Prevalence of tested resistance genes among isolated Enterococci.

<p>Prevalence of antimicrobial resistance genes tested among <i>E</i>. <i>faecalis</i> and <i>E</i>. <i>faecium</i> isolated from retail poultry products collected in 5 major Japanese cities between July and August 2012.</p><p>Prevalence of tested resistance genes among isolated Enterococci.</p

Final globally optimal additive Bayesian network model after adjustment for over-fitting.

<p>Final additive Bayesian network model after removing arcs that appeared in <50% of bootstrappings for the interrelationships between selected antimicrobial resistance genes and phenotypes. Solid lines and dashed lines represent positive and negative associations between variables, respectively. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0121189#pone.0121189.g002" target="_blank">Fig. 2</a> lists the variable names.</p

Clinical impact of endometrial cancer stratified by genetic mutational profiles, <i>POLE</i> mutation, and microsatellite instability

<div><p>Background</p><p>The molecular characterization of endometrial cancer (EC) can facilitate identification of various tumor subtypes. Although EC patients with <i>POLE</i> mutations reproducibly demonstrate better prognosis, the outcome of patients with microsatellite instability (MSI) remains controversial. This study attempted to interrogate whether genetic stratification of EC can identify distinct subsets with prognostic significance.</p><p>Materials and methods</p><p>A cohort of 138 EC patients who underwent surgical resection with curative intent was enrolled. Sanger sequencing was used to evaluate mutations in the <i>POLE</i> and <i>KRAS</i> genes. MSI analysis was performed using four mononucleotide repeat markers and methylation status of the <i>MLH1</i> promoter was measured by a fluorescent bisulfite polymerase chain reaction (PCR). Protein expression for mismatch repair (MMR) proteins was evaluated by immunohistochemistry (IHC).</p><p>Results</p><p>Extensive hypermethylation of the <i>MLH1</i> promoter was observed in 69.6% ECs with MLH1 deficiency and 3.5% with MMR proficiency, but in none of the ECs with loss of other MMR genes (<i>P</i> < .0001). MSI-positive and <i>POLE</i> mutations were found in 29.0% and 8.7% EC patients, respectively. Our MSI analysis showed a sensitivity of 92.7% for EC patients with MMR deficiency, and a specificity of 97.9% for EC patients with MMR proficiency. In univariate and multivariate analyses, <i>POLE</i> mutations and <i>MSI</i> status was significantly associated with progression-free survival (<i>P</i> = 0.0129 and 0.0064, respectively) but not with endometrial cancer-specific survival.</p><p>Conclusions</p><p>This study provides significant evidence that analyses of proofreading <i>POLE</i> mutations and MSI status based on mononucleotide repeat markers are potentially useful biomarkers to identify EC patients with better prognosis.</p></div

Posterior marginal log odds ratios for parameters.

<p>Posterior estimates for remaining arcs obtained from the final ABN model after bootstrapping. The median and 95% credibility intervals for each parameter estimate are shown.</p><p>^aMIC for dihydrostreptomycin: ≥128 μg/mL and ≤512 μg/mL.</p><p>^bMIC for dihydrostreptomycin: >512 μg/mL.</p><p>^cMIC for oxytetracycline: ≥16 μg/mL and ≤64 μg/mL.</p><p>^dMIC for oxytetracycline: >64 μg/mL.</p><p>Posterior marginal log odds ratios for parameters.</p

Unraveling Antimicrobial Resistance Genes and Phenotype Patterns among <i>Enterococcus faecalis</i> Isolated from Retail Chicken Products in Japan

<div><p>Multidrug-resistant enterococci are considered crucial drivers for the dissemination of antimicrobial resistance determinants within and beyond a genus. These organisms may pass numerous resistance determinants to other harmful pathogens, whose multiple resistances would cause adverse consequences. Therefore, an understanding of the coexistence epidemiology of resistance genes is critical, but such information remains limited. In this study, our first objective was to determine the prevalence of principal resistance phenotypes and genes among <i>Enterococcus faecalis</i> isolated from retail chicken domestic products collected throughout Japan. Subsequent analysis of these data by using an additive Bayesian network (ABN) model revealed the co-appearance patterns of resistance genes and identified the associations between resistance genes and phenotypes. The common phenotypes observed among <i>E</i>. <i>faecalis</i> isolated from the domestic products were the resistances to oxytetracycline (58.4%), dihydrostreptomycin (50.4%), and erythromycin (37.2%), and the gene <i>tet</i>(L) was detected in 46.0% of the isolates. The ABN model identified statistically significant associations between <i>tet</i>(L) and <i>erm</i>(B), <i>tet</i>(L) and <i>ant</i>(6)-Ia, <i>ant</i>(6)-Ia and <i>aph</i>(3’)-IIIa, and <i>aph</i>(3’)-IIIa and <i>erm</i>(B), which indicated that a multiple-resistance profile of tetracycline, erythromycin, streptomycin, and kanamycin is systematic rather than random. Conversely, the presence of <i>tet</i>(O) was only negatively associated with that of <i>erm</i>(B) and <i>tet</i>(M), which suggested that in the presence of <i>tet</i>(O), the aforementioned multiple resistance is unlikely to be observed. Such heterogeneity in linkages among genes that confer the same phenotypic resistance highlights the importance of incorporating genetic information when investigating the risk factors for the spread of resistance. The epidemiological factors that underlie the persistence of systematic multiple-resistance patterns warrant further investigations with appropriate adjustments for ecological and bacteriological factors.</p></div

Association between clinic-pathological features and EC patients stratified by genetic mutational profiles.

<p>Association between clinic-pathological features and EC patients stratified by genetic mutational profiles.</p

Initial optimal additive Bayesian network model.

<p>Identified interrelationships between selected antimicrobial resistance genes and their effects on the phenotypic expressions of resistance among 113 isolates of <i>Enterococcus faecalis</i> from domestic poultry products collected from retail shops in 5 major Japanese cities between July and August 2012. Abbreviations: ant6: <i>ant</i>(6)-Ia; aph3: <i>aph</i>(3’)-IIIa; EM: erythromycin resistance; DSM_L: MIC for dihydrostreptomycin ≥128 μg/mL and ≤512 μg/mL; DSM_H: MIC for dihydrostreptomycin >512 μg/mL; OTC_L: MIC for oxytetracycline ≥16 μg/mL and ≤64 μg/mL; OTC_H: MIC for oxytetracycline >64 μg/mL. Solid lines and dashed lines represent positive and negative associations between variables, respectively.</p

Prevalence of phenotypic resistance for the tested antimicrobials among isolated Enterococci.

<p>Prevalence of resistance to each tested antimicrobial in <i>E</i>. <i>faecalis</i> and <i>E</i>. <i>faecium</i> isolated from retail poultry products collected in 5 major Japanese cities between July and August 2012.</p><p>^aBreakpoints for <i>E</i>. <i>faecalis</i> and <i>E</i>. <i>faecium</i> were 64 and 8 μg/mL, respectively.</p><p>Prevalence of phenotypic resistance for the tested antimicrobials among isolated Enterococci.</p

Molecular and clinic-pathological features of 138 ECs.

<p>(A) Molecular and clinic–pathological landscape of 138 ECs. Genetic analysis, focusing on frequent hotspot mutations in the POLE gene, and MSI status result in the identification of three molecular subgroups: (1) <i>POLE</i>-mutant, (2) MSI and (3) non-MSI. (B) Progression-free survival and endometrial cancer-specific survival of 138 EC patients stratified by genetic profiles. <i>P</i> values were calculated by the log-rank test.</p

Detection of MSI and distribution of number of MSIs in 138 EC patients.

<p>(A) Example of MSI and non-MSI cases analyzed by four mononucleotide repeat markers (BAT26, NR21, NR27, and CAT25). (B) Association between MSI, <i>POLE</i> mutation, <i>MLH-1</i> promoter methylation and MMR protein expression. The number of mononucleotide repeat markers showing MSI are shown by color.</p