New diagnostic Approach for

Pneumonia as Syndromic Disease

Aryati
Suramade, 7-9 Agustus 2019

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 SYNDROMIC DISEASE
Same symptoms, many causes

VIRUS OR BACTERIA INFECTIONS? NORMAL FLORA OR PATHOGEN ?

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 Syndromic disease
Sindrom = kumpulan tanda + gejala yang non
spesifik, mengarah pada diagnosis tertentu

Gejala Tanda
Temp 39 ◦ C
Demam
Takikardia
Menggigil
Wheezing, rales
Batuk
Leukositosis
Nyeri kepala
LED meningkat
Nyeri otot
Thorax X-Ray

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 Pneumonia
Infeksi pada parenkim paru

Community Ventilator
Acquired Acquired
Pneumonia Hospital
Pneumonia
(CAP) Acquired
(VAP)
Pneumonia
(HAP)

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 Globally, in children < 5years,
S. pneumoniae is the leading cause of …
Disease Incidence

Meningitis 17*
(6-38)

Bacteremia 87*
& septicemia (36-192)

Pneumonia 2,228*
(462-3.397)

Acute otitis 93% (1st 24 months)

30-40%
media pneumococci
O`Brien et al. Lancet 2009;374:893-902
Black et al Lancet 2010:375;1969
*per 105
 FLM1-MKT-XXXX
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)

• Usia sangat muda atau sangat

Prevalensi tua
• Annual Incidence of 9.2 - 33 per
1,000 person-years

• Streptococcus pneumoniae (>>>)

Etiologi • Enterobacteriacea, Haemophilus
influenzae, and methicillin-
sensitive Staphyloccous aureus

Kaysin and viera, 2016 9

 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

Kaysin and viera, 2016 10

Kriteria Diagnosis

Kaysin and viera, 2016 11

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Kaysin and viera, 2016
 Tingkat deteksi 25% kasus CAP
patogen pada pasien diakibatkan oleh virus
dengan CAP 30- 40%  belum tersedia dx

Perkembangan baru penggunaan multiorganism

polymerase chain reaction–based testing for pathogen 
tingkat deteksi patogen (virus dan bakteri) ~ 86%

De-eskalasi terapi lebih awal

Penggunaan antibiotika spektrum luas menurun
Kaysin and viera, 2016 13
Hospital Acquired Pneumonia (HAP)

Pneumonia yang terjadi > 48 jam setelah MRS

tanpa ada tanda infeksi ketika MRS

Early onset HAP Late onset

(< 5 hari waktu (> 5 hari waktu
perawatan) perawatan)

Kieninger and lipsett 14

Hospital Acquired Pneumonia (HAP)

• 3 to 10 cases per 1000

Insidens hospital admissions

• Enterobacteriacea,
• Haemophilus influenzae,
Etiologi • Streptococcus pneumonia,
• Methicillin-sensitive Staphyloccous
aureus

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Kieninger & Lipsett, 2009
Patogenesis HAP

Alteration in
Poor nutrition patients’ immune
response

Impaired Aspiration of
mucocilliary oropharyngeal
clearance of the secretion (colonized
respiratory tract by enteric Gram
negative pathogens)

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Kieninger & Lipsett, 2009
Ventilator Acquired Pneumonia (VAP)

• pneumonia yang terjadi >

48 jam dari pemberian
Definisi ventilasi mekanik, tidak
lebih dari 72 jam dari awal
pemberian ventilasi

• 3% per hari dalam 5 hari

pertama ventilasi mekanik
Insidens • 2% per hari (hari ke 6-10)
• 1% per hari (ventilasi
mekanik > 10 hari)
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Risk factor

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Miller, 2018
 Diagnosis VAP - CPIS

A CPIS score of 6 or higher out of a maximum score of 12 indicates a likely diagnosis of VAP

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Miller, 2018
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SOP-ICMR-AMR, 2015
 Diagnosis Laboratorium

Kultur
(darah / Molekular (PCR) Antigen test
sputum)

Serologi DFA /IFA Kultur Virus

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Metode Diagnosis Berdasarkan Patogen

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Tores et al., 2016
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Tores et al., 2016
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Tores et al., 2016
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Tores et al., 2016
 The Challenge of Syndromic Disease

Age
Sex Travel
history
Bacteria,
virus,
yeast or
paracyte Immune
? status
Animal (pet)
exposure
Vaccinatio
n history

Past
Medical
History
Risk of Patient
exposure location
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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 FilmArray
One System & One Pouch for One Test

+
Conventional

2nd
Sample 1st Stage
Stage
Extraction &
MultiplexPCR
Preparation PCR

• Including : extraction reagents, control RNA & DNA, and mastermix

 The FilmArray Pouch

Reagent
Storage

Chemical
Circuit
Board

Sample First Second stage

Extraction & stage PCR
purification Multiplex
PCR
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Internal Control : mRNA Schizosacccharomyces pombe
 FilmArray

Workflow: Simple, Easy, Fast

 FLM1-MKT-XXXX
Sample Requirements
200 mL of:

Sputum -OR- BAL

(Bronchoalveolar lavage)
Non-invasive sample Invasive sample
collection like: collection like:
• Induced sputum • BAL
• Expectorated sputum • Mini-BAL
• Endotracheal aspirates

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
 FLM1-MKT-XXXX
Sample Requirements

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)
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 meningitidis 34
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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 FLM1-MKT-XXXX
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

Bacterium1

QSM

Bacterium2
 FLM1-MKT-XXXX
Semi-Quantitative
• 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”.

105.3
102.1

107.7

103.5 104.5 105.5 106.5

Bin Result
ND 10^4 10^5 10^6 ≥10^7
copies/mL copies/mL copies/mL copies/mL
 FLM1-MKT-XXXX
PNEUMONIA Panel (33)
Sample Requirements: Sputum (including ETA) and BAL (including mini-BAL)

Bacteria (15) Atypical Bacteria Antimicrobial

Semi-Quantitative Chlamydia Pneumoniae Resistance Gene
Acinetobacter calcoaceticus Legionella Pneumoniaphila METHICILLIN RESISTANCE
baumannii complex Mycoplasma Pneumoniae mec A/C and MREJ
Enterobacter cloacae complex
Escherichia coli CARBAPENEMASES
Haemophilus influenzae Viruses (8) KPC
Klebsiella aerogenes Adenovirus NDM
Klebsiella oxytoca Coronavirus Oxa-48-like
Klebsiella Pneumoniae group Human Rhinovirus/Enterovirus VIM
Moraxella catarrhalis Human MetaPneumoniavirus IMP
Proteus spp. Influenza A
Pseudomonas aeruginosa Influenza B ESBL
Serratia marcescens Parainfluenza Virus CTX-M
Staphylococcus aureus Respiratory Syncytial Virus
Streptococcus agalactiae MERS-CoV (Pneumoniaplus Only)*
Streptococcus Pneumoniae
Streptococcus pyogenes *Only available outside the U.S.
 FLM1-MKT-XXXX
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
 FLM1-MKT-XXXX
Panel Report

• Result Summary (lists all

targets that were tested)
 FLM1-MKT-XXXX
CAP HAP

Struthers, 2005
 Case 1 :
Day 1 Day 4 Day 5
• Female (18 bln) • Pasien masuk • Dikarenakan
• January IGD, batuk semakin
• Fever 37,9 ◦C • Tes rapid RSV parahnya kondisi
ulang masih pasien , Abx
• History infeksi diganti ke
telinga, asma negative
• Chest cefotaxime dan
ringan, batuk, dirawat ke ICU
hilang nafsu Radiography
makan, menunjukan
• Rapid test RSV indikasi ringan • Film Array RP
dan Flu A/B gangguan digunakan, 1 jam
negative pulmonary proses dan
• Didiagnosa : mild • Diberikan memberikan
Ampicillin dan di hasil : M.
bronchiolitis pneumoniae
obervasi
• Pasien dikirim
pulang dan
minum • Antibiotik diganti
acetaminophen ke Macrolide
RESEARCH ON SYNDROMIC
TESTING
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) 44
 FLM1-MKT-XXXX
FilmArray RP and multiple PCR had significantly high sensitivities and specificities for
the detection of respiratory viruses
 FLM1-MKT-XXXX
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
 FLM1-MKT-XXXX
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.
 FLM1-MKT-XXXX
 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
FLM1-MKT-XXXX
 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 50
 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
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2 minutes hands on time FAST : Extraction, PCR & detection in
45 minutes - 1 hour