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The African fig fly, Zaprionus indianus Gupta (Diptera: Drosophilidae), is an ecologically diverse pest species that interacts with and feeds on various microbial pathogens including bacteria and yeast found in decomposing fruits. However, the interaction of Z. indianus with its microbial community and microbial pathogens is obscure. To determine the presence of fungal pathogens, we collected wild Z. indianus from the northwestern part of the Indian subcontinent. Based on molecular identification and phylogenetic analysis, Debaryomyces hansenii (Zopf) Lodder & Kreger‐van Rij (isolate ziha1) was the most commonly observed fungus associated with Z. indianus. Furthermore, we identified two more opportunistic fungal pathogens: Aspergillus flavus Link (isolate zias2), and Pichia kudriavzevii Boidin, Pignal & Besson (isolate zibd3). The interaction of isolated fungi with Z. indianus was evaluated in terms of larval mortality, adult emergence, and fecundity. Debaryomyces hansenii ziha1 resulted in 90% emergence rate for adults, and did not cause significant mortality in the larval stage. In contrast, A. flavus zias2 and P. kudriavzevii zibd3 showed a significant reduction in fecundity and caused 99% and 74% larval mortality of Z. indianus, respectively. In the laboratory oviposition preference assay, mated females of Z. indianus preferred D. hansenii ziha1 supplemented food with a positive oviposition index compared to the uninfected control and compared to food infected with P. kudriavzevii zibd3 or A. flavus zias2. These findings underscore Z. indianus' potential to act as a reservoir for both symbiotic and pathogenic fungal species, some of which may be further harnessed for effective fruit fly pest control strategies. [ABSTRACT FROM AUTHOR]

Characteristics of microbiome of the pig's digestive tract play an important role in the animal's physiology, including metabolism, nutrient processing, the body's immune response, and disease resistance. This study aims to analyze the abundance and diversity of microorganisms (pathogenic and non-pathogenic) from the digestive system of pigs on farms in Tangerang District. The samples used in this research were pig feces from 43 pig farms in Tangerang District. Then DNA extraction was carried out using the Zymo Quick-DNA Fecal/Soil Microbe Kit according to manufacturing procedures. Sequencing was performed using an MGI DNBSEQ-G50 machine with a DNBSEQG50RS High-throughput sequencing set (FCL PE100) according to manufacturing procedures. The quality of fastq files was evaluated with FastQC. Taxonomic classification of the processed sequences was performed using Diamond, followed by MEGAN6. The microbiome of the pig's digestive system was dominated by bacteria (85%) with the taxonomic profile at the phylum level of abundance dominated by Firmicutes (84.46%) and Bacteroidetes (9.11%). Abundance at the genus level was dominated by Enterococcus (20.44%) and Clostridium (10.31%), and at the species level it was dominated by Escherichia coli (4.92%) and Levilactobacillus brevis (4.84%). There were 10 species of pathogenic bacteria detected, with E. coli showing the highest relative abundance (4.92%). Changes in the gut microbiome play an important role in the physiology of animal health and disease. In addition, the pathogenic bacteria detected not only affect the health and productivity of pigs but also have the potential to threaten public health. [ABSTRACT FROM AUTHOR]

Growing consumer awareness of the importance of food quality on their health is the main driving force for increasing the market for sustainable agricultural products. This makes sustainable, environmentally friendly production methods into non-chemical plant protection products against pathogens, including microbial biopreparations, increasingly important among farmers. Strawberry fruits (Fragaria x ananassa Duch.) are often negatively affected by fungal pathogens. The aim of this study was to evaluate the impact of five combinations of newly developed microbial biopreparations (from K2 to K6) on fungal pathogens and the yield of three strawberry cultivars. The research was conducted on a certified organic strawberry plantation in Poland in 2020–2021. In the first year of the study, no statistically significant positive impact of tested treatments on strawberry yields have been found. At the same time, yields of 'Honeoye' treated with K4 combination showed a tendency (with no statistical significance) to have higher yields than the control object by about 33%. In the second year of the study, yields of 'Honeoye' and 'Rumba' treated with K4 combination (containing Bacillus sp. Sp116AC*, Bacillus sp. Sp115AD, Bacillus sp. AF75BC and Bacillus subtilis AF75AB2, humic acids, yeast culture effluent, micronized dolomite, and mustard and rapeseed oil) significantly increased by 79% and 49%, respectively. Fruit infestation by fungal pathogens was reduced under some microbial treatments; however, the effect varied between years, cultivars, and tested biopreparations. The K2 combination showed a tendency (with no statistical significance) to limit B. cinerea infestation rate by 23% in 2020 and 21% in 2021, C. acutatum by 16% in 2021, and P. cactorum infestation rate by 30% in 2021. Tested microbial biopreparations showed a positive impact on the yield of strawberries and (to some extent) on disease infestation, with an impact on pathogen infestation strongly dependent on the year, variety, and biopreparation tested. [ABSTRACT FROM AUTHOR]

One of the main threats to aquaculture is represented by microbial pathogens, causing mass mortality episodes in hatcheries, which result in huge economic losses. Among the many disinfection methods applied to reduce this issue, the use of chemicals and beneficial microorganisms (probiotics) seems to be the most efficient. The aim of this study is to test the efficacy of two of them: a chemical, peracetic acid (PAA), and a probiotic, Phaeobacter inhibens. Tests were run on microalgae of the species Isochrysis galbana (var T-ISO). For both remedies, the microalgae survival rate and final cell concentration (cell/mL) were monitored. PAA analysis tested six different concentrations of the chemical: 7.5 µg, 10 µg/L, 20 µg/L, 30 µg/L, 40 µg/L, and 60 µg/L. Meanwhile, P. inhibens was tested with a concentration of 104 CFU/mL. Analysis for both the remedies was conducted on a laboratory scale using glass flasks, and on an industrial scale inside photobioreactors (PBRs). Among all the treatments, the one with PAA dosed with a concentration of 60 µg/L gave the best results, as the culture reached a final density of 8.61 × 106 cell/mL. However, none of the remedies involved in the experiment harmed microalgae or their growth. The results match perfectly with the condition requested for the tested remedies: to obtain an optimal breakdown of pathogens without interfering with culture growth. These features make PAA and P. inhibens good candidates for disinfection methods in aquaculture facilities. [ABSTRACT FROM AUTHOR]

The growing threat of antimicrobial-resistant (AMR) pathogens to human health worldwide emphasizes the need for more effective infection control strategies. Bacterial and fungal biofilms pose a major challenge in treating AMR pathogen infections. Biofilms are formed by pathogenic microbes encased in extracellular polymeric substances to confer protection from antimicrobials and the host immune system. Biofilms also promote the growth of antibiotic-resistant mutants and latent persister cells and thus complicate therapeutic approaches. Biofilms are ubiquitous and cause serious health risks due to their ability to colonize various surfaces, including human tissues, medical devices, and food-processing equipment. Detection and characterization of biofilms are crucial for prompt intervention and infection control. To this end, traditional approaches are often effective, yet they fail to identify the microbial species inside biofilms. Recent advances in artificial intelligence (AI) have provided new avenues to improve biofilm identification. Machine-learning algorithms and image-processing techniques have shown promise for the accurate and efficient detection of biofilm-forming microorganisms on biotic and abiotic surfaces. These advancements have the potential to transform biofilm research and clinical practice by allowing faster diagnosis and more tailored therapy. This comprehensive review focuses on the application of AI techniques for the identification of biofilm-forming pathogens in various industries, including healthcare, food safety, and agriculture. The review discusses the existing approaches, challenges, and potential applications of AI in biofilm research, with a particular focus on the role of AI in improving diagnostic capacities and guiding preventative actions. The synthesis of the current knowledge and future directions, as described in this review, will guide future research and development efforts in combating biofilm-associated infections. [ABSTRACT FROM AUTHOR]

Background: Land snails are considered a delicacy in many countries in Europe and sub-Saharan Africa. However, the interaction of microbial pathogens with land snails may present a public health threat when handling and/or consuming snails. This study examines the survival of Escherichia coli in edible land snails in a model system. Methods: Well-studied Shigatoxigenic (STEC) and non-STEC strains were compared. Mature Helix spp. were experimentally fed with E. coli-inoculated oats for 48 h. The snail feces after inoculation were periodically sampled and cultured for a 30-day period and subjected to microbiological analyses. Results: The average rate of decline of the non-STEC strain CSH-62 in the feces of live snails was significantly (p < 0.05) faster than that of STEC ERL 06-2503. In addition, the viable population of E. coli ERL 06-2503 significantly (p < 0.05) persisted for a longer time in the intestine of land snails than E. coli CSH-62. Conclusion: The results showed that the viable population of the E. coli strains examined demonstrated first-order kinetics, and their survival (CFU/mL) appeared significantly (p < 0.05) dependent on the E. coli pathotype. In addition, the continuous enumeration of E. coli in snail faeces indicated that land snails could serve as a mode of transmission of microbial pathogens to susceptible hosts, including humans. Further research is recommended to better quantify the direct and indirect health risks of pathogen transmission by edible snails to humans. [ABSTRACT FROM AUTHOR]

Microorganisms colonizing modern water-based metalworking fluids (MWFs) have been implicated in various occupational respiratory health hazards to machinists. An understanding of the exposure risks from specific microbial groups/genera/species (pathogenic or allergenic) and their endotoxins and the need for strategies for effective, timely fluid management warrant real-time extended tracking of the establishment of microbial diversity and the prevailing fluid-related factors. In the current study, the microbial community composition, succession, and dynamics of a freshly recharged industrial semi-synthetic MWF operation was tracked in real-time over a period of 50 weeks, using a combination of microbiological and molecular approaches. Substantial initial bacterial count (both viable and non-viable) even in the freshly recharged MWF pointed to the inefficiency of the dumping, cleaning, and recharge (DCR) process. Subsequent temporal analysis using optimized targeted genus/group-specific qPCR confirmed the presence of Pseudomonads, Enterics, Legionellae, Mycobacteria (M. immunogenum), Actinomycetes, and Fungi. In contrast, selective culturing using commercial culture media yielded non-specific isolates and collectively revealed Gram-negative (13 genera representing 19 isolates) and Gram-positive (2 genera representing 6 isolates) bacteria and fungi but not mycobacteria. Citrobacter sp. and Bacillus cereus represented the most frequent Gram-negative and Gram-positive isolates, respectively, across different media and Nectria haematococca isolation as the first evidence of this fungal pathogen colonizing semi-synthetic MWF. Unbiased PCR-DGGE analysis revealed a more diverse whole community composition revealing 22 bacterial phylotypes and their succession. Surges in the endotoxin level coincided with the spikes in Gram-negative bacterial population and biocide additions. Taken together, the results showed that semi-synthetic MWF is conducive for the growth of a highly diverse microbial community including potential bacterial and fungal pathogens, the current DCR practices are inefficient in combating microbial reestablishment, and the practice of periodic biocide additions facilitates the build-up of endotoxins and non-viable bacterial population. [ABSTRACT FROM AUTHOR]

In response to the growing global concern for environmental sustainability, a Life Cycle Assessment (LCA) study was conducted to evaluate the environmental benefits of the "Formula Servizi" GREEN protocol compared to a conventional cleaning protocol, as mandated by the updated Criteria for Environmental Sustainability (CAM—Criteri Ambientali Minimi) for cleaning services. The CAM, effective on 19 June 2021, requires companies to demonstrate the environmental advantages of their cleaning protocols over traditional methods. This study aligns with the new CAM guidelines and employs UNI EN ISO 14040–14044 technical standards for a comprehensive comparative analysis. The study highlights the significance of maintaining hygiene to ensure safety in various contexts, emphasizing the importance of environmental sampling and monitoring to prevent contamination and infection transmission. Despite the complexity and expenses associated with microbiological monitoring, this research affirms its crucial role in validating cleaning procedures, particularly in healthcare facilities, food service areas, and industrial settings. The findings reveal that both the "Traditional" and "GREEN" cleaning protocols demonstrate satisfactory effectiveness in controlling microbiological contamination according to established guidelines. Moreover, the LCA results indicate that the "GREEN" protocol, while exhibiting higher water consumption and wastewater treatment, showcases a strategic use of more sustainable cleaning and laundry detergents. Despite the increased water usage in certain phases, the significantly lower environmental impact per unit of weight demonstrates the potential for optimizing both environmental sustainability and operational efficiency in future Life Cycle Sustainability Assessment (LCSA) endeavors. The comparative LCA further reveals that the "GREEN" protocol enables an annual avoidance of 260 g of CO2-e emissions per square meter of cleaned surface. The most significant reduction in absolute terms is associated with the use of eco-labeled detergents in the laundry system, resulting in the avoidance of 654.1 kg of CO2-e per year of service (−77% compared to traditional laundry detergents). [ABSTRACT FROM AUTHOR]

This document is an editorial titled "The role of regulatory networks in virulence and antimicrobial resistance of microbial pathogens." It discusses the issue of antimicrobial resistance (AMR) and the need for research in various areas related to AMR, such as identifying resistance mechanisms, developing new therapeutic approaches, and improving epidemiological investigation and diagnostics. The editorial highlights several articles within the research topic that cover topics such as mechanisms of resistance in specific pathogens, the role of efflux pumps, and the impact of regulatory networks on virulence and drug resistance. The overall goal of the research topic is to advance our understanding of microbial drug resistance and regulatory networks in order to develop more effective intervention strategies. [Extracted from the article]

A significant number of people around the world suffer from illnesses that are related to the consumption of unsafe vegetable crops. Early identification of waterborne microbial pathogens affecting vegetable crops can be an important step towards the control of disease. Microbial pathogens secrete extracellular metabolic volatiles or molecular biomarkers that affect the yield and quality of vegetable crops. These secreted compounds can be investigated using several applied analytical techniques, such as metabolomics, proteomics and other 'omics' tools. Currently, it is possible to use these approaches to characterize a broad range of specialized metabolites present in vegetable crops affected by waterborne and soilborne microbial pathogens. Such approaches may be used to determine molecular biomarkers, which can subsequently be exploited for the diagnosis of microbial pathogens that affect vegetable crops. Molecular biomarkers are involved in complex pathogenic biological processes involving mechanisms of pathogenesis and could be of great interest in the field of metabolomics. This review investigates disease diagnostic strategies and emerging analytical metabolomics techniques for waterborne microbial pathogens in vegetable crops. These will be vital in building comprehensive and more reliable data regarding the nature of secreted proteins and other specialized metabolites in vegetable crops and will lead to an increased understanding of the interactions between the host and pathogenic oomycetes, fungi, bacteria and viruses. [ABSTRACT FROM AUTHOR]

Insects and microbial pathogens are ubiquitous and play significant roles in various biological processes, while microbial pathogens are microscopic organisms that can cause diseases in multiple hosts. Insects and microbial pathogens engage in diverse interactions, leveraging each other's presence. Metals are crucial in shaping these interactions between insects and microbial pathogens. However, metals such as Fe, Cu, Zn, Co, Mo, and Ni are integral to various physiological processes in insects, including immune function and resistance against pathogens. Insects have evolved multiple mechanisms to take up, transport, and regulate metal concentrations to fight against pathogenic microbes and act as a vector to transport microbial pathogens to plants and cause various plant diseases. Hence, it is paramount to inhibit insect–microbe interaction to control pathogen transfer from one plant to another or carry pathogens from other sources. This review aims to succinate the role of metals in the interactions between insects and microbial pathogens. It summarizes the significance of metals in the physiology, immune response, and competition for metals between insects, microbial pathogens, and plants. The scope of this review covers these imperative metals and their acquisition, storage, and regulation mechanisms in insect and microbial pathogens. The paper will discuss various scientific studies and sources, including molecular and biochemical studies and genetic and genomic analysis. [ABSTRACT FROM AUTHOR]

Introduction: Acute fascia dehiscence (FD) is a threatening complication occurring in 0.4–3.5% of cases after abdominal surgery. Prolonged hospital stay, increased mortality and increased rate of incisional hernias could be following consequences. Several risk factors are controversially discussed. Even though surgical infection is a known, indisputable risk factor, it is still not proven if a special spectrum of pathogens is responsible. In this study, we investigated if a specific spectrum of microbial pathogens is associated with FD. Methods: We performed a retrospective matched pair analysis of 53 consecutive patients with an FD after abdominal surgery in 2010–2016. Matching criteria were gender, age, primary procedure and surgeon. The primary endpoint was the frequency of pathogens detected intraoperatively, the secondary endpoint was the occurrence of risk factors in patients with (FD) and without (nFD) FD. Results: Intraabdominal pathogens were detected more often in the FD group (p = 0.039), with a higher number of Gram-positive pathogens. Enterococci were the most common pathogen (p = 0.002), not covered in 73% (FD group) compared to 22% (nFD group) by the given antibiotic therapy. Multivariable analysis showed detection of Gram-positive pathogens, detection of enterococci in primary laparotomy beside chronic lung disease, surgical site infections and continuous steroid therapy as independent risk factors. Conclusion: Risk factors are factors that reduce wound healing or increase intra-abdominal pressure. Furthermore detection of Gram-positive pathogens especially enterococci was detected as an independent risk factor and its empirical coverage could be advantageous for high-risk patients. [ABSTRACT FROM AUTHOR]

Poultry litter is a valuable crude protein feedstuff for ruminants, but it must be treated to kill pathogens before feeding. Composting effectively kills pathogens, but it risks losing ammonia to volatilization or leaching during degradation of uric acid and urea. Hops bitter acids also exert antimicrobial activity against certain pathogenic and nitrogen-degrading microbes. Consequently, the present studies were conducted to test if adding bitter acid-rich hop preparations to simulated poultry litter composts may improve nitrogen retention while simultaneously improving pathogen killing. Results from an initial study, testing doses of Chinook or Galena hops preparations designed to each deliver 79 ppm hops β-acid, revealed that, after nine days simulated composting of wood chip litter, ammonia concentrations were 14% lower (p < 0.05) in Chinook-treated composts than untreated composts (13.4 ± 1.06 µmol/g). Conversely, urea concentrations were 55% lower (p < 0.05) in Galena-treated than untreated composts (6.2 ± 1.72 µmol/g). Uric acid accumulations were unaffected by hops treatments in this study but were higher (p < 0.05) after three days than after zero, six, or nine days of composting. In follow-up studies, Chinook or Galena hops treatments (delivering 2042 or 6126 ppm of β-acid, respectively) for simulated composts (14 days) of wood chip litter alone or mixed 3:1 with ground Bluestem hay (Andropogon gerardii) revealed that these higher dosages had little effect on ammonia, urea, or uric acid accumulations when compared to untreated composts. Volatile fatty acid accumulations measured in these later studies were affected by the hops treatments, with butyrate accumulations being lower after 14 days in hops-treated composts than in untreated compost. In all studies, beneficial effects of Galena or Chinook hops treatments were not observed on the antimicrobial activity of the simulated composts, with composting by itself decreasing (p < 0.05) counts of select microbial populations by more than 2.5 log10 colony forming units/g compost dry matter. Thus, while hops treatments had little effect on pathogen control or nitrogen retention within the composted litter, they did lessen accumulations of butyrate, which may prevent adverse effects of this fatty acid on palatability of litter fed to ruminants. [ABSTRACT FROM AUTHOR]

Laboratory experiments in which blood‐borne parasitic microbes evolve in their animal hosts offer an opportunity to study parasite evolution and adaptation in real time and under natural settings. The main challenge of these experiments is to establish a protocol that is both practical over multiple passages and accurately reflects natural transmission scenarios and mechanisms. We provide a guide to the steps that should be considered when designing such a protocol, and we demonstrate its use via a case study. We highlight the importance of choosing suitable ancestral genotypes, treatments, number of replicates per treatment, types of negative controls, dependent variables, covariates, and the timing of checkpoints for the experimental design. We also recommend specific preliminary experiments to determine effective methods for parasite quantification, transmission, and preservation. Although these methodological considerations are technical, they also often have conceptual implications. To this end, we encourage other researchers to design and conduct in vivo evolution experiments with blood‐borne parasitic microbes, despite the challenges that the work entails. [ABSTRACT FROM AUTHOR]

Propolis has gained wide popularity over the last decades in several parts of the world. In parallel, the literature about propolis composition and biological properties increased markedly. A great number of papers have demonstrated that propolis from different parts of the world is composed mainly of phenolic substances, frequently flavonoids, derived from plant resins. Propolis has a relevant role in increasing the social immunity of bee hives. Experimental evidence indicates that propolis and its components have activity against bacteria, fungi, and viruses. Mechanisms of action on bacteria, fungi, and viruses are known for several propolis components. Experiments have shown that propolis may act synergistically with antibiotics, antifungals, and antivirus drugs, permitting the administration of lower doses of drugs and higher antimicrobial effects. The current trend of growing resistance of microbial pathogens to the available drugs has encouraged the introduction of propolis in therapy against infectious diseases. Because propolis composition is widely variable, standardized propolis extracts have been produced. Successful clinical trials have included propolis extracts as medicine in dentistry and as an adjuvant in the treatment of patients against COVID-19. Present world health conditions encourage initiatives toward the spread of the niche of propolis, not only as traditional and alternative medicine but also as a relevant protagonist in anti-infectious therapy. Production of propolis and other apiary products is environmentally friendly and may contribute to alleviating the current crisis of the decline of bee populations. Propolis production has had social-economic relevance in Brazil, providing benefits to underprivileged people. [ABSTRACT FROM AUTHOR]

The presence of microorganisms in water and food products is a chronic problem worldwide. This study attempts to develop pathogenic bacteria detection strategies using anti body-decorated gold nanorods (Au-NRs-Avidin-Ab-E) by electrochemical analysis. Escherichia coli ATCC 25922 was detected as the target with the antibody-modified Au-NRs. Cyclic voltammetry (CV) measurements were run on the Au-NRs-Avidin-Ab-E. coli immobilized on the surface of a screen-printed carbon electrode (SPCE) to capture the E. coli. The correlation between the different bacteria concentrations indicated excellent electrocatalytic activity within the linear range of 101 CFU/mL to 105 CFU/mL (R2 = 0.990), with a limit of detection (LOD) of 0.37 CFU/mL for the target. Findings revealed that electrochemical detection of the bacteria was enhanced after the deposition of antibody onto Au nanorods. The tailor-made approach offered multiple benefits, such as large sensing surface area and increased electron transfer abilities compared to the bare electrode. The developed dispersive electrode has potential selectivity towards the targeted bacteria among different bacteria electrochemically characterized. The developed E. coli ATCC 25922 antibody-based system optimized the sensing of the targeted bacteria in the presence of other bacteria, in particular E. coli O157/H7, Salmonella typhimurium, and Vibrio cholera, in real water samples. [ABSTRACT FROM AUTHOR]

Microbial infections and antibiotic resistance are some of the prime factors that are ascribed to endanger human health. Several reports have highlighted that drug-resistant pathogens assist in the etiology of various chronic diseases and lead to fatality. The present study deciphered the role of zinc oxide nanoparticles (ZnO NPs) as therapeutics against selected bacterial strains. The plant-based technique was followed to synthesize ZnO NPs. The synthesis was confirmed with different techniques viz. X-ray diffraction, transmission electron microscope (interplanar spacing at 0.126 nm), scanning electron microscope (flower-like structure), and Fourier transform infrared spectroscopy. The antibacterial analysis revealed that ZnO NPs inhibited the growth of all tested strains (Escherichia coli, Staphylococcus aureus, Salmonella typhi, Bacillus subtilis, and Klebsiella pneumoniae) to a greater extent (MIC ranged between 0.013±0.004-0.0625±0 mg/mL) as compared with ZnO compound (Bulk material). In the present study, ZnO NPs were produced in a cost-effective and environmentally sustainable way using a green process and can be used as a remedy for drug-resistant pathogens. [ABSTRACT FROM AUTHOR]

Nosocomial infections are a severe public health concern around the world, particularly in developing nations where infection control is difficult owing to financial constraints. Despite the significant drop in infectious disease due to advances in medical technology and medicine, it is well acknowledged that nosocomial infection has been one of the key impediments to better health conditions. The spread of bacterial species associated with number of medical devices for example commonly used stethoscope is one of the sources of infection. The presence of coagulase negative Staphylococcus species, Enterococci species, Escherichia coli, Klebsiella species and Acinetobacter species found to be common on stethoscope. The indiscriminate use of antibiotics without any regulation and proper screening certainly making many antibiotics non-functional to control their targeted pathogens. The hospital acquired pathogens mainly showcase increased incidences of antibiotic resistance. The purpose of this study is to examine epidemiologic characteristics of nosocomial infection and to find out effectives measures for their preventing. [ABSTRACT FROM AUTHOR]

Genetic interaction (GI) analysis is a powerful genetic strategy that analyzes the fitness and phenotypes of single- and double-gene mutant cells in order to dissect the epistatic interactions between genes, categorize genes into biological pathways, and characterize genes of unknown function. GI analysis has been extensively employed in model organisms for foundational, systems-level assessment of the epistatic interactions between genes. More recently, GI analysis has been applied to microbial pathogens and has been instrumental for the study of clinically important infectious organisms. Here, we review recent advances in systems-level GI analysis of diverse microbial pathogens, including bacterial and fungal species. We focus on important applications of GI analysis across pathogens, including GI analysis as a means to decipher complex genetic networks regulating microbial virulence, antimicrobial drug resistance and host–pathogen dynamics, and GI analysis as an approach to uncover novel targets for combination antimicrobial therapeutics. Together, this review bridges our understanding of GI analysis and complex genetic networks, with applications to diverse microbial pathogens, to further our understanding of virulence, the use of antimicrobial therapeutics and host−pathogen interactions. [ABSTRACT FROM AUTHOR]

Background The present research study was made to isolate and identify the pathogenic microorganism from environment of tertiary care hospital Lahore. This study also assessed the microbiological quality and efficacy of four commonly used disinfectants (Alpha Guard, Klortab NaDCC, Spray Off Virugard and UNISEPTA) in Jinnah Hospital Lahore in order to provide sterile environment. Material and Methods The sterilized cotton buds sticks wetted by dipping in normal saline were used to collect samples from various parts of hospital. A sum of 150 samples was obtained as many areas as possible of each surface. Disinfectants efficacy was determined for each isolate using the quantitative suspension test. Results The isolated microbial pathogens of work surfaces before disinfection were Staphylococcus aureus, Staphylococcus epidermidis, Pseudomonas aeruginosa, Klebsiella pneumoniae, Proteus mirabilis, Gram-positive bacilli, Micrococcus luteus and Candida species. All under study disinfectants were competent for disinfection in hospital at tested dilution which was taken as satisfactory on the basis of Log reduction, measured = 5. The Unisepta Plus disinfectant was more potent than Alpha Guard, Klortab NaDCC, and Spray off Virugard on the basis of bactericidal activity and individual killing rate. The bactericidal activity of the four disinfectants was time-dependent. Conclusions The results of this research study represents that there is need of assessing efficacy and quality of disinfectants from time to time to ensure the control of infections by choosing right disinfectant in right concentration for right contact time. [ABSTRACT FROM AUTHOR]

Platelets, small anucleate cells circulating in the blood, are critical mediators in haemostasis and thrombosis. Interestingly, recent studies demonstrated that platelets contain both pro-inflammatory and anti-inflammatory molecules, equipping platelets with immunoregulatory function in both innate and adaptive immunity. In the context of infectious diseases, platelets are involved in early detection of invading microorganisms and are actively recruited to sites of infection. Platelets exert their effects on microbial pathogens either by direct binding to eliminate or restrict dissemination, or by shaping the subsequent host immune response. Reciprocally, many invading microbial pathogens can directly or indirectly target host platelets, altering platelet count or/and function. In addition, microbial pathogens can impact the host auto- and alloimmune responses to platelet antigens in several immune-mediated diseases, such as immune thrombocytopenia, and fetal and neonatal alloimmune thrombocytopenia. In this review, we discuss the mechanisms that contribute to the bidirectional interactions between platelets and various microbial pathogens, and how these interactions hold relevant implications in the pathogenesis of many infectious diseases. The knowledge obtained from "well-studied" microbes may also help us understand the pathogenesis of emerging microbes, such as SARS-CoV-2 coronavirus. [ABSTRACT FROM AUTHOR]

The objective of the present study was the bioprospection of bioactive compounds from endophytic Thielaviopsis basicola with therapeutic applications, isolated from Ximenia americana, Western Ghats of Karnataka, India. The fresh and healthy leaves and roots of Ximenia americana were collected from the forests of Western Ghats of Karnataka, India. The collected explants were submerged for the enumeration and purification of fungal endophytes by using selective, and different media. Isolated fungal endophytes were processed for the production, extraction, phytochemical analysis, purification and evaluation of bioactive compounds by referring standard protocols. At a glance, endophyte derived bioactive compounds were used in in-vitro antagonistic, antioxidant antiurolithisis, and anticancer activity. A total of 32 pure isolates were obtained, 8 morphologically distinct fungal endophytes were identified from 200 explants of X. americana. Endophytic Thielaviopsis basicola was a core candidate identified and cultivated in solid-state fermentation on corn bran under the dark condition at 25° ± 2° for 15 days. Obtained 5.30g of aqueous crude extract per 100g of cornmeal were processed for qualitative phytochemical analysis, in alkaloids, terpenoids, flavonoids, phenols, tannins, and glycosides were found. The aqueous crude extract showed 0.761g of phenol and 0.276g of flavonoids content. From these crude extract TbCC1 and TbCC2, two fractions were purified by column chromatography and spotted potent bioactive compounds on thin layer chromatography. The FTIR data of TbCC1 and TbCC2 showed different functional groups such as alcohol, phenols, alkanes, alkenes, aromatic, alkyl halides, amines, ether, and nitrile. The TbCC1 exhibited prominent antagonistic activity and MIC against Staphylococcus aureus (24mm with 100µg/mL) and Candida albicans (22mm with 75µg/mL) while TbCC2 exhibited against Salmonella typhi (22mm with 75µg/mL) and Aspergillus fumigatus (18mm with 75µg/mL). The TbCC1 showed potent antioxidant activity (86.24±0.35) with 5.26µg/mL of IC50 value as compared with TbCC2. The maximum antiurolithiasis activity showed with 100% concentration at the rate of 67.5±1.49 of aqueous crude extract. The Sulphorodamine B assay showed MCF7 human breast cancer cell line viability 98.39±0.0250 at 100µg concentration and 40.81±0.0470 at 500µg with an IC50 value of 459.60µg. This is the first innovative report of endophytic Thielaviopsis basicola for their phytochemicals detection and prominent in-vitro activities from the selected plants. [ABSTRACT FROM AUTHOR]

This paper investigates the contamination of floodwaters in the urban center of Can Tho city, Vietnam. We sampled water from sewers, surface water bodies, and flood, before, during, and after specific flooding events. Total nucleic acid was extracted from the samples and subjected to a quantitative polymerase chain reaction (qPCR) to detect specific enteric pathogens. The difference between pathogen concentrations in floodwater and sewer water was compared by using the Mann Whitney U test. Correlations between the different pathogens were determined using the non-parametric Spearman test. E. coli and Rotavirus-A were the most prevalent pathogens in floodwater. We observed a weak association between E. coli and Rotavirus in flood-related waters (r < 0.5). Floodwater quality showed no difference to sewer water quality in terms of the E. coli and Rotavirus A concentrations (p > 0.05). Our results indicate that floodwater poses a significant urban public health risk due to the presence of enteric pathogens. [ABSTRACT FROM AUTHOR]

Aedes (Stegomyia) aegypti (L.) and Ae. (Stegomyia) albopictus (Skuse) mosquitoes can transmit dengue, chikungunya, yellow fever, and Zika viruses. Limited surveillance has led to uncertainty regarding the geographic ranges of these vectors globally, and particularly in regions at the present-day margins of habitat suitability such as the contiguous United States. Empirical habitat suitability models based on environmental conditions can augment surveillance gaps to describe the estimated potential species ranges, but model accuracy is unclear. We identified previously published regional and global habitat suitability models for Ae. aegypti (n = 6) and Ae. albopictus (n = 8) for which adequate information was available to reproduce the models for the contiguous U.S. Using a training subset of recently updated county-level surveillance records of Ae. aegypti and Ae. albopictus and records of counties conducting surveillance, we constructed accuracy-weighted, probabilistic ensemble models from these base models. To assess accuracy and uncertainty we compared individual and ensemble model predictions of species presence or absence to both training and testing data. The ensemble models were among the most accurate and also provided calibrated probabilities of presence for each species. The quantitative probabilistic framework enabled identification of areas with high uncertainty and model bias across the U.S. where improved models or additional data could be most beneficial. The results may be of immediate utility for counties considering surveillance and control programs for Ae. aegypti and Ae. albopictus. Moreover, the assessment framework can drive future efforts to provide validated quantitative estimates to support these programs at local, national, and international scales. [ABSTRACT FROM AUTHOR]

Blood stream infections rank among the top seven causes of death of the general population. The aim of our study was to better understand the epidemiology of BSI in order to improve diagnostics and patient outcome. We used retrospective aggregated laboratory data of blood samples received from all public hospitals in Tyrol, Austria between 2006 and 2015. Microorganisms were categorized into obligatory, facultative, unusual pathogens and contaminants. The distribution, the cumulative incidence and antimicrobial susceptibility patterns were compared between the tertiary (TH) and regional peripheral hospitals (PH). Among 256,364 blood samples, 76.1% were from the TH The incidence of obligatory pathogens was 1.7 fold, and up to 3 times higher for facultative, unusual pathogens and contaminants in the TH and increased mainly due to an increase of E.coli, which was the most common isolated pathogen (n = 2,869), followed by Staphylococcus aureus (n = 1,439), Enterococcus sp. (n = 953) and Klebsiella sp. (n = 816). The distribution of obligatory pathogens differed between the hospital settings: In the TH Enterococcus sp. accounted for 40.8% and E.coli for 70.4%, respectively, whereas in the PH for 25.4% (p<0.0001) and 57.8%, respectively (p<0.0001) Antibiotic resistance of Gram negative bacteria and Staphylococcus aureus did not change during the observation period. Carbapenem resistance of Klebsiella sp. and vancomycin and linezolid resistance of Enterococcus faecium showed a non-significant increase since 2010 in the TH setting. We concluded that the incidence of BSI in TH was higher compared to PH. We observed higher contamination rates in the TH. We could not interpret the data of coagulase negative staphylococci due to lack of clinical data. We strongly recommend enhancement of training on blood culture sampling to decrease the rate of contamination. Due to differences in pathogen distribution and antimicrobial resistance between different hospital settings we recommend separate treatment guidelines for BSI by hospital setting. [ABSTRACT FROM AUTHOR]

Purple seed stain (PSS) of soybean (Glycine max (L.) Merr.) is a prevalent seed disease. It results in poor seed quality and reduced seed lot market grade, and thus undermines value of soybean worldwide. The objectives of this research were to evaluate the reaction of selected soybean genotypes collected from 15 countries representing maturity groups (MGs) III, IV, and V to PSS, and to identify new sources of resistance to PSS based on three years of evaluation of natural field infection by Cercospora spp. in the Mississippi Delta of the U. S. In this study, 42 soybean genotypes were evaluated in 2010, 2011, and 2012. Seventeen lines including six MG III (PI 88490, PI 504488, PI 417361, PI 548298, PI 437482, and PI 578486), seven MG IV (PI 404173, PI 346308, PI 355070, PI 416779, PI 80479, PI 346307, and PI 264555), and four MG V (PI 417567, PI 417420, PI 381659, and PI 407749) genotypes had significantly lower percent seed infection by Cercospora spp. than the susceptible checks and other genotypes evaluated (P ≤ 0.05). These genotypes of soybean can be used in developing soybean cultivars or germplasm lines with resistance to PSS and for genetic mapping of PSS resistance genes. In addition, among these 17 lines with different levels of resistance to PSS, nine soybean genotypes (PI 417361, PI 504488, PI 88490, PI 346308, PI 416779, PI 417567, PI 381659, PI 417567, and PI 407749) were previously reported as resistant to Phomopsis seed decay. Therefore, they could be useful in breeding programs to develop soybean cultivars with improved resistance to both seed diseases. [ABSTRACT FROM AUTHOR]

Objectives: Hepatitis C virus (HCV) causes both acute and chronic infection, which can potentially develop into cirrhosis and liver cancer. Healthcare systems are struggling to finance costly direct-acting antiviral agents through public funding for uninsured patients, despite the unprecedented high cure rates of these agents. Vulnerable populations are at higher risk of HCV infection. The personal importation scheme is based on the legal right to import any unauthorized generics for personal use. This study was designed to assess the knowledge and perceptions of stakeholders on unauthorized generics. Methods: We conducted an anonymous online survey based on the fictitious situation of a patient diagnosed with HCV who lacked mandatory health insurance and personal financial resources. Results: We obtained a sample of 781 respondents: 445 physicians, 77 pharmacists, 51 patients and 207 non-healthcare professionals. We found that only 36% and 58% of respondents believe that the quality and efficacy, respectively, of unauthorized generics are equivalent to their corresponding brand. An overwhelming majority (98%) favoured quality control upon arrival, and 31% felt they could recognize fraudulent websites. A total of 79% expressed support for financial assistance for vulnerable patients, and support among physicians was 83%. Conclusions: Overall, the limited knowledge of the efficacy and quality of unauthorized generics, despite evidence in peer-reviewed literature, contrasts with the overwhelmingly positive attitudes toward financial assistance for personal import. This finding emphasizes the need for clearer information on imported generics and the potential safety provided by buyers' club schemes to complete the WHO agenda of eradicating viral hepatitis by 2030 within otherwise excluded vulnerable populations. [ABSTRACT FROM AUTHOR]

Thrips transmit one of the most devastating plant viruses worldwide–tomato spotted wilt tospovirus (TSWV). Tomato spotted wilt tospovirus is a type species in the genus Orthotospovirus and family Tospoviridae. Although there are more than 7,000 thrips species, only nine thrips species are known to transmit TSWV. In this study, we investigated the molecular factors that could affect thrips ability to transmit TSWV. We assembled transcriptomes of a vector, Frankliniella fusca [Hinds], and a non-vector, Frankliniella tritici [Fitch], and performed qualitative comparisons of contigs associated with virus reception, virus infection, and innate immunity. Annotations of F. fusca and F. tritici contigs revealed slight differences across biological process and molecular functional groups. Comparison of virus cell surface receptors revealed that homologs of integrin were present in both species. However, homologs of another receptor, heperan sulfate, were present in F. fusca alone. Contigs associated with virus replication were identified in both species, but a contig involved in inhibition of virus replication (radical s-adenosylmethionine) was only present in the non-vector, F. tritici. Additionally, some differences in immune signaling pathways were identified between vector and non-vector thrips. Detailed investigations are necessary to functionally characterize these differences between vector and non-vector thrips and assess their relevance in orthotospovirus transmission. [ABSTRACT FROM AUTHOR]

Background: Worldwide, the number of emerging and re-emerging infectious diseases is increasing, highlighting the importance of global disease pathogen surveillance. Traditional population-based methods may fail to capture important events, particularly in settings with limited access to health care, such as urban informal settlements. In such environments, a mixture of surface water runoff and human feces containing pathogenic microorganisms could be used as a surveillance surrogate. Method: We conducted a temporal metagenomic analysis of urban sewage from Kibera, an urban informal settlement in Nairobi, Kenya, to detect and quantify bacterial and associated antimicrobial resistance (AMR) determinants, viral and parasitic pathogens. Data were examined in conjunction with data from ongoing clinical infectious disease surveillance. Results: A large variation of read abundances related to bacteria, viruses, and parasites of medical importance, as well as bacterial associated antimicrobial resistance genes over time were detected. Significant increased abundances were observed for a number of bacterial pathogens coinciding with higher abundances of AMR genes. Vibrio cholerae as well as rotavirus A, among other virus peaked in several weeks during the study period whereas Cryptosporidium spp. and Giardia spp, varied more over time. Conclusion: The metagenomic surveillance approach for monitoring circulating pathogens in sewage was able to detect putative pathogen and resistance loads in an urban informal settlement. Thus, valuable if generated in real time to serve as a comprehensive infectious disease agent surveillance system with the potential to guide disease prevention and treatment. The approach may lead to a paradigm shift in conducting real-time global genomics-based surveillance in settings with limited access to health care. [ABSTRACT FROM AUTHOR]

In vitro and in vivo experiments were conducted to study the effects of synbiotic supplementation on Salmonella enterica ser. Enteritidis (SE) proliferation, cecal content load, and broiler carcass contamination. Lactobacillus reuteri, Enterococcus faecium, Bifidobacterium animalis, and Pediococcus acidilactici culture supernatants decreased (P < 0.05) the in vitro proliferation of SE at 1:1 supernatant: pathogen dilution. A total of 240 Cobb-500 broiler chicks were randomly allotted to three treatment groups (8 replicates/group with 10 birds/replicate): control (basal diet), antibiotic (Virginiamycin at 20 mg/kg feed), synbiotic (PoultryStar® ME at 0.5 g/kg feed containing L. reuteri, E. faecium, B. animalis, P. acidilactici and a Fructooligosaccharide) from day of hatch. At 21 d of age, all birds in experimental groups were orally inoculated with 250 μl of 1 X 109 CFU SE. Antibiotic supplementation increased (P < 0.05) body weight and feed consumption, compared to the control group. Birds in the synbiotic supplementation had intermediate body weight and feed consumption that were not significantly different from both the control and antibiotic group at 42 d of age in SE infected birds. No significant effects were observed in feed efficiency at 42 d of age among the groups. Antibiotic and synbiotic supplementation decreased (P < 0.05) SE load in cecal contents by 0.90 and 0.85 log units/ g and carcass SE load by 1.4 and 1.5 log units/mL of rinsate compared to the control group at 42 d of age (21 dpi). The relative abundance of IL-10, IL-1, TLR-4, and IFNγ mRNA was decreased (P < 0.05) in the antibiotic and synbiotic supplementation groups compared to the control birds at 42 d of age (21 dpi). It can be concluded that synbiotic supplementation decreased SE proliferation in vitro and decreased SE load in the cecal contents and broiler carcass. [ABSTRACT FROM AUTHOR]

Two recent reports suggested that the less common, less virulent enterococcal species, Enterococcus gallinarum and E. casseliflavus, with low-level vancomycin resistance due to chromosomally encoded vanC1 and vanC2/3, may influence host immunity. We reported that peri-transplant gut colonization with E. gallinarum and E. casseliflavus is associated with lower mortality after allogeneic hematopoietic cell transplantation (HCT). Because most acute leukemia patients undergoing HCT have received intensive chemotherapy (usually requiring prolonged hospitalization) for their underlying disease before HCT, we hypothesized that some may have acquired vanC-positive enterococci during chemotherapy. Therefore, we evaluated the presence of the vanC gene cluster using vanC1 and vanC2/3 qPCR in thrice-weekly collected stool samples from 20 acute leukemia patients undergoing intensive chemotherapy. We found that an unexpectedly large proportion of patients have detectable vanC1 and vanC2/3 (15% and 35%, respectively) in at least one stool sample. Comparing qPCR results with 16S rRNA gene sequencing results suggested that E. gallinarum may reach high abundances, potentially persisting into HCT and influencing transplant outcomes. [ABSTRACT FROM AUTHOR]

In the present study, antibiotic residues were detected in milk samples collected from the dairy herds located in Karnataka, India, by microbiological assay. Subsequently, the detected antibiotics were identified as azithromycin and tetracycline, by high-performance liquid chromatography, further both the antibiotics detected in the cow milk samples were found to be at high concentration (9708.7 and 5460 μg kg-1, respectively). We then investigated the effects of temperature and pH on the stabilities of azithromycin and tetracycline to determine the degradation rate constant k using first-order kinetic equation. Results indicated that significant reduction in stability and antibacterial activity of azithromycin solution when subjected to 70 and 100°C for 24 h. While stability of tetracycline was significantly reduced when subjected to 70 and 100°C for 24 h. However no significant reduction in antibacterial activity of tetracycline was observed at respective temperatures when compared with that of control. In addition, the stabilities of azithromycin and tetracycline were found to be decreased in acidic pH 4–5. The results of the present study revealed the high risk of contamination of milk sample with veterinary antibiotics and also demonstrated the effect of temperature and pH on stability of antibiotics. Therefore the study suggest that the qualitative and quantitative screening of milk for the presence of antibiotics need to be strictly performed to ensure safe drinking milk for consumers. [ABSTRACT FROM AUTHOR]

Background: Persons who inject drugs (PWID) have high HIV incidence and prevalence, and may have limited access to antiretroviral therapy (ART) in some settings. We evaluated HIV drug resistance in PWID in a randomized clinical trial (HPTN 074). The study intervention included ART at any CD4 cell count with enhanced support for ART and substance use treatment. Methods: HPTN 074 enrolled HIV-infected PWID (index participants) with viral loads ≥1,000 copies/mL and their HIV-uninfected injection-network partners in Indonesia, Ukraine, and Vietnam; the study limited enrollment of people who reported being on ART. HIV drug resistance testing and antiretroviral (ARV) drug testing were performed using samples collected from index participants at study enrollment. Results: Fifty-four (12.0%) of 449 participants had HIV drug resistance; 29 (53.7%) of the 54 participants had multi-class resistance. Prevalence of resistance varied by study site and was associated with self-report of prior or current ART, detection of ARV drugs, and a history of incarceration. Resistance was detected in 10 (5.6%) of 177 newly diagnosed participants. Participants with resistance at enrollment were less likely to be virally suppressed after 52 weeks of follow-up, independent of study arm. Conclusions: In HPTN 074, many of the enrolled index participants had HIV drug resistance and more than half of those had multi-class resistance. Some newly-diagnosed participants had resistance, suggesting that they may have been infected with drug-resistant HIV strains. Behavioral and geographic factors were associated with baseline resistance. Baseline resistance was associated with reduced viral suppression during study follow-up. These findings indicate the need for enhanced HIV care in this high-risk population to achieve sustained viral suppression on ART. [ABSTRACT FROM AUTHOR]

Four fungi isolated from trunks and branches of European hazelnut (Corylus avellana L.) from commercial orchards in the Willamette Valley, Oregon were characterized and pathogenicity was tested on potted hazelnut trees. The acreage of hazelnuts in Oregon has expanded greatly in recent years in response to the availability of Eastern filbert blight resistant cultivars. Fungi were characterized using the BLASTn algorithm and the GenBank database with multiple partial gene sequence(s). If BLASTn and GenBank were not sufficient for species-level identification, then a multilocus sequence analysis (MLSA) was performed. The four pathogens were identified as Diplodia mutilla (Fr.) Mont., Dothiorella omnivora B.T. Linaldeddu, A. Deidda & B. Scanu, Valsa cf. eucalypti Cooke & Harkn., and Diaporthe eres Nitschke. All pathogens but D. omnivora have not been previously reported from European hazelnut in the literature. All four pathogens caused lesions on trunks bare root hazelnut trees cv. 'Jefferson' planted in pots in the greenhouse and fungi were re-isolated from inoculated trees. D. mutilla appeared particularly aggressive in repeated inoculation experiments. [ABSTRACT FROM AUTHOR]

Introduction: Patients suffering from Sickle Cell Disease (SCD) are at increased risk for complications due to influenza virus. Annual influenza vaccination is strongly recommended but few clinical studies have assessed its immunogenicity in individuals with SCD. The aim of this study was to explore the biological efficacy of annual influenza vaccination in SCD patients by characterizing both their humoral and cell-mediated immunity against influenza antigen. We also aimed to investigate these immunological responses among SCD individuals according to their treatment (hydroxyurea (HU), chronic blood transfusions (CT), both HU and CT or none of them). Methods: Seventy-two SCD patients (49 receiving HU, 9 on CT, 7 with both and 7 without treatment) and 30 healthy controls were included in the study. All subjects received the tetravalent influenza α-RIX-Tetra® vaccine from the 2016–2017 or 2017–2018 season. Results: Protective anti-influenza HAI titers were obtained for the majority of SCD patients one month after vaccination but seroconversion rates in patient groups were strongly decreased compared to controls. Immune cell counts, particularly cellular memory including memory T and memory B cells, were greatly reduced in SCD individuals. Functional activation assays confirmed a poorer CD8+ T cell memory. We also document an imbalance of cytokines after influenza vaccination in SCD individuals with an INFγ/IL-10 ratio (Th1-type/Treg-type response) significantly lower in the SCD cohort. Conclusion: SCD patients undergoing CT showed altered immune regulation as compared to other treatment subgroups. Altogether, the cytokine imbalance, the high regulatory T cell levels and the low memory lymphocyte subset levels observed in the SCD cohort, namely for those on CT, suggest a poor ability of SCD patients to fight against influenza infection. Nevertheless, our serological data support current clinical practice for annual influenza vaccination, though immunogenicity to other vaccines involving immunological memory might be hampered in SCD patients and should be further investigated. [ABSTRACT FROM AUTHOR]

Background: Many countries have initiated school-based human papillomavirus (HPV) vaccination programs. The real-life effectiveness of HPV vaccines has become increasingly evident, especially among girls vaccinated before HPV exposure in countries with high vaccine uptake. In 2009, Norway initiated a school-based HPV vaccination program for 12-year-old girls using the quadrivalent HPV vaccine (Gardasil®), which targets HPV6, 11, 16, and 18. Here, we aim to assess type-specific vaginal and oral HPV prevalence in vaccinated compared with unvaccinated girls in the first birth cohort eligible for school-based vaccination (born in 1997). Methods: This observational, cross-sectional study measured the HPV prevalence ratio (PR) between vaccinated and unvaccinated girls in Norway. Facebook advertisement was used to recruit participants and disseminate information about the study. Participants self-sampled vaginal and oral specimens using an Evalyn® Brush and a FLOQSwab™, respectively. Sexual behavior was ascertained through a short questionnaire. Results: Among the 312 participants, 239 (76.6%) had received at least one dose of HPV vaccine prior to sexual debut. 39.1% of vaginal samples were positive for any HPV type, with similar prevalence among vaccinated and unvaccinated girls (38.5% vs 41.1%, PR: 0.93, 95% confidence interval [CI]: 0.62–1.41). For vaccine-targeted types there was some evidence of lower prevalence in the vaccinated (0.4%) compared to the unvaccinated (6.8%) group (PR: 0.06, 95%CI: 0.01–0.52). This difference remained after adjusting for sexual behavior (PR: 0.04, 95%CI: 0.00–0.42). Only four oral samples were positive for any HPV type, and all of these participants had received at least one dose of HPV vaccine at least 1 year before oral sexual debut. Conclusion: There is evidence of a lower prevalence of vaccine-targeted HPV types in the vagina of vaccinated girls from the first birth cohort eligible for school-based HPV vaccination in Norway; this was not the case when considering all HPV types or types not included in the quadrivalent HPV vaccine. [ABSTRACT FROM AUTHOR]

Neisseria gonorrhoeae antimicrobial resistance (AMR) surveillance is essential for tracking the emergence and spread of AMR strains in local, national and international populations. This is crucial for developing or refining treatment guidelines. N. gonorrhoeae multiantigen sequence typing (NG-MAST) is beneficial for describing the molecular epidemiology of gonococci at national and international levels. Elucidation of AMR determinants to β-lactam drugs, is a means of monitoring the development of resistance. In Ghana, little is known about the current gonococcal AMR prevalence and no characterization of gonococcal isolates has been previously performed. In this study, gonococcal isolates (n = 44) collected from five health facilities in Ghana from 2012 to 2015, were examined using AMR testing, NG-MAST and sequencing of penA. High rates of resistance were identified to tetracycline (100%), benzylpenicillin (90.9%), and ciprofloxacin (81.8%). One isolate had a high cefixime MIC (0.75 μg/ml). Twenty-eight NG-MAST sequence types (STs) were identified, seventeen of which were novel. The isolate with the high cefixime MIC contained a mosaic penA-34 allele and belonged to NG-MAST ST1407, an internationally spreading multidrug-resistant clone that has accounted for most cefixime resistance in many countries. In conclusion, AMR testing, NG-MAST, and sequencing of the AMR determinant penA, revealed high rates of resistance to tetracycline, benzylpenicillin, and ciprofloxacin; as well as a highly diverse population of N. gonorrhoeae in Ghana. It is imperative to continue with enhanced AMR surveillance and to understand the molecular epidemiology of gonococcal strains circulating in Ghana and other African countries. [ABSTRACT FROM AUTHOR]

Pseudomonas syringae is a taxon of plant pathogenic bacteria that can colonize and proliferate within the interior space of leaf tissue. This process requires P. syringae to rapidly upregulate the production of virulence factors including a type III secretion system (T3SS) that suppress host defenses. GacS/A is a two-component system that regulates virulence of many plant and animal pathogenic bacteria including P. syringae. We recently investigated the virulence defect of strain AC811, a Tn5: :gacA mutant of P. syringae pv. tomato DC3000 that is less virulent on Arabidopsis. We discovered that decreased virulence of AC811 is not caused by loss of GacA function. Here, we report the molecular basis of the virulence defect of AC811. We show that AC811 possesses a nonsense mutation in anmK, a gene predicted to encode a 1,6-anhydromuramic acid kinase involved in cell wall recycling. Expression of a wild-type allele of anmK partially increased growth of AC811 in Arabidopsis leaves. In addition to the defective anmK allele, we also show that the Tn5 insertion in gacA exerts a polar effect on uvrC, a downstream gene encoding a regulator of DNA damage repair. Expression of the wild-type anmK allele together with increased expression of uvrC fully restored the virulence of AC811 during infection of Arabidopsis. These results demonstrate that defects in anmK and uvrC are together sufficient to account for the decreased virulence of AC811, and suggest caution is warranted in assigning phenotypes to GacA function based on insertional mutagenesis of the gacA-uvrC locus. [ABSTRACT FROM AUTHOR]

The intracellular pathogen Listeria monocytogenes is distinguished by its ability to invade and replicate within mammalian cells. Remarkably, of the 15 serovars within the genus, strains belonging to serovar 4b cause the majority of listeriosis clinical cases and outbreaks. The Listeria O-antigens are defined by subtle structural differences amongst the peptidoglycan-associated wall-teichoic acids (WTAs), and their specific glycosylation patterns. Here, we outline the genetic determinants required for WTA decoration in serovar 4b L. monocytogenes, and demonstrate the exact nature of the 4b-specific antigen. We show that challenge by bacteriophages selects for surviving clones that feature mutations in genes involved in teichoic acid glycosylation, leading to a loss of galactose from both wall teichoic acid and lipoteichoic acid molecules, and a switch from serovar 4b to 4d. Surprisingly, loss of this galactose decoration not only prevents phage adsorption, but leads to a complete loss of surface-associated Internalin B (InlB),the inability to form actin tails, and a virulence attenuation in vivo. We show that InlB specifically recognizes and attaches to galactosylated teichoic acid polymers, and is secreted upon loss of this modification, leading to a drastically reduced cellular invasiveness. Consequently, these phage-insensitive bacteria are unable to interact with cMet and gC1q-R host cell receptors, which normally trigger cellular uptake upon interaction with InlB. Collectively, we provide detailed mechanistic insight into the dual role of a surface antigen crucial for both phage adsorption and cellular invasiveness, demonstrating a trade-off between phage resistance and virulence in this opportunistic pathogen. [ABSTRACT FROM AUTHOR]

Background: In endemic regions, asymptomatic Leishmania infection is common. In HIV patients, detection of asymptomatic Leishmania infection could potentially identify those at risk of visceral leishmaniasis (VL). However, data on the prevalence, incidence, and determinants of asymptomatic infection, and the risk of VL are lacking. Methods: We conducted a cross-sectional survey at a single ART centre, followed by a prospective cohort study amongst HIV-infected adults in HIV care in a district hospital in a VL-endemic area in North-West Ethiopia (9/2015-8/2016). Asymptomatic Leishmania infection was detected using the direct agglutination test (DAT), rK39-rapid diagnostic test (RDT)), PCR on peripheral blood and the KAtex urine antigen test, and defined as positivity on any Leishmania marker. All individuals were followed longitudinally (irrespective of the Leishmania test results). Risk factors for asymptomatic Leishmania infection were determined using logistic regression. Results: A total of 534 HIV-infected individuals enrolled in HIV care were included in the study. After excluding 13 patients with a history of VL and an 10 patients with incomplete baseline Leishmania tests, 511 were included in analysis. The median age was 38 years (interquartile range (IQR) 30–45), 62.6% were male. The median follow-up time was 12 months (IQR 9–12). No deaths were reported during the study period. Most (95.5%) were on antiretroviral treatment at enrolment, for a median of 52 months (IQR 27–79). The median CD4 count at enrolment was 377 cells/mm3 (IQR 250–518). The baseline prevalence of Leishmania infection was 12.8% in males and 4.2% in females. Overall, 7.4% tested positive for rK39, 4.3% for DAT, 0.2% for PCR and 0.2% for KAtex. Independent risk factors for a prevalent infection were male sex (odds ratio (OR) 3.2; 95% confidence intervals (CI) 14–7.0) and concurrent malaria infection (OR 6.1; 95% CI 1.9–18.9). Amongst the 49 prevalent (baseline) infections with further follow-up, the cumulative incidence of losing the Leishmania markers by one year was 40.1%. There were 36 incident infections during the course of the study, with a cumulative one-year risk of 9.5%. Only one case of VL was detected during follow-up. Conclusions: We found a high prevalence of asymptomatic Leishmania infection, persisting in most cases. The incidence was more modest and overt VL was rare. Larger and longer studies with more complete follow-up may help to decide whether a test and treat strategy would be justified in this context. Trial registration: ClinicalTrials.gov [ABSTRACT FROM AUTHOR]

Paracoccidioides spp. are thermodimorphic fungi that cause a neglected tropical disease (paracoccidioidomycosis) that is endemic to Latin America. These fungi inhabit the soil, where they live as saprophytes with no need for a mammalian host to complete their life cycle. Despite this, they developed sophisticated virulence attributes allowing them not only to survive in host tissues but also to cause disease. A hypothesis for selective pressures driving the emergence or maintenance of virulence of soil fungi is their interaction with soil predators such as amoebae and helminths. We evaluated the presence of environmental amoeboid predators in soil from armadillo burrows where Paracoccidioides had been previously detected and tested if the interaction of Paracoccidioides with amoebae selects for fungi with increased virulence. Nematodes, ciliates, and amoebae–all potential predators of fungi–grew in cultures from soil samples. Microscopical observation and ITS sequencing identified the amoebae as Acanthamoeba spp, Allovahlkampfia spelaea, and Vermamoeba vermiformis. These three amoebae efficiently ingested, killed and digested Paracoccidioides spp. yeast cells, as did laboratory adapted axenic Acanthamoeba castellanii. Sequential co-cultivation of Paracoccidioides with A. castellanii selected for phenotypical traits related to the survival of the fungus within a natural predator as well as in murine macrophages and in vivo (Galleria mellonella and mice). These changes in virulence were linked to the accumulation of cell wall alpha-glucans, polysaccharides that mask recognition of fungal molecular patterns by host pattern recognition receptors. Altogether, our results indicate that Paracoccidioides inhabits a complex environment with multiple amoeboid predators that can exert selective pressure to guide the evolution of virulence traits. [ABSTRACT FROM AUTHOR]

Defining cases of Zika virus (ZIKV) infection is a critical challenge for epidemiological research. Due to ZIKV’s overlapping clinical features and potential immunologic cross-reactivity with other flaviviruses and the current lack of an optimal ZIKV-specific diagnostic assay, varying approaches for identifying ZIKV infections have been employed to date. This paper presents the laboratory results and diagnostic criteria developed by the Microcephaly Epidemic Research Group for defining cases of maternal ZIKV infection in a cohort of pregnant women with rash (N = 694) recruited during the declining 2015–2017 epidemic in northeast Brazil. For this investigation, we tested maternal sera for ZIKV by quantitative reverse transcription polymerase chain reaction (qRT-PCR), Immunoglobulin (Ig) M and IgG3 enzyme-linked immunosorbent assays (ELISAs), and Plaque Reduction Neutralization Test (PRNT50). Overall, 23.8% of participants tested positive by qRT-PCR during pregnancy (range of detection: 0–72 days after rash onset). However, the inter-assay concordance was lower than expected. Among women with qRT-PCR-confirmed ZIKV and further testing, only 10.1% had positive IgM tests within 90 days of rash, and only 48.5% had ZIKV-specific PRNT50 titers ≥20 within 1 year of rash. Given the complexity of these data, we convened a panel of experts to propose an algorithm for identifying ZIKV infections in pregnancy based on all available lines of evidence. When the diagnostic algorithm was applied to the cohort, 26.9% of participants were classified as having robust evidence of a ZIKV infection during pregnancy, 4.0% as having moderate evidence, 13.3% as having limited evidence of a ZIKV infection but with uncertain timing, and 19.5% as having evidence of an unspecified flavivirus infection before or during pregnancy. Our findings suggest that integrating longitudinal data from nucleic acid and serologic testing may enhance diagnostic sensitivity and underscore the need for an on-going dialogue regarding the optimization of strategies for defining cases of ZIKV in research. [ABSTRACT FROM AUTHOR]

The case-fatality rate of yellow fever virus (YFV) is one of the highest among arthropod-borne viruses (arboviruses). Although historically, the Asia-Pacific region has remained free of YFV, the risk of introduction has never been higher due to the increasing influx of people from endemic regions and the recent outbreaks in Africa and South America. Singapore is a global hub for trade and tourism and therefore at high risk for YFV introduction. Effective control of the main domestic mosquito vector Aedes aegypti in Singapore has failed to prevent re-emergence of dengue, chikungunya and Zika viruses in the last two decades, raising suspicions that peridomestic mosquito species untargeted by domestic vector control measures may contribute to arbovirus transmission. Here, we provide empirical evidence that the peridomestic mosquito Aedes malayensis found in Singapore can transmit YFV. Our laboratory mosquito colony recently derived from wild Ae. malayensis in Singapore was experimentally competent for YFV to a similar level as Ae. aegypti controls. In addition, we captured Ae. malayensis females in one human-baited trap during three days of collection, providing preliminary evidence that host-vector contact may occur in field conditions. Finally, we detected Ae. malayensis eggs in traps deployed in high-rise building areas of Singapore. We conclude that Ae. malayensis is a competent vector of YFV and re-emphasize that vector control methods should be extended to target peridomestic vector species. [ABSTRACT FROM AUTHOR]

Evolutionarily conserved NusG protein enhances bacterial RNA polymerase processivity but can also promote transcription termination by binding to, and stimulating the activity of, Rho factor. Rho terminates transcription upon anchoring to cytidine-rich motifs, the so-called Rho utilization sites (Rut) in nascent RNA. Both NusG and Rho have been implicated in the silencing of horizontally-acquired A/T-rich DNA by nucleoid structuring protein H-NS. However, the relative roles of the two proteins in H-NS-mediated gene silencing remain incompletely defined. In the present study, a Salmonella strain carrying the nusG gene under the control of an arabinose-inducible repressor was used to assess the genome-wide response to NusG depletion. Results from two complementary approaches, i) screening lacZ protein fusions generated by random transposition and ii) transcriptomic analysis, converged to show that loss of NusG causes massive upregulation of Salmonella pathogenicity islands (SPIs) and other H-NS-silenced loci. A similar, although not identical, SPI-upregulated profile was observed in a strain with a mutation in the rho gene, Rho K130Q. Surprisingly, Rho mutation Y80C, which affects Rho’s primary RNA binding domain, had either no effect or made H-NS-mediated silencing of SPIs even tighter. Thus, while corroborating the notion that bound H-NS can trigger Rho-dependent transcription termination in vivo, these data suggest that H-NS-elicited termination occurs entirely through a NusG-dependent pathway and is less dependent on Rut site binding by Rho. We provide evidence that through Rho recruitment, and possibly through other still unidentified mechanisms, NusG prevents pervasive transcripts from elongating into H-NS-silenced regions. Failure to perform this function causes the feedforward activation of the entire Salmonella virulence program. These findings provide further insight into NusG/Rho contribution in H-NS-mediated gene silencing and underscore the importance of this contribution for the proper functioning of a global regulatory response in growing bacteria. The complete set of transcriptomic data is freely available for viewing through a user-friendly genome browser interface. [ABSTRACT FROM AUTHOR]

Phosphohexomutase superfamily enzymes catalyze the reversible intramolecular transfer of a phosphoryl moiety on hexose sugars. Bacillus subtilis phosphoglucomutase PgcA catalyzes the reversible interconversion of glucose 6-phosphate (Glc-6-P) and glucose 1-phosphate (Glc-1-P), a precursor of UDP-glucose (UDP-Glc). B. subtilis phosphoglucosamine mutase (GlmM) is a member of the same enzyme superfamily that converts glucosamine 6-phosphate (GlcN-6-P) to glucosamine 1-phosphate (GlcN-1-P), a precursor of the amino sugar moiety of peptidoglycan. Here, we present evidence that B. subtilis PgcA possesses activity as a phosphoglucosamine mutase that contributes to peptidoglycan biosynthesis. This activity was made genetically apparent by the synthetic lethality of pgcA with glmR, a positive regulator of amino sugar biosynthesis, which can be specifically suppressed by overproduction of GlmM. A gain-of-function mutation in a substrate binding loop (PgcA G47S) increases this secondary activity and suppresses a glmR mutant. Our results demonstrate that bacterial phosphoglucomutases may possess secondary phosphoglucosamine mutase activity, and that this dual activity may provide some level of functional redundancy for the essential peptidoglycan biosynthesis pathway. [ABSTRACT FROM AUTHOR]

Background: In Sub-Saharan Africa, both HIV/AIDS and anemia have considerable public health problems. Anemia has an adverse effect on treatment outcome and it decreases the quality of life among adult HIV patients. This study was aimed to assess the prevalence of anemia and its associated factors among adult HIV positive patients in Wolaita Sodo University Teaching Referral Hospital. Method: Institution based cross-sectional study was conducted at Wolaita Sodo University Teaching Referral Hospital from 01 October to December 30, 2016. A randomly selected 411 adult people living with the human immunodeficiency virus were included in the study. A pre-tested questionnaire was used to collect data. Variables with P-value ≤0.25 in the bivariable logistic regression model were taken into multivariable logistic regression analysis along with 95% confidence interval and Odds Ratio was used to examine the association between anemia and independent variables. P˗value ≤ 0.05 was taken as statistically significant. Result: Prevalence of anemia in this study was 36.5% with 95% CI (32%-41%). Factors associated with anemia among adult people living with HIV/AIDS were individuals who lived with HIV ≥9years (AOR = 2.6, 95% CI:-1.03–6.59),years lived with HIV 5–8 years (AOR = 2.59, 95% CI:-1.02–6.57),CD4 count <200cells/ul (AOR = 4.2, 95%CI:-2.03–8.67), CD4 count200-350cells/ul(AOR = 1.82,95%CI:-1.01–3.26),infection with intestinal parasites (AOR = 2.04, 95% CI:-1.06–3.95), Participants with BMI <18.5kg/m2 (AOR = 2.96, 95%CI:-1.37–6.390),BMI 18.5-25kg/m2(AOR = 1.98, 95%CI:-1.11–3.56) and being HAART naïve (AOR = 2.23, 95% CI:- 1.16–4.28). Conclusion: Prevalence of anemia among this study participant was high. This may affect the treatment outcome, increases morbidity and mortality of the participants. So periodic screening of anemia, a routine checkup of nutritional status, CD4 count and examination for intestinal parasite are essential. [ABSTRACT FROM AUTHOR]

Photorhabdus luminescens is an entomopathogenic bacterium found in symbiosis with the nematode Heterorhabditis. Dam DNA methylation is involved in the pathogenicity of many bacteria, including P. luminescens, whereas studies about the role of bacterial DNA methylation during symbiosis are scarce. The aim of this study was to determine the role of Dam DNA methylation in P. luminescens during the whole bacterial life cycle including during symbiosis with H. bacteriophora. We constructed a strain overexpressing dam by inserting an additional copy of the dam gene under the control of a constitutive promoter in the chromosome of P. luminescens and then achieved association between this recombinant strain and nematodes. The dam overexpressing strain was able to feed the nematode in vitro and in vivo similarly as a control strain, and to re-associate with Infective Juvenile (IJ) stages in the insect. No difference in the amount of emerging IJs from the cadaver was observed between the two strains. Compared to the nematode in symbiosis with the control strain, a significant increase in LT50 was observed during insect infestation with the nematode associated with the dam overexpressing strain. These results suggest that during the life cycle of P. luminescens, Dam is not involved the bacterial symbiosis with the nematode H. bacteriophora, but it contributes to the pathogenicity of the nemato-bacterial complex. [ABSTRACT FROM AUTHOR]

Head and neck squamous cell carcinoma (HNSCC) remains a morbid disease with poor prognosis and treatment that typically leaves patients with permanent damage to critical functions such as eating and talking. Currently only three targeted therapies are FDA approved for use in HNSCC, two of which are recently approved immunotherapies. In this work, we identify biological pathways involved with this disease that could potentially be targeted by current FDA approved cancer drugs and thereby expand the pool of potential therapies for use in HNSCC treatment. We analyzed 508 HNSCC patients with sequencing information from the Genomic Data Commons (GDC) database and assessed which biological pathways were significantly enriched for somatic mutations or copy number alterations. We then further classified pathways as either “light” or “dark” to the current reach of FDA-approved cancer drugs using the Cancer Targetome, a compendium of drug-target information. Light pathways are statistically enriched with somatic mutations (or copy number alterations) and contain one or more targets of current FDA-approved cancer drugs, while dark pathways are enriched with somatic mutations (or copy number alterations) but not currently targeted by FDA-approved cancer drugs. Our analyses indicated that approximately 35–38% of disease-specific pathways are in scope for repurposing of current cancer drugs. We further assess light and dark pathways for subgroups of patient tumor samples according to HPV status. The framework of light and dark pathways for HNSCC-enriched biological pathways allows us to better prioritize targeted therapies for further research in HNSCC based on the HNSCC genetic landscape and FDA-approved cancer drug information. We also highlight the importance in the identification of sub-pathways where targeting and cross targeting of other pathways may be most beneficial to predict positive or negative synergy with potential clinical significance. This framework is ideal for precision drug panel development, as well as identification of highly aberrant, untargeted candidates for future drug development. [ABSTRACT FROM AUTHOR]

Background: Since 2004, the President’s Emergency Plan for AIDS Relief (PEPFAR) has played a large role in Uganda’s HIV/AIDS response. To better target resources to high burden regions and facilities, PEPFAR planned to withdraw from 29% of previously-supported health facilities in Uganda between 2015 and 2017. Methods: We conducted a cross-sectional survey of 226 PEPFAR-supported health facilities in Uganda in mid-2017. The survey gathered information on availability, perceived quality, and access to HIV services before and after transition. We compare responses for facilities transitioned to those maintained on PEPFAR, accounting for survey design. We also extracted data from DHIS2 for the period October 2013–December 2017 on the number of HIV tests and counseling (HTC), number of patients on antiretroviral therapy (Current on ART), and retention on first-line ART (Retention) at 12 months. Using mixed effect models, we compare trends in service volume around the transition period. Results: There were 206 facilities that reported transition and 20 that reported maintenance on PEPFAR. Some facilities reporting transition may have been in a gap between implementing partners. The median transition date was September 2016, nine months prior to the survey. Transition facilities were more likely to discontinue HIV outreach following transition (51.6% vs. 1.4%, p<0.001) and to report declines in HIV care access (43.5% vs. 3.1%, p<0.001) and quality (35.6% vs. 0%, p<0.001). However, transition facilities did not differ in their trends in HIV service volume relative to maintenance facilities. Conclusions: Transition from PEPFAR resulted in facilities reporting worsening patient access and service quality for HIV care, but there is insufficient evidence to suggest negative impacts on volume of HIV services. Facility respondents’ perceptions about access and quality may be overly pessimistic, or they may signal forthcoming impacts. Unrelated to transition, declining retention on ART in Uganda is a cause for concern. [ABSTRACT FROM AUTHOR]

Background: Escherichia coli is currently unable to be reliably differentiated from Shigella species by routine matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) analysis. In the present study, a reliable and rapid identification method was established for Escherichia coli and Shigella species based on a short-term high-lactose culture using MALDI-TOF MS and artificial neural networks (ANN). Materials and methods: The Escherichia coli and Shigella species colonies, treated with (Condition 1)/without (Condition 2) a short-term culture with an in-house developed high-lactose fluid medium, were prepared for MALDI-TOF MS assays. The MS spectra were acquired in linear positive mode, with a mass range from 2000 to 12000 Da and were then compared to discover new biomarkers for identification. Finally, MS spectra data sets 1 and 2, extracted from the two conditions, were used for ANN training to investigate the benefit on bacterial classification produced by the new biomarkers. Results: Twenty-seven characteristic MS peaks from the Escherichia coli and Shigella species were summarized. Seven unreported MS peaks, with m/z 2330.745, m/z 2341.299, m/z 2371.581, m/z 2401.038, m/z 3794.851, m/z 3824.839 and m/z 3852.548, were discovered in only the spectra from the E. coli strains after a short-term high-lactose culture and were identified as belonging to acid shock protein. The prediction accuracies of the ANN models, based on data set 1 and 2, were 97.71±0.16% and 74.39±0.34% (n = 5), with an extremely remarkable difference (p < 0.001), and the areas under the curve of the receiver operating characteristic curve were 0.72 and 0.99, respectively. Conclusions: In summary, adding a short-term high-lactose culture approach before the analysis enabled a reliable and easy differentiation of Escherichia coli from the Shigella species using MALDI-TOF MS and ANN. [ABSTRACT FROM AUTHOR]