Biology subjects

Stalder, T.

Publications and source records attributed to Stalder, T..

10 recordsLinked to original sources

bioRxiv2026

Using Hi-C and target capture to monitor plasmid transfer in the barley rhizosphere

Emergence of multi-drug resistant (MDR) pathogens is facilitated by the mobilization of resistance genes from bacteria in animal and environmental habitats, a process often mediated by plasmids. While fertilization of agricultural soils with manure is hypothesized to serve as a pathway for transferring antimicrobial resistance plasmids to soil and crop bacteria, evidence is limited. In this study, we aimed to determine whether MDR-plasmids from manure transfer in soil, leading to the formation of long-term agricultural resistance reservoirs. To this end, we introduced a known MDR plasmid to agricultural soil where barley was subsequently grown and monitored spread of the plasmid over the course of a growing season (up to 190 days). Our experimental design mimicked conventional agricultural practices at a microcosm scale. A digital droplet PCR approach indicated plasmid transfer in the rhizosphere, which was confirmed by a targeted Hi-C method (termed Hi-C+). This demonstrated transfer of the plasmid to soil bacteria 10 days after barley planting but was not observed afterwards. The new plasmid hosts could not be identified, as plasmid-associated host Hi-C reads were absent from existing databases. This implies these hosts were rare and likely unculturable members of the soil microbiome. Our findings demonstrate that plasmid transfer from manure to soil can occur under conditions reflecting those found in agricultural settings. Furthermore, rare and uncharacterized members of the soil microbiomes may participate in acquiring MDR plasmids from manure bacteria, raising important questions about their role in spreading resistance plasmids.

microbiology↗

bioRxiv2024

Comparative genomic analysis identifies potential adaptive variation and virulence factors in Mycoplasma ovipneumoniae

Mycoplasma ovipneumoniae is associated with respiratory disease in wild and domestic Caprinae globally, with wide variation in disease outcomes within and between host species. To gain insight into phylogenetic structure and mechanisms of pathogenicity for this bacterial species, we compared M. ovipneumoniae genomes for 99 samples from six countries (Australia, Bosnia and Herzegovina, Brazil, China, France, USA) and four host species (domestic sheep, domestic goats, bighorn sheep, caribou). Core genome sequences of M. ovipneumoniae assemblies from domestic sheep and goats fell into two well-supported phylogenetic clades that are divergent enough to be considered different bacterial species, consistent with each of these two clades having an evolutionary origin in separate host species. Genome assemblies from bighorn sheep and caribou also fell within these two clades, indicating multiple spillover events, most commonly from domestic sheep. Pangenome analysis indicated a high percentage (91.4%) of accessory genes (i.e., genes found only in a subset of assemblies) compared to core genes (i.e., genes found in all assemblies), potentially indicating a propensity for this pathogen to adapt to within-host conditions. In addition, many genes related to carbon metabolism, which is a virulence factor for Mycoplasmas, showed evidence for homologous recombination, a potential signature of adaptation. The presence or absence of annotated genes was very similar between sheep and goat clades, with only two annotated genes significantly clade-associated. However, three M. ovipneumoniae genome assemblies from asymptomatic caribou in Alaska formed a highly divergent subclade within the sheep clade that lacked 23 annotated genes compared to other assemblies, and many of these genes had functions related to carbon metabolism. Overall our results provide evidence that adaptation of M. ovipneumoniae has involved evolution of carbon metabolism pathways and virulence mechanisms related to those pathways. The genes involved in these pathways, along with other genes identified as potentially involved in virulence in this study, are potential targets for future investigation into a possible genomic basis for the high variation observed in disease outcomes within and between wild and domestic host species. Data SummaryRaw sequence data and genome assemblies generated for this study have been deposited with the National Center for Biotechnology Information (NCBI) under BioProject number PRJNA1070810. Assemblies are also currently available for download through Dryad with the following link: https://datadryad.org/stash/share/aNet7o-xag3PTjJ0_A_BDoOPUpHHshArGW1eJMfLYl4 NCBI accession numbers and associated metadata for each assembly are available in the Supplemental Materials. DNA sequences extracted from these assemblies for four genetic markers (gyrB, rpoB, 16S, IGS) are available in the Supplemental Materials. Analysis code is available at https://github.com/kimandrews/Movi and an interactive phylogeny is available at https://nextstrain.org/community/narratives/kimandrews/Movi Impact statementMycoplasma ovipneumoniae causes respiratory disease in wild and domestic sheep and goats around the world, resulting in economic losses for the domestic sheep industry and severe population declines for wild species. Disease outcomes vary widely within and between host species, and this variation could be influenced by genomic differences across bacterial strains. We compared M. ovipneumoniae genomes from six countries and four host species and found species-level divergence for strains from domestic goats versus domestic sheep, indicating separate evolutionary origins in these two host species. All wildlife strains fell within these two groups, providing evidence that these strains originated by transmission from domestic populations. We identified genes potentially involved in adaptation to hosts, which could be responsible for differences in disease outcomes across bacterial strains and host species. Many of these genes had functions related to carbon metabolism, a potential virulence factor for Mycoplasmas.

evolutionary biology↗

bioRxiv2023

Detection of rare plasmid hosts using a targeted Hi-C approach

Despite the significant role plasmids play in microbial evolution, there is limited knowledge of their ecology, evolution, and transfer in microbial communities. Therefore, we developed and implemented a novel approach to identify rare plasmid hosts by combining Hi-C, a proximity ligation method, with enrichment for plasmid-specific DNA. We hereafter refer to this Hi-C enrichment approach as Hi-C+. Our experimental design mimicked scenarios in which the transfer of an antimicrobial resistance plasmid from a donor to a recipient in soil was increasingly rare. We established that Hi-C can link a plasmid to its host in soil when the relative abundance of that plasmid-host pair is as low as 0.001%. The Hi-C+ method further improved the detection limit of Hi-C 100-fold and allowed identification of plasmid hosts at the genus level. Therefore, Hi-C+ will facilitate the exploration of the ecological and evolutionary pathways that affect the spread of plasmids in natural environments. TeaserIn this study we demonstrate that a target-enriched Hi-C approach can identify rare hosts of a given plasmid in soil.

molecular biology↗

bioRxiv2022

Antimicrobial resistance genes predict plasmid generalism and network structure in wastewater

Plasmids are mobile genetic elements that can act as mutualists or parasites to their bacterial hosts depending on their accessory genes and environment. Ecological network theory predicts that mutualists, such as plasmids with antimicrobial resistance (AMR) genes in the presence of antimicrobials, should act as generalists, while plasmids without beneficial genes are expected to be more specialised. Therefore, whether the relationship between plasmid and host is mutualistic or antagonistic is likely to have a strong impact on the formation of interaction network structures and the spread of AMR genes across microbial networks. Here we re-analyse Hi-C metagenome data from wastewater samples and identify plasmid signatures with machine learning to generate a natural host-plasmid network. We found that AMR-carrying plasmids indeed interacted with more hosts than non-AMR plasmids (on average 14 versus 3, respectively). The AMR plasmid-host subnetwork showed a much higher connectedness and nestedness than the subnetwork associated with non-AMR plasmids. The overall network was clustered around Proteobacteria and AMR-carrying plasmids giving them a crucial role in network connectivity. Therefore, by forming mutualistic networks with their hosts, beneficial AMR plasmids lead to more connected network structures that ultimately share a larger gene pool of AMR genes across the network.

microbiology↗

bioRxiv2022

Biofilms preserve transmissibility of a multi-drug resistance plasmid

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. In contrast, in biofilms most plasmids retained their transfer genes, but on average plasmid persistence improved less over time. Our results showed that biofilms can act as refugia of MDR plasmids and favor the horizontal mode of plasmid transfer, which has important implications for the spread of MDR.

microbiology↗

bioRxiv2020

Contemplative mental training reduces hair glucocorticoid levels in a randomized clinical trial

ObjectiveThis study had the objective to investigate the effect of regular contemplative mental training on endocrine indices of long-term stress. MethodsAn open-label efficacy trial comprising three distinct 3-month modules targeting attention and interoception, socio-affective or socio-cognitive abilities through dyadic exercises and secularised meditation practices was designed and carried out in 332 healthy meditation-naive adults. Participants underwent the training for up to 9 months or were assigned to a retest control cohort. Chronic stress indices were assayed at four timepoints, i.e., pre-training and following each module. The main outcome measures were cortisol and cortisone concentration in hair and self-reported chronic stress ResultsN=362 initial individuals were randomized, of whom n=30 dropped out before study initiation, n=4 before first sampling and n=2 were excluded. N=99 participants did not provide hair samples. Data from three separate training cohorts revealed consistent decreases in hair cortisol and cortisone levels over the training period. This effect increased with practice frequency, was independent of training content and not associated with change in self-reported chronic stress. ConclusionsOur results point to the reduction of long-term cortisol exposure as a mechanism via which contemplative mental training may exert positive effects on practitioners health. Trial registrationClinicalTrials.gov identifier: NCT01833104

molecular biology↗

bioRxiv2018

Linking the Resistome and Plasmidome to the Microbiome

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.

microbiology↗

bioRxiv2018

The transferable resistome of produce

Produce is increasingly recognized as a reservoir of human pathogens and transferable antibiotic resistance genes. This study aimed to explore methods to characterize the transferable resistome of bacteria associated with produce. Mixed salad, arugula, and cilantro purchased from supermarkets were analyzed by means of cultivation- and DNA-based methods. Before and after a nonselective enrichment step, tetracycline (tet) resistant Escherichia coli were isolated and plasmids conferring tet resistance were captured by exogenous plasmid isolation. Tet resistant E. coli isolates, transconjugants and total community (TC)-DNA from the microbial fraction detached from leaves or after enrichment were analyzed for the presence of resistance genes, class 1 integrons and various plasmids by real-time PCR and PCR-Southern blot hybridization. Real-time PCR primers were developed for IncI and IncF plasmids. Tet resistant E. coli isolated from arugula and cilantro carried IncF, IncI1, IncN, IncH11, IncU and IncX1 plasmids. Three isolates from cilantro were positive for IncN plasmids and blaCTX-M-1. From mixed salad and cilantro, IncF, Inc11, and IncP-1{beta} plasmids were captured exogenously. Importantly, whereas direct detection of IncI and IncF plasmids in TC-DNA failed, these plasmids became detectable in DNA extracted from enrichment cultures. This confirms that cultivation-independent DNA-based methods are not always sufficiently sensitive to detect the transferable resistome in the rare microbiome. In summary, this study showed that an impressive diversity of self-transmissible multiple resistance plasmids was detected in bacteria associated with produce that is consumed raw, and exogenous capturing into E. coli suggests that they could transfer to gut bacteria as well.

microbiology↗

bioRxiv2017

Emerging patterns of plasmid-host coevolution that stabilize antibiotic resistance

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 system; iii) a mutation in the hosts global transcriptional regulator gene fur. Since each of these evolutionary solutions individually have been shown to increase plasmid persistence in other plasmid-host pairs, our work points towards common mechanisms of plasmid stabilization. These could become the targets of future alternative drug therapies to slow down the spread of antibiotic resistance.

evolutionary biology↗

bioRxiv2016

Phylodynamics on local sexual contact networks

Phylodynamic models are widely used in infectious disease epidemiology to infer the dynamics and structure of pathogen populations. However, these models generally assume that individual hosts contact one another at random, ignoring the fact that many pathogens spread through highly structured contact networks. We present a new framework for phylodynamics on local contact networks based on pairwise epidemiological models that track the status of pairs of nodes in the network rather than just individuals. Shifting our focus from individuals to pairs leads naturally to coalescent models that describe how lineages move through networks and the rate at which lineages coalesce. These pairwise coalescent models not only consider how network structure directly shapes pathogen phylogenies, but also how the relationship between phylogenies and contact networks changes depending on epidemic dynamics and the fraction of infected hosts sampled. By considering pathogen phylogenies in a probabilistic framework, these coalescent models can also be used to estimate the statistical properties of contact networks directly from phylogenies using likelihood-based inference. We use this framework to explore how much information phylogenies retain about the underlying structure of contact networks and to infer the structure of a sexual contact network underlying a large HIV-1 sub-epidemic in Switzerland.

epidemiology↗