Preweaned dairy calves and lactating dairy cows are known reservoirs of antibiotic-resistant bacteria. To further understand the differences in the resistomes and microbial communities between the two, we sequenced the metagenomes of fecal composite samples from preweaned dairy calves and lactating dairy cows on 17 commercial dairy farms (n = 34 samples). Results indicated significant differences in the structures of the microbial communities (analysis of similarities [ANOSIM] R = 0.81, p = 0.001) and resistomes (ANOSIM R = 0.93 to 0.96, p = 0.001) between the two age groups. Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria were the predominant members of the communities, but when the groups were compared, Bacteroidetes and Verrumicrobia were significantly more abundant in calf fecal composite samples, whereas Firmicutes, Spirochaetes, Deinococcus-Thermus, Lentisphaerae, Planctomycetes, Chlorofexi, and Saccharibacteria-(TM7) were more abundant in lactating cow samples. Diverse suites of antibiotic resistance genes (ARGs) were identified in all samples, with the most frequently detected being assigned to tetracycline and aminoglycoside resistance. When the two groups were compared, ARGs were significantly more abundant in composite fecal samples from calves than those from lactating cows (calf median ARG abundance = 1.8 × 100 ARG/16S ribosomal RNA [rRNA], cow median ARG abundance = 1.7 × 10−1 ARG/16S rRNA) and at the antibiotic resistance class level, the relative abundance of tetracycline, trimethoprim, aminoglycoside, macrolide-lincosamide-streptogramin B, β-lactam, and phenicol resistance genes was significantly higher in calf samples than in cow samples. Results of this study indicate that composite feces from preweaned calves harbor different bacterial communities and resistomes than composite feces from lactating cows, with a greater abundance of resistance genes detected in preweaned calf feces.
Get full access to this article
View all access options for this article.
References
1.
[APHIS] Animal and Plant Health Inspection Service. Antibiotic Use on U.S. Dairy Operations, 2002 and 2007. 2008. Available at: https://www.aphis.usda.gov/animal_health/nahms/dairy/downloads/dairy07/Dairy07_is_AntibioticUse.pdf, accessed May17, 2019.
2.
AverillJJ. Use of antimicrobial agents in dairy calves and the public health concern (Order No. 3363799). 2009. Available from Natural Science Collection. (304931071). Available at: https://search.proquest.com/docview/304931071?accountid=28147, accessed March6, 2020.
3.
BarlowJ.Mastitis therapy and antimicrobial susceptibility: A multispecies review with a focus on antibiotic treatment of mastitis in dairy cattle. J Mammary Gland Biol Neoplasia, 2011; 16:383–407.
4.
Bengtsson-PalmeJ, HartmannM, ErikssonKM, PalC, ThorellK, LarssonDG, NilssonRH. METAXA2: Improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data. Mol Ecol Resour, 2015; 15:1403–1414.
5.
BergeAC, HancockDD, SischoWM, BesserTE. Geographic, farm, and animal factors associated with multiple antimicrobial resistance in fecal Escherichia coli isolates from cattle in the western United States. J Am Vet Med Assoc, 2010; 236:1338–1344.
6.
BolgerAM, LohseM, UsadelB. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics, 2014; 30:2114–2120.
7.
CaoH, PradhanAK, KarnsJS, HovinghE, WolfgangDR, VinyardBT, KimSW, SalaheenS, HaleyBJ, Van KesselJAS. 2019. Age-associated distribution of antimicrobial-resistant Salmonella enterica and Escherichia coli isolated from Dairy Herds in Pennsylvania, 2013–2015. Foodborne Pathog Dis, 2019; 16:60–67.
8.
ChangQ, WangW, Regev-YochayG, LipsitchM, HanageWP. Antibiotics in agriculture and the risk to human health: How worried should we be?. Evol Appl, 2015; 8:240–247.
9.
de MenezesAB, LewisE, O'DonovanM, O'NeillBF, ClipsonN, DoyleEM. Microbiome analysis of dairy cows fed pasture or total mixed ration diets. FEMS Microbiol Ecol, 2011; 78:256–265.
10.
Dill-McFarlandKA, BreakerJD, SuenG. 2017. Microbial succession in the gastrointestinal tract of dairy cows from 2 weeks to first lactation. Sci Rep, 2017; 7:40864.
11.
GerzovaL, BabakV, SedlarK, FaldynovaM, VidenskaP, CejkovaD, JensenAN, DenisM, KerouantonA, RicciA, CibinV, ÖsterbergJ, RychlikI. Characterization of antibiotic resistance gene abundance and microbiota composition in feces of organic and conventional pigs from four EU Countries. PLoS One, 2015; 10:e0132892.
12.
HaleyBJ, PettengillJ, GorhamS, OttesenA, KarnsJS, Van KesselJA. Comparison of microbial communities isolated from feces of asymptomatic Salmonella-shedding and Non-Salmonella shedding dairy cows. Front Microbiol, 2016; 7:691.
13.
HendersonG, CoxF, GaneshS, JonkerA, Young W; Global Rumen CensusCollaborators, JanssenPH. Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range. Sci Rep, 2015; 5:14567.
14.
HintonM, LintonAH, HedgesAJ. The ecology of Escherichia coli in calves reared as dairy-cow replacements. J Appl Bacteriol, 1985; 58:131–138.
15.
HoyleDV, ShawDJ, KnightHI, DavisonHC, PearceMC, LowJC, GunnGJ, WoolhouseME. Age-related decline in carriage of ampicillin-resistant Escherichia coli in young calves. Appl Environ Microbiol, 2004; 70:6927–6930.
16.
KaneeneJB, WarnickLD, BolinCA, ErskineRJ, MayK, MillerR. Changes in tetracycline susceptibility of enteric bacteria following switching to nonmedicated milk replacer for dairy calves. J Clin Microbiol, 2008; 46:1968–1977.
17.
KennedyD.Time to deal with antibiotics. Science, 2013; 342:777.
18.
KhachatryanAR, HancockDD, BesserTE, CallDR. Role of calf-adapted Escherichia coli in maintenance of antimicrobial drug resistance in dairy calves. Appl Environ Microbiol, 2004; 70:752–757.
19.
KimM, KimJ, KuehnLA, BonoJL, BerryED, KalchayanandN, FreetlyHC, BensonAK, WellsJE. Investigation of bacterial diversity in the feces of cattle fed different diets. J Anim Sci, 2014; 92:683–694.
20.
Klein-JöbstlD, QuijadaNM, DzieciolM, FeldbacherB, WagnerM, DrillichM, Schmitz-EsserS, MannE. Microbiota of newborn calves and their mothers reveals possible transfer routes for newborn calves' gastrointestinal microbiota. PLoS One, 2019; 14:e0220554.
21.
Klein-JöbstlD, SchornsteinerE, MannE, WagnerM, DrillichM, Schmitz-EsserS. Pyrosequencing reveals diverse fecal microbiota in Simmental calves during early development. Front Microbiol, 2014; 5:622.
22.
LiB, YangY, MaL, JuF, GuoF, TiedjeJM, ZhangT. Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes. ISME J, 2015; 9:2490–2502.
23.
LiuJ, TaftDH, Maldonado-GomezMX, JohnsonD, TreiberML, LemayDG, DePetersEJ, MillsDA. The fecal resistome of dairy cattle is associated with diet during nursing. Nat Commun, 2019a;10:4406.
24.
LiuJ, ZhaoZ, AvillanJJ, CallDR, DavisM, SischoWM, ZhangA. Dairy farm soil presents distinct microbiota and varied prevalence of antibiotic resistance across housing areas. Environ Pollut, 2019b;254(Pt B):113058.
25.
MaoS, ZhangM, LiuJ, ZhuW. Characterising the bacterial microbiota across the gastrointestinal tracts of dairy cattle: Membership and potential function. Sci Rep, 2015; 5:16116.
26.
MorseD, NordstedtRA, HeadHH, Van HornHH. Production and characteristics of manure from lactating dairy cows in Florida. Trans Am Soc Agric Eng, 1994; 37:275–279.
27.
NennichT, HarrisonJH, MeyerD, WeissWP, HeinrichsAJ, KincaidRL, PowersWJ, KoelschRK, WrightPE. Development of standard methods to estimate manure production and nutrient characteristics from dairy cattle. Proceedings of the Ninth International Animal, Agricultural and Food Processing Wastes Symposium; 2003, pp. 263–268. Available at: https://digitalcommons.unl.edu/cgi/viewcontent.cgi?article=1000&context=biosysengpres, accessed March6, 2020.
28.
NoyesNR, WeinrothME, ParkerJK, DeanCJ, LakinSM, RaymondRA, RoviraP, DosterE, AbdoZ, MartinJN, JonesKL, RuizJ, BoucherCA, BelkKE, MorleyPS. Enrichment allows identification of diverse, rare elements in metagenomic resistome-virulome sequencing. Microbiome, 2017; 5:142.
29.
NoyesNR, YangX, LinkeLM, MagnusonRJ, CookSR, ZaheerR, YangH, WoernerDR, GeornarasI, McArtJA, GowSP, RuizJ, JonesKL, BoucherCA, McAllisterTA, BelkKE, MorleyPS. Characterization of the resistome in manure, soil and wastewater from dairy and beef production systems. Sci Rep, 2016; 6:24645.
30.
OksanenJ, BlanchetFG, FriendlyM, KindtR, LegendreP, McGlinnD, MinchinPR, O'HaraRB, SimpsonGL, SolymosP, StevensMHM, SzoecsE, WagnerH.vegan: Community Ecology Package. R package version 2.5-5, 2019. Available at: http://vegan.r-forge.r-project.org/, accessed March6, 2020.
31.
OliverSP, MurindaSE, JayaraoBM. Impact of antibiotic use in adult dairy cows on antimicrobial resistance of veterinary and human pathogens: A comprehensive review. Foodborne Pathog Dis, 2011; 8:337–355.
32.
PereiraR, LimaS, SilerJD, FoditschC, WarnickLD, BicalhoRC. Ingestion of milk containing very low concentration of antimicrobials: longitudinal effect on fecal microbiota composition in preweaned calves. PLoS One, 2016; 11:e0147525.
33.
PittaDW, DouZ, KumarS, InduguN, TothJD, VecchiarelliB, BhukyaB. Metagenomic evidence of the prevalence and distribution patterns of antimicrobial resistance genes in dairy agroecosystems. Foodborne Pathog Dis, 2016; 13:296–302.
34.
SatoK, BartlettPC, SaeedMA. Antimicrobial susceptibility of Escherichia coli isolates from dairy farms using organic versus conventional production methods. J Am Vet Med Assoc, 2005; 226:589–594.
35.
SchmiederR, EdwardsR. Fast identification and removal of sequence contamination from genomic and metagenomic datasets. PLoS One, 2011; 6:e17288.
ShanksOC, KeltyCA, ArchibequeS, JenkinsM, NewtonRJ, McLellanSL, HuseSM, SoginML. Community structures of fecal bacteria in cattle from different animal feeding operations. Appl Environ Microbiol, 2011; 77:2992–3001.
38.
SpringerHR, DenagamageTN, FentonGD, HaleyBJ, Van KesselJAS, HovinghEP. Antimicrobial resistance in fecal Escherichia coli and Salmonella enterica from dairy calves: A systematic review. Foodborne Pathog Dis, 2019; 16:23–34.
39.
ThamesCH, PrudenA, JamesRE, RayPP, KnowltonKF. Excretion of antibiotic resistance genes by dairy calves fed milk replacers with varying doses of antibiotics. Front Microbiol, 2012; 3:139.
40.
ThomasM, WebbM, GhimireS, BlairA, OlsonK, FenskeGJ, FonderAT, Christopher-HenningsJ, BrakeD, ScariaJ. Metagenomic characterization of the effect of feed additives on the gut microbiome and antibiotic resistome of feedlot cattle. Sci Rep, 2017; 7:12257.
41.
USDA. Escherichia coli O157 on U.S. Dairy Operations. Fort Collins, CO: USDA-APHIS-VS, CEAH, #N404.1203, 2003. Available at: https://www.aphis.usda.gov/aphis/ourfocus/animalhealth/monitoring-and-surveillance/nahms/nahms_dairy_studies, accessed March6, 2020.
42.
USDA. Salmonella, Listeria, and Campylobacter on U.S. Dairy Operations, 1996–2007. 2011. Available at: https://www.aphis.usda.gov/animal_health/nahms/dairy/downloads/dairy07/Dairy07_ir_Food_safety.pdf, accessed March6, 2020.
43.
USDA APHIS. Health and Management Practices on US Dairy Operations, 2014. 2014. Available at: https://www.aphis.usda.gov/aphis/ourfocus/animalhealth/monitoring-and-surveillance/nahms/nahms_dairy_studies, accessed March6, 2020.
44.
VikramA, RoviraP, AggaGE, ArthurTM, BosilevacJM, WheelerTL, MorleyPS, BelkKE, SchmidtJW. Impact of “raised without antibiotics” beef cattle production practices on occurrences of antimicrobial resistance. Appl Environ Microbiol, 2017; 83:pii:e01682-17.
45.
WichmannF, Udikovic-KolicN, AndrewS, HandelsmanJ. Diverse antibiotic resistance genes in dairy cow manure. MBio, 2014; 5:e01017.
46.
YoonSH, HaSM, KwonS, LimJ, KimY, SeoH, ChunJ. Introducing EzBioCloud: A taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol, 2017; 67:1613–1617.
Please find the following supplemental material available below.
For Open Access articles published under a Creative Commons License, all supplemental material carries the same license as the article it is associated with.
For non-Open Access articles published, all supplemental material carries a non-exclusive license, and permission requests for re-use of supplemental material or any part of supplemental material shall be sent directly to the copyright owner as specified in the copyright notice associated with the article.
