Genetics. 2024 Oct 30:iyae175. doi: 10.1093/genetics/iyae175. Online ahead of print.

ABSTRACT

Self-fertile Caenorhabditis nematodes carry a surprising number of Medea elements, alleles that act in heterozygous mothers and cause death or developmental delay in offspring that don't inherit them. At some loci, both alleles in a cross operate as independent Medeas, affecting all the homozygous progeny of a selfing heterozygote. The genomic coincidence of Medea elements and ancient, deeply coalescing haplotypes, which pepper the otherwise homogeneous genomes of these animals, raises questions about how these apparent gene-drive elements persist for long periods of time. Here I investigate how mating system affects the evolution of Medeas, and their paternal-effect counterparts, peels. Despite an intuition that antagonistic alleles should induce balancing selection by killing homozygotes, models show that, under partial selfing, antagonistic elements experience positive frequency dependence: the common allele drives the rare one extinct, even if the rare one is more penetrant. Analytical results for the threshold frequency required for one allele to invade a population show that a very weakly penetrant allele, one whose effects would escape laboratory detection, could nevertheless prevent a much more penetrant allele from invading under high rates of selfing. Ubiquitous weak antagonistic Medeas and peels could then act as localized barriers to gene flow between populations, generating genomic islands of deep coalescence. Analysis of gene expression data, however, suggest that this cannot be the whole story. A complementary explanation is that ordinary ecological balancing selection generates ancient haplotypes on which Medeas can evolve, while high homozygosity in these selfers minimizes the role of gene drive in their evolution.

PMID:39475455 | DOI:10.1093/genetics/iyae175

Microbiol Spectr. 2024 Oct 30:e0152124. doi: 10.1128/spectrum.01521-24. Online ahead of print.

ABSTRACT

Vulvovaginal candidiasis (VVC) is a common vaginal infectious disease caused by Candida. The high recurrence rate of VVC is a great clinical challenge, with recurrent VVC (RVVC) defined as four or more episodes within a year. In this study, we recruited 31 RVVC patients, 28 VVC patients, and 29 healthy women. Vaginal samples were collected for metagenomic and metabolic analysis. RVVC and VVC groups presented similar clinical symptoms, with only a significantly increased incidence of swelling in the VVC group. Vaginal microbiota in VVC/RVVC exhibited a decreased abundance of Lactobacillus and increased bacterial vaginosis-associated bacteria, such as Gardnerella, Prevotella, and Atopobium. Notably, Lactobacillus iners was higher in RVVC, suggesting not all Lactobacillus species are protective. Healthy women showed lower overall microbiota diversity, emphasizing single-species dominance for stability. Glycogen metabolism pathways were enriched in RVVC/VVC, and were correlated with Atopobium vaginae, Prevotella bivia, and Lactobacillus jensenii. Peptidoglycan synthesis pathways, associated with P. bivia, were enriched, with the substrate L-glutamate elevated in RVVC, possibly promoted by L. iners. These findings shed light on potential therapeutic targets for recurrent VVC, contributing to the understanding of the intricate interplay between the metabolism of vaginal microbiome and disease.

IMPORTANCE: This study enhances our knowledge of the vaginal microbiota dynamics and the role of associated metabolites in individuals with vulvovaginal candidiasis (VVC) and recurrent vulvovaginal candidiasis through shotgun sequencing and multi-omics analysis. The relationship between metabolites and vaginal microbiota and disease state was revealed. The accumulation of L-glutamate generated in glycogen metabolism, which is governed by Lactobacillus iners or bacterial vaginosis-associated bacteria, may contribute to the incidence and recurrence of VVC. Such insights have the potential to impact the treatment and prevention strategies for these common yet distressing conditions, potentially leading to targeted therapies and improved patient outcomes.

PMID:39475249 | DOI:10.1128/spectrum.01521-24

J Proteome Res. 2024 Oct 30. doi: 10.1021/acs.jproteome.4c00418. Online ahead of print.

ABSTRACT

Malaria is a deadly disease caused by Apicomplexan parasites of the Plasmodium genus. Several species of the Plasmodium genus are known to be infectious to humans, of which P. falciparum is the most virulent. Post-translational modifications (PTMs) of proteins coordinate cell signaling and hence regulate many biological processes in P. falciparum homeostasis and host infection, of which the most highly studied is phosphorylation. Phosphosites on proteins can be identified by tandem mass spectrometry (MS) performed on enriched samples (phosphoproteomics), followed by downstream computational analyses. We have performed a large-scale meta-analysis of 11 publicly available phosphoproteomics data sets to build a comprehensive atlas of phosphosites in the P. falciparum proteome, using robust pipelines aimed at strict control of false identifications. We identified a total of 26,609 phosphorylated sites on P. falciparum proteins, split across three categories of data reliability (gold/silver/bronze). We identified significant sequence motifs, likely indicative of different groups of kinases responsible for different groups of phosphosites. Conservation analysis identified clusters of phosphoproteins that are highly conserved and others that are evolving faster within the Plasmodium genus, and implicated in different pathways. We were also able to identify over 180,000 phosphosites within Plasmodium species beyond falciparum, based on orthologue mapping. We also explored the structural context of phosphosites, identifying a strong enrichment for phosphosites on fast-evolving (low conservation) intrinsically disordered regions (IDRs) of proteins. In other species, IDRs have been shown to have an important role in modulating protein-protein interactions, particularly in signaling, and thus warranting further study for their roles in host-pathogen interactions. All data have been made available via UniProtKB, PRIDE, and PeptideAtlas, with visualization interfaces for exploring phosphosites in the context of other data on Plasmodium proteins.

PMID:39475123 | DOI:10.1021/acs.jproteome.4c00418

Elife. 2024 Oct 30;13:e104040. doi: 10.7554/eLife.104040.

ABSTRACT

By inhibiting receptor-ligand interactions in sebaceous glands, antibodies may be able to treat certain skin conditions.

PMID:39475102 | DOI:10.7554/eLife.104040

iScience. 2024 Oct 2;27(10):110966. doi: 10.1016/j.isci.2024.110966. eCollection 2024 Oct 18.

ABSTRACT

Play is a widespread behavior present in phylogenetically distant taxa that, in its social form, relies on complex communication. Playful communication has been largely neglected in marine mammals. We focus on playful visual communication in bottlenose dolphins. The open mouth (OM) display was mainly emitted during social than during solitary play and occurred more frequently when the sender was in the receiver's field of view, suggesting that animals are attentive to the playmate's attentional state. Detecting an OM evoked the same facial display in the receiver, a result that strikingly matches with those obtained on cooperative social primates and carnivores. It is difficult to know whether such similarities derive from shared evolutionary pathways (homology) or from evolutionary convergence (homoplasy), as both have been suggested for play behavior. The pervasive presence of OM and rapid mimicry in the mammal phylogenetic tree indicates the relevance of visual mechanisms in shaping complex communication.

PMID:39474076 | PMC:PMC11519433 | DOI:10.1016/j.isci.2024.110966

Environ Health (Wash). 2024 May 9;2(7):499-513. doi: 10.1021/envhealth.4c00043. eCollection 2024 Jul 19.

ABSTRACT

As a key step in next-generation risk assessment (NGRA), in vitro to in vivo extrapolation (IVIVE) aims to mobilize a mechanism-based understanding of toxicology to translate bioactive chemical concentrations obtained from in vitro assays to corresponding exposures likely to induce bioactivity in vivo. This conversion can be achieved via physiologically-based toxicokinetic (PBTK) models and machine learning (ML) algorithms. The last 5 years have witnessed a period of rapid development in IVIVE, with the number of IVIVE-related publications increasing annually. This Review aims to (1) provide a comprehensive overview of the origin of IVIVE and initiatives undertaken by multiple national agencies to promote its development; (2) compile and sort out IVIVE-related publications and perform a clustering analysis of their high-frequency keywords to capture key research hotspots; (3) comprehensively review PBTK and ML model-based IVIVE studies published in the last 5 years to understand the research directions and methodology developments; and (4) propose future perspectives for IVIVE from two aspects: expanding the scope of application and integrating new technologies. The former includes focusing on metabolite toxicity, conducting IVIVE studies on susceptible populations, advancing ML-based quantitative IVIVE models, and extending research to ecological effects. The latter includes combining systems biology, multiomics, and adverse outcome networks with IVIVE, aiming at a more microscopic, mechanistic, and comprehensive toxicity prediction. This Review highlights the important value of IVIVE in NGRA, with the goal of providing confidence for its routine use in chemical prioritization, hazard assessment, and regulatory decision making.

PMID:39473885 | PMC:PMC11504544 | DOI:10.1021/envhealth.4c00043

Int J Breast Cancer. 2024 Oct 22;2024:8796102. doi: 10.1155/2024/8796102. eCollection 2024.

ABSTRACT

Background: Triple-negative breast cancer (TNBC) is an aggressive subtype with limited treatment options. This study is aimed at identifying potential therapeutic targets in TNBC using gene regulatory network analysis and a system biology approach. Methods: The GSE38959 dataset was reanalyzed to identify differentially expressed genes (DEGs) in TNBC tissues compared to normal breast samples. Protein-protein interaction networks were constructed, and hub genes were identified. Survival analysis was performed using GEPIA2. Gene regulatory networks were built to identify upstream regulators. Cross-platform verification was conducted using an independent RNA-seq dataset (GSE58135). Expression analysis of prognostic markers in TNBC versus non-TNBC samples was performed using bc-GenExMiner. Results: A total of 943 DEGs were identified in TNBC tissues. CHEK1 and PLK1 were identified as central hub genes, with overexpression correlating with poor prognosis. GABPB1 was identified as the most influential upstream regulator of CHEK1 and PLK1 through gene regulatory network analysis, while JUN exhibited the most interactions among regulators. A total of 302 consistently modulated genes were confirmed through cross-platform verification. The overexpression of CHEK1 and PLK1 in TNBC compared to non-TNBC samples was validated by expression analysis. Conclusion: This study provides insights into the molecular mechanisms of TNBC and suggests CHEK1, PLK1, and their upstream regulators as potential therapeutic targets for TNBC treatment.

PMID:39473450 | PMC:PMC11521586 | DOI:10.1155/2024/8796102

Sci Rep. 2024 Oct 30;14(1):26050. doi: 10.1038/s41598-024-77463-x.

ABSTRACT

Shiga toxin-producing Escherichia coli (STEC) is a foodborne pathogen with 6,534 annual reported cases in the EU in 2021. This pathotype generally contains strains with smooth LPS with O-antigen serogroup O157 being the predominant serogroup in the US. However, non-O157 STEC serogroups are becoming increasingly prevalent. Here we announce the complete genomes of three newly isolated phages that infect STEC serogroups O103 and O146, namely Escherichia phages vB_EcoP_PAS7, vB_EcoP_PAS59 and vB_EcoP_PAS61. The genome sequences revealed that they belong to three distinct genera, namely the newly proposed genus Cepavirus within the Slopekvirinae subfamily, the genus Suseptimavirus and the genus Uetakevirus, respectively. We identified the tailspikes of phages PAS7 and PAS61 as a primary specificity determinant for the O-antigens O103 and O146, respectively, and predicted their active site in silico.

PMID:39472643 | DOI:10.1038/s41598-024-77463-x

Sci Rep. 2024 Oct 29;14(1):26003. doi: 10.1038/s41598-024-74985-2.

ABSTRACT

We presented a method to find potential cancer attractors using single-cell RNA sequencing (scRNA-seq) data. We tested our method in a Glioblastoma Multiforme (GBM) dataset, an aggressive brain tumor presenting high heterogeneity. Using the cancer attractor concept, we argued that the GBM's underlying dynamics could partially explain the observed heterogeneity, with the dataset covering a representative region around the attractor. Exploratory data analysis revealed promising GBM's cellular clusters within a 3-dimensional marker space. We approximated the clusters' centroid as stable states and each cluster covariance matrix as defining confidence regions. To investigate the presence of attractors inside the confidence regions, we constructed a GBM gene regulatory network, defined a model for the dynamics, and prepared a framework for parameter estimation. An exploration of hyperparameter space allowed us to sample time series intending to simulate myriad variations of the tumor microenvironment. We obtained different densities of stable states across gene expression space and parameters displaying multistability across different clusters. Although we used our methodological approach in studying GBM, we would like to highlight its generality to other types of cancer. Therefore, this report contributes to an advance in the simulation of cancer dynamics and opens avenues to investigate potential therapeutic targets.

PMID:39472601 | DOI:10.1038/s41598-024-74985-2

Nat Commun. 2024 Oct 29;15(1):9330. doi: 10.1038/s41467-024-52909-y.

ABSTRACT

Dietary restriction (DR) is a potent method to enhance lifespan and healthspan, but individual responses are influenced by genetic variations. Understanding how metabolism-related genetic differences impact longevity and healthspan are unclear. To investigate this, we used metabolites as markers to reveal how different genotypes respond to diet to influence longevity and healthspan traits. We analyzed data from Drosophila Genetic Reference Panel (DGRP) strains raised under AL and DR conditions, combining metabolomic, phenotypic, and genome-wide information. We employed two computational and complementary methods across species-random forest modeling within the DGRP as our primary analysis and Mendelian randomization in human cohorts as a secondary analysis. We pinpointed key traits with cross-species relevance as well as underlying heterogeneity and pleiotropy that influence lifespan and healthspan. Notably, orotate was linked to parental age at death in humans and blocked the DR lifespan extension in flies, while threonine supplementation extended lifespan, in a strain- and sex-specific manner. Thus, utilizing natural genetic variation data from flies and humans, we employed a systems biology approach to elucidate potential therapeutic pathways and metabolomic targets for diet-dependent changes in lifespan and healthspan.

PMID:39472442 | DOI:10.1038/s41467-024-52909-y

J R Soc Interface. 2024 Oct;21(219):20240457. doi: 10.1098/rsif.2024.0457. Epub 2024 Oct 30.

ABSTRACT

Drawing on recent advances in biology, this paper describes a systems approach, 'Systems Public Affairs' (SPA), to integrate non-market strategies in corporate purposes and strategies. Just as the environment of organisms affects and is affected by their development and evolution, so individuals and businesses adjust to and can shape their non-market environment, which we define as 'a historically formed national and social sphere, including laws, regulations, and policies, which supports, maintains and restrains the operation and preservation of markets'. The paper uses cases from South Korea to illustrate this approach. Emergent ideas in biology have great relevance for micro-foundations of business. Traditionally, economic activities are outcomes of individualistic decision-makers, each promoting their distinct objectives within economic markets. In the SPA approach, decision makers in the domains of business, policy and civil society collaborate in shaping non-market environments to align business objectives with public interest. This requires agency to rise to higher levels than that of businesses, policymakers and civil society through collaboration and experimentation in the presence of stochasticity and radical uncertainty. Analogous to the advancement of organism evolution through emergence of nervous systems and learning, so alignment of organizations with their non-market environments accelerates economic and social development.

PMID:39471870 | DOI:10.1098/rsif.2024.0457

Proc Natl Acad Sci U S A. 2024 Nov 5;121(45):e2415631121. doi: 10.1073/pnas.2415631121. Epub 2024 Oct 29.

ABSTRACT

Reverse-transcribing animal DNA viruses include the hepadnaviruses, a well-characterized family of small enveloped viruses that infect vertebrates but also a sister group of nonenveloped viruses more recently discovered in fish and termed the nackednaviruses. Here, we describe the complete sequence of a virus found in the feces of an insectivorous bat, which encodes a core protein and a reverse transcriptase but no envelope protein. A database search identified a viral sequence from a permafrost sample as its closest relative. The two viruses form a cluster that occupies a basal phylogenetic position relative to hepadnaviruses and nackednaviruses, with an estimated divergence time of 500 My. These findings may lead to the definition of a "proto-nackednavirus" family and support the hypothesis that the ancestors of hepadnaviruses were nonenveloped.

PMID:39471221 | DOI:10.1073/pnas.2415631121

PLoS Genet. 2024 Oct 29;20(10):e1011464. doi: 10.1371/journal.pgen.1011464. Online ahead of print.

ABSTRACT

Three RpoD-family sigma factors, RpoD, RpoS, and RpoH, play critical roles in transcriptional regulation in Salmonella enterica serovar Typhimurium under heat shock conditions. However, the genome-wide regulatory mechanisms of these sigma factors in response to heat stress have remained elusive. In this study, we comprehensively identified 2,319, 2,226, and 213 genome-wide binding sites for RpoD, RpoS, and RpoH, respectively, under sublethal heat shock conditions (42°C). Machine learning-based transcriptome analysis was employed to infer the relative activity of iModulons, providing valuable insights into the transcriptional impact of heat shock. Integrative data analysis enabled the reconstruction of the transcriptional regulatory network of sigma factors, revealing how they modulate gene expression to adapt to heat stress, including responses to anaerobic and oxidative stresses. Notably, we observed a significant expansion of the RpoS sigmulon from 97 to 301 genes in response to heat shock, underscoring the crucial role of RpoS in regulating various metabolic processes. Moreover, we uncovered a competition mechanism between RpoD and RpoS within RpoS sigmulons, where RpoS significantly increases its binding within promoter regions shared with RpoD under heat shock conditions. These findings illuminate how three RpoD-family sigma factors coordinate multiple cellular processes to orchestrate the overall response of S. Typhimurium to heat stress.

PMID:39471211 | DOI:10.1371/journal.pgen.1011464

Asian Pac J Cancer Prev. 2024 Oct 1;25(10):3349-3361. doi: 10.31557/APJCP.2024.25.10.3349.

ABSTRACT

BACKGROUND: Despite advancements in breast cancer (BC) diagnosis and treatment, it continues to be a serious health concern among women due to its high incidence rate. Thus, prevention strategies in BC are essential. Some nutrients such as vitamin D may play a preventive role against BC through different genes which have a vital role in several pathways. These pathways include autophagy, tumorigenesis, apoptosis, immunity, and genome stability. This study aimed to review the role of vitamin D in BC via the network of vitamin D-regulated pathways.

METHODS: This systematic review was conducted following PRISMA guidelines. PubMed, ScienceDirect, and Scopus were searched using a combination of MeSH terms and keywords related to molecular and cellular mechanisms of the effects of vitamin D on breast cancer. A total of 200 articles were initially found, from which 14 relevant studies were selected based on specific inclusion and exclusion criteria.

RESULTS: Experimental studies have shown possible anti-carcinogenic effects of vitamin D-related genes due to their participation in regulating autophagy, tumorigenesis, apoptosis, immunity, and genome stability in normal and malignant breast cells. Moreover, vitamin D deficiency has the potential to create a supportive environment that promotes proangiogenic processes, tumor cell dissemination, metastasis, and establishment at secondary sites.

CONCLUSION: Vitamin D may have systematic roles against BC in humans through various interactions with different genes, which have roles in different and important pathways as underlying mechanisms in the pathophysiology of BC. More broadly, research is also needed to determine the exact protective effect of vitamin D on BC risk.

PMID:39471001 | DOI:10.31557/APJCP.2024.25.10.3349

Nucleic Acids Res. 2024 Oct 29:gkae968. doi: 10.1093/nar/gkae968. Online ahead of print.

ABSTRACT

With the escalating crisis of bacterial multidrug resistance, anti-virulence therapeutic strategies have emerged as a highly promising alternative to conventional antibiotic treatments. Anti-virulence compounds are specifically designed to target virulence factors (VFs), disarming pathogens without affecting bacterial growth and thus reduce the selective pressure for resistance development. However, due to the complexity of bacterial pathogenesis, no anti-virulence small molecules have been approved for clinical use thus far, despite the documentation of hundreds of potential candidates. To provide valuable reference resources for drug design, repurposing, and target selection, the virulence factor database (VFDB, http://www.mgc.ac.cn/VFs/) has systematically collected public data on anti-virulence compounds through extensive literature mining, and further integrated this information with its existing knowledge of bacterial VFs. To date, the VFDB has curated a comprehensive dataset of 902 anti-virulence compounds across 17 superclasses reported by 262 studies worldwide. By cross-linking the current knowledge of bacterial VFs with information on relevant compounds (e.g. classification, chemical structure, molecular targets and mechanisms of action), the VFDB aims to bridge the gap between chemists and microbiologists, providing crucial insights for the development of innovative and effective antibacterial therapies to combat bacterial infections and address antibiotic resistance.

PMID:39470738 | DOI:10.1093/nar/gkae968

Ann Bot. 2024 Oct 29:mcae191. doi: 10.1093/aob/mcae191. Online ahead of print.

ABSTRACT

BACKGROUND: Modern biotechnology is one of the last century's major advances in human science. Particularly in the agronomical field, the landscape of crop improvement technologies has witnessed a great expansion, driven by the integration of molecular and genetic engineering methodologies into the breeding toolbox. Latin America (LATAM) serves as a pioneering region in incorporating such techniques with several countries swiftly embracing these technologies.

SCOPE: This review aims to give a comprehensive overview of the elements that influenced agrobiotech acceptance in LATAM countries and how such cases could provide support for upcoming technologies to be considered worldwide.

CONCLUSIONS: Nearly 50 years of biotech breakthroughs have provided humankind with an impressive portfolio of tools already integrated into several life-sciences areas. The agronomical field has greatly progressed thanks to technologies derived from Genetically Modified Organisms (GMOs) and high promises are being made to also incorporate genome -editing products. LATAM's case is a prime example of how early introduction of novelties in the crop production chain can result in improved yields, paving the way for future developments to be easily integrated into the technological ecosystem of a region. The example set by LATAM can also be useful for the present gene-editing regulatory scenario. With several countries presently on the path to approving these methods in their current crop systems, basing their next steps on the southern continent's example, could represent a safe and practical pathway towards a new agronomical revolution.

PMID:39470392 | DOI:10.1093/aob/mcae191

Plant Cell Physiol. 2024 Oct 29:pcae112. doi: 10.1093/pcp/pcae112. Online ahead of print.

NO ABSTRACT

PMID:39470365 | DOI:10.1093/pcp/pcae112

J Urol. 2024 Oct 29:101097JU0000000000004305. doi: 10.1097/JU.0000000000004305. Online ahead of print.

ABSTRACT

PURPOSE: Patients with Ta low-grade (LG) non-muscle invasive bladder cancer (NMIBC) rarely develop metastases or die from it. Long-term data are scant and length of follow-up poorly defined.

MATERIAL AND METHODS: This retrospective study included 521 patients diagnosed with primary TaLG (n=491) or papillary urothelial neoplasm of low malignant potential (PUNLMP, n=30) from 1989-2019 at an Academic center. Patient data was acquired using patient records chart review and a bladder cancer informatics registry at the center. Risk of recurrence, progression in stage, to muscle invasion, metastases and death due to BC were analyzed. RNAseq assessed the transcriptomic profiles of four TaLG that metastasized. Interobserver variability in pathological grading (WHO 2004/2022 and 1973, n=80) was blindly assessed by three expert pathologists.

RESULTS: Median follow-up was 9.6 (95%CI: 8.6-10.2) years. Among 521 patients (73% men, median age 67.0 years), 350 recurred, 57 progressed in stage, 20 developed metastases, and 15 died from BC (median of 9.6 years after diagnosis). Cancer-specific survival probabilities were 0.99, 0.98 and 0.96 at 5-, 10- and 15- years, respectively. Fifty patients who were recurrence-free for the first 5 years developed late recurrences and 2 of them died of BC. Metastatic TaLG had more adverse transcriptomic findings in keeping with higher grade tumors despite phenotypically similar to indolent tumors. Grading concordance for the 2004/2022 system and WHO 1973 was 0.78 (95%CI: 0.65-0.90) and 0.41 (95%CI: 0.32-0.50), respectively.

CONCLUSION: This study with long-term data challenges the assumption that primary TaLG NMIBC nearly never progresses to lethal disease if followed long enough. However, the risk of BC-related mortality is extremely low in patients who are recurrence-free for the first 5 years. Minimizing variability in pathological grading remains an unmet need.

PMID:39470318 | DOI:10.1097/JU.0000000000004305

Microbiol Resour Announc. 2024 Oct 29:e0093724. doi: 10.1128/mra.00937-24. Online ahead of print.

ABSTRACT

Bulleidia sp. is a non-spore-forming, obligatory anaerobic, Gram-positive bacterium isolated from the stool samples of human colon cancer patients. We report the complete genome sequence of Bulleidia sp. 10714-15, comprising a single linear chromosome of 2,218,984 bp with a G + C content of 36.6%.

PMID:39470244 | DOI:10.1128/mra.00937-24

Antimicrob Agents Chemother. 2024 Oct 29:e0116524. doi: 10.1128/aac.01165-24. Online ahead of print.

ABSTRACT

Cephalosporin resistance in Neisseria gonorrhoeae has severely compromised the efficacy of World Health Organization (WHO)-recommended therapies. This study aimed to methodologically evaluate the optimized Six-CodonPlus assay, and additionally conducted a multicenter evaluation to assess its clinical application, especially for predicting antimicrobial resistance (AMR). For methodological evaluation, 397 sequence-known N. gonorrhoeae isolates were evaluated for specificity, 17 nongonococcal isolates were assessed for cross-reactivity, 159 uncultured urogenital swabs and urine samples were evaluated for sensitivity at the clinical level. For multicenter evaluation, 773 isolates with confirmed phenotypic data and 718 clinical urogenital swabs collected from four geographical cities were, respectively, utilized for the evaluation of AMR-prediction strategies and the clinical application of the assay. The assay accurately identified specific single-nucleotide polymorphisms in resistance-associated genes, the detection limits dropped to 10 copies/reaction for individual targets. The specificity reached 100% and no cross-reactivity occurred with double-target confirmation. The assay could be directly applied to clinical samples containing over 20 copies/reaction. Multicenter evaluation formulated two optimal strategies for decreased susceptibility prediction in specific scenarios, and one tactic for prediction of resistance and identification of FC428-like strains. High sensitivity of 86.84% (95% CI, 71.11-95.05) and specificity of 99.59% (95% CI, 98.71-99.89) for resistance prediction were demonstrated for ceftriaxone (CRO). Regarding N. gonorrhoeae identification among multicenter swabs, specificity reached 97.53% (95% CI, 95.49-98.69), and sensitivity reached 93.77% (95% CI, 90.04-96.22). The Six-CodonPlus assay exhibited excellent detection performance and formulated optimal AMR-related prediction strategy with regional adaptability, providing critical information for population screening and clinical treatment.

PMID:39470197 | DOI:10.1128/aac.01165-24