Most respiratory pathogens exhibit distinct seasonal and periodic outbreak patterns driven by climatic factors. However, predictive models that jointly consider climate, air quality index (AQI), and socioeconomic variables are lacking. We retrospectively analyzed targeted or metagenomic next-generation sequencing data from 153,544 respiratory samples collected from 1,880 centers across 30 provinces in China between September 2022 and September 2024. Monthly positivity rates were matched with geographic, climatic, AQI, and GDP data. CO(0.098 ± 0.016), HCHO(0.096 ± 0.021), O3(0.102 ± 0.019), sunshine hours(0.103 ± 0.028), wind speed(0.114 ± 0.024), and GDP(0.095 ± 0.019). were identified as the key geographical factors for the positivity across most respiratory pathogens via mean Gini index reduction, and a gradient boosting decision tree(GBDT) model was trained and benchmarked against other AI methods using the DISO metric. This model accurately simulated the epidemiological trends from September 2022 to September 2024 and outperformed alternative models with the lowest DISO metric of 0.12 in influenza A, 0.21 in SARS-CoV-2, 0.25 in RSV. The GBDT model was used to predict the short-term epidemic of 10 respiratory pathogens between October and December 2024. The predictions showed consistent trends with the external validation cohort for RNA viruses including SARS-CoV-2 and influenza A virus, but differed for bacterial pathogens. Integrating air quality, climatic, and socioeconomic data yields robust predictions of respiratory infection dynamics in the short-term by the GBDT model, bolstering public health surveillance and offering a framework potentially applicable to other infectious diseases.
The global health crisis of antimicrobial resistance necessitates the discovery of new antibacterial agents. Underexplored marine microbiomes, particularly from the biodiverse Indian coast, represent a rich potential source of antimicrobial peptides (AMPs). Targeting the urgent threat of multidrug-resistant ESKAPE pathogens, the present study aimed to computationally identify novel, membrane-active AMPs from these unique metagenomic datasets, with a focus on inhibiting Gram-negative bacteria. In this study, we computationally mined Indian marine high-resolution shotgun metagenomic datasets through quality filtering, de novo assembly, and small open reading frame prediction. An ensemble of six machine learning-based AMP prediction tools identified over 51,000 high-confidence candidate AMPs. Subsequent filtering based on physicochemical properties and AlphaFold3-predicted structures prioritized ten peptides with favourable membrane-active characteristics. Two lead candidates, c_AMP_1 and c_AMP_2, were subjected to all-atom molecular dynamics simulations within Gram-negative membrane mimetic models of Pseudomonas aeruginosa, Acinetobacter baumannii, and Klebsiella pneumoniae. Our simulations indicated distinct membrane interaction modes: c_AMP_1 adopted a stable, surface-associated α-helical orientation, while c_AMP_2 displayed a more flexible, membrane-inserting orientation in the simulations. Analysis of the MD simulations revealed distinct predicted peptide-membrane interaction profiles, characterized by specific hydrogen bonding patterns, peptide tilt angles, and membrane thinning, which collectively suggest differing biophysical interaction modes. Taken together, our work suggests the Indian marine microbiome as a promising reservoir for novel AMP candidates and suggests that an integrated computational pipeline - combining machine learning, structural biology, and biophysical simulation - may help prioritize candidate peptides for future experimental validation against critical pathogens.
Infection rates involving bacterial and viral pathogens have increased precipitously after the COVID-19 pandemic, though underlying causes remain elusive. Potential causes ranging from increased hospitalizations during the pandemic or greater use of antibiotics have been proposed, but precisely why rates remain high today remains unknown. Here, we demonstrate that decreased mitochondrial function in antigen-specific T cells post-COVID may contribute to higher infection susceptibility by metabolically immobilizing T cell responses. Using donor-matched peripheral blood samples from 31 COVID-naïve individuals who subsequently contracted COVID-19, we tracked how influenza A (IAV), Staphylococcus aureus (SA), and Varicella-zoster virus (VZV)-stimulated T cell responses were impacted by SARS-CoV-2 infection. Post-COVID CD4 memory T cells exhibited decreased activation- and increased mitochondrial redox-related gene expression. Despite this, mitochondrial flux and reactive oxygen species production were functionally limited in post-COVID antigen-specific T cells after stimulation with IAV, SA, and VZV. Post-COVID plasma was depleted in carnitine and TCA cycle species important for activating fatty acid oxidation, and this correlated with a disordered relationship between memory T cell mobilization of glycolysis, fatty acid metabolism, and oxidative phosphorylation pathways. Metabolic perturbations ultimately resulted in diminished use of catabolic, energy-generating pathways including glycolysis and fatty acid oxidation in antigen-specific T cells. Activating mitochondrial function with metformin and ubiquinol partially rescued the post-COVID decline in T cell catabolism. Collectively, these findings indicate that COVID-19 infection may inhibit T cell metabolism upon exposure to commonly encountered pathogens, which can be partly corrected with commonly available medications that activate mitochondrial metabolism. Our findings may have significant implications for the clinical care of immunologically vulnerable populations in the post-pandemic era.
Nature-based wastewater treatment systems are increasingly implemented to support water reuse in arid regions, yet their effectiveness in removing viable culturable opportunistic pathogens remains insufficiently characterized. In this exploratory, culture-based study, we assessed bacterial population dynamics across a five-stage natural wastewater treatment system (Wadi Hanifa, Riyadh, Saudi Arabia), tracking culturable bacteria from secondary-treated influent to sand-filtered effluent. Water samples were collected at five sequential treatment stages and analyzed for physicochemical parameters, total culturable bacterial abundance, bacterial diversity, taxonomic composition, and antimicrobial susceptibility of persistent isolates. Total culturable bacterial counts decreased by approximately 1.1 log10 CFU mL‒1 across the system, accompanied by an approximately 50% reduction in observed isolate richness. The fecal indicator Escherichia coli was detected only in upstream and intermediate stages (sampling locations L3.1-L3.3) and was absent from downstream samples. In contrast, the opportunistic pathogen Klebsiella pneumoniae was recovered across all five treatment stages and accounted for 44.4% (8/18) of all morphologically distinct isolates grown on the selected culture media. Turbidity declined by 71% along the treatment train and showed a strong positive correlation with bacterial richness (Kendall's τ = 0.84, p = 0.038), although this exploratory correlation should be interpreted with caution given the small sample size (n = 5 stages). Phenotypic antimicrobial susceptibility testing revealed multidrug resistance (MDR) in 62.5% (5/8) of K. pneumoniae isolates, although all remained susceptible to amikacin and meropenem. Under the conditions examined, multi-stage natural wastewater treatment substantially reduced overall bacterial abundance and diversity but did not eliminate viable, multidrug-resistant Klebsiella pneumoniae. The discordance between fecal-indicator removal and opportunistic pathogen recovery highlights system-specific limitations of indicator-based monitoring for assessing microbial safety in wastewater reuse systems. Given the limited isolate number (n = 8 K. pneumoniae) and the absence of molecular resistance-gene characterization, broader claims about wastewater as a dissemination pathway for antimicrobial resistance cannot be drawn from these data. These findings are based on a single cross-sectional sampling event and should be considered hypothesis-generating rather than confirmatory.
Global challenges associated with crop diseases and abiotic stress necessitate sustainable agricultural solutions. This study investigated the biocontrol and osmotic-stress mitigation potential of two endophytic fungi, which were isolated from native plants and subsequently identified as Aspergillus micronesiensis and Penicillium momoi. Their antagonistic activities against Fusarium oxysporum f. sp. lycopersici (FOL), F. oxysporum f. sp. radicis-lycopersici (FORL), and F. pseudograminearum (FPS) were evaluated. Complementary antagonistic mechanisms were observed: P. momoi primarily inhibited pathogen growth through direct mycelial competition, while A. micronesiensis predominantly exerted effects through antibiosis. In dual-culture assays, A. micronesiensis inhibited FOL, FORL, and FPS by 39.05%, 39.93%, and 54.59%, respectively, whereas P. momoi caused inhibition rates of 51.84%, 64.74%, and 60.66%, respectively, demonstrating strong biocontrol potential. The salt tolerance assay revealed that both endophytes were able to grow on media containing up to 3 M NaCl. Although, optimal growth for both isolates occurred at 1 M NaCl, A. micronesiensis showed a greater increase in growth relative to the control (2.06 times). In contrast, P. momoi maintained more consistent growth across the 0-1 M NaCl range. However, growth of both isolates declined at higher salt concentrations. The developed wettable powder formulation maintained high spore viability for at least 27 months under room-temperature conditions. This research highlights A. micronesiensis and P. momoi as promising agents for managing Fusarium diseases and enhancing plant salinity tolerance. Further metabolomics investigations are recommended to clarify the functional roles of these endophytes in crop protection under stress conditions.
Understanding how respiratory infectious diseases spread across cities of different socioeconomic tiers is crucial for regionally targeted interventions. However, most spatial prediction frameworks neglect the combined influence of urban hierarchy and human mobility in shaping transmission risk. We integrated large-scale intercity mobility data into an agent-based branching process model to simulate the spatial diffusion of respiratory pathogens across mainland China. Three COVID-19 outbreaks were used for validation: the Omicron outbreak in Shanghai, the Delta outbreak in Nanjing, and a multi-provincial Delta outbreak in northwestern China. We applied the framework to model the spread of SARS-CoV-2 (Omicron variant) and Influenza A to quantify tier-specific transmission risks. Tiers denote a hierarchical classification of Chinese cities based on concentration of commercial resources, transportation hub centrality, etc., ranging from super-tier metropolises to lower-tier cities. Predicted first arrival times showed strong agreement with observed data (r = 0.68 and 0.76), and mobility-based predictions more accurately identified outbreak origins than distance-based approaches. Markedly different tier-dependent diffusion patterns were observed across pathogens. Influenza A exhibited stable and stratified diffusion, with transmission confined mainly within the same or adjacent urban tiers and limited cross-tier seeding. In contrast, SARS-CoV-2 (Omicron) initially concentrated in super-tier and tier-1 cities but rapidly spread to lower-tier cities, producing a pronounced hierarchical pattern of spread that quickly diminished tier-level differences in transmission risk. Across pathogens, higher-tier cities consistently faced greater early importation risk; however, this disparity persisted for Influenza A but was rapidly attenuated for Omicron due to its high transmissibility and fast spatial expansion. A key limitation is that the model was validated against city-level first arrival times rather than full epidemic dynamics, and was parameterised using mobility data from China's "dynamic zero-COVID" period, which may limit direct quantitative generalisability to other settings. Spatial transmission risk reflects an interaction between pathogen-specific transmissibility and the hierarchical organisation of China's urban mobility system. These findings indicate that surveillance and response strategies effective for less transmissible pathogens may be insufficient for highly transmissible variants. Mobility-informed, tier-specific risk assessment may help inform early warning and support more adaptive public health responses. Because the framework relies on routinely available mobility data and minimal pathogen-specific inputs, it may provide a scalable approach for epidemic preparedness, including potential future emerging respiratory threats (Disease X).
Managing bloodstream infections in resource-constrained regions like Ethiopia is challenging due to scarce blood culture surveillance data. To guide empirical therapy, this study determines the bacterial profiles and antimicrobial resistance patterns among patients with suspected bloodstream infections at the Amhara Public Health Institute. This retrospective study analyzed blood culture records from the Amhara Public Health Institute spanning January 1, 2020, to December 30, 2023. Blood samples were processed using standardized manual culture techniques in accordance with World Health Organization (WHO) protocols. Antimicrobial susceptibility testing was performed using the Kirby-Bauer disk diffusion method following Clinical and Laboratory Standards Institute (CLSI) guidelines. Statistical analysis was conducted using SPSS version 20, employing descriptive statistics and regression models, with statistical significance defined as p < 0.05. True bacterial pathogens were isolated from 50.3% (N = 340) of the 676 patients, with Gram-negative bacteria predominating (61.2%, N = 208) over Gram-positive bacteria (38.8%, N = 132). Notably, ESKAPEE pathogens accounted for 96.5% (N = 328) of all isolates, led by Klebsiella spp. (25.9%, N = 88), Enterococcus spp. (20.9%, N = 71), and S. aureus (15.6%, N = 53). Among Gram-positive isolates, high resistance was observed against oxacillin (74.5%, N = 41), penicillin (72%, N = 36), and vancomycin (51.1%, N = 24). Gram-negative isolates exhibited critical resistance to national frontline therapeutics, including ampicillin (100%, N = 24), ceftriaxone (92.4%, N = 157), and trimethoprim-sulfamethoxazole (89.4%, N = 126). Overall, multidrug-resistant (MDR), extensively drug-resistant (XDR), and pandrug-resistant (PDR) profiles were detected in 43.8% (N = 149), 30.5% (N = 104) and 5.3% (N = 18) of isolates with similar distributions observed among ESKAPEE strains. Sex and age were the only independent predictors of culture positivity, with female sex reducing bloodstream infection odds by 44% (p = 0.002). Conversely, neonates (≤ 28 days) and young adults (15-24 years) had 4.7 times (p = 0.001) and 9.5-times (p = 0.001) higher odds compared to elderly patients. This study reveals a severe 50.3% (N = 340) bloodstream infection rate dominated by highly resistant Gram-negative and ESKAPEE pathogens, disproportionately affecting males, neonates, and young adults. Combating this threat requires immediate antibiotic stewardship, updated guidelines, and advanced laboratory testing (anaerobic culture, minimum inhibitory concentration, and molecular sequencing) to track and manage resistance.
Emerging zoonoses remain a global public health concern. Surveillance of infectious and vector-borne diseases is vital for predicting and mitigating detrimental effects of zoonotic spillover events. Beyond assessing what microorganisms are circulating in specific environments, it is important to understand how potential reservoir hosts, especially animals such as bats, participate in pathogen transmission. Bats can host and potentially spread infections caused by bacteria, viruses, fungi, and protozoa. However, bats can also act as sentinels that test positive for pathogenic microorganisms without necessarily contributing to the pathogen replication cycle. Metagenomic next-generation sequencing (mNGS) provides an efficient means to broadly screen for pathogens, although microorganism selectivity can sometimes be lower than targeted approaches. Pairing mNGS results with higher-sensitivity tests such as quantitative PCR (qPCR) can validate results and together these tools provide a relatively fast and reliable method for conducting surveillance. To test this approach, we conducted an exploratory study surveying the types of microorganisms circulating in Belize by collecting 263 blood samples from 20 different bat species captured in the Orange Walk District in 2019, 2022, and 2023. We used mNGS to initially characterize the microbial communities and qPCR to confirm presence and intensity of human pathogens of interest. We detected 1,430 different microorganisms with some relevance to human or animal health, including the protozoan Trypanosoma cruzi, which was detected in the phyllostomid bats Desmodus rotundus and Artibeus jamaicensis. qPCR confirmed the presence and intensity of Trypanosoma cruzi in mNGS-positive bat samples. We documented the types of pathogenic microorganisms circulating throughout the bat community in northern Belize to demonstrate the capacity for bats to serve as sentinels.
Invasive species can disrupt native epidemiological processes, potentially leading to the emergence of zoonotic pathogens. The relatively recent appearance and spread of the bank vole (Clethrionomys glareolus) in Ireland provides a unique model system to study these phenomena. The depauperate small mammal community in Ireland, combined with baseline data, allows us to identify the invasion gradient of C. glareolus and its effects on rodent-borne pathogens over time. A total of 498 C. glareolus and 584 Apodemus sylvaticus were sampled, via removal trapping, across nine sites in Ireland in 2016 and 2017, with six sites revisited in 2021 and 2022. 16S rRNA metabarcoding identified 10 putative pathogenic Operational Taxonomic Units (OTUs) present in these rodents, relating to four bacterial taxa, Bartonella spp., Mycoplasma coccoides, Mycoplasma haemomuris and Mycoplasma penetrans, and one family of protozoans, Sarcocystidae. Several epidemiological processes were found to be correlated with the C. glareolus invasion; firstly, C. glareolus in Ireland exhibited patterns consistent with the enemy release hypothesis, compared to native populations in France, and the native A. sylvaticus in Ireland. Secondly, a potential dilution effect, with reduced prevalence of M. haemomuris in A. sylvaticus at the C. glareolus invasion core compared to the invasion front, was observed. Finally, C. glareolus had increased prevalence of Sarcocystidae at the invasion front when compared to the invasion core, depending on the time and stage of invasion. These findings further our understanding of pathogen dynamics during biological invasions, demonstrating that invaders affect native host-pathogen communities differently as they advance through various stages of establishment.
Zoonotic neglected tropical diseases (NTDs) remain a substantial but under-recognised source of human morbidity and economic concern in the Greater Mekong Subregion, particularly in settings characterised by close human-animal interaction. This article represents a narrative synthesis of zoonotic disease research conducted in Laos and Cambodia between 2000 and 2025. The review integrates published literature with findings from long-term surveillance programmes conducted by the authors and collaborating institutions in Laos, with comparative insights from Cambodia, to examine the presence, distribution, diversity, and drivers of zoonotic pathogens at the human-animal interface. Evidence demonstrates the endemic presence of a wide range of parasitic, bacterial, and viral zoonoses, including Taenia solium, Trichinella spp., Streptococcus suis, rickettsial infections, melioidosis, hepatitis E virus, and Japanese encephalitis virus. Some of these pathogens are sustained within smallholder livestock systems, informal slaughter, farming practises, food networks, and wet market environments, where limited diagnostic capacity and fragmented surveillance obscure true disease presence. Surveillance innovations, including abattoir-based sampling, cross-sectoral serological studies, environmental surveillance approaches, and molecular diagnostic tools, have improved pathogen detection but have also highlighted persistent structural and behavioural barriers to control. Socio-cultural practices, occupational exposure, wildlife trade, and economic dependencies reinforce transmission dynamics, indicating that biomedical interventions alone are insufficient. Instead, zoonotic disease persistence reflects the interaction of livestock production systems, environmental conditions, diagnostic limitations, and entrenched human behaviours. This review emphasises the need for integrated One Health approaches that combine strengthened surveillance, improved diagnostics, behavioural interventions, and regional collaboration. Addressing zoonotic NTDs in Laos and Cambodia requires coordinated strategies that account for both biological complexity and socio-economic context to achieve sustainable disease control and improved public health outcomes.
Typhoid is a significant global health challenge due to its high pathogenicity and antimicrobial resistance. Salmonella typhi (S.typhi) can switch its lifestyles between biofilm and planktonic phase which allows it to evade host defenses and develop resistance to antibiotics. Salmonella sp. harbors multiple genes encoding efflux-pumps systems whose up-regulation contributes to multi-drug resistance (MDR) and extensive drug-resistance (XDR). To overcome the battle against resistant S. typhi strains, novel non-antibiotics inhibitors are required for inhibitory application. This study assesses the inhibitory effect of lignans against drug resistance of S. typhi. Clinical resistant and sensitive strains of S. typhi were obtained and characterized. The inhibitory effect of lignans, specifically Schisandrin A and B, purified from the plant Schisandra chinensis, are found to be effective non-antibiotic inhibitors were evaluated through standard microbiological techniques like growth curve and time-kill assays. Impact on bacterial morphology was analyzed using scanning electron microscopy (SEM). Our study explores two approaches, such as efflux pumps (EPs) inhibition and antibiofilm assays. Using colony-forming unit (CFU) assays, growth curve analysis, and SEM imaging, we observed significant bacteriostatic effects, with Schisandrin B causing notable membrane disruption. Schisandrin B also showed remarkable biofilm inhibition (90.33%) and strong efflux pumps inhibition. This study offers a strong basis for future research on addressing antibiotic resistance in clinically relevant pathogens.
C. burnetii is a Gram-negative, obligate intracellular bacterium and the causative agent of Q fever. The disease is either asymptomatic or manifests as a mild flu-like illness, but pneumonia or hepatitis might also occur. In most cases, the infection is self-limiting and the pathogen is cleared. In a small percentage of patients, the host immune system fails to eliminate the pathogen, potentially allowing the development of chronic Q fever months or even years after primary infection. The elimination of the bacteria, and thereby prevention of disease onset, would require an inflammatory response. Inflammasomes are multimeric protein complexes that induce a pro-inflammatory response to combat pathogens. Here we show that C. burnetii fails to induce strong activation of the non-canonical inflammasome, independently of its type IVB secretion system. However, the pathogen is unable to prevent external activation of the non-canonical inflammasome, which subsequently results in a reduction of the bacterial burden. Importantly, the acylation pattern of lipid A was identified to be involved in avoiding the activation of the non-canonical inflammasome. C. burnetii harbors a tetra-acylated lipid A. Modification of the C. burnetii lipid A to penta-/hexa-acylation in a small subpopulation resulted in increased secretion of IL1β and reduced bacterial load. Together, these results suggest that the acylation pattern of lipid A constitutes an important immune evasion strategy of C. burnetii by failing to activate the non-canonical inflammasome. In addition, evidence was provided that oxygen limitation arrests activation of the NLRP3 inflammasome in murine BMDM, which might prevent efficient elimination of bacteria under hypoxic conditions, such as in granulomas or in inflamed tissue.
Hypochlorite is an antiseptic that has been used for over a century for industrial sterilisation and antisepsis. More recently, the topical application of hypochlorite to severe burn patients increased their rate of survival post infection with Gram-negative bacteria, of which antisepsis cannot be solely responsible. Broth microdilution experiments were performed to confirm anti-microbial activity. Cytokine exposure was performed by dialytic exposure of serum spiked with either interleukin-6 or interleukin-10, accounting for contextually appropriate organic load. Cytokine degradation was measured by immunoassay and by functional bioassay utilising HEK-Blue cells. Hypochlorite mediated cytotoxicity against dermal cells was assessed via direct exposure, followed by a 1-hour attenuation period. Resazurin was utilised to assay the impact of hypochlorite on cell viability. We have shown that this formulation of hypochlorite in isotonic saline has multiple mechanisms. The first is that 7 mmol/L hypochlorite is capable of eliminating both Gram-negative and Gram-positive bacteria, and that the same concentration differentially degrades the function of IL-6 and IL-10. IL-6 was seen to be 3 times more susceptible to loss of function than IL-10 after only 5 minutes of exposure (P < 0.005). The asymmetrical effect on these cytokines was observed between 7 and 1.75 mmol/L, and across the entire time scale examined. This hypochlorite formulation has the capability to sterilize a wound, and by altering the cytokine profile reduce inflammation and scarring, and improve wound healing. These findings, taken with the burn survival study, suggest that the increased survival rate after application of hypochlorite could be due to the combined effect of elimination of infective pathogens, and the differential degradation of interleukin-6 and interleukin-10 at the site of injury.
Antibiotic resistance has emerged as one of the most urgent global health threats, undermining the effective treatment of bacterial infections. In response, scientific interest is increasingly focused on identifying natural and effective antimicrobial agents derived from medicinal plants. In Ethiopia, Ehretia cymosa (E. cymosa) is traditionally used to treat wound infections, fever, gastric ulcers, dysentery, and toothache. However, there is limited scientific evidence to support these traditional claims. Hence, the present study aimed to evaluate the in vitro and in vivo antibacterial activities and to screen the phytochemical profile of the 80% methanol extract of E. cymosa leaves. The air-dried and powdered leaves of E. cymosa were extracted using cold maceration with 80% methanol. The antibacterial activity of the crude extract was tested using the disk diffusion method against selected bacterial pathogens commonly associated with infections. An in vivo model of burn followed by infection was established in mice. Qualitative phytochemical screening was also performed. One-way analysis of variance followed by Tukey's post hoc multiple tests was used to compare the means of all parameters. The leaves of E. cymosa demonstrated significant antibacterial activity (p < 0.001) against the tested bacterial strains in a dose-dependent manner compared with the control. The minimum inhibitory concentration ranged from 6.25 to 75 mg/mL, while the minimum bactericidal concentration against P. aeruginosa and E. coli was 200 mg/mL. In the in vivo model, the extract resulted in faster wound contraction and a shorter epithelialization period against S. aureus than against P. aeruginosa. The plant leaf is also rich in flavonoids, terpenoids, and tannins. The 80% methanol extract of E. cymosa leaves exhibited antibacterial activity in vitro and in vivo, which corroborates the traditional use of the leaves against infectious diseases. Further studies involving the isolation and characterization of the active compounds are recommended.
Severe community-acquired pneumonia (CAP) remains a major cause of morbidity and mortality, requiring prompt empirical antibiotic therapy. The choice between amoxicillin/clavulanic acid (AMC) and third-generation cephalosporin (3GC) as first-line beta-lactam therapy in the ICU is still debated. To assess AMC and 3GC susceptibility in severe CAP or community-acquired aspiration pneumonia (CAAP) caused by Streptococcus pneumoniae (SP), Haemophilus influenzae (HI) and/or Staphylococcus aureus (SA), and to evaluate the appropriateness of empirical antibiotic therapy. We conducted a single-center retrospective study including patients admitted to the ICU between 01/01/2018 and 30/11/2022 for severe CAP/CAAP with microbiological documentation of at least one of the targeted pathogens. Clinical, microbiological, therapeutic, and outcome data were collected. The primary endpoint was AMC and 3GC susceptibility rates (expressed as percentage and [95% confidence intervals]). Among 104 included patients (median age 64 [48-71] years; 67% male), 60 (57.7%) had CAAP. AMC susceptibility rates were 81.5% [61.9-93.7], 78.0% [62.4-89.4], and 100% [92.6-100.0], while 3GC susceptibility rates were 96.3% [81.0-99.9], 95.1% [83.5-99.4], and 100% [92.6-100.0], for SP, HI, and SA, respectively. AMC was the empirical treatment in 59% of cases, and this choice was microbiologically appropriate in 86.9% of these prescriptions. Conversely, 3GC were prescribed empirically in 20% of cases, but this broad-spectrum choice was unjustified in 80% of those situations. Antibiotic de-escalation was performed in 28% of cases. In this single-center retrospective cohort, AMC appears to be a relevant empirical option for severe CAP/CAAP in the ICU, while 3GCs seem frequently overused. These findings required prospective multicenter validation before practice change can be recommended.
Controlled human infection studies play a critical role in advancing our knowledge of infectious diseases and developing therapeutics. However, these studies involve knowingly exposing research participants to pathogens, raising significant ethical, social, environmental and logistical concerns. Controlled human infection studies are being conducted in settings where individuals are economically disadvantaged and may have limited access to healthcare, education, and basic social amenities, making community engagement a central element in ensuring the ethical conduct of controlled human infection studies and the protection of participants' rights. In a cross-sectional qualitative study, we explored the views of research stakeholders on how to effectively engage local communities on controlled human infection studies. Twenty-seven key informant interviews were conducted with researchers, bioethics experts, research ethics committee members, and staff at national research regulatory bodies in Uganda between September 2023 - March 2024. A systematic inductive analysis approach was used. Due to the complexity and sensitivity of controlled human infection studies, findings reveal the necessity for early planning, adequate budgets and broad-based engagement using multiple approaches and activities. Research participants viewed the bottom-up approach as more appropriate for engaging communities. They also argued that meaningful community engagement should be a continuous process grounded in respect, justice and partnership, rather than merely a procedural or regulatory obligation. The acceptability and success of controlled human infection studies in low resource settings largely depends on effective intentional community engagement in the entire research process.
Pododermatitis (bumblefoot) is a chronic, debilitating disease of the plantar surface of the foot that affects birds of prey kept in captivity worldwide. Although bacterial pathogens, especially Staphylococcus aureus, are most commonly considered as causative agents, the contribution of opportunistic yeasts to chronic, non-healing footpad lesions remains poorly characterized. Keratinophilic yeasts may sustain the disease process by degrading keratin in superficial tissues, impairing wound healing and, owing to their thermotolerance and minimal nutritional requirements, persisting in the environment of the bird's enclosure. In this study, three captive steppe eagles (Aquila nipalensis) from a single aviary in Kazakhstan, all presenting with chronic pododermatitis unresponsive to antibacterial treatment, were investigated by integrated mycological, biochemical and molecular approaches. The yeast isolates were recovered from the deep footpad lesions and identified to species level by sequencing of the ITS1-5.8S-ITS2 rDNA region. All these isolates were assigned to Candida metapsilosis, and phylogenetic analysis confirmed their close clustering with reference C. metapsilosis sequences. Phenotypic characterization showed that all isolates were thermotolerant (growth at 8-37 °C), expressed strong urease and keratinolytic activity (the latter confirmed in vitro by the hair perforation test), high saccharolytic activity and selective, weak proteolytic activity. Disk diffusion screening showed susceptibility to azoles (ketoconazole, clotrimazole, fluconazole) and reduced susceptibility to polyenes (nystatin, amphotericin B). To our knowledge, this is the first report of C. metapsilosis isolated from chronic pododermatitis lesions in captive steppe eagles. Combined with the documented in vitro virulence-associated traits and the resolution of the lesions following targeted antifungal therapy, our findings support a contributory etiological role of C. metapsilosis as an opportunistic pathogen in raptor pododermatitis in immunocompromised birds maintained under suboptimal husbandry. Mycological work-up, including molecular identification, is therefore warranted in cases of chronic, non-resolving pododermatitis in captive birds of prey.
Herpes simplex virus (HSV) is an endemic pathogen, infecting over half of all adults world-wide. HSV infection can cause a wide spectrum of disease outcomes, ranging from asymptomatic infection or mild lesions to rare cases of infectious keratitis, encephalitis, and death. HSV genome sequences differ between individuals and within individuals. To date, the vast majority of publicly available HSV genomic data has come from Europe and North America. Populations in South America, Africa, and Asia are under-sampled, as are non-industrial (e.g., agricultural, pastoral) populations, for which the natural environment plays a large role in health and disease dynamics. We used Whatman FTA card stabilization of DNA to develop a procedure for capturing oral and genital swabs from a geographically isolated pastoralist population in a desert region of northern Namibia. This is the first study to document HSV genome sequences from this type of remote setting and these are the first HSV genomes from Namibia. The resulting HSV sequences, collected in 2015 and 2016 from remote settlements in Namibia, fit within the scope of viral genetic diversity previously defined by African strains. The methodological approaches developed in this study can be expanded to broaden viral detection, improve diagnostics, and raise public health awareness about the burden of pathogens in under-served populations.
The CAD (Cinnamyl Alcohol Dehydrogenase) gene family is a key determinant for lignin biosynthesis in plants. In legumes, CAD enzymes are involved in the development of vascular tissues such as xylem and Casparian strip and they contribute to the production of antimicrobial and antifungal compounds. Thereby, it offers defense against pathogens and pests. Despite their biological significance, a comparative genome-wide analysis of the CAD gene family in Medicago truncatula and Lotus japonicus has not been explored. Therefore, we conducted a comparative genome-wide study to investigate the characteristics and potential role of CAD genes in these two model legume species. A total of 51 CAD genes were identified in M. truncatula (MtCAD) and 35 in L. japonicus (LjCAD). The CAD proteins are prominently characterized by ADH_N and ADH_zinc_N domains that were distributed in 8 and 6 chromosomes of MtCAD and LjCAD, respectively. Structural organization and conserved motif analysis indicated notable similarities between MtCAD and LjCAD proteins. However, considering the ancestry and functionality and based on the evolutionary analysis, LjCAD showed more similarities with Arabidopsis than MjCAD. Gene duplication analysis identified twelve duplicated gene pairs in MtCAD and eight in LjCAD, including both tandem and segmental duplication events. Most MtCAD and LjCAD were found in the cytoplasm with some of the cis-acting regulatory elements associated with stress responses. Gene Ontology annotation suggested that most MtCAD genes were associated with biological processes whereas LjCAD genes are mainly enriched in molecular functions. Both MtCAD and LjCAD showed potential roles in secondary metabolite production. Three substantial transcription factor families such as bZIP, C2H2, and ERF and several unique microRNAs were predicted to target MtCAD and LjCAD in regulating their gene expression against certain abiotic stressors for instance cold, freezing, drought, and heat. The MtCAD and LjCAD expressed highly in stress-responsive tissues such as nodule, root, immature flower, seed, and leaf. Meanwhile, RNA-sequencing data further highlighted several potential stress-responsive genes. In M. truncatula, The MtCAD1, MtCAD3, MtCAD9, MtCAD15, MtCAD23, MtCAD27, and MtCAD47 exhibited higher expression under cold, drought, and freezing stress compared with control conditions. Whereas in L. japonicus, LjCAD6, LjCAD8, and LjCAD11 showed higher expression under cold, drought, and heat stress. Thus, these genes may serve as promising candidates for improving abiotic stress tolerance and provide molecular insights into their functional roles for future crop improvement programs and experimental validation.
As tick-borne disease cases continue to increase over time, there is a growing need to understand the ecological and epidemiological factors that contribute to disease risk. North Carolina is currently experiencing a rise in cases, yet tick-borne research in the state remains limited. In this study, we developed a framework for a community science program in collaboration with 22 county public health agencies to recruit participants to submit incidentally encountered ticks. As part of kit submissions, participants also completed a form describing where and when they encountered the tick, as well as the behaviors that led to the encounters. Submitted ticks were tested for several putative bacterial pathogens, including Borrelia burgdorferi, Ehrlichia spp., and Rickettsia amblyommatis. We additionally assessed how advertising methodology and frequency by county health agencies influenced tick kit submissions and evaluated correlations between agency perceptions of project performance and submission rates. Over two years, we received 444 ticks across 319 unique submissions. While species distributions were largely consistent with prior observations, we report the first published instance of Amblyomma americanum within the mountainous region of NC, indicating a potential range expansion into cooler, higher-altitude areas. Relative risk modeling identified recreational activities as consistently associated with higher likelihood of tick kit submissions. Multiple advertising types appeared to influence the number of kits submitted; however, these results should be interpreted cautiously due to small sample sizes. Overall, our study demonstrates a successful collaboration with state and county health agencies to engage the community in tick-borne disease research. Future studies should build on this framework to further optimize participation.