The document summarizes a study on the etiologies of community-acquired pneumonia (CAP) among refugees and host populations in Lebanon. Some key findings: - Viruses accounted for 81% of lower respiratory tract infections, with influenza alone causing 30%. Vaccine-preventable pathogens contributed to 43% of cases. - Etiologies varied between seasons and by age, suggesting treatment guidelines may need to change. It was difficult to determine the likelihood of viral vs. bacterial infections without point-of-care testing. - Streptococcus pneumoniae accounted for only 6% of cases, compared to higher rates in other studies. Pneumococcal vaccination started in 2016 and covered 44% of S

2. Results of the Pneumonias' Etiology
Among Refugees and Lebanese
population (PEARL) study
Thomas KESTEMAN, MD MPH PhD - Fondation Mérieux
Pneumonia Innovations Network webinar
Save The Children - Sep 09, 2019
thomas.kesteman@ext.fondation-merieux.org

3. • Lebanon: 1.5 M Syrian refugees
• Respiratory tract infection = major morbidity
among refugees, including Community-Acquired
Pneumonia (CAP)
• Treatment and guidelines blinded to the
pathogenic agents
• Objective:
o To estimate the proportion of CAP attributable to
specific viral and bacterial pathogens in a population of
refugees
Background
OPD in Bekaa valley, 2015
Source: MSF
56%
20%
8%
4%
5%
7%
RTI
Other
Other gastrointestinal
Watery diarrhoea
Skin
Musculo-skeletal

4. • Multi-centric prospective case-control study
• Inclusion over 2 winters: Nov 2016 – Mar 2018
• 2 regions, 4 Primary Health Care centres ():
o Bekaa (3 PHC)
o Tripoli (1 PHC)
o + 3 labs ()
• Case definition : clinically diagnosed CAP consulting at
PHC, all ages
o “Clinically diagnosed CAP” = lower respiratory tract infections (LRTI)
o Cough/dyspnea and tachypnea and onset <14 days (exclusion:
asthma, hospital-acquired infection, immunocompromised)
• Samples: nasopharyngeal swab, sputum, blood, urine
Study design

5. • 1372 individuals in the final dataset
686 cases, 686 controls
• Age variable by site (MDs)
o Mostly (62.1%) adults
o Under-fives: 13.2%
• 94% Syrian
• Mostly mild/moderate cases
o 1% hospitalized, 7% SaO2 <95%, 9% ≥1 WHO criteria
o (Very) severe cases skipped the inclusion process
• No significant association with tested variables:
o Sex (OR Male 0.98 [0.79 - 1.21]), socioeconomic quintile (OR poorest 1.14 [0.82 -
1.59]), housing type (OR living in tent 0.91 [0.67 - 1.23]), domestic use of
combustibles creating smoke (OR 1.04 [0.79 - 1.36]), increased risk in
“intermediate” smoking categories but not in smokers (e.g. OR heavy
smoker 1.07 [0.78 - 1.48])
o LBW or prematurity in infants (N=19): OR 4.50 [0.45 - 103.84]
Population & risk factors

6. • Viruses account for 81% of LRTI
o Influenza alone: 30%
o Top 5 are viruses
o Viruses often considered as benign
(Rhinovirus, Coronavirus) have an important
share
• Vaccine-preventable pathogens: 43%
• S. pneumoniae accounts for 6% “only”
and non-significant
o GABRIEL: 42%
o PERCH: 6%
o EPIC adults: 5%
• Atypical bacteria account for 9%
Population Attributable Fractions (PAF)

7. • Incidence 2016-2017 > 2017-2018
• Pathogens whose PAF 
o Influenza: 35  10%
o …
• Pathogens whose PAF 
o Parainfluenza: 3  20%
o …
PAF by year

8. • More important in children
o RSV: 7  30%
o Parainfluenza: 0  19%
o Adenovirus: 3  11%
• More important in adults
o Influenza: 4  36%
o Coronavirus: : [0]  17%
• Unclear :
o Str. pneumoniae
o Haemophilus influenzae b
PAF by age

9. • PCV13 vaccination started in
2016 for both refugees and
Lebanese populations
• Data from 286 individuals
• Most frequent serotype = 10F (not
in PCV13, but not in IPD* either)
• 6/10 most frequent serotypes
found in nasopharynx are
contained in the PCV13
• PCV13 covers 44% of serotypes
found
Serotypes Streptococcus pneumoniae
Serotype_2
Serotype_22F
Serotype_5
Serotype_1
Serotype_21
Serotype_8
Serotype_9V
Serotype_12F
Serotype_35B
Serotype_9N_L
Serotype_15A
Serotype_17F
Serotype_31
Serotype_38
Serotype_7F
Serotype_13
Serotype_4
Serotype_11A
Serotype_16F
Serotype_35F
Serotype_15B_C
Serotype_3
Serotype_33F
Serotype_20
Serotype_23A
Serotype_34
Serotype_6C
Serotype_10A
Serotype_19A
Serotype_7C
Serotype_Sg24
Serotype_Sg18
Serotype_14
Untypable
Serotype_19F
Serotype_23F
Serotype_6AB
Serotype_10F
0.0 2.5 5.0 7.5 10.0 12.5
% samples with S. pneumoniae
In PCV13
Not in PCV13
Untypable
* Hanna-Wakim et al., 2012

10. • Antibiotic consumption before visit at the center
o Self-reported antibiotic intake: 2%
o Presence of antibiotic in urine: 21%
o Higher in cases (32%) than controls (10%), increases with age
• Antibiotic treatment of LRTI
o Almost all cases have been prescribed antibiotics
 Only 2 cases (0.3%) sent home without antibiotics
o Mostly monotherapy (97%)
o Most frequent: Betalactams 72% > Macrolides 16% > FQ 14%
o Cases with atypical bacteria: only 10% had received macrolide (or tetracycline)
Antibiotics

11. • Viruses account for the major part (PEARL: 81%) of LRTI
o Influenza, RSV, Rhinovirus, Parainfluenza, Coronavirus
o The rest is half S. pneumoniae and H. influenzae (10%), half atypical bacteria (9%)
• Vaccine-preventable pathogens contribute to a great deal (43%) of LRTI
• Antibiotic treatment poorly addresses etiologic agents (atypical bacteria!)
• Etiologies differ considerably between seasons, but also age and severity
 change guidelines?
o How to deal with variability? Without PoC test, how to guess the likelihood to face
viral/atypical/bacterial LRTI?
o What is the cutoff below which one can safely withhold antibiotics? Probably well below
10%!
• No preventable risk factor of LRTI was identified
Conclusions

12. • Amel association
o Kamel MOHANNA
o Ali GHASSANI
o Mohamad AL ZAYED
o Valentina ABDEL KHELEK
o Ghadban AL GHADBAN
o Hussein MADI
o Zeinab FARHAT
o Haneen SATY
o Souraya NASSER
o Nahed ELBOOSH
o Maryam MENHEM
o Sahar SATY
o Virginie LEFEVRE
o Touffic HAIDAR
o Ihsan HAMMOUD
o Raghida YOUNES
o All other doctors: Rayan MADI, Ali
RIDA, Najib AL KHESHEN, Ali ALHAJJ,
Ghaleb AL KADI, Mark JABBOUR,
Mohammad MAHFOUZ, Mohammad
MOUHIEDDINE
• Bioteck
o Pierre SALLOUM
o Rolland SALLOUM
‫ا‬ً‫,شكر‬ Merci, Thanks … to the PEARL consortium
• Lebanese University, Tripoli
o Fawaz EL OMAR
o Mohamad KHALIL
o Monzer HAMZE
o Marwan OSMAN
o Majdeddine MOUZAWAK
o Assma ALLOUCH
o Taha ABDOU
o May IBRAHIM
• Nationwide Children’s Hospital
o Octavio RAMILO
o Samantha SHARPE
o Asunción MEJIAS
• Université Saint-Joseph
o Marianne ABI FADEL
o Dolla KARAM-SARKIS
o Crystel HAJJAR
o Danielle CHAAYA
o Tarek ITANI
o Andre ADAIME
o May MALLAH
o Rita BEYROUTHI
• External experts
o Rana HAJJEH, WHO EMRO
o Abdullah BROOKS, JHU/ICDDR,B
• Université de Lyon
o Philippe VANHEMS
o Thomas BENET
o Marie-Paule GUSTIN
• Bill & Melinda Gates
Foundation
o Gail RODGERS
o Hani KIM
o Keith KLUGMAN
• Biofire Diagnostics
o Rachel JONES
• Fondation Mérieux
o Hubert ENDTZ
o Thomas KESTEMAN
o Josette NAJJAR
o Valentina PICOT
o Cynthia BAKKALIAN
o Florence PRADEL
o Melina MESSAOUDI
o Marie MOROSO
o Leticia LOBO-LUPPI
o Yasmine AMRAOUI
o Samar HOUJEYRI
o Louise GRESHAM
• Bioteck (cont’d)
o Stéphanie SALLOUM
o Khaled S. AOUN
o Kamile, Shafiq BASSIL
o BioFire trainers
• Chtoura hospital
o Mohamad MESELMANI
o Zahraa ALNAJJAR
o Zeina JBARA
o All the lab techs
o Lama SEBLINI
o Slaiman SAID
o Khouloud MRAD
• El Bashaer Association
o Hicham Gh. SOULAIMAN
o Ahmad OBEID
o Hossam AL NAZER
o Ahmad AL HALLAK
o Mohammad ALABRASH
o Khaled HALLAK
o Anas ALTABAA
o Safa BUSH
o All other doctors: Rani ALALWI,
Ibrahim HASNA, Majed KHALIL,
Mohammad ABDEL RAZEK, Mona
ZEITOUN, Mountaser KABAKIBO

13. … and thank you!
PEARL study group

14. MSF Access Campaign
Protecting children caught in crisis from
pneumonia: MSF’s experience securing a more
affordable PCV for its medical operations.
Pneumonia Innovations Network
September 9, 2019
“What we as a civil society movement demand is change, not charity.“
-- Dr. James Orbinski, President of MSF International Council, acceptance speech for
Nobel Peace Prize (1999)

15. https://www.youtube.com/watch?v=Wcvb0Ip-Aac&feature=youtu.be

16. MSF need for PCV with limited access
• 2008: MSF unsuccessfully trying to purchase Wyeth’s PCV7
• 2009/10: GSK’s PCV10 approved (‘09); Pfizer’s PCV13 approved (‘10)
• 2010 Pfizer & GSK commit to Gavi Advance Market Commitment (AMC) for PCVs.
• 2010-2011: MSF can purchase GSK’s PCV10 for a limited time. Used in Dadaab
Refugee Camp; Blue House Project, Kenya (target pop: <1s & HIV+ children ages 1-
5yrs)
• 2013: MSF purchases GSK’s PCV10 after lengthy negotiations (since 2012) through
UNICEF SD for S Sudan. Due to price ($7/dose) MSF scales back target age from
5yrs -> 2yrs.
• 2014: MSF agrees to accept time-limited, multi-year PCV donations from both
Pfizer and GSK in a departure from institutional policy on medical donations.
Companies commit to longer-term solution by conclusion of donation period.
• 2015: MSF launches A Fair Shot global campaign targeting Pfizer and GSK to lower
PCV price to $5/child (for all three doses) for developing countries & humanitarian
orgs
• 2016 (September): GSK drops price for humanitarian orgs to lowest global price
• 2016 (October): MSF publicly rejects Pfizer offer of significant donation volumes
• 2016 (November): Pfizer drops price for humanitarian orgs to lowest global price
• 2017: Humanitarian Mechanism for Accessing Affordable and Timely Supply
of Vaccines for Use in Hum Emer launched (WHO, MSF, Save the Children, UNICEF)

18. 18
WHA RESOLUTION ON VACCINE PRICE TRANSPARENCY IN 2015
416,258 PETITION SIGNATORIES FROM 170 COUNTRIES
MEETINGS WITH PFIZER AND GSK CEOs
QUESTIONS AT PFIZER AND GSK ANNUAL SHAREHOLDER MEETINGS
WORKSHOPS IN JORDAN TO BUILD CAPACITIES
OPPOSITION TO PFIZER PATENT APPLICATION IN INDIA
MOBILIZATION OF FILIPINO DIASPORA
PRIZER PUBLISHED PRICING STRATEGY
UNPRECEDENTED PRESS COVERAGE OF VACCINE PRICE
HUNDREDS OF CALLS MADE TO PFIZER OFFICES
VACCINATION CAMPAIGN OF REFUGEE CHILDREN IN GREECE
OUTREACH TO PFIZER EMPLOYEES VIA POSTCARD CAMPAIGN
Select activities and impact

20. September 19, 2016:
GSK OFFERS
LOWEST PRICE
TO MSF & ALL
HUMANITARIAN ORGANISATIONS!
October 10, 2016:
MSF TURNS DOWN PFIZER DONATION OF 1 MILLION PCV
DOSES
November 11, 2016:
PFIZER OFFERS LOWEST PRICE TO MSF & ALL
HUMANITARIAN ORGANISATIONS!

21. A FAIR SHOT
CAMPAIGN
Bringing down barriers to access lower
price of new vaccines - Amman 21-25
August 2016
21
MSF’s PCV Use: 2008 – May 2019
1354
116
446
7026
1
24043
164783
225504
280684
388,002
50400
91200
0 50000 100000 150000 200000 250000 300000 350000 400000 450000
2008
2009
2010
2011
2012
2013
2014
2015
2016
2017
2018
2019 MAY
MSF use of PCV 2008 - May 2019
Note:
• 2008-2014: MSF’s purchase of PCV required price negotiation each time
• 2014-2016: PCV donation from Pfizer and GSK
• 2017-2019: Humanitarian Mechanism (HM) established in May 2017

22. A FAIR SHOT
CAMPAIGN
Bringing down barriers to access lower
price of new vaccines - Amman 21-25
August 2016
22
MSF’s Use of HM by Country:
2017 – May 2019
64,800
28,800
14,400
14,400
116,000
250,802
40,400
0 50,000 100,000 150,000 200,000 250,000 300,000
CAR
DRC
GREECE
NIGER
NIGERIA
SYRIA
S.SUDAN
Use of HM by Country 2017-May 2019
Total # PCV doses requested via HM, 2017 - May 2019: 529,202
Total # of people targeted with the HM, 2017- May 2019: 537,992
Syria accounts for 47% of all MSF’s PCV (PCV10) use via HM (2017-May ‘18)

23. Questions? Thank you!

24. Feasibility of training MSF Clinical Officers in
Point-of-Care Ultrasound (POCUS) for pediatric
respiratory diseases in Aweil, South Sudan
Adi Nadimpalli, Jim Tsung, Ramon Sanchez, Sachita Shah, Evgenia Zelikova,
Lisa Umphrey, Northan Hurtado, Alan Gonzalez, Carrie Teicher

25. Aweil, South Sudan

26. Introduction – what is POCUS?
The use of portable ultrasounds
by non-expert clinicians
using simple pattern-recognition
to answer clinical questions
at the patient’s bedside
to make a decision in real time.

27. Objective – proof-of-concept
• Evaluation of training exercise: can Clinical Officers (CO)
efficiently learn a lung ultrasound algorithm to diagnose
respiratory pathologies?
• Lower respiratory tract infections are leading cause of mortality
in children < 5 years old worldwide
• Lung ultrasound is moderately complex

28. Lung ultrasound – pattern recognition
LUNG ULTRASOUND DIAGNOSTIC KEY
Diagnostic Impression Ultrasound Findings
Normal Normal pleural sliding. A-line profile
Bronchiolitis or viral pneumonia
Normal pleural sliding, either sub-
pleural consolidations (<0.5cm) and/or
scattered B-profile (<5 of 6 zones)
Consolidation/Pneumonia (possibly
bacterial)
Normal or absent pleural sliding, > 1
consolidation of at least 0.5cm or
hepatization (solid appearing lung)
Interstitial syndrome
Normal sliding, diffuse B-lines
bilaterally
Pleural effusion
Clear area of liquid between parietal
and visceral pleura

29. Methodology
• 6 COs recruited for 12-hour field-
based training
• Each performed 60 lung ultrasounds
• Submit both images and interpretation
• Evaluation by 2 expert graders, with
tiebreaker
Photo: Adi Nadimpalli

30. Results (n= 355 exams)
• Images acceptable – 99.1%
• CO interpretations appropriate – 86.0%
• Inter-observer agreement (κ) between
COs and expert:
– Lung consolidation 0.73 (0.63–0.82)
– Viral LRTI/bronchiolitis 0.81 (0.74–0.87).

31. Limitations
• Evaluating training only, not diseases
• No comparison to chest x-ray
• 24% discordance rate between
expert 1 and 2
• Average time/exam 15 minutes
Photo: Adi Nadimpalli

32. Study Conclusions
• COs in South Sudan can
effectively learn a lung
ultrasound algorithm to
diagnose respiratory pathologies
• Additional work needs to be
done to standardize definitions
and decrease time/exam
Photo: Adi Nadimpalli

33. Next steps
• Add Cardiac component to make
cardio-pulmonary ultrasound for
respiratory distress
– Consolidations, pulmonary edema,
pleural effusions, pericardial
effusions, cardiomyopathies, mitral
valve diseases
• Consider Tuberculosis and HIV
Opportunistic Illnesses
Photo: Adi Nadimpalli

34. Next steps
• Feasibility of outpatient respiratory
diagnosis depends on time
• Artificial intelligence can help reduce
time
– Ethical questions on resource extraction
– Machine learning needs patient data
– Mitigations necessary before deployment
Photo: Adi Nadimpalli

35. Acknowledgements
• Justine Okello Ongom, Anyama
Agasi Legge, John Kuir Nyinguut,
Santino Garang Kuach, Moses
Mabior Madut, Masereka Ronald
• Aweil State Ministry of Health
• South Sudan Ministry of Health
We confirm that we have obtained permission to use images from the participants/patients/individuals included in this presentation
Photo: Adi Nadimpalli