The etiology of acute meningitis and encephalitis syndromes in a sentinel pediatric hospital, Shenzhen, China

Integrating DNA/RNA microbe detection and host response for accurate diagnosis, treatment and prognosis of childhood infectious meningitis and encephalitis

BACKGROUND

Infectious meningitis/encephalitis (IM) is a severe neurological disease that can be caused by bacterial, viral, and fungal pathogens. IM suffers high morbidity, mortality, and sequelae in childhood. Metagenomic next-generation sequencing (mNGS) can potentially improve IM outcomes by sequencing both pathogen and host responses and increasing the diagnosis accuracy.

METHODS

Here we developed an optimized mNGS pipeline named comprehensive mNGS (c-mNGS) to monitor DNA/RNA pathogens and host responses simultaneously and applied it to 142 cerebrospinal fluid samples. According to retrospective diagnosis, these samples were classified into three categories: confirmed infectious meningitis/encephalitis (CIM), suspected infectious meningitis/encephalitis (SIM), and noninfectious controls (CTRL).

RESULTS

Our pipeline outperformed conventional methods and identified RNA viruses such as Echovirus E30 and etiologic pathogens such as HHV-7, which would not be clinically identified via conventional methods. Based on the results of the c-mNGS pipeline, we successfully detected antibiotic resistance genes related to common antibiotics for treating Escherichia coli, Acinetobacter baumannii, and Group B Streptococcus. Further, we identified differentially expressed genes in hosts of bacterial meningitis (BM) and viral meningitis/encephalitis (VM). We used these genes to build a machine-learning model to pinpoint sample contaminations. Similarly, we also built a model to predict poor prognosis in BM.

CONCLUSIONS

This study developed an mNGS-based pipeline for IM which measures both DNA/RNA pathogens and host gene expression in a single assay. The pipeline allows detecting more viruses, predicting antibiotic resistance, pinpointing contaminations, and evaluating prognosis. Given the comparable cost to conventional mNGS, our pipeline can become a routine test for IM.

Diagnostic status and epidemiological characteristics of community-acquired bacterial meningitis in children from 2019 to 2020: a multicenter retrospective study

Community-acquired bacterial meningitis (CABM) is the main cause of morbidity and mortality in children. The epidemiology of CABM is regional and highly dynamic. To clarify the diagnostic status and epidemiological characteristics of children with CABM in this region, and pay attention to the disease burden, so as to provide evidence for the prevention and treatment of CABM. By retrospective case analysis, the clinical data of 918 CABM cases in children aged 0-14 years in Zhejiang Province from January, 2019 to December, 2020 were collected. The etiological diagnosis rate of CABM in children was 23.1%, the annual incidence rate 4.42-6.15/100,000, the annual mortality rate 0.06-0.09/100,000,the cure and improvement rate 94.4%, and the case fatality rate 1.4%. The total incidence of neuroimaging abnormalities was 20.6%. The median length of stay for CABM children was 20(16) days, with an average cost of 21,531(24,835) yuan. In addition, the incidence rate was decreased with age. Escherichia coli(E.coli) and group B Streptococcus agalactiae(GBS) were the principal pathogens in CABM infant<3 months(43.3%, 34.1%), and Streptococcus pneumoniae(S. pneumoniae) was the most common pathogen in children ≥ 3 months(33.9%). In conclusion, the annual incidence and mortality of CABM in children aged 0-14 years in Zhejiang Province are at intermediate and low level. The distribution of CABM incidence and pathogen spectrum are different in age; the incidence of abnormal neuroimaging is high; and the economic burden is heavy.

Pediatric central nervous system infections in the Amazon: clinical and laboratory profiles

Background

Central nervous system (CNS) infections are important causes of mortality and morbidity in children, and they are related to severe problems such as hearing loss, neurological sequelae, and death. The objective was to describe clinical and laboratory exam profiles of children who were diagnosed with CNS infections.

Methods

We conducted a cross-sectional study based on medical records, which included pediatric patients aged from 3 months to 15 years, with a clinical suspicion of CNS infection between January 2014 to December 2019. The pathogens were confirmed in cerebrospinal fluid (CSF) samples using Gram staining, cell culture, molecular diagnostics (PCR and qPCR), and serology.

Results

Out of the 689 enrolled patients, 108 (15.6%) had laboratory-confirmed infections in CSF. The most common bacterial pathogens isolated from the culture were Neisseria meningitidis serogroup C in 19, Streptococcus pneumoniae in 11, and Haemophilus influenzae in seven samples. The viruses identified were Enterovirus, Cytomegalovirus, Varicella-zoster virus, Epstein-Barr virus, and arbovirus. No patient was found to be positive for Herpes simplex virus 1 and 2. Patients with viral infections showed altered levels of consciousness (p = 0.001) when compared to bacterial infections.

Conclusion

This study shows the presence of important vaccine-preventable pathogens, and different families of viruses causing CNS infections in the pediatric patients of Manaus.

Epidemiology and Disease Burden of Hospitalized Children With Viral Central Nervous System Infections in China, 2016 to 2020

BACKGROUND

Viral central nervous system (CNS) infections seriously threaten the life and health of children, with a high mortality and severe sequelae in China and globally. Surveillance of viral CNS infections in children is important, especially in hospitalized children, to facilitate disease evaluation.

METHODS

In this study, we collected the data on the discharged Face Sheet of Medical Records from database from 2016 to 2020 and analyzed the epidemiologic characteristics and disease burden of hospitalized children (≤18 years old) with viral CNS infections in China. We classified the discharge diagnosis of viral CNS infection as viral encephalitis (VE), viral meningitis (VM), viral meningoencephalitis (VME), viral encephalomyelitis (VEM), and viral meningomyelitis (VMM).

RESULTS

A total of 42,641 cases of viral CNS infections were included in the database, consisting of 39,279 cases with VE (92.47%), 2011 cases with VM (4.73%), 1189 cases with VME (2.80%), 118 cases with VEM (0.28%), and 44 cases with VMM (0.10%). The number of hospitalized patients with viral CNS infections accounted for 0.74% (42,641 of 5,790,910) of all hospitalized cases. The onset of viral CNS infections presented seasonal characteristic, with peaks in June to July and December to January. Seizures are the most frequent complication of this disorder. Median length of stay and inpatient expenditures for patients with viral CNS infections were 9 days and 1144.36 USD. Causative viruses were identified in 4.33% (1848 of 42,641) of patients.

CONCLUSIONS

This study will help understand the clinical epidemiology and disease burden of hospitalized children with viral CNS infections in China.

Development of a multiplex droplet digital PCR assay for detection of enterovirus, parechovirus, herpes simplex virus 1 and 2 simultaneously for diagnosis of viral CNS infections

Background

Enterovirus (EV), parechovirus (HPeV), herpes simplex virus 1 and 2 (HSV1/2) are common viruses leading to viral central nervous system (CNS) infections which are increasingly predominant but exhibit deficiency in definite pathogen diagnosis with gold-standard quantitative PCR method. Previous studies have shown that droplet digital PCR (ddPCR) has great potential in pathogen detection and quantification, especially in low concentration samples.

Methods

Targeting four common viruses of EV, HPeV, HSV1, and HSV2 in cerebrospinal fluid (CSF), we developed a multiplex ddPCR assay using probe ratio-based multiplexing strategy, analyzed the performance, and evaluated it in 97 CSF samples collected from patients with suspected viral CNS infections on a two-channel ddPCR detection system.

Results

The four viruses were clearly distinguished by their corresponding fluorescence amplitude. The limits of detection for EV, HPeV, HSV1, and HSV2 were 5, 10, 5, and 10 copies per reaction, respectively. The dynamic range was at least four orders of magnitude spanning from 2000 to 2 copies per reaction. The results of 97 tested clinical CSF specimens were identical to those deduced from qPCR/qRT-PCR assays using commercial kits.

Conclusion

The multiplex ddPCR assay was demonstrated to be an accurate and robust method which could detect EV, HPeV, HSV1, and HSV2 simultaneously. It provides a useful tool for clinical diagnosis and disease monitoring of viral CNS infections.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12985-022-01798-y.

Epidemiology and Drug Resistance of Pathogens Isolated from Cerebrospinal Fluids at a Children's Medical Center in Eastern China During 2006-2020

Objective

To investigate the epidemiology and drug resistance of pathogens isolated from cerebrospinal fluid samples at a children's medical center in eastern China and provide the basis for anti-infection treatments.

Methods

In all, 307 non-duplicated strains of pathogens were isolated from cerebrospinal fluid samples in the Children's Hospital of Soochow University from January 2006 to December 2020. Mass spectrometry was used for pathogen identification. The VITEK 2 Compact system and Kirby-Bauer method were applied to determine antimicrobial susceptibility.

Results

Among the 307 isolates, gram-positive bacteria, gram-negative bacteria and fungi accounted for 60.26%, 34.53%, and 5.21%, respectively. The most prevalent pathogens were Streptococcus pneumoniae (26.06%), Escherichia coli (20.20%) and Streptococcus agalactiae (17.26%). The number of isolates was highest in winter. The most prevalent gram-positive bacterium in children <6 months old was Streptococcus agalactiae, while Streptococcus pneumoniae was the most in children were >6 months old. The drug resistance of gram-positive bacteria, fungi and Haemophilus influenza were not high. In addition, 35 strains of gram-negative bacteria produced extended-spectrum β-lactamases (ESBLs) and 6 strains were identified as multidrug-resistant (MDR) bacteria. These strains showed much higher resistance to the antibiotics than other strains.

Conclusion

Cases of meningitis among children have increased in the past 15 years and MDR bacteria were also identified. The emergence of MDR bacteria is a cause for great concern and requires further investigation.

Complicated Streptococcus agalactiae Sepsis with/without Meningitis in Young Infants and Newborns: The Clinical and Molecular Characteristics and Outcomes

Background: Streptococcus agalactiae (also known as group B streptococcus, GBS) is associated with high mortality and morbidity rates in infants, especially those with complicated GBS sepsis, defined as those with meningitis, severe sepsis and/or septic shock. We aimed to characterize the clinical and molecular characteristics and risk factors for adverse outcomes of neonates with invasive GBS diseases. Methods: From 2003 to 2020, all neonates with invasive GBS diseases who were hospitalized in a tertiary-level neonatal intensive care unit (NICU) were enrolled. The GBS isolates underwent serotyping, multilocus sequence typing (MLST) and antibiotic susceptibility testing. We compared cases of complicated GBS sepsis with uncomplicated GBS bacteremia. Results: During the study period, a total of 188 neonates (aged less than 6 months old) with invasive GBS diseases were identified and enrolled. Among them, 119 (63.3%) had uncomplicated GBS bacteremia and 69 (36.7%) neonates had complicated GBS sepsis, including meningitis (25.5%, n = 48) and severe sepsis or septic shock. Among neonates with complicated GBS sepsis, 45 (65.2%) had neurological complications, and 21 (42.0%) of 50 survivors had neurological sequelae at discharge. The overall final mortality rate was 10.1% (19 neonates died). Type III/ST-17 GBS isolates accounted for 56.5% of all complicated GBS sepsis and 68.8% of all GBS meningitis, but this strain was not significantly associated with worse outcomes. The antimicrobial resistance rate among the invasive GBS isolates was obviously increasing in the past two decades. After multivariate logistic regression analysis, neonates with thrombocytopenia and respiratory failure were independently associated with final adverse outcomes. Conclusions: a total of 36.7% of all neonatal invasive GBS diseases were associated with complicated sepsis with/without meningitis. Given the high mortality and morbidity rates in neonates with complicated GBS sepsis, further studies for early identification of specific strains, risk factors or genetic mechanisms that will cause complicated GBS sepsis are urgently needed in the future.

Epidemiology and Trends of Infective Meningitis in Neonates and Infants Less than 3 Months of Age in Hong Kong

INTRODUCTION AND AIMS

Meningitis in neonates and young infants leads to significant morbidity and mortality worldwide. This study aims to investigate pathogens, antibiotics resistance and secular change of incidence in Hong Kong.

METHODS

We performed a retrospective search on meningitis in neonates and infants <3 months old in three Hong Kong public hospitals from 2004 to 2019. Medical charts were reviewed, focusing on the identification and antibiotics resistance of the pathogens.

RESULTS

200 cases of meningitis were identified (67% were bacterial). Group B Streptococcus (GBS) and Escherichia coli (E. coli) were the commonest bacterial pathogens. The annual rates of early-onset GBS meningitis decreased since the implementation of the universal GBS screening and intrapartum antibiotics prophylaxis (IAP) in 2012, while that of late-onset GBS meningitis remained similar. A significant portion of E. coli isolates were resistant to ampicillin and/or gentamicin.

CONCLUSION

GBS and E. coli remained the commonest bacteria for meningitis in this age group. The annual rate of bacterial meningitis in Hong Kong declined in recent years, which was attributed by the decline in that of early-onset GBS meningitis due to the universal GBS screening and IAP. Antimicrobial-resistant bacterial strains that caused meningitis require further clinical and public health attention.

Etiology, Clinical Presentation and Incidence of Infectious Meningitis and Encephalitis in Polish Children

Little is known about the causes and the frequency of meningitis and encephalitis in Poland. We did a retrospective single-center cohort study of children under 18 years old hospitalized with infectious meningitis or encephalitis. Incidence rates were calculated using collected data from patients from the North-East Poland only. A total of 374 children hospitalized between 1 January 2015 and 31 December 2019 were included in the study. A total of 332 (89%) children had meningitis, and 42 (11%) had encephalitis. The etiology of the infection was established in 331 (89%) cases. Enteroviruses accounted for 224 (60%) of all patients. A total of 68 (18%) cases were tick-borne infections. Bacterial pathogens were detected in 26 (7%) children. The median length of hospital stay for children with enteroviral meningitis was 7 days (IQR 7–9), increasing to 11 days (8–13) in those treated with antibiotics. The incidence of meningitis was estimated to be 32.22 (95% CI, 25.33–40.98) per 100,000 and that of encephalitis to be 4.08 (95% CI, 2.07–8.02) per 100,000. By the broad use of molecular diagnostic methods, we managed to identify etiology of the infection in the majority of children. Our data suggest that thorough diagnostics of central nervous system infections are needed to rationalize treatment.