Isolation of Cryptococcus adeliensis from clinical samples and the environment in Germany.
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ABSTRACT:
SUBMITTER: Tintelnot K
PROVIDER: S-EPMC548102 | biostudies-literature | 2005 Feb
REPOSITORIES: biostudies-literature
Publications
Isolation of Cryptococcus adeliensis from clinical samples and the environment in Germany.
Tintelnot Kathrin K Losert Heidemarie H
Journal of clinical microbiology 20050201 2
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Project description:IntroductionmicroRNAs (miRNAs) are considered to be novel molecular biomakers that could be exploited in the diagnosis and treatment of different diseases. The present study aimed to develop an efficient miRNA isolation method from different clinical specimens.MethodsTotal RNAs were isolated by Trizol reagent followed by precipitation of the large RNAs with potassium acetate (KCH3COOH), polyethylene glycol (PEG) 4000 and 6000, and lithium chloride (LiCl). Then, small RNAs were enriched and recovered from the supernatants by applying a combination of LiCl and ethanol. The efficiency of the method was evaluated through the quality, quantity, and integrity of the recovered RNAs using the A260/280 absorbance ratio, reverse transcription PCR (RT-PCR), and quantitative real-time PCR (q-PCR).ResultsComparison of different RNA isolation methods based on the precipitation of DNA and large RNAs, high miRNA recovery and PCR efficiency revealed that applying potassium acetate with final precipitation of small RNAs using 2.5 M LiCl plus ethanol can provide high yield and quality small RNAs that can be exploited for clinical purposes.ConclusionThe current isolation method can be applied for most clinical samples including cells, formalin-fixed and paraffin-embedded (FFPE) tissues and even body fluids with a wide applicability in molecular biology investigations.
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Project description:The purpose of this study was to investigate the presence of Cryptococcus neoformans species complex isolates from environmental sources in Croatia and to determine their molecular types and antifungal susceptibility. Swab samples of tree hollows and bird excreta in the soil beneath trees were collected. Samples included 472 (92.73%) samples obtained from tree hollows and 37 (7.27%) samples from bird excreta. Four C. neoformans species complex isolates were recovered from tree hollow swabs along the Mediterranean coast, while there were no isolates recovered from bird excreta or from the continental area. Three isolates were identified as molecular types VNI and one as VNIV. All tested antifungals showed high in vitro activity against the four isolates. This is the first report proving the presence of C. neoformans species complex in the environment of Croatia. The results of the study suggest a major risk of exposure for inhabitants living along the Croatian coast and that both VNI and VNIV molecular types can be expected in clinical cases of cryptococcosis. Susceptibility to antifungals confirmed that no resistance should be expected in patients with cryptococcosis at the present time.
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Project description:BackgroundThe isolation and culture of Mycobacterium ulcerans (Mu) as a primary diagnostic modality for Buruli ulcer (BU) disease are limiting due to their low sensitivity and slow-growing nature. M. ulcerans cultures can also be overgrown with other bacteria and fungi. Culture, however, remains an important tool for the study of persisting viable M. ulcerans, drug susceptibility tests, and other molecular assays to improve management of the disease. The challenge of contamination with other fast-growing bacteria necessitates decontamination of clinical samples prior to culturing, but current methods may be too harsh, resulting in low yields of M. ulcerans. We aimed to evaluate a Tika-Kic decontamination process for M. ulcerans that uses supplements to stimulate M. ulcerans growth to improve recovery.MethodsSwab and Fine Needle Aspirate (FNA) samples were collected from 21 individuals with confirmed BU at baseline (week 0) and weeks 2 and 4 after initiating antibiotic treatment. Samples were decontaminated with Tika-Kic decontamination medium and the modified Petroff (NaOH) methods then inoculated each into Mycobacterium Growth Indicator Tube (MGIT) or Löwenstein Jensen (LJ) medium. Time to growth detection and confirmation by qPCR as well as the proportion of positive cultures for all three methods and the proportion of positive cultures for all three time points were documented. Common contaminating bacteria were also isolated and identified.ResultsThe proportion of M. ulcerans positive cultures obtained was higher for Tika-MGIT samples [14/43 (32%)] compared to Petroff-MGIT samples [10/43 (23%)] and Petroff-LJ samples [8/43 (19%)]. Baseline samples had a higher isolate proportion [17 (53%)] compared to samples collected after treatment initiation [9 (28%) for week 2 and 6 (19%) for week 4]. Contaminating bacteria isolated include Burkholderia cepacia, Pseudomonas aeruginosa, Pasteurella pneumotropica, Proteus mirabilis, Morganella morganii, Staphylococcus aureus and Enterococcus.ConclusionOur study shows an advantage for culturing Mycobacterium ulcerans from clinical samples using the Tika-Kic decontamination and growth medium. Further research is needed to refine sample processing to improve M. ulcerans recovery.
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2017-07-06 | GSE100819 | GEO
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Project description:Bacteroides fragilis is an extensively studied anaerobic bacterium comprising the normal flora of the human gut. B. fragilis is known to be one of the most commonly isolated species from clinical samples and has been shown to cause a wide range of pathologies in humans [1, 2]. As an opportunistic pathogen B. fragilis can cause abscess formation and bacteremia [2]. Additionally in its enterotoxigenic form, B. fragilis is a known cause of diarrheal illness, is associated with inflammatory bowel disease, and has been recently characterized in patients with colon cancer [3 - 5]. As research in the field of the gut microbiome continues to expand at an ever increasing rate due to advances in the availability of next generation sequencing and analysis tools it is important to outline various molecular methods that can be employed in quickly detecting and isolating relevant strains of B. fragilis. This review outlines methods that are routinely employed in the isolation and detection of B. fragilis, with an emphasis on characterizing enterotoxigenic B. fragilis (ETBF) strains.
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Project description:IntroductionEmpirical therapy for the treatment of urinary tract infections should be tailored to the current distribution and susceptibility of potential pathogens to ensure optimal treatment.AimWe aimed to provide an up-to-date overview of the epidemiology and susceptibility of Enterobacterales isolated from urine in Germany.MethodsWe retrospectively analysed antimicrobial susceptibility data from 201,152 urine specimens collected between January 2016 and June 2021 from in- and outpatients. Multiple logistic regression analysis was used to evaluate the association between year of investigation and antibiotic resistance, adjusted for age, sex and species subgroup. Subgroup analyses were performed for midstream urine samples obtained from (i) female outpatients aged 15 to 50 years, (ii) female outpatients older than 50 years and (iii) male outpatients.ResultsResistance rates of less than 20% were observed for nitroxoline (3.9%), fosfomycin (4.6%), nitrofurantoin (11.7%), cefuroxime (13.5%) and ciprofloxacin (14.2%). Resistance to trimethoprim/sulfamethoxazole (SXT) (20.1%), amoxicillin-clavulanic acid (20.5%), trimethoprim (24.2%), pivmecillinam (29.9%) and ampicillin (53.7%) was considerably higher. In the subgroup of outpatient women aged 15-50 years, resistance rates were generally lower. Resistance rates of all antibiotics decreased from 2016 to 2021. Multiple logistic regression revealed the lowest adjusted odds ratio (ORadj) of 0.838 (95% confidence interval (CI): 0.819-0.858; p < 0.001) for pivmecillinam and the highest ORadj of 0.989 (95% CI: 0.972-1.007; p = 0.226) for nitrofurantoin.ConclusionsResistance has generally decreased over the past years, independent of sex, age and causative pathogen. Our data provide an important basis for empirical antibiotic recommendations in various settings and patient collectives.
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Project description:The Cryptococcus genus comprises more than 100 species, of which C. neoformans and C. gattii are the leading cause of cryptococcosis. The distribution of C. gattii and C. neoformans species complexes has been extensively studied and widely reported globally. Other species such as Naganishia albida, Papiliotrema laurentii, and Papiliotrema flavescens have been reported as pathogenic yeasts. Since there are no reports of environmental isolation in the Boyacá region (Colombia), this study aimed to isolate and characterize Cryptococcus and Cryptococcus-like yeasts from pigeon feces, Eucalyptus, and olive trees distributed in the municipalities of Tunja and Ricaute Alto. The environmental data was recovered, and the isolations obtained were identified by microscopy, biochemical test, MALDI-TOF MS, URA5-RFLP, and sequencing of the ITS and LSU loci. For the 93 pigeon dropping samples collected in Tunja, 23 yielded to C. neoformans, 3 to N. globosa, 2 N. albida and 1 to P. laurentii. Of the 1188 samples collected from olive trees, 17 (1.43%) positive samples were identified as C. gattii species complex (4), C. neoformans species complex (2), P. laurentii (3), N. albida (2), N. globosa (5) and P. flavescens (1). Likewise, specimens of C. neoformans presented molecular type VNI and molecular type VNII; for C. gattii the molecular types found were VGIII and one VGIV by URA5-RFLP but VGIII by MALDI-TOF and sequencing of the ITS and LSU. Therefore, it can be concluded that the species of Cryptococcus, Naganishia and Papiliotrema genera, are present in the environment of Boyacá, and show a predilection for climate conditions that are typical of this region.
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