Group B streptococcal PCR testing in comparison to culture for diagnosis of late onset bacteraemia and meningitis in infants aged 7-90 days: a multi-centre diagnostic accuracy study

Molecular diagnostics in cerebrospinal fluid for the diagnosis of central nervous system infections

SUMMARYCentral nervous system (CNS) infections can be caused by various pathogens, including bacteria, viruses, fungi, and parasites. Molecular diagnostic methods are pivotal for identifying the different causative pathogens of these infections in clinical settings. The efficacy and specificity of these methods can vary per pathogen involved, and in a substantial part of patients, no pathogen is identified in the cerebrospinal fluid (CSF). Over recent decades, various molecular methodologies have been developed and applied to patients with CNS infections. This review provides an overview of the accuracy of nucleic acid amplification methods in CSF for a diverse range of pathogens, examines the potential value of multiplex PCR panels, and explores the broad-range bacterial and fungal PCR/sequencing panels. In addition, it evaluates innovative molecular approaches to enhance the diagnosis of CNS infections.

Burden of infant group B Streptococcus disease and impact of maternal screening and antibiotic prophylaxis in Ontario, Canada: a population-based cohort study

Background

Group B Streptococcus (GBS) significantly contributes to neonatal sepsis and meningitis, with varying disease rates reported globally and limited population-based data. We estimated infant GBS disease burden in Ontario, Canada and assessed the association of maternal GBS screening (35-37 weeks' gestation) and intrapartum antibiotic prophylaxis (IAP) provision with infant disease rates.

Methods

Our population-based cohort study included pregnant individuals and their offspring from April 2012 to March 2018, utilising the provincial birth registry linked to health administrative data. GBS cases were ascertained through culture results and diagnostic codes. We calculated incidence rates for early-onset disease (EOD: 0-6 days), late-onset disease (LOD: 7-89 days), and ultra-LOD (ULOD: 90-365 days). Adjusted incidence rate ratios (aIRR) were derived via log-binomial regression to compare infant GBS rates according to screening and IAP-receipt.

Findings

Among 776,148 liveborn infants, we identified 803 with GBS, with multiples exhibiting a threefold incidence increase. Incidence rates of EOD, LOD and ULOD were 0.49, 0.46 and 0.07 per 1000 livebirths, respectively. Of eligible pregnancies, 94% were screened; 23% screened positive, and 81% of them received IAP. Nearly 12% of term EOD infants had mothers who missed IAP despite screening positive. Maternal screening was associated with lower rates of any infant GBS disease (aIRR: 0.60; 95% CI: 0.45, 0.80). Among screen-positive births, IAP-receipt was associated with reduced rates of EOD (aIRR: 0.72, 95% CI: 0.48, 1.29) and LOD/ULOD (aIRR: 0.69; 95% CI: 0.46, 1.05), but confidence intervals included 1.0.

Interpretation

Our study, the largest Canadian investigation into infant GBS disease, highlights both widespread adoption and ongoing challenges of the current prevention strategy.

Funding

Canadian Institutes of Health Research.

Distinguishing community-acquired bacterial and viral meningitis: Microbes and biomarkers

Diagnostic tools to differentiate between community-acquired bacterial and viral meningitis are essential to target the potentially lifesaving antibiotic treatment to those at greatest risk and concurrently spare patients with viral meningitis from the disadvantages of antibiotics. In addition, excluding bacterial meningitis and thus decreasing antibiotic consumption would be important to help reduce antimicrobial resistance and healthcare expenses. The available diagnostic laboratory tests for differentiating bacterial and viral meningitis can be divided microbiological pathogen-focussed methods and biomarkers of the host response. Bacterial culture-independent microbiological methods, such as highly multiplexed nucleic acid amplification tests, are rapidly making their way into the clinical practice. At the same time, more conventional host protein biomarkers, such as procalcitonin and C-reactive protein, are supplemented by newer proteomic and transcriptomic signatures. This review aims to summarise the current state and the recent advances in diagnostic methods to differentiate bacterial from viral meningitis.

Lumbar Puncture and Meningitis in Infants with Proven Early- or Late-Onset Sepsis: An Italian Prospective Multicenter Observational Study

Background: To evaluate the rates of lumbar puncture (LP) in infants with culture-proven sepsis. Study design: We prospectively enrolled 400 infants with early- or late-onset sepsis due to Group B streptococcus (GBS) or Eschericha coli, diagnosed within 90 days of life. Rates of LP and potential variables associated with LP performance were evaluated. Moreover, cerebrospinal fluid (CSF) characteristics and results of the molecular analysis were investigated. Results: LP was performed in 228/400 (57.0%) infants; 123/228 LPs (53.9%) were performed after antibiotic initiation, hampering the ability to identify the pathogen in the CSF culture. However, polymerase chain reaction increased the probability of positive results of CSF analysis compared to microbiological culture (28/79, 35.4% vs. 14/79, 17.7%, p = 0.001). Severe clinical presentation and GBS infection were associated with higher LP rates. The rate of meningitis was 28.5% (65/228). Conclusions: Rates of LP are low in culture-proven neonatal sepsis and antibiotics are frequently given before LP is carried out. Thus meningitis may be underestimated, and the chances of giving an effective therapy to the newborn are reduced. LP should be performed before the start of antibiotics when there is a clinical suspicion of infection.

Mania: An atypical presentation of probable Streptococcus agalactiae meningoencephalitis

Streptococcus agalactiae, also known as Group B Streptococcus (GBS), is a common pathogen in the neonatal period, causing meningitis and sepsis. In non-pregnant adults it is an unusual cause of meningitis. We report about an elderly female with several risk factors for invasive GBS infection who developed GBS meningoencephalitis one month after treatment for COVID-19 upper respiratory tract infection. The patient presented with mania, and the classic triad of headache, neck stiffness, and fever was absent which contributed to the delay in diagnosis. Following initiation of treatment with intravenous ceftriaxone she attained full recovery, and her behavior returned to baseline. This case illustrates an unusual presentation of an emerging infection and should alert clinicians about this presentation. By reporting this case we want to raise awareness about mania as a presenting feature of meningoencephalitis. This should lead to more timely diagnosis and better outcomes for future patients.

Predicting treatment response to vancomycin using bacterial DNA load as a pharmacodynamic marker in premature and very low birth weight neonates: A population PKPD study

Background: While positive blood cultures are the gold standard for late-onset sepsis (LOS) diagnosis in premature and very low birth weight (VLBW) newborns, these results can take days, and early markers of possible treatment efficacy are lacking. The objective of the present study was to investigate whether the response to vancomycin could be quantified using bacterial DNA loads (BDLs) determined by real-time quantitative polymerase chain reaction (RT-qPCR). Methods: VLBW and premature neonates with suspected LOS were included in a prospective observational study. Serial blood samples were collected to measure BDL and vancomycin concentrations. BDLs were measured with RT-qPCR, whereas vancomycin concentrations were measured by LC-MS/MS. Population pharmacokinetic-pharmacodynamic modeling was performed with NONMEM. Results: Twenty-eight patients with LOS treated with vancomycin were included. A one-compartment model with post-menstrual age (PMA) and weight as covariates was used to describe the time PK profile of vancomycin concentrations. In 16 of these patients, time profiles of BDL could be described with a pharmacodynamic turnover model. The relationship between vancomycin concentration and first-order BDL elimination was described with a linear-effect model. Slope S increased with increasing PMA. In 12 patients, no decrease in BDL over time was observed, which corresponded with clinical non-response. Discussion: BDLs determined through RT-qPCR were adequately described with the developed population PKPD model, and treatment response to vancomycin using BDL in LOS can be assessed as early as 8 h after treatment initiation.

Group B Streptococcal Neonatal Meningitis

Neonatal bacterial meningitis is a devastating disease, associated with high mortality and neurological disability, in both developed and developing countries. Streptococcus agalactiae, commonly referred to as group B Streptococcus (GBS), remains the most common bacterial cause of meningitis among infants younger than 90 days. Maternal colonization with GBS in the gastrointestinal and/or genitourinary tracts is the primary risk factor for neonatal invasive disease. Despite prophylactic intrapartum antibiotic administration to colonized women and improved neonatal intensive care, the incidence and morbidity associated with GBS meningitis have not declined since the 1970s. Among meningitis survivors, a significant number suffer from complex neurological or neuropsychiatric sequelae, implying that the pathophysiology and pathogenic mechanisms leading to brain injury and devastating outcomes are not yet fully understood. It is imperative to develop new therapeutic and neuroprotective approaches aiming at protecting the developing brain. In this review, we provide updated clinical information regarding the understanding of neonatal GBS meningitis, including epidemiology, diagnosis, management, and human evidence of the disease's underlying mechanisms. Finally, we explore the experimental models used to study GBS meningitis and discuss their clinical and physiologic relevance to the complexities of human disease.

Neonatal Group B Streptococcal Meningitis: Predictors for Poor Neurologic Outcome at 18 Months

AIM

To find early predictors for poor neurodevelopmental outcome after neonatal group B streptococcal meningitis.

METHODS

We retrospectively analyzed clinical characteristics of 23 patients with neonatal group B streptococcal meningitis and their neurodevelopmental outcome at 18 months. Available group B Streptococcus strains were serotyped and their genomes characterized.

RESULTS

We found several differences between patients with early- (n = 5) and late-onset (n = 18) disease. Nine children had neurologic abnormalities at 18 months and 4 had epilepsy, all of them after late-onset disease. Most important risk factors for poor outcome were impaired consciousness at admission, hemodynamic instability, seizures, or abnormal electroencephalogram during the acute illness and abnormal neurologic and ophthalmologic examination at the end of treatment, whereas abnormalities in laboratory and imaging studies were not predictive. Hypervirulent serotype III, multilocus sequence type 17 group B Streptococcus was the predominant pathogen.

CONCLUSIONS

Neurodevelopmental impairment after neonatal group B streptococcal meningitis is likelier in those with clinical and neurophysiological features indicating worse disease severity.

Multiplex Droplet Digital Polymerase Chain Reaction Assay for Rapid Molecular Detection of Pathogens in Patients With Sepsis: Protocol for an Assay Development Study

BACKGROUND

Blood cultures are the cornerstone of diagnosis for detecting the presence of bacteria or fungi in the blood, with an average detection time of 48 hours and failure to detect a pathogen occurring in approximately 50% of patients with sepsis. Rapid diagnosis would facilitate earlier treatment and/or an earlier switch to narrow-spectrum antibiotics.

OBJECTIVE

The aim of this study is to develop and implement a multiplex droplet digital polymerase chain reaction (ddPCR) assay as a routine diagnostic tool in the detection and identification of pathogens from whole blood and/or blood culture after 3 hours of incubation.

METHODS

The study consists of three phases: (1) design of primer-probe pairs for accurate and reliable quantification of the most common sepsis-causing microorganisms using a multiplex reaction, (2) determination of the analytical sensitivity and specificity of the multiplex ddPCR assay, and (3) a clinical study in patients with sepsis using the assay. The QX200 Droplet Digital PCR System will be used for the detection of the following species-specific genes in blood from patients with sepsis: coa (staphylocoagulase) in Staphylococcus aureus, cpsA (capsular polysaccharide) in Streptococcus pneumoniae, uidA (beta-D-glucuronidase) in Escherichia coli, oprL (peptidoglycan-associated lipoprotein) in Pseudomonas aeruginosa, and the highly conserved regions of the 16S rRNA gene for Gram-positive and Gram-negative bacteria. All data will be analyzed using QuantaSoft Analysis Pro Software.

RESULTS

In phase 1, to determine the optimal annealing temperature for the designed primer-probe pairs, results from a gradient temperature experiment will be collected and the limit of detection (LOD) of the assay will be determined. In phase 2, results for the analytical sensitivity and specificity of the assay will be obtained after an optimization of the extraction and purification method in spiked blood. In phase 3, clinical sensitivity and specificity as compared to the standard blood culture technique will be determined using 301 clinical samples.

CONCLUSIONS

Successful design of primer-probe pairs in the first phase and subsequent optimization and determination of the LOD will allow progression to phase 3 to compare the novel method with existing blood culture methods.

INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID)

PRR1-10.2196/33746.

Pediatric sepsis cases diagnosed with group B streptococcal meningitis using next-generation sequencing: a report of two cases

BACKGROUND

Group B Streptococcus (GBS) is an important cause of invasive infection in neonates and infants. Cerebrospinal fluid (CSF) findings and culture may not show evidence of infection early in GBS meningitis. Next-generation sequencing (NGS) has the potential to detect microbial genetic material in patients with infectious diseases. We report two cases of infantile sepsis of GBS meningitis with negative results for CSF culture tests, but positive results for NGS analysis.

CASE PRESENTATION

Patient 1 was a 22-day-old male infant diagnosed with sepsis and meningitis. His CSF findings showed pleocytosis, decreased glucose, and increased protein levels. However, CSF and blood culture results at admission were negative. He received a total of 3 weeks of treatment with ampicillin and cefotaxime, and showed clinical improvement. GBS was detected through NGS analysis of CSF collected at admission. Patient 2 was a 51-day-old male infant with sepsis. CSF findings on admission were normal, and blood and CSF cultures were also negative. Intravenous ampicillin and cefotaxime treatment were initiated. Treatment was de-escalated to ampicillin alone because Enterococcus faecalis was cultured from urine. He was discharged after a total of 1 week of antibiotic treatment. Six days after discharge, he was re-hospitalized for sepsis. Blood and CSF cultures were negative, and E. faecalis was again cultured from urine. He received a total of 3 weeks of ampicillin treatment for enterococcal-induced nephritis and did not relapse thereafter. NGS pathogen searches were retrospectively performed on both blood and CSF collected at the first and second admission. GBS was detected in the CSF collected at the first admission, but no significant pathogen was detected in the other samples. Inadequate treatment for GBS meningitis at the first admission may have caused the recurrence of the disease.

CONCLUSION

Infantile sepsis may present bacterial meningitis that is not diagnosed by either culture testing or CSF findings. NGS analysis for CSF may be useful for confirming the diagnosis of bacterial meningitis.

Case Report: Prolonged CSF PCR Positivity in a Neonate With GBS Meningitis

Bacterial meningitis is one of the critical diseases that needs to be diagnosed and treated promptly. Recent diagnostics of high sensitivity and specificity rates, such as PCR, helped with such presentation, especially in cases with prior antibiotics that led to culture negativity. However, the time window of PCR positivity is not well-studied, with scattered reports of different periods of positivity. Here, we report a case of neonatal GBS meningitis with positive PCR for more than 80 days from starting antibiotics.

Enhanced identification of Group B streptococcus in infants with suspected meningitis in Ethiopia

Meningitis is one of the top ten causes of death among Ethiopian infants. Group B streptococcus (GBS) has emerged as a leading cause of meningitis in neonates and young infants, resulting in high mortality. Despite this, there is no report on GBS associated meningitis in Ethiopia where infant meningitis is common. Hence, the aim of this study was to determine the proportion of GBS associated meningitis among Ethiopian infants. PCR was prospectively used to detect GBS in culture-negative cerebrospinal fluid (CSF) samples, which were collected from infants suspected for meningitis, at Tikur Anbessa specialized hospital, Ethiopia, over a one-year period. GBS was detected by PCR in 63.9% of culture-negative CSF samples. Out of the 46 GBS positive infants, 10.9% (n = 5) of them died. The late onset of GBS (LOGBS) disease was noted to have a poor outcome with 3 LOGBS out of 5 GBS positive samples collected from patients with the final outcome of death. PCR was advantageous in the identification of GBS in culture-negative CSF samples. GBS was detected in 64% of the CSF samples from infants with meningitis compared with zero-detection rate by culture.

Towards accurate exclusion of neonatal bacterial meningitis: a feasibility study of a novel 16S rDNA PCR assay

Background

PCRctic is an innovative assay based on 16S rDNA PCR technology that has been designed to detect a single intact bacterium in a specimen of cerebro-spinal fluid (CSF). The assay’s potential for accurate, fast and inexpensive discrimination of bacteria-free CSF makes it an ideal adjunct for confident exclusion of bacterial meningitis in newborn babies where the negative predictive value of bacterial culture is poor. This study aimed to stress-test and optimize PCRctic in the “field conditions” to attain a clinically useful level of specificity.

Methods

The specificity of PCRctic was evaluated in CSF obtained from newborn babies investigated for meningitis on a tertiary neonatal unit. Following an interim analysis, the method of skin antisepsis was changed to increase bactericidal effect, and snap-top tubes (Eppendorf™) replaced standard universal containers for collection of CSF to reduce environmental contamination.

Results

The assay’s specificity was 90.5% in CSF collected into the snap-top tubes – up from 60% in CSF in the universal containers. The method of skin antisepsis had no effect on the specificity. All CSF cultures were negative and no clinical cases of neonatal bacterial meningitis occurred during the study.

Conclusions

A simple and inexpensive optimization of CSF collection resulted in a high specificity output. The low prevalence of neonatal bacterial meningitis means that a large multi-centre study will be required to validate the assay’s sensitivity and its negative predictive value.

Clinical characteristics and molecular epidemiology of children with meningitis in Tehran, Iran: a prospective study

The molecular epidemiology of meningitis in children is unclear in Iran, and data are scarce. We aimed to characterize its clinical and paraclinical features as well as to determine the distribution of genotype/capsular types of common bacterial meningitis agents in children in Iran. All children suspected to have meningitis aged 4 days to 15 years were enrolled onto a prospective cross-sectional study from January 2015 to September 2017. Diagnostic values of clinical features, cerebrospinal fluid and serum parameters were evaluated independently and in combination with each other by multivariate logistic regression to develop a diagnostic rule. Genotype/capsular types of all the isolates were determined by targeting serotype-specific genes with uniplex or multiplex PCR. Among 119 patients suspected of having meningitis, 43 had bacterial meningitis, 19 aseptic and one tuberculous; and there were 56 nonmeningitis cases (NMC). Presentation of four features at the same time-cerebrospinal fluid white blood cell count, protein, polymorphonuclear leukocytes and serum C-reactive protein-revealed 100% sensitivity and 86.4% specificity for diagnosis of bacterial meningitis. Haemophilus influenzae type b (60%), Streptococcus pneumoniae serotype 3 (28.5%) and Neisseria meningitidis B (63.5%) were the most prevalent serotypes. This study demonstrated that a well-designed combination of clinical and paraclinical features is useful, but these combinations are not good enough to be relied on as stand-alone exclusionary tests for the diagnosis of bacterial meningitis. In addition, public immunization of infants with the most prevalent bacterial meningitis serotypes is recommended.

Disease burden of neonatal invasive Group B Streptococcus infection in the Netherlands

BACKGROUND

Group B Streptococcus (GBS) is the leading cause of neonatal sepsis and meningitis worldwide. We aimed to estimate the current burden of neonatal invasive GBS disease in the Netherlands, as a first step in providing an evidence base for policy makers on the potential benefits of a future maternal GBS vaccine.

METHODS

Surveillance of neonatal invasive GBS occurs at the National Reference Laboratory for Bacterial Meningitis, where culture isolates from cerebrospinal fluid and blood are sent by diagnostic laboratories. From the number of cultures we estimated the incidence of neonatal (age 0-90 days) GBS meningitis and sepsis. We constructed a disease progression model informed by literature and expert consultation to estimate the disease burden of neonatal invasive GBS infection. As many neonates with a probable GBS sepsis are never confirmed by blood culture, we further estimated the disease burden of unconfirmed cases of probable GBS sepsis in sensitivity analyses.

RESULTS

An estimated 97 cases and 6.5 deaths occurred in the Netherlands in 2017 due to culture positive neonatal invasive GBS infection. This incidence comprised 15 cases of meningitis and 42 cases of sepsis per 100.000 births, with an estimated mortality of 3.8 per 100.000 live births. A disease burden of 780 disability-adjusted life years (DALY) (95% CI 650-910) or 460 DALY per 100.000 live births was attributed to neonatal invasive GBS infection. In the sensitivity analysis including probable neonatal GBS sepsis the disease burden increased to 71 cases and 550 DALY (95% CI 460-650) per 100.000 live births.

CONCLUSION

In conclusion, neonatal invasive GBS infection currently causes a substantial disease burden in the Netherlands. However, important evidence gaps are yet to be filled. Furthermore, cases of GBS sepsis lacking a positive blood culture may contribute considerably to this burden potentially preventable by a future GBS vaccine.

Pitfalls in the diagnosis of meningitis in neonates and young infants: the role of lumbar puncture

Meningitis occurs frequently in neonates and can lead to a number of acute, severe complications and long-term disabilities. An early diagnosis of neonatal meningitis is essential to reduce mortality and to improve outcomes. Initial clinical signs of meningitis are often subtle and frequently overlap with those of sepsis, and current haematologic tests do not distinguish sepsis from meningitis. Thus, lumbar puncture (LP) remains the gold standard for the diagnosis of meningitis in infants, and this procedure is recommended in clinical guidelines. Nevertheless, in clinical practice, LP is frequently deferred or omitted due to concerns regarding hypothetical adverse events or limited experience of the performer. Future studies should assess whether a combination of clinical findings and select haematologic tests at disease onset can identify those neonates with the highest risk of meningitis who should undergo LP. Furthermore, clinicians should be convinced that the actual benefits of an early diagnosis of meningitis far outweigh the hypothetical risks associated with LP.

Evaluation of the Clinical Utility of a Real-time PCR Assay for the Diagnosis of Streptococcus pneumoniae Bacteremia in Children: A Retrospective Diagnostic Accuracy Study

BACKGROUND

The widespread uptake of pneumococcal vaccines has substantially reduced the incidence of invasive pneumococcal disease, such that pneumococcal bacteremia in children is now considered a relatively rare event. The objective of this study was to ascertain the clinical utility of a Streptococcus pneumoniae real-time polymerase chain reaction (PCR) assay compared with standard blood culture for the diagnosis of pneumococcal bacteremia in children in the post-vaccine era.

METHODS

A systematic retrospective review of laboratory and patient records from Children's University Hospital, Temple Street, during a 6-year period was performed. Paired blood PCR and blood culture specimens from children younger than 16 years of age were investigated. Statistical analysis was performed to measure the diagnostic accuracy of PCR versus routine bacterial culture techniques.

RESULTS

More than 1900 PCR test requests were examined from 2010 to 2015, of which 1561 paired PCR and blood culture specimens met criteria for inclusion in the statistical analysis. The PCR assay demonstrated high specificity (99%, confidence interval 95%: 98.81%-99.69%); however, the sensitivity was low compared with that of blood culture (47%, confidence interval 95%: 21.27%-73.41%). Investigation of 10 PCR-positive/culture-negative cases revealed that these cases ranged from definite, probable, and possible significance, indicating a low false positivity rate associated with the assay.

CONCLUSION

This study demonstrates the limited utility of blood PCR testing for S. pneumoniae in pediatric patients without radiographic evidence pneumonia or empyema. Moreover, we report that PCR may be a useful diagnostic tool when blood cultures are negative because of antimicrobial therapy before sampling. Given that the incidence of pneumococcal disease has decreased considerably in recent years, justification of S. pneumoniae PCR requisition is necessary. Hence, new guidelines for pediatric pneumococcal blood PCR testing have been introduced at the Irish Meningitis and Sepsis Reference Laboratory.

Neonatal Meningitis: Overcoming Challenges in Diagnosis, Prognosis, and Treatment with Omics

Neonatal meningitis is a devastating condition. Prognosis has not improved in decades, despite the advent of improved antimicrobial therapy and heightened index of suspicion among clinicians caring for affected infants. One in ten infants die from meningitis, and up to half of survivors develop significant lifelong complications, including seizures, impaired hearing and vision, and delayed or arrested development of such basic skills as talking and walking. At present, it is not possible to predict which infants will suffer poor outcomes. Early treatment is critical to promote more favorable outcomes, though diagnosis of meningitis in infants is technically challenging, time-intensive, and invasive. Profound neuronal injury has long been described in the setting of neonatal meningitis, as has elevated levels of many pro- and anti-inflammatory cytokines. Mechanisms of the host immune response that drive clearance of the offending organism and underlie brain injury due to meningitis are not well understood, however. In this review, we will discuss challenges in diagnosis, prognosis, and treatment of neonatal meningitis. We will highlight transcriptomic, proteomic, and metabolomic data that contribute to suggested mechanisms of inflammation and brain injury in this setting with a view toward fruitful areas for future investigation.