Multiple Pathogens Research Articles

The circulating characteristics of common respiratory pathogens in Ningbo, China, both before and following the cessation of COVID-19 containment measures

To assess the circulating characteristics of common respiratory pathogens following the complete relaxation of non-pharmaceutical interventions (NPIs) and the cessation of the dynamic zero-COVID policy. The retrospective analysis was conducted from 14,412 patients with acute respiratory infections (ARIs) from January 24, 2020, to December 31, 2023, including Influenza A virus (IFV-A), Influenza B virus (IFV-B), Respiratory Syncytial Virus (RSV), Human Rhinovirus (HRV), Human Parainfluenza Virus (HPIV), Human Metapneumovirus (HMPV), Human Coronavirus (HCoV), Human Bocavirus (HBoV), Human Adenovirus (HAdV), and Mycoplasma pneumoniae (MP). Compared with 2020–2022, Joinpoint analysis indicated a monthly increase in overall pathogen activity in 2023, rising from an average of 43.05% to an average of 68.46%. The positive rates of IFV-A, IFV-B, HMPV, HPIV, HCoV, and MP increased, while those of HRV and RSV decreased, and no differences in HAdV and HBoV. The outbreak of IFV-A and MP was observed, the positive rate of MP has surpassed pre-COVID-19 pandemic levels and the spread of RSV was interrupted by IFV-A. Infants and toddlers were primarily infected by HRV and RSV, Children and adolescents exhibited a higher prevalence of infections with MP, IFV-A, and HRV, whereas Adults and the elderly were primarily infected by IFV-A. The incidence of co-infections rose from 4.25 to 13.73%. Restricted cubic spline models showed that the susceptible age ranges for multiple pathogens expanded. These changes serve as a reminder to stay alert in the future and offer clinicians a useful guide for diagnosing and treating.

Oral Microbial Changes in Oral Squamous Cell Carcinoma: Focus on Treponema denticola, Lactobacillus casei, and Candida albicans

Background and Objectives: In this study, we aimed to explore the oral bacteria and fungi that can help discern oral squamous cell carcinoma (OSCC) and investigate the correlations between multiple key pathogens. Materials and Methods: Twelve participants (8 females and 4 males; mean age, 54.33 ± 20.65 years) were prospectively recruited into three groups: Group 1: healthy control, Group 2: patients with stomatitis, and Group 3: patients with OSCC, with 4 individuals in each group. Unstimulated whole saliva samples from these participants were analyzed using real-time PCR to assess the presence and abundance of 14 major oral bacterial species and Candida albicans. Results: The analysis revealed significant differences for certain microorganisms, namely, Treponema denticola (T. denticola), Lactobacillus casei (L. casei), and Candida albicans. T. denticola was most abundant in the OSCC group (5,358,692.95 ± 3,540,767.33), compared to the stomatitis (123,355.54 ± 197,490.86) and healthy control (9999.21 ± 11,998.40) groups. L. casei was undetectable in the healthy control group but was significantly more abundant in the stomatitis group (1653.94 ± 2981.98) and even higher in the OSCC group (21,336.95 ± 9258.79) (p = 0.001). A similar trend was observed for C. albicans, with DNA copy numbers rising from the healthy control (464.29 ± 716.76) to the stomatitis (1861.30 ± 1206.15) to the OSCC group (9347.98 ± 5128.54) (p = 0.006). The amount of T. denticola was positively correlated with L. casei (r = 0.890, p < 0.001) and C. albicans (r = 0.724, p = 0.008). L. casei’s DNA copy number was strongly correlated with C. albicans (r = 0.931, p < 0.001). These three oral microbes exhibited strong positive correlations with each other and had various direct or indirect relationships with other species. Conclusions: In the OSCC group, T. denticola, L. casei, and C. albicans exhibited strong positive correlations with one another, further emphasizing the need for a deeper understanding of the complex microbial interactions in the OSCC environment.

Gene co-expression analysis reveals conserved and distinct gene networks between resistant and susceptible Lens ervoides challenged by hemibiotrophic and necrotrophic pathogens

As field crops are likely to be challenged by multiple pathogens during their development, the investigation of broad-spectrum resistance in the host is of great interest for crop genetic enhancement. In this study, we attempted to address this question by adopting a weighed gene co-expression approach to study the temporal transcriptome dynamics of resistant and susceptible recombinant inbred lines (RILs) derived from an intraspecific Len ervoides cross during the infection process with either the necrotrophic pathogens Ascochyta lentis or Stemphylium botryosum, or the hemibiotrophic pathogen Colletotrichum lentis. By comparing networks of resistant and susceptible RILs, seven network module pairs were found to possess high correlation coefficients (R > 0.70) and large number of overlapping genes (n > 100). The conserved co-regulation of genes in these network module pairs were involved in plant cell wall synthesis, cell division, cytoskeleton organization, and protein ubiquitin related processes and appeared to be common disease responses against these pathogens. On the other hand, we also identified eight modules with low correlation between resistance and susceptibility networks. Among those, a stronger gene co-expression in R-genes and small RNA processes in the resistant hosts may be enhancing L. ervoides resistance against A. lentis, C. lentis, and S. botryosum, whereas the higher level of synergistic regulation in the synthesis of arginine and glutamine and phospholipid and glycerophospholipids in the susceptible hosts may contribute to increased susceptibility in L. ervoides.

Electron-Beam-Killed Staphylococcus Vaccine Reduced Lameness in Broiler Chickens

Broiler chicken lameness caused by bacterial chondronecrosis with osteomyelitis (BCO) is presently amongst the most important economic and animal welfare issues faced by the poultry industry, and the estimated economic loss is around USD 150 million. BCO lameness is associated with multiple opportunistic bacterial pathogens inhabiting the respiratory and gastrointestinal tracts. In cases of immune deficiency resulting from stress, injury, or inflammation of the tissue, opportunistic pathogens, mainly Staphylococcus spp., can infiltrate the respiratory or gastrointestinal mucosa and migrate through the bloodstream to eventually colonize the growth plates of long bones, causing necrosis that leads to lameness. This is the first report of developing a Staphylococcus vaccine against BCO lameness disease in broiler chickens. Electron beam (eBeam) technology causes irreparable DNA damage, preventing bacterial multiplication, while keeping the epitopes of the cell membrane intact, helping the immune system generate a more effective response. Our results show a 50% reduction of lameness incidence in the eBeam-vaccinated chicken group compared to the control. Additionally, the eBeam-vaccinated chickens present higher titer of anti-Staphylococcus IgA, signifying the development of an efficient and more specific humoral immune response. Our data establish the eBeam-killed Staphylococcus vaccine as an effective approach to reducing the incidence of lameness in broiler chickens.

Phenazine-1-carboxamide Regulates Pyruvate Dehydrogenase of Phytopathogenic Fungi to Control Tea Leaf Spot Caused by Didymella segeticola.

Due to a lack of understanding of the disease epidemiology and comprehensive control measures, tea leaf spot caused by Didymella segeticola has a significant negative impact on tea yield and quality in the tea plantations of Southwest China. Phenazine-1-carboxamide (PCN) is a phenazine compound derived from Pseudomonas species, which exhibits antimicrobial activity against various pathogens. However, its inhibitory mechanism is not yet clear. The current study evaluated the inhibitory activity of PCN against various phytopathogenic fungi and found that PCN has inhibitory activity against multiple pathogens, with a half-maximal effective concentration (EC50) value for D. segeticola of 16.11 μg/mL in vitro and a maximum in-vivo curative activity of 72.28% toward tea leaf spot. Morphological changes in the hyphae after exposure to PCN were observed through microstructure and ultrastructure analysis, and indicated that PCN causes abnormalities in the hyphae, such as cytoplasmic coagulation, shortened hyphal inter-septum distances, and unclear boundaries of organelles. Transcriptomic analysis revealed that PCN upregulated the expression of genes related with energy metabolism. PCN significantly reduced the ATP concentration in the hyphae and decreased mitochondrial membrane potential. Molecular docking analysis indicated that PCN binds to one of the candidate target proteins, pyruvate dehydrogenase, with lower free energy of -10.7 kcal/mol. This study indicated that PCN can interfere with energy metabolism, reducing ATP generation, ultimately affecting hyphal growth. Overall, PCN shows potential for future application in the control of tea leaf spot due to its excellent antifungal activity and unique mode of action.

Unravelling the Current Status of Rice Stripe Mosaic Virus: Its Geographical Spread, Biology, Epidemiology, and Management

Rice stripe mosaic virus (RSMV) belongs to the Cytorhabdovirus species in the Rhabdoviridae family. Recently, RSMV was widely spread in East Asia and caused severe yield losses. RSMV is transmitted by the planthopper vectors, Recilia dorsalis, Nephotettix virescens, and Nilaparvata lugens, that mostly affect rice. The adult vectors can hibernate, transmit the virus, lay eggs on rice plants, and, finally, multiply in subsequent generations, resulting in new infection outbreaks. RSMV-infected rice varieties display striped mosaicism, mild dwarfism, stiff and twisted leaves, delayed heading, short panicles with large unfilled grains, and yield reduction. In nature, the infection of multiple pathogens in the same host is widespread, which is defined as co-infection. It can be antagonistic or synergistic. Pathological synergistic effects between RSMV and other viruses can generate strains with new genetic characteristics, leading to unpredictable epidemiological consequences. After the first identification of RSMV in 2015, significant advancements in understanding the disease’s characteristics, symptoms, cycles, geographic distribution, potential vectors, and synergistic interaction, as well as its management strategies, were developed. To reduce the damage due to RSMV infection, many scientists have recommended pest control techniques to target adult vectors. It is also essential to confirm the actual time of monitoring, development of resistant varieties, and changes in cultivation systems. Due to the limitations of the conventional plant disease control technologies, improvements in efficiency and safety are in high demand. Therefore, to find efficient and environmentally safe controls to mitigate these challenges, reviews of research are the foremost step. In this review, we summarize the basic epidemiological information about the origin of RSMV and its infection symptoms in the field, synergistic interaction with viruses during co-transmission, yield losses, formulation of the disease cycle, and control strategies from several case studies. Finally, we recommend the formulation of the disease cycle and management strategies of RSMV infection.

Emydomyces testavorans Surveillance in Multiple Free-Ranging Terrestrial and Aquatic Chelonian Species in Illinois, USA.

The order Onygenales contains multiple fungal pathogens that affect free-ranging and zoo-housed reptilian species. Emydomyces testavorans, an onygenalean fungus associated with skin and shell disease, has been sporadically detected in aquatic chelonians. Because of the recent discovery of this organism, little is known about its prevalence in free-ranging chelonians. The objective of this study was to perform surveillance for E. testavorans in six free-ranging aquatic and terrestrial chelonian species in Illinois, USA: Blanding's turtles (n=437; Emydoidea blandingii), painted turtles (n=199; Chrysemys picta), common snapping turtles (n=35; Chelydra serpentina), red-eared sliders (n=62; RES; Trachemys scripta elegans), eastern box turtles (n=73; Terrapene carolina carolina) and ornate box turtles (n=29; Terrapene ornata). Combined cloacal-oral swabs (COSs) or shell (carapace and plastron surfaces) swabs were collected from 2019 to 2021 and tested for E. testavorans using quantitative PCR. The PCR detected E. testavorans in COSs of an adult male, subadult female, and juvenile male Blanding's turtle (0.6%; 95% confidence interval [CI], 0.2-1.9%) and a shell swab from an adult female RES (1.6%; 95% CI, 0-8.7%). Shell lesions consistent with E. testavorans infection were present in two of the positive Blanding's turtles. These results document the rarity of this pathogen on the landscape in Illinois. Additional studies should determine this pathogen's impact on individuals and clarify its significance for conservation efforts of Blanding's turtle, in which E. testavorans has not been reported previously.

High phenotypic diversity correlated with genomic variation across the European Batrachochytrium salamandrivorans epizootic.

Recognizing the influence of pathogen diversity on infection dynamics is crucial for mitigating emerging infectious diseases. Characterising such diversity is often complex, for instance when multiple pathogen variants exist that interact differently with the environment and host. Here, we explore genotypic and phenotypic variation of Batrachochytrium salamandrivorans (Bsal), an emerging fungal pathogen that is driving declines among an increasing number of European amphibian species. For thirteen isolates, spanning most of the known temporal and geographical Bsal range in Europe, we mapped phenotypic diversity through numerous measurements that describe varying reproductive rates in vitro across a range of temperatures. Bsal isolates are revealed to have different thermal optima and tolerances, with phenotypic variation correlating with genomic diversity. Using a mechanistic niche model of the fire salamander (Salamandra salamandra) as an example, we illustrate how host steady-state body temperature and Bsal thermal range variation may influence pathogen growth through space and time across Europe. Our combined findings show how the identity of emergent pathogen variants may strongly influence when and which host populations are most at risk.

A Novel Secreted Protein of Fusarium oxysporum Promotes Infection by Inhibiting PR-5 Protein in Plant.

Fusarium oxysporum, an important soilborne fungal pathogen that causes serious Fusarium wilt disease, secretes diverse effectors during the infection. In this study, we identified a novel secreted cysteine-rich protein, FolSCP1, which contains unknown protein functional domain. Here, we characterized FolSCP1 as a secreted virulence factor that promotes the pathogen infection of host plants by inhibiting diverse plant defence responses. FolSCP1 interacted with the pathogenesis-related 5 (PR-5) protein SlPR5, a positive regulator of tomato plant immunity against multiple tomato pathogens, and effectively attenuated the antifungal activity of the tomato PR-5 protein. FoSCP1, a homologue of FolSCP1, was secreted by a F. oxysporum isolate from infected tobacco and targeted the tobacco PR-5 protein NtPR5 to suppress plant defence for further infection. In summary, our study revealed a fungal virulence strategy in which F. oxysporum secrete effectors that interfere with plant immunity by binding to the PR-5 protein of the host plant and inhibiting its biological activity, thereby promoting fungal infection.

Nationwide Survey of Vector-Borne Diseases in Rodents and Mites in Korea: Anaplasma, Ehrlichia, and Rickettsia.

Rodents are reservoirs for zoonotic pathogens, making it essential to study both rodents and their ectoparasites. In 2022 and 2023, we investigated the spatial distribution of rodents and their mites across Korea, focusing on three vector-borne diseases (VBDs): Anaplasma, Ehrlichia, and Rickettsia. A total of 835 wild rodents were collected from 16 locations, each consisting of five distinct environmental settings (mountains, waterways, reservoirs, fields, and paddy fields), with 20 traps per setting, totaling 100 Sherman live folding traps per site. Each rodent was identified using a taxonomic key, and post-mortem examinations led to the collection of 7971 mites (498 pools), followed by PCR analysis. Among the rodents, Anaplasma phagocytophilum was detected in 10.3%, Ehrlichia muris in 0.5%, Ehrlichia ruminantium in 0.2%, and Rickettsia raoultii in 2.9%. In mites, A. phagocytophilum was found in 8.8%, E. muris in 0.2%, R. raoultii in 0.2%, R. endosymbiont in 1.6%, and R. australis in 1.2%. This study marks the first detection of E. muris and R. raoultii in Korean rodents and the first global discovery of E. ruminantium in rodents. The detection of multiple pathogens in mites worldwide highlights the importance of continuous VBD monitoring to mitigate public health risks.

Clinical performance evaluation of the BioFire Joint Infection Panel.

The BioFire Joint Infection (JI) Panel offers a significant advancement in the rapid diagnosis of joint infections by facilitating the simultaneous detection of multiple bacterial and fungal pathogens, as well as resistance markers, directly from synovial fluid samples. An article published in the Journal of Clinical Microbiology by Moran et al. (J Clin Microbiol 62:e00182-24, 2024, https://doi.org/10.1128/jcm.00182-24) presents both prospective and retrospective analyses of the panel's real-world clinical application. The study highlights the panel's benefits, such as its rapid turnaround time and ability to identify challenging pathogens, while also discussing its limitations, particularly in detecting certain off-panel organisms.

A multi-pathogen behavioral exposure model for young children playing in public spaces in developing communities.

Diarrheal disease is the second leading cause of death among children under five in developing communities, despite active interventions to improve access to water, sanitation, and hygiene resources. Even interventions with high fidelity and compliance saw minimal improvements in health outcomes, necessitating a need for looking beyond traditionally targeted exposure pathways. This study focuses on the pathogen exposure a young child may receive while playing in the public spaces of informal settlements, where animal feces, human feces, and garbage are frequently observed. The study utilized 79 soil samples previously collected across ten cluster sites in Corail, Haiti and processed using DelAgua cultural assays and quantitative Polymerase Chain Reaction methods. Molecular assays screened for Aeromonas, Vibrio cholera, and several pathogenic Escherichia coli species. Behavioral observations of young children (<5 years old) were also conducted in overlapping areas with the environmental sampling to quantify frequency of risky and mitigating behaviors. Environmental and behavioral data were combined to obtain the posterior distribution of children's pathogen exposure from playing in a public space for one hour. The model estimated that children have a likelihood of approximately 70% of being exposed to a pathogen during one hour of play and a greater than 30% chance of being exposed to multiple pathogens in the same period. While children and toddlers practice fewer risky behaviors compared to infants, they were shown to have higher likelihood of exposure and slightly higher pathogen dose per exposure. As anticipated, a high correlation between genes from the same E. coli species was observed in the model output. These findings demonstrate the need to consider public spaces as an important exposure pathway for young children for both future research and interventions.

Castanet: a pipeline for rapid analysis of targeted multi-pathogen genomic data.

Target enrichment strategies generate genomic data from multiple pathogens in a single process, greatly improving sensitivity over metagenomic sequencing and enabling cost-effective, high-throughput surveillance and clinical applications. However, uptake by research and clinical laboratories is constrained by an absence of computational tools that are specifically designed for the analysis of multi-pathogen enrichment sequence data. Here we present an analysis pipeline, Castanet, for use with multi-pathogen enrichment sequencing data. Castanet is designed to work with short-read data produced by existing targeted enrichment strategies, but can be readily deployed on any BAM file generated by another methodology. Also included are an optional graphical interface and installer script. In addition to genome reconstruction, Castanet reports method-specific metrics that enable quantification of capture efficiency, estimation of pathogen load, differentiation of low-level positives from contamination, and assessment of sequencing quality. Castanet can be used as a traditional end-to-end pipeline for consensus generation, but its strength lies in the ability to process a flexible, pre-defined set of pathogens of interest directly from multi-pathogen enrichment experiments. In our tests, Castanet consensus sequences were accurate reconstructions of reference sequences, including in instances where multiple strains of the same pathogen were present. Castanet performs effectively on standard computers and can process the entire output of a 96-sample enrichment sequencing run (50M reads) using a single batch process command, in $<$2 h. Source code freely available under GPL-3 license at https://github.com/MultipathogenGenomics/castanet, implemented in Python 3.10 and supported in Ubuntu Linux 22.04. The data underlying this article are available in Europe Nucleotide Archives, at https://www.ebi.ac.uk/ena/browser/view/PRJEB77004.

Diagnostic Accuracy of the LabTurbo QuadAIO Common Flu Assay for Detecting Influenza A Virus, Influenza B Virus, RSV, and SARS-CoV-2.

Background: The coronavirus disease 2019 (COVID-19) pandemic has highlighted the urgent need for rapid and accurate diagnostic tools for upper respiratory tract infections (URTIs). Nucleic acid amplification tests (NAATs) have transformed URTI diagnostics by enabling the rapid detection of multiple pathogens simultaneously, thereby improving patient management and infection control. This study aimed to evaluate the diagnostic accuracy of the LabTurbo QuadAIO Common Flu Assay compared to that of the Xpert Xpress CoV-2/Flu/RSV Plus Assay for detecting SARS-CoV-2, Influenza A, Influenza B, and respiratory syncytial virus (RSV). Methods: A retrospective diagnostic accuracy study was conducted using nasopharyngeal samples from patients. Samples were tested using the LabTurbo QuadAIO Common Flu Assay and the comparator Xpert Xpress CoV-2/Flu/RSV Plus Assay. Positive and negative percent agreements (PPA and NPA) were calculated. Results: The LabTurbo Assay demonstrated a PPA of 100% and an NPA of 100% for SARS-CoV-2, Influenza A, and Influenza B, whereas it showed a PPA of 100% and an NPA of 98.3% for RSV. Conclusions: The LabTurbo QuadAIO Assay exhibited high diagnostic accuracy for detecting multiple respiratory pathogens, including SARS-CoV-2, Influenza A, Influenza B, and RSV. Despite the slight discrepancy in the NPA for RSV, the overall performance of the LabTurbo Assay supports its integration into routine diagnostic workflows to enhance patient management and infection control.

B-201 Clinical Performance Evaluation of IRON-qPCR™ RV, a Novel Molecular POCT system, for the Qualitative Detection of Respiratory Viruses in Nasopharyngeal Swab

Abstract Background The availability of Point-of-Care testing (POCT) based on molecular diagnostics to test simultaneously for multiple respiratory viruses is very limited though significant progress has been made in molecular testing for COVID-19 during the pandemic. Considering the similar symptoms presented by patients infected with various respiratory pathogens, it is crucial to have multiple POCT systems capable of detecting multiple respiratory pathogens while distinguishing SARS-CoV-2 from other pathogens. To meet the growing demand for multiplex testing for respiratory pathogens, a molecular POCT, IRON-qPCR™ RV has been developed. IRfON-qPCR™ RV is a multiplex real-time RT-PCR assay designed for the qualitative detection and differentiation of SARS-CoV-2, Influenza A, Influenza B, RSV-A, and RSV-B RNA from human nasopharyngeal swab specimens. The IRON-qPCR™ proceeds the entire process automatically from nucleic acid extraction to real-time RT-PCR within 40 minutes. The main goal of this study is to evaluate the clinical performance of IRON-qPCR™ RV in comparison with other assays and kits using nasopharyngeal swab samples. Methods To assess the clinical performance of the IRON-qPCR™ RV, specimen collection and evaluation were conducted at a clinical institution in France, utilizing a total of 980 nasopharyngeal swab samples. The comparators used were the Xpert® Xpress CoV-2/Flu/RSV plus Kit and the RealStar® RSV RT-PCR Kit 3.0. Since RSV subtypes are not distinguished by the Xpert kit, all RSV without subtype distinction were compared. Additionally, RealStar kit was used to compare the results of IRON-qPCR™ RV for RSV subtypes A and B. Clinical samples showing discrepancies between Xpert and RealStart, and the IRON-qPCR™ RV were further analyzed using Allplex™ SARS-CoV-2/FuA/FluB/RSV Assay and sequencing. Results Through the comparison of clinical performance of the IRON-qPCR™ RV with Xpert for SARS-CoV-2, Influenza A, and Influenza B in nasopharyngeal swab samples, the clinical sensitivity was analyzed to be over 95.5%, and the clinical specificity was over 99.6%. For RSV, compared to Xpert, the clinical sensitivity was analyzed to be 96.9%, and the clinical specificity was 98.9%. Furthermore, in comparison with RealStar, the clinical sensitivity and specificity of IRON-qPCR™ RV for RSV-A were determined to be 96.2% and 100%, respectively, and the clinical sensitivity and specificity for RSV-B were 96.0% and 100%. Additionally, discrepant samples in comparison with Xpert were further tested using the Allplex as a resolver kit. The result showed that the clinical sensitivity and specificity of IRON-qPCR™ RV for SARS-CoV-2, Influenza A, and Influenza B were over 98.3% and 100%. For RSV, the clinical sensitivity and specificity were 99.5% and 99.1%. Conclusions The clinical performance of IRON-qPCR™ RV was analyzed with the clinical sensitivity of over 95% and the clinical specificity of over 99%. Upon analysis including the results of the resolver kit for discrepant samples, increased clinical sensitivity and specificity were determined. The results of this study strongly support that the IRON-qPCR™ RV is a reliable POCT system for the simultaneous detection and differentiation of multiple respiratory viruses. Furthermore, it is applicable to district hospitals as well as clinical laboratories for accurate and timely testing.

B-206 Tick-borne disease molecular testing positivity and coinfection incidence in the northeastern united states: 2021-2023

Abstract Background The CDC estimates that Lyme disease affects hundreds of thousands of people each year in the United States. Tick-borne diseases caused by pathogens such as Anaplasma phagocytophilum, Babesia microti, Ehrlichia chaffeensis, and species of Borrelia follow a seasonal pattern due to the life cycle of disease-carrying ticks. In endemic areas, like the northeastern United States, the risk of coinfection by multiple tick-borne disease pathogens is higher and can complicate patient treatment. For example, while Anaplasma and Borrelia can be treated with doxycycline a Babesia coinfection would not be resolved with this medication. In this study, we performed a retrospective analysis of tick-borne disease molecular testing results to monitor positivity rates and incidence of coinfection. Methods This retrospective analysis included whole blood specimens submitted to a regional clinical laboratory in the northeastern United States for tick-borne disease molecular testing. Test results from 2021-2023 were analyzed for positivity rate trends and coinfection incidence. DNA was isolated from patient specimens and tested using laboratory developed real-time Taq polymerase PCR assays. Results Positivity rates for all tick-borne disease pathogens studied followed typical seasonal patterns (Table). Beginning in the early spring, as nymphs ended their dormancy and began to feed, infection rates of tick-borne disease climbed. Infections peaked in mid-summer and remained elevated through late autumn. For Anaplasma, a biphasic pattern was observed, with a smaller peak in late autumn when adult ticks are most active. Coinfections with Anaplasma and Babesia were observed in 136 specimens, while coinfections with Borrelia and Babesia were observed in 145 specimens. Conclusions Positivity rates for tick-borne disease pathogens followed expected seasonal patterns in the northeastern US. The incidence of coinfections involving Babesia microti highlights the importance of properly identifying tick-borne infections given the different treatment regimens indicated.

Modelling multiplex testing for outbreak control

During the SARS-CoV-2 pandemic, polymerase chain reaction (PCR) and lateral flow device (LFD) tests were frequently deployed to detect the presence of SARS-CoV-2. Many of these tests were singleplex, and only tested for the presence of a single pathogen. Multiplex tests can test for the presence of several pathogens using only a single swab, which can allow for: surveillance of more pathogens, targeting of antiviral interventions, a reduced burden of testing, and lower costs. Test sensitivity however, particularly in LFD tests, is highly conditional on the viral concentration dynamics of individuals. To inform the use of multiplex testing in outbreak detection it is therefore necessary to investigate the interactions between outbreak detection strategies and the differing viral concentration trajectories of key pathogens. Viral concentration trajectories are estimated for SARS-CoV-2, and Influenza A/B. Testing strategies for the first five symptomatic cases in an outbreak are then simulated and used to evaluate key performance indicators. Strategies that use a combination of multiplex LFD and PCR tests achieve; high levels of detection, detect outbreaks rapidly, and have the lowest burden of testing across multiple pathogens. Influenza B was estimated to have lower rates of detection due to its modelled viral concentration dynamics. Data availability statementThe SARS-CoV-2 viral load trajectory data may be accessed by contacting Killingley et. al. The influenza A/B viral load trajectory may be accessed at https://github.com/bcowling/pediatric-vaccine-trial/tree/master/data.

Comparative analysis of antifungal properties in medicinal plant extracts for sustainable agriculture

The escalating environmental repercussions of pesticide use in pest and disease management underscore the urgency for alternative strategies. One promising avenue involves harnessing natural antifungal properties present in plant extracts. This study aimed to assess the antifungal efficacy of aqueous and ethanolic extracts from five medicinal plants, viz., C. sativa L., S. moorcraftiana L., S. nigrum L., F. vesca L., and R. pseudoacacia, which were screened for their antifungal activity against various soil-borne fungi, viz., A. niger, A. flavus, A. terreus, R. stolonifer, M. mucedo, F. oxysporum, A. alternata, P. notatum, C. cladosporioides, and C. lunata. Phytochemical analysis exhibited the presence of phenols, alkaloids, tannins, flavonoids, quinines, and terpenoids. Results revealed potent antifungal activity across all tested fungi, significantly inhibiting mycelial growth compared to control. S. nigrum and C. sativa extracts exhibited the highest efficacy against multiple fungal pathogens. The inhibition in mycelial growth in ethanolic and aqueous plant extracts of C. sativa against A. niger varies between 3.00 mm to 6.00 mm and 4.00 mm–6.33 mm, against A. flavus 3.33 mm–11.66 mm and 4 mm–12.66 mm, A. terreus (3.00 mm–6.00 mm and 3.66 mm–7.00 mm), R. stolonifer (3.00 mm–5.33 and 3.66 mm–6.33 mm), M. mucedo (8.33 mm–17.66 mm and 9.66 mm–18.66 mm), F. oxysporum (6.66 mm–12.33 mm and 7.33 mm–13.33 mm), A. alternata (4.66 mm–11.33 mm and 5.33 mm–14.00 mm), P. notatum (9.33 mm–23.00 mm and 9.66 mm–24.33 mm), C. cladosporioides (4.33 mm–8.66 mm and 5.33 mm–9.66 mm), and C. lunata (14.00 mm–20.33 mm and 17.00 mm–21.33 mm) in different concentrations of plant extracts respectively. Likewise, the inhibition in mycelial growth in ethanolic and aqueous plant extracts of S. nigrum against A. niger at different concentrations varies between 8.00 mm to 17.66 mm and 9.00 mm–18.66 mm, A. flavus (8.33 mm–12.66 mm and 9 mm–14 mm), A. terreus (2.33 mm–5.66mm and 3 mm–7 mm), R. stolonifer (13.33 mm–20.33 mm and 17.66 mm–24.66 mm), M. mucedo (10.66 mm–12.00 mm and 11.66 mm–13.00 mm), F. oxysporum (15.66 mm–22.33 and 18.00 mm–24.00 mm), A. alternata (10.66 mm–13.00 mm and 11.66 mm–14.00 mm), P. notatum (5.33 mm–13.33 mm and 6.33 mm–18.66 mm, C. cladosporioides (3.33 mm–7.66 mm and 4.00 mm–8.00 mm), and C. lunata (3.66 mm–6.33 mm and 4.66 mm–6.66 mm), respectively. These findings suggest that these plant extracts have the potential to be natural fungicides, providing promising alternatives for disease management in agriculture.

Viability discrimination of bacterial microbiomes in home kitchen dish sponges using propidium monoazide treatment.

Dish sponges are known to support the proliferation of human bacterial pathogens, yet they are commonly used by consumers. Exposure to foodborne pathogens via sponge use may lead to illness, a serious concern among susceptible populations. The extent of exposure risks from sponge use has been limited by constraints associated with culture-independent or dependent methods for bacterial community characterization. Therefore, five used dish sponges were characterized to evaluate the presence of viable bacterial foodborne pathogens using the novel application of propidium monoazide (PMA) treatment and targeted 16S rRNA gene amplicon sequencing. Select pathogen viability was confirmed using targeted selective enrichment. The taxonomic abundance profiles of total and viable sponge microbiomes did not vary significantly. The numbers of unique bacterial species (p = 0.0465) and foodborne pathogens (p = 0.0102) identified were significantly lower in viable sponge microbiomes. Twenty unique bacterial foodborne pathogens were detected across total and viable sponge microbiomes, and three to six viable foodborne pathogens were identified in each sponge. Escherichia coli and Staphylococcus aureus were identified in each viable sponge microbiome, and viable E. coli were recovered from two sponges via targeted selective enrichment. These findings suggest that sponge-associated bacterial communities are primarily viable and contain multiple viable bacterial foodborne pathogens.

Pathogen distribution and infection patterns in pediatric severe pneumonia: A targeted next-generation sequencing study

ObjectiveSevere pneumonia in children represents a significant clinical challenge due to its high incidence and associated mortality. This study aimed to assess the distribution of pathogens and patterns of infection in pediatric patients with severe pneumonia. MethodsThis study included 110 pediatric patients diagnosed with severe pneumonia, who were admitted to Guangxi Maternal and Child Health Hospital between July 2021 and November 2023. Pathogen-targeted next-generation sequencing (tNGS) was employed to identify respiratory pathogens in these cases. ResultsPathogens were detected in 109 out of 110 cases, yielding a positive detection rate of 99.09%. Among these cases, 25 (22.72%) involved single-pathogen infections, while 84 (76.36%) were characterized by mixed infections. The infection pattern in children with severe pneumonia was relatively common with bacterial-viral coinfection (28.2%, 31/110). A total of 39 pathogens were identified from the 110 children with severe pneumonia, with the top three pathogens being Mycoplasma pneumoniae (30.91%, 34/110), Human Respiratory Syncytial Virus Type A (26.36%, 29/110), and Human Herpesvirus (18.18%, 20/110). Notably, 38.2% (13/34) of the cases were found to have macrolide-resistant Mycoplasma pneumoniae (MRMP). Additionally, 40% (44/110) of the children required admission to the intensive care unit (ICU). ConclusionThe application of tNGS demonstrates significant utility in the detection of pathogens in pediatric patients with severe pneumonia. The predominant pathogens identified in this study are Mycoplasma pneumoniae, Human Respiratory Syncytial Virus, and Human Herpesvirus. Furthermore, mixed infections involving multiple pathogens were observed in 76.36% of the cases, and a substantial proportion (40%) of these patients necessitated intensive care.