Diagnosis of Mycoplasma hyorhinis infection in pigs by PCR amplification of 16S-23S rRNA internal transcribed spacer region / 동물의과학연구지

Mycoplasma hyorhinis (M. hyorhinis) is considered an etiological agent of arthritis in suckling pigs. Recently, some M. hyorhinis strains were shown to produce pneumonia that is indistinguishable from the mycoplasmosis caused by M. hyopneumoniae. In this study, we developed a sensitive and specific PCR assay to detect M. hyorhinis and applied the developed PCR assay for detection of Mycoplasma infection in clinical piglets infected with M. hyorhinis. We developed a new PCR assay using a M. hyorhinis-specific primer pair, Mrhin-F and Mrhin-R, designed from the Mycoplasma 16S-23S rRNA internal transcribed spacer (ITS) region. The primers and probe for the assay were designed from regions in the Mycoplasma 16S-23S rRNA ITS unique to M. hyorhinis. The developed PCR assay was very specific and sensitive for the detection of M. hyorhinis. The assay could detect the equivalent of 1 pg of target template DNA, which indicates that the assay was very sensitive. In addition, M. hyorhinis PCR assay detected only M. hyorhinis and not any other Mycoplasma or bacterial spp. of other genera. The new developed PCR assay effectively detected M. hyorhinis infection in pigs. We suggest that this PCR assay using a M. hyorhinis-specific primer pair, Mrhin-F and Mrhin-R, could be useful and effective for monitoring M. hyorhinis infection in pigs.

Detección de Mycoplasma canadense y Mycoplasma californicum en ganado lechero de Argentina / Detection of Mycoplasma canadense and Mycoplasma californicum in dairy cattle from Argentina

Diferentes especies del género Mycoplasma pueden afectar al ganado bovino y causar varias enfermedades. La técnica de PCR, secuenciación y posterior análisis de la región ITS 16S-23S ARNr ha mostrado que existe una importante variabilidad interespecies entre Mollicutes. Se realizó la amplificación (región ITS 16S-23S ARNr) de 16 aislamientos sospechosos de corresponder a alguna especie de Mycoplasma, que habían sido obtenidos de muestras de leche provenientes de rodeos lecheros. Catorce de esos aislamientos fueron PCR positivos. Para confirmar la identidad de Mycoplasma bovis, dichos aislamientos fueron evaluados por otra PCR especie-específica. Siete aislamientos dieron un resultado positivo. Los productos de la PCR de la ITS 16S-23S ARNr de un aislamiento identificado como M. bovis y de otros dos aislamientos identificados como no-M. bovis fueron seleccionados al azar, secuenciados y analizados. Las tres secuencias (A, B y C) mostraron 100 % de similitud con cepas de M. bovis, Mycoplasma canadense y Mycoplasma californicum, respectivamente

Different species of Mycoplasma can affect bovine cattle, causing several diseases. PCR sequencing and further analysis of the 16S-23S rRNA ITS region have shown a significant interspecies variability among Mollicutes. Sixteen suspected isolates of Mycoplasma spp. obtained from milk samples from dairy herds were amplified (16S-23S rRNA ITS region). Fourteen out of those 16 suspected Mycoplasma spp. isolates were PCR-positive. To confirm the identity of Mycoplasma bovis, these 14 isolates were tested by another species-specific PCR. Seven of the isolates rendered a positive result. The products of 16S-23S rRNA ITS PCR from one isolate that was identified as M. bovis and from two other isolates, identified as non- M. bovis were randomly selected, sequenced and analyzed. The three sequences (A, B and C) showed 100% similarity with M. bovis, Mycoplasma canadense and Mycoplasma californicum respectively

Identification of Acinetobacter clinical isolates by polymerase chain reaction analysis of 16S-23S ribosomal ribonucleic acid internal transcribed spacer.

Background: The genus Acinetobacter is a diverse group of Gram‑negative bacteria involve at least 33 species using the molecular methods. Although the genus Acinetobacter comprises a number of definite bacterial species, some of these species are of clinical importance. Therefore, it is of vital importance to use a method which is able to reliably and efficiently differentiate the numerous Acinetobacter species. Objectives: This study aims to identify Acinetobacter of clinical isolates from Assir region to the species level by 16S‑23S intergenic spacers internal transcribed spacer (ITS) of ribosomal ribonucleic acid (rRNA). Materials and Methods: Deoxyribonucleic acid extraction, polymerase chain reaction amplification of 16S‑23S intergenic spacer sequences (ITS) was performed using the bacterium‑specific universal primers. Results: Based on the 16S‑23S intergenic spacers (ITS) of rRNA sequences, all isolates tested were identified as Acinetobacter baumannii. The isolates shared a common ancestral lineage with the prototypes A. baumannii U60279 and U60280 with 99% sequence similarities. Conclusion: These findings confirmed 16S‑23S rRNA ITS for the identification of A. baumannii of different genotypes among patients.

Queijo de minas artesanal da Serra da Canastra: influência da altitude das queijarias nas populações de bactérias acidolácticas / Influence of altitute on lactic acid bacteria population of minas artisanal cheese from Serra da Canastra

Amostras de queijo de minas artesanal foram coletadas em 18 queijarias localizadas em propriedades rurais da região da Serra da Canastra, Minas Gerais, com o objetivo de avaliar a influência da altitude sobre a população de bactérias acidolácticas. As queijarias estavam distribuídas nas altitudes de 600 a 900m, 900 a 1000m e mais de 1000m. Observaram-se populações mais elevadas de bactérias acidolácticas nas amostras de queijo da altitude de 600 a 900m. Lactobacillus rhamnosus, Lactobacillus casei e Lactobacillus plantarum foram os principais microrganismos isolados e identificados por PCR ARDRA 16S-23S rDNA, além de Enterococcus spp., Lactococcus spp. e outras espécies de Lactobacillus. Sugere-se que estas espécies estejam adaptadas ao ambiente de produção do queijo de minas artesanal produzido na região, o que resultaria em características sensoriais próprias do produto.

Samples of minas artisanal cheese were collected in 18 small-scale producer properties located in the rural region of Serra da Canastra, Minas Gerais state, aiming to evaluate the influence of three altitudes, from 600 to 900m, 900 to 1000m, and higher than 1000m, on the lactic acid bacteria (LAB) population. High populations of LAB were observed in the cheese samples, mainly in the lowest altitude. Lactobacillus rhamnosus, Lactobacillus casei, and Lactobacillus plantarum were the major LAB isolated from the cheese samples and identified according to PCR ARDRA 16S-23S rDNA. Enterococcus spp., Lactococcus spp., and other species of Lactobacillus genus were also found. It is suggested that these microorganisms are adapted to the production environment of the minas artisanal cheese which result in the unique sensorial properties of the product.

The genomic identification of Colombian Acinetobacter baumannii clinical isolates by RFLP-PCR analysis of the 16S-23S rRNA gene spacer region / Identificación genómica de aislamientos colombianos de Acinetobacter baumannii mediante RFLP-PCR de la región intergénica espaciadora de los genes 16S y 23S rRNA

The 16S-23S rRNA gene intergenic spacer (ITS) was analysed by RFLP in this study to identify A. baumannii from 139 isolates from four hospitals (identified as A, B, C and D). One hundred and twenty of these isolates (86.3%) belonged to the A. baumannii species; those identified as being A. baumannii were found to be polyclonal (19 clone groups) when determining the genetic relationships, 16 of them being found in hospital C. Hospitals A, B and D shared two clone groups isolated during different years. This study describes a rapid and easy method for genospecies identification of Acinetobacter baumannii.

Con el objeto de identificar la genomoespecie Acinetobacter baumannii, se estudiaron 189 aislamientos pertenecientes al Complejo Acinetobacter baumannii-Acinetobacter calcoaceticus provenientes de cuatro hospitales colombianos (denominados A,B,C,D) mediante el análisis por RFLP-PCR de la región intergénica espaciador (ITS) de los genes 16S y 23S rRNA. Se encontraron 120 aislamientos (86.3%) pertenecientes a la especie A. baumannii. La estructura de la población fue policlonal, con 19 grupos clonales, 16 de los cuales se hallaron en el hospital C. En los hospitales A,B y D se encontraron 2 grupos clonales aislados durante diferentes años. En este estudio se propone un método rápido y fácil para la identificación de Acinetobacter baumannii.

Genospecies Classification of Acinetobacter calcoaceticus-Acinetobacter baumannii Complex by Restriction Fragment Length Polymorphism

Acinetobacter calcoaceticus-Acinetobacter baumannii (A. calcoaceticus-A. baumannii) complex, which includes A. calcoaceticus (genospecies 1), A. baumannii (genospecies 2), Acinetobacter genospecies 3 and 13, has been identified as A. baumannii by automated bacteria identification system. The purpose of this study is to develop rapid genospecies classification of A. calcoaceticus-A. baumannii complex by molecular techniques. Random amplified polymorphic DNA (RAPD) and restriction fragment length polymorphism (RFLP) were determined for 4 reference strains and 80 isolates of A. calcoaceticus-A. baumannii complex from clinical sources. Four and eleven RAPD patterns were observed among the reference strains and the isolates, respectively. RAPD might be useful for genomic typing but not for genospecies classification of Acinetobacter spp. RFLP of 16S-23S rRNA intergenic spacer gene with three selected restriction enzymes (ApaLI, SwaI, and SalI) showed only four RFLP patterns in the reference and the isolates. Of 80 isolates, 10 of A. calcoaceticus (12.5%), 50 of A. baumannii (62.5%), 11 of A. genospecies 3 (13.75%), and 9 of A. genospecies 13 (11.25%) were classified by RFLP. This result suggests that RFLP of 16S-23S rRNA intergenic spacer gene of A. calcoaceticus-A. baumannii complex might be useful for genospecies classification.

IDENTIFICACIÓN MOLECULAR DE POBLACIONES BACTERIANAS ASOCIADAS AL CARACOL PALA (Strombus gigas) DEL CARIBE COLOMBIANO / Molecular Identification Of Bacterial Populations Associated To Queen Conch (Strombus gigas) From Colombian Caribbe

El caracol Pala, Strombus gigas (Strombidae), es de gran importancia ecológica y socioeconómica en el área caribeña colombiana. Sin embargo, es una especie catalogada como "vulnerable" y existe muy poca información referente a las especies bacterianas asociadas al caracol que puedan ser importantes para el desarrollo, manejo productivo y de seguridad acuícola de estos gastrópodos. En este trabajo, nosotros empleamos un estudio microbiológico y molecular de la región intergénica entre los genes 16S y 23S rDNA, análisis del gen rDNA 16S y secuenciación, para analizar las bacterias asociadas al caracol Pala (S. gigas). La composición de bacterias cultivables asociadas fue evaluada por su capacidad para crecer en agar marino y en medios de cultivos selectivos. De un total de 28 muestras analizadas encontramos que el número de bacterias cultivadas en condiciones aerobias fue de alrededor 10(6) ufc mL-1 donde las bacterias pertenecientes a la familia Vibrionacea fueron las más abundantes, cerca de >10(5) ufc mL-1. El análisis molecular de la región intergénica entre los genes 16S y 23S rDNA de las diferentes muestras, reveló una gran complejidad bacteriana asociada a S. gigas. Las secuencias de los amplificados del gen rDNA 16S identificó Pseudoalteromonas sp., Halomonas sp., Psycrobacter sp., Cobetia sp., Pseudomonas sp. y Vibrios sp. Nuestros resultados podrían sugerir un rol importante de estas bacterias como componentes de la comunidad asociada al S. gigas. Esta información puede complementar los estudios que se están implementando en los procesos para la conservación y repoblamiento de las poblaciones de S. gigas en Colombia.

The Queen Conch, Strombus gigas (Strombidae), is a species of great ecological and socioeconomic importance in the Caribbean area of Colombia. However, it is currently catalogued as "vulnerable"; there is limited information concerning the bacterial species associated with conch and important in the management of hatcheries for higher productivity and safety of these gastropods. In this study, we used a microbiology and molecular approach using the 16S-23S intergenic region, the 16S rDNA analysis and sequencing to determine the bacterial populations associated with Queen Conch (S. gigas). Also, the capacity to grow in marine agar and selective culture media was used to evaluate the composition of bacteria associated. The 28 total samples analysed we found the number of bacteria recovered after aerobic culture about 10ˆ6 cfu mL-1 and most belong to the Vibrionaceae family in the order of 10ˆ5 ufc mL-1. The molecular results of the spacer regions between the 16 and 23S genes from the different analyzed samples indicated a great complexity in the bacterial population associated to S. gigas. The sequencing of the amplicons of 16S rDNA identifies Pseudoalteromonas sp, Halomonas sp., Psycrobacter sp., Cobetia sp., Pseudomonas sp. and Vibrios sp. This suggests these bacteria can play an important role as components of the bacterial community associated to S. gigas. This information can help to improve both the management of hatcheries for higher productivity and for the implementation for the conservation processes of Colombian S. gigas.

PCR Amplification of 16S-23S rDNA Intergenic Spacer Regions of Bacteria in Trauma Infection by Universal Primers / 中华医院感染学杂志

OBJECTIVE To examine the feasibility of PCR amplification of 16S-23S rDNA intergenic spacer regions of bacteria in trauma infection by a pair of universal primers for gene diagnosis.METHODS The universal primers were designed at conserved regions of the 3' end of 16S rDNA and the 5' end of 23S rDNA.Bacterial genomic DNA from selected five commom bacteria in trauma infection were amplified by PCR.PCR products were examined using electrophoresis in agarose gel,and futher analyzed by sequencing.RESULTS The PCR products were similar to that we expected on the gel,which were confirmed by the results of sequencing and alignment.CONCLUSIONS Using the universal primers,16S-23S rDNA intergenic spacer regions of bacteria in trauma infection could be amplified by PCR,which lays a solid foundation for gene diagnosis in farther studies.

Identificition of Endophytic Bacteria EBS05 from Cinamonum camphra and Property of Its Antimicrobial Compound / 微生物学通报

An endophytic bacterium strain EBS05 from Cinamonum camphra was identified as Bacillus subtilis by morphological taxonomy and sequence analysis of 16S~23S rRNA intergenic spacer regions. Properties of antimicrobial compound produced by EBS05 were assayed. The active compound had the maximum absorbance peak at ?213.5 nm. The antimicrobial activity was stable in solution with pH value from 5 to 8, and decreased significantly in solution with pH value less than 4.0 or more than 9.0. The antimicrobial compound had thermodynamics stability. Its activity changed a little after treated at 60?C~80?C for two hours, and compared with 65% original activity after treated at 1?105 Pa for 30 minutes. The active substance had high resistance to ultraviolet radiation and protease K. Antimicrobial compound was soluble in alcohol solu- tion, which was easily dissolved in methanol and ethanol, but not dissolved in ethyl acetate, acetonitrile and petroleum et al.

Análise molecular de estirpes de Escherichia coli isoladas a partir de amostras de urina de pacientes ambulatoriais por RFLP da região intergência 16s-23s' / Molecular analysis based on intergenic 16s-23s RFLP of Escherichia coli strains obtained from urine samples of ambulatorial pacients

A análise de RFLP (Restriction Fragment Lenght Polymorphism) da região intergênica 16S-23S rDNA tem sido utilizada na diferenciação de estirpes de vários microrganismos. A digestão do produto de amplificação da região intergênica em isolados uropatogênicosde Escherichia coli com a enzima RsaI gerou dois padrões distintos, separando as estirpes em dois grupos: alfa e beta. Este trabalho teve como objetivo enquadrar dentro destes grupos 60 estirpes de E. coli isoladas a partir de urina de pacientes ambulatoriais no Laboratório Médico Santa Luzia (Florianópolis). Os produtos de amplificação foram digeridos com a enzima RsaI. Os fragmentos resultantes foram submetidos a análise eletroforética em gel de agarose 2% e as estirpes com padrões de restrição condizentes foram agrupadas. Através destas análises foi possível estabelecer correlações entre o perfil molecular e outros dados de análise bioquímicae de resistência a antibióticos.

RFLP analysis of 16S-23S rDNA intergenic region have been used in differentiation of many microorganisms strains. The digestion of the product of intergenic region amplification in uropathogenic strains of Escherichia coli with RsaI generated two distintpatterns: alpha and beta. This project had the aim of classify 60 Escherichia coli strains obtained from ambulatorial patients urine of the Laboratório Médico Santa Luzia (Florianópolis). The amplification products were digested with RsaI enzyme. The fragments weresubmitted to eletrophoretic analysis in 2% agarosis gel. Strains with the same restriction pattern were identified. This analysis allowed the correlation between molecular profile and biochemical and antibiotical resistence data.

Cloning and sequencing of the 16s rRNA intergenic spacer region of proteus mirabilis and acinetobacter iwoffii / 重庆医科大学学报

Objective:To clone and sequence of 16S~23S r RNA intergenic spacer region of Proteus mirabilis and Acinetobacter lowffii for further identification of these two bacteria by means of molecular probe.Methods: The PCR universal clinical common pathogenic bacteria primers for 16S and 23S rRNA's conserved sequences were designed.Then the genomes of these two bacteria were amplified,T Vector clones were constructed with PMD-18 T Vector ad PCR products.The vectors were sequenced and the sequence was submitted to Genbank.Results: T Vector clones were constructed with products amplified by using universal primers;according to Blast analyses,the results of sequencing were determined as ISR sequences of the two kinds of bacteria.And the reports to Genbank were accepted.Conclusion: Genbank accepted the cloning and sequencing results of Proteus mirabilis and Acinetobacter lwoffii as new sequences.And these sequences can be used to identify the two bacteria by universal primers.

Identification of Acinetobacter Genospecies by Analysis of rRNA Spacer Regions / 대한임상병리학회지

BACKGROUND: Recently, the genus Acinetobacter have become increasingly important as nosocomial pathogens. Colonization and infection caused by multiresistant epidemic strains are common manifestations in intensive care units. Up to now 21 genomic species have been described, of which 7 have been named. However, there is no approach about distribution of Acinetobacter species in Korea. The objective of this study was to evaluate the performance of PCR analysis for the accurate identification and distribution of Acinetobacter species. METHODS: tRNA intergenic spacer length polymorphism(tRNA-ILP), 16S-23S rRNA spacer length polymorphism(16S-23S ILP) and restriction analysis of the 16S-23S rRNA intergenic spacer sequences(RA 16S-23S) were performed to identify the 7 type strains and 83 clinical isolates of Acinetobacter. RESULTS: 1. In the 7 Acinetobacter type strains, tRNA-ILP data could be easily analyzed by visual comparision. Eighty one of 83(97.6%) clinical isolates of Acinetobacter were identified as A. baumannii and the others were identified as A. haemolyticus and A. calcoaceticus. 2. The 16S-23S ILP patterns were not distinguished among the species, except A. haemolyticus, A, johnonii and A. lwoffii. The three species could be discriminated by a number of specific DNA fragments. 3. In RA 16S-23S, restriction endonuclease Alu I was able to not only digest the amplification products but also gave characteristic restriction patterns for the 7 type strains. CONCLUSION: The tRNA-ILP analysis and RA 16S-23S can be used as a tool for the rapid identification of Acinetobacter species with a high degree of specificity.

Detection of Bacterial Pathogens by Nanogold-based Gene Chip Combining with One-time PCR with Common Primers / 中华医院感染学杂志

OBJECTIVE To develop a preparation technique of sample of one-time PCR with common primers based on ribotyping which was combined with the detection system of nanogold-based gene chip to detect clinical bacterial pathogens.METHODS According to the highly conserved regions of rDNA,the common primers were designed and used to amplify each target bacterial ISRs by one-time PCR,and the specific oligonucleotide probes for each target ISRs were designed,utilized to establish the new nanogold-based gene chips.After the characteristics of the chip such as sensitivity,specificity and reliability were determined,the chip was used to detect clinical samples.RESULTS The designed common primers could amplify the 12 target bacteria successfully by one-time PCR.All selected probes were of strong specificity and great reliability.The chip had high sensitivity,specificity and reliability,reaching 50 fmol/L of detection sensibility.Clinical detection results showed the chip had a great accuracy.CONCLUSIONS Compared to multi-PCR chip detection,the detection procedure and complexity of the chip are decreased significantly,and have more practical value in clinical pathogens detection.

Prediction of secondary structures of 16S and 23S rRNA from Escherichia coli.

Small and large subunits of Escherichia coli ribosome have three different rRNAs, the sequences of which are known. However, attempts by three groups to predict secondary structures of 16S and 23S rRNAs have certain common limitations namely, these structures are predicted assuming no interactions among various domains of the molecule and only 40% residues are involved in base pairing as against the experimental observation of 60 % residues in base paired state. Recent experimental studies have shown that there is a specific interaction between naked 16S and 23S rRNA molecules. This is significant because we have observed that the regions (oligonucleotides of length 9–10 residues), in 16S rRNA which are complementary to those in 23S rRNA do not have internal complementary sequences. Therefore, we have developed a simple graph theoretical approach to predict secondary structures of 16S and 23S rRNAs. Our method for model building not only uses complete sequence of 16S or 23S rRNA molecule along with other experimental observations but also takes into account the observation that specific recognition is possible through the complementary sequences between 16S and 23S rRNA molecules and, therefore, these parts of the molecules are not used for internal base pairing. The method used to predict secondary structures is discussed. A typical secondary structure of the complex between 16S and 23S rRNA molecules, obtained using our method, is presented and compared briefly with earlier model building studies.