Persistent effects of intramammary ceftiofur treatment on the gut microbiome and antibiotic resistance in dairy cattle

Karla A Vasco; Samantha Carbonell; Rebekah E Sloup; Bailey Bowcutt; Rita R Colwell; Karlis Graubics; Ronald Erskine; Bo Norby; Pamela L Ruegg; Lixin Zhang; Shannon D Manning

doi:10.1186/s42523-023-00274-4

Persistent effects of intramammary ceftiofur treatment on the gut microbiome and antibiotic resistance in dairy cattle

Anim Microbiome. 2023 Nov 9;5(1):56. doi: 10.1186/s42523-023-00274-4.

Authors

Karla A Vasco¹, Samantha Carbonell¹, Rebekah E Sloup¹, Bailey Bowcutt¹, Rita R Colwell^{2

3}, Karlis Graubics³, Ronald Erskine⁴, Bo Norby⁴, Pamela L Ruegg⁵, Lixin Zhang^{6

7}, Shannon D Manning⁸

Affiliations

¹ Department of Microbiology and Molecular Genetics, Michigan State University, E. Lansing, MI, 48824, USA.
² University of Maryland, Institute for Advanced Computer Studies, College Park, MD, 20742, USA.
³ Cosmos ID, Inc, Germantown, MD, 20874, USA.
⁴ Department of Large Animal Clinical Sciences, Michigan State University, E. Lansing, MI, 48824, USA.
⁵ Department of Large Animal Clinical Sciences, Michigan State University, E. Lansing, MI, 48824, USA. plruegg@msu.edu.
⁶ Department of Microbiology and Molecular Genetics, Michigan State University, E. Lansing, MI, 48824, USA. lxzhang@msu.edu.
⁷ Department of Epidemiology and Biostatistics, Michigan State University, E. Lansing, MI, 48824, USA. lxzhang@msu.edu.
⁸ Department of Microbiology and Molecular Genetics, Michigan State University, E. Lansing, MI, 48824, USA. mannin71@msu.edu.

Abstract

Background: Intramammary (IMM) ceftiofur treatment is commonly used in dairy farms to prevent mastitis, though its impact on the cattle gut microbiome and selection of antibiotic-resistant bacteria has not been elucidated. Herein, we enrolled 40 dairy (Holstein) cows at the end of the lactation phase for dry-cow therapy: 20 were treated with IMM ceftiofur (Spectramast®DC) and a non-antibiotic internal teat sealant (bismuth subnitrate) and 20 (controls) received only bismuth subnitrate. Fecal grab samples were collected before and after treatment (weeks 1, 2, 3, 5, 7, and 9) for bacterial quantification and metagenomic next-generation sequencing.

Results: Overall, 90% and 24% of the 278 samples had Gram-negative bacteria with resistance to ampicillin and ceftiofur, respectively. Most of the cows treated with ceftiofur did not have an increase in the number of resistant bacteria; however, a subset (25%) shed higher levels of ceftiofur-resistant bacteria for up to 2 weeks post-treatment. At week 5, the antibiotic-treated cows had lower microbiota abundance and richness, whereas a greater abundance of genes encoding extended-spectrum β-lactamases (ESBLs), CfxA, ACI-1, and CMY, was observed at weeks 1, 5 and 9. Moreover, the contig and network analyses detected associations between β-lactam resistance genes and phages, mobile genetic elements, and specific genera. Commensal bacterial populations belonging to Bacteroidetes most commonly possessed ESBL genes followed by members of Enterobacteriaceae.

Conclusion: This study highlights variable, persistent effects of IMM ceftiofur treatment on the gut microbiome and resistome in dairy cattle. Antibiotic-treated cattle had an increased abundance of specific taxa and genes encoding ESBL production that persisted for 9 weeks. Fecal shedding of ESBL-producing Enterobacteriaceae, which was classified as a serious public health threat, varied across animals. Together, these findings highlight the need for additional studies aimed at identifying factors associated with shedding levels and the dissemination and persistence of antibiotic resistance determinants on dairy farms across geographic locations.

Keywords: Antibiotic resistance; Cattle; Ceftiofur; Mastitis; Microbiome; Resistome; beta-lactam.

Abstract

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