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

Map of Japan showing the study area.

<p>A choropleth map of 46 Japanese administrative areas (prefectures) showing the origin of the purchased domestic chicken products and the quantity of products supplied from each prefecture. The origin of 82 domestic products (52.6%) was unavailable and is not shown. The superimposed points show the locations of the 5 Japanese cities where chicken products were purchased between July and August 2012.</p

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

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

Proportion of bootstrap samples detecting one or more <i>E. coli</i> isolates resistant to 12 different antimicrobials, obtained with 6 different sampling strategies and 10,000 bootstrap replications per strategy.

<p>ID = identification of sampling strategy shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0087147#pone-0087147-t001" target="_blank">Table 1</a>.</p><p>OTC = oxytetracycline, SIX = Sulfisoxazole, ST = sulfamethoxazole/trimethoprim, ABPC = ampicillin, CP = chloramphenicol, SM = dihydrostreptomycin, KM = kanamycin, NA = nalidixic acid, CEZ = cefazolin, GM = gentamicin, CPFX = ciprofloxacin, CTX = cefotaxime.</p

Proportions of <i>E. coli</i> isolates resistant to 12 different antimicrobials obtained with 6 different sampling strategies and 10,000 bootstrap replications per strategy.

<p>P = antimicrobial prevalence in 1,500 fecal samples.</p><p>ID = identification of sampling strategy shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0087147#pone-0087147-t001" target="_blank">Table 1</a>.</p><p>OTC = oxytetracycline, SIX = Sulfisoxazole, ST = sulfamethoxazole/trimethoprim, ABPC = ampicillin, CP = chloramphenicol, SM = dihydrostreptomycin, KM = kanamycin, NA = nalidixic acid, CEZ = cefazolin, GM = gentamicin, CPFX = ciprofloxacin, CTX = cefotaxime.</p

List of sampling strategies evaluated by bootstrap resampling.

<p>List of sampling strategies evaluated by bootstrap resampling.</p