Global phylogenetic analysis of Escherichia coli and plasmids carrying the mcr-1 gene indicates bacterial diversity but plasmid restriction

To understand the dynamics behind the worldwide spread of the mcr-1 gene, we determined the population structure of Escherichia coli and of mobile genetic elements (MGEs) carrying the mcr-1 gene. After a systematic review of the literature we included 65 E. coli whole genome sequences (WGS), adding 6 recently sequenced travel related isolates, and 312 MLST profiles. We included 219 MGEs described in 7 Enterobacteriaceae species isolated from human, animal and environmental samples. Despite a high overall diversity, 2 lineages were observed in the E. coli population that may function as reservoirs of the mcr-1 gene, the largest of which was linked to ST10, a sequence type known for its ubiquity in human faecal samples and in food samples. No genotypic clustering by geographical origin or isolation source was observed. Amongst a total of 13 plasmid incompatibility types, the IncI2, IncX4 and IncHI2 plasmids accounted for more than 90% of MGEs carrying the mcr-1 gene. We observed significant geographical clustering with regional spread of IncHI2 plasmids in Europe and IncI2 in Asia. These findings point towards promiscuous spread of the mcr-1 gene by efficient horizontal gene transfer dominated by a limited number of plasmid incompatibility types

Ice-dammed lake and ice-margin evolution during the Holocene in the Kangerlussuaq area of west Greenland

There is a lack of detailed information on the Holocene evolution of the west Greenland ice margin, not least because it was farther inland than at present and thus at present is covered by ice. Suggestions have been put forward, both of relatively quick ice-margin retreat and of relatively stable ice-margin positions. This study presents the first exploitation of sediments from an ice-dammed basin. Sediment that is rich in organic material records a period of time sufficient for vegetation to thrive; thus, without a lake and with a distal and diminished ice mass relative to the present. In contrast, sediment composed of suspension-settling deposits and with drop stones records an ice-dammed lake and a proximal calving ice-margin. Overall, we evidence relatively coarse-grained glacifluvial sedimentation predominantly from an ice-marginal delta and/or a proglacial, braided river soon after the early Holocene deglaciation of this area. Subsequent mid-Holocene aeolian activity deposited leaves, some vegetation (roots) developed in the basin, and ponding of water formed organic-rich “gyttja” sediments and thin layers of peat. The lake then became ice marginal, and ice advances are interpreted to have occurred at approximately 4000 cal. yr BP, and between 2776 ± 26 cal. yr BP and 2440 ± 45 cal. yr BP. The Little Ice Age ice-margin advance at Russell Glacier apparently reached its maximum extent after 147 ± 39 cal. yr BP, whereas at Isunnguata Sermia the maximum could have been as early as 245 ± 26 cal. yr BP. Given that ice-marginal lakes are becoming globally ubiquitous, improved resolution and new geological data on lake and ice-margin dynamics and interactions, such as ice-dammed lake-basin sediments, will be important for numerical models for assessing past and future ice-mass evolution

Author Correction: Global phylogenetic analysis of Escherichia coli and plasmids carrying the mcr-1 gene indicates bacterial diversity but plasmid restriction (Scientific Reports, (2017), 7, 1, (15364), 10.1038/s41598-017-15539-7)

In the original version of this Article, Martin C. J. Bootsma, Perry J. van Genderen, Abraham Goorhuis, Martin Grobusch, Nicky Molhoek, Astrid M. L. Oude Lashof, Ellen E. Stobberingh & Henri A. Verbrugh were incorrectly listed as the COMBAT consortium. This error has now been corrected in the HTML and PDF versions of the Article, and in the accompanying supplementary material

Toward Male Individualization with Rapidly Mutating Y-Chromosomal Short Tandem Repeats

Relevant for various areas of human genetics, Y-chromosomal short tandem repeats (Y-STRs) are commonly used for testing close paternal relationships among individuals and populations, and for male lineage identification. However, even the widely used 17-loci Yfiler set cannot resolve individuals and populations completely. Here, 52 centers generated quality-controlled data of 13 rapidly mutating (RM) Y-STRs in 14,644 related and unrelated males from 111 worldwide populations. Strikingly, >99% of the 12,272 unrelated males were completely individualized. Haplotype diversity was extremely high (global: 0.9999985, regional: 0.99836-0.9999988). Haplotype sharing between populations was almost absent except for six (0.05%) of the 12,156 haplotypes. Haplotype sharing within populations was generally rare (0.8% nonunique haplotypes), significantly lower in urban (0.9%) than rural (2.1%) and highest in endogamous groups (14.3%). Analysi

Toward Male Individualization with Rapidly Mutating Y-Chromosomal Short Tandem Repeats

Relevant for various areas of human genetics, Y-chromosomal short tandem repeats (Y-STRs) are com- monly used for testing close paternal relationships among individuals and populations, and for male lineage iden- tification. However, even the widely used 17-loci Yfiler set cannot resolve individuals and populations completely. Here, 52 centers generated quality-controlled data of 13 rapidly mutating (RM) Y-STRs in 14,644 related and unrelated males from 111 worldwide populations. Strik- ingly, >99% of the 12,272 unrelated males were com- pletely individualized. Haplotype diversity was extremely high (global: 0.9999985, regional: 0.99836\u20130.9999988). Haplotype sharing between populations was almost ab- sent except for six (0.05%) of the 12,156 haplotypes. Haplotype sharing within populations was generally rare (0.8% nonunique haplotypes), significantly lower in ur- ban (0.9%) than rural (2.1%) and highest in endogamous groups (14.3%). Analysis of molecular variance revealed 99.98% of variation within populations, 0.018% among populations within groups, and 0.002% among groups. Of the 2,372 newly and 156 previously typed male relative pairs,29% were differentiated including 27% of the 2,378 father\u2013son pairs. Relative to Yfiler, haplotype diversity was increased in 86% of the populations tested and over- all male relative differentiation was raised by 23.5%. Our study demonstrates the value of RM Y-STRs in identifying and separating unrelated and related males and provides a reference database