Longitudinal study of the short- and long-term effects of hospitalisation and oral trimethoprim-sulfadiazine administration on the equine faecal microbiome and resistome

Abstract

Background Hospitalisation and antimicrobial treatment are common in horses and significantly impact the intestinal microbiota. Antimicrobial treatment might also increase levels of resistant bacteria in faeces, which could spread to other ecological compartments, such as the environment, other animals and humans. In this study, we aimed to characterise the short- and long-term effects of transportation, hospitalisation and trimethoprim-sulfadiazine (TMS) administration on the faecal microbiota and resistome of healthy equids. Methods In a longitudinal experimental study design, in which the ponies served as their own control, faecal samples were collected from six healthy Welsh ponies at the farm (D0–D13-1), immediately following transportation to the hospital (D13-2), during 7 days of hospitalisation without treatment (D14–D21), during 5 days of oral TMS treatment (D22–D26) and after discharge from the hospital up to 6 months later (D27–D211). After DNA extraction, 16S rRNA gene sequencing was performed on all samples. For resistome analysis, shotgun metagenomic sequencing was performed on selected samples. Results Hospitalisation without antimicrobial treatment did not significantly affect microbiota composition. Oral TMS treatment reduced alpha-diversity significantly. Kiritimatiellaeota, Fibrobacteres and Verrucomicrobia significantly decreased in relative abundance, whereas Firmicutes increased. The faecal microbiota composition gradually recovered after discontinuation of TMS treatment and discharge from the hospital and, after 2 weeks, was more similar to pre-treatment composition than to composition during TMS treatment. Six months later, however, microbiota composition still differed significantly from that at the start of the study and Spirochaetes and Verrucomicrobia were less abundant. TMS administration led to a significant (up to 32-fold) and rapid increase in the relative abundance of resistance genes sul2, tetQ, ant6-1a, and aph(3”)-lb. lnuC significantly decreased directly after treatment. Resistance genes sul2 (15-fold) and tetQ (six-fold) remained significantly increased 6 months later. Conclusions Oral treatment with TMS has a rapid and long-lasting effect on faecal microbiota composition and resistome, making the equine hindgut a reservoir and potential source of resistant bacteria posing a risk to animal and human health through transmission. These findings support the judicious use of antimicrobials to minimise long-term faecal presence, excretion and the spread of antimicrobial resistance in the environment.

The Effect of Dietary Synbiotics in Actively Racing Standardbred Horses Receiving Trimethoprim/Sulfadiazine

“…All the horses given oral AB during this study remained clinically healthy, and this is consistent with others who report no clinically significant effect of TMS-associated decline in microbiome diversity [26]. No negative effects of any treatments were noted during weekly health assessments, and no evidence of diarrhea was observed during fecal scoring.…”

“…Reduced microbial diversity has also been noted in horses suffering from post-partum colic [24] and those presenting at a referral practice with a diagnosis of colic [25]. However, reduced microbial diversity is not a universal finding during disease, and, conversely, reduced microbial diversity can be observed in clinical healthy individuals [26]. As such, care must be taken to remember these data do not prove causation but rather they suggest that decreased microbial diversity may play a role in increased risk for gastrointestinal disease.…”

Differences in intestinal barrier function between Tianhua mutton sheep and Gansu alpine fine wool sheep (Ovis aries)

“…Among them, Verrucomicrobia had anti-in ammatory effects and maintained glucose homeostasis in the host microbiota 50 . Kiritimatiellaeota is involved in arginine and fatty acid biosynthetic pathways 51 . WCHB1-41 is involved in encoding arginine and fatty acid synthetic metabolic pathways which can effectively improve the e ciency of energy and nitrogen utilization in yaks 52 .…”

Characterising the gut microbiome of stranded harbour seals (Phoca vitulina) in rehabilitation

“…Illumina-sequenced data were transformed into an amplicon sequence variant (ASV) table following the DADA2 pipeline [ 27 ] tutorial v.1.6 with settings as described by Theelen and colleagues [ 28 ]. Finally, the ASV table was used to construct a phyloseq object, the initial dataset.…”