Short turnaround time of seven to nine hours from sample collection until informed decision for sepsis treatment using nanopore sequencing

Bloodstream infections (BSIs) and sepsis are major health problems, annually claiming millions of lives. Traditional blood culture techniques, employed to identify sepsis-causing pathogens and assess antibiotic susceptibility, usually take 2-4 days. Early and accurate antibiotic prescription is vital in sepsis to mitigate mortality and antibiotic resistance. This study aimed to reduce the wait time for sepsis diagnosis by employing shorter blood culture incubation times for BD BACTEC™ bottles using standard laboratory incubators, followed by real-time nanopore sequencing and data analysis. The method was tested on nine blood samples spiked with clinical isolates from the six most prevalent sepsis-causing pathogens. The results showed that pathogen identification was possible at as low as 102-104 CFU/mL, achieved after just 2 h of incubation and within 40 min of nanopore sequencing. Moreover, all the antimicrobial resistance genes were identified at 103-107 CFU/mL, achieved after incubation for 5 h and only 10 min to 3 h of sequencing. Therefore, the total turnaround time from sample collection to the information required for an informed decision on the right antibiotic treatment was between 7 and 9 h. These results hold significant promise for better clinical management of sepsis compared with current culture-based methods.

No place like home? A test of the natal habitat-biased dispersal hypothesis in Scandinavian wolves

Natal dispersal is an important mechanism for the viability of populations. The influence of local conditions or experience gained in the natal habitat could improve fitness if dispersing individuals settle in an area with similar habitat characteristics. This process, defined as 'natal habitat-biased dispersal' (NHBD), has been used to explain distribution patterns in large carnivores, but actual studies evaluating it are rare. We tested whether grey wolf Canis lupus territory establishment was influenced by the habitat characteristics of the natal territory using the long-term monitoring of the Scandinavian wolf population. We paired the locations of natal and established territories, accounted for available habitats along the dispersing route, and compared their habitat characteristics for 271 wolves during 1998-2012. Wolves with the shortest dispersal distances established in natal-like habitat types more than expected by chance, whereas wolves that dispersed longer distances did not show NHBD. The pattern was consistent for male and female wolves, with females showing more NHBD than males. Chances to detect NHBD increased with the size of habitat defined as available. This highlights the importance of considering the biological characteristics of the studied species when defining habitat availability. Our methodological approach can prove useful to inform conservation and management to identify habitats to be selected by reintroduced or naturally expanding populations.

Den site selection by male brown bears at the population's expansion front

Brown bears (Ursus arctos) spend about half of the year in winter dens. In order to preserve energy, bears may select denning locations that minimize temperature loss and human disturbance. In expanding animal populations, demographic structure and individual behavior at the expansion front can differ from core areas. We conducted a non-invasive study of male brown bear den sites at the male-biased, low-density western expansion front of the Scandinavian brown bear population, comparing den locations to the available habitat. Compared to the higher-density population core in which intraspecific avoidance may affect den site selection of subordinate bears, we expected resource competition in the periphery to be low, and all bears to be able to select optimal den sites. In addition, bears in the periphery had access to free-ranging domestic sheep during summer. We found that males in the periphery denned on high-elevation slopes, probably providing good drainage, longer periods of consistent, insulating snow cover and fewer melting-freezing events. Forests were the principal denning habitat and no dens were found in alpine areas. The Scandinavian brown bears have a history of intense harvest, including culling at the den. This may have exerted a selection pressure to avoid denning in open alpine habitat which compared to forests provide little cover. The bears denned away from main roads and in steep, rugged terrain, probably limiting human access. The odds for finding a bear den decreased with increasing distance to the population core where females could be found. Previous studies have documented directed movement of male brown bears from the male-biased population periphery toward the core areas during the mating season. In this way, denning males may be trading off between low resource competition and access to sheep in the low-density periphery, and mating opportunities in the higher-density population core.

Distribution of siderophore gene systems on a Vibrionaceae phylogeny: Database searches, phylogenetic analyses and evolutionary perspectives

Siderophores are small molecules synthesized and secreted by bacteria and fungi to scavenge iron. Extracellular ferri-siderohores are recognized by cognate receptors on the cell surface for transport over membranes. Several siderophore systems from Vibrionaceae representatives are known and well understood, e.g., the molecular structure of the siderophore, the biosynthesis gene cluster and pathway, and the gene expression pattern. Less is known about how these systems are distributed among the ~140 Vibrionaceae species, and which evolutionary processes contributed to the present-day distribution. In this work, we compiled existing knowledge on siderophore biosynthesis systems and siderophore receptors from Vibrionaceae and used phylogenetic analyses to investigate their organization, distribution, origin and evolution. Through literature searches, we identified nine different siderophore biosynthesis systems and thirteen siderophore receptors in Vibrionaceae. Homologs were identified by BLAST searches, and the results were mapped onto a Vibrionaceae phylogeny. We identified 81 biosynthetic systems distributed in 45 Vibrionaceae species and 16 unclassified Vibrionaceae strains, and 409 receptors in 89 Vibrionaceae species and 49 unclassified Vibrionaceae strains. The majority of taxa are associated with at least one type of siderophore biosynthesis system, some (e.g., aerobactin and vibrioferrin) of which are widely distributed in the family, whereas others (i.e., bisucaberin and vibriobactin) are found in one lineage. Cognate receptors are found more widespread. Phylogenetic analysis of three siderophore systems (piscibactin, vibrioferrin and aerobactin) show that their present-day distribution can be explained by an old insertion into Vibrionaceae, followed mainly by stable vertical evolution and extensive loss, and some cases of horizontal gene transfers. The present work provides an up to date overview of the distribution of siderophore-based iron acquisition systems in Vibrionaceae, and presents phylogenetic analysis of these systems. Our results suggest that the present-day distribution is a result of several evolutionary processes, such as old and new gene acquisitions, gene loss, and both vertical and horizontal gene transfers.