Clinical Utility of Universal Broad-Range Polymerase Chain Reaction Amplicon Sequencing for Pathogen Identification: A Retrospective Cohort Study

We assessed the real-world utility of universal broad-range polymerase chain reaction sequencing for pathogen detection. Among 1062 clinical samples, 107/1062 (10.1%) had a clinically significant, positive result, with substantial variation by specimen type. Clinical management was changed in 44/1062 (4.1%). These data can help maximize utility of this emerging diagnostic.

Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory

This review provides a state-of-the-art description of the performance of Sanger cycle sequencing of the 16S rRNA gene for routine identification of bacteria in the clinical microbiology laboratory. A detailed description of the technology and current methodology is outlined with a major focus on proper data analyses and interpretation of sequences. The remainder of the article is focused on a comprehensive evaluation of the application of this method for identification of bacterial pathogens based on analyses of 16S multialignment sequences. In particular, the existing limitations of similarity within 16S for genus- and species-level differentiation of clinically relevant pathogens and the lack of sequence data currently available in public databases is highlighted. A multiyear experience is described of a large regional clinical microbiology service with direct 16S broad-range PCR followed by cycle sequencing for direct detection of pathogens in appropriate clinical samples. The ability of proteomics (matrix-assisted desorption ionization-time of flight) versus 16S sequencing for bacterial identification and genotyping is compared. Finally, the potential for whole-genome analysis by next-generation sequencing (NGS) to replace 16S sequencing for routine diagnostic use is presented for several applications, including the barriers that must be overcome to fully implement newer genomic methods in clinical microbiology. A future challenge for large clinical, reference, and research laboratories, as well as for industry, will be the translation of vast amounts of accrued NGS microbial data into convenient algorithm testing schemes for various applications (i.e., microbial identification, genotyping, and metagenomics and microbiome analyses) so that clinically relevant information can be reported to physicians in a format that is understood and actionable. These challenges will not be faced by clinical microbiologists alone but by every scientist involved in a domain where natural diversity of genes and gene sequences plays a critical role in disease, health, pathogenicity, epidemiology, and other aspects of life-forms. Overcoming these challenges will require global multidisciplinary efforts across fields that do not normally interact with the clinical arena to make vast amounts of sequencing data clinically interpretable and actionable at the bedside.

Development of a DNA microarray assay for rapid detection of fifteen bacterial pathogens in pneumonia

Background

The rapid identification of pathogenic bacteria is important for determining an appropriate antimicrobial therapy for pneumonia, but traditional bacterial culture is time-consuming and labourious. The aim of this study was to develop and evaluate a DNA microarray assay for the simultaneous detection of fifteen bacterial species directly from respiratory tract specimens in patients with pneumonia. These species included Streptococcus pneumoniae, Staphylococcus aureus, Haemophilus influenzae, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter baumannii, Mycoplasma pneumoniae, Enterococcus faecalis, Enterococcus faecium, Enterobacter cloacae, Stenotrophomonas maltophilia, Burkholderia cepacia, Legionella pneumophila and Chlamydia pneumoniae. The 16S rDNA genes and other specific genes of each pathogen were chosen as the amplification targets, amplified via multiplex polymerase chain reaction (PCR), and hybridized to oligonucleotide probes in a microarray.

Results

The DNA microarray detection limit was 10³ copies/μL. Nineteen standard strains and 119 clinical isolates were correctly detected with our microarray, and 3 nontarget species from 4 clinical isolates were not detected. Additionally, bacterial pathogens were accurately identified when two or three bacterial targets were mixed together. Furthermore, the results for 99.4% (156/157) of clinical specimens were the same as those from a conventional assay.

Conclusions

We developed a DNA microarray that could simultaneously detect various bacterial pathogens in pneumonia. The method described here has the potential to provide considerable labour and time savings due to its ability to screen for 15 bacterial pathogens simultaneously.

Pleural Effusion in Adults-Etiology, Diagnosis, and Treatment

BACKGROUND

Pleural effusion is common in routine medical practice and can be due to many different underlying diseases. Precise differential diagnostic categorization is essential, as the treatment and prognosis of pleural effusion largely depend on its cause.

METHODS

This review is based on pertinent publications retrieved by a selective search in PubMed and on the authors' personal experience.

RESULTS

The most common causes of pleural effusion are congestive heart failure, cancer, pneumonia, and pulmonary embolism. Pleural fluid puncture (pleural tap) enables the differentiation of a transudate from an exudate, which remains, at present, the foundation of the further diagnostic work-up. When a pleural effusion arises in the setting of pneumonia, the potential devel- opment of an empyema must not be overlooked. Lung cancer is the most common cause of malignant pleural effusion, followed by breast cancer. Alongside the treatment of the underlying disease, the specific treatment of pleural effusion ranges from pleurodesis, to thoracoscopy and video-assisted thoracoscopy (with early consultation of a thoracic surgeon), to the placement of a permanently indwelling pleural catheter.

CONCLUSION

The proper treatment of pleural effusion can be determined only after meticulous differential diagnosis. The range of therapeutic options has recently become much wider. More data can be expected in the near future concerning diagnostic test- ing for the etiology of the effusion, better pleurodetic agents, the development of interventional techniques, and the genetic background of the affected patients.

Human intervertebral discs harbour a unique microbiome and dysbiosis determines health and disease

BACKGROUND

To document the role of sub-clinical infections in disc disorders and investigate the existence of microbiome in intervertebral discs (IVD).

METHODS

Genomic DNA from 24 lumbar IVDs [8-MRI normal discs (ND) from brain dead yet alive organ donors, 8-disc herniation (DH), 8-disc degeneration (DD)] was subjected to 16SrRNA sequencing for profiling the diversity of human disc microbiome in health and disease. The disc microbiome was further compared to established human gut and skin microbiomes.

RESULTS

All healthy MRI normal discs from brain dead yet alive organ donors also had a rich bacterial presence. A total of 424 different species (355-ND, 346-DD, and 322-DH) were detected, with 42.75% OTUs being classified at kingdom level, 44% at the phylum level, 22.62% at genus level, and 5.5% at species level. Varying biodiversity and abundance between healthy and diseased discs were documented with protective bacteria being abundant in normal discs, and putative pathogens abundant in DD and DH. Propionibacterium acnes had a similar but lower abundance to other pathogens in all three groups ND (3.07%), DD (3.88%), DH (1.56%). Fifty-eight bacteria were common between gut and IVD microbiomes, 29 between skin and IVD microbiomes, and six common to gut/skin/IVD.

CONCLUSION

Our study challenges the hitherto concept of sterility in healthy IVD and documented a microbiome even in MRI normal healthy discs. The varying abundance of bacteria between ND, DD, and DH documents 'dysbiosis' as a possible etiology of DD. Many known pathogens were identified in greater abundance than Propionibacterium acnes, and there was evidence for the presence of the gut/skin/spine microbiome axis.

Clinical utility and cost-effectiveness of bacterial 16S rRNA and targeted PCR based diagnostic testing in a UK microbiology laboratory network

16S ribosomal-ribonucleic acid polymerase chain reaction (PCR) and targeted PCR aid microbiological diagnosis in culture-negative clinical samples. Despite routine clinical use, there remains a paucity of data on their effectiveness across a variety of clinical sample types, and cost-effectiveness. In this 4 year multicentre retrospective observational study, all clinical samples referred for 16S PCR and/or targeted PCR from a laboratory network serving seven London hospitals were identified. Laboratory, clinical, prescribing, and economic variables were analysed. 78/607 samples were 16S PCR positive; pus samples were most frequently positive (29/84; p < 0.0001), and CSF least (8/149; p = 0.003). 210/607 samples had targeted PCR (361 targets requested across 23 organisms) with 43/361 positive; respiratory samples (13/37; p = 0.01) had the highest detection rate. Molecular diagnostics provided a supportive microbiological diagnosis for 21 patients and a new diagnosis for 58. 14/91 patients with prescribing information available and a positive PCR result had antimicrobial de-escalation. For culture-negative samples, mean cost-per-positive 16S PCR result was £568.37 and £292.84 for targeted PCR, equating to £4041.76 and £1506.03 respectively for one prescription change. 16S PCR is more expensive than targeted PCR, with both assisting in microbiological diagnosis but uncommonly enabling antimicrobial change. Rigorous referral pathways for molecular tests may result in significant fiscal savings.

Comparison of 16S Ribosomal RNA Targeted Sequencing and Culture for Bacterial Identification in Normally Sterile Body Fluid Samples: Report of a 10-Year Clinical Laboratory Review

As 16S ribosomal RNA (rRNA)-targeted sequencing can detect DNA from non-viable bacteria, it can be used to identify pathogens from clinical samples even in patients pretreated with antibiotics. We compared the results of 16S rRNA-targeted sequencing and culture for identifying bacterial species in normally sterile body fluid (NSBF): cerebrospinal, pericardial, peritoneal and pleural fluids. Over a 10-year period, a total of 312 NSBF samples were evaluated simultaneously using 16S rRNA-targeted sequencing and culture. Results were concordant in 287/312 (92.0%) samples, including 277 (88.8%) negative and 10 (3.2%) positive samples. Of the 16 sequencing-positive, culture-negative samples, eight showed clinically relevant isolates that included Fusobacterium nucleatum subsp. nucleatum, Streptococcus pneumoniae, and Staphylococcus spp. All these samples were obtained from the patients pretreated with antibiotics. The diagnostic yield of 16S rRNA-targeted sequencing combined with culture was 11.2%, while that of culture alone was 6.1%. 16S rRNA-targeted sequencing in conjunction with culture could be useful for identifying bacteria in NSBF samples, especially when patients have been pretreated with antibiotics and when anaerobic infection is suspected.

Optimization of 16S rRNA gene analysis for use in the diagnostic clinical microbiology service

Broad-range amplification and sequencing of the 16S rRNA gene, directly from clinical samples, is a method that potentially allows detection of any cultivable or non-cultivable bacteria. However, the method is prone to false positive results due to PCR contamination. Another concern is the human DNA abundance compared to bacterial DNA in samples from sterile sites. Those factors may decrease the sensitivity and specificity of the assay and can complicate the analysis and interpretation of the results. The objective of this prospective study was to try to avoid the most common pitfalls, mentioned above, and develop a molecular 16S assay with a high clinical sensitivity and specificity. Fifty-six consecutive tissue samples from patients with suspected deep infections were extracted by 3 different DNA-extraction methods; two based on a principle of bacterial DNA enrichment, and one conventional DNA extraction method. We compared three primer pairs, including both conventional and DPO principle, targeting different variable regions of the 16S rRNA gene. Results from routine tissue culture were used as reference. Clinical data was recorded from patient charts and analyzed in parallel. Of a total of 56 samples, collected from 39 patients, 70% (39 samples) were assessed as true infections by analysis of clinical data. Bacterial enrichment extraction increased sensitivity from 54% to 72%. The 2 sets of primer pairs defining region V1-V3 and V3-V4, showed similar sensitivity, but DPO-primers resulted in better specificity, i.e. less contaminations. The primer pairs covering V1-V8 show significantly lower sensitivity (p < .001) than V1-V3 and V3-V4. Optimizing extraction protocols and choice of primers can increase the sensitivity and specificity of a molecular 16S-analysis, rendering a valuable complement to tissue culture.

Molecular identification and diversity analysis of dental bacteria in diabetic and non-diabetic females from Saudi Arabia

Periodontal disease is a chronic infectious disease, which is characterized by the damaged dental hard tissue by lactic acid generated by microorganisms after the fermentation of carbohydrates rich diet. The risk of periodontal disease is known to be higher in diabetic patients. We compared the diversity of five commonly occurring dental bacteria including Porphyromonas gingivalis, Tannerella forsythia, Capnocytophaga ochracea, Prevotella intermedia, and Aggregatibacter actinomycetemcomitans in 14 type-2 diabetic patients and equal numbers of healthy controls. The subgingival samples were collected using sterile paper points. We used 16S rRNA sequence specific primers for PCR-based identification of dental bacteria. Our results showed that A. actinomycetemcomitans was completely absent in control subjects but present in 43% of diabetic patients. C. ochracea was highly prevalent in diabetic patients (100%) as compared to controls (28.5%). The frequency of other three bacterial species was also higher in diabetic patients than control subjects. These findings indicate that dental bacteria are highly prevalent in subgingival pockets of diabetic patients. Therefore, proper monitoring of diabetic patients for dental care is important to prevent bacterial growth and its sequela in risky individuals. Further case-control studies using larger sample size would help in validating the association between oral diseases and diabetes.

DAMIAN: an open source bioinformatics tool for fast, systematic and cohort based analysis of microorganisms in diagnostic samples

We describe DAMIAN, an open source bioinformatics tool designed for the identification of pathogenic microorganisms in diagnostic samples. By using authentic clinical samples and comparing our results to those from established analysis pipelines as well as conventional diagnostics, we demonstrate that DAMIAN rapidly identifies pathogens in different diagnostic entities, and accurately classifies viral agents down to the strain level. We furthermore show that DAMIAN is able to assemble full-length viral genomes even in samples co-infected with multiple virus strains, an ability which is of considerable advantage for the investigation of outbreak scenarios. While DAMIAN, similar to other pipelines, analyzes single samples to perform classification of sequences according to their likely taxonomic origin, it also includes a tool for cohort-based analysis. This tool uses cross-sample comparisons to identify sequence signatures that are frequently present in a sample group of interest (e.g., a disease-associated cohort), but occur less frequently in control cohorts. As this approach does not require homology searches in databases, it principally allows the identification of not only known, but also completely novel pathogens. Using samples from a meningitis outbreak, we demonstrate the feasibility of this approach in identifying enterovirus as the causative agent.

16S rRNA PCR on clinical specimens: Impact on diagnosis and therapeutic management

OBJECTIVE

16S rRNA PCR (16S PCR) performed on clinical samples contributes to bacterial identification in cases of negative culture due to an antibiotic therapy. Sensitivity of the 16S PCR is low (19-42%). Little data is available on its impact on the management of patients. We aimed to evaluate the contribution of 16S PCR to diagnosis and therapeutic management at the university hospital of Dijon, France.

PATIENTS AND METHODS

16S PCR was performed on the clinical specimens of 132 patients. Clinical settings, laboratory results, and data on antibiotic therapy were collected, as well as conclusions drawn from the 16S PCR result by physicians. Each case was analyzed to determine if the 16S PCR was helpful. The relevance of the 16S PCR was also assessed.

RESULTS

The 16S PCR yield was 27.3%, ranging from 14.3% to 64.3% depending on the type of specimen. 16S PCR had a positive impact on diagnosis in 28.8% of cases. Five negative 16S PCR results were considered helpful as they contributed to ruling out bacterial infection. 16S PCR led to treatment changes in six patients (4.5%): three narrower spectrums, two treatment adaptations, and one discontinuation. The 16S PCR was considered "non-relevant" in 35 cases (26.5%). None of these 35 PCRs contributed to the patient's management.

CONCLUSION

Physicians should be aware of performances of 16S PCR. Dialogue between physicians and bacteriologists is essential for appropriate selection of indications and correct interpretation of results.

Identification of uncultured bacteria from abscesses of exotic pet animals using broad-range nested 16S rRNA polymerase chain reaction and Sanger sequencing

Background:

The Sanger sequencing technique has been questioned and challenged by advanced high-throughput sequencing approaches. Sanger sequencing seems to be an obsolete technology. However, there are still research problems that could be answered using the Sanger sequencing technology. Fastidious obligate anaerobic bacteria are mostly associated with abscesses in animals. These bacteria are difficult to isolate from abscesses and are frequently excluded due to the bias of conventional bacterial culturing.

Aim:

This study demonstrated the usefulness of a broad-range polymerase chain reaction (PCR) with Sanger sequencing to identify the majority population of bacteria in abscesses from exotic pet animals.

Materials and Methods:

This study performed a pilot investigation of abscesses from 20 clinical cases (17 rabbits, 2 hedgehogs, and 1 sugar glider) using standard culture methods for both aerobes and anaerobes and broad-range nested PCR targeting the 16S rRNA gene followed by the Sanger sequencing technique.

Results:

The standard culture and PCR techniques detected bacteria in 9 and 17 of 20 samples, respectively. From the 17 sequencings of the 16S rRNA, 10 PCR products were found to be closely related with obligate anaerobes including Bacteroides spp., Fusobacterium spp., Prevotella spp. Phylogenetic analysis using the rpoB gene revealed that the species for the Bacteroides was thetaiotaomicron and for the Fusobacterium was varium and nucleatum. However, the amplification of the rpoB gene for the Prevotella spp. was unsuccessful. Correlations between the standard culture and PCR techniques were found in 9 (6 positive and 3 negative samples) of 20 samples. Eleven samples were discordant between the standard culture and PCR techniques which were composed of eight samples negative by culture but positive by PCR and three samples had different bacteria by the culture and PCR techniques.

Conclusion:

According to this study, broad-range PCR combined with Sanger sequencing might be useful for the detection of dominant anaerobic bacteria in abscesses that were overlooked based on conventional bacterial culture.

Bacteria Detected in both Urine and Open Wounds in Nursing Home Residents: a Pilot Study

Older adults, specifically those in nursing facilities, are more susceptible to developing chronic open nonhealing wounds. Chronic open nonhealing wounds severely impact an individual’s quality of life and can lead to other comorbidities, such as infection. Recent evidence suggests that the open wound bacterial community can influence wound healing and repair. It is important to understand all sources of open wound contamination to improve preventative infection measures and treatment protocols. In this pilot study, we investigated if bacterial species isolated from urine can also be isolated from open wounds located between the levels of the umbilicus and mid-thigh in the same patient at the same point in time. A growing body of evidence suggests that urine can harbor a microbial community, even in asymptomatic individuals, and older adults are more prone to urinary incontinence. This is the first study to investigate bacterial species concordance between these two anatomical sites. We found, using both culture-dependent and -independent methods, that the same bacterial species can colonize both the urine and wound in one patient at one point in time. Further studies are needed to investigate if these species are of the same lineage and if the urinary microbiota are able to seed colonization of these types of open wounds.

Nursing home residents are at a greater risk of developing pressure injuries that develop into an open wound, which can become colonized with bacteria. Understanding the factors that influence microbial colonization of open wounds can lead to the prevention of infections. The relationship between bacteria found in urine and those in open wounds is currently unknown. To determine if bacterial species colonizing open wounds are also found in the urine, we conducted a pilot study with nursing home residents, comparing bacterial species present in the urine with those present in wounds between the umbilicus and mid-thigh. To identify microbial species that were present in both urine and open wound at one time point in one patient, standard clinical bacteriologic culture techniques followed by matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) were used, as well as 16S rRNA-encoding gene amplicon sequencing. We found some bacterial species detected in urine were also detected in open wounds in one individual at one time point, using both culture-dependent and -independent techniques. Bacterial species that were more often detected, using culture-dependent and -independent methods, at both sites included Enterococcus faecalis, Proteus mirabilis, Escherichia coli, and Providencia stuartii. This pilot study provides evidence that bacterial species identified within the urine can also be identified in open wounds in the same patient at one point in time. Further studies are needed to investigate if these species are of the same lineage and if the urinary microbiota are able to seed colonization of open wounds below the umbilicus.

IMPORTANCE Older adults, specifically those in nursing facilities, are more susceptible to developing chronic open nonhealing wounds. Chronic open nonhealing wounds severely impact an individual’s quality of life and can lead to other comorbidities, such as infection. Recent evidence suggests that the open wound bacterial community can influence wound healing and repair. It is important to understand all sources of open wound contamination to improve preventative infection measures and treatment protocols. In this pilot study, we investigated if bacterial species isolated from urine can also be isolated from open wounds located between the levels of the umbilicus and mid-thigh in the same patient at the same point in time. A growing body of evidence suggests that urine can harbor a microbial community, even in asymptomatic individuals, and older adults are more prone to urinary incontinence. This is the first study to investigate bacterial species concordance between these two anatomical sites. We found, using both culture-dependent and -independent methods, that the same bacterial species can colonize both the urine and wound in one patient at one point in time. Further studies are needed to investigate if these species are of the same lineage and if the urinary microbiota are able to seed colonization of these types of open wounds.

Effectiveness of 16S ribosomal DNA real-time PCR and sequencing for diagnosing bacterial keratitis

PURPOSE

To evaluate the efficacy of real-time PCR for 16S ribosomal DNA (16S r-DNA) and sequencing for diagnosing microbial keratitis.

METHODS

We studied 272 eyes of 272 patients with keratitis. Eyes with keratitis were classified as "definite" (N = 118), "likely" (N = 71), or "non-bacterial" (N = 83) to have bacterial keratitis. The diagnostic efficacy of real-time PCR and conventional testing was determined by receiver operating characteristic analysis. The copy numbers of bacterial DNA and clinical characteristics were retrospectively analyzed for association with concordant culture results in the "definite" cases.

RESULTS

The level of bacterial DNA was significantly associated with the diagnostic probability of the three diagnostic categories. The level of bacterial DNA had comparable diagnostic efficacy with the area under the curve (AUC) at 0.67, by culture at 0.65, and by smear testing at 0.73. The efficacy was significantly improved by combining the DNA level with the conventional culture testing with an AUC of 0.81. Analysis of the "definite" cases showed culture positivity in 51.8% (58 eyes), and of these, 41 eyes (70.7%) were higher than the cutoff PCR values and 40 eyes were identified by 16S r-DNA sequencing. In the culture-negative eyes, the level of bacterial DNA was significantly lower (P = 0.0008). Eyes with higher bacterial DNA levels had significantly concordant outcomes with sequencing and culture results (P = 0.006). Previous antibiotic treatments decreased the bacterial DNA amount by 0.09-fold, and it was a significant factor for discordance (P = 0.006).

CONCLUSION

Quantification of the bacterial DNA level and conventional testing improves the diagnostic efficacy of infectious bacterial keratitis.

Broad-range PCR Application in a Large Academic Pediatric Center: Clinical Value and Challenges in Diagnosis of Infectious Diseases

BACKGROUND

Broad-range polymerase chain reaction (BR-PCR) detects infectious pathogens from clinical specimens using targets for bacteria (16S rRNA), fungi (28S rDNA), and mycobacteria (fluorescence resonance energy transfer and heat shock protein 65 gene) with reported diagnostic sensitivity and specificity ranging from 43% to 100% and 100%, respectively. We describe our experience when applying BR-PCR to clinical samples submitted for conventional infectious disease testing [conventional testing (CT)] from pediatric patients with concern for infection.

METHODS

Retrospective analysis of clinical samples obtained from Nationwide Children's Hospital microbiology laboratory from January 2011 to December 2014 and sent for BR-PCR. Medical record review collected data on patient characteristics, clinical manifestations, laboratory results and antimicrobials prescribed, and a determination of clinical value of BR-PCR was assigned.

RESULTS

There were 247 clinical samples from 163 patients identified; 71 (44%) patients were immunocompromised and 192 (78%) samples reflected pretreatment with antimicrobials. A clinically significant putative organism was identified for 59 samples (24%) between all diagnostic modalities. Conventional testing identified organisms in 41 (17%) samples, 17 of which were corroborated by BR-PCR. Broad-range polymerase chain reaction identified an organism in an additional 18 samples with negative CT results and was considered to provide additional important clinical information. Broad-range polymerase chain reaction detected a bacterial or fungal organism more frequently from tissue samples than from bronchoalveolar lavage or other fluid samples (P = 0.0096, χ).

CONCLUSIONS

In our cohort, BR-PCR was an important adjunctive diagnostic in identifying bacteria and fungi in complex clinical situations. Additional data are needed to define the optimal clinical circumstances and specimen type in which BR-PCR can provide the highest diagnostic yield.

Clinical metagenomics

Clinical metagenomic next-generation sequencing (mNGS), the comprehensive analysis of microbial and host genetic material (DNA and RNA) in samples from patients, is rapidly moving from research to clinical laboratories. This emerging approach is changing how physicians diagnose and treat infectious disease, with applications spanning a wide range of areas, including antimicrobial resistance, the microbiome, human host gene expression (transcriptomics) and oncology. Here, we focus on the challenges of implementing mNGS in the clinical laboratory and address potential solutions for maximizing its impact on patient care and public health.

Pleural Tap-Guided Antimicrobial Treatment for Pneumonia with Parapneumonic Effusion or Pleural Empyema in Children: A Single-Center Cohort Study

Parapneumonic effusion or pleural empyema (PPE/PE) is a frequent complication of community-acquired pneumonia (CAP) in children. Different management approaches exist for this condition. We evaluated a 14-day treatment with amoxicillin (AMX) with/without clavulanic acid (AMC) confirmed or modified by microbiological findings from pleural tap. Children ≤16 years of age with radiologically diagnosed PPE/PE and initial diagnostic pleural tap were included at University Children’s Hospital Zurich from 2001–2015. AMX/AMC was given for 14 days and rationalized according to microbiological pleural tap results. Clinical and radiological follow-up was scheduled until six months or full recovery. In 114 of 147 (78%) children with PPE/PE a pathogen was identified by culture, polymerase chain reaction (PCR), and/or antigen testing. Streptococcus pneumoniae was detected in 90 (79%), S. pyogenes in 13 (11%), and Staphylococcus aureus in seven cases (6%), all but two cultured pathogens (96%) were sensitive to AMX/AMC. One-hundred two of 147 (69%) patients received treatment with AMX/AMC for 14 days. They recovered more rapidly than patients with a different management (p = 0.026). Of 139 children with follow-up, 134 (96%) patients fully recovered. In conclusion, 14-day AMX/AMC treatment confirmed and rarely modified by microbiological findings from pleural tap resulted in full recovery in >95% of children with PPE/PE.

A Practical Guide to the Role of Ancillary Techniques in the Diagnosis of Infectious Agents in Fine Needle Aspiration Samples

Fine needle aspiration samples and small biopsies provide a minimally invasive diagnostic modality for mass lesions. When an infectious process is suspected based on initial evaluation, ancillary techniques can assist in making a specific diagnosis. Here we review the cytopathology that should prompt additional testing and review the availability and interpretation of special stains, immunohistochemistry, and in situ hybridization. In addition, this review addresses when special cultures may be necessary and the use of newer molecular techniques for pathogen identification.

Rapid identification and phylogenetic classification of diverse bacterial pathogens in a multiplexed hybridization assay targeting ribosomal RNA

Rapid bacterial identification remains a critical challenge in infectious disease diagnostics. We developed a novel molecular approach to detect and identify a wide diversity of bacterial pathogens in a single, simple assay, exploiting the conservation, abundance, and rich phylogenetic content of ribosomal RNA in a rapid fluorescent hybridization assay that requires no amplification or enzymology. Of 117 isolates from 64 species across 4 phyla, this assay identified bacteria with >89% accuracy at the species level and 100% accuracy at the family level, enabling all critical clinical distinctions. In pilot studies on primary clinical specimens, including sputum, blood cultures, and pus, bacteria from 5 different phyla were identified.

CSF inflammatory markers differ in gram-positive versus gram-negative shunt infections

Background

Cerebrospinal fluid (CSF) shunt placement is frequently complicated by bacterial infection. Shunt infection diagnosis relies on bacterial culture of CSF which can often produce false-negative results. Negative cultures present a conundrum for physicians as they are left to rely on other CSF indices, which can be unremarkable. New methods are needed to swiftly and accurately diagnose shunt infections. CSF chemokines and cytokines may prove useful as diagnostic biomarkers. The objective of this study was to evaluate the potential of systemic and CSF biomarkers for identification of CSF shunt infection.

Methods

We conducted a retrospective chart review of children with culture-confirmed CSF shunt infection at Children’s Hospital and Medical Center from July 2013 to December 2015. CSF cytokine analysis was performed for those patients with CSF in frozen storage from the same sample that was used for diagnostic culture.

Results

A total of 12 infections were included in this study. Patients with shunt infection had a median C-reactive protein (CRP) of 18.25 mg/dL. Median peripheral white blood cell count was 15.53 × 10³ cells/mL. Those with shunt infection had a median CSF WBC of 332 cells/mL, median CSF protein level of 406 mg/dL, and median CSF glucose of 35.5 mg/dL. An interesting trend was observed with gram-positive infections having higher levels of the anti-inflammatory cytokine interleukin (IL)-10 as well as IL-17A and vascular endothelial growth factor (VEGF) compared to gram-negative infections, although these differences did not reach statistical significance. Conversely, gram-negative infections displayed higher levels of the pro-inflammatory cytokines IL-1β, fractalkine (CX₃CL₁), chemokine ligand 2 (CCL2), and chemokine ligand 3 (CCL3), although again these were not significantly different. CSF from gram-positive and gram-negative shunt infections had similar levels of interferon gamma (INF-γ), tumor necrosis factor alpha (TNF-α), IL-6, and IL-8.

Conclusions

This pilot study is the first to characterize the CSF cytokine profile in patients with CSF shunt infection and supports the distinction of chemokine and cytokine profiles between gram-negative and gram-positive infections. Additionally, it demonstrates the potential of CSF chemokines and cytokines as biomarkers for the diagnosis of shunt infection.

Experimental procedures for decontamination and microbiological testing in cardiovascular tissue banks

IMPACT STATEMENT

Sterility testing is a critical issue in the recovery, processing, and release of tissue allografts. Contaminated allografts are often discarded, increasing costs, and reducing tissue stocks. Given these concerns, it is important to determine the most effective methodology for sterility testing. This work provides an overview of microbiological methods for sampling and culturing donor grafts for cardiovascular tissue banking.

Factors impairing cell proliferation in the granulation tissue of pressure ulcers: Impact of bacterial burden

The authors aimed to assess the factors that impair cell proliferation in the granulation tissue of pressure ulcers using immunohistochemistry for the cell proliferation marker Ki-67. This was a single center, cross-sectional study. The study included 86 patients with stage III or IV pressure ulcers. Two granulation tissue biopsy specimens were obtained from 86 patients. The specimens were used for histological examination, Ki-67 immunohistochemistry, and bacterial count assessment. The % of Ki-67-stained cells was considered as the Ki-67 index. Pearson's product-moment correlation coefficient (r) was used to assess the relationship between the Ki-67 index and other quantitative variables, including age, body mass index, bacterial count (Log10 CFU/g), serum albumin level, hemoglobin level, white blood cell count, and C-reactive protein level. The Mann-Whitney U test was used to compare the mean Ki-67 index according to gender, diabetes, smoking status, and wound culture. Univariate and multivariate linear regression analyses were used to assess the association between the Ki-67 index and other parameters. The Mann-Whitney U test revealed that the bacteria-positive group had a lower Ki-67 index (p = 0.045). Bacterial count demonstrated a significant negative correlation with the Ki-67 index (r = -0.325, p = 0.002). Multivariate linear regression analysis showed that bacterial count was a significant predictor of the Ki-67 index. The adjusted β-coefficient was -1.34 (95% confidence interval, -2.01 to -0.66, p < 0.001). Among the isolated bacteria, Corynebacterium spp. and Staphylococcus aureus were significantly associated with a low Ki-67 index, but Pseudomonas aeruginosa was not. These results suggest a negative relationship between bacterial count and cell proliferation in pressure ulcer granulation tissue, as indicated by the Ki-67 index. Granulation tissue formation in pressure ulcers may be accelerated if high bacterial load is treated appropriately.

Gram-negative multi-drug resistant bacteria influence survival to discharge for horses with septic synovial structures: 206 Cases (2010-2015)

Bacterial colonization of synovial structures can cause infections that are difficult to treat. Systemic and local antimicrobials and repeated joint lavages are the mainstays of therapy. However, despite aggressive treatments, infection may persist, leading to significant tissue damage or death of the patient. In order to investigate the impact of bacterial culture and antimicrobial resistance on survival to discharge, we reviewed medical records of horses admitted to the University of Pennsylvania's large animal teaching hospital from 2010-2015. Two-hundred and six cases with a definitive diagnosis of septic synovitis and a synovial fluid sample submitted for microbiological culture were included in the study. Of these horses, 48% were culture negative and 52% were positive for any bacterial growth, of which 66% were gram-positive and 28% were gram-negative aerobic organisms with 4% anaerobic and 2% fungal organisms. Overall survival to discharge from hospital was 86%. Horses that had negative growth on culture were more likely to survive until discharge (p < 0.02). Multivariable analyses revealed that the likelihood of euthanasia was significantly associated with identification of coagulase positive Staphylococcus spp. (OR 7.66, 5.46-10.74, p < 0.0001), β-hemolytic Streptococcus spp. (OR 5.18, 3.56-7.55, p < 0.0001), Enterococcus spp. (OR 18.38, 11.45-29.52, p = 0.002), Enterobacteriaceae (OR 31.37, 22.28-44.17, p < 0.0001), Pseudomonas aeruginosa (OR 9.31, 5.30-16.34, p = 0.0004) or other gram-negative species (OR 3.51, 2.07-5.94, p = 0.001). Multi-drug resistance and gram-negative bacteria species were associated with significantly decreased survival rates (OR 119.24, 70.57-201.46, p < 0.0001). In conclusion, prognosis for survival to discharge was poor for horses that were infected with gram-negative organisms, particularly those with MDR phenotypes.

Microbial Identification Using DNA Target Amplification and Sequencing: Clinical Utility and Impact on Patient Management

Broad-range polymerase chain reaction (PCR) is increasingly used in patients with culture-negative infections; however, few studies have assessed the diagnostic utility of this test in this context. We performed a retrospective cohort study of patients who had clinical specimens sent for broad-range PCR, aiming to evaluate performance and determine impact on patient management. Organisms were identified in 21/71 samples. High numbers of polymorphonuclear leukocytes on Gram stain (odds ratio [OR], 4.17; P = .04) and acute inflammation on histopathology (OR, 5.69; P = .02) were significantly associated with a positive result. Management was altered in 18 patients, 11 with positive and 7 with negative results. Overall, broad-range PCR assay had the highest impact in patients with microscopic evidence of inflammation. Physicians ordering this complex, difficult to interpret, and expensive test should carefully consider all available clinical information on an individualized basis to optimize its performance.

Clinical utility of pan-microbial PCR assays in the routine diagnosis of infectious diseases

The goals of the study were to examine the analytical properties and the clinical utility of pan-microbial PCR (PM-PCR) assays in a retrospective study conducted in 2014-2015 at the Tel-Aviv Sourasky Medical Center. PM-PCR included in-house assays for pan-bacterial, pan-fungal, and pan-mycobacterial PCR followed by sequencing. The clinical utility of the assays was decided based on defined criteria/categories. There were 585 PM-PCR tests performed on samples from 306 patients. The positivity rates of PM-PCR for bacterial, fungal, and mycobacterial infections were 72/316 (22.7%), 16/186 (8.6%), and 6/83 (7.2%), and the sensitivity values were 65%, 76%, and 85%, respectively. PCR results had influenced the management in 14/82 (17%) of PCR-positive cases and in 13/222 (5.8%) of PCR-negative cases (P = 0.005). The causes for the low clinical utility were related to lack of effect on the initial treatment in PCR-negative cases and concurrent positive cultures or presumed contamination in PCR-positive cases.

Conventional culture method and qPCR using 16S rDNA for tissue bank: a comparison using a model of cardiac tissue contamination

Real-time polymerase chain reaction (qPCR) using 16S rDNA is an alternative to conventional culture-based tests. The aim of this study was to compare the conventional culture method with qPCR using 16S rDNA in a model of cardiac tissue contamination. Samples of cardiac tissue for artificial contamination with Escherichia coli and control samples were submitted for DNA extraction, which was conducted by selective and alkaline lysis and purification steps. A standard curve for 16S rDNA was constructed to determine the efficiency and analytical sensitivity of the assay in concentrations from 10⁶ to 10² c.f.u. ml^-1 using TaqMan Master Mix. 16S rDNA was detected in all contaminated samples; however, it was not detected in the the final washing step solution of the sample with a bioburden of 10² c.f.u. ml^-1. Using qPCR is a potential alternative to conventional culture for microbiological safety testing of allograft tissues for biobanking, reducing the time and labour input required.

Isolation of bacterial DNA followed by sequencing and differing cytokine response in peritoneal dialysis effluent help in identifying bacteria in culture negative peritonitis

AIM

The treatment of peritoneal dialysis related culture negative peritonitis is empirical which increases the cost of therapy and moreover antibiotic resistance. We aimed the study to isolate bacterial DNA from PD effluent and indentify bacteria causing peritonitis in culture negative situations. We have also studied the cytokine response with different bacteria causing peritonitis.

METHODS

We have isolated bacterial DNA from PD effluent of culture negative and culture positive peritonitis patients. Bacterial DNA was subjected to polymerase chain reaction using universal bacteria specific primers and subsequently to Gram type specific primers for the differentiation of the etiologic agents into Gram-positive and Gram-negative. The amplified products were sequenced and subjected to blast search to identify agent at genus/ species level.

RESULTS

Of the 30 molecular method positive samples, 16 (53.33%) samples were positive for Gram-negative bacteria and 4 (13.33%) for Gram-positive, while the remaining10 (33.33%) were positive for both Gram-positive and Gram-negative bacteria. We have found organisms that usually do not grow on normal culture methods. TNF-α was significantly associated with Gram-positive peritonitis and regulatory cytokine IL-10 with Gram-negative peritonitis.

CONCLUSIONS

The molecular techniques are helpful in detecting and identifying organisms from culture negative PD effluent.

Increased Pathogen Identification in Vascular Graft Infections by the Combined Use of Tissue Cultures and 16S rRNA Gene Polymerase Chain Reaction

Background: Vascular graft infections (VGI) are difficult to diagnose and treat, and despite redo surgery combined with antimicrobial treatment, outcomes are often poor. VGI diagnosis is based on a combination of clinical, radiological, laboratory and microbiological criteria. However, as many of the VGI patients are already under antimicrobial treatment at the time of redo surgery, microbiological identification is often difficult and bacterial cultures often remain negative rendering targeted treatment impossible. We aimed to assess the benefit of 16S rRNA gene polymerase chain reaction (broad-range PCR) for better microbiological identification in patients with VGI.

Methods: We prospectively analyzed the clinical, microbiological, and treatment data of patients enrolled in the observational Vascular Graft Cohort Study (VASGRA), University Hospital Zurich, Switzerland. The routine diagnostic work-up involved microbiological cultures of minced tissue samples, and the use of molecular techniques in parallel. Patient-related and microbiological data were assessed in descriptive analyses, and we calculated sensitivity, specificity, negative and positive predictive value for broad-range 16S rRNA gene PCR versus culture (considered as gold standard).

Results: We investigated 60 patients (median age 66 years (Interquartile range [IQR] 59–75)) with confirmed VGI between May 2013 and July 2017. The prevalence of antimicrobial pretreatment at the time of sampling was high [91%; median days of antibiotics 7 days (IQR 1–18)]. We investigated 226 microbiological specimens. Thereof, 176 (78%) were culture-negative and 50 (22%) were culture-positive. There was a concordance of 70% (158/226) between conventional culture and broad-range PCR (sensitivity 58% (95% CI 43–72); specificity 74% (67–80%)). Among the group of 176 culture-negative specimens, 46 specimens were broad-range PCR-positive resulting in identification of overall 69 species. Among the culture and/or broad-range PCR-positive specimens (n = 96), 74 (77%) were monomicrobial and 22 (23%) polymicrobial, whereas the rate of polymicrobial samples was higher in broad-range PCR-positive specimens (93%).

Conclusions: Combined cultures and broad-range 16S rRNA gene PCR from periprosthetic tissue and/or explanted vascular grafts increased the diagnostic accuracy in VGI, particularly in patients already under antimicrobial treatment at the time of redo surgery. Ideally, antimicrobial treatment should be withheld until surgical sampling in order to optimize microbiological diagnostics.Clinical trials.gov identifier: NCT01821664

MALDI-TOF mass spectrometry technology for detecting biomarkers of antimicrobial resistance: current achievements and future perspectives

The laboratory diagnosis of infections is based on pathogen identification and antimicrobial susceptibility determination. The gold standard of cultivation, isolation and susceptibility testing is a time-consuming procedure and in some cases this can be threatening for patients' outcome. In the current review the applications of mass spectrometry in pathogen identification and especially in detecting biomarkers of antimicrobial resistance are analyzed. MALDI-TOF (matrix-assisted laser desorption/ionization time-of-flight) mass spectrometry is a new technology that has revolutionized pathogen identification and has also proven to accelerate detection of antimicrobial resistance compared to the traditional antibiotic susceptibility tests (AST) as well as DNA amplification methodologies. The technology has incorporated up to know four different methodologies: (I) the detection of differences of mass spectra of susceptible and resistant isolates of a given microorganism using the classical strain typing methodology; (II) the analysis of bacterial induced hydrolysis of β-lactam antibiotics; (III) the detection of stable (non-radioactive) isotope-labeled amino acids; and (IV) the analysis of bacterial growth in the presence and absence of antibiotics using an internal standard. The implementation of MALDI-TOF methodologies has improved detection of resistance in aerobic, Gram-positive and Gram-negative bacteria, mycobacteria, anaerobic bacteria, fungi and viruses. The MALDI-TOF is an easy to use, rapid, reliable, economical, and environmentally friendly methodology. However, this technology needs further development of research protocols that will be validated for routine application.

Vertebral Osteomyelitis Caused by Helicobacter cinaedi Identified Using Broad-range Polymerase Chain Reaction with Sequencing of the Biopsied Specimen

A 65-year-old man presented with gradually exacerbating low back pain. Magnetic resonance imaging revealed vertebral osteomyelitis in the Th11-L2 vertebral bodies and discs. The patient showed negative findings on conventional cultures. Direct broad-range polymerase chain reaction (PCR) with sequencing of the biopsied specimen had the highest similarity to the 16S rRNA gene of Helicobacter cinaedi. This case suggests that direct broad-range PCR with sequencing should be considered when conventional cultures cannot identify the causative organism of vertebral osteomyelitis, and that this method may be particularly useful when the pathogen is a fastidious organism, such as H. cinaedi.

Molecular analysis of endotracheal tube biofilms and tracheal aspirates in the pediatric intensive care unit

BACKGROUND

Ventilator-associated pneumonia (VAP) is a known complication of mechanically ventilated children in the pediatric intensive care unit (PICU). Endotracheal tube (ETT) biofilms are often implicated in the development of VAP by providing a conduit for pathogens to the lower respiratory tract.

METHODS

A prospective cohort study from April 2010-March 2011 of children 4 weeks to 18 years of age ventilated for greater than 72 hours to determine the microbiota of ETT biofilms and tracheal aspirates.

RESULTS

Thirty-three patients were included with a mean age of 6.1 years (SD ± 5.1 years) and average length of intubation of 8.8 days (SD ± 5.0 days). Bacterial communities from tracheal aspirates and the proximal and distal ends of ETTs were determined using 16S rRNA gene libraries. Statistical analysis utilized two-part statistics and the Wilcoxon signed rank sum test for comparison of bacterial communities. Sequencing revealed a predominance of oropharyngeal microbiota including Prevotella and Streptococcus spp. Pathogenic bacterial genera including Staphylococcus, Burkholderia, Moraxella, and Haemophilus were also represented. Bacterial load was greatest at the proximal aspect of the ETT. Duration of intubation did not significantly impact bacterial load. Morisita Horn analysis across sites showed similar communities in 24/33 (72%) of patients.

CONCLUSIONS

ETT biofilms and tracheal aspirates of intubated patients in the PICU primarily consisted of oropharyngeal microbiota, but had a significant representation of potentially pathogenic genera. While the majority of patients had similar microbiota when comparing their ETT biofilms and tracheal aspirates, a subset of patients showed a divergence between communities that requires further investigation.

Detection of bacterial pathogens from clinical specimens using conventional microbial culture and 16S metagenomics: a comparative study

Background

Infectious disease is the leading cause of death worldwide, and diagnosis of polymicrobial and fungal infections is increasingly challenging in the clinical setting. Conventionally, molecular detection is still the best method of species identification in clinical samples. However, the limitations of Sanger sequencing make diagnosis of polymicrobial infections one of the biggest hurdles in treatment. The development of massively parallel sequencing or next generation sequencing (NGS) has revolutionized the field of metagenomics, with wide application of the technology in identification of microbial communities in environmental sources, human gut and others. However, to date there has been no commercial application of this technology in infectious disease diagnostic settings.

Methods

Credence Genomics Rapid Infection Detection™ test, is a molecular based diagnostic test that uses next generation sequencing of bacterial 16S rRNA gene and fungal ITS1 gene region to provide accurate identification of species within a clinical sample. Here we present a study comparing 16S and ITS1 metagenomic identification against conventional culture for clinical samples. Using culture results as gold standard, a comparison was conducted using patient specimens from a clinical microbiology lab.

Results

Metagenomics based results show a 91.8% concordance rate for culture positive specimens and 52.8% concordance rate with culture negative samples. 10.3% of specimens were also positive for fungal species which was not investigated by culture. Specificity and sensitivity for metagenomics analysis is 91.8 and 52.7% respectively.

Conclusion

16S based metagenomic identification of bacterial species within a clinical specimen is on par with conventional culture based techniques and when coupled with clinical information can lead to an accurate diagnostic tool for infectious disease diagnosis.

Electronic supplementary material

The online version of this article (10.1186/s12879-017-2727-8) contains supplementary material, which is available to authorized users.

The potential contribution of 16S ribosomal RNA polymerase chain reaction to antimicrobial stewardship in culture-negative infection

Empiric broad-spectrum antimicrobial therapy frequently results in culture-negative specimens making rationalization of therapy difficult. We retrospectively reviewed 16S rRNA polymerase chain reaction (PCR) results from 78 specimens in 60 patients. 16S rRNA was detected in 28 (47%) patients with de-escalation of therapy in five (21%). Microbial DNA was not detected in 32 (53%) patients with antimicrobials discontinued in two (8%). Neurosurgical patients had a higher proportion of positive results (53% vs 34%) and treatment rationalizations (17% vs 12%). In specific patient groups, 16s rRNA PCR is a useful antimicrobial stewardship tool for targeting antimicrobial therapy.

Polymerase chain reaction based detection of bacterial 16S rRNA gene in the cerebrospinal fluid in the diagnosis of bacterial central nervous system infection in the course of external cerebrospinal fluid drainage. Comparison with standard diagnostics currently used in clinical practice

BACKGROUND AND PURPOSE

External drainage of cerebrospinal fluid (CSF) is a commonly used neurosurgical procedure. Complications of the procedure comprise central nervous system (CNS) bacterial infections, the frequency of which is estimated at around 6-10%. Detection of these infections is ineffective in many cases. The aim of the study was to evaluate the usefulness of a polymerase chain reaction (PCR)-based detection of bacterial 16S rRNA gene (16S rDNA) in the CSF.

MATERIAL AND METHODS

The study group consisted of 50 patients. Clinical signs of CNS infection were monitored and routine laboratory and microbiological tests were performed. The results of standard methods were compared with the bacterial 16S rDNA detection.

RESULTS

Using cultures, CNS infection was diagnosed in 8 patients, colonization of the drainage catheter in 6 patients, and sample contamination in 7 patients. In the group of the remaining 29 patients, no positive CSF culture was obtained and 13 of these patients also had all negative results for 16S rDNA detection. For the remaining 16 patients of this group, CNS infection, colonization of the catheter and sample contamination were diagnosed via PCR alone. Routine biochemical CSF tests and blood inflammatory parameters had a supporting value.

CONCLUSIONS

Routine hospital tests do not provide rapid and efficient detection of the external drainage related bacterial CNS infection. It is justified to use several diagnostic methods simultaneously. The16S rDNA determination in CSF can increase the probability of detection of possible pathogens.

Comparison of two commercial broad-range PCR and sequencing assays for identification of bacteria in culture-negative clinical samples

BACKGROUND

Culturing has long been the gold standard for detecting aetiologic agents in bacterial infections. In some cases, however, culturing fails to detect the infection. To further investigate culture-negative samples, amplification and subsequent sequencing of the 16S rRNA gene is often applied. The aim of the present study was to compare the current method used at our Department of Clinical Microbiology, based on the MicroSeq ID system (Applied Biosystems, USA) with the Universal Microbe Detection (UMD) SelectNA kit (Molzym, Germany).

METHODS

76 culture-negative samples were first processed with the MicroSeq ID analysis, where total DNA was extracted and the 16S gene amplified and sequenced with the MicroSeq ID system. Samples were subsequently processed with the UMD SelectNA analysis, where human DNA was removed during the DNA extraction procedure and the 16S gene amplified in a real-time PCR and sequenced.

RESULTS

22 of 76 samples (28.9%) were positive for bacteria with the UMD SelectNA, which was significantly more (p = 0.0055) than the MicroSeq ID where 11 of 76 samples (14.5%) were positive. The UMD SelectNA assay identified more relevant bacterial pathogens than the MicroSeq ID analysis (p = 0.0233), but also found a number of species that were considered contaminations.

CONCLUSIONS

The UMD SelectNA assay was valuable for the identification of pathogens in culture-negative samples; however, due to the sensitive nature of the assay, extreme care is suggested in order to avoid false positives.

Utility of 16S rRNA PCR performed on clinical specimens in patient management

BACKGROUND

Broad-range 16S rRNA PCR can be used for the detection and identification of bacteria from clinical specimens in patients for whom there is a high suspicion of infection and cultures are negative. The aims of this study were (1) to compare 16S rRNA PCR results with microbiological culture results, (2) to assess the utility of 16S rRNA PCR with regard to antimicrobial therapy, and (3) to compare the yield of 16S rRNA PCR for different types of clinical specimen and to perform a cost analysis of the test.

METHODS

A retrospective study was performed on different clinical specimens which had 16S performed over 3 years (2012-2015). Standard microbiological cultures were performed on appropriate media, as per the laboratory protocol. Patient clinical and microbiological data were obtained from the electronic medical records and laboratory information system, respectively. 16S rRNA PCR was performed in a reference laboratory using a validated method for amplification and sequencing. The outcomes assessed were the performance of 16S rRNA PCR, change of antimicrobials (rationalization, cessation, or addition), and duration of therapy. Concordance of 16S rRNA PCR with bacterial cultures was also determined for tissue specimens.

RESULTS

Thirty-two patients were included in the study, for whom an equal number of specimens (n=32) were sent for 16S rRNA PCR. 16S rRNA PCR could identify an organism in 10 of 32 cases (31.2%), of which seven were culture-positive and three were culture-negative. The sensitivity was 58% (confidence interval (CI) 28.59-83.5%) and specificity was 85% (CI 61.13-96%), with a positive predictive value of 70% (CI 35.3-91.9%) and negative predictive value of 77.2% (CI 54.17-91.3%). Antimicrobial therapy was rationalized after 16S rRNA PCR results in five patients (15.6%) and was ceased in four based on negative results (12.5%). Overall the 16S rRNA PCR result had an impact on antimicrobial therapy in 28% of patients (9/32). The highest concordance of 16S rRNA PCR with bacterial culture was found for heart valve tissue (80%), followed by joint fluid/tissue (50%).

CONCLUSIONS

Despite the low diagnostic yield, results of 16S rRNA PCR can still have a significant impact on patient management due to rationalization or cessation of the antimicrobial therapy. The yield of 16S rRNA PCR was highest for heart valves.

Infection after fracture osteosynthesis - Part I

Bone and surgical site infections after osteosynthesis are notoriously difficult to manage and pose a tremendous burden in fracture management. In this article, we use the term osteosynthesis-associated infection (OAI) to refer to this clinical entity. While relatively few surgically treated fractures become infected, it is challenging to perform a rapid diagnosis. Optimal management strategies are complex and highly customized to each scenario and take into consideration the status of fracture union, the presence of hardware and the degree of mechanical stability. At present, a high level of relevant evidence is unavailable; most findings presented in the literature are based on laboratory work and non-randomized clinical studies. We present this overview of OAI in two parts: an examination of recent literature concerning OAI pathogenesis, diagnosis and classification and a review of treatment options.

A case of Finegoldia magna (formerly Peptostreptococcus magnus) infection mimicking disseminated malignancy

A 44-year-old alcoholic (and therefore immunocompromised) hospital cleaner presented with general malaise, weight loss, and erythematous skin nodules. Computed tomography scanning revealed a neck mass invading the thyroid gland, pulmonary infiltrates, liver lesions, and deposits on the anterior abdominal wall, consistent with disseminated malignancy. However, tissue diagnosis showed a necro-inflammatory process with no evidence of malignancy. Microscopy and culture of samples failed to detect any infectious pathogen, but after an extended incubation period, Finegoldia magna was isolated. This case study illustrates the importance of tissue diagnosis in suspected disseminated malignancy and raises the risk of acquiring the rarer bacteria amongst hospital staff.

Similar efficacy of broad-range ITS PCR and conventional fungal culture for diagnosing fungal infections in non-immunocompromised patients

Background

Broad-range fungal inter spacer region (ITS) polymerase chain reaction (PCR) has been evaluated for the detection and identification of fungi in clinical specimens from severely immunocompromised patients, but not in non-selected patients. Thus, the aim of this study was to compare the diagnostic performance of ITS PCR with that of fungal culture and to investigate its clinical impact on the diagnosis of fungal infections in non-immunocompromised patients. The corresponding patients’ data were retrieved by detailed medical chart reviews.

Results

Results from 251 specimens showed a high concordance of 89.6 % for ITS PCR and fungal culture. The analytical sensitivity and specificity of ITS PCR considering culture as gold standard were 87.7 and 90.3 %, respectively, the positive and negative predictive value (PPV and NPV) were 76 and 95.5 %, respectively. Assessing the clinical probability of a fungal infection based on detailed chart reviews, PCR had a clinical sensitivity of 88.9 %, a specificity of 86.3 %, a PPV of 64.0 % and a NPV of 96.6 %. The overall performance of fungal broad-range PCR was similar to that of culture.

Conclusions

Our data show that, in non-selected and non-immunocompromised patients, the performance of ITS PCR is similar to that of culture for detecting fungal infections, not the least because sensitivity of culture in patients under antifungal treatment is surprisingly high. Compared to culture, PCR has the advantage of a rapid time-to-result (approximately two working days), proper identification of rare pathogens, prompt initiation of a species-targeted antifungal treatment, and prospects for automation.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-016-0752-1) contains supplementary material, which is available to authorized users.

Ureaplasma septic arthritis in an immunosuppressed patient with juvenile idiopathic arthritis

Mycoplasmas, including Ureaplasma and Mycoplasma species, are uncommon but important causes of septic arthritis, especially affecting immunosuppressed patients. Many of the reported cases have been associated with congenital immunodeficiency disorders, especially hypogammaglobulinemia. Mycoplasmas are difficult to grow in the laboratory, and these infections may be underdiagnosed using culture techniques. We report a case of a 21-year-old woman with juvenile idiopathic arthritis and hip arthroplasties treated with rituximab and adalimumab who developed urogenital infections and soft tissue abscesses followed by knee arthritis with negative routine cultures. Ureaplasma species was identified from synovial fluid on 2 separate occasions using a broad-range 16S ribosomal RNA gene polymerase chain reaction. Azithromycin led to rapid improvement in symptoms, but after completion of therapy, involvement of the hip prosthesis became apparent, and again, 16S rRNA gene polymerase chain reaction was positive for Ureaplasma species. The literature is reviewed with a discussion of risk factors for Mycoplasma septic arthritis, clinical presentation, methods of diagnosis, and treatment.

Cultivation-independent approach for the direct detection of bacteria in human clinical specimens as a tool for analysing culture-negative samples: a prospective study

Administration of empirical antibiotic therapy prior to microbiological diagnosis is thought to be associated the failure of subsequent bacterial growth in culture. The aim of this study was to detect bacterial pathogens via direct amplification and sequencing of the 16S rDNA gene in samples showing negative culture results as alternative diagnostic tools to troubleshoot difficult samples. Twenty-three (7.66 %) positive samples were detected, most of which were monomicrobial infections; 15 of the cases were identified as HAIs, 6 had catheter colonisation, and 2 had sample colonisation. The pathogens identified included Escherichia, Salmonella, Pseudomonas spp., Enterococcus spp. and coagulase-negative staphylococci (CoNS). The most frequent infections were bacteraemia and urinary tract infection, but meningitis, warm infection and soft tissue infection were also documented. These findings emphasise the efficacy and usefulness of molecular diagnosis, thus 16S rDNA gene analysis is strongly indicated by HAIs diagnostics.

Review of 16S and ITS Direct Sequencing Results for Clinical Specimens Submitted to a Reference Laboratory

We evaluated the performance of 16S and internal transcribed spacer (ITS) region amplification and sequencing of rDNA from clinical specimens, for the respective detection and identification of bacterial and fungal pathogens. Direct rDNA amplification of 16S and ITS targets from clinical samples was performed over a 4-year period and reviewed. All specimens were from sterile sites and submitted to a reference laboratory for evaluation. Results of 16S and ITS were compared to histopathology, Gram and/or calcofluor stain microscopy results. A total of 277 16S tests were performed, with 64 (23%) positive for the presence of bacterial DNA. Identification of an organism was more likely in microscopy positive 16S samples 14/21 (67%), compared to 35/175 (20%) of microscopy negative samples. A total of 110 ITS tests were performed, with 14 (13%) positive. The yield of microscopy positive ITS samples, 9/44 (21%), was higher than microscopy negative samples 3/50 (6%). Given these findings, 16S and ITS are valuable options for culture negative specimens from sterile sites, particularly in the setting of positive microscopy findings. Where microscopy results are negative, the limited sensitivity of 16S and ITS in detecting and identifying an infectious agent needs to be considered.