Phylogenetic analysis of H and N2 genes of avian influenza viruses detected in Ireland between 2003 and 2007.

Phylogenetic analysis was performed on the haemagglutinin and neuraminidase subtype N2 genes of low-pathogenic avian influenza viruses (LPAIVs) detected in Ireland between 2003 and 2007. Nucleotide sequences were compared to previously published sequences from the National Centre for Biotechnology Information. Sequences from viruses of the same subtype isolated in different years were compared to examine the possibility that LPAIVs may have been maintained in Ireland from year to year. All viruses had closest identity with published sequences of European lineage, supporting the conclusion that LPAIVs had been introduced to Ireland by dabbling ducks that had migrated from Europe. The data suggested that different subtypes of virus had been introduced each year. However, there was evidence that some LPAIVs may have been maintained in the sedentary waterfowl population for consecutive seasons. Furthermore, almost identical H6 and H10 sequences with different N types were found in isolates from the same season, suggesting that reassortment had occurred.

Avian influenza viruses detected by surveillance of waterfowl in Ireland during 2003-2007.

Specimens for the detection of avian influenza virus (AIV) were collected from 1937 waterfowl on the Wexford Sloblands, a major wetland reserve in southeast Ireland, between January 2003 and September 2007. During the same period, 1404 waterfowl were sampled at other locations in Ireland. Specimens were tested either by virus isolation or real-time reverse transcriptase polymerase chain reaction (rtRT-PCR). A total of 32 isolates of AIV, comprising nine subtypes, was obtained from specimens from the Sloblands compared with just one isolate from elsewhere in Ireland. Samples from nine other waterfowl, five of which were from the Sloblands, tested positive for AIV by rtRT-PCR. Ecological factors are likely to have contributed to the higher detection rate of AIV at the Sloblands compared with the rest of Ireland. It was concluded that targeted surveillance at such sites is a cost-effective means of monitoring the circulation of new AIVs in waterfowl, whereas widespread opportunistic sampling is unproductive and wasteful of resources.

Phenotypic and genotypic anti-microbial resistance profiles of campylobacters from untreated feedlot cattle and their environment.

Anti-microbial resistance is an emerging public health issue. Farmed animals may act as reservoirs and potential sources of anti-microbial resistant Campylobacters. The aim of this study was to investigate the anti-microbial resistance profile of cattle and environmental Campylobacter isolates from normal untreated feedlot cattle, the role of the gyrA Thr-86-Ile mutation in ciprofloxacin-resistant Campylobacter jejuni isolates and the involvement of the tripartite CmeABC efflux system for multi-resistant C. jejuni isolates. The phenotypic anti-microbial resistance testing was carried out on 500 Campylobacter isolates (445 cattle isolates and 55 environmental isolates). In general, there was a higher level of anti-microbial resistance for the environmental isolates compared with the animal isolates, 45% of the animal isolates were resistant to one or more of the seven anti-microbials compared with 84% of the environmental isolates. The combined cattle and environmental Campylobacters had 34 (6.8%) isolates resistant to three or more of the seven anti-microbials tested on all isolates and 11 (2.2%) isolates were resistant to the seven anti-microbials. There was a substantial level of ciprofloxacin-resistant Campylobacters in both animal (8.5%) and environmental (21.8%) isolates. The gyrA Thr-86-Ile mutation was only present in five of 22 ciprofloxacin-resistant C. jejuni isolates investigated. No multi-drug-resistant associated mutation was detected in the CmeB or the CmeR regions investigated. In conclusion, our study observed a substantial level of Campylobacter anti-microbial resistance, highlighting the need for an active anti-microbial surveillance program for food animals in Ireland and the importance of the chosen sampling point can have on the findings of such a program.

The characterisation of E. coli O157:H7 isolates from cattle faeces and feedlot environment using PFGE.

The objectives of this study were to investigate the diversity of Escherichia coli O157:H7 isolates obtained over a 3-month period from a cattle feedlot in order to assess the relationship between environmental and faecal isolates and to determine the pattern of transmission of E. coli O157:H7 between groups of cattle. Faecal samples were obtained from cattle housed in four adjacent feedlot pens at monthly intervals, with environmental pen samples collected simultaneously. All E. coli O157:H7 isolates obtained were examined by pulsed field gel electrophoresis (PFGE), polymerase chain reaction (PCR) to detect eaeA, ehxA, stx1 and stx2 genes and antibiotic sensitivity profiling. Ten isolates were subjected to acid shock to imitate conditions in the acidic cattle abomasum and assess the effect on PFGE profiles. E. coli O157:H7 was isolated from 69 faecal samples and 26 environmental samples. All isolates (n=95) carried the genes for eaeA, ehxA and stx2 and were sensitive to all antibiotics tested. The PFGE profiles of all isolates differed by no more than two bands and clustered within 80% similarity following dendrogram analysis. Acid shock had no effect on the subsequent PFGE patterns. A total of 8.7% (6/69) of cattle were shedding E. coli O157:H7 in the first month with faecal shedding increasing to 52% (36/69) by the third month of the study. A single isolate of E. coli O157:H7 may be passed rapidly through cattle pens, with the environment acting as a significant reservoir for transmission. PFGE is a useful tool for tracking the direct and indirect transmission of E. coli O157:H7 isolates on the farm.

Campylobacter spp. in Irish feedlot cattle: a longitudinal study involving pre-harvest and harvest phases of the food chain.

The aim of this study was to investigate faecal shedding and transmission of Campylobacter spp. in cohorts of cattle within a feedlot, to assess subsequent contamination of carcasses with this pathogen and to identify risk factors associated with faecal shedding of Campylobacter spp. A cohort of 133 heifers housed in four adjacent pens was examined over a five and a half month period, from entering the feedlot to slaughter. A parallel investigation of individual rectal faecal samples and pen environmental samples were taken at monthly intervals from November to February. The entire outer and inner surfaces of a carcass side of each animal were swabbed immediately following slaughter. Campylobacter spp. were isolated from 322 (54%) of the 600 rectal faecal samples. Campylobacter jejuni and C. coli accounted for 69 and 29.7% of the isolate recovered, respectively. A total of 159 environmental samples were examined, of these Campylobacter spp. was isolated from 46 samples (29%). Campylobacter jejuni and C. coli accounted for 35 and 59% of these isolates, respectively. Campylobacter spp. was not isolated from any of the dressed carcasses. Logistic regression indicated prevalence of Campylobacter spp. faecal shedding within pens was positively correlated to the pen, the month of sampling and the Campylobacter spp. contamination status of the pen dividing bars and the water trough surface. Campylobacter spp. should be considered as a pathogen shed in the faeces of a substantial proportion of feedlot cattle. However, with good hygienic practice during harvest, a very low level of this pathogen can be achieved on dressed carcasses.

An investigation on the effect of transport and lairage on the faecal shedding prevalence of Escherichia coli O157 in cattle.

The aim of the study was to investigate the effect of transport and lairage on the prevalence of Escherichia coli O157 faecal shedding and the subsequent contamination of beef carcasses. Individual rectal faecal samples were taken from two cohorts of cattle (109 and 59) at the farm before transport and at the abattoir post-transport and lairage. The entire outer and inner surfaces of the carcass of each animal were swabbed immediately following slaughter and dressing. The prevalence of E. coli O157 shedding in cattle sampled at farm, post-transport and lairage was 18% (20), 13% (14) and 12% (13) for cohort A and 1.7% (1), 1.7% (1) and 0 for cohort B, respectively. No E. coli O157 was recovered from the 168 dressed carcasses. In total, 98% (46 of 47) of the E. coli O157 isolates from cohort A were potentially pathogenic to man. Transport and lairage do not cause an increase in the prevalence of E. coli O157 faecal shedding in cattle. This study demonstrates that even positive cohorts of cattle may be slaughtered and processed to produce clean carcasses by following good hygienic practices.

The effect of commercial steam pasteurization on the levels of Enterobacteriaceae and Escherichia coli on naturally contaminated beef carcasses.

The aim of the study was to assess the reduction achieved by steam pasteurization of beef carcasses of Escherichia coli, Enterobacteriaceae and total aerobic mesophilic plate counts (APCs). In total, 30 carcass halves were exposed to steam pasteurization (90 degrees C, 10 s exposure time) and the 30 corresponding carcass halves remained as untreated controls. The neck, midline and rump were sampled on each carcass half. Significant reductions in E. coli incidence (P < 0.05) and counts, 0.5 log10 CFU 1000 cm(-2) (P < 0.05), were observed on rump sites only. Significant reductions (>0.8 log10 CFU 1000 cm(-2)) of Enterobacteriaceae were observed at all carcass sites sampled (P < 0.05). Enterobacteriaceae reductions (>2 log10 CFU 1000 cm(-2)) were highly significant at the more contaminated sites (P < 0.001). Reductions in total APCs were inconsistent. Steam pasteurization significantly reduced the level of E. coli and Enterobacteriaceae at more contaminated sites, but did not result in complete decontamination. Therefore, steam pasteurization should be classed as an aid to hygienic beef processing, but not as a critical control point.