Effects of Ceftiofur and Chlortetracycline on the Resistomes of Feedlot Cattle

Abstract

Treatment of food-producing animals with antimicrobial drugs (AMD) is controversial because of concerns regarding promotion of antimicrobial resistance (AMR). To investigate this concern, resistance genes in metagenomic bovine fecal samples during a clinical trial were analyzed to assess the impacts of treatment on beef feedlot cattle resistomes. Four groups of cattle were exposed, using a 2-by-2 factorial design, to different regimens of antimicrobial treatment. Injections of ceftiofur crystalline-free acid (a third-generation cephalosporin) were used to treat all cattle in treatment pens or only a single animal, and either chlortetracycline was included in the feed of all cattle in a pen or the feed was untreated. On days 0 and 26, respectively, pre- and posttrial fecal samples were collected, and resistance genes were characterized using shotgun metagenomics. Treatment with ceftiofur was not associated with changes to β-lactam resistance genes. However, cattle fed chlortetracycline had a significant increase in relative abundance of tetracycline resistance genes. There was also an increase of an AMR class not administered during the study, which is a possible indicator of coselection of resistance genes. Samples analyzed in this study had previously been evaluated by culture characterization (Escherichia coli and Salmonella) and quantitative PCR (qPCR) of metagenomic fecal DNA, which allowed comparison of results with this study. In the majority of samples, genes that were selectively enriched through culture and qPCR were not identified through shotgun metagenomic sequencing in this study, suggesting that changes previously documented did not reflect changes affecting the majority of bacterial genetic elements found in the predominant fecal resistome.IMPORTANCE Despite significant concerns about public health implications of AMR in relation to use of AMD in food animals, there are many unknowns about the long- and short-term impact of common uses of AMD for treatment, control, and prevention of disease. Additionally, questions commonly arise regarding how to best measure and quantify AMR genes in relation to public health risks and how to determine which genes are most important. These data provide an introductory view of the utility of using shotgun metagenomic sequencing data as an outcome for clinical trials evaluating the impact of using AMD in food animals.

Population Dynamics of Salmonella enterica within Beef Cattle Cohorts Followed from Single-Dose Metaphylactic Antibiotic Treatment until Slaughter

“…In our study, isolates were not resistant to azithromycin, ceftiofur, or ceftriaxone either before or after either ceftiofur or tulathromycin treatment. This result was supportive of metagenomic data analyses conducted by Weinroth et al and Doster et al but counter to the findings of Alali et al (33)(34)(35). The studies measured the effect of either ceftiofur or tulathromycin treatment on the microbiome and/or resistome of the fecal community of beef cattle; however, none of the studies focused directly on culturable bacteria, let alone Salmonella, as the outcome bacteria of interest.…”

“…According to their findings, ceftiofur treatment increased resistant E. coli populations after treatment; however, they observed that the population returned to preadministration resistance levels after a 2-week period. Weinroth et al also investigated the effects of ceftiofur use on the resistome of cattle feces, focusing on the bla CMY-2 and bla CTX-M-24 genes in the fecal microbiome on day 0 and day 26 (33). In contrast to the results of Alali et al, but similar to our results, their results did not indicate any significant changes in ceftriaxone resistance over a 26-day period, though they did not analyze the samples taken during peak antibiotic activity (i.e., days 4 to 12).…”

“…In the past 2 decades, numerous studies have been conducted to better understand the role of antibiotic use in both direct and indirect selection of resistant bacteria in food animals (28)(29)(30)(31)(32)(33)(34)(35)(36). A subset of these studies suggest use of antibiotics to control BRD in beef cattle may significantly or transiently increase the selection pressure for resistant bacterial populations during short periods (28)(29)(30)(31)(32)34).…”

“…Even though there are published studies focusing on the effect of metaphylactic ceftiofur treatment on fecal E. coli (30,31) and the resistome in cattle feces (33,34), studies measuring the effects of ceftiofur use on Salmonella specifically are very limited (32). Especially limited are those that follow animals from treatment early in the feeding period until slaughter.…”

Whole genome sequencing and metagenomics for outbreak investigation, source attribution and risk assessment of food‐borne microorganisms

“…ResFinder -Metagenomic read-mapping outperformed cultivation-based techniques in terms of predicting expected tetracycline resistance based on farm antimicrobial consumption Weinroth et al (2018) Bovine faecal samples during a clinical trial using ceftiofur and chlortetracycline MEGARes -Treatment with ceftiofur was not associated with changes in b-lactam resistance genes -Treatment with chlortetracycline had a significant increase in relative abundance of tetracycline resistance genes -There was an increase in resistance to an antimicrobial class not administered during the study, which is a possible indication of co-selection of resistance genes Munk et al (2018) Samples from pig and poultry farms ResFinder -Higher AMR gene loads were observed in pig farms, whereas poultry resistomes were more diverse -Several critical AMR genes, including mcr-1 and optrA, were detected, the abundance of which differed both between host species and between countries -The total acquired AMR genes level was associated with the overall country-specific antimicrobial usage in livestock The main advantages of shotgun metagenomics over classical methods for analysing the resistome is that this methodology is faster, allows for the simultaneous detection of a vast number of resistance genes of different microbial origins within a given sample and the estimation of their relative abundance, and in some cases it is possible to get important information on the genetic background of the detected AMR determinants (microbial species or strain of origin and/or association with mobile genetic elements, such as plasmids, integrons, transposons, prophages, etc.). In fact, shotgun metagenomics can be also used to characterise the so-called mobilome (pool of mobile genetic elements) in a given sample (Ravi et al, 2017).…”