Opportunistic Infections Research Articles

Integrating respiratory microbiome and host immune response through machine learning for respiratory tract infection diagnosis

At present, the diagnosis of lower respiratory tract infections (LRTIs) is difficult, and there is an urgent need for better diagnostic methods. This study enrolled 136 patients from 2020 to 2021 and collected bronchoalveolar lavage fluid (BALF) specimens. We used metatranscriptome to analyze the lower respiratory tract microbiome (LRTM) and host immune response. The diversity of the LRTM in LRTIs significantly decreased, manifested by a decrease in the abundance of normal microbiota and an increase in the abundance of opportunistic pathogens. The upregulated differentially expressed genes (DEGs) in the LRTIs group were mainly enriched in infection immune response-related pathways. Klebsiella pneumoniae had the most significant increase in abundance in LRTIs, which was strongly correlated with host infection or inflammation genes TNFRSF1B, CSF3R, and IL6R. We combined LRTM and host transcriptome data to construct a machine-learning model with 12 screened features to discriminate LRTIs and non-LRTIs. The results showed that the model trained by Random Forest in the validate set had the best performance (ROC AUC: 0.937, 95% CI: 0.832–1). The independent external dataset showed an accuracy of 76.5% for this model. This study suggests that the model integrating LRTM and host transcriptome data can be an effective tool for LRTIs diagnosis.

The bacterial and yeast microbiota in livestock forages in Hungary

BackgroundAlong bacteria, yeasts are common in forages and forage fermentations as spoilage microbes or as additives, yet few studies exist with species-level data on these fungi’s occurrence in feedstuff. Active dry yeast and other yeast-based products are also common feed additives in animal husbandry. Here, we aimed to characterize both fermented and non-fermented milking cow feedstuff samples from Hungary to assess their microbial diversity in the first such study from Central Europe.ResultsWe applied long-read bacterial metabarcoding to 10 fermented and 25 non-fermented types of samples to assess bacterial communities and their characteristics, surveyed culturable mold and yeast abundance, and identified culturable yeast species. Fermented forages showed the abundance of Aerococcaceae, Bacillaceae, Brucellaceae, Lactobacillaceae, Staphylococcaceae, and Thermoactinomycetaceae, non-fermented ones had Cyanothecaceae, Enterobacteriaceae, Erwiniaceae, Gomontiellaceae, Oxalobacteraceae, Rhodobiaceae, Rickettsiaceae, and Staphylococcaceae. Abundances of bacterial families showed mostly weak correlation with yeast CFU numbers, only Microcoleaceae (positive) and Enterococcaceae and Alcaligenaceae (negative correlation) showed moderate correlation. We identified 14 yeast species, most commonly Diutina rugosa, Pichia fermentans, P. kudriavzevii, and Wickerhahomyces anomalus. We recorded S. cerevisiae isolates only from animal feed mixes with added active dry yeast, while the species was completely absent from fermented forages. The S. cerevisiae isolates showed high genetic uniformity.ConclusionOur results show that both fermented and non-fermented forages harbor diverse bacterial microbiota, with higher alpha diversity in the latter. The bacterial microbiome had an overall weak correlation with yeast abundance, but yeasts were present in the majority of the samples, including four new records for forages as a habitat for yeasts. Yeasts in forages mostly represented common species including opportunistic pathogens, along with a single strain of Saccharomyces used as a feed mix additive.

Detection of Mycoplasma sp using next-generation DNA sequencing is common on nasal swabs from both healthy and unhealthy pet rabbits (Oryctolagus cuniculus).

Upper respiratory infections are a frequent problem in pet rabbits and rodents, and Mycoplasma pulmonis is 1 of the most common causes of respiratory infections in pet rats. M pulmonis was detected in 1967 in laboratory rabbits via culture of the nares and oropharynx, but overall, Mycoplasma is not commonly identified in the upper airway of rabbits. The objective of this study was to compare the prevalence of Mycoplasma sp detection via next-generation DNA sequencing on nasal swabs obtained from healthy and unhealthy rabbits. The results of nasal swabs from both healthy and unhealthy rabbits submitted for next-generation DNA sequencing from January 2022 to February 2023 were reviewed. Data gathered included signalment, whether or not Mycoplasma sp was detected, and the cell count and relative predominance of Mycoplasma sp compared to other organisms. 91 rabbits met the inclusion criteria, of which 49 were healthy and 42 were unhealthy. Overall, 52 of 91 (57.1%) rabbits were positive and 39 of 91 (42.8%) were negative for Mycoplasma sp. Mycoplasma positivity was significantly (P < .001) more common in healthy rabbits (37/49 [75.5%]) compared to unhealthy rabbits (15/42 [35.7%]). The fact that Mycoplasma positivity was common in both groups of rabbits, and particularly common in rabbits without upper respiratory signs, suggests that Mycoplasma may be normal nasal flora in rabbits. Further research is needed to determine whether Mycoplasma could function as an opportunistic pathogen in rabbits.

CROI 2024 BHIVA working group summary.

The Conference on Retroviruses and Opportunistic Infections (CROI) is usually the most significant HIV conference of the year in terms of basic and clinical scientific output. CROI 2024 in Denver, USA, felt very much back to 'business as usual' following COVID-19 disruptions that had impacted preceding years, but also felt more global and outward- facing. The British HIV Association supports a working group to attend CROI annually and deliver feedback in the UK. This article summarizes the highlights from that meeting.

The priority of bacteria Staphylococcus spp. in the etiology of PSI through the prism of new diagnostic capabilities. Literature review.

Representatives of the genus Staphylococcus spp. occupy a leading place in the etiology of infections caused by opportunistic bacteria. Staphylococcus spp., being symbionts of humans and/or animals, are constantly located on the surface of the skin and mucous membranes, which are their natural habitats. The importance of bacteria of the genus Staphylococcus spp. It is determined by their significant distribution in the population, as well as among patients and medical personnel, due to their transient and resident carrier, as well as their high adaptive potential, due to their ability to form biofilms and produce enzymes that provide them with protection from antimicrobial drugs. Modern molecular genetic methods for identifying Staphylococcus spp. and assessing their epidemic potential allow us to rethink their importance in the etiology of nosocomial purulent septic infections (PSI) in a new way. It is no coincidence that they entered the group of ESCAPE pathogens with a high level of priority. The ability of staphylococci to form biofilms ensures their survival in various hospital/environmental facilities, which in the conditions of a medical organization (MO) become additional, or so-called "inanimate" sources of infection. In recent years, despite the increasing role of coagulase-negative staphylococci (CoNS) in the etiology of PSI, S. aureus remains the most significant causative agent of PSI.

Pathogenic diversification of the gut commensal Providencia alcalifaciens via acquisition of a second type III secretion system.

Providencia alcalifaciens is a Gram-negative bacterium found in various water and land environments and organisms, including insects and mammals. Some P. alcalifaciens strains encode gene homologs of virulence factors found in pathogenic Enterobacterales members, such as Salmonella enterica serovar Typhimurium and Shigella flexneri. Whether these genes are pathogenic determinants in P. alcalifaciens is not known. In this study, we investigated P. alcalifaciens-host interactions at the cellular level, focusing on the role of two type III secretion systems (T3SS) belonging to the Inv-Mxi/Spa family. T3SS1b is widespread in Providencia spp. and encoded on the chromosome. A large plasmid that is present in a subset of P. alcalifaciens strains, primarily isolated from diarrheal patients, encodes for T3SS1a. We show that P. alcalifaciens 205/92 is internalized into eukaryotic cells, lyses its internalization vacuole, and proliferates in the cytosol. This triggers caspase-4-dependent inflammasome responses in gut epithelial cells. The requirement for the T3SS1a in entry, vacuole lysis, and cytosolic proliferation is host cell type-specific, playing a more prominent role in intestinal epithelial cells than in macrophages or insect cells. In a bovine ligated intestinal loop model, P. alcalifaciens colonizes the intestinal mucosa and induces mild epithelial damage with negligible fluid accumulation in a T3SS1a- and T3SS1b-independent manner. However, T3SS1b was required for the rapid killing of Drosophila melanogaster. We propose that the acquisition of two T3SS has allowed P. alcalifaciens to diversify its host range, from a highly virulent pathogen of insects to an opportunistic gastrointestinal pathogen of animals.

The Comparative Characterization of a Hypervirulent Acinetobacter baumannii Bacteremia Clinical Isolate Reveals a Novel Mechanism of Pathogenesis.

Acinetobacter baumannii is an opportunistic Gram-negative pathogen with exquisite survival capabilities under various environmental conditions and displays widespread resistance to common antibiotics. A. baumannii is a leading cause of nosocomial infections that result in high morbidity and mortality rates. Accordingly, when multidrug resistance rates surpass threshold levels, the percentage of A. baumannii clinical isolates surges. Research into A. baumannii has increased in the past decade, and multiple mechanisms of pathogenesis have been identified, including mechanisms underlying biofilm development, quorum sensing, exotoxin production, secretion system utilization, and more. To date, the two gold-standard strains used to investigate different aspects of A. baumannii pathogenesis include ATCC 17978 and ATCC 19606. Here, we report a comparative characterization study of three additional A. baumannii clinical isolates obtained from different infection types and derived from different anatomical regions of infected patients. The comparison of three clinical isolates in addition to the ATCC strains revealed that the hypervirulent bacteremia clinical isolate, known as HUMC1, employs a completely different mechanism of pathogenesis when compared to all its counterparts. In stark contrast to the other genetic variants, the hypervirulent HUMC1 isolate does not form biofilms, is antibiotic-susceptible, and has the capacity to reach higher levels of quorum compared to the other clinically relevant strains. Our data also reveal that HUMC1 does not shed endotoxin into the extracellular milieu, rather secretes the evolutionarily conserved, host-mimicking, Zonula occludens toxin (Zot). Taken together, our hypothesis that HUMC1 cells have the ability to reach higher levels of quorum and lack biofilm production and endotoxin shedding, accompanied by the substantial elaboration of Zot, suggests a novel mechanism of pathogenesis that appears to afford the hypervirulent pathogen with stealth-like capabilities when disseminating through the circulatory system in a state of bacteremia.

Gut Microbiome variation in patients with early-stage mild-to-moderate intracerebral hemorrhage: A pilot study exploring therapeutic targets

BackgroundThe significant morbidity and mortality rates of acute intracerebral hemorrhage (ICH) are well-known around the world. The link between gut microbiota and different types of strokes is becoming more studied. The goal of this study was to look at the relationships between intestinal flora and early-stage mild-to-moderate ICH (emICH), and to provide a new perspective for adjunctive treatment of emICH. MethodsFecal samples from 100 participants with emICH (n=50) and healthy individuals (n=50) in this study were collected as well as analyzed utilizing 16S rRNA gene amplicon sequencing in order to characterize the gut microbial community. ResultsDistinct microbial communities are present within each group, with emICH patients exhibiting a diminished diversity and uniformity in their microbial profiles. A notable shift in the gut microbiota composition of emICH patients has been observed, characterized by an upsurge in pro-inflammatory microbes belonging to the Euryarchaeota phylum and a concurrent decline in beneficial Bacteroidetes species. Concurrently, significant associations and patterns among operational taxonomic units (OTUs) were identified in emICH patients. A panel of biomarkers (WAL_1855D, Methanobrevibacter, Streptococcus, Bacteroides, Coprococcus, Lachnospira) has been effectively utilized to distinguish emICH patients from healthy individuals, with an area under the curve (AUC) of 0.845. Additionally, an analysis using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation uncovered several perturbed pathways in emICH patients, predominantly those related to metabolic processes and the inflammatory response. Moreover, predictive profiling of the microbiome's phenotypic traits suggests that emICH patients are likely to harbor a higher prevalence of Gram-negative bacteria and potential opportunistic pathogens compared to healthy controls. ConclusionsThe gut microbiota ecosystem of emICH patients is disrupted, characterized primarily by an increase in pro-inflammatory microbiota, elevated inflammatory signaling pathways, and metabolic dysregulation. Furthermore, microbiota modulation may be seen as a novel approach for the adjunctive treatment of emICH.

Opportunistic Features of Non-Clostridium botulinum Strains Containing bont Gene Cluster.

The cluster of genes determining the production of botulinum toxins is an attribute of not only the Clostridium botulinum species. This cluster is also found in other members of the Clostridium genus, such as C. baratii, C. butyricum, and C. sporogenes. The occurrence of a botulinum-like cluster has also been recorded in strains of other genera, i.e., Enterococcus faecium, as well as in a Gram-negative species isolated from freshwater sediments; however, the biological activity of bont-related genes has not been noted. It can be said that the mentioned species have a dual nature. Another species with a dual nature is C. butyricum. This bacterium is a common human and animal gut commensal bacterium and is also frequently found in the environment. Although non-toxigenic strains are currently used as probiotics in Asia, other strains have been implicated in pathological conditions, such as botulism in infants or necrotizing enterocolitis in preterm neonates. Additionally, C. baratii strains are rare opportunistic pathogens associated with botulism intoxication. They have been isolated from food and soil and can be carried asymptomatically or cause botulism outbreaks in animals and humans. In addition to the mentioned clostridia, the other microorganisms considered as non-toxigenic have also been suspected of carrying botulinum cluster Gram-negative bacteria, such as Chryseobacterium piperi isolated from freshwater sediments; however, the biological activity of bont-related genes has not been noted. Additionally, Enterococcus faecium strains have been discovered carrying BoNT-related clusters (BoNT/En). Literature data regarding the heterogeneity of BoNT-producing strains indicate the requirement to reclassify C. botulinum species and other microorganisms able to produce BoNTs or possess botulinum-like gene clusters. This article aims to show the dual nature of Clostridium strains not belonging to the C. botulinum species that are sporadically able to carry bont clusters, which are usually considered saprophytic and even probiotic, and bont-like clusters in microorganisms from other genera. The aim was also to consider the genetic mechanisms of botulinum cluster expression in strains that are considered opportunistic and the microbiological safety aspects associated with their occurrence in the environment.

Effects of tire particles and associated-chemicals on the Pacific oyster (Magallana gigas) physiology, reproduction and next-generation

By 2040, tire particles (TP) are expected to dominate marine plastic contamination, raising concerns about their effects on marine animals. This study employed a multidisciplinary and multigenerational approach on the Pacific oyster Magallana gigas to investigate the effects of TP and their leachates (LEA). Effects were analyzed at the individual scale, from cellular, molecular, and microbiota changes to reproductive outputs and offspring performance. Microbiota characterization revealed potential dysbiosis in oysters treated with high concentration of both TP and LEA. RNA-seq analyses highlighted the activation of energy metabolism and stress responses in the LEA treatment. Additionally, transcriptional changes in oocytes and the reduction of motile spermatozoa suggested potential effects on gamete quality. Notably, possible oyster resilience was pointed out by the lack of significant ecophysiological modifications in adults and impacts on the growth and reproductive outputs of the offspring. Overall, the implications of the observed oyster resilience under our experimental setting are discussed in relation to available toxicity data and within a comprehensive view of coastal ecosystems, where a higher diversity of plastic/rubber materials and harsher environmental conditions occur.

Analysis of the utility of a rapid vesicle isolation method for clinical strains of Pseudomonas aeruginosa.

Pseudomonas aeruginosa, a pathogen capable of causing diseases ranging from mild to life-threatening, has a large arsenal of virulence factors. Notably, extracellular vesicles have emerged as significant players in the pathogenesis of this organism. However, the full range of their functions is still being studied, and difficulties related to vesicle purification (long protocols, low yields, and specialized instruments) have become a major obstacle for their characterization. In this context, the utility of rapid new methods of vesicle isolation from clinical strains is still unknown. Here, we analyze the utility of the ExoBacteria OMV isolation kit for a collection of clinical strains of P. aeruginosa. We first phenotypically characterized 15 P. aeruginosa strains to ensure that our samples were heterogeneous. We then determined the best conditions for purifying vesicles from P. aeruginosa PAO1 reference strain by the rapid method and used them to isolate vesicles from clinical strains. Our results indicated that M9 minimal medium is the best for obtaining high purity with the rapid isolation kit. Although we were able to isolate vesicles from at least four strains, the low yield and the large number of strains with unpurifiable vesicles showed that the kit was not practical or convenient for clinical strains. Our findings suggest that although fast procedures for vesicle purification can be of great utility for Escherichia coli, the more complex phenotypes of clinical isolates of P. aeruginosa are a challenge for these protocols and new alternatives/optimizations need to be developed.IMPORTANCEPseudomonas aeruginosa is recognized as an opportunistic pathogen in humans and animals. It can effectively colonize various environments thanks to a large set of virulence factors that include extracellular vesicles. Different methods were recently developed to reduce the time and effort associated with vesicle purification. However, the utility of rapid vesicle isolation methods for clinical strains of P. aeruginosa (which are recognized as being highly diverse) is not yet known. In this context, we analyzed the utility of the ExoBacteria OMV Isolation kit for vesicle purification in P. aeruginosa clinical strains. Our findings showed that the kit does not seem to be convenient for research on clinical strains due to low vesicle recovery. Our results underscore the importance of developing new rapid vesicle purification protocols/techniques for specific clinical phenotypes.

Evolutionary dynamics in gut-colonizing Candida glabrata during caspofungin therapy: Emergence of clinically important mutations in sphingolipid biosynthesis.

Invasive fungal infections are associated with high mortality, which is exacerbated by the limited antifungal drug armamentarium and increasing antifungal drug resistance. Echinocandins are a frontline antifungal drug class targeting β-glucan synthase (GS), a fungal cell wall biosynthetic enzyme. Echinocandin resistance is generally low but increasing in species like Candida glabrata, an opportunistic yeast pathogen colonizing human mucosal surfaces. Mutations in GS-encoding genes (FKS1 and FKS2 in C. glabrata) are strongly associated with clinical echinocandin failure, but epidemiological studies show that other, as yet unidentified factors also influence echinocandin susceptibility. Furthermore, although the gut is known to be an important reservoir for emergence of drug-resistant strains, the evolution of resistance is not well understood. Here, we studied the evolutionary dynamics of C. glabrata colonizing the gut of immunocompetent mice during treatment with caspofungin, a widely-used echinocandin. Whole genome and amplicon sequencing revealed rapid genetic diversification of this C. glabrata population during treatment and the emergence of both drug target (FKS2) and non-drug target mutations, the latter predominantly in the FEN1 gene encoding a fatty acid elongase functioning in sphingolipid biosynthesis. The fen1 mutants displayed high fitness in the gut specifically during caspofungin treatment and contained high levels of phytosphingosine, whereas genetic depletion of phytosphingosine by deletion of YPC1 gene hypersensitized the wild type strain to caspofungin and was epistatic to fen1Δ. Furthermore, high resolution imaging and mass spectrometry showed that reduced caspofungin susceptibility in fen1Δ cells was associated with reduced caspofungin binding to the plasma membrane. Finally, we identified several different fen1 mutations in clinical C. glabrata isolates, which phenocopied the fen1Δ mutant, causing reduced caspofungin susceptibility. These studies reveal new genetic and molecular determinants of clinical caspofungin susceptibility and illuminate the dynamic evolution of drug target and non-drug target mutations reducing echinocandin efficacy in patients colonized with C. glabrata.

Characterization of acquired β-lactamases in Pseudomonas aeruginosa and quantification of their contributions to resistance.

Pseudomonas aeruginosa is a highly problematic opportunistic pathogen that causes a range of different infections. Infections are commonly treated with β-lactam antibiotics, including cephalosporins, monobactams, penicillins, and carbapenems, with carbapenems regarded as antibiotics of last resort. Isolates of P. aeruginosa can contain horizontally acquired bla genes encoding β-lactamase enzymes, but the extent to which these contribute to β-lactam resistance in this species has not been systematically quantified. The overall aim of this research was to address this knowledge gap by quantifying the frequency of β-lactamase-encoding genes in P. aeruginosa and by determining the effects of β-lactamases on susceptibility of P. aeruginosa to β-lactams. Genome analysis showed that β-lactamase-encoding genes are present in 3% of P. aeruginosa but are enriched in carbapenem-resistant isolates (35%). To determine the substrate antibiotics, 10 β-lactamases were expressed from an integrative plasmid in the chromosome of P. aeruginosa reference strain PAO1. The β-lactamases reduced susceptibility to a variety of clinically used antibiotics, including carbapenems (meropenem, imipenem), penicillins (ticarcillin, piperacillin), cephalosporins (ceftazidime, cefepime), and a monobactam (aztreonam). Different enzymes acted on different β-lactams. β-lactamases encoded by the genomes of P. aeruginosa clinical isolates had similar effects to the enzymes expressed in strain PAO1. Genome engineering was used to delete β-lactamase-encoding genes from three carbapenem-resistant clinical isolates and increased susceptibility to substrate β-lactams. Our findings demonstrate that acquired β-lactamases play an important role in β-lactam resistance in P. aeruginosa, identifying substrate antibiotics for a range of enzymes and quantifying their contributions to resistance.IMPORTANCEPseudomonas aeruginosa is an extremely problematic pathogen, with isolates that are resistant to the carbapenem class of β-lactam antibiotics being in critical need of new therapies. Genes encoding β-lactamase enzymes that degrade β-lactam antibiotics can be present in P. aeruginosa, including carbapenem-resistant isolates. Here, we show that β-lactamase genes are over-represented in carbapenem-resistant isolates, indicating their key role in resistance. We also show that different β-lactamases alter susceptibility of P. aeruginosa to different β-lactam antibiotics and quantify the effects of selected enzymes on β-lactam susceptibility. This research significantly advances the understanding of the contributions of acquired β-lactamases to antibiotic resistance, including carbapenem resistance, in P. aeruginosa and by implication in other species. It has potential to expedite development of methods that use whole genome sequencing of infecting bacteria to inform antibiotic treatment, allowing more effective use of antibiotics, and facilitate the development of new antibiotics.

Mass Mortality of the Invasive Sea Urchin Diadema setosum in Türkiye, Eastern Mediterranean Possibly Reveals Vibrio Bacteria Infection

ABSTRACTThe invasive Diadema setosum (Leske, 1778) long‐spined sea urchin has been in the Mediterranean Sea since 2006, and then, it has been known that its population density has reached high values on the southern Aegean coasts of Türkiye. This study aimed to report the mass mortality event of D. setosum with the determined agent on the Aegean coast of Türkiye. In addition, it was targeted to provide information on the current status of its density based on seasonal SCUBA diving observations for the period between January 2023 and November 2023. The results showed that the mass mortality of D. setosum was determined in Muğla, Aegean Sea, in August 2023. Spine loss, the mucoid layer at the bottom of the appendages, and the outer body surface were observed as the clinical symptoms of the diseased samples. Bacterial growth was detected on Vibrio‐selected TCBS agar plates, while no other parasitic agents were determined in the coelomic fluid of sea urchins. The results of the biochemical (API 20E) and molecular tests confirmed the isolated bacteria as Vibrio spp. The density of D. setosum showed statistically significant temporal changes, and the highest and lowest mean density values were recorded in autumn and spring, respectively. Environmental stressors, such as increasing sea temperature levels, affect the marine ecosystem and lead to opportunistic pathogens. Long‐term monitoring of disease outbreaks is necessary to understand the interactions between species and the ecosystem.

Increased levels of anti-Encephalitozoon intestinalis antibodies in patients with colorectal cancer.

The prevalence of microsporidiosis in the general population, or within specific groups of individuals/patients, is largely underestimated. The absence of specific seroprevalence tools limits knowledge of the epidemiology of these opportunistic pathogens, although known since the 1980s. Since microsporidia hijack the machinery of its host cell and certain species multiply within intestinal cells, a potential link between the parasite and colorectal cancer (CRC) has been suggested. To explore a potential epidemiological link between microsporidia and CRC, we evaluated the seroprevalence of Encephalitozoon intestinalis among CRC patients and healthy subjects using ELISA assays based on two recombinant proteins, namely rEiPTP1 and rEiSWP1, targeting polar tube and spore wall proteins. ELISA were performed in 141 CRC patients and 135 healthy controls. Patients with CRC had significantly higher anti-rEiPTP1 IgG levels than subjects in the control group. Anti-rEiPTP1 IgG, anti-rEiSWP1 IgG and anti-rEiPTP1 IgA levels were significantly increased among men with CRC compared to healthy men. Women with CRC who had died had higher rEiSWP1 IgG levels than those who were still alive. These higher antibody levels against microsporidia in patients with CRC suggest a relationship between microsporidia and pathophysiology of CRC.

Burkholderia cenocepacia epigenetic regulator M.BceJIV simultaneously engages two DNA recognition sequences for methylation

Burkholderia cenocepacia is an opportunistic and infective bacterium containing an orphan DNA methyltransferase called M.BceJIV with roles in regulating gene expression and motility of the bacterium. M.BceJIV recognizes a GTWWAC motif (where W can be an adenine or a thymine) and methylates N6 of the adenine at the fifth base position. Here, we present crystal structures of M.BceJIV/DNA/sinefungin ternary complex and allied biochemical, computational, and thermodynamic analyses. Remarkably, the structures show not one, but two DNA substrates bound to the M.BceJIV dimer, with each monomer contributing to the recognition of two recognition sequences. We also show that methylation at the two recognition sequences occurs independently, and that the GTWWAC motifs are enriched in intergenic regions in the genomes of B. cenocepacia strains. We further computationally assess the interactions underlying the affinities of different ligands (SAM, SAH, and sinefungin) for M.BceJIV, as a step towards developing selective inhibitors for limiting B. cenocepacia infection.

Perinatal HIV infection and opportunistic infectious pathology: morphological features of the placenta

Opportunistic infections account for more than 90% of all deaths associated with immunosuppression resulting from exposure to the human immunodeficiency virus (HIV). Fatal opportunistic infections include Pneumocystis pneumonia, cryptococcosis, cytomegalovirus infection, and viral hepatitis B and/or C. HIV-infected pregnant women have a high incidence of cytomegalovirus infection, which increases the risk of transplacental transmission of HIV from mother to fetus. In addition, an important factor in perinatal transmission of HIV is a genital infection caused by herpes simplex virus type 2 detected during pregnancy in HIV-infected women. Also, at present, there is no doubt about the possibility of damage to placental cells by the SARS-CoV-2 virus and its transplacental transmission.The aim of this study was to study the morphological features of the placenta in the presence of opportunistic infections caused by viruses of the herpes family (herpes simplex viruses types 1/2, cytomegalovirus, Epstein-Barr virus), as well as SARS-CoV2 in HIV-infected pregnant women.Materials and methods. A study was conducted of 21 placentas with various pregnancy outcomes in HIV-infected women, including 12 placentas obtained as a result of term birth, 1 placenta from premature birth at 29 weeks, and 8 observations of failed miscarriages (non-developing pregnancy).Results and discussion. Viral lesions were represented by the action of HIV with giant cell metamorphosis of trophoblast cells and placental macrophages, as well as infiltration by immunocompetent cells and fibrosis of the villous stroma. In addition, groups of immature villi were identified, the edematous stroma of which contained an increased number of large cells with light nuclei. In HIV-infected pregnant women with immunosuppression, the outcome of pregnancy in 8 cases was a miscarriage with a morphologically detected and immunohistochemically confirmed infection caused by herpes simplex virus types 1/2 (3 observations), cytomegalovirus (2 observations), and SARS-CoV-2 (3 observations), in 1 case the outcome of pregnancy was premature birth with morphologically identified and immunohistochemically confirmed infection caused by the Epstein-Barr virus.Conclusion. The placentas of HIV-infected pregnant women are characterized by impaired villous maturation with stromal fibrosis, which is the morphological substrate of chronic placental insufficiency with varying degrees of compensation. If HIVinfected pregnant women have opportunistic infections caused by viruses of the herpes family (herpes simplex viruses types 1/2, cytomegalovirus, Epstein-Barr virus), as well as SARS-CoV-2, pronounced involutive-dystrophic changes are observed in the placentas — perivillous deposition fibrinoid, petrification, which increases the likelihood of an unfavorable pregnancy outcome in the form of miscarriage or premature birth.

Features of the clinical course of the new coronavirus infection in HIV-infected patients

The aim. To study the features of the clinical course of a new coronavirus infection in patients infected with HIV.Materials and methods. The study included patients with HIV infection who received inpatient care for a new coronavirus infection (n=118). The diagnosis of U07.1 was made by detecting SARS-CoV-2 RNA. The diagnosis of U07.2 was made on the basis of epidemiological and clinical data in the presence of antibodies to SARS-CoV-2 in the blood.Results and discussion. The overall cohort of patients was dominated by women (55,9%), the average age of all co-infected patients was 37,5±2,78 years. The study was dominated by patients with a long history of HIV infection (66,1%), 43,2% received antiretroviral therapy (ART). The new coronavirus infection had a moderate course in 75,4% of patients. Severe form was recorded in 16,9% of patients. The mortality rate was 12,7%. The clinical picture of the new coronavirus infection upon admission was very variable due to comorbid pathology. The most frequently recorded symptoms upon admission were: increased body temperature (100%); weakness and increased fatigue (94,8%); cough (83,9%); shortness of breath (75,4%). Less frequently recorded: rhinorrhea (54,2%); sore throat (44,1%); gastrointestinal syndrome (21,2%); cerebral syndrome (17,8%); edematous-ascitic syndrome (13,5%); hepatolienal syndrome (13,5%); exanthema syndrome (10,2%). In 28,7% of patients, the number of CD4 lymphocytes was less than 200 cells/ml. The average level of CD4 lymphocytes was 321,3±43,6 cells/ml. The work revealed that as the degree of immunosuppression increased, there was a sharp increase in cases of severe forms of the new coronavirus infection, as well as an increase in deaths. The average HIV RNA level was 578 161,9±103 457,4 copecks/ml. A high HIV viral load (more than 100 000 cop/ml) was observed in 41,5% of cases, and only in this group of patients were severe forms of the new coronavirus infection recorded and, as a consequence, death. All observed patients had comorbid pathology in the form of opportunistic infections and/or concomitant diseases. The most frequently recorded opportunistic infections were: candidiasis (77,9%), cerebral toxoplasmosis (17,8%), Pneumocystis pneumonia (16,1%), tuberculosis (14,4%), central nervous system damage caused by the Epstein-Barr virus (10,2%), cytomegalovirus infection (6,78%), HIV-associated anemia (3,39%), cervical cancer (1,69%). Often opportunistic infections had a polyetiological cause. Of the concomitant diseases, bacterial pneumonia (66,9%), chronic viral hepatitis (40,7%), cardiovascular diseases (26,3%), diseases of the gastrointestinal tract (21,2%), and nervous system were most often recorded (5,93%), urinary system (5,08%) and cancer (5,03%). In 89,8% of coinfected patients, prolonged release of SARS-CoV-2 was observed, which affected the duration of antiviral therapy and the length of hospitalization.Conclusion. The new coronavirus infection and HIV infection are the intersection of two epidemics with the subsequent mutually aggravating effect of pathogens on each other. Among the co-infected patients, young people of working age, reproductive age (30–49 years) with a long history of HIV infection (66,1%) and not taking ART (56,3%) predominated. The new coronavirus infection in HIV-infected patients more often occurred in a moderate form (75,4%), pneumonia was recorded in 83,1%. A severe form of the new coronavirus infection was recorded in 16,9% of patients. The work shows that as the degree of immunosuppression increased, there was a sharp increase in the frequency of severe forms of the new coronavirus infection. In the general cohort of patients, comorbid pathology was recorded in the form of opportunistic infections and/or concomitant diseases. Often opportunistic infections had a polyetiological cause. Multimorbidity aggravated the condition of patients and largely increased the risk of an unfavorable outcome. Mortality in the group of coinfected patients was 12,7%.

The Influence of Silver-Containing Bionanomaterials Based on Humic Ligands on Biofilm Formation in Opportunistic Pathogens.

The uncontrolled use of antibiotics has led to a global problem of antimicrobial resistance. One of the main mechanisms of bacterial resistance is the formation of biofilms. In order to prevent the growth of antimicrobial resistance, it is crucial to develop new antibacterial agents that are capable of inhibiting the formation of biofilms. This makes this area of research highly relevant today. Promising candidates for these antibacterial agents are new bionanomaterials made from natural humic substances and silver nanoparticles. These substances have the potential to not only directly kill microorganisms but also penetrate biofilms and inhibit their formation. The goal of this study is to synthesize active pharmaceutical substances in the form of bionanomaterials, using ultradispersed silver nanoparticles in a matrix of coal humic substances, perform their characterization (NMR spectroscopy, TEM, and ICP-AES methods), and research their influence on biofilm formation in the most dangerous opportunistic pathogens (E. coli, Methicillin-resistant St. Aureus, K. pneumoniae, P. aeruginosa, St. aureus, A. baumannii, and K. Pneumonia). The results showed that all of the studied bionanomaterials had antibacterial activity against all of the opportunistic pathogens. Furthermore, they were found to have a suppressive effect on both pre-existing biofilms of these bacteria and their formation.

Genetic diversity and virulence properties of caprine Trueperella pyogenes isolates

BackgroundTrueperella pyogenes is an opportunistic pathogen that causes suppurative infections in various animal species, including goats. So far, only limited knowledge of phenotypic and genotypic properties of T. pyogenes isolates from goats has been gathered. In our study, we characterized the phenotypic and genotypic properties of caprine T. pyogenes isolates and established their relationship by Random Amplified Polymorphic DNA-Polymerase Chain Reaction (RAPD-PCR).ResultsFrom 2015 to 2023, 104 T. pyogenes isolates were obtained from 1146 clinical materials. In addition, two T. pyogenes isolates were obtained from 306 swabs collected from healthy goats. A total of 51 T. pyogenes isolates were subjected to detailed phenotypic and genotypic characterization. The virulence genotype plo/nanH/nanP/fimA/fimC/luxS was predominant. All of the tested isolates showed the ability to form a biofilm but with different intensities, whereby most of them were classified as strong biofilm formers (72.5%). The high level of genetic diversity among tested caprine T. pyogenes isolates (19 different RAPD profiles) was observed. The same RAPD profiles were found for isolates obtained from one individual, as well as from other animals in the same herd, but also in various herds.ConclusionsThis study provided important data on the occurrence of T. pyogenes infections in goats. The assessment of virulence properties and genetic relationships of caprine T. pyogenes isolates contributed to the knowledge of the epidemiology of infections caused by this pathogen in small ruminants. Nevertheless, further investigations are warranted to clarify the routes of transmission and dissemination of the pathogen.