Stephanie Lo

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.

🦠🧪🧬 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

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.

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

[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...

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...

[🚨 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...

A great collaboration with Dr Dan Neill and his team at University of Dundee and scientists from UCL, St. Jude Children's Research Hospital, Uni of Bern, Uni of Liverpool, Uni of Cape Town, Uni of Western Australia, Uni of Bath, Milner centre for Evolution and @sangerinstitute.bsky.social

However, this promoter variant does not thrive on its own and is usually co-occurence of the wild-type promoter without "A", showing heterogeneous gene expression during single infections provides population benefits.

This tiny mutation—found not only mouse colonization models but also clinical isolates from the #GPS_project — enhance S. pneumoniae colonization reducing mucus trapping.

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...

[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...

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...

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

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

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...

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...

@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

@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

Society Events Grant Funds are available to support eligible members attending the Society Annual Conference or one other Society meeting per year.

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

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

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...

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...

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...

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...

Graphical abstract for The Lancet Oncology paper "Incidence and prevalence of antimicrobial resistance in outpatients with cancer: a multicentre, retrospective, cohort study".

🆕 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

Issues · GlobalPneumoSeq/seroba A Fork of the Original SeroBA. Contribute to GlobalPneumoSeq/seroba development by creating an account on GitHub.

If you’d like us to add your new serotypes in SeroBA, create an issue on our GitHub page at github.com/GlobalPneumo...

Issues · GlobalPneumoSeq/seroba A Fork of the Original SeroBA. Contribute to GlobalPneumoSeq/seroba development by creating an account on GitHub.

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...

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...

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...

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...

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/

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!

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

A Portable and Scalable Genomic Analysis Pipeline for Streptococcus pneumoniae Surveillance: GPS Pipeline https://www.biorxiv.org/content/10.1101/2024.11.27.625679v1