Simultaneous monitoring of SARS-CoV-2 and bacterial profiles from the air of hospital environments with COVID-19-affected patients.

The SARS-CoV-2 presence and the bacterial community profile in air samples collected at the Intensive Care Unit (ICU) of the Operational Unit of Infectious Diseases of Santa Caterina Novella Hospital in Galatina (Lecce, Italy) have been evaluated in this study. Air samplings were performed in different rooms of the ICU ward with and without COVID-19 patients. No sample was found positive to SARS-CoV-2, according to Allplex 2019-nCoV Assay. The airborne bacterial community profiles determined by the 16S rRNA gene metabarcoding approach up to the species level were characterized by richness and biodiversity indices, Spearman correlation coefficients, and Principal Coordinate Analysis. Pathogenic and non-pathogenic bacterial species, also detected in outdoor air samples, were found in all collected indoor samples. Staphylococcus pettenkoferi, Corynebacterium tuberculostearicum, and others coagulase-negative staphylococci, detected at high relative abundances in all the patients' rooms, were the most abundant pathogenic species. The highest mean relative abundance of S. pettenkoferi and C. tuberculostearicum suggested that they were likely the main pathogens of COVID-19 patients at the ICU ward of this study. The identification of nosocomial pathogens representing potential patients' risks in ICU COVID-19 rooms and the still controversial airborne transmission of the SARS-CoV-2 are the main contributions of this study. Supplementary Information: The online version contains supplementary material available at 10.1007/s10453-022-09754-7.

Compositional Data Analysis of 16S rRNA Gene Sequencing Results from Hospital Airborne Microbiome Samples.

The compositional analysis of 16S rRNA gene sequencing datasets is applied to characterize the bacterial structure of airborne samples collected in different locations of a hospital infection disease department hosting COVID-19 patients, as well as to investigate the relationships among bacterial taxa at the genus and species level. The exploration of the centered log-ratio transformed data by the principal component analysis via the singular value decomposition has shown that the collected samples segregated with an observable separation depending on the monitoring location. More specifically, two main sample clusters were identified with regards to bacterial genera (species), consisting of samples mostly collected in rooms with and without COVID-19 patients, respectively. Human pathogenic genera (species) associated with nosocomial infections were mostly found in samples from areas hosting patients, while non-pathogenic genera (species) mainly isolated from soil were detected in the other samples. Propionibacterium acnes, Staphylococcus pettenkoferi, Corynebacterium tuberculostearicum, and jeikeium were the main pathogenic species detected in COVID-19 patients' rooms. Samples from these locations were on average characterized by smaller richness/evenness and diversity than the other ones, both at the genus and species level. Finally, the ρ metrics revealed that pairwise positive associations occurred either between pathogenic or non-pathogenic taxa.

Pollen Monitoring by Optical Microscopy and DNA Metabarcoding: Comparative Study and New Insights.

Environmental samples collected in Brindisi (Italy) by a Hirst-type trap and in Lecce (Italy) by a PM10 sampler were analysed by optical microscopy and DNA-metabarcoding, respectively, to identify airborne pollen and perform an exploratory study, highlighting the benefits and limits of both sampling/detection systems. The Hirst-type trap/optical-microscopy system allowed detecting pollen on average over the full bloom season, since whole pollen grains, whose diameter vary within 10-100 µm, are required for morphological detection with optical microscopy. Conversely, pollen fragments with an aerodynamic diameter ≤10 µm were collected in Lecce by the PM10 sampler. Pollen grains and fragments are spread worldwide by wind/atmospheric turbulences and can age in the atmosphere, but aerial dispersal, aging, and long-range transport of pollen fragments are favoured over those of whole pollen grains because of their smaller size. Twenty-four Streptophyta families were detected in Lecce throughout the sampling year, but only nine out of them were in common with the 21 pollen families identified in Brindisi. Meteorological parameters and advection patterns were rather similar at both study sites, being only 37 km apart in a beeline, but their impact on the sample taxonomic structure was different, likely for the different pollen sampling/detection systems used in the two monitoring areas.

Daytime and nighttime chemical and optical properties of fine and coarse particles at a central Mediterranean coastal site.

The characterization of the day-to-night changes of the atmospheric particle chemical and optical properties in autumn-winter (AW) and spring-summer (SS) is the main goal of this study to contribute to the characterization and understanding of the particulate matter (PM) impact on the environment and climate at one of the most vulnerable areas of the planet to climate change. To this end, PM10 and PM2.5 samples from 14 January 2016 to 5 January 2017 have been collected in Lecce, a coastal site of South-Eastern Italy (40.33°N, 18.11°E), and day-to-night changes of mass concentrations of both fine (PM2.5) and coarse (PM10-PM2.5) particles and corresponding chemical species have been assessed both in AW and in SS. The statistical analysis of local meteorological parameters and their correlations with PM2.5 and chemical species mass concentrations have indicated that the day-to-night changes of temperature (T) and wind speed (WS) likely affected the day-to-night changes of mass concentrations, because of the T and WS impact on the atmospheric turbulence and air particle dispersion. The daily evolution of the anthropogenic activities and the planetary-boundary-layer height likely contributed to the day-to-night changes of the particle chemical composition. The stagnant atmospheric conditions prevailing in SS all over the Mediterranean basin, which favoured the mixing and the accumulation of atmospheric particles from different pollution sources, likely contributed to the changes of the relationships between chemical species and meteorological parameters from AW to SS at daytime and nighttime. The analysis of the aerosol scattering coefficient, scattering Ångström exponent, and scattering Ångström exponent difference, retrieved from nephelometer measurements co-located in space and time with the PM samplings, has allowed characterizing the day-to-night change of the aerosol optical properties. The relationships between the particle chemical and optical properties allowed a good understanding of their changes both in AW and in SS.

Seasonal Variability of the Airborne Eukaryotic Community Structure at a Coastal Site of the Central Mediterranean.

The atmosphere represents an underexplored temporary habitat for airborne microbial communities such as eukaryotes, whose taxonomic structure changes across different locations and/or regions as a function of both survival conditions and sources. A preliminary dataset on the seasonal dependence of the airborne eukaryotic community biodiversity, detected in PM10 samples collected from July 2018 to June 2019 at a coastal site representative of the Central Mediterranean, is provided in this study. Viridiplantae and Fungi were the most abundant eukaryotic kingdoms. Streptophyta was the prevailing Viridiplantae phylum, whilst Ascomycota and Basidiomycota were the prevailing Fungi phyla. Brassica and Panicum were the most abundant Streptophyta genera in winter and summer, respectively, whereas Olea was the most abundant genus in spring and autumn. With regards to Fungi, Botrytis and Colletotrichum were the most abundant Ascomycota genera, reaching the highest abundance in spring and summer, respectively, while Cryptococcus and Ustilago were the most abundant Basidiomycota genera, and reached the highest abundance in winter and spring, respectively. The genus community structure in the PM10 samples varied day-by-day, and mainly along with the seasons. The impact of long-range transported air masses on the same structure was also proven. Nevertheless, rather few genera were significantly correlated with meteorological parameters and PM10 mass concentrations. The PCoA plots and non-parametric Spearman's rank-order correlation coefficients showed that the strongest correlations generally occurred between parameters reaching high abundances/values in the same season or PM10 sample. Moreover, the screening of potential pathogenic fungi allowed us to detect seven potential pathogenic genera in our PM10 samples. We also found that, with the exception of Panicum and Physcomitrella, all of the most abundant and pervasive identified Streptophyta genera could serve as potential sources of aeroallergens in the studied area.

Airborne bacteria in the Central Mediterranean: Structure and role of meteorology and air mass transport.

The 16S rRNA gene metabarcoding approach has been used to characterize the structure of the airborne bacterial community of PM10 samples, and investigate the dependence on meteorology, seasons, and long-range transported air masses. The PM10 samples were collected at a Central Mediterranean coastal site, away from large sources of local pollution. Proteobacteria, Cyanobacteria, Actinobacteria, Firmicutes, and Bacteroidetes, which were found in all samples, were the most abundant phyla. Calothrix, Pseudomonas, and Bacillus were the most abundant genera. The within-sample relative abundance (RA) of each phylum/genus varied from sample to sample. Calothrix was the most abundant genus during the advection of desert dust and Atlantic air masses, Pseudomonas was the most abundant genus when the advected air flows spent several hours over lands or close to lands affected by anthropogenic activities, before reaching the study site. The bacterial community richness and biodiversity of the PM10 samples on average increased from winter to spring, while the sample dissimilarity on average decreased from winter to spring. The spring meteorological conditions over the Mediterranean, which have likely contributed to maintain for longer time the bacterial community in the atmosphere, could have been responsible for the above results. The analysis of the presumptive species-level characterization of the airborne bacterial community has revealed that the abundance of human (opportunistic) pathogens was highly inhomogeneous among samples, without any significant change from winter to spring. We also found that the PM10 samples collected during the advection of desert dust and Atlantic air masses were on average the less enriched in human (opportunistic) pathogenic species.

Natural sources and heavy metals.

PTS, PM10 and PM2.5 samples have been collected at a rural site of south-east Italy (40 degrees 20' 13" N; 18 degrees 6' 47" E) from June to October, 2004 to investigate natural and anthropogenic contributions on particulate matter and heavy metal mass concentrations. It is shown that sharp-peak particulate-matter concentrations have been recorded during most African dust outbreaks occurred over south-east Italy. In particular, PM10 concentrations exceeding the 24-hour limit value of 50 microg/m3 have been monitored during dust events. Al, Cd, Cr, Cu, Fe, Mn, V, Ni, Pb, and Zn metal concentrations have been evaluated by an inductively coupled plasma atomic emission spectrometer and Al mass concentrations >500 ng/m3 have been observed in PTS and PM10 samples during the advection of African dust particles. Accordingly to geochemical calculations Al, Fe, and Mn, have a significant crustal origin while, Cd, Cu, Pb, and Zn are of anthropogenic origin. Moreover, Fe resulted predominant in the coarse particle fraction, while Ni, Pb, V, and Zn were predominant in the fine particle fraction. It is also shown that Cd, Mn, Ni, Pb, and V concentrations never exceeded guide and/or limit values recommended by the World Health Organization and the European Council Directives.

Imaginary refractive-index effects on desert-aerosol extinction versus backscatter relationships at 351 nm: numerical computations and comparison with Raman lidar measurements.

A numerical model is used to investigate the dependence at 351 nm of desert-aerosol extinction and backscatter coefficients on particle imaginary refractive index (mi). Three ranges (-0.005 < or = mi < or = -0.001, -0.01 < or = mi < or = -0.001, and -0.02 < or = mi < or = -0.001) are considered, showing that backscatter coefficients are reduced as /mi/ increases, whereas extinction coefficients are weakly dependent on mi. Numerical results are compared with extinction and backscatter coefficients retrieved by elastic Raman lidar measurements performed during Saharan dust storms over the Mediterranean Sea. The comparison indicates that a range of -0.01 to -0.001 can be representative of Saharan dust aerosols and that the nonsphericity of mineral particles must be considered.