Rapid identification of clinically relevant Enterococcus species by fluorescence in situ hybridization

Enterococci enhance Clostridioides difficile pathogenesis

Enteric pathogens are exposed to a dynamic polymicrobial environment in the gastrointestinal tract¹. This microbial community has been shown to be important during infection, but there are few examples illustrating how microbial interactions can influence the virulence of invading pathogens². Here we show that expansion of a group of antibiotic-resistant, opportunistic pathogens in the gut-the enterococci-enhances the fitness and pathogenesis of Clostridioides difficile. Through a parallel process of nutrient restriction and cross-feeding, enterococci shape the metabolic environment in the gut and reprogramme C. difficile metabolism. Enterococci provide fermentable amino acids, including leucine and ornithine, which increase C. difficile fitness in the antibiotic-perturbed gut. Parallel depletion of arginine by enterococci through arginine catabolism provides a metabolic cue for C. difficile that facilitates increased virulence. We find evidence of microbial interaction between these two pathogenic organisms in multiple mouse models of infection and patients infected with C. difficile. These findings provide mechanistic insights into the role of pathogenic microbiota in the susceptibility to and the severity of C. difficile infection.

Oral Corticosteroids Impair Mucin Production and Alter the Posttransplantation Microbiota in the Gut

INTRODUCTION

Gut microbiota alterations cause inflammation in patients with ulcerative colitis (UC). Fecal microbiota transplantation (FMT) enables manipulating the microbiota's composition, but the mechanisms underlying colonization of the posttransplantation microbiota are poorly understood.

METHODS

In this open-label, nonrandomized study, the FMT efficacy and changes in the gut microbiota were evaluated in 8 UC patients with mild-to-moderately active endoscopic colonic lesions. Compositional changes in the fecal and mucosal microbiotas between donors and recipients were examined via 16S rRNA-based sequencing. To investigate the effects of oral corticosteroids on microbiota colonization, FMT was performed in germ-free prednisolone (PSL)-administered mice to examine the factors determining colonization.

RESULTS

Four UC patients achieved clinical remission (CR) after FMT, and 3 also achieved endoscopic remission. The fecal microbiotas of the CR patients changed similar to those of the donors after FMT. The mucin-coding gene, MUC2, was less expressed in the colons of the PSL-dependent patients than in the PSL-free patients. In the mice, PSL treatment decreased the fecal mucin production and altered the posttransplantation fecal microbiota composition. Adding either exogenous mucin or the mucin secretagogue, rebamipide, partially alleviated the PSL-induced dysbiosis of the gut microbiota. Administering rebamipide with FMT from healthy donors relieved inflammation in mice with Enterococcus faecium-induced colitis.

CONCLUSION

Colonic mucin controlled the gut microbiota composition, and oral corticosteroid treatment modified the gut microbiota partly by reducing the colonic mucin.

Features and Colonization Strategies of Enterococcus faecalis in the Gut of Bombyx mori

The complex gut microbiome is a malleable microbial community that can undergo remodeling in response to many factors, including the gut environment and microbial properties. Enterococcus has emerged as one of the predominant gut commensal bacterial and plays a fundamental role in the host physiology and health of the major economic agricultural insect, Bombyx mori. Although extensive research on gut structure and microbiome diversity has been carried out, how these microbial consortia are established in multifarious niches within the gut has not been well characterized to date. Here, an Enterococcus species that was stably associated with its host, the model organism B. mori, was identified in the larval gut. GFP–tagged E. faecalis LX10 was constructed as a model bacterium to track the colonization mechanism in the intestine of B. mori. The results revealed that the minimum and optimum colonization results were obtained by feeding at doses of 10⁵ CFU/silkworm and 10⁷ CFU/silkworm, respectively, as confirmed by bioassays and fluorescence-activated cell sorting analyses (FACS). Furthermore, a comprehensive genome-wide exploration of signal sequences provided insight into the relevant colonization properties of E. faecalis LX10. E. faecalis LX10 grew well under alkaline conditions and stably reduced the intestinal pH through lactic acid production. Additionally, the genomic features responsible for lactic acid fermentation were characterized. We further expressed and purified E. faecalis bacteriocin and found that it was particularly effective against other gut bacteria, including Enterococcus casselifavus, Enterococcus mundtii, Serratia marcescens, Bacillus amyloliquefaciens, and Escherichia coli. In addition, the successful colonization of E. faecalis LX10 led to drastically increased expression of all adhesion genes (znuA, lepB, hssA, adhE, EbpA, and Lap), defense genes (cspp, tagF, and esp), regulation gene (BfmRS), secretion gene (prkC) and immune evasion genes (patA and patB), while the expression of iron acquisition genes (ddpD and metN) was largely unchanged or decreased. This work establishes an unprecedented conceptual model for understanding B. mori–gut microbiota interactions in an ecological context. Moreover, these results shed light on the molecular mechanisms of gut microbiota proliferation and colonization in the intestinal tract of this insect.

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.

A Novel Biofilm Model System to Visualise Conjugal Transfer of Vancomycin Resistance by Environmental Enterococci

Enterococci and biofilm-associated infections are a growing problem worldwide, given the rise in antibiotic resistance in environmental and clinical settings. The increasing incidence of antibiotic resistance and its propagation potential within enterococcal biofilm is a concern. This requires a deeper understanding of how enterococcal biofilm develops, and how antibiotic resistance transfer takes place in these biofilms. Enterococcal biofilm assays, incorporating the study of antibiotic resistance transfer, require a system which can accommodate non-destructive, real-time experimentation. We adapted a Gene Frame^® combined with fluorescence microscopy as a novel non-destructive platform to study the conjugal transfer of vancomycin resistance in an established enterococcal biofilm.A multi-purpose fluorescent in situ hybridisation (FISH) probe, in a novel application, allowed the identification of low copy number mobile elements in the biofilm. Furthermore, a Hoechst stain and ENU 1470 FISH probe identified Enterococcus faecium transconjugants by excluding Enterococcus faecalis MF06036 donors. Biofilm created with a rifampicin resistant E. faecalis (MW01105^Rif) recipient had a transfer efficiency of 2.01 × 10^-3; double that of the biofilm primarily created by the donor (E. faecalis MF06036). Conjugation in the mixed enterococcal biofilm was triple the efficiency of donor biofilm. Double antibiotic treatment plus lysozyme combined with live/dead imaging provided fluorescent micrographs identifying de novo enterococcal vancomycin resistant transconjugants inside the biofilm. This is a model system for the further study of antibiotic resistance transfer events in enterococci. Biofilms promote the survival of enterococci and reduce the effectiveness of drug treatment in clinical settings, hence giving enterococci an advantage. Enterococci growing in biofilms exchange traits by means of horizontal gene transfer, but currently available models make study difficult. This work goes some way to providing a non-destructive, molecular imaging-based model system for the detection of antibiotic resistance gene transfer in enterococci.

Quality Control in Diagnostic Fluorescence In Situ Hybridization (FISH) in Microbiology

This overview addresses fluorescence in situ hybridization (FISH) in a diagnostic microbiology setting with its associated problems and pitfalls and how to control them, but also the advantages and opportunities the method offers. This article focuses mainly on diagnostic FISH assays on tissue sections and on techniques and experiences in our laboratory. FISH in a routine diagnostic setting in microbiology requires strict quality control measures to ensure consistent high-quality and reliable assay results. Here, for the first time, we define quality control requirements for microbiological diagnostic FISH applications and discuss their impact and possible future developments of the FISH technique for infection diagnostics. We focus on diagnosis of biofilm-associated infections including infective endocarditis, oral biofilms, and device-associated infections as well as infections due to fastidious or yet uncultured microorganisms like Treponema spp., Tropheryma whipplei, Bartonella, Coxiella burnetii, or Brachyspira.

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.

Lactobacilli with superoxide dismutase-like or catalase activity are more effective in alleviating inflammation in an inflammatory bowel disease mouse model

Purpose

Some lactobacilli, which possess superoxide dismutase-like activity and catalase activity naturally, have strong antioxidative properties. The aim of this study was to identify such strains and check which of them play a crucial role in alleviating intestinal inflammation.

Methods

We selected two Lactobacillus strains for use in animal studies: L. plantarum 30B (which has the highest catalase activity) and L. acidophilus 900 (which has the highest dismutase-like activity). Forty mice (C57B1/6J) were divided into four experimental groups with ten mice in each group. Group I (control group) was not supplemented with Lactobacillus, group II (catalase group) was orally supplemented with L. plantarum 30B, group III (dismutase-like group) was supplemented with L. acidophilus 900, and group IV (mixed group) was supplemented with both Lactobacillus strains. For 23 days, the temperature and body mass of each mouse were recorded and fecal samples for microbiological examination were collected. On day 23, the animals were sacrificed, and their intestines were removed for microbiological and histopathological studies.

Results

Compared to the control group, the highest drop in the body temperature was observed in groups II (P<0.05) and IV (P<0.05). Similarly, groups II (P<0.05) and IV (P<0.05) had the highest drop in body mass. Moreover, histopathological evaluation of colon fragments showed intracryptic abscesses in these groups. Group III mice showed most limited degree of inflammation.

Conclusion

Lactobacillus strains with dismutase-like activity are more effective in alleviating intestinal inflammation than strains producing catalase, suggesting that superoxide anion radical decomposition is crucial in this process.

Seasonal and Sexual Differences in the Microbiota of the Hoopoe Uropygial Secretion

The uropygial gland of hoopoe nestlings and nesting females hosts bacterial symbionts that cause changes in the characteristics of its secretion, including an increase of its antimicrobial activity. These changes occur only in nesting individuals during the breeding season, possibly associated with the high infection risk experienced during the stay in the hole-nests. However, the knowledge on hoopoes uropygial gland microbial community dynamics is quite limited and based so far on culture-dependent and molecular fingerprinting studies. In this work, we sampled wild and captive hoopoes of different sex, age, and reproductive status, and studied their microbiota using quantitative polymerase chain reaction (qPCR), fluorescence in situ hybridization (FISH) and pyrosequencing. Surprisingly, we found a complex bacterial community in all individuals (including non-nesting ones) during the breeding season. Nevertheless, dark secretions from nesting hoopoes harbored significantly higher bacterial density than white secretions from breeding males and both sexes in winter. We hypothesize that bacterial proliferation may be host-regulated in phases of high infection risk (i.e., nesting). We also highlight the importance of specific antimicrobial-producing bacteria present only in dark secretions that may be key in this defensive symbiosis. Finally, we discuss the possible role of environmental conditions in shaping the uropygial microbiota, based on differences found between wild and captive hoopoes.

Translocation of a gut pathobiont drives autoimmunity in mice and humans

Despite multiple associations between the microbiota and immune diseases, their role in autoimmunity is poorly understood. We found that translocation of a gut pathobiont, Enterococcus gallinarum, to the liver and other systemic tissues triggers autoimmune responses in a genetic background predisposing to autoimmunity. Antibiotic treatment prevented mortality in this model, suppressed growth of E. gallinarum in tissues, and eliminated pathogenic autoantibodies and T cells. Hepatocyte-E. gallinarum cocultures induced autoimmune-promoting factors. Pathobiont translocation in monocolonized and autoimmune-prone mice induced autoantibodies and caused mortality, which could be prevented by an intramuscular vaccine targeting the pathobiont. E. gallinarum-specific DNA was recovered from liver biopsies of autoimmune patients, and cocultures with human hepatocytes replicated the murine findings; hence, similar processes apparently occur in susceptible humans. These discoveries show that a gut pathobiont can translocate and promote autoimmunity in genetically predisposed hosts.

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.

Neonatal piglet diarrhoea associated with enteroadherent Enterococcus hirae

Neonatal porcine diarrhoea of uncertain aetiology is an increasing problem in several countries. The aim of the present study was to investigate the unexpected finding of enteroadherent cocci in the small intestine of piglets selected for necropsy examination from six herds (18 diarrhoeic piglets and 11 healthy controls). Gross and microscopical lesions were characterized and selected intestinal sections were further examined by immunohistochemistry for expression of active caspase-3. The enteroadherent bacterium was characterized in situ by Gram staining, ultrastructural imaging, fluorescence in-situ hybridization (FISH) and 16S rRNA gene analysis. Species identification of enterococci from intestinal cultures was performed by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) for one diarrhoeic and one control animal per herd. Gross changes were mild. Microscopically, small intestinal colonization by gram-positive cocci was observed in diarrhoeic animals only and was accompanied by villus atrophy (4/18) and mild epithelial lesions (10/18), including increased apoptosis of enterocytes. Transmission electron microscopy revealed coccoid bacteria adjacent to the epithelium, but without effacement of microvilli. 16S rRNA gene analysis yielded a sequence identical to Enterococcus hirae and FISH identified the enteroadherent bacteria as Enterococcus spp. in all colonized animals. The proportion of bacterial isolates identified as E. hirae by MALDI-TOF MS analysis was significantly higher (P = 0.0138) in diarrhoeic pigs. Species identification was confirmed by species-specific polymerase chain reaction for one E. hirae isolate per herd. These isolates were further tested for antimicrobial susceptibility, which indicated decreased susceptibility to ciprofloxacin for one isolate (minimum inhibitory concentration >4 mg/l). These findings suggested that neonatal porcine diarrhoea was associated with small intestinal colonization by E. hirae accompanied by mucosal lesions.

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.

Mortality in kittens is associated with a shift in ileum mucosa-associated enterococci from Enterococcus hirae to biofilm-forming Enterococcus faecalis and adherent Escherichia coli

Approximately 15% of foster kittens die before 8 weeks of age, with most of these kittens demonstrating clinical signs or postmortem evidence of enteritis. While a specific cause of enteritis is not determined in most cases, these kittens are often empirically administered probiotics that contain enterococci. The enterococci are members of the commensal intestinal microbiota but also can function as opportunistic pathogens. Given the complicated role of enterococci in health and disease, it would be valuable to better understand what constitutes a "healthy" enterococcal community in these kittens and how this microbiota is impacted by severe illness. In this study, we characterized the ileum mucosa-associated enterococcal community of 50 apparently healthy and 50 terminally ill foster kittens. In healthy kittens, Enterococcus hirae was the most common species of ileum mucosa-associated enterococci and was often observed to adhere extensively to the small intestinal epithelium. These E. hirae isolates generally lacked virulence traits. In contrast, non-E. hirae enterococci, notably Enterococcus faecalis, were more commonly isolated from the ileum mucosa of kittens with terminal illness. Isolates of E. faecalis had numerous virulence traits and multiple antimicrobial resistances. Moreover, the attachment of Escherichia coli to the intestinal epithelium was significantly associated with terminal illness and was not observed in any kitten with adherent E. hirae. These findings identify a significant difference in the species of enterococci cultured from the ileum mucosa of kittens with terminal illness compared to the species cultured from healthy kittens. In contrast to prior case studies that associated enteroadherent E. hirae with diarrhea in young animals, these controlled studies identified E. hirae as more often isolated from healthy kittens and adherence of E. hirae as more common and extensive in healthy kittens than in sick kittens.

Quantitative detection of Staphylococcus aureus, Enterococcus faecalis and Pseudomonas aeruginosa in human oral epithelial cells from subjects with periodontitis and periodontal health

Epithelial cells in oral cavities can be considered reservoirs for a variety of bacterial species. A polymicrobial intracellular flora associated with periodontal disease has been demonstrated in buccal cells. Important aetiological agents of systemic and nosocomial infections have been detected in the microbiota of subgingival biofilm, especially in individuals with periodontal disease. However, non-oral pathogens internalized in oral epithelial cells and their relationship with periodontal status are poorly understood. The purpose of this study was to detect opportunistic species within buccal and gingival crevice epithelial cells collected from subjects with periodontitis or individuals with good periodontal health, and to associate their prevalence with periodontal clinical status. Quantitative detection of total bacteria and Staphylococcus aureus, Pseudomonas aeruginosa and Enterococcus faecalis in oral epithelial cells was determined by quantitative real-time PCR using universal and species-specific primer sets. Intracellular bacteria were visualized by confocal microscopy and fluorescence in situ hybridization. Overall, 33% of cell samples from patients with periodontitis contained at least one opportunistic species, compared with 15% of samples from healthy individuals. E. faecalis was the most prevalent species found in oral epithelial cells (detected in 20.6% of patients with periodontitis, P = 0.03 versus healthy individuals) and was detected only in cells from patients with periodontitis. Quantitative real-time PCR showed that high levels of P. aeruginosa and S. aureus were present in both the periodontitis and healthy groups. However, the proportion of these species was significantly higher in epithelial cells of subjects with periodontitis compared with healthy individuals (P = 0.016 for P. aeruginosa and P = 0.047 for S. aureus). Although E. faecalis and P. aeruginosa were detected in 57% and 50% of patients, respectively, with probing depth and clinical attachment level ≥6 mm, no correlation was found with age, sex, bleeding on probing or the presence of supragingival biofilm. The prevalence of these pathogens in epithelial cells is correlated with the state of periodontal disease.

Identification of pathogens in mastitis milk samples with fluorescent in situ hybridization

Traditionally, the bacteriological examination of mastitis milk samples is performed by culture followed by biochemical tests on the cultured bacteria to allow identification of the causative pathogen. Depending on the species involved, this classic identification is time-consuming compared to other techniques such as fluorescent in situ hybridization (FISH), a culture-independent method that utilizes oligonucleotides (labeled with a fluorophore) that are specific to a string of target DNA/RNA. In the current study, the applicability of FISH was evaluated for the detection of mastitis pathogens directly in milk samples. To remove interfering lipids and proteins from mastitis milk samples prior to FISH, a previously published enzymatic treatment with savinase was evaluated. FISH was performed using oligonucleotides specific for Staphylococcus aureus, Streptococcus agalactiae, Streptococcus uberis, Enterococcus faecalis, Enterococcus faecium, Escherichia coli, and Trueperella (Arcanobacterium) pyogenes. The enzymatic pretreatment and the sensitivity of FISH were evaluated using spiked whole milk samples and mastitis milk samples with bacterial loads of less than 10(3) up to 10(8) colony-forming units (CFU)/ml. Bacteria were reliably detected in milk samples with bacterial numbers of 10(6) CFU/ml or higher. However, bacteria present in numbers below 10(6) CFU/ml were not detectable in all cases. The ability of FISH to identify mastitis-causing pathogens directly in milk samples, and therefore earlier than classical culture methods, can supplement the classic diagnostic procedures for mastitis milk samples.

Development of a multispecies biofilm community by four root canal bacteria

INTRODUCTION

The development of multispecies biofilm models are needed to explain the interactions that take place in root canal biofilms during apical periodontitis. The aim of this study was to investigate the ability of 4 root canal bacteria to establish a multispecies biofilm community and to characterize the main structural, compositional, and physiological features of this community.

METHODS

Four clinical isolates isolated from infected root canals, Actinomyces naeslundii, Lactobacillus salivarius, Streptococcus gordonii, and Enterococcus faecalis, were grown together in a miniflow cell system. Simultaneous detection of the 4 species in the biofilm communities was achieved by fluorescence in situ hybridization in combination with confocal microscopy at different time points. The LIVE/DEAD BacLight technique (Molecular Probes, Carlsbad, CA) was used to assess cell viability and to calculate 3-dimensional architectural parameters such as biovolume (μm(3)). Redox fluorescence dye 5-cyano-2,3-ditolyl tetrazolium chloride was used to assess the metabolic activity of biofilm bacteria.

RESULTS

The 4 species tested were able to form stable and reproducible biofilm communities. The biofilms formed in rich medium generally showed continuous growth over time, however, in the absence of glucose biofilms showed significantly smaller biovolumes. A high proportion of viable cells (>90%) were generally observed, and biofilm growth was correlated with high metabolic activity of cells. The community structure of biofilms formed in rich medium did not change considerably over the 120-hour period, during which E. faecalis, L. salivarius, and S. gordonii were most abundant.

CONCLUSIONS

The ability of 4 root canal bacteria to form multispecies biofilm communities shown in this study give insights into assessing the community lifestyle of these microorganisms in vivo. This multispecies model could be useful for further research simulating stresses representative of in vivo conditions.

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.

Detection of microorganisms in blood specimens using matrix-assisted laser desorption ionization time-of-flight mass spectrometry: a review

Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) initiated a revolution in the identification of organisms grown on solid medium, including bacteria and fungi. Rapid identification of organisms responsible for septicaemia, which are typically grown in broth, is now expanding the field of application. Despite the fact that there are fewer than ten reports in the literature, published data indicate that MALDI-TOF MS yields accurate identification of blood-borne organisms in ≥80% of cases for inocula of >10⁷ organisms/mL. A major current limitation is failure to accurately identify Streptococcus pneumoniae among viridans steptococci. Identification is achieved in <2 h, sharply reducing the turn-around time for communication of identification to the clinician. Further progress in handling protocols and automation, and extraction of antibiotic resistance data from the MALDI-TOF MS spectra, will further push this emerging approach as the standard one in the laboratory diagnosis of septicaemia, paving the way to application in further clinical situations and clinical specimens.

In situ molecular diagnosis and histopathological characterization of enteroadherent Enterococcus hirae infection in pre-weaning-age kittens

The bacterial causes of diarrhea can be frustrating to identify, and it is likely that many remain undiagnosed. The pathogenic potential of certain bacteria becomes less ambiguous when they are observed to intimately associate with intestinal epithelial cells. In the present study we sought to retrospectively characterize the clinical, in situ molecular, and histopathological features of enteroadherent bacteria in seven unrelated kittens that were presumptively diagnosed with enteropathogenic Escherichia coli (EPEC) on the basis of postmortem light microscopic and, in some cases, microbiological examination. Characterization of the enteroadherent bacteria in each case was performed by Gram staining, in situ hybridization using fluorescence-labeled oligonucleotide probes, PCR amplification of species-specific gene sequences, and ultrastructural imaging applied to formalin-fixed paraffin-embedded sections of intestinal tissue. In only two kittens was EPEC infection confirmed. In the remaining five kittens, enteroadherent bacteria were identified as Enterococcus spp. The enterococci were further identified as Enterococcus hirae on the basis of PCR amplification of DNA extracted from the formalin-fixed, paraffin-embedded tissue and amplified by using species-specific primers. Transmission electron microscopy of representative lesions from E. coli- and Enterococcus spp.-infected kittens revealed coccobacilli adherent to intestinal epithelial cells without effacement of microvilli or cup-and-pedestal formation. Enterococci were not observed, nor were DNA sequences amplified from intestinal tissue obtained from age-matched kittens euthanized for reasons unrelated to intestinal disease. These studies suggest that E. hirae may be a common cause of enteroadherent bacterial infection in pre-weaning-age kittens and should be considered in the differential diagnosis of bacterial disease in this population.

Rapid identification of bacteria in positive blood culture broths by matrix-assisted laser desorption ionization-time of flight mass spectrometry

Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry is a rapid, accurate method for identifying bacteria and fungi recovered on agar culture media. We report herein a method for the direct identification of bacteria in positive blood culture broths by MALDI-TOF mass spectrometry. A total of 212 positive cultures were examined, representing 32 genera and 60 species or groups. The identification of bacterial isolates by MALDI-TOF mass spectrometry was compared with biochemical testing, and discrepancies were resolved by gene sequencing. No identification (spectral score of < 1.7) was obtained for 42 (19.8%) of the isolates, due most commonly to insufficient numbers of bacteria in the blood culture broth. Of the bacteria with a spectral score of > or = 1.7, 162 (95.3%) of 170 isolates were correctly identified. All 8 isolates of Streptococcus mitis were misidentified as being Streptococcus pneumoniae isolates. This method provides a rapid, accurate, definitive identification of bacteria within 1 h of detection in positive blood cultures with the caveat that the identification of S. pneumoniae would have to be confirmed by an alternative test.

Accelerated identification of Staphylococcus aureus from blood cultures by a modified fluorescence in situ hybridization procedure

This study evaluated fluorescence in situ hybridization (FISH) for rapid identification of Staphylococcus aureus and coagulase-negative staphylococci (CoNS) directly from blood cultures. Initially, 360 blood cultures containing Gram-positive cocci were investigated by a previously described microwave-FISH procedure: 44/49 (89.8 %) S. aureus and 298/299 (99.7 %) CoNS were correctly identified. Because FISH proved useful and reliable but handling was found to be inconvenient, the method was modified by employing a recently developed slide chamber. This reduced the time required from 60 to 30 min. The simplified execution allowed integration of the method into the workflow of a routine laboratory without difficulty. The modified method proved to be highly reliable, identifying 37/37 (100 %) S. aureus and 169/172 (98.2 %) CoNS directly from blood cultures.

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

A newly designed probe for rapid identification of Propionibacterium acnes by fluorescence in situ hybridization was evaluated using 111 isolates from subculture and showed 100% sensitivity and specificity. A sensitivity of 95% and a specificity of 100% were achieved with direct application on 55 blood cultures containing Gram-positive rods.

Detection and identification of specific bacteria in wound biofilms using peptide nucleic acid fluorescent in situ hybridization (PNA FISH)

Biofilms provide a reservoir of potentially infectious micro-organisms that are resistant to antimicrobial agents, and their importance in the failure of medical devices and chronic inflammatory conditions is increasingly being recognized. Particular research interest exists in the association of biofilms with wound infection and non-healing, i.e. chronic wounds. In this study, fluorescent in situ hybridization (FISH) was used in combination with confocal laser scanning microscopy (CLSM) to detect and characterize the spatial distribution of biofilm-forming bacteria which predominate within human chronic skin wounds (Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus sp. and Micrococcus sp.). In vitro biofilms were prepared using a constant-depth film fermenter and a reconstituted human epidermis model. In vivo biofilms were also studied using biopsy samples from non-infected chronic venous leg ulcers. The specificity of peptide nucleic acid (PNA) probes for the target organisms was confirmed using mixed preparations of planktonic bacteria and multiplex PNA probing. Identification and location of individual bacterial species within multi-species biofilms demonstrated that P. aeruginosa was predominant. CLSM revealed clustering of individual species within mixed-species biofilms. FISH analysis of archive chronic wound biopsy sections showed bacterial presence and allowed bacterial load to be determined. The application of this standardized procedure makes available an assay for identification of single- or multi-species bacterial populations in tissue biopsies. The technique provides a reliable tool to study bacterial biofilm formation and offers an approach to assess targeted biofilm disruption strategies in vivo.

Rapid identification of beta-hemolytic streptococci by fluorescence in situ hybridization (FISH)

Rapid identification of pathogenic, beta-hemolytic streptococci is important for treatment decisions. We evaluated fluorescence in situ hybridization (FISH) for this purpose using 23 reference strains, 157 clinical isolates, and 80 blood cultures showing streptococci in the Gram stain. With a sensitivity and specificity in excess of 99%, FISH proved to be suitable for rapid identification of beta-hemolytic streptococci in a diagnostic laboratory.

Detection of mutations conferring resistance to linezolid in Enterococcus spp. by fluorescence in situ hybridization

A fluorescence in situ hybridization (FISH) assay was established to detect linezolid resistance (conferred by the mutation 2576G>T in the gene coding for the 23 string of the ribosomal RNA) in enterococci. The assay was evaluated with 106 Enterococcus isolates; it showed a sensitivity of 100% for the detection of phenotypic resistance and was even able to identify a single mutated allele in phenotypically linezolid-susceptible isolates.