Stephanie Lo
@stephlo.bsky.social
Senior Staff Scientist @ Sanger Institute
Senior Lecturer @ University of Bath
Leading the Global Pneumococcal Sequencing project, inform vaccine design and promote equality in science
Senior Lecturer @ University of Bath
Leading the Global Pneumococcal Sequencing project, inform vaccine design and promote equality in science
[🚨New Paper 🚨]SeroBA recognised 102/107 known pneumococcal serotypes and its companion resources webpage SeroBAnk are now published on Microbial Genomics @microbiologysociety.org
www.microbiologyresearch.org/content/jour...
www.microbiologyresearch.org/content/jour...
November 8, 2025 at 1:40 PM
[🚨New Paper 🚨]SeroBA recognised 102/107 known pneumococcal serotypes and its companion resources webpage SeroBAnk are now published on Microbial Genomics @microbiologysociety.org
www.microbiologyresearch.org/content/jour...
www.microbiologyresearch.org/content/jour...
Reposted by Stephanie Lo
🦠🧪🧬 Excited to share that our GPS Pipeline, the portable and scalable genomic pipeline for Streptococcus pneumoniae surveillance, is now published in @natcomms.nature.com
🔗 nature.com/articles/s41... #GPS_project
🔗 nature.com/articles/s41... #GPS_project
GPS Pipeline: portable, scalable genomic pipeline for Streptococcus pneumoniae surveillance from Global Pneumococcal Sequencing Project - Nature Communications
The GPS Pipeline enables accessible and scalable genomic surveillance of Streptococcus pneumoniae. It performs quality control and in silico typing of sequencing reads with high accuracy using a single simple command, without requiring the internet.
nature.com
September 24, 2025 at 1:02 PM
🦠🧪🧬 Excited to share that our GPS Pipeline, the portable and scalable genomic pipeline for Streptococcus pneumoniae surveillance, is now published in @natcomms.nature.com
🔗 nature.com/articles/s41... #GPS_project
🔗 nature.com/articles/s41... #GPS_project
Reposted by Stephanie Lo
It's likely the next pandemic will come from wildlife. But how can we prepare for the next spillover event, if we don't understand the diversity of viruses out there? 🦔🦠
Check out our Genomewatch article, where we discuss using meta-genomics to study viral diversity in wild mammals 🖥️🧬
rdcu.be/eHIBl
Check out our Genomewatch article, where we discuss using meta-genomics to study viral diversity in wild mammals 🖥️🧬
rdcu.be/eHIBl
Zoonotic threats hidden in wildlife
Nature Reviews Microbiology - This Genome Watch article explores how metagenomics can be used to investigate viral diversity and track emerging zoonotic disease threats from wildlife.
urldefense.proofpoint.com
September 23, 2025 at 10:09 AM
It's likely the next pandemic will come from wildlife. But how can we prepare for the next spillover event, if we don't understand the diversity of viruses out there? 🦔🦠
Check out our Genomewatch article, where we discuss using meta-genomics to study viral diversity in wild mammals 🖥️🧬
rdcu.be/eHIBl
Check out our Genomewatch article, where we discuss using meta-genomics to study viral diversity in wild mammals 🖥️🧬
rdcu.be/eHIBl
Reposted by Stephanie Lo
[New pre-print🚨] When a single genotype (pbp) confer resistance (penicillin, amoxicillin, cephalosporins) to multiple antibiotics, how do we make sense of genetic changes and their impact on AMR?
A new concept - AMR cartography is invented.
www.biorxiv.org/content/10.1...
A new concept - AMR cartography is invented.
www.biorxiv.org/content/10.1...
www.biorxiv.org
September 22, 2025 at 11:48 AM
[New pre-print🚨] When a single genotype (pbp) confer resistance (penicillin, amoxicillin, cephalosporins) to multiple antibiotics, how do we make sense of genetic changes and their impact on AMR?
A new concept - AMR cartography is invented.
www.biorxiv.org/content/10.1...
A new concept - AMR cartography is invented.
www.biorxiv.org/content/10.1...
Reposted by Stephanie Lo
[🚨 New paper] The first nationwide, longitudinal WGS analysis of Streptococcus pneumoniae in Taiwan (2006–2022).
1,343 isolates from 27 hospitals, we track serotype, AMR, and genomic lineage before and after PCV13.
#GPS_project #PCV13_impact #Taiwan
www.microbiologyresearch.org/content/jour...
1,343 isolates from 27 hospitals, we track serotype, AMR, and genomic lineage before and after PCV13.
#GPS_project #PCV13_impact #Taiwan
www.microbiologyresearch.org/content/jour...
Genomic analysis of the Streptococcus pneumoniae in Taiwan: a nationwide study from 2006 to 2022
Streptococcus pneumoniae remains a leading respiratory pathogen for children and the elderly. In Taiwan, a national PCV13 catch-up vaccination programme for children began in March 2013. This study in...
www.microbiologyresearch.org
September 18, 2025 at 8:11 AM
[🚨 New paper] The first nationwide, longitudinal WGS analysis of Streptococcus pneumoniae in Taiwan (2006–2022).
1,343 isolates from 27 hospitals, we track serotype, AMR, and genomic lineage before and after PCV13.
#GPS_project #PCV13_impact #Taiwan
www.microbiologyresearch.org/content/jour...
1,343 isolates from 27 hospitals, we track serotype, AMR, and genomic lineage before and after PCV13.
#GPS_project #PCV13_impact #Taiwan
www.microbiologyresearch.org/content/jour...
[New paper alert 🚨 ] What happens when pneumococci 'slip' and 'add' just one extra A in a promoter spacer of a sugar scavenging gene? 🧬
www.cell.com/cell-host-mi...
www.cell.com/cell-host-mi...
Naturally acquired promoter variation influences Streptococcus pneumoniae infection outcomes
Barton et al. identify Streptococcus pneumoniae promoters containing repetitive nucleotide
sequences that promote DNA strand slippage and accumulation of promoter sequence mutations.
This drives popul...
www.cell.com
September 3, 2025 at 10:00 AM
[New paper alert 🚨 ] What happens when pneumococci 'slip' and 'add' just one extra A in a promoter spacer of a sugar scavenging gene? 🧬
www.cell.com/cell-host-mi...
www.cell.com/cell-host-mi...
Our team is hiring an ambitious senior bioinformatician to look into bacterial capsules . This position will closely collaborate with EMBL-EBI
Stephen Bentley, John Lees, Steph Lo
Closing date: 20 July 2025
sanger.wd103.myworkdayjobs.com/en-GB/Wellco...
Stephen Bentley, John Lees, Steph Lo
Closing date: 20 July 2025
sanger.wd103.myworkdayjobs.com/en-GB/Wellco...
Bioinformatician – Bacterial Genomics
Do you want to help us improve human health and understand life on Earth? Make your mark by shaping the future to enable or deliver life-changing science to solve some of humanity’s greatest challenge...
sanger.wd103.myworkdayjobs.com
July 6, 2025 at 1:48 AM
Our team is hiring an ambitious senior bioinformatician to look into bacterial capsules . This position will closely collaborate with EMBL-EBI
Stephen Bentley, John Lees, Steph Lo
Closing date: 20 July 2025
sanger.wd103.myworkdayjobs.com/en-GB/Wellco...
Stephen Bentley, John Lees, Steph Lo
Closing date: 20 July 2025
sanger.wd103.myworkdayjobs.com/en-GB/Wellco...
It’s my great pleasure to present the Global Pneumoocccal Sequencing project at #LISSSD25
I feel humbled to learn more about Group A and Group B streptococci and other species, and meet great minds to discuss science.
#GPS_project
I feel humbled to learn more about Group A and Group B streptococci and other species, and meet great minds to discuss science.
#GPS_project
June 4, 2025 at 4:11 AM
It’s my great pleasure to present the Global Pneumoocccal Sequencing project at #LISSSD25
I feel humbled to learn more about Group A and Group B streptococci and other species, and meet great minds to discuss science.
#GPS_project
I feel humbled to learn more about Group A and Group B streptococci and other species, and meet great minds to discuss science.
#GPS_project
Dr Dorota Jamrozy presents a well-powered GWAS to identify genetic features associated with invasive #GBS disease as compared with carriage at #LISSSD25
Thanks to the >20,000 GBS genomes in the #JUNO_project funded by @gatesfoundation.bsky.social
Thanks to the >20,000 GBS genomes in the #JUNO_project funded by @gatesfoundation.bsky.social
June 4, 2025 at 2:11 AM
Dr Dorota Jamrozy presents a well-powered GWAS to identify genetic features associated with invasive #GBS disease as compared with carriage at #LISSSD25
Thanks to the >20,000 GBS genomes in the #JUNO_project funded by @gatesfoundation.bsky.social
Thanks to the >20,000 GBS genomes in the #JUNO_project funded by @gatesfoundation.bsky.social
Reposted by Stephanie Lo
Each year, over half a million of pneumococcal disease in children were reported in China
Our paper showed
1) 94.3% serotypes covered by PCV13
2) 99.8% isolates resistant to ≥1 antibiotics
Routine PCV in children will ↘️ pneumococcal disease and AMR!
www.microbiologyresearch.org/content/jour...
Our paper showed
1) 94.3% serotypes covered by PCV13
2) 99.8% isolates resistant to ≥1 antibiotics
Routine PCV in children will ↘️ pneumococcal disease and AMR!
www.microbiologyresearch.org/content/jour...
Genomic analysis of invasive and non-invasive disease-causing Streptococcus pneumoniae isolated from children between 2014 and 2023 in Suzhou, China
In 2017, 553,000 clinical cases of Streptococcus pneumoniae in children were reported in China, although the pneumococcal conjugate vaccine (PCV), which targets the pneumococcal capsule, is not includ...
www.microbiologyresearch.org
June 3, 2025 at 12:25 PM
Each year, over half a million of pneumococcal disease in children were reported in China
Our paper showed
1) 94.3% serotypes covered by PCV13
2) 99.8% isolates resistant to ≥1 antibiotics
Routine PCV in children will ↘️ pneumococcal disease and AMR!
www.microbiologyresearch.org/content/jour...
Our paper showed
1) 94.3% serotypes covered by PCV13
2) 99.8% isolates resistant to ≥1 antibiotics
Routine PCV in children will ↘️ pneumococcal disease and AMR!
www.microbiologyresearch.org/content/jour...
@sophiebelman.bsky.social carried out this spatiotemporal analysis to quantify how fast a pneumococcal lineage can travel across the country, and this work was published on pmc.ncbi.nlm.nih.gov/articles/PMC...
#LISSSD25
#LISSSD25
June 2, 2025 at 1:50 AM
@sophiebelman.bsky.social carried out this spatiotemporal analysis to quantify how fast a pneumococcal lineage can travel across the country, and this work was published on pmc.ncbi.nlm.nih.gov/articles/PMC...
#LISSSD25
#LISSSD25
Reposted by Stephanie Lo
@stephlo.bsky.social & global partners describe the extent (worldwide) of intra-country spread (<4 years) of pneumococcus through in silico genotyping, then outlines genotypic methods of predicting vaccine escape (capsules 33F -> 33E) using this in silico data. #LISSSD25 #idsky
June 2, 2025 at 12:45 AM
@stephlo.bsky.social & global partners describe the extent (worldwide) of intra-country spread (<4 years) of pneumococcus through in silico genotyping, then outlines genotypic methods of predicting vaccine escape (capsules 33F -> 33E) using this in silico data. #LISSSD25 #idsky
Good morning Brisbane! What a nice view to prepare my very first talk at #LISSSD25 !
Looking forward to meeting people at the conference.
#GPS_project #pneumococci #Genomics
Looking forward to meeting people at the conference.
#GPS_project #pneumococci #Genomics
May 31, 2025 at 10:16 PM
Good morning Brisbane! What a nice view to prepare my very first talk at #LISSSD25 !
Looking forward to meeting people at the conference.
#GPS_project #pneumococci #Genomics
Looking forward to meeting people at the conference.
#GPS_project #pneumococci #Genomics
Reposted by Stephanie Lo
Society Event Grant – applications for funding to attend EC Summer Conference 2025 are now open until 24 May at 23:59 BST. Check your eligibility and apply now- microb.io/3S9T6cO
Society Events Grant
Funds are available to support eligible members attending the Society Annual Conference or one other Society meeting per year.
microb.io
May 17, 2025 at 3:02 PM
Society Event Grant – applications for funding to attend EC Summer Conference 2025 are now open until 24 May at 23:59 BST. Check your eligibility and apply now- microb.io/3S9T6cO
The SeroBA(v2.0) is now available in the GPS pipeline github.com/GlobalPneumo...
#GPS_project #pneumococci #serotype #bioinformatics
#GPS_project #pneumococci #serotype #bioinformatics
May 7, 2025 at 5:09 PM
The SeroBA(v2.0) is now available in the GPS pipeline github.com/GlobalPneumo...
#GPS_project #pneumococci #serotype #bioinformatics
#GPS_project #pneumococci #serotype #bioinformatics
Reposted by Stephanie Lo
Keeping track on the number of hashtag#pneumococcal serotypes?
SeroBAnk is an atlas of pneumococcal capsule to display its genetics, biochemical structure and serological profiles
www.pneumogen.net/gps/#/serobank
SeroBAnk is an atlas of pneumococcal capsule to display its genetics, biochemical structure and serological profiles
www.pneumogen.net/gps/#/serobank
GPS :: Global Pneumococcal Sequencing Project
Homepage of The Global Pneumococcal Sequencing Project
www.pneumogen.net
May 1, 2025 at 3:56 PM
Keeping track on the number of hashtag#pneumococcal serotypes?
SeroBAnk is an atlas of pneumococcal capsule to display its genetics, biochemical structure and serological profiles
www.pneumogen.net/gps/#/serobank
SeroBAnk is an atlas of pneumococcal capsule to display its genetics, biochemical structure and serological profiles
www.pneumogen.net/gps/#/serobank
Reposted by Stephanie Lo
Do you need a #bioinformatic tool to detect almost all serotypes in #pneumococci?
The new SeroBA v2.0 can detect 102 of 107 known pneumococcal serotypes
www.biorxiv.org/content/10.1...
The new SeroBA v2.0 can detect 102 of 107 known pneumococcal serotypes
www.biorxiv.org/content/10.1...
SeroBA(v2.0) and SeroBAnk: a robust genome-based serotyping scheme and comprehensive atlas of capsular diversity in Streptococcus pneumoniae
The unprecedented number of Streptococcus pneumoniae (the pneumococcus) genomes sequenced in recent years has accelerated the discovery of novel serotypes and highlighted the genetic diversity both be...
www.biorxiv.org
May 1, 2025 at 3:43 PM
Do you need a #bioinformatic tool to detect almost all serotypes in #pneumococci?
The new SeroBA v2.0 can detect 102 of 107 known pneumococcal serotypes
www.biorxiv.org/content/10.1...
The new SeroBA v2.0 can detect 102 of 107 known pneumococcal serotypes
www.biorxiv.org/content/10.1...
Reposted by Stephanie Lo
Happy to share the first preprint from my lab. Great work by Lewis Fisher and collaboration with Jukka Corander
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
High frequency body site translocation of nosocomial Pseudomonas aeruginosa
Pseudomonas aeruginosa is an important nosocomial pathogen which can cause serious infections across diverse anatomic locations. Infections can spread within an individual to different body sites, but...
www.biorxiv.org
May 1, 2025 at 6:32 AM
Happy to share the first preprint from my lab. Great work by Lewis Fisher and collaboration with Jukka Corander
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Stephanie Lo
🆕 Rates of AMR up to 3 times greater in outpatients with cancer compared to those without cancer, suggests USA data.
Find out more in @thelancetoncol.bsky.social: tinyurl.com/2uy9ttvv
Find out more in @thelancetoncol.bsky.social: tinyurl.com/2uy9ttvv
May 1, 2025 at 2:04 PM
🆕 Rates of AMR up to 3 times greater in outpatients with cancer compared to those without cancer, suggests USA data.
Find out more in @thelancetoncol.bsky.social: tinyurl.com/2uy9ttvv
Find out more in @thelancetoncol.bsky.social: tinyurl.com/2uy9ttvv
Do you need a #bioinformatic tool to detect almost all serotypes in #penumococci ?
The new SeroBA v2.0 can detect 102 of 107 pneumococcal serotypes
github.com/GlobalPneumo...
The new SeroBA v2.0 can detect 102 of 107 pneumococcal serotypes
github.com/GlobalPneumo...
Issues · GlobalPneumoSeq/seroba
A Fork of the Original SeroBA. Contribute to GlobalPneumoSeq/seroba development by creating an account on GitHub.
github.com
May 1, 2025 at 1:00 PM
Do you need a #bioinformatic tool to detect almost all serotypes in #penumococci ?
The new SeroBA v2.0 can detect 102 of 107 pneumococcal serotypes
github.com/GlobalPneumo...
The new SeroBA v2.0 can detect 102 of 107 pneumococcal serotypes
github.com/GlobalPneumo...
Reposted by Stephanie Lo
As part of the #GPS_project, @Abel_AberaN
led us to understand the circulating #pneumococcal lineages (carriage and disease)!in Ethiopia after #PCV10
www.microbiologyresearch.org/content/jour...
led us to understand the circulating #pneumococcal lineages (carriage and disease)!in Ethiopia after #PCV10
www.microbiologyresearch.org/content/jour...
Genomic characterization of Streptococcus pneumoniae isolates obtained from carriage and disease among paediatric patients in Addis Ababa, Ethiopia
Background and aims. Despite the introduction of pneumococcal conjugate vaccines (PCVs), Streptococcus pneumoniae still remains an important cause of morbidity and mortality, especially among children...
www.microbiologyresearch.org
March 24, 2025 at 11:45 AM
As part of the #GPS_project, @Abel_AberaN
led us to understand the circulating #pneumococcal lineages (carriage and disease)!in Ethiopia after #PCV10
www.microbiologyresearch.org/content/jour...
led us to understand the circulating #pneumococcal lineages (carriage and disease)!in Ethiopia after #PCV10
www.microbiologyresearch.org/content/jour...
An up-to-date review on the evolving landscape of pneumococcal capsule
- seroepidemiology
-recently recognised novel serotypes
-mitis expressed pneumo capsule
-future research direction
#pneumococcus #vaccine #PCV #NahmLab led by @FerozeGanaie
pubmed.ncbi.nlm.nih.gov/39878373/
- seroepidemiology
-recently recognised novel serotypes
-mitis expressed pneumo capsule
-future research direction
#pneumococcus #vaccine #PCV #NahmLab led by @FerozeGanaie
pubmed.ncbi.nlm.nih.gov/39878373/
Update on the evolving landscape of pneumococcal capsule types: new discoveries and way forward - PubMed
SUMMARY<i>Streptococcus pneumoniae</i> (the "pneumococcus") is a significant human pathogen. The key determinant of pneumococcal fitness and virulence is its ability to produce a protective polysaccha...
pubmed.ncbi.nlm.nih.gov
February 17, 2025 at 1:09 PM
An up-to-date review on the evolving landscape of pneumococcal capsule
- seroepidemiology
-recently recognised novel serotypes
-mitis expressed pneumo capsule
-future research direction
#pneumococcus #vaccine #PCV #NahmLab led by @FerozeGanaie
pubmed.ncbi.nlm.nih.gov/39878373/
- seroepidemiology
-recently recognised novel serotypes
-mitis expressed pneumo capsule
-future research direction
#pneumococcus #vaccine #PCV #NahmLab led by @FerozeGanaie
pubmed.ncbi.nlm.nih.gov/39878373/
Reposted by Stephanie Lo
There are four (that's right four!) academic posts open at the School of Biological sciences at Cambridge University. Check them out here: www.jobs.cam.ac.uk/job/?categor... Gr10/11 (AssocProf/Reader; now Prof) Closing 26/1/25. Looking for excellent, collaborative people. Spread the word!
Job Opportunities - University of Cambridge
Current Academic jobs at the University of Cambridge.
www.jobs.cam.ac.uk
November 29, 2024 at 8:22 PM
There are four (that's right four!) academic posts open at the School of Biological sciences at Cambridge University. Check them out here: www.jobs.cam.ac.uk/job/?categor... Gr10/11 (AssocProf/Reader; now Prof) Closing 26/1/25. Looking for excellent, collaborative people. Spread the word!
Reposted by Stephanie Lo
A Portable and Scalable Genomic Analysis Pipeline for Streptococcus pneumoniae Surveillance: GPS Pipeline https://www.biorxiv.org/content/10.1101/2024.11.27.625679v1
A Portable and Scalable Genomic Analysis Pipeline for Streptococcus pneumoniae Surveillance: GPS Pipeline https://www.biorxiv.org/content/10.1101/2024.11.27.625679v1
Ever increasing global sequencing capacity provides an unprecedented opportunity in utilising genomi
www.biorxiv.org
November 30, 2024 at 3:33 AM
A Portable and Scalable Genomic Analysis Pipeline for Streptococcus pneumoniae Surveillance: GPS Pipeline https://www.biorxiv.org/content/10.1101/2024.11.27.625679v1