General dynamics of the URT microbiome and microbial signs of recovery in COVID-19 patients

COVID-19 is caused by an airborne virus, SARS-CoV-2. The upper respiratory tract (URT) is, therefore, the first system to endure the attack. Inhabited by an assemblage of microbial communities, a healthy URT wards off the invasion. However, once invaded, it becomes destabilised, which could be crucial to the establishment and progression of the infection. We examined 696 URT samples collected from 285 COVID-19 patients at three time-points throughout their hospital stay and 100 URT samples from 100 healthy controls. We used 16S ribosomal RNA sequencing to evaluate the abundance of various bacterial taxa, α-diversity, and β-diversity of the URT microbiome. Ordinary least squares regression was used to establish associations between the variables, with age, sex, and antibiotics as covariates. The URT microbiome in the COVID-19 patients was distinctively different from that of healthy controls. In COVID-19 patients, the abundance of 16 genera was significantly reduced. A total of 47 genera were specific to patients, whereas only 2 were unique to controls. The URT samples collected at admission differed more from the control than from the samples collected at later stages of treatment. The following four genera originally depleted in the patients grew significantly by the end of treatment: Fusobacterium, Haemophilus, Neisseria, and Stenotrophomonas. Our findings strongly suggest that SARS-CoV-2 caused significant changes in the URT microbiome, including the emergence of numerous atypical taxa. These findings may indicate increased instability of the URT microbiome in COVID-19 patients. In the course of the treatment, the microbial composition of the URT of COVID-19 patients tended toward that of controls. These microbial changes may be interpreted as markers of recovery.

Phenotypic and genomic characteristics of oxacillin-susceptible mecA-positive Staphylococcus aureus, rapid selection of high-level resistance to beta-lactams

The aim of this study is to describe the phenotypic and genetic properties of oxacillin-susceptible methicillin-resistant Staphylococcus aureus (OS-MRSA) isolates and their beta-lactam resistant derivatives obtained after selection with oxacillin. A collection of hospital- (HA-) and community-acquired (CA-) MRSA was screened for oxacillin susceptibility. Antibiotic susceptibility testing, population analysis profile (PAP), mecA expression analysis, and whole genome sequencing (WGS) were performed for 60 mecA-positive OS-MRSA isolates. Twelve high-level beta-lactam resistant derivatives selected during PAP were also subjected to WGS. OS-MRSA were more prevalent among CA-MRSA (49/205, 24%) than among HA-MRSA (11/575, 2%). OS-MRSA isolates belonged to twelve sequence types (ST), with a predominance of ST22-t223-SCCmec IVc and ST59-t1950-SCCmec V lineages. OS-MRSA were characterized by mecA promoter mutations at - 33 (C→T) or - 7 (G→T/A) along with PBP2a substitutions (S225R or E246G). The basal and oxacillin-induced levels of mecA expression in OS-MRSA isolates were significantly lower than those in control ST8-HA-MRSA isolates. Most of the OS-MRSA isolates were heteroresistant to oxacillin. High-level beta-lactam resistant OS-MRSA derivatives selected with oxacillin carried mutations in mecA auxiliary factors: relA (metabolism of purines), tyrS, cysS (metabolism of tRNAs), aroK, cysE (metabolism of amino acids and glycolysis). Cefoxitin-based tests demonstrated high specificity for OS-MRSA detection. The highest positive predictive values (PPV > 0.95) were observed for broth microdilution, the VITEK® 2 automatic system, and chromogenic media. Susceptibility testing of CA-MRSA requires special attention due to the high prevalence of difficult-to-detect OS-MRSA among them. Mis-prescription of beta-lactams for the treatment of OS-MRSA may lead to selection of high-level resistance and treatment failures.

Comparative Analysis of Library Preparation Approaches for SARS-CoV-2 Genome Sequencing on the Illumina MiSeq Platform

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been responsible for over two years of the COVID-19 pandemic and a global health emergency. Genomic surveillance plays a key role in overcoming the ongoing COVID-19 pandemic despite its relative successive waves and the continuous emergence of new variants. Many technological approaches are currently applied for the whole genome sequencing (WGS) of SARS-CoV-2. They differ in key stages of the process, and they feature some differences in genomic coverage, sequencing depth, and in the accuracy of variant-calling options. In this study, three different protocols for SARS-CoV-2 WGS library construction are compared: an amplicon-based protocol with a commercial primer panel; an amplicon-based protocol with a custom panel; and a hybridization capture protocol. Specific differences in sequencing depth and genomic coverage as well as differences in SNP number were found. The custom panel showed suitable results and a predictable output applicable for the epidemiological surveillance of SARS-CoV-2 variants.

A psychometric study of the Russian-language version of the “Bayley Scales of Infant and Toddler Development–third edition”: An assessment of reliability and validity

Introduction

The Bayley Scales of Infant and Toddler Development–third edition (Bayley-III) is one of the most widely used tools for assessing child development, and adapted versions of this instrument have been successfully used in many countries. No comprehensive psychometric studies of the Bayley-III have yet been performed in Russia.

Materials and methods

This psychometric study was part of the longitudinal study conducted by the Ural Federal University in 2016–2020. Within the project, the original Bayley-III manual was translated into Russian and then used in a cohort of 333 infants to assess cognition, expressive/receptive communication, and fine/gross motor skills. For the purpose of psychometric analysis, we selected the data for four age groups of children from the longitudinal study database: 4–6 months (N = 149), 10 months (N = 138), 15 months (N = 151), and 24 months (N = 124). The development scores of the sample children were compared with the original Bayley-III norms in each age strata separately. Reliability and validity of the translated instrument were examined using correlation analysis, tests of internal consistency, and confirmatory factor analysis (CFA).

Results

The average scaled scores of the examined children were generally comparable with the original (US) Bayley-III norms, with the exception of those older than 1 year, who demonstrated 1.2–1.9 points better performance in cognitive development and gross motor skills and 0.9–2.6 points lower performance in expressive communication. The correlation of both raw and scaled scores between different scales was low to moderate in all age groups (Spearman’s ρ mostly within the range of 0.3–0.6; p < 0.001 for all pairwise correlations). Internal consistency tests confirmed high reliability of the translated instrument (Cronbach’s α = 0.74–0.87, McDonald’s ω = 0.79–0.89). CFA demonstrated a good fit of the three-factor model (cognitive, communicative, and motor components) in all age strata.

Conclusion

The Russian version of the Bayley-III proved to be a psychometrically valid and reliable tool for assessing child development, at least in a research context. The development of the examined children was close to the original US norms, with some deviation in cognitive, gross motor, and expressive communication scores mostly in older children, which could be attributed to the biased sample.

Quantitative screening level assessment of human risk from PCBs released in glacial meltwater: Silvretta Glacier, Swiss Alps

Persistent organic pollutants (POPs) are entrained within glaciers globally, reemerging in many alpine ecosystems. Despite available data on POP flux from glaciers, a study of human health risk caused by POPs released in glacial meltwater has never been attempted. Glaciers in the European Alps house the largest known quantity of POPs in the Northern Hemisphere, presenting an opportunity for identification of potential risk in an endmember scenario case study. With methodology developed by the US Environmental Protection Agency (EPA), we provide a regional screening level human risk analysis of one class of POPs, polychlorinated-biphenyls (PCB) that have been measured in melt waters from the Silvretta Glacier in the Swiss Alps. Our model suggests the potential for both cancer and non-cancer impacts in residents with lifetime exposure to current levels of PCB in glacial meltwater and average consumption of local fish. For residents with an abbreviated 30-year exposure timeframe, the risk for cancer and non-cancer impacts is low. Populations that consume higher quantities of local fish are predicted to be at a greater risk, with risk to lifetime consumers higher by an order of magnitude. Based on the results of our screening study, we suggest that local government move to the next step within the risk assessment framework: local monitoring and management. Within the Alps, other glacial watersheds of a similar size and latitude may see comparable risk and our model framework can be adapted for further implementation therein.

Legacy organochlorine pollutants in glacial watersheds: a review

Northern Hemisphere alpine glaciers have been identified as a point of concentration and reemergence of legacy organochlorine pollutants (OCPs). In this review, we compile a selection of published literature combining long-range, global atmospheric transport and distribution-based compartmental environmental flux models, as well as data from glacial meltwater, ice core, crevasse and proglacial lake sediment studies. Regional studies of ice and meltwater in alpine glaciers of the northern latitudes show similarities in sample deposition profiles and concentration due to chemical atmospheric residence time, precipitation type and glacier flow rates. In glaciated locations near areas of extensive OCPs use, such as the Swiss and Italian Alps, glacier sample concentrations are higher, while in areas more distant from use, including Arctic nations, OCPs concentrations in glaciers are significantly lower. Our review identifies alpine glaciers co-located with regions characterized by OCPs use as a significant organochlorine pollutant distribution source, secondary in timing and location to direct deposition, with subsequent bioaccumulation and potential human risk impacts.

[Age-related characteristics of reactivity of school children during mental processes]

An examination of 300 students was carried out, aged 9, 12 and 15, in the process of their training, aiming at the establishment of the characteristics of their reactivity to mental loading. Modern psychophysiological and biochemical methods were used in the dynamic follow up of the changes in CNS and neuroendocrine activity. Definite age and sex discrepancies were found, on the base of the analysis, in the CNS reactivity to mental loading. With the growing up, the volume and speed of the work performed were increased and their accuracy enhanced. The boys showed faster reactions and less accuracy at work. The girls were distinguished with a better characteristic of their capacity for work. The curves of the daily and weekly dynamics of mental capacity for work were outlined.

[Free plasma cortisol in mothers and newborn infants immediately after birth]

Free plasma cortisol levels were determined in 60 mothers and their newborn infants by the method of Ousvatova and Pankov. Twenty healthy, nonpregnant women were used as a control group. The data showed that the level of free plasma cortisol was higher in the mothers than in the healthy, nonpregnant women. The free plasma cortisol level in the newborn infants was lower than in the mothers but higher than in the non-pregnant women.