Journal: PLoS ONE

Article Title: Distribution, Numbers, and Diversity of ESBL-Producing E . coli in the Poultry Farm Environment

doi: 10.1371/journal.pone.0135402

Figure Lengend Snippet: Numbers of characterized ESBL-producing E . coli isolates per matrix and farm type.

Article Snippet: Multiple dilutions of each sample were streaked on ChromID ESBL agar (Biomerieux, Boxtel, the Netherlands) for the isolation of ESBL-producing E . coli and on tryptone bile x-glucuronide agar (TBX) for the isolation of E . coli , in accordance with ISO 16649–2 [ ] (for details on sample preparation, see ).

Techniques:

Journal: PLoS ONE

Article Title: Distribution, Numbers, and Diversity of ESBL-Producing E . coli in the Poultry Farm Environment

doi: 10.1371/journal.pone.0135402

Figure Lengend Snippet: ESBL-producing E . coli and E . coli concentrations in poultry manure and the environment.

Article Snippet: Multiple dilutions of each sample were streaked on ChromID ESBL agar (Biomerieux, Boxtel, the Netherlands) for the isolation of ESBL-producing E . coli and on tryptone bile x-glucuronide agar (TBX) for the isolation of E . coli , in accordance with ISO 16649–2 [ ] (for details on sample preparation, see ).

Techniques: Concentration Assay

Journal: PLoS ONE

Article Title: Distribution, Numbers, and Diversity of ESBL-Producing E . coli in the Poultry Farm Environment

doi: 10.1371/journal.pone.0135402

Figure Lengend Snippet: Shown are the proportions of ESBL-producing isolates with the indicated phylogenetic group and ESBL-genotype combinations, among the isolates from poultry faeces and barn rinse water sampled from drains and pits. Lh = laying hen farms, Br = broiler farms.

Article Snippet: Multiple dilutions of each sample were streaked on ChromID ESBL agar (Biomerieux, Boxtel, the Netherlands) for the isolation of ESBL-producing E . coli and on tryptone bile x-glucuronide agar (TBX) for the isolation of E . coli , in accordance with ISO 16649–2 [ ] (for details on sample preparation, see ).

Techniques:

Journal: PLoS ONE

Article Title: Distribution, Numbers, and Diversity of ESBL-Producing E . coli in the Poultry Farm Environment

doi: 10.1371/journal.pone.0135402

Figure Lengend Snippet: Simpson’s Index of Diversity (1-D) among isolates from poultry faeces and farm environment.

Article Snippet: Multiple dilutions of each sample were streaked on ChromID ESBL agar (Biomerieux, Boxtel, the Netherlands) for the isolation of ESBL-producing E . coli and on tryptone bile x-glucuronide agar (TBX) for the isolation of E . coli , in accordance with ISO 16649–2 [ ] (for details on sample preparation, see ).

Techniques:

Journal: PLoS ONE

Article Title: Distribution, Numbers, and Diversity of ESBL-Producing E . coli in the Poultry Farm Environment

doi: 10.1371/journal.pone.0135402

Figure Lengend Snippet: Maximum parsimony trees constructed based on the concatenated sequences of the seven MLST alleles, using Bionumerics 7.1 software. Node sizes reflect the number of isolates per ST and node colours represent different matrices. Additionally indicated are the phylogenetic group, ESBL-genotype and ABR profiles of isolates in every node (i.e., ST). Note that per sample maximally one isolate of each variant was included, and that multiple isolates of a specific variant reflects detection in multiple samples. ABR profiles represent antibiotics to which resistance was observed additionally to 3rd generation cephalosporins. In between brackets are antibiotics with MICs just above and just below epidemiological cut-off values (i.e. with a maximal 2-fold difference) among isolates with the same ST and/or ESBL genotype. Sx = sulfamethoxazole, Tm = trimethoprim; Te = tetracycline, Ci = ciprofloxacin, Na = nalidixic acid, St = streptomycin, Ge = gentamycin, Ax = amoxicillin+clavulanic acid, Ch = chloramphenicol; u.i.d. = unidentified.

Article Snippet: Multiple dilutions of each sample were streaked on ChromID ESBL agar (Biomerieux, Boxtel, the Netherlands) for the isolation of ESBL-producing E . coli and on tryptone bile x-glucuronide agar (TBX) for the isolation of E . coli , in accordance with ISO 16649–2 [ ] (for details on sample preparation, see ).

Techniques: Construct, Software, Variant Assay

Journal: PLoS ONE

Article Title: Distribution, Numbers, and Diversity of ESBL-Producing E . coli in the Poultry Farm Environment

doi: 10.1371/journal.pone.0135402

Figure Lengend Snippet: Maximum parsimony trees constructed based on the concatenated sequences of the seven MLST alleles, using Bionumerics 7.1 software. Node sizes reflect the number of isolates per ST and node colours represent different matrices. Additionally indicated are the phylogenetic group, ESBL-genotype and ABR profiles of isolates in every node (i.e., ST). Note that per sample maximally one isolate of each variant was included, and that multiple isolates of a specific variant reflects detection in multiple samples. ABR profiles represent antibiotics to which resistance was observed additionally to 3rd generation cephalosporins. In between brackets are antibiotics with MICs just above and just below epidemiological cut-off values (i.e. with a maximal 2-fold difference) among isolates with the same ST and/or ESBL genotype. Sx = sulfamethoxazole, Tm = trimethoprim; Te = tetracycline, Ci = ciprofloxacin, Na = nalidixic acid, St = streptomycin, Ge = gentamycin, Ax = amoxicillin+clavulanic acid, Ch = chloramphenicol. Br1 was sampled during three production rounds: August/September 2011 (Br1_1), November 2011 (Br1_2), and August/September 2012 (Br1_3); underlined are variants that were detected at multiple time-points.

Article Snippet: Multiple dilutions of each sample were streaked on ChromID ESBL agar (Biomerieux, Boxtel, the Netherlands) for the isolation of ESBL-producing E . coli and on tryptone bile x-glucuronide agar (TBX) for the isolation of E . coli , in accordance with ISO 16649–2 [ ] (for details on sample preparation, see ).

Techniques: Construct, Software, Variant Assay

Journal: PLoS ONE

Article Title: Distribution, Numbers, and Diversity of ESBL-Producing E . coli in the Poultry Farm Environment

doi: 10.1371/journal.pone.0135402

Figure Lengend Snippet: Indicated are the proportions of isolates from the different environmental matrices, with identical counterparts in manure and rinse water and/or other environmental matrices at the same farm, based on phylogenetic group, ESBL-genotype, ABR profile and ST. White bars represent broiler farms, black bars represent laying hen farms, and hatched bars represent the results for all farms combined.

Article Snippet: Multiple dilutions of each sample were streaked on ChromID ESBL agar (Biomerieux, Boxtel, the Netherlands) for the isolation of ESBL-producing E . coli and on tryptone bile x-glucuronide agar (TBX) for the isolation of E . coli , in accordance with ISO 16649–2 [ ] (for details on sample preparation, see ).

Techniques: