The data provided are the estimates that resulted from raw qPCR fluorescence data (available upon... more The data provided are the estimates that resulted from raw qPCR fluorescence data (available upon request). The data are those used in the analyses described in the associated manuscript. See the ReadMe file for column descriptions
Introduction : Pathogens resistant to multiple antibiotics are rapidly emerging and can acquire t... more Introduction : Pathogens resistant to multiple antibiotics are rapidly emerging and can acquire their resistance genes by conjugation from non-pathogenic bacteria inhabiting a multitude of environments. In spite of the concern that foodborne pathogens can become multi-drug resistant by acquiring plasmids from environmental strains, little is known about the success of that natural genetic exchange. This study investigated if the multiresistance plasmid pB10, isolated from a wastewater treatment plant and harbouring amoxicillin, streptomycin, sulfonamides and tetracycline resistance genes, can be transferred to the foodborne pathogens Salmonella and Escherichia coli O157:H7 and how this alters the phenotype of the recipients. Material and methods : The strains used in this study were the donor strain Pseudomonas putida SM1443 (pB10::gfp) and the recipient strains Salmonella spp. (n=10) and E. coli O157:H7 (n=5). The Salmonella spp. strains belonged to the serovars S. Enteritidis (n=3), S. Typhimurium (n=4), S. Virchow (n=1), S. Infantis (n=1) and S. Hadar (n=1). Conjugation experiments were performed by filter mating on 0.22 µm polycarbonate filters. The transfer ratio was determined by plating and by flow cytometry in which gfp was used as reporter gene [1]. Antibiotic resistance profiles were determined for both recipients and transconjugants using the disc diffusion method according to the Clinical and Laboratory Standards Institute (CLSI) guidelines [2]. Results : For 14 of the 15 recipient strains, transconjugants were obtained by plating and/or by flow cytometry. Based on plating, transfer ratios were between 6.8 x 10-9 and 3.0 x 10-2 while using flow cytometry, transfer ratios were between <1.0 x 10-5 and 1.9 x 10-2. The highest transfer ratio was observed for one of the S. Enteritidis strains. No transconjugants were detected with either method for the S. Hadar strain. The transfer ratios detected in the E.coli strains were lower than those detected in the Salmonella spp. strains, except for one E. coli strain. With a few exceptions, the transconjugants showed phenotypically increased resistance. Discussion : We showed that an environmental plasmid can be transferred to foodborne pathogenic bacteria at high transfer ratios; however the transfer ratio seemed strain dependent. Moreover, the newly acquired resistance genes turned antimicrobial sensitive strains into resistant ones. This event can lead to treatment failure and thus compromise public health [3]. In future work, the possible role of food matrices on the transfer of this plasmid will be examined. References 1. 1. Sorensen S.J. et al. (2003). Current Microbiology 47: 129–133. 2. Clinical and Laboratory Standards Institute (CLSI) (2010). 3. Su L.H. et al. (2003). Antimicrob Agents Chemother 47(2): 563–565.
Self-transmissible multidrug resistance (MDR) plasmids are a major health concern because they ca... more Self-transmissible multidrug resistance (MDR) plasmids are a major health concern because they can spread antibiotic resistance to pathogens. Even though most pathogens form biofilms, little is known about how MDR plasmids persist and evolve in biofilms. We hypothesize that (i) biofilms act as refugia of MDR plasmids by retaining them in the absence of antibiotics longer than well-mixed planktonic populations, and that (ii) the evolutionary trajectories that account for the improvement of plasmid persistence over time differ between biofilms and planktonic populations. In this study, we evolved Acinetobacter baumannii with an MDR plasmid in biofilm and planktonic populations with and without antibiotic selection. In the absence of selection biofilm populations were better able to maintain the MDR plasmid than planktonic populations. In planktonic populations plasmid persistence improved rapidly but was accompanied by a loss of genes required for the horizonal transfer of plasmids. I...
The history of soil microbiology contains several important lessons about approaches and attempts... more The history of soil microbiology contains several important lessons about approaches and attempts to alter the indigenous microbial community. Currently, a number of novel and powerful strategies are available. Yet, it is important for the scientist to be pragmatic concerning their potential usages. Moreover, the validity of concepts such as ‘Isolating - controlling - monitoring’, ‘Environmentally Acceptable Endpoint’ and ‘Nonextractable Residues’ warrants delineation.
The rapid spread of antibiotic resistance is a global health threat. A range of environments have... more The rapid spread of antibiotic resistance is a global health threat. A range of environments have been identified as reservoirs of the antibiotic resistance genes (ARGs) found in pathogens, but we lack understanding of the origins of these ARGs and their spread from environment to clinic. This is partly due to an inability to identify the bacterial hosts of ARGs and the mobile genetic elements that mediate horizontal gene transfer due to the loss of intra-cellular contiguity upon DNA extraction. In two recent studies we describe the application of proximity-ligation methods for the determination of the in situ host range of numerous ARGs, viruses, plasmids, and integrons within complex microbiome samples. This method forms physical junctions between sequences present within the same cell prior to DNA extraction. Subsequent sequencing generates a dataset that robustly connects mobile elements to their hosts and can assemble de novo genomes from mixed communities. Our application of t...
The rapid spread of antibiotic resistance is a serious human health threat. A range of environmen... more The rapid spread of antibiotic resistance is a serious human health threat. A range of environments have been identified as reservoirs of the antibiotic resistance genes (ARGs) found in pathogens. However, we lack understanding of the origins of these ARGs and their spread from environment to clinic. This is partly due to our inability to identify the bacterial hosts of ARGs and the mobile genetic elements that mediate this spread, such as plasmids and integrons. Here we demonstrated that the in vivo proximity ligation method Hi-C can determine the in situ host range of ARGs, plasmids, and integrons in a wastewater sample by physically linking them to their host chromosomes. Hi-C detected both previously known and novel associations between ARGs, mobile elements and host genomes, mostly validating this method. A better identification of the natural carriers of ARGs will aid the development of strategies to limit resistance spread to pathogens.
Multidrug resistant bacterial pathogens have become a serious global human health threat, and con... more Multidrug resistant bacterial pathogens have become a serious global human health threat, and conjugative plasmids are important drivers of the rapid spread of resistance to last-resort antibiotics. Whereas antibiotics have been shown to select for adaptation of resistance plasmids to their new bacterial hosts, or vice versa , a general evolutionary mechanism has not yet emerged. Here we conducted an experimental evolution study aimed at determining general patterns of plasmid-bacteria evolution. Specifically, we found that a large conjugative resistance plasmid follows the same evolutionary trajectories as its non-conjugative mini-replicon in the same and other species. Furthermore, within a single host-plasmid pair three distinct patterns of adaptive evolution led to increased plasmid persistence: i) mutations in the replication protein gene ( trfA1 ); ii) the acquisition by the resistance plasmid of a transposon from a co-residing plasmid encoding a putative toxin-antitoxin syste...
The data provided are the estimates that resulted from raw qPCR fluorescence data (available upon... more The data provided are the estimates that resulted from raw qPCR fluorescence data (available upon request). The data are those used in the analyses described in the associated manuscript. See the ReadMe file for column descriptions
Introduction : Pathogens resistant to multiple antibiotics are rapidly emerging and can acquire t... more Introduction : Pathogens resistant to multiple antibiotics are rapidly emerging and can acquire their resistance genes by conjugation from non-pathogenic bacteria inhabiting a multitude of environments. In spite of the concern that foodborne pathogens can become multi-drug resistant by acquiring plasmids from environmental strains, little is known about the success of that natural genetic exchange. This study investigated if the multiresistance plasmid pB10, isolated from a wastewater treatment plant and harbouring amoxicillin, streptomycin, sulfonamides and tetracycline resistance genes, can be transferred to the foodborne pathogens Salmonella and Escherichia coli O157:H7 and how this alters the phenotype of the recipients. Material and methods : The strains used in this study were the donor strain Pseudomonas putida SM1443 (pB10::gfp) and the recipient strains Salmonella spp. (n=10) and E. coli O157:H7 (n=5). The Salmonella spp. strains belonged to the serovars S. Enteritidis (n=3), S. Typhimurium (n=4), S. Virchow (n=1), S. Infantis (n=1) and S. Hadar (n=1). Conjugation experiments were performed by filter mating on 0.22 µm polycarbonate filters. The transfer ratio was determined by plating and by flow cytometry in which gfp was used as reporter gene [1]. Antibiotic resistance profiles were determined for both recipients and transconjugants using the disc diffusion method according to the Clinical and Laboratory Standards Institute (CLSI) guidelines [2]. Results : For 14 of the 15 recipient strains, transconjugants were obtained by plating and/or by flow cytometry. Based on plating, transfer ratios were between 6.8 x 10-9 and 3.0 x 10-2 while using flow cytometry, transfer ratios were between <1.0 x 10-5 and 1.9 x 10-2. The highest transfer ratio was observed for one of the S. Enteritidis strains. No transconjugants were detected with either method for the S. Hadar strain. The transfer ratios detected in the E.coli strains were lower than those detected in the Salmonella spp. strains, except for one E. coli strain. With a few exceptions, the transconjugants showed phenotypically increased resistance. Discussion : We showed that an environmental plasmid can be transferred to foodborne pathogenic bacteria at high transfer ratios; however the transfer ratio seemed strain dependent. Moreover, the newly acquired resistance genes turned antimicrobial sensitive strains into resistant ones. This event can lead to treatment failure and thus compromise public health [3]. In future work, the possible role of food matrices on the transfer of this plasmid will be examined. References 1. 1. Sorensen S.J. et al. (2003). Current Microbiology 47: 129–133. 2. Clinical and Laboratory Standards Institute (CLSI) (2010). 3. Su L.H. et al. (2003). Antimicrob Agents Chemother 47(2): 563–565.
Self-transmissible multidrug resistance (MDR) plasmids are a major health concern because they ca... more Self-transmissible multidrug resistance (MDR) plasmids are a major health concern because they can spread antibiotic resistance to pathogens. Even though most pathogens form biofilms, little is known about how MDR plasmids persist and evolve in biofilms. We hypothesize that (i) biofilms act as refugia of MDR plasmids by retaining them in the absence of antibiotics longer than well-mixed planktonic populations, and that (ii) the evolutionary trajectories that account for the improvement of plasmid persistence over time differ between biofilms and planktonic populations. In this study, we evolved Acinetobacter baumannii with an MDR plasmid in biofilm and planktonic populations with and without antibiotic selection. In the absence of selection biofilm populations were better able to maintain the MDR plasmid than planktonic populations. In planktonic populations plasmid persistence improved rapidly but was accompanied by a loss of genes required for the horizonal transfer of plasmids. I...
The history of soil microbiology contains several important lessons about approaches and attempts... more The history of soil microbiology contains several important lessons about approaches and attempts to alter the indigenous microbial community. Currently, a number of novel and powerful strategies are available. Yet, it is important for the scientist to be pragmatic concerning their potential usages. Moreover, the validity of concepts such as ‘Isolating - controlling - monitoring’, ‘Environmentally Acceptable Endpoint’ and ‘Nonextractable Residues’ warrants delineation.
The rapid spread of antibiotic resistance is a global health threat. A range of environments have... more The rapid spread of antibiotic resistance is a global health threat. A range of environments have been identified as reservoirs of the antibiotic resistance genes (ARGs) found in pathogens, but we lack understanding of the origins of these ARGs and their spread from environment to clinic. This is partly due to an inability to identify the bacterial hosts of ARGs and the mobile genetic elements that mediate horizontal gene transfer due to the loss of intra-cellular contiguity upon DNA extraction. In two recent studies we describe the application of proximity-ligation methods for the determination of the in situ host range of numerous ARGs, viruses, plasmids, and integrons within complex microbiome samples. This method forms physical junctions between sequences present within the same cell prior to DNA extraction. Subsequent sequencing generates a dataset that robustly connects mobile elements to their hosts and can assemble de novo genomes from mixed communities. Our application of t...
The rapid spread of antibiotic resistance is a serious human health threat. A range of environmen... more The rapid spread of antibiotic resistance is a serious human health threat. A range of environments have been identified as reservoirs of the antibiotic resistance genes (ARGs) found in pathogens. However, we lack understanding of the origins of these ARGs and their spread from environment to clinic. This is partly due to our inability to identify the bacterial hosts of ARGs and the mobile genetic elements that mediate this spread, such as plasmids and integrons. Here we demonstrated that the in vivo proximity ligation method Hi-C can determine the in situ host range of ARGs, plasmids, and integrons in a wastewater sample by physically linking them to their host chromosomes. Hi-C detected both previously known and novel associations between ARGs, mobile elements and host genomes, mostly validating this method. A better identification of the natural carriers of ARGs will aid the development of strategies to limit resistance spread to pathogens.
Multidrug resistant bacterial pathogens have become a serious global human health threat, and con... more Multidrug resistant bacterial pathogens have become a serious global human health threat, and conjugative plasmids are important drivers of the rapid spread of resistance to last-resort antibiotics. Whereas antibiotics have been shown to select for adaptation of resistance plasmids to their new bacterial hosts, or vice versa , a general evolutionary mechanism has not yet emerged. Here we conducted an experimental evolution study aimed at determining general patterns of plasmid-bacteria evolution. Specifically, we found that a large conjugative resistance plasmid follows the same evolutionary trajectories as its non-conjugative mini-replicon in the same and other species. Furthermore, within a single host-plasmid pair three distinct patterns of adaptive evolution led to increased plasmid persistence: i) mutations in the replication protein gene ( trfA1 ); ii) the acquisition by the resistance plasmid of a transposon from a co-residing plasmid encoding a putative toxin-antitoxin syste...
Uploads
Papers by Eva Top