Abstract
Through the use of polymerase chain reaction (PCR)-electron spray ionization (ESI)-time of flight (TOF)-mass spectrometry (MS), we identified multiple periodontal pathogens within joint tissues of individuals undergoing replacement arthroplasties of the knee. The most prevalent of the periodontal pathogens were Treponema denticola and Enterococcus faecalis, the latter of which is commonly associated with apical periodontitis. These findings were unique to periprosthetic joint infections (PJI) of the knee and were never observed for PJIs of other lower extremity joints (hip and ankle) or upper extremity joints (shoulder and elbow). These data were confirmed by multiple independent methodologies including fluorescent in situ hybridization (FISH) which showed the bacteria deeply penetrated inside the diseased tissues, and 454-based deep 16S rDNA sequencing. The site-specificity, the tissue investment, and the identical findings by multiple nucleic-acid-based techniques strongly suggests the presence of infecting bacteria within these diseased anatomic sites. Subsequently, as part of a control program using PCR-ESI-TOF-MS, we again detected these same periodontal pathogens in aspirates from patients with osteoarthritis who were undergoing primary arthroplasty of the knee and thus who had no history of orthopedic implants. This latter finding raises the question of whether hematogenic spread of periodontal pathogens to the knee play a primary or secondary- exacerbatory role in osteoarthritis.
J Appl Biomater Funct Mater 2014; 12(1): 13 - 20
Article Type: ORIGINAL RESEARCH ARTICLE
DOI:10.5301/jabfm.5000203
Authors
Garth D. Ehrlich, Fen Z. Hu, Nicholas Sotereanos, Jeffrey Sewicke, Javad Parvizi, Peter L. Nara, Carla Renata ArciolaArticle History
- • Accepted on 09/11/2013
- • Available online on 02/06/2014
- • Published online on 12/06/2014
Disclosures
This article is available as full text PDF.
INTRODUCTION
Bacterial biofilms are frequently formed in biological systems and are characterized by bacteria adopting a multicellular lifestyle (1-2-3). In the case of pathogens, the development of the biofilm state is related to their intrinsically high resistances to both the host’s immune defenses and standard antimicrobial treatments. These factors together with powerful adherence mechanisms provide for the extraordinary abilities of bacterial biofilms to persist within the host leading to chronic, often incurable conditions (4-5-6-7-8-9-10-11-12-13-14). Thus, bacterial biofilms are the prototypical population-level virulence factor (15), as they manifest only when bacteria adopt a multicellular life style. This includes promoting other population-based virulence behaviors such as horizontal gene transfer (8, 16-17-18) and quorum sensing capabilities (19-20-21). Like many virulence factors, these mechanisms evolved in response to the internecine battles between bacteria (22). Implantable medical devices are at a high risk of becoming encrusted with bacterial (and fungal) biofilms (3, 23-24-25). Due to the ineffectiveness of traditional, culture-based, microbial detection strategies and antimicrobial strategies for the control of biofilms, respectively, great effort is being expended to identify biofilm-specific targets for both diagnostics (26, 27) and interventions (28-29-30-31-32-33).
We and others have previously documented periprosthetic joint infections (PJIs) of the ankle, knee, hip, elbow and shoulder in culture-negative cases (11, 34-35-36-37-38-39-40) and in cases of hip fracture associated with osteoporosis (41). Some of these PJIs are associated with known medically-important pathogens such as
One of the biggest challenges in the treatment of biofilm infections is their accurate diagnosis. Biofilm bacteria are intrinsically difficult to culture, and prior treatment with antibiotics greatly exacerbates this problem (47).Thus, other methods must be developed and employed for their clinical detection. Until recently, however, DNA-based molecular diagnostic (MDx) methods also suffered from many limitations, most importantly from a lack of breadth (48, 49). This manifested as a high positive predictive value for the test organism, but a very low negative predictive value overall, as infectious disease physicians and clinical microbiologists essentially had to guess what species to test for; and if they guessed wrong there was no test that provided adequate coverage. The Ibis technology revolutionized MDx and essentially did away with the need for culturing (50-51-52-53). This technology combined the exquisite sensitivity of PCR-based methods with unheard-of breadth of coverage. This was accomplished by uniting multiple technical advances with powerful diagnostic algorithms capable of accessing immense databases (50, 53). In practice, the Ibis technology utilizes multiple PCR primers to a battery of highly conserved (pan-domain) sequences, as well as employing primers specific to various mid-level taxa. Each primer comes with its own internal standard that serves as a test for amplification and also for quantifying the number of genome equivalents of any identified target sequence. This makes it possible to determine the relative levels of different species in a polymicrobial infection. After amplification (and a desalting step) the amplimers are ionized via electrospray ionization (ESI) which serves to gently denature the two strands such that each intact strand enters the TOF and is weighed. The ESI is critical in this regard as it does not produce fragmentation as MALDI would, thus the exact amplimer weight is determined twice – once for each strand, with each strand serving as a control for the other. The MW of each strand is then used to determine the exact base composition of the amplimer, i.e., how many As, Gs, Cs, and Ts there are using a deconvolution algorithm. This works similarly to weighing a pocket full of change and from the weight deciphering how many each quarters, dime, nickels, and pennies there are. Once the base composition is determined, it is compared against a massive database which holds the DNA sequence data for each species. Through an iterative process of examining the base compositions of multiple amplimers, a species-level diagnosis is achievable in essentially all cases.
In the incumbent study, we evaluated both PJIs and native knees undergoing primary arthroplasty for osteoarthritis for the presence of periodontal and apical periodontal pathogens using the Ibis technology and compared these results with deep 16S sequence analysis and/or 16S FISH.
METHODS AND MATERIALS
DNA extraction and Ibis T5000 eubacterial domain assay
In summary, total DNA was extracted from aspirates and tissue samples, and the bacterial DNAs were amplified by polymerase chain reaction (PCR) (49) using the 16 primer pair BAC system developed by Ibis (50). The individual amplicons were then “weighed” using the Ibis T5000 electrospray ionization (ESI) time-of-flight (TOF) mass spectrometer (MS). The species identities of the amplicons were then revealed using a database containing base composition data on virtually all bacterial species sequenced to date.
For the tissue and membrane samples, 1 mm3 of tissue or membrane was placed into a sterile microcentrifuge tube containing 270 μL of ATL Lysis buffer (Qiagen, Germantown, MD, USA; cat# 19076) and 30 μL proteinase K (Qiagen; cat# 19131). For aspirate samples 1 ml of aspirate (in RNA later) was centrifuged at 10000 rpm x 3 min, then 900 μL of supernatant was removed. ATL lysis buffer and proteinase K were then added as above. Samples were incubated at 56°C until lysis of the material was noted by visual inspection (typically ~12 h). One hundred microliters of a mixture containing 50 μL each of 0.1 mm and 0.7 mm Zirconia beads (Biospec, Bartlesville, OK, USA; cat# 11079101z, 11079107zx, respectively) were added to the samples which were then homogenized for 10 min at 25 Hz using a Qiagen Tissuelyser. Nucleic acid from the lysed sample was then extracted using the Qiagen DNeasy Tissue kit (Qiagen; cat# 69506). Ten microliters of each sample was loaded per well onto the BAC detection PCR plate (Abbott Molecular, Carlsbad, CA, USA; cat# PN 05N13-01). The BAC detection plate is a 96-well plate containing 16 primer pairs per assay that survey all bacterial organisms by using omnipresent loci (e.g., 16S rDNA sequences), phylum/class/order specific loci, while some are targeted to specific pathogens of interest (e.g., the Staphylococcus-specific
Fluorescence in situ hybridization
Fluorescence
Deep 16 S rDNA sequencing
Samples from patients in this series were analyzed by the creation of 16S clone libraries in cases in which there was sufficient material to provide bacterial DNA for this process. These clone libraries were then analyzed using the GS titanium system developed by 454 Life Sciences (Branford, CT, USA), and bacteria were identified at the species or (more commonly) at the genus level. We designed 114 different Multiplex Identifier (MID) tagged 16S PCR primers. The primers were generated by combining the 454 sequencing primer keys, an exclusive 10-base MID adaptor, and a 16S rRNA targeted sequence. DNAs from 113 different orthopedic samples and one negative control were used as PCR templates. PCR were performed in 50 µL reactions containing 1× High Fidelity PCR Buffer, 2.0 mM MgCl2 solution, 0.8 mM dNTP Mix, 1 U Platinum Taq High-Fidelity (Invitrogen, Carlsbad, CA, USA), 0.4 µM each primer (Integrated DNA Technologies, Coralville, IA, USA) and 5 µL of DNA extract. Cycling was performed with an initial denaturation step at 94°C for 2 min followed by 30 cycles of 94°C for 30 seconds, 55°C for 30 s and 72°C for 60 s, followed by a final extension of 7 min at 72°C. Five microliters of the PCR products were visualized on 1% agarose gels. Positive PCR products were purified using the Agencourt AMPure XP system (Beckman Coulter, Brea, CA, USA) and quantified using Quanti-iT PicoGreen dsDNA Assay Kit (Invitrogen). All primers that produced 16S PCR fragments were diluted to equimolar concentrations (48 pg/µl). PCR products were then pooled into two groups of samples to create two amplicon libraries. GS Titanium SV emPCR (Lib-A) and GS Titanium sequencing (454 Life Sciences) were then performed on the amplicon libraries according to the manufacturer’s guidelines. Following conclusion of the sequencing run, reads from the 454 16S sequencing run were separated by MID (sample), and the MIDs were stripped from the reads. Each sample’s reads were then analyzed using the RDP classifier online tool (http://rdp.cme.msu.edu/classifier/classifier.jsp).
RESULTS
Patient population, specimen types, and testing modalities
A series of 40 revision arthroplasties of the knee (n=25), hip (n=14), and ankle (n=1) were evaluated by microbial culture and molecular diagnostics (MDx) for the presence of microbial infection, regardless of the clinical indication for surgery. Thus, the patient population included both individuals with clinical signs and/or symptoms of infection, as well as subjects suspected of having sterile loosening in the absence of infection. Specimen types included pre-surgical aspirates, and tissue and pseudomembrane (biofilm) collected during the surgical arthroplasty excision process. Patients were considered culture-positive even if only a single culture (often out of five or more) supported growth of a pathogen. All specimens were also evaluated using the Ibis T-5000 BAC assay which is an MDx based on PCR-ESI-TOF-MS that provides eubacterial pan-domain detection, speciation, and quantification of both single agents and polymicrobial infections. In addition, the BAC assay provides coverage for
Ibis BAC assay results vs. microbial culture
Periodontal pathogens were detected by the Ibis BAC assay in 12/25 (48%) of knees, in 0/13 hips and 0/1 ankles. The difference between knees and hips was highly statistically significant using a Chi-square analysis (p=0.0032; 95% CI=1.96). Microbial culture did not detect periodontal pathogens in any of these specimens. This joint specificity to the knee was striking, and supported the veracity of these results, arguing against some external source of contamination. Moreover, in the majority of these cases the periodontal pathogens were found in multiple specimen types. In total, 32/63 (52%) of all Ibis tests from all subjects having at least one specimen positive for a given periodontal pathogen were periodontal pathogen-positive for that species.
Results of confirmatory and validating tests
To confirm the detection of the periodontal pathogens identified by Ibis, but not by culture, 16S FISH analyses were performed on tissue/pseudomembrane specimens using probes specific to the species (or genera) identified by the primary detection modalities (
Detection of Treponena denticola from a periprosthetic infection of the knee. The presence of T. denticola detected by the Ibis BAC assay was confirmed via 16S FISH performed on tissue removed during excisional surgery for this primary arthroplasty. The bacteria appear as redish pink, the blue is reflected light.
Detection of Enterococcus faecalis from a periprosthetic infection of the knee. The presence of E. faecalis, originally detected by the Ibis BAC assay, was confirmed via 16S FISH specific for E. faecalis which was performed on tissue removed during excisional surgery for this primary arthroplasty. The bacteria appear as redish pink, the blue is reflected light.
Detection of Brevundimonas diminuta from a periprosthetic infection of the knee. The presence of Brevundimonas diminuta, originally detected by the Ibis BAC assay, was confirmed via 16S FISH generic for Brevundimonas sp. which was performed on tissue removed during excisional surgery for this primary arthroplasty. The bacteria appear as redish pink, the blue is reflected light.
PROBES USES FOR 16S FLUORESCENT IN SITU HYBRIDIZATION
Probe name | Target organism | Sequence (5’ -> 3’) | Reference |
---|---|---|---|
Pdi |
|
TTC CAC ATA CCT CTC TCA | Schleifer K et al, Molecular Biology and Biotechnology., 1992 |
TRE II |
|
GCTCCTTTCCTCATTTACCTTTAT | Moter et al, Microbiology, 1998. |
ENF 191 |
|
GAAAGCGCCTTTCACTCTTATGC | Wellinghausen, J. Clin. Microb., 2007 |
Analyses of native knees for periodontal pathogens
Following our findings that periodontal pathogens were likely associated with a large percentage of infected arthroplasties of the knee, we decided to evaluate native knees from patients planning to undergo primary arthroplasty for osteoarthritis. From a series of pre-surgical aspirates of six such knees, by Ibis we detected
DISCUSSION
Our experience with the Ibis technology versus traditional microbial culture over the last seven years extends to several thousands of specimens collected and analyzed under the auspices of several national and multi-center bioburden studies (unpublished data). Collectively, the data from these studies indicate, that on average, culture detects an organism in only approximately 20% of the cases that the Ibis does. In all of these studies, the Ibis technology has been verified by either deep 16S rDNA sequence analysis and species- or genera-specific 16S
One of the reasons given for the necessity of culture is the need to determine antibiotic resistances and sensitivities of infecting organisms; however, if an infection is only detected by culture 20% of the time in 80% of cases there will be no sensitivity data. Here again the Ibis technology has an advantage, because there are primers included in the BAC eubacterial pan-domain assay to provide a molecular antibiogram. The latter is accomplished by amplification of the genetic determinants of major antibiotic resistances. As a test of the accuracy of this system we examined the identification of the mecA gene in the current PJI study. This gene encodes methicillin resistance among the staphylococci, and therefore should be found preferentially when staphylococci species are also detected. In the current study
In this study, in the absence of bacterial culture, multiple periodontal pathogens were identified both in the knees of patients with arthroplasties who were undergoing revisional surgery for either periprosthetic joint infections or “sterile” loosening as well as in the knees of osteoarthritis patients prior to the placement of any arthroplasty. The bacterial species detected included
In the incumbent PJI study we confirmed the Ibis T5000 findings of periodontal bacterial DNA via direct visualization of the Ibis-identified microbes with FISH probes and confocal microscopy as well as by deep 16S pyrosequencing of individual 16S amplicon libraries prepared from individual specimens, when sufficient material was available. In all 10 Ibis-positive cases, 16S FISH verified the presence of the same periodontal bacteria (identified by Ibis) as being present within tissue-embedded biofilms, despite all these cases being culture negative. It is important to point out that the tissue processing steps involved in preparing the specimens for FISH, as well as the FISH procedure itself (54, 55), are very harsh in terms of shear forces encountered by the bacterial biofilms. This results in a very substantial debulking of the biofilm such that any remaining bacteria must be tightly attached to the tissue (hardware) under evaluation. Thus, any contaminating bacteria would not survive the process. This means that FISH-based visualization of a given bacterial taxa is essentially proof-positive not only of its presence but also of its penetration into the tissue.
In our Ibis evaluation of aspirates from native knees prior to their undergoing primary knee arthroplasty (PKA) for treatment of osteoarthritis, we detected the same periodontal pathogens (
ACKNOWLEDGEMENTS
The authors thank all of the physicians and clinical staff members who provided specimens.
Disclosures
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Sotereanos N Second-generation molecular diagnostics and strategies for preventing periprosthetic joint infections. In: Ehrlich GD DeMeo P Costerton JW Winkler H eds. Culture-Negative Orthopedic Biofilm Infections. Berlin, Heidelberg Springer-Verlag (Series on Biofilms) 2012 -
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Ehrlich GD DeMeo P Costerton JW Winkler H eds. Culture-Negative Orthopedic Biofilm Infections. Berlin, Heidelberg Springer-Verlag (Series on Biofilms) 2012 -
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Authors
- Ehrlich, Garth D. [PubMed] [Google Scholar] 1, 3, * Corresponding Author ([email protected])
- Hu, Fen Z. [PubMed] [Google Scholar] 1, 3
- Sotereanos, Nicholas [PubMed] [Google Scholar] 4
- Sewicke, Jeffrey [PubMed] [Google Scholar] 4
- Parvizi, Javad [PubMed] [Google Scholar] 5
- Nara, Peter L. [PubMed] [Google Scholar] 6
- Arciola, Carla Renata [PubMed] [Google Scholar] 7, 8, * Corresponding Author ([email protected])
Affiliations
-
Center for Genomic Sciences, Institute for Molecular Medicine and Infections Disease, Drexel University College of Medicine, Philadelphia, PA - USA -
Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA - USA -
Department of Otolaryngology, Drexel University College of Medicine, Philadelphia, PA - USA -
Department of Orthopedic Surgery, Allegheny General Hospital, Pittsburgh, PA - USA -
Rothman Institute at Thomas Jefferson University, Philadelphia, PA - USA -
Biological Mimetics Inc., Frederick, MD - USA -
Research Unit on Implant Infections, Rizzoli Orthopedic Institute, Bologna - Italy -
DIMES, University of Bologna, Bologna - Italy
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