Changes in the oropharyngeal microbiome in patients with viral-bacterial pneumonia associated with сovid-19 on the background of antibiotic therapy and monitoring of antibioticaresistentie strains

2021 ◽  
Vol 43 (3-4) ◽  
pp. 37-41
Author(s):  
L. B. Romanyuk ◽  
Keyword(s):  
Antibiotic Resistance ◽  
Bacterial Pneumonia ◽  
Antibacterial Agents ◽  
Cost Of Treatment ◽  
E Coli ◽  
Intestinal Dysbiosis ◽  
New Antibiotics ◽  
Resistant Strains ◽  
Clinically Significant ◽  
The Cost

The relevance of the infection caused by COVID-19 today is beyond doubt. According to the Protocol “Provision of medical care for the treatment of coronavirus disease (COVID-19)” approved by the order of the Ministry of Health of Ukraine dated April 2, 2020 № 762, antibacterial drugs are prescribed only in the presence of confirmed bacterial co-infection ( after receiving positive bacteriological results) blood and / or sputum analysis). But given that the results of the analysis must wait a few days, antibiotics, under certain indications, can be prescribed empirically. The aim of our work was to analyze the structure of the oropharyngeal microbiome, patients with viral and bacterial pneumonia who received antibiotics, to determine clinically significant strains and their sensitivity to antibacterial agents. In the structure of the oropharyngeal microbiome, fungi of the genus Candida significantly prevailed, which were found in 50 (45.6%) subjects, in second place in terms of frequency of detection were S. pneumoniae – 29 (26.4%). Much less often from the oropharynx of patients with viral-bacterial pneumonia associated with COVID-19 were isolated K. pneumoniae – 13 (11.8%), S. aureus – 11 (10.0%) and E. coli – 7 (6.4 %). Among the isolated S. pneumoniae, the maximum number of resistant strains was detected for such fairly new antibiotics as ceftriaxone – 37.9% and azithromycin – 31.0%. Among fungi of the genus Candida resistant to nystatin and amphotericin were 38.5% and 26.9%, respectively. Therefore, the administration of antibacterial agents, taking into account the sensitivity of clinically significant strains, will guarantee effective treatment, prevent the development of antibiotic resistance, prevent the development of oropharyngeal and intestinal dysbiosis, and thus reduce the cost of treatment of antibiotic side effects, including probiotics.

scholarly journals Thinking Outside the Bug: Molecular Targets and Strategies to Overcome Antibiotic Resistance

2019 ◽  
Vol 20 (6) ◽  
pp. 1255 ◽  
Author(s):  
Ana Monserrat-Martinez ◽  
Yann Gambin ◽  
Emma Sierecki
Keyword(s):  
Antibiotic Resistance ◽  
Bacterial Infections ◽  
Rational Design ◽  
Disease Onset ◽  
Resistant Bacteria ◽  
Antibiotic Resistant ◽  
New Antibiotics ◽  
Resistant Strains ◽  
Vancomycin Resistant ◽  
Antibiotic Discovery

Since their discovery in the early 20th century, antibiotics have been used as the primary weapon against bacterial infections. Due to their prophylactic effect, they are also used as part of the cocktail of drugs given to treat complex diseases such as cancer or during surgery, in order to prevent infection. This has resulted in a decrease of mortality from infectious diseases and an increase in life expectancy in the last 100 years. However, as a consequence of administering antibiotics broadly to the population and sometimes misusing them, antibiotic-resistant bacteria have appeared. The emergence of resistant strains is a global health threat to humanity. Highly-resistant bacteria like Staphylococcus aureus (methicillin-resistant) or Enterococcus faecium (vancomycin-resistant) have led to complications in intensive care units, increasing medical costs and putting patient lives at risk. The appearance of these resistant strains together with the difficulty in finding new antimicrobials has alarmed the scientific community. Most of the strategies currently employed to develop new antibiotics point towards novel approaches for drug design based on prodrugs or rational design of new molecules. However, targeting crucial bacterial processes by these means will keep creating evolutionary pressure towards drug resistance. In this review, we discuss antibiotic resistance and new options for antibiotic discovery, focusing in particular on new alternatives aiming to disarm the bacteria or empower the host to avoid disease onset.

scholarly journals Nosocomial post-cesarean endometritis: a rationalized strategy of antibacterial therapy

2018 ◽  
Vol 12 (2) ◽  
pp. 12-20
Author(s):  
N. A. Korobkov ◽  
N. N. Volkov ◽  
E. R. Tsoy ◽  
S. М. Mikaelyan
Keyword(s):  
Antibacterial Therapy ◽  
Antibacterial Agents ◽  
Antimicrobial Agents ◽  
Multidrug Resistant ◽  
E Coli ◽  
Number Of Patients ◽  
Previously Treated ◽  
New Mother ◽  
Clinically Significant ◽  
Klebsiella Spp

The number of patients with nosocomial post-cesarean endometritis is steadily growing. Aim: to study the etiology of nosocomial post-cesarean endometritis and to propose a rationalized antimicrobial therapy. Material and methods. Sixty six puerperas with post-cesarean endometritis were examined. The spectrum of microflora and its resistance to antimicrobial agents were determined using an automatic microbiological analyzer based on mass spectrometry. Results. Enterococci, E. coli, staphylococci and streptococci were the most clinically significant pathogens found in the examined patients with post-cesarean endometritis. The microflora spectrum in the endometrium reflected the previous «antibacterial history»; this association must be taken into account when developing antibacterial therapy. Conclusion. If the new mother was previously treated with antibacterial agents, it is recommended to use a combination of the reserve antibiotics in order to block the entire spectrum of possible multidrug-resistant pathogens. In cases of the resistant Gram-positive microflora (MRSE, MRSA, E. faecium), it is advisable to prescribe vancomycin. For the resistant Gram-negative microflora (Enterobacter spp., Citrobacter spp., E. coli-ESBL+ and Klebsiella spp.-ESBL+), vancomycin should be combined with carbapenems.

scholarly journals Development of evolution drugs - antibacterial compounds that block pathways to resistance

2020 ◽  
Author(s):  
Yanmin Zhang ◽  
Sourav Chowdhury ◽  
João V. Rodrigues ◽  
Eugene Shakhnovich
Keyword(s):  
Antibiotic Resistance ◽  
Dihydrofolate Reductase ◽  
Experimental Approach ◽  
Whole Genome ◽  
Bacterial Protein ◽  
Antibacterial Compounds ◽  
E Coli ◽  
Resistant Strains ◽  
Resistant Mutants

AbstractAntibiotic resistance is a worldwide challenge. A potential approach to block resistance is to simultaneously inhibit WT and known escape variants of the target bacterial protein. Here we applied an integrated computational and experimental approach to discover compounds that inhibit both WT and trimethoprim (TMP) resistant mutants of E. coli dihydrofolate reductase (DHFR). We identified a novel compound (CD15-3) that inhibits WT DHFR and its TMP resistant variants L28R, P21L and A26T with IC50 50-75 μM against WT and TMP-resistant strains. Resistance to CD15-3 was dramatically delayed compared to TMP in in vitro evolution. Whole genome sequencing of CD15-3 resistant strains showed no mutations in the target folA locus. Rather, gene duplication of several efflux pumps gave rise to weak (about twofold increase in IC50) resistance against CD15-3. Altogether, our results demonstrate the promise of strategy to develop evolution drugs - compounds which block evolutionary escape routes in pathogens.

scholarly journals Precise prediction of antibiotic resistance in Escherichia coli from full genome sequences

2018 ◽  
Author(s):  
Danesh Moradigaravand ◽  
Martin Palm ◽  
Anne Farewell ◽  
Ville Mustonen ◽  
Jonas Warringer ◽  
...  
Keyword(s):  
Machine Learning ◽  
Antibiotic Resistance ◽  
Population Structure ◽  
Genome Sequencing ◽  
Diagnostic Tools ◽  
Clinical Settings ◽  
Whole Genome ◽  
Genome Sequences ◽  
E Coli ◽  
Resistant Strains

AbstractThe emergence of microbial antibiotic resistance is a global health threat. In clinical settings, the key to controlling spread of resistant strains is accurate and rapid detection. As traditional culture-based methods are time consuming, genetic approaches have recently been developed for this task. The diagnosis is typically made by measuring a few known determinants previously identified from whole genome sequencing, and thus is restricted to existing information on biological mechanisms. To overcome this limitation, we employed machine learning models to predict resistance to 11 compounds across four classes of antibiotics from existing and novel whole genome sequences of 1936 E. coli strains. We considered a range of methods, and examined population structure, isolation year, gene content, and polymorphism information as predictors. Gradient boosted decision trees consistently outperformed alternative models with an average F1 score of 0.88 on held-out data (range 0.66-0.96). While the best models most frequently employed all inputs, an average F1 score of 0.73 could be obtained using population structure information alone. Single nucleotide variation data were less useful, and failed to improve prediction for ten out of 11 antibiotics. These results demonstrate that antibiotic resistance in E. coli can be accurately predicted from whole genome sequences without a priori knowledge of mechanisms, and that both genomic and epidemiological data are informative. This paves way to integrating machine learning approaches into diagnostic tools in the clinic.SummaryOne of the major health threats of 21st century is emergence of antibiotic resistance. To manage its economic impact, efforts are made to develop novel diagnostic tools that rapidly detect resistant strains in clinical settings. In our study, we employed a range machine learning tools to predict antibiotic resistance from whole genome sequencing data for E. coli. We used the presence or absence of genes, population structure and isolation year of isolates as predictors, and could attain average precision of 0.93 and recall of 0.83, without prior knowledge about the causal mechanisms. These results demonstrate the potential application of machine learning methods as a diagnostic tool in healthcare settings.

scholarly journals Gene Amplification Uncovers Large Previously Unrecognized Cryptic Antibiotic Resistance Potential in E. coli

2021 ◽  
Author(s):  
Stacy A. Suarez ◽  
Adam C. Martiny
Keyword(s):  
Antibiotic Resistance ◽  
Gene Amplification ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Bacterial Cells ◽  
Adaptive Resistance ◽  
E Coli ◽  
New Antibiotics

Predicting where new antibiotic resistance genes will rise is a challenge and is especially important when new antibiotics are developed. Adaptive resistance allows sensitive bacterial cells to become transiently resistant to antibiotics.

scholarly journals Susceptibility to antibiotics in escherichiae isolated in a multidisciplinary medical centre

2016 ◽  
Vol 65 (4) ◽  
pp. 83-89
Author(s):  
Nadezda S. Kozlova ◽  
Natalia E. Barantsevich ◽  
Elena P. Barantsevich
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Multidrug Resistance ◽  
Antimicrobial Resistance ◽  
Antimicrobial Agents ◽  
E Coli ◽  
Microdilution Method ◽  
Carbapenem Resistant ◽  
Resistant Strains ◽  
High Level

Relevance. Antimicrobial resistance in nosocomial strains currently presents a very important problem.  Aim of the study: Study of antibiotic resistance in Escherichia coli, isolated in a multidisciplinary centre.  Materials and Methods. Susceptibility of 151 E. coli strains to 15 antibiotics was studied by microdilution method. Results. The majority of the studied strains were resistant to antibiotics, including: ampicillin (57.0%), ciprofloxacin and moxifloxacin (42.4% each), III and IV generation cephalosporins (37.1% and 34.4%, respectively) and gentamycin (29.1%). The highest activity against E. coliwas shown for carbapenems (resistance to erthapenem – 2.6%, meropenem – 0.7%), in particular, for imipenem – no strains resistant to this drug were isolated. Resistance to amikacin and phosphomycin was low: 3.3% and 1.3% respectively. Wide diversity of antibiotic resistance spectra was revealed in studied strains, with a high level of multidrug resistance (48.0%). Conclusion. Study of susceptibility to antimicrobial agents in E. coli, isolated in a multidisciplinary centre, showed predominance of resistant strains with a high level of multidrug resistance. The appearance of carbapenem-resistant strains in a multidisciplinary centre presents a rising problem.

scholarly journals Differential Susceptibility of Catheter Biomaterials to Biofilm-Associated Infections and Their Remedy by Drug-Encapsulated Eudragit RL100 Nanoparticles

2019 ◽  
Vol 20 (20) ◽  
pp. 5110 ◽  
Author(s):  
Vivek Kumar Pandey ◽  
Kumar Rohit Srivastava ◽  
Gufran Ajmal ◽  
Vijay Kumar Thakur ◽  
Vijai Kumar Gupta ◽  
...  
Keyword(s):  
Differential Susceptibility ◽  
Therapeutic Index ◽  
Cost Of Treatment ◽  
Water Contact ◽  
E Coli ◽  
Gentamicin Sulfate ◽  
The Cost ◽  
Complex Architecture ◽  
Contact Angle Analysis

Biofilms are the cause of major bacteriological infections in patients. The complex architecture of Escherichia coli (E. coli) biofilm attached to the surface of catheters has been studied and found to depend on the biomaterial’s surface properties. The SEM micrographs and water contact angle analysis have revealed that the nature of the surface affects the growth and extent of E. coli biofilm formation. In vitro studies have revealed that the Gram-negative E. coli adherence to implanted biomaterials takes place in accordance with hydrophobicity, i.e., latex > silicone > polyurethane > stainless steel. Permanent removal of E. coli biofilm requires 50 to 200 times more gentamicin sulfate (G-S) than the minimum inhibitory concentration (MIC) to remove 90% of E. coli biofilm (MBIC90). Here, in vitro eradication of biofilm-associated infection on biomaterials has been done by Eudragit RL100 encapsulated gentamicin sulfate (E-G-S) nanoparticle of range 140 nm. It is 10–20 times more effective against E. coli biofilm-associated infections eradication than normal unentrapped G-S. Thus, Eudragit RL100 mediated drug delivery system provides a promising way to reduce the cost of treatment with a higher drug therapeutic index.

scholarly journals Comparison of Antibiotic Resistance Profile and Biofilm Production of Staphylococcus aureus Isolates Derived from Human Specimens and Animal-Derived Samples

Antibiotics ◽  
2019 ◽  
Vol 8 (3) ◽  
pp. 97 ◽  
Author(s):  
Maria Vitale ◽  
Paola Galluzzo ◽  
Patrizia Giuseppina Buffa ◽  
Eleonora Carlino ◽  
Orazio Spezia ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Antibiotic Resistance ◽  
Antimicrobial Resistance ◽  
Meca Gene ◽  
Multidrug Resistant ◽  
Animal Origin ◽  
Antibiotic Resistance Profile ◽  
Biofilm Production ◽  
New Antibiotics ◽  
Resistant Strains

Background: The diffusion of antimicrobial resistance is a significant concern for public health worldwide. Staphylococcus aureus represents a paradigm microorganism for antibiotic resistance in that resistant strains appear within a decade after the introduction of new antibiotics. Methods: Fourteen S. aureus isolates from human specimens and twenty-one from samples of animal origin, were compared for their antimicrobial resistance and biofilm capability. In addition, they were characterized at the molecular level to detect the antimicrobial resistance mecA gene and genes related with enterotoxin, toxin, and biofilm production. Results: Both phenotypic and molecular analysis showed main differences among human- and animal-derived isolates. Among the human-derived isolates, more multidrug-resistant isolates were detected and mecA gene, enterotoxin, and toxin genes were more prevalent. Different genes involved in biofilm production were detected with bap present only in animal-derived isolates and sasC present in both isolates, however, with a higher prevalence in the human-derived isolates. Biofilm capability was higher in human-derived isolates mainly associated to the sasC gene. Conclusions: The overall results indicate that human S. aureus isolates are more virulent and resistant than the isolates of animal origin randomly selected with no infection anamnesis. This study confirms that selection for more virulent and resistant S. aureus strains is related to the clinical practice.

Antibiotic Resistance of Escherichia coliO157:H7 and O157:NM Isolated from Animals, Food, and Humans

1998 ◽  
Vol 61 (11) ◽  
pp. 1511-1514 ◽  
Author(s):  
JIANGHONG MENG ◽  
SHAOHUA ZHAO ◽  
MICHAEL P. DOYLE ◽  
SAM W. JOSEPH
Keyword(s):  
Antibiotic Resistance ◽  
Ground Beef ◽  
E Coli ◽  
Resistance To Antibiotics ◽  
Development Of Resistance ◽  
Resistant Strains

Antibiotic resistance was determined for 118 E. coli O157:H7 and 7 O157:NM isolates from Animals, foods, and humans. Among the 125 isolates, 30 (24%) were resistant to at least one antibiotic and 24 (19%) were resistant to three or more antibiotics. Cattle isolates had the highest rate (34%) of antibiotic resistance. The seven resistant food isolates were all from ground beef. The most frequent resistance type overall was streptomycin-sulfisoxazole-tetracycline, which accounted for over 70% of the resistant strains. Two E. coli O157:NM isolates from cattle were resistant to six antibiotics: ampicillin, kanamycin, sulfisoxazole, streptomycin, tetracycline, and ticarcillin. Streptomycin was the most common antibiotic to which E. coli O157:H7 and O157:NM were resistant (29 out of 30 isolates), followed by tetracycline (26 isolates). This study suggests that E. coli O157:H7 and O157:NM have developed resistance to antibiotics. Research is needed to define mechanisms of antibiotic resistance in E. coli O157:H7 and to minimize the development of resistance.

scholarly journals In vitro and in vivo antibacterial activities of CS-834, a novel oral carbapenem.

1997 ◽  
Vol 41 (12) ◽  
pp. 2652-2663 ◽  
Author(s):  
T Fukuoka ◽  
S Ohya ◽  
Y Utsui ◽  
H Domon ◽  
T Takenouchi ◽  
...  
Keyword(s):  
Antibacterial Activity ◽  
Bacterial Species ◽  
Antibacterial Activities ◽  
Gram Positive ◽  
Beta Lactamases ◽  
E Coli ◽  
Resistant Strains ◽  
Clinically Significant

CS-834 is a novel oral carbapenem antibiotic. This compound is an ester-type prodrug of the active metabolite R-95867. The antibacterial activity of R-95867 was tested against 1,323 clinical isolates of 35 species and was compared with those of oral cephems, i.e., cefteram, cefpodoxime, cefdinir, and cefditoren, and that of a parenteral carbapenem, imipenem. R-95867 exhibited a broad spectrum of activity covering both gram-positive and -negative aerobes and anaerobes. Its activity was superior to those of the other compounds tested against most of the bacterial species tested. R-95867 showed potent antibacterial activity against clinically significant pathogens: methicillin-susceptible Staphylococcus aureus including ofloxacin-resistant strains, Streptococcus pneumoniae including penicillin-resistant strains, Clostridium perfringens, Neisseria spp., Moraxella catarrhalis, most members of the family Enterobacteriaceae, and Haemophilus influenzae (MIC at which 90% of strains are inhibited, < or =0.006 to 0.78 microg/ml). R-95867 was quite stable to hydrolysis by most of the beta-lactamases tested except the metallo-beta-lactamases from Stenotrophomonas maltophilia and Bacteroides fragilis. R-95867 showed potent bactericidal activity against S. aureus and Escherichia coli. Penicillin-binding proteins 1 and 4 of S. aureus and 1Bs, 2, 3, and 4 of E. coli had high affinities for R-95867. The in vivo efficacy of CS-834 was evaluated in murine systemic infections caused by 16 strains of gram-positive and -negative pathogens. The efficacy of CS-834 was in many cases superior to those of cefteram pivoxil, cefpodoxime proxetil, cefdinir, and cefditoren pivoxil, especially against infections caused by S. aureus, penicillin-resistant S. pneumoniae, E. coli, Citrobacter freundii, and Proteus vulgaris. Among the drugs tested, CS-834 showed the highest efficacy against experimental pneumonia in mice caused by penicillin-resistant S. pneumoniae.

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