Maho Yokoyama
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View article: Microbial diversity and antimicrobial resistance in faecal samples from acute medical patients assessed through metagenomic sequencing
Microbial diversity and antimicrobial resistance in faecal samples from acute medical patients assessed through metagenomic sequencing Open
Antimicrobial resistance (AMR) is a threat to global public health. However, unsatisfactory approaches to directly measuring the AMR burden carried by individuals has hampered efforts to assess interventions aimed at reducing selection for…
View article: Klebsiella pneumonia in Sudan: Multidrug Resistance, Polyclonal Dissemination, and Virulence
Klebsiella pneumonia in Sudan: Multidrug Resistance, Polyclonal Dissemination, and Virulence Open
The emergence and global expansion of hyper-virulent and multidrug resistant (MDR) Klebsiella pneumoniae is an increasing healthcare threat worldwide. The epidemiology of MDR K. pneumoniae is under-characterized in many parts of the world,…
View article: Undetected carriage explains apparent Staphylococcus aureus acquisition in a non-outbreak healthcare setting
Undetected carriage explains apparent Staphylococcus aureus acquisition in a non-outbreak healthcare setting Open
View article: Using metagenomics to investigate the impact of hospital stay and the ARK intervention on the human gut resistome
Using metagenomics to investigate the impact of hospital stay and the ARK intervention on the human gut resistome Open
Antimicrobials are vital for modern medicine. Antimicrobial use selects for antimicrobial resistant bacteria, particularly among the gut microflora. Minimising antimicrobial resistance (AMR) selection by avoiding unnecessary antibiotic use…
View article: Evolution and Global Transmission of a Multidrug-Resistant, Community-Associated Methicillin-Resistant Staphylococcus aureus Lineage from the Indian Subcontinent
Evolution and Global Transmission of a Multidrug-Resistant, Community-Associated Methicillin-Resistant Staphylococcus aureus Lineage from the Indian Subcontinent Open
The Bengal Bay clone (ST772) is a community-associated and multidrug-resistant Staphylococcus aureus lineage first isolated from Bangladesh and India in 2004. In this study, we showed that the Bengal Bay clone emerged from a virulent proge…
View article: Timing Is Everything: Impact of Naturally Occurring <i>Staphylococcus aureus</i> AgrC Cytoplasmic Domain Adaptive Mutations on Autoinduction
Timing Is Everything: Impact of Naturally Occurring <i>Staphylococcus aureus</i> AgrC Cytoplasmic Domain Adaptive Mutations on Autoinduction Open
Virulence factor expression in Staphylococcus aureus is regulated via autoinducing peptide (AIP)-dependent activation of the sensor kinase AgrC, which forms an integral part of the agr quorum sensing system. In response to bound AIP, the c…
View article: Epistasis analysis uncovers hidden antibiotic resistance-associated fitness costs hampering the evolution of MRSA
Epistasis analysis uncovers hidden antibiotic resistance-associated fitness costs hampering the evolution of MRSA Open
View article: Additional file 2: of Epistasis analysis uncovers hidden antibiotic resistance-associated fitness costs hampering the evolution of MRSA
Additional file 2: of Epistasis analysis uncovers hidden antibiotic resistance-associated fitness costs hampering the evolution of MRSA Open
Table S3. Protein profile differences between SH1000 (mupS) and MY40 (mupR). Proteins highlighted in yellow are also differentially produced by exposure to mupirocin. (XLSX 32 kb)
View article: Additional file 3: of Epistasis analysis uncovers hidden antibiotic resistance-associated fitness costs hampering the evolution of MRSA
Additional file 3: of Epistasis analysis uncovers hidden antibiotic resistance-associated fitness costs hampering the evolution of MRSA Open
Table S4. Effect of exposure to mupirocin on SH1000 protein profile. Proteins highlighted in yellow are those also differentially produced in the mupR mutant. (XLSX 13 kb)
View article: Clonal differences in Staphylococcus aureus bacteraemia-associated mortality
Clonal differences in Staphylococcus aureus bacteraemia-associated mortality Open
View article: Hidden antibiotic resistance fitness costs revealed by GWAS-based epistasis analysis
Hidden antibiotic resistance fitness costs revealed by GWAS-based epistasis analysis Open
Understanding how multi-drug resistant pathogens evolve is key to identifying means of curtailing their further emergence and dissemination. Fitness costs imposed on bacteria by resistance mechanisms are believed to hamper their disseminat…
View article: The use of Oxford Nanopore native barcoding for complete genome assembly
The use of Oxford Nanopore native barcoding for complete genome assembly Open
Background The Oxford Nanopore Technologies MinION(TM) is a mobile DNA sequencer that can produce long read sequences with a short turn-around time. Here we report the first demonstration of single contig genome assembly using Oxford Nanop…
View article: Low levels of toxicity are associated with invasive <i>S</i>. <i>aureus</i> infections across two collections of clinical isolates.
Low levels of toxicity are associated with invasive <i>S</i>. <i>aureus</i> infections across two collections of clinical isolates. Open
a: Individual isolates from seven time points were assayed for toxicity and their genome sequenced. Early nose cultures (ENCs) from months 1, 2, 4, 6, and 8 were all highly toxic. Late nose culture (LNC) isolates at month 12 and blo…
View article: Evolution towards increased levels of virulence.
Evolution towards increased levels of virulence. Open
Two competing MRSA strains with different levels of toxicity are considered, where higher toxicity is assumed to increase the transition rate from carriage to infection (SSTI) but also increases treatment-induced clearance of infections. A…
View article: The highly toxic isolates are less fit than the low-toxicity isolates in the presence of human serum.
The highly toxic isolates are less fit than the low-toxicity isolates in the presence of human serum. Open
We quantified the relative fitness of six high- and six low-toxicity isolates from the single patient collection (A), 10 high- and 10 low-toxicity isolates from the USA300 collection (B) and an Agr wild type and mutant isogenic pair (C) in…
View article: Toxicity levels and disease origin distributed across the USA300 collection.
Toxicity levels and disease origin distributed across the USA300 collection. Open
The clinical origin (carriage = C, SSTI = S, or blood = B) and the toxicity (low = green, medium = orange or high = red) of 134 USA300 isolates are mapped onto a maximum likelihood tree based on their whole genome sequence.
View article: The identification of six novel toxicity-affecting loci.
The identification of six novel toxicity-affecting loci. Open
Transposon mutagenesis was used to functionally verify the role of loci associated with toxicity by genome-wide association study (GWAS; PLINK). Mean of six replicates are presented, error bars represent the 95% confidence intervals. The m…
View article: Explaining the association between toxicity and infection severity.
Explaining the association between toxicity and infection severity. Open
A range of virulence assays were performed on a subset of 10 high- and 10 low-toxicity isolates from the USA300 collection to identify the biological feature that explains the observed inverse correlation between toxicity and disease sever…
View article: Evolutionary Trade-Offs Underlie the Multi-faceted Virulence of Staphylococcus aureus
Evolutionary Trade-Offs Underlie the Multi-faceted Virulence of Staphylococcus aureus Open
Bacterial virulence is a multifaceted trait where the interactions between pathogen and host factors affect the severity and outcome of the infection. Toxin secretion is central to the biology of many bacterial pathogens and is widely acce…