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Fischer, E. A. J.

Publications and source records attributed to Fischer, E. A. J..

6 recordsLinked to original sources

Post-transfer instability, not initial transfer, limits dissemination of IncI1-blaCTX-M-1 plasmids between chicken and human Escherichia coli.

Plasmids are key vectors in the dissemination of antibiotic resistance genes. Within Escherichia coli, IncI1 plasmids carrying blaCTX-M-1 significantly contribute to extended-spectrum beta-lactamase (ESBL) resistance. To investigate their zoonotic dissemination potential, we compared the conjugative transfer rates, post-transfer stability, and short-term evolution of two IncI1-blaCTX-M-1 plasmids transferred from their original chicken E. coli host to a panel of chicken and human E. coli. In vitro conjugation assays revealed that transfer rates were not affected by recipient host origin or temperature and were primarily governed by recipient genotype. However, post-transfer plasmid loss rates were host-dependent, with four-fold higher loss rates in human than chicken-derived transconjugants. The total number of mutations accumulated post-acquisition was determined by the identity of the specific plasmid rather than the host origin, with each plasmid following a distinct evolutionary trajectory involving convergent parallel deletions. Specifically, one trajectory involved the loss of genes associated with plasmid stability, observed more frequently in human than in chicken strains, while the other involved the loss of part of the conjugation machinery. Our findings show that, although these plasmids transfer easily between bacteria from chicken to human hosts, they are less stable in their new host environment, which may restrict their overall spread. A comprehensive One Health risk assessment must consider these critical downstream dynamics of plasmid stability and host-specific evolution.

microbiology↗

Extended period of selection for antimicrobial resistance due to persistency of antimicrobials in broilers

Antimicrobials can select for antimicrobial resistant bacteria. After treatment the active compound is excreted through urine and faeces. As some antimicrobials are chemically stable and very persistent, recirculation of sub-inhibitory concentrations of antimicrobials may occur due to coprophagic behaviour of animals such as chickens. The persistence of three antimicrobials over time and their potential effects on antimicrobial resistance were determined in four groups of broilers. Groups were left untreated (control) or were treated with amoxicillin (non-persistent), doxycycline or enrofloxacin (persistent). Antimicrobials were extracted from the faecal samples and concentrations were measured by LC-MS/MS. We determined the resistome genotypically using shotgun metagenomics and phenotypically by using Escherichia coli as indicator microorganism. Up to 37 days after treatment, persistent antimicrobials (doxycycline and enrofloxacin) had concentrations in faeces equal to or higher than the minimal selective concentration (MSC), in contrast to the non-persistent (amoxicillin) treatment. The amoxicillin treatment showed a significant difference (p [≤] 0.01 and p [≤] 0.0001) in the genotypic resistance only directly after treatment. On the other hand, the doxycycline treatment showed approximately 52% increase in phenotypic and a significant difference (p [≤] 0.05 and p [≤] 0.0001) in genotypic resistance throughout the trial. Furthermore, the enrofloxacin treatment resulted in a complete enrofloxacin-resistant E. coli population but the quantity of resistance genes was similar to the control group, likely because resistance is mediated by point mutations. Based on our findings, we suggest that persistency of antimicrobials should be taken into consideration in the assessment of priority classification of antimicrobials in livestock.

microbiology↗

Defining minimal selective concentrations of amoxicillin, doxycycline and enrofloxacin in broiler-derived cecal fermentations by phenotype, microbiome and resistome

Antimicrobial resistance (AMR) is an emerging worldwide problem. Exposure to antimicrobials selects for resistant bacteria which are a health threat for humans and animals. The concentration at which selection for resistant bacteria occurs is often lower than the minimum inhibitory concentration (MIC) and also differs between environments. Defining this minimal selective concentration (MSC) under natural conditions is essential to understand the selective window for resistant bacteria which are exposed to residual antimicrobials in humans, animals and the environment. In this study we estimated the MSCs of three antimicrobial compounds, amoxicillin, doxycycline and enrofloxacin in a complex microbial community by conducting fermentation assays with cecal material derived from broilers. We examined the phenotypic resistance of Escherichia coli, resistome and microbiome after 6 and 30 hours of fermenting in the presence of antimicrobials of interest. The concentrations are 10 to 100 times lower than the epidemiological cut-off values in E. coli for the respective antimicrobials as determined by EUCAST (https://mic.eucast.org/). In contrast to the amoxicillin and doxycycline exposure we could not determine any molecular resistance mechanism in the resistome analysis for the enrofloxacin exposure, likely because they are the result of point mutations. Our findings show at which concentrations there still is selection for AMR bacteria. This knowledge can be used to manage the risk of the emergence of AMR bacteria. ImportanceAntimicrobial resistance is an emerging threat to the health of humans and animals; it might affect economic prosperity in the future. The rise of antimicrobial resistant bacteria is a consequence of the use of antimicrobial compounds in humans and animals which selects for resistant bacteria. It is critical to understand the relation between the concentrations of antimicrobial compounds and their selection for antimicrobial resistant bacteria. In our study we are providing the minimal selective concentrations for amoxicillin, doxycycline and enrofloxacin by using cecal fermentations assays.

microbiology↗

Comparing the transmission of carbapenemase-producing and extended-spectrum beta-lactamase-producing Escherichia coli between broiler chickens.

The emergence of carbapenemase-producing Enterobacteriaceae (CPE) is a threat to public health, because of their resistance to clinically important carbapenem antibiotics. The emergence of CPE in meat-producing animals is particularly worrying because consumption of meat contaminated with resistant bacteria similar to CPE, such as extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae, contributed to colonization in humans worldwide. Currently, no data on the transmission of CPE in livestock is available. We performed a transmission experiment to quantify the transmission of CPE between broilers to fill this knowledge gap and to compare the transmission rates of CPE and other antibiotic-resistant E. coli. A total of 180 Ross 308 broiler chickens were distributed on the day of hatch (day 0) over 12 pens. On day 5, half of the chickens in each pen were orally inoculated with 5{middle dot}102 colony-forming units of CPE, ESBL, or chloramphenicol-resistant E. coli (catA1). Amoxicillin drinking water treatment was given twice daily in 6 of the 12 pens from days 2 to 6 to evaluate the effect of antibiotic treatment on the transmission rates. Cloacal swabs of all animals were taken to determine the number of infectious broilers. We used a Bayesian hierarchical model to quantify the transmission of the E. coli strains. E. coli can survive in the environment and serve as a reservoir. Therefore, the susceptible-infectious transmission model was adapted to account for the transmission of resistant bacteria from the environment. In addition, the caecal microbiome was analyzed on day 5 and at the end of the experiment on day 14 to assess the relationship between the caecal microbiome and the transmission rates. The transmission rates of CPE were 52 - 68 per cent lower compared to ESBL and catA1, but it is not clear if these differences were caused by differences between the resistance genes or between the E. coli strains. Differences between the groups in transmission rates and microbiome diversity did not correspond to each other, indicating that differences in transmission rates were probably not caused by major differences in the community structure in the caecal microbiome. Amoxicillin treatment from day 2 to 6 increased the transmission rate more than three-fold in all inoculums. It also increased alpha-diversity compared to untreated animals on day 5, but not on day 14, suggesting only a temporary effect. Future research could incorporate more complex transmission models with different species of resistant bacteria into the Bayesian hierarchical model.

microbiology↗

Adaptation, spread and transmission of SARS-CoV-2 in farmed minks and related humans in the Netherlands

In the first wave of the COVID-19 pandemic (April 2020), SARS-CoV-2 was detected in farmed minks and genomic sequencing was performed on mink farms and farm personnel. Here, we describe the outbreak and use sequence data with Bayesian phylodynamic methods to explore SARS-CoV-2 transmission in minks and related humans on farms. High number of farm infections (68/126) in minks and farm related personnel (>50% of farms) were detected, with limited spread to the general human population. Three of five initial introductions of SARS-CoV-2 lead to subsequent spread between mink farms until November 2020. The largest cluster acquired a mutation in the receptor binding domain of the Spike protein (position 486), evolved faster and spread more widely and longer. Movement of people and distance between farms were statistically significant predictors of virus dispersal between farms. Our study provides novel insights into SARS-CoV-2 transmission between mink farms and highlights the importance of combing genetic information with epidemiological information at the animal-human interface.

microbiology↗

Estimating the rate of plasmid transfer in liquid mating cultures

Plasmids are important vectors for the spread of genes among diverse populations of bacteria. However, there is no standard method to determine the rate at which they spread horizontally via conjugation. Here, we compare commonly used methods on simulated and experimental data, and show that the resulting conjugation rate estimates often depend strongly on the time of measurement, the initial population densities, or the initial ratio of donor to recipient populations. Differences in growth rate, e.g. induced by sub-lethal antibiotic concentrations or temperature, can also significantly bias conjugation rate estimates. We derive a new end-point measure to estimate conjugation rates, which extends the well-known Simonsen method to include the effects of differences in population growth and conjugation rates from donors and transconjugants. We further derive analytical expressions for the parameter range in which these approximations remain valid. We present an easy to use R package and web interface which implement both new and previously existing methods to estimate conjugation rates. The result is a set of tools and guidelines for accurate and comparable measurement of plasmid conjugation rates. HighlightsO_LIWe present an R package and Shiny app to estimate conjugation rates from experimental data C_LIO_LIWe highlight the diversity of existing measures used to estimate conjugation rates C_LIO_LIWe show these measures are biased for populations with differing growth and conjugation rates from donors or transconjugants C_LIO_LIWe develop a new end-point measure which accounts for such differences in growth and conjugation rates C_LI

microbiology↗