Characterization of integron mediated antimicrobial resistance in Salmonella isolated from diseased swine

Forty-two Salmonella isolates obtained from diseased swine were genetically characterized for the presence of specific antimicrobial resistance mechanisms. Twenty of these isolates were characterized as S. Typhimurium DT104 strains. Pulsed-field gel electrophoresis was used to determine genetic relatedness and revealed 20 distinct genetic patterns among the 42 isolates. However, all DT104 isolates fell within 2 closely related genetic clusters. Other Salmonella isolates were genetically grouped together according to serotype. All DT104 isolates displayed the penta-resistance phenotype to ampicillin, chloramphenicol, streptomycin, sulfamethoxazole, and tetracycline. Resistance to sulfamethoxazole, tetracycline, streptomycin, kanamycin, and ampicillin was most common among the non-DT104 Salmonella isolates. All DT104 strains contained 2 chromosomal integrons of 1000 and 1200 base pairs. The DNA sequencing revealed that the 2 integrons contained genes encoding a resistance to streptomycin and ampicillin, respectively. None of the non-DT104 strains showed the same pattern, although several strains possessed integrons of 1000 base pairs or larger. However, the majority of non-DT104 Salmonella strains did not possess any integrons. Two Salmonella isolates displayed tolerance to the organic solvent cyclohexane, indicating the possibility that they are overexpressing chromosomal regulatory genes marA or soxS or the associated multidrug efflux pump, acrAB. This research suggests that integrons contribute to antimicrobial resistance among specific swine Salmonella serotypes; however, they are not as widely disseminated among non-Typhimurium swine Salmonella serotypes as previously thought.     

Detection of antimicrobial resistance genes of pathogenic Salmonella from swine with DNA microarray.

A glass-based microarray was developed to detect 11 antimicrobial resistance genes that confer resistance to aminoglycosides, tetracyclines, sulfonamides, and chloramphenicols. The target genes for microarray were generated from Salmonella isolates by PCR and confirmed by sequencing. The specificity of the microarray was tested using 11 positive DNA probes. The sensitivity was tested with tetA gene and Salmonella isolates. Using detection threshold of signal-to-noise ratio (S/N) > or = 1.5 or median pixel intensity > or =1000, antimicrobial resistance genes carried by 30 Salmonella isolates were detected. Common genes included sul I(76.7%, 23/30), aph(3')-IIa (60%, 18/30), tetC (60%, 18/30), cat] (43.3%, 13/30), tetA (40%, 12/30) and aadA1 (36.7%, 11/30), and the results were confirmed to be correct by PCR.     

全基因组测序技术在猪源沙门氏菌血清分型和耐药性分析中的应用

【目的】为研究全基因组测序技术在猪源沙门氏菌血清型和耐药性检测方面的应用能力。【方法】以60株猪源沙门氏菌为研究对象,应用传统玻片凝集法和微量肉汤稀释法对其进行血清分型和耐药性检测,并提取所有菌株核酸进行全基因组测序组装,利用SeqSero2和ResFinder4在线预测每株菌的血清型和耐药基因,然后与传统方法进行比较分析。【结果】血清凝集试验共鉴定出8种沙门氏菌血清型,而全基因组测序鉴定出9种血清型,二者分型结果的符合率为90.0%;对11种抗菌药物的药敏试验显示：沙门氏菌对四环素（73.3%）的耐药率最高,其次为氨苄西林（66.7%）、磺胺异噁唑（66.7%）和复方新诺明（53.3%）,基于全基因组预测的恩诺沙星、美罗培南、头孢噻呋和阿奇霉素的耐药性与药敏试验结果完全一致,对氨苄西林、磺胺异噁唑、四环素预测的结果符合率也均大于90.0%。【结论】全基因组测序分析的沙门氏菌血清型和耐药性与常规检测方法的符合率较高,且具有操作简便的优势,可以作为分析沙门氏菌血清型和耐药性的有效方法。     

Evaluation of stocking density and subtherapeutic chlortetracycline on Salmonella enterica subsp. enterica shedding in growing swine

The objective of this research was to determine the effect of stocking density and inclusion of subtherapeutic chlortetracycline in the diet on Salmonella fecal prevalence and antimicrobial resistance in growing swine. A 2 x 2 factorial design was employed on a privately owned commercial swine farm. Four finisher rooms were included in the study. Two of the rooms received 50 g/tonnes of chlortetracycline in the ration, two rooms received no antimicrobials in the feed. In each room, alternate pens were assigned to either high stocking density (0.60 m2/pig) or low stocking density (0.74 m2/pig). Pigs were placed in the finisher rooms at 10 weeks of age and followed for 6 weeks. Individual fecal samples were collected from the floors of each pen and cultured once weekly. Antimicrobial resistance phenotypes were determined. Data were analyzed using multilevel, multivariable logistic regression. Pigs fed chlortetracycline were at increased odds (OR 6.88, 95% CI 2.77-17.12) to shed Salmonellae. No other associations between treatments (CTC and stocking density) and Salmonella prevalence or reduced susceptibility to antimicrobials were identified. Variance in the odds of a fecal sample to be positive was distributed mostly at the lowest level, the individual fecal sample. The increased risk of shedding associated with inclusion of subtherapeutic chlortetracycline in swine diets is discordant with previous results by our group, suggesting farm or strain specific factors may impact this association. Understanding this risk may provide a potential intervention for controlling Salmonella pre-harvest.     

Molecular epidemiology and antimicrobial resistance of Salmonella typhimurium DTI04 on Ontario swine farms.

This study was conducted to examine antimicrobial resistances, plasmid profiles, and pulsed-field gel electrophoresis patterns of 80 Salmonella Typhimurium (including var. Copenhagen) DT104 strains (including DT104a and DT104b) recovered from pig and environmental fecal samples on 17 swine farms in Ontario. No resistance was observed to amoxicillin/clavulanic acid, apramycin, carbadox, cephalothin, ceftriaxone, ceftiofur, cefoxitin, ciprofloxacin, nalidixic acid, trimethoprim, and tobramycin. However, the isolates exhibited resistance against 4 to 10 antimicrobials with the most frequent resistance being to sulfonamides (Su), ampicillin (A), streptomycin (S), spectinomycin (Sp), chloramphenicol (C), tetracycline (T), and florfenicol (F). Thirteen distinct resistance patterns were determined but 88% of isolates shared the typical resistance pattern "ACSpSSuT." Twelve different plasmid profiles were observed; the 62 MDa virulence-associated plasmid was detected in 95% of the isolates. The 2.1 MDa plasmid was the second most frequent one, which was harbored by 65% isolates. The isolates were classified into 23 distinct genotypes by PFGE-SpeI + BlnI when difference in at least one fragment was defined as a distinct genotype. In total, 39 distinct "types" were observed when defining a "type" based on the combination of antimicrobial resistance, plasmid pattern, and PFGE-SpeI + BlnI for each isolate. The highest diversity was 0.96 (95% CI: 0.92, 0.96) for the "type" described above followed by 0.92 (95% CI: 0.88, 0.93) for PFGE-SpeI + BlnI. The diversity of DT104 isolates indicates there might be multiple sources for this microorganism on swine farms. This knowledge might be used to track these sources, as well as to study the extent of human salmonellosis attributed to pork compared to food products derived from other food-producing animals.     

Effect of 2-deoxy-d-glucose induced stress on Salmonella choleraesuis shedding and persistence in swine

A glucose analog, 2-deoxy-d-glucose (2DG), previously shown in swine to induce many of the hallmark parameters of stress, was administered to Salmonella choleraesuis carrier-swine and the effects on Salmonella fecal shedding and tissue colonization were evaluated. Initially, pigs were divided into two groups, one that received 1 x 10 (6) S. choleraesuis and one group that received saline. At 3 or 6 weeks post inoculation (PI), half of each group received an injection of 2DG and the other half received saline. Throughout the study, individual fecal samples were collected and quantitatively cultured for Salmonella, tonsil and nasal swabs were qualitatively cultured, clinical signs were monitored, temperatures were measured and whole blood collected. Pigs were necropsied 8-18 days after 2DG treatment. The experimental stress induced by 2DG was not sufficient to cause recrudescence of Salmonella fecal shedding even when tissues were culture positive for Salmonella. In addition, persistent shedding was not affected by 2DG administration. Although the complex set of parameters that constitute the stress phenomenon is still relatively unknown, it is now apparent that the stressful event(s) sufficient to trigger Salmonella recrudescence involves more than just increased blood glucose, increased cortisol, and inhibition of lymphocyte proliferation.     

Risk factors for fecal shedding of Salmonella in 91 US dairy herds in 1996

In 1996, data on management practices used on US dairy operations were collected and analyzed for association with fecal shedding of Salmonella by dairy cows. A total of 4299 fecal samples from 91 herds was cultured for Salmonella isolation. Herd-size (adjusted odds ratios (OR) = 5.8, 95% CI 1.1, 31.3), region (OR = 5.7, CI 1.4, 23.5), use of flush water systems (OR = 3.5, CI 0.9, 14.7), and feeding brewers' products to lactating cows (OR = 3.4, CI 0.9, 12.9) were identified as the most important predictive risk factors. The population attributable risks (PARs) for herd-size, region, flush water system, and feeding brewers' products to lactating cows were 0.76, 0.46, 0.37, and 0.42, respectively. The estimated PAR for all four risk factors combined was 0.95. The effects of these factors need to be more-closely evaluated in more-controlled studies, in order to develop intervention programs that reduce Salmonella shedding.     

Risk factors for fecal shedding of Salmonella from horses in a veterinary teaching hospital

Identification of risk factors for horses shedding Salmonella in their feces helps identify patients at-risk of infection and protect the overall population through heightened biosecurity. Fecal samples from 230 hospitalized horses were cultured for Salmonella spp. Historical data were collected on 21 putative risk factors and assessed for association with the risk of a horse being culture positive using forwards stepwise logistic regression. Salmonella was isolated from 13 horses—most commonly from either the first (n=5) or second (n=4) sample collected. Only presenting complaint (confounded by age, breed and gender) was significantly (P≤0.05) associated with positive Salmonella-culture results. Analysis of residuals showed that the model was robust, but individual risk-factor estimates were changed by removal of outliers. Overall, presenting complaint (for example, lower-respiratory-tract disease) was the most important indicator of culture status.     

Comparison of antimicrobial resistance in generic Escherichia coli and Salmonella spp. cultured from identical fecal samples in finishing swine

The objectives of this study were to investigate the associations between antimicrobial resistance patterns in generic Escherichia coli and Salmonella spp. isolates recovered from identical pen pooled fecal samples, and to evaluate potential clustering of multiple isolates of these organisms within identical fecal samples. Up to 5 generic E. coli (n = 922 isolates) and Salmonella spp. (n = 922 isolates) isolates were obtained from each of 188 pen pooled fecal samples that had been collected from 45 finishing swine farms in Alberta in 2000, and tested for susceptibility to 15 antimicrobials. No isolates of either organism were resistant to 3rd generation cephalosporins or fluoroquinolones, which in Canada are considered antimicrobials of very high importance to human health. Approximately twice as many generic E. coli isolates as Salmonella spp. isolates were resistant to at least 1 antimicrobial. In addition, E. coli isolates showed more multidrug-resistance patterns. No significant association was observed between the resistance phenotypes of Salmonella spp. and E. coli at the fecal sample level. More clustering at the sample level was observed for proportions of antimicrobial resistance (AMR) in Salmonella spp. isolates than E. coli indicating that in future studies it might be sufficient to test fewer than 5 Salmonella spp. isolates per sample.     

Evaluation of commercial probiotics for antimicrobial resistance genes

The objective of this study was to determine if transferable antimicrobial resistance (AMR) genes are present in commercial animal probiotics. DNA was extracted from 50 probiotics, tested for the presence of bacterial DNA, and analyzed by polymerase chain reaction (PCR) for the presence of 8 transferrable AMR genes, including tetracycline, erythromycin, aminoglycoside, sulfonamide, and trimethoprim. Samples that were positive by PCR were confirmed by genome sequencing. Forty-seven (94%) products contained bacterial DNA. Of these, 97% contained at least 1 AMR gene, and 82% contained 2 or more. These results indicate that further evaluation of the risk for transmission of these AMR genes may be warranted.     

Risk factors associated with the antimicrobial resistance of staphylococci in canine pyoderma

This study reports the susceptibility to antimicrobial agents of staphylococci (n=105) isolated from dogs, and the factors associated with this resistance. The study animals were 23 healthy dogs (group A), 24 with first-time pyoderma (group B), and 27 with recurrent pyoderma that had undergone long-term antibiotic treatment (group C). Staphylococci were more commonly isolated from the pyoderma-affected than the healthy dogs (p<0.0001). Some 78% of the isolates were resistant to at least one antimicrobial agent. Resistance to amoxicillin-clavulanate, cephalosporins (OR 4.29, 95% CI [1.15, 16.3] respectively), enrofloxacin (OR 9.47, 95% CI [1.53, 58.5]) and ciprofloxacin (OR 79.7 95% CI [3.26, 1947.4]) was more common among group C isolates. Some 32% of all the isolates were multiresistant (MR) and 10.4% were methicillin-resistant (MRS). The probability of isolating MRS staphylococci in group C increased by a factor of four (95% CI [1.18, 17.9]) compared to A plus B. Multi-resistant (MR) isolates were obtained more commonly from urban than rural dogs (OR 3.79, 95% CI [1.09, 13.17]). All the MRS staphylococci encountered were obtained from urban dogs and more commonly from male dogs (p=0.07). This study shows that dogs bred in urban habitat, with a history of antibiotic therapy in the past year represents significant risk of being carriers of isolates resistant to methicillin (MRS) and other antimicrobials. These factors should be considered before applying an antimicrobial treatment in veterinary clinics.     

Evaluation of farm management practices as risk factors for clinical listeriosis and fecal shedding of Listeria monocytogenes in ruminants

OBJECTIVE: To assess seasonal variation in prevalence of Listeria monocytogenes on ruminant farms and identify management practices associated with ruminant listeriosis and fecal shedding of L. monocytogenes. STUDY DESIGN: Case-control study. SAMPLE POPULATION: 2056 samples of feces, feed, soil, and water from 24 case farms with listeriosis and 28 control farms without listeriosis. PROCEDURE: Samples were collected and evaluated via bacterial culture for L. monocytogenes. Univariate associations between farm management practices and listeriosis and fecal shedding of L. monocytogenes were assessed. Multivariate models were developed to identify farm management practices associated with listeriosis and fecal shedding of L. monocytogenes. RESULTS: The prevalence of L. monocytogenes on cattle, goat, and sheep farms was seasonal, especially in fecal samples, with peak prevalence in winter. Although the prevalence of L. monocytogenes in feedstuffs from small-ruminant farms also peaked during winter, the bacterium was detected at a constant rate in cattle farm feedstuffs throughout the year. Farm management practices, animal health and hygiene, and feedstuff quality and storage were associated with ruminant listeriosis and fecal shedding of L. monocytogenes. CONCLUSIONS AND CLINICAL RELEVANCE: Results suggest that the prevalence of L. monocytogenes on ruminant farms is seasonal, management practices are associated with ruminant listeriosis and fecal shedding of L. monocytogenes, and the epidemiologic features of listeriosis differ in cattle versus small ruminants. Awareness of risk factors may be used to develop control measures to reduce animal disease and introduction of L. monocytogenes into the human food chain.     

Differences in antibiotic resistance in Escherichia coli,isolated from East-European swine herds with or without prophylactic use of antibiotics

The aim of the study was to compare the resistance patterns of Escherichia coli isolates from pig herds with or without prophylactic use of anti-microbial substances. The presented pig units received either antibiotics or oregano as preventive feed additives. The trial was performed from April to October 2001, in the large 'country-corner', Hungary-Rumania-Serbia. Thirty of 39 evaluated herds suffered E. coli O139 K88 ac or ad LT STb caused losses, the remaining were negative for E. coli O139. Thirteen of the selected 30 herds produced with oregano feed supplementation (Oregpig Pecs, Hungary) antibiotic-free pigs. These units had no history of prophylactic antibiotic use since 1995. The remaining 17 herds routinely used prophylactic antibiotic feed supplementation. In each herd, pigs of four different age groups (suckling piglets, weaners. fattening swine and breeding sows), showing the clinical symptoms of wasting, were investigated. E. coli O139 K88 ac or ad LT STb were tested for their resistance to antibiotics, available in this region. Oregano-fed herds demonstrated high significantly (P < 0.001) lower MICs (microg/ml) for ampicillin, doxycyclin, enrofloxacin, gentamycin, oxytetracyclin and sulfamethacin compared to herds with prophylactic use of antibiotics. Resistance to ceftiofur revealed significant (P < 0.05) differences between the antibiotic- or oregano-treated units. The present results confirm literature data, that prophylactic use of antibiotics likely plays a role in inducing resistance of E. coli and other intestinal bacteria. Thus, imposing greater restrictions on antibiotic use in animal agriculture is likely to reduce but not eliminate the occurrence of resistant isolates.     

Antimicrobial resistance of Salmonella isolated from finishing swine and the environment of 60 Alberta swine farms

The study objective was to describe and evaluate antimicrobial resistance profiles in Salmonella isolated from Alberta swine finishing farms. Salmonella isolates (n = 322) were obtained from 192 fecal and 84 environmental samples of the 60 Salmonella-positive swine finishing farms. Isolates were classified susceptible, intermediate or resistant based on NCCLS guidelines. More than half of the isolates (53.4%) were susceptible to all of the 18 antimicrobials in the testing panel. No resistance was observed to amikacin, amoxicillin/clavulanic acid, cefoxitin, ceftiofur, ceftriaxone, cephalothin, ciprofloxacin, imipenem or nalidixic acid. Less than 1% of isolates were resistant to apramycin, gentamicin and trimethoprim/sulfamethoxazole. Higher frequencies of resistance were observed for chloramphenicol (4.7%), ampicillin (7.8%), kanamycin (11.8%), sulfamethoxazole (21.1%), streptomycin (25.5%) and tetracycline (38.8%). Eleven Salmonella serovars had isolates with resistance to > or =3 antimicrobials. The most frequently resistant serovar was Salmonella Derby, with 27 (38.0%) isolates resistant to > or =3 antimicrobials, including resistance to five and six antimicrobials. An absence of resistance to cephalosporins and fluoroquniolones and a low proportion of isolates resistant to amikacin, amoxicillin/clavulanic acid, apramycin, gentamicin and trimethoprim/sulfamethoxazole are encouraging findings from public health and animal health perspectives. Frequent resistance observed for ampicillin, kanamycin, sulfamethoxazole, streptomycin and tetracycline, antimicrobials commonly used in veterinary medicine for decades, indicates an urgent need to utilize these antimicrobials more prudently if their benefits are to be preserved.     

Risk factors associated with fecal Salmonella shedding among hospitalized horses with signs of gastrointestinal tract disease

OBJECTIVE: To estimate prevalence of and identify risk factors for fecal Salmonella shedding among hospitalized horses with signs of gastrointestinal tract disease. DESIGN: Cross-sectional study. ANIMALS: 465 hospitalized horses with gastrointestinal tract disease. PROCEDURE: Horses were classified as positive or negative for fecal Salmonella shedding during hospitalization by means of standard aerobic bacteriologic methods. The relationship between investigated exposure factors and fecal Salmonella shedding was examined by means of logistic regression. RESULTS: The overall prevalence of fecal Salmonella shedding was 13%. Salmonella serotype Newport was the most commonly isolated serotype (12/60 [20%]), followed by Anatum (8/60 [13%]), Java (13%), and Saint-paul (13%). Foals with gastrointestinal tract disease were 3.27 times as likely to be shedding Salmonella organisms as were adult horses with gastrointestinal tract disease. Adult horses that had been treated with antimicrobial drugs prior to hospitalization were 3.09 times as likely to be shedding Salmonella organisms as were adult horses that had not been treated with antimicrobial drugs prior to hospitalization. Adult horses that underwent abdominal surgery were 2.09 times as likely to be shedding Salmonella organisms as were adult horses that did not undergo abdominal surgery. CONCLUSIONS AND CLINICAL RELEVANCE: Results suggest that a history of exposure to antimicrobial drugs prior to hospitalization and abdominal surgery during hospitalization were associated with Salmonella shedding in adult horses with gastrointestinal tract disease. Foals with gastrointestinal tract disease were more likely to shed Salmonella organisms than were adult horses with gastrointestinal tract disease.     

Towards incorporating spatial risk analysis for Salmonella sero-positivity into the Danish swine surveillance programme

An increased incidence of pork-related human salmonellosis in Denmark led to the development of a national control programme for Salmonella in Danish swine herds in 1993. The aim of the programme has been met and now the issue of cost-effectiveness is receiving greater attention. An appropriate way to address this is to bring a risk-based focus to the programme.

We describe a practical approach to risk-based surveillance through spatial risk assessment using serological and questionnaire data from 2280 herds in 1995. A mixed effects logistic regression model was fitted and both first- and second-order spatial properties of the random effects were investigated. We identified wet-feeding (OR: 0.64; 95% CI: 0.54–0.75) and SPF health status (OR: 0.65; 95% CI: 0.52–0.81) as protective factors for Salmonella sero-positivity. Purchasing feed (OR: 1.81; 95% CI: 1.61–2.04) was a risk factor. The west of the study area generally, and the north of Jutland in particular, experienced the greatest disease risk after controlling for the covariates. There was some evidence for spatial dependency between farms at distances of 6 km (95% CI: 2–35 km) on the Jutland peninsula.

We conclude that when farm location details are analysed in conjunction with routinely recorded surveillance information (such as that collected by the Danish swine Salmonella control programme) and targeted industry surveys (such as those conducted by slaughterhouse co-operatives), our knowledge of the behaviour of disease in animal populations is enhanced and this provides a more informed framework for designing efficient, risk-based surveillance strategies.     

Prevalence and risk factors associated with Cryptosporidium oocysts shedding in pigs in Central Vietnam

We investigated the prevalence and risk factors associated with Cryptosporidium oocysts shedding in pigs in Central Vietnam. A total of 740 single fecal samples collected from diarrheic and non-diarrheic pigs on 89 farms were screened by the modified Ziehl-Neelsen staining method. Prevalence at the animal and the farm levels were 18.1% (134/740) and 71.9% (64/89), respectively. Risk factors for the infection were identified using univariate and multivariate logistic regression analysis. The results revealed that age, sanitary condition and topography were significantly associated with oocyst shedding (P<0.05). Pre-weaned piglets were at the highest risk for infection, followed by post-weaners, sows and finishing pigs. Good sanitary conditions showed positive effects in decreasing oocysts shedding. Topographically, Cryptosporidium was more common in mountainous zone than that in coastal delta zone. There was an association between the occurrence of diarrhea and the level of Cryptosporidium oocyst excretion within infected pigs. This is the first epidemiological investigation of prevalence and risk factors of Cryptosporidium in pigs in Vietnam.     

Risk factors for Salmonella enterica subsp. enterica shedding by market-age pigs in French farrow-to-finish herds

Fattening-pigs carriers of Salmonella enterica are believed to be a main source of carcass and pork contamination at the later steps of the meat process. We did a prospective study in 2000-2001 in 105 French farrow-to-finish pig farms. In each farm, a batch of contemporary fattening pigs housed in the same room was followed throughout the fattening period. Salmonella shedding was assessed on environmental samples of faecal material (taken by means of pairs of gauze socks) analysed by classical bacteriological methods. 36.2% of the batches studied had at least one contaminated environmental sample and therefore were classified as Salmonella-shedding batches. Logistic regression was used to assess the association between managerial and hygiene practices and health status and the shedding risk at the end of the finishing period. Emptying the pit below the slatted floor after the previous batch of sows was removed and frequent removal of sow dung during the lactation period were protective. Presence of residual Salmonella contamination of the floor and pen partitions in the fattening rooms before loading the growing pigs also was a risk factor. The risk for Salmonella shedding at the end of the fattening period was increased when dry feed (versus wet feed) was provided during the fattening period. Lastly, Lawsonia intracellularis seroconversion and PRRSV seropositivity during the fattening period also was a risk factor for Salmonella shedding.