Early life antimicrobial prophylaxis had no effect on individual weight gain, or mortality but it was associated with minor shifts in the composition of fecal microbiota and noticeable changes in the abundance of selected Antimicrobial Resistant Genes
The shifts in fecal microbiota structure caused by perinatal antimicrobial intervention are modest and limited to particular groups of microbial taxa
Early life PPG and TUL intervention could promote the selection of Anrimicrobial Resistant Genes in herds
This is a favorite on the blog. Once a month, we are sharing with you a presentation given at the Allen D. Leman swine conference, on topics that the swine group found interesting, innovative or that lead to great discussions.
We can find all of the presentations selected from the previous years’ conferences on the blog here.
Our sixth presentation is by Dr. Matheus Costa, our newest colleague in the swine group, about his work on colitis and antimicrobial resistance when he was working at the University of Saskatchewan.
The emergence of antimicrobial resistance in humans, animals
and the environment is a major global public health threat to both human and
veterinary medicine. Efforts to address
this important issue involve government, industry, academia, and most notably,
veterinary diagnostic laboratories (VDLs).
These efforts include surveillance to assess the extent resistance in
human and animal pathogens and the development of policies to monitor and
control antimicrobial resistance.
A collaborative effort involving the stakeholders listed above is the key to addressing this emerging threat of antimicrobial resistance and VDLs play major roles in these collaborative efforts. As reported in a Commentary by GK Hendrix in the Journal of Veterinary Diagnostic Investigation in 2018, VDLs are the “nexus in the battle against antimicrobial resistance” (1). The University of Minnesota VDL Bacteriology Section performs almost 30,000 bacterial cultures annually, and most of the pathogenic isolates are archived for future use. These uses include further testing (subtyping, virulence gene assays, serotyping, etc.), use in disease control efforts (autogenous vaccines, etc.), various research projects, and surveillance studies. Almost 5,000 of these pathogenic bacteria are subjected to antimicrobial resistance testing annually, and these antimicrobial minimum inhibitory concentration data are archived for decades for further use.
For our part in this aforementioned collaborative effort in
antimicrobial stewardship, the University of Minnesota VDL is actively involved
in two collaborative government-organized antimicrobial resistance projects as
well as several collaborative academic research projects on antimicrobial
resistance. The common goal of the
collaborative government projects is to determine the population and
distribution of resistant bacteria in the U.S.
The first of these projects is the U.S. Department of Agriculture (USDA) Animal and Plant Health Inspection Service National Animal
Health Laboratory Network (NAHLN) project (2).
This project has 19 AAVLD-accredited laboratories throughout the U.S.
and Canada participating with the objective of monitoring antimicrobial
resistance profiles in animal pathogens routinely isolated from VDLs. Ultimately, this project will result in a national
centralized data collection and reporting process, using harmonized methods and
antimicrobial resistance interpretation and reporting standards. It aims to monitor data for trends in
antimicrobial resistance phenotypes (and eventually genotypes) by identifying
new or emerging resistance profiles, monitoring usefulness of antimicrobials
over time, and reporting these trends to facilitate antimicrobial stewardship
This USDA project
began in January, 2018, and initially involved collection of isolates and
antimicrobial resistance data from Escherischia
coli (all species), Salmonella
enterica (all species), Mannheimia
haemolytica (cattle) and Staphylococcus
intermedius group (companion animals) from routine VDL submissions. A target of about 3,000 isolates will be collected
from the participating VDLs annually and archived for further testing. The antimicrobial testing data will be
tracked and stored by USDA for each
isolate and an annual report will be prepared for stakeholders. This report will include antimicrobial
resistance trends for antibiotics important for human and animal health and the
distribution of minimum inhibitory concentrations for each antimicrobial
monitored for each bacterial pathogen for each animal species included in the
The second of these collaborative antimicrobial resistance projects
is the Food and Drug Administration
(FDA), Center for Veterinary
Medicine, Veterinary-Laboratory Investigation and Response Network (Vet-LIRN)
project (3). This project has 21 AAVLD-accredited laboratories participating
with the objective of performing surveillance of antimicrobial susceptibility
testing results and whole genome sequencing of pathogens from the National
Antimicrobial Resistance Monitoring System scope of interest (4).
This FDA project began in January, 2017, and initially involved collection of isolates and data for three zoonotic bacterial pathogens, with several other bacterial species added to the project in July, 2018. About 2,000 isolates have been collected since project inception, and the FDA has randomly selected about 200 of these isolates for whole genome sequencing. The remaining isolates have been archived for future studies. As an additional benefit related to this project, the University of Minnesota VDL received funds from FDA to purchase an Illumina iSeq Sequencer and participate in a collaborative project designed to increase the number and capabilities of network laboratories involved in the whole genome sequencing portion of this FDA project. Standardization and harmonization of these bacterial genome sequencing abilities among participating laboratories is further designed to increase the network capacity and facilitate future outbreak investigations.
In summary, in support of antimicrobial stewardship efforts, the University of Minnesota VDL Bacteriology Section provides clinical isolates and antimicrobial susceptibility testing data for two collaborative government-initiated projects, one in collaboration with the USDA and the other with the FDA. Further, the VDL as a whole provides leadership in antimicrobial stewardship on a daily basis, cooperating with disease outbreak investigations, collaborating with academic and industrial researchers, and educating veterinarians, clients and the public on issues of antimicrobial stewardship (1).
Nearly one-third of clinical E. coli isolates collected from swine samples were ceftiofur or enrofloxacin resistant
Genetic analysis revealed presence of rarely reported genes in antimicrobial resistant isolates
Most of the isolates were multi-drug resistant on both routine lab tests and genetic analysis
In a previous study, we analyzed the antimicrobial resistance in Escherichia coli isolates recovered from swine clinical samples from across USA during 2006-2016 at the University of Minnesota Veterinary Diagnostic Laboratory (UMN-VDL), and found a 47% annual increase in the prevalence of enrofloxacin resistance (from 1.5% in 2006 to 32% in 2016) while no trend was observed for the resistance to ceftiofur (that ranged between 32-39%). A follow-up study was conducted to evaluate the genetic basis of resistance against enrofloxacin and ceftiofur in E. coli isolates using whole genome sequencing (WGS).
153 swine clinical E. coli isolates collected in 2014-15 from 14 states across USA were selected and genes causing ceftiofur and enrofloxacin resistance were identified using WGS.
21 (out of 106) enrofloxacin-resistant isolates from 6 states harbored diverse plasmid mediated quinolone resistance (PMQR) genes (qnrB19, qnrB2, qnrS1, qnrS2 and qnrS15). The presence of PMQR genes alone was associated with clinical levels of resistance.
The most prevalent genes associated with ceftiofur resistance were blaCMY-2 (89/106, 84%). Moreover, 24 ceftiofur-resistant isolates harbored various blaCTX-M and blaSHV genes.
Additionally, bacteria carrying blaCTX-M and qnr genes also contained genes coding for resistance mechanisms against other antimicrobial classes and were commonly resistant against ampicillin, tetracyclines, gentamycin, trimethoprim and sulfonamides.
These genes (blaCTX-M, qnr) have been rarely reported from farm animals in USA and have been implicated as important genetic mechanisms behind extended spectrum cephalosporin and fluoroquinolone resistance in human and animal populations in several countries. These genes are present on plasmids, making their dissemination across bacterial populations faster by horizontal transfer.
The presence of multiple antimicrobial resistance genes on the same plasmids also makes mitigation of this problem more difficult because of the possibility that using one antimicrobial class will exert positive selection pressure for resistance against other antimicrobial classes.
We launched a new series on the blog last year. Once a month, we are sharing with you a presentation given at the Allen D. Leman swine conference, on topics that the swine group found interesting, innovative or that lead to great discussions.
We can find all of the presentations selected from last year’s conference on the blog here.