Global epidemiology, seasonality and climatic drivers of the four human parainfluenza virus types

Objectives: Human parainfluenza viruses (hPIV) are a common cause of acute respiratory infections, especially in children under five years and the elderly. hPIV can be subclassified as types 1–4: these showed various seasonality patterns worldwide, and it is unclear how climatic factors might consistently explain their global epidemiology. Methods: This study collected time-series incidence data from the literature and hPIV surveillance programs worldwide (47 locations). Wavelet analysis and circular statistics were used to detect the seasonality and the months of peak incidence for each hPIV type. Relationships between climatic drivers and incidence peaks were assessed using a generalized estimating equation. Results: The average positive rate of hPIV among patients with respiratory symptoms was 5.6% and ranged between 0.69–3.48% for different types. In the northern temperate region, the median peak incidence months for hPIV1, hPIV2, and hPIV4 were from September to October, while for hPIV3, it was in late May. Seasonal peaks of hPIV3 were associated with higher monthly temperatures and lower diurnal temperatures range throughout the year; hPIV4 peaks appeared to correlate with lower monthly temperatures and higher precipitation throughout the year. Different hPIV types exhibit different patterns of global epidemiology and transmission. Conclusions: Climate drivers may play a role in hPIV transmission. More comprehensive and coherent surveillance of hPIV types would enable more in-depth analyses and inform the timing of preventive measures.</p

Chasing organohalide respirers: ecogenomics approaches to assess the bioremediation capacity of soils

Het opsporen van organohalogeen-reducerende bacteriën: ecogenomics benaderingen om de bioremediatie-capaciteit van de bodem te beoordelen. Organohalogeen-reducerende bacteriën (OHRB) zijn efficiënte afbrekers van organische chloorverbindingen, zoals gechloreerde ethenen, chloorfenolen en andere gehalogeneerde alifatische en aromatische koolwaterstoffen. Desondanks, lijken deze organische chloorverbindingen te volharden op verschillende locaties. De reden voor dit gebrek aan afbraak kan worden toegeschreven aan het ontbreken van OHRB in voldoende aantallen of aan verkeerde fysisch-chemische omstandigheden voor hun groei en activiteit. Derhalve is er een dringende behoefte aan snelle, robuuste en gevoelige methoden die het voorspellen van en het toezicht houden op het bioremediatie potentieel en de activiteit van OHRB mogelijk maken. Moleculaire monitoring en modelsimulaties werden toegepast om de in-situ afbraak prestaties van een on-site dechlorerende bioreactor te bepalen en zijn invloed op de vervuilingsspluim. De toepasbaarheid van dit systeem werd getest in verschillende verontreinigde bodems

A pilot metagenomic study reveals that community derived mobile phones are reservoirs of viable pathogenic microbes

There is increasing attention focussed on the risks associated with mobile phones possibly serving as ‘Trojan Horse’ fomites for microbial transmission in healthcare settings. However, little is reported on the presence of microbes on community derived mobile phones which in 2021, numbered in the billions in circulation with majority being used on a daily basis. Identify viable microbial organisms swabbed from smartphones on a university campus. Entire surfaces of 5 mobile phones were swabbed and examined for their microbial content using pre-agar-based growths followed by downstream DNA metagenomic next-generation sequencing analysis. All phones were contaminated with viable microbes. 173 bacteria, 8 fungi, 8 protists, 53 bacteriophages, 317 virulence factor genes and 41 distinct antibiotic resistant genes were identified. While this research represents a pilot study, the snapshot metagenomic analysis of samples collected from the surface of mobile phones has revealed the presence of a large population of viable microbes and an array of antimicrobial resistant factors. With billions of phones in circulation, these devices might be responsible for the rise of community acquired infections. These pilot results highlight the importance of public health authorities considering mobile phones as ‘Trojan Horse’ devices for microbial transmission and ensure appropriate decontamination campaigns are implemented

TLR5 participates in the TLR4 receptor complex and promotes MyD88- dependent signaling in environmental lung injury

Lung disease causes significant morbidity and mortality, and is exacerbated by environmental injury, for example through lipopolysaccharide (LPS) or ozone (O3). Toll-like receptors (TLRs) orchestrate immune responses to injury by recognizing pathogen- or danger-associated molecular patterns. TLR4, the prototypic receptor for LPS, also mediates inflammation after O3, triggered by endogenous hyaluronan. Regulation of TLR4 signaling is incompletely understood. TLR5, the flagellin receptor, is expressed in alveolar macrophages, and regulates immune responses to environmental injury. Using in vivo animal models of TLR4-mediated inflammations (LPS, O3, hyaluronan), we show that TLR5 impacts the in vivo response to LPS, hyaluronan and O3. We demonstrate that immune cells of human carriers of a dominant negative TLR5 allele have decreased inflammatory response to O3 exposure ex vivo and LPS exposure in vitro. Using primary murine macrophages, we find that TLR5 physically associates with TLR4 and biases TLR4 signaling towards the MyD88 pathway. Our results suggest an updated paradigm for TLR4/TLR5 signaling

Determination and control of some pollutants in indoor environments

Unsatisfactory indoor air quality (IAQ) may result from polluting emissions that are spread from building materials such as volatile organic compounds (VOCs) and/or microbial components or from various kinds of human activity such as smoking. Different methods are available to limit the exposure to unwanted pollutants and improve human wellbeing and health. One goal of this thesis was to determine two microbial markers (3-hydroxy fatty acids of bacterial lipopolysaccharide and ergosterol of fungal biomass) in waterpipe smoke. A second goal was to study the influence of relative humidity (RH) on room air concentrations of VOCs. A third goal was to study the performance of a new device called the surface emissions trap (cTrap) in controlling indoor pollutants. Smoking waterpipe was found to generate a bioaerosol rich in microbial components, policyclic aromatic hydrocarbons (PAHs), and small size particles. Rapidly increasing RH was found to influence air concentrations of VOCs emitted from building materials as studied both in a climate chamber and in a room with dampness-related floor emissions. The cTrap cloth was found to be efficient in reducing emissions of VOCs, stopping mycotoxins, and improving the perceived IAQ in a damp school building. The device was proved to be efficient in reducing and trapping moisture-driven floor emissions. Preliminary results also showed that the cloth may be used in reducing smoking generated VOCs and particles which may migrate between rooms within a building

Microcystins and Liver Disease Mortality, Insights from an Ecological Study

Microcystins (MCs) are toxic secondary metabolites produced by freshwater cyanobacteria. Algal bloom subsidence can stimulate MC release, which can impair liver function if orally exposed to in large doses. The purpose of this retrospective, U.S. ecological study was to determine if MC exposure represented an environmental risk factor for liver disease mortality using a socioecological approach. A longitudinal ecological substudy investigated the association between average total MCs in Lake Washington and Lake Manatee and age-adjusted chronic liver disease (CLD)/cirrhosis death rates in Brevard County and Manatee County, Florida (FL). A prediction model of total MCs was deduced by quantifying levels of nitrites and phosphates in Lake Washington and Lake Manatee. According to multiple linear regression analysis, there was a significant positive association between average total MCs and age-adjusted CLD/cirrhosis death rates in the United States. Daily sunlight and state of residence also significantly predicted U.S. liver mortality rates. Average total MCs demonstrated predictive value in reference to age-adjusted CLD/cirrhosis death rates in Brevard County, FL. Positive social change can educate the federal and state governments to improve the surveillance of MCs. Results may encourage water treatment plants in Brevard County and Manatee County, FL to monitor and manage cyanobacterial contamination in drinking water sources

In Silico Bioinformatics Followed by Molecular Validation Using Archival FFPE Tissue Biopsies Identifies a Panel of Transcripts Associated with Severe Asthma and Lung Cancer

Severe asthma and lung cancer are both heterogeneous pathological diseases affecting the lung tissue. Whilst there are a few studies that suggest an association between asthma and lung cancer, to the best of our knowledge, this is the first study to identify common genes involved in both severe asthma and lung cancer. Publicly available transcriptomic data for 23 epithelial brushings from severe asthmatics and 55 samples of formalin-fixed paraffin-embedded (FFPE) lung cancer tissue at relatively early stages were analyzed by absolute gene set enrichment analysis (GSEA) in comparison to 37 healthy bronchial tissue samples. The key pathways enriched in asthmatic patients included adhesion, extracellular matrix, and epithelial cell proliferation, which contribute to tissue remodeling. In the lung cancer dataset, the main pathways identified were receptor tyrosine kinase signaling, wound healing, and growth factor response, representing the early cancer pathways. Analysis of the enriched genes derived from the pathway analysis identified seven genes expressed in both the asthma and lung cancer sets: BCL3, POSTN, PPARD, STAT1, MYC, CD44, and FOSB. The differential expression of these genes was validated in vitro in the cell lines retrieved from different lung cancer and severe asthma patients using real-time PCR. The effect of the expression of the seven genes identified in the study on the overall survival of lung cancer patients (n = 1925) was assessed using a Kaplan–Meier plot. In vivo validation performed in the archival biopsies obtained from patients diagnosed with both the disease conditions provided interesting insights into the pathogenesis of severe asthma and lung cancer, as indicated by the differential expression pattern of the seven transcripts in the mixed group as compared to the asthmatics and lung cancer samples alone

Population genomics uncovers global distribution, antimicrobial resistance, and virulence genes of the opportunistic pathogen <i>Klebsiella </i>aerogenes

Klebsiella aerogenes is an understudied and clinically important pathogen. We therefore investigate its population structure by genome analysis aligned with metadata. We sequence 130 non-duplicated K. aerogenes clinical isolates and identify two inter-patient transmission events. We then retrieve all publicly available K. aerogenes genomes (n = 1,026, accessed by January 1, 2023) and analyze them with our 130 genomes. We develop a core-genome multi-locus sequence-typing scheme. We find that K. aerogenes is a species complex comprising four phylogroups undergoing evolutionary divergence, likely forming three species. We delineate remarkable clonal diversity and identify three worldwide-distributed carbapenemase-encoding clonal clusters, representing high-risk lineages. We uncover that K. aerogenes has an open genome equipped by a large arsenal of antimicrobial resistance genes. We identify two genetic regions specific for K. aerogenes, encoding a type VI secretion system and flagella/chemotaxis for motility, respectively, both contributing to the virulence. These results provide much-needed insights into the population structure and pan-genomes of K. aerogenes.</p

The microbiome of diabetic foot ulcers and the role of biofilms

Diabetic Foot Ulcers are a common precursor to the development of infection and amputations. A breach in the protective skin barrier represents a portal of entry for invading microorganisms, where infective episodes frequently pursue. Three key areas that may augment clinical care are one. understanding what microorganisms are present in Diabetic Foot Ulcers, two. differentiating if microorganisms are planktonic microbial cells or slow growing microbial biofilms and three. treating Diabetic Foot Ulcers complicated by microorganisms with effective topical agents. As part of this thesis, 16S rDNA next generation sequencing was utilised to profile the microbiota of infected Diabetic Foot Ulcers (DFUs). Clinical / laboratory data and treatment outcomes were collected and correlated against microbiota data. Thirty-nine patients with infected DFUs were recruited over twelve-months. Shorter duration DFUs (less than six weeks) all had one dominant bacterial species (n= five of five, 100%, p <⋅001), S. aureus in three cases and S. agalactiae in two. Longer duration DFUs (≥six weeks) were diversely polymicrobial (p = .01) with an average of 63 (range 19-125) bacterial species. Severe Diabetic Foot Infections (DFIs) had complex microbiota’s and were distinctly dissimilar to less severe infections (p = .02), characterised by the presence of low frequency microorganisms. Our results confirm that short DFUs have a simpler microbiota’s consisting of pyogenic cocci but chronic DFUs have a highly polymicrobial microbiota. The duration of a DFU may be useful as a guide to directing antimicrobial therapy. Secondly, we utilised Scanning electron microscopy (SEM) and Fluorescent in situ Hybridisation (FISH) techniques to determine if DFUs were complicated by sessile, slow growing bacteria referred to as biofilms. 65 DFU specimens were obtained from subjects with infected chronic ulcers. Of the 65 DFU specimens evaluated by microscopy, all were characterized as containing biofilm (100%, p < .001). Molecular analyses of DFU specimens revealed diverse polymicrobial communities. No clinical visual cues were identified in aiding clinicians identify wound biofilm. Microscopy visualization when combined with molecular approaches, confirms biofilms are ubiquitous in DFUs and a paradigm shift of managing these complicated wounds needs to consider anti-biofilm strategies. Lastly, the effectiveness of various topical antimicrobials commonly used in woundcare were tested in two separate studies by employing in vitro models, ex vivo porcine skin explant models and in vivo human studies. In the first study, 17 participants with chronic non-healing DFUs due to suspected biofilm involvement were recruited to receive one-week application of Cadexomer Iodine ointment. Real-time qPCR was used to determine the microbial load with 11 participants exhibiting one-two Log10 reductions in microbial load after treatment, in comparison to six patients who experienced less than one log10 reduction (p =.04). Scanning electron microscopy (SEM) and/or fluorescent in situ hybridisation (FISH) confirmed the presence or absence of biofilm in all 17 participants. 16SrDNAnextgenerationsequencing provided useful insights that these wounds support complex polymicrobial communities and demonstrated that Cadexomer Iodine had a broad level of antimicrobial activity in reducing both facultative anaerobes such as Staphylococcus spp., Serratia spp., aerobes including Pseudomonas spp., and obligate anaerobes including Clostridiales family XI. In the second study, a range of topical antimicrobial wound solutions were tested under three different conditions; (in vitro) 4 % w/v melaleuca oil, polyhexamethylene biguanide, chlorhexidine, povidone iodine and hypochlorous acid were tested at short duration exposure times for 15-minutes against three-day mature biofilms of S. aureus and P. aeruginosa. (ex vivo) Hypochlorous acid was tested in a porcine skin explant model with twelve cycles of tenminute exposure, over 24 hours, against three-day mature P. aeruginosa biofilms. (in vivo) 4 % w/v Melaleuca Oil was applied for 15-minutes exposure, daily, for seven days, in ten patients with chronic non-healing Diabetic Foot Ulcers (DFUs) complicated by biofilm. In vitro assessment demonstrated variable efficacy in reducing biofilms ranging between 0.5 log10 reductions to full eradication. Repeated instillation of hypochlorous acid in a porcine model achieved less than one log10 reduction (0.77 log10, p < 0.1). Application of 4 % w/v melaleuca oil in vivo, resulted in no change to the total microbial load of DFUs complicated by biofilm (median log10 microbial load pre-treatment = 4.9 log10 versus 4.8 log10 (p = .43). In conclusion, to the best of our knowledge, the in vivo human studies testing the performances of topical antimicrobials represents the first in vivo evidence employing a range of molecular and microscopy techniques. These demonstrate the ability of Cadexomer Iodine (sustained release over 48-72 hours) to reduce the microbial load of chronic non-healing DFUs complicated by biofilm. In contrast, short durations of exposure to topical antimicrobial wound solutions commonly utilised by clinicians are ineffective against microbial biofilms, particularly when used in vivo