The comparison of pyrosequencing molecular Gram stain, culture, and conventional Gram stain for diagnosing orthopaedic infections

Detection of mecA and 16S rRNA Genes Using Real-Time PCR Can Be Useful in Diagnosing Iliopsoas Abscess, Especially in Culture-Negative Cases: RT-PCR for Iliopsoas Abscess

The rapid detection of etiological agents is important for the successful treatment of iliopsoas abscess (IPA). The purpose of this study was to investigate the clinical utility of a real-time polymerase chain reaction (PCR) that targets the mecA gene for methicillin-resistant staphylococci (MRS) and the 16S rRNA gene for pan-bacteria. Our retrospective diagnostic study included 22 patients exhibiting IPAs and four patients with noninfectious iliopsoas mass regions who underwent computerized tomography or ultrasonography-guided biopsy and/or surgical treatment. Clinical symptoms, serum data, imaging analysis, and tissue microbiological culture were utilized for the diagnosis of IPA. The diagnostic accuracy of real-time PCR was determined based on the diagnosis of IPA and microbiological culture results. The microbiological culture was positive for 12 IPA cases that included 2 MRSA infections. Among 12 culture-positive IPA cases, 16S rRNA-PCR was positive in 12 and MRS-PCR in two. Among 10 culture-negative IPA cases, including 3 TB cases, 16S rRNA-PCR was positive in 8 and MRS-PCR in 2. In noninfectious iliopsoas mass patients, neither 16S rRNA nor MRS-PCR detected bacterial DNA. The sensitivity, specificity, positive predictive, and negative predictive values of 16S rRNA-PCR for diagnosing IPA were 0.91, 1.00, 1.00, and 0.67, respectively, while those for the diagnosis of MRS infection with MRS-PCR were 1.00, 0.92, 1.00, and 0.50, respectively. Real-time PCR targeting bacterial DNA can detect bacterial DNA in culture-negative cases and offer improved detectability of MRS infection in IPA patients.

Killing Effects of an Isolated Serratia marcescens KH-001 on Diaphorina citri via Lowering the Endosymbiont Numbers

Huanglongbing (HLB) is the most devastating citrus disease worldwide, and suppression of the Asian citrus psyllid (Diaphorina citri) is regarded as an effective method to inhibit the spread of HLB. In this study, we isolated a strain named as Serratia marcescens KH-001 from D. citri nymphs suffering from disease, and evaluated its killing effect on D. citri via toxicity test and effect on microbial community in D. citri using high-throughput sequencing. Our results indicated that S. marcescens KH-001 could effectively kill 83% of D. citri nymphs, while the fermentation products of S. marcescens KH-001 only killed 40% of the D. citrinymphs. High-throughput sequencing results indicated that the S. marcescens KH-001 increased the OTU numbers from 62.5 (PBS buffer) to 81.5, while significantly lowered the Shannon index compared with Escherichia coli DH5α (group E) (p < 0.05). OTU analysis showed that the S. marcescens KH-001 had significantly reduced the relative abundance of endosymbionts Wolbachia, Profftella, and Carsonella in group S compared with that in other groups (p < 0.05). Therefore, the direct killing effect of the fermentation products of S. marcescens KH-001 and the indirect effect via reducing the numbers of endosymbionts (Wolbachia, Profftella, and Carsonella) of D. citri endow S. marcescens KH-001 a sound killing effect on D. citri. Further work need to do before this strain is used as a sound biological control agents.

Prevalence of fecal viruses and bacteriophage in Canadian farmed mink (Neovison vison)

Recent viral metagenomic studies have demonstrated the diversity of eukaryotic viruses and bacteriophage shed in the feces of domestic species. Although enteric disease is a major concern in the commercial mink farming industry, few etiologic agents have been well characterized. This study aimed to identify viruses shed in the fecal matter of clinically healthy commercial mink from 40 southern Ontario farms. Viral RNA was extracted from 67 pooled fecal samples (30 adult female mink and 37 kit) and amplified for Illumina sequencing on the NextSeq platform, and the resulting contigs were trimmed and assembled using Trimmomatic 0.36.0 and Spades 3.8.0 in iVirus (CyVerse, AZ, USA) and SeqMan NGen 12 (DNAStar, WI, USA). Identification of assembled sequences >100 bp (Geneious 10.1.3) showed an abundance of bacteriophage sequences, mainly from families Siphoviridae (53%), Podoviridae (22%), Myoviridae (20%), Inoviridae (1%), Leviviridae (0.04%), Tectiviridae (0.01%), and Microviridae (0.01%). A diverse range of vertebrate viruses were detected, of which posavirus 3, mink bocavirus, gyroviruses, and avian‐associated viruses were most abundant. Additionally, sequences from nonvertebrate viruses with water and soil‐associated amebal and algal hosts were also highly prevalent. The results of this study show that viruses shed in the fecal matter of healthy commercial mink are highly diverse and could be closely associated with diet, and that more research is necessary to determine how the detected viruses may impact mink health.

Comparison of the common bacteria in human and mouse tumours using high-throughput sequencing

Evidence has indicated that gut bacteria may serve an important role in cancer development and therapy, while little work has been done to explore the microbial diversity inside tumours. In the present study, high‑throughput sequencing was first used to identify and compare the microbial diversity in human and mouse tumours. Principal component analysis (PCA) and β-diversity indicated a low microbial similarity among mouse artificial tumours (M.AT group), mouse spontaneous tumours (M.T group) and human tumours (H.T group), and Serratia (35.85 vs. 32.64 vs. 73.32%), Pseudomonas (24.10 vs. 16.62 vs. 1.72%) and Ochrobactrum (6.28 vs. 11.08 vs. 11.90%) were identified as dominant bacteria at the genus level. In addition, Venn results indicated 103 common operational taxonomic units (OTUs) in the M.AT, M.T and H.T groups, and only 2 and 1 OTUs belonged to Lactobacillus and Escherichia, respectively, while no OTUs belonging to Salmonella, Bifidobacteria or Clostridium were identified. In the present study, the common bacteria between human and mouse tumours were identified, which may serve as potential strains for bacteriotherapy of cancers.

High‑throughput sequencing analyses of oral microbial diversity in healthy people and patients with dental caries and periodontal disease

Recurrence of oral diseases caused by antibiotics has brought about an urgent requirement to explore the oral microbial diversity in the human oral cavity. In the present study, the high-throughput sequencing method was adopted to compare the microbial diversity of healthy people and oral patients and sequence analysis was performed by UPARSE software package. The Venn results indicated that a mean of 315 operational taxonomic units (OTUs) was obtained, and 73, 64, 53, 19 and 18 common OTUs belonging to Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria and Fusobacteria, respectively, were identified in healthy people. Moreover, the reduction of Firmicutes and the increase of Proteobacteria in the children group, and the increase of Firmicutes and the reduction of Proteobacteria in the youth and adult groups, indicated that the age bracket and oral disease had largely influenced the tooth development and microbial development in the oral cavity. In addition, the traditional ‘pathogenic bacteria’ of Firmicutes, Proteobacteria and Bacteroidetes (accounted for >95% of the total sequencing number in each group) indicated that the ‘harmful’ bacteria may exert beneficial effects on oral health. Therefore, the data will provide certain clues for curing some oral diseases by the strategy of adjusting the disturbed microbial compositions in oral disease to healthy level.

Application of Pyrosequencing® in Food Biodefense

The perpetration of a bioterrorism attack poses a significant risk for public health with potential socioeconomic consequences. It is imperative that we possess reliable assays for the rapid and accurate identification of biothreat agents to make rapid risk-informed decisions on emergency response. The development of advanced methodologies for the detection of biothreat agents has been evolving rapidly since the release of the anthrax spores in the mail in 2001, and recent advances in detection and identification techniques could prove to be an essential component in the defense against biological attacks. Sequence-based approaches such as Pyrosequencing(®), which has the capability to determine short DNA stretches in real time using biotinylated PCR amplicons, have potential biodefense applications. Using markers from the virulence plasmids and chromosomal regions, my laboratory has demonstrated the power of this technology in the rapid, specific, and sensitive detection of B. anthracis spores and Yersinia pestis in food. These are the first applications for the detection of the two organisms in food. Furthermore, my lab has developed a rapid assay to characterize the antimicrobial resistance (AMR) gene profiles for Y. pestis using Pyrosequencing. Pyrosequencing is completed in about 60 min (following PCR amplification) and yields accurate and reliable results with an added layer of confidence, thus enabling rapid risk-informed decisions to be made. A typical run yields 40-84 bp reads with 94-100 % identity to the expected sequence. It also provides a rapid method for determining the AMR profile as compared to the conventional plate method which takes several days. The method described is proposed as a novel detection system for potential application in food biodefense.

Synovial IL-6 as inflammatory marker in periprosthetic joint infections

We analyzed serum and synovial biomarkers of 69 patients. 31 of them suffered from a periprosthetic joint infection (PJI) and 38 from aseptic arthralgia after total joint arthroplasty. We used Receiver-Operating-Characteristic-curves to calculate the Area-under-the-curve (AUC), cutoff-values, positive (+LR), negative (-LR) and interval-Likelihood-Ratios (iLR) for predicting a PJI. The most significant parameter was synovial interleukin-6 (IL-6) (cutoff-value ≥ 30,750 pg/ml, AUC = 0.959, SE = 90.0%, SP = 94.7%, +LR = 17.27), followed by synovial lactate (cutoff-value ≥ 8.3 mmol/l, AUC = 0.844, SE = 71.4%, SP=88.0%, +LR = 5.95), and synovial glucose (cutoff-value ≤ 44 mg/dl, AUC = 0.829, SE = 79.2%, SP = 78.6%, +LR = 3.69). IL-6 ≥ 30,750 pg/ml and lactate ≥ 10 mmol/l make a PJI very likely, IL-6 <10,000pg/ml or lactate <4.3 mmol/l makes a PJI very unlikely. If none of these thresholds are met, physicians should use the iLR of IL-6, glucose and lactate to estimate the likelihood of PJI.

Rapid sensitive molecular diagnosis of pyogenic spinal infections using methicillin-resistant Staphylococcus-specific polymerase chain reaction and 16S ribosomal RNA gene-based universal polymerase chain reaction

BACKGROUND CONTEXT

Rapid diagnosis and accurate detection of etiological agents in pyogenic spinal infection (PSI) patients are important.

PURPOSE

The purpose of this study was to evaluate the clinical usefulness of methicillin-resistant Staphylococcus-specific polymerase chain reaction (MRS-PCR) and broad-range universal PCR (U-PCR) for diagnosing PSI.

STUDY DESIGN

A prospective diagnostic study.

PATIENTS

Thirty-two clinically suspect PSI patients and six control patients who underwent computerized tomography-guided biopsy and/or surgical treatment were enrolled.

METHODS

Tissue samples were examined by microbiological culture, histopathology, and real-time PCR (MRS-PCR and U-PCR). The diagnostic accuracy of real-time PCR was analyzed based on the definitive diagnosis of infection, defined as a positive result from microbiological culture or histopathology.

RESULTS

All six control subjects were negative for PSI for all analyses. Twelve clinically suspect PSI subjects received definitive diagnoses (PSI group). The non-PSI group consisted of six control subjects plus the remaining 20 patients from the PSI clinically suspect group. MRS-PCR results were positive for all MRS-cultured PSI subjects. U-PCR was positive for all subjects in the PSI group with one discrepancy between real-time PCR and microbiological culture results in differentiation between gram-positive and gram-negative bacteria. In the non-PSI group, MRS-PCR and U-PCR were positive in three and seven cases, respectively. The sensitivity, specificity, positive predictive value, and negative predictive value of MRS-PCR for diagnosing MRS infection were 1.00, 0.91, 0.57, and 1.00, respectively; those for the diagnosis of bacterial infection with U-PCR were 1.00, 0.73, 0.63, and 1.00, respectively.

CONCLUSION

Identification of MRS infection and ability to differentiate between gram-positive and gram-negative bacteria is rapidly achieved using MRS-PCR and U-PCR. Real-time PCR provides a sensitive molecular diagnosis of PSI and may contribute to antibiotic selection.

Use of real-time polymerase chain reaction for the diagnosis of infection and differentiation between gram-positive and gram-negative septic arthritis in children

BACKGROUND

Diagnosis and identification of the etiological agent of septic arthritis (SA) in children is an important issue, as early treatment based on accurate diagnosis of joint infections can prevent potentially disabling complications. The purpose of this study was to evaluate the efficacy of real-time polymerase chain reaction (PCR) for the diagnosis of SA in children.

PATIENTS AND METHODS

Twenty children with suspected SA who had joint pain and underwent surgical treatment were enrolled in this study. Their preoperative clinical and laboratory findings were investigated. Tissues obtained during operation were subjected to microbiological culture and real-time PCR, including methicillin-resistant Staphylococcus (MRS)-specific PCR and broad range universal PCR. Infection was confirmed if the result of microbiological culture was positive. Furthermore, abnormal clinical and laboratory findings and improvement in the symptoms and posttreatment data were also defined as the final diagnosis of infection.

RESULTS

Out of the 20 patients, 19 were diagnosed with the infection. The remaining patient was postoperatively diagnosed with juvenile idiopathic arthritis. Abnormal preoperative body temperatures, white blood cell counts, C-reactive protein levels, and erythrocyte sedimentation rates were observed in 6, 9, 15, and 12 cases, respectively. The results of microbiological culture, MRS-PCR, and universal PCR were positive in 9, 2, and 15 cases, respectively. Analysis of the melting peak in universal PCR revealed that of the 15 cases, 10 had gram-positive and 5 had gram-negative infections. The sensitivity and specificity for the diagnosis of SA were, respectively, 0.47 and 1.00 in microbiological culture and 0.79 and 1.00 in real-time PCR.

CONCLUSIONS

Successful diagnosis of infection and differentiation between gram-positive and gram-negative bacteria were achieved using MRS-PCR and universal PCR. Hence, real-time PCR is useful and has greater sensitivity than microbial culture for diagnosing SA in children.

LEVEL OF EVIDENCE

Level II diagnostic study investigating a diagnostic test.

Use of F-18 fluoride PET to differentiate septic from aseptic loosening in total hip arthroplasty patients

PURPOSE

The preoperative differentiation of aseptic and septic loosening following a total hip arthroplasty (THA) remains a challenging issue for clinicians to which several molecular imaging techniques have been applied. In our current study, we used F-18 fluoride positron emission tomography (PET) to evaluate THA cases with stable, septic or septic loosened implants to assess the possibility of differentiating these clinical settings using a novel uptake-type classification approach.

MATERIALS AND METHODS

A total of 65 joints were enrolled in this prospective study comprising 27 asymptomatic stable hips (control group), 11 painful hips conservatively treated after THA due to a suspicion of loosening, and 27 painful hips surgically treated after THA. PET imaging was classified into 3 types according to the uptake pattern. The maximum standardized uptake value (SUVmax) was then measured for each joint. A final diagnosis was made via tissue examinations of surgically treated cases, and by serological and radiographic findings in conservatively treated cases.

RESULTS

There were significant differences found between the SUVmax values for the aseptic and septic loosening THA cases. In the diagnosis of infection with type 3 pattern, the sensitivity and specificity were measured at 0.95 and 0.98 for all cases, and 0.95 and 0.88 for surgically treated cases, respectively.

CONCLUSIONS

The results of our current study demonstrate that F-18 fluoride PET has considerable potential as a method for differentiating septic from aseptic loosening following a THA. The type classification of the uptake pattern can be performed relatively simply, and quantifications using the SUVmax values can then provide an objective evaluation.

Molecular markers for diagnosis of periprosthetic joint infection

Despite a battery of tests available for diagnosing periprosthetic joint infection, as yet, no gold standard has been identified. Our purpose was to measure inflammatory proteins in synovial fluid from patients undergoing revision arthroplasty for septic or aseptic failure. We analyzed 74 synovial fluid samples: 31 infected and 43 uninfected, based on clinical and laboratory criteria. Proteomics analysis and receiver operating characteristic curve analyses were conducted on 46 inflammatory proteins for each sample. Of 46 proteins, 5 (interleukin 6, interleukin 8, α(2)-macroglobulin, C-reactive protein, and vascular endothelial growth factor) had an area under the curve greater than 0.90. This prospective study has demonstrated promising results for the use of molecular markers in diagnosis of periprosthetic joint infection. Future studies will focus on designing assays with these proteins in mind.

Use of 18F-fluoride PET to determine the appropriate tissue sampling region for improved sensitivity of tissue examinations in cases of suspected periprosthetic infection after total hip arthroplasty

BACKGROUND AND PURPOSE

The accurate diagnosis of periprosthetic infection requires assessment of intraoperative tissues. These must be sampled from the appropriate sites. We used (18)F-fluoride positron emission tomography (PET) to identify sites of inflammation in order to improve the sensitivity of histopathology, microbiological culture, and real-time PCR in total hip arthroplasty (THA) patients.

PATIENTS AND METHODS

23 THA patients (23 hips) scheduled for revision surgery (the revision group) and 17 uninfected THA patients (23 hips; control group) were enrolled. Uptake was classified into major, minor, and no uptake. To evaluate the association between the (18)F-fluoride uptake and intraoperative tissue results in the revision group, we calculated their sensitivity on each of the major, minor, and no-uptake sides.

RESULTS

17 revision patients showed major uptake and all were diagnosed as having septic loosening from intraoperative tissue results. Minor uptake was observed in the other 6 revision patients and all were diagnosed as having aseptic loosening. Apart from 3 cases that showed minor uptake regions, control subjects showed no uptake. In the revision group, the sensitivities of histopathology, microbiological culture, real-time PCR separately and also in combination were 0.78, 0.58, 0.96, and 0.96, respectively, on the major (18)F-fluoride uptake sides, 0.0, 0.0, 0.1, and 0.1 on the minor-uptake sides, and 0, 0, 0.18, and 0.18 on the no-uptake sides.

INTERPRETATION

Our findings suggest that preoperative assessment of major uptake of (18)F-fluoride markedly improves the accuracy of tissue sampling, and thus the sensitivity of subsequent tissue examinations. More definitive diagnosis of periprosthetic infection is therefore possible.

Incidence of low-grade infection in aseptic loosening of total hip arthroplasty

PURPOSE

We investigated the hypothesis that many total hip arthroplasty revisions that are classified as aseptic are in fact low-grade infections missed with routine diagnostics.

METHODS

In 7 Dutch hospitals, 176 consecutive patients with the preoperative diagnosis of aseptic loosening of their total hip arthroplasty were enrolled. During surgery, between 14 and 20 tissue samples were obtained for culture, pathology, and broad-range 16S rRNA PCR with reverse line blot hybridization. Patients were classified as either not being infected, suspected of having infection, or infected according to strict, predefined criteria. Each patient had a follow-up visit after 1 year.

RESULTS

7 patients were classified as infected, 4 of whom were not identified by routine culture. 15 additional patients were suspected of having infection. 20 of these 22 patients received a cemented prosthesis, fixated with antibiotic-loaded bone cement. All 22 patients received prophylactic systemic antibiotics. 7 of them reported complaints one year after surgery, but only one showed signs of early loosening. However, additional surgery was not performed in any of the patients.

INTERPRETATION

Although the proportions were not as high as previously reported in the literature, between 4% and 13% of patients with the preoperative diagnosis of aseptic loosening were infected. However, as thorough debridement was performed during surgery and prophylactic antibiotics were used, the diagnosis of infection did not have any obvious clinical consequences, as most patients performed well at the 1-year follow-up. Whether this observation has implications for long-term implant survival remains to be seen.

Distinction between intact and antibiotic-inactivated bacteria by real-time PCR after treatment with propidium monoazide

One limitation to the use of the polymerase chain reaction (PCR) to identify orthopedic infections has been apparent false-positive results, possibly due to the detection of dead bacteria. We recently showed that the use of DNA-binding agent propidium monoazide (PMA) could distinguish viable from heat-inactivated bacteria, and, in this study, we investigated whether the same technique can be applied to bacteria killed by two antibiotics with distinctly different mechanisms of action, a test of greater clinical relevance than thermal inactivation. Staphylococcus aureus and S. epidermidis were inactivated by vancomycin and gentamicin and treated with PMA or left untreated before DNA extraction. The threshold cycle difference of antibiotic-treated bacteria with and without PMA pretreatment was investigated with PCR primers for the 16S rDNA and tuf genes. Our results indicated that PMA effectively inhibited detection by PCR of bacteria, which had been inactivated by either vancomycin or gentamicin. The effect was statistically significant at 24 h after treatment (C(t) difference consistently >3; p < 0.05) and after 10 days of treatment (C(t) difference >4; p < 0.01), when compared to viable cells (C(t) difference 1-2). Vancomycin had a stronger effect on the C(t) value than gentamicin, reflecting the different mechanism of action of each antibiotic. Techniques of this type may help reduce clinically false-positive PCR results caused by the detection of dead bacteria, and may be especially useful in patients who have received antibiotics, such as patients undergoing the second stage of a two-stage revision for infected arthroplasty.

Improving clinical significance of PCR: use of propidium monoazide to distinguish viable from dead Staphylococcus aureus and Staphylococcus epidermidis

Molecular techniques, such as the polymerase chain reaction (PCR) have high sensitivity when used to diagnose infection, but may detect DNA, RNA, and proteins from dead, as well as viable, bacteria. Propidium monoazide (PMA) is a DNA binding agent, that has the ability to penetrate only dead cells with compromised membranes and has been used in conjunction with real-time PCR to distinguish intact from dead bacterial cells. In this study, intact, heat-inactivated (dead), and intact/dead admixed Staphylococcus aureus (S. aureus) and Staphylococcus epidermidis (S. epidermidis) were treated with PMA or left untreated before DNA extraction. We quantified levels of 16S rDNA and tuf gene by real-time quantitative PCR (qPCR), to test the ability of PMA to distinguish intact from dead bacteria. Our results indicated that PMA inhibited detection of dead bacteria, and the qPCR results reflected the number of intact bacteria without being impacted by the presence of the dead bacteria. This approach of combining qPCR with and without PMA treatment has promise to limit false-positive PCR results when used to diagnose infections, but needs to be further validated in clinical samples.

Improved detection of biofilm-formative bacteria by vortexing and sonication: a pilot study

Bacteria such as staphylococci commonly encountered in orthopaedic infections form biofilms and adhere to bone implants and cements. Various methods to disrupt the biofilm and enhance bacterial detection have been reported. We will describe the effectiveness of vortexing and sonication to improve the detection of biofilm-formative bacteria from polymethylmethacrylate by conventional quantitative bacterial culture and real-time quantitative PCR. We used a single biofilm-formative Staphylococcus aureus strain and 20 polymethylmethacrylate coupons as an in vitro biofilm model; four coupons were used for each of two control groups or three experimental sonication times (1, 5, and 30 minutes). Vortexing the cement without sonication increased the yield of adherent bacteria to a considerable extent. The combination of vortexing and sonication further enhanced the yield regardless of the duration of sonication. Quantitative conventional cultures correlated with quantitative PCR assay. The combination of vortexing and sonication to disrupt the bacterial biofilm followed by quantitative PCR and/or culture seems to be a sensitive method for detecting bacteria adherent to bone cement.

Utility of pyrosequencing in identifying bacteria directly from positive blood culture bottles

Growth in liquid media is the gold standard for detecting microorganisms associated with bloodstream infections. The Gram stain provides the first clue as to the etiology of infection, with phenotypic identification completed 1 or 2 days later. Providing more detailed information than the Gram stain can impart, and in less time than subculturing, would allow the use of more directed empirical therapy and, thus, reduce the patient's exposure to unnecessary or ineffective antibiotics sooner. The study had two objectives, as follows: (i) to identify new targets to improve our ability to differentiate among certain enteric gram-negative rods or among certain Streptococcus species and (ii) to determine whether real-time PCR and pyrosequencing could as accurately identify organisms directly from positive blood culture bottles as culture-based methods. Two hundred and fifty-five consecutive positive blood culture bottles were included. The results showed a high level of agreement between the two approaches; of the 270 bacteria isolated from the 255 blood culture bottles, results for pyrosequencing and culture-based identifications were concordant for 264/270 (97.8%) bacteria with three failed sequences, and three sequences without match. Additionally, compared to the universal 16S rRNA gene target, the new 23S rRNA gene targets greatly improved our ability to differentiate among certain enteric gram-negative rods or among certain Streptococcus species. In conclusion, combining real-time PCR and pyrosequencing provided valuable information beyond that derived from the initial Gram stain and in less time than phenotypic culture-based identification. This strategy, if implemented, could result in a more directed empirical therapy in patients and would promote responsible antibiotic stewardship.

Molecular identification of bacteria from aseptically loose implants

Polymerase chain reaction (PCR) assays have been used to detect bacteria adherent to failed orthopaedic implants, but some PCR assays have had problems with probable false-positive results. We used a combination of a Staphylococcus species-specific PCR and a universal PCR followed by DNA sequencing to identify bacteria on implants retrieved from 52 patients (92 implants) at revision arthroplasty. We addressed two questions in this study: (1) Is this method able to show the existence of bacterial DNA on presumed aseptic loosed implants?; and (2) What proportion of presumed aseptic or culture-negative implants was positive for bacterial DNA by PCR? Fourteen implants (15%) were believed infected, whereas 74 implants (85%) were believed aseptic. Each implant was sonicated and the resulting solution was submitted for dual real-time PCR assay and culture. All implants believed aseptically loose were culture-negative, but nine of the 74 (12%) had bacterial DNA by PCR; two (2.7%) were PCR-positive and also showed histologic findings suggestive of infection. Uniquely developed PCR and bacterial sequencing assays showed bacterial DNA on 12% of implants removed for presumed aseptic loosening. Additional studies are needed to determine the clinical importance of bacterial DNA detected by PCR but not by conventional culture.

LEVEL OF EVIDENCE

Level III, diagnostic study.

Identifications of pathogens - a bioinformatic point of view

Over the past 15 years, microbiology has undergone a momentous shift toward molecular methods. New sequences appear daily in the public databases and new computer tools and web servers are published on a regular basis. Major advances in molecular identifications of pathogens have been made because new biotechnology methods have appeared that often require a thorough in silico analysis of sequences. However, significant difficulties partly remain in developing efficient methods because the public databases contain many poorly annotated or partial sequences (often of environmental origin) and also because there are few dedicated web servers and curated databases.

Molecular diagnostics for the detection and characterization of microbial pathogens

New and advanced methods of molecular diagnostics are changing the way we practice clinical microbiology, which affects the practice of medicine. Signal amplification and real-time nucleic acid amplification technologies offer a sensitive and specific result with a more rapid turnaround time than has ever before been possible. Numerous methods of postamplification analysis afford the simultaneous detection and differentiation of numerous microbial pathogens, their mechanisms of resistance, and the construction of disease-specific assays. The technical feasibility of these assays has already been demonstrated. How these new, often more expensive tests will be incorporated into routine practice and the impact they will have on patient care remain to be determined. One of the most attractive uses for such techniques is to achieve a more rapid characterization of the infectious agent so that a narrower-spectrum antimicrobial agent may be used, which should have an impact on resistance patterns.

DNA pyrosequencing-based bacterial pathogen identification in a pediatric hospital setting

Sole reliance on biochemical methods can limit the clinical microbiology laboratory's ability to identify bacterial pathogens. This study describes the incorporation of DNA pyrosequencing-based identification for routine pathogen identification of atypical clinical isolates in a large children's hospital. The assay capitalized on the highly conserved nature of 16S rRNA genes by positioning amplification and sequencing primers in conserved target sequences flanking the variable V1 and V3 regions. A total of 414 isolates of 312 pediatric patients were tested by DNA pyrosequencing during the time period from December 2003 to July 2006. Seventy-eight different genera were specified by DNA pyrosequencing, and isolates were derived from diverse specimen types. By integrating DNA sequencing of bacterial pathogens with conventional microbiologic methods, isolates that lacked a definitive identification by biochemical testing yielded genus- or species-level identifications in approximately 90% of cases by pyrosequencing. Improvements incorporated into the assay process during the period of clinical testing included software enhancements, improvements in sequencing reagents, and refinements in database search strategies. Coupled with isolation by bacteriologic culture and biochemical testing, DNA pyrosequencing-based bacterial identification was a valuable tool that markedly improved bacterial pathogen identification in a pediatric hospital setting.

Development of a molecular methodology to quantify Staphylococcus epidermidis in surgical wash-out samples from prosthetic joint replacement surgery

Prosthetic joint infection is a serious complication of total joint arthroplasty that causes great morbidity in affected individuals. The most common cause of prosthesis associated infections are members of Staphylococcus spp., including Staphylococcus epidermidis. Culture has served as the gold standard for diagnosis, despite obvious shortcomings in terms of sensitivity and time. Bacterial genomic DNA extraction methodologies were evaluated for optimal recovery of genomic DNA from sterilised wash-out samples, spiked with S. epidermidis. Real time Polymerase chain reaction (PCR) assays targeting the S. epidermidis specific gseA gene were designed to reliably detect and quantify S. epidermidis. Sixty post-operative wash-out samples from primary hip and knee arthroplasties were taken aseptically. All were shown to be culture negative using the culture-dependent approach. These were samples were subjected to S. epidermidis-specific real time PCR. Standard curve showed good linearity. Sensitivity limit of the assay was <10 CFU S. epidermidis per sample. Reproducibility of the assay was confirmed. S. epidermidis was not identified in any of these samples using the novel species specific SYBR Green real time PCR technique. Results indicated that wash-out samples were true negatives and did not harbour S. epidermidis. To support this, patients displayed no symptoms of infection. To illustrate the full effectiveness of the novel real time PCR assay, a larger number of samples need to be tested (>1,000 patients).

Identification of orthopaedic infections using broad-range polymerase chain reaction and reverse line blot hybridization

BACKGROUND

Culture remains the gold standard in the diagnosis of bacterial infection, but molecular biological techniques have yielded promising results. In this study, we validated a combined polymerase chain reaction and reverse line blot hybridization protocol for identifying musculoskeletal infections.

METHODS

Samples were obtained from seventy-six patients undergoing orthopaedic surgery for various aseptic and septic indications. The diagnosis of infection was based on a review of all available clinical and culture data. In addition to routine culture for aerobic and anaerobic growth, samples were analyzed with a broad-range 16S rRNA polymerase chain reaction and subsequent reverse line blot hybridization with use of twenty-eight group, genus, and species-specific oligonucleotide probes.

RESULTS

An infection was diagnosed on the basis of patient data in thirty-one patients. All but one of the patients with a clinical diagnosis of infection had a positive result of the polymerase chain reaction-reverse line blot hybridization. Five of the forty-five patients in whom an infection was not suspected on the basis of patient data had at least one positive result of the polymerase chain reaction-reverse line blot hybridization. Cultures demonstrated microorganisms in twenty-five patients with an infection and in two patients in whom an infection was not suspected on the basis of the patient data. Staphylococcus aureus was the most common organism grown on culture. The species identified by the polymerase chain reaction-reverse line blot hybridization was in full accordance with that grown on culture in all but one patient.

CONCLUSIONS

Polymerase chain reaction-reverse line blot hybridization performed well in detecting and identifying the various bacterial species and was more sensitive than routine culture. It identified Staphylococcus aureus as the most frequently found microorganism. Five patients in whom an infection was not suspected on the basis of the patient data had a positive result of the polymerase chain reaction, which may have been caused by contamination of the samples. However, three of these patients had aseptic loosening of a total hip prosthesis, suggesting the presence of a low-grade bacterial infection that remained undetected by the culture but was detected by the polymerase chain reaction-reverse line blot hybridization.

LEVEL OF EVIDENCE

Diagnostic Level III.