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.

A new multidrug resistant Salmonella enterica serotype found in Midwestern swine

Text reproduced from the Center for Infectious Disease Research and Policy (CIDRAP)

A new study by Dr. Julio Alvarez‘s team from the STEMMA laboratory, published  in Clinical infectious Diseases suggests that a Salmonella strain circulating in pigs in the US Midwest is part of an emerging clade from Europe that is resistant to multiple antibiotics and may pose a public health risk.

The strain, Salmonella 4,[5],12:i:-, causes many foodborne disease outbreaks mostly tied to pigs and pork products and is expanding in the United States, according to the report by researchers from Minnesota and the United Kingdom.

The team used whole-genome sequencing to assess the relatedness of 659 S 4,[5],12:i:- isolates and 325 S Typhimurium isolates from various sources and locations in the United States and Europe. They also searched for resistance genes and other virulence factors and, for 50 livestock isolates and 22 human isolates, determined the antimicrobial resistance phenotypes.

The researchers found that the S 4,[5],12:i:- isolates fell into two main clades, regardless of their host or place of origin. Eighty-four percent of the US isolates recovered from 2014 through 2016, including nearly all those from pigs in the Midwest, were part of an emerging clade. This clade carried multiple genetic markers for antimicrobial resistance, including resistance to ampicillin, streptomycin, sulphonamides, and tetracyclines.

In addition, phenotypic (actual) resistance to enrofloxacin and ceftiofur was found in 11 of the 50 tested livestock isolates and 9 of the 22 human isolates. This was accompanied by plasmid-mediated resistance genes.

The authors conclude that S 4,[5],12:i:- strains circulating in Midwestern swine herds “are likely part of an emerging multidrug resistant clade first reported in Europe, and can carry plasmid-mediated resistance genes that may be transmitted horizontally to other bacteria and thus could represent a public-health concern.”

Click on the banner below to access the entire article.

salmonella enterica multidru resistant Alvarez 2017

Abstract

Background
Salmonella 4,[5],12:i:-, a worldwide emerging pathogen that causes many foodborne outbreaks mostly attributed to pig and pig products, is expanding in the U.S

Methods
Whole genome sequencing was applied to conduct multiple comparisons of 659 S. 4,[5],12:i:- and 325 S. Typhimurium from different sources and locations (i.e. U.S. and Europe) to assess their genetic heterogeneity, with a focus on strains recovered from swine in the U.S. Midwest. In addition, presence of resistance genes and other virulence factors was detected and the antimicrobial resistance phenotype of 50 and 22 isolates of livestock and human origin, respectively, was determined.

Results
The S. 4,5,12:i:- strains formed two main clades regardless of their source and geographical origin. Most (84%) of the U.S. isolates recovered in 2014–2016, including those (50/51) recovered from swine in the U.S. Midwest, were part of an emerging clade. In this clade, multiple genotypic resistance determinants were predominant, including resistance against ampicillin, streptomycin, sulphonamides and tetracyclines (ASSuT). Phenotypic resistance to enrofloxacin (11/50) and ceftiofur (9/50) was found in conjunction with the presence of plasmid-mediated resistance genes (qnrB19/qnrB2/qnrS1 and blaCMY-2/blaSHV-12, respectively). Also, higher similarity was found between S. 4,[5],12:i:- from the emerging clade and S. Typhimurium from Europe than with S. Typhimurium from the U.S.

Conclusions
Salmonella 4,[5],12:i:- currently circulating in swine in the U.S. Midwest are likely part of an emerging multidrug resistant clade first reported in Europe, and can carry plasmid-mediated resistance genes that may be transmitted horizontally to other bacteria and thus could represent a public-health concern.

Science Page: Salmonella antimicrobial resistance and emergence of a new serotype S.4,[5],12:i:-

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.

Monitoring antimicrobial resistance is a research topic of utmost importance in the swine industry. Dr. Julio Alvarez at the University of Minnesota is leading some of this effort and this week, his team is presenting the latest results regarding Salmonella antimicrobial resistance in the strains isolated by the University of Minnesota – Veterinary Diagnostic Laboratory between the years 2006 and 2015 and the emergence of a new serotype S.4,[5],12:i:-

Key Points

  • Swine is the reservoir most commonly associated with the S.4,[5],12:i: serotype.
  • The prevalence of S. agona and S. 4,[5],12:i:- in isolates of swine origin recovered from clinical samples received at the Minnesota Veterinary Diagnostic Laboratory (MVDL) in 2006-2015 has increased.
  • In these serotypes an increased proportion of isolates were resistant to ceftiofur and enrofloxacin, compared with other serotypes.
  • The increase in the frequency of isolation of the S.4,[5],12:i:- serotype in humans may be paralleled by a similar increase in swine clinical samples received in the MVDL.

The information synthesized in the figure below is the evolution, over the years, of the percentages of Salmonella isolated at the UMN – VDL, belonging to each of other the following serotypes: typhimurium, agona, derby, typhymurium var5, and 4,5,12:i:-. The increase in the proportion of S.4,5,12:i:- can be seen starting back in 2011-2012.

Salmonella antibiotic resistance

Click here to read the full report about Salmonella serotypes isolated at the UMN – VDL

What does antimicrobial-resistant bacteria really mean?

Antimicrobial resistance is an expression that everyone in swine production has heard at least once but what does it really mean?  How are you as a producer or veterinarian affected?

Villalta NHF antimicrobial resistance 2017.gif

In this column for the National Hog Farmer, Dr. Carles Vilalta explains that beyond the definition of a bacterium that is not affected by an antimicrobial, there are two different approaches to think about resistance:

  • One is determined by the Minimal Inhibitory Concentration or MIC, which records the minimum medicine concentration required to stop the growth of the bacteria.
  • The other focuses on the presence of genes enabling the bacterium to counteract the effect of the antimicrobial.

These genes are usually present in a sub-population of bacteria called mutants. The video below created by Harvard Medical School shows how these mutants can develop, adapt, and survive the highest antimicrobial concentrations. (video length < 2min)

 

 

Monitoring Salmonella resistance to antimicrobials in Minnesota during the past 9 years

The STEMMA laboratory at the University of Minnesota and more particularly Dr. Alvarez’s team is aiming at monitoring of antimicrobial resistance in animal and human bacteria. Therefore, the research they present in this article published this month, focused on Salmonella species both in swine and cattle. Records from the Veterinary Diagnostic Laboratory between 2006 and 2015 were compiled to study the evolution of the proportion of resistant strains of Salmonella in Minnesota.

Dr Hong, in collaboration with researchers from the U of MN, captured the number and the type of antimicrobials each strain was resistant to. He also monitored the evolution of the resistances over the nine-year period.

Evolution in antimicrobial resistant Salmonella isolates
recovered from swine at the MVDL in 2006–2015.

Explanation of the figure: Proportion of Salmonella isolates recovered from swine samples that were resistant to ampicillin (A), ceftiofur (C), enrofloxacin (E), florfenicol (F), gentamicin (G), neomycin (N), oxytetracycline (O), sulfadimethoxine (Sul), spectomycin (Sp) and trimethorpim/ sulfamethoxazole (Ts)

Abstract: Salmonellosis remains one of the leading causes of foodborne disease worldwide despite preventive efforts at various stages of the food production chain. The emergence of multi-drug resistant (MDR) non-typhoidal Salmonella enterica represents an additional challenge for public health authorities. Food animals are considered a major reservoir and potential source of foodborne salmonellosis; thus, monitoring of Salmonella strains in livestock may help to detect emergence of new serotypes/MDR phenotypes and to gain a better understanding of Salmonella epidemiology. For this reason, we analyzed trends over a nine-year period in serotypes, and antimicrobial resistance, of Salmonella isolates recovered at the Minnesota Veterinary Diagnostic Laboratory (MVDL) from swine (n = 2,537) and cattle (n = 1,028) samples. Prevalence of predominant serotypes changed over time; in swine, S. Typhimurium and S. Derby decreased and S. Agona and S. 4,5,12:i:- increased throughout the study period. In cattle, S. Dublin, S. Montevideo and S. Cerro increased and S. Muenster became less frequent. Median minimum inhibitory concentration (MIC) values and proportion of antibiotic resistant isolates were higher for those recovered from swine compared with cattle, and were particularly high for certain antibiotic-serotype combinations. The proportion of resistant swine isolates was also higher than observed in the NARMS data, probably due to the different cohort of animals represented in each dataset. Results provide insight into the dynamics of antimicrobial resistant Salmonella in livestock in Minnesota, and can help to monitor emerging trends in antimicrobial resistance.

Link to the full article