Characterization of Alternaria blotch disease of apple in Himachal Pradesh, India: insights on morphology, pathogenicity, and molecular features

BACKGROUND

Alternaria blotch disease in Himachal Pradesh, India, caused by Alternaria spp., adversely affects apple cultivars, resulting in reduced fruit size and quality accompanied by premature leaf fall.

METHODS AND RESULTS

Sixteen Alternaria isolates from apple growing regions underwent comprehensive analysis including morphology, pathogenicity, and molecular characterization. Variations in conidiophore and conidia dimensions, shapes, and divisions were observed among isolates. Pathogenicity assays revealed differences in incubation periods, latent phases, and disease responses. Molecular characterization via nuclear ITS rDNA and RAPD analysis indicated 99-100% homology with Alternaria alternata, Alternaria mali, and other Alternaria spp., with a close phylogenetic relationship to Chinese isolates. Differentiation of isolates based on origin, cultural characteristics, and morphology was achieved using RAPD markers.

CONCLUSIONS

The study identifies diverse genotypes and morphotypes of Alternaria contributing to apple blotch disease in Himachal Pradesh. These findings highlight the complexity of the pathogenic environment and hold significant implications for disease management in apple orchards.

Advances in understanding bioaerosol release characteristics and potential hazards during aerobic composting

Bioaerosol emissions and their associated risks are attracting increasing attention. Bioaerosols are generated during the pretreatment, fermentation, and screening of mature compost when processing various types of solid waste at composting plants (e.g., municipal sludge and animal manure). In this review, we summarize research into bioaerosols at different types of composting plants by focusing on the methods used for sampling bioaerosols, stages when emissions potentially occur, major components of bioaerosols, survival and diffusion factors, and possible control strategies. The six-stage Andersen impactor is the main method used for sampling bioaerosols in composting plants. In addition, different composting management methods mainly affect bioaerosol emissions from composting plants. Studies of the components of bioaerosols produced by composting plants mainly focused on bacteria and fungi, whereas few considered others such as endotoxin. The survival and diffusion of bioaerosols are influenced by seasonal effects due to changes in environmental factors, such as temperature and relative humidity. Finally, three potential strategies have been proposed for controlling bioaerosols in composting plants. Improved policies are required for regulating bioaerosol emissions, as well as bioaerosol concentration diffusion models and measures to protect human health.

Bacterial community profiles within the water samples of leptospirosis outbreak areas

Background

Leptospirosis is a water-related zoonotic disease. The disease is primarily transmitted from animals to humans through pathogenic Leptospira bacteria in contaminated water and soil. Rivers have a critical role in Leptospira transmissions, while co-infection potentials with other waterborne bacteria might increase the severity and death risk of the disease.

Methods

The water samples evaluated in this study were collected from four recreational forest rivers, Sungai Congkak, Sungai Lopo, Hulu Perdik, and Gunung Nuang. The samples were subjected to next-generation sequencing (NGS) for the 16S rRNA and in-depth metagenomic analysis of the bacterial communities.

Results

The water samples recorded various bacterial diversity. The samples from the Hulu Perdik and Sungai Lopo downstream sampling sites had a more significant diversity, followed by Sungai Congkak. Conversely, the upstream samples from Gunung Nuang exhibited the lowest bacterial diversity. Proteobacteria, Firmicutes, and Acidobacteria were the dominant phyla detected in downstream areas. Potential pathogenic bacteria belonging to the genera Burkholderiales and Serratia were also identified, raising concerns about co-infection possibilities. Nevertheless, Leptospira pathogenic bacteria were absent from all sites, which is attributable to its limited persistence. The bacteria might also be washed to other locations, contributing to the reduced environmental bacterial load.

Conclusion

The present study established the presence of pathogenic bacteria in the river ecosystems assessed. The findings offer valuable insights for designing strategies for preventing pathogenic bacteria environmental contamination and managing leptospirosis co-infections with other human diseases. Furthermore, closely monitoring water sample compositions with diverse approaches, including sentinel programs, wastewater-based epidemiology, and clinical surveillance, enables disease transmission and outbreak early detections. The data also provides valuable information for suitable treatments and long-term strategies for combating infectious diseases.

Pathogenic potential of an environmental Aspergillus fumigatus strain recovered from soil of Pygoscelis papua (Gentoo penguins) colony in Antarctica

Aspergillus fumigatus is a common opportunistic pathogen in different animals, including birds such as penguins. For the first time, a fungal strain identified as A. fumigatus was isolated from soil in the nests of gentoo penguins, Pygoscelis papua, on Livingston Island, South Shetland Islands (maritime Antarctica). This isolate (A. fumigatus UFMGCB 11829) displayed a series of potentially pathogenic characteristics in vitro. We evaluated its detailed molecular taxonomy and submitted the A. fumigatus UFMGCB 11829 Antarctic strain to in vivo pathogenic modelling. The isolate was confirmed to represent A. fumigatus morphological and phylogenetic analysis showed that it was closely related to A. fumigatus sequences reported from animals, immunosuppressed humans, storage grains, plants and soils. The strain displayed the best mycelial growth and conidia production at 37 ºC; however, it was also able to grow and produce conidia at 15º, demonstrating its capability to survive and colonize penguin nest at least in the summer season in maritime Antarctica. In pathogenicity tests, healthy mice did not showed symptoms of infection; however, 50% lethality was observed in immunosuppressed mice that were inoculated with 106 and 107 spores. Lethality increased to 100% when inoculated with 108 spores. Our data highlight the potential pathogenicity of opportunistic A. fumigatus that may be present in the Antarctic, and the risks of both their further transfer within Antarctica and outwards to other continents, risks which may be exacerbated due global climatic changes.

Intestinal Parasites Associated with American Cockroach (Periplaneta americana) in Akure, Ondo State, Nigeria

American cockroach (Periplaneta americana) has been implicated as mechanical vector of parasites of humans and animals. Therefore, this study aimed to identify and determine the prevalence of human intestinal parasites associated with the body surface and gut of P. americana. A total of 221 cockroaches which include 104 males and 117 females were collected from household kitchen, toilet area and canteen after which they were brought to laboratory for study. The body surface of the cockroach was washed with 5 ml normal saline solution to remove external parasites on the body surface for examination and later rinsed with 70% alcohol and dried before dissecting. The cockroach was dissected to examine internal parasites. Eleven parasites were recovered and identified, these include Ascaris lumbricoides (51.58%), Strongyloides stercoralis (48.42%) Trichuris trichiura (52.49%), Enterobius vermicularis (37.10%), Taenia spp (14.93%), Toxocara (31.67%), Ancylostoma spp (34.84%), Necator americanus (53.39%), and Diphylidium spp (66.23%) Balantidium coli (66.52%). The parasites were recorded both on the body surface and gut of the cockroach. There is no significant difference (p > 0.05) between parasites infection rate comparing both sexes; though, female cockroach having a higher infection rate (91.45%) than male (81.5%). Cockroach collected from toilets carried more parasites (96.34%) as compared to those from restaurants/canteen (89.71%) and household kitchens (81.69%). All parasites encountered were pathogenic to human and animals. This study has revealed that P. americana can act as mechanical vector by transporting and transmitting these parasites easily to man and animal. Good sanitary practices, reinforcement of worms' eradication programs, and the fight against these insects remain a necessity to contain the menace of parasites burden and cockroach control.

Diverse functions of myeloid-derived suppressor cells in autoimmune diseases

Since myeloid-derived suppressor cells (MDSCs) were found suppressing immune responses in cancer and other pathological conditions, subsequent researchers have pinned their hopes on the suppressive function against immune damage in autoimmune diseases. However, recent studies have found key distinctions of MDSC immune effects in cancer and autoimmunity. These include not only suppression and immune tolerance, but MDSCs also possess pro-inflammatory effects and exacerbate immune disorders during autoimmunity, while promoting T cell proliferation, inducing Th17 cell differentiation, releasing pro-inflammatory cytokines, and causing direct tissue damage. Additionally, MDSCs could interact with surrounding cells to directly cause tissue damage or repair, sometimes even as an inflammatory indicator in line with disease severity. These diverse manifestations could be partially attributed to the heterogeneity of MDSCs, but not all. The different disease types, disease states, and cytokine profiles alter the diverse phenotypes and functions of MDSCs, thus leading to the impairment or obversion of MDSC suppression. In this review, we summarize the functions of MDSCs in several autoimmune diseases and attempt to elucidate the mechanisms behind their actions.

Spotting disease disrupts the microbiome of infected purple sea urchins, Strongylocentrotus purpuratus

BACKGROUND

Spotting disease infects a variety of sea urchin species across many different marine locations. The disease is characterized by discrete lesions on the body surface composed of discolored necrotic tissue that cause the loss of all surface appendages within the lesioned area. A similar, but separate disease of sea urchins called bald sea urchin disease (BSUD) has overlapping symptoms with spotting disease, resulting in confusions in distinguishing the two diseases. Previous studies have focus on identifying the underlying causative agent of spotting disease, which has resulted in the identification of a wide array of pathogenic bacteria that vary based on location and sea urchin species. Our aim was to investigate the spotting disease infection by characterizing the microbiomes of the animal surface and various tissues.

RESULTS

We collected samples of the global body surface, the lesion surface, lesioned and non-lesioned body wall, and coelomic fluid, in addition to samples from healthy sea urchins. 16S rRNA gene was amplified and sequenced from the genomic DNA. Results show that the lesions are composed mainly of Cyclobacteriaceae, Cryomorphaceae, and a few other taxa, and that the microbial composition of lesions is the same for all infected sea urchins. Spotting disease also alters the microbial composition of the non-lesioned body wall and coelomic fluid of infected sea urchins. In our closed aquarium systems, sea urchins contracted spotting disease and BSUD separately and therefore direct comparisons could be made between the microbiomes from diseased and healthy sea urchins.

CONCLUSION

Results show that spotting disease and BSUD are separate diseases with distinct symptoms and distinct microbial compositions.

Microbial diversity and potential health risks of household municipal solid waste in China: A case study in winter during outbreak of COVID-19

Microbial (bacteria and fungi) community structures and their distributions in urban household municipal solid waste (HMSW) were characterized in a sampling campaign in 38 cities of China covering 5 climatic zones. All samples were collected from garbage containers in residential communities during the Winter of 2022, from January 11 to 26. A total of 247 bacterial genera belonging to 22 phyla were identified among the samples. Firmicutes (44.3 %), Bacteroidetes (33.77 %) and Proteobacteria (21.54 %) were the top 3 dominant phyla, and Arcicella (33.11 %) and Leuconostoc (21.87 %) were the dominant genera. Meanwhile, 124 fungal genera from 7 fungal phyla were detected. Ascomycota was the most dominant phylum, with an average relative abundance of 77.31 %. Hanseniaspora (24.03 %), Debaryomyces (13.47 %), Candida (12.18) were the top 3 dominant fungal genera. Alpha-diversity analysis showed that the species richness and diversity of bacterial and fungal communities of HMSW samples belonging to different climatic zones did not differ significantly. Nonmetric multidimensional scaling (NMDS) analysis confirmed that climatic had an effect on microbial communities but did not show a significant correlation. In addition, the distribution of microbial community in different samples from the same climate zone varied considerably, suggesting the HMSW source play important role in shaping microbial community composition. Considering that residential HMSW is relatively fresh, we speculates that the original microorganisms residing in different components of HMSW are key influencing factor for the community, while the reshaping force driven by environmental conditions are relatively weak. In addition, the study identified 13 bacterial and 16 fungal pathogens with Pseudomonas putida (0.25 %) and Sclerotinia sclerotiorum (2.12 %) as the most abundant potential pathogenic bacteria and fungi, respectively. These findings provide valuable information for characterizing microbial features and potential risks of HMSW in its management system.

Proteases of Acanthamoeba

The members of genus Acanthamoeba are the etiological agent of uncommon but severe or even fatal opportunistic infections in human beings. The presence of different classes of intracellular and extracellular proteases including serine proteases, cysteine proteases, and metalloproteases has been well documented in environmental and clinical isolates of Acanthamoeba spp. However, the role of the proteolytic enzymes in physiological, biological, and pathological mechanisms of the amoeba remains partially investigated. Some attempts have been conducted using various methods to determine the profile of proteases (number, class, optimal conditions, and activity of the enzymes), and possible pathogenicity mechanism of the proteolytic enzymes (various protein substrate degradation, cytopathic effect on different cell lines). In some cases, it was attempted to correlate intracellular and extracellular protease profile with pathogenicity potential of strains. This review revealed that the protease profile of different strains of Acanthamoeba was extremely complex, therefore, further comprehensive studies with application of a combination of various methods may help to elucidate the role of the enzymes.

Deleterious and ethnic-related BRCA1/2 mutations in tissue and blood of Egyptian colorectal cancer patients and its correlation with human papillomavirus

This study aimed to identify BRCA1/2 mutational patterns in the tissue and blood of Egyptian colorectal cancer (CRC) patients and to study the possible correlation of this mutational pattern with Human papillomavirus (HPV) infection. Eighty-two colonoscopic biopsies and forty-six blood samples were collected from Egyptian CRC patients, as well as blood samples of age and sex-matched healthy controls (n = 43) were enrolled. The libraries were performed using Qiaseq Human BRCA1 and BRCA2 targeted DNA panel and sequenced via Ion proton sequencer. Also, the CRC tissues were subjected to conventional PCR targeting the HPV Late 1 (L1) region. Our analysis revealed that the BRCA-DNA damage pathway had been altered in more than 65% of the CRC patients. Comparing tissue and blood samples from CRC patients, 25 somatic mutations were found exclusively in tissue, while 41 germline mutations were found exclusively in blood. Additionally, we identified 23 shared BRCA1/2 pathogenic (PVs) mutations in both blood and tissue samples, with a significantly higher frequency in blood samples compared to tissue samples. The most affected exon in BRCA1 was exon 10, while the most affected exons in BRCA2 were 11, 14, 18, 24, and 27 exons. Notably, we revealed an ethnic-related cluster of polymorphism variants in our population closely related to South Asian and African ethnicities. Novel PVs were identified and submitted to the ClinVar database. HPV was found in 23.8% of the CRC tissues, and 54% of HPV-positive cases had somatic BRCA1/2 PVs. The results of this research point to a possible connection between infection with HPV and BRCA1/2 mutations in the occurrence of colorectal cancer in the Egyptian population, which has a mixed ethnic background. Our data also indicate that liquid biopsy (blood samples) may be more representative than tissue samples for detecting BRCA1/2 mutations. These findings may have implications for cancer screening and the development of personalized, targeted therapies, such as PARP inhibitors, which can effectively target BRCA1/2 mutations.

The role of the Mediator complex in fungal pathogenesis and response to antifungal agents

Mediator is a complex of polypeptides that plays a central role in the recruitment of RNA polymerase II to promoters and subsequent transcriptional activation in eukaryotic organisms. Studies have now shown that Mediator has a role in regulating expression of genes implicated in virulence and antifungal drug resistance in pathogenic fungi. The roles of specific Mediator subunits have been investigated in several species of pathogenic fungi, particularly in the most pathogenic yeast Candida albicans. Uniquely, pathogenic yeast also present several interesting examples of divergence in Mediator structure and function, most notably in C. glabrata, which possesses two orthologues of Med15, and in C. albicans, which has a massively expanded family of Med2 orthologues known as the TLO gene family. This review highlights specific examples of recent progress in characterizing the role of Mediator in pathogenic fungi.

Epstein-Barr virus and genetic risk variants as determinants of T-bet+ B cell-driven autoimmune diseases

B cells expressing the transcription factor T-bet are found to have a protective role in viral infections, but are also considered major players in the onset of different types of autoimmune diseases. Currently, the exact mechanisms driving such 'atypical' memory B cells to contribute to protective immunity or autoimmunity are unclear. In addition to general autoimmune-related factors including sex and age, the ways T-bet+ B cells instigate autoimmune diseases may be determined by the close interplay between genetic risk variants and Epstein-Barr virus (EBV). The impact of EBV on T-bet+ B cells likely relies on the type of risk variants associated with each autoimmune disease, which may affect their differentiation, migratory routes and effector function. In this hypothesis-driven review, we discuss the lines of evidence pointing to such genetic and/or EBV-mediated influence on T-bet+ B cells in a range of autoimmune diseases, including systemic lupus erythematosus (SLE) and multiple sclerosis (MS). We provide examples of how genetic risk variants can be linked to certain signaling pathways and are differentially affected by EBV to shape T-bet+ B-cells. Finally, we propose options to improve current treatment of B cell-related autoimmune diseases by more selective targeting of pathways that are critical for pathogenic T-bet+ B-cell formation.

A Multi-landscape Assessment of Leptospira Prevalence on a Diversity of Small Mammals

Leptospirosis is a major zoonotic disease, especially in the tropics, and rodents were known to be carriers of this bacterium. There was established information on Leptospira prevalence among animal reservoirs in human-dominated landscapes from previous literature. However, there was very little focus given comparing the prevalence of Leptospira in a wide range of habitats. An extensive sampling of small mammals from various landscapes was carried out, covering oil palm plantations, paddy fields, recreational forests, semi-urbans, and wet markets in Peninsular Malaysia. This study aims to determine the prevalence of pathogenic Leptospira in a diversity of small mammals across different landscapes. Cage-trapping was deployed for small mammals' trappings, and the kidneys of captured individuals were extracted, for screening of pathogenic Leptospira by polymerase chain reaction (PCR) using LipL32 primer. Eight microhabitat parameters were measured at each study site. Out of 357 individuals captured, 21 (5.9%) were positive for pathogenic Leptospira of which recreational forest had the highest prevalence (8.8%) for landscape types, whereas Sundamys muelleri shows the highest prevalence (50%) among small mammals' species. Microhabitat analysis reveals that rubbish quantity (p < 0.05) significantly influenced the Leptospira prevalence among small mammals. Furthermore, nMDS analysis indicates that the presence of faeces, food waste, and exposure to humans in each landscape type also were linked with high prevalence of pathogenic Leptospira among the small mammals. This study supplements previous studies on pathogenic Leptospira prevalence across different landscape types, and the major microhabitat factors associated with Leptospira prevalence. This information is crucial for epidemiological surveillance and habitat management to curb the possibility of the disease outbreaks.

Hypothesis: functional age and onset of autosomal dominant genetic prion disease

Autosomal dominant diseases typically have an age-related onset. Here, I focus on genetic prion disease (gPrD), caused by various mutations in the PRNP gene. While gPrD typically occurs at or after middle age, there can be considerable variability in the specific age of onset. This variability can occur among patients with the same PRNP mutation; in some cases, these differences occur not only between families but even within the same family. It is not known why gPrD onset is typically delayed for decades when the causative mutation is present from birth. Mouse models of gPrD manifest disease; however, unlike human gPrD, which typically takes decades to manifest, mouse models exhibit disease within months. Therefore, the time to onset of prion disease is proportional to species lifespan; however, it is not known why this is the case. I hypothesize that the initiation of gPrD is strongly influenced by the process of aging; therefore, disease onset is related to proportional functional age (e.g., mice vs. humans). I propose approaches to test this hypothesis and discuss its significance with respect to delaying prion disease through suppression of aging.

Study on the effectiveness of membrane separation + N2 deoxidation process for the treatment of bacteria in ballast water

Effects of the membrane separation + N₂ deoxidation process on the abundance and activity of bacteria were examined under two salinity conditions at Yangshan Port, Shanghai, China. Sequencing of 16S rRNA gene amplicons demonstrated a decrease in the diversity and activity of bacteria in fresh water and marine water, with a total removal rate of approximately 63 % and 69 %, respectively. Indicator bacteria decreased to 10 CFU·100 mL^-1, which met the IMO D-2 standard. A total of 13 potential pathogens were detected after treatment, indicating that there is still a risk of pathogenic bacteria invasion in the discharge water, particularly marine bacteria, and that the D-2 standard may be insufficient as a preventive measure against pathogenic bacteria transfer. The results will provide reference for government supervision, and will also be important for monitoring foreign bacteria and technology development.

When Vibrios Take Flight: A Meta-Analysis of Pathogenic Vibrio Species in Wild and Domestic Birds

Of the over 100 species in the genus Vibrio, approximately twelve are associated with clinical disease, such as cholera and vibriosis. Crucially, eleven of those twelve, including Vibrio cholerae and Vibrio vulnificus, have been isolated from birds. Since 1965, pathogenic Vibrio species have been consistently isolated from aquatic and ground-foraging bird species, which has implications for public health, as well as the One Health paradigm defined as an ecology-inspired, integrative framework for the study of health and disease, inclusive of environmental, human, and animal health. In this meta-analysis, we identified 76 studies from the primary literature which report on or examine birds as hosts for pathogenic Vibrio species. We found that the burden of disease in birds was most commonly associated with V. cholerae, followed by V. metschnikovii and V. parahaemolyticus. Meta-analysis wide prevalence of our Vibrio pathogens varied from 19% for V. parahaemolyticus to 1% for V. mimicus. Wild and domestic birds were both affected, which may have implications for conservation, as well as agriculturally associated avian species. As pathogenic Vibrios become more abundant throughout the world as a result of warming estuaries and oceans, susceptible avian species should be continually monitored as potential reservoirs for these pathogens.

Clinical, neuroimaging and genetic findings in children with hereditary ataxia: single center study

BACKGROUND

The genetics of hereditary ataxia (HA) are complex and multigenic. The diversity of genes that cause ataxia varies considerably between populations. We aimed to investigate the clinical, neuroimaging, and genetic findings of HA in children from a tertiary center in Turkey.

METHODS

The clinical and neuroimaging evaluations of patients, laboratory investigations, and molecular genetic evaluations of those with ataxia were performed at the pediatrics, pediatric neurology, and genetics outpatient clinics between October 2020 and October 2021. With repeated expansions in the ATXN 1, 2, 3, 7, and 8 genes for spinocerebellar ataxia (SCA) and FXN genes for Friedreich's ataxia (FA), whole-exome sequencing (WES) was used to analyze every patient.

RESULTS

25 patients from 24 families had ataxia and an unsteady gait as their main symptoms. The patients had a mean age of 8.5 ± 3.78 years, and the symptoms had begun at a mean age of 2 ± 0.62 years; five of these were males and three were females. A genetic cause of ataxia was found in 8/25 patients (32%). Seven of the eight gene mutations detected in the patients were novel mutations. Spinocerebellar ataxia was found in 16% of cases (n = 4), L-2-Hydroxyglutaric aciduria was found in 12% of cases (n = 3), and ataxia-telangiectasia was found in 4% of cases (n = 1).

CONCLUSION

Our research adds to the body of knowledge by describing the clinical and genetic traits of HA patients in our area and by finding unusual gene changes linked to ataxia.

Weissella and the two Janus faces of the genus

The genus Weissella belongs to the lactic acid bacteria group. It occurs naturally in foods and is a component of the human microbiome. A few Weissella species are candidate probiotics due to their potential for survival under the harsh conditions present in the gastrointestinal tract of humans and animals. Various species have also shown potential for treating and preventing periodontal disease, skin pathologies, and atopic dermatitis; some are used as starters for the fermentation of foods due to their production of exopolysaccharides; and others are used as protective cultures due to their production of weissellicin, a bacteriocin. However, a few Weissella species are opportunistic pathogens, such as W. ceti, which is the etiological agent of weissellosis, a disease in rainbow trout. Additionally, most Weissella species are intrinsically vancomycin-resistant. Thus, the Weissella genus is important from both medical and industrial points of view, and the Janus faces of this genus should be considered in any expected biotechnological applications. In this review, we present an overview of the probiotic potential and pathogenic cases of the Weissella genus reported in the literature.

Genomic Comparisons of Two Armillaria Species with Different Ecological Behaviors and Their Associated Soil Microbial Communities

Armillaria species show considerable variation in ecological roles and virulence, from mycorrhizae and saprophytes to important root pathogens of trees and horticultural crops. We studied two Armillaria species that can be found in coniferous forests of northwestern USA and southwestern Canada. Armillaria altimontana not only is considered as a weak, opportunistic pathogen of coniferous trees, but it also appears to exhibit in situ biological control against A. solidipes, formerly North American A. ostoyae, which is considered a virulent pathogen of coniferous trees. Here, we describe their genome assemblies and present a functional annotation of the predicted genes and proteins for the two Armillaria species that exhibit contrasting ecological roles. In addition, the soil microbial communities were examined in association with the two Armillaria species within a 45-year-old plantation of western white pine (Pinus monticola) in northern Idaho, USA, where A. altimontana was associated with improved tree growth and survival, while A. solidipes was associated with reduced growth and survival. The results from this study reveal a high similarity between the genomes of the beneficial/non-pathogenic A. altimontana and pathogenic A. solidipes; however, many relatively small differences in gene content were identified that could contribute to differences in ecological lifestyles and interactions with woody hosts and soil microbial communities.

Infection with pathogenic Blastocystis ST7 is associated with decreased bacterial diversity and altered gut microbiome profiles in diarrheal patients

Background

Blastocystis is a common protistan parasite inhabiting the gastrointestinal tract of humans and animals. While there are increasing reports characterizing the associations between Blastocystis and the gut microbiome in healthy individuals, only a few studies have investigated the relationships between Blastocystis and the gut microbiota in diarrheal patients.

Methods

The effects of a specific subtype (ST7) of Blastocystis on the composition of gut microbiota in diarrheal patients were investigated using 16S ribosomal RNA (rRNA) gene sequencing and bioinformatic analyses.

Results

Compared with diarrheal patients without Blastocystis, diarrheal patients infected with Blastocystis ST7 exhibited lower bacterial diversity. Beta diversity analysis revealed significant differences in bacterial community structure between ST7-infected and Blastocystis-free patients. The proportion of Enterobacteriaceae and Escherichia-Shigella were significantly enriched in ST7-infected patients. In contrast, the abundance of Bacteroides and Parabacteroides were more prevalent in Blastocystis-free patients.

Conclusions

The results of this study revealed, for the first time, that infection with Blastocystis ST7 is associated with lower bacterial diversity and altered microbial structure in diarrheal patients. Our study on clinical diarrheal patients is also the first to reinforce the notion that ST7 is a pathogenic subtype of Blastocystis.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s13071-022-05435-z.

AuNP-based biosensors for the diagnosis of pathogenic human coronaviruses: COVID-19 pandemic developments

The outbreak rate of human coronaviruses (CoVs) especially highly pathogenic CoVs is increasing alarmingly. Early detection of these viruses allows treatment interventions to be provided more quickly to people at higher risk, as well as helping to identify asymptomatic carriers and isolate them as quickly as possible, thus preventing the disease transmission chain. The current diagnostic methods such as RT-PCR are not ideal due to high cost, low accuracy, low speed, and probability of false results. Therefore, a reliable and accurate method for the detection of CoVs in biofluids can become a front-line tool in order to deal with the spread of these deadly viruses. Currently, the nanomaterial-based sensing devices for detection of human coronaviruses from laboratory diagnosis to point-of-care (PoC) diagnosis are progressing rapidly. Gold nanoparticles (AuNPs) have revolutionized the field of biosensors because of the outstanding optical and electrochemical properties. In this review paper, a detailed overview of AuNP-based biosensing strategies with the varied transducers (electrochemical, optical, etc.) and also different biomarkers (protein antigens and nucleic acids) was presented for the detection of human coronaviruses including SARS-CoV-2, SARS-CoV-1, and MERS-CoV and lowly pathogenic CoVs. The present review highlights the newest trends in the SARS-CoV-2 nanobiosensors from the beginning of the COVID-19 epidemic until 2022. We hope that the presented examples in this review paper convince readers that AuNPs are a suitable platform for the designing of biosensors.

Genomic characteristics, virulence and antimicrobial resistance in avian pathogenic Escherichia coli MTR_BAU02 strain isolated from layer farms in Bangladesh

BACKGROUND

Colibacillosis, caused by avian pathogenic Escherichia coli (APEC), is one of the most significant infectious diseases affecting poultry worldwide.

OBJECTIVE

This study was aimed to determine the genomic diversity, virulence factor genes (VFGs) and antimicrobial resistance genes (ARGs) in the APEC MTR_BAU02 strain isolated from layer chickens using whole-genome sequencing (WGS).

METHOD

Paired-end (2 × 250) WGS was performed using Illumina MiSeq sequencer and de novo assembly was performed using SPAdes. Core genome MLST (cgMLST) analysis between APEC MTR_BAU02 and all of the ST1196 E. coli strains retrieved from the NCBI GenBank database was performed using BacWGSTdb 2.0 server. We further utilized different databases to detect ARGs, VFGs and genomic functional features of the APEC MTR_BAU02 strain.

RESULTS

The complete genome of APEC MTR_BAU02 consists of 94 contigs comprising 4,924,680 bp (51.1% GC content) including 4,681 protein-coding sequences, one chromosome, one plasmid, and was assigned to ST1196. The closest relatives of APEC MTR_BAU02 were another four isolates originating from human clinical (diarrhoeic stool) specimens in Bangladesh and two clinical isolates originating from chicken in India, which differed by 694 cgMLST alleles. One hundred twenty-two ARGs and 92 VFGs were identified in APEC MTR_BAU02 genome. Metabolic functional annotations detected 380 SEED subsystems including genes coding for carbohydrate metabolism, protein metabolism, cofactors, vitamins, prosthetic groups and pigments, respiration, membrane transport, stress response, motility and chemotaxis, and virulence, disease and defense.

CONCLUSION

This study reports the genome sequence of a multidrug resistant APEC strain isolated from layer birds in Bangladesh. The ARGs and VFGs, widespread in APEC MTR_BAU02, are similar to those found in human isolates, and highlight the growing threat of antimicrobial resistance in both poultry and humans.

Identification and isolation of pathogenic Theileria orientalis Ikeda genotype from confined dairy cattle, in Hebei, China

Theileria orientalis is known to be a group of benign cattle parasites with a cosmopolitan distribution, and has been classified into 11 genotypes through MPSP gene phylogenetic analysis. In China, T. orientalis is the most prevalent Theileria species, with several genotypes, but few fatal cases have been reported. In June 2020, dairy cattle in Zhangjiakou, Hebei Province, showed clinical symptoms of piroplasmosis, causing many animals to die. Blood smears and PCR detection results confirmed T. orientalis infection with a 66.7% positive rate of collected blood samples. The MPSP sequences analysis revealed parasite genotypes 1 (Chitose) and 2 (Ikeda). Aiming to isolate the pathogens, experimental animal was infected with T. orientalis via inoculation of the positive blood samples. The results has shown that only T. orientalis genotype 2 (Ikeda) was obtained that has confirmed by MPSP and 18S rRNA sequences analysis, indicating that the Ikeda type was predominant and responsible for the disease. Although many T. orientalis genotypes are present in China, the possibility of T. orientalis genotypes 1 and 2 infections in confined dairy cattle should be considered to avoid additional economic losses.

Comparative Analyses of the Transport Proteins Encoded within the Genomes of nine Bifidobacterium Species

The human microbiome influences human health in both negative and positive ways. Studies on the transportomes of these organisms yield information that may be utilized for various purposes, including the identification of novel drug targets and the manufacture of improved probiotic strains. Moreover, these genomic analyses help to improve our understanding of the physiology and metabolic capabilities of these organisms. The present study is a continuation of our studies on the transport proteins of the major gut microbes. Bifidobacterium species are essential members of the human gut microbiome, and they initiate colonization of the gut at birth, providing health benefits that last a lifetime. In this study we analyze the transportomes of nine bifidobacterial species: B. adolescentis, B. animalis, B. bifidum, B. breve, B. catenulatum, B. dentium, B. longum subsp. infantis, B. longum subsp. longum, and B. pseudocatenulatum. All of these species have proven probiotic characteristics and exert beneficial effects on human health. Surprisingly, we found that all nine of these species have similar pore-forming toxins and drug exporters that may play roles in pathogenesis. These species have transporters for amino acids, carbohydrates, and proteins, essential for their organismal lifestyles and adaption to their respective ecological niches. The strictly probiotic species, B. bifidum, however, contains fewer such transporters, thus indicative of limited interactions with host cells and other gut microbial counterparts. The results of this study were compared with those of our previous studies on the transportomes of multiple species of Bacteroides, Escherichia coli/Salmonella, and Lactobacillus. Overall, bifidobacteria have larger transportomes (based on percentages of total proteins) than the previously examined groups of bacterial species, with a preference for primary active transport systems over secondary carriers. Taken together, these results provide useful information about the physiologies and pathogenic potentials of these probiotic organisms as reflected by their transportomes.

Incorporating structural features to improve the prediction and understanding of pathogenic amino acid substitutions

BACKGROUND

The wide application of gene sequencing has accumulated numerous amino acid substitutions (AAS) with unknown significance, posing significant challenges to predicting and understanding their pathogenicity. While various prediction methods have been proposed, most are sequence-based and lack insights for molecular mechanisms from the perspective of protein structures. Moreover, prediction performance must be improved.

METHODS

Herein, we trained a random forest (RF) prediction model, namely AAS3D-RF, underscoring sequence and three-dimensional (3D) structure-based features to explore the relationship between diseases and AASs.

RESULTS

AAS3D-RF was trained on more than 14,000 AASs with 21 selected features, and obtained accuracy (ACC) between 0.811 and 0.839 and Matthews correlation coefficient (MCC) between 0.591 and 0.684 on two independent testing datasets, superior to seven existing tools. In addition, AAS3D-RF possesses unique structure-based features, context-dependent substitution score (CDSS) and environment-dependent residue contact energy (ERCE), which could be applied to interpret whether pathogenic AASs would introduce incompatibilities to the protein structural microenvironments.

CONCLUSION

AAS3D-RF serves as a valuable tool for both predicting and understanding pathogenic AASs.

Escherichia coli strain INF32/16/A: Dataset of raw reads and assembled draft genome

Escherichia coli strain INF32/16/A is a gram-negative bacteria which is an extended-spectrum beta-lactamases (ESBL). ESBL is an enzyme that is produced by bacteria to become resistant to existing antibiotic such as extended-spectrum penicillin, cephalosporins, and have been threatening the ability to treat an infection. Therefore, genome analysis will provide an insight of how this bacteria able to evolve and the information obtained will able to facilitate in designing new antibiotics. The genome of E. coli strain was sequenced using Illumina MiSeq and raw genome sequence have been submitted into NCBI SRA database (SRR15334628) under Bioproject accession number PRJNA726861.

First report of a disease caused by Bacillus cereus in cultured loach Paramisgurnus dabryanus

Bacillus cereus is commonly considered a bacterium pathogenic to mammals, but several studies have suggested that it also induces diseases in fish. In 2017 and 2018, 2 strains of B. cereus, NQ-2017-17 and NQ-2018-8, were isolated from diseased large-scale loach Paramisgurnus dabryanus in Tianjin, China, and were considered to be the pathogens responsible for the disease. These stains were identified as B. cereus based on the results of 16S rDNA gene sequence analysis, Vitek biochemical tests, physiological and biochemical tests, and B. cereus group species-specific PCR. Strains NQ-2017-7 and NQ-2018-8 were found to contain virulence genes (e.g. hblA, hblC, hblD, entFM, and bceT) causing pathological damage to the spleen, kidneys, liver, and gills of loach. The median lethal dose (LD50) of NQ-2017-7 and NQ-2018-8 for loach were 1.0 ×106.64 and 1.0 ×106.49 CFU ml-1, respectively. To our knowledge, this is the first report of loach disease caused by a member of the genus Bacillus.

Effects of Bacterial Metabolites on the Immune System: Enemies and Friends

Metabolites produced by bacteria can influence the immune system. These metabolites are produced by pathogenic bacteria as well as the friendly microbiota. This review sheds light on the major bacterial metabolites and their structures. It also describes the capacity of these molecules to stimulate and inhibit the immune responses in a way that affects their capacity to control different diseases.

Pathogenic hitchhiker diversity on international ships' ballast water at West Malaysia port

This study investigates bacterial diversity and potential pathogens in the international ships' ballast water at Tanjung Pelepas Port, Malaysia, using 16S rRNA amplicon sequencing. Thirty-four bacterial phylum, 305 families, 577 genera, and 941 species were detected in eight ballast water samples of different origins. The similarity of the bacterial composition between samples was found to be random and not tied to geographical locations. The bacterial abundance did not seem to be affected by related physicochemical except for temperature. Ballast water samples with a temperature lower than 25 °C showed a relatively lower bacterial abundance. A total of 33 potential pathogens were detected from all ballast water samples. Pseudomonas spp., Tenacibaculum spp., Flavobacteriaceae spp., Halomonas spp., and Acinetobacter junii are the potential pathogens with more than 10% OTU prevalence. This study would provide beneficial information for further enhancing ballast water microorganism guidelines in Malaysia.

DNA variant classification-reconsidering "allele rarity" and "phenotype" criteria in ACMG/AMP guidelines

Recent guidance suggested modified DNA variant pathogenicity assignments based on genome-wide allele rarity. Different a priori probabilities of pathogenicity operate where patients already have clinical diagnoses, and are found to have a very rare variant in a gene known to cause their disease, compared to predictive testing of a clinically unaffected individual. We tested new recommendations from the ClinGen Sequence Variant Interpretation Working Group for ClinVar-listed, loss-of-function variants meeting the very strong evidence of pathogenicity criterion [PVS1] in genes for 3 specific diseases where causal gene identification can modify clinical care of an individual- Von Willebrand disease, cystic fibrosis and hereditary haemorrhagic telangiectasia. Across these diseases, current rules leave 20/1,278 (1.6%) of loss-of-function variants as variants of uncertain significance (VUS that may not be reported to clinicians), and 207/1,278 (17.2%) as likely pathogenic. Applying the new ClinGen rule enabling PVS1 and the allele rarity criterion PM2 to delineate likely pathogenicity still left 8/1,278 (0.9%) as VUS (reflecting non-PVS1 calls by the submitters), and the majority of null alleles meeting PVS1 as merely likely pathogenic. We favour an approach whereby, for PVS1 variants in patients who personally meet the phenotypic PP4 criterion for a disease where casual variants are commonly family-specific, that PM2 is upgraded to permit a pathogenic call. Of 1,278 ClinVar-listed frameshift, nonsense and canonical splice site variants that met PVS1 in the 3 conditions, 16.0% (204/1,278) would be newly designated as pathogenic, avoiding misinterpretation outside of clinical genetics communities. We suggest further discussion around variant assessment across different clinical applications, potentially guided by PP4 alerts to distinguish personal versus family phenotypic history.

Incorporating mucosal-associated invariant T cells into the pathogenesis of chronic liver disease

Mucosal-associated invariant T (MAIT) cells have been described in liver and non-liver diseases, and they have been ascribed antimicrobial, immune regulatory, protective, and pathogenic roles. The goals of this review are to describe their biological properties, indicate their involvement in chronic liver disease, and encourage investigations that clarify their actions and therapeutic implications. English abstracts were identified in PubMed by multiple search terms, and bibliographies were developed. MAIT cells are activated by restricted non-peptides of limited diversity and by multiple inflammatory cytokines. Diverse pro-inflammatory, anti-inflammatory, and immune regulatory cytokines are released; infected cells are eliminated; and memory cells emerge. Circulating MAIT cells are hyper-activated, immune exhausted, dysfunctional, and depleted in chronic liver disease. This phenotype lacks disease-specificity, and it does not predict the biological effects. MAIT cells have presumed protective actions in chronic viral hepatitis, alcoholic hepatitis, non-alcoholic fatty liver disease, primary sclerosing cholangitis, and decompensated cirrhosis. They have pathogenic and pro-fibrotic actions in autoimmune hepatitis and mixed actions in primary biliary cholangitis. Local factors in the hepatic microenvironment (cytokines, bile acids, gut-derived bacterial antigens, and metabolic by-products) may modulate their response in individual diseases. Investigational manipulations of function are warranted to establish an association with disease severity and outcome. In conclusion, MAIT cells constitute a disease-nonspecific, immune response to chronic liver inflammation and infection. Their pathological role has been deduced from their deficiencies during active liver disease, and future investigations must clarify this role, link it to outcome, and explore therapeutic interventions.

Visceral mycobacteriosis in amphibians from the Brazilian Caatinga region

Emerging infectious diseases in wild animals related to humans have received greater attention in recent years. Mycobacteriosis is a bacterial disease of animal and human importance. Mycobacterium gordonae infects the skin and internal organs of free-ranging amphibians and is considered the least pathogenic member of the Mycobacteriaceae to humans. However, information about its infection and pathogenesis in wild amphibians is still lacking. A total of 1306 amphibian specimens belonging to 6 families, 12 genera, and 21 species were collected and dissected during a helminthological survey of 7 municipalities in southern Ceará state, Caatinga (eco)region, northeast Brazil. Of these, 17 specimens (0.76%), belonging to 2 families and 4 species (Leptodactylus macrosternum, n = 2; L. vastus, n = 10; Pseudopaludicola pocoto, n = 2; Rhinella jimi, n = 3), presented infections that consisted of calcification nodules in the coelomic cavity, kidney, liver, lung, gut, and pancreas. The nodules were examined by histopathology and PCR. The bacteria were identified as M. gordonae by molecular analyses. Infected animals presented with hepatocellular vacuolar degeneration, karyolysis, and karyorrhexis, hepatic portal congestion, hemorrhage, mononuclear cellular infiltration, melanomacrophage center hyperplasia, and granulomas in varying stages of development with intralesional acid-fast bacilli. This study is the first report of M. gordonae in these amphibian species, in which results of molecular analyses confirmed the presence of M. gordonae in natural environments and histopathology confirmed the typical lesion of mycobacteriosis in amphibians from northeastern Brazil.

Indian coastal waters: a concoction of sewage indicator bacteria! An assessment on recreational beaches

Coastal water quality assessment is important to maintain a healthy environment for various uses including fisheries and recreation. Microbial populations are used as biological indicators of contamination to monitor water quality and are considered by the government to be one of the critical features for issuing safety guidelines. Different bacterial groups (pathogenic, vibrio and faecal) from five major recreational beaches of Chennai, India, were monitored for the assessment of coastal water quality. Faecal coliforms (FC) were high at all the beaches, with up to 4.2 × 10⁵ CFU/mL and exceeding the normal standard limits of 100 CFU/100 mL set by the Central Pollution Control Board (CPCB) of India. Rainfall was found to have a role in the variability and distribution of indicator and pathogenic bacteria. The seasonal dry period witnessed elevated FC, while dilution in the wet period reduced Escherichia coli-like organisms (ECLO). High microbial counts were detected near the beach situated close to the river mouth, mainly due to discharges of untreated domestic sewage and industrial wastes. Similarly, the biological oxygen demand (BOD) was also high, 0.32 to 10.32 mg/L. Dissolved inorganic nitrogen (DIN) ranged from 2.21 to 134.53 μmol/L and inorganic phosphate (IP) ranged from 0 to 57.53 μmol/L. These values indicated the presence of significant untreated sewage in the coastal water. This study revealed that Chennai coastal waters carry high levels of faecal and pathogenic bacteria, detrimental for recreational and other contact activities. The quantitative and qualitative analyses will be useful for modelling and prediction of coastal water quality and management of other recreational beaches in India.

The pathogenic, therapeutic and diagnostic role of exosomal microRNA in the autoimmune diseases

Exosomes are a nano-vesicle surrounded by a bilipid layer that can release from almost all cells and could be detected in tissues and biological liquids. These vesicles contain lipids, proteins, and nucleic acids (including DNA, mRNA, and miRNA) inside and on the exosomes' surface constitute their content. Exosomes can transfer their cargo into the recipient cell, which can modify recipient cells' biological activities. Recently it has been deciphering that the miRNA pattern of exosomes reveals the cellular pathophysiological situation and modifies various biological processes. Increasing data regarding exosomes highlights that the exosomes and their cargo, especially miRNAs, are implicated in the pathophysiology of various disorders, such as autoimmune disease. The current evidence on the deciphering of mechanisms in which exosomal miRNAs contributed to autoimmunity was indicated that exosomal miRNA might hold information that can reprogram the function of many of the immune cells involved in autoimmune diseases' pathogenesis. In the present study, we summarized the pathogenic role of exosomal miRNAs in several autoimmune diseases, including myasthenia gravis (MG), psoriasis, inflammatory bowel disease (IBD), type 1 diabetes (T1D), multiple sclerosis (MS), systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), Sjogren's Syndrome (SS), systemic sclerosis (SSc), vitiligo, and autoimmune thyroid diseases (AITD). Moreover, in this work, we present evidence of the potential role of exosomal miRNAs as therapeutic and diagnostic agents in autoimmune diseases.

The divergent roles of sortase in the biology of Gram-positive bacteria

The bacterial cell wall contains numerous surface-exposed proteins, which are covalently anchored and assembled by a sortase family of transpeptidase enzymes. The sortase are cysteine transpeptidases that catalyzes the covalent attachment of surface protein to the cell wall peptidoglycan. Among the reported six classes of sortases, each distinct class of sortase plays a unique biological role in anchoring a variety of surface proteins to the peptidoglycan of both pathogenic and non-pathogenic Gram-positive bacteria. Sortases not only exhibit virulence and pathogenesis properties to host cells, but also possess a significant role in gut retention and immunomodulation in probiotic microbes. The two main distinct functions are to attach proteins directly to the cell wall or assemble pili on the microbial surface. This review provides a compendium of the distribution of different classes of sortases present in both pathogenic and non-pathogenic Gram-positive bacteria and also the noteworthy role played by them in bacterial cell wall assembly which enables each microbe to effectively interact with its environment.

Mutational analysis of mitochondrial tRNA genes in 138 patients with Leber's hereditary optic neuropathy

INTRODUCTION

Mutations in mitochondrial DNA (mtDNA) are the most important causes for Leber's hereditary optic neuropathy (LHON). Of these, three primary mtDNA mutations account for more than 90% cases of this disease. However, to date, little is known regarding the relationship between mitochondrial tRNA (mt-tRNA) variants and LHON.

AIM

In this study, we aimed to investigate the association between mt-tRNA variants and LHON.

METHODOLOGY

One hundred thirty-eight LHON patients lacking three primary mutations (ND1 3460G > A, ND4 11778Gxs > A, and ND6 14484 T > C), as well as 266 controls were enrolled in this study. PCR-Sanger sequencing was performed to screen the mt-tRNA variants. Moreover, the phylogenetic analysis, pathogenicity scoring system, as well as mitochondrial functions were performed.

RESULTS

We identified 8 possible pathogenic variants: tRNA^Phe 593 T > C, tRNA^Leu(UUR) 3275C > T, tRNA^Gln 4363 T > C, tRNA^Met 4435A > G, tRNA^Ala 5587 T > C, tRNA^Glu 14693A > G, tRNA^Thr 15927G > A, and 15951A > G, which may change the structural and functional impact on the corresponding tRNAs, and subsequently lead to a failure in tRNA metabolism. Furthermore, significant reductions in mitochondrial ATP and MMP levels and an overproduction of ROS were observed in cybrid cells containing these mt-tRNA variants, suggesting that these variants may lead to mitochondrial dysfunction which was responsible for LHON.

CONCLUSION

Our study indicated that mt-tRNA variants were associated with LHON, and screening for mt-tRNA variants were recommended for early detection, diagnosis, and prevention of maternally inherited LHON.

Effects of sub-lethal doses of nisin on the virulence of Salmonella enterica in Galleria mellonella larvae

Salmonella enterica is a pathogen that induces self-limiting gastroenteritis and is of worldwide concern. Nisin, an antimicrobial peptide, has emerged as an alternative for the control of microbial growth but its effect on the virulence of pathogenic bacteria is not yet well-explored. This work aimed to evaluate the virulence of S. enterica in the presence of sub-inhibitory nisin using the experimental model Galleria mellonella. Sub-inhibitory concentrations of nisin of 11.72 and 46.88 μM did not affect the cellular viability of S. enterica but promoted changes in gene expression within 1 h of treatment, with increases of up to 3-fold of pagC, 1.8-fold of invA and 2.3-fold of invF. Larvae of G. mellonella inoculated with S. enterica combined with nisin at 46.88 μM presented mortality, and TL₅₀ noticeably increased to 50% and 80% at 24 and 48 h post-infection, respectively. Defence responses, such as melanisation, nodulation, pseudopodia, immune response, and expression of defence proteins of the larvae G. mellonella were enhanced when the treatments with S. enterica were combined with 11.72 or 46.88 μM nisin. These results show an increase in virulence of S. enterica by sub-MIC concentration of nisin that needs to be explored.

Phenotype and multi-omics comparison of Staphylococcus and Streptococcus uncovers pathogenic traits and predicts zoonotic potential

BACKGROUND

Staphylococcus and Streptococcus species can cause many different diseases, ranging from mild skin infections to life-threatening necrotizing fasciitis. Both genera consist of commensal species that colonize the skin and nose of humans and animals, and of which some can display a pathogenic phenotype.

RESULTS

We compared 235 Staphylococcus and 315 Streptococcus genomes based on their protein domain content. We show the relationships between protein persistence and essentiality by integrating essentiality predictions from two metabolic models and essentiality measurements from six large-scale transposon mutagenesis experiments. We identified clusters of strains within species based on proteins associated to similar biological processes. We built Random Forest classifiers that predicted the zoonotic potential. Furthermore, we identified shared attributes between of Staphylococcus aureus and Streptococcus pyogenes that allow them to cause necrotizing fasciitis.

CONCLUSIONS

Differences observed in clustering of strains based on functional groups of proteins correlate with phenotypes such as host tropism, capability to infect multiple hosts and drug resistance. Our method provides a solid basis towards large-scale prediction of phenotypes based on genomic information.

Sea foam-associated pathogenic bacteria along the west coast of India

Anthropogenic activities release effluents containing nutrients and pathogenic bacteria that change the characteristics of coastal ecosystems. An important type of marine pollution which has occurred in 3 different states in India during 2019 is sea foam. Sea foam was found on Hole beach, Goa (Lat: 15.404° N, Long: 73.787° E), where nutrients (NO₃^- = 137 μM and organic nitrogen = 121 μM) from a garbage dumpyard are released directly via streams/gutters to coastal waters. This resulted in a bloom of the diatom Thalassiosira pseudonana, associated with high concentration of total organic carbon and fucoxanthin. Decay of this bloom along with strong agitation due to rocks and wave action resulted in sea foam. We isolated foam-associated bacteria and identified pathogenic bacteria including Enterobacter cancerogenus through 16S rRNA gene sequencing. Such foam-associated pathogenic bacteria, could be antibiotic resistant, and may have adverse effects on human health. This can also hamper the tourism industry of a small state like Goa that relies heavily on tourism.

Telomere Dysfunction as an Initiator of Inflammation: Clues to an Age-Old Mystery

Inflammatory Bowel Disease (IBD) is a challenging medical condition that is driven by various genetic and environmental factors. Therapeutic opportunities for this disease remain limited due to the lack of in-depth understanding of the pathogenetic mechanisms and actionable targets driving the disease. Analysis of telomere dysfunctional mice and patients with genetic defects in telomere maintenance unexpectedly revealed phenotypes mirroring those observed in IBD. Molecular characterization of this model identified a pathway driven by telomere DNA damage-mediated activation of the ATM/cABL/YAP1 pathway, which directly regulates genes central to IBD pathogenesis and amenable to therapeutic intervention. This review summarizes the evidence correlating telomere dysfunction with IBD and colitis-associated cancer and proposes therapeutic opportunities for such inflammatory conditions targeting this newly identified pathway.

A porcine epidemic diarrhea virus strain with distinct characteristics of four amino acid insertion in the COE region of spike protein

In recent years, a novel, highly virulent variant of porcine epidemic diarrhea virus (PEDV) has emerged, causing substantial economic losses to the pork industry worldwide. In this study, a PEDV strain named LNsy was successfully isolated in China. Phylogenetic analysis based on the whole genome revealed that PEDV LNsy belonged to the G2 subtype. For the first time, a unique four amino acids (4-aa) insertion was identified in the COE region of the spike (S) protein (residues 499-640), resulting in an extra alpha helix in the spatial structure of the COE region. To determine changes in virus-neutralization (VN) antibody reactivity of the virus, polyclonal antibodies (PAbs) against the S protein of different subtypes were used in a VN test. Both PAbs against the S protein of the G1 and G2 subtype showed reduced VN reactivity to PEDV LNsy. Further, recombination analyses revealed that PEDV LNsy was the result of recombination between PEDV GDS13 and GDS46 strains at the genomic breakpoints (nt 17,959-20,594 in the alignment) in the ORF1b gene of the genomes. Pathological examination showed gross morphological pathological changes in the gut, including significant villus atrophy and shedding of the infected piglets. These results indicated that a 4-aa insertion in the COE region of the S protein may have partly altered the profiles of VN antibodies and thus it will be important to develop vaccine candidates to resist wild virus infection and to monitor the genetic diversity of PEDV.

Pathogenic variants identified by whole-exome sequencing in 43 patients with epilepsy

Background

Epilepsy is a group of neurological disorders characterized by recurrent epileptic seizures. Epilepsy is affected by many factors, approximately 20–30% of cases are caused by acquired conditions, but in the remaining cases, genetic factors play an important role. Early establishment of a specific diagnosis is important to treat and manage this disease.

Methods

In this study, we have recruited 43 epileptic encephalopathy patients and the molecular genetic analysis of those children was performed by whole-exome sequencing (WES).

Results

Fourteen patients (32.6%, 14/43) had positive genetic diagnoses, including fifteen mutations in fourteen genes. The overall diagnostic yield was 32.6%. A total of 9 patients were diagnosed as pathogenic mutations, including 4 variants had been reported as pathogenic previously and 6 novel variants that had not been reported previously. Therefore, WES heralds promise as a tool for clinical diagnosis of patients with genetic disease.

Conclusion

Early establishment of a specific diagnosis, on the one hand, is necessary for providing an accurate prognosis and recurrence risk as well as optimizing management and treatment options. On the other hand, to unveil the genetic architecture of epilepsy, it is of vital importance to investigate the phenotypic and genetic complexity of epilepsy.

Combining Ramachandran plot and molecular dynamics simulation for structural-based variant classification: Using TP53 variants as model

The wide application of new DNA sequencing technologies is generating vast quantities of genetic variation data at unprecedented speed. Developing methodologies to decode the pathogenicity of the variants is imperatively demanding. We hypothesized that as deleterious variants may function through disturbing structural stability of their affected proteins, information from structural change caused by genetic variants can be used to identify the variants with deleterious effects. In order to measure the structural change for proteins with large size, we designed a method named RP-MDS composed of Ramachandran plot (RP) and Molecular Dynamics Simulation (MDS). Ramachandran plot captures the variant-caused secondary structural change, whereas MDS provides a quantitative measure for the variant-caused globular structural change. We tested the method using variants in TP53 DNA binding domain of 219 residues as the model. In total, RP-MDS identified 23 of 38 (60.5%) TP53 known Pathogenic variants and 17 of 42 (41%) TP53 VUS that caused significant changes of P53 structure. Our study demonstrates that RP-MDS method provides a powerful protein structure-based tool to screen deleterious genetic variants affecting large-size proteins.

In vitro antibacterial activities and molecular characterization of bacterial species isolated from farmlands against selected pathogens

This study aims to screen bacterial isolates from Olabisi Onabanjo University Farmland for antibacterial activity against pathogenic microorganisms. Agar well diffusion method was used. Isolates were identified molecularly. Chi-square test revealed significant association between isolates, antibacterial activity with likelihood p-value = 0.000 and 5% significant level. Six among thirty-five isolates exhibited antibacterial activity against the test pathogenic species. A greater antibacterial activity (50 % inhibition) was observed in Lysinibacillus sphearicus strain PRE16. It inhibited the growth of Bacillus subtilis, Staphylococcus aureus and Escherichia coli by 23.00 ± 2.00, 18.00 ± 2.00 and 20.00 ± 4.00 respectively. DNA sequencing revealed antagonist isolates as Bacillus sp. BCN2, Brochothrix thermosphacta strain P30C4, Bacillus aryabhattai strain KNUC205, Alcaligenes faecalis strain KEM24, Bacillus arsenicus strain CSD05 and Lysinibacillus sphaericus strain PRE16. Phylogenetic analysis revealed close relatedness of most isolates with Bacillus species strains. These strains are suggested to be effective for the discovery of new antibacterial agents.

Emerging of a SARS-CoV-2 viral strain with a deletion in nsp1

BACKGROUND

The new Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), which was first detected in Wuhan (China) in December of 2019 is responsible for the current global pandemic. Phylogenetic analysis revealed that it is similar to other betacoronaviruses, such as SARS-CoV and Middle-Eastern Respiratory Syndrome, MERS-CoV. Its genome is ∼ 30 kb in length and contains two large overlapping polyproteins, ORF1a and ORF1ab that encode for several structural and non-structural proteins. The non-structural protein 1 (nsp1) is arguably the most important pathogenic determinant, and previous studies on SARS-CoV indicate that it is both involved in viral replication and hampering the innate immune system response. Detailed experiments of site-specific mutagenesis and in vitro reconstitution studies determined that the mechanisms of action are mediated by (a) the presence of specific amino acid residues of nsp1 and (b) the interaction between the protein and the host's small ribosomal unit. In fact, substitution of certain amino acids resulted in reduction of its negative effects.

METHODS

A total of 17,928 genome sequences were obtained from the GISAID database (December 2019 to July 2020) from patients infected by SARS-CoV-2 from different areas around the world. Genomes alignment was performed using MAFFT (REFF) and the nsp1 genomic regions were identified using BioEdit and verified using BLAST. Nsp1 protein of SARS-CoV-2 with and without deletion have been subsequently modelled using I-TASSER.

RESULTS

We identified SARS-CoV-2 genome sequences, from several Countries, carrying a previously unknown deletion of 9 nucleotides in position 686-694, corresponding to the AA position 241-243 (KSF). This deletion was found in different geographical areas. Structural prediction modelling suggests an effect on the C-terminal tail structure.

CONCLUSIONS

Modelling analysis of a newly identified deletion of 3 amino acids (KSF) of SARS-CoV-2 nsp1 suggests that this deletion could affect the structure of the C-terminal region of the protein, important for regulation of viral replication and negative effect on host's gene expression. In addition, substitution of the two amino acids (KS) from nsp1 of SARS-CoV was previously reported to revert loss of interferon-alpha expression. The deletion that we describe indicates that SARS-CoV-2 is undergoing profound genomic changes. It is important to: (i) confirm the spreading of this particular viral strain, and potentially of strains with other deletions in the nsp1 protein, both in the population of asymptomatic and pauci-symptomatic subjects, and (ii) correlate these changes in nsp1 with potential decreased viral pathogenicity.

Co-expression of master transcription factors determines CD4+ T cell plasticity and functions in auto-inflammatory diseases

Master CD4⁺ T cell lineage determined transcription factors are found to be dysregulated in pathogenesis of autoimmune and inflammatory diseases. CD4⁺ T cells categorized into different lineages based on their functions, cell surface markers and master transcription factors those required for expression of lineage specific cytokines. T-bet, GATA3, RORγt and Foxp3 are major transcription regulators of Th1, Th2, Th17 and Treg cells respectively. Significant progress has been made in understanding expression of lineage specific master regulators that drives CD4⁺ T cell differentiation. It is known that each CD4⁺ T cell lineage express precise determined transcription factor and due to cross regulation between these factors the CD4⁺ T cells able to maintain thier specific phenotype. However, recent studies shows that the lineage specifying transcription factors frequently co-expressed. There is an emerging area of research revealing that the co-expression of lineage-specifying transcription factors alters the potential function and flexibility of subsets of CD4⁺ T cell, this in turn favors the autoimmune pathology. Here, we discuss similarities and differences between mutually co-expressed transcription factors in CD4⁺ T cell subsets and then recapitulates on cell type specific and dynamic balance between the lineage restricted transcription factors in determining plasticity of CD4⁺ T cell subsets. Furthermore, we discuss abnormal regulation of such transcription factors that establishes a pathogenic CD4⁺ T cell phenotype in autoimmune diseases and how this understanding will provide further insight into potential therapeutic development.

Biological characteristics and genetic evolutionary analysis of emerging pathogenic Bacillus cereus isolated from Père David's deer (Elaphurus davidianus)

Bacillus cereus (B. cereus) is widely distributed in the environment. It is one of the most common opportunistic food-borne pathogens associated with food poisoning, not only being majorly reported to cause fatal infections of the gastrointestinal tract, but also responsible for abdominal distress and vomiting. The current study was undertaken to evaluate the biological characteristics and the genetic evolution of B. cereus isolated from infected organs of dead Elaphurus davidianus (E. davidianus). B. cereus was characterized through antibiotic sensitivity tests, mouse lethality assay, whole genome sequencing analysis, and genome annotation. The results revealed that the isolated B. cereus strain was highly resistant to rifampicin, lincomycin, sulfamethoxazole, erythromycin, and ampicillin, with a high pathogenicity phenotype. KEGG annotation revealed that "metabolic pathways" had the largest number of unigenes, followed by "biosynthesis of secondary metabolites" and "biosynthesis of antibiotics". GO analysis resulted in 8039 unigenes categorized. Meanwhile, 54,779 unigenes were annotated and grouped into 23 categories based on COG functional classifications. Moreover, one gene (codY) was found to be related to the host in conformity with the analysis done on PHI-base. Other tests led to the identification of 16 B. cereus virulence factor genes and five resistance types, with potential resistance against bacitracin, penicillin, and fosfomycin. We isolated a highly drug-resistant and pathogenic B. cereus strain from E. davidianus, showing that a variety of antimicrobial drugs should be avoided in clinical treatments. Furthermore, to the best of our knowledge, this is the first study to report whole genome sequencing of a emergence of food-borne B. cereus strain isolated from E. davidianus deer; it will be helpful to extensively investigate the genetic and molecular mechanisms of drug resistance and pathogenesis about B. cereus in both humans and animals.

Draft genome assembly dataset of the Basidiomycete pathogenic fungus, Ganoderma boninense

Ganoderma boninense is a soil-borne Basidiomycete pathogenic fungus that eminent as the key causal of devastating disease in oil palm, named basal stem rot. Being a threat to sustainable palm oil production, it is essential to comprehend the fundamental view of this fungus. However, there is gap of information due to its limited number of genome sequence that is available for this pathogenic fungus. This implies the hitches in performing biological research to unravel the mechanism underlying the pathogen attack in oil palm. Therefore, here we report a dataset of draft genome of G. boninense that was sequenced using Illumina Hiseq 2000. The raw reads were deposited into NCBI database (SRX7136614 and SRX7136615) and can be accessed via Bioproject accession number PRJNA503786.

Molecular detection of Leptospira spp. in wild boar (Sus scrofa) hunted in Liguria region (Italy)

Leptospirosis is a re-emerging and widespread zoonosis, worldwide distributed, due to a wide variety of wild and domestic animal species able to act as natural or accidental hosts. During last years, in Europe, as in Italy, wild boar (Sus scrofa) population is increased. This animal represents a reservoir for different etiological agents, such as Leptospira. The aim of this investigation was to evaluate the prevalence of Leptospira spp. in wild boar hunted in Liguria region (Italy) during two-year hunting seasons. From 611 hunted wild boar, kidneys were collected. DNA was extracted from each organ and different targets were used to detect pathogenic (lipL32 gene), intermediate (16S rRNA gene) and saprophytic (23S rRNA gene) Leptospira by Taqman-based RealTime-PCR assays. Overall, kidneys were sampled from 282 adults, 155 sub-adults and 174 young wild boar (in total 314 males and 298 females). By RealTime PCR 77 kidneys were positive and, among these, 74 resulted positive for pathogenic (96.10%) and 3 (3.90%) for intermediate Leptospira. No significant differences in pathogenic Leptospira infection ratio were detected between male (11.50%) and female (12.75%). Only 13 sub-adult animals (8.39%) resulted infected by pathogenic Leptospira; 23 young animals (13.22%) and 38 adult animals (13.47%) were positive. The results of this study confirmed the importance of wild boar in the epidemiology of leptospirosis, which is able to infect other animal species (domestic and wild) including humans. Rarely, intermediate Leptospira could be able to infect wild boar with a renal localization that can contribute to their shedding and circulation.