The place of molecular genetic methods in the diagnostics of human pathogenic anaerobic bacteria. A minireview

Anaerobic infections are common and can cause diseases associated with severe morbidity, but are easily overlooked in clinical settings. Both the relatively small number of infections due to exogenous anaerobes and the much larger number of infections involving anaerobic species that are originally members of the normal flora, may lead to a life-threatening situation unless appropriate treatment is instituted. Special laboratory procedures are needed for the isolation, identification and susceptibility testing of this diverse group of bacteria. Since many anaerobes grow more slowly than the facultative or aerobic bacteria, and particularly since clinical specimens yielding anaerobic bacteria commonly contain several organisms and often very complex mixtures of aerobic and anaerobic bacteria, considerable time may elapse before the laboratory is able to provide a final report. Species definition based on phenotypic features is often time-consuming and is not always easy to carry out. Molecular genetic methods may help in the everyday clinical microbiological practice in laboratories dealing with the diagnostics of anaerobic infections. Methods have been introduced for species diagnostics, such as 16S rRNA PCR-RFLP profile determination, which can help to distinguish species of Bacteroides, Prevotella, Actinomyces, etc. that are otherwise difficult to differentiate. The use of DNA-DNA hybridization and the sequencing of special regions of the 16S rRNA have revealed fundamental taxonomic changes among anaerobic bacteria. Some anaerobic bacteria are extremely slow growing or not cultivatable at all. To detect them in special infections involving flora changes due to oral malignancy or periodontitis, for instance, a PCR-based hybridization technique is used. Molecular methods have demonstrated the spread of specific resistance genes among the most important anaerobic bacteria, the members of the Bacteroides genus. Their detection and investigation of the IS elements involved in their expression may facilitate following of the spread of antibiotic resistance among anaerobic bacteria involved in infections and in the normal flora members. Molecular methods (a search for toxin genes and ribotyping) may promote a better understanding of the pathogenic features of some anaerobic infections, such as the nosocomial diarrhoea caused by C. difficile and its spread in the hospital environment and the community. The investigation of toxin production at a molecular level helps in the detection of new toxin types. This mini-review surveys some of the results obtained by our group and others using molecular genetic methods in anaerobic diagnostics.     

Molecular tools for the detection and identification of Ichthyobodo spp. (Kinetoplastida), important fish parasites

Ichthyobodo spp. are ectoparasitic flagellates of fish that may cause disease (ichthyobodosis), a common problem affecting the aquaculture industry worldwide. Ichthyobodosis in farmed fish is often associated with a range of other infectious agents and diagnosis in for example gill disease may be difficult. Sensitive and effective methods for detection and identification of Ichthyobodo spp. are needed to aid diagnosis of ichthyobodosis and epizootiological studies on Ichthyobodo spp. We have designed a specific quantitative real-time PCR assay targeting SSU rDNA for the detection of Ichthyobodo spp. infections. Also, several novel primer sets are presented for use in identification of Ichthyobodo spp. through PCR and sequencing. These PCR methods have been optimized and tested on samples from wild caught and farmed fish from different geographical areas in Norway. The real-time PCR assay has been tested for sensitivity and efficiency, and we present data demonstrating its use for absolute quantification of Ichthyobodo salmonis in tissue samples through RT-qPCR and qPCR. We demonstrate the use of the described set of molecular tools for the detection and sequencing of Ichthyobodo spp. from farmed and wild fish, and also show that they may aid the discovery of new Ichthyobodo species. The detection of light Ichthyobodo spp. infections through microscopy is time consuming and less sensitive compared to PCR methods. Initial real-time PCR testing and subsequent sequencing of positive samples is a powerful method that will increase diagnostic precision, aid carrier detection and promote species discoveries in the Ichthyobodonidae. Our preliminary observations indicate a high Ichthyobodo spp. diversity.     

肺放线菌病1 例报告并文献复习

目的：分析肺放线菌病的临床表现、诊断及治疗,提高对肺放线菌病的认识。方法：回顾性分析我科收治的1 例肺放线菌病 患者的临床资料,并对相关文献进行复习。结果：本例患者,43 岁,男性,以咳嗽、咳血性痰为主要临床表现,胸部CT 提示右肺上 叶结节,经皮肺穿刺活检结果确诊肺放线菌病,青霉素治疗效果好。结论：肺放线菌病是放线菌感染引起的一种少见的呼吸系统 疾病,起病隐匿,呈渐进性过程,临床表现及影像学检查均无特异性,放线菌可在肺部引起化脓性肺炎,并经叶间隙、胸膜侵犯胸 壁、肋骨,形成窦道及破坏骨质。确诊有赖于病理学或微生物学证据,主要可采用青霉素抗感染治疗,在疑似肿瘤的情况下,需通 过外科手术治疗,既可以明确诊断也避免病变进一步引起肺、胸壁等组织的不可逆性破坏。     

肺放线菌病1例报告并文献复习

目的：分析肺放线菌病的临床表现、诊断及治疗,提高对肺放线菌病的认识。方法：回顾性分析我科收治的1例肺放线菌病患者的临床资料,并对相关文献进行复习。结果：本例患者,43岁,男性,以咳嗽、咳血性痰为主要临床表现,胸部CT提示右肺上叶结节,经皮肺穿刺活检结果确诊肺放线菌病,青霉素治疗效果好。结论：肺放线菌病是放线菌感染引起的一种少见的呼吸系统疾病,起病隐匿,呈渐进性过程,临床表现及影像学检查均无特异性,放线菌可在肺部引起化脓性肺炎,并经叶间隙、胸膜侵犯胸壁、肋骨,形成窦道及破坏骨质。确诊有赖于病理学或微生物学证据,主要可采用青霉素抗感染治疗,在疑似肿瘤的情况下,需通过外科手术治疗,既可以明确诊断也避免病变进一步引起肺、胸壁等组织的不可逆性破坏。     

真菌感染的实验室诊断研究进展

随着易感人群逐渐增多,对临床真菌感染标本的快速检测及真菌培养的分离鉴定日益重要。所幸目前有新的检测方法用来辅助早期诊断及指导经验性的抗真菌治疗。主要的进展集中在对标本的真菌抗原直接检测方面(如半乳甘露聚糖和β-葡聚糖);假丝酵母产色培养基等快速培养鉴定法;微生物生化自动分析系统(VITEK2)和显微扫描(MicroScan)等生化自动检测平板;多肽核苷酸原位杂交,特异性的大范围聚合酶链反应(PCR)检测以及针对临床标本或培养阳性标本直接DNA测序技术。     

Hepatic actinomycosis diagnosed by fine needle aspiration. A case report

A 43-year-old woman, a long-term intrauterine contraceptive device (IUD) wearer with a history of Actinomyces organisms seen in cervicovaginal smears, developed hepatic actinomycosis 13 months after removal of the IUD. The liver involvement was diagnosed by fine needle aspiration (FNA) cytology and the use of immunocytochemical techniques. Histopathologic examination of a right pelvic mass removed at surgical exploration revealed an Actinomyces tuboovarian abscess, the primary lesion in this case. The importance of cytologic detection of Actinomyces in cervicovaginal smears for the prevention of IUD-related pelvic inflammatory disease (PID) is discussed, as is the usefulness of FNA cytology in the diagnosis of systemic actinomycosis.     

Actinomyces hongkongensis sp. nov. a novel Actinomyces species isolated from a patient with pelvic actinomycosis

A bacterium was isolated from the pus of a patient with pelvic actinomycosis. The cells were strictly anaerobic, straight, non-sporulating, Gram-positive rods. It grows on sheep blood agar as non-haemolytic, pinpoint colonies after 24 hours of incubation at 37 degrees C in anaerobic environment. It is non-motile and does not produce catalase. 16S ribosomal RNA (rRNA) gene sequencing showed that there were 6.6% difference between the 16S rRNA gene sequence of the bacterium that of Actinomyces marimammalium (GenBank Accession no. AJ276405), a new species described in 2001, isolated from two seals and a porpoise. For these reasons a new species, Actinomyces hongkongensis sp. nov., is proposed, for which HKU8(T) is the type strain. Further studies should be performed to ascertain the potential of this bacterium to become an important cause of actinomycosis.     

Evaluation of Agar Candida ID2 (bioMerieux) a chromogenic medium for yeasts differentiation

Invasive diagnostic and therapeutic methods, widespread antibiotic therapy and rising percent of the immunocompromised patients cause incrementation of frequency of occurrence of the yeast infection. C. albicans is the most commonly isolated species of Candida from clinical samples. However, recently growth of frequency of isolation Candida non - albicans from clinical specimens have been observed. Yeast-like fungi different from C. albicans have become serious clinical problem. Conventional methods of identification of the yeast-like fungi carry away a lot time enough. Employment of chromogenic agar shortens latency on result. We decided to examine the usefulness ofAgar Candida ID2 (CAN2) (bioMérieux) in the identification of Candida species. The subjects within the study were 146 of Candida spp strains which were isolated from the clinical specimens of patients hospitalized at the University Hospital in Bydgoszcz. Germ tube test. Api 20C AUX test (bioMérieux) and Agar Candida ID2 (bioMérieux) were used. We have ascertained correspondence of identifying species amounted to 82.2% of analyzed Candida species between API 20C AUX test and kind of growth on CAN2 medium. Divergence of results received between CAN2 medium and API 20C AUX test suggests necessity of conducting of verification data with other methods. In conclusion, our study shows that Agar Candida ID2 is an effective medium for the isolation yeast-like fungi and in preliminary identification of Candida species direct from clinical materials.     

Black-pigmented Gram-negative anaerobes in endodontic infections

Abstract Necrotic dental root canal infections are polymicrobial infections dominated by anaerobic bacteria. The number of different species in one canal is usually low, approx. 4–7 species. The species isolated most frequently belong to the genera Prevotella, Porphyromonas, Fusobacterium, Peptostreptococcus, Eubacterium and Streptococcus . The frequency of isolation of black-pigmented Gram-negative anaerobes in endodontic infections varies from 25% to >50%. Pr. intermedia is the most commonly found pigmented species, followed by Pr. denticola and two Porphyromonas species, P. gingivalis and P. endodontalis . Several studies have shown that P. gingivalis and P. endodontalis are closely related to the presence of acute symptoms in endodontic infections, whereas other black-pigmented Gram-negative anaerobes are not. However, several other species may also be involved in acute infections. Moreover, Porphyromonas species have occasionally been isolated from cases with no symptoms. Although Porphyromonas spp. are clearly related to symptoms at the beginning of therapy, they are not important for the prognosis of the treatment.     

Cytologic diagnosis of suppurative cholecystitis due to Candida albicans and actinomyces. A report of 2 cases

BACKGROUND: Cholecystitis is a common inflammatory disease of the gallbladder. Actinomycosis and candidiasis of the gallbladder are uncommon causes of acute cholecystitis. There has been no previous report on the cytologic diagnosis of actinomycosis and candidiasis from aspirated gallbladder bile intraoperatively. CASES: Purulent bile was intraoperatively aspirated from the gallbladder of 71-year-old Indian and a 30-year-old Australian woman. The specimens were sent for cytologic examination. The first case revealed sulphur granules characteristic of Actinomyces spp. The second case showed budding spores and pseudohyphae of Candida spp. Pure colonies of Candida albicans grew from the bile culture. CONCLUSION: Actinomycosis and candidiasis rarely cause acute suppurative cholecystitis. Initial diagnosis can be made by cytologic examination of the aspirated purulent bile intraoperatively.     

Anaerobic bacteria cultured from the tongue dorsum of subjects with oral malodor

The bacteria on the dorsum of the tongue are the most frequent cause of oral malodor; however, the bacterial flora of the tongue has not been well defined. Although recent studies have used DNA probes to detect the presence of certain periodontal pathogens, cultural studies have been limited because of the complexity of the flora of the tongue dorsum. The purpose of this study was to grow and to identify maximum numbers of capnophylic Gram-negative bacilli and anaerobic micro-organisms by culturing tongue samples on to several selective and non-selective media. The most frequently isolated species included Peptostreptococcus anaerobius, Collinsella aerofaciens, Eubacterium group, Actinomyces spp., Eikenella corrodens, Veillonella spp., Fusobacterium nucleatum, pigmented Prevotella spp. and Selenomonas spp. Reported for the first time are Actinomyces turicensis, Collinsella aerofaciens, Eubacterium saburreum, E. timidum, Prevotella tannerae, Campylobacter concisus, Campylobacter mucosalis, Leptotrichia buccalis, Selenomonas flueggei, and Centipeda periodontii. Species not previously reported in studies that used only molecular techniques were identified in the present study.     

Detection and identification of Listeria monocytogenes in cooked sausage products and in milk by in vitro amplification of haemolysin gene fragments

Recent outbreaks of listeriosis have emphasized the urgent need for rapid and reliable detection methods for Listeria spp., especially in food. Haemolysin production is a major factor in the pathogenesis of listeriosis and the polymerase chain reaction (PCR) was used to amplify two specific DNA fragments of the alpha- and the beta-haemolysin genes. The amplification system specifically recognized L. monocytogenes strains. The detection limit determined with pure cultures was 10 bacteria when estimated with alpha-haemolysin primers. In the analysis of 50 samples of cooked sausage products, bacterial colonies suspected to be Listeria spp. were isolated by conventional methods from six samples. PCR analysis identified three of six as L. monocytogenes. Subsequent serotyping showed perfect agreement with the PCR results. Since enrichment is the most time consuming step in conventional methods a PCR procedure which allows the direct detection of L. monocytogenes in milk was developed. Pasteurized milk was artificially contaminated with various levels of L. monocytogenes. The detection limit was determined to be 10 bacteria/10 ml milk and direct detection and identification of L. monocytogenes took less than two working days. These results show that this haemolysin gene amplification system is very rapid and reliable and therefore avoids cumbersome and lengthy cultivation steps.     

The tentative identification of actinomycetes of the oral cavity by a complex of key morphophysiological signs

In this work the results obtained in the study of the morphology of 208 Actinomyces strains isolated from the oral cavity and a wide spectrum of their enzymatic activity are presented. The identification of these strains was carried out on the basis of chemotaxonomic criteria. Bacteria belonging to the same taxonomic group were found to have considerable similarity in their morphological and physiological features. On the basis of the data obtained in this study a simplified scheme of the tentative identification of fermentative Actinomyces, suitable for use by a wide circle of researchers, is presented.     

Detection and identification of Listeria monocytogenes in cooked sausage products and in milk by in vitro amplification of haemolysin gene fragments

Recent outbreaks of listeriosis have emphasized the urgent need for rapid and reliable detection methods for Listeria spp., especially in food. Haemolysin production is a major factor in the pathogenesis of listeriosis and the polymerase chain reaction (PCR) was used to amplify two specific DNA fragments of the α- and the β-haemolysin genes. The amplification system specifically recognized L. monocytogenes strains. The detection limit determined with pure cultures was 10 bacteria when estimated with α-haemolysin primers. In the analysis of 50 samples of cooked sausage products, bacterial colonies suspected to be Listeria spp. were isolated by conventional methods from six samples. PCR analysis identified three of six as L. monocytogenes. Subsequent serotyping showed perfect agreement with the PCR results. Since enrichment is the most time consuming step in conventional methods a PCR procedure which allows the direct detection of L. monocytogenes in milk was developed. Pasteurized milk was artificially contaminated with various levels of L. monocytogenes. The detection limit was determined to be 10 bacteria/10 ml milk and direct detection and identification of L. monocytogenes took less than two working days. These results show that this haemolysin gene amplification system is very rapid and reliable and therefore avoids cumbersome and lengthy cultivation steps.     

Group-specific differentiation of Rhizobium from clover species by PCR amplification of 23S rDNA sequences

Two 20-bp primers that provide group-specific detection of Rhizobium spp. by polymerase chain reaction (PCR) have been used to differentiate strains that belong to different effectiveness groups within the Rhizobium-Trifolium cross-inoculation group. The target for DNA amplification was a 370-bp fragment of the 23S rDNA region. Analysis of additional root-nodule forming, as well as root-associated bacterial species by PCR-primer assay revealed that variability within this 20-bp segment of the 23S rDNA region may be widespread and provide an effective identification tool. Our data suggest that strains of Rhizobium isolated from the perennial clover Trifolium semipilosum may be phylogenetically more closely related to Rhizobium etli.     

Direct identification in food samples of Listeria spp. and Listeria monocytogenes by molecular methods

A new molecular approach for the detection and identification of Listeria spp. and Listeria monocytogenes in food is presented here. The method is based on the PCR amplification of a fragment of the iap gene from the five species belonging to the genus and on the analysis of the PCR products obtained by denaturing gradient gel electrophoresis (DGGE). The protocol was first optimized by using strains from international collections. Based on the differences present in the sequences amplified, it was possible to obtain species-specific DGGE migration that allowed fast and easy identification of L. monocytogenes, L. innocua, L. welshimeri, L. seeligeri, and L. ivanovii. Moreover, for L. monocytogenes serotypes, partial differentiation was possible. The optimized protocol was used for identification of Listeria strains traditionally isolated from food and for direct detection and identification of Listeria members in food after an overnight enrichment. Identification of 48 food isolates and direct detection of Listeria spp. in 73 food samples show the potential of the method that can be used as a fast screening test to investigate the presence of Listeria spp. and L. monocytogenes in food.     

Epidemiological characteristics of infections caused by Bacteroides, Prevotella and Fusobacterium species: a prospective observational study

In order to investigate differences among infections due to Gram-negative anaerobic bacteria (Bacteroides, Prevotella and Fusobacterium spp.), clinical, epidemiological, and microbiological data were collected and evaluated from 206 anaerobic infections. The most frequently isolated species was Bacteroides fragilis. The majority of the cases were intra-abdominal infections (49%) followed by skin and soft tissue infections (24.7%). Logistic regression analysis showed that Bacteroides spp. strains were more often isolated from intra-abdominal infections (p?=?0.002), whereas Prevotella spp. were isolated more frequently from cases with shorter duration of hospitalization (p?=?0.026), and less frequently from bloodstream infections (p?=?0.049). In addition, Bacteroides spp. were associated with coinfection due to Enterobacteriaceae species (p?=?0.007), whereas Prevotella spp. were associated with coinfection due to Staphylococcus spp. (p?=?0.002). Patients with an infection due to B.?fragilis, were more frequently admitted in a general surgical ward (p?=?0.017), or have been treated with a 2nd generation cephalosporin before anaerobic infection onset (p?=?0.05). Total mortality was 10.9% and was associated with bacteremia (p?=?0.026), and hematological (p?=?0.028), or solid organ malignancy (p?=?0.007). Metronidazole resistance was detected only among Prevotella spp. (16.2%) and B. fragilis group (0.8%) isolates. In conclusion, this study indicated differences between infections due to the most frequently isolated Gram-negative anaerobic species, differences that may affect the design and implementation of empirical antimicrobial chemotherapy guidelines.     

Growth of oral Streptococcus species and Actinomyces viscosus in human saliva.

Microorganisms in dental plaque live in constant association with saliva. The role of saliva in the adherence of bacteria to the teeth and the antibacterial properties of saliva have been well investigated; less interest has been shown in the possible role of saliva as a substrate for oral microorganisms. In this study it was shown that saliva can serve as a growth medium for oral Streptococcus spp. and Actinomyces viscosus. The cell production of these organisms on saliva was carbohydrate limited. The doubling times for growth on glucose-supplemented saliva (4 to 5 mmol/liter) ranged from 1.6 to 4.0 h. The availability of carbohydrate sources for the oral microflora is discussed in relation to microbial growth in the oral cavity.