Disease Pathogen Research Articles

A novel vaccine construct against Zika virus fever: insights from epitope-based vaccine discovery through molecular modeling and immunoinformatics approaches.

The Zika virus (ZIKV) is an emerging virus associated with the Flaviviridae family that mainly causes infection in pregnant women and leads to several abnormalities during pregnancy. This virus has unique properties that may lead to pathological diseases. As the virus has the ability to evade immune response, a crucial effort is required to deal with ZIKV. Vaccines are a safe means to control different pathogenic infectious diseases. In the current research, a multi-epitope-based vaccination against ZIKV is being designed using in silico methods. For the epitope prediction and prioritization phase, ZIKV polyprotein (YP_002790881.1) and flavivirus polyprotein (>YP_009428568.1) were targeted. The predicted B-cell epitopes were used for MHC-I and MHC-II epitope prediction. Afterward, several immunoinformatics filters were applied and nine (REDLWCGSL, MQDLWLLRR, YKKSGITEV, TYTDRRWCF, RDAFPDSNS, KPSLGLINR, ELIGRARVS, AITQGKREE, and EARRSRRAV) epitopes were found to be probably antigenic in nature, non-allergenic, non-toxic, and water soluble without any toxins. Selected epitopes were joined using a particular GPGPG linker to create the base vaccination for epitopes, and an extra EAAAK linker was used to link the adjuvant. A total of 312 amino acids with a molecular weight (MW) of 31.62762 and an instability value of 34.06 were computed in the physicochemical characteristic analysis, indicating that the vaccine design is stable. The molecular docking analysis predicted a binding energy of -329.46 (kcal/mol) for TLR-3 and -358.54 (kcal/mol) for TLR-2. Moreover, the molecular dynamics simulation analysis predicted that the vaccine and receptor molecules have stable binding interactions in a dynamic environment. The C-immune simulation analysis predicted that the vaccine has the ability to generate both humoral and cellular immune responses. Based on the design, the vaccine construct has the best efficacy to evoke immune response in theory, but experimental analysis is required to validate the in silico base approach and ensure its safety.

Analysis of the causes of sheep endoparasites in farms of the Luga district of the Leningrad region

This article reflects current data on the assessment of the epizootic situation for the main endoparasitoses of small cattle in two peasant (farm) farms of the Luga district of the Leningrad region with similar animal conditions. The level of extensive invasion (EI) of sheep by pathogens of parasitic diseases was established, and the age and seasonal dynamics of the spread were studied. The level of infection of livestock with strongylates of the gastrointestinal tract with an EI of 87-97%, protostrongylidoses of the genus Mullerius (M. capillaris) with EI – 53%, tapeworms of the genus Moniezia (M. expansa) – 69%, trematodes Fasciola hepatica with EI – 24-28% and eimeria with EI – 96-98%. The analysis of the causes of diseases in the territories of the studied farms was carried out, and the main mechanisms of transmission of pathogens to susceptible animals were considered. A number of violations of the conditions of keeping small cattle in the conditions of the farms under study were identified: crowded livestock, untimely change of bedding and manure cleaning, keeping young animals together with adult animals, as well as violations of microclimate conditions (reduced air velocity and increased concentration of inert gases harmful to animals). In addition, an important factor in the spread of pathogens of invasive diseases among animals on the farms under study is the deworming of livestock without taking into account the characteristics of the life cycle of parasites and the timing of their preimaginal stages, as well as the duration of endogenous and exogenous stages of development of protozoa of the Eimeria genus.Thus, causal relationships in the occurrence and circulation of pathogens of invasive diseases of small cattle among livestock in the territory of the farms of the Luga district of the Leningrad region were studied and determined, taking into account the climatic and geographical features of the area and the seasons of the year

BEECH FORESTS OF THE "VYZHNYTSKYI NATIONAL NATURAL PARK": CURRENT SANITARY CONDITION AND PROBLEMS OF PRESERVATION

The beech primeval forests of the Vyzhnytskyi National Natural Park are a unique cultural heritage and play a special role for the Carpathian region and Ukraine as a whole, therefore they are strictly protected in the territories of the nature reserve fund, performing ecological, educational and scientific-cognitive functions. In this regard, monitoring the current state of the beech forests of the Vyzhnytskyi National Natural Park and highlighting the problem of their preservation becomes relevant. In the course of conducting research, classical and modern methods of forestry research were used, as well as specific methods of phytosanitary monitoring and comparative ecology. The massif of primeval beech forests of the Vyzhnytskyi National Natural Park is characterized by a remarkable diversity of fungi. We identified fruiting bodies of wood-destroying fungi on the trunks of beech trees: Fomes fomentarius (L. ex Fr.) Gill., Daedalea quercina L. ex Fr., Phellinus igniarius (L.: Fr.) Quel, Laetiporus sulphureus (Bull.: Fr.) Bond. et Sing., Coriolus versicolor (L.) Quél., Stereum hirsutum (Willd.) Pers., Daldinia concentrica (Bolton) Ces. & De Not., Аrmillariella mellea (Vahl) P.Karst., and Pleurotus ostreatus (Jacq.) P.Kumm. Groups of Coprinus micaceus (Fr.) and Hypholoma capnoides (Fr. ex Fr.) Kumm were noted near rotten beech stumps. We also came across a unique find the invasive red-listed Clathrus archeri (Berk.) Dring. In the course of surveys, fruiting bodies of typical representatives of the marsupial class Xylaria polymorpha (Pers.) Grev., and Xylaria hypoxylon (L.: Fr.) Grev). Representatives of xylophilic ascomycetes were identified on the dead trunk of a European beech Bisporella citrina (Batsch) Korf et S.E. Carp. Symptoms of dieback of central shoots and side branches, dieback of European beech bark, which is directly related to the vital activity of Nectria ditissima Tul., were recorded. & C.Tul. Cumulative manifestations of infectious and non-infectious pathologies were noted. The problems of preserving the beech forests of the Vyzhnytskyi National Natural Park should include: intensive and uncontrolled economic activity; irresponsible behavior of tourists (arson, mechanical damage, littering, poaching, etc.); construction of highways and tourist centers in the immediate vicinity of primeval forests; damage to forest stands due to atmospheric air pollution, climate change; significant spread of pests or pathogens of forest diseases; danger of forest fires; recreational load and livestock grazing. Given the role and importance of the beech forests of the Vyzhnytskyi National Natural Park, a comprehensive study of the forest systems is necessary to preserve these unique resources.

Weather-related changes in the dehydration of respiratory droplets on surfaces bolster bacterial endurance

HypothesisThe study shows for the first time a fivefold difference in the survivability of the bacterium Pseudomonas Aeruginosa (PA) in a realistic respiratory fluid droplet on fomites undergoing drying at different environmental conditions. For instance, in 2023, the annual average outdoor relative humidity (RH) and temperature in London (UK) is 71 % and 11 °C, whereas in New Delhi (India), it is 45 % and 26 °C, showing that disease spread from fomites could have a demographic dependence. Respiratory fluid droplet ejections containing pathogens on inanimate surfaces are crucial in disease spread, especially in nosocomial settings. However, the interplay between evaporation dynamics, internal fluid flow and precipitation and their collective influence on the distribution and survivability of pathogens at different environmental conditions are less known. ExperimentsShadowgraphy imaging is employed to study evaporation, and optical microscopy imaging is used for precipitation dynamics. Micro-particle image velocimetry (MicroPIV) measurements reveal the internal flow dynamics. Confocal imaging of fluorescently labelled PA elucidates the bacterial distribution within the deposits. FindingsThe study finds that the evaporation rate is drastically impeded during drying at elevated solutal concentrations, particularly at high RH and low temperature conditions. MicroPIV shows reduced internal flow under high RH and low temperature (low evaporation rate) conditions. Evaporation rate influences crystal growth, with delayed efflorescence and extending crystallization times. PA forms denser peripheral arrangements under high evaporation rates and shows a fivefold increase in survivability under low evaporation rates. These findings highlight the critical impact of environmental conditions on pathogen persistence and disease spread from inanimate surfaces.

YOLOv8's advancements in tuberculosis identification from chest images.

Tuberculosis (TB) is a chronic and pathogenic disease that leads to life-threatening situations like death. Many people have been affected by TB owing to inaccuracy, late diagnosis, and deficiency of treatment. The early detection of TB is important to protect people from the severity of the disease and its threatening consequences. Traditionally, different manual methods have been used for TB prediction, such as chest X-rays and CT scans. Nevertheless, these approaches are identified as time-consuming and ineffective for achieving optimal results. To resolve this problem, several researchers have focused on TB prediction. Conversely, it results in a lack of accuracy, overfitting of data, and speed. For improving TB prediction, the proposed research employs the Selection Focal Fusion (SFF) block in the You Look Only Once v8 (YOLOv8, Ultralytics software company, Los Angeles, United States) object detection model with attention mechanism through the Kaggle TBX-11k dataset. The YOLOv8 is used for its ability to detect multiple objects in a single pass. However, it struggles with small objects and finds it impossible to perform fine-grained classifications. To evade this problem, the proposed research incorporates the SFF technique to improve detection performance and decrease small object missed detection rates. Correspondingly, the efficacy of the projected mechanism is calculated utilizing various performance metrics such as recall, precision, F1Score, and mean Average Precision (mAP) to estimate the performance of the proposed framework. Furthermore, the comparison of existing models reveals the efficiency of the proposed research. The present research is envisioned to contribute to the medical world and assist radiologists in identifying tuberculosis using the YOLOv8 model to obtain an optimal outcome.

Identification, Genetic Characterization, and Pathogenicity of Three Feline Herpesvirus Type 1 Isolates from Domestic Cats in China.

(1) Background: Feline herpesvirus (FHV-1) is a significant pathogen in cats, causing respiratory and ocular diseases with consequential economic and welfare implications. (2) Methods: This study aimed to isolate and characterize FHV-1 from clinical samples and assess its pathogenicity. We collected 35 nasal and ocular swabs from cats showing symptoms of upper respiratory tract infection and FHV positivity detected by polymerase chain reaction (PCR). Viral isolation was carried out using feline kidney (F81) cell lines. Confirmation of FHV-1 presence was achieved through PCR detection, sequencing, electron microscopy, and indirect immunofluorescence assay. The isolated strains were further characterized by evaluating their titers, growth kinetics, and genetic characteristics. Additionally, we assessed the pathogenicity of the isolated strains in a feline model, monitoring clinical signs, viral shedding, and histopathological changes. (3) Results: Three strains of FHV-1 were isolated, purified, and identified. The isolated FHV-1 strains exhibited high homology among themselves and with domestic isolates and FHV-1 viruses from around the world. However, they showed varying degrees of virulence, with one strain (FHV-A1) causing severe clinical signs and histopathological lesions. (4) Conclusion: This study advances our understanding of the genetic and pathogenic characteristics of FHV-1 in China. These findings underscore FHV-A1 isolate as a potentially ideal candidate for establishing a challenge model and as a potential vaccine strain for vaccine development.

Alterations to metabolic hormones in amyotrophic lateral sclerosis and frontotemporal dementia postmortem human tissue.

Metabolic changes are observed in patients with both amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Although regulation of metabolic processes in the CNS is predominantly carried out within the hypothalamus, extra-hypothalamic CNS areas contain metabolic hormone receptors, including those for leptin (LEPR), insulin (INSR), and neuropeptide Y (NPY), indicating that they may play a role in biological processes underlying pathogenic disease processes. The status of these hormones within regions vulnerable in ALS/FTD is not well described. This study sought to determine whether the expression of these hormones and their receptors is altered in pathology-rich regions in cases of human FTD (superior frontal gyrus and insular cortex) and ALS (primary motor cortex and lumbar spinal cord) with TDP-43 pathology compared to matched healthy controls. LEPR mRNA was increased within the superior frontal gyrus of FTD cases and within primary motor cortex and lumbar spinal cord of ALS cases; INSR mRNA was increased in superior frontal gyrus and insular cortex of FTD cases. NPY protein was decreased in primary motor cortex and lumbar spinal cord of ALS cases. Our results demonstrate that metabolic hormones undergo complex alterations in ALS and FTD and suggest that these hormones could play critical roles in the pathogenesis of these diseases.

Comprehensive profiling of social mixing patterns in resource poor countries: A mixed methods research protocol.

Low-and-middle-income countries (LMICs) bear a disproportionate burden of communicable diseases. Social interaction data inform infectious disease models and disease prevention strategies. The variations in demographics and contact patterns across ages, cultures, and locations significantly impact infectious disease dynamics and pathogen transmission. LMICs lack sufficient social interaction data for infectious disease modeling. To address this gap, we will collect qualitative and quantitative data from eight study sites (encompassing both rural and urban settings) across Guatemala, India, Pakistan, and Mozambique. We will conduct focus group discussions and cognitive interviews to assess the feasibility and acceptability of our data collection tools at each site. Thematic and rapid analyses will help to identify key themes and categories through coding, guiding the design of quantitative data collection tools (enrollment survey, contact diaries, exit survey, and wearable proximity sensors) and the implementation of study procedures. We will create three age-specific contact matrices (physical, nonphysical, and both) at each study site using data from standardized contact diaries to characterize the patterns of social mixing. Regression analysis will be conducted to identify key drivers of contacts. We will comprehensively profile the frequency, duration, and intensity of infants' interactions with household members using high resolution data from the proximity sensors and calculating infants' proximity score (fraction of time spent by each household member in proximity with the infant, over the total infant contact time) for each household member. Our qualitative data yielded insights into the perceptions and acceptability of contact diaries and wearable proximity sensors for collecting social mixing data in LMICs. The quantitative data will allow a more accurate representation of human interactions that lead to the transmission of pathogens through close contact in LMICs. Our findings will provide more appropriate social mixing data for parameterizing mathematical models of LMIC populations. Our study tools could be adapted for other studies.

Cytogenetic and Genomic Characterization of a Novel Wheat-Tetraploid Thinopyrum elongatum 1BS⋅1EL Translocation Line with Stripe Rust Resistance.

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is a destructive wheat disease pathogen. Thinopyrum elongatum is a valuable germplasm including diploid, tetraploid, and decaploid with plenty of biotic and abiotic resistance. In a previous study, we generated a stripe rust-resistant wheat-tetraploid Th. elongatum 1E/1D substitution line, K17-841-1. To further apply the wild germplasm for wheat breeding, we selected and obtained a new homozygous wheat-tetraploid Th. elongatum translocation line, T1BS⋅1EL, using genomic in situ hybridization, fluorescence in situ hybridization (FISH), oligo-FISH painting, and the wheat 55K single nucleotide polymorphism genotyping array. The T1BS⋅1EL is highly resistant to stripe rust at the seedling and adult stages. Pedigree and molecular marker analyses revealed that the resistance gene was located on the chromosome arm 1EL of tetraploid Th. elongatum, tentatively named Yr1EL. In addition, we developed and validated 32 simple sequence repeat markers and two kompetitive allele-specific PCR assays that were specific to the tetraploid Th. elongatum chromosome arm 1EL to facilitate marker-assisted selection for alien 1EL stripe rust resistance breeding. This will help us explore and locate the stripe rust resistance gene mapping on the 1E chromosome and deploy it in the wheat breeding program.

Natural Prenylflavonoids from Sophora flavescens Root Bark against Multidrug-Resistant Methicillin-Sensitive Staphylococcus aureus Targeting the Membrane Permeability.

The overuse of antibiotics in animal farming and aquaculture has led to multidrug-resistant methicillin-sensitive Staphylococcus aureus (MR-MSSA) becoming a common pathogen in foodborne diseases. Sophora flavescens Ait. serves as a traditional plant antibacterial agent and functional food ingredient. A total of 30 compounds (1-30) were isolated from the root bark of S. flavescens, consisting of 20 new compounds (1-20). In the biological activity assay, compound 1 demonstrated a remarkable inhibitory effect on MR-MSSA, with an MIC of 2 μg/mL. Furthermore, 1 was found to rapidly eliminate bacteria, inhibit biofilm growth, and exhibit exceptionally low cytotoxicity. Mechanistic studies have revealed that 1 possesses an enhanced membrane-targeting ability, binding to the bacterial cell membrane components phosphatidylglycerol (PG), phosphatidylethanolamine (PE), and cardiolipin (CL). This disruption of bacterial cell membrane integrity increases intracellular reactive oxygen species, protein and DNA leakage, reduced bacterial metabolism, and ultimately bacterial death. In summary, these findings suggest that compound 1 holds promise as a lead compound against MR-MSSA.

First Report of Rust Caused by Puccinia sasicola on Corylopsis coreana in South Korea.

Korean winter hazel (Corylopsis coreana) is an endemic species of the South Korea (Seo et al. 2016; Kim et al. 2021), which is cultivated as an ornamental plant in this country, but also in China and Japan (Yoon et al. 2016). In July 2022, typical symptoms of a rust disease were observed on C. coreana at Jirisan National Park (35°22'07.7"N 127°34'57.7"E) in Namwon, South Korea. Spermogonia were epiphyllous, densely grouped, pale brown or orange-yellow, round, and 0.23 - 0.38 × 0.19 - 0.41 mm in size. Aecia were hypophyllous, mostly densely grouped, yellow or pale orange, resembling small wart-like galls, and 0.04 - 0.06 × 0.89 - 1.68 mm in size. Aeciospores were hyaline, mostly angularly globose, ellipsoid or oblong-ellipsoid, and 17.8 - 25.2 × 15 - 26.5 μm (average 19.2 × 19.1 μm; n=50) in size. Aeciospore walls were echinulate-verrucose, and 1.1 - 2.2 µm (average 1.7 µm; n=50) in thickness. In December 2022, dark brown telia were observed on the lower surface of Sasa borealis leaves near C. coreana. Telia were mostly scattered but often compacted, brown to dark brown, round, and 1.5 - 1.95 × 1.24 - 1.55 mm in size. Teliospores were either one- or two-celled with a long tapering apex, and light brown to brown in color. One-celled teliospores were globose, and 95.1 - 186.5 × 20.5 - 36.4 μm (average 136.4 × 27.7 μm; n=50) in size. Two-celled teliospores were ellipsoid-cylindrical, and 111.4 - 180.3 × 13.5 - 32.6 μm (average 149 × 21.1 μm; n=50) in size. Side walls of teliospores were golden and 2.2 - 5.5 µm thick (average 3.5 µm; n=50), and pedicels were hyaline, measuring 150 - 300 μm long. Uredinial stage was not observed. Disease symptomology and pathogen morphology were mostly consistent with that of Puccinia sasicola reported in Japan (Hino. 1955). For phylogenetic analysis, genomic DNA was extracted from the aeciospores collected from C. coreana and the teliospores collected from S. borealis. The internal transcribed spacer (ITS) rDNA and the large subunit (LSU) rDNA regions were amplified using ITS5u/ITS4rust (Pfunder and Schürch 2001) and LRust1R/LRust3 (Beenken et al. 2012) primers, respectively. Both sequences were identical for the spores collected from the two different hosts. The sequences were deposited in GenBank (PP171665, PP174211 [ITS], PP171709, PP174356 [LSU]). A GenBank BLAST search revealed 89.53% and 96.78% similarity with Puccinia kusanoi (KX610657) and Puccinia sp. (MT7298241) for ITS and LSU sequences, respectively. In maximum-likelihood phylogenetic analysis of ITS and LSU sequences, the isolates from C. coreana and S. borealis formed a separate clade from other Puccinia species. To test Koch's postulates, leaf disks with telia from S. borealis were directly attached to the adaxial surface of six healthy C. coreana leaves with tape. As controls, healthy S. borealis leaf disks were attached to the adaxial surface of six C. coreana leaves. After four weeks, four inoculated leaves developed small yellow wart-like galls on the abaxial surface, while the control leaves remained symptom-free. The isolates obtained from the inoculated leaves had identical sequences to the original isolate. There are no publicly available sequences for P. sasicola, nor did we find any sequences that match our Puccinia samples. Nevertheless, based on morphological characteristics and life cycle, our isolates closely matched with the previous description of P. sasicola by Hino (1955). To our knowledge, this is the first report of P. sasicola causing leaf rust in C. coreana in South Korea.

First report of large-berry coffee (Coffea liberica) anthracnose caused by Colletotrichum kahawae in China.

Large-berry coffee (Coffea liberica) is one of the three cultivated coffee species and a precious breeding germplasm in China (Yan et al, 2019). Anthracnose is a damaging epidemic disease on coffee worldwide (Mohammed et al. 2015). Between June and September 2022, anthracnose was observed on coffee plants in Puer area, Yunnan, China and disease incidence (% plants diseased) of 8.5%-28.2% was recorded in the field. The disease symptoms were observed at all growth stages. Lesions on leaves were circular or oval, with a white to gray central zone outlined by a brown margin and surrounded by a chlorotic halo, Φ5.1-18.5 mm; some lesions extended and coalesced later to form large, blighted areas, leading to complete leaf senescence, defoliation and bare blighted branches on heavily infected trees. The spots on coffee berries were oval or fusiform, sunken and brown-black; diseased berries became gray-black and dried-out but remained on the tree. Leaves with typical anthracnose lesions were collected from fields in Simao ( 22.07°E,100.98°N) to isolate the pathogen. Leaf pieces (5×5mm) from the lesion margin were cut, surface-sterilized with 75% ethanol and 2% NaClO, and cultured on PDA at 25°C. Three isolates with the same colony morphology were obtained by hyphal tip purification. Detached and intact leaves of 6-month coffee seedlings were inoculated with Φ5mm mycelial discs of the isolates. Anthracnose lesions developed on the inoculated leaves, with all 3 isolates, 7d after incubation in a growth chamber (25°C, > 90% RH and lighting 8 h/d at 11000 lux). Pathogens with the same colony morphology as those of the original isolates were re-isolated from the infected tissues of inoculated leaves, thus fulfilling Koch's Postulates. The ITS sequence (PP550861) for the isolate was PCR-amplified and Blast-n analyses showed 100 % (554/554bp) identity to Colletotrichum kahawae LWTJ01; so they were the same population and coded as KFTJ02. The actin (ACT), calmodulin(CAL), glyceraldehydes-3-phosphate dehydrogenase (GAPHD) and histone 3 (HIS3) genes (Qiu et al. 2020) were amplified from one of KFTJ02 isolates, sequenced and deposited in NCBI GenBank (OR842543, OR842544, OR842545 & OR842546). A phylogenetic tree was generated based on the concatenated sequences of the four genes and those of related Colletotrichum spp. using MEGA 6.0 and KFTJ02 clustered in the same clade with C. kahawae IMI319418 on the tree (Bootstrap sup.=88%). When cultured at 25°C on PDA for 7 days, its colonies were near round or ovoid, gray-white, contoured, Φ73.2-80.1 (76.2±2.3)mm or growth rate 10.2-11.1(8.1) mm/d (n=10). The hyphae were hyaline, septated, branching at near right angles. Conidial masses formed 14 days after incubation. The conidia were elliptical, hyaline, monocellular, 10.2-15.5 (12.7±1.06)×3.8-5.2 (4.3±0.52) µm (n=50). The appressoria were black-brown, oval or irregular, 7.8-9.3 (8.5±0.81)μm (n= 50). These morphological characteristics were consistent with those of C. kahawae (Bridge et al, 2008). Therefore, KFTJ02 was identified as C. kahawae, which has been found to infect Camellia oleifera, Areca catechu and Ficus microcarpa (Wei et al, 2023; Zhang et al, 2020; Lin 2023). The coffee berry disease pathogen (C. kahawae) is a quarantine species which has not been recorded and so it is first reported on coffee crops in China. Results of the present study provide important references for further studies on this disease.

Lessons Learned from the Sea Star Wasting Disease Investigation.

Marine invertebrate mass mortality events (MMEs) threaten biodiversity and have the potential to catastrophically alter ecosystem structure. A proximal question around acute MMEs is their etiologies and/or environmental drivers. Establishing a robust cause of mortality is challenging in marine habitats due to the complexity of the interactions among species and the free dispersal of microorganisms from surrounding waters to metazoan microbiomes. The 2013-2014 sea star wasting disease (SSWD) MME in the northeast Pacific Ocean highlights the difficulty in establishing responsible agents. In less than a year of scientific investigation, investigators identified a candidate agent and provided at the time convincing data of pathogenic and transmissible disease. However, later investigation failed to support the initial results, and critical retrospective analyses of experimental procedures and reinterpretation of early findings disbanded any candidate agent. Despite the circuitous path that the investigation and understanding of SSWD have taken, lessons learned from the initial investigation-improving on approaches that led to misinterpretation-have been successfully applied to the 2022 Diadema antillarum investigation. In this review, we outline the history of the initial SSWD investigation, examine how early exploration led to spurious interpretations, summarize the lessons learned, provide recommendations for future work in other systems, and examine potential links between the SSWD event and the Diadema antillarum MME.

The role of microbiological monitoring in the prevention and control of antibiotic resistance

The article deals with the problem of antibiotic resistance of opportunistic microorganisms. The aim of the study is to determine the predominant microflora of a medical organization and to develop protocols for empirical antibacterial therapy in infectious and inflammatory processes. The main groups of infectious agents in the departments for the treatment of patients with new coronavirus infection of the Oryol region «Botkin City Hospital» for 2020–2022 are analyzed. Isolation, identification and determination of antibiotic sensitivity were carried out using standard methods. The results of the study made it possible to identify priority microorganisms and assess their antibiotic resistance. The growth of resistance to carbapenems of microorganisms isolated from patients in 2020–2021 was revealed. The effect obtained from the correction of antibiotic therapy has been shown, which has significantly reduced the resistance of isolated strains to carbapenems. To ensure effective epidemiological surveillance of clinically significant microorganisms and curb the growth of antimicrobial resistance in medical organizations of the Orel region, it is important to consider the possibility of maintaining a regional medical information system in order to monitor the prevalence of potential pathogens of infectious diseases, including those related to the provision of medical care resistant to antimicrobial drugs.

Review of antibiotic agents active against infectious mastitis pathogens

The effectiveness of animal treatment largely depends on correctly selected veterinary drugs. In recent years, there has been a decrease in the activity of antimicrobial agents against both gram-positive and gram-negative microorganisms. This trend is associated with the natural processes of adaptation of bacteria to living conditions. Once inside the animal’s body, bacterial cells react flexibly to both the immune response and treatment with antimicrobial agents. In cases where medical care was provided with antibiotics with low activity against a specific pathogen, there was a failure to comply with deadlines or deviations from the treatment regimen, some bacterial cells may not only not die, but also acquire drug resistance. Surviving microorganisms can change the type of colonial growth, the shape of the shell (many modern studies are devoted to L-forms of bacteria, which are formed under the influence of unfavorable factors, including antibiotics) or acquire new qualities through mutational changes. It is these processes that drive the emergence of bacterial strains resistant to antimicrobial drugs. As a result, many treatment regimens cease to give the desired result, since they include drugs whose active components do not have the proper bactericidal effect on resistant strains. In order for the treatment of animals to have therapeutic effectiveness, careful monitoring of antimicrobial agents and the compilation of an up-to-date list of them is necessary, based on the active substances and drug resistance of pathogens of infectious diseases. Thus, reviews of effective antibiotic therapy are a current area of veterinary medicine.

Identification of genetic markers of resistance to macrolide class antibiotics in Mannheimia haemolytica isolates from a Saskatchewan feedlot.

Mannheimia haemolytica is a major contributor to bovine respiratory disease (BRD), which causes substantial economic losses to the beef industry, and there is an urgent need for rapid and accurate diagnostic tests to provide evidence for treatment decisions and support antimicrobial stewardship. Diagnostic sequencing can provide information about antimicrobial resistance genes in M. haemolytica more rapidly than conventional diagnostics. Realizing the full potential of diagnostic sequencing requires a comprehensive understanding of the genetic markers of antimicrobial resistance. We identified genetic markers of resistance in M. haemolytica to macrolide class antibiotics commonly used for control of BRD. Genome sequences were determined for 99 M. haemolytica isolates with six different susceptibility phenotypes collected over 2 years from a feedlot in Saskatchewan, Canada. Known macrolide resistance genes estT, msr(E), and mph(E) were identified in most resistant isolates within predicted integrative and conjugative elements (ICEs). ICE sequences lacking antibiotic resistance genes were detected in 10 of 47 susceptible isolates. No resistance-associated polymorphisms were detected in ribosomal RNA genes, although previously unreported mutations in the L22 and L23 ribosomal proteins were identified in 12 and 27 resistant isolates, respectively. Pangenome analysis led to the identification of 79 genes associated with resistance to gamithromycin, of which 95% (75 of 79) had no functional annotation. Most of the observed phenotypic resistance was explained by previously identified antibiotic resistance genes, although resistance to the macrolides gamithromycin and tulathromycin was not explained in 39 of 47 isolates, demonstrating the need for continued surveillance for novel determinants of macrolide resistance.IMPORTANCEBovine respiratory disease is the costliest disease of beef cattle in North America and the most common reason for injectable antibiotic use in beef cattle. Metagenomic sequencing offers the potential to make economically significant reductions in turnaround time for diagnostic information for evidence-based selection of antibiotics for use in the feedlot. The success of diagnostic sequencing depends on a comprehensive catalog of antimicrobial resistance genes and other genome features associated with reduced susceptibility. We analyzed the genome sequences of isolates of Mannheimia haemolytica, a major bovine respiratory disease pathogen, and identified both previously known and novel genes associated with reduced susceptibility to macrolide class antimicrobials. These findings reinforce the need for ongoing surveillance for markers of antimicrobial resistance to support improved diagnostics and antimicrobial stewardship.

Drug design of new anti-EBOV inhibitors: QSAR, homology modeling, molecular docking and molecular dynamics studies

Ebola virus disease is a deadly pathogenic disease with a fatality rate of 25–90 % as recorded in previous outbreaks. The Ebola Virus glycoprotein (EBOV-GP) plays a crucial role in the entry of viruses into human cells, making it an interesting target for therapeutic discovery. Therefore, inhibiting this protein can directly limit the virus replication and disease progression at an early stage of infection. The present study focuses on the design of novel potent EBOV-GP inhibitors using multiple computational techniques. In this context, two QSAR models were built from a set of 86 amodiaquine derivatives as anti-EBOV-GP using Monte Carlo and genetic algorithm multiple linear regression methods. Both models confirmed their predictive performance with satisfactory statistical parameters of the validation (R2 = 0.9129; Q2 = 0.8848 for the CORAL model and R2 = 0.8848; Q2 = 0.8148 for the GA-MLR model). From the outputs of the CORAL model, the structural fragments responsible for increasing and decreasing the inhibition activity were extracted and interpreted. This molecular information was used to design 26 new potentially safe and active candidate drugs. Molecular docking and dynamics simulations have affirmed the efficacy of the designed compounds. Specifically, compounds D2 (pIC50_coral = 7.12; pIC50_GA-MLR = 7.07), D3 (pIC50_coral = 7.83; pIC50_GA-MLR = 7.10), and D5 (pIC50_coral = 7.26; pIC50_GA-MLR = 7.55) displayed notable predicted inhibitory activity, according to both models. These compounds also exhibited conformational and structural stability, as well as a favorable binding profile. Furthermore, these potential drug candidates were found to be non-toxicity and have acceptable pharmacological properties.

Pathogenic differences of cynomolgus macaques after Taï Forest virus infection depend on the viral stock propagation.

Taï Forest virus (TAFV) is a negative-sense RNA virus in the Filoviridae family. TAFV has caused only a single human infection, but several disease outbreaks in chimpanzees have been linked to this virus. Limited research has been done on this human-pathogenic virus. We sought to establish an animal model to assess TAFV disease progression and pathogenicity at our facility. We had access to two different viral stock preparations from different institutions, both originating from the single human case. Type I interferon receptor knockout mice were inoculated with TAFV stock 1 or stock 2 by the intraperitoneal route. Inoculation resulted in 100% survival with no disease regardless of viral stock preparation or infectious dose. Next, cynomolgus macaques were inoculated with TAFV stock 1 or stock 2. Inoculation with TAFV stock 1 resulted in 100% survival and robust TAFV glycoprotein-specific IgG responses including neutralizing antibodies. In contrast, macaques infected with TAFV stock 2 developed disease and were euthanized 8-11 days after infection exhibiting viremia, thrombocytopenia, and increased inflammatory mediators identified by transcriptional analysis. Histopathologic analysis of tissue samples collected at necropsy confirmed classic filovirus disease in numerous organs. Genomic differences in both stock preparations were mapped to several viral genes which may have contributed to disease severity. Taken together, we demonstrate that infection with the two TAFV stocks resulted in no disease in mice and opposing disease phenotypes in cynomolgus macaques, highlighting the impact of viral stock propagation on pathogenicity in animal models.

Vaginal flora in HPV infection: a cross‑sectional analysis

Objective The vaginal flora has been reported to be associated with human papillomavirus (HPV) infection. The purpose of this study was to investigate the characteristics of the cervical microbiota in patients with HPV infection and to analyse the changes in the vaginal flora and enzyme profiles in females with HPV infection. Methods We conducted a cross-sectional study involving 206 participants who underwent HPV genotyping, sexually transmitted diseases pathogen testing, cytology examination, and microbiome analysis. Additionally, we collected 115 HPV-negative samples and 48 HPV-positive samples for 16S rRNA amplicon sequencing. The vaginal microbial communities of both groups were analysed for diversity and differences to explore their association with HPV infection. Results The abundance of Lactobacillus was found to be reduced, while Gardnerella vaginalis was significantly more prevalent in the HPV + group. In terms of alpha diversity indices, the Shannon index (P = .0036) and Simpson index (P = .02) were higher in the HPV + group compared to the HPV − group, indicating greater community diversity in the HPV + group. Among the 10 sexually transmitted diseases pathogens analysed, Uup3 and Uup6 were significantly associated with HPV infection. Statistically significant differences were observed in Nugent scores and bacterial vaginosis between the two groups (P < .05). In functional analysis, 11 proteins and 13 enzymes were found to be significantly altered in the HPV + group. Conclusion Our study demonstrates that disruptions in the vaginal flora are associated with HPV infection. Reduced levels of Lactobacillus, increased prevalence of Gardnerella, and abnormal enzyme profiles are closely linked to HPV infection.

Modularization of dual recognized CRISPR/Cas12a system for the detection of Staphylococcus aureus assisted by hydrazone chemistry

In this work, a dual recognized CRISPR/Cas12a system has been proposed, in which the activation chain is cleverly divided into two parts that can serve for precise dual target recognition, and hydrazone chemistry is introduced for the formation of a whole activation chain. It has been further explored to construct a new method for the specific and sensitive detection of Staphylococcus aureus (SA) as one of the most common pathogens in infectious diseases. In virtue of proximity effect contributed by complementary base pairing, hydrazone chemistry accelerates the formation of the whole activation strand and improves the specificity of the CRISPR/Cas12a system, serving for the accurate analysis of SA. Moreover, the temporary aggregation of CRISPR/Cas12a around SA enhances its catalytical efficiency so as to further amplify signal. With high sensitivity, stability, reproducibility and specificity, the established method has been successfully applied to detect SA in complex substrates. Meanwhile, our established method can well evaluate the inhibition effect of chlorogenic acid and congo red in comparison with flow cytometry. Environmental implicationBacterial pathogens exist widely in the environment and seriously threaten the safety of human health. Staphylococcus aureus (SA) is the most common pathogen of human suppurative infection, which can cause local suppurative infection, pneumonia, and even systemic infections such as sepsis. In this work, a dual recognized CRISPR/Cas12a system mediated by hydrazone chemistry has been proposed. With high sensitivity and low detection limit, the established method can specifically detect SA and effectively evaluate the antibacterial effect of inhibitors. This method is expected to be further developed into a detection method in different scenarios such as environmental monitoring and clinical diagnosis.