Detection of bacterial DNA in joint samples from patients with undifferentiated arthritis and reactive arthritis, using polymerase chain reaction with universal 16S ribosomal RNA primers

Diagnosis and Treatment of Culture-Negative Periprosthetic Joint Infection

Identification of the causative organism(s) in periprosthetic joint infection (PJI) is a challenging task. The shortcomings of traditional cultures have been emphasized in recent literature, culminating in a clinical entity known as "culture-negative PJI." Amidst the growing burden of biofilm infections that are inherently difficult to culture, the field of clinical microbiology has seen a paradigm shift from culture-based to molecular-based methods. These novel techniques hold much promise in the demystification of culture-negative PJI and revolutionization of the microbiology laboratory. This article outlines the clinical implications of culture-negative PJI, common causes of this diagnostic conundrum, established strategies to improve culture yield, and newer molecular techniques to detect infectious organisms.

Changes in the Composition of the Soil Bacterial Community in Heavy Metal-Contaminated Farmland

The structural changes of microorganisms in soil are the focus of soil indicators research. The purpose of this study was to investigate the changes in the composition of the soil bacterial community in heavy metal-contaminated soil. A total of six soil samples (two sampling times) were collected from contaminated farmland at three different depths (surface, middle, and deep layer). The pH value was measured. The concentrations of heavy metals (Cr, Ni, Cu, Zn, Cd, and Pb) and the soil bacterial community were analyzed using ICP-OES and 16S rRNA gene sequencing. The results of the two samplings showed that the pH value in the deep layer decreased from 6.88 to 6.23, and the concentrations of Cu, Zn, Cd, and Pb, with a smaller ion radius, increased by 16-28%, and Shannon, Chao1 increased by ~13%. The bacteria community composition at the three depths changed, but Proteobacteria, Acidobacteria, and Actinobacteria were the dominant phyla. In the copper and zinc tolerance test, the isolated bacterium that was able to tolerate copper and zinc was Bacillus sp. We found that, the longer the heavy metal pollution was of concern, the higher the tolerance. These results can be used as references for the microbial remediation of heavy metal-contaminated farmland.

Elizabethkingia miricola bacteraemia in a haemodialysis patient

We report a case of catheter-associated Elizabethkingia miricola bacteraemia in a haemodialysis patient. The patient was a 73-year-old home haemodialysis patient who presented with a history of recurrent falls and fevers. Blood cultures grew Gram-negative bacilli identified by MALDI-TOF MS (matrix-assisted laser desorption/ionization time-of-flight mass spectrometry 6903 MSP Library) and 16S rRNA gene sequencing as E. miricola. E. miricola is an emerging human pathogen and is multidrug-resistant, making the choice of antimicrobial therapy challenging. There are only a small number of case reports of human infection worldwide and this is the second reported case of catheter-related bacteraemia. It has also been found in the hospital environment in South Korea and is pathogenic in black-spotted frogs.

Usefulness of complex bacteriological and serological analysis in patients with spondyloarthritis

Spondyloarthritis (SpA) is a group of associated chronic systemic inflammatory immune-mediated rheumatic diseases affecting axial and peripheral joints and entheses. The aim of the present study was to identify what parameters are useful to determine in order to better understand the correlation between the disease activity/severity and the microbiological results/immune status against intestinal and/or urogenital pathogens. Microorganisms known to trigger SpA, including Klebsiella spp., Yersinia spp., Salmonella spp., Campylobacter spp. and Chlamydia spp., were analyzed in various specimens (stool, urine, synovial fluid and serum) collected from 27 randomly selected SpA patients and 26 healthy controls using a combined direct and indirect approach relying on conventional culture technique and nucleic acid-based assays together with serological testing by ELISA. Although Escherichia coli derived from phylogroup A prevailed in the gut microflora of the patients and controls, differences were observed regarding the representatives of the other phylogroups with a higher prevalence of E.coli members of phylogenetic group B1 in the stool specimens of patients. Antibodies against the targeted species were detected in SpA patients and controls, and the serological profiles of the former were more diverse and complex. In conclusion, the detection of anti-bacterial antibodies combined with other specific laboratory investigations should be more extensively used to monitor SpA patients in association with their symptoms and in order to determine and administer more effective therapeutics.

Detection of Shigella spp. nucleic acids in the synovial tissue of Tunisian rheumatoid arthritis patients and other forms of arthritis by quantitative real-time polymerase chain reaction

Enterobacterial components in the joints of patients are believed to contribute to a perpetuating inflammation leading to a reactive arthritis (ReA), a condition in which microbial agents cannot be recovered from the joint. At present, it is unclear whether nucleic acids from Shigella spp. are playing a pathogenic role in causing not only ReA but also other forms of arthritis. Quantitative real-time polymerase chain reaction assay (qPCR) is the method of choice for the identification of bacteria within the synovium. The aim of our study was to detect the presence of Shigella spp. nucleic acids in the synovial tissue (ST) of Tunisian arthritis patients. We investigated 57 ST samples from rheumatoid arthritis (RA) n = 38, undifferentiated oligoarthritis (UOA) n = 12, and spondyloarthritis (SpA) n = 7 patients; 5 ST samples from healthy individuals were used as controls. Shigella spp. DNA and mRNA transcripts encoding the virulence gene A (VirA) were examined using an optimized qPCR with newly designed primers and probes. Using qPCR, Shigella spp. DNA was found in 37/57 (65%) ST samples (24/38, i.e., 63.2% of RA, 8/12, i.e., 67% of UOA, and 5/7, i.e., 71.4% of SpA patients). Paired DNA and mRNA were extracted from 39 ST samples, whose VirA cDNA was found in 29/39 (74.4%) patients. qPCR did not yield any nucleic acids in the five healthy control ST samples. The qPCR assay was sensitive and showed a good intra- and inter-run reproducibility. These preliminary findings generated by an optimized, highly sensitive PCR assay underline a potential role of past gastrointestinal infections. In Tunisian patients, a bacterial etiology involving Shigella spp. in the manifestation of arthritic disorders including RA might be more common than expected.

Antimicrobial Treatment Options for Granulomatous Mastitis Caused by Corynebacterium Species

Corynebacterium species are increasingly recognized as important pathogens in granulomatous mastitis. Currently, there are no published treatment protocols for Corynebacterium breast infections. This study describes antimicrobial treatment options in the context of other management strategies used for granulomatous mastitis. Corynebacterium spp. isolated from breast tissue and aspirate samples stored from 2002 to 2013 were identified and determined to the species level using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), 16S RNA sequencing, and rpoB gene targets. The MICs for 12 antimicrobials were performed using Etest for each isolate. Correlations of these with antimicrobial characteristics, choice of antimicrobial, and disease outcome were evaluated. Corynebacterium spp. from breast tissue and aspirate samples were confirmed in 17 isolates from 16 patients. Based on EUCAST breakpoints, Corynebacterium kroppenstedtii isolates (n = 11) were susceptible to seven antibiotic classes but resistant to β-lactam antibiotics. Corynebacterium tuberculostearicum isolates (n = 4) were multidrug resistant. Two nonlipophilic species were isolated, Corynebacterium glucuronolyticum and Corynebacterium freneyi, both of which have various susceptibilities to antimicrobial agents. Short-course antimicrobial therapy was common (median, 6 courses per subject; range, 1 to 9 courses). Patients with C. kroppenstedtii presented with a hot painful breast mass and underwent multiple surgical procedures (median, 4 procedures; range, 2 to 6 procedures). The management of Corynebacterium breast infections requires a multidisciplinary approach and includes culture and appropriate sensitivity testing to guide antimicrobial therapy. Established infections have a poor outcome, possibly because adequate concentrations of some drugs will be difficult to achieve in lipophilic granulomata. Lipophilic antimicrobial therapy may offer a therapeutic advantage. The role of immunotherapy has not been defined.

The role of microbes in the pathogenesis of acute rhinosinusitis in young adults

Objectives/Hypothesis

To provide information on the course of acute rhinosinusitis (ARS) with sequential nasal and paranasal microbiological data and their correlation with clinical outcomes.

Study Design

We conducted a prospective cohort study among 50 Finnish military recruits with clinically diagnosed ARS in spring 2012.

Methods

We collected symptom, nasal endoscopy, and cone‐beam CT (CBCT) scores during the early (2–3 days from onset) and later phases (9–10 days). We took viral samples from the nasopharynx (multiplex respiratory virus polymerase chain reaction [PCR]), bacterial culture from the middle meatus during both phases, and both viral and bacterial samples from the maxillary sinus aspirate (respiratory virus PCR, bacterial culture, broad‐range bacterial PCR) during the later phase. Cilia destruction and microbial biofilms were sought from a nasal mucosal biopsy sample.

Results

We found that 42 (84%) of the subjects had viral nucleic acid in the nasopharynx during ARS. During the early phase, 28 (56%) of the subjects had nontypeable H. influenzae (NTHi) in the middle meatus, which was associated with wider paranasal mucosal changes in CBCT scans and increased symptoms during the study period. After 9 to 10 days from the onset, NTHi was found in the maxillary sinus in eight subjects (40%, 8/20) and led to prolonged symptoms. Bacterial biofilm was ruled out in 39 (78%) cases, and cilia destruction did not correlate with microbiological or clinical outcomes.

Conclusion

Nasal and paranasal H. influenzae coinfection during viral infection may modify the symptoms and the extent of sinonasal mucosal disease observed in CBCT scans already from the beginning of the ARS episode.

Level of Evidence

N/A. Laryngoscope, 125:E1–E7, 2015

A 5-year retrospective report of Gallibacterium anatis and Pasteurella multocida isolates from chickens in Mississippi

A 5-yr retrospective study (November 2006-December 2011) was conducted to determine the isolation frequency of Pasteurella multocida and Gallibacterium anatis and their antibiograms from chickens submitted to the Mississippi Poultry Research and Diagnostic Laboratory. The number of isolations of G. anatis increased over the last 5 yr in broiler and broiler breeder type chickens. For P. multocida, the number of isolations increased from 2006 to 2010, but decreased through 2011 with all isolations being from boiler breeder type chickens. Gallibacterium anatis demonstrated almost complete resistance to novobiocin, tylosin, lincosamide, and tetracycline antimicrobials with moderate to high sensitivity to sulfonamides, fluoroquinolones, and florfenicol. There was intermediate sensitivity for spectinomycin and erythromycin and variable resistance to β-lactam and aminoglycoside antimicrobials. In sharp contrast, P. multocida showed moderate to high sensitivity to β-lactam, novobiocin, and tetracycline antimicrobials, but had antibiograms similar to G. anatis for the other antimicrobials. Sensitivities were determined using minimum inhibitory concentration. This study examines the trends over a 5-yr period of the number of isolates of P. multocida and G. anatis and their sensitivities. These 2 pathogens produce very similar clinical signs and lesions (fowl cholera-like) in breeders despite having extremely antagonistic sensitivity patterns. This study shows the necessity for producers to attempt culture and sensitivity in suspect fowl cholera-like flocks before initiating antimicrobial treatment commonly used with P. multocida for fear that the culprit may actually be the more antimicrobial-resistant G. anatis.

How to perform and analyse synovial biopsies

Although most of the rheumatologic diseases can be diagnosed based on clinical examination combined with additional laboratory and radiographic tests, histological examination of synovial tissue may lead to the correct diagnosis and adjustment of therapy when neoplastic or granulomatous disease, deposition disease or infection in spite of negative synovial fluid culture is suspected. For research purposes synovial tissue analysis is used to investigate the pathological changes of the synovium in studies aimed at elucidating the aetiology and pathogenetic mechanisms involved in arthritis. In addition, the use of synovial biomarkers has been shown to be instrumental in the developmental process of new therapeutics. In this chapter, several minimally invasive techniques for acquiring synovial tissue samples, handling of the tissue and the analysis thereof are described.

Porphyromonas gingivalis and the pathogenesis of rheumatoid arthritis: analysis of various compartments including the synovial tissue

Introduction

We evaluated the presence of Porphyromonas gingivalis (Pg) DNA in the synovial tissue through synovial biopsy and in other compartments of rheumatoid arthritis (RA) patients in comparison with patients affected by other arthritides. Possible links with clinical, immunologic and genetic features were assessed.

Methods

Peripheral blood (PB), sub-gingival dental plaque, synovial fluid (SF) and synovial tissue samples were collected from 69 patients with active knee arthritis (32 with RA and 37 with other arthritides, of which 14 had undifferentiated peripheral inflammatory arthritis - UPIA). Demographic, clinical, laboratory and immunological data were recorded. The presence of Pg DNA was evaluated through PCR. The HLA-DR haplotype was assessed for 45 patients with RA and UPIA.

Results

No differences arose in the positivity for Pg DNA in the sub-gingival plaque, PB and SF samples between RA and the cohort of other arthritides. Full PB samples showed a higher positivity for Pg DNA than plasma samples (11.8% vs. 1.5%, P = 0.04). Patients with RA showed a higher positivity for Pg DNA in the synovial tissue compared to controls (33.3% vs. 5.9%, P <0.01). UPIA and RA patients carrying the HLA DRB1*04 allele showed a higher positivity for Pg DNA in the synovial tissue compared to patients negative for the allele (57.1% vs. 16.7%, P = 0.04). RA patients positive for Pg DNA in the sub-gingival plaque had a lower disease duration and a higher peripheral blood leucocyte and neutrophil count. The presence of Pg DNA did not influence disease activity, disease disability or positivity for autoantibodies.

Conclusions

The presence of Pg DNA in the synovial tissue of RA patients suggests a pathogenic role of the bacterium. The higher positivity of Pg DNA in full peripheral blood and synovial tissue samples compared to plasma and synovial fluid suggests a possible intracellular localization of Pg, in particular in patients positive for HLA-DR4.

Prevalence and genetic characterization of second-line drug-resistant and extensively drug-resistant Mycobacterium tuberculosis in Rural China

This study aimed to investigate the prevalence of resistance to second-line antituberculosis (anti-TB) drugs and its association with resistance-related mutations in Mycobacterium tuberculosis isolated in China. In the present study, we collected 380 isolates from a population-based study in China and tested the drug susceptibility to first- and selected second-line drugs. These results were compared with polymorphisms in the DNA sequences of genes associated with drug resistance and MIC values of the studied second-line drugs. Of 43 multidrug-resistant M. tuberculosis isolates, 13 showed resistance to fluoroquinolones or injectable second-line drugs (preextensively drug-resistant TB [pre-XDR-TB]), and 4 were resistant to both and thus defined as extensively drug-resistant TB (XDR-TB). Age and previous TB therapy, including use of second-line drugs, were two independent factors associated with increased resistance to both first- and second-line drugs. Molecular analysis identified the most frequent mutations in the resistance-associated genes: D94G in gyrA (29.1%) and A1401G in rrs (30.8%). Meanwhile, all 4 XDR-TB isolates had a mutation in gyrA, and 3 of them carried the A1401G mutation in rrs. Mutations in gyrA and rrs were associated with high-level resistance to fluoroquinolones and the second-line injectable drugs. In addition to the identification of resistance-associated mutations and development of a rapid molecular test to diagnose the second-line drug resistance, it should be a priority to strictly regulate the administration of second-line drugs to maintain their efficacy to treat multidrug-resistant TB.

Bacterial agents in spondyloarthritis: a destiny from diversity?

The spondyloarthritides (SpAs) are a group of diseases that share clinical, radiographic and laboratory features; these arthritides also display a tendency for family aggregation. Given the intimate relationship that these types of arthritis share, it suggests that the SpAs might share a common aetiology. Of all the SpAs, the role of bacteria is most clearly defined in reactive arthritis. Tremendous recent insights into the pathophysiology of reactive arthritis have been made, demonstrating that the causative bacteria play a much more complex role than previously thought. The bacteria that are proven to cause reactive arthritis, one of the five types of SpA, will be reviewed and their role in the pathophysiology of reactive arthritis will be examined. The speculative data suggesting links between various other bacteria and the other types of SpAs will be critically analysed. Although these data are not definitive, when viewed using the paradigm that the SpAs might actually represent a common end point from several diverse starting points, they are provocative, suggesting that bacteria might, indeed, be aetiological for the entire group of SpAs.

Rheumatoid arthritis and the role of oral bacteria

Rheumatoid arthritis (RA) and periodontal disease (PD) have shown similar physiopathologic mechanisms such as chronic inflammation with adjacent bone resorption in an immunogenetically susceptible host; however, PD has a well-recognized bacterial etiology while the cause of RA is unclear. Some reports have indicated that an infectious agent in a susceptible host could be one possible trigger factor for RA, and it has been suggested that oral microorganisms, specialty periodontal bacteria could be the infectious agent (mainly Porphyromonas gingivalis). It has been reported that PD is more frequent and more severe in patients with RA, suggesting a positive association between both diseases. There have been reports regarding the detection of antibodies against periodontal bacteria while other studies have identified periodontal bacterial DNA in serum and synovial fluid of RA patients and have explored the possible pathways of transport of periodontal bacterial DNA. In conclusion, there is no question that RA and PD have pathologic features in common and there is strong evidence of an association between both diseases, but further studies, including experimental models, are needed to demonstrate the arthritogenicity of oral microorganisms.

Multinational evidence-based recommendations on how to investigate and follow-up undifferentiated peripheral inflammatory arthritis: integrating systematic literature research and expert opinion of a broad international panel of rheumatologists in the 3E Initiative

Objective

To develop evidence-based recommendations on how to investigate and follow-up undifferentiated peripheral inflammatory arthritis (UPIA).

Methods

697 rheumatologists from 17 countries participated in the 3E (Evidence, Expertise, Exchange) Initiative of 2008–9 consisting of three separate rounds of discussions and modified Delphi votes. In the first round 10 clinical questions were selected. A bibliographic team systematically searched Medline, Embase, the Cochrane Library and ACR/EULAR 2007–2008 meeting abstracts. Relevant articles were reviewed for quality assessment, data extraction and synthesis. In the second round each country elaborated a set of national recommendations. Finally, multinational recommendations were formulated and agreement among the participants and the potential impact on their clinical practice was assessed.

Results

A total of 39 756 references were identified, of which 250 were systematically reviewed. Ten multinational key recommendations about the investigation and follow-up of UPIA were formulated. One recommendation addressed differential diagnosis and investigations prior to establishing the operational diagnosis of UPIA, seven recommendations related to the diagnostic and prognostic value of clinical and laboratory assessments in established UPIA (history and physical examination, acute phase reactants, autoantibodies, radiographs, MRI and ultrasound, genetic markers and synovial biopsy), one recommendation highlighted predictors of persistence (chronicity) and the final recommendation addressed monitoring of clinical disease activity in UPIA.

Conclusions

Ten recommendations on how to investigate and follow-up UPIA in the clinical setting were developed. They are evidence-based and supported by a large panel of rheumatologists, thus enhancing their validity and practical use.

Is the role of Chlamydia trachomatis underestimated in patients with suspected reactive arthritis?

Reactive arthritis is usually caused by bacteria of either the enteric or genital tracts. In the genital tract, Chlamydia trachomatis is perhaps the only aetiological agent. In Iran, newer evidence suggests that as C. trachomatis is more commonly found in the general population than was previously believed, its role in reactive arthritis may well be currently overlooked. In this review, as well as emphasizing the potential role of C. trachomatis in reactive arthritis in patients from developing countries, we also make recommendations for further clinical studies to determine its prevalence. Moreover, we also stress the need for standardization of new testing methodologies for C. trachomatis, including the use of new commercial systems in an attempt to determine a truer picture of chlamydial infection in reactive arthritis.

Corynebacterium accolens-associated pelvic osteomyelitis

Corynebacterium accolens is a rare human pathogen. We encountered a case of C. accolens isolated from a thigh collection in a man with osteomyelitis of the adjacent pubic symphysis.

Direct detection of pathogens in osteoarticular infections by polymerase chain reaction amplification and microarray hybridization

BACKGROUND

Molecular biological techniques such as the polymerase chain reaction (PCR) and DNA microarray are used for the detection/identification of microorganisms; however, few reports have discussed the clinical utility of microarray analysis for identification of causative organisms of osteoarticular infections. It is important to examine the utility of PCR amplification followed by analysis of DNA microarray carrying specific oligonucleotides.

METHODS

This study included 101 biological samples obtained from 96 patients who underwent conservative and/or surgical treatment for osteoarticular infections. In this double-blind comparative study, routine conventional testing and the research groups were unaware of each other's interpretation until identical specimens were identified by culture and microarray analysis.

RESULTS

Results of PCR microarray analysis were positive for 25 samples and negative for the remaining 76 samples within 24 h, and the results of the cultures (available after a mean of 3.54 days) were positive in 26 samples and negative for the remaining 75 samples. The sensitivity of microarray analysis was 84.6% (22/26) and specificity was 88.0% (22/25). Discrepant results were identified in seven samples, including a negative culture and a positive microarray in three cases and a positive culture and a negative microarray in four other cases.

CONCLUSIONS

The PCR microarray analysis is complementary to routine cultures in identifying causative microorganisms and should be used in patients with highly suspected infections and negative bacterial culture and in patients who require prompt diagnosis and early initiation of antibiotic therapy.

[Applications of molecular pathology in the diagnosis of joint infections]

The diagnosis of infections in patients with arthritis and/or joint prostheses requires interdisciplinary cooperation and the use of up-to-date methods. Massive bacterial infection can be identified by bacterial culture, and minimal infection can be detected by molecular pathological methods. These processes include specific enrichment of bacterial and fungal DNA, amplification, and identification of the DNA by gel electrophoresis, sequencing techniques, and chip technologies.Anamnesis (enteral or urogenital infection), the clinical picture (oligoarthritis), and further parameters (e.g., HLA B27 status) are important for the diagnosis of reactive arthritis. In many cases of reactive arthritis, molecular methods allow detection of bacterial DNA or RNA in synovial fluid or tissue. Molecular pathological methods allow the fast and reliable differential diagnosis of granulomatous synovialitis without prior cultivation of bacteria or fungi. The development of new molecular pathological methods for detecting bacterial and fungal nucleic acids will increase diagnostic accuracy.

Seasonal variation in detection of bacterial DNA in arthritic stifle joints of dogs with cranial cruciate ligament rupture using PCR amplification of the 16S rRNA gene

An underappreciated cause and effect relationship between environmental bacteria and arthritis may exist. Previously, we found that stifle arthritis in dogs was associated with the presence of environmental bacteria within synovium. Cranial cruciate ligament rupture (CCLR) is often associated with stifle arthritis in dogs. We now wished to determine whether seasonal variation in detection of bacterial material may exist in affected dogs, and to also conduct analyses of both synovium and synovial fluid. We also wished to analyze a larger clone library of the 16S rRNA gene to further understanding of the microbial population in the canine stifle. Synovial biopsies were obtained from 117 affected dogs from January to December 2006. Using PCR, synovium and synovial fluid were tested for Borrelia burgdorferi and Stenotrophomonas maltophilia DNA. Broad-ranging 16S rRNA primers were also used and PCR products were cloned and sequenced for bacterial identification. Overall, 41% of arthritic canine stifle joints contained bacterial DNA. Detection of bacterial DNA in synovial fluid samples was increased, when compared with synovium (p<0.01). Detection rates were highest in the winter and spring and lowest in the summer period, suggesting environmental factors influence the risk of translocation to the stifle. Organisms detected were predominately Gram's negative Proteobacteria, particularly the orders Rhizobiales (32.8% of clones) and Burkholderiales (20.0% of clones), usually as part of a polymicrobial population. PCR-positivity was inversely correlated with severity of arthritis assessed radiographically and with dog age. Bacterial translocation to the canine stifle may be associated with changes to the indoor environment.

Rapid identification of bacterial pathogens using a PCR- and microarray-based assay

Background

During the course of a bacterial infection, the rapid identification of the causative agent(s) is necessary for the determination of effective treatment options. We have developed a method based on a modified broad-range PCR and an oligonucleotide microarray for the simultaneous detection and identification of 12 bacterial pathogens at the species level. The broad-range PCR primer mixture was designed using conserved regions of the bacterial topoisomerase genes gyrB and parE. The primer design allowed the use of a novel DNA amplification method, which produced labeled, single-stranded DNA suitable for microarray hybridization. The probes on the microarray were designed from the alignments of species- or genus-specific variable regions of the gyrB and parE genes flanked by the primers. We included mecA-specific primers and probes in the same assay to indicate the presence of methicillin resistance in the bacterial species. The feasibility of this assay in routine diagnostic testing was evaluated using 146 blood culture positive and 40 blood culture negative samples.

Results

Comparison of our results with those of a conventional culture-based method revealed a sensitivity of 96% (initial sensitivity of 82%) and specificity of 98%. Furthermore, only one cross-reaction was observed upon investigating 102 culture isolates from 70 untargeted bacteria. The total assay time was only three hours, including the time required for the DNA extraction, PCR and microarray steps in sequence.

Conclusion

The assay rapidly provides reliable data, which can guide optimal antimicrobial treatment decisions in a timely manner.

Functional TLR9 modulates bone marrow B cells from rheumatoid arthritis patients

TLR9 recognizes unmethylated CpG-rich, pathogen-derived DNA sequences and represents the component of the innate immune system that heavily influences adaptive immunity and may contribute to the immunological disturbances in rheumatoid arthritis (RA). Accumulating data indicate that BM of RA patients participates in the pathogenesis of this disease as a site of proinflammatory cytokines overproduction and lymphocytes activation. Here, we investigated the functionality of TLR9 and its role in the modulation of RA BM B-cell functions. We report that BM B cells isolated from RA patients express TLR9 at the mRNA and protein levels acquired at the stage of preB/immature B-cell maturation. Stimulation of BM CD20(+) B cells by CpG-containing oligodeoxynucleotide-enhanced expression of activation markers (CD86 and CD54) triggered IL-6 and TNF-alpha secretion and cell proliferation. Significantly higher levels of eubacterial DNA encoding 16S-rRNA were found in BM samples from RA than osteoarthritis patients. Moreover, RA BM B cells exerted higher expression of CD86 than their osteoarthritis counterparts, suggesting their in situ activation via TLR9. Thus, our data indicate that TLR9 may participate in direct activation and proliferation of B cells in BM, and therefore could play a role in the pathogenesis of RA.

Broad-range PCR, cloning and sequencing of the full 16S rRNA gene for detection of bacterial DNA in synovial fluid samples of Tunisian patients with reactive and undifferentiated arthritis

Introduction

Broad-range rDNA PCR provides an alternative, cultivation-independent approach for identifying bacterial DNA in reactive and other form of arthritis. The aim of this study was to use broad-range rDNA PCR targeting the 16S rRNA gene in patients with reactive and other forms of arthritis and to screen for the presence of DNA from any given bacterial species in synovial fluid (SF) samples.

Methods

We examined the SF samples from a total of 27 patients consisting of patients with reactive arthritis (ReA) (n = 5), undifferentiated arthritis (UA) (n = 9), rheumatoid arthritis (n = 7), and osteoarthritis (n = 6) of which the latter two were used as controls. Using broad-range bacterial PCR amplifying a 1400 bp fragment from the 16S rRNA gene, we identified and sequenced at least 24 clones from each SF sample. To identify the corresponding bacteria, DNA sequences were compared to the EMBL (European Molecular Biology Laboratory) database.

Results

Bacterial DNA was identified in 20 of the 27 SF samples (74, 10%). Analysis of a large number of sequences revealed the presence of DNA from more than one single bacterial species in the SF of all patients studied. The nearly complete sequences of the 1400 bp were obtained for most of the detected species. DNA of bacterial species including Shigella species, Escherichia species, and other coli-form bacteria as well as opportunistic pathogens such as Stenotrophomonas maltophilia and Achromobacter xylosoxidans were shared in all arthritis patients. Among pathogens described to trigger ReA, DNA from Shigella sonnei was found in ReA and UA patients. We also detected DNA from rarely occurring human pathogens such as Aranicola species and Pantoea ananatis. We also found DNA from bacteria so far not described in human infections such as Bacillus niacini, Paenibacillus humicus, Diaphorobacter species and uncultured bacterium genera incertae sedis OP10.

Conclusions

Broad-range PCR followed by cloning and sequencing the entire 16S rDNA, allowed the identification of the bacterial DNA environment in the SF samples of arthritic patients. We found a wide spectrum of bacteria including those known to be involved in ReA and others not previously associated with arthritis.

Optimization of bacterial diagnosis yield after needle aspiration in immunocompetent adults with brain abscesses

OBJECTIVE

Brain abscesses (BA) are life threatening, even in immunocompetent patients, in part because microbiological diagnosis is often lacking and management is empirical. Recent epidemiological changes make it all the more important to have a precise microbiological diagnosis. Our purpose was to evaluate the efficacy of a strategy aimed at obtaining a microbiological diagnosis in immunocompetent patients presenting with suspected BAs.

METHODS

We conducted a cohort study including all consecutive patients suspected of having BAs according to clinical, biological, and radiological findings. Severely immunocompromised patients were excluded. Aspiration was performed free-hand in patients with superficial abscesses (<1 cm depth from the cortical surface) and under stereotactic guidance in patients with deep-seated abscesses. Microbiological diagnosis was optimized, using the best aerobic and anaerobic growth conditions, blood culture bottles inoculated in the operating room, and molecular biology techniques if necessary. Antibiotic treatment was adapted according to the findings.

RESULTS

Twenty-six patients were suspected of having BAs during the study period. Twenty-four patients benefited from aspiration (stereotactic puncture in 3 cases), which was safe, confirmed the diagnosis of BAs, and yielded microbiological diagnosis in all cases, even in those patients who had previously received antibiotics (n = 8; 33%). In 10 patients (42%), microbiological results led to a different choice in antibiotic therapy than the recommended empirical regimen.

CONCLUSION

Microbiological diagnosis can be obtained in all cases of BA. This is achieved by the conjunction of rapid needle aspiration and the optimization of microbiological diagnosis resulting from fast management of the surgical specimen, good anaerobic culture conditions, and the use of blood culture bottles and molecular biology techniques when appropriate. Moreover, it is of clinical and therapeutic interest when BAs are suspected in immunocompetent patients.

Leptospira wolffii sp. nov., isolated from a human with suspected leptospirosis in Thailand

A single Leptospira strain (designated Khorat-H2(T)) was isolated from the urine of an adult male patient with suspected leptospirosis from the province of Nakornrachasima, Thailand. The isolate showed typical Leptospira motility and morphology under dark-field microscopy. Cells were 10-13 mum long and 0.2 mum in diameter, with a wavelength of 0.5 mum and an amplitude of approximately 0.3 mum. Phenotypically, strain Khorat-H2(T) did not grow at 13 degrees C but grew at 30 and 37 degrees C and in the presence of 8-azaguanine. Serological identification using the microscopic agglutination test revealed that strain Khorat-H2(T) had no cross-reaction with any recognized Leptospira serogroups. Phylogenetic analysis of the 16S rRNA gene sequence placed the novel strain within the radiation of the genus Leptospira, with sequence similarities of 88.1-97.7 % to recognized Leptospira species. DNA-DNA hybridization against the type strains of the three most closely related Leptospira species was used to confirm the results of the 16S rRNA sequence analysis. The G+C content of strain Khorat-H2(T) was 41.8 mol%. On the basis of phenotypic, serological and phylogenetic data, strain Khorat-H2(T) represents a novel species of the genus Leptospira, for which the name Leptospira wolffii sp. nov. is proposed. The type strain is Khorat-H2(T) (=WHO LT1686(T) =KIT Khorat-H2(T)).

Analysis of bacterial DNA in synovial tissue of Tunisian patients with reactive and undifferentiated arthritis by broad-range PCR, cloning and sequencing

Introduction

Bacteria and/or their antigens have been implicated in the pathogenesis of reactive arthritis (ReA). Several studies have reported the presence of bacterial antigens and nucleic acids of bacteria other than those specified by diagnostic criteria for ReA in joint specimens from patients with ReA and various arthritides. The present study was conducted to detect any bacterial DNA and identify bacterial species that are present in the synovial tissue of Tunisian patients with reactive arthritis and undifferentiated arthritis (UA) using PCR, cloning and sequencing.

Methods

We examined synovial tissue samples from 28 patients: six patients with ReA and nine with UA, and a control group consisting of seven patients with rheumatoid arthritis and six with osteoarthritis (OA). Using broad-range bacterial PCR producing a 1,400-base-pair fragment from the 16S rRNA gene, at least 24 clones were sequenced for each synovial tissue sample. To identify the corresponding bacteria, DNA sequences were compared with sequences from the EMBL (European Molecular Biology Laboratory) database.

Results

Bacterial DNA was detected in 75% of the 28 synovial tissue samples. DNA from 68 various bacterial species were found in ReA and UA samples, whereas DNA from 12 bacteria were detected in control group samples. Most of the bacterial DNAs detected were from skin or intestinal bacteria. DNA from bacteria known to trigger ReA, such as Shigella flexneri and Shigella sonnei, were detected in ReA and UA samples of synovial tissue and not in control samples. DNA from various bacterial species detected in this study have not previously been found in synovial samples.

Conclusion

This study is the first to use broad-range PCR targeting the full 16S rRNA gene for detection of bacterial DNA in synovial tissue. We detected DNA from a wide spectrum of bacterial species, including those known to be involved in ReA and others not previously associated with ReA or related arthritis. The pathogenic significance of some of these intrasynovial bacterial DNAs remains unclear.

Rapid PCR-based diagnosis of septic arthritis by early Gram-type classification and pathogen identification

Septic arthritis (SA) is a rheumatologic emergency associated with significant morbidity and mortality. Delayed or inadequate treatment of SA can lead to irreversible joint destruction and disability. Current methods of diagnosing SA rely on synovial fluid analysis and culture which are known to be imprecise and time-consuming. We report a novel adaptation of a probe-based real-time PCR assay targeting the 16S rRNA gene for early and accurate diagnosis of bacterial SA. The assay algorithm consists of initial broad-range eubacterial detection, followed by Gram typing and species characterization of the pathogen. The platform demonstrated a high analytical sensitivity with a limit of detection of 10(1) CFU/ml with a panel of SA-related organisms. Gram typing and pathogen-specific probes correctly identified their respective targets in a mock test panel of 36 common clinically relevant pathogens. One hundred twenty-one clinical synovial fluid samples from patients presenting with suspected acute SA were tested. The sensitivity and specificity of the assay were 95% and 97%, respectively, versus synovial fluid culture results. Gram-typing probes correctly identified 100% of eubacterial positive samples as to gram-positive or gram-negative status, and pathogen-specific probes correctly identified the etiologic agent in 16/20 eubacterial positive samples. The total assay time from sample collection to result is 3 h. We have demonstrated that a real-time broad-based PCR assay has high analytical and clinical performance with an improved time to detection versus culture for SA. This assay may be a useful diagnostic adjunct for clinicians, particularly those practicing in the acute care setting where rapid pathogen detection and identification would assist in disposition and treatment decisions.

Detection of parvovirus B19 in synovial fluids of patients with osteoarthritis

We aimed to determine the possible role of parvovirus B19 (PVB19) in the etiology of osteoarthritis. PVB19 DNA, anti-VP1 IgM and IgG, and interleukin IL-6 levels were also assayed in synovial fluids of 42 patients with osteoarthritis and 10 controls. PVB19 DNA was detected in 28 of 42 (66.66%) in patients and in 3 of 10 (30%) in controls. IgG and IgM response were detected in 21 of 42 (50.00%) and in 2 of 42 (4.76%) patients, respectively. IL-6 were positive in 15 of 42 (36%) patients and in 3 of 10 (30%) controls. All IgG (+) samples had PVB19 DNA (100%, P < 0.001). Eleven of 15 IL-6 (+) samples had PVB19 DNA (+) (73.33%, P < 0.05). Moreover, all IL-6 (+) samples (n = 5) in stage IV had PVB19 DNA (+) (100%, P < 0.001). We have detected a significant association between the stages of osteoarthritis and PVB19 DNA (P < 0.05). These findings support the presence of PVB19 acting as a transactivator of IL-6 expression as reported earlier. Our results also suggest that the higher stages of osteoarthritis might be related to the increased inflammation and cell damage on joint cartilage due to PVB19.

Evaluation of a modified Taqman assay detecting pathogenic Leptospira spp. against culture and Leptospira-specific IgM enzyme-linked immunosorbent assay in a clinical environment

A Taqman assay for the detection of pathogenic Leptospira was modified to suit the LightCycler instrument. The modified assay was found to have an analytical sensitivity of 10 copies/reaction. The assay was then compared to the current gold standard for acute phase detection, culture, and to a commercially available Leptospira-specific IgM enzyme-linked immunosorbent assay (ELISA). Of the 236 samples including serum and ethylenediaminetetraacetic acid anticoagulated blood sample submitted for testing, polymerase chain reaction (PCR) was able to detect Leptospira DNA in 27 of the 28 culture positives and in 1 negative culture. Discrepant results were resolved by using the microscopic agglutination test on convalescent sera. The PCR was found to have a clinical specificity and sensitivity of 99.5% and 96.4%, respectively, when compared to the culture. Comparisons between culture and ELISA showed that the ELISA lack sensitivity (4.2%) and positive predictability (3.6%) for the detection of acute phase Leptospira infections. These results show that the modified LightCycler Taqman assay could be used as a replacement of culture for the detection of pathogenic Leptospira in a clinical setting.

Detection of DNA from a range of bacterial species in the knee joints of dogs with inflammatory knee arthritis and associated degenerative anterior cruciate ligament rupture

Mixtures of bacterial nucleic acids can often be detected in synovial joints affected with arthritis. We investigated the potential role of such mixtures of bacterial nucleic acids in the pathogenesis of arthritis in a naturally occurring canine model. Dogs with a common inflammatory knee arthritis in which associated pathological degenerative anterior cruciate ligament (ACL) rupture often develops were studied. Synovial biopsies were obtained from 43 dogs with the naturally occurring ACL rupture arthropathy, 12 dogs with normal knees and intact ACL, and 16 dogs with normal knees and experimentally induced ACL rupture. Using PCR, specimens were tested for Borrelia burgdorferi OspA and p66 gene sequences. Broad-ranging 16S rRNA primers were also used; 'panbacterial' PCR products were cloned and multiple clones were sequenced for bacterial identification. Synovium was also studied histologically. The presence of bacterial DNA within the synovium was significantly associated with the naturally occurring ACL rupture arthropathy (p<0.05); knee joints from 37% of these dogs were PCR-positive. Mixtures of bacterial DNA were common and often included environmental bacteria; predominant organisms included Borrelia burgdorferi and Stenotrophomonas maltophilia. DNA from environmental bacteria was only found in dogs with the naturally occurring ACL rupture arthopathy; joints from 33% of affected dogs contained such bacterial DNA. Synovial inflammation developed in dogs with both naturally occurring and experimentally induced ACL rupture, when compared with intact ACL controls (p<0.01). These results indicate that mixtures of DNA derived from environmental bacteria are commonly found in the knee joint of a naturally occurring canine arthropathy, often in association with a recognized joint pathogen. Our results also suggest that knee instability alone is not responsible for this finding and have led us to hypothesize that mixtures of bacterial DNA are an important causative factor in the pathogenesis of inflammatory arthritis in this canine model.

Broad range 16S rRNA gene PCR compared to bacterial culture to confirm presumed synovial infection in horses

The objectives of the present study were to evaluate the accuracy of broad range 16S rRNA gene PCR compared to bacterial culture for the detection of synovial infection in horses. The study included 57 synovial fluid samples from horses with presumed synovial infection and a control group consisting of 31 synovial fluid samples originating from clinically normal horses and horses with aseptic synovial inflammation. All samples were analysed by 16S PCR with reverse line blot (RLB) hybridisation. Synovial fluid samples were cultured using conventional agar plate methods (APM) and/or blood culture medium (BCM). The results of the study showed a superior detection rate (89.5%) for 16S PCR with RLB. Bacterial culture had lower sensitivity, but highly acceptable detection rates (77.6%) were observed using BCM. APM had very low sensitivity (37.8%) and infection was never detected by plate isolation without positive incubation in BCM. The highest sensitivity (91.8%) for the detection of synovial infection was achieved when the results of incubation in BCM and 16S PCR were combined. For all the tests, the specificity was higher than 90%.

Clinical Applications of the Polymerase Chain Reaction: An Update

The development, in the past decade, of nucleic acid amplification and detection methods is useful in the study of the etiopathogenesis, diagnosis, and management of a variety of clinical (including rheumatologic) disorders. An association between infectious agents and rheumatic disorders has been established through such methods as polymerase chain reaction. This article describes the principles behind polymerase chain reaction-based diagnosis and updates its clinical applications. It is beyond the scope of this article, however, to describe other nucleic acid amplification methods or to include a complete list of all polymerase chain reaction assays that have been developed. Other recent reviews offer additional details.

Identification of pathogenic Leptospira species by conventional or real-time PCR and sequencing of the DNA gyrase subunit B encoding gene

Background

Leptospira is the causative genus of the disease, leptospirosis. Species identification of pathogenic Leptospira in the past was generally performed by either DNA-DNA hybridisation or 16s rRNA gene sequencing. Both methods have inherent disadvantages such as the need for radio-labelled isotopes or significant homology between species. A conventional and real-time PCR amplification and sequencing method was developed for an alternate gene target: DNA gyrase subunit B (gyrB). Phylogenetic comparisons were undertaken between pathogenic Leptospira 16srRNA and gyrB genes using clustering and minimum evolution analysis. In addition 50 unidentified Leptospira isolates were characterised by gyrB sequencing and compared with conventional 16s rRNA sequencing.

Results

A conventional and real-time PCR methodology was developed and optimised for the amplification of the gyrB from pathogenic Leptospira species. Non pathogenic and opportunistic Leptospira species such as L. fainei and L. broomi were not amplified. The gyrB gene shows greater nucleotide divergence (3.5% to 16.1%) than the 16s rRNA gene (0.1% to 1.4%). Minimum evolution analysis reveals that the gyrB has a different evolution topology for L. kirschneri and L. interrogans. When the two genes were compared for the identification of the 50 unknown isolates there was 100% agreement in the results.

Conclusion

This research has successfully developed a methodology for the identification of pathogenic Leptospira using an alternate gene to 16s rRNA. The gyrB encoding gene shows higher nucleotide/evolutionary divergence allowing for superior identification and also the potential for the development of DNA probe based identification.

Fatal myocardial necrosis caused by Staphylococcus lugdunensis and cytomegalovirus in a patient with scleroderma

A 42-year-old woman developed a rapidly progressing fatal heart failure. At the autopsy extensive necrosis of the myocardium was seen, with an almost complete absence of inflammatory cells and the presence of bacterial structures identified as Staphylococcus lugdunensis by PCR. In addition, the cytomegalovirus genome was found to be located inside the cardiomyocytes.

A high prevalence of parvovirus B19 DNA in patients with psoriasis

Psoriasis is a common inflammatory skin disease. Infectious models are considered to be of pathophysiological importance in psoriasis. The immunological profile of stable psoriasis plaques suggests that viral antigens may be important. Human parvovirus B19 (PVB19) is a single-stranded DNA virus that causes various clinical symptoms. Several case reports have suggested associations between PVB19 infection and various chronic autoimmune and dermatologic diseases. There has so far been no information regarding the role of PVB19 in psoriasis, except psoriatic arthritis. In this report, to investigate the role of PVB19 in psoriasis, we analyzed PVB19 DNA of peripheral blood from psoriatic patients (n = 47) in comparison with blood donors (n = 20). We also determined the presence of anti-PVB19 IgG and IgM antibodies by using enzyme-linked immunosorbent assay (ELISA). We found that the presence of PVB19 DNA in patients with psoriasis (38%) was significantly higher than in controls (0%, P < 0.01). Anti-PVB19 IgG antibodies were detected in 79% of the cases while only 6% had anti-PVB19 IgM antibodies. PVB19 DNA presence was associated with seropositivity for anti-PVB19 IgG (P < 0.05) but not with IgM antibodies, indicating subclinical activation of latent infection. No correlation was found between the presence of PVB19 DNA and a patient's age, sex, type of psoriasis, or psoriasis area and severity index. The data demonstrated a statistically significant association between psoriasis and PVB19. Therefore, we suggest that PVB19 infection may be of pathophysiological importance in psoriasis.

Characterization of the chromosomal class A β-lactamase CKO fromCitrobacter koseri

The gene bla(CKO) encoding the chromosomal class A beta-lactamase of Citrobacter koseri was cloned and sequenced. CKO was found to display only 41% identity with SED-1 from Citrobacter sedlakii and 36% with CdiA from Citrobacter amalonaticus (formerly Citrobacter diversus). No transcriptional regulator was found upstream from bla(CKO). Silent and missense mutations were detected in four bla(CKO) genes amplified from different C. koseri clinical isolates, but the CKO variants displayed identical biochemical behaviours. A bla(CKO)-specific polymerase chain reaction confirmed that bla(CKO) is present only in C. koseri and therefore represents an interesting tool with which to differentiate C. koseri from the other Citrobacter spp.

Synovial biopsy

In patients with arthritis, synovial tissue is easily accessible for analysis. Blind needle biopsy is a simple and safe procedure. Arthroscopic biopsy is also safe, it allows access to most sites in the joint and it can provide adequate tissue for extensive laboratory investigations, both before and after successful therapy. Synovial tissue analysis has been successfully applied to the study of disease mechanisms and response to treatment. In addition, there may be an indication for diagnostic synovial biopsy in selected cases.

Recurrent breast abscess caused by Gordonia bronchialis in an immunocompetent patient

We present the first reported case of a recurrent breast infection caused by Gordonia bronchialis. The infection occurred in a 43-year-old immunocompetent female, and species level identification was obtained with 16S rRNA sequencing.

Demonstration by PCR and DNA sequencing of Corynebacterium pseudodiphtheriticum as a cause of joint infection and isolation of the same organism from a surface swab specimen from the patient

A case of infectious arthritis following arthroscopy is described. Real-time PCR, using universal bacterial primers targeting the 16S rRNA gene, and subsequent DNA sequencing of the PCR product demonstrated the presence of DNA from Corynebacterium pseudodiphtheriticum in the synovial fluid from the affected knee. Culture from a surface swab from the site of purulent discharge from the knee was initially reported as growing normal skin microbiota. Knowing the result of the DNA analysis, the specimen was re-examined and a diphtheroid bacterium was isolated. The DNA sequence of the isolated bacterium was identical to that of the DNA in the joint. The isolated bacterium was tested for susceptibility to relevant antibiotics. Demonstration and identification of bacterial DNA by PCR and gene sequencing may not by itself give information on important characteristics such as susceptibility to antibiotics of the infecting bacterium. The present case illustrates that the results obtained by the method can be used to isolate the relevant bacterium in culture from other sites and thereby characterize it. It furthermore demonstrates that C. pseudodiphtheriticum can cause severe arthritis when inoculated into joints.

Detection and identification of Mycobacterium tuberculosis in joint biopsy specimens by rpoB PCR cloning and sequencing

Osteoarticular tuberculosis (OAT) is an extrapulmonary tuberculosis and accounts for 1 to 3% of all tuberculosis cases. We used an rpoB PCR-plasmid TA cloning-sequencing method to detect and identify tubercle bacilli in surgical specimens from patients suspected of having OAT. By comparing the similarities of the rpoB sequences determined with those in GenBank, Mycobacterium tuberculosis was detected in 23 of 43 samples. Three of the 23 positive samples had mutations at codon 531, which are commonly observed in rifampin-resistant M. tuberculosis strains. Our results suggest that the rpoB PCR-TA cloning-sequencing method developed, which detects M. tuberculosis and which simultaneously determines its rifampin susceptibility, can also be used efficiently for the diagnosis of OAT.

Decreased pain and synovial inflammation after etanercept therapy in patients with reactive and undifferentiated arthritis: An open-label trial

OBJECTIVE

Elevated levels of tumor necrosis factor alpha (TNFalpha) have been identified in the synovium of patients with reactive and undifferentiated arthritis, implicating TNFalpha in the pathogenesis of these disorders. This finding has provided a rationale for the use of TNFalpha antagonists in the treatment of reactive arthritis; however, the possibility that the triggering microorganism might persist in affected joints and become activated with use of these agents has been of concern.

METHODS

The efficacy and safety of etanercept (25 mg subcutaneous twice weekly) in 16 patients with undifferentiated or reactive arthritis was assessed in a 6-month open-label trial. Synovial biopsies were performed before and after treatment with etanercept. Polymerase chain reaction (PCR) analysis was performed on the synovial biopsy samples to evaluate for the presence of nucleic acid material of bacterial organisms. Outcome measures including tender and swollen joint counts, pain assessment on a 10-point visual analog scale, and functional ability as measured by the Health Assessment Questionnaire were determined before and after etanercept therapy.

RESULTS

Ten of 16 patients completed the trial. Six patients withdrew, but none had a worsening of arthritis or infection. Of the 10 completers, 9 could be classified as treatment responders, despite the evidence of bacterial organisms on PCR analysis prior to initiating etanercept in 3 patients; 2 patients became PCR negative on etanercept. Five of 6 patients with adequate synovial biopsy specimens showed improvement, but not normalization of histology.

CONCLUSION

Etanercept was well-tolerated without clinical exacerbation of any suspected underlying infections and appeared to provide therapeutic benefit in our cohort of patients with reactive and undifferentiated arthritis.

Use of an oligonucleotide array for laboratory diagnosis of bacteria responsible for acute upper respiratory infections

We developed a diagnostic array of oligonucleotide probes targeting species-specific variable regions of the genes encoding topoisomerases GyrB and ParE of respiratory bacterial pathogens. Suitable broad-range primer sequences were designed based on alignment of gyrB/parE sequences from nine different bacterial species. These species included Corynebacterium diphtheriae, Fusobacterium necrophorum, Haemophilus influenzae, Legionella pneumophila, Moraxella catarrhalis, Mycoplasma pneumoniae, Staphylococcus aureus, Streptococcus pneumoniae, and Streptococcus pyogenes. Specific probe sequences were selected by comparative analysis against the European Bioinformatics Database, as well as gyrB/parE sequences generated for this study. To verify specificity, at least six initial oligonucleotide probe sequences per bacterial species were tested by hybridization on a solid glass support using culture collection strains as templates. Finally, three oligonucleotide probes per bacterial species were utilized to examine 65 middle ear fluid and 29 throat swab samples. The sensitivities of the developed assay compared to classic culture from middle ear fluid samples for H. influenzae, M. catarrhalis, and S. pneumoniae were 96 (93 for culture), 73 (93 for culture), and 100% (78% for culture), respectively. No cross-reactivity with bacterial species belonging to the normal oral flora was observed when the 29 throat swab samples were studied. The sensitivity of the assay to detect S. pyogenes from these samples was 93% (80% for culture). These results provide a proof of concept for the diagnostic use of microarray technology based on broad-range topoisomerase gene amplification, followed by hybridization and specific detection of bacterial species.

Detection of bacterial DNA in synovial fluid from horses with infectious synovitis

Standard culturing techniques are often unrewarding in confirming diagnosis of synovial infection in the equine patient. Several human studies report the use of sensitive polymerase chain reaction (PCR) techniques for the detection of bacterial involvement in acute synovitis. However, successful extraction of bacterial DNA directly from clinical samples from horses without prior culture has not been reported yet. The goal of this study was to develop a sensitive and reliable method for molecular detection and identification of bacterial species in synovial fluid from horses with infectious synovitis. Synovial fluid samples from 6 horses with culture confirmed synovial infection were used for broad range 16S rRNA gene PCR. Synovial aspirates of 2 healthy horses were used as negative controls. Following extraction and purification of synovial fluid DNA, all samples were processed by touchdown PCR. Amplicons were detected by reverse line blot hybridisation and visualised with chemiluminescence. Pathogen-specific detection of 16S rRNA gene sequences was successful in all 6 synovial fluid samples. No bacterial DNA was detected in the aspirates from the negative control horses using touchdown PCR followed by 25 additional cycles of amplification. The identity of the pathogens was confirmed by DNA sequencing of the amplicons. It can be concluded that broad range 16S rRNA gene PCR followed by reverse line blot hybridisation is a promising technique for detection of bacterial DNA in synovial fluid samples. Further research should aim at the detection of bacterial DNA in synovial fluid samples suspected of infection but having negative culture results. When the 16S PCR proves to be reliable and more sensitive than standard culturing techniques, it may become a powerful tool in the diagnosis of synovial infection.