Microbiome response in an urban river system is dominated by seasonality over wastewater treatment upgrades.

BACKGROUND: Microorganisms such as coliform-forming bacteria are commonly used to assess freshwater quality for drinking and recreational use. However, such organisms do not exist in isolation; they exist within the context of dynamic, interactive microbial communities which vary through space and time. Elucidating spatiotemporal microbial dynamics is imperative for discriminating robust community changes from ephemeral ecological trends, and for improving our overall understanding of the relationship between microbial communities and ecosystem health. We conducted a seven-year (2013-2019) microbial time-series investigation in the Chicago Area Waterways (CAWS): an urban river system which, in 2016, experienced substantial upgrades to disinfection processes at two wastewater reclamation plants (WRPs) that discharge into the CAWS and improved stormwater capture, to improve river water quality and reduce flooding. Using culture-independent and culture-dependent approaches, we compared CAWS microbial ecology before and after the intervention. RESULTS: Examinations of time-resolved beta distances between WRP-adjacent sites showed that community similarity measures were often consistent with the spatial orientation of site locations to one another and to the WRP outfalls. Fecal coliform results suggested that upgrades reduced coliform-associated bacteria in the effluent and the downstream river community. However, examinations of whole community changes through time suggest that the upgrades did little to affect overall riverine community dynamics, which instead were overwhelmingly driven by yearly patterns consistent with seasonality. CONCLUSIONS: This study presents a systematic effort to combine 16S rRNA gene amplicon sequencing with traditional culture-based methods to evaluate the influence of treatment innovations and systems upgrades on the microbiome of the Chicago Area Waterway System, representing the longest and most comprehensive characterization of the microbiome of an urban waterway yet attempted. We found that the systems upgrades were successful in improving specific water quality measures immediately downstream of wastewater outflows. Additionally, we found that the implementation of the water quality improvement measures to the river system did not disrupt the overall dynamics of the downstream microbial community, which remained heavily influenced by seasonal trends. Such results emphasize the dynamic nature of microbiomes in open environmental systems such as the CAWS, but also suggest that the seasonal oscillations remain consistent even when perturbed.

Mortality rates among COVID-19 patients hospitalised during the first three waves of the epidemic in Milan, Italy: A prospective observational study.

INTRODUCTION: This paper describes how mortality among hospitalised COVID-19 patients changed during the first three waves of the epidemic in Italy. METHODS: This prospective cohort study used the Kaplan-Meier method to analyse the time-dependent probability of death of all of the patients admitted to a COVID-19 referral centre in Milan, Italy, during the three consecutive periods of: 21 February-31 July 2020 (first wave, W1), 1 August 2020-31 January 2021 (second wave, W2), and 1 February-30 April 2021 (third wave, W3). Cox models were used to examine the association between death and the period of admission after adjusting for age, biological sex, the time from symptom onset to admission, disease severity upon admission, obesity, and the comorbidity burden. RESULTS: Of the 2,023 COVID-19 patients admitted to our hospital during the study period, 553 (27.3%) were admitted during W1, 838 (41.5%) during W2, and 632 (31.2%) during W3. The crude mortality rate during W1, W2 and W3 was respectively 21.3%, 23.7% and 15.8%. After adjusting for potential confounders, hospitalisation during W2 or W3 was independently associated with a significantly lower risk of death than hospitalisation during W1 (adjusted hazard ratios [AHRs]: 0.75, 95% confidence interval [CI] 0.59-0.95, and 0.58, 95% CI 0.44-0.77). Among the patients aged >75 years, there was no significant difference in the probability of death during the three waves (AHRs during W2 and W3 vs W1: 0.93, 95% CI 0.65-1.33, and 0.88, 95% CI 0.59-1.32), whereas those presenting with critical disease during W2 and W3 were at significantly lower risk of dying than those admitted during W1 (AHRs 0.61, 95% CI 0.43-0.88, and 0.44, 95% CI 0.28-0.70). CONCLUSIONS: Hospitalisation during W2 and W3 was associated with a reduced risk of COVID-19 death in comparison with W1, but there was no difference in survival probability in patients aged >75 years.

Parietal intrahemispheric source connectivity of resting-state electroencephalographic alpha rhythms is abnormal in Naïve HIV patients.

Previous evidence showed abnormal parietal sources of resting-state electroencephalographic (EEG) delta (< 4 Hz) and alpha (8-12 Hz) rhythms in treatment-Naïve HIV (Naïve HIV) subjects, as cortical neural synchronization markers in quiet wakefulness. Here, we tested the hypothesis that these local abnormalities may be related to functional cortical dysconnectivity as an oscillatory brain network disorder. The present EEG database regarded 128 Naïve HIV and 60 Healthy subjects. The eLORETA freeware estimated lagged linear EEG source connectivity (LLC). The area under receiver operating characteristic (AUROC) curve indexed the accuracy in the classification between Healthy and HIV individuals. Parietal intrahemispheric LLC solutions in alpha sources were abnormally lower in the Naïve HIV than in the control group. Furthermore, those abnormalities were greater in the Naïve HIV subgroup with executive and visuospatial deficits than the Naïve HIV subgroup with normal cognition. AUROC curves of those LLC solutions exhibited moderate/good accuracies (0.75-0.88) in the discrimination between the Naïve HIV individuals with executive and visuospatial deficits vs. Naïve HIV individuals with normal cognition and control individuals. In quiet wakefulness, Naïve HIV subjects showed clinically relevant abnormalities in parietal alpha source connectivity. HIV may alter a parietal "hub" oscillating at the alpha frequency in quiet wakefulness as a brain network disorder.

Off-label use of tocilizumab for the treatment of SARS-CoV-2 pneumonia in Milan, Italy.

BACKGROUND: Tocilizumab, a humanized monoclonal antibody, targets IL-6 receptors blocking downstream pro-inflammatory effects of IL-6. In preliminary reports it was suggested to be beneficial in patients with severe COVID-19. METHODS: In this open-label prospective study we describe clinical characteristics and outcome of 51 patients hospitalized with confirmed and severe COVID-19 pneumonia treated with tocilizumab intravenously. All patients had elevated IL-6 plasma level (>40 pg/mL) and oxygen saturation <93% in ambient air. Clinical outcomes, oxygen support, laboratory data and adverse events were collected over a follow-up of 30 days. RESULTS: Forty-five patients (88%) were on high-flow oxygen supplementation, six of whom with invasive ventilation. From baseline to day 7 after tocilizumab we observed a dramatic drop of body temperature and CRP value with a significant increase in lymphocyte count (p<0.001). Over a median follow-up time of 34 days from tocilizumab, 34 patients (67%) showed an improvement in their clinical severity class; 31 were discharged; 17 (33%) showed a worsening of their clinical status, of these 14 died (27%). The mortality rate was significantly associated with mechanical ventilation at baseline (83.3% vs 20% of patients on non-invasive oxygen support; p=0.0001). The most frequent side effects were an increase of hepatic enzymes (29%), thrombocytopenia (14%), and serious bacterial and fungal infections (27%). CONCLUSION: Tocilizumab exerts a rapidly beneficial effect on fever and inflammatory markers, although no significant impact on the clinical outcome can be inferred by our results. Critically ill patients seem to have a high risk of serious infections with this drug.

Genomic Characterization of an ST1153 PVL-producing Methicillin Resistant Staphylococcus aureus Clinical Isolate in Italy.

Methicillin-resistant Staphylococcus aureus (MRSA) clones are rapidly increasing beyond the hospital into the community, livestock farming and environmental settings. An Italian man, a professional diver working in Egypt, was admitted to Infectious Diseases Clinic-ASST Fatebenefratelli Sacco for ulcerative skin lesions. An MRSA strain was isolated from the lesions' purulent exudate and the nasal colonization was also ascertained. The strain, characterized by whole genome sequencing, resulted to be Panton-Valentine Leukocidin (PVL) positive, SCCmecI - spa-type t504, and belonging to the sequence type 1153, sporadically described worldwide.

Trends in hospital admissions at a Department for Infectious Diseases in Italy from 1995 to 2011 and implications for health policies.

BACKGROUND: Interactions among several environmental, behavioral, social, and biological variables contribute to the epidemiology of infectious diseases (IDs) and have an impact on the healthcare system and hospitalizations. We evaluated trends in ID hospitalizations at our Department for Infectious Diseases in the last two decades to aid decision-makers in defining appropriate healthcare strategies. METHODS: The discharge diagnoses of all patients admitted to the ID Department of L Sacco University Hospital between 1995 and 2011 were classified by the International Classification of Diseases (ICD-9) grouped in Major Diagnostic Categories (MDC). Linear regression was used to determine the trends in hospitalizations for each MDC. Estimates of the average annual change were based on the slope of the regression line. RESULTS: A sharp decline in HIV/AIDS cases (-22.5 +/-6.0 cases per calendar year), and an increase in admissions for respiratory, cardiovascular, renal and musculoskeletal infections were recorded. The mean age of the patients increased by 1.2 years (+/-0.049) for each calendar year of observation (linear trend, p < 0.0001), increasing from 37.02 +/-11.91 years in 1995 to 56.02 +/-19.62 years in 2011 (p < 0.0001). The mean number of comorbidities per patient increased significantly over time (Mann-Whitney U test, p = 0.0153). From 1998/1999 to 2010/2011 the hospital length of stay (LOS) increased for cardiovascular, digestive system, musculoskeletal, and skin/subcutaneous infections, and infectious and parasitic diseases (p < 0.01). The rate of hospital stay over threshold (HSOT) increased in the last 5 years by 1.12% for every 10-year age group. CONCLUSIONS: Older age, a higher number of comorbidities, a longer hospital LOS for certain conditions, and a higher rate of HSOT characterize the patients admitted to this ID department in recent years. Despite progress in treatment and management, infectious diseases continue to be a major threat to human health. The current challenge for ID departments is the treatment of complex cases, often associated with chronic diseases in elderly patients. Continuous monitoring at a local and national level will allow early identification of changes in the epidemiological patterns of IDs and provide information for healthcare system planning.

Anti-Toxocara spp. antibodies in an adult healthy population:serosurvey and risk factors in Southeast Brazil

Objective: To evaluate the frequency of anti-Toxocara spp. antibodies in an adult healthy population. Methods: The study was performed by interviewing 253 blood donors, from 19 to 65 years of age, in a hematological centre in Presidente Prudente, S?o Paulo, southeast Brazil. A survey was applied to blood donors in order to evaluate the possible factors associated to the presence of antibodies, including individual (gender and age), socioeconomic (scholarship, familial income and sanitary facilities) and habit information (contact with soil, geophagy, onycophagy and intake of raw/undercooked meat) as well as the presence of dogs or cats in the household. ELISA test was run for detection of the anti-Toxocara spp. IgG antibodies. Bivariate analysis followed by logistic regression was performed to evaluate the potential risk factors associated to seropositivity. Results: The overall prevalence observed in this study was 8.7%(22/253). Contact with soil was the unique risk factor associated with the presence of antibodies (P=0.017 8;OR=3.52; 95%CI=1.244-9.995). Conclusions: The results of this study reinforce the necessity in promoting preventive public health measures, even for healthy adult individual, particularly those related to the deworming of pets to avoid the soil contamination, and hygiene education of the population.

Microorganisms form exocellular structures, trophosomes, to facilitate biodegradation of oil in aqueous media.

Cytochemical staining and microscopy were used to study the trophic structures and cellular morphotypes that are produced during the colonization of oil-water interfaces by oil-degrading yeasts and bacteria. Among the microorganisms studied here, the yeasts (Schwanniomyces occidentalis, Torulopsis candida, Candida tropicalis, Candida lipolytica, Candida maltosa, Candida paralipolytica) and two representative bacteria (Rhodococcus sp. and Pseudomonas putida) produced exocellular structures composed of biopolymers during growth on petroleum hydrocarbons. Four of the yeasts including S. occidentalis, T. candida, C. tropicalis and C. maltosa excreted polymers through modified sites in their cell wall ('canals'), whereas C. lipolytica and C. paralipolytica and the two bacterial species secreted polymers over the entire cell surface. These polymers took the form of fibrils and films that clogged pores and cavities on the surfaces of the oil droplets. A three-dimensional reconstruction of the cavities using serial thin sections showed that the exopolymer films isolated the ambient aqueous medium together with microbial cells and oil to form both closed and open granules that contained pools of oxidative enzymes utilized for the degradation of the oil hydrocarbons. The formation of such granules, or 'trophosomes,' appears to be a fundamental process that facilitates the efficient degradation of oil in aqueous media.