Development and evaluation of a novel fast broad-range 16S ribosomal DNA PCR and sequencing assay for diagnosis of bacterial infective endocarditis: multi-year experience in a large Canadian healthcare zone and a literature review

Novel Diagnostic Methods for Infective Endocarditis

Infective endocarditis (IE) remains a dangerous disease and continues to have a high mortality rate. Unfortunately, despite continuous improvements in diagnostic methods, in many cases, blood cultures remain negative, and the pathogen causing endocarditis is unknown. This makes targeted therapy and the selection of appropriate antibiotics impossible. Therefore, we present what methods can be used to identify the pathogen in infective endocarditis. These are mainly molecular methods, including PCR and MGS, as well as imaging methods using radiotracers, which offer more possibilities for diagnosing IE. However, they are still not widely used in the diagnosis of IE. The article summarizes in which cases we should choose them and what we are most hopeful about in further research into the diagnosis of IE. In addition, registered clinical trials that are currently underway for the diagnosis of IE are also presented.

Gastrointestinal Variant of Lemierre Syndrome due to Fusobacterium nucleatum: A Case Report

Introduction

Pyogenic liver abscess is a noteworthy health concern in North America, characterized by a mortality rate ranging from 2 to 12%. This condition is often polymicrobial, with Streptococcus species and Escherichia coli as the predominant causal pathogens in Western countries. Fusobacterium species, typically commensals of gastrointestinal, genital, and oral flora, have been implicated in the rare formation of tonsillar abscesses and Lemierre syndrome, including its gastrointestinal variant known as pylephlebitis.

Case Presentation

We present the case of an immunocompetent male with a 2-week history of abdominal distention and pain. Abdominal magnetic resonance imaging revealed multiseptated cystic hepatic masses and portal vein thrombosis. A subsequent liver biopsy confirmed Fusobacterium nucleatum etiology. The patient was initiated on intravenous cefepime and oral metronidazole antibiotics. Unfortunately, the patient succumbed to cardiac arrest before a final diagnosis could be established.

Conclusion

Fusobacterium species-associated liver abscess, coupled with the rare gastrointestinal variant of Lemierre syndrome (pylephlebitis), poses a significant mortality risk. This case underscores the rarity and clinical challenges associated with these conditions. Increased awareness among clinicians is crucial for early diagnosis and prompt intervention, potentially improving outcomes in such cases.

Development of a scoring system to identify high-yield specimens for bacterial broad-range 16S rRNA gene PCR with sequencing at a tertiary care medical center

OBJECTIVES

Broad-range bacterial polymerase chain reaction with sequencing (BRBPS) provides valuable diagnostic data, especially in cases of culture-negative infections. However, as BRBPS testing demonstrates generally low positivity, cost per impactful result can be high and commonly involves longer turnaround times compared with other methods, targeting use of this assay to high-yield situations remains a challenging goal. Diagnostic stewardship can help alleviate these challenges and increase clinical utility, yet not all laboratories have a dedicated stewardship team, and little formal guidance exists on identifying high-yield samples outside of specific clinical syndromes. In this study, we performed a retrospective review of 86 BRBPS orders from a tertiary care medical center, with a focus on identifying high-yield cases using an infectious markers scoring system, visualized inflammation or organism (VIO) score, to predict return of actionable diagnostic data.

METHODS

Using chart review, we evaluated how results from high VIO score or low VIO score specimens contributed to clinical management.

RESULTS

Testing low VIO score samples identified an organism in only 10% of samples, and of these positive results, 33% were considered to represent contamination. Despite negative routine workup and no identified pathogen via BRBPS, broad antimicrobial treatment was continued in 85% of cases with a low VIO score. In contrast, specimens with high VIO scores were more predictably positive by BRBPS, identified organisms that were universally considered pathogens, and provided opportunities to target or de-escalate antimicrobial therapy.

CONCLUSIONS

This study describes the VIO scoring system to guide the identification of high-yield samples and steward the appropriate use of BRBPS testing.

Microbiologic diagnostics and pathogen spectrum in infective endocarditis of surgically treated patients: a five-year, retrospective, monocentric study

PURPOSE

The spectrum of causative organisms in infective endocarditis (IE) has changed significantly in the last decades. Reliable pathogen detection is crucial for appropriate antimicrobial therapy for IE. The aim of the study was to evaluate the diagnostic value of microbiological methods for detecting the causative microorganism of IE and to analyze the spectrum of pathogens.

METHODS

A total of 224 cases (211 unique patients, some with multiple surgeries) were included into this retrospective study. Patients were diagnosed with IE according to the modified Duke criteria from January 2016 to July 2021 and underwent heart valve surgery in a tertiary hospital. Pathogen detection was performed by blood culture, microbiological culture and 16S rDNA PCR of explanted heart valve material.

RESULTS

A causative pathogen of IE was detected in 95.5% (n = 214) of cases. Blood cultures were positive in 83.3%, while a pathogen in the examined heart valve samples was identified in 32.6% by culture and in 88.2% by 16S rDNA PCR. A microorganism was identified by 16S rDNA PCR in 61.1% of blood culture negative cases but only in 19.4% by heart valve culture. The most common pathogens were Staphylococcus aureus (27%), viridans group streptococci (20%), enterococci (19%) and coagulase-negative staphylococci (CoNS 8%). Cutibacterium acnes (7%) was detected in prosthetic valve IE cases only.

CONCLUSION

Blood culture as a comparatively non-invasive and straightforward technique remains an important and reliable method for initial detection of the causative organism in IE. Diagnostic stewardship programs should broadly emphasize proper collection of blood cultures, particularly sampling prior to any antibiotic treatment. Additionally, molecular testing using 16S rDNA tissue PCR can be used with culture techniques to increase the diagnostic yield, especially in the case of a negative blood culture.

Recent updates in the development of molecular assays for the rapid identification and susceptibility testing of MRSA

INTRODUCTION

Methicillin-resistant Staphylococcus aureus (MRSA) is a frequent cause of healthcare- and community-associated infections. Nasal carriage of MRSA is a risk factor for subsequent MRSA infections. Increased morbidity and mortality are associated with MRSA infections and screening and diagnostic tests for MRSA play an important role in clinical management.

AREAS COVERED

A literature search was conducted in PubMed and supplemented by citation searching. In this article, we provide a comprehensive review of molecular-based methods for MRSA screening and diagnostic tests including individual nucleic acid detection assays, syndromic panels, and sequencing technologies with a focus on their analytical performance.

EXPERT OPINION

Molecular based-assays for the detection of MRSA have improved in terms of accuracy and availability. Rapid turnaround enables earlier contact isolation and decolonization for MRSA. The availability of syndromic panel tests that include MRSA as a target has expanded from positive blood cultures to pneumonia and osteoarticular infections. Sequencing technologies allow detailed characterizations of novel methicillin-resistance mechanisms that can be incorporated into future assays. Next generation sequencing is capable of diagnosing MRSA infections that cannot be identified by conventional methods and metagenomic next-generation sequencing (mNGS) assays will likely move closer to implementation as front-line diagnostics in the near future.

New Perspectives for Prosthetic Valve Endocarditis: Impact of Molecular Imaging by FISHseq Diagnostics

BACKGROUND

The microbial etiology of prosthetic valve infective endocarditis (PVE) can be difficult to identify. Our aim was to investigate the benefit of molecular imaging technique fluorescence in situ hybridization (FISH) combined with 16S rRNA-gene polymerase chain reaction (PCR) and sequencing (FISHseq) for the analysis of infected prosthetic heart valves.

METHODS

We retrospectively evaluated the diagnostic outcome of 113 prosthetic valves from 105 patients with suspected PVE, treated in 2003-2013 in the Department of Cardiac Surgery, Charité University Medicine Berlin. Each prosthetic valve underwent cultural diagnostics and was routinely examined by FISH combined with 16S rRNA gene PCR and sequencing. We compared classical microbiological culture outcomes (blood and valve cultures) with FISHseq results and evaluated the diagnostic impact of the molecular imaging technique.

RESULTS

Conventional microbiological diagnostic alone turned out to be insufficient, as 67% of preoperative blood cultures were noninformative (negative, inconclusive, or not obtained) and 67% of valve cultures remained negative. FISHseq improved the conventional cultural diagnostic methods in PVE in 30% of the cases and increased diagnostic accuracy. Of the valve culture-negative PVE cases, FISHseq succeeded in identifying the causative pathogen in 35%.

CONCLUSIONS

FISHseq improves PVE diagnostics, complementing conventional cultural methods. In addition to species identification, FISH provides information about the severity of PVE and state of the pathogens (eg, stage of biofilm formation, activity, and localization on and within the prosthetic material). As a molecular imaging technique, FISHseq enables the unambiguous discrimination of skin flora as contaminant or infectious agent.

Effect of Antibiotic Therapy on the Sensitivity of Etiological Diagnostic Methods in Patients with Infective Endocarditis after Surgery

Aim. Assessment of impact  of the duration  of preoperative  antimicrobial  therapy  (AMT) on the sensitivity  of microbiological examination and polymerase  chain reaction (PCR) of blood/tissues of resected valves in operated patients with infective endocarditis  (IE).

Materials and methods. 52 operated patients with active IE were included prospectively (Duke criteria, 2015). All patients underwent microbiological examination of blood  before  admission  to the cardiac  surgery  hospital,  as well as parallel  simultaneous microbiological examination and  PCR  of blood/tissues of excised  valves,  followed  by Sanger  sequencing. The duration  of preoperative  treatment  was  calculated  from the first day of AMT according to IE diagnosis to the day of surgery.

Results. The causative agent of IE was established in 84.6% (n=44) patients by means of complex etiological diagnosis. A significant  decrease in the sensitivity of microbiological examination of venous blood was revealed when performed  in the period before and after hospitalization to a surgical hospital (up 44.2% to 17.3%, p<0.05). When comparing microbiological examination of blood/tissues of resected valves and PCR of blood/tissues of resected valves, molecular biological  methods demonstrated the greatest sensitivity, with a great advantage when examining the tissues of resected valves (17.3% and 19.2% vs. 38.5% and 75.0%, respectively;  p<0.001). The microbiological examination of venous blood performed  at an early date before admission  to the cardiac  surgery  hospital was comparable in sensitivity to the PCR blood test performed  at a later date after prolonged AMT,  and significantly less sensitive in relation to the PCR of resected valve tissues [44.2% and 38.5% (p>0.05) vs. 75.0% (p<0.05)]. In course of AMT 1-28 days,  there were comparable results of microbiological examination with PCR blood examination and significantly better results of PCR of resected valve tissues [31.0% and 34.5% and 41.4% (p>0.05) vs 72.4% (p<0.001), respectively], and with AMT ≥ 29 days, microbiological examination of any biological  material was negative  in all patients,  and PCR of blood/tissues of resected valves retained high sensitivity (0% and 0% vs. 34.8% and 78.3%, respectively; p<0.01).

Conclusion. Long-term preoperative AMT significantly reduced the sensitivity of microbiological examination of resected valve blood/tissue in operated patients with IE, whereas PCR of resected valve blood/tissue was highly sensitive even with preoperative AMT for more than 29 days.

Hepatosplenic mucormycosis due to Rhizomucor pusillus identified by panfungal PCR/sequencing of ribosomal ITS2 and LSU regions in a patient with acute myelogenous leukemia: A case report

Background:

Angioinvasive Rhizomucor pusillus infection with dissemination to the liver and spleen is exceedingly uncommon, representing less than 1% of reported cases of mucormycosis.

Methods:

Diagnosis of mucormycosis is often difficult using conventional methods that rely on broad-based non-septate hyphae present on histologic examination and morphological identification of the cultured organism. Our laboratory also uses an in-house panfungal molecular assay to rapidly diagnose invasive fungal infection when conventional methods do not provide definitive results.

Results:

Herein we present a case of disseminated mucormycosis with hepatosplenic involvement in a 49-year-old female with acute myelogenous leukemia following induction chemotherapy. But in this case repeated tissue biopsy cultures were negative. R. pusillus infection was diagnosed using an in-house panfungal PCR/sequencing assay based on dual priming oligonucleotide primers.

Conclusions:

New molecular assays facilitate prompt diagnosis of invasive fungal infections.

Diagnostic Yield and Impact on Antimicrobial Management of 16S rRNA Testing of Clinical Specimens

16S rRNA gene sequencing is increasingly used in clinical practice for bacterial identification of clinical specimens. However, studies on its applicability to direct clinical specimens are limited. Here, we studied the diagnostic yield and impact of 16S rRNA gene sequencing from direct clinical specimens on antimicrobial management. Adult inpatients whose attending physician requested 16S rRNA gene sequencing and corresponding bacterial culture from a direct clinical specimen between January and December 2021 in a university hospital were prospectively included in this study. A total of 434 specimens from 374 patients were requested. Of these, 253 (58.3%) specimens were collected from patients whose final diagnosis indicated a bacterial infection, whereas 181 (41.7%) specimens were from nonbacterial infections. Using the final diagnosis as a "gold standard," the sensitivity and specificity of 16S rRNA gene sequencing were 38.3% and 93.9%, respectively. Among the bacterial infection cases, the proportion of 16S rRNA gene sequencing-positive and culture-positive cases was 32.4%, and the proportion of sequencing-positive and culture-negative cases was 5.9%. The impact on antimicrobial management was evident in 10 (2.3%) specimens, which all resulted in the continuation of antibiotics. The impact on antimicrobial management was highest in skin and soft tissue infections, followed by bone and joint infections. In this study, the long turnaround time of 16S rRNA gene sequencing of clinical specimens was a limiting factor. In conclusion, the overall diagnostic yield of 16S rRNA gene sequencing in bacterial infection cases was fair, being useful in selected cases. Restrictions on test requests may improve test utilization in this setting. IMPORTANCE 16S rRNA gene sequencing has been increasingly used in clinical practice. Using the final diagnosis as a gold standard, the sensitivity of 16S rRNA gene sequencing was fair. In the setting with no 16S rRNA gene sequencing test ordering restrictions, only small percentages of the test results had an impact on antimicrobial management. Restrictions on test requests should be developed to maximize the benefit of the test.

Endocarditis in the intensive care unit: an update

PURPOSE OF REVIEW

The incidence of infective endocarditis (IE) is increasing worldwide, resulting in a higher number of patients with IE being admitted to intensive care units (ICU). Nearly half of patients with IE develop a complication during their clinical course. However, few well conducted studies or reviews are devoted to critically ill IE patients. This review discusses the contemporary perioperative and intensive care literature.

RECENT FINDINGS

IE epidemiology is changing towards elderly and frail patients. ICU patients are at risk of risk of developing IE because they are often in a pro-inflammatory state and many also have several indwelling catheters, which favors infection. Increased performance and recent advances in cardiac imaging allow for easier diagnosis of EI, but the applicability of these techniques to ICU patients is still relatively limited. New developments in antibiotic treatment and adjunctive therapies are explored further in this review.

SUMMARY

The lack of evidence on ICU patients with IE highlights the critical importance of multidisciplinary decision-making and the need for further research.

Multi-year comparison of VITEK® MS and 16S rRNA gene sequencing performance for the identification of rarely encountered anaerobes causing invasive human infections in a large Canadian region: can our laboratory abandon 16S rRNA gene sequencing?

BACKGROUND

Our large regional laboratory routinely provides a definitive identification (ID) for 800-1,200 anaerobic bacteria per annum that cause invasive human infections. An increasing number of isolates (i.e., 10-13%) recovered from clinical specimens from these cases were more unusual or rarely isolated genera and/or species (i.e., ≤5 individual cases/annum).

METHODS

VITEK® MS (MALDI-TOF MS)is done initially on all anaerobic bacteria, but rare isolates undergo in-house PCR/sequencing when proteomics provides a wrong ID or no results despite repeat testing. A clinical microbiologist in consultation with the Infectious Diseases service approves molecular analyses. This multi-year comparison (2014-19) of the performance of MALDI-TOF MS and 16S rRNA gene sequencing using the IDNS Smart Gene bacterial dataset shows both method's abilities to provide a genus-level and/or species-level ID for rare isolates.

RESULTS

489 rare anaerobes were recovered from a variety of clinical specimens: 57% blood cultures, 19% other sterile fluids, 14% sterile tissues, 8% deep wounds/abscesses, and 2% prosthetic implants. 16S rRNA gene sequencing gave an accurate genus-vs. species level ID for 487/489 (99.6%) and 401/489 (82.0%) of isolates respectively. Accurate genus-vs species-level ID were obtained by MALDI-TOF MS for 269/489 (53.4%) and 187/489 (37.3%) of isolates respectively. MALDI-TOF MS gave wrong or no results for 35.1% of Gram-negative anaerobic cocci (GNAC), 62% of Gram-negative anaerobic bacilli (GNAB), 30.8% of Gram-positive anaerobic cocci (GPAC) and 46.3% of Gram-positive anaerobic bacilli (GPAB). Neither method gave an ID for one GNAB and one GPAC isolate. MALDI-TOF MS genus-level ID of GNAC and genus/species-level ID of GPAB improved during the study but its performance remained stable for genus- or species-level ID of other organism groups.

CONCLUSIONS

MALDI-TOF MS provides accurate ID for most common anaerobes, but molecular analyses need to be available for rare isolates. Large complex laboratories should have a workflow for sending rare isolates for 16S rRNA gene sequencing in invasive cases where a definitive ID is clinically required.

Molecular Analysis With 16S rRNA PCR/Sanger Sequencing and Molecular Antibiogram Performed on DNA Extracted From Valve Improve Diagnosis and Targeted Therapy of Infective Endocarditis: A Prospective Study

BACKGROUND

Molecular analysis (MA) on heart valve (HV) improves the microbiologic diagnosis of infectious endocarditis (IE). The main drawback of MA is the lack of antimicrobial susceptibility information.

METHODS

We conducted a prospective cohort observational study of consecutive adult patients from April 2012 to May 2021 who underwent valve surgery at our hospital. The performance of MA, blood cultures (BC) and valve cultures (VC), and the diagnostic and therapeutic impact of MA were evaluated. Molecular antibiogram results were compared to culture-based antimicrobial susceptibility testing (AST).

RESULTS

A total of 137 patients with definite IE and 52 patients with no IE were enrolled in the study. Among IE cases BC, VC, and MA were positive in 75 (55%), 30 (22%), and 120 (88%) of IE cases, respectively. Among 62 cases of BC-negative IE (BCNE), 57 achieved diagnosis with MA. MA led to a change of antimicrobial therapy in 92% of BCNE. MA was negative in 100% of patients with no IE. Molecular antibiogram performed on 17 valve specimens that resulted positive for pathogens potential carrier of genes encoding for multidrug resistant mechanisms showed 100% concordance with AST.

CONCLUSIONS

MA showed a high specificity and sensitivity in etiological diagnosis of IE. Molecular antibiogram could overcome the major limitation of MA that is the lack of susceptibility testing. We advocate for the inclusion of MA among diagnostic criteria for IE and for a more extensive use of molecular antibiogram when the culture result is negative, and MA is the only positive test.

Automated 16S Sequencing Using an R-Based Analysis Module for Bacterial Identification

Sanger sequencing of the 16S rRNA gene is routinely used for the identification of bacterial isolates. However, this method is still performed mostly in more-specialized reference laboratories, and traditional protocols can be labor intensive. In this study, 99 clinical bacterial isolates were used to validate a fast, simplified, and largely automated protocol for 16S sequencing. The workflow combines real-time PCR of the first 500 bp of the bacterial 16S rRNA gene and amplicon sequencing on an automated, cartridge-based sequence analyzer. Sequence analysis, NCBI BLAST search, and result interpretation were performed using an automated R-based script. The automated workflow and R analysis described here produced results equal to those of manual sequence analysis. Of the 96 sequences with adequate quality, 90 were concordantly identified to the genus (n = 62) or species level (n = 28) compared with routine laboratory identification of the organism. One organism identification was discordant, and 5 resulted in an inconclusive identification. For sequences that gave a valid result, the overall accuracy of identification to at least the genus level was 98.9%. This simplified sequencing protocol provides a standardized approach to clinical 16S sequencing, analysis, and quality control that would be suited to frontline clinical microbiology laboratories with minimal experience. IMPORTANCE Sanger sequencing of the 16S rRNA gene is widely used as a diagnostic tool for bacterial identification, especially in cases where routine diagnostic methods fail to provide an identification, for organisms that are difficult to culture, or from specimens where cultures remain negative. Our simplified protocol is tailored toward use in frontline laboratories with little to no experience with sequencing. It provides a highly automated workflow that can deliver fast results with little hands-on time. Implementing 16S sequencing in-house saves additional time that is otherwise required to send out isolates/specimens for identification to reference laboratories. This makes results available much faster to physicians who can in turn initiate or adjust patient treatment accordingly.

Development and evaluation of a novel fast broad-range PCR and sequencing assay (FBR-PCR/S) using dual priming oligonucleotides targeting the ITS/LSU gene regions for rapid diagnosis of invasive fungal diseases: multi-year experience in a large Canadian healthcare zone

Background

This study evaluated the performance of a novel fast broad range PCR and sequencing (FBR-PCR/S) assay for the improved diagnosis of invasive fungal disease (IFD) in high-risk patients in a large Canadian healthcare region.

Methods

A total of 114 clinical specimens (CS) including bronchoalveolar lavages (BALs) were prospectively tested from 107 patients over a 2-year period. Contrived BALs (n = 33) inoculated with known fungi pathogens were also tested to increase diversity. Patient characteristics, fungal stain and culture results were collected from the laboratory information system. Dual-priming oligonucleotide (DPO) primers targeted to the internal transcribed spacer (ITS) (~ 350 bp) and large subunit (LSU) (~ 550 bp) gene regions were used to perform FBR-PCR/S assays on extracted BALs/CS. The performance of the molecular test was evaluated against standard microbiological methods and clinical review for the presence of IFD.

Results

The 107 patients were predominantly male (67, 62.6%) with a mean age of 59 years (range = 0–85 years): 74 (69.2%) patients had at least one underlying comorbidity: 19 (34.5%) had confirmed and 12 (21.8%) had probable IFD. Culture recovered 66 fungal isolates from 55 BALs/CS with Candida spp. and Aspergillus spp. being most common. For BALs, the molecular assay vs. standard methods had sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV), and efficiency of 88.5% vs.100%, 100% vs. 61.1%, 100% vs. 88.5%, 61.1% vs. 100%, and 90.2% for both. For other CS, the molecular assay had similar performance to standard methods with sensitivity, specificity, PPV, NPV and efficiency of 66.7%, 87.0%, 66.7%, 87.0% and 81.3% for both methods. Both methods also performed similarly, regardless of whether CS stain/microscopy showed yeast/fungal elements. FBR-PCR/S assays results were reported in ~ 8 h compared to fungal cultures that took between 4 and 6 weeks.

Conclusions

Rapid molecular testing compared to standard methods have equivalent diagnostic efficiency but improves clinical utility by reporting a rapid species-level identification the same dayshift (~ 8 h).

Utility of Broad-Range PCR Sequencing for Infectious Diseases Clinical Decision Making: a Pediatric Center Experience

Broad-range PCR (BRPCR) sequencing is a promising tool for diagnosis of infectious conditions when traditional microbiologic strategies fail to identify a pathogen. Data on the optimal clinical scenarios in which to use this tool are limited.

Disseminated nocardiosis in an immunocompetent host with occupational exposure

Nocardia is a genus of Gram-positive, partially acid-fast bacteria consisting of over 120 species, of which 50 are recognized as human pathogens. Nocardia spp. are common colonizers in the environment, particularly in soil and water. Nocardia spp. typically cause opportunistic infections in the immunocompetent host, although cases of nocardiosis have been described in those with a normal immune system. Nocardiosis can be localized, most often in the skin or lung, or be disseminated, with involvement of the brain, bone, and visceral organs. Treatment of nocardiosis is complex, as multiple culture-directed antibacterials with appropriate tissue penetration may need to be used for a prolonged duration. To our knowledge, we describe the first successfully treated case of disseminated Nocardia beijingensis infection in an immunocompetent host with doxycycline and trimethoprim-sulfamethoxazole and hypothesize that his occupational exposure to ubiquitous saprophytes may have led to his infection.

Infective endocarditis: Role of molecular techniques in early diagnosis

Infective endocarditis (IE), a heart valve infection primarily caused by bacteria such as streptococci or staphylococci, causes significant morbidity and mortality. Despite the long-term use of broad-spectrum antimicrobials, the infection is often difficult to manage. The latest diagnostic modalities for IE are discussed in this study. Blood culture use in pathogen identification can lead to loss of precious time as well as generation of false negative reports. The first steps in diagnosis are blood cultures and echocardiography, but molecular techniques can be extremely useful and may be used for an accurate and early diagnosis.

Evaluation of 16S rDNA Heart Tissue PCR as a Complement to Blood Cultures for the Routine Etiological Diagnosis of Infective Endocarditis

Identification of the causative pathogen is required to optimize the effective therapy in infective endocarditis (IE). The aim of this study was to assess a 16S rDNA PCR to identify bacteria from heart valve tissues and to evaluate its usefulness as a complement to blood and removed valves cultures. A total of 266 patients diagnosed with IE from January 2015 to December 2019 were evaluated. Results between 16S rDNA PCR from heart valve tissues were compared with microbiological cultures. Blood cultures were positive in 83.5% of patients diagnosed with IE, while 39.6% and 71.8% of the evaluated heart valve samples were positive by culture and 16S rDNA PCR, respectively. For 32 (12%) patients, 16S rDNA tissue PCR provided valuable information supporting the results of blood cultures in the case of bacteria characteristic from the skin microbiota. Additionally, a microorganism was identified by using 16S rDNA PCR in 36% of blood culture-negative cases. The present study reveals that molecular diagnosis using 16S rDNA tissue PCR provides complementary information for the diagnosis of IE, and it should be recommended in surgical endocarditis, especially when blood cultures are negative.

Diagnostic performance of Ion 16S metagenomics kit and Ion reporter metagenomics workflow for bacterial pathogen detection in culture-negative clinical specimens from sterile sources

PCR-based deep sequencing of 16S rRNA gene allows for detection of a wide array of bacterial pathogens in culture-negative specimens. Ion 16S metagenomics kit and Ion Reporter metagenomics workflow (Ion 16S mNGS) provides an end-to-end solution with integrated workflow. Ninety-eight clinical samples with the diagnosis generated with 16S rRNA gene PCR/chain termination (Sanger) sequencing (16S CS) was used to assess the performance of Ion 16S mNGS. Compared to species level detection of 16S CS, the Ion 16S mNGS had 88% sensitivity and 76% specificity. When accounting for genus level of detection, the Ion 16S mNGS had 100% sensitivity. Notably, Ion 16S mNGS generated diagnosis in 13% of 16S CS and culture-negative samples. In addition, Ion 16S mNGS had the advantage of detecting more than 1 pathogen in 16S CS positive samples. We showed that the workflow had high reproducibility.

Clinical utility of 16S rRNA PCR in pleural infection

Pleural infections cause major morbidity and mortality, particularly amongst paediatric and elderly populations. The aetiology is broad, but pleural culture fails to yield a causative pathogen in approximately 40 % of cases. Alternative pathogen identification methods are therefore required. The aim of the study was to investigate the yield from and impact on patient care when performing 16S rRNA PCR on culture-negative pleural fluid specimens and to determine whether any individual laboratory parameters were associated with a positive 16S rRNA PCR result. We conducted a study on 90 patients with suspected pleural infection, who had a culture-negative pleural fluid specimen, which underwent 16S rRNA PCR analysis between August 2017 and June 2019. This study was undertaken at a large NHS Trust in London, UK. Thirty-one per cent of culture-negative pleural fluid specimens tested by 16S rRNA PCR yielded a positive PCR result. Our data demonstrated that 16S rRNA PCR detected a significantly higher proportion of Streptococcus pneumoniae (P<0.0001) and fastidious, slow-growing and anaerobic pathogens (P=0.0025) compared with culture-based methods. Of the 25 16S rRNA PCR results that were positive for a causative pathogen, 76 % had a direct impact on clinical management. No single laboratory variable was found to be associated with a positive 16S rRNA PCR result. The findings from our real-world evaluation highlight the importance of 16S rRNA PCR in confirming pleural infection when the aetiology is unknown, and its direct, positive impact on clinical management.

Revised version (INFD-D-20-00242): impact of 16S rDNA sequencing on clinical treatment decisions: a single center retrospective study

Background

PCRs targeting 16S ribosomal DNA (16S PCR) followed by Sanger’s sequencing can identify bacteria from normally sterile sites and complement standard analyzes, but they are expensive. We conducted a retrospective study in the Strasbourg University Hospital to assess the clinical impact of 16S PCR sequencing on patients’ treatments according to different sample types.

Methods

From 2014 to 2018, 806 16S PCR samples were processed, and 191 of those were positive.

Results

Overall, the test impacted the treatment of 62 of the 191 patients (32%). The antibiotic treatment was rationalized in 31 patients (50%) and extended in 24 patients (39%), and an invasive procedure was chosen for 7 patients (11%) due to the 16S PCR sequencing results. Positive 16S PCR sequencing results on cerebrospinal fluid (CSF) had a greater impact on patients’ management than positive ones on cardiac valves (p = 0.044). The clinical impact of positive 16S PCR sequencing results were significantly higher when blood cultures were negative (p < 0.001), and this difference appeared larger when both blood and sample cultures were negative (p < 0.001). The diagnostic contribution of 16S PCR was higher in patients with previous antibiotic treatment (p < 0.001).

Conclusion

In all, 16S PCR analysis has a significant clinical impact on patient management, particularly for suspected CSF infections, for patients with culture-negative samples and for those with previous antibiotic treatments.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-021-05892-4.

Molecular Approach to Diagnosis of Cardiovascular Implantable Electronic Device Infection

BACKGROUND

Sonicate fluid (SF), a solution derived from vortexing and sonication of explanted cardiovascular implantable electronic devices (CIEDs), is a higher-yield specimen compared with swabs or tissues for culture-based detection of microorganisms associated with CIED infection. Despite this, SF culture fails to identify a causative organism in ~50% of cases. We aimed to evaluate the diagnostic performance of 16S ribosomal RNA gene (rRNA) polymerase chain reaction (PCR)/sequencing of SF and compare it with that of SF culture.

METHODS

We identified 322 SF specimens from extracted CIEDs and reviewed clinical data for each patient. Subjects were classified as having or not having CIED infection. Cases were subcategorized as culture negative if no significant growth was reported from SF cultures and as culture positive if an organism was detected above predefined thresholds. 16S rRNA PCR/sequencing was performed, with the organisms identified reported according to Clinical and Laboratory Standards Institute guidelines for sequence data interpretation.

RESULTS

A total of 278 SF samples corresponded to infected cases, of which 160 were culture positive and 118 culture negative. The remaining 44 were from noninfected cases, of which 2 were culture positive. Compared with SF culture, the sensitivity of 16S rRNA PCR/sequencing was higher (64% vs 57.5%, P = .003). 16S rRNA PCR/sequencing detected a potential pathogen in 28 of 118 culture-negative cases, identifying staphylococci in the majority (18/28).

CONCLUSIONS

16S rRNA PCR/sequencing has higher sensitivity to detect bacteria in SF from extracted CIEDs than does SF culture.

Current Capabilities of Gut Microbiome-Based Diagnostics and the Promise of Clinical Application

There is increasing evidence for the importance of the gut microbiome in human health and disease. Traditional and modern technologies - from cell culture to next generation sequencing - have facilitated these advances in knowledge. Each of the tools employed in measuring the microbiome exhibits unique capabilities that may be leveraged for clinical diagnostics. However, much still needs to be done to standardize the language and metrics by which a microbiome is characterized. Here we review the capabilities of gut microbiome-based diagnostics, review selected examples, and discuss the outlook towards clinical application.

Infective endocarditis is associated with worse outcomes in stroke: A Thailand National Database Study

BACKGROUND

There is lack of data on the association between infective endocarditis (IE) and outcomes of mortality and complications in stroke. We aimed to compare characteristics and outcomes of stroke patients with and without IE.

METHODS

We retrospectively examined the above association using data obtained from an insurance database which covers ~75% of the Thai population. All hospitalised strokes between 8 January 2003 and 31 December 2013 were included in the current study. Characteristics and outcomes were compared between stroke patients with or without IE, and then between two main stroke types. Multiple logistic regression models including propensity score-matched analyses were constructed to assess study outcomes controlling for age, sex, stroke type and comorbidities.

RESULTS

A total of 590 115 stroke patients (mean (SD) age = 64.2 ± 13.7 years; ischaemic = 51.7%; haemorrhagic = 32.6%; undetermined = 15.7%) were included, of whom 2129 (0.36%) had stroke associated with IE. After adjustment, we found that IE was significantly associated with the following complications: arrhythmias (adjusted odds ratio (95% CI) 6.94 (6.29-7.66)), sepsis (1.24 (1.01-1.52)), pneumonia (1.34 (1.17-1.53)), respiratory failure (1.43 (1.24-1.66)) and in-hospital mortality (1.29 (1.13-1.47)) (P for all <.001). Patients with haemorrhagic stroke with IE had poorer outcomes for in-hospital mortality and respiratory failure compared with their counterparts with ischaemic stroke. Propensity score-matched analysis showed similar results.

CONCLUSIONS

Our results suggest that stroke patients with IE differ from that of the general stroke population and these patients have worse outcomes. Future studies are needed to determine the best treatment strategies for stroke patients with IE.

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.

The diagnostic benefit of 16S rDNA PCR examination of infective endocarditis heart valves: a cohort study of 146 surgical cases confirmed by histopathology

Aims

Upon suspicion of infective endocarditis, the causative microorganism must be identified to optimize treatment. Blood cultures and culturing of removed valves are the mainstay of this diagnosis and should be complemented by growth-independent methods. We assessed the diagnostic benefit of examining removed endocarditis valves by broad-range bacterial PCR to detect causative bacteria in cases where culturing was not available, negative, or inconclusive because a skin commensal was detected, in patients from our clinical routine practice.

Methods and results

Patients from Heidelberg University Hospital with suspicion of endocarditis, followed by valve replacement and analysis by 16S rDNA PCR, between 2015 and 2018, were evaluated. 146 patients with definite infective endocarditis, confirmed by the valve macroscopics and/or histology, were included. Valve PCRs were compared to corresponding blood and valve culture results. Overall, valve PCR yielded an additional diagnostic benefit in 34 of 146 cases (23%) and was found to be more sensitive than valve culture. In 19 of 38 patients with both negative blood and valve cultures, valve PCR was the only method rendering a pathogen. In 23 patients with positive blood cultures detecting skin commensals, 4 patients showed discordant valve PCR results, detecting a more plausible pathogen, and in 11 of 23 cases, valve PCR confirmed commensals in blood culture as true pathogens. Only the remaining 8 patients had negative valve PCRs.

Conclusion

Valve PCR was found to be a valuable diagnostic tool in surgical endocarditis cases with negative blood cultures or positive blood cultures of unknown significance.

Trial registration

S-440/2017 on 28.08.2017 retrospectively registered.

Graphic abstract

Subdividing of all infective endocarditis patients in this study, showing that valve PCR yields valuable information for patients with skin commensals in blood cultures, which were either confirmed by the same detection in valve PCR or refuted by the detection of a different and typical pathogen in valve PCR. Additionally, benefit was determined in patients with negative or not available blood cultures and only positive detection in valve PCR. +: Positive; −: negative; n/a: not available results

Electronic supplementary material

The online version of this article (10.1007/s00392-020-01678-x) contains supplementary material, which is available to authorized users.

Fluorescence in situ hybridization for identification and visualization of microorganisms in infected heart valve tissue as addition to standard diagnostic tests improves diagnosis of endocarditis

OBJECTIVES

In infective endocarditis (IE), identification of the causative organism and consecutive treatment are crucial for patient survival. Although the macroscopic aspect resembles infected tissue, standard diagnostic tests often fail to allow one to identify bacteria. Fluorescence in situ hybridization (FISH) is a molecular, culture-independent technique that allows one to identify and visualize microorganisms within tissue and to recognize their morphology, number and activity. We analysed the diagnostic benefit of FISH/polymerase chain reaction (PCR) by comparing its results to those of standard diagnostic tests.

METHODS

From September 2015 to April 2018, 128 patients underwent first-time or redo valve surgery to treat IE. Patients were designated according to the modified Duke criteria as definite (n = 61), possible (n = 34) or rejected (n = 33) IE. Tissue specimens obtained intraoperatively were analysed using FISH/PCR in addition to undergoing standard diagnostic testing and PCR alone.

RESULTS

We used blood cultures to detect microorganisms in 67/128 patients; valve cultures, in 34/128; PCR, in 67/128; histopathological diagnosis showed IE in 72/128 cases. We were able to detect microorganisms in 103/128 cases using FISH/PCR, with 55/61 in definite IE. Furthermore, we were able to identify 26 cases of bacterial biofilm using FISH/PCR, despite antibiotic treatment of 61 in the definite, 13 in the possible and 1 in the rejected group, including 8/33 patients in the rejected group with active bacteria. In all cases, the patient's therapy was altered.

CONCLUSIONS

FISH/PCR was used to identify microorganisms in cases in which standard diagnostic tests failed to provide sufficient results for various reasons. Furthermore, FISH/PCR enabled us to identify bacterial biofilms and to differentiate between active versus degraded bacteria, thus indicating the impact of treatment. Therefore, we suggest FISH/PCR as an additional diagnostic tool in IE alongside standard diagnostic tests.

Ureaplasma urealyticum disseminated multifocal abscesses in an immunocompromised adult patient: a case report

BACKGROUND

Ureaplasma urealyticum is a fastidious bacteria which lacks a cell wall. Extragenital infections are rare in immunocompetent adults. There are few literature reports of perinephric abscess. We present a case of non-resolving multifocal "culture-negative" abscesses in a hypogammaglobulinemic adult female due to U. urealyticum.

CASE PRESENTATION

66-year-old female with a one-week history of fever, malaise and new right hip and leg pain. Past medical history was notable for chronic pancytopenia secondary to in remission B cell follicular lymphoma, ESRD on intermittent hemodialysis with bilateral nephrostomy tubes and Crohn's. CT abdomen/pelvis revealed a small left perinephric hematoma and proximal right femur fluid collection. Persistent right thigh pain led to additional ultrasound with anterior thigh collection and CT revealed an irregular rim-enhancing fluid collection in the left posterior pararenal space. Antimicrobial therapy included ertapenem and vancomycin followed by meropenem, trimethoprim-sulfamethoxazole, daptomycin and metronidazole in setting of persistent culture-negative results and clinical deterioration. Following detection of U. urealyticum by 16S rDNA PCR in both left pararenal and right trochanteric bursa abscesses doxycycline was started. Despite this, the patient died four days later.

CONCLUSIONS

Disseminated infection by U. urealyticum has been documented in immunocompromised adult patients with few reports of perinephric abscess. We propose that ascending genitourinary route led to perinephric abscess. The multiple disseminated fluid collections make it highly suspicious for hematogenous spread given the lack of radiographic enhancement to suggest contiguous spread. Diagnosis and treatment of U. urealyticum-disseminated infection is extremely challenging as culture is laborious and not routinely performed. Furthermore, the lack of cell wall renders beta-lactams and vancomycin ineffective and therefore requirement for "atypical" coverage. Early diagnosis and treatment are key to prevent further complications and death.

Utility of Histologic and Histochemical Screening for 16S Ribosomal RNA Gene Sequencing of Formalin-Fixed, Paraffin-Embedded Tissue for Bacterial Endocarditis

OBJECTIVES

16S ribosomal RNA (rRNA) sequencing is a powerful but expensive tool for the identification of bacteria in culture-negative endocarditis. Histologic criteria to screen formalin-fixed, paraffin-embedded (FFPE) specimens for testing are evaluated.

METHODS

Sixty-eight cases of infective endocarditis and controls were histologically reviewed and analyzed by 16S rRNA gene sequencing.

RESULTS

Sequencing identified a specific pathogenic organism in 33 (49%) of 68 cases with acute inflammation and in 0 of 10 controls (P = .004). Visualization of organisms by Gram or Grocott methenamine silver stains had the strongest association with positive sequencing, while antibiotic treatment effect and acid decalcification decreased sensitivity. Molecular identifications were concordant with blood culture results in 90% of the cases, and a positive sequencing result was obtained in approximately half of the cases with negative valve cultures.

CONCLUSIONS

Histologic screening criteria are extremely helpful for identifying cases likely to be positive by molecular testing and can provide significant cost savings in filtering out low-yield specimens.

Molecular characterisation of emerging pathogens of unexplained infectious disease syndromes

Introduction: The discoveries of HIV and Helicobacter pylori in the 1980s were landmarks in identification of novel pathogens causing unexplained infectious syndromes using conventional microbiological technologies. In the last few decades, advancement of molecular technologies has provided us with more robust tools to expand our armamentarium in this microbial hunting process. Areas covered: In this article, we give a brief overview of the most important molecular technologies we use for identification of emerging microbes associated with unexplained infectious syndromes, including 16S rRNA and other conserved targets sequencing for bacteria, internal transcribed spacer (ITS) and other target gene sequencing for fungi, polymerase and other gene sequencing for viruses, as well as deep sequencing. Then, we use several representative examples to illustrate how these techniques have been used for the discoveries of a few notable bacterial, fungal and viral pathogens associated with unexplained infectious syndromes in the last 20-30 years. Expert opinion: In the past and present, characterization of emerging pathogens of unexplained infectious disease syndromes has relied on a combination of conventional culture- and phenotype-based technologies and nucleic acid amplification and sequencing. In the next era, we envisage more widespread adoption of next generation technologies that can detect both known and previously undescribed pathogens.

Impact of pre-operative antimicrobial treatment on microbiological findings from endocardial specimens in infective endocarditis

Treatment of infective endocarditis (IE) should be initiated promptly. This might hamper the chances to identify the causative organism in blood cultures. Microbiological sampling of infected valve in patients undergoing surgery might identify the causative organism. The impact of pre-operative antimicrobial treatment on the yield of valve samples is not known. This study evaluated the impact of the duration of the pre-operative antibiotic treatment on valve culture and 16S rRNA PCR findings from resected endocardial samples. Patients meeting the modified Duke criteria of definite or possible IE and undergoing valve surgery due to IE during 2011–2016 were included from Southern Finland. Eighty-seven patients were included. In patients with shorter than 2 weeks of pre-operative antimicrobial treatment, PCR was positive in 91% (n = 42/46) and valve culture in 41% (n = 19/46) of cases. However, in patients who had 2 weeks or longer therapy before operation, PCR was positive in 53% (n = 18/34) and all valve cultures were negative. In 14% of patients, PCR had a diagnostic impact. In blood-culture negative cases (n = 13), PCR could detect the causative organism in ten patients (77%). These included five cases of Bartonella quintana, one Tropheryma whipplei, and one Coxiella burnetii. Long pre-operative antimicrobial treatment was shown to have a negative impact on microbiological tests done on resected endocardial material. After 2 weeks of therapy, all valve cultures were negative, but PCR was positive in half of the cases. PCR aided in diagnostic work-up, especially in blood culture negative cases.

Multidrug-resistant Aeromonas hydrophila causing fatal bilateral necrotizing fasciitis in an immunocompromised patient: a case report

BACKGROUND

Aeromonas hydrophila is a water-dwelling, gram-negative rod-shaped bacterium, associated with diarrheal illness and, less commonly, necrotizing skin and soft tissue infections, especially among immunocompromised patients. Necrotizing fasciitis is associated with a high mortality rate, especially when caused by Aeromonas spp. Our patient was infected with an extremely aggressive form of multidrug-resistant Aeromonas spp. that produced both an extended-spectrum β-lactamase and an AmpC enzyme. Aeromonads are being recognized as important emerging pathogens because of their inherent antibiotic resistance profiles compounded by other virulence factors. These difficult-to-treat organisms can have significant implications in both clinical and public health settings.

CASE PRESENTATION

A 37-year-old Caucasian male with immunosuppression due to aplastic anemia being treated with cyclosporine, presented to hospital with relapsed disease. While in hospital, he subsequently developed overwhelming sepsis secondary to bilateral lower extremity necrotizing fasciitis. The necrotizing fasciitis was caused by a multidrug-resistant strain of A. hydrophila. Despite broad-spectrum antibiotics and aggressive surgical debridement, he succumbed to this severe invasive infection.

CONCLUSIONS

Necrotizing fasciitis caused by Aeromonas spp. is a rare infection that may have a poor clinical outcome, particularly if the diagnosis is delayed and/or the organism is highly virulent and multidrug resistant. Enhanced education of clinicians and microbiologists is required to prevent unnecessary complications and improve survival.

The use of broad-range bacterial PCR in the diagnosis of infectious diseases: a prospective cohort study

OBJECTIVES

Broad-range PCR has the potential to detect virtually any bacterial species via amplification and nucleotide sequencing of a DNA region common to all bacteria. We aimed to evaluate its usefulness and clinical relevance when applied to a wide variety of primary sterile materials.

METHODS

A prospective study including 1370 samples (75 heart valves, 151 joint tissue samples, 230 joint aspirates, 848 whole blood samples and 66 culture-negative cerebrospinal fluid samples) were studied by using a commercial PCR system for detecting 16S rDNA (Molzym). The PCR results were compared with culture and were considered to provide added diagnostic value only if the PCR approach revealed new pathogens that were missed by culture.

RESULTS

The added value of PCR was evident in 173 of 555 PCR-positive samples (0.126; 0.109-0.144 (proportion from all tested samples; 95% confidence interval)), most frequently in examinations of heart valves (0.56; 0.448-0.672) and joint tissue samples (0.219; 0.153-0.284). In contrast, the lowest rate of PCR with added value was noted for blood samples, regardless of the patient cohort they had been drawn from (nononcologic patients from intensive care: 0.065; 0.043-0.087, haematooncologic children: 0.048; 0.027-0.070). Moreover, PCR missed up to 7.1% of blood culture findings (0.071; 0.048-0.095) regarded as clinically relevant, which was the second highest failure rate after joint tissue samples (0.099; 0.052-0.147).

CONCLUSIONS

Broad-range PCR substantially increases detection rate of pathogens, especially from heart valves and joint samples. However, a concurrent risk of false-negative PCR results justifies the need for parallel culture.

Utility of a Direct 16S rDNA PCR and Sequencing for Etiological Diagnosis of Infective Endocarditis

Background

Cases of infective endocarditis (IE) require prompt etiological diagnosis for effective treatment. Molecular methods can aid in rapid and reliable diagnosis of culture-negative IE cases. We evaluated the utility of 16S rDNA PCR and sequencing in determining the causative agents of IE in valve tissues, especially when specimens were obtained after initiation of antimicrobial therapy.

Methods

We performed 16S rDNA PCR and sequencing in heart valve specimens and medical records review of 80 patients who underwent protocol-based cardiac surgery from 2013 to 2015. One patient did not meet the criteria for IE. Sixty-five (81.3%) and 14 pa-tients (17.5%) were diagnosed as having definite IE and possible IE, respectively. Blood and heart valve biopsy tissue were examined by using routine microbiological methods.

Results

Blood cultures in our hospital were IE-positive for 33 patients (41.8%), whereas 49 patients (62.0%) showed positive blood cultures when initial blood cultures performed at the referring hospital were included. Eighteen (22.8%) and 40 patients (50.6%) were IE-positive in valve tissue cultures and 16S rDNA PCR, respectively. Bacteria in the Streptococcus mitis group (n=26) were the most common etiological agents of IE. Eight (10.1%) culture-negative specimens tested positive by 16S rDNA PCR. In five of eight PCR-positive and culture-negative cases, fastidious or anaerobic organisms were the cause of IE.

Conclusions

Direct 16S rDNA PCR and sequencing can be used as a supplementary method to conventional blood and biopsy culture testing, especially in culture-negative IE cases that are negative for IE by culture.

Molecular Diagnosis of Bacterial Definite Infective Endocarditis by Real-Time Polymerase Chain Reaction

Infective endocarditis (IE) can be diagnosed using the Duke criteria, which cannot be conclusive especially when the results of blood cultures are negative. This study aimed at using real-time polymerase chain reaction (PCR) technique to isolate bacteria present in whole blood samples of patients with definitive IE on the basis of the method designed in this study. This laboratory and test study was conducted on 20 whole blood samples taken from patients with definitive IE. Real-time PCR of the 16s rRNA was utilized to directly analyze whole blood samples to diagnose bacterial IE. Of 20 whole blood samples with definitive IE, only one blood culture (5%) was positive and the isolated bacterium belonged to Streptococci viridans group. Also, 13 whole blood samples were positive using real-time PCR technique. The isolated bacteria were Enterococcus faecalis with seven (35%) cases, Streptococcus gallolyticus with two (10%) cases, Streptococcus mutans with one (5%) case, Streptococcus sanguinis with one (5%) case, Streptococcus salivarius with one (5%) case, and Staphylococcus aureus with one (5%) case. Sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) using real-time PCR technique were 65%, 100%, 100%, and 74%, respectively. The developed real-time PCR method allows us to detect bacteria in whole blood samples and is much more sensitive than culturing method. It also permits the differentiation of the main group of bacteria within a few hours for IE.

The diagnosis of microorganism involved in infective endocarditis (IE) by polymerase chain reaction (PCR) and real-time PCR: A systematic review

Broad-range bacterial rDNA polymerase chain reaction (PCR) followed by sequencing may be identified as the etiology of infective endocarditis (IE) from surgically removed valve tissue; therefore, we reviewed the value of molecular testing in identifying organisms' DNA in the studies conducted until 2016. We searched Google Scholar, Scopus, ScienceDirect, Cochrane, PubMed, and Medline electronic databases without any time limitations up to December 2016 for English studies reporting microorganisms involved in infective endocarditis microbiology using PCR and real-time PCR. Most studies were prospective. Eleven out of 12 studies used valve tissue samples and blood cultures while only 1 study used whole blood. Also, 10 studies used the molecular method of PCR while 2 studies used real-time PCR. Most studies used 16S rDNA gene as the target gene. The bacteria were identified as the most common microorganisms involved in infective endocarditis. Streptococcus spp. and Staphylococcus spp. were, by far, the most predominant bacteria detected. In all studies, PCR and real-time PCR identified more pathogens than blood and tissue cultures; moreover, the sensitivity and specificity of PCR and real-time PCR were more than cultures in most of the studies. The highest sensitivity and specificity were 96% and 100%, respectively. The gram positive bacteria were the most frequent cause of infective endocarditis. The molecular methods enjoy a greater sensitivity compared to the conventional blood culture methods; yet, they are applicable only to the valve tissue of the patients undergoing cardiac valve surgery.