Accurate bacterial outbreak tracing with Oxford Nanopore sequencing and reduction of methylation-induced errors.

Our study investigates the effectiveness of Oxford Nanopore Technologies for accurate outbreak tracing by resequencing 33 isolates of a 3-year-long outbreak with Illumina short-read sequencing data as the point of reference. We detect considerable base errors through cgMLST and phylogenetic analysis of genomes sequenced with Oxford Nanopore Technologies, leading to the false exclusion of some outbreak-related strains from the outbreak cluster. Nearby methylation sites cause these errors and can also be found in other species besides Based on these data, we explore PCR-based sequencing and a masking strategy, which both successfully address these inaccuracies and ensure accurate outbreak tracing.

A multicenter study on accuracy and reproducibility of nanopore sequencing-based genotyping of bacterial pathogens.

Nanopore sequencing has shown the potential to democratize genomic pathogen surveillance due to its ease of use and low entry cost. However, recent genotyping studies showed discrepant results compared to gold-standard short-read sequencing. Furthermore, although essential for widespread application, the reproducibility of nanopore-only genotyping remains largely unresolved.

Core genome multilocus sequence typing (cgMLST) applicable to the monophyletic species complex.

The environmental bacterium displays an alarming increase of antibiotic-resistant strains that frequently cause outbreaks in intensive care units. Due to its prevalence in the environment and opportunistic presence in humans, molecular surveillance (including resistance marker screening) and high-resolution cluster analysis are of high relevance. Furthermore, previously described in studies is rather a species complex (KoSC) than a single species comprising at least six closely related species that are not easily differentiated by standard typing methods.

Aggression and spatial positioning of kin and non-kin fish in social groups.

Group-living animals are faced with the challenge of sharing space and local resources amongst group members who may be either relatives or non-relatives. Individuals may reduce the inclusive fitness costs they incur from competing with relatives by either reducing their levels of aggression toward kin, or by maintaining physical separation between kin. In this field study, we used the group-living cichlid to examine whether within-group aggression is reduced among group members that are kin, and whether kin occupy different regions of their group's territory to reduce kin competition over space and local resources.

Real-Time Nanopore Q20+ Sequencing Enables Extremely Fast and Accurate Core Genome MLST Typing and Democratizes Access to High-Resolution Bacterial Pathogen Surveillance.

Next-generation whole-genome sequencing is essential for high-resolution surveillance of bacterial pathogens, for example, during outbreak investigations or for source tracking and escape variant analysis. However, current global sequencing and bioinformatic bottlenecks and a long time to result with standard technologies demand new approaches. In this study, we investigated whether novel nanopore Q20+ long-read chemistry enables standardized and easily accessible high-resolution typing combined with core genome multilocus sequence typing (cgMLST).

Complete Genome Sequence of Klebsiella oxytoca Strain AHC-6, Isolated from a Patient during Acute Antibiotic-Associated Hemorrhagic Colitis.

Klebsiella oxytoca is a ubiquitous bacterium that is increasingly associated with inflammatory diseases. Here, we report the hybrid assembled genome for cytotoxic K. oxytoca strain AHC-6.

Patterns of sex-biased dispersal are consistent with social and ecological constraints in a group-living cichlid fish.

Background: Sex-biased dispersal is a common and widespread phenomenon that can fundamentally shape the genetic structure of the social environments in which animals live. For animals that live in and move between social groups, sex-biased dispersal can result in an asymmetry in the degree of relatedness among cohabiting males and females, which can have strong implications for their social evolution. In this study, we measured the relatedness structure within and across groups of a wild population of Neolamprologus multifasciatus, a highly-social, shell-dwelling cichlid fish endemic to Lake Tanganyika, East Africa.

Parentage analysis across age cohorts reveals sex differences in reproductive skew in a group-living cichlid fish, Neolamprologus multifasciatus.

Group-living animals are often faced with complex reproductive decisions, namely how to partition within-group reproduction, how to obtain extra-group reproduction and how these two means of reproduction should be balanced. The solutions to these questions can be difficult to predict because ecological conditions can affect the scopes for within-group and extra-group reproduction in complex ways. For example, individuals that are restricted from moving freely around their habitats may have limited extra-group reproductive opportunities, but at the same time, groups may live in close proximity to one another, which could potentially have the opposite effect.