Take-Home Summaries

Discussions of Recent Publications from the CSU Microbial Ecology Group

  • Summaries and discussion of our recent publications to highlight:
    • Key research questions being addressed by the study
    • Novel aspects of the study design
    • What we view as the most important research findings

Summary Topic: “Resistome diversity in cattle and the environment decreases during beef production”, published March 8, 2016, in eLife. See Discussion by Paul Morley here.

Summary Topic: “Use of metagenomic shotgun sequencing technology to detect foodborne pathogens within their microbiome in beef production chain”, published February 12, 2016, in Applied and Environmental Microbiology. See Discussion by Crystal Yang here.

Investigating the Effects of Tulathromycin Metaphylaxis on the Fecal Resistome and Microbiome of Commercial Feedlot Cattle Early in the Feeding Period
Enrique Doster, Pablo Rovira, Noelle R. Noyes, Brandy A. Burgess, Xiang Yang, Margaret D. Weinroth, Steven M. Lakin, Christopher J. Dean, Lyndsey Linke, Roberta Magnuson, Kenneth I. Jones, Christina Boucher, Jamie Ruiz, Keith E. Belk, Paul S. Morley. Frontiers In Microbiology, 30 July 2018 |

Effects of Ceftiofur and Chlortetracycline on the Resistome of Feedlot Cattle
Margaret D. WeinrothH. Morgan ScottBo NorbyGuy H. LoneraganNoelle R. NoyesPablo RoviraEnrique DosterXiang YangDale R. WoernerPaul S. MorleyKeith E. Belk. Applied and Environmental Microbiology, 04 May 2018. doi: 10.1128/AEM.00610-18

Enrichment Allows Identification of Diverse, Rare Elements in Metagenomic Resistome-Virulome Sequencing
Noelle R. NoyesMaggie E. WeinrothJennifer K. ParkerChris J. DeanSteven M. LakinRobert A. RaymondPablo RoviraEnrique DosterZaid AbdoJennifer N. MartinKenneth L. JonesJaime RuizChristina A. BoucherKeith E. Belk, Paul S. Morley. Microbiome 2017. no. 5, vol. 142.

Rapid Communication: 16S Ribosomal Ribonucleic Acid Characterization of Liver Abscesses in Feedlot Cattle From Three States in the United States
M. D. Weinroth C. R. Carlson J. N. Martin J. L. Metcalf P. S. MorleyK. E. Belk. Journal of Animal Science, Volume 95, Issue 10, 1 October 2017, Pages 4520–4525,

Impact of “Raised Without Antibiotics” Beef Cattle Production Practices on Occurrences of Antimicrobial Resistance
Amit VikramPablo RoviraGetahun E. AggaTerrance M. ArthurJoseph M. BosilevacTommy L. WheelerPaul S. MorleyKeith E. BelkJohn W. Schmidt. Applied and Environmental Microbiobiology 2017 doi:10.1128/AEM.01682-17

Whole-Genome Sequencing and Concordance Between Antimicrobial Susceptibility Genotypes and Phenotypes of Bacterial Isolates Associated with Bovine Respiratory Disease
Joseph R. OwenNoelle NoyesAmy E. YoungDaniel J. PrincePatricia C. BlanchardTerry W. LehenbauerSharif S. AlyJessica H. DavisSean M. O’RourkeZaid AbdoKeith BelkMichael R. MillerPaul Morley,  and Alison L. Van Eenennaam. 

Succinct Colored de Bruijn Graphs
Martin D. Muggli, Alexander Bowe, Noelle R. Noyes, Paul Morley, Keith Belk, Robert Raymond, Travis Gagie, Simon J. Puglisi, Christina Boucher; Succinct Colored de Bruijn Graphs. Bioinformatics 2017 btx067. doi: 10.1093/bioinformatics/btx067

MEGARes: an antimicrobial resistance database for high throughput sequencing
Lakin S*, Dean C*, Noyes NR*, Dettenwanger A, Ross A, Doster E, Rovira P, Abdo Z, Jones K, Ruiz J, Belk KE, Morley PS, Boucher C. MEGARes: an antimicrobial resistance database for high throughput sequencing. Nucleic Acid Res 2016 epub [doi: 10.1093/nar/gkw1009].

Characterization of the resistome in manure, soil and wastewater from dairy and beef production systems
Noyes, N. R., Yang, X., Linke, L. M., Magnuson, R. J., Cook, S. R., Zaheer, R., … Morley, P. S. (2016). Scientific Reports, 6, 24645.

Resistome diversity in cattle and the environment decreases during beef production
Noyes NR, Yang X, Linke LM, Magnuson RJ, Dettenwanger A, Cook S, Geornaras I, Woerner DR, Gow SP, McAllister TA, Yang H, Ruiz J, Jones KL, Boucher CA, Morley PS, Belk KE. eLife, accepted 02/2016.

Use of metagenomic shotgun sequencing technology to detect foodborne pathogens within their microbiome in beef production chain
Yang X, Noyes NR, Doster E, Martin JN, Linke LM, Magnuson RJ, Yang H, Geornaras I, Woerner D, Jones KL, Ruiz J, Boucher C, Morley PS, Belk KE. Appl Environ Microbiol. 2016 Feb 12. pii: AEM.00078-16. [Epub ahead of print].

Modelling considerations in the analysis of associations between antimicrobial use and resistance in beef feedlot cattle.
Noyes NR, Benedict KM, Gow SP, Waldner CL, Reid-Smith RJ, Booker CW, McAllister TA, Morley PS. Epidemiology and Infection 2015; 144:1313–1329 [doi:10.1017/S0950268815002423]

Antimicrobial resistance in Escherichia coli recovered from feedlot cattle and associations with antimicrobial use.
Benedict KM, Gow SP, McAllister TA, Booker CW, Hannon SJ, Checkley SL, Noyes NR, Morley PS. PLoS One. 2015; 10(12): e0143995 [doi:10.1371/journal.pone.0143995].

ACVIM consensus statement on therapeutic antimicrobial use in animals and antimicrobial resistance.
Weese JS, Giguѐre S, Guardabassi L, Morley PS, Papich M, Ricciuto DR, Sykes JE. J Vet Intern Med. 2015 Mar-Apr;29(2):487-98. doi: 10.1111/jvim.12562. Epub 2015 Mar 17.

Mannheimia haemolytica in feedlot cattle: prevalence of recovery and associations with antimicrobial use, resistance, and health outcomes.
Noyes NR, Benedict KM, Gow SP, Booker CW, Hannon SJ, McAllister TA, Morley PS. J Vet Intern Med 2015;29:705–713 [doi:10.1111/jvim.12547].

Latent class comparison of test accuracy when evaluating antimicrobial susceptibility using disk diffusion and broth microdilution to test Escherichia coli and Mannheimia haemolytica isolates recovered from beef feedlot cattle.
Benedict KM, Gow SP, Reid-Smith RJ, Booker CW, McAllister TA, Morley PS. Epidemiol Infect. 2014 Nov;142(11):2314-25. doi: 10.1017/S0950268813003300. Epub 2014 Jan 24.

Comparison of two sampling and culture systems for detection of Salmonella enterica in the environment of a large animal hospital.
Ruple-Czerniak A, Bolte DS, Burgess BA, Morley PS. Equine Vet J. 2014 Jul;46(4):499-502. doi: 10.1111/evj.12193. Epub 2013 Dec 5.

Understanding the role of cleaning in the control of Salmonella Typhimurium in grower-finisher pigs: a modelling approach.
Gautam R, Lahodny G Jr, Bani-Yaghoub M, Morley PS, Ivanek R. Epidemiol Infect. 2014 May;142(5):1034-49. doi: 10.1017/S0950268813001805. Epub 2013 Aug 7.

Using syndromic surveillance to estimate baseline rates for healthcare-associated infections in critical care units of small animal referral hospitals.
Ruple-Czerniak A, Aceto HW, Bender JB, Paradis MR, Shaw SP, Van Metre DC, Weese JS, Wilson DA, Wilson JH, Morley PS. J Vet Intern Med. 2013 Nov-Dec;27(6):1392-9. doi: 10.1111/jvim.12190. Epub 2013 Oct 17.

Methodological comparisons for antimicrobial resistance surveillance in feedlot cattle.
Benedict KM, Gow SP, Checkley S, Booker CW, McAllister TA, Morley PS. BMC Vet Res. 2013 Oct 21;9:216. doi: 10.1186/1746-6148-9-216.

Evidence-based infection control in clinical practice: if you buy clothes for the emperor, will he wear them?
Morley PS. J Vet Intern Med. 2013 May-Jun;27(3):430-8. doi: 10.1111/jvim.12060. Epub 2013 Mar 20.

Report of the third Havemeyer workshop on infection control in equine populations.
Morley PS, Anderson ME, Burgess BA, Aceto H, Bender JB, Clark C, Daniels JB, Davis MA, Hinchcliff KW, Johnson JR, McClure J, Perkins GA, Pusterla N, Traub-Dargatz JL, Weese JS, Whittem TL.Equine Vet J. 2013 Mar;45(2):131-6. doi: 10.1111/evj.12000.

Comparison of routine urinalysis and urine Gram stain for detection of bacteriuria in dogs.
Way LI, Sullivan LA, Johnson V, Morley PS. J Vet Emerg Crit Care (San Antonio). 2013 Jan-Feb;23(1):23-8. doi: 10.1111/vec.12012. Epub 2013 Jan 14.

Metrics for quantifying antimicrobial use in beef feedlots.
Benedict KM, Gow SP, Reid-Smith RJ, Booker CW, Morley PS. Can Vet J. 2012 Aug;53(8):841-8.

Salmonella enterica shedding in hospitalized horses and associations with diarrhea occurrence among their stablemates and gastrointestinal-related illness or death following discharge.
Hartnack AK, Van Metre DC, Morley PS. J Am Vet Med Assoc. 2012 Mar 15;240(6):726-33. doi: 10.2460/javma.240.6.726.

Prevalence and molecular characterization of Clostridium difficile isolated from feedlot beef cattle upon arrival and mid-feeding period.
Costa MC, Reid-Smith R, Gow S, Hannon SJ, Booker C, Rousseau J, Benedict KM, Morley PS, Weese JS. BMC Vet Res. 2012 Mar 28;8:38. doi: 10.1186/1746-6148-8-38.

Effects of restricted antimicrobial exposure on antimicrobial resistance in Escherichia coli from feedlot cattle.
Morley PS, Dargatz DA, Hyatt DR, Dewell GA, Patterson JG, Burgess BA, Wittum TE. Foodborne Pathog Dis. 2011 Jan;8(1):87-98. doi: 10.1089/fpd.2010.0632. Epub 2010 Oct 30.

Association of dry cow therapy with the antimicrobial susceptibility of fecal coliform bacteria in dairy cows.
Mollenkopf DF, Glendening C, Wittum TE, Funk JA, Tragesser LA, Morley PS. Prev Vet Med. 2010 Aug 1;96(1-2):30-5. doi: 10.1016/j.prevetmed.2010.05.014. Epub 2010 Jun 22.

Control of EHV-1 viremia and nasal shedding by commercial vaccines.
Goehring LS, Wagner B, Bigbie R, Hussey SB, Rao S, Morley PS, Lunn DP. Vaccine. 2010 Jul 19;28(32):5203-11. doi: 10.1016/j.vaccine.2010.05.065. Epub 2010 Jun 9.

Detection and control of a nosocomial outbreak caused by Salmonella newport at a large animal hospital.
Steneroden KK, Van Metre DC, Jackson C, Morley PS. J Vet Intern Med. 2010 May-Jun;24(3):606-16. doi: 10.1111/j.1939-1676.2010.0484.x. Epub 2010 Mar 15.

Antimicrobial drug use and antimicrobial resistance in enteric bacteria among cattle from Alberta feedlots.
Rao S, Van Donkersgoed J, Bohaychuk V, Besser T, Song XM, Wagner B, Hancock D, Renter D, Dargatz D, Morley PS. Foodborne Pathog Dis. 2010 Apr;7(4):449-57. doi: 10.1089/fpd.2009.0400.

Development of a syndromic surveillance system for detection of disease among livestock entering an auction market
Van Metre D, Barkey DQ, Salman MD, Morley PS. J Am Vet Med Assoc 2009; 234:658-664.

Survival of Streptococcus equi on surfaces in an outdoor environment.
Weese JS, Jarlot C, Morley PS. Can Vet J. 2009 Sep;50(9):968-70.

Retrospective multicentre study of methicillin-resistant Staphylococcus aureus infections in 115 horses.
Anderson ME, Lefebvre SL, Rankin SC, Aceto H, Morley PS, Caron JP, Welsh RD, Holbrook TC, Moore B, Taylor DR, Weese JS. Equine Vet J. 2009 Apr;41(4):401-5.

Genetic and phenotypic characterization of the bla(CMY) gene from Escherichia coli and Salmonella enterica isolated from food-producing animals, humans, the environment, and retail meat.
Heider LC, Hoet AE, Wittum TE, Khaitsa ML, Love BC, Huston CL, Morley PS, Funk JA, Gebreyes WA. Foodborne Pathog Dis. 2009 Dec;6(10):1235-40. doi: 10.1089/fpd.2009.0294.

Risk associated with transportation and lairage on hide contamination with Salmonella enterica in finished beef cattle at slaughter.
Dewell GA, Simpson CA, Dewell RD, Hyatt DR, Belk KE, Scanga JA, Morley PS, Grandin T, Smith GC, Dargatz DA, Wagner BA, Salman MD.J Food Prot. 2008 Nov;71(11):2228-32.

Characteristics of biosecurity and infection control programs at veterinary teaching hospitals.
Benedict KM, Morley PS, Van Metre DC. J Am Vet Med Assoc. 2008 Sep 1;233(5):767-73. doi: 10.2460/javma.233.5.767.

A multiplex polymerase chain reaction assay for the identification of Mannheimia haemolytica, Mannheimia glucosida and Mannheimia ruminalis.
Alexander TW, Cook SR, Yanke LJ, Booker CW, Morley PS, Read RR, Gow SP, McAllister TA. Vet Microbiol. 2008 Jul 27;130(1-2):165-75. doi: 10.1016/j.vetmic.2008.01.001. Epub 2008 Jan 19.

Impact of transportation and lairage on hide contamination with Escherichia coli O157 in finished beef cattle.
Dewell GA, Simpson CA, Dewell RD, Hyatt DR, Belk KE, Scanga JA, Morley PS, Grandin T, Smith GC, Dargatz DA, Wagner BA, Salman MD. J Food Prot. 2008 Jun;71(6):1114-8.

Microbiological and histopathological findings in cases of fatal bovine respiratory disease of feedlot cattle in Western Canada.
Booker CW, Abutarbush SM, Morley PS, Jim GK, Pittman TJ, Schunicht OC, Perrett T, Wildman BK, Fenton RK, Guichon PT, Janzen ED. Can Vet J. 2008 May;49(5):473-81.

The effect of bovine viral diarrhea virus infections on health and performance of feedlot cattle.
Booker CW, Abutarbush SM, Morley PS, Guichon PT, Wildman BK, Jim GK, Schunicht OC, Pittman TJ, Perrett T, Ellis JA, Appleyard G, Haines DM. Can Vet J. 2008 Mar;49(3):253-60.

Comparison of Salmonella enterica serotype Infantis isolates from a veterinary teaching hospital.
Dunowska M, Morley PS, Traub-Dargatz JL, Davis MA, Patterson G, Frye JG, Hyatt DR, Dargatz DA. J Appl Microbiol. 2007 Jun;102(6):1527-36.

Pilot study to evaluate 3 hygiene protocols on the reduction of bacterial load on the hands of veterinary staff performing routine equine physical examinations.
Traub-Dargatz JL, Weese JS, Rousseau JD, Dunowska M, Morley PS, Dargatz DA. Can Vet J. 2006 Jul;47(7):671-6.

Impact of hospitalization and antimicrobial drug administration on antimicrobial susceptibility patterns of commensal Escherichia coli isolated from the feces of horses.
Dunowska M, Morley PS, Traub-Dargatz JL, Hyatt DR, Dargatz DA. J Am Vet Med Assoc. 2006 Jun 15;228(12):1909-17.

Evaluation of the efficacy of a peroxygen disinfectant-filled footmat for reduction of bacterial load on footwear in a large animal hospital setting.
Dunowska M, Morley PS, Patterson G, Hyatt DR, Van Metre DC. J Am Vet Med Assoc. 2006 Jun 15;228(12):1935-9.

A simulation model to evaluate sampling strategies for characterization of antimicrobial resistance in non-type-specific E. coli recovered from dairy cows.
Villarroel A, Morley PS, Wittum TE, Bolte DS. Am J Vet Res. 2006 Jun;67(6):951-6.

Evaluation of the association between feeding raw meat and Salmonella enterica infections at a Greyhound breeding facility.
Morley PS, Strohmeyer RA, Tankson JD, Hyatt DR, Dargatz DA, Fedorka-Cray PJ. J Am Vet Med Assoc. 2006 May 15;228(10):1524-32.

Evaluation of the effects of footwear hygiene protocols on nonspecific bacterial contamination of floor surfaces in an equine hospital.
Stockton KA, Morley PS, Hyatt DR, Burgess BA, Patterson G, Dunowska M, Lee DE. J Am Vet Med Assoc. 2006 Apr 1;228(7):1068-73.

Evaluation of bacterial and protozoal contamination of commercially available raw meat diets for dogs.
Strohmeyer RA, Morley PS, Hyatt DR, Dargatz DA, Scorza AV, Lappin MR. J Am Vet Med Assoc. 2006 Feb 15;228(4):537-42.

Investigation of falsely reported resistance of Streptococcus equi subsp. zooepidemicus isolates from horses to trimethoprim-sulfamethoxazole.
Feary DJ, Hyatt D, Traub-Dargatz J, Roach S, Jones RL, Wu CC, Morley PS. J Vet Diagn Invest. 2005 Sep;17(5):483-6.

Efficacy of directed misting application of a peroxygen disinfectant for environmental decontamination of a veterinary hospital.
Patterson G, Morley PS, Blehm KD, Lee DE, Dunowska M. J Am Vet Med Assoc. 2005 Aug 15;227(4):597-602.

Comparison of the odds of isolation, genotypes, and in vivo production of major toxins by Clostridium perfringens obtained from the gastrointestinal tract of dairy cows with hemorrhagic bowel syndrome or left-displaced abomasum.
Dennison AC, Van Metre DC, Morley PS, Callan RJ, Plampin EC, Ellis RP. J Am Vet Med Assoc. 2005 Jul 1;227(1):132-8.

Antimicrobial drug use in veterinary medicine.
Morley PS, Apley MD, Besser TE, Burney DP, Fedorka-Cray PJ, Papich MG, Traub-Dargatz JL, Weese JS. J Vet Intern Med. 2005 Jul-Aug;19(4):617-29.

Evaluation of the efficacy of disinfectant footbaths as used in veterinary hospitals.
Morley PS, Morris SN, Hyatt DR, Van Metre DC. J Am Vet Med Assoc. 2005 Jun 15;226(12):2053-8.

The effect of Virkon S fogging on survival of Salmonella enterica and Staphylococcus aureus on surfaces in a veterinary teaching hospital.
Dunowska M, Morley PS, Hyatt DR. Vet Microbiol. 2005 Feb 25;105(3-4):281-9. Epub 2005 Jan 20.

Characterization of Escherichia coli and Salmonella enterica from cattle feed ingredients.
Dargatz DA, Strohmeyer RA, Morley PS, Hyatt DR, Salman MD. Foodborne Pathog Dis. 2005 Winter;2(4):341-7.

Surveillance for nosocomial infections in veterinary hospitals.
Morley PS. Vet Clin North Am Equine Pract. 2004 Dec;20(3):561-76, vi-vii.

An overview of infection control strategies for equine facilities, with an emphasis on veterinary hospitals.
Traub-Dargatz JL, Dargatz DA, Morley PS, Dunowska M. Vet Clin North Am Equine Pract. 2004 Dec;20(3):507-20, v.

Environmental surveillance for Salmonella enterica in a veterinary teaching hospital.
Burgess BA, Morley PS, Hyatt DR. J Am Vet Med Assoc. 2004 Nov 1;225(9):1344-8.

Analysis methods for evaluating bacterial antimicrobial resistance outcomes.
Wagner BA, Dargatz DA, Morley PS, Keefe TJ, Salman MD. Am J Vet Res. 2003 Dec;64(12):1570-9.

Short-term repeatability of measurements of antimicrobial susceptibility of Escherichia coli isolated from feces of feedlot cattle.
Wagner B, Morley PS, Dargatz DA, Wittum TE, Keefe TJ, Salman MD. J Vet Diagn Invest. 2003 Nov;15(6):535-42.

Factor analysis of minimum-inhibitory concentrations for Escherichia coli isolated from feedlot cattle to model relationships among antimicrobial-resistance outcomes.
Wagner BA, Salman MD, Dargatz DA, Morley PS, Wittum TE, Keefe TJ. Prev Vet Med. 2003 Mar 20;57(3):127-39.

Survey of antimicrobial susceptibility testing practices of veterinary diagnostic laboratories in the United States.
Brooks MB, Morley PS, Dargatz DA, Hyatt DR, Salman MD, Akey BL. J Am Vet Med Assoc. 2003 Jan 15;222(2):168-73.

American Association of Feline Practitioners 2003 report on feline zoonoses.
Brown RR, Elston TH, Evans L, Glaser C, Gulledge ML, Jarboe L, Lappin MR, Marcus LC, Breitschwerdt EB, Greene CE, Morley PS, Rosychuk R, Schantz P, Wolf AM. Comp Cont Ed Pract Vet 2003; 25(12): 936-965.

Comparison of sampling techniques for measuring the antimicrobial susceptibility of enteric Escherichia coli recovered from feedlot cattle.
Wagner BA, Dargatz DA, Salman, Morley PS, Wittum TE, Keefe TJ. Am J Vet Res. 2002 Dec;63(12):1662-70

Detection of Salmonella spp in fecal specimens by use of real-time polymerase chain reaction assay.
Kurowski PB, Traub-Dargatz JL, Morley PS, Gentry-Weeks CR. Am J Vet Res. 2002 Sep;63(9):1265-8.

Survey of complications and antimicrobial use in equine patients at veterinary teaching hospitals that underwent surgery because of colic.
Traub-Dargatz JL, George JL, Dargatz DA, Morley PS, Southwood LL, Tillotson K. J Am Vet Med Assoc. 2002 May 1;220(9):1359-65.

Identification of two phylogenetically related organisms from feces by PCR for detection of Salmonella spp.
Gentry-Weeks C, Hutcheson HJ, Kim LM, Bolte D, Traub-Dargatz J, Morley P, Powers B, Jessen M. J Clin Microbiol. 2002 Apr;40(4):1487-92.

Factors associated with Salmonella shedding among equine colic patients at a veterinary teaching hospital.
Kim LM, Morley PS, Traub-Dargatz JL, Salman MD, Gentry-Weeks C. J Am Vet Med Assoc. 2001 Mar 1;218(5):740-8.

Trends in mortality ratios among cattle in U.S. feedlots
Loneragan GH, Dargatz DA, Morley PS, Smith MA. J Am Vet Med Assoc 2001; 219:1122-1127.