Evaluation of a multiplex polymerase chain reaction for early diagnosis of ventriculostomy-related infections

The incidence of ventriculostomy-related infections as diagnosed by 16S rRNA polymerase chain reaction: A prospective observational study

BACKGROUND

Ventriculostomy-related infections (VRIs) are reported in about 10 % of patients with external ventricular drains (EVDs). VRIs are difficult to diagnose due to clinical and laboratory abnormalities caused by the primary neurological injury which led to insertion of the EVD. Polymerase chain reaction (PCR) of the cerebrospinal fluid (CSF) may enable more accurate diagnosis of VRI. We performed a prospective cohort study to measure the incidence of VRI as diagnosed by 16S rRNA PCR.

METHODS

Patients admitted to intensive care with a primary diagnosis of subarachnoid haemorrhage (SAH), traumatic brain injury (TBI), or intracerebral haemorrhage (ICH), who required an EVD, were assessed for inclusion in this study. Data were extracted from the electronic medical record, bedside charts, or from a prospectively collected database, the Neuroscience Outcomes in Intensive CarE database (NOICE). 16S rRNA PCR was performed on routinely collected CSF as per laboratory protocol. VRI was also diagnosed based on pre-existing definitions.

RESULTS

237 CSF samples from 39 patients were enrolled in the study. The mean patient age was 55.7 years, and 56.4 % were female. The most common primary neurological diagnosis was SAH (61.5 %). The incidence of a positive PCR was 2.6 % of patients (1 in 39) and 0.8 % of CSF samples (2 in 237). The incidence of VRI according to pre-published diagnostic criteria was 2.6 % - 41 % of patients and 0.4 % - 17.6 % of CSF samples. 28.2 % of patients were treated for VRI. Pre-published definitions which relied on CSF culture results had higher specificity and lower false positive rates for predicting a PCR result when compared to definitions incorporating non-microbiological markers of VRI. In CSF samples with a negative 16S rRNA PCR, there was a high proportion of non-microbiological markers of infection, and a high incidence of fever on the day the CSF sample was taken.

CONCLUSIONS

The incidence of VRI as defined as a positive PCR was lower than the incidence of VRI according to several published definitions, and lower than the incidence of VRI as defined as treatment by the clinical team. Non-microbiological markers of VRI may be less reliable than a positive CSF culture in diagnosing VRI.

Diagnosis of external ventricular drainage related infections with real-time 16S PCR and third-generation 16S sequencing

OBJECTIVE

Investigate the performance of real-time 16S PCR and third-generation 16S sequencing in the diagnosis of external ventricular drain related infections (EVDRI).

METHODS

Subjects with suspected EVDRI were prospectively included at Uppsala University Hospital. Subjects were included into three groups: subjects with negative CSF culture with and without antibiotic treatment and subjects with positive CSF culture, respectively. CSF was analysed with real-time 16S PCR and third-generation 16S sequencing. Real-time 16S PCR positivity/negativity and number of 16S sequence reads were compared between groups. For culture positive subjects, species identification in third-generation sequencing and routine culture was compared.

RESULTS

84 subjects were included. There were 18, 44 and 22 subjects in the three groups. Real-time PCR was positive in 17 of 22 subjects in the culture positive group and negative in 61 of the 62 subjects in the two culture negative groups. The sensitivity and specificity for real-time 16S PCR compared to culture was estimated to 77% and 98%, respectively. Species identification in 16S sequencing and culture was concordant in 20 of 22 subjects. The number of 16S sequence reads were significantly higher in the culture positive group than in both culture negative groups (p < 0.001). There was no significant difference in number of 16S sequences between the two culture negative groups.

CONCLUSIONS

Real-time 16S PCR predict culture results with sufficient reliability. Third-generation 16S sequencing could enhance sensitivity and species identification in diagnostics of EVD-related infections. False negative culture results appear to be uncommon in patients with suspected EVDRI.

Broad Range Eubacterial Polymerase Chain Reaction of Cerebrospinal Fluid Reduces the Time to Exclusion of and Costs Associated with Ventriculostomy-Related Infection in Hemorrhagic Stroke

BACKGROUND

Patients with hemorrhagic stroke and an external ventricular drain in situ are at risk for ventriculostomy-related-infections (VRI). Because of the contamination of the cerebrospinal fluid (CSF) with blood and the high frequency of false negative CSF culture, the diagnosis of VRI remains challenging. This study investigated the introduction of CSF broad range eubacterial polymerase chain reaction (ePCR) and its effect on frequency and duration of antibiotic therapy for VRI, neurocritical care unit (NCCU) length of stay, related costs, and outcome.

METHODS

Between 2020 and 2022, we prospectively included 193 patients admitted to the NCCU of the University Hospital of Zürich with hemorrhagic stroke and an external ventricular drain for more than 48 h. Patient characteristics, serum inflammatory markers, white blood cell count in CSF, use and duration of antibiotic treatment for VRI, microbiological findings (CSF cultures and ePCR tests), and NCCU length of stay were compared in patients with no infection, noncerebral infection, suspected VRI, and confirmed VRI. Data of patients with suspected VRI of this cohort were compared with a retrospective cohort of patients with suspected VRI treated at our NCCU before the introduction of CSF ePCR testing (2013-2019).

RESULTS

Out of 193 patients, 12 (6%) were diagnosed with a confirmed VRI, 66 (34%) with suspected VRI, 90 (47%) with a noncerebral infection, and 25 (13%) had no infection at all. Compared with the retrospective cohort of patients, the use of CSF ePCR resulted in a reduction of patients treated for suspected VRI for the whole duration of 14 days (from 51 to 11%). Furthermore, compared with the retrospective group of patients with suspected VRI (n = 67), after the introduction of CSF ePCR, patients with suspected VRI had shorter antibiotic treatment duration of almost 10 days and, hence, lower related costs with comparable outcome at 3 months.

CONCLUSIONS

The use of CSF ePCR to identify VRI resulted in shorter antibiotic treatment duration without changing the outcome, as compared with a retrospective cohort of patients with suspected VRI.

Etiology and Outcomes of Healthcare-Associated Meningitis and Ventriculitis—A Single Center Cohort Study

Healthcare associated meningitis and ventriculitis (HCAMV) are serious complications of neurosurgical procedures. We conducted a retrospective cohort study of patients with HCAMV treated at the University Hospital for Infectious Diseases Zagreb during the 2013–2019 period. A total of 144 patients with 151 episodes of HCAMV were included. The most common indications for neurosurgical procedures were brain tumor, hemorrhage and hydrocephalus. Etiology was identified in 90 (59.6%) episodes (either positive CSF culture or positive PCR), and in other 61 (40.39%) the diagnosis of HCAMV was made based on clinical and CSF parameters, without microbiologic confirmation. Carbapenem-resistant Acinetobacter baumannii was the most common pathogen (15.89%), followed by Staphylococcus aureus (13.91%), Pseudomonas aeruginosa (13.25%) and Coagulase negative staphylococci (7.95%). Overall, 24 (16.3%) patients died, and the majority had adverse outcomes, persistent vegetative state (8, 5.56%) and severe disability (31, 21.53%). The worst clinical outcomes were observed in A. baumannii infections. High rate of complications, the need for external ventricular drainage (re)placement often complicated with nosocomial infections and prolonged stay in intensive care units were observed. Clinicians should be aware of local microbial epidemiology on guiding proper empirical antimicrobial treatment in patients with HCAMV.

Current Perspectives on the Diagnosis and Management of Healthcare-Associated Ventriculitis and Meningitis

Ventriculitis or post-neurosurgical meningitis or healthcare-associated ventriculitis and meningitis (VM) is a severe infection that complicates central nervous system operations or is related to the use of neurosurgical devices or drainage catheters. It can further deteriorate patients who have already presented significant neurologic injury and is associated with high morbidity, mortality, and poor functional outcome. VM can be difficult to distinguish from aseptic meningitis, inflammation that follows hemorrhagic strokes and neurosurgical operations. The associated microorganisms can be either skin flora or nosocomial pathogens, most commonly, Gram-negative bacteria. Classical microbiology can fail to isolate the culprit pathogen. Novel cerebrospinal fluid (CSF) biomarkers and molecular microbiology can fill the diagnostic gap and expedite pathogen identification and treatment. The pathogens may demonstrate significant resistant patterns and their antibiotic treatment can be difficult, as many important drug classes, including the beta-lactams and the glycopeptides, hardly penetrate to the CSF, and do not achieve therapeutic levels at the site of the infection. Treatment modifications, such as higher daily dose and prolonged or continuous administration, might increase antibiotic levels in the site of infection and facilitate pathogens clearance. However, in the case of therapeutic failure or infection due to difficult-to-treat bacteria, the direct antibiotic instillation into the CSF, in addition to the intravenous antibiotic delivery, may help in the resolution of infection. However, intraventricular antibiotic therapy may result in aseptic meningitis and seizures, concerning the administration of aminoglycosides, polymyxins, and vancomycin. Meanwhile, bacteria form biofilms on the catheter or the device that should routinely be removed. Novel neurosurgical treatment modalities comprise endoscopic evacuation of debris and irrigation of the ventricles. VM prevention includes perioperative antibiotics, antimicrobial impregnated catheters, and the implementation of standardized protocols, regarding catheter insertion and manipulation.

Evaluation of a commercial multiplex PCR for diagnosis of central nervous system (CNS) nosocomial infections

Nosocomial Central Nervous System (CNS) infections are often serious complications of neurosurgical procedures. Their diagnosis is complex and frequently based on microbiological culture. The aim of this work was to evaluate the effectiveness of the FilmArray® Blood Culture Identification (BCID) panel, a multiplex PCR designed to identify the most common etiologic agents of sepsis involved with nosocomial CNS infections. A total of ninety samples were analyzed with the BCID panel. The sensitivity and specificity achieved were 77.4% and 100% respectively, when compared with the reference method (culture). Based on the analysis of the melting curves, another cut-off was established improving sensitivity to 83.9% whilst maintaining 98.3% specificity. The BCID panel seems to be a helpful tool for the prompt diagnosis of CNS nosocomial infections. The cut-off proposed here can increase sensitivity, but further studies are required to confirm its effectiveness and its applicability in clinical microbiology laboratories.

Detection of bacterial DNA on neurostimulation systems in patients without overt infection

OBJECTIVE

Hardware-related infection remains a major problem in patients with neurostimulation systems. The role of bacterial colonization and the formation of biofilm on the surface of implanted devices remain unclear. Here, we analysed the incidence of bacterial DNA on the surface of implantable pulse generators (IPGs) using 16S rRNA gene sequencing in a consecutive series of patients who underwent routine IPG replacement without clinical signs of infection.

PATIENTS AND METHODS

We included 36 patients who underwent scheduled replacement surgery of 44 IPGs. The removed IPGs were processed and whole genomic DNA was extracted. The detection of bacterial DNA was carried out by Polymerase Chain Reaction (PCR) using universal bacterial primers targeting the 16S rRNA gene. The DNA strands were analysed by single-strand conformation polymorphism (SSCP) analysis.

RESULTS

Indications for chronic neurostimulation were Parkinson disease, tremor, dystonia, neuropathic pain and peripheral artery occlusion disease. Mean age of patients at the time of implantation was 48 ± 17.6 years. The mean interval between implantation and replacement of the IPG was 24.8 months. PCR/SSCP detected bacterial DNA of various species in 5/36 patients (13.9%) and in 5/44 pacemakers (11.4%), respectively. There was no evidence of clinical infection or wound healing impairment during follow-up time of 45.6 ± 19.6 months.

CONCLUSION

Bacterial DNA can be detected on the surface of IPGs of neurostimulation systems in patients without clinical signs of infection by using PCR techniques. It remains unclear, similar to other permanently implanted devices, which mechanisms and processes promote progression to the point of overt infection.

Neutrophil CD64 index in cerebrospinal fluid as a marker of bacterial ventriculitis in children with external ventricular drainage

Background

Bacterial ventriculitis is a common complication in children with temporary external ventricular drains (EVD) and the diagnosis is challenging. The present study compared the diagnostic accuracy of novel cerebrospinal fluid (CSF) marker - CD64 expression on neutrophils measured as neutrophil CD64 index (CD64in) to routine laboratory CSF and blood markers for bacterial ventriculitis in children with EVD.

Methods

We conducted a prospective, observational study, enrolling children with EVD. CD64in in CSF together with CSF markers (leukocyte count, percentage of neutrophils, glucose, and proteins) and blood markers (leukocyte and differential count, C-reactive protein (CRP), and procalcitonin (PCT)) were studied at the time of suspected bacterial ventriculitis. CD64in was measured by flow cytometry. Diagnostic accuracy determined by the area under the receiver–operating characteristic (ROC) curves (AUC) was defined for each marker.

Results

Thirty-three episodes of clinically suspected ventriculitis in twenty-one children were observed during a 26-month period. Episodes were classified into those with microbiologically proven ventriculitis (13 episodes) and into those with microbiologically negative CSF (20 episodes). CD64in and leukocyte count were the only CSF markers that could differentiate between groups with diagnostic accuracy of 0.875 and 0.694, respectively. Among blood markers only CRP and band neutrophils differentiated between groups with diagnostic accuracy of 0.792 and 0.721, respectively.

Conclusions

CD64in in CSF is a promising diagnostic marker of bacterial ventriculitis in children with EVD as it has higher diagnostic accuracy than routine blood and CSF markers for diagnosing bacterial ventriculitis at the time of clinical suspicion.

Probe-free label system for rapid detection of Cronobacter genus in powdered infant formula

Cronobacter species previously known as Enterobacter sakazakii poses high risks to neonates and infants. In this work a rapid detection method was developed which combined loop-mediated isothermal amplification with lateral flow assay for detection of Cronobacter species in powdered infant formula. The fast amplification reaction without betaine was established and capable of performing DNA replication within 25 min. Based on the novel probe-free labeling methods, we established a lateral flow assay to capture the specific loop-mediated isothermal amplification amplicons which were labeled with fluorescein isothiocyanate and biotin. And the final detection time of this system was within 40 min. The false positive results of the lateral flow assay induced by primer dimer tagged with fluorescein isothiocyanate and biotin were eliminated by Taq single strand DNA binding protein (4 ng/μL). Simultaneously, the efficiency of the fast loop-mediated isothermal amplification assay was achieved. By injection of Taq SSB into the amplification assay as a replacement for betaine, the novel probe-free method could detect Cronobacter species with high specificity and sensitivity at the detection limit in PIF of 10¹ cfu/g. Our overall strategy has excellent potential in the rapid diagnosis of Cronobacter species label-free by integrating loop-mediated isothermal amplification and lateral flow assay.

New York City House Mice (Mus musculus) as Potential Reservoirs for Pathogenic Bacteria and Antimicrobial Resistance Determinants

House mice (Mus musculus) thrive in large urban centers worldwide. Nonetheless, little is known about the role that they may play in contributing to environmental contamination with potentially pathogenic bacteria. Here, we describe the fecal microbiome of house mice with emphasis on detection of pathogenic bacteria and antimicrobial resistance genes by molecular methods. Four hundred sixteen mice were collected from predominantly residential buildings in seven sites across New York City over a period of 13 months. 16S rRNA sequencing identified Bacteroidetes as dominant and revealed high levels of Proteobacteria A targeted PCR screen of 11 bacteria, as indicated by 16S rRNA analyses, found that mice are carriers of several gastrointestinal disease-causing agents, including Shigella, Salmonella, Clostridium difficile, and diarrheagenic Escherichia coli Furthermore, genes mediating antimicrobial resistance to fluoroquinolones (qnrB) and β-lactam drugs (bla_SHV and bla_ACT/MIR) were widely distributed. Culture and molecular strain typing of C. difficile revealed that mice harbor ribotypes associated with human disease, and screening of kidney samples demonstrated genetic evidence of pathogenic Leptospira species. In concert, these findings support the need for further research into the role of house mice as potential reservoirs for human pathogens and antimicrobial resistance in the built environment.IMPORTANCE Mice are commensal pests often found in close proximity to humans, especially in urban centers. We surveyed mice from seven sites across New York City and found multiple pathogenic bacteria associated with febrile and gastrointestinal disease as well as an array of antimicrobial resistance genes.

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.