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Maurer JJ, Cheng Y, Pedroso A, Thompson KK, Akter S, Kwan T, Morota G, Kinstler S, Porwollik S, McClelland M, Escalante-Semerena JC, Lee MD. Peeling back the many layers of competitive exclusion. Front Microbiol 2024; 15:1342887. [PMID: 38591029 PMCID: PMC11000858 DOI: 10.3389/fmicb.2024.1342887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/19/2024] [Indexed: 04/10/2024] Open
Abstract
Baby chicks administered a fecal transplant from adult chickens are resistant to Salmonella colonization by competitive exclusion. A two-pronged approach was used to investigate the mechanism of this process. First, Salmonella response to an exclusive (Salmonella competitive exclusion product, Aviguard®) or permissive microbial community (chicken cecal contents from colonized birds containing 7.85 Log10Salmonella genomes/gram) was assessed ex vivo using a S. typhimurium reporter strain with fluorescent YFP and CFP gene fusions to rrn and hilA operon, respectively. Second, cecal transcriptome analysis was used to assess the cecal communities' response to Salmonella in chickens with low (≤5.85 Log10 genomes/g) or high (≥6.00 Log10 genomes/g) Salmonella colonization. The ex vivo experiment revealed a reduction in Salmonella growth and hilA expression following co-culture with the exclusive community. The exclusive community also repressed Salmonella's SPI-1 virulence genes and LPS modification, while the anti-virulence/inflammatory gene avrA was upregulated. Salmonella transcriptome analysis revealed significant metabolic disparities in Salmonella grown with the two different communities. Propanediol utilization and vitamin B12 synthesis were central to Salmonella metabolism co-cultured with either community, and mutations in propanediol and vitamin B12 metabolism altered Salmonella growth in the exclusive community. There were significant differences in the cecal community's stress response to Salmonella colonization. Cecal community transcripts indicated that antimicrobials were central to the type of stress response detected in the low Salmonella abundance community, suggesting antagonism involved in Salmonella exclusion. This study indicates complex community interactions that modulate Salmonella metabolism and pathogenic behavior and reduce growth through antagonism may be key to exclusion.
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Affiliation(s)
- John J. Maurer
- School of Animal Sciences, College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Ying Cheng
- Department of Population Health, University of Georgia, Athens, GA, United States
| | - Adriana Pedroso
- Department of Population Health, University of Georgia, Athens, GA, United States
| | - Kasey K. Thompson
- Department of Population Health, University of Georgia, Athens, GA, United States
| | - Shamima Akter
- Department of Biomedical Sciences and Pathobiology, College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Tiffany Kwan
- Department of Population Health, University of Georgia, Athens, GA, United States
| | - Gota Morota
- School of Animal Sciences, College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Sydney Kinstler
- School of Animal Sciences, College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Steffen Porwollik
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA, United States
| | - Michael McClelland
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA, United States
| | | | - Margie D. Lee
- Department of Biomedical Sciences and Pathobiology, College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
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2
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Botta C, Franciosa I, Coisson JD, Ferrocino I, Colasanto A, Arlorio M, Cocolin L, Rantsiou K. Beef carcass microbiota after slaughtering and primary cooling: A metataxonomic assessment to infer contamination drivers. Food Res Int 2023; 174:113466. [PMID: 37986409 DOI: 10.1016/j.foodres.2023.113466] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/29/2023] [Accepted: 09/10/2023] [Indexed: 11/22/2023]
Abstract
The impact of primary cooling on beef microbiota was investigated on six beef carcasses consecutively processed with the parallel use of metataxonomic and culture-dependent analysis. Samples were collected immediately after slaughtering (AS) and after the 24th-hour post-cooling (PC) from three different surfaces, namely neck, flank and thigh. The main objective was to examine whether the microbiota composition of beef carcasses changes as function of the surface sampled, primary cooling (from AS to PC) and animal's origin (breeder). The outcomes underline that primary cooling did not affect qualitatively the composition of the potentially active microbiota or the carcass superficial counts. Although slight changes in chemical-physical parameters like volatile organic compounds (VOCs) were observed after cooling, the carcasses microbiota and its inferred metabolic pathways varied among animals as a function of their origin. Co-occurrence and co-exclusion analyses underlined competition for the colonisation of the carcass surface between Brochothrix-Psychrobacter and Carnobacterium-Serratia-Pseudomonas. Once integrated in a comprehensive monitoring of the supply chain, the metataxonomic characterisation of the beef carcasses microbiota might represent a valid integrative approach to define the cuts' perishability and their appropriateness to specific packaging and storage methods. These new bits of knowledge could be the base to define good strategies for the prevention of meat spoilage.
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Affiliation(s)
- C Botta
- Department of Agricultural, Forest and Food Sciences, University of Torino, Italy
| | - I Franciosa
- Department of Agricultural, Forest and Food Sciences, University of Torino, Italy
| | - J D Coisson
- Dipartimento di Scienze del Farmaco - Università del Piemonte Orientale, Largo Donegani 2, I-28100 Novara, Italy
| | - I Ferrocino
- Department of Agricultural, Forest and Food Sciences, University of Torino, Italy
| | - A Colasanto
- Dipartimento di Scienze del Farmaco - Università del Piemonte Orientale, Largo Donegani 2, I-28100 Novara, Italy
| | - M Arlorio
- Dipartimento di Scienze del Farmaco - Università del Piemonte Orientale, Largo Donegani 2, I-28100 Novara, Italy
| | - L Cocolin
- Department of Agricultural, Forest and Food Sciences, University of Torino, Italy
| | - K Rantsiou
- Department of Agricultural, Forest and Food Sciences, University of Torino, Italy.
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3
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Al-Awwal N, Anderson SH, El-Dweik M, Udawatta RP, Yang J, Zaid F. Effects of conservation buffer systems on adsorption of fluorescent-labeled Escherichia coli. JOURNAL OF ENVIRONMENTAL QUALITY 2023; 52:303-314. [PMID: 36382799 DOI: 10.1002/jeq2.20436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 11/04/2022] [Indexed: 06/16/2023]
Abstract
The magnitude of bacterial transport through runoff into surface water or infiltration into groundwater is influenced by the adsorption processes in soil. The objective of this study was to evaluate fluorescent-labeled Escherichia coli (E. coli) adsorption by soil under agroforestry buffer (AB), grass buffer (GB), and row crop (RC) management. Adsorption experiments were conducted by inoculating three masses (0.5, 1, and 10 g) of each treatment (AB, GB, and RC) with E. coli O157:H7-GFP with concentration ranges of 105 -108 colony-forming units (cfu) ml-1 . Adsorption data were evaluated using Langmuir, Freundlich, and Temkin adsorption isotherm models. The Freundlich isotherm model described the observed data well for all treatments using the 10-g soil mass, with the R2 values closer to unity in all treatments. The Freundlich Kf parameter, an indicator of adsorption capacity, was higher for the AB treatment (9.93 cfu ml-1 ) compared with the GB and RC treatments (2.32 and 1.27 cfu ml-1 , respectively). The multiple pairwise comparisons test (Tukey test) of the Freundlich 1/nf parameter demonstrated a significant difference (p < .05) between the AB treatment and the RC and GB treatments. Similarly, the Kf values were significantly (p = .05) higher for the 10-g mass under the same test conditions, but no significant differences were observed in the 0.5- and 1-g masses. This study demonstrated that AB has a higher E. coli adsorption capacity and the potential for mitigating the effects of E. coli O157:H7 transport to surface or groundwater through the soil ecosystem.
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Affiliation(s)
- Nasruddeen Al-Awwal
- School of Natural Resources, Univ. of Missouri-Columbia, 302 Anheuser-Busch Natural Resources Building, Columbia, MO, USA
- Dep. of Agriculture and Environmental Sciences and Cooperative Research Program, Lincoln Univ., Jefferson City, MO, USA
| | - Stephen H Anderson
- School of Natural Resources, Univ. of Missouri-Columbia, 302 Anheuser-Busch Natural Resources Building, Columbia, MO, USA
| | - Majed El-Dweik
- Dep. of Agriculture and Environmental Sciences and Cooperative Research Program, Lincoln Univ., Jefferson City, MO, USA
| | - Ranjith P Udawatta
- School of Natural Resources, Univ. of Missouri-Columbia, 302 Anheuser-Busch Natural Resources Building, Columbia, MO, USA
- The Center for Agroforestry, Univ. of Missouri-Columbia, 203 Anheuser-Busch Natural Resources Building, Columbia, MO, USA
| | - John Yang
- Dep. of Agriculture and Environmental Sciences and Cooperative Research Program, Lincoln Univ., Jefferson City, MO, USA
| | - Faraj Zaid
- Dep. of Chemical Engineering, Sirte Univ., Sirte, Libya
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4
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Guevarra RB, Kim ES, Cho JH, Song M, Cho JH, Lee JH, Kim H, Kim S, Keum GB, Lee CH, Cho WT, Watthanaphansak S, Kim HB. Gut microbial shifts by synbiotic combination of Pediococcus acidilactici and lactulose in weaned piglets challenged with Shiga toxin-producing Escherichia coli. Front Vet Sci 2023; 9:1101869. [PMID: 36713861 PMCID: PMC9879705 DOI: 10.3389/fvets.2022.1101869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 12/28/2022] [Indexed: 01/13/2023] Open
Abstract
Development of alternatives to in-feed antibiotics in the swine industry have been the focused of many pig gut microbiota studies to improve animal health. In this study, we evaluated the effects of probiotic Pediococcus acidilactici (PRO), prebiotic lactulose (PRE), and their synbiotic combination (SYN) on gut microbiota using 16S rRNA gene sequencing in weaned piglets challenged with Shiga-toxin producing Escherichia coli (STEC). Our data showed that prebiotics, probiotics and synbiotics improved the intestinal health in weaned piglets. No significant differences were observed in species richness and species diversity in weaned piglets fed prebiotics, probiotics and their synbiotic combination. However, beta diversity analysis revealed distinct clustering of the microbiota of according to dietary treatment and by oral challenge of STEC. At the phylum level, Firmicutes to Bacteroidetes ratio was lower in the dietary treatment groups than the control group. Oral supplementation of prebiotics, probiotics and synbiotics enriched the abundance of Prevotella and Roseburia. Succinivibrio was elevated in PRO group; however, Phascolarctobacterium was depleted with STEC challenge regardless of dietary treatment. Overall, our data showed that administration of synbiotics in piglets improved intestinal health through gut microbiota modulation. Our data indicated that prebiotics, probiotics and their synbiotic combination could promote intestinal health through gut microbiota modulation in weaned piglets.
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Affiliation(s)
- Robin B. Guevarra
- Department of Animal Resources Science, Dankook University, Cheonan, Republic of Korea
| | - Eun Sol Kim
- Department of Animal Resources Science, Dankook University, Cheonan, Republic of Korea
| | - Jin Ho Cho
- Division of Food and Animal Sciences, Chungbuk National University, Cheongju, Republic of Korea
| | - Minho Song
- Division of Animal and Dairy Science, Chungnam National University, Daejeon, Republic of Korea
| | - Jae Hyoung Cho
- Department of Animal Resources Science, Dankook University, Cheonan, Republic of Korea
| | - Jun Hyung Lee
- Department of Animal Resources Science, Dankook University, Cheonan, Republic of Korea
| | - Hyeri Kim
- Department of Animal Resources Science, Dankook University, Cheonan, Republic of Korea
| | - Sheena Kim
- Department of Animal Resources Science, Dankook University, Cheonan, Republic of Korea
| | - Gi Beom Keum
- Department of Animal Resources Science, Dankook University, Cheonan, Republic of Korea
| | - Chan Ho Lee
- Gene Bio Tech Co., Ltd., Gongju, Republic of Korea
| | - Won Tak Cho
- Gene Bio Tech Co., Ltd., Gongju, Republic of Korea
| | - Suphot Watthanaphansak
- Department of Veterinary Medicine, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Hyeun Bum Kim
- Department of Animal Resources Science, Dankook University, Cheonan, Republic of Korea,*Correspondence: Hyeun Bum Kim ✉
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5
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Lee MD, Pedroso AA, Maurer JJ. Bacterial composition of a competitive exclusion product and its correlation with product efficacy at reducing Salmonella in poultry. Front Physiol 2023; 13:1043383. [PMID: 36699689 PMCID: PMC9868637 DOI: 10.3389/fphys.2022.1043383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 12/20/2022] [Indexed: 01/11/2023] Open
Abstract
The mature intestinal microbiome is a formidable barrier to pathogen colonization. Day-old chicks seeded with cecal contents of adult hens are resistant to colonization with Salmonella, the basis of competitive exclusion. Competitive exclusion products can include individual microbes but are commonly undefined intestinal communities taken from adult animals and in commercial production is amplified in fermentator and sold commercially in freeze dried lots. While superior to single and multiple species probiotics, reducing Salmonella colonization by multiple logs, undefined products have limited acceptance because of their uncharacterized status. In this study, the bacterial composition of the master stock, preproduction seed stocks and commercial lots of a poultry competitive exclusion product, was defined by 16S rRNA sequence analysis, targeting the 16S rRNA variable region (V1-V3). The samples contained a diversity of genera (22-52 distinct genera) however, the commercial lots displayed less diversity compared to the seeds and the master stock. Community composition varied between seeds and the master stock and was not a good predictor of potency, in terms of log10 reduction in Salmonella abundance. While there was significant correlation in composition between seeds and their commercial lots, this too was a not a good predictor of potency. There was linear correlation between unclassified Actinobacteria, Peptococcus, and unclassified Erysipelotrichaceae, and Salmonella abundance (r 2 > .75) for commercial seeds. However, upon review of the literature, these three genera were not consistently observed across studies or between trials that examined the correlation between intestinal community composition and Salmonella prevalence or abundance.
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Affiliation(s)
- Margie D. Lee
- Poultry Diagnostic and Research Center, College of Veterinary Medicine, The University of Georgia, Athens, GA, United States,Department of Biomedical Sciences and Pathobiology, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States,*Correspondence: Margie D. Lee,
| | - Adriana A. Pedroso
- Poultry Diagnostic and Research Center, College of Veterinary Medicine, The University of Georgia, Athens, GA, United States
| | - John J. Maurer
- Poultry Diagnostic and Research Center, College of Veterinary Medicine, The University of Georgia, Athens, GA, United States,School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
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6
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Vasco K, Nohomovich B, Singh P, Venegas-Vargas C, Mosci RE, Rust S, Bartlett P, Norby B, Grooms D, Zhang L, Manning SD. Characterizing the Cattle Gut Microbiome in Farms with a High and Low Prevalence of Shiga Toxin Producing Escherichia coli. Microorganisms 2021; 9:microorganisms9081737. [PMID: 34442815 PMCID: PMC8399351 DOI: 10.3390/microorganisms9081737] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/06/2021] [Accepted: 08/12/2021] [Indexed: 12/20/2022] Open
Abstract
Cattle are the main reservoirs of Shiga toxin producing Escherichia coli (STEC), a major foodborne pathogen associated with acute enteric disease and hemolytic-uremic syndrome in humans. A total of 397 beef and dairy cattle from 5 farms were included in this study, of which 660 samples were collected for 16S rRNA gene sequencing. The microbiota of farms with a high-STEC prevalence (HSP) had greater richness compared to those of farms with a low-STEC prevalence (LSP). Longitudinal analyses showed STEC-shedders from LSP farms had higher microbiome diversity; meanwhile, changes in the microbiome composition in HSP farms were independent of the STEC shedding status. Most of the bacterial genera associated with STEC shedding in dairy farms were also correlated with differences in the percentage of forage in diet and risk factors of STEC carriage such as days in milk, number of lactations, and warm temperatures. Identifying factors that alter the gut microbiota and enable STEC colonization in livestock could lead to novel strategies to prevent fecal shedding and the subsequent transmission to humans.
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Affiliation(s)
- Karla Vasco
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA; (K.V.); (B.N.); (P.S.); (R.E.M.); (L.Z.)
| | - Brian Nohomovich
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA; (K.V.); (B.N.); (P.S.); (R.E.M.); (L.Z.)
| | - Pallavi Singh
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA; (K.V.); (B.N.); (P.S.); (R.E.M.); (L.Z.)
| | - Cristina Venegas-Vargas
- Department of Large Animal Clinical Sciences, College Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA; (C.V.-V.); (P.B.); (B.N.); (D.G.)
| | - Rebekah E. Mosci
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA; (K.V.); (B.N.); (P.S.); (R.E.M.); (L.Z.)
| | - Steven Rust
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA;
| | - Paul Bartlett
- Department of Large Animal Clinical Sciences, College Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA; (C.V.-V.); (P.B.); (B.N.); (D.G.)
| | - Bo Norby
- Department of Large Animal Clinical Sciences, College Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA; (C.V.-V.); (P.B.); (B.N.); (D.G.)
| | - Daniel Grooms
- Department of Large Animal Clinical Sciences, College Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA; (C.V.-V.); (P.B.); (B.N.); (D.G.)
| | - Lixin Zhang
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA; (K.V.); (B.N.); (P.S.); (R.E.M.); (L.Z.)
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI 48824, USA
| | - Shannon D. Manning
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA; (K.V.); (B.N.); (P.S.); (R.E.M.); (L.Z.)
- Correspondence:
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7
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Pedroso AA, Lee MD, Maurer JJ. Strength Lies in Diversity: How Community Diversity Limits Salmonella Abundance in the Chicken Intestine. Front Microbiol 2021; 12:694215. [PMID: 34211451 PMCID: PMC8239400 DOI: 10.3389/fmicb.2021.694215] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 05/24/2021] [Indexed: 12/12/2022] Open
Abstract
The transfer of the intestinal microbiota from adult to juvenile animals reduces Salmonella prevalence and abundance. The mechanism behind this exclusion is unknown, however, certain member species may exclude or promote pathogen colonization and Salmonella abundance in chickens correlates with intestinal community composition. In this study, newly hatched chicks were colonized with Salmonella Typhimurium and 16S rRNA libraries were generated from the cecal bacterial community at 21, 28, 35, and 42 days of age. Salmonella was quantified by real-time PCR. Operational taxonomic units (OTUs) were assigned, and taxonomic assignments were made, using the Ribosomal Database Project. Bacterial diversity was inversely proportional to the Salmonella abundance in the chicken cecum (p < 0.01). In addition, cecal communities with no detectable Salmonella (exclusive community) displayed an increase in the abundance of OTUs related to specific clostridial families (Ruminococcaceae, Eubacteriaceae, and Oscillospiraceae), genera (Faecalibacterium and Turicibacter) and member species (Ethanoligenens harbinense, Oscillibacter ruminantium, and Faecalibacterium prausnitzii). For cecal communities with high Salmonella abundance (permissive community), there was a positive correlation with the presence of unclassified Lachnospiraceae, clostridial genera Blautia and clostridial species Roseburia hominis, Eubacterium biforme, and Robinsoniella peoriensis. These findings strongly support the link between the intestinal bacterial species diversity and the presence of specific member species with Salmonella abundance in the chicken ceca. Exclusive bacterial species could prove effective as direct-fed microbials for reducing Salmonella in poultry while permissive species could be used to predict which birds will be super-shedders.
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Affiliation(s)
- Adriana A Pedroso
- Department of Population Health, University of Georgia, Athens, GA, United States
| | - Margie D Lee
- Department of Population Health, University of Georgia, Athens, GA, United States.,Department of Biomedical Sciences and Pathobiology, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - John J Maurer
- Department of Population Health, University of Georgia, Athens, GA, United States.,Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
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8
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Jeyanathan A, Ramalhete R, Blunn G, Gibbs H, Pumilia CA, Meckmongkol T, Lovejoy J, Coathup MJ. Lactobacillus cell-free supernatant as a novel bioagent and biosurfactant against Pseudomonas aeruginosa in the prevention and treatment of orthopedic implant infection. J Biomed Mater Res B Appl Biomater 2021; 109:1634-1643. [PMID: 33634961 DOI: 10.1002/jbm.b.34821] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 01/13/2021] [Accepted: 02/14/2021] [Indexed: 01/09/2023]
Abstract
The hypothesis was that probiotic Lactobacillus species (spp.) or their cell-free supernatant (CFS) are effective in inhibiting (a) planktonic growth of Pseudomonas aeruginosa (PA), (b) its adhesion to a Ti6Al4V-alloy surface, and (c) in dispersing biofilm once formed. (a) A planktonic co-culture containing PA(104 colony-forming unit [CFU]/ml) was combined with either Lactobacillus acidophilus, Lactobacillus plantarum (LP), or Lactobacillus fermentum (LF) at a suspension of 104 (1:1) or 108 CFU/ml (1:2). Lactobacillus and PA CFUs were then quantified. (b) Ti-6Al-4V discs were inoculated with PA followed by supplementation with CFS and adherent PA quantified. (c) Biofilm covered discs were supplemented with Lactobacillus CFS and remaining PA activity quantified. Results showed that whole-cell cultures were ineffective in preventing PA growth; however, the addition of CFS resulted in a 99.99 ± 0.003% reduction in adherent PA in all Lactobacillus groups (p < .05 in all groups) with no viable PA growth measured in the LF and LP groups. Following PA biofilm formation, CFS resulted in a significant reduction in PA activity in all Lactobacillus groups (p ≤ .05 in all groups) with a 29.75 ± 15.98% increase measured in control samples. Supplementation with CFS demonstrated antiadhesive, antibiofilm, and toxic properties to PA.
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Affiliation(s)
- Augustina Jeyanathan
- Institute of Orthopaedics and Musculoskeletal Science, Division of Surgery and Interventional Science, Royal National Orthopaedic Hospital, University College London, Stanmore, UK
| | - Rita Ramalhete
- Institute of Orthopaedics and Musculoskeletal Science, Division of Surgery and Interventional Science, Royal National Orthopaedic Hospital, University College London, Stanmore, UK
| | - Gordon Blunn
- Institute of Orthopaedics and Musculoskeletal Science, Division of Surgery and Interventional Science, Royal National Orthopaedic Hospital, University College London, Stanmore, UK.,School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth, UK
| | - Hannah Gibbs
- Biionix (Bionic Materials, Implants & Interfaces) Cluster, Department of Internal Medicine, College of Medicine, University of Central Florida, Orlando, Florida, USA
| | - Cyrus Anthony Pumilia
- Biionix (Bionic Materials, Implants & Interfaces) Cluster, Department of Internal Medicine, College of Medicine, University of Central Florida, Orlando, Florida, USA
| | - Teerin Meckmongkol
- Biionix (Bionic Materials, Implants & Interfaces) Cluster, Department of Internal Medicine, College of Medicine, University of Central Florida, Orlando, Florida, USA.,Department of General Surgery, Nemours Children's Hospital, Orlando, Florida, USA
| | - John Lovejoy
- Biionix (Bionic Materials, Implants & Interfaces) Cluster, Department of Internal Medicine, College of Medicine, University of Central Florida, Orlando, Florida, USA.,Department of Orthopaedics, Sports Medicine and Physical Medicine and Rehabilitation, Nemours Children's Hospital, Orlando, Florida, USA
| | - Melanie J Coathup
- Institute of Orthopaedics and Musculoskeletal Science, Division of Surgery and Interventional Science, Royal National Orthopaedic Hospital, University College London, Stanmore, UK.,Biionix (Bionic Materials, Implants & Interfaces) Cluster, Department of Internal Medicine, College of Medicine, University of Central Florida, Orlando, Florida, USA
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9
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Changes in STEC and bacterial communities during enrichment of manufacturing beef in selective and non-selective media. Food Microbiol 2020; 96:103711. [PMID: 33494892 DOI: 10.1016/j.fm.2020.103711] [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] [Received: 05/13/2020] [Revised: 11/26/2020] [Accepted: 12/01/2020] [Indexed: 11/22/2022]
Abstract
Detection and isolation of Shiga toxin-producing Escherichia coli (STEC) from manufacturing beef is challenging and it may be affected by microbial changes during enrichment. This study was designed to understand population changes during enrichment of beef from an integrated (Samples A and B) and a fragmented (Samples C and D) abattoir. The samples were enriched in buffered peptone water (BPW), Assurance GDS MPX top 7 STEC mEHEC®, BAX® E. coli O157:H7 MP and PDX-STEC media then were processed for 16 S rRNA sequencing. Escherichia dominated Sample B enrichment broths regardless of the media used (71.6-97.9%) but only in mEHEC broth (79.6%) of Sample A. Escherichia was dominant in Sample C in mEHEC (95.2%) and PDX-STEC (99.2%) broths but less in BPW (58.5%) and MP (64.9%) broths. In Sample D, Clostridium dominated in mEHEC (65.5%), MP (80.2%) and PDX-STEC (90.6%) broths. O157 STEC was isolated from Sample C only. The study suggested that MP may not be as effective as mEHEC and PDX-STEC and that Clostridium could interfere with enrichment of Escherichia. Understanding the ecological changes during enrichment provides meaningful insight to optimising the enrichment protocol for STEC and subsequently enhance the efficiency of STEC detection.
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10
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Kang S, Ravensdale JT, Coorey R, Dykes GA, Barlow RS. Analysis of Bacterial Diversity in Relation to the Presence of the Top 7 Shiga Toxin-Producing Escherichia coli throughout Australian Beef Abattoirs. J Food Prot 2020; 83:1812-1821. [PMID: 32502254 DOI: 10.4315/jfp-20-109] [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] [Received: 03/22/2020] [Accepted: 06/02/2020] [Indexed: 11/11/2022]
Abstract
ABSTRACT There is increasing evidence that diversity changes in bacterial communities of beef cattle correlate to the presence of Shiga toxin-producing Escherichia coli (STEC). However, studies that found an association between STEC and bacterial diversity have been focused on preslaughter stages in the beef supply chain. This study was designed to test a hypothesis that there are no differences in bacterial diversity between samples with and those without the presence of the top 7 STEC (O26, O45, O103, O111, O121, O145, and O157) throughout processing in an integrated (abattoir A) and a fragmented (abattoir B) Australian beef abattoir. Slaughter and boning room surface samples from each abattoir were analyzed using 16S rRNA amplicon sequencing and tested for the top 7 STEC following the Food Safety and Inspection Service protocol. Potential positives through slaughter were similar between the abattoirs (64 to 81%). However, abattoir B had substantially reduced potential positives in the boning room compared with abattoir A (abattoir A: 23 and 48%; abattoir B: 2 and 7%). Alpha diversity between the sample groups was not significantly different (P > 0.05) regardless of different STEC markers. Nonmetric multidimensional scaling of slaughter samples showed that the bacterial composition in fecal and hide samples shared the least similarity with the communities in carcass and environmental samples. Surface samples from slaughter (carcass and environmental) and boning (carcass, beef trim, and environmental) all appeared randomly plotted on the scale. This indicated that the STEC presence also did not have a significant effect (P > 0.05) on beta diversity. Although presence of STEC appeared to correlate with changes in diversity of fecal and hide bacterial communities in previous studies, it did not appear to have the same effect on other samples throughout processing. HIGHLIGHTS
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Affiliation(s)
- Sanga Kang
- School of Public Health, Queensland, Australia.,CSIRO Agriculture and Food, Coopers Plains, Queensland, Australia.,(ORCID: https://orcid.org/0000-0002-9074-5043 [S.K.])
| | | | - Ranil Coorey
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | | | - Robert S Barlow
- CSIRO Agriculture and Food, Coopers Plains, Queensland, Australia
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11
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Moore RM, Harrison AO, McAllister SM, Polson SW, Wommack KE. Iroki: automatic customization and visualization of phylogenetic trees. PeerJ 2020; 8:e8584. [PMID: 32149022 PMCID: PMC7049256 DOI: 10.7717/peerj.8584] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 01/17/2020] [Indexed: 12/26/2022] Open
Abstract
Phylogenetic trees are an important analytical tool for evaluating community diversity and evolutionary history. In the case of microorganisms, the decreasing cost of sequencing has enabled researchers to generate ever-larger sequence datasets, which in turn have begun to fill gaps in the evolutionary history of microbial groups. However, phylogenetic analyses of these types of datasets create complex trees that can be challenging to interpret. Scientific inferences made by visual inspection of phylogenetic trees can be simplified and enhanced by customizing various parts of the tree. Yet, manual customization is time-consuming and error prone, and programs designed to assist in batch tree customization often require programming experience or complicated file formats for annotation. Iroki, a user-friendly web interface for tree visualization, addresses these issues by providing automatic customization of large trees based on metadata contained in tab-separated text files. Iroki’s utility for exploring biological and ecological trends in sequencing data was demonstrated through a variety of microbial ecology applications in which trees with hundreds to thousands of leaf nodes were customized according to extensive collections of metadata. The Iroki web application and documentation are available at https://www.iroki.net or through the VIROME portal http://virome.dbi.udel.edu. Iroki’s source code is released under the MIT license and is available at https://github.com/mooreryan/iroki.
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Affiliation(s)
- Ryan M Moore
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, United States of America
| | - Amelia O Harrison
- School of Marine Science and Policy, University of Delaware, Newark, DE, United States of America
| | - Sean M McAllister
- School of Marine Science and Policy, University of Delaware, Newark, DE, United States of America
| | - Shawn W Polson
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, United States of America
| | - K Eric Wommack
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, United States of America
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12
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Kang S, Ravensdale J, Coorey R, Dykes GA, Barlow R. A Comparison of 16S rRNA Profiles Through Slaughter in Australian Export Beef Abattoirs. Front Microbiol 2019; 10:2747. [PMID: 31849891 PMCID: PMC6895009 DOI: 10.3389/fmicb.2019.02747] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 11/12/2019] [Indexed: 01/29/2023] Open
Abstract
Microbial contamination of beef cattle carcases and subsequent cross-contamination during processing is inevitable and virtually impossible to prevent. The understanding of microbial contamination in the beef industry is currently limited to hypotheses based on traditional microbiological tools. Additionally, the complex structural and functional responses of beef cattle microbial communities to the fragmentation in the supply chain remain unknown. This study used 16S rRNA gene sequencing in combination with traditional microbiology to monitor and compare changes in the microbiota throughout slaughter in an integrated (abattoir A) and a fragmented (abattoir B) beef abattoir in Australia. Briefly, the primary difference between an integrated and a fragmented abattoir is that fragmented abattoirs receive cattle from multiple sources, whereas integrated abattoirs typically receive cattle that has been produced using the same production system and from a limited number of sources. The composition in the bacterial communities varied between the abattoirs, though the presence of the most predominant bacterial species within the microbiota at each abattoir was similar. Lactobacillales (2.4-56.2%) and Pseudomonadales (2.4-59.4%) most notably dominated hides, carcases, and the environment in abattoir B. In abattoir A, Bacteroidales (3.9-43.8%), Lactobacillales (0.0-61.9%), and Pseudomonadales (0.5-72.1%) fluctuated but generally shared the dominance over the rest. Combined results of total viable count (TVC) and 16S rRNA gene profiling indicated that an upward hide pulling system adopted by abattoir B may lead to increased transmission of hide contaminants to post-hide pull carcases. Abattoir B had 3.2 log10CFU/cm2 reduction from hide to carcase, where abattoir A had 4.5 log10CFU/cm2 reduction. The findings from this study indicated that common beef-associated microbiota exist in varying composition in Australian abattoirs, and 16S rRNA amplicon sequencing is a powerful tool to understand in-depth movement of microbial contaminants.
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Affiliation(s)
- Sanga Kang
- School of Public Health, Curtin University, Bentley, WA, Australia.,Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Brisbane, QLD, Australia
| | | | - Ranil Coorey
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Gary A Dykes
- School of Public Health, Curtin University, Bentley, WA, Australia
| | - Robert Barlow
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Brisbane, QLD, Australia
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13
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Stromberg ZR, Redweik GAJ, Mellata M. Detection, Prevalence, and Pathogenicity of Non-O157 Shiga Toxin-Producing Escherichia coli from Cattle Hides and Carcasses. Foodborne Pathog Dis 2019; 15:119-131. [PMID: 29638166 DOI: 10.1089/fpd.2017.2401] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Cattle are a major reservoir for Shiga toxin-producing Escherichia coli (STEC) and harbor these bacteria in the intestinal tract. The prevalence, concentration, and STEC serogroup isolated in cattle varies between individuals. Hide removal at slaughter serves as a major point of carcass contamination and ultimately beef products. Certain STEC serogroups, such as O26, O45, O103, O111, O121, O145, and O157, containing the intestinal adherence factor intimin, pose a large economic burden to food producers because of testing and recalls. Human infection with STEC can cause illnesses ranging from diarrhea to hemorrhagic colitis and hemolytic uremic syndrome, and is commonly acquired through ingestion of contaminated foods, often beef products. Previously, most studies focused on O157 STEC, but there is growing recognition of the importance of non-O157 STEC serogroups. This review summarizes detection methods, prevalence, and methods for prediction of pathogenicity of non-O157 STEC from cattle hides and carcasses. A synthesis of procedures is outlined for general non-O157 STEC and targeted detection of specific STEC serogroups. Standardization of sample collection and processing procedures would allow for more robust comparisons among studies. Presence of non-O157 STEC isolated from cattle hides and carcasses and specific factors, such as point of sample collection and season, are summarized. Also, factors that might influence STEC survival on these surfaces, such as the microbial population on hides and microbial adherence genes, are raised as topics for future investigation. Finally, this review gives an overview on studies that have used genetic and cell-based methods to identify specific phenotypes of non-O157 STEC strains isolated from cattle to assess their risk to human health.
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Affiliation(s)
- Zachary R Stromberg
- Department of Food Science and Human Nutrition, Iowa State University , Ames, Iowa
| | - Graham A J Redweik
- Department of Food Science and Human Nutrition, Iowa State University , Ames, Iowa
| | - Melha Mellata
- Department of Food Science and Human Nutrition, Iowa State University , Ames, Iowa
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Stenkamp-Strahm C, Lombard J, Magnuson R, Linke L, Magzamen S, Urie N, Shivley C, McConnel C. Preweaned heifer management on US dairy operations: Part IV. Factors associated with the presence of Escherichia coli O157 in preweaned dairy heifers. J Dairy Sci 2018; 101:9214-9228. [DOI: 10.3168/jds.2018-14659] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 07/09/2018] [Indexed: 01/03/2023]
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Stenkamp‐Strahm C, McConnel C, Magzamen S, Abdo Z, Reynolds S. Associations between
Escherichia coli
O157 shedding and the faecal microbiota of dairy cows. J Appl Microbiol 2018; 124:881-898. [DOI: 10.1111/jam.13679] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 12/01/2017] [Accepted: 12/15/2017] [Indexed: 12/20/2022]
Affiliation(s)
- C. Stenkamp‐Strahm
- College of Veterinary Medicine and Biomedical Sciences Colorado State University Fort Collins CO USA
| | - C. McConnel
- College of Veterinary Medicine and Biomedical Sciences Colorado State University Fort Collins CO USA
| | - S. Magzamen
- College of Veterinary Medicine and Biomedical Sciences Colorado State University Fort Collins CO USA
| | - Z. Abdo
- College of Veterinary Medicine and Biomedical Sciences Colorado State University Fort Collins CO USA
| | - S. Reynolds
- College of Veterinary Medicine and Biomedical Sciences Colorado State University Fort Collins CO USA
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Newell DG, La Ragione RM. Enterohaemorrhagic and other Shiga toxin-producing Escherichia coli (STEC): Where are we now regarding diagnostics and control strategies? Transbound Emerg Dis 2018; 65 Suppl 1:49-71. [PMID: 29369531 DOI: 10.1111/tbed.12789] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Indexed: 12/24/2022]
Abstract
Escherichia coli comprises a highly diverse group of Gram-negative bacteria and is a common member of the intestinal microflora of humans and animals. Generally, such colonization is asymptomatic; however, some E. coli strains have evolved to become pathogenic and thus cause clinical disease in susceptible hosts. One pathotype, the Shiga toxigenic E. coli (STEC) comprising strains expressing a Shiga-like toxin is an important foodborne pathogen. A subset of STEC are the enterohaemorrhagic E. coli (EHEC), which can cause serious human disease, including haemolytic uraemic syndrome (HUS). The diagnosis of EHEC infections and the surveillance of STEC in the food chain and the environment require accurate, cost-effective and timely tests. In this review, we describe and evaluate tests now in routine use, as well as upcoming test technologies for pathogen detection, including loop-mediated isothermal amplification (LAMP) and whole-genome sequencing (WGS). We have considered the need for improved diagnostic tools in current strategies for the control and prevention of these pathogens in humans, the food chain and the environment. We conclude that although significant progress has been made, STEC still remains an important zoonotic issue worldwide. Substantial reductions in the public health burden due to this infection will require a multipronged approach, including ongoing surveillance with high-resolution diagnostic techniques currently being developed and integrated into the routine investigations of public health laboratories. However, additional research requirements may be needed before such high-resolution diagnostic tools can be used to enable the development of appropriate interventions, such as vaccines and decontamination strategies.
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Affiliation(s)
- D G Newell
- Department of Pathology and Infectious Diseases, Faculty of Health and Medical Sciences, School of Veterinary Medicine, University of Surrey, Guildford, UK
| | - R M La Ragione
- Department of Pathology and Infectious Diseases, Faculty of Health and Medical Sciences, School of Veterinary Medicine, University of Surrey, Guildford, UK
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Kim M, Kuehn LA, Bono JL, Berry ED, Kalchayanand N, Freetly HC, Benson AK, Wells JE. The impact of the bovine faecal microbiome on Escherichia coli O157:H7 prevalence and enumeration in naturally infected cattle. J Appl Microbiol 2017; 123:1027-1042. [PMID: 28736954 DOI: 10.1111/jam.13545] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 07/05/2017] [Accepted: 07/10/2017] [Indexed: 12/24/2022]
Abstract
AIMS The objective of this study was to determine if the faecal microbiome has an association with Escherichia coli O157:H7 prevalence and enumeration. METHODS AND RESULTS Pyrosequencing analysis of faecal microbiome was performed from feedlot cattle fed one of three diets: (i) 94 heifers fed low concentrate (LC) diet, (ii) 142 steers fed moderate concentrate (MC) diet, and (iii) 132 steers fed high concentrate (HC) diet. A total of 322 585 OTUs were calculated from 2,411,122 high-quality sequences obtained from 368 faecal samples. In the LC diet group, OTUs assigned to the orders Clostridiales and RF39 (placed within the class Mollicutes) were positively correlated with both E. coli O157:H7 prevalence and enumeration. In the MC diet group, OTUs assigned to Prevotella copri were positively correlated with both E. coli O157:H7 prevalence and enumeration, whereas OTUs assigned to Prevotella stercorea were negatively correlated with both E. coli O157:H7 prevalence and enumeration. In both the MC diet group and the HC diet group, OTUs assigned to taxa placed within Clostridiales were both positively and negatively correlated with both E. coli O157:H7 prevalence and enumeration. However, all correlations were weak. In both the MC diet group and the HC diet group, stepwise linear regression through backward elimination analyses indicated that these OTUs were significantly correlated (P < 0·001) with prevalence or enumeration, explaining as much as 50% of variability in E. coli O157:H7 prevalence or enumeration. CONCLUSIONS Individual colonic bacterial species have little impact on E. coli O157:H7 shedding but collectively groups of bacteria were strongly associated with pathogen shedding. SIGNIFICANCE AND IMPACT OF THE STUDY Bacterial groups in the bovine colon may impact faecal shedding of the zoonotic pathogen E. coli O157:H7, and manipulation of the intestinal microbiota to alter these bacteria may reduce shedding of this pathogen and foodborne illnesses.
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Affiliation(s)
- M Kim
- U.S. Meat Animal Research Center, USDA, ARS, Clay Center, NE, USA
| | - L A Kuehn
- U.S. Meat Animal Research Center, USDA, ARS, Clay Center, NE, USA
| | - J L Bono
- U.S. Meat Animal Research Center, USDA, ARS, Clay Center, NE, USA
| | - E D Berry
- U.S. Meat Animal Research Center, USDA, ARS, Clay Center, NE, USA
| | - N Kalchayanand
- U.S. Meat Animal Research Center, USDA, ARS, Clay Center, NE, USA
| | - H C Freetly
- U.S. Meat Animal Research Center, USDA, ARS, Clay Center, NE, USA
| | - A K Benson
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - J E Wells
- U.S. Meat Animal Research Center, USDA, ARS, Clay Center, NE, USA
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18
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Cameron A, McAllister TA. Antimicrobial usage and resistance in beef production. J Anim Sci Biotechnol 2016; 7:68. [PMID: 27999667 PMCID: PMC5154118 DOI: 10.1186/s40104-016-0127-3] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 10/28/2016] [Indexed: 11/10/2022] Open
Abstract
Antimicrobials are critical to contemporary high-intensity beef production. Many different antimicrobials are approved for beef cattle, and are used judiciously for animal welfare, and controversially, to promote growth and feed efficiency. Antimicrobial administration provides a powerful selective pressure that acts on the microbial community, selecting for resistance gene determinants and antimicrobial-resistant bacteria resident in the bovine flora. The bovine microbiota includes many harmless bacteria, but also opportunistic pathogens that may acquire and propagate resistance genes within the microbial community via horizontal gene transfer. Antimicrobial-resistant bovine pathogens can also complicate the prevention and treatment of infectious diseases in beef feedlots, threatening the efficiency of the beef production system. Likewise, the transmission of antimicrobial resistance genes to bovine-associated human pathogens is a potential public health concern. This review outlines current antimicrobial use practices pertaining to beef production, and explores the frequency of antimicrobial resistance in major bovine pathogens. The effect of antimicrobials on the composition of the bovine microbiota is examined, as are the effects on the beef production resistome. Antimicrobial resistance is further explored within the context of the wider beef production continuum, with emphasis on antimicrobial resistance genes in the food chain, and risk to the human population.
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Affiliation(s)
- Andrew Cameron
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB Canada ; Agriculture and Agri-Food Canada, Lethbridge, AB Canada
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