Domain-directed polymerase chain reaction capable of distinguishing bacterial from host DNA at the single-cell level: characterization of a systematic method to investigate putative bacterial infection in idiopathic disease

Ceftiofur reduced Fusobacterium leading to uterine microbiota alteration in dairy cows with metritis

BACKGROUND

Metritis is an inflammatory uterine disease found in ~ 20% of dairy cows after parturition and associated with uterine microbiota with high abundance of Fusobacterium, Bacteroides, and Porphyromonas. Ceftiofur is a common treatment, but the effect on uterine microbiota is poorly understood. Herein, we investigated the short-term impact of ceftiofur on uterine microbiota structure and function in cows with metritis. Eight cows received ceftiofur (CEF) and 10 remained untreated (CON). Uterine swabs were collected for PCR and metagenomic analysis at diagnosis before treatment (5 ± 1 DPP) and 2 days after diagnosis/treatment (7 ± 1 DPP) from the same individuals. Seven CEF and 9 CON passed quality control and were used for 16S rRNA gene sequencing.

RESULTS

Ceftiofur treatment resulted in uterine microbiota alteration, which was attributed to a decrease in relative abundance of Fusobacterium and in gene contents involved in lipopolysaccharide biosynthesis, whereas uterine microbiota diversity and genes involved in pantothenate and coenzyme A biosynthesis increased. Ceftiofur treatment also reduced rectal temperature and tended to reduce total bacteria in the uterus. However, other uterine pathogens such as Bacteroides and Porphyromonas remained unchanged in CEF. The bla_CTX-M gene was detected in 37.5% of metritic cows tested but was not affected by CEF. We found that β-hydroxybutyric acid, pyruvic acid, and L-glutamine were preferentially utilized by Fusobacterium necrophorum according to metabolic activity with 95 carbon sources.

CONCLUSIONS

Ceftiofur treatment leads to alterations in the uterine microbiota that were mainly characterized by reductions in Fusobacterium and genes involved in LPS biosynthesis, which may be associated with a decrease in rectal temperature. The increase in pantothenate and coenzyme A biosynthesis indicates microbial response to metabolic stress caused by ceftiofur. Preference of Fusobacterium for β-hydroxybutyric acid may help to explain why this strain becomes dominant in the uterine microbiota of cows with metritis, and it also may provide a means for development of new therapies for the control of metritis in dairy cows.

Quantitative dynamics of Salmonella and E. coli in feces of feedlot cattle treated with ceftiofur and chlortetracycline

Antibiotic use in beef cattle is a risk factor for the expansion of antimicrobial-resistant Salmonella populations. However, actual changes in the quantity of Salmonella in cattle feces following antibiotic use have not been investigated. Previously, we observed an overall reduction in Salmonella prevalence in cattle feces associated with both ceftiofur crystalline-free acid (CCFA) and chlortetracycline (CTC) use; however, during the same time frame the prevalence of multidrug-resistant Salmonella increased. The purpose of this analysis was to quantify the dynamics of Salmonella using colony counting (via a spiral-plating method) and hydrolysis probe-based qPCR (TaqMan® qPCR). Additionally, we quantified antibiotic-resistant Salmonella by plating to agar containing antibiotics at Clinical & Laboratory Standards Institute breakpoint concentrations. Cattle were randomly assigned to 4 treatment groups across 16 pens in 2 replicates consisting of 88 cattle each. Fecal samples from Days 0, 4, 8, 14, 20, and 26 were subjected to quantification assays. Duplicate qPCR assays targeting the Salmonella invA gene were performed on total community DNA for 1,040 samples. Diluted fecal samples were spiral plated on plain Brilliant Green Agar (BGA) and BGA with ceftriaxone (4 μg/ml) or tetracycline (16 μg/ml). For comparison purposes, indicator non-type-specific (NTS) E. coli were also quantified by direct spiral plating. Quantity of NTS E. coli and Salmonella significantly decreased immediately following CCFA treatment. CTC treatment further decreased the quantity of Salmonella but not NTS E. coli. Effects of antibiotics on the imputed log10 quantity of Salmonella were analyzed via a multi-level mixed linear regression model. The invA gene copies decreased with CCFA treatment by approximately 2 log10 gene copies/g feces and remained low following additional CTC treatment. The quantities of tetracycline or ceftriaxone-resistant Salmonella were approximately 4 log10 CFU/g feces; however, most of the samples were under the quantification limit. The results of this study demonstrate that antibiotic use decreases the overall quantity of Salmonella in cattle feces in the short term; however, the overall quantities of antimicrobial-resistant NTS E. coli and Salmonella tend to remain at a constant level throughout.

Impact of treatment strategies on cephalosporin and tetracycline resistance gene quantities in the bovine fecal metagenome

The study objective was to determine the effects of two treatment regimens on quantities of ceftiofur and tetracycline resistance genes in feedlot cattle. The two regimens were ceftiofur crystalline-free acid (CCFA) administered to either one or all steers within a pen and subsequent feeding/not feeding of therapeutic doses of chlortetracycline. A 26-day randomized controlled field trial was conducted on 176 steers. Real-time PCR was used to quantify bla_CMY-2, bla_CTX-M, tet(A), tet(B), and 16S rRNA gene copies/gram of feces from community DNA. A significant increase in ceftiofur resistance and a decrease in tetracycline resistance elements were observed among the treatment groups in which all steers received CCFA treatment, expressed as gene copies/gram of feces. Subsequent chlortetracycline administration led to rapid expansion of both ceftiofur and tetracycline resistance gene copies/gram of feces. Our data suggest that chlortetracycline is contraindicated when attempting to avoid expansion of resistance to critically important third-generation cephalosporins.

An efficient strategy for broad-range detection of low abundance bacteria without DNA decontamination of PCR reagents

Background

Bacterial DNA contamination in PCR reagents has been a long standing problem that hampers the adoption of broad-range PCR in clinical and applied microbiology, particularly in detection of low abundance bacteria. Although several DNA decontamination protocols have been reported, they all suffer from compromised PCR efficiency or detection limits. To date, no satisfactory solution has been found.

Methodology/Principal Findings

We herein describe a method that solves this long standing problem by employing a broad-range primer extension-PCR (PE-PCR) strategy that obviates the need for DNA decontamination. In this method, we first devise a fusion probe having a 3′-end complementary to the template bacterial sequence and a 5′-end non-bacterial tag sequence. We then hybridize the probes to template DNA, carry out primer extension and remove the excess probes using an optimized enzyme mix of Klenow DNA polymerase and exonuclease I. This strategy allows the templates to be distinguished from the PCR reagent contaminants and selectively amplified by PCR. To prove the concept, we spiked the PCR reagents with Staphylococcus aureus genomic DNA and applied PE-PCR to amplify template bacterial DNA. The spiking DNA neither interfered with template DNA amplification nor caused false positive of the reaction. Broad-range PE-PCR amplification of the 16S rRNA gene was also validated and minute quantities of template DNA (10–100 fg) were detectable without false positives. When adapting to real-time and high-resolution melting (HRM) analytical platforms, the unique melting profiles for the PE-PCR product can be used as the molecular fingerprints to further identify individual bacterial species.

Conclusions/Significance

Broad-range PE-PCR is simple, efficient, and completely obviates the need to decontaminate PCR reagents. When coupling with real-time and HRM analyses, it offers a new avenue for bacterial species identification with a limited source of bacterial DNA, making it suitable for use in clinical and applied microbiology laboratories.

Scavenger Receptor BI Protects against Septic Death through Its Role in Modulating Inflammatory Response

Sepsis is a leading cause of death that is characterized by uncontrolled inflammatory response. In this study, we report that scavenger receptor BI (SR-BI), a high density lipoprotein receptor, is a critical survival factor of sepsis. We induced sepsis using an established septic animal model, cecal ligation and puncture (CLP). CLP induced 100% fatality in SR-BI-null mice but only 21% fatality in wild type littermates. SR-BI-null mice exhibited aberrant inflammatory responses with delayed inflammatory cytokine generation at the early stage of sepsis and highly elevated inflammatory cytokine production 20 h after CLP treatment. To understand the mechanisms underlying SR-BI protection, we elucidated the effect of macrophage SR-BI on inflammatory cytokine generation. Macrophages from SR-BI-null mice produced significantly higher levels of inflammatory cytokines than those of wild type controls in response to LPS. Importantly, transgenic mice overexpressing SR-BI were more resistant to CLP-induced septic death. Using an HEK-Blue(TM) cell system, we demonstrated that expression of SR-BI suppressed TLR4-mediated NF-kappaB activation. To understand why SR-BI-null mice had a delayed inflammatory response, we elucidated the effect of SR-BI on LPS clearance during sepsis. Compared with wild type controls, SR-BI-null mice had lower plasma LPS levels in the early stage of sepsis and elevated plasma LPS levels 20 h following CLP treatment. In conclusion, our findings demonstrate that SR-BI is a critical protective modulator of sepsis in mice. SR-BI exerts its protective function through its role in modulating inflammatory response in macrophages and facilitating LPS recruitment and clearance.

Rapid detection and identification of clinically important bacteria by high-resolution melting analysis after broad-range ribosomal RNA real-time PCR

BACKGROUND

Broad-range PCR provides valuable information for detecting bacterial infections. This study assesses the combined use of broad-range real-time PCR and high-resolution melting analysis for rapid detection and identification of clinically important bacteria.

METHODS

We subjected 46 bacterial culture colonies representing 25 clinically important bacterial species to LightCycler real-time PCR amplification of the 16S rRNA gene in the presence of LCGreen I fluorescent dye. We performed high-resolution melting analysis of the PCR products with the HR-1 instrument and used melting profiles as molecular fingerprints for bacterial species identification. We validated this method via assessment of 54 consecutive bacteria culture colonies obtained from a clinical microbiology laboratory.

RESULTS

The 16S rRNA gene of all 25 bacterial species was amplifiable by this method, with PCR product lengths of 216 or 217 bp. Of the 25 bacterial species, we identified 11 via a 1-step post-PCR high-resolution melting analysis. The remaining bacterial species were identified via the high-resolution melting plots obtained by heteroduplex formation between the PCR products of the tested and reference bacterial species or by a 2nd real-time PCR targeting a different region of the 16S rRNA gene. A high-resolution melting database and a working protocol were established for identifying these 25 bacterial species. In the validation assay, a 94% accuracy rate was achieved when the bacterial species were in the high-resolution melting database.

CONCLUSIONS

This assay requires no multiplexing or hybridization probes and provides a new approach for bacterial species identification in a molecular diagnostic laboratory.

Biodegradation, bioaccessibility, and genotoxicity of diffuse polycyclic aromatic hydrocarbon (PAH) pollution at a motorway site

Diffuse pollution of surface soil with polycyclic aromatic hydrocarbons (PAHs) is problematic in terms of the large areas and volumes of polluted soil. The levels and effects of diffuse PAH pollution at a motorway site were investigated. Surface soil was sampled with increasing distance from the asphalt pavement and tested for total amounts of PAHs, amounts of bioaccessible PAHs, total bacterial populations, PAH degrader populations, the potential for mineralization of 14C-PAHs, and mutagenicity. Elevated PAH concentrations were found in the samples taken 1-8 m from the pavement. Soil sampled at greater distances (12-24 m) contained only background levels of PAHs. The total bacterial populations (CFU and numbers of 16S rDNA genes) were similar for all soil samples, whereas the microbial degrader populations (culturable PAH degraders and numbers of PAH dioxygenase genes) were most abundant in the most polluted samples close to the pavement. Hydroxypropyl-beta-cyclodextrin extraction of soil PAHs, as a direct estimate of the bioaccessibility, indicated that only 1-5% of the PAHs were accessible to soil bacteria. This low bioaccessibility is suggested to be due to sorption to traffic soot particles. The increased PAH level close to the pavement was reflected in slightly increased mutagenic activity (1 m, 0.32 +/- 0.08 revertants g(-1) soil; background/ 24 m: 0.08 +/- 0.04), determined by the Salmonella/ microsome assay of total extractable PAHs activated by liver enzymes. The potential for lighter molecular weight PAH degradation in combination with low bioaccessibility of heavier PAHs is proposed to lead to a likely increase in concentration of heavier PAHs over time. These residues are, however, likely to be of low biological significance.

Positron emission tomography in a patient with renal malacoplakia

Positron emission tomography is increasingly used for the diagnosis of occult infection or malignancy. The altered metabolic rate of cells in areas of malignancy or infection provides a sensitive method to identify pathology that is otherwise not identified by standard imaging methods. This case report describes a patient who presented with a pyrexia of unknown origin and renal impairment. She had a positron emission tomography scan that showed intense accumulation of fluoro-deoxy-glucose in both kidneys. Subsequent renal biopsy results showed a diagnosis of malacoplakia, the treatment of which resulted in a resolution of the fever and a stabilization of renal function. This is the first report of the positron emission tomographic appearance of renal malacoplakia.

Detection of kappa- and lambda-expressing cells in the endometrium by in situ hybridization

The detection of kappa- and lambda-expressing cells in endometrial biopsies using in situ hybridization was correlated with the histologic findings. Forty endometrial biopsies were examined in conjunction with kappa and lambda expression in serial sections, recorded as the number of positive cells per 10 x100 fields. Cells expressing kappa or lambda were found in 39/40 (98%) biopsies with the average total number per 10 x100 fields as follows: proliferative (n = 13) 13; secretory (n = 6) 16; endometritis (n = 6) 623; polyp (n = 4) 72; adenocarcinoma (n = 6) 677; oral contraceptive effect (n = 5) 8. Many of the B lymphocytes expressing kappa and lambda did not have the cytologic features of plasma cells. The diagnosis of chronic endometritis can be made when the histologic findings of out-of-phase endometrial glands and focal fibrosis are seen with increased plasma cells; in cases where the latter is equivocal, in situ hybridization testing for light chain expression can be useful. Cells expressing kappa and lambda mRNA are relatively common in normally cycling endometrium, implying that mild chronic antigenic stimulation is present in most endometrial tissues. In situ hybridization for light chain expression can be helpful in endometria where only very rare plasma cells are seen; a baseline result would rule out chronic endometritis.

Amplification and sequence analysis of partial bacterial 16S ribosomal RNA gene in gallbladder bile from patients with primary biliary cirrhosis

BACKGROUND/AIMS

The etiopathogenesis of bile duct lesion in primary biliary cirrhosis is unknown, though the participation of bacteria and/or their components and products is suspected. In this study, we tried to detect and identify bacteria in the bile of patients with primary biliary cirrhosis by polymerase chain reaction using universal bacterial primers of the 16S ribosomal RNA gene.

METHODS

Gallbladder bile samples from 15 patients with primary biliary cirrhosis, 5 with primary sclerosing cholangitis, 5 with hepatitis C virus-related liver cirrhosis, 11 with cholecystolithiasis, and from 12 normal adult gallbladders were used. In addition to the culture study, partial bacterial 16S ribosomal RNA gene was amplified by polymerase chain reaction (PCR) taking advantage of universal primers that can amplify the gene of almost all bacterial species, and the amplicons were cloned and sequenced. Sequence homology with specific bacterial species was analyzed by database research. Bacterial contamination at every step of the bile sampling, DNA extraction and PCR study was avoided. Furthermore, to confirm whether bacterial DNA is detectable in liver explants, the same analysis was performed using 10 liver explants of patients with primary biliary cirrhosis.

RESULTS

In primary biliary cirrhosis, 75% (p<0.0001) of 100 clones were identified as so-called gram-positive cocci while these cocci were positive in only 5% in cholecystolithiasis (p<0.0001). In cholecystolithiasis gram-negative rods were predominant instead. One bacterial species detected in a normal adult was not related to those detected in primary biliary cirrhosis and cholecystolithiasis patients. No bacterial DNA was detected by PCR amplification in 10 liver explants of patients with primary biliary cirrhosis.

CONCLUSIONS

The present results raise several possible roles of gram-positive bacteria in bile in the etiopathogenesis of primary biliary cirrhosis. However, these results could also reflect an epiphenomenon due to decreased bile flow in the patients with primary biliary cirrhosis at an advanced stage.

Identification of bacteria from a non-healing diabetic foot wound by 16 S rDNA sequencing

Approximately 10-20% of diabetic foot wounds fail initial antibiotic treatment. It is generally believed that several bacterial species may be present in these types of wounds. Because some of these organisms cannot be easily cultured, proper identification is problematic and thus, appropriate treatment modalities cannot be applied. This report examined the bacterial flora present in a chronic diabetic foot wound that failed antibiotic treatment. A tissue sample was collected from the base of the wound and used for standard microbiological culturing. DNA from the sample was used to amplify bacterial 16 S rDNA gene sequences and a library of these sequences was made. The clones were placed into two major groups on the basis of their melting temperatures. Representatives of these groups were sequenced, and information was used to identify the bacteria present in the wound. The culture-based method identified a single anaerobic species, Bacteroides fragilis. The method employing rDNA sequencing identified B. fragilis as a dominant organism and Pseudomonas (Janthinobacterium) mephitica as a minor component. The results indicate that rDNA sequencing approach can be an important tool in the identification of bacteria from wounds.

Detection of bacterial DNA in serial synovial samples obtained during antibiotic treatment from patients with septic arthritis

OBJECTIVE

The management of septic arthritis could benefit from sensitive tests that detect the persistence of microorganisms in the joint. The aim of this study was to determine the feasibility of monitoring the presence of bacterial DNA in synovial samples from septic arthritis patients during antibiotic treatment.

METHODS

Synovial fluid (SF) and synovial tissue (ST) samples were collected serially from 6 patients with septic arthritis before and during antibiotic therapy. In addition, peripheral blood (PB) samples were available for polymerase chain reaction (PCR) analysis from 5 of the 6 patients before treatment. All samples were analyzed for the presence of bacterial DNA with the use of a PCR with universal 16S ribosomal RNA primers. Automated sequencing and comparative data analysis were performed to identify the species. These data were compared with Gram staining and culture results.

RESULTS

The bacterial species cultured from the synovium could be identified in all 6 patients using PCR and subsequent sequence analysis of the amplicons. In virtually all cases, positive Gram stain and culture findings in the synovial samples became negative after 2-3 days of antibiotic treatment. Bacterial DNA persisted in the SF and/or ST after culture conversion; in 2 patients, bacterial DNA was still detected at day 10, in 1 patient, at day 20, and in another patient, at day 22 after the initiation of treatment. Synovial samples were available for PCR analysis from 2 patients at day 26. At this time point, bacterial DNA could not be detected anymore. All PB samples were negative by both culture and PCR analysis.

CONCLUSION

PCR analysis can be used to monitor the presence of bacterial DNA in synovial samples from patients with septic arthritis during antibiotic treatment. The absence of bacterial DNA could help in the decision to discontinue antibiotic treatment.

The use of polymerase chain reaction to detect septicemia in critically ill patients

OBJECTIVE

To describe the use of bacterial DNA amplification of conserved bacterial 16S ribosomal DNA nucleotide sequences by polymerase chain reaction (PCR) to detect the presence of septicemia in critically ill septic patients.

DESIGN

Case series of blood samples from septic patients comparing the PCR results with conventional blood culture results.

SETTING

A general intensive care unit in a tertiary referral hospital.

PATIENTS

Two sets of samples (n = 101 and n = 55) from patients diagnosed as clinically septic and requiring blood cultures. They were classified by internationally accepted criteria into systemic inflammatory response syndrome, severe sepsis, and septic shock groups.

INTERVENTIONS

Blood samples taken in a sterile fashion concurrently for blood culture, and PCR of the bacterial 16S ribosomal RNA gene in leukocytes and plasma. Two different DNA extraction techniques for PCR were tried sequentially.

MEASUREMENTS AND MAIN RESULTS

Blood culture and PCR positivity were measured in relation to the clinical classification of severity of sepsis. Using the initial extraction method (n = 101), ten patients were positive by both PCR and blood culture, eight patients were PCR positive and blood culture negative, and seven patients were blood culture positive and PCR negative. From the clinical criteria, PCR detected at least six true positives that had been missed on blood culture and missed four true Gram-positive bacteremias. When the initial code was broken, this deficiency was rectified using the improved extraction technique (n = 55), in which ten patients were positive by PCR and blood culture, 29 patients were PCR positive and blood culture negative, and two patients were PCR negative and PCR positive.

CONCLUSIONS

We conclude that the use of PCR (for the 16S ribosomal DNA in the plasma) was significantly more sensitive than the use of conventional blood culturing techniques for the detection of bacteremia in seriously ill patients. This could prove to be a valuable adjunct to conventional blood cultures.

Radiologic diagnosis and pathology of the spondyloarthropathies

Five different subtypes of spondyloarthropathy (SpA) are now recognized. Clinical and radiologic involvement of the sacroiliac joint is an outstanding feature of the SpA, especially ankylosing spondylitis (AS). In this partly debilitating form of SpA a unique type of inflammatory axial involvement is observed which is characterized by inflammation and new bone formation at different spinal sites. In longstanding disease sacroiliitis, spondylitis and spondylodiscitis are easily recognized by conventional radiography and even better by computed tomography--especially when bony changes have already taken place. The advantage of dynamic magnetic resonance imaging (MRI) is to visualize morphologic changes and inflammation at the same time. This facilitates detection of sacroiliitis and spondylitis/spondylodiscitis at early time points. Hopefully, this will lead to other forms of therapy to prevent ankylosis of the spine. The origin of the granulation tissue infiltrating cartilage and bone in AS might be the synovium, the subchondrium or the bone marrow itself. T cells and macrophages seem to play an important role in this inflammatory process in which TNF-alpha is present in severe cases. The mechanisms responsible for the increased bone formation observed in the course of AS are unknown.

The polymerase chain reaction in infectious and post-infectious arthritis. A review

Polymerase chain reaction and other DNA amplification techniques to identify elusive infections should prove to be an effective tool for the clinical and investigative rheumatologist. The capability to identify and characterize infectious organisms in fluids and tissue will enable early, specific, and potentially curative treatment. Similarly, the capability to exclude infection and differentiate postinfectious diseases will enable other therapies to control the inflammation. Understanding these molecular techniques will most certainly improve clinicians' effectiveness for diagnosis and care.

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

OBJECTIVE

Bacteria are considered to be important in the pathogenesis of several forms of arthritis. The goal of this study was to apply the 16S ribosomal RNA (rRNA)-polymerase chain reaction method for the detection of bacterial DNA in synovial fluid (SF) and synovial tissue (ST) from inflamed joints.

METHODS

Samples from 5 patients with septic arthritis and from 7 with osteoarthritis or arthritis secondary to joint trauma were used as controls. Samples from 6 patients with spondylarthropathy (SpA) and from 20 with undifferentiated arthritis (UA) were analyzed for the presence of bacterial DNA using universal 16S rRNA primers. Automated sequencing and comparative data analysis were performed to identify the species.

RESULTS

In the positive control group, the bacterial species cultured from the synovium could be identified in all cases. No bacterial DNA was detected in the SF and ST from patients in the negative control group. In 4 of 6 patients with SpA and 7 of 20 with UA, the analysis of joint samples revealed the presence of bacterial DNA. Sequence analysis indicated the presence of multiple species, which was confirmed by sequencing of cloned products.

CONCLUSION

When the the above techniques were used with a stringent regimen, we were able to demonstrate that it is possible to collect and analyze joint samples without contaminating bacterial DNA. The accumulation of phagocytic cells that contain bacterial DNA of various species could play a role in the pathogenesis of both SpA and UA.