Abstract
The objective of this study was to determine the prevalence and characteristics of Salmonella spp. isolated from feces of cattle in feedlots in the United States. Fecal samples were collected from up to three pens of cattle in each of 68 feedlots in 12 states. Samples included up to 25 individual fecal pats from the pen floors and up to five composite samples from the floors of the same pens. The prevalence of Salmonella-positive samples was 9.1% (460/5050) and 11.3% (114/1009) for individual and composite samples, respectively. The prevalences of Salmonella at the pen level were 35.6% (72/202) and 22.8% (46/202) for individual and composite samples, respectively. Dietary factors, including inclusion of cottonseed hulls, coccidiostats, and antimicrobial drugs, were associated with differences in prevalence of Salmonella isolation. Overall, 32 serotypes of Salmonella were identified, but six serotypes accounted for 69.1% (495/716) of the isolates. Nearly two-thirds (64.7%, 44/68) of feedlots had at least one positive sample. All isolates were evaluated for susceptibility to a panel of 15 antimicrobial drugs. Most isolates (74.4%, 533/716) were susceptible to all antimicrobial drugs in the panel. When resistance was detected, it was most commonly to tetracycline (21.7%, 155/716 of isolates) or sulfisoxazole (12.4%, 89/716 of isolates). Less than 10% of the isolates were resistant to any other antimicrobials in the panel. The results of this study indicate that the prevalence of Salmonella in individual fecal samples was less than 10%, but that Salmonella is widely distributed among feedlot cattle. Furthermore, when Salmonella is present in feedlot cattle, there is a low occurrence of antimicrobial resistance with the exception of tetracycline and sulfisoxazole. More research is indicated to understand the ecology of Salmonella and antimicrobial resistance, when present, in cattle-feeding operations.
Introduction
S
Previous studies of cattle feedlots have reported on prevalence and characteristics of Salmonella in cattle feedlots in 1994 and 1999 (Dargatz et al., 2002; Dargatz et al., 2003; Van Donkersgoed, 2009; Rao, 2010). There is potential for much to have changed over the preceding 12 years with regard to prevalent serotypes and their characteristics. Some of these changes may be related to the inclusion of new nutritional management strategies and other contemporary management changes for cattle in feedlots. In addition, as in other ecologic settings (e.g., other livestock production streams or public health), there appears to be temporal variation in serotype distribution and characteristics that remains unexplained. For these and other reasons, there is a need for updated information for feedlot cattle in the United States. Furthermore, there is a need to identify optimal surveillance strategies for pathogen prevalence. Collection and testing of large numbers of samples can be cumbersome and expensive. The objectives of this study were (1) to provide more current estimates of the prevalence of Salmonella in cattle feedlots in the United States, (2) to describe the serotype and resistance characteristics of Salmonella isolates, (3) to compare these data when collected by two sampling strategies (individual and composite samples), and (4) to investigate regional and dietary associations with Salmonella prevalence.
Materials and Methods
Sample collection
Feedlots participating in the USDA National Animal Health Monitoring System (NAHMS) Feedlot 2011 study were eligible to participate in the pathogen sampling component of the study (USDA, 2013). Sixty-eight feedlots distributed across 12 states were recruited for sample collection. In each feedlot three pens of cattle were selected for sampling, including the pen of cattle that had been in the feedlot the shortest time, the pen of cattle that had been in the feedlot the longest time, and a randomly selected pen (pen type for subsequent analysis). Samples were collected between April 2 and August 15, 2011. In each pen up to 25 fecal samples were collected from individual fecal pats from the pen floor during a serpentine walk of the pen (individual samples). Efforts were made to minimize the chance of collecting multiple samples from the same animal. An additional five composite samples were collected from fecal pats on the pen floor by conducting another serpentine walk of the pen and aggregating feces from up to five fecal pats into a single collection (composite samples). Samples (individual or composite) were collected in separate plastic bags, chilled, and transported by overnight delivery to the USDA–ARS Bacterial Epidemiology and Antimicrobial Resistance research laboratory for bacterial culture and initial characterization beginning on the day of arrival.
Salmonella isolation
Fecal samples were cultured as previously described (Wells et al., 2001). Fecal samples were enriched in selective media (1 g of sample in 10 mL of broth: GN Hajna incubated for 24 h at 37°C and Tetrathionate Broth incubated 48 h at 37°C), and 0.1 mL of each selective enrichment culture was transferred to Rappaport R-10 broth (10 mL) for a secondary selective enrichment and incubated for 24 h at 37°C. Broth was streaked for isolation on selective brilliant green sulfa agar (BGS) and Xylose Lysine Tergitol 4 (XLT4) agar plates and incubated for 24 h at 37°C. On BGS plates, presumptive Salmonella colonies were lactose negative, forming a pink colony, and on XLT4 plates, presumptive Salmonella colonies were typically yellow to red with a black center (indicating hydrogen sulfide production). Up to four presumptive Salmonella colonies were inoculated on triple sugar iron (TSI) and lysine iron agar slants and incubated for 24 h at 37°C. On TSI, the presence of Salmonella produced a K/A+ alkaline (red) reaction on the slant surface and an acid (yellow) reaction with hydrogen sulfide production in the stabbed agar butt. Up to four presumptive Salmonella colonies from each sample were serogrouped by slide agglutination with serogroup-specific antisera (Difco; BD; personal communication). When all isolates were of the same serogroup, a single isolate was chosen for serotyping.
Serotyping of the isolates
All the isolates were submitted to the USDA–APHIS National Veterinary Services Laboratories in Ames, IA, for serotyping using previously described methods (Ewing, 1986). Antigenic formulae for somatic (O) and flagellar (H) antigens were used to determine serotype (Grimont and Weill, 2007).
Antimicrobial susceptibility testing
The susceptibility of each of the isolates was tested using a semiautomated system (Sensititre; TREK Diagnostic Systems, Inc.) using a panel of 15 antimicrobial drugs. To allow comparison with other antimicrobial resistance surveillance systems, the Sensititre Gram Negative Plate (CMV3AGPF) used in the National Antimicrobial Resistance Monitoring System (NARMS) was used and included the following antimicrobial agents: amoxicillin–clavulanic acid, ampicillin, azithromycin, cefoxitin, ceftiofur, ceftriaxone, chloramphenicol, ciprofloxacin, gentamicin, kanamycin, nalidixic acid, streptomycin, sulfisoxazole, tetracycline, and trimethoprim–sulfamethoxazole. Breakpoints used in the NARMS program were used to classify the isolates as susceptible, intermediate, or resistant (FDA, 2013). The quality control organism used for the study was Escherichia coli ATCC 25922. Isolates were classified as multidrug resistant if they were resistant to three or more antimicrobial drugs in the panel.
Statistical analysis
At the time of sample collection, a questionnaire was administered to collect data on animal gender, breed type, average placement weight, average current weight, use of E. coli or Salmonella vaccines, metaphylaxis,
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morbidity levels, mortality levels, single source or multisource, chlorination of drinking water, feed ingredients used in the last 7 d, and any use of specific feed or water antimicrobials since arrival (questionnaire available at
Analyses were done at the sample level and at the pen level—separately for individual and composite samples—using SAS version 9.3 (SAS Institute version 9.3). For sample-level inferential analyses, logistic regression models were constructed using SAS PROC GENMOD, with samples nested within pens and feedlots. Variables significant at p < 0.10 in univariable models were included in a multivariable model, and variables significant at p < 0.05 were retained in the final multivariable model after backward elimination. Pen-level inferential analyses were done similarly, with pens nested within feedlots.
Results
Prevalence of Salmonella
Overall 5050 individual and 1009 composite samples were collected from 202 pens in 68 feedlots (Table 1). Among the 68 feedlots, 44 had at least one Salmonella-positive sample. Individual samples were positive on 41 feedlots and composite samples were positive on 30 feedlots.
The overall pen-level prevalences for individual samples and composite samples were 35.6% (72/202) and 22.8% (46/202), respectively, with no differences by type of pen (p = 0.59 and p = 0.88, respectively). Pens in feedlots from the Central region were more likely to have a positive individual sample (42.4%, p = 0.043) compared with pens from the Other region (24.7%). The prevalence of positive pens based on individual samples was not different among the North and South regions. However, pens from the South region were more likely to have positive composite samples (39.2%, p = 0.028) compared with pens from the North region (17.2%).
The sample-level prevalences for individual and composite samples were 9.1% and 11.3%, respectively, again with no differences by type of pen (p = 0.93 and p = 0.55, respectively). The prevalence of positive individual samples was higher from the Central region (11.3%, p = 0.045) compared with the Other region (5.6%) (Table 2). Similarly, the prevalence of positive composite samples was also higher in the Central region (14.1%, p = 0.034) compared with the Other region (6.8%). Considering feedlot latitude, the prevalence of positive individual samples was higher in the South region (20.0%, p = 0.003) compared with the North region (5.4%). The prevalence of positive composite samples was also higher in the South region (25.9%, p = 0.001) compared with the North region (6.4%).
Serotyping of isolates
Among the 716 Salmonella isolates from the individual and composite samples (n = 6059), there were 33 serotypes represented. The top six serotypes comprised 69.1% of the isolates (Table 3). The relative proportions of isolates by serotype were similar regardless of sample type.
6;7:g;m;s:e;n;z15, Worthington, Agona, Infantis, Schwarzengrund, Reading, Dublin, Give, Muenchen, Sundsvall, Bareilly, Derby, Minnesota, Thompson, Uganda, Cubana, Javiana, Kiambu, Lexington var 15+, Orion, Rough 0:l;v:1;7, Senftenberg, and Soerenga.
Antimicrobial resistance phenotypes
Most of the Salmonella isolates (74.4%; 533/716) were susceptible to all antimicrobial drugs in the panel tested (Table 4). An additional 16.3% (117/716) of isolates were resistant to only one antimicrobial drug tested. When resistance was present it was most commonly to tetracycline (21.7%; 155/216) or sulfisoxazole (12.4%; 89/216) (Table 5). The resistance characteristics of Salmonella isolates were similar regardless of whether they were from individual or composite samples. Isolates among some serotypes were more likely to be multidrug resistant (i.e., resistant to three or more antimicrobials) (Table 6).
Includes serotypes 6;7:g;m;s:e;n;z15, Worthington, Agona, Infantis, Schwarzengrund, Reading, Dublin, Give, Muenchen, Sundsvall, Bareilly, Derby, Minnesota, Thompson, Uganda, Cubana, Javiana, Kiambu, Lexington var 15+, Orion, Rough 0:l;v:1;7, Senftenberg, and Soerenga.
For serotypes represented by at least 10 isolates, the highest proportion of multidrug resistance was seen for serotypes Newport (89.5%, 17/19), Typhimurium (56.7%, 17/30), Infantis (33.3%, 4/12), Meleagridis (12.8%, 5/39), Muenster (4.2%, 1/24), and Montevideo (3.9%, 5/129). Among the 49 isolates that were resistant to 9 or more antimicrobial drugs, the serotypes were Montevideo (n = 3), Typhimurium (n = 14), Newport (n = 15), Infantis (n = 4), Reading (n = 7), Dublin (n = 4), Uganda (n = 1), and S. Rough O:I;v:1;7 (n = 1).
Factors associated with Salmonella presence
Modeling the prevalence of Salmonella in individual samples, three factors remained in the multivariable model (Table 7). Ration inclusion of cottonseed hulls in the last 7 d (increasing prevalence), inclusion of decoquinate (decreasing prevalence), and inclusion of oxytetracycline (decreasing prevalence) any time since arrival were associated with the outcome.
In modeling the prevalence of Salmonella in composite samples, four factors remained in the model, including the inclusion of a beta-agonist in the last 7 d (increasing prevalence), inclusion of cottonseed hulls in the last 7 d (increasing prevalence), inclusion of decoquinate (decreasing prevalence) any time since arrival, and being located in the South region (increasing prevalence).
For the model of pen-level Salmonella prevalence based on results from individual samples, only one factor remained in the model. Pens that had lasalocid in the ration any time since arrival were more likely to be positive than pens not receiving lasalocid.
Finally, for the model of pen-level prevalence based on results of composite samples, three factors remain in the model. Ration inclusion of a beta-agonist in the last 7 d (increasing prevalence), longer time on feed (decreasing prevalence), and being located in the South region (increasing prevalence) were associated with the outcome.
Factors associated with Salmonella resistance
Modeling the prevalence of Salmonella resistant to tetracycline or sulfisoxazole in individual samples, two factors remained in the multivariable models (Table 8)—ration inclusion of cottonseed hulls in the last 7 d (decreasing prevalence) and region location of the feedlot. Samples positive for Salmonella from animals collected in feedlots in the Central region were more likely to have tetracycline- or sulfisoxazole-resistant Salmonella than samples with Salmonella from feedlots in the Other region.
Discussion
The sample and pen-level prevalence of Salmonella from this study were similar to those described for feedlots from 1999 (Dargatz et al., 2003). Prevalence estimates were similar regardless of whether individual or composite samples were used. This result suggests that when the outcome of interest is an overall prevalence, and distribution of serotypes across a broad population of animals in multiple facilities that a more cost-effective design for sample collection could involve the collection of composite samples from the pen floors rather than the collection of a larger number of samples representing individual animals. While the precision of the estimates may be lower with composite sampling and some rare serotypes may not be identified, the overall description of prevalence and distribution are not severely compromised.
Relatively few variables were associated with finding Salmonella either in individual samples or in composite samples collected in cattle feedlots. Most of the variables associated with positive samples were related to diet components. Some of these dietary factors were the same or similar to those associated with Salmonella-positive samples from two previous similar studies (Losinger et al., 1997; Green et al., 2010). In the 1994 and 1999 studies, the odds of a positive sample were 3.5 and 5.2 times higher if cottonseed hulls were included in the ration. Cottonseeds or cottonseed meal have been associated with Salmonella contamination in a number of studies evaluating the prevalence of contamination of animal feed components (Van et al., 1966; Rutqvist et al., 1983; Jardy and Michard, 1992; Davis et al., 2003; Jones and Richardson, 2004; Myint et al., 2007).
In the current study, as with the 1999 study, the use of a coccidiostat—decoquinate—in the ration decreased the likelihood of a sample positive for Salmonella. However, in some cases the inclusion of lasalocid, another compound with anticoccidial activity, was associated with a higher expected percentage of positive samples. Inclusion of coccidiostats in the diet of poultry has also been associated with decreased prevalence of Salmonella shedding (Bolder et al., 1999). Inclusion of tetracycline in the ration was associated with a decreased likelihood of positive samples in both studies as well. The finding of a higher predicted percentage of positive samples with animals receiving a beta agonist is consistent with findings from others (Edrington et al., 2006).
Samples from more southern latitudes were more likely to be positive for Salmonella in the current study and in the 1994 and 1999 studies. This observation is consistent with anecdotal observations and other research to document the presence of Salmonella in samples from cattle in feedlots across a broad geographic continuum from the southern edge of the United States, where the prevalence is expected to be higher to Canada where the prevalence is very low. The reasons for this regional variation are unclear at this time.
Relatively few of the Salmonella isolates were resistant to one or more of the antimicrobial drugs tested in the panel. Less than 10% of the isolates were resistant to antimicrobial drugs considered critical for treatment of human salmonellosis, such as cephalosporins and fluoroquinolones. However, the low frequency of resistance preclude an extensive look at the factors associated with resistance among the isolates. While the prevalence of Salmonella was positively associated with the inclusion of cottonseed or cottonseed meal in the ration, the salmonellae were less likely to be resistant, with 89.3% (293/328) of those isolates being pansusceptible. The most common serotypes of Salmonella among the cattle pens exposed to cottonseed or cottonseed meal were S. Anatum (29.9% = 98/328), followed by S. Kentucky (19.8% = 65/328), S. Montevideo (19.5% = 64/328), and S. Cerro (12.8% = 42/328). The remainder of the isolates (18.0% = 59/328) were from 10 additional serotypes. More work is indicated to define those modifiable factors that might serve to mitigate the risk of both resistant and nonresistant Salmonella shedding by feedlot cattle.
Footnotes
Acknowledgments
The skilled technical assistance of Sandra House and Takiyah Ball of the USDA–ARS Bacterial Epidemiology and Antimicrobial Resistance unit is gratefully acknowledged.
Disclosure Statement
No competing financial interests exist.
