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PubMed2026

Survey of diagnostic laboratories highlights need for improved standards in somatic genomic testing and reporting.

There is a growing international need to support somatic genomic testing, standardised variant curation and improved patient access to molecular profiling for somatic conditions, including cancer. We conducted a survey of scope, curation, reporting and sharing practices of diagnostic laboratories performing somatic testing in Australia and New Zealand. Laboratories with accreditation (n = 41) were invited in 2023 to complete a semi-structured, 25-question interview. Responses were received for 27 laboratories (66% response rate) offering solid tumour, haematological malignancy and non-cancer services. Only 36% of laboratories offered tests capturing the full breadth of variants, from single-nucleotide variants to gene fusions. Knowledge sharing was rare, with only one laboratory submitting variant classifications to a public knowledge base. Most laboratories (96%) conducted somatic testing in oncology. Of cancer laboratories, 35% offered testing considered capable of comprehensive genomic profiling (CGP). Almost half of cancer laboratories had already adopted the 2022 ClinGen/CGC/VICC oncogenicity guidelines, and 84% were using AMP/ASCO/CAP 2017 clinical significance guidelines. Only 47% of mixed discipline cancer laboratories reported biomarkers such as tumour mutational burden, with wide variation in reporting of matched therapy options. Our study has generated a unique overview of somatic laboratory practices in the region, and areas for global standardisation in somatic molecular testing and reporting. We also provide a model for practice and guideline uptake assessment, for application by other country-wide networks. This is particularly relevant in anticipation of CGP mainstreaming, with the increasing complexity of sequencing interpretation for laboratories and clinicians.

Humans↗

PubMed2026

Comprehensive Genomic Profiling Timeliness Beyond Laboratory Turnaround Time: A Patient-Facing Pathway Analysis.

AIM: We evaluated the timeliness of the patient-facing comprehensive genomic profiling (CGP) pathway by separating laboratory and post-laboratory intervals within an expert panel-mediated process, using direct disclosure of results to patients as the endpoint. METHODS: This single-center retrospective study included adult CGP test episodes performed under government-funded cancer genomic medicine at a Japanese university hospital between October 2019 and November 2025. The primary outcome was patient-centered turnaround time (TAT), defined as the interval from informed consent to direct disclosure of the CGP result to the patient. Laboratory TAT and pathway intervals were summarized descriptively, and laboratory TAT was compared across assays. RESULTS: Among 882 CGP test episodes, median laboratory TAT was 14 days (interquartile range [IQR], 12-16) among 871 evaluable episodes. Among 828 evaluable episodes, median patient-centered TAT was 41 days (IQR 35-45). The laboratory analysis retained observed long intervals, including a maximum of 72 days; no episode was excluded solely because laboratory TAT exceeded 56 days. These findings indicate that laboratory TAT was only one component of the longer consent-to-disclosure pathway. CONCLUSION: In this routine-care CGP pathway, patient-facing timeliness depended on the full process from consent to direct patient disclosure. Patient-centered TAT should be monitored alongside laboratory TAT as a care-delivery measure.

comprehensive genomic profiling↗

PubMed2025

Impact of laboratory-driven proactive reanalysis: Reclassification to positive in 5% of initially negative or uncertain exome sequencing cases.

PURPOSE: Reanalysis of exome sequencing (ES) data increases diagnostic utility; however, there is no consensus on when and under what circumstances reanalysis should occur. Requesting and performing ES reanalysis burdens both clinical and laboratory workflows. Maximizing the potential for reclassification is essential. Here, we describe the impact of a laboratory-driven proactive reanalysis process that triggers reanalysis when new evidence is identified. METHODS: We reviewed reanalysis outcomes of an ES cohort. Reanalysis events were categorized based on initiating factors (laboratory-driven proactive, family studies, and clinician-initiated). Laboratory-driven proactive reclassifications are prompted by systematic review of new scientific data. Outcomes were evaluated by initiating factors, reclassification types, evidence used, and time since original report. RESULTS: Overall, 23% of cases underwent at least 1 reanalysis, with 35% of reanalyses resulting in reclassification. There was a 4% increase in diagnostic yield, including 5% of initially unsolved ES receiving diagnostic reports. Diagnostic reclassifications rates were significantly higher for laboratory-driven proactive reanalyses (54%; P < .0001) than family studies (18%) and clinician-initiated reanalyses (4%). New gene-disease relationships were the most efficacious evidence source. Laboratory-driven proactive reclassifications occurred steadily over time. CONCLUSION: Laboratory-driven proactive reanalysis effectively provides more diagnostic reclassifications compared with clinician-initiated reanalysis. Laboratories should curate and integrate emerging evidence into ES reanalysis.

Humans↗

PubMed2026

The role of pathology laboratories in integrating genetic testing into Australian primary care: an implementation science perspective.

As genomic testing moves into mainstream healthcare, non-genetic healthcare professionals, including general practitioners (GPs), play a critical role as gatekeepers to genetic services. Laboratories are essential in supporting this transition by providing not only high-quality genetic tests but also point-of-care tools, educational materials and clinical guidance to support their use. This study aimed to explore how these tools and supports are conceptualized, developed, implemented and evaluated and how laboratories integrate them into their relationships with GPs, an essential process for paving the way toward better use of genomics in primary care. A qualitative study design was employed using semi-structured, in-depth interviews with representatives from genetic laboratories across Australia. The Consolidated Framework for Implementation Research (CFIR) guided deductive content analysis of data. Findings spanned the four CFIR domains (Intervention Characteristics, Outer Setting, Inner Setting and Implementation Process) across 34 constructs. Participants reported that laboratories viewed point-of-care tools and resources as essential responses to persistent genomic knowledge gaps among GPs. Development of evidence-based, practice-driven and adaptable resources was supported and rewarded within laboratory organisations. A strong culture of clinical responsibility and implementation readiness, combined with robust networks and communications, enabled timely support for GPs. Gaps identified included lack of implementation planning, misalignments between laboratory-developed resources and GPs' real-world needs and inadequate mechanisms for obtaining GPs' feedback, which made evaluation problematic. By applying an implementation science framework, these findings provide insights for future efforts to build and sustain the provision of point-of-care tools and support, ultimately improving the integration of genomics in primary care.

Journal Article↗

PubMed2026

AI'm Here to Help: Enhancing Laboratory Genetic Counseling with Artificial Intelligence.

BACKGROUND: Artificial intelligence (AI) is transforming the fields of genetics and genetic counseling, enhancing both clinical and laboratory practices. The rise of AI technologies has drawn attention to their potential impact on genetic counseling, particularly in patient diagnosis and the counseling processes. CONTENT: In the laboratory, AI plays a critical role in improving communication between laboratory genetic counselors and healthcare providers by automating routine tasks and optimizing workflows. These advancements allow genetic counselors to dedicate more time to addressing complex inquiries, improving genetic test selection, and helping providers interpret genetic test results. As AI continues to integrate into laboratory genetic counseling practice, it presents both opportunities and challenges. At the time of submission, there is a large knowledge gap regarding AI and its application to laboratory genetic counseling, given the lack of published information on this topic. SUMMARY: This article summarizes existing literature, the history and current applications of AI in laboratory genetic counseling, examines its benefits and limitations, and explores future directions for its implementation in the field.

Humans↗

PubMed2024

Mass Spectrometry-Based Proteomics for the Masses: Peptide and Protein Identification in the Hunt Laboratory During the 2000's.

There has been a rapid increase in the number of individuals utilizing mass spectrometry-based proteomics to study complex biological systems and questions since the start of the 2000's. Building off the advancements in ionization and liquid chromatography scientists continued to push towards technology that would enable in-depth analysis of biological specimen. Donald F Hunt and the Hunt laboratory were major contributors to this effort with their work on improving upon existing Fourier Transform MS, development of electron transfer dissociation, and continued work on ion-ion reactions to improve intact protein analysis. Collaboration with other instrumentation laboratories and instrument companies led to the sharing of technology and eventual commercialization providing greater access. Additionally, the Hunt laboratory spread the gospel of MS-based proteomics through collaborations that lasted decades with other scientists who were experts in immunology, cellular signaling, epigenetics, and other fascinating fields. This article attempts to highlight the many contributions of Don and the Hunt laboratory to peptide and protein identification since the year 2000.

Humans↗

PubMed2026

Intra-strain genomic microevolution and phage resistance in Pseudomonas aeruginosa PAO1 laboratory isolates.

Pseudomonas aeruginosa is a major opportunistic pathogen, and its laboratory reference strain, PAO1, is widely used in microbiological and genetic studies. However, PAO1 often exhibits phenotypic variability that can affect experimental reproducibility. Our PAO1 stock, obtained from a public biobank, is resistant to PP7, a pilus-dependent single-stranded RNA phage known to infect PAO1. This suggests the presence of genetic variants in the stock. To check this possibility, we isolated six phenotypically distinct variants (GU1-GU6) and performed genomic and phenotypic analyses. Notable differences were observed among the isolates in terms of motility, pyocyanin production, and susceptibility to PP7. Whole-genome sequencing revealed that four of the six variants harbored mutations in pilus-associated genes. Among these, GU3 carried a mutation in pilT, which encodes a motor protein essential for type IV pilus retraction, and the loss of retraction led to the PP7 resistance. GU2, GU4, and GU6 shared a nonsense mutation in pilJ, a gene involved in chemotaxis and pilus extension, resulting in reduced twitching motility and lower PP7 infection efficiency. Additionally, we found that a mutation in lasR, a master regulator of quorum sensing, promoted the replication of prophage Pf6, which was integrated into the PAO1 genome. Pf6 replication interferes with PP7 infection, providing an alternative mechanism of resistance. These findings offer new insights into the complexity of phage-host interactions and emphasize the importance of routine verification and careful handling of P. aeruginosa sublines used in bacteriological and phage research.IMPORTANCEPhenotypic and genotypic variability in Pseudomonas aeruginosa PAO1 has been widely reported, raising concerns regarding the reproducibility of laboratory studies that rely on this reference strain. In this study, we isolated six PAO1 variants from a single laboratory stock and demonstrated that they differed markedly in motility, pyocyanin production, and susceptibility to the ssRNA phage PP7. Whole-genome sequencing has revealed that even a single mutation in a pilus-associated gene can profoundly affect bacterial motility and phage susceptibility. Furthermore, we showed that a mutation in lasR, a key regulator of the quorum-sensing system, triggered replication of the Pf6 prophage, which in turn hindered PP7 infection. These findings underscore the dynamic nature of laboratory strains and highlight the need for caution when interpreting results from phage-host interaction studies using reference strains. Our results provide a new understanding of how subtle genetic changes in model strains influence experimental outcomes in microbiology.

Pseudomonas aeruginosa↗

PubMed2025

Venous thromboembolism laboratory testing (factor V Leiden and factor II c.∗97G>A), 2025 revision: A technical standard of the American College of Medical Genetics and Genomics (ACMG).

Venous thromboembolism (VTE) occurs when a blood clot forms in a vein. The etiology of VTE is multifactorial, including both environmental and genetic factors. Among the genetic factors, factor V Leiden and factor II c.∗97G>A (formerly referred to as prothrombin 20210G>A) are the 2 most common genetic variants associated with VTE. Testing for these variants is one of the most common referrals in clinical genetics laboratories. Although the methodologies for testing these 2 variants are relatively straightforward, the clinical implementation can be complicated regarding test indications, risk assessment for occurrence, and recurrence of VTE and related genetic counseling. This document provides an overview of VTE, information about the variants and their influence on risk, considerations before initiating genetic testing, and the clinical and analytical sensitivity and specificity of the tests. Key information that should be included in the laboratory report is also provided. This document supersedes the Technical Standards and Guidelines for Venous Thromboembolism Laboratory Testing originally published in 2005 and revised in 2018. It is designed for genetic testing professionals familiar with the disease and the analysis methods.

Humans↗

PubMed2025

Laboratory Evolution Reveals Transcriptional Mechanisms Underlying Thermal Adaptation of Escherichia coli.

Adaptive laboratory evolution is able to generate microbial strains, which exhibit extreme phenotypes, revealing fundamental biological adaptation mechanisms. Here, we use adaptive laboratory evolution to evolve Escherichia coli strains that grow at temperatures as high as 45.3 °C, a temperature lethal to wild-type cells. The strains adopted a hypermutator phenotype and employed multiple systems-level adaptations that made global analysis of the DNA mutations difficult. Given the challenge at the genomic level, we were motivated to uncover high-temperature tolerance adaptation mechanisms at the transcriptomic level. We employed independently modulated gene set (iModulon) analysis to reveal five transcriptional mechanisms underlying growth at high temperatures. These mechanisms were connected to acquired mutations, changes in transcriptome composition, sensory inputs, phenotypes, and protein structures. They are as follows: (i) downregulation of general stress responses while upregulating the specific heat stress responses, (ii) upregulation of flagellar basal bodies without upregulating motility and upregulation fimbriae, (iii) shift toward anaerobic metabolism, (iv) shift in regulation of iron uptake away from siderophore production, and (v) upregulation of yjfIJKL, a novel heat tolerance operon whose structures we predicted with AlphaFold. iModulons associated with these five mechanisms explain nearly half of all variance in the gene expression in the adapted strains. These thermotolerance strategies reveal that optimal coordination of known stress responses and metabolism can be achieved with a small number of regulatory mutations and may suggest a new role for large protein export systems. Adaptive laboratory evolution with transcriptomic characterization is a productive approach for elucidating and interpreting adaptation to otherwise lethal stresses.

Escherichia coli↗

PubMed2026

Thermal biology characteristics of the Caspian whipsnake (Dolichophis caspius, Gmelin, 1789) under natural and laboratory conditions.

Reptiles rely on behavioural thermoregulation to maintain optimal body temperature (Tb), essential for many physiological functions. However, thermal biology remains poorly studied in many snake species, including the Caspian whipsnake (Dolichophis caspius, Gmelin, 1789). This study examined the thermal biology of the Caspian whipsnake under natural and laboratory conditions. In the field, we investigated the influence of sex, age category, season, time of day, air temperature, detection status, feeding status, and shedding phase on Tb. Under controlled conditions, we assessed preferred Tb variation and its relationship to active thermoregulation. In the field, Tb was significantly affected by sex, season, time of day, air temperature, feeding status, and shedding phase, but not age category, body size or detection status. Males had lower Tb than females and snakes with food in their stomachs exhibited higher Tb. Tb increased from March to June and from morning to afternoon, and air temperature had a positive effect on Tb. In the laboratory, mean Tb (24.5 ± 4.9 °C) was lower than in the field (26.9 ± 5.2 °C) and was significantly associated with body posture and terrarium part, indicating active behavioural thermoregulation. In the laboratory, males had lower Tb than females, and juveniles had lower Tb than adults. The lower thermal preference suggests a cooler thermal niche than many colubrids, potentially increasing their susceptibility to climate warming. However, the broad Tb variation and behavioural thermoregulation indicate some flexibility in responding to environmental changes. These findings highlight the role of behavioural thermoregulation in snake thermal responses to environmental variation.

Behavioural thermoregulation↗

PubMed2026

Associations of clinical and laboratory parameters with pediatric urolithiasis composition: A retrospective, single-center study.

OBJECTIVE: To investigate demographic, clinical, and laboratory factors associated with distinct stone compositions in children. METHODS: This retrospective study included 237 children aged <14 years who underwent stone composition analysis between July 2008 and November 2023. Demographic, clinical, and laboratory data were collected, and propensity score matching (PSM) was used to control for confounding factors. RESULTS: The urate component (uric acid anhydrous, ammonium acid urate, and sodium urate) was most prevalent in infants, males, and non-Han children, whereas the calcium oxalate component predominated in older children. Analysis of coexisting components revealed urate is the most common partner to calcium oxalate (67.6%), and vice versa (82.8%). Struvite most frequently coexisted with carbonate apatite (60%), while carbonate apatite most often coexisted with calcium oxalate (54%). After PSM, the urate component was independently associated with host metabolic dysregulation, including lower high-density lipoprotein (β = -0.175, 95% CI: -0.279 to -0.071, p = 0.001) and with coagulation dysfunction, as evidenced by a prolonged prothrombin time (β = 0.595, 95% CI: 0.125 to 1.064, p = 0.014). Additionally, preoperative urinary tract infection (UTI) and congenital urinary tract anomalies were independently associated with both carbonate apatite and struvite components, with directionally consistent but quantitatively unstable signals in the struvite cohort, whereas the calcium oxalate component exhibited an inverse association with UTI (OR = 0.156, 95% CI: 0.030 to 0.819, p = 0.028). Furthermore, the carbonate apatite component was also independently associated with an elevated systemic immune-inflammation index (β = 416.53, 95% CI: 60.05 to 773.01, p = 0.024) and systemic inflammation response index (β = 1.286, 95% CI: 0.086 to 2.487, p = 0.038). CONCLUSION: Urate component was prevalent in infants, males, and non-Han children, whereas calcium oxalate predominated in older children. After adjusting for confounders, urate composition was associated with metabolic abnormalities, the carbonate apatite component was linked to infection and anatomical malformations, and a similar directional pattern was observed in the struvite cohort.

Humans↗

PubMed2025

Adaptive laboratory evolution of Micrococcus luteus and identification of genes associated with radioresistance through genome-wide association study.

Micrococcus luteus (V017) is a Gram-positive bacterium that was isolated from a sterilization area exposed to 60Co radiation. In this study, we performed an adaptive laboratory evolution experiment with M. luteus, exposing it to 24 continuous cycles of gamma irradiation at four different doses (1.5 kGy, 3.5 kGy, 5.5 kGy, and 7.5 kGy). This led to the creation of four evolved populations with different levels of radioresistance, which were positively correlated with the radiation dose applied. The survival rate of the evolved population that underwent adaptive treatment at the highest dose (7.5 kGy) was 0.69% after exposure to 5.5 kGy, which is about five orders of magnitude higher than that of the original strain V017. Furthermore, 76 evolved strains were selected from these populations, and their genomes were re-sequenced, uncovering a total of 3072 mutations. A genome-wide association study identified 56 single nucleotide polymorphisms (SNPs) significantly associated with radioresistance, linked to 62 candidate genes. Ultimately, 9 genes were selected for functional validation. Inactivating 6 of these genes, including H0H31_RS03855 (SMC family ATPase, SbcC), H0H31_RS04250 (ribonuclease HII), H0H31_RS04570 (endonuclease VIII), H0H31_RS07595 (bifunctional 3'-5' exonuclease/DNA polymerase I), H0H31_RS00170 (serine/threonine phosphatase PPP), and H0H31_RS05860 (CBS-domain-containing protein), significantly increased sensitivity to gamma radiation, underscoring their importance in radioresistance.

Micrococcus luteus↗

PubMed2025

Adaptive laboratory evolution of Saccharomyces cerevisiae CEN.PK 113-7D to enhance ethanol tolerance.

Saccharomyces cerevisiae is a widely used yeast for industrial production of ethanol. However, elevated ethanol, temperature, and osmotic stress adversely affect fermentation efficiency. In this study, adaptive laboratory evolution for S. cerevisiae CEN.PK 113-7D on higher concentrations of ethanol was performed. After 144 days, the maximum specific growth rate (µmax) increased from 0.0240 to 0.1150 h-1 for the strain evolved on 9% v/v ethanol, and from 0.0002 to 0.0530 h-1 for the strain evolved on 11% v/v ethanol, and the specific glucose uptake rate increased by 30%. The strain evolved on 11% ethanol produced 94.5 g/L ethanol in a fermentation as compared to 78.5 g/L production by a non-evolved strain. By whole-genome sequencing of the evolved clones, we identified multiple coding mutations in genes involved in processes such as stress response, cell growth regulation, pentose phosphate pathway, lipid synthesis, and redox balance. The selected mutations in RKI1, CYC2, ANR2, RGA2, RGA1, LPX1, and LRE1 genes were validated by introducing them in the nonevolved yeast, showing 1.7-5-fold growth improvement at 9% ethanol (P < 0.05). Notably, RGA2, RGA1 and LPX 1 carried an identical missense mutation across three independent clones. The RKI1I208V mutant showed the highest ethanol tolerance, while CYC2N342A achieved the highest ethanol production.

Ethanol↗

PubMed2026

Adaptive laboratory evolution enables carbon-negative mixotrophic fermentation and enhanced chain elongation in Clostridium sp. JS66.

Improving carbon recovery during sugar fermentation remains a major challenge because a substantial fraction of substrate carbon is lost as CO2 during central metabolism. To overcome this limitation, Clostridium sp. JS66 (JS66), an acetogen producing hexanoic acid from glucose, was subjected to adaptive laboratory evolution under autotrophic CO2/H2 conditions to enhance H2-assisted CO2 reassimilation during glucose fermentation. The evolved strain, ALECO2, exhibited CO2 consumption without a lag phase under autotrophic conditions and reached a 9.5-fold higher CO2 uptake rate than JS66. Under fed-batch mixotrophic conditions, glucose-only fermentation yielded a carbon molar yield (Cmetabolite/Csugar, CM/CS) of 0.60, whereas H2 supplementation increased CM/CS to 0.91 and redirected carbon flux toward C6 products (hexanoic acid and hexanol), which accounted for 49% of total C_output. With additional CO2 supplementation, ALECO2 further assimilated externally supplied CO2, increasing the CM/CS to 1.10 and demonstrating carbon-negative fermentation. Assimilation of externally supplied CO2 further redirected carbon flux toward chain elongation, producing 7.14 g/L hexanoic acid and increasing the C6 carbon fraction to 57% of total C_output. Constraint-based flux analysis supported increased acetyl-CoA formation through the Wood-Ljungdahl pathway and enhanced flux toward reverse β-oxidation under H2- and CO2/H2-supplemented conditions. Genome analysis identified mutations including genes encoding a putative HytB homolog and a LysR-type transcriptional regulator. These results establish ALECO2 as a promising evolved anaerobic non-photosynthetic (ANP) mixotrophy platform that links CO2 reassimilation and external CO2 assimilation with chain elongation, enabling carbon-neutral and carbon-negative production of value-added C6 products from glucose.

Anaerobic non-photosyntheticmixotrophy (ANP)↗

PubMed2026

CRISPR-Cas-based diagnostics for point-of-care detection of sexually transmitted infections: a laboratory development and evaluation study.

BACKGROUND: Timely, point-of-care diagnosis of sexually transmitted infections (STIs) is crucial for enabling prompt treatment and reducing transmission. We aimed to develop a portable, multiplexed, CRISPR-based assay panel for the detection of Neisseria gonorrhoeae (including the ciprofloxacin resistance marker gyrA S91F), Chlamydia trachomatis, Treponema pallidum, and herpes simplex virus (HSV). METHODS: In this laboratory development and evaluation study, we developed and optimised four multiplexed, CRISPR-based, diagnostic STI assays for point-of-care use. The complete assay panel comprised a CRISPR TP-HSV (cTP-HSV) panel for the detection of T pallidum and pan-HSV, with reflex testing to distinguish HSV-1 from HSV-2, and a CRISPR NG-CT (cNG-CT) panel for the detection of N gonorrhoeae and C trachomatis, with reflex testing to detect N gonorrhoeae using two additional genome regions and to identify the gyrA S91F mutation. Each pathogen was targeted at two independent genomic regions by isothermal amplification and CRISPR-Cas reaction using Cas12a and Cas13a, each with distinct fluorescent reporters. Analytical specificity and limits of detection (LODs) were determined, and a retrospective, masked concordance study was conducted on genomic DNA from 900 clinical samples (400 for cTP-HSV and reflex testing and 500 for cNG-CT and reflex testing), using quantitative PCR as the reference standard. The diagnostic accuracy of the test was assessed by analysis of receiver operating characteristic curves. FINDINGS: The overall sensitivity of the TP-HSV CRISPR assay was 82·5% (95% CI 74·0-88·7) for T pallidum and 94·4% (90·2-97·0) for pan-HSV; LODs were 6·2 copies per μL for T pallidum and 7·8 copies per μL for HSV. Reflex testing gave sensitivities of 97·0% (91·1-99·3) for HSV-1 and 96·0% (89·7-98·7) for HSV-2. The NG-CT CRISPR assay had an overall sensitivity of 80·0% (74·0-84·9) for N gonorrhoeae and 73·0% (65·5-79·3) for C trachomatis, with a LOD of 3·9 copies per μL for both pathogens. Reflex testing for the detection of the gyrA S91F mutation in N gonorrhoeae showed an overall sensitivity of 63·1% (55·1-70·4); however, this was dependent on sample type, with a sensitivity of 85·7% (46·7-99·5) in genital samples and 61·2% (52·8-68·9) in extragenital samples. For all pathogens, assay sensitivity was positively correlated with pathogen load. Area under the curve (AUC) values were 0·90 for T pallidum and 0·99 for pan-HSV in the TP-HSV assay, with values of 0·99 for HSV-1 and 0·97 for HSV-2 obtained in the reflex HSV-1-HSV-2 assay. For the cNG-CT assay, AUC values were 0·90 for N gonorrhoeae and 0·85 for C trachomatis, with a value of 0·72 obtained for gyrA S91F in the reflex cNG-gyrA assay. INTERPRETATION: Our multiplexed, CRISPR-based, point-of-care platform achieved performance consistent with WHO target product profiles for N gonorrhoeae and T pallidum. Proof-of-concept detection of the gyrA S91F resistance marker highlights its potential for resistance-guided therapy. Although optimisation is required before large-scale deployment, this suite offers a promising approach for rapid, decentralised, and resistance-informed STI diagnosis, particularly in resource-limited settings. FUNDING: Victorian Government Department of Health, Australian Government Department of Health, Disability and Ageing and Aged Care, and Australian Research Council.

Humans↗

PubMed2026

Influence of ovarian maturity, age, and mating status on the antennal responses of wild and laboratory reared Xyleborus affinis (Coleoptera: Curculionidae: Scolytinae) to ethanol.

Xyleborus affinis Eichthoff is a neotropical ambrosia beetle that, in certain regions such as the United States and Mexico, has been associated with exotic phytopathogenic fungi causing extensive tree mortality. Although studies relating its olfactory response to volatile compounds and trapping systems have been published, factors such as the insect's physiological condition, which can affect its recognition or response to odors, have not been studied. Here, we evaluated the electroantennographic (EAG) response of wild and laboratory reared X. affinis females to 70% ethanol, a compound known to attract these insects. The experimental design was developed to consider and compare the following conditions: (i) females collected inside and outside host-galleries, (ii) sexual maturity (with mature and immature ovaries), (iii) age (0, 1, 3, and 5 d after emergence), and (iv) mating status (virgins and mated). Our results indicate that most of the wild females located outside the galleries were sexually mature but exhibited significantly lower EAG response than those inside the galleries. Regarding mating status, mated females exhibited significantly stronger antennal responses compared to virgins, whereas age did not affect antennal sensitivity. Finally, we provide images of the hitherto undescribed reproductive system of X. affinis females, a key element that enabled this investigation. The information generated offers a useful foundation for future studies aimed at understanding the physiological mechanisms and other critical factors related to sensory perception and reproductive condition. For example, factors that may influence the behavior and attraction of X. affinis females to host semiochemicals.

Animals↗

PubMed2025

Novel insights into the genetic architecture and mechanisms of host/microbiome interactions from a multi-cohort analysis of outbred laboratory rats.

The intestinal microbiome influences health and disease. Its composition is affected by host genetics and environmental exposures. Understanding host genetic effects is critical but challenging in humans, due to the difficulty of detecting, mapping and interpreting them. To address this, we analysed host genetic effects in four cohorts of outbred laboratory rats exposed to distinct but controlled environments. We found that polygenic host genetic effects were consistent across environments. We identified three replicated microbiome-associated loci, one of which involved a sialyltransferase gene and Paraprevotella. We found a similar association in a human cohort, between ST6GAL1 and Paraprevotella, both of which have been linked with immune and infectious diseases. Moreover, we found evidence of indirect genetic effects on microbiome phenotypes, which substantially increased their total genetic variance. Finally, we identified a novel mechanism whereby indirect genetic effects can contribute to "missing heritability".

Journal Article↗

PubMed2026

Metagenome-assembled genomes for N2-fixing cyanobacterium Nostoc sp. TISTR 8405 and co-occurring microorganisms from a long-term laboratory culture.

We report here metagenome-assembled genomes from a long-term laboratory culture of the nitrogen-fixing cyanobacterium Nostoc sp. TISTR 8405, originally sourced from a Thai freshwater lake. The community consists of two additional co-occurring microorganisms, Erythrobacter sp. THAI-01 and Allorhizobium sp. THAI-01, and contains putative plasmids associated with Nostoc and Allorhizobium, respectively.

co-culture↗