A multi-target real-time PCR assay for rapid identification of meningitis-associated microorganisms

Risk factors and pathogen characteristics associated with unfavorable outcomes among adults with pneumococcal meningitis in Japan, 2006 to 2016

PURPOSE

In this study, we aimed to clarify the risk factors associated with unfavorable outcomes in adults with pneumococcal meningitis (PnM).

METHODS

Surveillance was conducted between 2006 and 2016. Adults with PnM (n = 268) were followed up for outcomes within 28 days after admission using the Glasgow Outcome Scale (GOS). After classifying the patients into the unfavorable (GOS1-4) and favorable (GOS5) outcome groups, i) the underlying diseases, ii) biomarkers at admission, and iii) serotype, genotype, and antimicrobial susceptibility for all isolates were compared between both groups.

RESULTS

Overall, 58.6% of patients with PnM survived,15.3% died, and 26.1% had sequelae. The number of living days in the GOS1 group was highly heterogeneous. Motor dysfunction, disturbance of consciousness, and hearing loss were the commonest sequelae. Of the underlying diseases identified in 68.9% of the PnM patients, liver and kidney diseases were significantly associated with unfavorable outcomes. Of the biomarkers, creatinine and blood urea nitrogen, followed by platelet and C-reactive protein had the most significant associations with unfavorable outcomes. There was a significant difference in the high protein concentrations in the cerebrospinal fluid between the groups. Serotypes 23F, 6C, 4, 23A, 22F, 10A, and 12F were associated with unfavorable outcomes. These serotypes were not penicillin-resistant isolates possessing three abnormal pbp genes (pbp1a, 2x, and 2b), except for 23F. The expected coverage rate of the pneumococcal conjugate vaccine (PCV) was 50.7% for PCV15 and 72.4% for PCV20.

CONCLUSIONS

In the introduction of PCV for adults, the risk factors for underlying diseases should be prioritized over age, and serotypes with unfavorable outcomes should be considered.

Polymicrobial Anaerobic Meningitis Detected by Next-Generation Sequencing: Case Report and Review of the Literature

Background

Anaerobic meningitis is a severe central nervous system infection associated with significant neurological sequelae and high mortality. However, the precise detection of causative pathogen(s) remains difficult because anaerobic bacteria are difficult to culture. Next-generation sequencing is a technology that was developed recently and has been applied in many fields. To the best of our knowledge, the use of next-generation sequencing for cerebrospinal fluid analysis in the diagnosis of anaerobic meningitis has been rarely reported.

Case presentation

Here, we report a case of polymicrobial anaerobic meningitis diagnosed using next-generation sequencing of cerebrospinal fluid in a 16-year-old girl. Five species of anaerobic bacteria (Porphyromonas gingivalis, Prevotella enoeca, Campylobacter rectus, Fusobacterium uncleatum, and Actinomyces israelii) were detected by next-generation sequencing and treated with antibacterial agents (ceftriaxone, vancomycin, and metronidazole). The patient responded well to antibacterial treatment. Further inspection revealed bone destruction at the base of the skull, which further confirmed that these bacteria had originated from the oral cavity. One month later, the patient's condition improved significantly. At the same time, we performed a literature review on anaerobic meningitis using studies published in the last 20 years.

Conclusions

This case emphasizes the importance of applying metagenomic next-generation sequencing to clinch the clinical diagnosis for patients with central nervous system infection. Metagenomic next-generation sequencing has been reported to be an important diagnostic modality for identifying uncommon pathogens.

Simultaneous detection of Neisseria meningitidis, Streptococcus pneumoniae and Haemophilus influenzae by quantitative PCR from CSF samples with negative culture in Morocco

Bacteriological cultures from cerebrospinal fluids (CSF) have less sensitivity and specificity compared to quantitative PCR (RT-PCR), and multiple facts still conduct to the increase of negative culture. The aims of this study are to determine the molecular epidemiology and the simultaneous detection of bacterial meningitis in Morocco by using RT-PCR and compared this molecular approach with culture method to improve the etiological diagnosis of meningitis. The CSFs were collected over one-year period in 2018 in different hospitals covering all regions of the Kingdom of Morocco, from patients with suspected meningitis. The results showed the confirmation rate per culture recorded a rate of 33% and the RT-PCR of 70%. Molecular epidemiology is predominant of Neisseria meningitidis followed by Streptococcus pneumoniae and a dramatic reduction in meningitis due to Haemophilus influenzae following the introduction of conjugate vaccine in 2007. Also, the epidemiological profile shows a sex ratio M/F of 1.4 and a median age of 2 years. The national distribution showed a predominant of meningococcal disease followed by pneumococcal disease, especially a dominance of N. meningitidis over S. pneumoniae in two regions and a slight predominance of S. pneumoniae in the other two regions over N. meningitidis. Our research shows that culture in our country has less sensitivity and specificity than RT-PCR in diagnosis of bacterial meningitis and that molecular biology technique at bacteriology laboratories is desirable for diagnosis, early management of meningitis cases and in the context of the surveillance of meningitis in Morocco in parallel with culture.

Molecular diagnostic assays for the detection of common bacterial meningitis pathogens: A narrative review

Bacterial meningitis is a major global cause of morbidity and mortality. Rapid identification of the aetiological agent of meningitis is essential for clinical and public health management and disease prevention given the wide range of pathogens that cause the clinical syndrome and the availability of vaccines that protect against some, but not all, of these. Since microbiological culture is complex, slow, and often impacted by prior antimicrobial treatment of the patient, molecular diagnostic assays have been developed for bacterial detection. Distinguishing between meningitis caused by Neisseria meningitidis (meningococcus), Streptococcus pneumoniae (pneumococcus), Haemophilus influenzae, and Streptococcus agalactiae and identifying their polysaccharide capsules is especially important. Here, we review methods used in the identification of these bacteria, providing an up-to-date account of available assays, allowing clinicians and diagnostic laboratories to make informed decisions about which assays to use.

Diagnostic accuracy of two multiplex real-time polymerase chain reaction assays for the diagnosis of meningitis in children in a resource-limited setting

INTRODUCTION

Accurate etiological diagnosis of meningitis is important, but difficult in resource-limited settings due to prior administration of antibiotics and lack of viral diagnostics. We aimed to develop and validate 2 real-time multiplex PCR (RT-PCR) assays for the detection of common causes of community-acquired bacterial and viral meningitis in South African children.

METHODS

We developed 2 multiplex RT- PCRs for detection of S. pneumoniae, N. meningitidis, H. influenzae, enteroviruses, mumps virus and herpes simplex virus. We tested residual CSF samples from children presenting to a local paediatric hospital over a one-year period, whose CSF showed an abnormal cell count. Results were compared with routine diagnostic tests and the final discharge diagnosis. We calculated accuracy of the bacterial RT-PCR assay compared to CSF culture and using World Health Organisation definitions of laboratory-confirmed bacterial meningitis.

RESULTS

From 292 samples, bacterial DNA was detected in 12 (4.1%) and viral nucleic acids in 94 (32%). Compared to CSF culture, the sensitivity and specificity of the bacterial RT-PCR was 100% and 97.2% with complete agreement in organism identification. None of the cases positive by viral RT-PCR had a bacterial cause confirmed on CSF culture. Only 9/90 (10%) of patients diagnosed clinically as bacterial meningitis or partially treated bacterial meningitis tested positive with the bacterial RT-PCR.

DISCUSSION

In this population the use of 2 multiplex RT-PCRs targeting 6 common pathogens gave promising results. If introduced into routine diagnostic testing, these multiplex RT-PCR assays would supplement other diagnostic tests, and have the potential to limit unnecessary antibiotic therapy and hospitalisation.

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

The aim of this study was to compare an in-house real-time PCR assay, with bacterial culture as the reference, for the diagnosis of late onset group B Streptococcal (GBS) disease. This was a retrospective review. All children aged 7-90 days presenting to four paediatric centres that had a blood or CSF sample tested by GBS PCR were included. Of 7,686 blood and 2,495 cerebrospinal fluid (CSF) samples from patients of all ages received for PCR testing, 893 and 859 samples were eligible for the study, respectively. When compared to culture, the sensitivity of blood PCR was 65% (13/20) in comparison to the CSF PCR test which was 100% (5/5). Ten of 23 PCR-positive blood samples and 17 of 22 PCR-positive CSF samples were culture negative. The median threshold Ct values for culture-positive/PCR-positive CSF samples was lower than that of culture-negative/PCR-positive CSF samples (p = 0.08). Clinical details of 17 available cases that were culture negative/PCR positive were reviewed; seven were deemed to be definite cases, eight were probable and two were possible. The results showed that detection of GBS by PCR is useful for CSF samples from infants aged 7-90 days with suspected meningitis; however, analysis of blood samples by PCR is of limited value as a routine screening test for late onset GBS sepsis and should not replace bacterial culture.

Real-time polymerase chain reaction and culture in the diagnosis of invasive group B streptococcal disease in infants: a retrospective study

Group B streptococcus (GBS) is a leading cause of invasive disease in infants. Accurate and rapid diagnosis is crucial to reduce morbidity and mortality. Real-time polymerase chain reaction (PCR) targeting the dltR gene was utilised for the direct detection of GBS DNA in blood and cerebrospinal fluid (CSF) from infants at an Irish maternity hospital. A retrospective review of laboratory and patient records during the period 2011-2013 was performed in order to evaluate PCR and culture for the diagnosis of invasive GBS disease. A total of 3570 blood and 189 CSF samples from 3510 infants had corresponding culture and PCR results. Culture and PCR exhibited concordance in 3526 GBS-negative samples and 13 (25%) GBS-positive samples (n = 53). Six (11%) and 34 (64%) GBS-positive samples were positive only in culture or PCR, respectively. Culture and PCR identified more GBS-positive infants (n = 47) than PCR (n = 43) or culture (n = 16) alone. Using culture as the reference standard, the sensitivity, specificity, and positive and negative predictive values for PCR on blood samples were 71.4%, 99.2%, 25% and 99.9%, and for CSF samples, they were 60%, 97.8%, 42.9% and 98.9%, respectively. The sensitivity and positive predictive values were improved (blood: 84.6% and 55%; CSF: 77.8% and 100%, respectively) when maternal risk factors and other laboratory test results were considered. The findings in this study recommend the use of direct GBS real-time PCR for the diagnosis of GBS infection in infants with a clinical suspicion of invasive disease and as a complement to culture, but should be interpreted in the light of other laboratory and clinical findings.

Comparative genome analysis identifies novel nucleic acid diagnostic targets for use in the specific detection of Haemophilus influenzae

Haemophilus influenzae is recognised as an important human pathogen associated with invasive infections, including bloodstream infection and meningitis. Currently used molecular-based diagnostic assays lack specificity in correctly detecting and identifying H. influenzae. As such, there is a need to develop novel diagnostic assays for the specific identification of H. influenzae. Whole genome comparative analysis was performed to identify putative diagnostic targets, which are unique in nucleotide sequence to H. influenzae. From this analysis, we identified 2H. influenzae putative diagnostic targets, phoB and pstA, for use in real-time PCR diagnostic assays. Real-time PCR diagnostic assays using these targets were designed and optimised to specifically detect and identify all 55H. influenzae strains tested. These novel rapid assays can be applied to the specific detection and identification of H. influenzae for use in epidemiological studies and could also enable improved monitoring of invasive disease caused by these bacteria.

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

OBJECT

Diagnosis of ventriculostomy-related infections (VRIs) is challenging due to the lack of rapid, sensitive assays for pathogen detection. The authors report the development of a multiplex polymerase chain reaction (PCR) assay for differential diagnosis of common VRI pathogens.

METHODS

MassTag PCR was used to develop a multiplex assay for detection of 11 VRI pathogens. The assay was established and optimized using cloned template standards and spiked samples and was then evaluated on CSF specimens from ventricular drains. Subjects were grouped into definite VRI, possible VRI, or no VRI based on conventional microbiology, CSF evaluation, and clinical parameters.

RESULTS

CSF specimens were obtained from 45 subjects (median age 49 years, interquartile range 32-63 years; 51% were male). The assay detected 10-100 genome copies. It detected a pathogen in 100% (6 of 6) of definite VRI cases in which a pathogen targeted by the assay was present; these represented 67% of all definite VRIs (6 of 9). Among subjects with a possible VRI, the assay detected a pathogen in 29% (5 of 17). In subjects without overt infection the presence of a pathogen was detected in 32% of subjects (6 of 19), albeit with lower signal compared with the VRI group.

CONCLUSIONS

MassTag PCR enabled parallel testing of CSF specimens for 11 pathogens of VRI. The high sensitivity of PCR combined with possible device colonization, specimen contamination, and concurrent antibiotic treatments limit the clinical value of the assay, similar to other current diagnostic approaches. With further optimization, multiplex PCR may provide timely identification of multiple possible VRI pathogens and guide management, complementing classic culture approaches.

Bacterial etiologies of five core syndromes: laboratory-based syndromic surveillance conducted in Guangxi, China

BACKGROUND

Under the existing national surveillance system in China for selected infectious diseases, bacterial cultures are performed for only a small percentage of reported cases. We set up a laboratory-based syndromic surveillance system to elucidate bacterial etiologic spectrum and detect infection by rare etiologies (or serogroups) for five core syndromes in the given study area.

METHODS

Patients presenting with one of five core syndromes at nine sentinel hospitals in Guagnxi, China were evaluated using laboratory-based syndrome surveillance to elucidate bacterial etiologies. We collected respiratory and stool specimens, as well as CSF, blood and other related samples for bacterial cultures and pulse field gel electrophoresis (PFGE) assays.

RESULTS

From February 2009 to December 2011, 2,964 patients were enrolled in the study. Etiologies were identified in 320 (10.08%) patients. Streptococcus pneumonia (37 strains, 24.18%), Klebsiella pneumonia (34, 22.22%), Pseudomonas aeruginosa (19, 12.42%) and Haemophilus influenza (18, 11.76%) were the most frequent pathogens for fever and respiratory syndrome, while Salmonella (77, 81.05%) was most often seen in diarrhea syndrome cases. Salmonella paratyphi A (38, 86.36%) occurred in fever and rash syndrome, with Cryptococcus neoformans (20, 35.09%), Streptococcus pneumonia (5, 8.77%), Klebsiella pneumonia (5, 8.77%),streptococcus suis (3, 5.26%) and Neisseria meningitides group B (2, 3.51%) being the most frequently detected in encephalitis-meningitis syndrome. To date no pathogen was isolated from the specimens from fever and hemorrhage patients.

CONCLUSIONS

In addition to common bacterial pathogens, opportunistic pathogens and fungal infections require more attention. Our study contributes to the strengthening of the existing national surveillance system and provides references for other regions that are similar to the study area.

Multiplex real-time PCR probe-based for identification of strains producing: OXA48, VIM, KPC and NDM

The spread of multi-resistant enterobacteria, particularly carbapenem-resistant Enterobacteriaceae (CRE), in both community and hospital settings is a global problem. The phenotypic identification of CRE is complex, occasionally inconclusive and time consuming. However, commercially available molecular assays are very expensive, and many do not allow the simultaneous identification of all genetic markers of resistance that have been recognised in CRE (bla KPC, bla OXA-48, bla VIM and bla NDM). The aim of the present study is to describe a new test: a multiplex real time PCR probe-based assay designed for the simultaneous detection of KPC, OXA-48, VIM and NDM in a short time (no longer than 90 min from the extraction of DNA to detection). Our assay correctly identified 63 CRE isolates and all standard reference strains tested, in agreement with and extending the results of phenotypic identification tests; additionally, a KPC-VIM co-expressing Enterobacter aerogenes isolate was identified using the new assay, whereas traditional methods failed to detect it. The assay was also able to correctly detect 28 CRE-producers from 50 positive blood cultures, again detecting, in four specimens, the presence of CRE co-expressing KPC and VIM, which were only partially identified by traditional methods. Finally, when used directly on rectal swabs, the assay enabled the identification of CRE-carrier patients, for whom isolation is mandatory in a hospital setting.

Evolution of bacterial meningitis diagnosis in São Paulo State-Brazil and future challenges

Bacterial meningitis (BM) is a severe disease and still represents a serious public health problem with high rates of morbidity and mortality. The most common cases of BM around the world, mainly in Brazil, have been caused by Neisseria meningitidis, Streptococcus pneumoniae, and Haemophilus influenzae type b. Bacterial culture is the gold-standard technique for BM confirmation, but approximately 50% of suspected cases are not culture-confirmed, due to problems related to improper transportation and seeding or previous antibiotic treatment. Immunological methods present low sensitivity and have possibility of cross-reactions. Real time PCR (qPCR) is a molecular technique and has been successful used for BM diagnosis at Instituto Adolfo Lutz in São Paulo State, Brazil, since 2007. The incorporation of qPCR in the Public Health surveillance routine in our state resulted in diminishing 50% of undetermined BM cases. Our efforts are focused on qPCR implementation in the BM diagnostic routine throughout Brazil.

Application of microarray technology for the detection of intracranial bacterial infection

The aim of this study was to assess the value of microarray technology for the detection of intracranial bacterial infection. A small gene chip was prepared based on the four pathogens commonly known to cause intracranial infection and the corresponding six types of common resistance genes in The Affiliated Hospital of Nantong University and The Affiliated Haian People’s Hospital of Nantong University. Cerebrospinal fluid samples were then collected from 30 patients with clinically diagnosed intracranial infection for the detection of the bacteria and resistance genes. The results were compared with the bacterial culture and sensitivity test results from the Department of Clinical Laboratories. The laboratory bacterial culture took 4–5 days, and revealed that 12 cases were positive and 18 cases were negative for bacteria. The microarray analysis took 1 day, and bacteria and resistance genes were detected in 15 cases. The 16S gene and drug resistance genes were detected in 8 cases; however, the bacterial strain was not identified. Seven cases appeared negative for bacteria and resistance genes. Microarray technology is rapid, sensitive and suitable for use in the detection of intracranial infections and other diseases for which conventional bacterial culture has a low positive rate.