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We observed bacterial or fungal co-infections in COVID-19 patients admitted between March 1 – April 18, 2020 (152/4267, 3.6%). Mortality was 57%; 74% were intubated; 51% with bacteremia had central venous catheters. Time to culture positivity was 6-7 days; 79% received preceding antibiotics. Metallo-beta-lactamase-producing E. cloacae co-infections occurred in 5 patients.
The work reported in this research communication investigated the occurrence of Mycoplasma bovis (M. bovis) in milk samples from cows with clinical mastitis on dairy farms from seven Brazilian states. We hypothesized that M. bovis was present in bovine clinical mastitis milk in Brazil. A total of 561 milk samples were cultured on Hayflick agar and incubated in a microaerophilic atmosphere at 5% CO2. Polymerase chain reaction (PCR) was performed for the detection of Mycoplasma spp. and Mycoplasma bovis in milk samples. Mycoplasma spp. were isolated in 2% of the milk samples, and Mycoplasma bovis was verified in 3% of the milk samples by PCR. The results showed that Mycoplasma bovis is involved in clinical mastitis in Brazilian dairy herds. We emphasize the need for further studies to investigate the infection by this agent in clinical mastitis cases, particularly in Brazil, due to the lack of knowledge about its prevalence.
Critical care transport organizations are nimble, operationally focused institutions that can aid in managing crises. Ornge provides air ambulance and critical care transport services to Ontario. From 12 bases, Ornge operates four PC-12 Next Generation fixed wing (FW) aircraft, eight AW-139 rotary wing (RW) aircraft, and four critical care land ambulances (CCLA) on a 24/7 basis. Ornge also contracts with private air carriers to provide lower acuity air ambulance services. Ornge performs over 20,000 patient-related transports annually. We discuss Ornge's approach to preparing for the coronavirus disease 2019 (COVID-19) pandemic, and identify potential unconventional roles.
Our objective was to examine the performance characteristics of a bladder stimulation technique for urine collection among infants presenting to the emergency department (ED).
This prospective cohort study enrolled a convenience sample of infants aged ≤ 90 days requiring urine testing in the ED. Infants were excluded if critically ill, moderately to severely dehydrated, or having significant feeding issues. Bladder stimulation consisted of finger tapping on the lower abdomen with or without lower back massage while holding the child upright. The primary outcome was successful midstream urine collection within 5 minutes of stimulation. Secondary outcomes included sample contamination, bladder stimulation time for successful urine collection, and perceived patient distress on a 100-mm visual analog scale (VAS).
We enrolled 151 infants and included 147 in the analysis. Median age was 53 days (interquartile range [IQR] 27–68 days). Midstream urine sample collection using bladder stimulation was successful in 78 infants (53.1%; 95% confidence interval [CI] 45–60.9). Thirty-nine samples (50%) were contaminated. Most contaminated samples (n = 31; 79.5%) were reported as “no significant growth” or “growth of 3 or more organisms”. Median bladder stimulation time required for midstream urine collection was 45 seconds (IQR 20–120 seconds). Mean VAS for infant distress was 22 mm (standard deviation 23 mm).
The success rate of this bladder stimulation technique was lower than previously reported. The contamination rate was high, however most contaminated specimens were easily identified and had no clinical impact.
Employer- and school-mandated verification of minor illness leads patients to use healthcare resources solely to obtain a “sick note.” This puts unnecessary strain on the patient and the emergency department (ED), and threatens to spread communicable diseases in our community.
The use of antibiotics as performance enhancers in animal feeding is declining, so Lippia gracilis Schauer essential oil (LGSEO) could be used as a potential substitute for the conventionally used growth promoters. The LGSEO contains components such as carvacrol and thymol, which kill and/or control pathogenic bacteria, increase population of beneficial organisms, act against oxidative processes and onto nutrient digestibility and absorption. The aim of this study was to investigate the action and the effects of LGSEO as a growth promoter in the diet of Japanese quail by examining their productive performance, intestinal microbiology, blood biochemical parameters, hepatic thiobarbituric acid reactive substances (TBARS) content and intestinal gene expression. A total of 252 two-day-old quail (Coturnix coturnix japonica) were assigned to 3 treatments in 7 replicates, using 12 birds per experimental unit. The treatments consisted of a basal diet, basal diet + LGSEO at 400 mg/kg of diet and basal diet + chemical antimicrobial (bacitracin methylene disalicylate) at 500 mg/kg of diet. The experimental period was 34 days. The highest feed intake (P < 0.01) was found in the group receiving the conventional antimicrobial, whereas the best feed conversion (P < 0.01) was shown by the animals receiving LGSEO. Escherichia coli growth was restricted in the quail receiving the growth promoters. Salmonella spp. growth was controlled by the treatment containing the conventional antimicrobial. There was no difference between the treatments (P > 0.05) for the concentration of aspartate aminotransferase and alanine aminotransferase enzymes in the blood or hepatic TBARS content. Birds receiving negative-control treatment exhibited a higher expression of sodium-glucose cotransporter (SGLT1), while those receiving the treatment with essential oil showed lower catalase (CAT) and glutathione peroxidase (GPX7) expressions compared to the conventional antimicrobial and control groups, respectively. Lippia gracilis Schauer essential oil is a powerful performance enhancer for Japanese quail by virtue of its abilities to improve their intestinal environment, balance the microbial population and reduce energy expenditure for oxidative processes.
We investigate the spatial distribution, spectral properties and temporal variability of primary producers (e.g. communities of microbial mats and mosses) throughout the Fryxell basin of Taylor Valley, Antarctica, using high-resolution multispectral remote-sensing data. Our results suggest that photosynthetic communities can be readily detected throughout the Fryxell basin based on their unique near-infrared spectral signatures. Observed intra- and inter-annual variability in spectral signatures are consistent with short-term variations in mat distribution, hydration and photosynthetic activity. Spectral unmixing is also implemented in order to estimate mat abundance, with the most densely vegetated regions observed from orbit correlating spatially with some of the most productive regions of the Fryxell basin. Our work establishes remote sensing as a valuable tool in the study of these ecological communities in the McMurdo Dry Valleys and demonstrates how future scientific investigations and the management of specially protected areas could benefit from these tools and techniques.
The aim of this study was to describe the clinical and laboratory characteristics of invasive group A streptococcal infections in a geographic area that sees a high volume of cases.
We conducted a health records review of consecutive patients presenting to the Thunder Bay Regional Health Sciences Centre Emergency Department (ED) in 2016–2017 with a diagnosis of invasive group A streptococcal infection using ICD-10 codes. Patient demographics, host characteristics, triage vital signs, laboratory values, culture sites, and disposition were described using univariate and bivariate statistics.
Forty-four adult cases were identified over 2 years, with a median age of 44 years (interquartile range, 35–52). The most prevalent risk factors were diabetes mellitus (45%), current or previous alcohol abuse (39%), and current or previous intravenous drug use (34%). The two most abnormal triage vitals signs were a heart rate ≥ 100 beats per minute in 32 (73%) cases and a respiratory rate ≥ 20 breaths per minute in 27 (63%) cases. The temperature was ≥ 38°C in only 14 (32%) of cases. The C-reactive protein (CRP) was always elevated when measured, and greater than 150 mg/L in 20 (71%) of cases. One-third of patients had an ED visit in the preceding 7 days before the diagnosis of invasive group A Streptococcus.
Invasive group A streptococcal infections often present insidiously in adult patients with mild tachycardia and tachypnea at triage. The CRP was the most consistently abnormal laboratory investigation.
Recent advances in nucleic acid extraction and sequencing have changed and expanded our understanding of the diversity of life in the terrestrial and marine subsurface. This chapter highlights recent developments in sequencing genetic material from the deep biosphere (spurred in part by the Census of Deep Life) and new bioinformatics approaches to present a synthesis of our current understanding of the biogeography of life in the deep biosphere. Building from this data framework, this chapter also explores emerging trends in understanding the ecology and evolution of subsurface life.
Ruminants are unique among livestock due to their ability to efficiently convert plant cell wall carbohydrates into meat and milk. This ability is a result of the evolution of an essential symbiotic association with a complex microbial community in the rumen that includes vast numbers of bacteria, methanogenic archaea, anaerobic fungi and protozoa. These microbes produce a diverse array of enzymes that convert ingested feedstuffs into volatile fatty acids and microbial protein which are used by the animal for growth. Recent advances in high-throughput sequencing and bioinformatic analyses have helped to reveal how the composition of the rumen microbiome varies significantly during the development of the ruminant host, and with changes in diet. These sequencing efforts are also beginning to explain how shifts in the microbiome affect feed efficiency. In this review, we provide an overview of how meta-omics technologies have been applied to understanding the rumen microbiome, and the impact that diet has on the rumen microbial community.
About 400 subglacial lakes are known from Antarctica. The question of whether life unique of subglacial lakes exists has been paramount since their discovery. Despite frequent evidence of microbial life mostly from accretion ice, subglacial lakes are characterized by physiologically hostile conditions to metazoan life, as we know it. Pure water (salinity ≤0.4–1.2%), extreme cold (−3°C), high hydrostatic pressure, areas of limited or no oxygen availability and permanent darkness altogether require physiological adaptations to these harsh conditions. The record of gene sequences including some associated with hydrothermal vents does foster the idea of metazoan life in Lake Vostok. Here, we synthesize the physico-chemical environment surrounding sub-glacial lakes and potential sites of hydrothermal activity and advocate that the physico-chemical stability found at these sites may be the most likely sites for metazoan life to exist. The unique conditions presented by Lake Vostok may also offer an outlook on life to be expected in extra-terrestrial subglacial environments, such as on Jupiter's moon Europa or Saturn's moon Enceladus.
Microorganisms are the most abundant organisms on Earth, and microbial abundance records preserved in ice cores have been connected to records of environmental change. As an alternative to high resolution abundance records, which can be difficult to recover, we used culture-dependent and culture-independent methods to examine bacteria in glacier ice from the Tibetan Plateau (TP). We recovered a total of 887 bacterial isolates from ice cores of up to 164 m in depth retrieved from seven glaciers, located across the TP. These isolates were related to 53 genera in the Actinobacteria, Firmicutes, Bacteroidetes, and Proteobacteria, with 13 major genera accounting for 78% of isolates. Most of the genera were common across the geographic region covered by our sampling, but there were differences in the genera recovered from different depths in the ice, with the deepest portions of the ice cores dominated by a single genus (Sporosarcina). Because microorganisms deposited on glaciers must survive atmospheric transport under a range of temperatures, temperature tolerance should be an important survival mechanism. We tested isolate growth across a range of temperatures (0–35 °C), and found psychrotolerance to be common. Together, our results show that ice depth, and by extension age, are characterized by different types of microorganisms, providing new information about microbial records in ice.
To understand the geological origins of minerals in cryoconite and the nutrients sources for microbes on glaciers, we analyzed the Sr–Nd isotopic ratios of the four mineral fractions in cryoconites including saline, carbonate, phosphate, silicate and the organic fraction obtained from Gulkana Glacier in Alaska. The isotopes in the silicate mineral fraction exhibited spatial variation within the glacier (87Sr/86Sr: 0.704533–0.709563, εNd (0): −16.0 to 0.5), which can be explained by the different mixing ratios of the two distinct sources: one of the sources is lateral and terminal moraines or soil, and the other is the medial moraine of the glacier. The minerals in the cryoconite at the lower sites in the glacier are likely derived from the former source, whereas those at the upper sites are from latter sources. The mineralogical and elemental compositions also support mixing of the silicate minerals from the two local sources. The Sr isotopic ratios of the organic fraction also showed spatial variation on the glacier in the middle sites – a trend similar to those of the phosphate fraction. The results suggest that the organic matter is mostly the byproducts of microbes using the phosphate minerals as a nutrient source.
This survey presents the first high-throughput characterisation of fungal distribution based on ITS2 Illumina sequencing of uncultured microbiome from a 1500 years old perennial ice deposit in Scărișoara Ice Cave, Romania. Of the total of 1 751 957 ITS2 sequences, 64% corresponded to 182 fungal operational taxonomic units, showing a low diversity, particularly in older ice strata, and a distinct temporal distribution pattern. Ascomycota was the major phylum in all ice samples, dominating the 400 and 1500 years old ice strata deposited during the cold Little Ice Age (LIA) and Dark Ages Cold Period, while Basidiomycota was mostly present in 900-years old ice formed during the Medieval Warm Period (MWP). Chytridiomycota and Mucoromycota phyla were present in recently formed and 400-years old ice, respectively. Among the 80 identified genera, Cryptococcus victoriae, commonly found in glacial habitats, was identified in all strata. A positive correlation between fungal distribution and ice conductivity, Ca, Na and Sr concentrations was observed across the ice block, with pH values trailing climate variations during LIA and MWP, respectively. Our record highlighted the presence of a complex climate and environmental-driven fungal community in perennial ice strata accumulated during the last 1500 years in Scărișoara Ice Cave.
Glaciers retreating in response to climate warming are progressively exposing primary mineral substrates to surface conditions. As primary production is constrained by nitrogen (N) availability in these emerging ecosystems, improving our understanding of how N accumulates with soil formation is of critical concern. In this study, we quantified how the distribution and speciation of N, as well as rates of free-living biological N fixation (BNF), change along a 2000-year chronosequence of soil development in a High Arctic glacier forefield. Our results show the soil N pool increases with time since exposure and that the rate at which it accumulates is influenced by soil texture. Further, all N increases were organically bound in soils which had been ice-free for 0–50 years. This is indicative of N limitation and should promote BNF. Using the acetylene reduction assay technique, we demonstrated that microbially mediated inputs of N only occurred in soils which had been ice-free for 0 and 3 years, and that potential rates of BNF declined with increased N availability. Thus, BNF only supports N accumulation in young soils. When considering that glacier forefields are projected to become more expansive, this study has implications for understanding how ice-free ecosystems will become productive over time.
Proglacial environments are ideal for studying the development of soils through the changes of rocks exposed by glacier retreat to weathering and microbial processes. Carbon (C) and nitrogen (N) contents as well as soil pH and soil elemental compositions are thought to be dominant factors structuring the bacterial, archaeal and fungal communities in the early stages of soil ecosystem formation. However, the functional linkages between C and N contents, soil composition and microbial community structures remain poorly understood. Here, we describe a multivariate analysis of geochemical properties and associated microbial community structures between a moraine and a glaciofluvial outwash in the proglacial area of a High Arctic glacier (Longyearbreen, Svalbard). Our results reveal distinct differences in developmental stages and heterogeneity between the moraine and the glaciofluvial outwash. We observed significant relationships between C and N contents, δ13Corg and δ15N isotopic ratios, weathering and microbial abundance and community structures. We suggest that the observed differences in microbial and geochemical parameters between the moraine and the glaciofluvial outwash are primarily a result of geomorphological variations of the proglacial terrain.
Cryoconite holes are water-filled cylindrical holes formed on ablation ice surfaces and commonly observed on glaciers worldwide. Temporal changes of cryoconite holes characteristically <5 cm in diameter were monitored with a time-lapse interval camera over 15 d during the melting season on Qaanaaq Glacier in northwest Greenland. The holes drastically changed their dimensions and synchronously collapsed twice during the study period. When the holes collapsed, the coverage of cryoconite on the ice surface increased from 1.0 to 3.5% in the field of view of the camera, and then decreased again to 0.4% after the holes reformed. Comparison with meteorological data showed that the collapses occurred in cloudy and rainy or windy weather conditions, corresponding to low shortwave solar radiation (68–126 W m−2, 40–55% of the incoming flux). In contrast, holes developed in sunny conditions correspond to high solar radiation (186–278 W m−2, 63–88%). Results suggest that the dimensions of holes drastically changed depending on the weather conditions and that frequent cloudy, warm and windy conditions would cause a decay of holes and weathering crust, inducing an increase in the cryoconite coverage on the ice, consequently darkening the glacier surface.
Snow can be considered an independent ecosystem that hosts active microbial communities. Snow microbial communities have been extensively investigated in the Arctic and in the Antarctica, but rarely in mid-latitude mountain areas. In this study, we investigated the bacterial communities of snow collected in four glacierized areas (Alps, Eastern Anatolia, Karakoram and Himalaya) by high-throughput DNA sequencing. We also investigated the origin of the air masses that produced the sampled snowfalls by reconstructing back-trajectories. A standardized approach was applied to all the analyses in order to ease comparison among different communities and geographical areas. The bacterial communities hosted from 25 to 211 Operational Taxonomic Units (OTUs), and their structure differed significantly between geographical areas. This suggests that snow bacterial communities may largely derive from ‘local’ air bacteria, maybe by deposition of airborne particulate of local origin that occurs during snowfall. However, some evidences suggest that a contribution of bacteria collected during air mass uplift to snow communities cannot be excluded, particularly when the air mass that originated the snow event is particularly rich in dust.