Comparison of three molecular methods for typing Aeromonas popoffii isolates

Three typing methods, restriction fragment length polymorphism (RFLP) of the 16S-23S intergenic spacer region (ISR), PCR amplification of the enterobacterial repetitive intergenic consensus (ERIC) and of the repetitive extragenic palindromic units (REP), were evaluated for typing 26 isolates of Aeromonas popoffii from different geographical origins. When the methods were independently studied, ERIC showed the highest discriminatory power. When the methods were combined, the best combination of two methods was ERIC with REP since strains showed a tendency to cluster according to their geographical origin. However, this tendency was reinforced with the addition of ISR-RFLP. This revised version was published online in June 2006 with corrections to the Cover Date.     

我国17株绵羊肺炎支原体分子分型及其菌体蛋白免疫印迹

【目的】分别从基因和蛋白水平研究我国部分地区绵羊肺炎支原体(Mycoplasma ovipneumoniae)分离株的分子特征,并了解其免疫原性蛋白的差异。【方法】对分离自8个地区的17株绵羊肺炎支原体进行扩增片段长度多态性(Amplified Fragment Length Polymorphism,AFLP)和十二烷基磺酸钠-聚丙烯酰胺凝胶电泳(Sodium Dodecyl Sulphate-Polyacrylamide Gel Electrophoresis,SDS-PAGE)分析,采用NTsys-2.10e软件对AFLP和SDS-PAGE结果进行聚类,并用绵羊肺炎支原体模式株Y98高免血清对部分分离株进行免疫印迹分析。【结果】当相似系数分别为0.78和0.85时,绵羊肺炎支原体分离株可根据8个来源地区分成8个AFLP群和8个SDS-PAGE群;用8株分离株进行免疫印迹共出现6条蛋白条带,分子质量分别为105 kDa、83 kDa、65 kDa、42 kDa、40 kDa或26 kDa,其中83 kDa和40 kDa蛋白为8个菌株保守的免疫原性蛋白。【结论】我国部分地区绵羊肺炎支原体分离株之间存在遗传差异,不同分离株的主要免疫原性蛋白也存在一定差异,但83 kDa和40 kDa蛋白为其保守的免疫原性蛋白。本研究首次对我国部分地区绵羊肺炎支原体分离株进行了分子分型与免疫印迹分析,结果将为绵羊肺炎支原体病的新型诊断技术开发和疫苗研制奠定理论基础。     

Epidemiology and molecular typing of Candida isolates from burn patients

This study, spread over a span of 2 years describes Candida infections in burn patients of an Indian hospital. A total of 220 burn patients were monitored and Candida could be isolated from 138 patients. A total of 228 different Candida species were obtained from various body locations of these patients. Species identification revealed that Candida albicans was the most predominant (45) followed by Candida tropicalis(33), Candida glabrata (13.5), C. parapsilosis (4), C. krusei (2.75) and C. kefyr (1.75). DNA fingerprinting of all C. albicans isolates was done by using CARE-2 probe. Fingerprinting analyses of all the C. albicans strains revealed that strains collected from different patients were different. It is noteworthy that patients with disseminated candidiasis had a similar, but unique strain isolated from all body locations, suggesting a possibility that commensal isolates might be turning pathogenic. Taken together, this is probably the first ever detailed survey of Candidainfections in burn patients in India and is expected to lead to better clinical management of this group of patients.     

3株禽滑液囊支原体分离株致病性的比较和评价

【背景】禽滑液囊支原体是感染鸡的一种重要病原体,给我国的家禽养殖业带来了严重的经济损失。【目的】评价从病鸡中分离到的3株禽滑液囊支原体的致病性,以期丰富不同区域来源的分离株对鸡致病性的认识。【方法】分别用分离株CHN-WF224-2016、CHN-BZJ2-2015、CHN-JNB19-2016感染商品肉鸡,并在攻毒后第10天和21天进行实验室解剖,通过气囊和足垫的临床病变、血清学检测结果及气管粘膜病理形态学改变来比较评价分离株的致病力。【结果】CHN-BZJ2-2015和CHN-WF224-2016分离株能引起明显足垫肿胀和关节滑膜炎,其中CHN-BZJ2-2015分离株致病力最强,感染21 d后的血清学检测和气管粘膜厚度与CHN-JNB19-2016分离株和MS-H疫苗株比较差异显著(P<0.05)。【结论】本研究表明我国目前流行的禽滑液囊支原体菌株其致病力存在明显差异,强调养殖场要积极控制和预防禽滑液囊支原体感染的重要性,同时为今后该疫苗的研发积累了实验数据。     

Identification of Mycoplasma hyopneumoniae with a DNA probe

From a genomic library of Mycoplasma hyopneumoniae a 1.3 kb DNA fragment was cloned which showed specific Southern hybridization and dot hybridization with the type strain of several porcine and bovine Mycoplasma species. This probe selectively recognized M. hyopneumoniae sequences in purified DNA or in broth-grown organisms. The 35S-labelled probe could detect as little as 100 pg of DNA or 10(5) colour changing units. This is a possible alternative diagnostic procedure for enzootic pneumonia of pigs.     

Proteogenomic mapping of Mycoplasma hyopneumoniae virulent strain 232

Background

Mycoplasma hyopneumoniae causes respiratory disease in swine and contributes to the porcine respiratory disease complex, a major disease problem in the swine industry. The M. hyopneumoniae strain 232 genome is one of the smallest and best annotated microbial genomes, containing only 728 annotated genes and 691 known proteins. Standard protein databases for mass spectrometry only allow for the identification of known and predicted proteins, which if incorrect can limit our understanding of the biological processes at work. Proteogenomic mapping is a methodology which allows the entire 6-frame genome translation of an organism to be used as a mass spectrometry database to help identify unknown proteins as well as correct and confirm existing annotations. This methodology will be employed to perform an in-depth analysis of the M. hyopneumoniae proteome.

Results

Proteomic analysis indicates 483 of 691 (70%) known M. hyopneumoniae strain 232 proteins are expressed under the culture conditions given in this study. Furthermore, 171 of 328 (52%) hypothetical proteins have been confirmed. Proteogenomic mapping resulted in the identification of previously unannotated genes gatC and rpmF and 5-prime extensions to genes mhp063, mhp073, and mhp451, all conserved and annotated in other M. hyopneumoniae strains and Mycoplasma species. Gene prediction with Prodigal, a prokaryotic gene predicting program, completely supports the new genomic coordinates calculated using proteogenomic mapping.

Conclusions

Proteogenomic mapping showed that the protein coding genes of the M. hyopneumoniae strain 232 identified in this study are well annotated. Only 1.8% of mapped peptides did not correspond to genes defined by the current genome annotation. This study also illustrates how proteogenomic mapping can be an important tool to help confirm, correct and append known gene models when using a genome sequence as search space for peptide mass spectra. Using a gene prediction program which scans for a wide variety of promoters can help ensure genes are accurately predicted or not missed completely. Furthermore, protein extraction using differential detergent fractionation effectively increases the number of membrane and cytoplasmic proteins identifiable my mass spectrometry.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-576) contains supplementary material, which is available to authorized users.     

Loop-mediated isothermal amplification for rapid and convenient detection of Mycoplasma hyopneumoniae

Loop-mediated isothermal amplification (LAMP), a novel method of gene amplification, was employed in this study for detecting Mycoplasma hyopneumoniae in the respiratory tract or lungs of swine. The pathogen can be detected in LAMP reactions containing as few as 10 fg purified target DNA (10 copies of M. hyopneumoniae genome) within 30 min, which was comparable to real-time PCR. After 30-min reaction at 63 °C, the addition of a certain amount of dye (SYBR Green I and hydroxyl naphthol blue at a proper ratio) into the LAMP reaction system makes the results easily determined as positive or negative by visual inspection. In addition, the LAMP was able to distinguish between M. hyopneumoniae and other closely-related mycoplasma strains, indicating a high degree of specificity. The LAMP assay was more simple and cheap, since the reaction could be completed under isothermal conditions and less laboratorial infrastructure are required. And, it was proven reliable for M. hyopneumoniae diagnosis of nasal swab and lung samples from the field.     

A two-step strategy for molecular typing of multidrug-resistant Mycobacterium tuberculosis clinical isolates from Poland

Tuberculosis (TB) continues to be one of the most challenging public health problems in the world. An important contributor to the global burden of the disease is the emergence and spread of drug-resistant and particularly multidrug-resistant Mycobacterium tuberculosis strains (MDR), defined as being resistant to at least isoniazid and rifampicin. In recent years, the introduction of different DNA-based molecular typing methods has substantially improved the knowledge of the epidemiology of TB. The purpose of this study was to employ a combination of two PCR-based genotyping methods, namely spoligotyping and IS6110-Mtb1/Mtb2 PCR to investigate the clonal relatedness of MDR M. tuberculosis clinical isolates recovered from pulmonary TB patients from Poland. Among the 50 isolates examined, 28 (56%) were clustered by spoligotyping, whereas IS6110-Mtb1/Mtb2 PCR resulted in 16 (32%) clustered isolates. The isolates that clustered in both typing methods were assumed to be clonally related. A two-step strategy consisting of spoligotyping as a first-line test, performed on the entire pool of isolates, and IS6110-Mtb1/Mtb2 PCR typing as a confirmatory subtyping method, performed only within spoligotype-defined clusters, is an efficient approach for determining clonal relatedness among M. tuberculosis clinical isolates.     

Complete genome sequence of Mycoplasma hyopneumoniae strain 168

Mycoplasma hyopneumoniae strain 168, a pathogenic strain prevalent in China, was isolated in 1974. Although this strain has been widespread for a long time, the genome sequence had not been determined. Here, we announce the complete genome sequence of M. hyopneumoniae strain 168.     

PCR技术检测猪肺炎支原体的研究进展

猪肺炎支原体(Mycopiasma hyopneumoniae)是引起猪支原体肺炎的重要病原,该病常引起继发感染和混合感染,严重威胁养猪业发展,造成巨大的经济损失.利用PCR技术对猪支原体肺炎早期正确诊断具有非常重要的意义.从猪肺炎支原体的特异性靶基因、临床样品采集方法与样品DNA处理方法、关键技术因素及普通PCR技术、多重PCR技术、套式PCR技术、荧光定量PCR技术、芯片检测和环介导等温扩增技术等在猪肺炎支原体检测中的研究进展、主要优缺点及应用进行综述.     

Comparison of (GTG)5-oligonucleotide and ribosomal intergenic transcribed spacer (ITS)-PCR for molecular typing of Klebsiella isolates

Molecular typing of Klebsiella species has become important for monitoring dissemination of β-lactamase-producers in hospital environments. The present study was designed to evaluate poly-trinucleotide (GTG)₅- and rDNA intergenic transcribed spacer (ITS)-PCR fingerprint analysis for typing of Klebsiella pneumoniae and Klebsiella oxytoca isolates. Multiple displacement amplified DNA derived from 19 K. pneumoniae (some with an ESBL-phenotype), 35 K. oxytoca isolates, five K. pneumoniae, two K. oxytoca, three Raoultella, and one Enterobacter aerogenes type and reference strains underwent (GTG)₅ and ITS-PCR analysis. Dendrograms were constructed using cosine coefficient and the Neighbour joining method. (GTG)₅ and ITS-PCR analysis revealed that K. pneumoniae and K. oxytoca isolates, reference and type strains formed distinct cluster groups, and tentative subclusters could be established. We conclude that (GTG)₅ and ITS-PCR analysis combined with automated capillary electrophoresis provides promising tools for molecular typing of Klebsiella isolates.     

Leishmania donovani complex (Kinetoplastida, Trypanosomatidae): Comparison of deoxyribonucleic acid based techniques for typing of isolates from Ethiopia

In Ethiopia, visceral leishmaniasis (VL) is an increasing public health concern. Recently, a new outbreak of VL claimed the lives of hundreds of Ethiopians. Mapping its distribution and the identification of the causative Leishmania species is important for proper use of resources and for control planning. The choice of appropriate typing technique is the key for determining the infecting species. Here we compared three deoxyribonucleic acid (DNA) based markers. We used, for the first time, cpbE and cpbF (cpbE/F) PCR-RFLP and demonstrated that it clearly differentiates Leishmania donovani from Leishmania infantum. The cpbE/F PCR-RFLP gave identical banding pattern for all L. donovani strains irrespective of their geographic origin. With the K26 (primers) PCR-RFLP, the L. donovani strains gave a banding pattern different from L. infantum and showed variation with geographic origin. The Ethiopian isolates typed as L. donovani by the PCR-RFLP of the cpbE/F (gene) and K26 (primers) showed two types of patterns with the T2/B4 (primers) PCR-RFLP; one group with L. infantum-like and the other L. donovani-like pattern. Phylogenetic analysis using cpbE/F sequences showed variation with geographic origin of strains and the African strains of L. donovani are more distantly related to L. infantum. Moreover, the Ethiopian isolates were seen to be closely related to the Sudanese, Kenyan and Indian strains. Thus, we recommend the use of more than one marker to study the population genetics of L. donovani complex.     

Antigenic characteristics and stability of microencapsulated Mycoplasma hyopneumoniae vaccine

The in vitro stability (temperature, pH, and trypsin) of Mycoplasma hyopneumoniae antigen (MHA) with and without enteric-coated microencapsulation were examined. Microencapsulation of MHA with cellulose acetate phthalate (CAP) is an effective route to produce enteric-coated vaccine microspheres for oral administration. The effect of temperature on the rate of inactivation of MHA was studied by exposing MHA to various temperatures, such as 25, 37, 50 and 60 degrees C. The MHA microspheres were thermally more stable than that of the unencapsulated MHA. The kinetic parameters were observed to follow an Arrhenius-type temperature dependence. The MHA microspheres were also more stable in acidic regions (pH 1.2-4.0) than that of the free one. The enteric-coated MHA microspheres exhibited an excellent enteric function to prevent acidic degradation. A model similar to the well-known Michaelis-Menten equation was formulated to describe the effect of trypsin on the antigenic degradation of MHA. The equilibrium constant K(A) and the maximum reaction velocity V(m) were obtained from experimental data for both free and microencapsulated MHA. Both K(A) and V(m) values of the microencapsulated MHA were smaller than that of the free one, i.e., the resistance to proteolytic enzyme such as trypsin was enhanced by microencapsulation. The storage stability of enteric-coated MHA microspheres has been satisfactorily prolonged that they could preserve more than 90% of original antigenicity after 30 days, and over 80% of antigenicity of MHA was retained in the microspheres for 95 days when it was stored at 4 degrees C.     

Chromosomal heterogeneity of various Mycoplasma hyopneumoniae field strains.

Restriction enzyme digestion and field inversion gel electrophoresis were used to analyze the chromosomes of strains of Mycoplasma hyopneumoniae and the related organism Mycoplasma flocculare. The chromosome size for the M. hyopneumoniae type strain was calculated from individual fragments to be 1,011.3 +/- 32.9 kbp. The chromosomes of M. hyopneumoniae field strains were approximately the same size. The restriction patterns obtained for the chromosomes of phenotypically similar M. hyopneumoniae strains were quite different. Therefore, the species M. hyopneumoniae seems to be very heterogeneous. A field inversion gel electrophoresis analysis of the entire chromosomes allowed us to distinguish M. hyopneumoniae strains easily and hence to characterize further the species M. hyopneumoniae. The chromosome size for M. flocculare was calculated to be 988.3 +/- 39.5 kbp. Restriction enzyme XhoI, which statistically should cut the M. hyopneumoniae chromosome frequently, did not cut the DNA of any of the M. hyopneumoniae strains but did digest M. flocculare DNA, indicating that there is a site-specific modification at CTCGAG which probably belongs to a restriction modification system in M. hyopneumoniae and is absent in M. flocculare.     

一种快速鉴定猪肺炎支原体免疫显性蛋白抗原的ELISA方法的建立

旨在建立一种快速鉴定猪肺炎支原体(Mycoplasma hyopneumoniae,Mhp)血清体液免疫显性蛋白抗原的方法。通过构建p GEX-6P-1-mhp366重组表达质粒并转入大肠杆菌BL21(DE3),将GST-Mhp366重组蛋白进行原核表达。将GST-Mhp366重组菌和GST工程菌裂解液加入谷胱甘肽包被板进行抗原包被,分别与17份Mhp阳性血清和13份Mhp阴性血清反应,通过对抗原包被量、封闭液、血清和二抗稀释度的优化,确定间接ELISA的反应条件。最终确定GST-Mhp366重组菌和GST工程菌裂解液原液为抗原的最佳包被量,PBS+10%FBS+2.5%脱脂奶粉为最佳封闭液,分别将血清按照1∶500稀释、酶标二抗按照1∶40 000稀释作为最佳工作浓度,从而建立了一种基于间接ELISA的快速鉴定Mhp血清体液免疫显性蛋白抗原的方法,同时通过已知的血清体液免疫显性蛋白Mhp156和Mhp364对所建立的方法进行了验证。该方法的建立能够用于在基因组水平高通量筛选Mhp血清体液免疫显性蛋白抗原,并为Mhp初乳体液免疫和黏膜免疫显性蛋白抗原鉴定方法的建立奠定基础。     

A technique for typing Cryptosporidium isolates.

Antigens extracted from Cryptosporidium oocysts, which had been purified from faeces or chick egg culture, were electrophoresed in sodium dodecyl sulfate-polyacrylamide gels, and blotted onto nitrocellulose membranes. A Cryptosporidium genus-specific monoclonal antibody MAb-C1 bound to multiple bands using several detection techniques, and these corresponded to bands detected using immune rabbit antisera. Using a detection system with fluorescein isothiocyanate (FITC)-labelled MAb-C1 and alkaline phosphatase-labelled anti-FITC, bands were detected between 50 and 300 kDa. Blots were examined directly and by using a laser scanner. The system was shown to be specific for Cryptosporidium spp., giving no staining with a variety of other pathogens, and with negative samples. The oocyst antigen which bound MAb-C1 was stable, and banding patterns were not significantly affected by pretreatment of oocysts with proteinase K, trypsin, formalin, or sodium hypochlorite, methods commonly used during preparation and storage of C. parvum oocysts. However, banding was reduced with potassium dichromate. Of 76 samples containing Cryptosporidium oocysts, 53 showed one or more MAb-C1 staining bands. Cryptosporidium baileyi and C. parvum could be clearly differentiated by their banding patterns, indicating that the system will distinguish between species. Some isolates, including a single isolate of C. muris, produced weak bands which made interpretation difficult. The technique showed differences between isolates of C. parvum, with two different banding types found in human isolates, and other banding types seen in calf and lamb isolates. This method provides a useful way of characterising isolates which may be new species.