Fig 1.
Map of the Netherlands showing locations of the sampled poultry farms.
Table 1.
Numbers of characterized ESBL-producing E. coli isolates per matrix and farm type.
Fig 2.
Prevalence of ESBL-producing E. coli in poultry faeces and environmental samples at laying hen and broiler farms.
White bars represent broiler farms, black bars represent laying hen farms. In between brackets (n = a; b) are indicated the numbers of analysed samples at broiler (a) and laying hen farms (b) respectively; ns = not sampled; *includes water from pits and storage basins as well as run-off water and sediment from gullies.
Table 2.
ESBL-producing E. coli and E. coli concentrations in poultry manure and the environment.
Fig 3.
Diversity among ESBL-producing E. coli variants in poultry faeces and barn rinse water.
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.
Table 3.
Simpson’s Index of Diversity (1-D) among isolates from poultry faeces and farm environment.
Fig 4.
ESBL-producing E. coli variants on laying hen farms.
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.
Fig 5.
ESBL-producing E. coli variants on broiler farms.
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.
Fig 6.
Relationship between ESBL-producing variants from different matrices.
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.