Our sequencing endeavors continue as the NextSeq 2000 arrives!

23 December, 2020

In Bangladesh. With Bangladesh. For Bangladesh.

Map screenshot of empowering medical detectives on the frontlines

In 2018, we got a small grant from the Bill and Melinda Gates Foundation to buy our first next-generation sequencing machine – it was a small machine called the iSeq100. It had just been released, and we got the first one in Bangladesh. Using that machine we sequenced the first Dengue virus in Bangladesh. We also sequenced influenza virus, and respiratory syncytial virus, in addition to various bacteria and fungi that cause severe infections in children. But the iSeq100 only came to life when we started sequencing SARS-CoV2 in May 2020…

We were the first, but we were not the last. Our usage of the iSeq100 was so successful that the Gates Foundation, in collaboration with the Chan Zuckerberg Biohub, decided to fund 10 other countries like us to buy their own iSeq100s!

Did you know Chikungunya caused a meningitis outbreak in Bangladesh in 2017?

The success of this project was followed up by a grant to attain our own sequencer (iSeq) to do our own sequencing in our brand new laboratory, at real time.

CHRF's new sequencing lab

We are all very proud of Shahidul Islam, an old and trusted member of CHRF, who just started his PhD in collaboration with CHRF and University of Edinburgh. His thesis focuses on long-term impact of respiratory syncytial virus (RSV) infections in children – and that brings us to arguably the most exciting new of the year – the ANISA paper in the Lancet – which showed that RSV is the primary cause of infection and illness in newborns.

If you want to know more – read “Bangladesh leads the world one step closer to understanding causes of deaths in newborns” and here is the original paper. With 84,971 pregnant mothers and 63,114 babies, ANISA was the first of its kind- it showed that a bacterium called Ureaplasma is the leading cause of death due to infection in babies, and that RSV causes the greatest number of illnesses. The study also talks about the best choice of antibiotics in newborns; only small proportion of the suspected infections appear to be infections at all!

Our other PhD student, Tanmoy, is gearing up to be Dr. Tanmoy! He has already published his first PhD paper in mBio, where the authors analyzed the genomes of >400 Salmonella Typhi strains isolated by our group.

Zabed and Naziat, in the midst of their crazy lab work, have been squeezing in trips to Lucknow and Pune working with our collaborators there and spreading the expertise of pneumococcal detection and serotyping. Want to learn how to lean on a microscope and serotype pneumococcus perfectly for hours using capsular swelling reactions? Naziat is your friend. Naziat also published her first first author paper (causes of otitis media in Bangladeshi children) this year!

Popy and Hasan went to St. Paul, Minnesota, to brush up their qPCR techniques for bacterial meningitis identification, guided by the CDC, USA. Popy went back with Hafiz soon after, this time to Atlanta, Georgia, to polish their microbiology techniques on pathogen identification. This was hosted by the CDC and Association of Public Health Labs, USA.

Senjuti was also in Atlanta, however at a different time, to present CHRF’s work on meningitis at the American Society of Microbiology as a Gates Fellow from Low- and Middle Income Countries.

Group Photo at Georgia Public Health Lab

In addition to going places, CHRF members also “brought places” to Dhaka by organizing the second global meeting of RESPIRE, NIHR Global Health Research Unit on Respiratory Health at The University of Edinburgh, where the experts representing seven countries in Europe, Australia, and Asia shared their ideas to tackle respiratory illnesses in the south and south-east Asian countries. Additionally, a policy dialog on respiratory health was arranged to discuss the current respiratory health problems in Bangladesh.

group photo from Global Meeting of RESPIRE in Dhaka

We also took part in the world pneumonia day in Dhaka and the rally. Dr. Samir gave an inspirational key note speech to remember.

CHRF in World Pneumonia Day rally in Dhaka

Looking forward – in 2018 CHRF geared up to start two big studies that will look at the impact of Rotaviral diarrhea and RSV infections on the health system of Bangladesh. These studies are being coordinated by two amazing coordinators – Zabed and Kawser, who have probably gotten very little sleep in the last few months trying to coordinate a large group of clinicians, microbiologists, technicians and research assistants in both the outpatient and inpatient departments of the Dhaka Shishu Hospital, the largest pediatric hospital of Bangladesh. We also started a project to automatically interpret pediatric chest X-rays in collaboration with RESPIRE and our Canadian collaborator Mark Sun. On top of those, a project on neonatal sepsis treatment guidelines has just started. And these are in addition to our ongoing studies like the invasive bacterial disease surveillance, surveillance of enteric fever in South Asia (SEAP), TuNDRA study on antimicrobial resistance, etc, etc, etc.

And with all of the exciting new projects, CHRF expanded significantly in 2018: 25 people joined our Dhaka Shishu team and 5 joined our Shishu Shasthya team in Dhaka and 7 joined our Kumudini team in Mirzapur.

Also, Hasan – our favourite lab manager of all time – expanded his family this December!

We were sad to see Popy, Raktim and Ishtiaque join our alumni list – but also very proud of their new roles. While Popy is now teaching in Noakhali University, Raktim is doing great work in Cox’s Bazar and Ishtiaque has landed a job at the WHO.

In 2018, together we published 22 (12 from our core research group), papers in fields from rotavirus to typhoid to GBS to pneumococcus. In addition to ANISA, our paper in eLife on Barriers in Bangladesh to conducting research was definitely a highlight, which was also covered by the Johns Hopkins Global Health Magazine, Global Health NOW– “Closing the Scientific Gap.

Sajib published his first paper (on ceftriaxone resistant Salmonella Typhi)  in 2018 too – which was followed by two more papers!

While several members like Maksuda, Jamal, Gautam, Shampa and Nawshad are not specifically mentioned here – we would not have reached Feb 05 of 2019 without the invisible support they provide every day, every minute. We are also very grateful to Shafiq, Afi and Sharif for managing the enormous amount of data we generate every day and keeping us from drowning and to Ruma for keeping us alive. And so thankful to so many others who make CHRF CHRF.

With all the exciting projects in place – we can’t wait for Highlights of 2019. Gotta beat 2018!

We will continue to work for Bangladesh, in Bangladesh, with Bangladesh.

Candid photo of team members from 2018 CHRF movie night 2018

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