Comparing culture and molecular methods for the identification of microorganisms involved in necrotizing soft tissue infections.

BACKGROUND: Necrotizing soft tissue infections (NSTIs) are a group of infections affecting all soft tissues. NSTI involves necrosis of the afflicted tissue and is potentially life threatening due to major and rapid destruction of tissue, which often leads to septic shock and organ failure. The gold standard for identification of pathogens is culture; however molecular methods for identification of microorganisms may provide a more rapid result and may be able to identify additional microorganisms that are not detected by culture. METHODS: In this study, tissue samples (n = 20) obtained after debridement of 10 patients with NSTI were analyzed by standard culture, fluorescence in situ hybridization (FISH) and multiple molecular methods. The molecular methods included analysis of microbial diversity by 1) direct 16S and D2LSU rRNA gene Microseq 2) construction of near full-length 16S rRNA gene clone libraries with subsequent Sanger sequencing for most samples, 3) the Ibis T5000 biosensor and 4) 454-based pyrosequencing. Furthermore, quantitative PCR (qPCR) was used to verify and determine the relative abundance of Streptococcus pyogenes in samples. RESULTS: For 70 % of the surgical samples it was possible to identify microorganisms by culture. Some samples did not result in growth (presumably due to administration of antimicrobial therapy prior to sampling). The molecular methods identified microorganisms in 90 % of the samples, and frequently detected additional microorganisms when compared to culture. Although the molecular methods generally gave concordant results, our results indicate that Microseq may misidentify or overlook microorganisms that can be detected by other molecular methods. Half of the patients were found to be infected with S. pyogenes, but several atypical findings were also made including infection by a) Acinetobacter baumannii, b) Streptococcus pneumoniae, and c) fungi, mycoplasma and Fusobacterium necrophorum. CONCLUSION: The study emphasizes that many pathogens can be involved in NSTIs, and that no specific "NSTI causing" combination of species exists. This means that clinicians should be prepared to diagnose and treat any combination of microbial pathogens. Some of the tested molecular methods offer a faster turnaround time combined with a high specificity, which makes supplemental use of such methods attractive for identification of microorganisms, especially for fulminant life-threatening infections such as NSTI.

Unexpected Diagnosis of Cerebral Toxoplasmosis by 16S and D2 Large-Subunit Ribosomal DNA PCR and Sequencing.

The protozoan parasite Toxoplasma gondii causes severe opportunistic infections. Here, we report an unexpected diagnosis of cerebral toxoplasmosis. T. gondii was diagnosed by 16S and D2 large-subunit (LSU) ribosomal DNA (rDNA) sequencing of a cerebral biopsy specimen and confirmed by T. gondii-specific PCR and immunohistochemistry. The patient was later diagnosed with HIV/AIDS.

Sinus biofilms in patients with cystic fibrosis: is adjusted eradication therapy needed?

The paranasal sinuses can be a focus for colonisation of the cystic fibrosis (CF) lungs with pathogens. In the sinuses, bacteria can adapt to the lung environment and enhance their antibiotic resistance, with biofilm formation thought to be the most important adaptive mechanism, causing recalcitrant disease. The presence of biofilms in CF sinuses is sparsely described. In this descriptive cross-sectional study, the sinus mucosa from 16 CF patients were analysed by fluorescence in situ hybridization using specific peptide nucleic acid (PNA-FISH) probes for Pseudomonas aeruginosa and Staphylococcus aureus to demonstrate the presence of biofilms. Small clusters of biofilm were visualised lining the sinus mucosa of CF patients. Biofilms were found in 10 out of 18 cases; 7 with intermittent lung colonisation, 2 chronically infected, and one lung transplanted patient. Finding P. aeruginosa biofilms in intermittently lung-colonised patients encourage us to intensify the attempt to eradicate pathogenic bacteria from the CF sinuses in an early stage using combined antibiotic therapy in the prolonged exposure of the sinus-mucosal surface.

Bacterial infection as a likely cause of adverse reactions to polyacrylamide hydrogel fillers in cosmetic surgery.

BACKGROUND: The etiology of long-lasting adverse reactions to gel fillers used in cosmetic surgery is not known. Bacterial infection and immunological reaction to the product have been suggested. METHODS: We performed a case-control study, with 77 biopsies and 30 cytology specimens originating from 59 patients with adverse reactions to polyacrylamide gel, and 54 biopsies and 2 cytology specimens from 28 control subjects with no adverse reactions. Samples from 5 patients and 4 controls could not be investigated for presence of bacteria owing to limited material. Samples from the remaining 54 patients and 24 controls were systematically examined for the presence of bacteria by culture, 16S rRNA gene sequencing, Gram stain, and fluorescence in situ hybridization. RESULTS: Bacteria, mostly normal skin bacteria such as Staphylococcus epidermidis and Propionibacterium acnes, were identified in bacteriologically investigated samples from 53 of 54 patients (98%), and in none of the 24 controls (0%). The bacteria were lying in small clusters, which in symptomatic lesions were detected up to 5 years postinjection. CONCLUSIONS: Commensal bacteria of low virulence are capable of producing long-term infection in the presence of polyacrylamide filler in cosmetic surgery, possibly due to a biofilm mode of growth. Adequate skin preparation and use of sterile technique in these procedures are mandatory, but antibiotic prophylaxis prior to injection of nondegradable gels like polyacrylamide should be explored as well.

Direct sequencing and RipSeq interpretation as a tool for identification of polymicrobial infections.

In this study, RipSeq Mixed, a software resolving uninterpretable mixed DNA sequencing chromatograms, revealed the bacterial content of 15 polymicrobial samples. Direct sequencing combined with RipSeq Mixed constitutes a valuable supplement to cultivation, particularly when cultivation is negative and direct sequencing is inconclusive despite continued clinical indications of infection.

Bacterial Aggregates Establish at the Edges of Acute Epidermal Wounds.

Objective: The bacterial composition and distribution were evaluated in acute standardized epidermal wounds and uninjured skin by a molecular in situ technology benchmarked to conventional culturing. This was done to reveal whether bacterial biofilm is present in acute wounds. Approach: On the buttock of 26 healthy volunteers, 28 suction blisters were made and de-roofed. Four wounds were biopsied immediately after wounding, whereas the remaining 24 wounds were treated daily with sterile deionized water and covered with a moisture-retaining dressing. On day 4 post-wounding, swabs were obtained for culturing from the wounds and adjacent skin, and the wounds including adjacent skin were excised. Tissue sections were stained with peptide nucleic acid (PNA) fluorescence in situ hybridization (FISH) probes, counterstained by 4',6-diamidino-2-phenylindole, and evaluated by confocal laser scanning microscopy (CLSM). Results: No bacterial aggregates were detected at day 0. At day 4, coagulase-negative staphylococci (CoNS) were the sole bacteria identified by CLSM/PNA-FISH and culturing. CoNS was isolated from 78% of the wound swabs and 48% of the skin swabs. Bacterial aggregates (5-150 µm) were detected by PNA-FISH/CLSM in the split stratum corneum and fibrin deposits at the wound edges and in the stratum corneum and the hair follicles of the adjacent skin. The bacterial aggregates were more common (p = 0.0084) and larger (p = 0.0083) at wound edges than in the adjacent skin. Innovation: Bacterial aggregates can establish in all wound types and may have clinical significance in acute wounds. Conclusion: Bacterial aggregates were observed at the edges of acute epidermal wounds, indicating initiated establishment of a biofilm.

Implants induce a new niche for microbiomes.

Although much work is being done to develop new treatments, research and knowledge regarding factors underlying implant-related microbial colonization leading to infection are less comprehensive. Presence of microorganisms in and around implants clinically characterized as uninfected remains unknown. The objective of this study was to detect and identify bacteria and fungi on implants from various groups of patients with no prior indications of implant related infections. Patient samples (implants and tissue) were collected from five different hospitals in the Capital region of Denmark. By in-depth microbiological detection methods, we examined the prevalence of bacteria and fungi on 106 clinically uninfected implants from four patient groups (aseptic loosening, healed fractures, craniofacial complications and recently deceased). Of 106 clinically uninfected implants and 39 negative controls investigated, 66% were colonized by bacteria and 40% were colonized by fungi (p < 0.0001 compared to negative controls). A large number of microbes were found to colonize the implants, however, the most prevalent microbes present were not common aetiological agents of implant infections. The findings indicate that implants provide a distinct niche for microbial colonization. These data have broad implications for medical implant recipients, as well as for supporting the idea that the presence of foreign objects in the body alters the human microbiome by providing new colonization niches.

Specific Antibodies to Staphylococcus aureus Biofilm Are Present in Serum from Pigs with Osteomyelitis.

BACKGROUND: The Achilles heel in osteomyelitis is that bacteria, primarily Staphylococcus aureus, grow as a biofilm in the bone lesions. MATERIALS AND METHODS: In the present study, we explored the serum level of specific antibodies to S. aurues biofilm in porcine models of osteomyelitis. RESULTS: Significantly increased levels of antibodies towards the specific biofilm antigen SA0688 were measured in serum from pigs with S. aureus-associated acute and chronic osteomyelitis 5-7 and 10-14 days after inoculation, respectively. Simultaneously with raised antibody levels, an increase in serum interleukin 6 (IL 6) levels was also seen. CONCLUSION: The observed biofilm-specific antibody response represents a T-helper cell 17 (Th17) response and potentially a T-helper cell 1 (Th1) response. This is in agreement with previous studies in mice and rabbits speculating that S. aureus induces a Th1- and Th17-biased adaptive immune response, instead of a protective Th2 response, in order to evade the immune system, resulting in a chronic infection.

Autofluorescence in samples obtained from chronic biofilm infections--"all that glitters is not gold".

When looking at tissue sections of ex vivo samples, autofluorescence can be a major cause of artifacts and misinterpretations. We here reiterate evidence that autofluorescing granules, often hemosiderin but also ceroid or mucinogen granules, are severe obstacles when imaging and diagnosing biofilm infections through fluorescent imaging techniques. We used confocal laser scanning microscopy with spectral analysis for autofluorescence detection as well as standard histological stains in order to identify the culprit and show that these granules might very well be mistaken for bacterial biofilms. Furthermore, we hypothesize that the increased amount of autofluorescing granules may be a consequence of prolonged inflammation as a consequence of chronic biofilm infections.

Bacterial biofilm formation and treatment in soft tissue fillers.

Injection of soft tissue fillers plays an important role in facial reconstruction and esthetic treatments such as cosmetic surgery for lip augmentation and wrinkle smoothening. Adverse events are an increasing problem, and recently, it has been suggested that bacteria are the cause of a vast fraction these. We developed a novel mouse model and evaluated hyaluronic acid gel, calcium hydroxyl apatite microspheres, and polyacrylamide hydrogel for their potential for sustaining bacterial infections and their possible treatments. We were able to culture Pseudomonas aeruginosa, Staphylococcus epidermidis, and Probionibacterium acnes in all three gels. When contaminated gels were left for 7 days in a mouse model, we found sustainment of bacterial infection with the permanent gel, less with the semi-permanent gel, and no growth within the temporary gel. Evaluation of treatment strategies showed that once the bacteria had settled (into biofilms) within the gels, even successive treatments with high concentrations of relevant antibiotics were not effective. Our data substantiate bacteria as a cause of adverse reactions reported when using tissue fillers, and the sustainability of these infections appears to depend on longevity of the gel. Most importantly, the infections are resistant to antibiotics once established but can be prevented using prophylactic antibiotics.

A case of human babesiosis in Denmark.

We report the first human case of Babesia microti infection imported to Denmark from the United States by a 64 year old female traveller with fever of unknown origin. The case raises the possibility that Babesia-infections may be under-diagnosed, illustrates the importance of a thorough travel history and discusses important diagnostic pitfalls.

A non-fatal case of invasive zygomycete (Lichtheimia corymbifera) infection in an allogeneic haematopoietic cell transplant recipient.

Post-transplant infections in allogeneic haematopoietic cell transplant (allo-HCT) recipients often have severe consequences. This is especially the case when dealing with zygomycete infections where the result is often fatal. A major problem when dealing with zygomycete infections is the need for an accurate and fast diagnosis as the phylum is highly resistant towards the conventional antifungals. We herein describe a non-fatal case of Lichtheimia corymbifera infection in an allo-HCT recipient.

Complete genome sequence of the cystic fibrosis pathogen Achromobacter xylosoxidans NH44784-1996 complies with important pathogenic phenotypes.

Achromobacter xylosoxidans is an environmental opportunistic pathogen, which infects an increasing number of immunocompromised patients. In this study we combined genomic analysis of a clinical isolated A. xylosoxidans strain with phenotypic investigations of its important pathogenic features. We present a complete assembly of the genome of A. xylosoxidans NH44784-1996, an isolate from a cystic fibrosis patient obtained in 1996. The genome of A. xylosoxidans NH44784-1996 contains approximately 7 million base pairs with 6390 potential protein-coding sequences. We identified several features that render it an opportunistic human pathogen, We found genes involved in anaerobic growth and the pgaABCD operon encoding the biofilm adhesin poly-ß-1,6-N-acetyl-D-glucosamin. Furthermore, the genome contains a range of antibiotic resistance genes coding efflux pump systems and antibiotic modifying enzymes. In vitro studies of A. xylosoxidans NH44784-1996 confirmed the genomic evidence for its ability to form biofilms, anaerobic growth via denitrification, and resistance to a broad range of antibiotics. Our investigation enables further studies of the functionality of important identified genes contributing to the pathogenicity of A. xylosoxidans and thereby improves our understanding and ability to treat this emerging pathogen.