Diversity and distribution of the tick-borne relapsing fever spirochete Borrelia turicatae

Borrelia turicatae is a causative agent of tick-borne relapsing fever (TBRF) in the subtropics and tropics of the United States and Latin America. Historically, B. turicatae was thought to be maintained in enzootic cycles in rural areas. However, there is growing evidence that suggests the pathogen has established endemic foci in densely populated regions of Texas. With the growth of homelessness in the state and human activity in city parks, it was important to implement field collection efforts to identify areas where B. turicatae and its vector circulate. Between 2017 and 2020 we collected Ornithodoros turicata ticks in suburban and urban areas including public and private parks and recreational spaces. Ticks were fed on naïve mice and spirochetes were isolated from the blood. Multilocus sequence typing (MLST) was performed on eight newly obtained isolates and included previously reported sequences. The four chromosomal loci targeted for MLST were 16S ribosomal RNA (rrs), flagellin B (flaB), DNA gyrase B (gyrB), and the intergenic spacer (IGS). Given the complexity of Borrelia genomes, plasmid diversity was also evaluated. These studies indicate that the IGS locus segregates B. turicatae into four genomic types and plasmid diversity is extensive between isolates. Furthermore, B. turicatae and its vector have established endemic foci in parks and recreational areas in densely populated settings of Texas.

The dilution effect limits plasmid horizontal transmission in multispecies bacterial communities

By transferring ecologically important traits between species, plasmids drive genomic divergence and evolutionary innovation in their bacterial hosts. Bacterial communities are often diverse and contain multiple coexisting plasmids, but the dynamics of plasmids in multi-species communities are poorly understood. Here, we show, using experimental multi-species communities containing two plasmids, that bacterial diversity limits the horizontal transmission of plasmids due to the ‘dilution effect’; this is an epidemiological phenomenon whereby living alongside less proficient host species reduces the expected infection risk for a focal host species. In addition, plasmid horizontal transmission was also affected by plasmid diversity, such that the rate of plasmid conjugation was reduced from co-infected host cells carrying both plasmids. In diverse microbial communities, plasmid spread may be limited by the dilution effect and plasmid–plasmid interactions, reducing the rate of horizontal transmission.

The dilution effect limits plasmid horizontal transmission in multispecies bacterial communities

By transferring ecologically important traits between species, plasmids drive genomic divergence and evolutionary innovation in their bacterial hosts. Bacterial communities are often diverse and contain multiple coexisting plasmids, but the dynamics of plasmids in multispecies communities are poorly understood. Here, we show, using experimental multispecies communities containing two plasmids, that bacterial diversity limits the horizontal transmission of plasmids due to the dilution effect; an epidemiological phenomenon whereby living alongside less proficient host species reduces the expected infection risk for a focal host species. In addition, plasmid horizontal transmission was also affected by plasmid diversity, such that the rate of plasmid conjugation was reduced from coinfected host cells carrying both plasmids. In diverse microbial communities, plasmid spread may be limited by the dilution effect and plasmid-plasmid interactions reducing the rate of horizontal transmission.

Genomic network analysis of environmental and livestock F-type plasmid populations

F-type plasmids are diverse and of great clinical significance, often carrying genes conferring antimicrobial resistance (AMR) such as extended-spectrum β-lactamases, particularly in Enterobacterales. Organising this plasmid diversity is challenging, and current knowledge is largely based on plasmids from clinical settings. Here, we present a network community analysis of a large survey of F-type plasmids from environmental (influent, effluent and upstream/downstream waterways surrounding wastewater treatment works) and livestock settings. We use a tractable and scalable methodology to examine the relationship between plasmid metadata and network communities. This reveals how niche (sampling compartment and host genera) partition and shape plasmid diversity. We also perform pangenome-style analyses on network communities. We show that such communities define unique combinations of core genes, with limited overlap. Building plasmid phylogenies based on alignments of these core genes, we demonstrate that plasmid accessory function is closely linked to core gene content. Taken together, our results suggest that stable F-type plasmid backbone structures can persist in environmental settings while allowing dramatic variation in accessory gene content that may be linked to niche adaptation. The association of F-type plasmids with AMR may reflect their suitability for rapid niche adaptation.

Discovering plasmids in metagenomes based on genetic architecture

ABSTRACTPlasmids play a critical role in rapid bacterial adaptation by encoding accessory functions that may increase the host’s fitness. However, the diversity and ecology of plasmids is poorly understood due to computational and experimental challenges in plasmid identification. Here, we report the Plasmid Classification System (PCS), a machine learning classifier that recognizes plasmid sequences based on gene functions. To train PCS, we performed a large-scale discovery and comparison of gene functions in a reference set of >16,000 plasmids and >14,000 chromosomes. PCS accurately recognizes a diverse range of plasmid subtypes, and it outperforms the previous state-of-the-art approach based on k-mer decomposition of sequences. Armed with this model, we conducted, to our knowledge, the largest search for naturally occurring human gut plasmids in 406 publicly available metagenomes representing 5 countries. This search yielded 6,257 high-confidence predicted plasmids, of which 576 had evidence of a circular conformation based on pair-end mapping. These predicted plasmids were found to be highly prevalent across the metagenomes compared to the reference set of known plasmids, suggesting there is extensive and uncharacterized plasmid diversity in the human gut microbiome.

Self-organisation and persistence of antibiotic resistance in evolving plasmid communities

ABSTRACTA key source of genetic variation of microbial populations are plasmids: extrachromosomal genetic elements that replicate autonomously and can be highly mobile between individual cells. Diverse plasmids were found in environmental samples and bacterial populations. Here we explore the mechanisms that help to preserve this gene pool as a fundamental basis for bacterial adaptation. An individual-based model of the plasmidome is presented and used to investigate how intra- and intercellular competition between diverse plasmid types affects the evolution of plasmid communities. It indicates the relative importance of stochastic and deterministic drivers of plasmid persistence both under neutral conditions and when the environment selects for specific plasmid-encoded traits such as antibiotic resistance for a certain period of time. We found that evolving plasmid communities exhibit a cyclical dynamics that contributes to the maintenance of plasmid diversity and the persistence of costly plasmid-mediated antibiotic resistance after stopped abiotic selection.

Genomic network analysis of an environmental and livestock IncF plasmid population

IncF plasmids are diverse and of great clinical significance, often carrying genes conferring antimicrobial resistance (AMR) such as extended-spectrum β-lactamases, particularly in Enterobacteriaceae. Organising this plasmid diversity is challenging, and current knowledge is largely based on plasmids from clinical settings. Here, we present a network community analysis of a large survey of IncF plasmids from environmental (influent, effluent, and upstream/downstream waterways surrounding wastewater treatment works) and livestock settings. We use a tractable and scalable methodology to examine the relationship between plasmid metadata and network communities. This reveals how niche (sampling compartment and host genera) partition and shape plasmid diversity. We also perform pangenome-style analyses on network communities. We show that such communities define unique combinations of core genes, with limited overlap. Building plasmid phylogenies based on alignments of these core genes, we demonstrate that plasmid accessory function is closely linked to core gene content. Taken together, our results suggest that stable IncF plasmid backbone structures can persist in environmental settings while allowing dramatic variation in accessory gene content that may be linked to niche adaptation. The recent association of IncF plasmids with AMR likely reflects their suitability for rapid niche adaptation.