Stephanie W. Lo
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View article: The capsule and genetic background, rather than specific individual loci, strongly influence in vitro pneumococcal growth kinetics
The capsule and genetic background, rather than specific individual loci, strongly influence in vitro pneumococcal growth kinetics Open
Bacterial growth characteristics intrinsic to each strain can impact and influence gene expression, antibiotic susceptibility, and disease pathogenesis. However, little is known about specific genomic variations that influence these bacter…
View article: SeroBA(v2.0) and SeroBAnk: a robust genome-based serotyping scheme and comprehensive atlas of capsular diversity in Streptococcus pneumoniae
SeroBA(v2.0) and SeroBAnk: a robust genome-based serotyping scheme and comprehensive atlas of capsular diversity in Streptococcus pneumoniae Open
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 between and within each serotype. A novel…
View article: Within-host genetic diversity of pneumococcal serotype 3 during one-year prolonged carriage in a healthy adult
Within-host genetic diversity of pneumococcal serotype 3 during one-year prolonged carriage in a healthy adult Open
Streptococcus pneumoniae adapts within hosts through genetic variation and genome plasticity, facilitating persistence under antibiotic and immune pressures. Here, we investigated a prolonged pneumococcal carriage episode (>337 days) in a …
View article: GPS Pipeline: portable, scalable genomic pipeline for Streptococcus pneumoniae surveillance from Global Pneumococcal Sequencing Project
GPS Pipeline: portable, scalable genomic pipeline for Streptococcus pneumoniae surveillance from Global Pneumococcal Sequencing Project Open
Streptococcus pneumoniae (pneumococcus) is a major pathogen globally, responsible for an estimated one million deaths annually and contributing significantly to the global burden of antimicrobial resistance. Ongoing surveillance of its vac…
View article: <i>Streptococcus pneumoniae</i> vaccine serotype persistence following 13-valent pneumococcal conjugate vaccine introduction in Mongolia: investigating changes in epidemiology, immunology and virulence
<i>Streptococcus pneumoniae</i> vaccine serotype persistence following 13-valent pneumococcal conjugate vaccine introduction in Mongolia: investigating changes in epidemiology, immunology and virulence Open
Background Streptococcus pneumoniae is a leading cause of pneumonia globally. Vaccine serotypes can persist despite pneumococcal conjugate vaccine (PCV) introduction. To examine serotype persistence, we leveraged 6,545 nasopharyngeal swabs…
View article: Antimicrobial Resistance Cartography: A Generalisable Framework for Studying Multivariate Drug Resistance
Antimicrobial Resistance Cartography: A Generalisable Framework for Studying Multivariate Drug Resistance Open
The global rise in antimicrobial resistance (AMR) has motivated large-scale surveillance studies of bacterial pathogens. Although these datasets contain rich information on drug resistance, they are both complex and multivariate, with each…
View article: Genomic analysis of the Streptococcus pneumoniae in Taiwan: a nationwide study from 2006 to 2022
Genomic analysis of the Streptococcus pneumoniae in Taiwan: a nationwide study from 2006 to 2022 Open
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 investigates the population structure and…
View article: Serotype replacement and mobile genetic elements in Streptococcus pneumoniae: a systematic review
Serotype replacement and mobile genetic elements in Streptococcus pneumoniae: a systematic review Open
Streptococcus pneumoniae causes otitis media and severe diseases including pneumonia, meningitis and bacteraemia. The rise of antimicrobial resistance (AMR) in S. pneumoniae , facilitated by mobile genetic elements (MGEs), complicates infe…
View article: Changes in carriage and serotype diversity of Streptococcus pneumoniae and other respiratory pathobionts in the UK between pre-PCV13 (2006-10), early-PCV13 (2010-12) and late-PCV13 (2012-23) periods
Changes in carriage and serotype diversity of Streptococcus pneumoniae and other respiratory pathobionts in the UK between pre-PCV13 (2006-10), early-PCV13 (2010-12) and late-PCV13 (2012-23) periods Open
Background: The ongoing burden of mortality and morbidity associated with Streptococcus pneumoniae infections requires that monitoring of carriage epidemiology continues. Here, we present data from the annual, cross-sectional surveillance …
View article: The capsule and genetic background, rather than specific individual loci, strongly influence in vitro pneumococcal growth kinetics
The capsule and genetic background, rather than specific individual loci, strongly influence in vitro pneumococcal growth kinetics Open
Bacterial growth characteristics intrinsic to each strain can impact and influence gene expression, antibiotic susceptibility, and disease pathogenesis. However, little is known about specific genomic variations that influence these bacter…
View article: Naturally acquired promoter variation influences Streptococcus pneumoniae infection outcomes
Naturally acquired promoter variation influences Streptococcus pneumoniae infection outcomes Open
Streptococcus pneumoniae colonizes human airways, where it acquires sugars from glycosylated mucins using glycoside hydrolases and sugar transport systems. This study identifies widespread nucleotide sequence variation in the promoter of a…
View article: High Propensity for Multidrug-Resistant Pneumococcal Shedding Among Adults Living With HIV on Stable Antiretroviral Therapy in Malawi
High Propensity for Multidrug-Resistant Pneumococcal Shedding Among Adults Living With HIV on Stable Antiretroviral Therapy in Malawi Open
Background People living with human immunodeficiency virus (HIV; PLHIV) on antiretroviral therapy (ART) are still at risk of pneumococcal disease and have over 2-fold higher pneumococcal carriage prevalence than HIV-uninfected (HIV−) adult…
View article: Genomic analysis of invasive and non-invasive disease-causing Streptococcus pneumoniae isolated from children between 2014 and 2023 in Suzhou, China
Genomic analysis of invasive and non-invasive disease-causing Streptococcus pneumoniae isolated from children between 2014 and 2023 in Suzhou, China Open
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 included in the Chinese National Immunization…
View article: SeroBA(v2.0) and SeroBAnk: a robust genome-based serotyping scheme and comprehensive atlas of capsular diversity in Streptococcus pneumoniae
SeroBA(v2.0) and SeroBAnk: a robust genome-based serotyping scheme and comprehensive atlas of capsular diversity in Streptococcus pneumoniae Open
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 between and within each serotype. A novel…
View article: Within-host pneumococcal serotype 3 genetic diversity and evolution during a one-year prolonged carriage episode in a healthy adult
Within-host pneumococcal serotype 3 genetic diversity and evolution during a one-year prolonged carriage episode in a healthy adult Open
Streptococcus pneumoniae can rapidly evolve within hosts through genetic mutations, recombination, and mobile genetic elements, enabling adaptation to antibiotics and immune pressures. Here, we detail a longitudinal phenotypic and genomic …
View article: The capsule and genetic background, rather than specific loci, strongly influence pneumococcal growth kinetics
The capsule and genetic background, rather than specific loci, strongly influence pneumococcal growth kinetics Open
Bacterial growth characteristics intrinsic to each strain can impact and influence gene expression, antibiotic susceptibility, and disease pathogenesis. However, little is known about specific genomic variations that influence these bacter…
View article: The capsule and genetic background, rather than specific individual loci, strongly influence in vitro pneumococcal growth kinetics
The capsule and genetic background, rather than specific individual loci, strongly influence in vitro pneumococcal growth kinetics Open
Bacterial growth characteristics intrinsic to each strain can impact and influence gene expression, antibiotic susceptibility, and disease pathogenesis. However, little is known about specific genomic variations that influence these bacter…
View article: Streptococcus pneumoniae serotype 33H: a novel serotype with frameshift mutations in the acetyltransferase gene wciG
Streptococcus pneumoniae serotype 33H: a novel serotype with frameshift mutations in the acetyltransferase gene wciG Open
Background Streptococcus pneumoniae (the pneumococcus) is a leading cause of community-acquired pneumonia. Pneumococci are categorised into serotypes, based on the type of capsular polysaccharide produced, which has important implications …
View article: Genomic characterization of Streptococcus pneumoniae isolates obtained from carriage and disease among paediatric patients in Addis Ababa, Ethiopia
Genomic characterization of Streptococcus pneumoniae isolates obtained from carriage and disease among paediatric patients in Addis Ababa, Ethiopia Open
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 under 5 years in sub-Saharan Africa. W…
View article: The capsule and genetic background, rather than specific individual loci, strongly influence <i>in vitro</i> pneumococcal growth kinetics
The capsule and genetic background, rather than specific individual loci, strongly influence <i>in vitro</i> pneumococcal growth kinetics Open
Bacterial growth characteristics intrinsic to each strain can impact and influence gene expression, antibiotic susceptibility, and disease pathogenesis. However, little is known about specific genomic variations that influence these bacter…
View article: New pneumococcal serotype 20C is a WciG O-acetyltransferase deficient variant of canonical serotype 20B
New pneumococcal serotype 20C is a WciG O-acetyltransferase deficient variant of canonical serotype 20B Open
The polysaccharide (PS) capsule of Streptococcus pneumoniae (pneumococcus) is the immunodominant surface structure that shields the bacteria from the host immune system. Since the capsule is the primary target of currently available pneumo…
View article: A Portable and Scalable Genomic Analysis Pipeline for<i>Streptococcus pneumoniae</i>Surveillance: GPS Pipeline
A Portable and Scalable Genomic Analysis Pipeline for<i>Streptococcus pneumoniae</i>Surveillance: GPS Pipeline Open
Ever increasing global sequencing capacity provides an unprecedented opportunity in utilising genomic information captured from whole-genome sequencing to enhance pathogen surveillance. However, there is a growing need for developing user-…
View article: Essential role of proline synthesis and the one-carbon metabolism pathways for systemic virulence of <i>Streptococcus pneumoniae</i>
Essential role of proline synthesis and the one-carbon metabolism pathways for systemic virulence of <i>Streptococcus pneumoniae</i> Open
Virulence screens have indicated potential roles during Streptococcus pneumoniae infection for the one-carbon metabolism pathway component Fhs and proline synthesis mediated by ProABC. To define how these metabolic pathways affect S. pneum…
View article: Comparison of gene-by-gene and genome-wide short nucleotide sequence-based approaches to define the global population structure of Streptococcus pneumoniae
Comparison of gene-by-gene and genome-wide short nucleotide sequence-based approaches to define the global population structure of Streptococcus pneumoniae Open
Defining the population structure of a pathogen is a key part of epidemiology, as genomically related isolates are likely to share key clinical features such as antimicrobial resistance profiles and invasiveness. Multiple different methods…
View article: Pan-pathogen deep sequencing of nosocomial bacterial pathogens in Italy in spring 2020: a prospective cohort study
Pan-pathogen deep sequencing of nosocomial bacterial pathogens in Italy in spring 2020: a prospective cohort study Open
Wellcome Trust, European Research Council, Academy of Finland Flagship program, Trond Mohn Foundation, and Research Council of Norway.
View article: Pneumococcal carriage and changes in serotype distribution post- PCV13 introduction in children in Matiari, Pakistan
Pneumococcal carriage and changes in serotype distribution post- PCV13 introduction in children in Matiari, Pakistan Open
Replacing PCV10 with PCV13 rapidly decreased prevalence of PCV13 carriage among vaccinated children in Matiari, Pakistan. Vaccine-driven selection pressure may have been responsible for the increase of non-PCV13 serotypes.