June 2018 Member Newsletter


A Comment from the Coordinator, Announcements, Deep Breaths blog post by Dr. Debby Bogaert, Upcoming events, and PIN Member and Partner Updates for June 2018.



A Comment from the Coordinator

A special thank you to Drs. Jeremy Keenan and Charles Knirsch for their Pneumonia Innovations Network webinar presentations for the MORDOR webinar. The next PIN webinar is being planned for late June 2018. Keep your eyes open for an upcoming email with more info.




CALL FOR MEMBER UPDATES: Do you have news, updates/ announcements or publications that you would like to share with the Pneumonia Innovations Network? Send them to Mari Couasnon at This email address is being protected from spambots. You need JavaScript enabled to view it. for a PIN newsletter feature!



Deep Breaths: Blogs from Network Members 

Development of low-cost microbiome-based diagnostic tools for respiratory infections may be key to future antimicrobial stewardship

By Dr. Debby Bogaert

In low and middle-income countries (LMICs), major efforts have been devoted to improving the availability of vaccines, antibiotics and standardized treatment protocols, to reduce the incidence of respiratory infections and the resulting fatalities. However, despite these efforts we can still regard pneumonia as the biggest killer of children on a global scale. Meanwhile, due to the chronic overuse of antimicrobials globally, the threat of antibiotic resistance has emerged among common disease-causing bugs. This disproportionally affects LMICs, where the burden of these infections is greatest. Greater efforts are required to understand the exact mechanisms and drivers of disease severity leading to childhood illness, since this could directly help to design new preventive strategies and guide effective antibiotic treatment.


In this context, I would like to highlight the new emerging science of the human microbiome. Trillions of bacteria, fungi, and viruses inhabit the human body, and together provide a multitude of beneficial functions for its host. These are all functions that human cells cannot provide for themselves, such as the digestion of food, keeping potential harmful pathogens at bay, and teaching the immune system what is friend or foe. Unfortunately, many beneficial microbes are highly susceptible to commonly used broad-spectrum antibiotics. As a result, treatment for infectious diseases, such as pneumonia, is not only driving antimicrobial resistance, but also depriving the host of beneficial microbes, with knock on effects on the host’s and microbiome’s defense mechanisms.


This new research field is rapidly unraveling the role of the human microbiome in preventing pneumonia in children. Recent studies have suggested respiratory infections are merely a result of interplay between viruses and bacteria, or even more complex mixed infections, rather than caused by a single organism. They also identified potential beneficial microbes that may protect infants and young children against viral and bacterial acquisition and infection, and may even alter severity of disease. Importantly, those bacteria seem to be universally present, depending on natural resources such as the mothers gut and vaginal microbes, and breastmilk components, while varying less with genetic background and socio-economic status. Although this is promising, we must move further to try to understand exactly what role these microbes play in the protection against infections.


Interestingly, however, since microbiome profiling provides in-depth detail of any types of microbes and their relative abundance at time of infection, it could potentially be used as diagnostic tool as well. Where conventional microbial techniques often fail to identify the causative pathogen, due to lack of specificity and their targeted approach, microbiome profiling could provide the level of detail and certainty required. Using microbiome-based diagnostics, including detection of resistance genes, may thereby improve targeted therapy and reduce blind treatment with broad-spectrum antibiotics.


Real-time sequencing, such as the MinION Nanopore sequencing technology (Oxford Nanopore), is the newest platform available for this type of diagnostics. In principle, the technique is fast, simple and does not require sophisticated laboratory equipment allowing for remote testing. Single specimen sequencing, combined with a rapid turnaround time, could affect current practice dramatically, bringing antimicrobial stewardship to a whole new level. Targeted therapy, in combination with microbiome-centered antibiotic stewardship, would also help to avoid damage to the diverse range of beneficial microbes and reduce the risk of short- and long-term health problems related to antimicrobial use. Several institutes in the UK and the USA are already studying the applications of this technique for improved diagnostics and treatment in severe adult community-acquired pneumonia and ventilator-associated pneumonia. However, there are few initiatives visible on the pediatric side of the spectrum, let alone in LMICs. This might be a consequence of several ‘pediatric’ hurdles, such as the heterogeneity of disease and the most likely mixed origin of infections. Also, since far fewer children than adults die of complicated pneumonia in western countries, attempting to prove cost-effectiveness of the technology when applied to pediatric pneumonia might be problematic. However, the former does not apply to pediatric pneumonia in LMIC, where this disease fatally affects an inordinate number of children, and where antimicrobial resistance disproportionally affects treatment failure. It therefore deserves investments in testing and improving low-cost diagnostic sequence technology for pediatric pneumonia in LMICs as well; for too long these children came last in benefiting from medical innovations, let them now come first.


Professor Debby Bogaert is the Chair of Paediatric Medicine at the Centre for Inflammation Research, University of Edinburgh, and works as a paediatric infectious diseases specialist at the Royal Hospital for Sick Children Edinburgh. She also leads a research group at the University Medical Center Utrecht, Netherlands. Her research groups have a major focus on investigating the physiology and pathophysiology of respiratory infections and inflammation from an ecological perspective, with the ultimate goal to design new or improved treatment and preventive measures for respiratory infections in susceptible populations. To this purpose, the teams use a fully translational approach, combining epidemiological, molecular microbiological, immunological and systems biology approaches to answer their research questions. 



Upcoming Events

36th Annual Meeting of the European Society for Paediatric Infectious Diseases (ESPID).

Malmö, Sweden. May 28 – June 2, 2018.

Building on the success and innovation of previous meetings, ESPID 2018 will feature a wide range of sessions and learning opportunities showcasing the latest research and developments in the field hosted by leading international experts.

Register to attend here.


9th IPCRG World Conference & 1st Ibero-American Primary Care Respiratory Meeting

Porto, Portugal. May 31 – June 2, 2018.

A varied and inspiring programme that addresses many of the issues to improving the care of people seen in primary care with respiratory conditions. IPCRG 2018 offers a comprehensive scientific programme as well as important networking opportunities allowing delegates to come together with colleagues to discuss respiratory care and new developments.

Register to attend here.



Pneumonia Innovations Network Member and Partner Updates

Commentary by Ammara Mushtaq: Investigating pneumonia – a neglected tragedy

On April 19, 2018, the University of Southampton launched their Sizing Up Pneumonia Research report at the Commonwealth Heads of Government Meeting in London, UK. The report expands on research funding for therapeutics, vaccines, the paediatric population, antimicrobial resistance, and research in high-risk areas. Investigators uncovered some striking findings:

"13% of deaths in children worldwide are caused by pneumonia. Despite this figure, pneumonia received only 3% of the global US$100 billion funding for infection-related research. Pneumonia received lower funding per death than HIV, tuberculosis, malaria, and enteric diseases. For example, in 2011 only 2% of development assistance for health funding was allocated to pneumonia despite the 13% mortality in children due to pneumonia worldwide."

Full of key insights from leaders in the field, this commentary by Ammara Mushtaq places a spotlight on this issue and forces us to see that something isn't adding up. The commentary also addresses other factors contributing to the slow pace of decreasing pneumonia mortality in children siting geographical disparity in funding, the need for capacity building and educational initiatives, and poor health access as big contributors.

Read the full commentary here.


EssentialTech releases new GlobalO2 video

EssentialTech recently released their new video, “GlobalO2: Universal Access to Essential Oxygen Therapy.” Project GlobalO2 aims to provide sustainable access to oxygen with a goal to design a low-cost, robust oxygen concentrator. Watch the video and share within your networks.


Pneumonia features strongly in new WHO Quality of Healthcare Standards for Children & Adolescents

A sign of progress: child pneumonia prevention, diagnosis and treatment are strong features in the new WHO standards for quality healthcare for children and adolescents.

From Quality statement 1.3: “All children with cough or difficult breathing are correctly assessed, classified, and investigated and receive appropriate care and/ or antibiotics for pneumonia according to WHO guidelines.”

The new standards require health facilities to have a written, up-to-date, evidence-based clinical protocol for identifying and managing children with cough or difficult breathing, basic laboratory and diagnostic tests (e.g. pulse oximetry, full blood count, culture, ultrasound and chest X-ray), and adequate supplies of antibiotics (first- and second-line) for treatment of severe pneumonia. Inhalation bronchodilators, pulse oximeters, and a reliable and functioning oxygen supply should be available at all times. Health facility clinical staff who care for children must receive training and regular refresher sessions in assessing and managing children with cough or wheeze at least once every 12 months.

See the new WHO standards here.


Every Breath Counts supports identification of critical gaps in child pneumonia and implements strategies to close them

In a letter to Commonwealth Heads of Government Meeting leaders, Leith Greenslade and the Every Breath Counts Coalition call for countries to recognize just how vulnerable their children are and to make faster progress in closing gaps to prevent child pneumonia deaths:

“If more than 5% of your children are wasted, if less than 50% are exclusively breastfed, and if less than 80% are fully vaccinated with both the Hib and pneumococcal (PCV) vaccines, your children are vulnerable. 

If less than 70% of parents in your country seek care when a child has pneumonia symptoms, and if your healthcare workers don’t routinely use diagnostic tools like pulse oximeters and respiratory rate timers, your children are vulnerable.

If your health workers don’t rationally dispense amoxicillin in child friendly form (i.e. dispersible tablets) and your hospitals don't provide oxygen safely and reliably, your children are vulnerable.

And if you don't know how your country is performing on these measures because there are so many data gaps, your children are vulnerable.”

Read this powerful letter, complete with country data tables here.




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Monday, 17 February 2020