A gentle introduction to pangenomics.

Pangenomes have emerged in response to limitations associated with traditional linear reference genomes. In contrast to a traditional reference that is (usually) assembled from a single individual, pangenomes aim to represent all of the genomic variation found in a group of organisms. The term 'pangenome' is currently used to describe multiple different types of genomic information, and limited language is available to differentiate between them.

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.

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.

Discordance between different bioinformatic methods for identifying resistance genes from short-read genomic data, with a focus on .

Several bioinformatics genotyping algorithms are now commonly used to characterize antimicrobial resistance (AMR) gene profiles in whole-genome sequencing (WGS) data, with a view to understanding AMR epidemiology and developing resistance prediction workflows using WGS in clinical settings. Accurately evaluating AMR in Enterobacterales, particularly , is of major importance, because this is a common pathogen. However, robust comparisons of different genotyping approaches on relevant simulated and large real-life WGS datasets are lacking.

Plassembler: an automated bacterial plasmid assembly tool.

Summary: With recent advances in sequencing technologies, it is now possible to obtain near-perfect complete bacterial chromosome assemblies cheaply and efficiently by combining a long-read-first assembly approach with short-read polishing. However, existing methods for assembling bacterial plasmids from long-read-first assemblies often misassemble or even miss bacterial plasmids entirely and accordingly require manual curation. Plassembler was developed to provide a tool that automatically assembles and outputs bacterial plasmids using a hybrid assembly approach.

Integrated chromosomal and plasmid sequence analyses reveal diverse modes of carbapenemase gene spread among .

Molecular and genomic surveillance systems for bacterial pathogens currently rely on tracking clonally evolving lineages. By contrast, plasmids are usually excluded or analyzed with low-resolution techniques, despite being the primary vectors of antibiotic resistance genes across many key pathogens. Here, we used a combination of long- and short-read sequence data of isolates ( = 1,717) from a European survey to perform an integrated, continent-wide study of chromosomal and plasmid diversity.

Reconciling the Potentially Irreconcilable? Genotypic and Phenotypic Amoxicillin-Clavulanate Resistance in .

Resistance to amoxicillin-clavulanate, a widely used beta-lactam/beta-lactamase inhibitor combination antibiotic, is rising globally, and yet susceptibility testing remains challenging. To test whether whole-genome sequencing (WGS) could provide a more reliable assessment of susceptibility than traditional methods, we predicted resistance from WGS for 976 bloodstream infection isolates from Oxfordshire, United Kingdom, comparing against phenotypes from the BD Phoenix (calibrated against EUCAST guidelines). A total of 339/976 (35%) isolates were amoxicillin-clavulanate resistant.

Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes.

Illumina sequencing allows rapid, cheap and accurate whole genome bacterial analyses, but short reads (<300 bp) do not usually enable complete genome assembly. Long-read sequencing greatly assists with resolving complex bacterial genomes, particularly when combined with short-read Illumina data (hybrid assembly). However, it is not clear how different long-read sequencing methods affect hybrid assembly accuracy.

The Role of in Challenges with Fosfomycin Susceptibility Testing of Multispecies Klebsiella pneumoniae Carbapenemase-Producing Clinical Isolates.

With multidrug-resistant (MDR) on the rise, a nontoxic antimicrobial agent with a unique mechanism of action such as fosfomycin seems attractive. However, establishing accurate fosfomycin susceptibility testing for non- isolates in a clinical microbiology laboratory remains problematic. We evaluated fosfomycin susceptibility by multiple methods with 96 KPC-producing clinical isolates of multiple strains and species collected at a single center between 2008 and 2016.

Don't overlook the little guy: An evaluation of the frequency of small plasmids co-conjugating with larger carbapenemase gene containing plasmids.

As the spread of antimicrobial resistance (AMR) genes becomes an increasing global threat, improved understanding of mobile genetic elements which contribute to the spread of antimicrobial resistance genes, becomes more critical. We created transconjugants from the mating of three chromosomally isogenic Klebsiella pneumoniae carbapenemase (bla) positive Citrobacter freundii isolates with a laboratory strain of Escherichia coli and evaluated the movement of small cryptic plasmids (SCPs), p3223 and p1916, when larger bla-plasmids were transferred. In all of the 143 transconjugants, multiple plasmids, both large and small, transferred with each mating.

Provides a Window into Carbapenemase Gene Transfer, Plasmid Rearrangements, and Patient Interactions with the Hospital Environment.

Several emerging pathogens have arisen as a result of selection pressures exerted by modern health care. was recently defined as a new species, yet its prevalence, niche, and propensity to acquire antimicrobial resistance genes are not fully described. We have been tracking inter- and intraspecies transmission of the carbapenemase (KPC) gene, , between bacteria isolated from a single institution.

TETyper: a bioinformatic pipeline for classifying variation and genetic contexts of transposable elements from short-read whole-genome sequencing data.

Much of the worldwide dissemination of antibiotic resistance has been driven by resistance gene associations with mobile genetic elements (MGEs), such as plasmids and transposons. Although increasing, our understanding of resistance spread remains relatively limited, as methods for tracking mobile resistance genes through multiple species, strains and plasmids are lacking. We have developed a bioinformatic pipeline for tracking variation within, and mobility of, specific transposable elements (TEs), such as transposons carrying antibiotic-resistance genes.

A Candida auris Outbreak and Its Control in an Intensive Care Setting.

Background: Candida auris is an emerging and multidrug-resistant pathogen. Here we report the epidemiology of a hospital outbreak of C. auris colonization and infection.

Severe infections emerge from commensal bacteria by adaptive evolution.

Bacteria responsible for the greatest global mortality colonize the human microbiota far more frequently than they cause severe infections. Whether mutation and selection among commensal bacteria are associated with infection is unknown. We investigated de novo mutation in 1163 genomes from 105 infected patients with nose colonization.

Resolving plasmid structures in using the MinION nanopore sequencer: assessment of MinION and MinION/Illumina hybrid data assembly approaches.

This study aimed to assess the feasibility of using the Oxford Nanopore Technologies (ONT) MinION long-read sequencer in reconstructing fully closed plasmid sequences from eight isolates of six different species with plasmid populations of varying complexity. Species represented were , , , and , with plasmid populations ranging from 1-11 plasmids with sizes of 2-330 kb. Isolates were sequenced using Illumina (short-read) and ONT's MinION (long-read) platforms, and compared with fully resolved PacBio (long-read) sequence assemblies for the same isolates.

Complete genome sequence of the nematicidal Bacillus thuringiensis MYBT18247.

The Gram-positive spore forming bacterium Bacillus thuringiensis MYBT18247 encodes three cry toxin genes, (cry6Ba2, cry6Ba3 and cry21-like) which are active against nematodes. For a better understanding of the evolution of virulence and cry toxins, we present here the complete genome sequence of Bacillus thuringiensis MYBT18247. Various additional virulence factors such as bacteriocins, proteases and hemolysins were identified.

Complete Genome sequence of the nematicidal MYBT18246.

10.1601/nm.5000 is a rod-shaped facultative anaerobic spore forming bacterium of the genus 10.

A curated dataset of complete Enterobacteriaceae plasmids compiled from the NCBI nucleotide database.

Thousands of plasmid sequences are now publicly available in the NCBI nucleotide database, but they are not reliably annotated to distinguish complete plasmids from plasmid fragments, such as gene or contig sequences; therefore, retrieving complete plasmids for downstream analyses is challenging. Here we present a curated dataset of complete bacterial plasmids from the clinically relevant Enterobacteriaceae family. The dataset was compiled from the NCBI nucleotide database using curation steps designed to exclude incomplete plasmid sequences, and chromosomal sequences misannotated as plasmids.

Enhanced Klebsiella pneumoniae Carbapenemase Expression from a Novel Tn Deletion.

The carbapenemase gene () is typically located within mobile transposon Tn Enhanced KPC expression has been associated with deletions in the putative promoter region upstream of Illumina sequences from -positive clinical isolates from a single institution were mapped to a Tnb reference sequence, which carries no deletions. The novel isoform Tnh (188-bp deletion [between and ]) was present in 14% (39/281) of clinical isolates. MICs showed that strains containing plasmids with Tna and Tnh were more resistant to meropenem (≥16 and ≥16, respectively), ertapenem (≥8 and 4, respectively), and cefepime (≥64 and 4, respectively) than strains with Tnb (0.

Ordering the mob: Insights into replicon and MOB typing schemes from analysis of a curated dataset of publicly available plasmids.

Plasmid typing can provide insights into the epidemiology and transmission of plasmid-mediated antibiotic resistance. The principal plasmid typing schemes are replicon typing and MOB typing, which utilize variation in replication loci and relaxase proteins respectively. Previous studies investigating the proportion of plasmids assigned a type by these schemes ('typeability') have yielded conflicting results; moreover, thousands of plasmid sequences have been added to NCBI in recent years, without consistent annotation to indicate which sequences represent complete plasmids.

Plasmid Classification in an Era of Whole-Genome Sequencing: Application in Studies of Antibiotic Resistance Epidemiology.

Plasmids are extra-chromosomal genetic elements ubiquitous in bacteria, and commonly transmissible between host cells. Their genomes include variable repertoires of 'accessory genes,' such as antibiotic resistance genes, as well as 'backbone' loci which are largely conserved within plasmid families, and often involved in key plasmid-specific functions (e.g.

Chromosomal Integration of the Klebsiella pneumoniae Carbapenemase Gene, , in Klebsiella Species Is Elusive but Not Rare.

Carbapenemase genes in are mostly described as being plasmid associated. However, the genetic context of carbapenemase genes is not always confirmed in epidemiological surveys, and the frequency of their chromosomal integration therefore is unknown. A previously sequenced collection of -positive from a single U.

Complete Sequencing of Plasmids Containing blaOXA-163 and blaOXA-48 in Escherichia coli Sequence Type 131.

OXA-48-like enzymes have emerged as important extended-spectrum β-lactamases/carbapenemases in Escherichia coli sequence type 131 (ST131). We report the structures of the first fully sequenced bla plasmid and of two other bla plasmids in this lineage. bla was located on a 71-kb IncN plasmid with other resistance genes.