Odour and ammonia emissions from intensive poultry units in Ireland

Odour and ammonia emissions were measured from three broiler, two layer and two turkey houses in Ireland. The broiler units gave a large range of odour and ammonia emission rates depending on the age of the birds and the season. A considerable variation between the odour and ammonia emission rates was evident for the two layer units which may have been due to the different manure handling systems utilised in the houses. There was relatively little difference in the odour and ammonia emissions from the two turkey houses. As a precautionary principle, odour emission rates utilised in atmospheric dispersion models should use the maximum values for broilers and turkeys (1.22 and 10.5 ou(E) s(-1) bird(-1) respectively) and the mean value for the layers depending on the manure handling system used (0.47 or 1.35 ou(E) s(-1) bird(-1)).     

Speciating Campylobacter jejuni and Campylobacter coli isolates from poultry and humans using six PCR-based assays

Six previously published polymerase chain reaction (PCR) assays each targeting different genes were used to speciate 116 isolates previously identified as Campylobacter jejuni using routine microbiological techniques. Of the 116 isolates, 84 were of poultry origin and 32 of human origin. The six PCR assays confirmed the species identities of 31 of 32 (97%) human isolates and 56 of 84 (67%) poultry isolates as C. jejuni. Twenty eight of 84 (33%) poultry isolates were identified as Campylobacter coli and the remaining human isolate was tentatively identified as Campylobacter upsaliensis based on the degree of similarity of 16S rRNA gene sequences. Four of six published PCR assays showed 100% concordance in their ability to speciate 113 of the 116 (97.4%) isolates; two assays failed to generate a PCR product with four to 10 isolates. A C. coli-specific PCR identified all 28 hippuricase gene (hipO)-negative poultry isolates as C. coli although three isolates confirmed to be C. jejuni by the remaining five assays were also positive in this assay. A PCR-restriction fragment length polymorphism assay based on the 16S rRNA gene was developed, which contrary to the results of the six PCR-based assays, identified 28 of 29 hipO-negative isolates as C. jejuni. DNA sequence analysis of 16S rRNA genes from four hipO-negative poultry isolates showed they were almost identical to the C. jejuni type strain 16S rRNA sequences ATCC43431 and ATCC33560 indicating that assays reliant on 16S rRNA sequence may not be suitable for the differentiation of these two species.     

Genetic diversity and quinolone resistance in Campylobacter jejuni isolates from poultry in Senegal

We used the multilocus sequence typing (MLST) method to evaluate the genetic diversity of 46 Campylobacter jejuni isolates from chickens and to determine the link between quinolone resistance and sequence type (ST). There were a total of 16 ST genotypes, and the majority of them belonged to seven clonal complexes previously identified by using isolates from human disease. The ST-353 complex was the most common complex, whereas the ST-21, ST-42, ST-52, and ST-257 complexes were less well represented. The resistance phenotype varied for each ST, and the Thr-86-Ile substitution in the GyrA protein was the predominant mechanism of resistance to quinolone. Nine of the 14 isolates having the Thr-86-Ile substitution belonged to the ST-353 complex. MLST showed that the emergence of quinolone resistance is not related to the diffusion of a unique clone and that there is no link between ST genotype and quinolone resistance. Based on silent mutations, different variants of the gyrA gene were shown to exist for the same ST. These data provide useful information for understanding the epidemiology of C. jejuni in Senegal.     

Penner serotyping of Campylobacter isolates from poultry, with absorbed pooled antisera

The Penner serotyping system, based on detection of heat-stable antigens with a passive haemagglutination technique, was used in studies on Campylobacter epidemiology in poultry. Preparation of specific antisera by absorption allowed the use of pooled antisera. Over 80% of the Campylobacter isolates were typable with this modified Penner serotyping system. Typability of strains was clearly affected by storage of the strains before actual typing. Extracted antigens appeared to be stable for at least 6 months at 4°C. Therefore, it is advisable to store extracted antigens from freshly isolated Campylobacter strains instead of reculturing frozen-stored strains, when actual typing cannot be performed directly after primary isolation. Untypability of isolates may partly be explained by the detection of Campylobacter serovars not yet represented in the serotyping system. Experiments on repeated serotyping of several Campylobacter strains did not suggest any serovar instability within the strains.     

Molecular characterization of the diversity of Campylobacter spp. isolates collected from a poultry slaughterhouse: analysis of cross-contamination

Investigations of a free-range broiler flock during the rearing period and at the slaughterhouse by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) of the flagellin (flaA) gene (flaA typing) have shown that poultry carcasses are contaminated by Campylobacter spp. strains which were previously present in the poultry faces. Moreover, the investigation of the previous and the following batches in the processing plant using flaA typing have shown that cross-contamination between batches coming from different flocks occurs and is also a risk factor for the presence of Campylobacter spp. on poultry carcasses.     

A dispersion modelling approach to determine the odour impact of intensive poultry production units in Ireland

The use of atmospheric dispersion modelling has become more common for the determination of odour impacts from existing poultry production facilities and the assessment of setback distances for new facilities. Setback distances for broiler, layer and turkey units were determined using the atmospheric dispersion model ISCST3 and the Environmental Protection Agency (EPA, Ireland) recommended criterion (C(98,1-h)6.0 ou(E) m(-3)) and a new odour annoyance criterion (C(98,1-h) 9.7 ou(E) m(-3)) developed in this study. For a typical size unit in Ireland, maximum setback distances of 660, 665 and 1035 m were calculated for 40,000 broilers, 40,000 layers and 10,000 turkeys respectively at the current limit (C(98,1-h) 6.0 ou(E) m(-3)). However, if the suggested odour impact criterion (C(98,1-h) 9.7 ou(E) m(-3)) is implemented, the maximum setback distances decrease to 460, 500 and 785 m for broilers, layers and turkeys, respectively.     

Antimicrobial resistance of Campylobacter jejuni and Campylobacter coli isolates from broiler chickens isolated at an Irish poultry processing plant

AIMS: The antibiotic susceptibility of Campylobacter jejuni and Campylobacter coli isolates from broiler chickens were determined in order to evaluate the level of antibiotic resistance of Campylobacter species in the Irish poultry industry. METHODS AND RESULTS: Seventy-eight Camp. jejuni and 22 Camp. coli strains were examined for susceptibility to eight antibiotics using the disc diffusion assay. The highest level of resistance of the Camp. jejuni isolates was recorded to ampicillin (35.9%), followed by 20.5% to tetracycline, 20.5% to naladixic acid, 17.9% to ciprofloxacin, 10.2% to erythromycin, 2.5% to streptomycin and 1.2% to kanamycin. Multidrug resistance to two or more antibiotics was seen for 30.7% of Camp. jejuni strains. Resistance of the Camp. coli isolates was shown to ampicillin (9%) and tetracycline (18.2%). CONCLUSIONS: The majority of Camp. jejuni strains were susceptible to antibiotics commonly used for human therapy. Camp. coli strains showed very low resistance levels and were susceptible to six of the eight antimicrobial agents studied. SIGNIFICANCE AND IMPACT OF THE STUDY: Levels of Camp. jejuni and Camp. coli antimicrobial resistance in Irish poultry production was assessed to determine the current situation in Ireland. The prevalence of antibiotic resistance of Campylobacter strains isolated from broiler chickens was low.     

Prevalence of antimicrobial resistance among serotypes of Campylobacter jejuni isolates from cattle and poultry in Japan

Penner serotypes of C. jejuni in a total of 601 isolates from apparently healthy cattle, layer and broiler chickens in Japan were examined between 2001 and 2006. Predominant serotypes were B (O: 2, 19.1%), D (O: 4, 13.5%), Y (O: 37, 7.3%) and G (O: 8, 5.8%), whereas the remaining serotypes made up less than 5% of the total isolates. The frequency of ampicillin resistance in serotype G (65.6%) was significantly higher than in serotypes D (12.5%), B (11.2%), and Y (0%). Our results suggest that serotype is one factor contributing to the prevalence of ampicillin resistance in C. jejuni isolates.     

Molecular epidemiology of ceftiofur-resistant Escherichia coli isolates from dairy calves

Healthy calves (n = 96, 1 to 9 weeks old) from a dairy herd in central Pennsylvania were examined each month over a five-month period for fecal shedding of ceftiofur-resistant gram-negative bacteria. Ceftiofur-resistant Escherichia coli isolates (n = 122) were characterized by antimicrobial resistance (disk diffusion and MIC), serotype, pulsed-field gel electrophoresis subtypes, beta-lactamase genes, and virulence genes. Antibiotic disk diffusion assays showed that the isolates were resistant to ampicillin (100%), ceftiofur (100%), chloramphenicol (94%), florfenicol (93%), gentamicin (89%), spectinomycin (72%), tetracycline (98%), ticarcillin (99%), and ticarcillin-clavulanic acid (99%). All isolates were multidrug resistant and displayed elevated MICs. The E. coli isolates belonged to 42 serotypes, of which O8:H25 was the predominant serotype (49.2%). Pulsed-field gel electrophoresis classified the E. coli isolates into 27 profiles. Cluster analysis showed that 77 isolates (63.1%) belonged to one unique group. The prevalence of pathogenic E. coli was low (8%). A total of 117 ceftiofur-resistant E. coli isolates (96%) possessed the bla(CMY2) gene. Based on phenotypic and genotypic characterization, the ceftiofur-resistant E. coli isolates belonged to 59 clonal types. There was no significant relationship between calf age and clonal type. The findings of this study revealed that healthy dairy calves were rapidly colonized by antibiotic-resistant strains of E. coli shortly after birth. The high prevalence of multidrug-resistant nonpathogenic E. coli in calves could be a significant source of resistance genes to other bacteria that share the same environment.     

Prevalence of Campylobacter spp. in a subset of intensive poultry flocks in Ireland

Aim:  The aim of this study was to investigate the prevalence of Campylobacter species in a subset of intensive poultry flocks by examining samples collected in geographically disparate areas on the island of Ireland.
Methods and Results:  Faecal, water and environmental samples were collected from the interior of poultry houses on nine farms. Three cultural methods were used for Campylobacter isolation: direct plating, enrichment culture and a recovery method for emerging Campylobacter spp. Presumptive Campylobacter isolates were confirmed using biochemical tests and further identified to species level by multiplex PCR. All flocks sampled in this study were found to be contaminated with Campylobacter at the time of sampling. Structural and air samples taken from the interior of broiler houses were also found to be Campylobacter positive. All water samples were found to be Campylobacter negative. The Campycheck method was used for the isolation of emerging Campylobacter spp.
Conclusions:  Campylobacter spp. were recovered (as contaminants) from the poultry house interior, air and environmental samples in all intensive poultry flocks surveyed.
Significance and Impact of the Study:  This study highlights the need for improved biosecurity on selected poultry farms.     

Molecular subtype analyses of Campylobacter spp. from Arkansas and California poultry operations

Campylobacter isolates from diverse samples within broiler production and processing environments were typed by using flaA short variable region DNA sequence analysis. Sixteen flocks from four different farms representing two broiler producers in Arkansas and California were analyzed. Fourteen of the flocks (87.5%) were Campylobacter-positive; two remained negative throughout the 6-week rearing period. In general, multiple clones were present within a flock. Additionally, clones found within a flock were also present on the final product, although the diversity of Campylobacter spp. on the final product appeared to be reduced relative to that observed within the flock. Comparison of clones between flocks on the same farm revealed that some clones of Campylobacter persisted in multiple flocks. Furthermore, some clones were identified across the two farms that were under the same management. In two sampling periods, environmental isolates were positive for Campylobacter prior to flock shedding. Environmental samples associated with five additional flocks were positive for Campylobacter concomitantly with recovery of Campylobacter from the birds. Analysis of the environmental isolates that were positive prior to flock shedding demonstrated that in some instances the environmental isolates possessed genotypes identical to those of isolates originating from the flock, while in other cases the environmental isolates possessed genotypes that were distantly related to isolates obtained from the flock. Analyses of environmental isolates that tested positive concurrently with the positive isolates from the flocks demonstrated varied results; in some instances the environmental isolates possessed genotypes identical to those of isolates originating from the flock, while in other cases the environmental isolates possessed genotypes that were distantly related to isolates obtained from the flock. These data suggest that the external environment may contribute to Campylobacter contamination during poultry production and processing. However, environmental contamination with Campylobacter does not appear to be the sole contributing factor.     

Molecular epidemiology of pseudomonas aeruginosa clinical isolates from Portuguese Central Hospital

The relatedness between clinical isolates of P. aeruginosa obtained from patients during their stay in a Portuguese Central Hospital was evaluated. Genotypic fingerprinting (M13-PCR), phenotypic methods (biotyping and antibiotyping) and epidemiological information (spatial and temporal links) were used to evaluate the relatedness between 88 clinical isolates (68 patients), selected randomly out of 189. Sixty-two M13 types were found, 12 of them containing isolates from more than one patient. Thirty-four antibiotypes were found, as well as a significant association (p < 0.05) between epidemic isolates and multiresistance patterns. The nosocomial transmission of P. aeruginosa strains may be limited since M13 typing demonstrated a high degree of diversity among all the isolates, suggesting the occurrence of mainly independent infectious episodes. The results show the possible occurrence of cross-acquisition, cross-colonization and cross-infection and suggest an epidemic population structure for P. aeruginosa in this hospital.     

Study on the epidemiology and control of Campylobacter jejuni in poultry broiler flocks.

Broiler flocks are frequently infected with Campylobacter jejuni. The origin of the infection is still unclear. The question of whether colonization of flocks results from transmission of C. jejuni from breeder flocks to progeny (vertical transmission) or from environmental sources (horizontal transmission) remains to be answered. Therefore, in this study samples were taken from successive broiler flocks in two broiler houses (house A on farm A and house B1 on farm B) as well as from the environment of the houses. All C. jejuni isolates were typed by using the Penner serotyping system, and part of the isolates from farm B were typed by using a randomly amplified polymorphic DNA-typing system. In poultry house A, C. jejuni was isolated from the first flock but not from subsequent flocks. In poultry house B1, C. jejuni strains of the same Penner serotypes and exhibiting identical DNA profiles were isolated from successive flocks. Infection of the flocks from a common source via horizontal pathways is suspected, while a vertical route of infection is not likely to exist. Application of measures to control horizontal transmission of C. jejuni on farm B was successful.     

Study on the epidemiology and control of Campylobacter jejuni in poultry broiler flocks.

Broiler flocks are frequently infected with Campylobacter jejuni. The origin of the infection is still unclear. The question of whether colonization of flocks results from transmission of C. jejuni from breeder flocks to progeny (vertical transmission) or from environmental sources (horizontal transmission) remains to be answered. Therefore, in this study samples were taken from successive broiler flocks in two broiler houses (house A on farm A and house B1 on farm B) as well as from the environment of the houses. All C. jejuni isolates were typed by using the Penner serotyping system, and part of the isolates from farm B were typed by using a randomly amplified polymorphic DNA-typing system. In poultry house A, C. jejuni was isolated from the first flock but not from subsequent flocks. In poultry house B1, C. jejuni strains of the same Penner serotypes and exhibiting identical DNA profiles were isolated from successive flocks. Infection of the flocks from a common source via horizontal pathways is suspected, while a vertical route of infection is not likely to exist. Application of measures to control horizontal transmission of C. jejuni on farm B was successful.     

Molecular epidemiology of isolates of the Cryptococcus neoformans species complex from Spain

To study genetic diversity of Cryptococcus neoformans species complex in Spain, 97 isolates of the yeast recovered from human, animal and environmental samples have been analysed using three molecular epidemiological techniques. One of these, URA5 gene fragment length polymorphism (RFLP) analysis, has been previously described as a molecular epidemiology tool. Thus, standard profiles and reference strains have been defined for it. In addition, 5S rDNA/IGS RFLP and [GACA]₄ microsatellite PCR fingerprinting were also used. Our results show five of the previously defined URA5 genotypes with a high frequency (33%) of the VNI type, which is in concordance with other studies. The high presence of VNIII pattern (28.9%) among our strains is remarkable and could be a specific feature of the isolates from our country. 5S rDNA/IGS RFLP showed a low intra-species discriminative power. Three different molecular profiles (S1-3), which showed a good correlation with the different species, varieties and genotypes, were obtained. [GACA]₄ microsatellite PCR-fingerprinting analysis showed a high variability of patterns among the studied strains. Molecular profiles represented in a dendrogram clustered strains in four main groups related with the source of the yeast and also in concordance with some of the described genotypes (VNI-IV and VGI).     

进口水产品中单增李斯特菌的分子流行病学特点

摘要：[目的] 探明进口水产品中单增李斯特菌的污染状况、致病性和分子特征。[方法] 针对2007年7月至2008年11月间从29个国家进口的1275批水产品,进行单增李斯特菌鉴定、谱系与血清型分析、小鼠毒力试验与多位点序列分析。[结果] 检出单增李斯特菌33批次（2.6%）,其中以4b型为主（65.2%）,而1/2a型、1/2b型与1/2c型仅分别占13.0%、17.4%与4.4%。这些分离株对小鼠均具有与强毒参考株相当的毒力。基于actA-hisJ-ribC-sigB的多位点序列分析可将32个菌株分为23个序列型,分辨力达0.97。其中3个序列型包含3个以上分离株,其中序列型9属于流行性克隆I。[结论] 进口水产品中单增李斯特菌污染率与国内水产品相近,但血清型分布以4b型为主,且有流行性克隆I检出,因此要加强对进口水产品中单增李斯特菌的监测。     

Molecular epidemiology and microbiological characteristics of Cryptococcus gattii VGII isolates from China

Cryptococcus gattii (C. gattii) is a fungal pathogen that once caused an outbreak of cryptococcosis on Vancouver Island, and had spread worldwide, while few data were available in China. In this study, seven clinical isolates of C. gattii VGII were collected from 19 hospitals, Multi-locus Sequence Typing (MLST) analysis and whole-genome sequencing (WGS) was performed, combined with published data for phylogenetic analysis. In addition, in vitro antifungal susceptibility testing, phenotypic analysis, and in vivo virulence studies were performed, subsequently, histopathological analysis of lung tissue was performed. C.gattii VGII infected patients were mainly immunocompetent male, and most of them had symptoms of central nervous system (CNS) involvement. MLST results showed that isolates from China exhibited high genetic diversity, and sequence type (ST) 7 was the major ST among the isolates. Some clinical isolates showed a close phylogenetic relationship with strains from Australia and South America. All clinical isolates did not show resistance to antifungal drugs. In addition, there was no correlation between virulence factors (temperature, melanin production, and capsule size) and virulence while in vivo experiments showed significant differences in virulence among strains. Lung fungal burden and damage to lung tissue correlated with virulence, and degree of damage to lung tissue in mice may highlight differences in virulence. Our work seeks to provide useful data for molecular epidemiology, antifungal susceptibility, and virulence differences of C. gattii VGII in China.