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 ß-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.

Molecular Mechanisms of Ceftaroline Susceptibility Reduction in Methicillin-Resistant Staphylococcus aureus.

Ceftaroline is a unique cephalosporin with activity against methicillin resistant Staphylococcus aureus (MRSA). It was approved for clinical use in the USA, Europe and Russian Federation since 2010 for the treatment of the skin and soft tissue infection and community-acquired pneumoniae. In the present study there was used molecular typing of 24 isolates of MRSA with reduced susceptibility to ceftaroline. For 8 isolates belonging to different genetic lines (ST8, ST239 and ST228) and requiring MICs there were determined antibiotic concentrations preventing formation of resistant mutants (mutant prevention concentration) and the ranges of the mutant selection window (MSW). The last majority of the isolates with reduced susceptibility to ceftaroline (MIC of 2 mcg/ml) belonged to the clonal line ST228. The whole genome sequencing of two isolates of ST228 showed that they belonged to the epidemic South Germany genetic line and were characterized by the presence of mutations in PBP2a (N146K) and PBP2 (C197Y) responsible for reduced susceptibility. The highest rates of MPC (32 mcg/ml) and MSW (2-16 mcg/ml) were observed in the clinical isolates belonging to the genetic line ST8. The isolates of ST239 and ST228 had the selection window within 2-4 mcg/ml. No dependence of the MIC and MPC/MSW levels was detected.

SNP Polymorphism in Genomes of CC320 Isolates of Streptococcuspneumoniae Resistant to Beta-Lactams.

Bioinformatic analysis of the data on the genome sequencing of the isolates of the Streptococcuspneumoniae clonal complex SS320 from the Russian Federation, as well as the data on SS320 isolates from public sources in the penicillin resistant isolates resulted in detection of 139 missense mutations in 45 genes. In addition to the mutations in the genes of the main penicillin-binding proteins (PSB - PBP1A, PBP2B and PBP2X) there was detected high frequency of mutations in the genes of the (division and cell wall) dcw-cluster, as well as in RegR protein belonging to the transcription regulators of the LacI/GaIR family. Development of resistance to beta-lactams in S.pneumoniae is defined not only by modification of the PSB, but also by adaptive changes in the metabolic pathways involved in the bacterial cell growth and division.

[Antibiotic Resistance of MRSA in the Russian Federation].

The results of the multicentre trial on estimation of MRSA antibiotic susceptibility to 17 antibiotics are presented. 474 nonrepeting isolates of MRSA (mecA+), collected in 2011-2014 in 10 cities of the Russian Federation were used in the trial. The antibiotic susceptibility was determined by the method of serial microdilutions in broth with estimation of the MICs in accordance with the international standards CLSI 2014 and EUCAST 2014. The highest levels of the MRSA resistance were stated against ciprofloxacin--92%(MIC50 32 mcg/ml), gentamicin--85% (MIC50 128 mcg/ml), erythromycin--54% (MIC50 32-mcg/ml) and clindainycin - 45% (MIC50 0.03 mcg/ml), as well as against rifampicin--38% (MIC50 0.06 mcg/ml). The frequency of MRSA isolated at the vancomycin dose of 2 mcg/ml equaled 26%. No correlation of the decrease in susceptibility to vancomycin and rifampicin was observed. In 5% of MRSA isolated from infected surgical wounds in patients with bone infection or sepsis, there was observed a decrease in the susceptibility to ceftarolin (MIC 2-4 mcg/ml). Co-trimoxasole, fusidic acid (MIC50 0.06 mcg/ml) and mupirocin (MIC50 0.5 mcg/ml) showed high antibacterial activity, 93-98% of the isolates being susceptible to the drugs. No resistance to linezolid and tigecycline was detected. By the associate resistance spectrum, most of the MRSA isolates were characterized by resistance to drugs of 3-7 groups (56%). The phenotypes with simultaneous resistance to drugs of 8-10 groups amounted to 6%. As a whole, 70 variants of associate resistance combinations were detected.

[Antibiotic Resistance and Serotype Pattern of Streptococcus pneumoniae Isolated from Children in St. Petersburg in 2010-2013].

The surveillance of the serotype pattern and antibiotic resistance of S. pneumoniae in various geographical regions is required for the validity of rational etiotrophic therapy of pneumococcal infections and the choice of the optimal vaccines for their prophylaxis. 250 S. pneumoniae isolates from children with acute otitis or pneumonia and healthy carriers in St. Petersburg in 2010-2013 were investigated. The analysis of the serotype pattern of the pneumococci showed that 13-valent conjugate vaccine was the most active (86.1% of pneumococci causing pneumonia and 86.4% of pneumococci causing acute otitis). The isolates were higly resistant to beta-lactams and macrolides. By the EUCAST criteria, the decrease in the susceptibility to penicillin, cefotaxime, erythromycin and ceftarolin was observed in 32.4%, 14%, 33.2 and 6% of the isolates respectively. 22.4% of the isolates showed associate resistance to penicillin and erythromycin.. No resistance to moxifloxacin was detected. The frequency of resistance to tetracycline, co-trimoxasole and chloramphenicol in various patients ranged within 30-50%. The prevalence of the antibiotic resistance was mainly characteristic of the isolates serotypes 19A, 19F, 14 and serogroup 6.

[Antibiotic Resistance of Coagulase-Negative Staphylococci Isolated at Hospitals of St. Petersburg and Moscow].

Antibiotic susceptibility of 119 coagulase-negative staphylococci isolated at hospitals of St. Petersburg and Moscow was investigated and estimated at the local laboratories as oxacillin resistant. The following species were identified: Staphylococcus epidermidis, S. haemolyticus, S. hominis, S.capitis, S. simulans, S. pettenkoferi, S. lentus, S. carnosus and S. warneri. The oxacillin resistance was confirmed in 79.8% of the isolates. The frequency of the associated resistance to non-beta-lactams was much higher in the oxacillin resistant isolates vs. the oxacillin susceptible ones. When the CLSI and EUCAST susceptibility criteria were used, 1-3% difference in the resistance levels was recorded. Among the oxacillin resistant isolates the frequency of resistance to gentamicin, ciprofloxacin, erythromycin, moxifloxacin, tetracycline and clindamycin equaled 90, 88, 88, 63, 43 and 26% respectively. Two linezolid resistant isolates of S. epidermidis with lower susceptibility to tedizolid were isolated. Eight isolates of S. epidermidis showed lower resistance to mupirocin. The MIC of ceftarolin for oxacillin resistant coagulase-negative staphylococci varied from 0.5 to 2.0 mcg/ml, while for the oxacillin susceptible ones it was lower than 0.25 mcg/ml. No resistance to tigecyclin and vancomycin was observed.