scholarly journals Molecular detection and characterization of bacteria from CSF samples of patients with suspected cerebrospinal meningitis in parts of northern Nigeria using metagenomic DNA extracts

2021 ◽  
Vol 22 (3) ◽  
pp. 365-376
Author(s):  
I.C. Peletiri ◽  
E.I. Ikeh ◽  
G.M. Ayanbimpe ◽  
E. Nna
Keyword(s):  
Streptococcus Pneumoniae ◽  
Haemophilus Influenzae ◽  
Neisseria Meningitidis ◽  
Real Time Pcr ◽  
Molecular Detection ◽  
Northern Nigeria ◽  
Rt Pcr ◽  
Metagenomic Dna ◽  
Pcr Multiplex

Background: The most commonly used approaches for detection and characterization of bacterial pathogens of meningitis in developing countries include culture, Gram stain, and latex agglutination. The positivity rate of culture is relatively low due to suboptimal storage and transportation conditions, culture practice, and/or antibiotic treatment administered before specimens are collected. Specimens that yield no growth in culture can still be analyzed using molecular methods, and metagenomic DNA (mDNA) extracted directly from clinical samples (CSF) can be used. We aimed to detect and characterize three major bacterial causes of cerebrospinal meningitis (CSM); Neisseria meningitidis, Haemophilus influenzae, and Streptococcus pneumoniae using mDNA extracted directly from CSF samples. Methodology: Metagenomic DNA templates were prepared directly from CSF specimens collected from 210 patients with suspected CSM. A multiplex Real Time PCR (mRT-PCR) using the ABI StepOne Plus Machine and Taqman Probe chemistry was used in the molecular detection, while serogroup/serotype-specific singleplex RT-PCR was used to characterize all positives samples. Results: Eighty-eight (41.9%) of the 210 samples were positive with the mRT-PCR assay for one or a combination of two of the three bacteria. Of these, 59 (67.1%) were N. meningitidis, 2 (2.3%) were H. influenzae, 3 (3.4%) were S. pneumoniae, 15 (17 %) had co-infections of N. meningitidis with H. influenzae, and 9 (10.2%) had co-infections of H. influenzae and S. pneumoniae. The serogroups of N. meningitidis encountered were A (13.5%), B (23%), C (8.1%), W135 (8.1%), X (5.4%), Y (32.4%), and non-groupable (9.5%). The serotypes of H. influenzae were Hia (3.8%), Hib (57.7%), Hic (3.85%), Hie (11.5%) and Hif (23.1%). The serotypes of S. pneumoniae were Wxy1 (8.3%), Wxy4 (33.3%), Wxy5 (50.0%), and Wxy9 (8.3%). Conclusion: Multiplex RT-PCR is a fast and accurate method for detecting and characterizing serogroups/serotypes of major bacteria implicated in CSM. Isolating DNA directly from CSF improves turnaround time, which will speed up patient care and management. Keywords: Cerebrospinal meningitis, metagenomic DNA, multiplex Real Time PCR, Northern Nigeria   French title: Détection moléculaire et caractérisation de bactéries à partir d'échantillons de LCR de patients suspectés de méningite cérébrospinale dans certaines parties du nord du Nigéria à l'aide d'extraits d'ADN métagénomique   Contexte: Les approches les plus couramment utilisées pour la détection et la caractérisation des agents pathogènes bactériens de la méningite dans les pays en développement comprennent la culture, la coloration de Gram et l'agglutination au latex. Le taux de positivité de la culture est relativement faible en raison des conditions de stockage et de transport sous-optimales, des pratiques de culture et/ou du traitement antibiotique administré avant le prélèvement des échantillons. Les échantillons qui ne donnent pas de croissance en culture peuvent toujours être analysés à l'aide de méthodes moléculaires, et l'ADN métagénomique (ADNm) extrait directement d'échantillons cliniques (LCR) peut être utilisé. Nous visions à détecter et à caractériser trois causes bactériennes majeures de la méningite cérébrospinale (CSM); Neisseria meningitidis, Haemophilus influenzae et Streptococcus pneumoniae à l'aide d'ADNm extrait directement d'échantillons de LCR. Méthodologie: Des matrices d'ADN métagénomique ont été préparées directement à partir d'échantillons de LCR prélevés sur 210 patients suspects de CSM. Une PCR multiplex en temps réel (mRT-PCR) utilisant la chimie de la machine ABI StepOne Plus et de la sonde Taqman a été utilisée pour la détection moléculaire, tandis que la RT-PCR monoplex spécifique au sérogroupe/sérotype a été utilisée pour caractériser tous les échantillons positifs. Résultats: Quatre-vingt-huit (41,9%) des 210 échantillons étaient positifs avec le test mRT-PCR pour une ou une combinaison de deux des trois bactéries. Parmi ceux-ci, 59 (67,1%) étaient N. meningitidis, 2 (2,3%) étaient H. influenzae, 3 (3,4%) étaient S. pneumoniae, 15 (17%) avaient des co-infections de N. meningitidis avec H. influenzae et 9 (10,2%) avaient des co-infections à H. influenzae et S. pneumoniae. Les sérogroupes de N. meningitidis rencontrés étaient A (13,5%), B (23%), C (8,1%), W135 (8,1%), X (5,4%), Y (32,4%) et non groupables (9,5%). Les sérotypes de H. influenzae étaient Hia (3,8%), Hib (57,7%), Hic (3,85%), Hie (11,5%) et Hif (23,1%). Les sérotypes de S. pneumoniae étaient Wxy1 (8,3%), Wxy4 (33,3%), Wxy5 (50,0%) et Wxy9 (8,3%). Conclusion: La RT-PCR multiplex est une méthode rapide et précise de détection et de caractérisation des sérogroupes/sérotypes des principales bactéries impliquées dans le CSM. Isoler l'ADN directement du LCR améliore le temps de traitement, ce qui accélérera les soins et la gestion des patients. Mots clés: méningite cérébro-spinale, ADN métagénomique, PCR multiplex en temps réel, nord du Nigéria

scholarly journals Accuracy of real-time PCR, Gram stain and culture for Streptococcus pneumoniae, Neisseria meningitidis and Haemophilus influenzae meningitis diagnosis

2013 ◽  
Vol 13 (1) ◽  
Author(s):  
Henry M Wu ◽  
Soraia M Cordeiro ◽  
Brian H Harcourt ◽  
Maria da Gloria S Carvalho ◽  
Jailton Azevedo ◽  
...  
Keyword(s):  
Streptococcus Pneumoniae ◽  
Haemophilus Influenzae ◽  
Neisseria Meningitidis ◽  
Real Time ◽  
Real Time Pcr ◽  
Gram Stain

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

2021 ◽  
Author(s):  
Youssef Ikken ◽  
Amina Benaouda ◽  
Latifa Ibn Yaich ◽  
Farida Hilali ◽  
Yassine Sekhsokh ◽  
...  
Keyword(s):  
Streptococcus Pneumoniae ◽  
Bacterial Meningitis ◽  
Haemophilus Influenzae ◽  
Molecular Epidemiology ◽  
Neisseria Meningitidis ◽  
Quantitative Pcr ◽  
Sensitivity And Specificity ◽  
Simultaneous Detection ◽  
Rt Pcr ◽  
Negative Culture

AbstractBacteriological 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.

scholarly journals Identification of Common Bacterial Pathogens Causing Meningitis in Culture-Negative Cerebrospinal Fluid Samples Using Real-Time Polymerase Chain Reaction

2016 ◽  
Vol 2016 ◽  
pp. 1-5 ◽  
Author(s):  
Walaa Shawky Khater ◽  
Safia Hamed Elabd
Keyword(s):  
Streptococcus Pneumoniae ◽  
Bacterial Meningitis ◽  
Haemophilus Influenzae ◽  
Neisseria Meningitidis ◽  
Real Time ◽  
Real Time Pcr ◽  
Latex Agglutination ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Culture Negative

Background. Meningitis is a serious communicable disease with high morbidity and mortality rates. It is an endemic disease in Egypt caused mainly byStreptococcus pneumoniae,Neisseria meningitidis, andHaemophilus influenzae. In some settings, bacterial meningitis is documented depending mainly on positive cerebrospinal fluid (CSF) culture results or CSF positive latex agglutination test, missing the important role of prior antimicrobial intake which can yield negative culture and latex agglutination test results. This study aimed to utilize molecular technology in order to diagnose bacterial meningitis in culture-negative CSF samples.Materials and Methods. Forty culture-negative CSF samples from suspected cases of bacterial meningitis were examined by real-time polymerase chain reaction (real-time PCR) for the presence oflytA,bexA, andctrAgenes specific forStreptococcus pneumoniae,Haemophilus influenzae, andNeisseria meningitidis, respectively.Results. Positive real-time PCR results forStreptococcus pneumoniaewere detected in 36 (90%) of culture-negative CSF samples while no positive results forHaemophilus influenzaeorNeisseria meningitidiswere detected. Four (10%) samples were negative by real-time PCR for all tested organisms.Conclusion. The use of molecular techniques as real-time PCR can provide a valuable addition to the proportion of diagnosed cases of bacterial meningitis especially in settings with high rates of culture-negative results.

scholarly journals Đồng nhiễm vi khuẩn gây viêm phổi nặng mắc phải tại cộng đồng ở trẻ em

2021 ◽  
Vol 139 (3) ◽  
pp. 45-54
Author(s):  
Trần Quang Khải ◽  
Nguyễn Thị Diệu Thúy ◽  
Trần Đỗ Hùng ◽  
Phạm Hùng Vân
Keyword(s):  
Streptococcus Pneumoniae ◽  
Haemophilus Influenzae ◽  
Real Time ◽  
Mycoplasma Pneumoniae ◽  
Real Time Pcr ◽  
Moraxella Catarrhalis ◽  
Rt Pcr

Viêm phổi là một trong những nguyên nhân hàng đầu dẫn đến tử vong ở trẻ dưới 5 tuổi. Từ trước đến nay, vi rút là nguyên nhân phổ biến nhất gây viêm phổi mắc phải tại cộng đồng ở trẻ em. Đồng nhiễm vi khuẩn là vấn đề được quan tâm nhiều vì tác động của nó đến định hướng điều trị cho các nhà lâm sàng. Real - time PCR (RT - PCR) là một xét nghiệm hiện đại giúp phát hiện nhiều tác nhân mới, đặc biệt đồng nhiễm vi khuẩn. Chúng tôi sử dụng kỹ thuật RT - PCR nhằm xác định nguyên nhân gây viêm phổi nặng. Qua phân tích 95 trẻ ghi nhận tỷ lệ PCR dương tính là 90,5%. Đồng nhiễm vi rút - vi khuẩn chiếm tỷ lệ cao nhất (43,1%), kế đến đồng nhiễm vi khuẩn - vi khuẩn (33,7%), đơn nhiễm vi rút 7,4%, đơn nhiễm vi khuẩn 6,3%, còn lại 9,5% không phân lập được. Trong nhóm đồng nhiễm, có sự tham gia của năm loài vi khuẩn sau theo thứ tự giảm dần Streptococcus pneumoniae, Haemophilus influenzae, MRSA, Moraxella catarrhalis và Mycoplasma pneumoniae. Do đó, lựa chọn kháng sinh trong điều trị viêm phổi nặng nên tập trung vào các vi khuẩn này.

Epidemiología de la meningitis producida por Haemophilus influenzae tipo b, Neisseria meningitidis y Streptococcus pneumoniae en niños de la Comunidad Valenciana, España

1998 ◽  
Vol 26 (149) ◽  
pp. 34 ◽  
Author(s):  
Mª Amparo Morant Gimeno ◽  
J. Díez Domingo ◽  
C. Gimeno ◽  
N. de la Muela ◽  
I. Pereiró ◽  
...  
Keyword(s):  
Streptococcus Pneumoniae ◽  
Haemophilus Influenzae ◽  
Neisseria Meningitidis
Sign in / Sign up

Export Citation Format

Share Document