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.

Prevalence and Antibiotic Resistance of Carbapenemase-Producing Gram-Negative Bacteria in Saint Petersburg and Some Other Regions of the Russian Federation.

Carbapenemase-producing gramnegative bacteria, which hydrolyze most offi-lactams, including carbapenems, is of global health care system threat. The number of the known carbapenemases is constantly increasing, however only four types are widely distributed: NDM-type, KPC-type, OXA-48-type and VIM-type. The frequency of carbapenemase-producing Klebsiellapneumoniae in hospitals of Saint Petersburg reached 9.2% (5.9% for NDM-type, 1.4% for OXA-48-type, 1.9% for NDM-type + OXA-48-type). Carbapenemase producers were also detected in hospitals of Moscow, Yekaterinburg, Vologda, Murmansk, Kurgan, Krasnoyarsk, Izhevsk, Krasnodar and Perm. In total 281 carbapenemase producers were recorded within 2011-2016, which were isolated from infected or colonized patients (K.pneumoniae - 247 isolates, Acinetobacter spp - 29 isolates, Enterobacter cloacae - 2 isolates, Serratia marcescens - 1 isolate, Escherichia coli - 1 isolate and Proteus mirabifis - 1 isolate). The carbapenemase-producing K.pneumoniae isolates were distinguished by considerable genetic diversity, the NDM-type carbapenemase-producers belonged to eight, KPC-type - to three and OXA-48-type - to four different sequence-types (STs) respectively. The representatives of the globally dominant genetic line, Clonal Group 258 (CG258), and also a number of the less common lines (ST147, ST273, ST307 and ST377) were detected. The K.pneumoniae strains were distinguished by a high frequency of cross-resistance and the associated resistance to antibiotics of different groups. The frequency of resistance to cephalosporins and fluoroquinolones reached 100%. Among the NDM-type carbapenemase producers the frequency of resistance to aminoglycosides exceeded 90%, among the KPC-type carbapenemase producers the frequency of resistance corresponded to 66% for amikacin and 93% for gentamicin, among the OXA-48 type carbapenemase producers the frequency of resistance was even lower (50% and 73% respectively). Approximately 80% of the NDM-type, 90% of the KPC-type and only 60% of the OXA-48-type carbapenemase producers showed a high level of resistance to imipenem and meropenem. The frequency of resistance to tigecycline varied within 6.7% to 14.8% and the frequency of resistance to polymyxin was within 4.2% to 20%. The OXA-40- and OXA-23-types carbapenemase-producing Acinetobacter spp. remained susceptible only to polymyxin. It is obvious that the possibility of antibacterial therapy of infections caused by carbapenemases producers is limited.

[Discovery of Genetic Markers of Resistance to ß-Lactams in Gramnegative Microorganisms by PCR Diagnosis].

Fifteen specimens of the hemoculture and 89 specimens of the broncho-alveolar lavage were used in the study. Monocultures of gramnegative bacteria resistant to cefotaxime, cefepime, imipenem and meropenem were isolated from the specimens. The PCR method with detection of the results in the real time regimen (PCR test-system Litekh) provided detection of the beta-lactamase genes: bla(CTX-M-like) (72/104, 69.2%), bla(NDM) (6/104, 5.8%), bla(VIM) (49/104, 47.1%) and bla(OXA48-like) (59/104, 56.7%). There was identified correlation between the phenotype of resistance of Acinetobacter spp., Pseudomonas aeruginosa, Klebsiella pneumoniae and Escherichia coli to cefotaxime and carbopenems and detection of the bla(CTX-M-like) and bla(NDM) genes. At the same time, up to 70% of the K. pneumoniae isolates from the biological specimes positive with respect to the presence of the carbapenase bla(VIM) and bla(OXA48-like) genes demonstrated their phenotypic susceptibility to carbopenems. The results of the study confirmed the prognostic value of the genetic diagnosis for improvement of the routine bacteriological investigations.

[Susceptibility of gramnegative carbapenemase-producing bacteria to various group antibiotics].

The study involved 25 isolates of gramnegative carbapenemase-producing bacteria. 17 isolates of Klebsiella pneumonia produced carbapenemase NDM-1 and were highly resistant to cephalosporins (MIC>128 mcg/ml), carbapenems (MIC>16 mcg/ml), aminoglycosides and fluoroquinoiones, while among them 4 isolates preserved susceptibility to azthreonam and all of them were susceptible to tigecycline and polymyxin. 2 isolates of Acinetobacter genomospecies 13 produced NDM-1 and were resistant to all the beta-lactams and amikacin, while preserved susceptibility to gentamicin, co-trimoxazole, tigecycline and polymyxin, the susceptibility to ciprofloxacin being lowered. Carbapenemase VIM-4 was produced by 2 isolates of Enterobacter cloacae, which were highly resistant to cephalosporins and azthreonam, significant synergism being observed between cefepim and clavulanate. The resistance of the isolates to carbapenems was low (MIC 0.5-4.0 mcg/ml), they also being resistant to aminoglycosides and ciprofioxacin and susceptible to tigecycline and polymyxin. Carbapenemases KPC-2 were detected in 2 isolates of K.pneumoniae and in 1 isolate of E.cloacae. The above isolates were resistant to all the beta-lactams, ciprofloxacin, aminoglycosides and co-trimoxazole. I isolate of E.cloacae showed resistance to tigecychine and I isolate of K.pneumoniae was resistant to polymyxin. Carbapenemase OXA-48 was detected in 1 isolate of K.pneumoniae. It was resistant to all the beta-lactams, ciprofloxacin and co-trimoxazole and susceptible to aminoglycosides, tigecycline and polymyxin.