Prevalence and types of Campylobacter on poultry farms and in their direct environment.

To study whether broiler and layer farms contribute to the environmental Campylobacter load, environmental matrices at or close to farms, and caecal material from chickens, were examined. Similarity between Campylobacter from poultry and environment was tested based on species identification and Multilocus Sequence Typing. Campylobacter prevalence in caecal samples was 97% at layer farms (n = 5), and 93% at broiler farms with Campylobacter-positive flocks (n = 2/3). Campylobacter prevalence in environmental samples was 24% at layer farms, and 29% at broiler farms with Campylobacter-positive flocks. Campylobacter was detected in soil and surface water, not in dust and flies. Campylobacter prevalence in adjacent and remote surface waters was not significantly (P > 0.1) different. Detected species were C. coli (52%), C. jejuni (40%) and C. lari (7%) in layers, and C. jejuni (100%) in broilers. Identical sequence types (STs) were detected in caecal material and soil. A deviating species distribution in surface water adjacent to farms indicated a high background level of environmental Campylobacter. STs from layer farms were completely deviant from surface water STs. The occasional detection of identical STs in broilers, wastewater at broiler farms and surface water in the farm environment suggested a possible contribution of broiler farms to the aquatic environmental Campylobacter load

Prevalence and types of Campylobacter on poultry farms and in their direct environment.

To study whether broiler and layer farms contribute to the environmental Campylobacter load, environmental matrices at or close to farms, and caecal material from chickens, were examined. Similarity between Campylobacter from poultry and environment was tested based on species identification and Multilocus Sequence Typing. Campylobacter prevalence in caecal samples was 97% at layer farms (n = 5), and 93% at broiler farms with Campylobacter-positive flocks (n = 2/3). Campylobacter prevalence in environmental samples was 24% at layer farms, and 29% at broiler farms with Campylobacter-positive flocks. Campylobacter was detected in soil and surface water, not in dust and flies. Campylobacter prevalence in adjacent and remote surface waters was not significantly (P > 0.1) different. Detected species were C. coli (52%), C. jejuni (40%) and C. lari (7%) in layers, and C. jejuni (100%) in broilers. Identical sequence types (STs) were detected in caecal material and soil. A deviating species distribution in surface water adjacent to farms indicated a high background level of environmental Campylobacter. STs from layer farms were completely deviant from surface water STs. The occasional detection of identical STs in broilers, wastewater at broiler farms and surface water in the farm environment suggested a possible contribution of broiler farms to the aquatic environmental Campylobacter load

ESBL-producing <i>E</i>. <i>coli</i> variants on laying hen farms.

<p>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.</p

ESBL-producing <i>E</i>. <i>coli</i> and <i>E</i>. <i>coli</i> concentrations in poultry manure and the environment.

<p>^aFor some of the samples total <i>E</i>. <i>coli</i> was not determined (*): in these cases the number of samples analyzed for ESBL-producing <i>E</i>. <i>coli</i> (a) and <i>E</i>. <i>coli</i> (b) are indicated separately (n = a; b).</p><p>^bPercentages of samples positive for the indicated bacteria.</p><p>^c Concentration ranges observed in the positive samples</p><p>^d Indicated after fly species/family (n = x, y) is the number of pools (x) and the number of flies (y)</p><p>cfu = colony forming units; Geo-mean = geometric mean; n.a. = not applicable.</p><p>ESBL-producing <i>E</i>. <i>coli</i> and <i>E</i>. <i>coli</i> concentrations in poultry manure and the environment.</p

Relationship between ESBL-producing variants from different matrices.

<p>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.</p

Numbers of characterized ESBL-producing <i>E</i>. <i>coli</i> isolates per matrix and farm type.

<p>* Indicated between brackets are the numbers of isolates that were not characterized using MLST.</p><p>Numbers of characterized ESBL-producing <i>E</i>. <i>coli</i> isolates per matrix and farm type.</p

Prevalence of ESBL-producing <i>E</i>. <i>coli</i> in poultry faeces and environmental samples at laying hen and broiler farms.

<p>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.</p

ESBL-producing <i>E</i>. <i>coli</i> variants on broiler farms.

<p>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.</p

Map of the Netherlands showing locations of the sampled poultry farms.

<p>Map of the Netherlands showing locations of the sampled poultry farms.</p

Diversity among ESBL-producing <i>E</i>. <i>coli</i> variants in poultry faeces and barn rinse water.

<p>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.</p