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1. Antimicrobial resistance in commensal Escherichia coli and Enterococcus spp. isolated from pigs subjected to different antimicrobial administration protocols

Author:
Heather K. Allen,   et al.   ; Caroline Pissetti; Jalusa Deon Kich; Claudia Navarrete; Eduardo de Freitas Costa; Nelson Morés; Marisa Cardoso;     Show all 7 Authors
Source:
Research in veterinary science 2021 v.137 pp. 174-185
ISSN:
0034-5288
Subject:
Enterococcus; Escherichia coli; antibiotic resistance; colistin; digestive system; humans; multiple drug resistance; probability; research; swine; veterinary medicine
Abstract:
... The antimicrobial resistance (AMR) in human and animal pathogens is a global concern, and antimicrobial use (AMU) is considered the most important driver for its increase. The aim of this study was to assess AMR in Escherichia coli and Enterococcus spp. in faecal samples of pigs subjected to four different AMU protocols from birth to finishing: G1, no in-feed antimicrobials; G2: a total average do ...
DOI:
10.1016/j.rvsc.2021.05.001

2. Paenibacillus 79R4, a potential rumen probiotic to enhance nitrite detoxification and methane mitigation in nitrate-treated ruminants

Author:
Heather K. Allen,   et al.   ; Elizabeth A. Latham; William E. Pinchak; Julian Trachsel; Todd R. Callaway; David J. Nisbet; Robin C. Anderson;     Show all 7 Authors
Source:
Science of the total environment 2019 v.671 pp. 324-328
ISSN:
0048-9697
Subject:
Holstein; Paenibacillus; blood sampling; body weight; cannulas; denitrification; fermentation; methane; methane production; microbial ecology; nitrites; probiotics; rumen bacteria; rumen fermentation; rumen fluids; sodium nitrate; steers; toxicity; volatile fatty acids
Abstract:
... The effects of supplemental nitrate administered alone or with a denitrifying ruminal bacterium, designated Paenibacillus 79R4 (79R4) intentionally selected for enhanced nitrate- and nitrite-metabolizing ability, on select rumen fermentation characteristics was examined in vivo. Rumen and blood samples were collected from cannulated Holstein steers one day prior to and one day after initiation of ...
Handle:
10113/6350779
DOI:
10.1016/j.scitotenv.2019.03.390

3. Porcine Response to a Multidrug-Resistant to a Multidrug-Resistan serovar l 4,[5],12:i;:-Outbreak Isolate serovar I 4,[5],12:i:- Outbreak Isolate

Author:
Heather K. Allen,   et al.   ; Daniel C. Shippy; Bradley L. Bearson; Devin B. Holman; Brian Brunelle; Shawn M. D. Bearson;     Show all 6 Authors
Source:
Foodborne pathogens & disease 2018 v.15 no.5 pp. 253-261
ISSN:
1535-3141
Subject:
Salmonella Typhimurium; antibodies; bacterial motility; blood serum; diarrhea; feces; fever; foodborne illness; genes; human diseases; immune response; interferon-gamma; intestinal microorganisms; intestines; lipopolysaccharides; microbial communities; multiple drug resistance; nucleotide sequences; pathogenesis; pork; ribosomal RNA; serotypes; signs and symptoms (animals and humans); swine; swine diseases; virulence; water content
Abstract:
... Salmonella enterica serovar I 4,[5],12:i:- has emerged as a common nontyphoidal Salmonella serovar to cause human foodborne illness. An interesting trait of serovar I 4,[5],12:i:- is that it only expresses the fliC gene for bacterial motility (i.e., monophasic), while most Salmonella strains alternately express two flagellin genes (fliC and fljB). The goal of this study was to characterize the porcine ...
Handle:
10113/6723271
DOI:
10.1089/fpd.2017.2378

4. Isolation, characterization and strain selection of a Paenibacillus species for use as a probiotic to aid in ruminal methane mitigation, nitrate/nitrite detoxification and food safety

Author:
Heather K. Allen,   et al.   ; Elizabeth A. Latham; William E. Pinchak; Julian Trachsel; Todd R. Callaway; David J. Nisbet; Robin C. Anderson;     Show all 7 Authors
Source:
Bioresource technology 2018 v.263 pp. 358-364
ISSN:
0960-8524
Subject:
Campylobacter jejuni; Escherichia coli O157; Paenibacillus; coculture; denitrifying bacteria; fermentation; food safety; in vitro studies; methane; methane production; nitrates; nitrites; nitrogen; probiotics; rumen fluids; rumen microorganisms
Abstract:
... The effects of dietary nitrate and Paenibacillus 79R4 (79R4), a denitrifying bacterium, when co-administered as a probiotic, on methane emissions, nitrate and nitrite-metabolizing capacity and fermentation characteristics were studied in vitro. Mixed populations of rumen microbes inoculated with 79R4 metabolized all levels of nitrite studied after 24 h in vitro incubation. Results from in vitro si ...
Handle:
10113/6472381
DOI:
10.1016/j.biortech.2018.04.116

5. Antibiotic resistance gene discovery in food-producing animals

Author:
Heather K. Allen
Source:
Current opinion in microbiology 2014 v.19 no. pp. 25-29
ISSN:
1879-0364
Subject:
antibiotic resistance; antibiotics; food animals; gene transfer; genes; intestinal microorganisms; metagenomics; polymerase chain reaction
Abstract:
... Numerous environmental reservoirs contribute to the widespread antibiotic resistance problem in human pathogens. One environmental reservoir of particular importance is the intestinal bacteria of food-producing animals. In this review I examine recent discoveries of antibiotic resistance genes in agricultural animals. Two types of antibiotic resistance gene discoveries will be discussed: the use o ...
Handle:
10113/59369
DOI:
10.1016/j.mib.2014.06.001

6. Altered egos: antibiotic effects on food animal microbiomes

Author:
Heather K. Allen,   et al.   ; Thad B. Stanton;     Show all 2 Author
Source:
Annual Review of Microbiology 2014 v.68 no. pp. 297-315
ISSN:
0066-4227
Subject:
animal diseases; animal growth; animal husbandry; antibiotic resistance; antibiotics; bacteria; feed additives; food animals; food safety; genes; human food chain; intestinal microorganisms; medicated feeds; poultry
Abstract:
... The human food chain begins with upwards of 1000 species of bacteria that inhabit the intestinal tracts of poultry and livestock. These intestinal denizens are responsible for the health and safety of a major protein source for humans. The use of antibiotics to treat animal diseases was followed by the surprising discovery that antibiotics enhanced food animal growth, both of which led to six deca ...
Handle:
10113/59366
DOI:
10.1146/annurev-micro-091213-113052

7. Editorial on virus ecology and disturbances: impact of environmental disruption on the viruses of microorganisms

Author:
Heather K. Allen,   et al.   ; Stephen T. Abedon;     Show all 2 Author
Source:
Frontiers in microbiology 2014 v.5 no.article 700 pp. 1-2
ISSN:
1664-302X
Subject:
environmental impact; bacteriophages; microbial ecology; community ecology; microbial genetics; technology; bacteria
Abstract:
... Viruses of microorganisms (VoMs) can be both responsive to and the source of change in their environment. Defining the diverse VoMs in an environment has become easier with the advent of various new technologies, so analyzing VoM populations or communities involved with disturbances could be the next step to drive research forward. Contributions assembled in this Research Topic explore the effects ...
Handle:
10113/60071
DOI:
10.3389/fmicb.2014.00700
PubMed:
25566216
PubMed Central:
PMC4264494

8. Chlortetracycline Enhances Tonsil Colonization and Fecal Shedding of Multidrug-Resistant Serovar Typhimurium DT104 without Major Alterations to the Porcine Tonsillar and Intestinal Microbiota

Author:
Heather K. Allen,   et al.   ; Devin B. Holman; Bradley L. Bearson; Daniel C. Shippy; Crystal L. Loving; Brian Kerr; Shawn M. D. Bearson; Brian W. Brunelle; Donald Schaffner;     Show all 9 Authors
Source:
Applied and environmental microbiology 2019 v.85 no.4 pp. -12
ISSN:
0099-2240
Subject:
Salmonella Typhimurium; cecum; chlortetracycline; foodborne illness; humans; ileum; intestinal microorganisms; multiple drug resistance; pathogenesis; pork; risk; salmonellosis; serotypes; swine; swine production; tonsils; transcriptome
Abstract:
... Salmonella spp. are estimated to cause 1.2 million cases of human foodborne illness each year in the United States, and pigs can often be asymptomatically colonized with Salmonella spp. (>50% of farms). Recent reports state that 18.3% of Salmonella enterica serovar Typhimurium isolates are resistant to ≥3 antimicrobial classes, and multidrug-resistant (MDR) strains are associated with an increased ...
Handle:
10113/6579862
DOI:
10.1128/AEM.02354-18
PubMed:
30530706
PubMed Central:
PMC6365817

9. Shifts in the nasal microbiota of swine in response to different dosing regimens of oxytetracycline administration

Author:
Heather K. Allen,   et al.   ; Kathy T. Mou; David P. Alt; Julian Trachsel; Samantha J. Hau; Johann F. Coetzee; Devin B. Holman; Steven Kellner; Crystal L. Loving; Susan L. Brockmeier;     Show all 10 Authors
Source:
Veterinary microbiology 2019 pp. -
ISSN:
0378-1135
Subject:
Actinobacillus; Streptococcus; acute exposure; bacterial communities; community structure; intramuscular injection; microorganisms; necropsy; nose; oxytetracycline; swine; tonsils
Abstract:
... The impacts of antibiotic treatment and dosing regimen of an antibiotic on the swine respiratory microbiota are poorly defined. To begin to address this, this study characterized the impact of oxytetracycline administration, given either parenterally or in feed, on the diversity of the nasal and tonsil microbiotas of post-weaned pigs over a two-week period. One group received a single intramuscula ...
DOI:
10.1016/j.vetmic.2019.108386
CHORUS:
10.1016/j.vetmic.2019.108386

10. Finding alternatives to antibiotics

Author:
Heather K Allen,   et al.   ; Julian Trachsel; Torey Looft; Thomas A. Casey;     Show all 4 Authors
Source:
Annuals of the New York Academy of Sciences 2014 v. no. pp. -
ISSN:
0077-8923
Subject:
antibiotic resistance; antibiotics; bacteria; bacteriocins; bacteriophages; disease prevention; feed additives; intestinal microorganisms; microbial communities; pathogens; therapeutics
Abstract:
... The spread of antibiotic-resistant pathogens requires new treatments. As the rate of development of new antibiotics has severely declined, alternatives to antibioticsmust be considered in both animal agriculture and humanmedicine. Products for disease prevention are different from those for disease treatment, and examples of both are discussed here. For example, modulating the gut microbial commun ...
Handle:
10113/59368
DOI:
10.1111/nyas.12468
CHORUS:
10.1111/nyas.12468
Chorus Open Access:
10.1111/nyas.12468

11. Function and Phylogeny of Bacterial Butyryl Coenzyme A:Acetate Transferases and Their Diversity in the Proximal Colon of Swine

Author:
Heather K. Allen,   et al.   ; Julian Trachsel; Darrell O. Bayles; Torey Looft; Uri Y. Levine;     Show all 5 Authors
Source:
Applied and environmental microbiology 2016 v.82 no.22 pp. 6788-6798
ISSN:
0099-2240
Subject:
CoA-transferases; DNA; RNA; bacteria; bacterial communities; butyrates; colon; ecosystems; enzyme activity; genes; homeostasis; intestinal microorganisms; phylogeny; swine
Abstract:
... Studying the host-associated butyrate-producing bacterial community is important because butyrate is essential for colonic homeostasis and gut health. Previous research has identified the butyryl-coA:acetate transferase (2.3.8.3) as a the main gene for butyrate production in intestinal ecosystems; however, this gene family (but) remains poorly defined. To develop analysis tools for this community, ...
Handle:
10113/63276
DOI:
10.1128/AEM.02307-16
PubMed:
27613689
PubMed Central:
PMC5086572

12. Treatment, promotion, commotion: antibiotic alternatives in food-producing animals

Author:
Heather K Allen,   et al.   ; Uri Y. Levine; Torey Looft; Meggan Bandrick; Thomas A. Casey;     Show all 5 Authors
Source:
Trends in microbiology 2013 v.21 no.3 pp. 114-119
ISSN:
0966-842X
Subject:
animal performance; antibiotic resistance; antibiotics; disease prevention; drug therapy; feed additives; feed conversion; food animals; growth promotion; medicated feeds; prebiotics; probiotics; vaccination; vaccines
Abstract:
... Alternatives to antibiotics are urgently needed in animal agriculture. The form these alternatives should take presents a complex problem due to the various uses of antibiotics in agriculture, including disease treatment, disease prevention, and growth promotion, ant the relative contribution of these uses to the antibiotic resistance problem. Numerous antibiotic alternatives, such as feed amended ...
Handle:
10113/56315
DOI:
10.1016/j.tim.2012.11.001
PubMed:
23473629

13. Estimation of viral richness from shotgun metagenomes using a frequency count approach

Author:
Heather K. Allen,   et al.   ; John Bunge; James A. Foster; Darrell O. Bayles; Thaddeus B. Stanton;     Show all 5 Authors
Source:
Microbiome 2013 v.1 no.5 pp. 1-7
ISSN:
2049-2618
Subject:
bacteriophages; computer software; ecosystems; feces; freshwater; genes; metagenomics; nucleotide sequences; species diversity; statistical analysis; swine; water reuse
Abstract:
... Viruses are important drivers of ecosystem functions, yet little is known about the vast majority of viruses. Viral shotgun metagenomics enables the investigation of broad ecological questions in phage communities. One ecological characteristic is species richness, which is the number of different species in a community. Viruses do not have a phylogenetic marker analogous to the bacterial 16S rRNA ...
Handle:
10113/56338
DOI:
10.1186/2049-2618-1-5
PubMed:
24451229
PubMed Central:
PMC3869190

14. Bacteria, phages and pigs: the effects of in-feed antibiotics on the microbiome at different gut locations

Author:
Heather K. Allen,   et al.   ; Torey Looft; Brandi L. Cantarel; Uri Y. Levine; Darrell O. Bayles; David P. Alt; Bernard Henrissat; Thaddeus B. Stanton;     Show all 8 Authors
Source:
Journal of the International Society for Microbial Ecology 2014 v.8 pp. 1566-1576
ISSN:
1751-7370
Subject:
Escherichia; Lachnobacterium; bacteria; bacterial communities; bacteriophages; cecum; cell wall components; chlortetracycline; colon; feces; feed conversion; food safety; genes; ileum; inoculum; intestinal microorganisms; metagenomics; mucosa; nucleotide sequences; penicillins; ribosomal RNA; swine
Abstract:
... Disturbance of the beneficial gut microbial community is a potential collateral effect of antibiotics, which have many uses in animal agriculture (disease treatment or prevention and feed efficiency improvement). Understanding antibiotic effects on bacterial communities at different intestinal locations is essential to realize the full benefits and consequences of in-feed antibiotics. In this stud ...
Handle:
10113/58451
DOI:
10.1038/ismej.2014.12
PubMed:
24522263
PubMed Central:
PMC4817603

15. Effect of sole or combined administration of nitrate and 3-nitro-1-propionic acid on fermentation and Salmonella survivability in alfalfa-fed rumen cultures in vitro

Author:
Heather K. Allen,   et al.   ; Alejandro Castañeda Correa; Julian Trachsel; Agustin Corral-Luna; Hector Gutierrez-Bañuelos; Pedro Antonia Ochoa-Garcia; Oscar Ruiz-Barrera; Michael E. Hume; Todd R. Callaway; Roger B. Harvey; Ross C. Beier; Robin C. Anderson; David J. Nisbet;     Show all 13 Authors
Source:
Bioresource technology 2017 v.229 pp. 69-77
ISSN:
0960-8524
Subject:
Salmonella; digestion; emissions; energy; feed supplements; fermentation; methane; methane production; nitrates; nitrites; rumen; rumen microorganisms; volatile fatty acids
Abstract:
... Ruminal methanogenesis is a digestive inefficiency resulting in the loss of dietary energy consumed by the host and contributing to environmental methane emission. Nitrate is being investigated as a feed supplement to reduce rumen methane emissions but safety and efficacy concerns persist. To assess potential synergies of co-administering sub-toxic amounts of nitrate and 3-nitro-1-propionate (NPA) ...
Handle:
10113/5613810
DOI:
10.1016/j.biortech.2017.01.012

16. Antibiotics in feed induce prophages in swine fecal microbiomes

Author:
Heather K. Allen,   et al.   ; Torey Looft; Darrell O. Bayles; Samuel Humphrey; Uri Y. Levine; David Alt; Thaddeus B. Stanton;     Show all 7 Authors
Source:
mBio 2011 v.2 no.6 pp. -
ISSN:
2150-7511
Subject:
Streptococcus; antibiotic resistance; aquatic communities; bacteria; bacterial communities; bacteriophages; carbadox; chlortetracycline; digestive system; disease prevention; drug therapy; ecosystems; feces; feed additives; feed conversion; gene transfer; genes; intestinal microorganisms; lysogeny; medicated feeds; metagenomics; models; multiple drug resistance; population; population dynamics; population structure; predator-prey relationships; predators; ribosomal RNA; risk reduction; sequence analysis; strains; swine; transporters
Abstract:
... Antibiotics are a cost-effective tool for improving feed efficiency and preventing disease in agricultural animals, but the full scope of their collateral effects is not understood. Antibiotics have been shown to mediate gene transfer by inducing prophages in certain bacterial strains; therefore, one collateral effect could be prophage induction in the gut microbiome at large. Here we used metagen ...
Handle:
10113/59214
DOI:
10.1128/mBio.00260-11
PubMed:
22128350
PubMed Central:
PMC3225969

17. Profiling the gastrointestinal microbiota in response to Salmonella: Low versus high Salmonella shedding in the natural porcine host

Author:
Heather K. Allen,   et al.   ; Shawn M.D. Bearson; Bradley L. Bearson; Torey Looft; Brian W. Brunelle; Jalusa D. Kich; Christopher K. Tuggle; Darrell O. Bayles; David Alt; Uri Y. Levine; Thaddeus B. Stanton;     Show all 11 Authors
Source:
Infection, genetics, and evolution 2013 v.16 pp. 330-340
ISSN:
1567-1348
Subject:
Prevotella; intestinal microorganisms; ribosomal RNA; community structure; hosts; DNA; Salmonella Typhimurium; feces; Catenibacterium; salmonellosis; nucleotide sequences; bacterial communities; species diversity; colonizing ability; piglets; excretion
Abstract:
... Controlling Salmonella in the food chain is complicated by the ability of Salmonella to colonize livestock without causing clinical symptoms/disease. Salmonella-carrier animals are a significant reservoir for contamination of naïve animals, the environment, and our food supply. Salmonella carriage and shedding in pigs varies greatly both experimentally and on-farm. To investigate the dynamics betw ...
Handle:
10113/56318
DOI:
10.1016/j.meegid.2013.03.022

18. In-feed antibiotic effects on the swine intestinal microbiome

Author:
Heather K. Allen,   et al.   ; Torey Looft; Timothy A. Johnson; Darrell O. Bayles; David P. Alt; Robert D. Stedtfeld; Woo Jun Sul; Tiffany M. Stedtfeld; Benli Chai; James R. Cole; Syed A. Hashsham; James M. Tiedje; Thad B. Stanton;     Show all 13 Authors
Source:
Proceedings of the National Academy of Sciences of the United States of America 2012 v.109 no.5 pp. 1691-1696
ISSN:
0027-8424
Subject:
Escherichia coli; antibiotic resistance; chlortetracycline; cost benefit analysis; diet; disease prevention; genes; growth promotion; human diseases; intestinal microorganisms; metagenomics; swine
Abstract:
... Antibiotics have been administered to agricultural animals for disease treatment, disease prevention, and growth promotion for over 50 y. The impact of such antibiotic use on the treatment of human diseases is hotly debated. We raised pigs in a highly controlled environment, with one portion of the littermates receiving a diet containing performance-enhancing antibiotics [chlortetracycline, sulfam ...
DOI:
10.1073/pnas.1120238109
PubMed:
22307632
PubMed Central:
PMC3277147