Rapid identification of Propionibacterium acnes from blood cultures by fluorescence in situ hybridization

The Presence of Biofilms in Instrumented Spinal Fusions

Study Design: Prospective observational cohort study. Objective: To determine whether biofilms exist on spinal instrumentation recovered during revision surgery in which microbial cultures were negative. Background: Biofilm bacteria are extremely difficult to detect by conventional culture methods used in the standard hospital setting. Chronic infections in which bacteria form biofilms have been demonstrated to slow healing and prevent bony fusion. These slime encased microbial communities serve to isolate the bacteria from the body's immune responses, while simultaneously providing metabolic resistance to antimicrobial therapy. Methods: Traditional debridement wound cultures were taken from each specimen and sent for microbiological analyses. Bacterial DNA testing was performed using polymerase chain reaction (PCR) electrospray ionization-mass spectrometry (ESI-MS). Based on the PCR/ESI-MS results, specific crossed immune electrophoresis was used to detect the bacterial species within biofilms observed on the removed instrumentation. In addition, fluorescent in situ hybridization (FISH) probes corresponding to the bacterial species identified by PCR/ESI-MS were used with confocal microscopy to visualize and confirm the infecting bacteria. Results: Fifteen patients presented for surgical revision of thoracolumbar spinal implantation: four for clinical suspicion of infection, six for adjacent segment disease (ASD), one with ASD and pseudoarthrosis (PA), three with PA, and one for pain. Infections were confirmed with PCR/ESI-MS for all four patients who presented with clinical infection, and for five of the patients for whom infection was not clinically suspected. Of the presumed non-infected implants, 50% demonstrated the presence of infectious biofilms. Half of the revisions due to pseudoarthrosis were shown to harbour biofilms. The revisions that were performed for pain demonstrated robust biofilms but did not grow bacteria on traditional culture media. Conclusions: Culture is inadequate as a diagnostic modality to detect indolent/subclinical biofilm infections of spinal instrumentation. The PCR/ESI-MS results for bacterial detection were confirmed using species-specific microscopic techniques for both bacterial nucleic acids and antigens. Biofilms may contribute to pseudoarthrosis and back pain in postoperative wounds otherwise considered sterile.

Bacterial Identification and Visualization of Bacterial Biofilms Adjacent to Fracture Sites After Internal Fixation

Objectives: The primary aims of this study were to determine if any correlation exists in cases of fracture fixation among: (1) bacterial profiles recovered from the instrumentation and adjacent tissues; (2) the type of orthopedic injury; and (3) the clinical outcome-union versus nonunion. A secondary goal was to compare culture and molecular diagnostics for identifying the bacterial species present following fracture fixation. Design: Single-institution, prospective case-control cohort study. Setting: Single level 1 trauma center. Patients: Forty-nine bony nonunion cases undergoing revision internal fixation and 45 healed fracture controls undergoing removal of hardware. Intervention: Bacterial infection was detected by standard microbial culture methods and by a pan-eubacterial domain, molecular diagnostic (MDx) assay. Confirmation of culture and MDx results was achieved with bacterial ribosomal 16S rRNA fluorescence in situ hybridization (FISH) to visualize bacterial biofilms. Main Outcome Measurements: MDx and microbial culture methods results were the primary study outcomes. Results: Ninety-four percent of the nonunion cohort and 93% of the union cohort had bacteria detected by the MDx. Seventy-eight percent of the nonunion cases and 69% of the controls were culture negative, but MDx positive. Although no significant differences in bacterial composition were observed between the cases and controls, differences were observed when cases were divided by comorbidities. Conclusion: The MDx is more sensitive than microbial culture in detecting bacterial presence. The lack of significantly different findings with regard to bacterial profile identified between the cases and controls suggests that host factors and environmental conditions are largely responsible for determining if bony union will occur. Level of Evidence: Diagnostic Level III. See Instructions for Authors for a complete description of levels of evidence.

Fluorescence In Situ Hybridization and Polymerase Chain Reaction to Detect Infections in Patients With Left Ventricular Assist Devices

The development of driveline infections following left ventricular assist device (LVAD) implantation remains a major problem. We investigated the impact of fluorescence in situ hybridization (FISH) combined with 16S rRNA gene sequencing on the diagnosis of driveline infections. LVAD drivelines (n = 61) from 60 consecutive patients were obtained during LVAD explantation and subjected to FISH analysis. 16S rRNA gene polymerase chain reaction (PCR) and sequencing to identify the microorganisms were performed. Results were compared with those of a standard microbiological culture. The reasons for pump removal were heart transplantation (n = 22), weaning (n = 14), pump exchange due to pump thrombosis (n = 12), technical problems (n = 7), or death (n = 5). Of the 60 patients, 26 exhibited clinical signs of a VAD-specific infection, while 34 (with 35 drivelines) showed no clinical signs of infection before explantation. The spectrum of identified pathogens differed between FISH/PCR and conventional microbiological diagnostics. In general, the bacterial spectrum was more diverse in FISH/PCR as compared with conventional microbiology, which more often showed only typical skin flora (coagulase-negative staphylococci and Corynebacteriaceae). In addition to identifying the species, FISH/PCR provided information about the spatial distribution and invasiveness of the microorganisms. Cultures usually represent the only source of microbiological information for clinicians and often prove to be unsatisfactory in complex LVAD cases. FISH/PCR not only identified a greater number and variety of microorganisms than standard culture did, but it also provided information about the number, localization, and biofilm state of the pathogens, making it a useful tool for diagnosing the specific cause of LVAD driveline infections.

Cutibacterium avidum resists surgical skin antisepsis in the groin-a potential risk factor for periprosthetic joint infection: a quality control study

BACKGROUND

The skin commensal Cutibacterium avidum has been recognized as an emerging pathogen for periprosthetic joint infections (PJI). One currently assumes that the early occurring PJIs are a consequence of skin commensals contaminating the peri-implant tissue during surgery. We addressed whether standard skin antisepsis with povidone-iodine/alcohol before total hip arthroplasty (THA) is effective to eliminate colonizing bacteria with focus on C. avidum.

METHODS

In a single-center, prospective study, we screened all patients for skin colonizing C. avidum in the groin before THA. Only in the patients positive for C. avidum, we preoperatively repeated skin swabs after the first and third skin antisepsis and antibiotic prophylaxis. We also obtained dermis biopsies for microbiology and fluorescence in situ hybridization (FISH).

RESULTS

Fifty-one out of 60 patients (85%) were colonized on the skin with various bacteria, in particular with C. avidum in 12 out of 60. Skin antisepsis eliminated C. avidum in eight of ten (20%) colonized patients undergoing THA. Deeper skin (dermis) biopsies were all culture negative, but FISH detected single positive ribosome-rich C. avidum in one case near sweat glands.

CONCLUSION

Standard skin antisepsis was not effective to completely eliminate colonizing C. avidum on the skin in the groin of patients undergoing THA. Colonizing with C. avidum might pose an increased risk for PJI when considering a THA. Novel more effective antisepsis strategies are needed. Trial registration No clinical trial.

Evaluation of FISH for Blood Cultures under Diagnostic Real-Life Conditions

BACKGROUND

The study assessed a spectrum of previously published in-house fluorescence in-situ hybridization (FISH) probes in a combined approach regarding their diagnostic performance with incubated blood culture materials.

METHODS

Within a two-year interval, positive blood culture materials were assessed with Gram and FISH staining. Previously described and new FISH probes were combined to panels for Gram-positive cocci in grape-like clusters and in chains, as well as for Gram-negative rod-shaped bacteria. Covered pathogens comprised Staphylococcus spp., such as S. aureus, Micrococcus spp., Enterococcus spp., including E. faecium, E. faecalis, and E. gallinarum, Streptococcus spp., like S. pyogenes, S. agalactiae, and S. pneumoniae, Enterobacteriaceae, such as Escherichia coli, Klebsiella pneumoniae and Salmonella spp., Pseudomonas aeruginosa, Stenotrophomonas maltophilia, and Bacteroides spp.

RESULTS

A total of 955 blood culture materials were assessed with FISH. In 21 (2.2%) instances, FISH reaction led to non-interpretable results. With few exemptions, the tested FISH probes showed acceptable test characteristics even in the routine setting, with a sensitivity ranging from 28.6% (Bacteroides spp.) to 100% (6 probes) and a specificity of >95% in all instances.

CONCLUSION

If sophisticated rapid diagnostic methods like mass spectrometry from blood culture materials are not available, FISH provides an option for rapid differentiation for laboratories in resource-limited settings.

Regulation of Monospecies and Mixed Biofilms Formation of Skin Staphylococcus aureus and Cutibacterium acnes by Human Natriuretic Peptides

Staphylococcus aureus and Cutibacterium acnes are common representatives of the human skin microbiome. However, when these bacteria are organized in biofilm, they could be involved in several skin disorders such as acne or psoriasis. They inhabit in hollows of hair follicles and skin glands, where they form biofilms. There, they are continuously exposed to human hormones, including human natriuretic peptides (NUPs). We first observed that the atrial natriuretic peptide (ANP) and the C-type natriuretic peptide (CNP) have a strong effect S. aureus and C. acnes biofilm formation on the skin. These effects are significantly dependent on the aero-anaerobic conditions and temperature. We also show that both ANP and CNP increased competitive advantages of C. acnes toward S. aureus in mixed biofilm. Because of their temperature-dependent effects, NUPs appear to act as a thermostat, allowing the skin to modulate bacterial development in normal and inflammatory conditions. This is an important step toward understanding how human neuroendocrine systems can regulate the cutaneous microbial community and should be important for applications in fundamental sciences, medicine, dermatology, and cosmetology.

Detection of Acinetobacter spp. in Blood Cultures by an Improved Fluorescent in Situ Hybridization Assay

Fluorescent in situ hybridization (FISH) allows rapid detection of microorganisms. We aimed (i) to evaluate the sensitivity and specificity of FISH for the detection of Acinetobacter spp. in blood culture specimens and (ii) to test the simultaneous application of two genus-specific probes labeled with the same fluorochrome to increase the fluorescent signal intensity and improve the detection of Acinetobacter spp. Three hundred and twenty blood culture specimens were tested via both the conventional laboratory methods and FISH to detect Acinetobacter spp. The specimens were examined separately with each genus-specific probe Aci and ACA, and also using a mixture of the both probes Aci and ACA. In all examinations, probe EUB338 was used accompanied by Aci and ACA. The specificity of FISH was 100% (97.5% confidence interval [CI] = 98.7% – 100%). The sensitivity of FISH by the use of probe Aci was 96.4% (95% CI = 81.7% – 99.9%), whereas, the sensitivity of this technique by the use of probe ACA as well as by the combination of both probes Aci and ACA was 100% (97.5% CI = 87.7% – 100%). Moreover, simultaneous hybridization by probes Aci and ACA increased the fluorescent signal of Acinetobacter spp. cells to 3+ in 13 specimens. In conclusion, FISH, particularly using a combination of Aci and ACA, is a highly accurate method for the detection of Acinetobacter spp. in blood cultures. Furthermore, simultaneous hybridization by the both probes Aci and ACA can increase the fluorescent signal intensity of Acinetobacter spp. cells in some blood culture specimens and facilitate the detection of these microorganisms.

Microbiological diagnosis of device-related biofilm infections

Medical device-related infections cause undue patient distress, increased morbidity and mortality and pose a huge financial burden on healthcare services. The pathogens are frequently distributed heterogeneously in biofilms, which can persist without being effectively cleared by host immune defenses and antibiotic therapy. At present, there is no 'gold standard' available to reveal the presence of device-related biofilm infections. However, adequate sample collection and logistics, standardised diagnostic methods, and interpretation of results by experienced personnel are important steps in efficient diagnosis and treatment of these infections. The focus of this mini review is on prosthethic joint and cardiovascular implantable device infections, which exemplify permanent devices that are placed in a sterile body site. These device-related infections represent some of the most challenging in terms of both diagnosis and treatment.

Fluorescence in situ hybridization (FISH) in the microbiological diagnostic routine laboratory: a review

Early identification of microbial pathogens is essential for rational and conservative antibiotic use especially in the case of known regional resistance patterns. Here, we describe fluorescence in situ hybridization (FISH) as one of the rapid methods for easy identification of microbial pathogens, and its advantages and disadvantages for the diagnosis of pathogens in human infections in the laboratory diagnostic routine. Binding of short fluorescence-labeled DNA or nucleic acid-mimicking PNA probes to ribosomes of infectious agents with consecutive analysis by fluorescence microscopy allows identification of bacterial and eukaryotic pathogens at genus or species level. FISH analysis leads to immediate differentiation of infectious agents without delay due to the need for microbial culture. As a microscopic technique, FISH has the unique potential to provide information about spatial resolution, morphology and identification of key pathogens in mixed species samples. On-going automation and commercialization of the FISH procedure has led to significant shortening of the time-to-result and increased test reliability. FISH is a useful tool for the rapid initial identification of microbial pathogens, even from primary materials. Among the rapidly developing alternative techniques, FISH serves as a bridging technology between microscopy, microbial culture, biochemical identification and molecular diagnostic procedures.

Propionibacterium acnes: from commensal to opportunistic biofilm-associated implant pathogen

Propionibacterium acnes is known primarily as a skin commensal. However, it can present as an opportunistic pathogen via bacterial seeding to cause invasive infections such as implant-associated infections. These infections have gained more attention due to improved diagnostic procedures, such as sonication of explanted foreign materials and prolonged cultivation time of up to 14 days for periprosthetic biopsy specimens, and improved molecular methods, such as broad-range 16S rRNA gene PCR. Implant-associated infections caused by P. acnes are most often described for shoulder prosthetic joint infections as well as cerebrovascular shunt infections, fibrosis of breast implants, and infections of cardiovascular devices. P. acnes causes disease through a number of virulence factors, such as biofilm formation. P. acnes is highly susceptible to a wide range of antibiotics, including beta-lactams, quinolones, clindamycin, and rifampin, although resistance to clindamycin is increasing. Treatment requires a combination of surgery and a prolonged antibiotic treatment regimen to successfully eliminate the remaining bacteria. Most authors suggest a course of 3 to 6 months of antibiotic treatment, including 2 to 6 weeks of intravenous treatment with a beta-lactam. While recently reported data showed a good efficacy of rifampin against P. acnes biofilms, prospective, randomized, controlled studies are needed to confirm evidence for combination treatment with rifampin, as has been performed for staphylococcal implant-associated infections.

Can we trust intraoperative culture results in nonunions?

OBJECTIVES

To identify the presence of bacterial biofilms in nonunions comparing molecular techniques (multiplex polymerase chain reaction and mass spectrometry, fluorescent in situ hybridization) with routine intraoperative cultures.

METHODS

Thirty-four patients with nonunions were scheduled for surgery and enrolled in this ongoing prospective study. Intraoperative specimens were collected from removed implants, surrounding tissue membrane, and local soft tissue followed by standard culture analysis, Ibis's second generation molecular diagnostics (Ibis Biosystems), and bacterial 16S rRNA-based fluorescence in situ hybridization (FISH). Confocal microscopy was used to visualize the tissue specimens reacted with the FISH probes, which were chosen based on the Ibis analysis.

RESULTS

Thirty-four patient encounters were analyzed. Eight were diagnosed as infected nonunions by positive intraoperative culture results. Ibis confirmed the presence of bacteria in all 8 samples. Ibis identified bacteria in a total of 30 of 34 encounters, and these data were confirmed by FISH. Twenty-two of 30 Ibis-positive samples were culture-negative. Four samples were negative by all methods of analysis. No samples were positive by culture, but negative by molecular techniques.

CONCLUSIONS

Our preliminary data indicate that molecular diagnostics are more sensitive for identifying bacteria than cultures in cases of bony nonunion. This is likely because of the inability of cultures to detect biofilms and bacteria previously exposed to antibiotic therapy.

LEVEL OF EVIDENCE

Diagnostic Level I. See Instructions for Authors for a complete description of levels of evidence.

16S rRNA-targeted oligonucleotide probes for direct detection of Propionibacterium freudenreichii in presence of Lactococcus lactis with multicolour fluorescence in situ hybridization

Multicolour fluorescence in situ hybridization (FISH) has been applied to detect Lactococcus lactis and Propionibacterium freudenreichii cells in mixed populations in medium and skimmed milk, using epifluorescent microscopy. The 16S rRNA-targeted 18-mer oligonucleotide probes, specific for P. freudenreichii were designed and evaluated. Based on multiple alignments of designed sequences, eight 16S rRNA probes were selected for in vitro studies. The permeabilization protocol was optimized for simultaneous hybridization of propionibacteria and lactococci cells. The probes GLO62 (62-80), PEU64 (64-82) and PFX311 (311-329) were found specific for P. freudenreichii in analysis in vitro. Lactococcus lactis cells were labelled with LactV5 (822-840), (S-S-L.lact-0821-a-A-18) probe. The following combinations of oligonucleotide probes: LactV5/GLO62 , LactV5/PEU64 and LactV5/PFX311 , enabled differentiation of Lc. lactis and P. freudenreichii cells in culture media and in skimmed milk.

SIGNIFICANCE AND IMPACT OF THE STUDY

Results showed that three newly designed 16S rRNA-targeted oligonucleotide probes specific for Propionibacterium freudenreichii in combination with a probe specific for Lactococcus lactis can be used to differentiate lactic and propionic acid bacteria in mixed communities using multicolour fluorescence in situ hybridization (FISH), without applying permeabilization step. This is a first study on simultaneous detection of both bacterial species with FISH, which was found as rapid, useful and culture-independent tool for direct visualization of bacteria on single cell level. It might be applied in monitoring of mixed starter cultures in dairy industry.

Imaging bacteria and biofilms on hardware and periprosthetic tissue in orthopedic infections

Infection is a major complication of total joint arthroplasty (TJA) surgery, and even though it is now as low as 1 % in some hospitals, the increasing number of primary surgeries translates to tens of thousands of revisions due to prosthetic joint infection (PJI). In many cases the only solution is revision surgery in which the hardware is removed. This process is extremely long and painful for patients and is a considerable financial burden for the health-care system. A significant proportion of the difficulties in diagnosis and treatment of PJI are associated with biofilm formation where bacteria attach to the surface of the prosthesis and periprosthetic tissue and build a 3-D biofilm community encased in an extracellular polymeric slime (EPS) matrix. Bacteria in biofilms have a low metabolic rate which is thought to be a major contributor to their recalcitrance to antibiotic treatment. The diagnosis of biofilm infections is difficult due to the fact that bacteria in biofilms are not readily cultured with standard clinical microbiology techniques. To identify and visualize in situ biofilm bacteria in orthopedic samples, we have developed protocols for the collection of samples in the operating room, for molecular fluorescent staining with 16S rRNA fluorescence in situ hybridization (FISH), and for imaging of samples using confocal laser scanning microscopy (CLSM). Direct imaging is the only method which can definitively identify biofilms on implants and complements both culture and culture-independent diagnostic methods.

Fluorescence in situ hybridization (FISH) for rapid identification of Salmonella spp. from agar and blood culture broth--an option for the tropics?

BACKGROUND

Salmonella enterica is an important cause of diarrhea with the potential to cause systemic infection including sepsis, particularly in the tropics. Sepsis in particular requires quick and reliable identification to allow a rapid optimization of antibiotic therapy. We describe the establishment and evaluation of fluorescence in situ hybridization (FISH) as a rapid and easy-to-perform molecular identification procedure from agar and blood culture broths.

METHODS

Two newly developed FISH probes with specificity for Salmonella spp. were evaluated with 10 reference strains, 448 clinical isolates of Gram-negative bacteria from Germany and Ghana including 316 Salmonella spp. strains, and 39 environmental Salmonella spp. isolates from rivers and streams in Ghana. One FISH probe was further tested with 207 pre-incubated blood culture broths from Germany with Gram-negative rod-shaped bacteria in Gram stain.

RESULTS

Evaluation of the newly designed FISH probes demonstrated sensitivity of 99.2% and specificity of 98.4% for clinical isolates, sensitivity of 97.4% for environmental Salmonella spp. isolates, and sensitivity of 100% and specificity of 99.5% for blood culture materials.

CONCLUSIONS

FISH proved to be highly reliable for a rapid identification of Salmonella spp. directly from pre-incubated blood culture broths as well as after growth on agar. The inexpensive and easy-to-perform procedure is particularly suitable for resource-limited areas where more sophisticated procedures are not available.

Rapid identification of Acinetobacter spp. by fluorescence in situ hybridization (FISH) from colony and blood culture material

Multi-drug-resistant strains of the Acinetobacter baumannii complex cause nosocomial infections. Rapid identification of Acinetobacter spp. is desirable in order to facilitate therapeutic or hygiene decisions. We evaluated a newly designed DNA probe that can be used under standard conditions in both a microwave oven and a slide chamber for the rapid identification of Acinetobacter spp. by fluorescence in situ hybridization (FISH). Using FISH, the new probe correctly identified 81/81 Acinetobacter spp. isolates and excluded 109/109 tested non-target organisms from agar culture. Furthermore, the new probe correctly identified 7/7 Acinetobacter spp. in 214 blood cultures determined to contain Gram-negative bacteria by Gram staining. Using either the microwave oven or slide chamber technique, the new probe was able to identify Acinetobacter spp. in 100% of the samples tested. FISH used in conjunction with our newly designed probe provides an easy, cheap, precise, and rapid method for the preliminary identification of Acinetobacter spp., especially in laboratories where more sophisticated methods like matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) are not available.