Differentiation of two biovars of Ureaplasma urealyticum based on the 16S-23S rRNA intergenic spacer region

Ureaplasma infections: update on epidemiology, antimicrobial resistance, and pathogenesis

Human Ureaplasma species are being increasingly recognized as opportunistic pathogens in human genitourinary tract infections, infertility, adverse pregnancy, neonatal morbidities, and other adult invasive infections. Although some general reviews have focused on the detection and clinical manifestations of Ureaplasma spp., the molecular epidemiology, antimicrobial resistance, and pathogenesis of Ureaplasma spp. have not been adequately explained. The purpose of this review is to offer valuable insights into the current understanding and future research perspectives of the molecular epidemiology, antimicrobial resistance, and pathogenesis of human Ureaplasma infections. This review summarizes the conventional culture and detection methods and the latest molecular identification technologies for Ureaplasma spp. We also reviewed the global prevalence and mechanisms of antibiotic resistance for Ureaplasma spp. Aside from regular antibiotics, novel antibiotics with outstanding in vitro antimicrobial activity against Ureaplasma spp. are described. Furthermore, we discussed the pathogenic mechanisms of Ureaplasma spp., including adhesion, proinflammatory effects, cytotoxicity, and immune escape effects, from the perspectives of pathology, related molecules, and genetics.

External quality assessment for molecular detection of Ureaplasma urealyticum in China

BACKGROUND AND AIMS

A pilot external quality assessment (EQA) scheme for molecular detection of Ureaplasma urealyticum (UU) was conducted by the National Center for Clinical Laboratories (NCCL) to evaluate the testing capabilities of clinical laboratories and the actual performance of DNA-based nucleic acid amplification tests (NAAT) and RNA-based NAATs when applied in clinical settings.

MATERIALS AND METHODS

The EQA panel contained twelve lyophilized samples, including positive samples containing inactivated cell culture supernatants of UU at different concentrations and sterile saline for negative samples. The positive samples were further divided into three groups of high, moderate and low concentrations. The panels were distributed to the participants and the datasets were analyzed according to the qualitative results.

RESULTS

A total of 365 laboratories participated in the EQA scheme, and 360 results submitted by 338 laboratories were collected, of which 96.11 % (346/360) of the returned results and 95.86 % (324/338) of the laboratories were deemed competent. The positive percentage agreement (PPA) was ≥ 97.5 % for high and moderate concentration samples, but varied significantly for low concentration samples, decreasing from 86.94 % to 51.94 % as the sample concentration decreased. Additionally, for low concentration samples, RNA-based NAAT showed higher PPAs than DNA-based NAATs, but these results were specific to UU supernatants used in this study.

CONCLUSION

Most of UU detection assays employed by the participants were generally consistent with their estimated limit of detection (LOD), and the majority of participants can reliably detect UU samples with high and moderate concentrations, while the poor analytical performance for low concentration samples requires further improvement and optimization.

Molecular genetic techniques and oligonucleotides for mycoplasma identification – a review

Control of distribution of mycoplasmal infections in cattle herds is essential in the majority of countries world-wide. Various PCR procedures are available to detect mycoplasmas in cell cultures and bovine mycoplasma in different types of samples. We reviewed some common PCR techniques and specific primers targeted to different bacterial genetic regions of mycoplasma. Several researchers used the same PCR approach and Mycoplasma spp. as a target but their results could not be compared because different primer pairs were used. These methods and primers were first developed to identify mycoplasma species that contaminate animal cell cultures, and then were used by other researchers to differentiate mycoplasmas as a cow infecting agent. Our analysis of the specificity of these primer pairs to nucleotide sequences of five Mycoplasma spp. showed that oligonucleotides have less specificity to them. Numerous commercially available PCR kits are applicable to find mycoplasma contamination in cell cultures and fewer of them can be used in veterinary diagnostics. Although serological and culture techniques are still used, it is necessary to develop a new multiplex PCR technique with a more specific primer set especially in agrarian countries.

Molecular Detection of Ureaplasma urealyticum from Prostate Tissues using PCR-RFLP, Tehran, Iran

BACKGROUND

In most cases, prostatitis can be caused by a bacterial agent such as Ureaplasma urealyticum. Considering to the cumbersome of the culture method for the detection of Ureaplasma species in clinical samples such as prostate; PCR method that is faster and more appropriate than the cultivation methods, can be utilized for the detection of U. urealyticum and U. parvum. PCR-RFLP method can differentiate both biovars and assist in studies of the clinical diagnosis, epidemiology and pathology of this species in human. The aim of this study was to molecular detection of U. urealyticumin in prostate tissue samples based on PCR- RFLP.

METHODS

Two hundred prostate tissue samples were collected from patient suffering from prostatitis. The PCR assay was used to amplify a 559 bp fragment of 16S-23SRNA interspace region of Ureaplasma. After sequencing, PCR products from positive samples were digested with TaqI restriction enzyme.

RESULTS

Seven cases (3.5%) out of 200 prostate tissue samples were positive for U. urealyticum. Results of PCR products sequencing demonstrated that all isolates were U. parvum biovar. PCR-RFLP results shown that there was not any differentiation in pattern of enzymatic digestion, in addition, all isolates were U. parvum, serovar 3.

DISCUSSION

U. urealyticum can be one of the causing agents of prostatitis. Using PCR-RFLP with specific primer and restriction enzyme is a rapid and cost-effect method for detection and differentiation of Ureaplasma from clinical samples.

Susceptibility of Ureaplasma urealyticum to Methylene Blue-Mediated Photodynamic Antimicrobial Chemotherapy: An in vitro Study

The aim of this study was to detect the susceptibility of Ureaplasma urealyticum to methylene blue-mediated photodynamic antimicrobial chemotherapy (PACT). Three U. urealyticum strains including the standard serotype 1 and 5, and a clinically collected strain were used in this study. Strains were first incubated in 96-well culture plates in the presence of methylene blue with decreasing concentrations (from 1 to 0.015625 mg mL(-1)) for 20 or 60 min, and then submitted to irradiation with a light-emitting diode laser with a power density of 100 mW cm(-2) for 8, 17, 34 or 68 min. Regrowth of the strains was performed soon after irradiation. A significant inactivation effect was observed after PACT. Longer incubation time induced more extensive inactivation of U. urealyticum. No difference in response to PACT was observed between the two biovars of U. urealyticum. It was concluded that PACT had a significant inactivation effect on U. urealyticum, and it might be a promising alternative treatment for resistant U. urealyticum infections.

A sensible technique to detect mollicutes impurities in human cells cultured in GMP condition

In therapeutic trials the use of manipulated cell cultures for clinical applications is often required. Mollicutes microorganism contamination of tissue cultures is a major problem because it can determine various and severe alterations in cellular function. Thus methods able to detect and trace cell cultures with Mollicutes contamination are needed in the monitoring of cells grown under good manufacturing practice conditions, and cell lines in continuous culture must be tested at regular intervals. We here describe a multiplex quantitative polymerase chain reaction assay able to detect contaminant Mollicutes species in a single-tube reaction through analysis of 16S-23S rRNA intergenic spacer regions and Tuf and P1 cytoadhesin genes. The method shows a sensitivity, specificity, and robustness comparable with the culture and the indicator cell culture as required by the European Pharmacopoeia guidelines and was validated following International Conference on Harmonization guidelines and Food and Drug Administration requirements.

Development of a multilocus sequence typing scheme for Ureaplasma

Ureaplasma is a commensal of the human urogenital tract but is always associated with invasive diseases such as non-gonococcal urethritis and infertility adverse pregnancy outcomes. To better understand the molecular epidemiology and population structure of Ureaplasma, a multilocus sequence typing (MLST) scheme based on four housekeeping genes (ftsH, rpL22, valS, thrS) was developed and validated using 283 isolates, including 14 serovars of reference strains and 269 strains obtained from clinical patients. A total of 99 sequence types (STs) were revealed: the 14 type strains of the Ureaplasma serovars were assigned to 12 STs, and 87 novel and special STs appeared among the clinical isolates. ST1 and ST22 were the predominant STs, which contained 68 and 70 isolates, respectively. Two clonal lineages (CC1 and CC2) were shown by eBURST analysis, and linkage disequilibrium was revealed through a standardized index of association (I A (S)). The neighbor-joining tree results of 14 Ureaplasma serovars showed two genetically significantly distant clusters, which was highly congruent with the species taxonomy of ureaplasmas [Ureaplasma parvum (UPA) and Ureaplasma urealyticum (UUR)]. Analysis of the biotypes of 269 clinical isolates revealed that all the isolates of CC1 were UPA and those of CC2 were UUR. Additionally, CC2 was found more often in symptomatic patients with vaginitis, tubal obstruction, and cervicitis. In conclusion, this MLST scheme is adequate for investigations of molecular epidemiology and population structure with highly discriminating capacity.

Current concepts of genetic variability of genital mycoplasmas and their role in the development of inflammatory diseases of the urogenital system

The authors disclose current concepts of the taxonomic and morphologic characteristics of genital mycoplasmas and their role in the development of inflammatory urogenital diseases and reproductive disorders. They also discuss such issues as genetic variability of genital mycoplasmas and possible interrelation with different variants of the clinical course of inflammatory processes in the urogenital tract.

Hemotropic mycoplasma infection in wild black bears (Ursus thibetanus japonicus)

This is the first report on Mycoplasma infection in wild bears. We report a novel hemotropic Mycoplasma (also called hemoplasma) detected in a free-ranging black bear (Ursus thibetanus japonicus) in Japan. We then used real-time PCR to look for hemoplasma DNA in blood samples collected from 15 bears and found that eight (53%) were positive. Among these eight PCR samples, seven showed a melting temperature of around 85.5°C, while the remaining one showed a single peak at 82.26°C. Almost the entire region of the 16S rRNA gene as well as the 16S-23S rRNA intergenic transcribed spacer (ITS) region from the sample that showed a melting temperature of 82.26°C was successfully amplified by means of end-point PCR. The nucleotide sequences of the 16S rRNA gene and the ITS region were then determined and compared with those of authentic Mycoplasma species. Our examinations revealed the presence of a novel hemoplasma in Japanese black bears.

Two clusters among Mycoplasma haemomuris strains, defined by the 16S-23S rRNA intergenic transcribed spacer sequences

Mycoplasma haemomuris is a causative organism of infectious anemia or splenomegaly in rodents. Here, we report two distinct genetic groups among M. haemomuris strains detected from rats and mice, respectively, by examining the nucleotide sequences of the 16S-23S rRNA intergenic transcribed spacer region that has been shown to be a stable genetic marker for mycoplasma species. Our results may reveal host-tropism of each cluster of M. haemomuris strains, and suggest an idea to distinguish M. haemomuris into two different genetic clusters.

Two genotypes among 'Candidatus Mycoplasma haemobos' strains based on the 16S-23S rRNA intergenic spacer sequences

'Candidatus Mycoplasma haemobos', sometimes causative of bovine infectious anemia at various extents, has been demonstrated throughout the world. Here, we show two distinct types of 'Ca. M. haemobos' are distributed among cattle in Japan, by examining the primary and secondary structures of the 16S-23S rRNA intergenic spacer region that has been shown to be a stable genetic marker for mycoplasma species. Our results may explain differences in severity of anemic condition as well as provide a genetic marker for an epidemiological study of bovine hemoplasma infections.

A diagnostic polymerase chain reaction for Mycoplasma iowae using primers located in the intergenic spacer region and the 23S rRNA gene

Mycoplasma iowae is primarily a pathogen of turkeys and, although uncommon, it still persists in some areas of the world, where it may cause embryo mortality and leg lesions. A species-specific diagnostic polymerase chain reaction was developed using a forward primer based in the intergenic spacer region between the 16S rRNA and the 23S rRNA ribosomal genes and a reverse primer located within the 23S rRNA gene. The polymerase chain reaction proved to be both sensitive and specific. It detected M. iowae DNA in the six reference strains of serotypes I, J, K, N, Q and R and in 28 field isolates. With the six serotypes the test detected between 1 and 5 pg of M. iowae DNA. There were no non-specific reactions with the other avian Mycoplasma species. When the closest phylogenetically related species were checked, a weak reaction with Mycoplasma muris was observed that disappeared when the annealing temperature was increased by 2°C.

Molecular methods for the detection of Mycoplasma and ureaplasma infections in humans: a paper from the 2011 William Beaumont Hospital Symposium on molecular pathology

Mycoplasma and Ureaplasma species are well-known human pathogens responsible for a broad array of inflammatory conditions involving the respiratory and urogenital tracts of neonates, children, and adults. Greater attention is being given to these organisms in diagnostic microbiology, largely as a result of improved methods for their laboratory detection, made possible by powerful molecular-based techniques that can be used for primary detection in clinical specimens. For slow-growing species, such as Mycoplasma pneumoniae and Mycoplasma genitalium, molecular-based detection is the only practical means for rapid microbiological diagnosis. Most molecular-based methods used for detection and characterization of conventional bacteria have been applied to these organisms. A complete genome sequence is available for one or more strains of all of the important human pathogens in the Mycoplasma and Ureaplasma genera. Information gained from genome analyses and improvements in efficiency of DNA sequencing are expected to significantly advance the field of molecular detection and genotyping during the next few years. This review provides a summary and critical review of methods suitable for detection and characterization of mycoplasmas and ureaplasmas of humans, with emphasis on molecular genotypic techniques.

Comparative genome analysis of 19 Ureaplasma urealyticum and Ureaplasma parvum strains

Background

Ureaplasma urealyticum (UUR) and Ureaplasma parvum (UPA) are sexually transmitted bacteria among humans implicated in a variety of disease states including but not limited to: nongonococcal urethritis, infertility, adverse pregnancy outcomes, chorioamnionitis, and bronchopulmonary dysplasia in neonates. There are 10 distinct serotypes of UUR and 4 of UPA. Efforts to determine whether difference in pathogenic potential exists at the ureaplasma serovar level have been hampered by limitations of antibody-based typing methods, multiple cross-reactions and poor discriminating capacity in clinical samples containing two or more serovars.

Results

We determined the genome sequences of the American Type Culture Collection (ATCC) type strains of all UUR and UPA serovars as well as four clinical isolates of UUR for which we were not able to determine serovar designation. UPA serovars had 0.75−0.78 Mbp genomes and UUR serovars were 0.84−0.95 Mbp. The original classification of ureaplasma isolates into distinct serovars was largely based on differences in the major ureaplasma surface antigen called the multiple banded antigen (MBA) and reactions of human and animal sera to the organisms. Whole genome analysis of the 14 serovars and the 4 clinical isolates showed the mba gene was part of a large superfamily, which is a phase variable gene system, and that some serovars have identical sets of mba genes. Most of the differences among serovars are hypothetical genes, and in general the two species and 14 serovars are extremely similar at the genome level.

Conclusions

Comparative genome analysis suggests UUR is more capable of acquiring genes horizontally, which may contribute to its greater virulence for some conditions. The overwhelming evidence of extensive horizontal gene transfer among these organisms from our previous studies combined with our comparative analysis indicates that ureaplasmas exist as quasi-species rather than as stable serovars in their native environment. Therefore, differential pathogenicity and clinical outcome of a ureaplasmal infection is most likely not on the serovar level, but rather may be due to the presence or absence of potential pathogenicity factors in an individual ureaplasma clinical isolate and/or patient to patient differences in terms of autoimmunity and microbiome.

Development and validation of a multiplex quantitative polymerase chain reaction assay for the detection of Mollicutes impurities in human cells, cultured under good manufacturing practice conditions, and following European Pharmacopoeia requirements and the International Conference on Harmonization guidelines

BACKGROUND AIMS

The clinical applications of in vitro manipulated cultured cells and their precursors are often made use of in therapeutic trials. However, tissue cultures can be easily contaminated by the ubiquitous Mollicutes micro-organisms, which can cause various and severe alterations in cellular function. Thus methods able to detect and trace Mollicutes impurities contaminating cell cultures are required before starting any attempt to grow cells under good manufacturing practice (GMP) conditions.

METHODS

We developed a multiplex quantitative polymerase chain reaction (qPCR) assay specific for the 16S-23S rRNA intergenic spacer regions, for the Tuf and P1 cytoadhesin genes, able to detect contaminant Mollicutes species in a single tube reaction. The system was validated by analyzing different cell lines and the positive samples were confirmed by 16S and P1 cytoadhesin gene dideoxy sequencing.

RESULTS

Our multiplex qPCR detection system was able to reach a sensitivity, specificity and robustness comparable with the culture and the indicator cell culture method, as required by the European Pharmacopoeia guidelines.

CONCLUSIONS

We have developed a multiplex qPCR method, validated following International Conference on Harmonization (ICH) guidelines, as a qualitative limit test for impurities, assessing the validation characteristics of limit of detection and specificity. It also follows the European Pharmacopoeia guidelines and Food and Drug Administration (FDA) requirements.

Analysis of the 16S to 23S rRNA intergenic spacer region of Mycoplasma synoviae field strains

Mycoplasma synoviae has been associated with economic loss in the chicken and turkey industries. The molecular characterization of M. synoviae at strain level allows the analysis of relationships between strains that may be valuable in epidemiological investigations. In the present study, the intergenic spacer region (ISR) between the 16S and 23S rRNA genes was examined to see whether useful information about strains could be derived. M. synoviae has two copies of this region, which may not be exactly the same (intercistronic heterogeneity). Sequencing of the ISRs of 21 M. synoviae isolates and the type strain revealed that 19 of them had such heterogeneity so DNA cloning was performed where necessary. All sequences were analysed and aligned; the percentage similarity of the DNA was calculated and a dendrogram was constructed. The length of the ISRs varied between 305 and 309 base pairs. Apart from having extra A/Ts in poly-A or poly-T regions and the presence of a few polymorphisms, the sequences of the M. synoviae strains were similar. Based on phylogenetic analysis, the strains were assigned to 10 groups-taking into account that within each group the DNA similarity was 100%, while the lowest similarity between groups was 95.8%. The results were compared with those obtained with the vlhA gene, resulting in very similar M. synoviae groups. Although the ISR could be a good target for strain typing, as has been shown by others for Mycoplasma gallisepticum, the method may be too cumbersome for routine use with M. synoviae because of complications with intercistronic heterogeneity. However, if the ISR sequence information was to be combined with other mutation detection techniques it could increase the discriminatory power.

Ureaplasma antigenic variation beyond MBA phase variation: DNA inversions generating chimeric structures and switching in expression of the MBA N-terminal paralogue UU172

Phase variation of the major ureaplasma surface membrane protein, the multiple-banded antigen (MBA), with its counterpart, the UU376 protein, was recently discussed as a result of DNA inversion occurring at specific inverted repeats. Two similar inverted repeats to the ones within the mba locus were found in the genome of Ureaplasma parvum serovar 3; one within the MBA N-terminal paralogue UU172 and another in the adjacent intergenic spacer region. In this report, we demonstrate on both genomic and protein level that DNA inversion at these inverted repeats leads to alternating expression between UU172 and the neighbouring conserved hypothetical ORF UU171. Sequence analysis of this phase-variable ‘UU172 element’ from both U. parvum and U. urealyticum strains revealed that it is highly conserved among both species and that it also includes the orthologue of UU144. A third inverted repeat region in UU144 is proposed to serve as an additional potential inversion site from which chimeric genes can evolve. Our results indicate that site-specific recombination events in the genome of U. parvum serovar 3 are dynamic and frequent, leading to a broad spectrum of antigenic variation by which the organism may evade host immune responses.

Detection and characterization of human Ureaplasma species and serovars by real-time PCR

We designed primers and probes for the detection and discrimination of Ureaplasma parvum and U. urealyticum and their 14 serovars by real-time PCR. The analytical sensitivity and specificity of the multiplex species-specific PCR were determined by testing corresponding American Type Culture Collection (ATCC) type strains, 47 other microbial species, and human genomic DNA. The limits of the multiplex PCR were 2.8 x 10(-2) CFU/microl PCR mixture for detecting U. parvum and 4.1 x 10(-2) CFU/microl PCR mixture for detecting U. urealyticum. Clinical specificity and sensitivity were proven by comparison with culture and traditional PCR. For the detection of any Ureaplasma species, the clinical sensitivity and specificity of real-time PCR were 96.9% and 79.0%, respectively, using culture as a reference. Multiplex real-time PCR was also more sensitive than traditional PCR in discriminating the two Ureaplasma species in culture-positive subcultures. Each of the 14 monoplex serovar-specific PCR assays was specific for the corresponding ATCC type strain serovar. This new species identification PCR is specific and sensitive in the detection of Ureaplasma species in clinical specimens, and the serovar-specific PCR assays are the first set of complete genotypic assays to differentiate all 14 known Ureaplasma serovars. These assays provide quick and reliable means for investigating the epidemiology and pathogenicity of ureaplasmas at the serovar level.

Development and evaluation of a diagnostic PCR for Mycoplasma synoviae using primers located in the intergenic spacer region and the 23S rRNA gene

Mycoplasma synoviae (Ms) is an important pathogen of poultry, causing economic losses to this industry. Early and reliable diagnosis is a key to controlling the spread of this organism. In this study, a polymerase chain reaction with one primer based on the intergenic spacer region (ISR) was validated for detection of Ms. The ISR primer was paired with a general primer from within the 23S rRNA gene. The PCR primers were tested with the 22 other recognised avian Mycoplasma species to check the specificity and with 21 field isolates of Ms from various hosts and countries, and with several swab samples. The PCR appeared to be specific and sensitive. Four different sample preparation methods were compared for use in this PCR, and the amplification protocol was compared with three others, confirming the comparative sensitivity of the new PCR.

Evaluation of amplified rDNA restriction analysis (ARDRA) for the identification of Mycoplasma species

Background

Mycoplasmas are present worldwide in a large number of animal hosts. Due to their small genome and parasitic lifestyle, Mycoplasma spp. require complex isolation media. Nevertheless, already over 100 different species have been identified and characterized and their number increases as more hosts are sampled. We studied the applicability of amplified rDNA restriction analysis (ARDRA) for the identification of all 116 acknowledged Mycoplasma species and subspecies.

Methods

Based upon available 16S rDNA sequences, we calculated and compared theoretical ARDRA profiles. To check the validity of these theoretically calculated profiles, we performed ARDRA on 60 strains of 27 different species and subspecies of the genus Mycoplasma.

Results

In silico digestion with the restriction endonuclease AluI (AG^CT) was found to be most discriminative and generated from 3 to 13 fragments depending on the Mycoplasma species. Although 73 Mycoplasma species could be differentiated using AluI, other species gave undistinguishable patterns. For these, an additional restriction digestion, typically with BfaI (C^TAG) or HpyF10VI (GCNNNNN^NNGC), was needed for a final identification. All in vitro obtained restriction profiles were in accordance with the calculated fragments based on only one 16S rDNA sequence, except for two isolates of M. columbinum and two isolates of the M. mycoides cluster, for which correct ARDRA profiles were only obtained if the sequences of both rrn operons were taken into account.

Conclusion

Theoretically, restriction digestion of the amplified rDNA was found to enable differentiation of all described Mycoplasma species and this could be confirmed by application of ARDRA on a total of 27 species and subspecies.

Differentiation of group VIII Spiroplasma strains with sequences of the 16S-23S rDNA intergenic spacer region

Spiroplasma species (Mollicutes: Spiroplasmataceae) are associated with a wide variety of insects, and serology has classified this genus into 34 groups, 3 with subgroups. The 16S rRNA gene has been used for phylogenetic analysis of spiroplasmas, but this approach is uninformative for group VIII because the serologically distinct subgroups generally have similarity coefficients >0.990. Therefore, we investigated the utility of the 16S-23S rRNA spacer region as a means to differentiate closely related subgroups or strains. We generated intergenic sequences and detailed serological profiles for 8 group VIII Spiroplasma strains. Sequence analyses using Maximum Parsimony, Neighbor Joining, and Maximum Likelihood placed the strains into 2 clades. One clade consisted of strains BARC 2649 and GSU5367. The other clade was divided into clusters containing representatives of the 3 designated group VIII subgroups (EA-1, DF-1, and TAAS-1) and 3 previously unclassified strains. The stability of the positions of the strains in various analytical models and the ability to provide robust support for groupings tentatively supported by serology indicates that the 16S-23S intergenic rDNA sequence will prove useful in intragroup analysis of group VIII spiroplasmas.

Restriction Fragment Length Polymorphism of 16S–23S rDNA Intergenic Spacer of Aeromonas spp

We analyzed restriction fragment length polymorphism (RFLP) of 16S-23S rDNA intergenic spacer region (ISR) of Aeromonas species. A total of 69 isolates belonging to 18 DNA hybridization groups (HG; equivalent of genomic species) were used in this study. ISRs were amplified by PCR and the products were digested with four restriction endonucleases: Hin6I, Csp6I, TaqI, and TasI. The RFLP patterns obtained after digesting by particular enzymes revealed ISR polymorphism of isolates allocated to individual genomic species. The combined Hin6I, Csp6I, TaqI, and TasI restriction profiles were examined by Dice coefficient (SD) and unweighted pair group method of clustering (UPGMA). The isolates were allocated into 15 groups, three strains were unclustered. The strains belonging to the following genomic species: A. hydrophila, A. bestiarum, A. salmonicida, A. caviae, A. media, A. schubertii, A. allosaccharophila, A. popoffii, and A. culicicola formed distinct clusters. Strains belonging to HG 6, HG 7, HG 11, and HG 16 revealed similar combined RFLP patterns and constituted one group. Similarly, the strains of A. jandaei (HG 9) and the type strain of A. trota were allocated into one cluster. Two isolates of HG 14 formed distinct cluster. We noticed a genetic diversity among A. veronii isolates, the strains were clustered in two groups. Our study showed that combined ISR-RFLP analysis may be used for identification of some species of Aeromonas.

Ureaplasma urealyticum biovar determination in women attending a family planning clinic in Guiné-Bissau, using polymerase chain reaction of the multiple-banded antigen gene

Although Ureaplasma urealyticum is commonly found in the genital tract of asymptomatic women, it has been suggested that only certain subgroups of this microorganism are disease associated. Vaginal specimens were collected to determine the distribution of U. urealyticum biovars and to estimate their possible association with age, absence of lactobacilli, and tetracycline resistance. Of the 94 women studied, 40 (43%) carried U. urealyticum and were biotyped by polymerase chain reaction (PCR). Twenty-nine (73%) strains presented with parvo biovar, 10 (25%) with T960 biovar, and one (2.5%) with both biovars. Parvo biovar was predominant in all age groups and appears to be more frequent in women 20-25 years of age (41%), whereas T960 was common in women 30-35 years of age (22%). In this study, U. urealyticum was not associated with changes in vaginal flora, although the inverse apparently was true for Mycoplasma hominis. However, T960 biovar was more associated with the loss of lactobacilli than was parvo biovar. The number of T960 biovar strains that presented tetracycline (40%) or multiple (100%) resistance was higher than that of parvo biovar strains (27% and 69%, respectively).

Species-specific PCR for identification of common contaminant mollicutes in cell culture

Mycoplasma arginini, M. fermentans, M. hyorhinis, M. orale, and Acholeplasma laidlawii are the members of the class Mollicutes most commonly found in contaminated cell cultures. Previous studies have shown that the published PCR primer pairs designed to detect mollicutes in cell cultures are not entirely specific. The 16S rRNA gene, the 16S-23S rRNA intergenic spacer region, and the 5' end of the 23S rRNA gene, as a whole, are promising targets for design of mollicute species-specific primer pairs. We analyzed the 16S rRNA genes, the 16S-23S rRNA intergenic spacer regions, and the 5' end of the 23S rRNA genes of these mollicutes and developed PCR methods for species identification based on these regions. Using high melting temperatures, we developed a rapid-cycle PCR for detection and identification of contaminant mollicutes. Previously published, putative mollicute-specific primers amplified DNA from 73 contaminated cell lines, but the presence of mollicutes was confirmed by species-specific PCR in only 60. Sequences of the remaining 13 amplicons were identified as those of gram-positive bacterial species. Species-specific PCR primers are needed to confirm the presence of mollicutes in specimens and for identification, if required.

Simple method for determining biovar and serovar types of Ureaplasma urealyticum clinical isolates using PCR-single-strand conformation polymorphism analysis

Ureaplasma urealyticum has been associated with urethritis in men, obstetric problems in women, and respiratory distress syndrome in preterm infants. U. urealyticum can be divided into two biovars comprising 14 serovars. Partial sequences of genes encoding the multiple-banded antigens of the cell surface are known. Using a commercially available precast DNA mutation detection gel system, we have developed a simple and reproducible PCR-single-strand conformation polymorphism analysis method for differentiating the biovars of this species that reveals five patterns among the 14 serovars and enables clinical isolates to be typed directly from broth cultures.