Resistome diversity in cattle and the environment decreases during beef production

  1. Noelle R Noyes  Is a corresponding author
  2. Xiang Yang
  3. Lyndsey M Linke
  4. Roberta J Magnuson
  5. Adam Dettenwanger
  6. Shaun Cook
  7. Ifigenia Geornaras
  8. Dale E Woerner
  9. Sheryl P Gow
  10. Tim A McAllister
  11. Hua Yang
  12. Jaime Ruiz
  13. Kenneth L Jones
  14. Christina A Boucher
  15. Paul S Morley
  16. Keith E Belk
  1. Colorado State University, United States
  2. Agriculture and Agri-Food Canada Research Centre, Canada
  3. University of Saskatoon, Canada
  4. University of Colorado Denver School of Medicine, United States
7 figures, 2 tables and 3 additional files

Figures

Overview of sampling design.

Cattle in this study were born on ranches and entered the feedlots between 3 and 12 months of age. In the feedlots, we collected pooled fecal (black pin), soil (red pin), and drinking water (blue …

https://doi.org/10.7554/eLife.13195.003
Figure 1—source data 1

Sample collection details, by location, sample matrix and pen.

https://doi.org/10.7554/eLife.13195.004
ARD abundance and frequency, by sample type.

(A) Heatmap of the 319 ARDs (rows) identified in 87 samples (columns) collected from the beef production system. Columns are grouped by sampling location but are unclustered. ARDs are clustered …

https://doi.org/10.7554/eLife.13195.006
Figure 2—source data 1

Raw and normalized count matrix of ARDs (rows) identified by sample (columns).

https://doi.org/10.7554/eLife.13195.007
NMDS ordination plots of ARD composition, by sample type and location.

Non-metric multidimensional scaling (NMDS) ordination plots of pre-slaughter sample ARD composition, depicting significant sample separation by (A) matrix (Stress=0.13, R=0.41, p=0.001), and …

https://doi.org/10.7554/eLife.13195.008
Procrustes analysis of ARD content (filled circles) and species composition (open circles) at arrival (A) and exit (B) using Hellinger transformation and NMDS ordination (Legendre and Gallagher, 2001).

Stress values for ARD ordination at arrival and exit were 0.08 and 0.03, respectively, and for microbiome species ordination at arrival and exit were 0.06 and 0.07, respectively. Soil (red), water …

https://doi.org/10.7554/eLife.13195.009
Changes in prevalence of resistance mechanisms during the feedlot period (arrival to exit).

Proportion of arrival (n=8 soil, 8 fecal, 8 water) and exit (n=8 soil, 8 fecal, 8 water) samples that contained at least one ARD in each resistance mechanism (n=33), grouped by resistance class.

https://doi.org/10.7554/eLife.13195.010
Non-metric multidimensional scaling (NMDS) ordination plots at the ARD, mechanism and class levels, visualized by pens (n=8), feedlots (n=4) and states (n=2).

In each NMDS plot, a polygon corresponds to one unit (i.e., pen, feedlot or state) and represents the convex hull for that unit (i.e. the smallest amount of space within the graph that contains all …

https://doi.org/10.7554/eLife.13195.012
Figure 6—source data 1

NMDS ordination, adonis, and anosim results at the ARD, mechanism and class levels, by pen, feedlot, and state variables.

https://doi.org/10.7554/eLife.13195.013
Figure 7 with 1 supplement
Microbiome changes from pre- to post-slaughter in all samples.

(A) Boxplot of Shannon’s diversity at the species level, pre- vs. post-slaughter across all sample matrices. Shannon’s diversity was significantly lower in post-slaughter samples when tested using …

https://doi.org/10.7554/eLife.13195.014
Figure 7—source data 1

Shannon’s diversity, taxa table and model output for Figure 7.

Sheet 1 ('Figure 7A') includes sample metadata and Shannon's Diversity Index calculated at the species level. Sheet 2 ('Figure 7B taxa table') includes the taxa count matrix, by sample, that was used to model log2-fold changes in abundance for Figure 7B and Figure 7—figure supplement 1. Sheet 3 ('Figure 7B model output') shows model output for log2-fold change in abundance at the genus level across all pre- and post-slaughter samples. Sheet 4 ('Figure 7 supp. Model output') shows model output for log2-fold change in abundance at the genus level between pre- and post-slaughter swab samples.

https://doi.org/10.7554/eLife.13195.015
Figure 7—figure supplement 1
Microbiome changes from pre- to post-slaughter in swab samples only.

Log2-fold change in abundance of genera from pre- to post-slaughter versus adjusted P–value, using only swab samples. Dot size is proportional to the average abundance of the genus across all …

https://doi.org/10.7554/eLife.13195.016

Tables

Table 1

Antimicrobial drug usage in the study population.

https://doi.org/10.7554/eLife.13195.005
Drug (dosage)Drug ClassPrimary Reason for UseNumber of Animals treated (%)
Pen APen BPen CPen DPen EPen FPen GPen H
Tylosin phosphate
(11 mg/kg diet dry matter)a
MacrolideLiver abscess prevention244
(100)
281
(100)
152
(100)
189
(100)
230
(100)
230
(100)
265
(100)
150
()
Tulathromycinb
(2.5 mg/kg BWc)
MacrolideBRDd Treatment15
(6.1)
16
(5.7)
12
(7.9)
3
(1.6)
19
(8.3)
3
(1.3)
8
(3.0)
5
(3.3)
Oxytetracyclinee
(20 mg/kg BW)
TetracyclineBRD Treatment1
(0.4)
1
(0.4)
43
(28.3)
9
(4.8)
6
(2.6)
2
(0.9)
13
(4.9)
10
(6.7)
Oxytetracycline and Flunixin meglumineb
(30 mg/kg BW and 2 mg/kg BW)
TetracyclineBRD Treatment0
(0.0)
0
(0.0)
0
(0.0)
0
(0.0)
1
(0.4)
0
(0.0)
0
(0.0)
0
(0.0)
Danofloxacin mesylateb
(8 mg/kg BW)
FluoroquinoloneBRD Treatment0
(0.0)
4
(1.4)
1
(0.7)
0
(0.0)
4
(1.7)
7
(3.0)
2
(0.8)
0
(0.0)
Enrofloxacinb
(7.7 mg/kg BW)
FluoroquinoloneBRD Treatment0
(0.0)
0
(0.0)
0
(0.0)
0
(0.0)
0
(0.0)
0
(0.0)
2
(0.8)
0
(0.0)
Ceftiofur sodiume
(1 mg/kg BW)
β-lactamBRD Treatment0
(0.0)
0
(0.0)
2
(1.3)
0
(0.0)
0
(0.0)
0
(0.0)
0
(0.0)
0
(0.0)
Ceftiofur crystalline free acidb
(6.6 mg/kg BW)
β-lactamBRD Treatment0
(0.0)
0
(0.0)
0
(0.0)
0
(0.0)
0
(0.0)
0
(0.0)
4
(1.5)
1
(0.7)
  1. aThis AMD was in all rations of all cattle for the duration of the feeding period

  2. bEach treated animal received a dose that persisted in target tissues at effective therapeutic concentrations for 3 days, according to the drug label.

  3. cBW = body weight

  4. dBRD = bovine respiratory disease

  5. eEach treated animal received a dose that persisted in target tissues at effective therapeutic concentrations for 1 day, according to the drug label.

Table 2

ARDs to critically important antimicrobials that were specifically searched for in all 87 samples.

https://doi.org/10.7554/eLife.13195.011
ClassificationGroupARD ID (database)Sample Type, LocationAlignment characteristics
Carbapenemasesbla(OXA)Bla)OXA-347:JN086160 (ARG-ANNOT)a
(Bla)OXA-235:JQ820240
(ARG-ANNOT)
1 x water, holding
1 x soil, arrival
1 x soil, arrival
100% nucleotide homology with reference across ≥ 80% of gene (≥ 1x coverage)
100% nucleotide homology to KSG, FGN and STFK motifs
bla(SME)Not identifiedNot identifiedNot identified
bla(IMI)Not identifiedNot identifiedNot identified
bla(NDM)Not identifiedNot identifiedNot identified
bla(GES)Not identifiedNot identifiedNot identified
bla(KPC)Not identifiedNot identifiedNot identified
bla(cphA)bcphA1_2_AYAY261377
(Resfinder)
3 x water, holding100% amino acid homology to reference (4 silent substitutions)
Extended-spectrum β-lactamasebla(TEM)(Bla)TEM-116:AY425988
(ARG-ANNOT)
1 x water, holding100% nucleotide homology with reference across ≥ 80% of gene (≥ 1x coverage)
bla(SHV)Not identifiedNot identifiedNot identified
bla(CTX-M)Not identifiedNot identifiedNot identified
bla(CMY)Not identifiedNot identifiedNot identified
Quinupristin-dalfopristin resistancevga/vatGQ205627.2.gene3 (CARD)
AND
(MLS)VgaD:GQ205627:1394-2971:1578
1 x soil, arrival100% nucleotide homology to Walker A and B motifs; silent substitution in RSGG motif
100% nucleotide homology to LβH hexapeptide repeat domain
Multi-drug resistance to PhLOPSA ccfr(MLS)CfrA:AM408573
(ARG-ANNOT)
4 x swab, truck (all in Texas)100% nucleotide homology with reference across ≥ 95% of gene (≥ 1x coverage)
  1. aNote that phenotypic resistance to carbapenems has not been confirmed for this ARD

  2. bbla(cphA) is a strict carbapenemase

  3. cConfers multi-drug resistance to phenicol, lincosamide, oxazolidinones (linezolid), pleuromutilins, and streptogramin A

Additional files

Supplementary file 1

Sequencing, filtering and host removal statistics for all samples.

https://doi.org/10.7554/eLife.13195.017
Supplementary file 2

List of 319 ARDs identified across all 87 samples.

https://doi.org/10.7554/eLife.13195.018
Supplementary file 3

Resistance classification by class and mechanism

https://doi.org/10.7554/eLife.13195.019

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