High levels of contamination and antimicrobial-resistant non-typhoidal Salmonella serovars on pig and poultry farms in the Mekong Delta of Vietnam.

We investigated the prevalence, diversity, and antimicrobial resistance (AMR) profiles of non-typhoidal Salmonella (NTS) and associated risk factors on 341 pig, chicken, and duck farms in Dong Thap province (Mekong Delta, Vietnam). Sampling was stratified by species, district (four categories), and farm size (three categories). Pooled faeces, collected using boot swabs, were tested using ISO 6575: 2002 (Annex D). Isolates were serogrouped; group B isolates were tested by polymerase chain reaction to detect S. Typhimurium and (monophasic) serovar 4,[5],12:i:- variants. The farm-level adjusted NTS prevalence was 64·7%, 94·3% and 91·3% for chicken, duck and pig farms, respectively. Factors independently associated with NTS were duck farms [odds ratio (OR) 21·2], farm with >50 pigs (OR 11·9), pig farm with 5-50 pigs (OR 4·88) (vs. chickens), and frequent rodent sightings (OR 2·3). Both S. Typhimurium and monophasic S. Typhimurium were more common in duck farms. Isolates had a high prevalence of resistance (77·6%) against tetracycline, moderate resistance (20-30%) against chloramphenicol, sulfamethoxazole-trimethoprim, ampicillin and nalidixic acid, and low resistance (<5%) against ciprofloxacin and third-generation cephalosporins. Multidrug resistance (resistance against ⩾3 classes of antimicrobial) was independently associated with monophasic S. Typhimurium and other group B isolates (excluding S. Typhimurium) and pig farms. The unusually high prevalence of NTS on Mekong Delta farms poses formidable challenges for control.

A longitudinal observational study of Salmonella shedding patterns by commercial turkeys during rearing and fattening, showing limitations of some control measures.

1. The onset and progression of Salmonella infections was investigated in commercial turkey flocks from placement at 1 d old until slaughter in "brood and move" systems using a longitudinal observational approach based on faeces and environmental sampling with subsequent culture of Salmonella. 2. Persistent Salmonella Newport contamination was found within rearing houses and on their external concrete aprons after cleaning and disinfection between crops of heavily shedding young birds. 3. Salmonella shedding was often detected by 5 d of age and the frequency of positive samples peaked at 14-35 d. Thereafter Salmonella isolations declined, especially in the later (fattening) stages. Samples were still Salmonella-positive at low prevalence in half of the intensively sampled houses at slaughter age. 4. A number of management interventions to combat Salmonella infection of flocks, including sourcing policy, competitive exclusion cultures and cleaning and disinfection, were inadequate to prevent flock infection, although improved disinfection on one unit was associated with a delay in the onset of flock infection.

An epidemiological investigation of Campylobacter in pig and poultry farms in the Mekong delta of Vietnam.

Campylobacter are zoonotic pathogens commonly associated with gastroenteritis. To assess the relevance of Campylobacter in Vietnam, an economically transitioning country in SE Asia, we conducted a survey of 343 pig and poultry farms in the Mekong delta, a region characterized by mixed species farming with limited biosecurity. The animal-level prevalence of Campylobacter was 31·9%, 23·9% and 53·7% for chickens, ducks and pigs, respectively. C. jejuni was predominant in all three host species, with the highest prevalence in pigs in high-density production areas. Campylobacter isolates demonstrated high levels of antimicrobial resistance (21% and 100% resistance against ciprofloxacin and erythromycin, respectively). Multilocus sequence type genotyping showed a high level of genetic diversity within C. jejuni, and predicted C. coli inter-species transmission. We suggest that on-going intensification of animal production systems, limited biosecurity, and increased urbanization in Vietnam is likely to result in Campylobacter becoming an increasingly significant cause of human diarrhoeal infections in coming years.

Sensitivity of environmental sampling methods for detecting Salmonella Enteritidis in commercial laying flocks relative to the within-flock prevalence.

The objective of this study was to estimate the sensitivity of three different sampling/testing methodologies for the detection of Salmonella Enteritidis in commercial egg-laying flocks relative to the within-flock prevalence. The following methods were compared on 21 farms: (1) The European Union (EU) baseline survey method (five faecal and two dust samples); (2) an in-house method that involved collecting 10 dust and 10 faecal samples into jars with buffered peptone water, and (3) a method involving single samples of pooled faeces and dust that has been adopted as a monitoring method for the National Control Programme across the EU (the NCP method). Testing of individual bird ovaries/oviduct and caeca was carried out on each flock, and the sensitivity of each sampling method was estimated relative to the within-flock prevalence using Bayesian methods. Results showed that the sensitivity of all the sampling methods increased as the within-flock prevalence increased, and that all were more efficient than individual bird sampling for detection of S. Enteritidis in commercial flocks. The in-house method was the most sensitive of the methods compared, with a 98% power to detect a 0.1% prevalence, and the NCP method the least sensitive, with a 93% power to detect a prevalence of 20%.

Investigation of risk factors for Salmonella on fattening-turkey farms.

A cross-sectional study into risk factors for Salmonella was undertaken using data gathered from 252 fattening turkey flocks in the UK. The data was derived from the EU baseline survey conducted during 2006 and 2007, in addition to a voluntary questionnaire. Multivariate logistic regression models identified significant risk factors for Salmonella spp. and Salmonella Typhimurium. A decreased risk of Salmonella spp. infection was associated with a history of intestinal illness in the sampled flock (OR 0.17), the use of wood shavings as litter (OR 0.21), use of disinfectant in the cleaning process (OR 0.25), incineration of dead birds on farm (OR 0.29), seasonal production (OR 0.31), farm staff also working with cattle (OR 0.31), and the presence of pigs on neighbouring farms (OR 0.38). The risk of isolating Salmonella spp. varied according to the company from which the poults were sourced. A reduced risk of S. Typhimurium infection was associated with the use of wax blocks to control rodents (OR 0.09), using mains water (OR 0.19) and having a Salmonella test programme (OR 0.23). An increased risk of S. Typhimurium infection was associated with storage of items around the turkey house (OR 5.20), evidence of mice (OR 4.71) and a soil surface surrounding the turkey house (OR 2.70). This study therefore identifies a number of important practical measures which can be implemented by farmers and veterinarians within the turkey industry to assist in the control of salmonellosis at the farm level.

A comparison of the efficacy of different disinfection methods in eliminating Salmonella contamination from turkey houses.

AIMS: This study aimed to compare the efficacy of different disinfection methods in eliminating Salmonella contamination from turkey houses. METHODS AND RESULTS: Fifty depopulated turkey houses which had all housed Salmonella-positive flocks were visited after cleaning and disinfection. A minimum of 45 swab samples from different surfaces were taken per house and analysed for the presence of Salmonella. The sampled surfaces included intact floor surfaces, floor cracks, walls, feeders, drinkers, anteroom, nestboxes and miscellaneous items. Houses were grouped according to the disinfectant which had been used and the efficacy of the different groups of disinfectants was compared. Sixty-eight % of houses tested positive for Salmonella after C&D. Out of 4440 samples, 207 tested positive for Salmonella, giving an overall sample prevalence of 4.7%. There was no significant difference in the level of residual contamination between breeding, rearing and finishing houses. Products containing a mixture of formaldehyde, glutaraldehyde and quaternary ammonium compounds (QAC) performed significantly better than products containing hydrogen peroxide and peracetic acid. Cleaning and disinfection was least effective in nestboxes and anterooms. CONCLUSIONS: Thorough cleaning and the choice of a suitable disinfectant are crucial if Salmonella contamination of turkey houses is to be eliminated. SIGNIFICANCE AND IMPACT OF THE STUDY: This study shows that disinfectants containing a mixture of formaldehyde, glutaraldehyde and QAC perform significantly better under field conditions than oxidising products and should therefore be the first choice for disinfection of turkey premises where Salmonella is present.

Salmonella serovars and their antimicrobial resistance in British turkey flocks in 1995 to 2006.

Serovar and antimicrobial resistance data from the scanning surveillance of British turkey flocks for Salmonella between 1995 and 2006 were analysed and compared with prevalence data from other livestock and animal feed. A total of 2753 incidents of 57 different serovars were reported. The five most prevalent serovars were Salmonella Typhimurium (20.8%), Salmonella Newport (14.7%), Salmonella Derby (10.6%), Salmonella Indiana (8.3%) and Salmonella Agona (6.4%). S. Typhimurium reports peaked in the mid- to late 1990s; this occurred in parallel with the S. Typhimurium DT104 epidemic in other livestock species. S. Enteritidis reports peaked in mid- to late 1990s, followed by a considerable decrease after 2000, which was also noted in flocks of domestic fowl. S. Newport, Salmonella Montevideo, Salmonella Senftenberg and Salmonella Binza occurred in marked clusters, indicating that they were introduced into one or more flocks at a certain time (i.e. via contaminated feed or infected 1-day-old chicks). A proportion of 43.1% of the reported Salmonella isolates were resistant to at least one antimicrobial, while 17.7% were multi-resistant. No isolates were resistant to ciprofloxacin or to the third-generation cephalosporins ceftazidime and cefotaxime. Resistance to ampicillin, chloramphenicol, streptomycin, sulphonamide compounds and tetracycline was common, and it was mainly a characteristic of S. Typhimurium DT104 compared with S. Typhimurium non-DT104 and non-S. Typhimurium isolates (P<0.001). Resistance to nalidixic acid decreased from 16.9% in 1995 to 11.8% in 2006. Nalidixic acid resistance was most frequently found in Salonella Hadar (71.4%), S. Typhimurium DT104 (30.0%), S. Newport (17.9%) and S. Typhimurium non-DT104 (11.1%).

Comparison of three plating media for the isolation of Salmonella from poultry environmental samples in Great Britain using ISO 6579:2002 (Annex D).

AIMS: To evaluate the performance of three Salmonella plating media (Rambach, Xylose Lysine Deoxycholate agar and modified Brilliant Green Agar plus Novobiocin) as part of the ISO 6579: 2002 (Annex D) on poultry environmental samples. METHODS AND RESULTS: The samples analysed were those for the European Union Salmonella baseline surveys of laying (N = 3087), broiler (N = 1550), turkey fattening (N = 1540) and turkey breeding (N = 580) flocks for Great Britain. Results were considered separately for Rambach (including and excluding pale orange colonies) and for growth on selective media [Modified semi-solid Rappaport Vassiliadis (MSRV)] after 24 and 48 h of incubation. Overall, Rambach was the most sensitive medium, provided that pale orange colonies were checked. In all cases, an increase in the sensitivity of detection was obtained by plating growth on MSRV after 48 h of incubation. In broilers and laying flocks, the specificity significantly improved when Rambach only was used. CONCLUSION: The use of Rambach results in considerable savings compared with the two-plate method prescribed by ISO 6579:2002 (Annex D) without compromising sensitivity. SIGNIFICANCE AND IMPACT OF THE STUDY: Salmonella isolation protocols should be reviewed in terms of their efficiency and cost.

The estimation of pooled-sample sensitivity for detection of Salmonella in turkey flocks.

AIMS: To investigate the effectiveness of pooled sampling methods for detection of Salmonella in turkey flocks. METHODS AND RESULTS: Individual turkey droppings were taken from 43 flocks, with half the dropping tested for Salmonella as an individual sample and the other half included in a pool of five. A pair of boot swabs and a dust sample were also taken from each flock. The results were analysed using Bayesian methods in the absence of a gold standard. This showed a dilution effect of mixing true-positive with negative samples, but even with this the pooled faecal samples were found to be a highly efficient method of testing compared with individual faecal samples. The more samples included in the pool, the more sensitive the pooled sampling method was predicted to be. The sensitivity of dust sampling was much more sensitive than faecal sampling at low prevalence. CONCLUSIONS: Pooled faecal sampling is an efficient method of Salmonella detection in turkey flocks. The additional testing of a dust sample greatly increased the effectiveness of sampling, especially at low prevalence. SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first study to relate the sensitivity of the sampling methods to the within-flock prevalence.

Comparison of sampling methods to detect Salmonella infection of turkey flocks.

AIMS: To compare the efficiency of various sampling methods for detection of Salmonella in turkey flocks. METHODS AND RESULTS: In a field study that compared various sampling methods one pair of boot swabs taken from the whole turkey house provided suitably sensitive results for fattening and rearing flocks and was no less sensitive than two pairs, each from half the house, tested as a pooled sample. The sensitivity was further enhanced by adding a dust sample. The dust sample appeared to be particularly useful in flocks with a low prevalence, especially in breeding flocks, and was more sensitive than a method which used five pairs of boot swabs per flock. Combined incubation of a boot swab and a dust sample showed no interference between the two sample types and a maximum sensitivity of detection. Litter samples and commercial sponge drag swabs provided a lower level of detection. CONCLUSIONS: A single pair of boot swabs taken from the whole house is recommended for routine sampling of commercial rearing or fattening flocks. An additional dust sample could be added to increase detection in flocks with a low prevalence or in breeding flocks, but adding an additional pair of boot swabs would not increase detection compared with a single pair. SIGNIFICANCE AND IMPACT OF THE STUDY: This study demonstrates that significant efficiencies can be made in sampling programmes for detection of Salmonella in turkey flocks without detracting from the sensitivity. Similar studies are recommended for other poultry sectors, particularly in chicken breeding flocks.

Salmonella colonisation of laying hens following vaccination with killed and live attenuated commercial Salmonella vaccines.

The aim of this study was to determine the efficacy of a killed Salmonella vaccine and three live vaccines in preventing caecal colonisation of Hy-line Brown pullets by Salmonella Enteritidis PT 4. The lowest number of Salmonella-positive birds following the largest challenge (10(8) cfu) was recorded for live vaccine 1. However, birds treated with the killed vaccine had a significantly lower number of salmonellae in their caeca compared with both the control group and the other vaccine groups (P<0.05).

Risks for bovine tuberculosis in British cattle farms restocked after the foot and mouth disease epidemic of 2001.

The foot and mouth disease (FMD) epidemic of 2001 was used to investigate herd breakdown (HBD) with bovine tuberculosis (bTB) in totally restocked herds of cattle. By August 2004, 2941 restocked cattle herds, with cattle movements from before and after 2001, had been tested for bTB for the first time since restocking. A total of 6% (177) of these herds broke down at the first bTB test. A binomial logistic regression model with HBD (at least one reactor bovine) at the first test after restocking as the outcome was used to investigate risks associated with HBD. The final model contained three risk factors. There was an increased risk for HBD in restocked herds with every log increase in herd size with an OR=1.38 (CI 1.16-1.64) to a maximum OR of 10.75. When there was a history of bTB on the restocked farm before 2001 the OR, with CI not including unity, were 5.92, 4.63, 3.8 and 2.9 for last HBD in 2000, 1999, 1998 and 1997, respectively, indicating a persistence in increased risk for restocked herds from farms with a history of HBD in the previous herd before restocking, i.e. a different population of cattle. Finally, for every log increase in the number of cattle purchased from herds with a greater than biennial frequency of testing for bTB in the previous 8 years (i.e. perceived high risk herds for bTB) there was an OR=1.35 (95% CI 1.22-1.49). The maximum OR was 9.27. These results indicate that both introduction of bTB through the purchase of cattle from farms with a high perceived risk of bTB infection and persistence of bTB on the restocked farm, (not the farm's original herd), were associated with an increased risk of HBD in the newly formed herds after restocking.

Comparison of environmental sampling methods for detecting Salmonella in commercial laying flocks in the UK.

AIMS: To investigate the performance of the Salmonella National Control Programme (NCP) sampling/testing methods in laying flocks of domestic fowl. METHODS AND RESULTS: Eighty-five visits were made to 69 flocks representative of the main production systems (cage, barn and free-range) infected with Salmonella. In each visit, three methodologies were compared: (i) the European Union (EU) baseline survey method (five faeces and two dust samples); (ii) an in-house (Veterinary Laboratories Agency, VLA) 'wet' method that involved collecting 10 dust and 10 faeces samples into jars with buffered peptone water; and (iii) a method involving two samples of pooled faeces and one of dust (cultured as one sample of each type), which has been adopted for the NCP for laying flocks across the EU. CONCLUSIONS: The 'wet' method was the most sensitive, and the NCP the least, although individual NCP samples were the most sensitive ones. SIGNIFICANCE AND IMPACT OF THE STUDY: The apparent lower sensitivity of the NCP method may be compensated by repeated sampling of flocks (twice during rear and several times during lay). Sampling using VLA methodology should be advocated for farms aiming to disclose low-level Salmonella before restrictions on the sale of eggs from Salmonella Enteritidis or Salmonella Typhimurium-infected flocks are in place.

Bacteriological detection of Salmonella enteritidis in eggs: a review.

The detection of Salmonella enterica serovar Enteritidis (SE) in eggs is hampered by a typically low prevalence of contaminated eggs, the low number of SE organisms in such eggs, and the presence of inhibitory substances in the egg albumin. For these reasons, the analysis of large pools of eggs is normally necessary, which presents logistic and microbiological challenges associated with a low number of target organisms from a large volume of sample matrix. In some studies using artificially inoculated eggs the standard procedure for Salmonella culture consisting of pre-enrichment, followed by selective enrichment and plating has been replaced by incubation of the egg pools at 25 degrees C to 37 degrees C followed by direct plating. However, in most cases using pools of naturally contaminated eggs, it may be necessary to enhance the traditional three-step method by addition of antibiotics or iron supplements.

Sampling and bacteriological detection of Salmonella in poultry and poultry premises: a review.

The detection of Salmonella in primary poultry production is an issue of great concern in the European Union (EU), since control of this zoonotic disease is in part based on the reduction of the prevalence at the farm level. Success of detection is likely to be highly dependent on the choice of an adequate sampling procedure combined with a sensitive culture method. In poultry farms 'naturally pooled' faeces/litter and dust are the matrices of choice. In floor systems boot swabs are the preferred method for the collection of faeces. A wide range of culture methods is available, but ISO 6579:2002 (Annex D) is currently the standard for poultry environmental samples in the EU. In this review, the authors discuss in detail the range of sampling and culture methodologies for Salmonella in poultry farms. The review also covers sampling and testing of poultry hatcheries, live birds and poultry carcasses.

Trends in phage types and antimicrobial resistance of Salmonella enterica serovar Enteritidis isolated from animals in Great Britain from 1990 to 2005.

Surveillance data for Salmonella enterica serovar Enteritidis incidents and isolations from food animals in Great Britain from 1990 to 2005 were analysed to detect any trends and provide the basis for a comparison between phage types (pt) and antimicrobial sensitivity patterns in human beings and animals. During 2001 to 2005 there was a decrease in incidents involving most species except ducks. Only the numbers of incidents involving pts 6, 6a, 9b and 14b (in ducks) and pts 6a and 13a (in mammals) increased significantly during this period, whereas there were 93 per cent fewer incidents involving pt 4 than in 1990 to 2000. After adjustment for pt, the isolates from ducks were more resistant to nalidixic acid, tetracyclines and sulfonamides, and were more likely to be multiresistant than isolates from chickens. Isolates from turkeys tended to be more resistant to sulfonamides than isolates from chickens. pts 1, 5a, 6, 6a and 35 had the highest level of resistance after adjusting for species. During 2001 to 2005 there was an increase in resistance among pts 1, 6 and 7, in most cases involving nalidixic acid.

Survey of the prevalence of Salmonella on commercial broiler farms in the United Kingdom, 2005/06.

Between October 2005 and September 2006, all European Union member states were required to carry out standardised surveys of the prevalence of Salmonella in broiler flock holdings to establish baseline data from which to derive national targets for disease reduction. In the uk 382 holdings were sampled, 41 of which were positive for Salmonella, giving an estimated weighted prevalence of 10.7 per cent (95 per cent confidence interval [ci] 8.1 to 13.1 per cent). The serotype most frequently isolated was Salmonella Ohio, with a weighted prevalence of 2.2 per cent (95 per cent ci 1.2 to 3.7 per cent), followed by Salmonella Kedougou at 1.7 per cent (95 per cent ci 0.9 to 3.2 per cent). There were no isolates of Salmonella Enteritidis and only a single isolation of Salmonella Typhimurium (0.2 per cent, 95 per cent ci 0.0 to 1.6 per cent). Of the three other serotypes given top priority by the eu owing to their public health significance, Salmonella Virchow was isolated from one holding, but Salmonella Hadar and Salmonella Infantis were not detected on any of the holdings.

Detection of potentially novel paramyxovirus and coronavirus viral RNA in bats and rats in the Mekong Delta region of southern Viet Nam.

Bats and rodents are being increasingly recognized as reservoirs of emerging zoonotic viruses. Various studies have investigated bat viruses in tropical regions, but to date there are no data regarding viruses with zoonotic potential that circulate in bat and rat populations in Viet Nam. To address this paucity of data, we sampled three bat farms and three wet markets trading in rat meat in the Mekong Delta region of southern Viet Nam. Faecal and urine samples were screened for the presence of RNA from paramyxoviruses, coronaviruses and filoviruses. Paramyxovirus RNA was detected in 4 of 248 (1%) and 11 of 222 (4.9%) bat faecal and urine samples, respectively. Coronavirus RNA was detected in 55 of 248 (22%) of bat faecal samples; filovirus RNA was not detected in any of the bat samples. Further, coronavirus RNA was detected in 12 of 270 (4.4%) of rat faecal samples; all samples tested negative for paramyxovirus. Phylogenetic analysis revealed that the bat paramyxoviruses and bat and rat coronaviruses were related to viruses circulating in bat and rodent populations globally, but showed no cross-species mixing of viruses between bat and rat populations within Viet Nam. Our study shows that potentially novel variants of paramyxoviruses and coronaviruses commonly circulate in bat and rat populations in Viet Nam. Further characterization of the viruses and additional human and animal surveillance is required to evaluate the likelihood of viral spillover and to assess whether these viruses pose a risk to human health.

Hepatitis E in southern Vietnam: Seroepidemiology in humans and molecular epidemiology in pigs.

Viral pathogens account for a significant proportion of the burden of emerging infectious diseases in humans. The Wellcome Trust-Vietnamese Initiative on Zoonotic Infections (WT-VIZIONS) is aiming to understand the circulation of viral zoonotic pathogens in animals that pose a potential risk to human health. Evidence suggests that human exposure and infections with hepatitis E virus (HEV) genotypes (GT) 3 and 4 results from zoonotic transmission. Hypothesising that HEV GT3 and GT4 are circulating in the Vietnamese pig population and can be transmitted to humans, we aimed to estimate the seroprevalence of HEV exposure in a population of farmers and the general population. We additionally performed sequence analysis of HEV in pig populations in the same region to address knowledge gaps regarding HEV circulation and to evaluate if pigs were a potential source of HEV exposure. We found a high prevalence of HEV GT3 viral RNA in pigs (19.1% in faecal samples and 8.2% in rectal swabs) and a high HEV seroprevalence in pig farmers (16.0%) and a hospital-attending population (31.7%) in southern Vietnam. The hospital population was recruited as a general-population proxy even though this particular population subgroup may introduce bias. The detection of HEV RNA in pigs indicates that HEV may be a zoonotic disease risk in this location, although a larger sample size is required to infer an association between HEV positivity in pigs and seroprevalence in humans.

Survey of the prevalence of Salmonella species on commercial laying farms in the United Kingdom.

A survey of salmonella infection on 454 commercial layer flock holdings in the uk was carried out between October 2004 and September 2005. Fifty-four (11.7 per cent, 95 per cent confidence interval 9.3 to 14.0 per cent) were salmonella positive. The most common serovar identified was Salmonella Enteritidis at a prevalence of 5.8 per cent, and 70 per cent of these isolates were phage types 4, 6, 7 and 35. Salmonella Typhimurium was the second most prevalent serovar, found in 1.8 per cent of the farms. Of the three other serovars given top priority by the eu because of their public health significance, Salmonella Virchow and Salmonella Infantis were each isolated from one holding, but Salmonella Hadar was not isolated from any of the holdings. Analysis of antimicrobial resistance patterns revealed that over 76 per cent of the isolates were sensitive to all of the 16 drugs tested, and all the isolates were sensitive to ciprofloxacin, gentamicin, ceftazidime, apramycin, amikacin, amoxicillin/clavulanic acid, neomycin and cefotaxime.