new diagnostic approach for pneumonia as syndromic...
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New diagnostic Approach for Pneumonia as Syndromic Disease
Aryati
Suramade, 7-9 Agustus 2019
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SYNDROMIC DISEASE
Same symptoms, many causes
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VIRUS OR BACTERIA INFECTIONS? NORMAL FLORA OR PATHOGEN ?
Syndromic disease
Sindrom = kumpulan tanda + gejala yang non spesifik, mengarah pada diagnosis tertentu
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Gejala Tanda
Demam Menggigil Batuk Nyeri kepala Nyeri otot
Temp 39 ◦ CTakikardia Wheezing, rales Leukositosis LED meningkatThorax X-Ray
PneumoniaInfeksi pada parenkim paru
Community Acquired
Pneumonia (CAP)
Hospital Acquired
Pneumonia (HAP)
Ventilator Acquired
Pneumonia (VAP)
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Meningitis
Bacteremia & septicemia
Pneumonia
Acute otitismedia
Globally, in children < 5years, S. pneumoniae is the leading cause of …
Disease Incidence
17*(6-38)
87*(36-192)
2,228*(462-3.397)
93% (1st 24 months)
30-40%pneumococci
O`Brien et al. Lancet 2009;374:893-902
Black et al Lancet 2010:375;1969
*per 105
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Pneumonia :the forgotten killer of children
• More than 1 million
children die from
Pneumonia
• Pneumonia kills a
child every 15
second
• Pneumonia is the
cause of death in 1
of 5 children under 5
years
http://www.depkes.go.id/resources/download/info-terkini/hasil-riskesdas-2018.pdf
Respiratory Infection
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Community Acquired Pneumonia (CAP)
Kaysin and viera, 2016 9
• Usia sangat muda atau sangat tua
• Annual Incidence of 9.2 - 33 per 1,000 person-years
Prevalensi
• Streptococcus pneumoniae (>>>)
• Enterobacteriacea, Haemophilus influenzae, and methicillin-sensitive Staphyloccous aureus
Etiologi
Faktor risiko dan Patogen pada CAP
Faktor risiko Patogen
Alkoholisme Anaerobic oral flora, Klebsiella pneumoniae, Mycobacterium
tuberculosis, Streptococcus pneumoniae
Merokok atau COPD Chlamydophila pneumoniae, Haemophilus influenzae,
Legionella species, Moraxella catarrhalis, Pseudomonas
aeruginosa or other gram-negative rods, S. pneumoniae
Infeksi HIV (awal) H. influenzae, M. tuberculosis, S. pneumoniae
Infeksi HIV (Lanjut) Aspergillus and Cryptococcus species, H. capsulatum, H.
influenzae, Nocardia species, non-tuberculous mycobacteria,
Pneumocystis jiroveci
Influenza H. influenzae, influenza and other respiratory viruses, S.
pneumoniae, Staphylococcus aureus (including MRSA)
Injection Drug abuse Anaerobes, M. tuberculosis, S. aureus(including MRSA), S.
pneumoniae
10Kaysin and viera, 2016
Kriteria Diagnosis
11Kaysin and viera, 2016
12Kaysin and viera, 2016
13Kaysin and viera, 2016
Tingkat deteksi
patogen pada pasien
dengan CAP 30- 40%
Perkembangan baru penggunaan multiorganism
polymerase chain reaction–based testing for pathogen
tingkat deteksi patogen (virus dan bakteri) ~ 86%
25% kasus CAP
diakibatkan oleh virus
belum tersedia dx
De-eskalasi terapi lebih awal
Penggunaan antibiotika spektrum luas menurun
Hospital Acquired Pneumonia (HAP)
14Kieninger and lipsett
Pneumonia yang terjadi > 48 jam setelah MRS
tanpa ada tanda infeksi ketika MRS
Early onset HAP
(< 5 hari waktu
perawatan)
Late onset
(> 5 hari waktu
perawatan)
Hospital Acquired Pneumonia (HAP)
15Kieninger & Lipsett, 2009
• 3 to 10 cases per 1000 hospital admissionsInsidens
• Enterobacteriacea,
• Haemophilus influenzae,
• Streptococcus pneumonia,
• Methicillin-sensitive Staphyloccous aureus
Etiologi
Patogenesis HAP
16Kieninger & Lipsett, 2009
Alteration in patients’ immune
response
Aspiration of oropharyngeal
secretion (colonized by enteric Gram
negative pathogens)
Impaired mucocilliary
clearance of the respiratory tract
Poor nutrition
Ventilator Acquired Pneumonia (VAP)
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• pneumonia yang terjadi > 48 jam dari pemberian ventilasi mekanik, tidak lebih dari 72 jam dari awal pemberian ventilasi
Definisi
• 3% per hari dalam 5 hari pertama ventilasi mekanik
• 2% per hari (hari ke 6-10)
• 1% per hari (ventilasi mekanik > 10 hari)
Insidens
Risk factor
18Miller, 2018
Diagnosis VAP - CPIS
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A CPIS score of 6 or higher out of a maximum score of 12 indicates a likely diagnosis of VAP
Miller, 2018
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SOP-ICMR-AMR, 2015
Diagnosis Laboratorium
Kultur
(darah / sputum)
Molekular (PCR) Antigen test
Serologi DFA /IFA Kultur Virus
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Metode Diagnosis Berdasarkan Patogen
22Tores et al., 2016
23Tores et al., 2016
24Tores et al., 2016
25Tores et al., 2016
Age
The Challenge of Syndromic Disease
Past Medical History
Travel history
Vaccination history
Patient location
Risk of exposure
Animal (pet) exposure
Immune status
Sex
Bacteria, virus, yeast or paracyte?
Syndromic testing : the new one
Multiplexed “panels” capable of detecting a
broad array of pathogens bacterial, viral,
fungal, parasitic associated with a clinical
“syndrome”
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One System & One Pouch for One Test
• Including : extraction reagents, control RNA & DNA, and mastermix
2nd
Stage PCR
1st StageMultiplex
PCR
SampleExtraction &Preparation
+FilmArray
Conventional
Reagent
Storage
Chemical
Circuit
Board
The FilmArray Pouch
Sample
Extraction &
purification
First
stage
Multiplex
PCR
Second stage
PCR
29Internal Control : mRNA Schizosacccharomyces pombe
Workflow: Simple, Easy, Fast
FilmArray
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Sample Requirements
200 mL of:
Sputum BAL(Bronchoalveolar lavage)
Non-invasive sample
collection like:
• Induced sputum
• Expectorated sputum
• Endotracheal aspirates
Invasive sample
collection like:
• BAL
• Mini-BAL
-OR-
Notes: • Specimen should not be pre-processed, centrifuged, treated with any mucolytic or
decontaminating agents or placed into transport media before testing
• Institutions should follow their own established rules for acceptance/rejection of sputum specimens (e.g. using Gram stain/Q-score/Bartlett’s/Murray and Washington grading system) and therefore apply appropriate guidelines locally for acceptance/rejection of a sample for testing
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Transport and Storage
• Specimens should be tested as soon
as possible
• If storage is required, specimen can
be held refrigerated for up to 1 day
(2-8oC)
Sample Requirements
Selected Commencal Microbiota and Potential
Pathogens in the Respiratory Tract
Koneman’s., 2017
Normal flora of the Respiratory Tract
A. The nares (nostrils)
1. Staphylococcus epidermidis
2. Corynebacterium
3. Staphylococcus
4. Neisseria sp.
5. Haemophilus sp.
6. Streptococcus pneumonia
B. The Upper Respiratory Tract (Nasopharynx)
1. Non-hemolytic streptococci
2. Alpha-hemolytic streptococci
3. Neisseria sp.
4. Streptococcus pneumonia
5. Streptococcus pyogenes
6. Hemophilus influenzae
7. Neisseria meningitidis34
Normal flora of the Respiratory Tract
C. The Lower Respiratory Tract
(trachea, bronchi, and pulmonary
tissues)
• Usually sterile
• The individual may become susceptible to
infection by pathogens descending from
the nasopharynx e.g.
Haemophilus influenzae
Streptococcus pneumonia
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Semi-Quantitative
The FilmArray Pneumonia Panel uses real-time amplification data
from the assays relative to the Quantified Standard Material (QSM)
included in the pouch to provide an estimated value in genomic
copies per milliliter (copies/mL) for bacterial analytes
QSM
Bacterium1
Bacterium2
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Semi-Quantitative
ND 10^4copies/mL
10^5copies/mL
10^6copies/mL
≥10^7copies/mL
103.5 104.5 105.5 106.5
Bin Result
102.1
105.3
107.7
• Quantitative values for a target are calculated by comparing
the real-time PCR data of the QSM relative to the target.
• Calculated values rounded to the nearest one-log “Bin”.
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PNEUMONIA Panel (33)
Bacteria (15)Semi-Quantitative
Acinetobacter calcoaceticus
baumannii complex
Enterobacter cloacae complex
Escherichia coli
Haemophilus influenzae
Klebsiella aerogenes
Klebsiella oxytoca
Klebsiella Pneumoniae group
Moraxella catarrhalis
Proteus spp.
Pseudomonas aeruginosa
Serratia marcescens
Staphylococcus aureus
Streptococcus agalactiae
Streptococcus Pneumoniae
Streptococcus pyogenes
Atypical BacteriaChlamydia Pneumoniae
Legionella Pneumoniaphila
Mycoplasma Pneumoniae
Viruses (8)Adenovirus
Coronavirus
Human Rhinovirus/Enterovirus
Human MetaPneumoniavirus
Influenza A
Influenza B
Parainfluenza Virus
Respiratory Syncytial Virus
MERS-CoV (Pneumoniaplus Only)*
*Only available outside the U.S.
AntimicrobialResistance GeneMETHICILLIN RESISTANCE
mec A/C and MREJ
CARBAPENEMASES
KPC
NDM
Oxa-48-like
VIM
IMP
ESBL
CTX-M
Sample Requirements: Sputum (including ETA) and BAL (including mini-BAL)
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Antimicrobial Resistance Genes
• A resistance marker(s) is only reported if a microorganism is detected that could
potentially contain that resistance gene.
• Detected resistance markers cannot be definitively linked to detected microorganisms
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Panel Report
• Result Summary (lists all targets that were tested)
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CAP HAP
Struthers, 2005
Day 1
• Female (18 bln)
• January
• Fever 37,9 ◦C
• History infeksitelinga, asmaringan, batuk, hilang nafsumakan,
• Rapid test RSV dan Flu A/B negative
• Didiagnosa : mild bronchiolitis
• Pasien dikirimpulang dan minumacetaminophen
Day 4
• Pasien masukIGD, batuk
• Tes rapid RSV ulang masihnegative
• Chest Radiography menunjukanindikasi ringangangguanpulmonary
• DiberikanAmpicillin dan di obervasi
Day 5
• Dikarenakansemakinparahnya kondisipasien , Abx diganti kecefotaxime dan dirawat ke ICU
• Film Array RP digunakan, 1 jam proses dan memberikanhasil : M. pneumoniae
• Antibiotik digantike Macrolide
Case 1 :
RESEARCH ON SYNDROMIC
TESTING
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Positivity rate 42,4% kelompok mPCR vs 14.4% kelompok konvensional (non mPCR)Persentase RSV dan influenza hampir sama (J pediatr 2016; 173:196-201)
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FilmArray RP and multiple PCR had significantly high sensitivities and specificities for the detection of respiratory viruses
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FilmArray RP had higher sensitivity in detecting the dual viral infection than
multiple PCR.
Mycoplasma pneumoniae is a causative agent of community-acquired atypical pneumonia, and Chlamydophila pneumoniae is an obligate intracellular bacterium that causes acute respiratory infections and is a common cause of CAP.
To Mycoplasma pneumoniae and Chlamydia pneumonia detection, culture is highly specific but it is a complex process that has a long turnaround time, technically demanding, and offers limited sensitivity. Serology and PCR methods may
provide a rapid diagnosis
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FILMARRAY® RP decreased the time to diagnosis and was associated with trends
toward decreased admission rates, shorter length of stay, shorter duration of
antimicrobial therapy and fewer chest radiographs compared to conventional
methods.
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Implementation of the FILMARRAY® RP was associated with:- significant decreases in the median length of antibiotic therapy (P<0.01), - a reduction in chest radiographs performed during the first two days of hospitalization (P<0.01),- an increase in the proportion of patients placed on isolation precautions (P=0.01) during the first two days of hospitalization.Use of the FILMARRAY® RP resulted in dramatic reductions in testing turnaround time (2-5 days to ~3 hours)FILMARRAY® RP has the capability to replace traditional testing methods, including EIA, DFA, viral culture and traditional or low multiplex PCR methods
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Kesimpulan
• Syndromic disease memiliki gejala yang sama
namun berbagai penyebab berbeda
• Pneumonia merupakan salah satu syndromic
disease dan terdiri dari CAP, HAP, VAP. Agen
penyebab yaitu bakteri, bakteri atipik, virus, jamur
dan parasit.
• 25% kasus Community Acquired Pneumonia
disebabkan oleh virus yang saat ini sulit dideteksi.
• Diagnosis laboratorium infeksi pneumonia meliputi
darah lengkap, serologi (CRP, PCT, IgM
antiMycoplasma), antigen spesifik patogen, direct
fluorescent antibody (DFA), kultur dan molekuler .
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Kesimpulan
• Pemeriksaan molekular terdiri dari metode
konvensional, multiplex PCR dan microarray
(Biofire FilmArray)
• FilmArray Pneumonia panel menggunakan sputum
(termasuk ETA) dan BAL yang terdiri dari 26
patogen (15 bakteri-semikuantitatif, 3 bakteri atipik,
8 virus dan 7 marker resistensi antibiotika)
• FilmArray Pneumonia panel memberikan hasil
dalam waktu 1 jam bermanfaat untuk
penanganan pasien yang lebih cepat 51
2 minutes hands on time FAST : Extraction, PCR & detection in
45 minutes - 1 hour