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Ishengoma VL, Amachawadi RG, Habib KA, Shi X, Mahmood T, Hutchens WM, Tokach MD, Dritz SS, Woodworth JC, Goodband RD, DeRouchey JM, Apley MD, Nagaraja TG. 18 Impact of in-feed vs. in-water antibiotic administrations on the fecal prevalence and antimicrobial susceptibilities of Campylobacter and Salmonella in piglets. J Anim Sci 2020. [DOI: 10.1093/jas/skaa054.063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Campylobacter and Salmonella are common food borne pathogens in the gut of pigs and are shed in the feces. The control of these bacteria in pigs is of importance in reducing the potential for transmission to humans. In swine, oral route, either in-feed or in-water, is by far the most common route of administration of antibiotics. Because the distribution of the antibiotic in the gut and the dosage are different, the impact of in-feed vs. in-water administration of antibiotics on the fecal shedding of food borne pathogens, Campylobacter and Salmonella, and on the development of antimicrobial resistance (AMR) in gut bacteria is a largely unexplored area. Therefore, a study was conducted to compare the effects of in-feed and in-water antibiotic administration on fecal prevalence of Campylobacter and Salmonella and AMR development in nursery piglets. A total of 1,296 weaned piglets were allocated into pens (48 pens; 27 pigs per pen) distributed in a single room. Pens were assigned randomly to six treatment groups; Control (No antibiotic), In-feed chlortetracycline (CTC), In-water CTC, In-feed tiamulin, In-water tiamulin, and a combination of CTC and tiamulin (In-feed). Fresh fecal samples were collected randomly from 5 of 27 piglets from each pen on pre-treatment (days -7, 0), treatment (days 7, 14) and post-treatment (days 21, 28) phases. Bacterial isolations and identifications were done by culture method and PCR, respectively. Overall prevalence of Campylobacter and Salmonella were 18.2% (262/1,440) and 3.9% (56/1,440) respectively. Speciation of Campylobacter isolates indicated C. hyointestinalis (17.9%; 258/1,440) and C. coli (0.3%; 4/1,440). Pigs from control group had a higher prevalence (P< 0.05) of both Campylobacter and Salmonella when compared to other treatment groups. Both treatment and post-treatment phases had a significant effect on the prevalence of Campylobacter and Salmonella (P< 0.05).
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Dewsbury DMA, Cernicchiaro N, Depenbusch B, Nagaraja TG, Renter DG. Effectiveness of a Direct-Fed Microbial Product Containing Lactobacillus acidophilus and Lactobacillus casei in Reducing Fecal Shedding of Escherichia coli O157:H7 in Commercial Feedlot Cattle. Foodborne Pathog Dis 2020; 18:16-23. [PMID: 32898446 DOI: 10.1089/fpd.2020.2828] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The objective of this study was to evaluate the effectiveness of a direct-fed microbial (DFM) product in reducing fecal shedding of Escherichia coli O157:H7 in finishing commercial feedlot cattle in Kansas (KS) and Nebraska (NE). Utilizing a randomized complete block design within the feedlot (KS, n = 1; NE, n = 1), cattle were randomly allocated to 20 pens, grouped in blocks of two based on allocation date, and then, within the block, randomly assigned to a treatment group (DFM or negative control). The DFM product was included in the diet at a targeted daily dose of 1 × 109 colony-forming units (CFU) of the Lactobacillus acidophilus and Lactobacillus casei combination per animal for at least 60 d before sampling. Feedlots were sampled for four consecutive weeks; weekly sampling consisted of collecting 20 pen floor fecal samples per pen. Fecal samples were subjected to culture-based methods for detection and isolation of E. coli O157, and positive samples were quantified using real-time polymerase chain reaction. Primary outcomes of interest were fecal prevalence of E. coli O157:H7 and E. coli O157 supershedding (≥104 CFU/g of feces) prevalence. Data for each feedlot were analyzed at the pen level using mixed models accounting for the study design features. Model-adjusted mean E. coli O157:H7 fecal prevalence estimates (standard error of the mean [SEM]) for DFM and control groups were 8.2% (SEM = 2.2%) and 9.9% (SEM = 2.5%) in KS and 14.6% (SEM = 2.8%) versus 14.3% (SEM = 2.6%) in NE; prevalence did not differ significantly between treatment groups at either site (KS, p = 0.51; NE, p = 0.92). Mean E. coli O157 supershedding prevalence estimates for DFM and control groups were 2.2% (SEM = 0.7%) versus 1.8% (SEM = 0.7%) in KS (p = 0.66) and 6.7% (SEM = 1.5%) versus 3.2% (SEM = 1.0%) in NE (p = 0.04). In conclusion, administering the DFM product in the finishing diet of feedlot cattle did not significantly reduce E. coli O157:H7 fecal prevalence or supershedding prevalence in study pens at either commercial feedlot.
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Caton JS, Engle T, Crouse MS, Archibeque S, Nagaraja TG, Huntington G. Frontiers in ruminant nutrition: An ASAS-CSAS-WSASAS 2020 Symposium overview. J Anim Sci 2020; 98:5906045. [PMID: 32931569 DOI: 10.1093/jas/skaa276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 08/23/2020] [Indexed: 11/15/2022] Open
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Ludwig JB, Shi X, Shridhar PB, Roberts EL, DebRoy C, Phebus RK, Bai J, Nagaraja TG. Multiplex PCR Assays for the Detection of One Hundred and Thirty Seven Serogroups of Shiga Toxin-Producing Escherichia coli Associated With Cattle. Front Cell Infect Microbiol 2020; 10:378. [PMID: 32850480 PMCID: PMC7403468 DOI: 10.3389/fcimb.2020.00378] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/18/2020] [Indexed: 12/16/2022] Open
Abstract
Escherichia coli carrying prophage with genes that encode for Shiga toxins are categorized as Shiga toxin-producing E. coli (STEC) pathotype. Illnesses caused by STEC in humans, which are often foodborne, range from mild to bloody diarrhea with life-threatening complications of renal failure and hemolytic uremic syndrome and even death, particularly in children. As many as 158 of the total 187 serogroups of E. coli are known to carry Shiga toxin genes, which makes STEC a major pathotype of E. coli. Seven STEC serogroups, called top-7, which include O26, O45, O103, O111, O121, O145, and O157, are responsible for the majority of the STEC-associated human illnesses. The STEC serogroups, other than the top-7, called “non-top-7” have also been associated with human illnesses, more often as sporadic infections. Ruminants, particularly cattle, are principal reservoirs of STEC and harbor the organisms in the hindgut and shed in the feces, which serves as a major source of food and water contaminations. A number of studies have reported on the fecal prevalence of top-7 STEC in cattle feces. However, there is paucity of data on the prevalence of non-top-7 STEC serogroups in cattle feces, generally because of lack of validated detection methods. The objective of our study was to develop and validate 14 sets of multiplex PCR (mPCR) assays targeting serogroup-specific genes to detect 137 non-top-7 STEC serogroups previously reported to be present in cattle feces. Each assay included 7–12 serogroups and primers were designed to amplify the target genes with distinct amplicon sizes for each serogroup that can be readily identified within each assay. The assays were validated with 460 strains of known serogroups. The multiplex PCR assays designed in our study can be readily adapted by most laboratories for rapid identification of strains belonging to the non-top-7 STEC serogroups associated with cattle.
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Magossi G, Lambertini E, Noll L, Bai J, Jones C, Nagaraja TG, Phebus R, Woodworth J, Trinetta V. Potential risk-factors affecting Salmonella sp. and Escherichia coli occurrence and distribution in Midwestern United States swine feed mills. J Appl Microbiol 2020; 129:1744-1750. [PMID: 32648660 DOI: 10.1111/jam.14758] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 06/19/2020] [Accepted: 06/22/2020] [Indexed: 11/29/2022]
Abstract
AIM This study aimed to evaluate the patterns and potential risk factors associated with the occurrence of Salmonella sp. and Escherichia coli in selected United States swine feed mills. METHODS AND RESULTS A total of 405 samples were collected during fall 2018, spring and summer 2019 from selected sites including floors, equipment, shoes and feed in six feed mills in the US Midwest region. Each sample was analysed for the presence of Salmonella and E. coli with culture methods and confirmed by PCR. A survey regarding production volumes, hygiene practices and microbial testing capabilities was conducted in each facility All mills had at least one sampling site positive for either Salmonella or E. coli. Of the 405 samples, 4·7, and 14·1% were positive for Salmonella sp., and E. coli respectively. Sites with higher percentages of positive samples were the receiving, manufacturing, and control area floors. The survey responses indicated that the age of the mill might be a risk factor for bacterial contamination: the older the facility, the higher the number of positive samples. Other risk factors evaluated, such as the production capacity, did not appear to relate to bacterial prevalence. CONCLUSION The data documents the presence of E. coli and Salmonella in selected US swine feed mills, and an association between E. coli occurrence and number of ingredient suppliers to feed mill. SIGNIFICANCE AND IMPACT OF THE STUDY This information could be used to understand risk factors affecting the occurrence of Salmonella sp. and E. coli in feed mills and help implement monitoring and mitigation strategies for public health.
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Amachawadi R, Shi X, George L, Theurer M, Marston T, Holder V, Nagaraja TG. 449 Late-Breaking: Impact of feeding a propriety yeast-based synbiotic product on fecal shedding of top-7 Shiga toxin-producing Escherichia coli in feedlot cattle. J Anim Sci 2019. [DOI: 10.1093/jas/skz258.288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Shiga toxin-producing E. coli (STEC) belonging to serogroups O26, O45, O111, O103, O121, O145, and O157, called ‘top-7’, are major foodborne pathogens. Cattle are a major reservoir, in which STEC colonize the hindgut and are shed in the feces, which is a major source of contamination of food. Our objective was to evaluate the impact of a proprietary yeast-based synbiotic product (prebiotic and probiotic; Alltech, Inc., Nicholasville, KY) on fecal shedding of top-7 STEC in feedlot cattle. Twenty existing pens, housing 40–112 steers per pen, with an estimated 60 to 90 days to slaughter, were randomly assigned to a control group or a treatment group that received 22 g of the synbiotic product per steer per day, as a top dress, in a finishing diet. Twenty pen-floor fecal samples were collected from each pen on days 0, 21, 42, and 54. Fecal samples were enriched and subjected to a multiplex PCR assay targeting serogroup-specific genes for the top-7 STEC and three major virulence genes, stx1 (Shiga toxin 1), stx2 (Shiga toxin 2), and eae (intimin). Bivariate descriptive statistics for the major serogroups and virulence genes were assessed prior to multivariable analysis using mixed effects logistic regression. The overall prevalence of the top-7 serogroups were 44.5% of O26, 41.3% of O157, 15.1% of O103, 13.7% of O45, 7.8% of O121, and 0.6% of O111. The overall prevalence of stx1, stx2, and eae were 43.9%, 70.8%, and 49%, respectively. E. coli O26, O157, and O45 had a significant treatment and sampling day interaction (P < 0.0001). On d 42, fecal samples from treated group had lower prevalence (P < 0.01) of O26, O103, and O45 compared to the control group. In conclusion, the in-feed administration of the synbiotic product appears to reduce fecal shedding of certain top-7 STEC serogroups in the feedlot cattle.
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Sorensen RJ, Stewart SC, Jones CK, Crane AR, Nagaraja TG, Lattimer JM. PSVII-8 Efficacy of corn dried distillers grains with solubles as a replacement for soybean meal in a Boer goat diet. J Anim Sci 2019. [DOI: 10.1093/jas/skz122.286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Due to increased use of dried distillers grains with solubles (DDGS) in animal feed and accessibility of ethanol plants in the Midwest, this study evaluated the effect of feeding DDGS in place of soybean meal (SBM) on the fecal microbiome of Boer goats. Twenty-four Boer goat kids (apx. 70 d of age; 28.21 ± 0.96 kg) were blocked by BW and randomly assigned to 1 of 2 treatment diets for 47 d. Treatments were 0% (0DDGS) and 100% (30DDGS) DDGS in place of SBM. Goats were placed in 8 pens (4 pens/treatment; 3 goats/pen) with ad libitum access to feed and water. Fecal pellets were collected on d 47 via rectal grab and stored at -80°C until microbiome sequencing was performed. The V4 region of the 16S rRNA gene was sequenced by MR DNA (MR DNA, Shallowater, TX) on the Illumina HiSeq 2500 platform (Illumina, Inc., San Diego, CA). Data were analyzed using ANOVA with Tukey’s test for pairwise comparisons. Genera impacted by DDGS inclusion with individual relative abundances greater than 1% included increased Ruminococcus (P = 0.01) and Methanobrevibacter (P = 0.009) and decreased Lachnoclostridium (P = 0.02). Ruminococcus and Methanobrevibacter most likely increased in 30DDGS due to greater amounts of soluble fiber passing through the rumen, thus being fermented in the hindgut. The overall percentage of the phyla Bacteroidetes (P = 0.36) and Firmicutes (P = 0.12) did not differ between treatments; however, Firmicutes:Bacteroidetes increased (P = 0.05) in the 30DDGS diet. Treatment did not impact β-diversity (P = 0.47) although species richness increased (P = 0.09) in DDGS-fed goats as more soluble fiber was available for fermentation in the hindgut. In all, results of this study found replacing SBM with DDGS did not greatly alter the fecal microbiome of Boer goats.
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Shridhar PB, Patel IR, Gangiredla J, Noll LW, Shi X, Bai J, Nagaraja TG. DNA Microarray-Based Genomic Characterization of the Pathotypes of Escherichia coli O26, O45, O103, O111, and O145 Isolated from Feces of Feedlot Cattle †. J Food Prot 2019; 82:395-404. [PMID: 30794460 DOI: 10.4315/0362-028x.jfp-18-393] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Shiga toxin-producing Escherichia coli (STEC) serogroups O26, O45, O103, O111, O121, and O145, referred to as the top six non-O157 serogroups, are responsible for more than 70% of human non-O157 STEC infections in North America. Cattle harbor non-O157 strains in the hindgut and shed them in the feces. The objective of this study was to use the U.S. Food and Drug Administration (FDA) E. coli identification (ECID) DNA microarray to identify the serotype, assess the virulence potential of each, and determine the phylogenetic relationships among five of the six non-O157 E. coli serogroups isolated from feedlot cattle feces. Forty-four strains of STEC, enterohemorrhagic E. coli (EHEC), enteropathogenic E. coli (EPEC), or putative nonpathotype E. coli (NPEC) of cattle origin and five human clinical strains of EHEC were assayed with the FDA-ECID DNA microarray. The cattle strains harbored diverse flagellar genes. The bovine and human strains belonging to serogroups O26, O45, and O103 carried stx1 only, O111 carried both stx1 and stx2, and O145 carried either stx1 or stx2. The strains were also positive for various subtypes of intimin and other adhesins (IrgA homologue adhesin, long polar fimbriae, mannose-specific adhesin, and curli). Both human and cattle strains were positive for LEE-encoded type III secretory system genes and non-LEE-encoded effector genes. SplitsTree4, a program used to determine the phylogenetic relationship among the strains, revealed that the strains within each serogroup clustered according to their pathotype. In addition to genes encoding Shiga toxins, bovine non-O157 E. coli strains possessed other major virulence genes, including those for adhesins, type III secretory system proteins, and plasmid-borne virulence genes, similar to human clinical strains. Because virulence factors encoded by these genes are involved in the pathogenesis of various pathotypes of E. coli, the bovine non-O157 strains could cause human illness. The FDA-ECID DNA microarray assay rapidly provided a profile of the virulence genes for assessment of the virulence potential of each strain.
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Ekong PS, Sanderson MW, Shridhar PB, Cernicchiaro N, Renter DG, Bello NM, Bai J, Nagaraja TG. Bayesian estimation of sensitivity and specificity of culture- and PCR-based methods for the detection of six major non-O157 Escherichia coli serogroups in cattle feces. Prev Vet Med 2018; 161:90-99. [PMID: 30466664 DOI: 10.1016/j.prevetmed.2018.10.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 10/12/2018] [Accepted: 10/22/2018] [Indexed: 11/18/2022]
Abstract
Non-O157 Shiga toxin-producing Escherichia coli (non-O157 STEC, O26, O45, O103, O111, O121, and O145) are foodborne pathogens of public health importance. Culture and PCR-based methods have been developed for the detection of these serogroups in cattle feces. The objectives of this study were to evaluate diagnostic sensitivity and specificity of PCR- and culture-based methods for the detection of the six non-O157 serogroups, and to estimate their true prevalence in cattle feces, using a Bayesian latent class modeling approach that accounts for conditional dependence among the three methods. A total of 576 fecal samples collected from the floor of pens of finishing feedlot cattle during summer 2013 were used. Fecal samples, suspended in E. coli broth, were enriched and subjected to three detection methods: culture (involving immunomagnetic separation with serogroup specific beads and plating on a selective medium), conventional (cPCR), and multiplex quantitative PCR (mqPCR) assays. Samples were considered serogroup positive if the sample or the recovered isolate tested positive by PCR for an O gene of interest; neither Shiga toxin (stx) nor intimin (eae) genes were assessed. Prior information on the performance of the three methods was elicited from three subject experts. Culture was generally the least sensitive and most specific of the 3 tests across serogroups, mqPCR was generally the most sensitive test and cPCR more specific than mqPCR. Sensitivity analysis indicated that posterior inferences on test performance and prevalence were susceptible to prior specification in cases where few or no detections present in the data for selected combinations of diagnostic methods (i.e. extreme category problem). Our results characterize performance of detection methods and true prevalence of non-O157 serogroups, thus informing necessary adjustments for test bias in risk modeling.
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Amachawadi RG, Giok F, Shi X, Soto J, Narayanan SK, Tokach MD, Apley MD, Nagaraja TG. Antimicrobial resistance of Enterococcus faecium strains isolated from commercial probiotic products used in cattle and swine. J Anim Sci 2018; 96:912-920. [PMID: 29584914 DOI: 10.1093/jas/sky056] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 03/14/2018] [Indexed: 01/07/2023] Open
Abstract
Probiotics, an antibiotic alternative, are widely used as feed additives for performance benefits in cattle and swine production systems. Among bacterial species contained in probiotics, Enterococcus faecium is common. Antimicrobial resistance (AMR), particularly multidrug resistance, is a common trait among enterococci because of their propensity to acquire resistance and horizontally transfer AMR genes. Also, E. faecium is an opportunistic pathogen, and in the United States, it is the second most common nosocomial pathogen. There has been no published study on AMR and virulence potential in E. faecium contained in probiotic products used in cattle and swine in the United States. Therefore, our objectives were to determine phenotypic susceptibilities or resistance to antimicrobials, virulence genes (asa1, gelE, cylA, esp, and hyl) and assess genetic diversity of E. faecium isolated from commercial products. Twenty-two commercially available E. faecium-based probiotic products used in cattle (n = 13) and swine (n = 9) were procured and E. faecium was isolated and species confirmed. Antimicrobial susceptibility testing to determine minimum inhibitory concentrations was done by micro-broth dilution method using National Antimicrobial Resistance Monitoring Systems Gram-positive Sensititre panel plate (CMV3AGPF), and categorization of strains as susceptible or resistant was as per Clinical Laboratory and Standards Institute's guidelines. E. faecium strains from 7 products (3 for swine and 4 for cattle) were pan-susceptible to the 16 antimicrobials tested. Strains from 15 products (6 for swine and 9 for cattle) exhibited resistance to at least one antimicrobial and a high proportion of strains was resistant to lincomycin (10/22), followed by tetracycline (4/22), daptomycin (4/22), ciprofloxacin (4/22), kanamycin (3/22), and penicillin (2/22). Four strains were multidrug resistant, with resistant phenotypes ranging from 3 to 6 antimicrobials or class. None of the E. faecium strains were positive for any of the virulence genes tested. The clonal relationships among the 22 E. faecium strains were determined by pulsed-field gel electrophoresis (PFGE) typing. A total of 10 PFGE patterns were observed with 22 strains and a few of the strains from different probiotic products had identical (100% Dice similarity) PFGE patterns. In conclusion, the E. faecium strains in a few commercial probiotics exhibited AMR to medically-important antimicrobials, but none contained virulence genes.
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Noll LW, Shridhar PB, Ives SE, Cha E, Nagaraja TG, Renter DG. Detection and Quantification of Seven Major Serogroups of Shiga Toxin-Producing Escherichia coli on Hides of Cull Dairy, Cull Beef, and Fed Beef Cattle at Slaughter †. J Food Prot 2018; 81:1236-1244. [PMID: 29969294 DOI: 10.4315/0362-028x.jfp-17-497] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Dehiding during beef cattle processing can introduce fecal contaminants, including Shiga toxin-producing Escherichia coli (STEC), from hides onto carcass surfaces, creating the potential for contaminated beef. Fecal shedding of major STEC serogroups (O26, O45, O103, O111, O121, O145, and O157; STEC-7) may differ among cattle populations, yet no study has been conducted to isolate STEC-7 on hides of multiple cattle types on the same production days at the same processing plant. Our objective was to estimate and compare prevalence and concentrations of STEC-7 on hides of cull dairy, cull beef, and fed beef cattle from the same date and processing plant. Overall, 1,500 cattle hides were sponge sampled from cull dairy ( n = 500), cull beef ( n = 500) and fed beef cattle ( n = 500) over 10 processing days. To determine prevalence, samples were subjected to an immunomagnetic separation culture method, and presumptive STEC isolates were tested by PCR for serogroup and major virulence genes. A spiral plate method was used to enumerate STEC-7 from hide samples. Data were analyzed with linear mixed models. All STEC-7 serogroups except O121 were detected and quantified on cattle hides in this study population. Slightly more fed beef hides (77 of 500; 15.4%) and cull beef hides (76 of 500; 15.2%) were positive for at least one STEC-7 strain compared with cull dairy hides (57 of 500; 11.4%), but cattle type was not significantly associated ( P = 0.19) with STEC-7 prevalence. Fed beef hides had a significantly higher prevalence ( P < 0.05) of STEC O103, O145, and O157 serogroups than did either of the other cattle types. The highest proportions of quantifiable samples were for STEC O145 (32 of 1,500 samples; 2.1%) and O157 (31 of 1,500 samples; 2.1%) serogroups, with the majority of concentrations at 3 to 5 and 2 to 4 log CFU/100 cm2 of hide, respectively. Results indicate that hide contamination with some major STEC serogroups differs significantly among cattle types at harvest, even within the same day and location.
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Noll LW, Chall R, Shridhar PB, Liu X, Bai J, Delannoy S, Fach P, Nagaraja TG. Validation and Application of a Real-Time PCR Assay Based on the CRISPR Array for Serotype-Specific Detection and Quantification of Enterohemorrhagic Escherichia coli O157:H7 in Cattle Feces †. J Food Prot 2018; 81:1157-1164. [PMID: 29939793 DOI: 10.4315/0362-028x.jfp-18-049] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Several real-time quantitative PCR (qPCR) assays have been developed for detection and quantification of Escherichia coli O157:H7 in complex matrices by targeting genes for serogroup-specific O-antigen ( rfbEO157), H7 antigen, and one or more major virulence factors (Shiga toxin and intimin). A major limitation of such assays is that coamplification of H7 and virulence genes in a sample does not signal association of those genes with the O157 serogroup. Clusters of regularly interspaced short palindromic repeats (CRISPR) polymorphisms are highly correlated with certain enterohemorrhagic E. coli (EHEC) serotypes, including O157:H7, and the presence of genes for Shiga toxin ( stx1 and stx2) and intimin ( eae). Our objectives were to develop and validate a qPCR assay targeting the CRISPR array for the detection and quantification of EHEC O157:H7 in cattle feces and to evaluate the applicability of the assay for detection of and comparison with a four-plex qPCR assay targeting rfbEO157, stx1, stx2, and eae genes and a culture method. Detection limits of the CRISPRO157:H7 qPCR assay for cattle feces spiked with pure cultures were 2.1 × 103 and 2.3 × 100 CFU/g before and after enrichment, respectively. Detection of E. coli O157 in feedlot cattle fecal samples ( n = 576) was compared among the CRISPRO157:H7 qPCR assay, culture method, and four-plex qPCR assay. The CRISPRO157:H7 qPCR detected 42.2% of the samples (243 of 576 samples) as positive for E. coli O157:H7, compared with 30.4% (175 samples) by the culture method. Nearly all samples (97.2%; 560 samples) were positive for rfbEO157 by the four-plex PCR, but 21.8% (122 of 560 samples) were negative for the stx and/or eae genes, making it unlikely that EHEC O157:H7 was present in these samples. Cohen's kappa statistic indicated a fair and poor agreement beyond that due to chance between the CRISPR assay and the culture method and four-plex assay, respectively. This novel qPCR assay can detect the EHEC O157:H7 serotype in cattle feces by targeting CRISPR polymorphisms.
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Sylvester EW, Cochrane RA, Amachawadi RG, Remfry S, Lerner AB, Nagaraja TG, Pluske JR, Niederwerder MC, Paulk CB, Stark CR, Woodworth JC, Dritz SS, Tokach MD, DeRouchey JM, Goodband RD, Jones CK. 503 Defining the Minimum Inhibitory Concentration of Synthetic and Commercial Medium Chain Fatty Acid Based Products Against Salmonella Typhimurium. J Anim Sci 2018. [DOI: 10.1093/jas/sky073.500] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Wu F, Tokach MD, DeRouchey JM, Dritz SS, Woodworth JC, Goodband RD, Capps K, Remfry S, Chitakasempornkul K, Bello NM, Nagaraja TG, Amachawadi RG. 351 Effects of Tylosin Administration Route on the Development of Antimicrobial Resistance in Fecal Enterococci of Finishing Swine. J Anim Sci 2018. [DOI: 10.1093/jas/sky073.348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Cochrane RA, Amachawadi RG, Remfry S, Lerner AB, Gebhardt JT, Nagaraja TG, Pluske JR, Niederwerder MC, Woodworth JC, Dritz SS, Jones CK. 105 Young Scholar Presentation: A Review of Medium Chain Fatty Acids and Their Recent Role in Feed Safety. J Anim Sci 2018. [DOI: 10.1093/jas/sky073.103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Menegat MB, Woodworth JC, Dritz SS, Amachawadi RG, Nagaraja TG, Capps K, Tokach MD, DeRouchey JM, Goodband RD. 223 Impact of Added Copper and Chlortetracycline on Growth Performance of Nursery Pigs. J Anim Sci 2018. [DOI: 10.1093/jas/sky073.220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Swanson AJ, Cochrane RA, Amachawadi RG, Remfry S, Lerner AB, Nagaraja TG, Pluske JR, Niederwerder MC, Stark CR, Paulk CB, Woodworth JC, Dritz SS, Tokach MD, DeRouchey JM, Goodband RD, Jones CK. 482 Determination of the Minimum Inhibitory Concentration of Various Medium Chain Fatty Acid-Based Products in E. coli, Enterotoxigenic E. coli, and Campylobacter coli. J Anim Sci 2018. [DOI: 10.1093/jas/sky073.479] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Shridhar PB, Patel IR, Gangiredla J, Noll LW, Shi X, Bai J, Elkins CA, Strockbine NA, Nagaraja TG. Genetic Analysis of Virulence Potential of Escherichia coli O104 Serotypes Isolated From Cattle Feces Using Whole Genome Sequencing. Front Microbiol 2018; 9:341. [PMID: 29545780 PMCID: PMC5838399 DOI: 10.3389/fmicb.2018.00341] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 02/12/2018] [Indexed: 11/13/2022] Open
Abstract
Escherichia coli O104:H4, a Shiga toxin-producing hybrid pathotype that was implicated in a major foodborne outbreak in Germany in 2011, has not been detected in cattle. However, serotypes of O104, other than O104:H4, have been isolated from cattle feces, with O104:H7 being the most predominant. In this study, we investigated, based on whole genome sequence analyses, the virulence potential of E. coli O104 strains isolated from cattle feces, since cattle are asymptomatic carriers of E. coli O104. The genomes of ten bovine E. coli O104 strains (six O104:H7, one O104:H8, one O104:H12, and two O104:H23) and five O104:H7 isolated from human clinical cases were sequenced. Of all the bovine O104 serotypes (H7, H8, H12, and H23) that were included in the study, only E. coli O104:H7 serotype possessed Shiga toxins. Four of the six bovine O104:H7 strains and one of the five human strains carried stx1c. Three human O104 strains carried stx2, two were of subtype 2a, and one was 2d. Genomes of stx carrying bovine O104:H7 strains were larger than the stx-negative strains of O104:H7 or other serotypes. The genome sizes were proportional to the number of genes carried on the mobile genetic elements (phages, prophages, transposable elements and plasmids). Both bovine and human strains were negative for intimin and other genes associated with the type III secretory system and non-LEE encoded effectors. Plasmid-encoded virulence genes (ehxA, epeA, espP, katP) were also present in bovine and human strains. All O104 strains were negative for antimicrobial resistance genes, except one human strain. Phylogenetic analysis indicated that bovine E. coli O104 strains carrying the same flagellar antigen clustered together and STEC strains clustered separately from non-STEC strains. One of the human O104:H7 strains was phylogenetically closely related to and belonged to the same sequence type (ST-1817) as the bovine O104:H7 STEC strains. This suggests that the bovine feces could be a source of human illness caused by E. coli O104:H7 serotype. Because bovine O104:H7 strains carried virulence genes similar to human clinical strains and one of the human clinical strains was phylogenetically related to bovine strains, the serotype has the potential to be a diarrheagenic pathogen in humans.
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Hoehn AN, Titgemeyer EC, Nagaraja TG, Drouillard JS, Miesner MD, Olson KC. Effects of high condensed-tannin substrate, prior dietary tannin exposure, antimicrobial inclusion, and animal species on fermentation parameters following a 48 h in vitro incubation. J Anim Sci 2018; 96:343-353. [PMID: 29365124 PMCID: PMC6140839 DOI: 10.1093/jas/skx018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 11/27/2017] [Indexed: 11/14/2022] Open
Abstract
Condensed tannins (CT), prior dietary CT exposure, animal species, and antimicrobial inclusion effects on 48 h extent of in vitro fermentation were measured in an experiment with a 3 × 2 × 2 × 3 factorial arrangement of treatments. Treatments included species of inoculum donor (Bos taurus, Ovis aries, or Capra hircus; n = 3/species), prior adaptation to dietary CT (not adapted or adapted), culture substrate (low-CT or high-CT), and antimicrobial additive (none, bacterial suppression with penicillin + streptomycin, or fungal suppression with cycloheximide). Low-CT or high-CT substrates were incubated in vitro using inoculum from animals either not exposed (period 1) or previously exposed to dietary CT (period 2). The extent of IVDMD after 48 h of incubation was greater (P < 0.001) for cultures with low-CT substrate (21.5%) than for cultures with high-CT substrate (16.5%). Cultures with high-CT substrate or with suppressed bacterial activity had less (P < 0.001) gas pressure than cultures with low-CT substrate or cultures with suppressed fungal activity. Total VFA concentrations were greater (P < 0.001) in low-CT cultures when inoculum donors were without prior CT exposure (83.7 mM) than when inoculum was from CT-exposed animals (79.6 mM). Conversely, total VFA concentrations were greater (P < 0.001) in high-CT cultures with tannin-exposed inoculum (59.4 mM) than with nonexposed inoculum (52.6 mM). As expected, CT and suppression of bacterial fermentative activities had strong negative effects on fermentation; however, prior exposure to dietary CT attenuated some negative effects of dietary CT on fermentation. In our experiment, the magnitude of inoculum-donor species effects on fermentation was minor.
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Noll LW, Worley JN, Yang X, Shridhar PB, Ludwig JB, Shi X, Bai J, Caragea D, Meng J, Nagaraja TG. Comparative genomics reveals differences in mobile virulence genes of Escherichia coli O103 pathotypes of bovine fecal origin. PLoS One 2018; 13:e0191362. [PMID: 29389941 PMCID: PMC5794082 DOI: 10.1371/journal.pone.0191362] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 01/03/2018] [Indexed: 01/09/2023] Open
Abstract
Escherichia coli O103, harbored in the hindgut and shed in the feces of cattle, can be enterohemorrhagic (EHEC), enteropathogenic (EPEC), or putative non-pathotype. The genetic diversity particularly that of virulence gene profiles within O103 serogroup is likely to be broad, considering the wide range in severity of illness. However, virulence descriptions of the E. coli O103 strains isolated from cattle feces have been primarily limited to major genes, such as Shiga toxin and intimin genes. Less is known about the frequency at which other virulence genes exist or about genes associated with the mobile genetic elements of E. coli O103 pathotypes. Our objective was to utilize whole genome sequencing (WGS) to identify and compare major and putative virulence genes of EHEC O103 (positive for Shiga toxin gene, stx1, and intimin gene, eae; n = 43), EPEC O103 (negative for stx1 and positive for eae; n = 13) and putative non-pathotype O103 strains (negative for stx and eae; n = 13) isolated from cattle feces. Six strains of EHEC O103 from human clinical cases were also included. All bovine EHEC strains (43/43) and a majority of EPEC (12/13) and putative non-pathotype strains (12/13) were O103:H2 serotype. Both bovine and human EHEC strains had significantly larger average genome sizes (P < 0.0001) and were positive for a higher number of adherence and toxin-based virulence genes and genes on mobile elements (prophages, transposable elements, and plasmids) than EPEC or putative non-pathotype strains. The genome size of the three pathotypes positively correlated (R2 = 0.7) with the number of genes carried on mobile genetic elements. Bovine strains clustered phylogenetically by pathotypes, which differed in several key virulence genes. The diversity of E. coli O103 pathotypes shed in cattle feces is likely reflective of the acquisition or loss of virulence genes carried on mobile genetic elements.
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Amachawadi RG, Purvis TJ, Lubbers BV, Homm JW, Maxwell CL, Nagaraja TG. Bacterial flora of liver abscesses in crossbred beef cattle and Holstein steers fed finishing diets with or without tylosin. J Anim Sci 2018; 95:3425-3434. [PMID: 28805921 DOI: 10.2527/jas.2016.1198] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Holstein steers raised for beef production consistently have a higher prevalence and more severe form of liver abscesses than cattle of beef breeds. A study was conducted to compare bacterial flora of liver abscesses collected from multiple abattoirs from 4 groups of cattle, arranged in a 2 × 2 factorial design, consisting of crossbred cattle and Holstein steers, and each group fed a finishing diet supplemented with or without tylosin. A total of 383 liver abscess samples, consisting of 94 and 81 from crossbred cattle and 89 and 119 from Holstein steers fed finishing diets with or without tylosin, respectively, were subjected for anaerobic and aerobic bacterial isolations. The minimum inhibitory concentrations (MIC) of tylosin to the predominant bacterial species were determined. The likelihood chi-square test was performed to assess unadjusted differences in bacterial prevalence proportions between the 2 types of cattle (crossbred and Holstein steers) and feed type (tylosin or no tylosin). There was no interaction between cattle type and tylosin inclusion on the prevalence of any of the bacterial species isolated. Liver abscesses from Holstein steers yielded a higher total number of isolates compared to liver abscesses from crossbred cattle (1060 vs. 788). subsp. was isolated from all abscesses. The prevalence of subsp. was 19.1% and was not affected by the cattle type or tylosin. The prevalence of was higher ( < 0.01) in crossbred cattle (73.7%) compared to Holstein steers (29.8%). Also, the prevalence of was higher in abscesses from tylosin-fed (66.1%) cattle than no tylosin-fed cattle (35%). The overall prevalence of was 25.3% and was similar ( = 0.58) between cattle type, but the prevalence was lower ( < 0.01) in tylosin-fed (16.9%) compared to no tylosin-fed group (33%). Mean MIC of tylosin for and were similar across both cattle types and tylosin inclusion. Although bacterial flora of liver abscesses from Holstein steers appeared to be more diverse than that of crossbred cattle, there was no difference in the prevalence of the and and in fact, prevalence of was higher in crossbred than Holstein steers. Therefore, the difference in bacterial flora is not the likely reason for higher prevalence and severity of liver abscesses in Holstein steers than crossbred beef cattle.
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Meredith CM, Weiss CP, Gentry WW, Amachawadi RG, Narayanan SK, Nagaraja TG, McCollum FT, Jennings JS. 566 Isolation of Fusobacterium necrophorum , Trueperella pyogenes , and Salmonella enterica from ruminal, ileal, and colonic epithelial tissues of finishing beef steers receiving different levels of dietary roughage with and without tylosin. J Anim Sci 2017. [DOI: 10.2527/asasann.2017.566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Shridhar PB, Noll LW, Cull CA, Shi X, Cernicchiaro N, Renter DG, Bai J, Nagaraja TG. Spiral Plating Method To Quantify the Six Major Non-O157 Escherichia coli Serogroups in Cattle Feces. J Food Prot 2017; 80:848-856. [PMID: 28414257 DOI: 10.4315/0362-028x.jfp-16-360] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Accepted: 12/20/2016] [Indexed: 01/01/2023]
Abstract
Cattle are a major reservoir of the six major Shiga toxin-producing non-O157 Escherichia coli (STEC) serogroups (O26, O45, O103, O111, O121, and O145) responsible for foodborne illnesses in humans. Besides prevalence in feces, the concentrations of STEC in cattle feces play a major role in their transmission dynamics. A subset of cattle, referred to as super shedders, shed E. coli O157 at high concentrations (≥4 log CFU/g of feces). It is not known whether a similar pattern of fecal shedding exists for non-O157. Our objectives were to initially validate the spiral plating method to quantify the six non-O157 E. coli serogroups with pure cultures and culture-spiked fecal samples and then determine the applicability of the method and compare it with multiplex quantitative PCR (mqPCR) assays for the quantification of the six non-O157 E. coli serogroups in cattle fecal samples collected from commercial feedlots. Quantification limits of the spiral plating method were 3 log, 3 to 4 log, and 3 to 5 log CFU/mL or CFU/g for individual cultures, pooled pure cultures, and cattle fecal samples spiked with pooled pure cultures, respectively. Of the 1,152 cattle fecal samples tested from eight commercial feedlots, 122 (10.6%) and 320 (27.8%) harbored concentrations ≥4 log CFU/g of one or more of the six serogroups of non-O157 by spiral plating and mqPCR methods, respectively. A majority of quantifiable samples, detected by either spiral plating (135 of 137, 98.5%) or mqPCR (239 of 320, 74.7%), were shedding only one serogroup. Only one of the quantifiable samples was positive for a serogroup carrying Shiga toxin (stx1) and intimin (eae) genes; 38 samples were positive for serogroups carrying the intimin gene. In conclusion, the spiral plating method can be used to quantify non-O157 serogroups in cattle feces, and our study identified a subset of cattle that was super shedders of non-O157 E. coli. The method has the advantage of quantifying non-O157 STEC, unlike mqPCR that quantifies serogroups only.
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Samii SS, Wallace N, Nagaraja TG, Engstrom MA, Miesner MD, Armendariz CK, Titgemeyer EC. Effects of limonene on ruminal concentrations, fermentation, and lysine degradation in cattle. J Anim Sci 2017; 94:3420-3430. [PMID: 27695807 DOI: 10.2527/jas.2016-0455] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Previous in vitro data showed that was inhibited by limonene. We further evaluated effects of limonene on growth of in vitro as well as on ruminal concentrations of in vivo. With in vitro cultivation in anaerobic brain-heart infusion broth, limonene decreased growth of . Thymol also reduced growth of , but it was less effective than limonene. Tylosin effectively reduced growth of in vitro. Although the response over fermentation times and concentrations of antimicrobials differed somewhat between tylosin and limonene, the 2 antimicrobial agents yielded similar inhibitory effects on growth of at concentrations ranging from 6 to 24 mg/L. The effects of limonene on ruminal concentration in vivo were tested in 7 ruminally cannulated heifers (225 kg initial BW) used in a 7 × 4 Youden square design. Treatments included: 1) control, 2) limonene at 10 mg/kg diet DM, 3) limonene at 20 mg/kg diet DM, 4) limonene at 40 mg/kg diet DM, 5) limonene at 80 mg/kg diet DM, 6) CRINA-L (a blend of essential oil components) at 180 mg/kg diet DM, and 7) tylosin at 12 mg/kg diet DM. Each period included 11 d with 10 d washouts between periods. Samples of ruminal contents were collected before treatment initiation and after 4, 7, and 10 d of treatment for measuring by the most probable number method using selective culture medium. Limonene linearly decreased ( = 0.03) ruminal concentration, with the lowest concentration achieved with 40 mg of limonene/kg dietary DM. Limonene tended ( ≤ 0.07) to linearly reduce ruminal molar proportions of propionate and valerate while tending to linearly increase ( ≤ 0.10) those of butyrate and 2-methyl butyrate. Limonene did not affect ruminal NH concentrations or degradation rates of lysine. Neither CRINA-L ( = 0.52) nor tylosin ( = 0.19) affected ruminal concentrations. CRINA-L significantly decreased ruminal concentrations of NH and molar proportions of 3-methyl butyrate, whereas tylosin significantly decreased molar proportions of propionate while increasing those of butyrate and tending to increase those of acetate. Limonene supplementation reduced ruminal concentrations of suggesting that it may have the potential to reduce the prevalence of liver abscesses, although further research is needed to assess the effect of limonene in feedlot cattle.
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