Biology subjects

McGarry, N.

Publications and source records attributed to McGarry, N..

3 recordsLinked to original sources

bioRxiv2026

A capsule polysaccharide synthesis locus database for the Klebsiella oxytoca Species Complex

The Klebsiella oxytoca Species Complex (SC) represents an emerging healthcare-associated group of opportunistic pathogens. The capsular polysaccharide is a virulence determinant and target for novel vaccines, monoclonal antibodies and phage therapy. In the absence of broadly accessible phenotyping techniques, prediction of capsule types from whole-genome sequence data is critical for understanding capsule diversity and epidemiology, and to prioritise capsule types as targets for novel anti-K. oxytoca SC interventions. Here we present the first comprehensive capsule synthesis locus (K locus) database targeted for the K. oxytoca SC, comprising 88 distinct loci defined by gene content and which is compatible with the rapid genome typing tool Kaptive. The database provides high coverage of publicly available K. oxytoca SC genomes (97.6% of 2,244 genomes, dereplicated from a total of 4,055), and the typing rate is significantly higher than that achieved with the pre-existing Klebsiella K locus database (97.6% vs 50.3%, p <0.0001), which primarily targets the Klebsiella pneumoniae SC. We demonstrate the utility of the novel K. oxytoca SC database by application to three diverse clinical K. oxytoca SC isolate collections (n=61 to 102 genomes each), suggesting a high diversity of K types. The novel K. oxytoca SC K locus database (github.com/klebgenomics/KoSC-surface-antigen-loci) will provide a key resource to support larger systematic studies and ongoing genomics surveillance efforts for the K. oxytoca SC. IMPACT STATEMENTMembers of the Klebsiella oxytoca Species Complex (SC) are an emerging cause of infections in humans and are frequently associated with antimicrobial resistance. Klebsiella species produce two key surface antigen sugars (capsular polysaccharide and lipopolysaccharide) that are immunogenic and are targets for novel control strategies such as vaccines and phage therapy. Phenotypic typing of these surface antigen sugars (serotyping) is costly and laborious, with genotyping (predicting the serotype from whole-genome sequence data) a useful alternative. Here, we present a curated capsule (K) locus reference database for the K. oxytoca SC, which represents a useful tool to assist in the epidemiological surveillance of this emerging pathogen. DATA SUMMARYAll Klebsiella oxytoca Species Complex genomes used in this work were publicly available, with accession details listed in Supplementary Tables 1, 2 and 3. The K. oxytoca Species Complex K locus reference database is available under GNU public license at github.com/klebgenomics/KoSC-surface-antigen-loci.

bioinformatics↗

bioRxiv2024

Synergy between Group 2 capsules and lipopolysaccharide underpins serum resistance in Extra-intestinal Pathogenic Escherichia coli

Escherichia coli (E. coli) is a major cause of urinary tract infections, bacteraemia, and sepsis. CFT073 is a prototypic, urosepsis isolate of sequence type (ST) 73. This laboratory, among others, has shown that strain CFT073 is resistant to serum, with capsule and other extracellular polysaccharides imparting resistance. The interplay of such polysaccharides remains under-explored. This study has shown that CFT073 mutants deficient in lipopolysaccharide (LPS) O-antigen and capsule display exquisite serum sensitivity. Additionally, O-antigen and LPS outer core mutants displayed significantly reduced surface K2 capsule, coupled with increased unbound K2 capsule being detected in the supernatant. The R1 core and O6 antigen are involved in the tethering of K2 capsule to the CFT073 cell surface, highlighting the importance of the R1 core in serum resistance. The dependence of capsule on LPS was shown to be post-transcriptional and related to changes in cell surface charge. Furthermore, immunofluorescence microscopy suggested that the surface pattern of capsule is altered in such LPS core mutants, which display a punctate capsule expression. Finally, targeting LPS biosynthesis using sub-inhibitory concentrations of a WaaG inhibitor resulted in increased serum sensitivity, antibiotic sensitivity, and reduced capsule in CFT073. Interestingly, the dependency of capsule on LPS has been observed previously in several Klebsiella pneumoniae isolates and a neonatal meningitic E. coli strain, indicating that the synergy between these polysaccharides is not just strain, serotype or species-specific but may be conserved across several pathogenic Gram-negative species. Therefore, using WaaG inhibitor derivatives or phage-derived depolymerases to target LPS is a promising avenue for co-administration with antibiotics to reduce morbidity and mortality by reducing or eliminating surface capsule. Impact statementDisseminated infections caused by E. coli place a large burden on healthcare systems globally, with incidence as well as antimicrobial resistance on the rise (1, 2). The key to designing successful therapeutic strategies is to understand how and why bacteria can cause infection, with an increased need for alternative/ preventative therapies in the age of antimicrobial resistance. ST131 is the predominant and most significant clonal group of bloodstream isolates currently (3-6). The second-most frequently isolated clonal group in E. coli bloodstream infections is that of ST73, into which the prototype used in this study, CFT073, is categorised (3, 5-7). Whilst antimicrobial resistance is not currently widespread in the ST73 clonal group, patterns of drug resistance are emerging (7). The clonal group is also associated with higher virulence scores than ST131, highlighting a need to better understand ST73 virulence to identify potential therapeutic intervention strategies (6). This study has identified a synergy between common virulence factors of sepsis-associated E. coli, capsule and LPS, which can be exploited to reduce virulence, a promising prospect in the age of antimicrobial resistance. Data summaryOligonucleotide primers for mutagenesis as well as schematic representations of gene clusters were designed based on the assembled genome sequence of strain CFT073 (GenBank accession number: AE014075.1). The authors confirm all other supporting data, code and protocols have been provided within the article or through supplementary data files.

microbiology↗

bioRxiv2021

Double stranded RNA drives innate immune responses, sickness behavior and cognitive impairment dependent on dsRNA length, IFNAR1 expression and age

Double stranded RNA is generated during viral replication. The synthetic analogue poly I:C is frequently used to mimic anti-viral innate immune responses in models of psychiatric and neurodegenerative disorders including schizophrenia, autism, Parkinsons disease and Alzheimers disease. Many studies perform limited analysis of innate immunity despite these responses potentially differing as a function of dsRNA molecular weight and age. Therefore fundamental questions relevant to impacts of systemic viral infection on brain function and integrity remain. Here, we studied innate immune-inducing properties of poly I:C preparations of different lengths and responses in adult and aged mice. High molecular weight (HMW) poly I:C (1-6kb, 12 mg/kg) produced more robust sickness behavior and more robust IL-6, IFN-I and TNF responses than poly I:C of <500 bases (low MW) preparations. This was partly overcome with higher doses of LMW (up to 80 mg/kg), but neither circulating IFN{beta} nor brain transcription of Irf7 were significantly induced by LMW poly I:C, despite brain Ifnb transcription, suggesting that brain IFN-dependent gene expression is predominantly triggered by circulating IFN{beta} binding of IFNAR1. In aged animals, poly I:C induced exaggerated IL-6, IL-1{beta} and IFN-I in the plasma and similar exaggerated brain cytokine responses. This was associated with acute working memory deficits selectively in aged mice. Thus, we demonstrate dsRNA length-, IFNAR1- and age-dependent effects on anti-viral inflammation and cognitive function. The data have implications for CNS symptoms of acute systemic viral infection such as those with SARS-CoV-2 and for models of maternal immune activation.

neuroscience↗