Real-time qpcr improves meningitis pathogen detection in invasive bacterial-vaccine preventable disease surveillance in Fiji

Transcription

1 Real-time qpcr improves meningitis pathogen detection in invasive bacterial-vaccine preventable disease surveillance in Fiji Eileen M. Dunne, Silivia Mantanitobua, Shalini P. Singh, Rita Reyburn, Evelyn Tuivaga, Eric Rafai, Lisi Tikoduadua, Barbara Porter, Catherine Satzke, Janet E. Strachan, Kimberly Fox, Kylie M. Jenkins, Adam Jenney, Silo Baro, E. Kim Mulholland, Mike Kama, and Fiona M. Russell New Vaccine Evaluation Project Bacterial meningitis Severe infection with high mortality Streptococcus pneumoniae, Haemophilus influenzae, and Neisseria meningitidis are the most common causes The WHO conducts surveillance on these species as part of Invasive Bacterial - Vaccine Preventable Disease (IB-VPD) Surveillance Surveillance is important for Determining the main causes of meningitis Outbreak detection Monitoring changes following vaccine introduction Pneumococcus H. influenzae Meningococcus 1

2 Detection of bacterial meningitis Cerebrospinal fluid (CSF) collected from suspected meningitis patients Bacteria identified by traditional microbiology methods Culture Gram stain Latex agglutination CSF analysed for indicators of bacterial infection* White blood cell count (WCC) Elevated (eg. >100 cells/mm 3 ) Glucose Low (eg. <1.6 mmol/l) Protein Elevated (eg. >1 g/l) microbeworld.org *interpretation guidelines from RCH thermofisher.com Quantitative PCR of CSF samples Molecular methods are sensitive and can identify culturenegative bacteria Exposure to antibiotics Low bacterial loads Improper handling and/or storage WHO recommends qpcr testing of CSF samples for IB-VPD surveillance sodc for N. meningitidis hpd for H. influenzae lyta for S. pneumoniae 2

3 Immunisation in Fiji Hib vaccine introduced in 1997 PCV10 introduced in October (6, 10, 14 wk), no catch up Meningococcal vaccine not used New Vaccine Evaluation Project established to monitor impact of PCV, rotavirus, and HPV immunisation IPD surveillance at Colonial War Memorial Hospital in Suva qpcr detection of meningitis pathogens at Fiji Centre for Communicable Disease Control Fiji joined WHO Global IB-VPD laboratory network in 2015 Study aims 1. To identify the major aetiologic agents causing meningitis in the years immediately following PCV introduction 2. To to examine whether the use of qpcr improved detection of S. pneumoniae, N. meningitidis, and H. influenzae compared to traditional microbiological approaches 3

4 Meningitis surveillance flowchart SOPs based on WHO IB-VPD guidelines Clinician identifies potential case, collects CSF CSFs sent to CWMH Micro lab CSFs cultured, examined by microscopy and antigen testing Leftover CSFs sent to FCCDC Molecular testing of CSFs by qpcr Laboratory methods Traditional Culture on human blood agar, chocolate agar, and MacConkey agar Direct antigen testing (DAT) using commercial kit (Wellcogen) Hib, S. pneumoniae, N. meningitidis A/C/Y/W135, N. meningitidis B, E. coli K1, GBS qpcr DNA extraction from CSF: enzymatic digest + commercial kit (Qiagen) qpcr for N. meningitidis, H. influenzae, S. pneumoniae (WHO manual) typing Hib detection by Hib-specific qpcr (bcsb) Meningococcal typing by latex agglutination (isolates) and qpcr (CSF DNA), WHO IB-VPD Regional Reference Laboratory, Melbourne Pneumococcal typing by latex/quellung (isolates) and microarray or qpcr (CSF DNA), MCRI and IB-VPD RRL, Melbourne 4

5 Quality control Extraction controls, no template controls, and positive controls included in each qpcr run qpcr results interpretation according to CDC Meningitis lab Ct values < 35 are positive Ct values are equivocal (re-test) Ct values > 40 are negative Participation in WHO external quality assessment program Study aims 1. To identify the major aetiologic agents causing meningitis in the years immediately following PCV introduction 2. To to examine whether the use of qpcr improved detection of S. pneumoniae, N. meningitidis, and H. influenzae compared to traditional microbiological approaches 5

6 Results: meningitis aetiology 330 CSF samples examined from Nov Dec 2016 Bacterial pathogen identified in 63 (19.1%) samples 48/63 (76%) from children < 5 years Age N (%) 0 1 month 85 (25.8) 2-11 months 128 (38.8) months 28 (8.5) 2-4 years 25 (7.6) 5 18 years 22 (6.7) not identified identified not identified 19+ years 39 (11.8) Results: meningitis aetiology Pneumococcus most common (n = 23) followed by meningococcus (n = 19) All GBS identified by DAT E. coli (n = 3) H. influenzae (n = 5) Other* (n = 6) S. pneumoniae (n = 23) N. meningitidis (n = 19) *Other includes Acinetobacter baumannii (n = 2), Klebsiella oxytoca, Streptococcus mitis, group D streptococcus, and coagulase-negative staphylococci. 6

7 No. of meninogococcal cases Jan Mar May Jul Sep Nov Jan Mar May Jul Sep Nov Jan Mar May Jul Sep Nov Jan Mar May Jul Sep Nov Jan 12-Jul-17 Results: bacterial typing Of the 5 H. influenzae cases 2 were type b (Hib) 1 vaccine failure Pneumococcal serotyping by microarray conducted to test feasibility of direct molecular typing from clinical specimens 9/16 (56%) had a serotype identified, including 4 culturenegative samples Only samples with a lyta Ct value <30 were serotypeable by microarray Pneumococcal serotypes identified from 14 samples 8 (n=3), 23B (n=2), 6A, 7B, 7C, 16F, 19A, 23F, 31, 33, and 44 Only 23F included in PCV10, patient not age eligible for vaccination Results: bacterial typing Concerns about possible increase in meningococcal cases 5 4 Meningococcal Cases at CWMH Meningococcal serogrouping results from CSF and blood: B ( n = 13), C (n = 2), W (n = 1) WGS on 3 N. meningitidis isolates from 2015 (MDU) 2 related to each other, 1 distinct Not closely related to epidemic NZ serogroup B strains serogroup PorA FetA MLST NM2 B 7-2,4 F1-5 - NM4 B 22,9 F NM5 B 7-2,4 F

8 Study aims 1. To identify the major aetiologic agents causing meningitis in the years immediately following PCV introduction 2. To to examine whether the use of qpcr improved detection of S. pneumoniae, N. meningitidis, and H. influenzae compared to traditional microbiological approaches Results method comparison 266 CSF samples examined from Nov May /266 (91%) had white blood cell counts > 10 cells/mm 3 Total* Culture identified/ tested (%) Direct Antigen Testing identified/ tested (%) Gram stain identified/ tested (%) qpcr identified/ tested (%) Increased detection due to qpcr + (%) S. pneumoniae 17 7/17 (41) 6/11 (54) 8/16 (50) 16/16 (100) 200 N. meningitidis 13 1/13 (8) 2/9 (29) 3/12 (25) 12/13 (92) 400 H. influenzae 5 2/5 (40) 1/2 (50) 1/5 (20) 5/5 (100) 250 * identified by culture, DAT, and/or qpcr + not identified by culture or DAT qpcr significantly increased detection of IB-VPD (P = 0.001, Fisher s exact test) Of 35 IB-VPD cases, only 10 were culture positive qpcr identified an additional 23 cases 8

9 Results method comparison Sensitivity: qpcr 97%, DAT 45%, 29% culture True positives: detected by culture, DAT, and/or qpcr Samples not tested by a method excluded from sensitivity analysis DAT kits often out of stock (only 17/35 samples tested) 1 false negative by qpcr for N. meningitidis, only 1 µl used for DNA extraction Summary S. pneumoniae and N. meningitidis were the most common causes of meningitis in Fiji qpcr detection of IB-VPD successfully implemented at FCCDC qpcr significantly improved detection of IB-VPD pathogens Particularly important for meningococcus Almost all pneumococcal cases were due to non-vaccine serotypes Pneumococcal serotyping by microarray can be performed directly on CSF Requires sufficient pneumococcal DNA (lyta Ct < 30) Meningococcal meningitis may be increasing in Fiji Planned expansion of surveillance to Lautoka and Labasa 9

10 Acknowledgements Fiji MoHMS Eric Rafai Mike Kama Rachel Devi Joseph Kado Lisi Tikoduadua Reapi Mataika Ilisapeci Vereti Silo Baro Liti Volavola NVEP Silivia Mantanitobua Evelyn Tuivaga Rita Reyburn Tupou Ratu Mere Gunaivalu MCRI Fiona Russell Kim Mulholland Catherine Satzke Barbara Porter Kathryn Bright Adam Jenney Pneumococcal Research lab WHO PCR Facility Shalini P Singh Patrick Reading Eric Nilles FHSSP Rosalina Sa'aga-Banuve Kelly Robertson Atelini Wainiveikoso Kylie Jenkins Clinicians and CWMH Micro lab Mataika House staff WHO Kimberly Fox Janet Strachan (MDU) Department of Foreign Affairs and Trade of the Australian Government and Fiji Health Sector Support Program (FHSSP). FHSSP is implemented by Abt JTA on behalf of the Australian Government. 10