The fecal resistome of dairy cattle is associated with diet during nursing

Liu, Jinxin; Taft, Diana H.; Maldonado-Gómez, María X.; Johnson, Daisy; Treiber, Michelle L.; Lemay, Danielle G.; DePeters, E.J.; Mills, David A.

doi:10.1038/s41467-019-12111-x

Cited by 112 publications

(126 citation statements)

References 76 publications

Supporting

Mentioning

114

Contrasting

Order By: Relevance

“…tetQ and ermB) were present in higher copy numbers than the 16S rRNA gene at the majority of the studied time points. This is consistent with the work of other groups, www.nature.com/scientificreports www.nature.com/scientificreports/ which has demonstrated overall AMR gene abundances of 0.77-5.14 40 and 0.54-3.1 gene copies 41 per 16S rRNA gene in agricultural faecal and wastewater samples. It is worth noting that these AMR gene copy numbers are orders of magnitude higher than in samples obtained from other environments, such as sediments, soil and river water 41,42 .…”

Section: Measured Amr Genes Consistently High Across the Unit Althousupporting

confidence: 92%

Resistance to change: AMR gene dynamics on a commercial pig farm with high antimicrobial usage

Pollock

Muwonge

Hutchings

et al. 2020

Sci Rep

View full text Add to dashboard Cite

Group antimicrobial administration is used to control disease in livestock, but we have little insight into how this impacts antimicrobial resistance (AMR) gene dynamics. Here, a longitudinal study was carried out during a single production cycle on a commercial pig unit with high historic and current antimicrobial usage. Quantitative PCR, 16S rRNA gene metabarcoding and shotgun metagenomic sequencing were used to track faecal AMR gene abundance and diversity and microbiome alpha diversity. Shotgun metagenomic sequencing identified 144 AMR genes in total, with higher AMR gene diversity present in young pigs compared to dry sows. Irrespective of in-feed antibiotic treatment or changes in microbiome diversity, mean AMR gene copy number was consistently high, with some AMR genes present at copy numbers comparable to the bacterial 16S rRNA gene. In conclusion, AMR gene prevalence and abundance were not influenced by antibiotic use, either during the production cycle or following whole-herd medication. The high levels of certain genes indicate they are widely disseminated throughout the microbial population, potentially aiding stability. Despite the high and relatively stable levels of resistance genes against the main antimicrobials used, these compounds continue to control production limiting diseases on this unit.Antimicrobial agents are used regularly in many agricultural systems worldwide to improve the health, welfare and productivity of livestock 1,2 . This has led to concerns about the anthropogenic selection of antimicrobial-resistant bacteria in livestock systems 2-4 , particularly due to the potential transfer of antimicrobial resistance (AMR) genes from livestock to humans 5-7 and into the environment 8,9 . In the United Kingdom, 52% of all antimicrobials sold for livestock were used in the pig and poultry sectors, with tetracyclines being reported as the highest sold antibiotic class 10 . Given the substantial use of antimicrobials in pig production, the association between antimicrobial use and AMR has been an area of intensive study. Specifically, antimicrobial administration has been associated with increased AMR in sentinel bacteria such as Escherichia coli [11][12][13] , Staphylococcus aureus 14,15 , and Campylobacter 16 , Salmonella 17 and Enterococcus 18 species. Molecular studies have revealed a higher richness and diversity of AMR genes in pigs administered oxytetracycline in-feed 19 , with farm origin being associated with AMR gene abundances in faeces at slaughter using both quantitative PCR 20 and metagenomic 21 datasets. However, there are currently few longitudinal studies of AMR in livestock systems, specifically for pig production 22 , with information on antimicrobial use in these systems often derived from national figures, rather than from farm medicines records 12,21 .Here, we examine microbial population dynamics and both AMR gene abundance and diversity on a single pig farm during a six-month production cycle. Faecal samples were collected weekly from a batch of young pigs that were ...

show abstract

Section: Measured Amr Genes Consistently High Across the Unit Althousupporting

confidence: 92%

Resistance to change: AMR gene dynamics on a commercial pig farm with high antimicrobial usage

Pollock

Muwonge

Hutchings

et al. 2020

Sci Rep

View full text Add to dashboard Cite

show abstract

“…The effect of the antibiotic treatments was small relative to the longitudinal changes (Additional le 6: Tables S2, S3 and S4), consistent with ndings in pre-weaned dairy calves receiving enro oxacin and tulathromycin metaphylactic treatment [24] and beef cattle receiving oxytetracycline or tulathromycin injection [6]. These ndings can be explained by the existence of a natural resistome, independently of any antibiotic treatment, carried by certain abundant families in the fecal microbiota of pre-weaned calves, as recently shown [28]. Genera of these antibiotic-resistance gene carrying families were found to be dominant in the feces of the veal calves, such as Anaerostipes, Blautia, and Roseburia (Lachnospiraceae family), Enterococcus (Enterococcaceae family), Faecalibacterium and Pseudo avonifractor (Ruminococcaceae family), Bacteroides (Bacteroidaceae family), and Streptococcus (Streptococcaceae).…”

Section: Discussionsupporting

confidence: 87%

“…Moreover, it has been shown that this natural resistome is shaped by the bacterial phylogeny of the fecal microbiome and decreases as the calves age. One of the main drivers of such a decrease was the decrease in abundance of the Enterobacteriaceae family, in which 90% of the members were classi ed as E. coli [28]. It is wellknown that commensal E. coli populations of veal calves harbor high levels of antibiotic-resistance genes [3,29], and that they are diverse.…”

Section: Discussionmentioning

confidence: 99%

Temporal dynamics of the fecal microbiota in veal calves in a 6-month field trial

Haenni

Nguyễn

Madec

et al. 2020

Preprint

View full text Add to dashboard Cite

Background Little is known about maturation of calves’ gut microbiome in veal farms, in which animals are confined under intensive-farming conditions and the administration of collective antibiotic treatment in feed is common. We conducted a field study on 45 calves starting seven days after their arrival in three veal farms. We collected monthly fecal samples over six months and performed 16S rRNA gene sequencing and quantitative PCR of Escherichia coli to follow the dynamics of their microbiota, including that of their commensal E. coli populations. We used mixed-effect models to characterize the dynamics of α-diversity indices and numbers of E. coli, and searched for an effect of collective antibiotic treatments on the estimated parameters. On two farms, we also searched for associations between recommended daily doses of milk powder and bacterial abundance. Results There was high heterogeneity between calves’ microbiota upon their arrival at the farms, followed by an increase in similarity, starting at the first month. From the second month, 16 genera were detected at each sampling in all calves, representing 67.5% (± 9.9) of their microbiota. Shannon diversity index showed a two-phase increase, an inflection occurring at the end of the first month. Calves receiving antibiotics had a lower intercept estimate for Shannon index (-0.17 CI95%[0.27; -0.06], p = 0.003) and a smaller number of E. coli/ gram of feces during the treatment and in the 15 days following it (-0.37 log10 (E. coli/g) CI95%[-0.66; -0.08], p = 0.01) than unexposed calves. There were moderate to strong positive associations between the dose of milk powder and the relative abundances of the genera Megasphaera, Enterococcus, Dialister and Mitsuokella, and the number of E. coli (rs ≥ 0.40; Bonferroni corrected p < 0.05).Conclusions This observational study shows early convergence of the developing microbiota between veal calves and associations between the dose of milk powder and members of their microbiota. It suggests that administration of collective antibiotic treatment results in a reduction of diversity and size of the E. coli population and highlights the need for additional work to fully understand the impact of antibiotic treatment in the veal industry.

show abstract

“…Consumption of antimicrobials in livestock, as well as antimicrobial residues in food have been proposed to contribute to antimicrobial resistance (AMR) in humans [3,4] and aquatic/soil environments [5,6]. The AMR found in food-producing animals not only reduces the therapeutic e cacy of antimicrobials against diseases but also selects for reservoirs of resistance that could be transferred to humans via the food chain or through the environment [7]. Therefore, reducing antimicrobial resistance and preventing antimicrobial residues from entering the food chain is a priority for livestock industry to address the food safety and public health concerns [8].…”

Section: Introductionmentioning

confidence: 99%

“…It is largely unknown the extent to which ARGs are expressed in the rumen of cattle that are not under the selective pressure antibiotics used in human is unclear. Recent studies have assessed wastewater treatment plant resistome at both metagenomic and metatranscripome levels and reveals that plant locations not only affected the ARGs but also their transcripts [7,17]. However, comparing to largely identi ed resistomes in the animal system, their functionality and activity in vivo has not been reported.…”

Section: Introductionmentioning

confidence: 99%

Host genetics affected the resistome and its expression patterns in the rumen of beef cattle raised without antibiotics used in humans

Ma¹,

Li²,

Zaheer³

et al. 2020

Preprint

View full text Add to dashboard Cite

Background: The rumen microbiome is a potential reservoir of antimicrobial-resistant genes (ARGs), termly resistome. However, the activity of ARGs and what factors affect expression of ARGs in the rumen is unknown. Here, the rumen resistome was evaluated using metagenomic and metatranscriptomic datasets, with the aim to identify the active rumen resistome and whether it can be affected by cattle breed and feed efficiency.Results: Genes encoding resistance to 12 ARG classes representing 62 individual ARGs were detected in the rumen metagenomes of Angus, Charolais or Kinsella composite hybrid (KC) beef steers (n = 48) with high and low feed efficiency. Three genes encoding tetracycline (tetQ, tetW) and macrolide (mefA) resistance constituted 75.3% of abundance of total ARGs identified in all animals, suggesting they are ‘core’ resistome in the rumen of steers. Only about 20.96% (13/62) of the total ARGs identified were expressed, among which genes encoding resistance to tetracycline, macrolide-licosamide-streptogramin (MLS), aminoglycoside, and multidrug exhibited the highest level of expression. More than half (56.2%) of the ARGs identified were plasmid-associated, while only 5 plasmid-associated ARGs were expressed. The abundance of 17, 14, and 5 individual ARGs were significantly affected by breed, feed efficiency, and breed × feed efficiency, respectively, while the expression of ARGs did not differ among breeds or between feed efficiency groups. In KC cattle, less number of total ARGs, ARG transcripts, as well as total active bacteria (estimated by 16S rRNA copies) was observed than AN. The total active bacteria were negatively correlated with expression of MLS and tetracycline ARG (mefA, tet40, tetM, tetW, and an unidentified tet), and tended to be negatively correlated with the expression of plasmid-associated tetracycline ARG t only in the rumen of KC cattle.Conclusions: Our results suggest that a large portion of the ARGs are not expressed in the rumen of cattle raised without antibiotics used in humans. The identified less diversified active resistome and total active bacteria, and the significant correlation between total active bacteria and the abundance of ARG transcripts in KC cattle suggest that the expression of resistome in the rumen may be breed specific and driven by ruminal microbiota.

show abstract

The fecal resistome of dairy cattle is associated with diet during nursing

Cited by 112 publications

References 76 publications

Resistance to change: AMR gene dynamics on a commercial pig farm with high antimicrobial usage

Resistance to change: AMR gene dynamics on a commercial pig farm with high antimicrobial usage

Temporal dynamics of the fecal microbiota in veal calves in a 6-month field trial

Host genetics affected the resistome and its expression patterns in the rumen of beef cattle raised without antibiotics used in humans

Contact Info

Product

Resources

About