers may mistakenly attribute characteristics observed in division II strains to the more extensively studied division I B. fragilis . Our findings underscore the necessity of recognizing these divisions as separate species with distinct functions. We unveil new findings of differential gene prevalence between division I and II strains in genes associated with intestinal colonization and survival strategies, potentially influencing their role as gut commensals and their pathogenicity in extraintestinal sites. Despite the significant niche overlap and colonization patterns between these groups, our study highlights the complex dynamics that govern strain distribution and behavior, emphasizing the need for a nuanced understanding of these microorganisms.

The emergence of antibiotic-resistant bacteria (ARB) has necessitated the development of alternative therapies to deal with this global threat. Bacteriophages (viruses that target bacteria) that kill ARB are one such alternative. Although phages have been used clinically for decades with inconsistent results, a number of recent advances in phage selection, propagation, and purification have enabled a reevaluation of their utility in contemporary clinical medicine. In most phage therapy cases, phages are administered in combination with antibiotics to ensure that patients receive the standard-of-care treatment. Some phages may work cooperatively with antibiotics to eradicate ARB, as often determined using non-standardized broth assays. We sought to develop a solid media-based assay to assess cooperativity between antibiotics and phages to offer a standardized platform for such testing. We modeled the interactions that occur between antibiotics and phages on solid medium to measure additive, antagonistic, and synergistic interactions. We then tested the method using different bacterial isolates and identified a number of isolates where synergistic interactions were identified. These interactions were not dependent on the specific organism, phage family, or antibiotic used. A priori susceptibility to the antibiotic or the specific phage were not requirements to observe synergistic interactions. Our data also confirm the potential for the restoration of vancomycin to treat vancomycin-resistant Enterococcus (VRE) when used in combination with phages. Solid media assays for the detection of cooperative interactions between antibiotics and phages can be an accessible technique adopted by clinical laboratories to evaluate antibiotic and phage choices in phage therapy.IMPORTANCEBacteriophages have become an important alternative treatment for individuals with life-threatening antibiotic-resistant bacteria (ARB) infections. Because antibiotics represent the standard-of-care for treatment of ARB, antibiotics and phages often are delivered together without evidence that they work cooperatively. Testing for cooperativity can be difficult due to the equipment necessary and a lack of standardized means for performing the testing in liquid medium. We developed an assay using solid medium to identify interactions between antibiotics and phages for gram-positive and gram-negative bacteria. We modeled the interactions between antibiotics and phages on solid medium, and then tested multiple replicates of vancomycin-resistant Enterococcus (VRE) and Stenotrophomonas in the assay. For each organism, we identified synergy between different phage and antibiotic combinations. The development of this solid media assay for assessing synergy between phages and antibiotics will better inform the use of these combinations in the treatment of ARB infections.

Surveillance for genetic variation of microbial pathogens, both within and among species, plays an important role in informing research, diagnostic, prevention, and treatment activities for disease control. However, large-scale systematic screening for novel genotypes remains challenging in part due to technological limitations. Towards addressing this challenge, we present an advancement in universal microbial high resolution melting (HRM) analysis that is capable of accomplishing both known genotype identification and novel genotype detection. Specifically, this novel surveillance functionality is achieved through time-series modeling of sequence-defined HRM curves, which is uniquely enabled by the large-scale melt curve datasets generated using our high-throughput digital HRM platform. Taking the detection of bacterial genotypes as a model application, we demonstrate that our algorithms accomplish an overall classification accuracy over 99.7% and perform novelty detection with a sensitivity of 0.96, specificity of 0.96 and Youden index of 0.92. Since HRM-based DNA profiling is an inexpensive and rapid technique, our results add support for the feasibility of its use in surveillance applications.

Bacterial pathogens are becoming greater threats given the rise in antibiotic resistance, where traditional therapies may no longer work to cure some infections. Chief amongst these multidrug resistant infections (MDR) and extensively drug-resistant infections (XDR) is Klebsiella pneumoniae, which is known to sometimes harbor genetic elements that render it incredibly difficult to treat with conventional antibiotics. Treatments like bacteriophages have not had much success against such pathogens because resistance to the phages used often develops rapidly. We adapted a co-evolutionary technique to develop K. pneumoniae phages to be highly active longitudinally against K. pneumoniae clinical isolates. In as few as 30 days, we were able to vastly expand the host ranges of K. pneumoniae phages against MDR and XDR clinical isolates and that maintain their infectivity over clinically relevant time periods. By adapting these established techniques to clinical MDR and XDR K. pneumoniae isolates, we believe we can establish similar techniques for expanding phage host ranges against most antibiotic-resistant bacteria. As such, phages can be viable alternatives to antibiotics when antibiotic resistance exists in hospitals and communities. ### Competing Interest Statement The authors declare no conflicts of interest. RAW III is the CEO of RAW Molecular Systems (RAW), LLC, but no financial, IP, or others from RAW LLC were used or contributed to this study.

Bacteroides fragilis is a prominent member of the human gut microbiota, playing crucial roles in maintaining gut homeostasis and host health. Although it primarily functions as a beneficial commensal, B. fragilis can become pathogenic. To determine the genetic basis of its duality, we conducted a comparative genomic analysis of 813 B. fragilis strains, representing both commensal and pathogenic origins. Our findings reveal that pathogenic strains emerge across diverse phylogenetic lineages, due in part to rapid gene exchange and the adaptability of the accessory genome. We identified 16 phylogenetic groups, differentiated by genes associated with capsule composition, interspecies competition, and host interactions. A microbial genome-wide association study identified 44 genes linked to extra-intestinal survival and pathogenicity. These findings reveal how genomic diversity within commensal species can lead to the emergence of pathogenic traits, broadening our understanding of microbial evolution in the gut.

ABSTRACTFast and accurate diagnosis of bloodstream infection is necessary to inform treatment decisions for septic patients, who face hourly increases in mortality risk. Blood culture remains the gold standard test but typically requires ∼15 hours to detect the presence of a pathogen. Here, we assess the potential for universal digital high-resolution melt (U-dHRM) analysis to accomplish faster broad-based bacterial detection, load quantification, and species-level identification directly from whole blood. Analytical validation studies demonstrated strong agreement between U-dHRM load measurement and quantitative blood culture, indicating that U-dHRM detection is highly specific to intact organisms. In a pilot clinical study of 21 whole blood samples from pediatric patients undergoing simultaneous blood culture testing, U-dHRM achieved 100% concordance when compared with blood culture and 90.5% concordance when compared with clinical adjudication. Moreover, U-dHRM identified the causative pathogen to the species level in all cases where the organism was represented in the melt curve database. These results were achieved with a 1 mL sample input and sample-to-answer time of 6 hrs. Overall, this pilot study suggests that U-dHRM may be a promising method to address the challenges of quickly and accurately diagnosing a bloodstream infection.Universal digital high resolution melt analysis for the diagnosis of bacteremiaApril Aralar, Tyler Goshia, Nanda Ramchandar, Shelley M. Lawrence, Aparajita Karmakar, Ankit Sharma, Mridu Sinha, David Pride, Peiting Kuo, Khrissa Lecrone, Megan Chiu, Karen Mestan, Eniko Sajti, Michelle Vanderpool, Sarah Lazar, Melanie Crabtree, Yordanos Tesfai, Stephanie I. Fraley

Quantitative assessment of nucleophosmin 1 (NPM1) mutation status is integral to evaluating measurable residual disease (MRD) in NPM1-mutated acute myeloid leukemia (AML) patients. In a retrospective study, leftover peripheral blood (PB) specimens (n = 40) which were collected for routine clinical diagnostic evaluations of AML disease burden were tested by both a novel automated RT-qPCR quantitative NPM1 assay (Xpert NPM1 mutation assay) and the NPM1 mutA, mutB&D MutaQuant kit. Based on a Deming regression analysis, there was a high correlation (slope = 0.92; intercept = 0.12; Pearson’s r = 0.982) between the quantitative results of the Xpert NPM1 mutation assay and the NPM1 mutA, mutB&D MutaQuant kit. The Xpert test quantitative results are thus highly correlated with the comparator method and the former has potential as a useful alternative for the monitoring of AML patients with a known NPM1 mutation.

Background: Detection and treatment of individuals with presumed latent tuberculosis (TB) infection (i.e., excluding active disease; LTBI) is imperative to achieve global TB control, as they represent a potential transmission reservoir. However, more sensitive and user–friendly diagnostic tools are needed. Methods: We evaluated the accuracy for TB infection detection of the new VIDAS® TB–IGRA (bioMérieux), a fully automated, single tube (thus eliminating the need for batch testing) overnight incubation assay, compared to the QuantiFERON®–TB Gold Plus (QFT–Plus, QIAGEN), in a global multi–centre cross–sectional study ([NCT04048018][1]) that included patients with TB disease (n=200) or participants at varying levels of TB exposure (n=1460; mixed exposure–risk–population). Results: VIDAS® TB–IGRA identified TB disease with greater sensitivity than QFT–Plus (97.5% vs. 80.7%, P<0.01%), and yielding significantly fewer false–negatives (2.5% vs. 17.5%; P<0.01%) and indeterminate results (1.0% vs. 9.5%; P=0.02%). In the mixed exposure–risk–population, negative (NPA) and positive percent agreement (PPA) were 90.1% (1097/1217) and 92.1% (223/242), respectively. PPA increased with TB–exposure risk (up to 95.7% for high–risk participants), whereas NPA decreased (starting from 96.9% for low–risk participants). Regression analyses revealed that VIDAS® TB–IGRA had a better fit with the risk–exposure gradient than the QFT‑Plus. Specificity in extremely low TB–exposure risk participants (n = 125) was high for both VIDAS® TB–IGRA and QFT–Plus (97.6% vs. 95.2%; P=8.33%). Conclusions: VIDAS® TB–IGRA displayed greater sensitivity than QFT–Plus, had a lower indeterminate rate, correlated better with an exposure gradient, and was highly specific, suggesting that it is a potentially valuable tool for the diagnosis of LTBI. ### Competing Interest Statement All authors had financial support from bioMérieux for performing this study. ### Clinical Trial NCT04048018 ### Funding Statement This study was funded by bioMérieux ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The following gave ethical approval for this work: - The French National Ethics committee (CPP, ref. 2019-A00998-49) - The UK Health Research Authority (Wales Research Ethics Committee 7, REC refs: 19/WA/0284 and 19/WA/0285) - The INMI "L. Spallanzani" (Rome, Italy) Ethics Committee (approval n°35/2019) - The "Comité de Ética en Investigación del Hospital General de Mexicali" (Mexico, ref. 02-01-HGMXL/FMED-UABC-2019-08-29-254) - In South Africa: - Pharma ethics refs. 190822774 and 190822777 - University of Cape Town Human Research Ethics Committee ref. 840/2019 - In USA: - Western Institutional Review Board (WIRB, tracking numbers: 20191965; 20192037; 20192039) - The Rutgers University Institutional Review Board (Refs: Pro2019001840 and Pro2019001936) - The Stanford University Institutional Review Board (eProtocol number: 53485) - The University of Illinois at Chicago Institutional Review Board (research protocol number: 2019-1145) I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data produced in the present study are available upon reasonable request to the authors [1]: /lookup/external-ref?link_type=CLINTRIALGOV&access_num=NCT04048018&atom=%2Fmedrxiv%2Fearly%2F2024%2F07%2F05%2F2024.07.03.24309158.atom

Citation classification aims to identify the purpose of the cited article in the citing article. Previous citation classification methods rely largely on supervised approaches. The models are trained on datasets with citing sentences or citation contexts annotated for a citation's purpose or function or intent. Recent advancements in Large Language Models (LLMs) have dramatically improved the ability of NLP systems to achieve state-of-the-art performances under zero or few-shot settings. This makes LLMs particularly suitable for tasks where sufficiently large labelled datasets are not yet available, which remains to be the case for citation classification. This paper systematically investigates the effectiveness of different prompting strategies for citation classification and compares them to promptless strategies as a baseline. Specifically, we evaluate the following four strategies, two of which we introduce for the first time, which involve updating Language Model (LM) parameters while training the model: (1) Promptless fine-tuning, (2) Fixed-prompt LM tuning, (3) Dynamic Context-prompt LM tuning (proposed), (4) Prompt + LM fine-tuning (proposed). Additionally, we test the zero-shot performance of LLMs, GPT3.5, a (5) Tuning-free prompting strategy that involves no parameter updating. Our results show that prompting methods based on LM parameter updating significantly improve citation classification performances on both domain-specific and multi-disciplinary citation classifications. Moreover, our Dynamic Context-prompting method achieves top scores both for the ACL-ARC and ACT2 citation classification datasets, surpassing the highest-performing system in the 3C shared task benchmark. Interestingly, we observe zero-shot GPT3.5 to perform well on ACT2 but poorly on the ACL-ARC dataset.