Clinical Microbiology and Antimicrobial Chemotherapy

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ISSN / EISSN : 1684-4386 / 2686-9586
Total articles ≅ 156
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, N.I. Eremeeva, D.V. Vakhrusheva
Clinical Microbiology and Antimicrobial Chemotherapy, Volume 23; https://doi.org/10.36488/cmac.2021.4.404-408

Abstract:
Objective. To develop a technology for freezing and long-term storage of mycobacteria cultures and implement into a microbiological laboratory routine practice. Materials and Methods. For comparison between different condition, the media for freezing mycobacteria containing 0.9% NaCl or Middlebrook’s 7H9 medium with the addition of glycerol at various concentrations: 0%, 4.0%, 20.0%, 50.0% (by final volume) was evaluated. To freeze suspensions of cultures, two methods were used: one – using a cryo-freezer (cooling rate of 1°C/min), the second – direct placement in a deep freeze at a temperature of -80°C. Suspension of a museum strain of Mycobacterium tuberculosis H37Rv was used for preparing suspension. The efficiency of the chosen storage method was assessed by the proportion of viable cells obtained after thawing the suspensions (total number of cells according to quantitative PCR data/number of CFU in Lowenstein-Jensen medium). Results. After storage under various conditions, from 1.2% to 16.9% of mycobacterial cells remained viable. The maximum percentage of viable cells of 16.9% (95% CI 8.6–42.4%) reached when stored in a freezer at a temperature of -80°C without using a cryo-freezer in a medium consisting of 0.9% NaCl with glycerol (20.0% by final volume). However, no statistically significant differences in viable cells were found in the medium containing 0.9% NaCl solution with the addition of 4.0%, 50.0% glycerol, as well as Middlebrook’s 7H9 medium with and without glycerol. Conclusions. A technology for long-term storage of mycobacterial cultures has been developed, based on freezing a cell suspension at a temperature of -80°C in a medium consisting of a 0.9% NaCl solution with the glycerol (20.0% volume fraction), which provides a high degree of cell viability preservation, is lowcost and can be easily integrated into the routine work of a microbiological laboratory.
, A.I. Yaremenko, A.A. Zubareva, S.A. Karpischenko, Marina O. Popova, A.A. Kurus, G.V. Portnov, O.N. Pinegina, O.V. Lukina, M.V. Malyarevskaya, et al.
Clinical Microbiology and Antimicrobial Chemotherapy, Volume 23; https://doi.org/10.36488/cmac.2021.4.347-358

Abstract:
Currently, the relevance of the issues of diagnosis and treatment of invasive fungal diseases has increased significantly due to the pandemic of a new coronavirus infection COVID-19 and the massive use of corticosteroids for the treatment. The key success factors in the outcome of invasive fungal diseases are early diagnosis and treatment, including the applying of an adequate systemic antifungal therapy and surgical treatment. Extensive areas of mycotic lesions of the facial bones and paranasal sinuses are lifethreatening conditions due to anatomical proximity to brain structures and a high risk of dissemination of I invasive fungal diseases with a fatal outcome. The objective of this work was to study the risk factors, possible pathogenesis, diagnosis and treatment strategy of invasive fungal diseases of the orofacial region in convalescents of COVID-19. We present case-series data on six patients in the clinics of maxillofacial surgery and otorhinolaryngology of the Pavlov First Saint Petersburg State Medical University over the period of 2021–2022. Predisposing factors, clinical and radiological symptoms, features of diagnosis, therapy and surgical strategy were analyzed. The presented observations confirm the relevance and danger of complications after a COVID-19 in the form of the development of invasive fungal diseases with damage to the maxillofacial region caused by mucormycetes and Aspergillus spp., as well as importance of early diagnosis and treatment.
Clinical Microbiology and Antimicrobial Chemotherapy, Volume 23; https://doi.org/10.36488/cmac.2021.4.359-366

Abstract:
This article presents a review of currently available data on etiology and antimicrobial resistance in surgical site infections (SSI) following cardiac surgery. Author performed analysis of the references on etiology and antimicrobial resistance in SSI after cardiac surgery from the Scopus, Medline, EMBASE, PubMed and Google Scholar over January 2010 to December 2020. The selected most cited earlier (January 1990 to December 2009) publications were also included in the analysis.
, Yu.A. Rogacheva
Clinical Microbiology and Antimicrobial Chemotherapy, Volume 23; https://doi.org/10.36488/cmac.2021.3.226-238

Abstract:
Over the last decade, the introduction of new antifungal drugs and diagnostic procedures has improved the prognosis of hematological patients with invasive fungal disease (IFD), primarily invasive aspergillosis. Despite effective antifungal prophylaxis against the most common IFD caused by Aspergillus spp., rates of IFD due to rare pathogens being resistant to most antifungal drugs, including mucormycosis have been increased. The main group of patients having a high risk of mucormycosis is deeply immunocompromised patients who received chemotherapy for acute leukemia, patients undergoing allogeneic bone marrow transplantation, or treated with corticosteroids for graft-versushost disease. Currently, the urgency of this complication is significantly higher due to COVID-19 pandemic and extensive use of corticosteroids for the treatment of COVID-19. Despite the fact that the criteria for the diagnosis of IFD EORTC/MSG 2008 and 2020 have been developed and implemented into practice in most countries, mucormycosis still remains a difficult-to-diagnose IFD, where the factor of rapid diagnosis is a main factor of treatment success. Medications available for the treatment of IFD include polyenes, triazoles, and echinocandins. For a long time, the drug of choice for the treatment of mucormycosis was liposomal amphotericin B. However, a new effective drug has been approved for the treatment of both mucormycosis and IFD, caused by multiple pathogens – isavuconazole. This review presents new data on the epidemiology of mucormycosis, diagnosis approaches and current international treatment guidelines.
N.V. Ovsyannikov, Olga A. Bilevich
Clinical Microbiology and Antimicrobial Chemotherapy, Volume 23; https://doi.org/10.36488/cmac.2021.3.239-246

Abstract:
The novel coronavirus (COVID-19) pandemic announced by the World Health Organization in March 2020 assigned medical community to the new tasks that require immediate solutions. Recent studies have shown that invasive aspergillosis associated with COVID-19 often complicates a course of the disease and leads to death. This review aims to describe the diagnosis and therapy challenges due to COVID-19 associated invasive pulmonary aspergillosis.
, , , , Alexey Yu. Kuzmenkov, Alexey А. Martinovich, Anna V. Mikotina, Marina V. Sukhorukova, Ivan V. Trushin,
Clinical Microbiology and Antimicrobial Chemotherapy, Volume 23; https://doi.org/10.36488/cmac.2021.3.280-291

Abstract:
Objective. To evaluate in vitro activity of biapenem and other clinically available carbapenems against Russian clinical isolates of Enterobacterales, Pseudomonas aeruginosa и Acinetobacter spp., including isolates with acquired fermentative mechanisms of resistance to β-lactams. Materials and Methods. A total of 3139 Enterobacterales isolates, 793 P. aeruginosa isolates and 634 Acinetobacter spp. isolates from hospitalized patients in 63 hospitals from 35 Russian cities were included in the study during 2018-2019. Minimal inhibitory concentrations (MIC) for biapenem and other antimicrobials were determined in accordance with ISO 20776-1:2006. Carbapenemases genes were detected by commercially available real-time PCR kits AmpliSens® MDR KPC/OXA-48-FL and AmpliSens® MDR MBL-FL (Central Research Institute of Epidemiology, Russia). Data analysis and reporting was performed using AMRcloud online platform (www.amrcloud.net). Results. For all tested Escherichia coli isolates MIC50/90 were 0.06/0.125 mg/l for biapenem, 0.125⁄0.25 mg/l for imipenem, and 0.06/0.06 mg/l for meropenem. When MIC50/90 for ertapenem (0.015/0.125 mg/l for all isolates tested) were comparable to those of biapenem, a greater number of nosocomial E. coli isolates had MIC >4 mg/l for ertapenem (3.6%) than for biapenem (2.6%). MIC50/90 of Klebsiella pneumoniae for biapenem were 0.5⁄16 mg/l, for both imipenem and meropenem – 0.5⁄32 mg/l, for ertapenem – 2⁄32 mg/l. Resistance to oxyimino-β-lactams had no significant influence on activity of biapenem against Enterobacterales isolates. For 321 carbapenemase-producing K. pneumoniae isolates (ОХА-48 – 63.9%, NDM – 27.7%) biapenem has shown no advantages over imipenem and meropenem. МПК50/90 for nosocomial and community-acquired P. aeruginosa isolates were 8⁄64 mg/l and 0,5⁄16 mg/l for biapenem, 8⁄128 mg/l and 1⁄16 mg/l – for imipenem, 16⁄64 mg/l and 0,5⁄32 mg/l – for meropenem. All carbapenems, including biapenem, had very low in vitro activity against carbapenemaseproducing P. aeruginosa isolates. МПК50/90 of Acinetobacter spp. were 64⁄128 mg/l for biapenem, 64⁄128 mg/l – for imipenem, and 128⁄128 mg/l – for meropenem. Conclusions. According to the MIC distributions and MICs50/90 values independently of the presence of fermentative mechanisms of resistance to β-lactams, in vitro activity of biapenem against Russian clinical isolates of Enterobacterales, P. aeruginosa and Acinetobacter spp. was comparable to those of imipenem and meropenem.
A.V. Zhestkov, , D.D. Ismatullin, A.A. Martinovich, E.V. Haykina
Clinical Microbiology and Antimicrobial Chemotherapy, Volume 23; https://doi.org/10.36488/cmac.2021.1.66-91

Abstract:
Non-tuberculous mycobacteria (NTM) include more than 190 species and subspecies. Some NTM species can cause human diseases of the lungs or extrapulmonary infections. The guidelines focus on pulmonary mycobacteriosis in adult patients without cystic fibrosis or HIV infection caused by the most common NTMs, such as Mycobacterium avium complex, Mycobacterium kansasii, and Mycobacterium xenopi among slow-growing NTMs and Mycobacterium abscessus complex among fast-growing species. Experts of American Thoracic Society (ATS), European Respiratory Society (ERS), European Society for Clinical Microbiology and Infectious Diseases (ESCMID), and American Society for Infectious Diseases (IDSA) contributed to the development of the guidelines. A total of 31 evidence-based recommendations are provided for the diagnosis and treatment of NTM-induced lung infections.
, Мarina V. Sukhorukova, Аida N. Chagaryan, Ivan V. Trushin, ,
Clinical Microbiology and Antimicrobial Chemotherapy, Volume 23; https://doi.org/10.36488/cmac.2021.1.92-99

Abstract:
Objective. To determine in vitro activity of thiamphenicol and other clinically available antimicrobials against clinical isolates of Haemophilus influenzae, Streptococcus pneumoniae and Streptococcus pyogenes. Materials and Methods. We included in the study 875 clinical isolates from 20 Russian cities during 2018–2019. Among tested strains, 126 were H. influenzae, 389 – S. pneumoniae, 360 – S. pyogenes. Antimicrobial susceptibility testing was performed using broth microdilution method according to ISO 20776-1:2006. AST results were interpreted according to EUCAST v.11.0 clinical breakpoints. Results. The minimum inhibitory concentrations (MICs) of thiamphenicol did not exceed 2 mg/L for 94.4% of H. influenzae strains (MIC50 and MIC90 were 0.5 and 1 mg/L, respectively). Thiamphenicol was active against 76.9% of ampicillin-resistant H. influenzae strains (MIC of thiamphenicol < 2 mg/L). The MIC of thiamphenicol was in the range of 0.06–2 mg/L for 96.7% of S. pneumoniae strains (MIC50 and MIC90 were 0.5 and 2 mg/L, respectively). The MIC of thiamphenicol for 90.6% of S. pneumoniae strains with reduced susceptibility to penicillin (MIC of penicillin > 0.06 mg/L) did not exceed 2 mg/L. A total of 88.1% of S. pneumoniae strains resistant to erythromycin were highly susceptible to thiamphenicol (MIC < 2 mg/L). The MIC of thiamphenicol did not exceed 8 mg/L for 96.1% of S. pyogenes strains (MIC50 and MIC90 were 2 and 4 mg/L, respectively). Conclusions. Thiamphenicol was characterized by relatively high in vitro activity, comparable to that of chloramphenicol, against tested strains of H. influenzae, S. pneumoniae and S. pyogenes, including S. pneumoniae isolates with reduced susceptibility to penicillin.
, Vladimir A. Bagin, D.V. Belsky, Maria N. Astafyeva, N.N. Nevskaya, G.B. Kolotova, S.M. Rosanova, T.I. Bykova
Clinical Microbiology and Antimicrobial Chemotherapy, Volume 23; https://doi.org/10.36488/cmac.2021.1.17-25

Abstract:
Objective. To review a literature published over the past 5 years and our own data on the etiology of lower respiratory tract infections (LRTI), antimicrobial resistance and its relationships between sepsis and choice of appropriate antibiotic therapy. Materials and Methods. National Nosocomial Infections Surveillance (NNIS) criteria were used to diagnose LRTI. A review of the articles regarding LRTI from the Russian and international English language journals published over 6 years was performed. Identification of microorganisms was performed by culture over the period of 2003–2013; since 2014, MALDI-TOF MS method was used for this purpose. Results. Despite the ongoing policy to limit the use of antimicrobial therapy in the ICUs, there is an increase in carbapenemase-producing isolates in the ICUs from 2.2% (2018) to 11.7% (2020, 9 months). Along with the trend to increase in carbapenemase-producing pathogens causing LRTI, their variability is also increasing. In particular, it applies to strains producing carbapenemases OXA-48 or combination of OXA-48 with KPC; with the trend to combined production of carbapenemase beginning at 2019. Conclusions. Carbapenemase producers are becoming more widespread in the ICU settings, including the lower respiratory tract in mechanically ventilated patients. Practitioners didn’t get used to associate VAP with the Sepsis-3 criteria. The changes in etiology include the increased rate of carbapenem-resistant Enterobacterales and non-fermenting Gram-negative bacteria, primarily Acinetobacter spp., in Russia. It’s due to improved quality of respiratory support and increased consumption of carbapenems, tigecycline and polymyxins. Significant increase of OXA-48-producing pathogens is likely to be associated with a poor compliance with temporary guidelines on COVID-19 with regard to antibiotic therapy.
Dmitry Y. Ruzanov, A.M. Skriagina, I.V. Buinevich, S.V. Goponiako, G.S. Balasaniantc, E.S. Khimova
Clinical Microbiology and Antimicrobial Chemotherapy, Volume 23; https://doi.org/10.36488/cmac.2021.1.27-42

Abstract:
Rapid tests detecting Mycobacterium tuberculosis and drug resistance which are universally implemented in medical practice has dramatically improved the diagnosis of rifampicin-resistant tuberculosis and shortened turnaround time thus enabling early etiotropic therapy. However, permanently increasing drug resistance of M. tuberculosis makes treatment less effective. Furthermore, long treatment courses are required due to low sterilizing activity of treatment regimens used for drug-resistant tuberculosis which leads to greater toxic effects, reduces patients’ adherence to treatment and consumes resources of medical care systems. Current phthisiology needs new effective medications and short treatment regimens, otherwise elimination of tuberculosis by 2050 is impossible. This review summarizes the information about treatment of drugresistant TB, including repurposed drugs, new medications and treatment regimens.
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