The presence of bacteria and yeast like fungi in specimens from surgical patients

The aim of this study was to determine the incidence of Candida spp. strains in specimens obtained from surgically treated patients as well as to analyze the accompanying bacterial flora, both aerobic and anaerobic. The material came from two groups of patients. In the first group consisting of patients operated for colon and rectum carcinoma, the samples included peritoneal fluid, colon or rectum bioptates, pus, blood, and wound swabs. In the other group, biopsy material and smears from post operation wounds were taken from patients who underwent a surgical treatment of larynx carcinoma. Altogether, 282 various clinical specimens from 165 patients were analysed, and 41 Candida spp. strains were isolated: 39 strains of C. albicans and 2 strains of C. tropicalis. In 20 out of 41 specimens infected with Candida spp. (48.8%) the co-infection with bacterial aerobic flora was found. In 10 cases (24.4%), the fungi were isolated together with aerobic and anaerobic bacterial flora, whereas in 2 specimens (4.9%) the anaerobes and Candida albicans were diagnosed. The remaining 9 samples showed only the presence of Candida spp. (21.9%). From among aerobic bacterial flora Enterococcus spp. strains (n = 17) and Gram negative rods from Enterobacteriaceae family (n = 13) were the most frequently isolated. The bacterial strains of Streptococcus spp. (n = 5), Pseudomonas spp. (n = 3), Staphylococcus spp. and Corynebacterium spp. (2 strains, both) were identified more rarely. Bacteroides spp. were the most frequent members of bacterial anaerobic flora (n = 10). Other isolated anaerobic bacteria were classified as Fusobacterium spp. or Peptostreptococcus spp. (1 strain each). E. coli and Enterococcus spp. strains of aerobic bacterial flora were more frequently isolated together with Candida spp. CONCLUSIONS: (i) Mixed bacterial flora was found to predominate in the clinical material from the patients after surgery. (ii) Candida spp. were most frequently found together with aerobic bacterial flora.     

Quantitative and qualitative studies of the microflora of barley malt production

Populations of aerobic heterotrophic bacteria, mycelial fungi and yeasts occurring in malting barley were estimated by a plate technique and scanning electron microscopy. There was an increase in the total number of micro-organisms during germination, although populations declined after kilning. Bacteria dominated on all samples, with progressively lower populations of yeasts and filamentous fungi. There was no obvious spatial distribution of micro-organisms on the samples although there appeared to be high populations of bacteria and fungal hyphae on the inner surface of the kernels. The dominant groups of aerobic heterotrophic bacteria were presumptively identified as Alcaligenes sp., Arthrobacter globiformis, Clavibacter iranicum, Erwinia herbicola, Lactobacillus spp. and Pseudomonas fluorescens. The principal filamentous fungi were identified as Aiternaria alternata, Aspergillus glaucus (group), Cladosporium macrocarpum, Epicoccum purpurascens, Fusarium avenaceum, Geotrichum candidum and Penicillium spp. The yeasts isolated most frequently were Candida catenulata, C. vini, Debaryomyces hansenii, Hansenula polymorpha, Kloeckera apiculata, Rhodotorula mucilaginosa, Sporobolomyces roseus and Trichosporon beigelii.     

Identification of medically significant fungal genera by polymerase chain reaction followed by restriction enzyme analysis

Rapid non-culture-dependent assays for identification of fungi quicken diagnosis and prompt treatment of invasive fungal disease. Fungal DNA extracts from pure cultures of the most frequently isolated fungal pathogens belonging to the Genera Aspergillus, Candida and Cryptococcus along with less common pathogenic Genera were amplified with the general fungal primer pair internal transcribed spacer-1/4. Subsequently, the amplicon was digested with the restriction endonucleases MspI, HaeIII, HinfI and EcoRI in order to generate genus- or species-specific patterns for identification of the fungus. HinfI produced indistinguishable fingerprints for all Aspergillus species tested. MspI produced species-specific patterns for: Cryptococcus neoformans, Cryptococcus non-neoformans, Candida albicans and Candida tropicalis. EcoRI succeeded in differentiating penicillia from aspergilli and cryptococci from Candida spp. It is concluded that this procedure can differentiate genera and occasionally species of medically important fungi and that following the necessary validation experiments, it can be used directly on clinical samples to assist prompt diagnosis of systemic fungal infections.     

Significance of Molecular Identification and Antifungal Susceptibility of Clinically Significant Yeasts and Moulds in a Global Antifungal Surveillance Programme

The increasing diversity of opportunistic fungi causing serious invasive fungal infections (IFI) has been documented. Accurate identification (ID) is important in guiding therapy, determining prognosis for IFIs and in epidemiological surveys. We assessed the utility of PCR-based methods for the ID of yeasts and moulds that either were uncommon, failed conventional ID, or represented unusual biochemical or phenotypic profiles of common species. Among 1,790 viable fungal clinical isolates received during the SENTRY Program in 2010, 322 strains from 40 study sites had ID confirmed by molecular methods. Isolates were previously identified in participant institutions. Yeasts that were not confirmed by morphology on CHROMagar, growth at 45?°C (Candida albicans/dubliniensis), or assimilation of trehalose (C. glabrata) as well as non-Candida yeasts and all moulds were amplified and sequenced using primers amplifying one or more of the following genes: ITS, 28S, β-tubulin (Aspergillus spp.), TEF (Fusarium spp.), IGS (Trichosporon spp.). The isolates selected for molecular ID included 149 isolates of Candida species, 77 of Aspergillus species, 73 non-Candida yeasts, and 23 other moulds (a total of 41 different species). Overall, the ID determined by the submitting site was confirmed for 189 isolates (58.7?%): Aspergillus spp. (64.1?% correct); Candida spp. (60.1?% correct); non-Candida yeasts (58.9?% correct); non-Aspergillus moulds (30.4?% correct). Species with high levels of concordance between conventional and molecular ID included A. fumigatus (95.0 %), C. lusitaniae (100?%), C. dubliniensis (92.3?%), C. kefyr (100?%), and C. neoformans (90.2?%). Only 50.0?% of isolates of C. albicans and 59.1?% of C. glabrata selected due to unusual phenotypic or biochemical features were found to be correctly identified by the submitting site. Molecular methods for the identification of fungal pathogens are an important adjunct to the conventional identification of many less common clinically relevant yeasts and moulds including species of Candida with unusual or erroneous phenotypic or biochemical profiles. Molecular confirmation of fungal identification is essential in epidemiological surveys such as SENTRY.     

濮阳市部分浅部真菌病中癣菌和念珠菌混合感染的分析

目的了解濮阳地区部分浅部真菌病中两种及两种以上真菌混合感染的情况。方法对临床确诊为浅部真菌病的患者456例,取标本行10%KOH直接镜检、真菌培养及菌种鉴定。登记确诊患者相关临床资料,分析其中混合感染的发病特点。结果确诊皮肤癣菌和念珠菌混合感染病例36例,分离率为7.89%,多见于股部(58.33%)和足部(27.78%);分离菌株72株,皮肤癣菌中以红色毛癣菌为主(75.00%),念珠菌中以非白念珠菌为主(72.22%)。结论濮阳地区部分浅部真菌病中混合感染主要为皮肤癣菌和念珠菌的混合感染,多见于股部和足部;致病菌以红色毛癣菌和非白念珠菌为主。     

Occurrence ofCandida strains in cases of paronychia

A total of 43 patients, 11 males and 32 females, with paronychia of the fingernails were examined for the presence of Candida spp. The yeast species isolated were identified using standard laboratory methods, including germ-tube production, morphology on rice agar with Tween 80, and mainly fermentation and assimilation of saccharides. In the male group, two Candida species were detected: C. albicans as the dominant species in 9 patients and C. parapsilosis in 2 cases. Similarly, C. albicans was the prevalent species also in females (n = 17); other Candida species detected were C. parapsilosis (n = 7), C. tropicalis (5) and C. krusei (3). In addition to the genus Candida, the following anaerobic and aerobic microorganisms were isolated from patients of both groups: Fusobacterium spp., Bacteroides spp., Staphylococcus aureus, alpha-hemolytic streptococci, group A beta-hemolytic streptococci, Klebsiella pneumoniae, Neisseria spp. and Pseudomonas aeruginosa.     

Occurrence of mites and fungi in the homes of patients with allergic manifestations

This survey was carried out to evaluate mites and moulds concentrations in the homes of patients with allergic manifestations and positive skin-test for mites and/or fungi. The home environments of 277 patients were evaluated by questionnaire, by sampling of airborne fungal spores and by determining the occurrence of mites and moulds in dust samples. Among the 277 patients examined, 83% reacted positively to house dust mites. The fungal allergen most frequently responsible for skin positivity was Alternaria tenuis. The prevalent airborne fungi were Cladosporium, Penicillium and Alternaria, followed by Aspergillus and Aureobasidium. The other genera were found in less than 50% of the homes. The presence of domestic mites in dust was documented in more than 85% of the homes sampled. The occurrence of fungi in dust was generally higher than in the air. The most common genera recovered were Penicillium, Candida, Aspergillus, Aureobasidium, Alternaria and Cladosporium. The homes investigated were divided into two groups, damp and dry, on the basis of the reported presence of wet or damp spots on inside surfaces and moulds growing inside the home. Our results showed that the concentration of mites and moulds in dust was significantly higher (p < 0.01) in damp homes as compared to dry ones.In general, a good agreement between skin positivity and presence of the same allergens in patients' home environment was observed for mites and, among fungi, for Alternaria, Cladosporium and Aspergillus. Our results seem to confirm that the study of mycoaeroflora and the quantification of mites and moulds in dust samples of allergic patients' homes could lead to more precise diagnoses and therefore to better prophylactic and therapeutic programs for each individual patient.     

Occurrence of fungal spores in the respiratory tract and homes of patients with positive skin test to fungi

The occurrence of fungal spores in the upper respiratory tract and in the homes of 86 patients with allergic manifestations and positive skin tests for fungi has been investigated.Alternaria tenuis andCladosporium herbarum have been more frequently found to give positive reactions, followed byAspergillus mix,Candida albicans andPenicillium notatum. Cladosporium andAlternaria represented also the most common moulds isolated from nasal specimens. The prevalent fungi isolated from patients' environments wereCladosporium, Penicillium andAlternaria, occurring respectively in 93%, 78% and 72% of the homes sampled. An examination of individual cases have revealed a surprisingly close correlation, in 47 out of 86 patients, between positive skin test response and presence in high amount of the same fungi in patient's respiratory tract and home. In the majority of cases the fungi involved wereAlternaria and/orCladosporium.     

Occurrence of fungal spores in the respiratory tract and homes of patients with positive skin test to fungi

The occurrence of fungal spores in the upper respiratory tract and in the homes of 86 patients with allergic manifestations and positive skin tests for fungi has been investigated.Alternaria tenuis andCladosporium herbarum have been more frequently found to give positive reactions, followed byAspergillus mix,Candida albicans andPenicillium notatum. Cladosporium andAlternaria represented also the most common moulds isolated from nasal specimens. The prevalent fungi isolated from patients' environments wereCladosporium, Penicillium andAlternaria, occurring respectively in 93%, 78% and 72% of the homes sampled. An examination of individual cases have revealed a surprisingly close correlation, in 47 out of 86 patients, between positive skin test response and presence in high amount of the same fungi in patient's respiratory tract and home. In the majority of cases the fungi involved wereAlternaria and/orCladosporium.     

The broad-scale distribution of microfungi in the Windmill Islands region, continental Antarctica

Microfungi were isolated from soils, mosses, algae and lichens in the Windmill Islands region of Antarctica. From a total of 1,228 isolates, 22 genera were identified. The most frequently isolated fungi from mosses were Mycelia sterilia (47% of total isolates), Phoma spp. (18%), Penicillium spp. (11%), Chrysosporium spp. (7%) and Thelebolus microsporus (6%). Mycelia sterilia, Penicillium spp., Mortierella spp., Chrysosporium cf. pannorum and Thelebolus microsporus were also frequently isolated from algae. Fungal distribution and diversity were poor in samples of lichens, compared to samples from mosses and algae. The frequency of occurrence of microfungi was most often associated with strong biotic influence. There was a marked increase in fungal diversity in human-disturbed sites. Twelve taxa were restricted to soils from near the Australian Casey Station, suggesting significant introduction of fungi into this environment by human activities. Away from the station, fungal distribution appeared to be related to substrata and nutrient status rather than dispersal opportunities. Suggestions for future research and the need for constant monitoring to clarify the role of human disturbance on Antarctic fungi are discussed. Received: 1 April 1997 / Accepted: 17 August 1997     

Distribution of bacteria and fungi in the earthworm Libyodrillus violaceous (Annelida: Oligochaeta), a native earthworm from Nigeria

Earthworms are soil invertebrates that play a key role in recycling organic matter in soils. In Nigeria, earthworms include Libyodrillus violaceous. Aerobic and anaerobic bacterial counts, as well as fungal counts of viable microorganisms in soils and gut sections, were made on twenty L. violaceous collected from different sites on the campus of the University of Agriculture, Abeokuta, Nigeria. The samples were collected between April and November, 2002. Numbers of microorganisms were higher in castings and gut sections than in un-ingested soil samples. The guts and their contents also had higher moisture and total nitrogen contents than the un-ingested soils. Bacteria and fungi isolated from the samples were identified by standard microbiological procedures on the bases of their morphological and biochemical characteristics. Isolated bacteria were identified as Staphylococcus, Bacillus spp., Pseudomonas aeruginosa, Streptococcus mutans, Clostridium, Spirocheata spp., Azotobacter spp., Micrococcus lylae, Acinetobacter spp., Halobacterium for bacteria. Yeast isolates were identified as Candida spp., Zygosaccharomyces spp., Pichia spp., and Saccharomyces spp while molds were identified as, Aspergillus spp., Pytium spp., Penicillium spp., Fusarium spp and Rhizopus spp. Of the five locations examined, the refuse dump area had the highest numbers of both aerobic and anaerobic organisms, followed by the arboretum while the cultivated land area recorded the lowest counts. The higher numbers of microorganisms observed in the gut sections and casts of the earthworms examined in this work reinforce the general concept that the gut and casts of earthworms show higher microbial diversity and activity than the surrounding soil.     

Nasal fungal microbiota in allergic and healthy subjects

Environmental fungi, moulds and yeasts could reach the nasal cavity with the inhaled air causing respiratory symptoms in atopic subjects, but little is known about the fungal flora of this site. In the present study samples of the nasal cavities of 135 subjects aged 18-35 years (48 allergic patients to fungi, mites and/or cat fur and from 87 normal subjects--healthy, control group) were cultured. All of them lived in the metropolitan area of Barcelona. Fungi were isolated from 41.5% of healthy people and in 14.8% of allergy patients (p = 0.011). Morphologically, 50.4% of the isolates were located within 4 genera: Cladosporium, Penicillium, Aspergillus and Alternaria, fungi which are considered the most allergenic. The most prevalent species were: Cladosporium herbarum and C. cladosporioides (23.6%). Alternaria alternata was isolated only in 8.8% of samples from the allergic group, although most subjects were sensitive to this species. There were not differences in the isolation rate between genera and smoking-no-smoking groups. The lower prevalence of nasal fungi from allergic patients could be related to the nasal insufficiency, the hypersecretion and the larger use of handkerchiefs.     

Bacterial flora from bronchoalveolar lavage and occurrence of class IgG and IgA antibodies to Chlamydia pneumoniae in patients with chronic obstructive pulmonary disease (COPD)

Bronchoalveolar lavage taken from 46 patients (ranging in age from 21 to 71 years, mean 50.6 +/- 13.9) was examined for aerobic and anaerobic bacterial flora. Sera taken from 39 of patients as well as sera taken from 25 healthy blood donors of similar age (P = 0.99) were examined to determine IgG and IgA antibodies to C. pneumoniae. Bacterial flora was routinely cultured and determined using ATB computer system (bioMérieux,). IgG and IgA antibodies were tested by the enzyme immunoassays (Labsystems, Finland, Helsinki). Sera containing anti -C. pneumoniae IgG antibodies with titers of 45 EIU or higher and IgA with titers of 12 EIU or higher were considered positive. 143 of aerobic and 74 of anaerobic bacterial strains were cultured. Streptococci group viridans, pneumococci, enteric bacilli, Haemophilus spp., Prevotella spp., Actinomyces spp., Bifidobacterium spp. and Veilonella spp. were most often cultured. 66.6% of patients had IgG or IgA antibodies, in contrast, to the control group in which 60.0% and 44.0% of examined blood donors had IgG and IgA antibodies respectively. COPD patients were more frequently positive for specific anti-C. pneumoniae antibodies than the healthy donors (p = 0.003). The difference in a seropositivity rate of specific IgA and IgG antibodies was significant (p = 0.00002 and p = 0.003 respectively). Bronchoalveolar lavage of patients suffering from COPD can be contaminated with high number of aerobic and anaerobic bacterial species, and immunological status of the patients indicated persistent infection caused by C. pneumoniae more often than in controls.     

深部真菌感染临床特点分析

目的了解深部真菌感染患者的性别、年龄、感染部位、住院科室、菌种分布及真菌耐药情况,为临床防治真菌感染提供研究依据。方法收集荆州市中心医院2009年1月至2009年12月微生物实验室分离的真菌446株,采用科马嘉显色琼脂及API220C Aux鉴定系统鉴定,并使用ATMTMFUNGUS3真菌药敏卡进行体外药敏试验。结果临床真菌感染男性占72%,以老年患者为主,大于60岁者占54.9%;感染的真菌主要分布于呼吸内科和ICU,分别占35.5%、24.9%;主要感染部位为呼吸道,占91.3%;主要菌种为白假丝酵母菌、热带念株菌、近平滑假丝酵母菌、光滑念株菌和克柔念株菌,分别占64.2%、13.2%、9.6%、7.6%和5.4%;合并细菌感染的感染真菌100株,占22.2%,细菌中以革兰阴杆性菌为主,占96%;药敏试验结果显示真菌对各抗真菌药具有较好的敏感性。结论临床真菌感染已日益突出,以呼吸科及ICU患者老年男性为主,儿童真菌感染亦不容忽视,感染菌种以白假丝酵母菌和热带念株菌为主,临床应加强对这些真菌感染的预防和监测,防止真菌感染。     

Characterization of the skin fungal microbiota in patients with atopic dermatitis and in healthy subjects

Patients with atopic dermatitis (AD) are highly susceptible to viral, bacterial, and fungal skin infections because their skin is dry and this compromises the barrier function of the skin. Therefore, the skin microbiota of patients with AD is believed to be different from that of healthy individuals. In the present study, the skin fungal microbiota of nine patients with mild, moderate, or severe AD and ten healthy subjects were compared using an rRNA clone library. Fungal D1/D2 large subunit analysis of 3647 clones identified 58 species and seven unknown phylotypes in face scale samples from patients with AD and healthy subjects. Malassezia species were predominant, accounting for 63%-86% of the clones identified from each subject. Overall, the non-Malassezia yeast microbiota of the patients was more diverse than that of the healthy individuals. In the AD samples 13.0 ± 3.0 species per case were detected, as compared to 8.0 ± 1.9 species per case in the samples taken from healthy individuals. Notably, Candida albicans, Cryptococcus diffluens, and Cryptococcus liquefaciens were detected in the samples from the patients with AD. Of the filamentous fungal microbiota, Cladosporium spp. and Toxicocladosporium irritans were the predominant species in these patients. Many pathogenic fungi, including Meyerozyma guilliermondii (anamorphic name, Candida guilliermondii), and Trichosporon asahii, and allergenic microorganisms such as Alternaria alternata and Aureobasidium pullulans were found on the skin of the healthy subjects. When the fungal microbiota of the samples from patients with mild/moderate to severe AD and healthy individuals were clustered together by principal coordinates analysis they were found to be clustered according to health status.     

Fungal infection in the oncologic clinic]

Fungal infection in oncologic hospitals is a serious threat for the patients that can undermine the results of the specific treatment of the main disease. Most frequently fungal infection is developing in localities naturally disseminated with microbial flora. The infection is usually mixed: bacterial/fungal and even fungal/fungal. The most frequent members of the associations are the representatives of Candida albicans: 63 per cent in the bacteria + fungi associations and up to 60 per cent in the fungi + fungi associations. The preventive use of azoles can lower the threat of fungal affection of the organs. However, the danger of mixed fungal/bacterial infection remains rather high.     

Aerobic microorganisms associated with alfalfa leafcutter bees (megachile rotundata)

Characterization of microorganisms associated with alfalfa leaf-cutter bee (Megachile rotundata) nectar, pollen, provisions, larval guts, and frass (excreta) in Alberta demonstrated a varied aerobic microflora. Yeasts were isolated frequently from nectar, pollen, and provisions but rarely from guts or frass. The most prevalent yeast taxa were: Candida bombicola, Cryptococcus albidus, Metschnikowia reukaufii, and Rhodotorula glutinis. Although few filamentous fungi were found in nectar, they were frequently isolated from pollen and provisions; the predominant taxa were Alternaria alternata, Cladosporium cladosporioides, C. herbarum, Epicoccum nigrum, and Penicillium chrysogenum. Bacteria, including species of Bacillus, Corynebacterium, Micrococcus, and the actinomycete Streptomyces, also were prevalent in provisions and/or on pollen. In general, the diversity of microorganisms isolated from alimentary canals and frass was lower than from nectar, pollen, and provisions. Bacillus firmus, B. licheniformis, B. megaterium, B. pumilus, and Streptomyces spp. were the most frequently isolated bacteria, whereas Trichosporonoides megachiliensis was the most common filamentous fungus isolated from larval guts and/or frass. These taxa may be part of the resident microflora of the alimentary canal. Populations of bacteria and filamentous fungi, but not yeasts, were larger from Ascosphaera aggregata-infected larvae than from healthy larvae. However, with the exception of Aspergillus niger and T. megachiliensis in frass from healthy larvae, no taxon of filamentous fungi was conspicuously present or absent in infected larvae, healthy larvae, or their frass. Offprint reauests to: M.S. Goettel.     

眼部真菌感染菌种分布特征

目的分析眼部真菌感染的致病情况和菌种分布特征。方法统计山东省眼科研究所2000～2005年间所有真菌感染病例的培养结果,按照感染部位分类并分析不同菌种的致病情况。结果6年间共有970份真菌培养资料,阳性结果691份,阳性率为71.2%(691/970)。其中角膜溃疡阳性率为86.2%(669/776),镰刀菌占73.2%(490/669);眼内炎阳性率为10.4%(19/182),曲霉菌占68.4%(13/19);泪囊炎阳性率为25.0%(3/12),念珠菌占100.0%(3/3)。结论不同的感染部位常见的真菌菌种不同,镰刀菌是真菌性角膜溃疡的主要致病菌,曲霉菌是真菌性眼内炎的主要致病菌,而念珠菌则是泪囊炎的主要致病菌。     

The Occurrence of Fungi in the Recently Discovered Jarkowicka Cave in the Karkonosze Mts. (Poland)

Our study is one of the very few cases of speleomycological research in recently discovered caves. The aim of this research was to assess the population size of fungal colonies and their species composition in the Jarkowicka cave, discovered in 2012. The air samples were taken from one location outside the cave and from two locations inside of it. Mycological evaluation of the rocks inside the cave was performed usingswab sampling procedure. In the Jarkowicka cave we found 22 species of fungi, including 13 isolated from air at the entrance and from the walls, and 8 species from air inside the cave. Cladosporium spp. were the fungi most frequently isolated from internal atmosphere of the Jarkowicka cave, and from the external air. On the other hand, the fungi most frequently isolated from the rocks were Mucor spp. We found several species not yet described as cave inhabitants: Hypocrea pachybasioides, Cladosporium uredinicola, and Embellisia abundans. Our study may provide a basis for comparison to other similar studies conducted in frequently visited caves by tourists.     

Fungi inhabiting the healthy human gastrointestinal tract: a diverse and dynamic community

Fungal DNA was selectively amplified, and the ITS region sequenced, from fecal samples taken from 45 healthy human volunteers at one (21 volunteers) or two (24 volunteers) time points. Seventy-two operational taxonomic units, representing two phyla and ten classes of fungi, were recovered. Candida yeasts, notably Candida tropicalis (present in 51 samples), and yeasts in the Dipodascaceae (39 samples), dominated, while 38 OTUs were detected in a single sample each. Fungi included known human symbionts (Candida, Cryptococcus, Malassezia and Trichosporon spp.), common airborne fungi (Cladosporium sp.) and fungi known to be associated with food (Debaryomyces hansenii and high salt fermented foods; Penicillium roqueforti and blue cheese). In contrast with gut-associated bacteria, fungi occurred in much lower abundance and diversity, and fungal composition appeared unstable over time.