- MeSH
- bakteriální nálož MeSH
- barvení a značení metody MeSH
- Escherichia coli MeSH
- fenaziny * MeSH
- genciánová violeť * MeSH
- gramnegativní bakteriální infekce diagnóza MeSH
- gramnegativní bakterie izolace a purifikace MeSH
- krev mikrobiologie MeSH
- kultivační vyšetření krve MeSH
- senzitivita a specificita MeSH
- Staphylococcus aureus MeSH
- techniky typizace bakterií metody MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
BACKGROUND: While the resistance rates of commonly detected uropathogens are well described, those of less frequent Gram-negative uropathogenic bacteria have seldom been reported. The aim of this study was to examine the resistance rates of less frequent uropathogenic Gram-negatives in a population of patients treated in a Department of Urology of a tertiary referral centre in Central Europe over a period of 9 years. METHODS: Data on all positive urine samples from urological in- and out-patients were extracted form the Department of Clinical Microbiology database from 2011 to 2019. Numbers of susceptible and resistant isolates per year were calculated for these uropathogens: Acinetobacter spp. (n = 74), Citrobacter spp. (n = 60), Enterobacter spp. (n = 250), Morganella morganii (n = 194), Providencia spp. (n = 53), Serratia spp. (n = 82) and Stenotrophomonas maltophilia (n = 27). Antimicrobial agents selected for the survey included: ampicillin, amoxicillin/clavulanic acid, piperacillin/tazobactam; cefuroxime, cefotaxime, ceftazidime and cefepime; ciprofloxacin and ofloxacin; gentamicin and amikacin; ertapenem, meropenem and imipenem; trimethoprim-sulfamethoxazole (co-trimoxazole), nitrofurantoin and colistin. RESULTS: Penicillin derivatives have generally poor effect except piperacillin/tazobactam. Cefuroxime is not efficient unlike cefotaxime (except against Acinetobacter spp. and S. maltophilia). Susceptibility to fluoroquinolones is limited. Amikacin is somewhat more efficient than gentamicine but susceptibilities for both safely exceed 80%. Nitrofurantoin shows virtually no efficiency. Cotrimoxazole acts well against Citrobacter spp., Serratia spp. and it is the treatment of choice for S. maltophilia UTIs. Among carbapenems, ertapenem was less efficient than meropenem and imipenem except for S. maltophilia whose isolates were mostly not suceptible to any carbapenems. CONCLUSIONS: Uropathogenic microorganisms covered in this report are noteworthy for their frequently multi-drug resistant phenotypes. Knowledge of resistance patterns helps clinicians choose the right empirical antibiotic treatment when the taxonomical assignment of the isolate is known but sensitivity results are pending.
- MeSH
- bakteriální léková rezistence * MeSH
- časové faktory MeSH
- centra terciární péče MeSH
- gramnegativní bakterie účinky léků izolace a purifikace MeSH
- infekce močového ústrojí mikrobiologie MeSH
- lidé středního věku MeSH
- lidé MeSH
- nemocniční oddělení MeSH
- retrospektivní studie MeSH
- senioři MeSH
- urologie MeSH
- Check Tag
- lidé středního věku MeSH
- lidé MeSH
- mužské pohlaví MeSH
- senioři MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- pozorovací studie MeSH
- Geografické názvy
- Česká republika MeSH
Úvod: Včasná a kauzální aplikace antibiotik u pacientů s pozitivní hemokulturou patří mezi základní předpoklady úspěšné léčby infekce. Izolace a následná identifikace bakterií z hemokultury klasickými (kultivačními) metodami však může trvat až několik dní. MALDI-TOF MS patří mezi metody, které umožňují rychlou identifikaci bakterií, a to nejen kultur z kultivačních médií, ale i přímo v klinickém materiálu. Metodika: Do studie byly zařazeny vzorky pozitivních hemokultur, které byly v letech 2016 až 2018 odebrány od pacientů Fakultní nemocnice Olomouc a následně byly vyšetřeny na Ústavu mikrobiologie Lékařské fakulty Univerzity Palackého v Olomouci. Vzorky pozitivních hemokultur byly zpracovány pomocí vlastního modifikovaného postupu, zahrnujícího odstranění krevních buněk pomocí centrifugace za nižších otáček. Následně byla pomocí centrifugace za vyšších otáček a promývání vzorku získána peleta, která byla testována pomocí MALDI-TOF MS. Výsledky: Ve studii bylo metodou přímé identifikace vyšetřeno celkem 110 pozitivních hemokultur. Správná identifikace na úrovni druhu byla vyšší u gramnegativních bakterií (88 %) v porovnání s grampozitivními bakteriemi (79 %) a také u nich bylo dosaženo vyšších hodnot identifikačního skóre. Hodnota identifikačního skóre vyšší nebo rovna než 2,0 byla u 62 % hemokultur obsahujících gramnegativní bakterie a 17 % hemokultur obsahujících bakterie grampozitivní. Hodnota identifikačního skóre v rozmezí 1,7–2,0 byla zjištěna u 21 % hemokultur gramnegativních a 33 % hemokultur s grampozitivními bakteriemi. Závěr: Přímá identifikace mikroorganismů z pozitivních hemokultur metodou MALDI-TOF MS umožňuje rychlejší diagnostiku a v důsledku zkrácení doby potřebné k dosažení výsledku identifikace patogenu může pozitivním způsobem významně ovlivnit antibiotickou léčbu pacientů.
Background: Early and causal administration of antibiotics in patients with a positive blood culture is an essential prerequisite for successful treatment of infection. However, isolation and subsequent identification of bacteria in a blood culture by classical (culture) methods may last several days. MALDI-TOF MS is a method allowing rapid identification of bacteria, not only cultures from culture media, but also directly in clinical specimens. Methods: The study included samples of positive blood cultures taken from patients in the University Hospital Olomouc between 2016 and 2018 and examined at the Department of Microbiology of the Faculty of Medicine, Palacký University Olomouc. Positive blood culture samples were processed using an in-house method involving the removal of blood cells by low-speed centrifugation. Subsequently, a pellet obtained by high-speed centrifugation and sample washing was tested by MALDI-TOF MS. Results: A total of 110 positive blood cultures were examined using the method of direct identification. At a species level, more Gramnegative bacteria (88 %) than Gram-positive bacteria (79 %) were correctly identified, with higher identification score values being obtained for the former. Identification score values of 2.0 or higher were found in 62 % of blood cultures containing Gram-negative bacteria and 17 % of blood cultures containing Gram-positive bacteria. Identification score values ranging from 1.7 to 2.0 were found in 21 % of Gram-negative blood cultures and 33 % of blood cultures containing Gram-positive bacteria. Conclusion: Direct identification of microorganisms from positive blood cultures using MALDI-TOF MS enables more rapid diagnosis. By reducing the time required to obtain the result of pathogen identification, it may positively affect the antibiotic treatment of patients.
- MeSH
- bakteriemie * diagnostické zobrazování mikrobiologie MeSH
- gramnegativní bakterie izolace a purifikace patogenita MeSH
- grampozitivní bakterie izolace a purifikace patogenita MeSH
- lidé MeSH
- senzitivita a specificita MeSH
- spektrometrie hmotnostní - ionizace laserem za účasti matrice metody přístrojové vybavení MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- práce podpořená grantem MeSH
OBJECTIVES: The Tigecycline Evaluation and Surveillance Trial (T.E.S.T.) is a global surveillance programme monitoring the in vitro activity of a panel of antimicrobial agents against clinically important bacterial isolates. Data for Gram-positive and Gram-negative isolates collected in Eastern Europe between 2011 and 2016 are presented here. METHODS: Minimum inhibitory concentrations (MICs) were determined by the broth microdilution method using CLSI guidelines. Antimicrobial susceptibility was assessed using EUCAST breakpoints. RESULTS: Nine Eastern European countries submitted 4289 isolates. Among Acinetobacter baumannii, resistance to levofloxacin, amikacin and meropenem was 77.5%, 63.4% and 62.2%, respectively. Multidrug resistance among A. baumannii was higher in 2015 than in previous years (44.1% in 2011 and 71.0% in 2015), decreasing to 51.7% in 2016. The multidrug resistance percentage for Pseudomonas aeruginosa was 26.9% and was relatively stable over time. The percentage of extended-spectrum β-lactamase (ESBL)-positive isolates among Escherichia coli and Klebsiella pneumoniae was 20.1% and 55.7%, respectively. Resistance to amikacin, meropenem and tigecycline was low among E. coli and K. pneumoniae and the ESBL-producing subset (≤5.9%). Among Staphylococcus aureus isolates, 36.7% were methicillin-resistant (MRSA); percentages varied year-on-year. No S. aureus isolates, including MRSA, were resistant to linezolid, vancomycin or tigecycline. Among Enterococcus faecium isolates, resistance was 22.6% to vancomycin and 2.3% to linezolid; no isolates were resistant to tigecycline. CONCLUSION: This study shows low resistance to meropenem and tigecycline among Enterobacteriaceae isolates and continued activity of linezolid, vancomycin and tigecycline against Gram-positive organisms. However, antimicrobial resistance continues to be problematic in Eastern Europe and requires continued surveillance.
- MeSH
- antibakteriální látky farmakologie MeSH
- bakteriální léková rezistence MeSH
- dospělí MeSH
- gramnegativní bakteriální infekce mikrobiologie MeSH
- gramnegativní bakterie klasifikace účinky léků genetika izolace a purifikace MeSH
- grampozitivní bakteriální infekce mikrobiologie MeSH
- grampozitivní bakterie klasifikace účinky léků genetika izolace a purifikace MeSH
- lidé středního věku MeSH
- lidé MeSH
- mikrobiální testy citlivosti MeSH
- mladiství MeSH
- mladý dospělý MeSH
- senioři MeSH
- tigecyklin farmakologie MeSH
- Check Tag
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- mladiství MeSH
- mladý dospělý MeSH
- mužské pohlaví MeSH
- senioři MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- východní Evropa MeSH
Many studies correlate changes in human gut microbiome with the onset of various diseases, mostly by 16S rRNA gene sequencing. Setting up the optimal sampling and DNA isolation procedures is crucial for robustness and reproducibility of the results. We performed a systematic comparison of several sampling and DNA isolation kits, quantified their effect on bacterial gDNA quality and the bacterial composition estimates at all taxonomic levels. Sixteen volunteers tested three sampling kits. All samples were consequently processed by two DNA isolation kits. We found that the choice of both stool sampling and DNA isolation kits have an effect on bacterial composition with respect to Gram-positivity, however the isolation kit had a stronger effect than the sampling kit. The proportion of bacteria affected by isolation and sampling kits was larger at higher taxa levels compared to lower taxa levels. The PowerLyzer PowerSoil DNA Isolation Kit outperformed the QIAamp DNA Stool Mini Kit mainly due to better lysis of Gram-positive bacteria while keeping the values of all the other assessed parameters within a reasonable range. The presented effects need to be taken into account when comparing results across multiple studies or computing ratios between Gram-positive and Gram-negative bacteria.
- MeSH
- DNA bakterií genetika MeSH
- dospělí MeSH
- feces mikrobiologie MeSH
- fylogeneze MeSH
- gramnegativní bakterie klasifikace genetika izolace a purifikace MeSH
- grampozitivní bakterie klasifikace genetika izolace a purifikace MeSH
- lidé středního věku MeSH
- lidé MeSH
- mladý dospělý MeSH
- reagenční diagnostické soupravy MeSH
- reprodukovatelnost výsledků MeSH
- RNA ribozomální 16S genetika MeSH
- sekvenční analýza DNA MeSH
- vysoce účinné nukleotidové sekvenování metody MeSH
- zdraví dobrovolníci pro lékařské studie MeSH
- Check Tag
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- mladý dospělý MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- srovnávací studie MeSH
Non-fermentative Gram-negative bacilli are now one of the most important causes of severe infections in Polish hospitals. Acinetobacter species are serious concern because of the high prevalence of multi-drug resistance among strains. Resistance profiles for 53 Gram-negative non-fermentative blood isolates were done. MLST was carried out using 44 strains representing the most commonly isolated species: A. baumannii, P. aeruginosa, and S. maltophilia. MLST revealed that all 22 A. baumannii belonged to sequence type (ST) 2. The P. aeruginosa isolates belonged to 10 different STs. Four S. maltophilia isolates matched STs present in the database (ST4, ST15, ST116, ST142), seven isolates showing novel sequence types. Among P. aeruginosa and S. maltophilia PFGE confirmed the genetical variety of strains.
- MeSH
- antibakteriální látky farmakologie MeSH
- bakteriemie mikrobiologie MeSH
- fylogeneze MeSH
- gramnegativní bakterie klasifikace účinky léků genetika izolace a purifikace MeSH
- infekce spojené se zdravotní péčí krev mikrobiologie MeSH
- lidé středního věku MeSH
- lidé MeSH
- mikrobiální testy citlivosti MeSH
- multilokusová sekvenční typizace MeSH
- senioři MeSH
- Check Tag
- lidé středního věku MeSH
- lidé MeSH
- mužské pohlaví MeSH
- senioři MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Polsko MeSH
OBJECTIVE: Evaluation of tear production (Schirmer's tear test, STT) and measurement of intraocular pressure (IOP) were performed in a population of captive wild ungulates in a Slovenian ZOO during routine annual health check. ANIMALS STUDIED: In total, 10 fallow deer (Dama dama), 25 mouflons (Ovis aries musimon), 20 alpine ibexes (Capra ibex), and three alpine chamois (Rupicapra rupicapra) were included in the study. METHODS: Tear production was performed by Schirmer's tear test, IOP was measured with an applanation tonometer, and ophthalmological examination was conducted with slit-lamp biomicroscopy and indirect ophthalmoscopy. Conjunctival swabs were taken and submitted for aerobic bacteriology and for detection of Chlamydia spp. and Mycoplasma spp. tested by PCR. RESULTS: Average tear production (in mm/min) was 17.8 ± 3.16 for fallow deer, 17.9 ± 3.87 for mouflons, and 11.7 ± 3.87 for ibexes. Mean intraocular pressure (IOP, in mm Hg) was 14.1 ± 2.48 for fallow deer, 14.9 ± 2.20 for mouflons, and 13.1 ± 2.43 for ibexes. For chamois, average tear production and IOP were 14.5 ± 3.0 and 10.2 ± 2.5, respectively; this is the first record of STT I and IOP in chamois. Bacteriological swabs were positive for bacteria in 100% of the fallow deer, 56% of mouflons, 35% of ibexes, and 100% of chamois. Gram-positive bacteria were predominant. Moraxella spp., Chlamydia spp., and Mycoplasma spp. were not detected. CONCLUSION: The reported values were obtained in animals under manual restraint only to be applicative in similar conditions.
- MeSH
- divoká zvířata MeSH
- gramnegativní bakterie genetika izolace a purifikace MeSH
- grampozitivní bakterie genetika izolace a purifikace MeSH
- konjunktiva mikrobiologie MeSH
- kozy MeSH
- nitrooční tlak MeSH
- oči - fyziologické jevy * MeSH
- ovce domácí MeSH
- přežvýkavci fyziologie MeSH
- Rupicapra MeSH
- slzy fyziologie MeSH
- tonometrie oční veterinární MeSH
- vysoká zvěř MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Slovinsko MeSH
Národní referenční laboratoř pro antibiotika a Česká národní sbírka typových kultur (CNCTC) dourčily v letech 2016–2018 na základě výsledků analýzy MALDI-TOF hmotnostní spektrometrie a sekvenační analýzy části genu pro 16S rRNA celkem 14 izolátů, které pocházely z terénních laboratoří a které se na původních pracovištích pomocí standardních biochemických metod nepodařilo dourčit. Ve všech případech se jednalo o kmeny velmi vzácně izolované nebo neobvyklé ve spojení s danou diagnózou.
In 2016-2018, the National Reference Laboratory for Antibiotics and the Czech National Collection of Type Cultures (CNCTC) identified, based on results of MALDI-TOF mass spectrometry and sequence analysis of a part of the 16S rRNA gene, 14 isolates from field laboratories which could not be identified by the standard biochemical methods. All these strains were either rare or uncommon in the context of the given diagnosis.
- Klíčová slova
- bakteriální izoláty,
- MeSH
- gramnegativní bakterie izolace a purifikace MeSH
- grampozitivní bakterie izolace a purifikace MeSH
- kultivační vyšetření krve MeSH
- lidé MeSH
- odběr biologického vzorku * metody MeSH
- RNA ribozomální 16S MeSH
- spektrometrie hmotnostní - ionizace laserem za účasti matrice * MeSH
- techniky typizace bakterií MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- práce podpořená grantem MeSH
- tabulky MeSH
BACKGROUND: Catheter-related bloodstream infection (CRBSI) is a common complication in patients receiving home parenteral nutrition (HPN). Data regarding catheter salvage after a CRBSI episode are limited. We aimed to determine the incidence of CRBSI and rates of catheter salvage in adult patients receiving HPN. MATERIALS AND METHODS: We retrospectively searched our prospectively maintained HPN database for the records of all adult patients receiving HPN from January 1, 1990, to December 31, 2013, at our tertiary referral center. Data abstracted from the medical records included demographics, diseases, treatments, and outcomes. The incidence of CRBSI and rates of catheter salvage were determined. RESULTS: Of 1040 patients identified, 620 (59.6%) were men. The median total duration on HPN was 124.5 days (interquartile range, 49.0-345.5 days). Mean (SD) age at HPN initiation was 53.3 (15.3) years. During the study period, 465 CRBSIs developed in 187 patients (18%). The rate of CRBSI was 0.64/1000 catheter days. Overall, 70% of catheters were salvaged (retained despite CRBSI) during the study period: 78% of infections with coagulase-negative staphylococci, 87% with methicillin-sensitive Staphylococcus aureus, and 27% with methicillin-resistant S aureus. The percentage of catheters salvaged was 63% from 1990 to 1994, 63% from 1995 to 1999, 61% from 2000 to 2004, 72% from 2005 to 2009, and 76% from 2010 to 2013. CONCLUSION: Catheter salvage is possible after a CRBSI episode. Since most episodes of CRBSI are caused by skin commensals, effective treatment without removal of the central venous catheter is possible in most cases.
- MeSH
- bakteriemie epidemiologie MeSH
- Candida izolace a purifikace MeSH
- centra terciární péče MeSH
- centrální žilní katétry škodlivé účinky mikrobiologie MeSH
- gramnegativní bakterie izolace a purifikace MeSH
- grampozitivní bakterie izolace a purifikace MeSH
- incidence MeSH
- katétrové infekce epidemiologie mikrobiologie MeSH
- lidé středního věku MeSH
- lidé MeSH
- methicilin rezistentní Staphylococcus aureus izolace a purifikace MeSH
- následné studie MeSH
- parenterální výživa doma * MeSH
- retrospektivní studie MeSH
- senioři MeSH
- socioekonomické faktory MeSH
- stafylokokové infekce epidemiologie MeSH
- Check Tag
- lidé středního věku MeSH
- lidé MeSH
- mužské pohlaví MeSH
- senioři MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- Research Support, N.I.H., Extramural MeSH
BACKGROUND: Against a background of rapid increase of β-lactamase-producing or multi-resistant pathogenic bacteria and the resulting lack of effective antibiotic treatment, some older antibiotics have been tested for new therapeutic uses. One of these is fosfomycin, to which according to studies these resistant bacteria are very sensitive. Our study was designed because there is no data on the fosfomycin susceptibility rate in the Czech Republic. METHOD: In this study from January 2013 to June 2014 3295 unique isolates of Gram-negative bacteria which had caused urinary tract infections were examined. The antibiotic susceptibility was measured by disk diffusion test. Both EUCAST and CLSI guidelines criteria (for fosfomycin only) were used for the antibiotic susceptibility evaluation. RESULTS: The most frequently tested bacterial isolates were Escherichia coli (51.3%, n = 1703), Klebsiella pneumoniae (19.4%, n = 643) and Proteus spp. (11.8%, n = 392). Among all isolates 29.0% (n = 963) were resistant to fluoroquinolones, 11.3% (n = 374) produced extended spectrum β-lactamase and 4.2% (n = 141) produced AmpC β-lactamase. The overall in vitro susceptibility was significantly higher for fosfomycin compared to the other tested per-oral antibiotics (nitrofurantoin, ampicillin, co-trimoxazole, ciprofloxacin and cefuroxime) against all tested Gram-negative rod isolates (excluding Morganella morgani and Acinetobacter spp. isolates). Fosfomycin also remained highly active against those isolates with extended spectrum β-lactamase (ESBL) production (95.8% in Escherichia coli isolates and 85.3% in Klebsiella pneumoniae isolates), unlike other tested per-oral antibiotics, which showed significant (p < 0.0001) susceptibility decrease. CONCLUSION: We have confirmed in the Czech Republic the very high susceptibility to fosfomycin trometamol of urinary tract infection pathogens, particularly Gram-negative rods including those producing β-lactamase.
- MeSH
- antibakteriální látky farmakologie MeSH
- beta-laktamasy MeSH
- fosfomycin farmakologie MeSH
- gramnegativní bakterie účinky léků izolace a purifikace MeSH
- infekce močového ústrojí mikrobiologie MeSH
- lidé MeSH
- mikrobiální testy citlivosti MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Česká republika MeSH