What Is Resistance? Impact of Phenotypic versus Molecular Drug Resistance Testing on Therapy for Multi- and Extensively Drug-Resistant Tuberculosis.

Rapid and accurate drug susceptibility testing (DST) is essential for the treatment of multi- and extensively drug-resistant tuberculosis (M/XDR-TB). We compared the utility of genotypic DST assays with phenotypic DST (pDST) using Bactec 960 MGIT or Löwenstein-Jensen to construct M/XDR-TB treatment regimens for a cohort of 25 consecutive M/XDR-TB patients and 15 possible anti-TB drugs. Genotypic DST results from Cepheid GeneXpert MTB/RIF (Xpert) and line probe assays (LPAs; Hain GenoType MTBDRplus 2.0 and MTBDRsl 2.0) and whole-genome sequencing (WGS) were translated into individual algorithm-derived treatment regimens for each patient. We further analyzed if discrepancies between the various methods were due to flaws in the genotypic or phenotypic test using MIC results. Compared with pDST, the average agreement in the number of drugs prescribed in genotypic regimens ranged from just 49% (95% confidence interval [CI], 39 to 59%) for Xpert and 63% (95% CI, 56 to 70%) for LPAs to 93% (95% CI, 88 to 98%) for WGS. Only the WGS regimens did not contain any drugs to which pDST showed resistance. Importantly, MIC testing revealed that pDST likely underestimated the true rate of resistance for key drugs (rifampin, levofloxacin, moxifloxacin, and kanamycin) because critical concentrations (CCs) were too high. WGS can be used to rule in resistance even in M/XDR strains with complex resistance patterns, but pDST for some drugs is still needed to confirm susceptibility and construct the final regimens. Some CCs for pDST need to be reexamined to avoid systematic false-susceptible results in low-level resistant isolates

Supplementary Data for "Population structure of multidrug resistant Klebsiella oxytoca within the UK and Ireland identifies sharing of virulence and resistance genes with K. pneumoniae"

Supplemental Data for "Population structure of multidrug resistant Klebsiella oxytoca within the UK and Ireland identifies sharing of virulence and resistance genes with K. pneumoniae" Danesh Moradigaravand, Veronique Martin, Sharon J. Peacock and Julian Parkhill 1- Multi-fasta files of genes in pan-genome 2- Metadata of genes in pan-genom

Supplemental data for "Whole genome sequencing reveals high-resolution epidemiological links between clinical and environmental Klebsiella pneumoniae

Data for "Whole genome sequencing reveals high-resolution epidemiological links between clinical and environmental Klebsiella pneumoniae" Authors: Chakkaphan Runcharoen*, Danesh Moradigaravand*, Elizabeth Blane, Suporn Paksanont, Jeeranan Thammachote, Suthatip Anun, Julian Parkhill, Narisara Chantratita** and Sharon J. Peacock** * Joint first author ** Joint senior author 1- List of genes in the pan-genome of 77 Klebsiella pneumoniae isolates from Thailand 2- Multiple alignment of the genes in the pan-genom

Pan-genome multi-fasta files for the Serratia marcescens population study

multifasta files for the pan-genome analysis conducted in "Recent independent emergence of multiple multi-drug resistant Serratia marcescens clones within the United Kingdom and Ireland" 2016 Authors: Danesh Moradigaravand, Christine J. Boinett, Veronique Martin, Sharon J. Peacock and Julian Parkhil

Pan-genome data for the genes in "Prediction of antibiotic resistance in Escherichia coli from large-scale pan-genome data"

The pan-genome data for the paper under review. Files are in fasta format

Assembly data for newly sequenced genomes used in "Prediction of antibiotic resistance in Escherichia coli from large-scale pan-genome data"

These are 256 assembly files for the genomes sequenced for the manuscript. The file "accession.txt" contains tags and accession number

Supplemental Data for 'The dissemination of multidrug resistant Enterobacter cloacae throughout the UK and Ireland'

The dissemination of multidrug resistant Enterobacter cloacae throughout the UK and Ireland Danesh Moradigaravand, Sandra Reuter, Veronique Martin, Sharon J. Peacock and Julian Parkhill List of files and folders: 1- RCode.R: R code for the regression analysis 2- Metadata.csv: MIC and MLST data used as input for regression models 3- gene_presence_absence.csv: Output of pan-genome analysis used as input for regression models 4- SNP.out: List of SNPs identified used as input for regression models 5- pan_genome_sequences folder contains sequences of the genes in the pan-genom

Evolution of the community-onset invasive Staphylococcus argenteus ST2250 clone in northeast Thailand is linked with the acquisition of livestock-associated staphylococcal genes

$\textit{Staphylococcus argenteus}$ is a newly named species previously described as a divergent lineage of Staphylococcus aureus that has recently been shown to have a global distribution. Despite growing evidence of the clinical importance of this species, knowledge about its population epidemiology and genomic architecture is limited. We used whole-genome sequencing to evaluate and compare $\textit{S. aureus}$ (n 251) and $\textit{S. argenteus}$ (n 68) isolates from adults with staphylococcal sepsis at several hospitals in northeastern Thailand between 2006 and 2013. The majority (82%) of the $\textit{S. argenteus}$ isolates were of multilocus sequence type 2250 (ST2250). $\textit{S. aureus}$ was more diverse, although 43% of the isolates belonged to ST121. Bayesian analysis suggested an $\textit{S. argenteus}$ ST2250 substitution rate of 4.66 (95% confidence interval [CI], 3.12 to 6.38) mutations per genome per year, which was comparable to the $\textit{S. aureus}$ ST121 substitution rate of 4.07 (95% CI, 2.61 to 5.55). $\textit{S. argenteus}$ ST2250 emerged in Thailand an estimated 15 years ago, which contrasts with the $\textit{S. aureus}$ ST1, ST88, and ST121 clades that emerged around 100 to 150 years ago. Comparison of $\textit{S. argenteus}$ ST2250 genomes from Thailand and a global collection indicated a single introduction into Thailand, followed by transmission to local and more distant countries in Southeast Asia and further afield. $\textit{S. argenteus}$ and $\textit{S. aureus}$ shared around half of their core gene repertoire, indicating a high level of divergence and providing strong support for their classification as separate species. Several gene clusters were present in ST2250 isolates but absent from the other $\textit{S. argenteus}$ and $\textit{S. aureus}$ study isolates. These included multiple exotoxins and antibiotic resistance genes that have been linked previously with livestock-associated $\textit{S. aureus}$, consistent with a livestock reservoir for $\textit{S. argenteus}$. These genes appeared to be associated with plasmids and mobile genetic elements and may have contributed to the biological success of ST2250.This publication presents independent research supported by the Health Innovation Challenge Fund (HICF-T5-342 and WT098600), a parallel funding partnership between the UK Department of Health and the Wellcome Trust. This project was also funded by a grant awarded to the Wellcome Trust Sanger Institute (098051). This study was also funded by a Wellcome Trust Career Development award in Public Health and Tropical Medicine (087769/Z/08/Z) to N.C

Population Structure of Multidrug-Resistant Klebsiella oxytoca\textit{Klebsiella oxytoca} within Hospitals across the United Kingdom and Ireland Identifies Sharing of Virulence and Resistance Genes with K. pneumoniae\textit{K. pneumoniae}

$\textit{Klebsiella oxytoca}$, a member of the Enterobacteriaceae, is a gram-negative pathogenic bacterium of environmental origin, which can cause infection in healthcare settings. Outbreaks of multidrug-resistant $\textit{K. oxytoca}$ infection have been increasingly reported in hospitalized patients. Despite the growing importance of this pathogen, there is limited knowledge about the population structure and epidemiology of antimicrobial resistant $\textit{K. oxytoca}$. We investigated the population structure and genomic basis of antimicrobial resistance of 41 multidrug resistant $\textit{K. oxytoca}$ isolates recovered from bloodstream infections across the UK and Ireland. Our results show that $\textit{K. oxytoca}$ has a highly diverse population, which is composed of several distinct clades, and we identified one recent expansion of a clone within our dataset. Although the $\textit{K. oxytoca}$ genomes are clearly distinct from the genomes of a global collection of $\textit{Klebsiella pneumoniae}$ complex, pre-dominantly composed of $\textit{K. pneumoniae}$, we found evidence for sharing of core genes through recombination, as well as the exchange of accessory antimicrobial resistance and virulence factor genes between the species. Our findings also suggest that the different $\textit{K. oxytoca}$ clades have acquired antimicrobial resistance and virulence factor genes independently. This highlights the clinical and therapeutic importance of genetic flexibility in $\textit{K. oxytoca}$ and the relevance of this in its role as an opportunistic pathogen.This publication presents independent research supported by the Health Innovation Challenge Fund (HICF-T5-342 and WT098600), a parallel funding partnership between the UK Department of Health and Wellcome Trust. The views expressed in this publication are those of the authors and not necessarily those of the Department of Health, Public Health England or the Wellcome Trust. This project was also funded by a grant awarded to the Wellcome Trust Sanger Institute (098051)