Best of Leman 2018 series #6: M. Costa – Guts and bugs: understanding colitis to fight AMR

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.

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.

Continue reading “Best of Leman 2018 series #6: M. Costa – Guts and bugs: understanding colitis to fight AMR”

Antimicrobial Resistance Projects: Towards Antimicrobial Stewardship

This article was written by Drs. CJ Gebhart, KE Olsen and JL Torrison from the Veterinary Diagnostic Laboratory, University of Minnesota.

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.

Performing one of many antimicrobial susceptibility tests in the University of Minnesota Veterinary Diagnostic Laboratory, Bacteriology Section.

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 efforts. 

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 study.

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).


1.  Hendrix, GK. 2018.  The Role of Veterinary Diagnostic Laboratories in the Fight Against Antimicrobial Resistance

2.  USDA. 2018. USDA’s Role in Combatting Antimicrobial Resistance. 

3.  FDA. 2018.  Veterinary Laboratory Investigation and Response Network

Science Page: Emerging enrofloxacin and ceftiofur resistance in E. coli isolated from US swine clinical samples

This is our Friday rubric: every week a new Science Page from the Bob Morrison’s Swine Health Monitoring Project. The previous editions of the science page are available on our website.

This week we are sharing a report from Dr. Shivdeep Singh Hayer from the STEMMA lab, on the emerging enrofloxacin and ceftiofur resistance in E.coli in swine.

Key points:

  • 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.

Best of Leman 2018 series #1: Dr. Noelle Noyes – AMU and AMR: How will we ever understand it?

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.

Our first presenter to kick off this year’ selection is Dr. Noelle Noyes who recently joined the University of Minnesota to bring her expertise in Antimicrobial Resistance in human and livestock. The Center for Animal Health and Food Safety wrote a great article on how Dr. Noyes plans to bring her research to the farms and help producers solve their issues.

Click on the image below to watch her presentation at the conference:

Noyes Leman 2018 AMR understanding

Science Page: Salmonella monophasic harboring plasmid mediated resistance genes to enrofloxacin and ceftiofur is expanding in swine in the Midwest

This is our Friday rubric: every week a new Science Page from the Bob Morrison’s Swine Health Monitoring Project. The previous editions of the science page are available on our website.

This week, we are sharing a report by Dr. Elnekave and the STEMMA lab regarding a multiresistant clad of Salmonella isolated in the Midwest.

Key Points:

  • A genetically distinct clade of Salmonella 4,[5],12:i:- (also referred to as S. monophasic), harboring multiple antimicrobial resistance genes (including to ampicillin,streptomycin, sulfonamides, and tetracyclines) became the predominant S. monophasic type in swine in the U.S. during 2014-2016.
  • Phenotypic resistance to enrofloxacin (fluoroquinolone) and ceftiofur (3rd generation cephalosporin) was present in a proportion these isolates, and whole genome sequencing revealed the presence of the plasmid-mediated genes.
  • These plasmid-mediated resistance genes could potentially transfer horizontally to other microorganisms and augment the problem of antimicrobial resistance to these critically important antibiotics.

S. monophasic emerged globally in the recent years and pig products have been identified as a source in some foodborne outbreaks. The prevalence of S. monophasic, and phenotypic resistance (minimum inhibitory concentration (MIC) above the cut-off value for this bacteria) to enrofloxacin increased in swine clinical samples in the Midwest during 2006 and 2016.

During this period, injectable enrofloxacin was approved by the Food and Drug Administration (FDA) for treatment of swine respiratory disease and colibacillosis in piglets (in 2008 and 2014, respectively); therefore, the objective of the study was to characterize the S. monophasic in swine in the U.S Midwest.

Salmonella genotypic profile
Maximum likelihood tree of S. monophasic collected in the U.S. and Europe during 1991-2016. Tip colors indicate of the period of sample collection: 1991-2009 (red), 2010-2013 (green), 2014-2016 (turquoise) and not available (n.a.; purple). The location of samples collection is indicated by the background color: Europe (red), U.S. (blue) and not available (green). ASSUT= presence of resistance genes against ampicillin, streptomycin, sulfonamides, and tetracyclines. qnr genes – conferring resistance to quinolones.

We used whole genome sequencing to compare S. monophasic isolates collected from livestock in the Midwest with isolates collected from different sources in the U.S. and Europe. We then determined the antimicrobial resistance genotypes and presence of other virulence factors that could help to explain the emergence of this variant.

Salmonella monophasic formed two main genetic clades regardless of source and geographical origin (Figure 1). Most (84%) isolates recovered in the U.S. during 2014-2016, including 50 isolates (out of 51) originating mainly from swine in the Midwest, were part of an emerging clade genotypically resistant to ampicillin, streptomycin, sulphonamides and tetracyclines. In the Midwest samples, phenotypic resistance to enrofloxacin (11 out of 50; 22%) and ceftiofur (9 out of 50; 18%) was found in conjunction with plasmid-mediated resistance genes. This is of particular concern because fluoroquinolones and 3rd generation cephalosporins are often used to treat invasive Salmonella infections in people. Furthermore, because the genes were plasmid borne there is greater likelihood for horizontal transfer of these genes to other bacterial strains.