Plassembler: an automated bacterial plasmid assembly tool

Vibrio harveyi plasmids as drivers of virulence in barramundi (Lates calcarifer)

Vibrio species are an emerging public and animal health risk in marine environments and the opportunistic bacterial pathogen Vibrio harveyi is a major disease risk for tropical aquaculture. Current understanding of virulence in V. harveyi is limited by strain-specific variability and complex host-pathogen dynamics. This study sought to integrate genomic investigation, phenotypic characterisation and in vivo challenge trials in barramundi (Lates calcarifer) to increase our understanding of V. harveyi virulence. We identified two hypervirulent isolates, Vh-14 and Vh-15 that caused 100% mortality in fish within 48 hours, and that were phenotypically and genotypically distinct from other V. harveyi isolates. Virulent isolates contained multiple plasmids, including a 105,412 bp conjugative plasmid with type III secretion system genes originally identified in Yersinia pestis. The emergence of this hypervirulent plasmid-mediated patho-variant poses a potential threat to the sustainable production of marine finfish in Southeast Asia, the Mediterranean and Australia. In addition, we observed an effect of temperature on phenotypic indicators of virulence with an increase in activity at 28°C and 34°C compared to 22°C. This suggests that temperature fluctuations associated with climate change may act as a stressor on bacteria, increasing virulence gene secretion and host adaptation. Our results utilising a myriad of technologies and tools, highlights the importance of a holistic view to virulence characterisation.

Draft genome assemblies of ciprofloxacin-resistant derivatives of Bacillus cereus strain ATCC14579

Ciprofloxacin resistance in Bacillus cereus involves diverse and understudied mechanisms. Here, we present draft genome assemblies of 95 experimentally evolved Bacillus cereus strains that exhibit increased growth in the presence of ciprofloxacin, many containing novel mutations not previously described for this phenotype.

Clonal expansion of chromosome-borne CTX-M-55 extended-spectrum β-lactamase-producing Salmonella enterica serovar Agona, Taiwan

We investigated emerging multidrug-resistant (MDR) Salmonella enterica serovar Agona in Taiwan. These MDR strains commonly harbored the efflux pump activator gene ramAp and up to 15 resistance genes, including aac (3)-IId, aadA22, aph(3')-Ia, aph (6)-Id, arr-2, blaCTX-M-55, blaLAP-2, blaTEM-1, dfrA14, floR, lnu(F), qnrS13, sul2, sul3, and tet(A), within IncHI2-IncHI2A plasmids or diverse chromosomal resistance genomic islands (RGIs). These newly emerging MDR strains comprised 44.9% and 74.4% of S. Agona isolates collected in 2023 and 2024, respectively. Through analysis of chromosomal insertion sites, we identified 11 distinct RGIs. Strains containing RGI_SA11 became predominant, comprising 59.2% of S. Agona isolates collected in 2024.IMPORTANCEThe emergence and clonal expansion of MDR S. Agona represent a growing public health concern. This study identifies a significant shift in resistance mechanisms, driven by chromosomally integrated resistance genomic islands (RGIs), which likely originated from IncHI2-IncHI2A plasmids. The chromosomal integration of antimicrobial resistance genes enhances the evolutionary fitness of these strains, facilitating their persistence and dissemination in both human and animal populations. These findings underscore the urgent need for enhanced surveillance, targeted interventions, and global antimicrobial stewardship to curb the spread of MDR pathogens and safeguard public health.

Double carbapenemases in Klebsiella pneumoniae blood isolates: dissemination in a single medical center via multiple plasmids and a variety of highly efficient clones

Acquisition of multiple carbapenemase genes by Klebsiella pneumoniae (Kp) is an emerging public health threat. Here, we aim to elucidate the population structure of Kp blood isolates carrying two different carbapenemase genes and identify the mechanism facilitating their dissemination. The study was conducted in a tertiary healthcare center between 2014 and 2022. Twenty-four patients with bacteremia caused by Kp carrying two different carbapenemase genes were identified. All 24 blood isolates were analyzed by short-read genome sequences supplemented by long reads in a selected number of isolates. All isolates carried blaKPC (23 blaKPC-2, 1 blaKPC-3) and blaVIM-1 genes, along with a variety of antimicrobial resistance determinants. The isolates were clustered in six clonal lineages (ST39, ST147, ST323, ST258, ST3035, and ST340). Long-read genome sequences demonstrated that each carbapenemase gene was located in a separate group of plasmids: the blaKPC-2 on a fusion of IncFIB(pQil) and IncFII(K) plasmids, the blaKPC-3 on IncX3, the blaVIM-1 on IncC, or a fusion of the IncFIB(pNDM-Mar) and IncHI1B(pNDM-MAR) plasmids. Comparison of plasmid content of eight isolates carrying a single carbapenemase gene from a previous study with eight isolates carrying two carbapenemase genes from the present study, matched by clonal lineages, revealed that the second carbapenemase gene was acquired by addition of another plasmid. Identical plasmids were found within the same lineage and across lineages. These findings suggest that dissemination of carbapenemase genes in our hospital setting was driven by multiple plasmids across a variety of highly efficient clones.

High intra-laboratory reproducibility of nanopore sequencing in bacterial species underscores advances in its accuracy

Nanopore sequencing is a third-generation technology known for its portability, real-time analysis and ability to generate long reads. It has great potential for use in clinical diagnostics, but thorough validation is required to address accuracy concerns and ensure reliable and reproducible results. In this study, we automated an open-source workflow (freely available at https://gitlab.com/FLI_Bioinfo/nanobacta) for the assembly of Oxford Nanopore sequencing data and used it to investigate the reproducibility of assembly results under consistent conditions. We used a benchmark dataset of five bacterial reference strains and generated eight technical sequencing replicates of the same DNA using the Ligation and Rapid Barcoding kits together with the Flongle and MinION flow cells. We assessed reproducibility by measuring discrepancies such as substitution and insertion/deletion errors, analysing plasmid recovery results and examining genetic markers and clustering information. We compared the results of genome assemblies with and without short-read polishing. Our results show an average reproducibility accuracy of 99.999955% for nanopore-only assemblies and 99.999996% when the short reads were used for polishing. The genomic analysis results were highly reproducible for the nanopore-only assemblies without short read in the following areas: identification of genetic markers for antimicrobial resistance and virulence, classical MLST, taxonomic classification, genome completeness and contamination analysis. Interestingly, the clustering information results from the core genome SNP and core genome MLST analyses were also highly reproducible for the nanopore-only assemblies, with pairwise differences of up to two allele differences in core genome MLST and two SNPs in core genome SNP across replicates. After polishing the assemblies with short reads, the pairwise differences for cgMLST were 0 and for cgSNP were 0-1 SNP across replicates. These results highlight the advances in sequencing accuracy of nanopore data without the use of short reads.

Complete genome sequence of Dorea formicigenerans JCM 31256

We describe a complete genome sequence of Dorea formicigenerans JCM 31256. The genome consists of a single circular chromosome with a length of 3,090,452 base pairs and a GC content of 40.8%, and was predicted to contain 3,061 total genes, encoding for 2,907 proteins.

Complete genome sequence of Roseburia faecis M72/1T

We describe a complete genome sequence of Roseburia faecis strain M72/1T (= JCM 17581T = DSM 16840T = NCIMB 14031T). The genome assembly consists of a single circular chromosome with a length of 3,385,415 base pairs and was predicted to contain 3,338 genes and encode for 3,180 proteins.

Sphae: an automated toolkit for predicting phage therapy candidates from sequencing data

Motivation

Phage therapy offers a viable alternative for bacterial infections amid rising antimicrobial resistance. Its success relies on selecting safe and effective phage candidates that require comprehensive genomic screening to identify potential risks. However, this process is often labor intensive and time-consuming, hindering rapid clinical deployment.

Results

We developed Sphae, an automated bioinformatics pipeline designed to streamline the therapeutic potential of a phage in under 10 minutes. Using Snakemake workflow manager, Sphae integrates tools for quality control, assembly, genome assessment, and annotation tailored specifically for phage biology. Sphae automates the detection of key genomic markers, including virulence factors, antimicrobial resistance genes, and lysogeny indicators such as integrase, recombinase, and transposase, which could preclude therapeutic use. Among the 65 phage sequences analyzed, 28 showed therapeutic potential, 8 failed due to low sequencing depth, 22 contained prophage or virulent markers, and 23 had multiple phage genomes. This workflow produces a report to assess phage safety and therapy suitability quickly. Sphae is scalable and portable, facilitating efficient deployment across most high-performance computing and cloud platforms, accelerating the genomic evaluation process.

Availability and implementation

Sphae source code is freely available at https://github.com/linsalrob/sphae, with installation supported on Conda, PyPi, Docker containers.

Sequencing Strategy to Ensure Accurate Plasmid Assembly

Despite the wide use of plasmids in research and clinical production, the need to verify plasmid sequences is a bottleneck that is too often underestimated in the manufacturing process. Although sequencing platforms continue to improve, the method and assembly pipeline chosen still influence the final plasmid assembly sequence. Furthermore, few dedicated tools exist for plasmid assembly, especially for de novo assembly. Here, we evaluated short-read, long-read, and hybrid (both short and long reads) de novo assembly pipelines across three replicates of a 24-plasmid library. Consistent with previous characterizations of each sequencing technology, short-read assemblies had issues resolving GC-rich regions, and long-read assemblies commonly had small insertions and deletions, especially in repetitive regions. The hybrid approach facilitated the most accurate, consistent assembly generation and identified mutations relative to the reference sequence. Although Sanger sequencing can be used to verify specific regions, some GC-rich and repetitive regions were difficult to resolve using any method, suggesting that easily sequenced genetic parts should be prioritized in the design of new genetic constructs.

Plaseval: a framework for comparing and evaluating plasmid detection tools

BACKGROUND

Plasmids play a major role in the transfer of antimicrobial resistance (AMR) genes among bacteria via horizontal gene transfer. The identification of plasmids in short-read assemblies is a challenging problem and a very active research area. Plasmid binning aims at detecting, in a draft genome assembly, groups (bins) of contigs likely to originate from the same plasmid. Several methods for plasmid binning have been developed recently, such as PlasBin-flow, HyAsP, gplas, MOB-suite, and plasmidSPAdes. This motivates the problem of evaluating the performances of plasmid binning methods, either against a given ground truth or between them.

RESULTS

We describe PlasEval, a novel method aimed at comparing the results of plasmid binning tools. PlasEval computes a dissimilarity measure between two sets of plasmid bins, that can originate either from two plasmid binning tools, or from a plasmid binning tool and a ground truth set of plasmid bins. The PlasEval dissimilarity accounts for the contig content of plasmid bins, the length of contigs and is repeat-aware. Moreover, the dissimilarity score computed by PlasEval is broken down into several parts, that allows to understand qualitative differences between the compared sets of plasmid bins. We illustrate the use of PlasEval by benchmarking four recently developed plasmid binning tools-PlasBin-flow, HyAsP, gplas, and MOB-recon-on a data set of 53 E. coli bacterial genomes.

CONCLUSION

Analysis of the results of plasmid binning methods using PlasEval shows that their behaviour varies significantly. PlasEval can be used to decide which specific plasmid binning method should be used for a specific dataset. The disagreement between different methods also suggests that the problem of plasmid binning on short-read contigs requires further research. We believe that PlasEval can prove to be an effective tool in this regard. PlasEval is publicly available at https://github.com/acme92/PlasEval.

phage therapy candidates from Sphae: An automated toolkit for predicting sequencing data

Motivation

Phage therapy is a viable alternative for treating bacterial infections amidst the escalating threat of antimicrobial resistance. However, the therapeutic success of phage therapy depends on selecting safe and effective phage candidates. While experimental methods focus on isolating phages and determining their lifecycle and host range, comprehensive genomic screening is critical to identify markers that indicate potential risks, such as toxins, antimicrobial resistance, or temperate lifecycle traits. These analyses are often labor-intensive and time-consuming, limiting the rapid deployment of phage in clinical settings.

Results

We developed Sphae, an automated bioinformatics pipeline designed to streamline therapeutic potential of a phage in under ten minutes. Using Snakemake workflow manager, Sphae integrates tools for quality control, assembly, genome assessment, and annotation tailored specifically for phage biology. Sphae automates the detection of key genomic markers, including virulence factors, antimicrobial resistance genes, and lysogeny indicators like integrase, recombinase, and transposase, which could preclude therapeutic use. Benchmarked on 65 phage sequences, 28 phage samples showed therapeutic potential, 8 failed during assembly due to low sequencing depth, 22 samples included prophage or virulent markers, and the remaining 23 samples included multiple phage genomes per sample. This workflow outputs a comprehensive report, enabling rapid assessment of phage safety and suitability for phage therapy under these criteria. Sphae is scalable, portable, facilitating efficient deployment across most high-performance computing (HPC) and cloud platforms, expediting the genomic evaluation process.

Availability

Sphae is source code and freely available at https://github.com/linsalrob/sphae, with installation supported on Conda, PyPi, Docker containers.

Complete genome sequence of Serratia marcescens D1_6, isolated from peat soil

We present a complete genome of Serratia marcescens D1_6 isolated from peat swamp forest. The complete genome for the isolate D1_6 was constructed using data from Oxford Nanopore Technologies and Illumina. The genome of D1_6 has a total length of 4,996,151 bp, comprising a chromosome and a plasmid.

Proposal of Acinetobacter thermotolerans sp. nov. to accommodate bovine feces-dwelling bacteria growing at 47 °C

This study aimed to determine the taxonomic status of a new group of bovine strains of the genus Acinetobacter characterized by the rare ability to grow at temperatures above 44 °C. Initially, 24 strains were isolated from cattle feces collected at 11 farms in Czechia in 2022, representing a tentative new species based on preliminary whole-cell MALDI-TOF MS identification and rpoB gene sequencing. Twelve strains encompassing the within-group diversity were studied in detail, including whole genome de novo sequencing. Core genome-based phylogenetic analysis revealed that the 12 strains form a distinct clade within the genus. The genomic average nucleotide identity based on BLAST (ANIb) values within the clade were ≥ 98.2%, whereas the ANIb values between the clade and the known Acinetobacter species were < 83%. Each of the 12 genomes consisted of a circular chromosome (3.05-3.28 Mb) and 1-6 extrachromosomal elements (1.43-122.5 kb). All strains were non-glucose oxidizing, non-hemolytic, non-proteolytic, and prototrophic, and used acetate, ethanol, and DL-lactate as sole carbon and energy sources. Unrestricted growth at 47 °C was their unique diagnostic characteristic in a genus-wide comparative analysis and their growth kinetics at 37-46 °C differed from that of Acinetobacter baumannii. The studied strains were susceptible to 18 antibiotics except for sporadic resistance to streptomycin, tetracycline, and sulfonamides associated with the presence of strA/strB, tet(Y), and sul2 genes, respectively. We conclude that the studied strains represent a new species, for which we propose the name Acinetobacter thermotolerans sp. nov. The type strain is ANC 7454T (= CCM 9356T = CCUG 77195T = CNCTC 8200T).

Enterobacter adelaidei sp. nov. Isolation of an extensively drug resistant strain from hospital wastewater in Australia and the global distribution of the species

BACKGROUND

Enterobacter species are included among the normal human gut microflora and persist in a diverse range of other environmental niches. They have become important opportunistic nosocomial pathogens known to harbour plasmid-mediated multi-class antimicrobial resistance (AMR) determinants. Global AMR surveillance of Enterobacterales isolates shows the genus is second to Klebsiella in terms of frequency of carbapenem resistance. Enterobacter taxonomy is confusing and standard species identification methods are largely inaccurate or insufficient. There are currently 27 named species and a total of 46 taxa in the genus distinguishable via average nucleotide identity (ANI) calculation between pairs of genomic sequences. Here we describe an Enterobacter strain, ECC3473, isolated from the wastewater of an Australian hospital whose species could not be determined by standard methods nor by ribosomal RNA gene multi-locus typing.

AIM

To characterise ECC3473 in terms of phenotypic and genotypic antimicrobial resistance, biochemical characteristics and taxonomy as well as to determine the global distribution of the novel species to which it belongs.

METHODS

Standard broth dilution and disk diffusion were used to determine phenotypic AMR. The strain's complete genome, including plasmids, was obtained following long- and short read sequencing and a novel long/short read hybrid assembly and polishing, and the genomic basis of AMR was determined. Phylogenomic analysis and quantitative measures of relatedness (ANI, digital DNA-DNA hybridisation, and difference in G+C content) were used to study the taxonomic relationship between ECC3473 and Enterobacter type-strains. NCBI and PubMLST databases and the literature were searched for additional members of the novel species to determine its global distribution.

RESULTS

ECC3473 is one of 21 strains isolated globally belonging to a novel Enterobacter species for which the name, Enterobacter adelaidei sp. nov. is proposed. The novel species was found to be resilient in its capacity to persist in contaminated water and adaptable in its ability to accumulate multiple transmissible AMR determinants.

CONCLUSION

E. adelaidei sp. nov. may become increasingly important to the dissemination of AMR.

Extraction of high-molecular-weight DNA from Streptococcus spp. for nanopore sequencing in resource-limited settings

The long-read sequencing platform MinION, developed by Oxford Nanopore Technologies, enables the sequencing of bacterial genomes in resource-limited settings, such as field conditions or low- and middle-income countries. For this purpose, protocols for extracting high-molecular-weight DNA using nonhazardous, inexpensive reagents and equipment are needed, and some methods have been developed for gram-negative bacteria. However, we found that without modification, these protocols are unsuitable for gram-positive Streptococcus spp., a major threat to fish farming and food security in low- and middle-income countries. Multiple approaches were evaluated, and the most effective was an extraction method using lysozyme, sodium dodecyl sulfate, and proteinase K for lysis of bacterial cells and magnetic beads for DNA recovery. We optimized the method to consistently achieve sufficient yields of pure high-molecular-weight DNA with minimal reagents and time and developed a version of the protocol which can be performed without a centrifuge or electrical power. The suitability of the method was verified by MinION sequencing and assembly of 12 genomes of epidemiologically diverse fish-pathogenic Streptococcus iniae and Streptococcus agalactiae isolates. The combination of effective high-molecular-weight DNA extraction and MinION sequencing enabled the discovery of a naturally occurring 15 kb low-copy number mobilizable plasmid in S. iniae, which we name pSI1. We expect that our resource-limited settings-adapted protocol for high-molecular-weight DNA extraction could be implemented successfully for similarly recalcitrant-to-lysis gram-positive bacteria, and it represents a method of choice for MinION-based disease diagnostics in low- and middle-income countries.

Complete genome sequence of three Staphylococcus epidermidis strains isolated from patients with skin diseases in Japan

Staphylococcus epidermidis is a member of the human skin microbiota as a commensal organism but could be an important opportunistic pathogen for immunocompromised individuals. Here, we report the complete genome sequence of three S. epidermidis strains isolated from patients with skin diseases.

The usefulness of nanopore sequencing in whole-genome sequencing-based genotyping of Listeria monocytogenes and Salmonella enterica serovar Enteritidis

Bacterial genotyping through whole-genome sequencing plays a crucial role in disease surveillance and outbreak investigations in public health laboratories. This study assessed the effectiveness of Oxford Nanopore Technologies (ONT) sequencing in the genotyping of Listeria monocytogenes and Salmonella enterica serovar Enteritidis. Our results indicated that ONT sequences, generated with the R10.4.1 flow cell and basecalled using the Dorado 0.5.0 Super Accurate 4.3 model, exhibited comparable accuracy to Illumina sequences, effectively discriminating among bacterial strains from outbreaks. These findings suggest that ONT sequencing has the potential to be a promising tool for rapid whole-genome sequencing of bacterial pathogens in public health laboratories for epidemiological investigations.

IMPORTANCE

This study unveils that Oxford Nanopore Technologies sequencing, by itself, holds the potential to serve as a whole-genome sequencing-based genotyping tool in public health laboratories, enabling routine subtyping of bacterial isolates for disease surveillance and outbreak investigations.

Sequencing Strategy to Ensure Accurate Plasmid Assembly

Despite the wide use of plasmids in research and clinical production, the need to verify plasmid sequences is a bottleneck that is too often underestimated in the manufacturing process. Although sequencing platforms continue to improve, the method and assembly pipeline chosen still influence the final plasmid assembly sequence. Furthermore, few dedicated tools exist for plasmid assembly, especially for de novo assembly. Here, we evaluated short-read, long-read, and hybrid (both short and long reads) de novo assembly pipelines across three replicates of a 24-plasmid library. Consistent with previous characterizations of each sequencing technology, short-read assemblies had issues resolving GC-rich regions, and long-read assemblies commonly had small insertions and deletions, especially in repetitive regions. The hybrid approach facilitated the most accurate, consistent assembly generation and identified mutations relative to the reference sequence. Although Sanger sequencing can be used to verify specific regions, some GC-rich and repetitive regions were difficult to resolve using any method, suggesting that easily sequenced genetic parts should be prioritized in the design of new genetic constructs.

PlasCAT: Plasmid Cloud Assembly Tool

SUMMARY

PlasCAT (Plasmid Cloud Assembly Tool) is an easy-to-use cloud-based bioinformatics tool that enables de novo plasmid sequence assembly from raw sequencing data. Nontechnical users can now assemble sequences from long reads and short reads without ever touching a line of code. PlasCAT uses high-performance computing servers to reduce run times on assemblies and deliver results faster.

AVAILABILITY AND IMPLEMENTATION

PlasCAT is freely available on the web at https://sequencing.genofab.com. The assembly pipeline source code and server code are available for download at https://bitbucket.org/genofabinc/workspace/projects/PLASCAT. Click the Cancel button to access the source code without authenticating. Web servers implemented in React.js and Python, with all major browsers supported.

Hybracter: enabling scalable, automated, complete and accurate bacterial genome assemblies

Improvements in the accuracy and availability of long-read sequencing mean that complete bacterial genomes are now routinely reconstructed using hybrid (i.e. short- and long-reads) assembly approaches. Complete genomes allow a deeper understanding of bacterial evolution and genomic variation beyond single nucleotide variants. They are also crucial for identifying plasmids, which often carry medically significant antimicrobial resistance genes. However, small plasmids are often missed or misassembled by long-read assembly algorithms. Here, we present Hybracter which allows for the fast, automatic and scalable recovery of near-perfect complete bacterial genomes using a long-read first assembly approach. Hybracter can be run either as a hybrid assembler or as a long-read only assembler. We compared Hybracter to existing automated hybrid and long-read only assembly tools using a diverse panel of samples of varying levels of long-read accuracy with manually curated ground truth reference genomes. We demonstrate that Hybracter as a hybrid assembler is more accurate and faster than the existing gold standard automated hybrid assembler Unicycler. We also show that Hybracter with long-reads only is the most accurate long-read only assembler and is comparable to hybrid methods in accurately recovering small plasmids.

Hybracter: Enabling Scalable, Automated, Complete and Accurate Bacterial Genome Assemblies

Improvements in the accuracy and availability of long-read sequencing mean that complete bacterial genomes are now routinely reconstructed using hybrid (i.e. short- and long-reads) assembly approaches. Complete genomes allow a deeper understanding of bacterial evolution and genomic variation beyond single nucleotide variants (SNVs). They are also crucial for identifying plasmids, which often carry medically significant antimicrobial resistance (AMR) genes. However, small plasmids are often missed or misassembled by long-read assembly algorithms. Here, we present Hybracter which allows for the fast, automatic, and scalable recovery of near-perfect complete bacterial genomes using a long-read first assembly approach. Hybracter can be run either as a hybrid assembler or as a long-read only assembler. We compared Hybracter to existing automated hybrid and long-read only assembly tools using a diverse panel of samples of varying levels of long-read accuracy with manually curated ground truth reference genomes. We demonstrate that Hybracter as a hybrid assembler is more accurate and faster than the existing gold standard automated hybrid assembler Unicycler. We also show that Hybracter with long-reads only is the most accurate long-read only assembler and is comparable to hybrid methods in accurately recovering small plasmids.

Metagenomic assembly is the main bottleneck in the identification of mobile genetic elements

Antimicrobial resistance genes (ARG) are commonly found on acquired mobile genetic elements (MGEs) such as plasmids or transposons. Understanding the spread of resistance genes associated with mobile elements (mARGs) across different hosts and environments requires linking ARGs to the existing mobile reservoir within bacterial communities. However, reconstructing mARGs in metagenomic data from diverse ecosystems poses computational challenges, including genome fragment reconstruction (assembly), high-throughput annotation of MGEs, and identification of their association with ARGs. Recently, several bioinformatics tools have been developed to identify assembled fragments of plasmids, phages, and insertion sequence (IS) elements in metagenomic data. These methods can help in understanding the dissemination of mARGs. To streamline the process of identifying mARGs in multiple samples, we combined these tools in an automated high-throughput open-source pipeline, MetaMobilePicker, that identifies ARGs associated with plasmids, IS elements and phages, starting from short metagenomic sequencing reads. This pipeline was used to identify these three elements on a simplified simulated metagenome dataset, comprising whole genome sequences from seven clinically relevant bacterial species containing 55 ARGs, nine plasmids and five phages. The results demonstrated moderate precision for the identification of plasmids (0.57) and phages (0.71), and moderate sensitivity of identification of IS elements (0.58) and ARGs (0.70). In this study, we aim to assess the main causes of this moderate performance of the MGE prediction tools in a comprehensive manner. We conducted a systematic benchmark, considering metagenomic read coverage, contig length cutoffs and investigating the performance of the classification algorithms. Our analysis revealed that the metagenomic assembly process is the primary bottleneck when linking ARGs to identified MGEs in short-read metagenomics sequencing experiments rather than ARGs and MGEs identification by the different tools.

The intra-host evolutionary landscape and pathoadaptation of persistent Staphylococcus aureus in chronic rhinosinusitis

Chronic rhinosinusitis (CRS) is a common chronic sinonasal mucosal inflammation associated with Staphylococcus aureus biofilm and relapsing infections. This study aimed to determine rates of S. aureus persistence and pathoadaptation in CRS patients by investigating the genomic relatedness and antibiotic resistance/tolerance in longitudinally collected S. aureus clinical isolates. A total of 68 S. aureus paired isolates (34 pairs) were sourced from 34 CRS patients at least 6 months apart. Isolates were grown into 48 h biofilms and tested for tolerance to antibiotics. A hybrid sequencing strategy was used to obtain high-quality reference-grade assemblies of all isolates. Single nucleotide variants (SNV) divergence in the core genome and sequence type clustering were used to analyse the relatedness of the isolate pairs. Single nucleotide and structural genome variations, plasmid similarity, and plasmid copy numbers between pairs were examined. Our analysis revealed that 41 % (14/34 pairs) of S. aureus isolates were persistent, while 59 % (20/34 pairs) were non-persistent. Persistent isolates showed episode-specific mutational changes over time with a bias towards events in genes involved in adhesion to the host and mobile genetic elements such as plasmids, prophages, and insertion sequences. Furthermore, a significant increase in the copy number of conserved plasmids of persistent strains was observed. This was accompanied by a significant increase in biofilm tolerance against all tested antibiotics, which was linked to a significant increase in biofilm biomass over time, indicating a potential biofilm pathoadaptive process in persistent isolates. In conclusion, our study provides important insights into the mutational changes during S. aureus persistence in CRS patients highlighting potential pathoadaptive mechanisms in S. aureus persistent isolates culminating in increased biofilm biomass.