Tracing <i>Mycobacterium tuberculosi</i>s transmission by whole genome sequencing in a high incidence setting:A retrospective population-based study in East Greenland

In East Greenland, a dramatic increase of tuberculosis (TB) incidence has been observed in recent years. Classical genotyping suggests a genetically similar Mycobacterium tuberculosis (Mtb) strain population as cause, however, precise transmission patterns are unclear. We performed whole genome sequencing (WGS) of Mtb isolates from 98% of culture-positive TB cases through 21 years (n = 182) which revealed four genomic clusters of the Euro-American lineage (mainly sub-lineage 4.8 (n = 134)). The time to the most recent common ancestor of lineage 4.8 strains was found to be 100 years. This sub-lineage further diversified in the 1970s, and massively expanded in the 1990s, a period of lowered TB awareness in Greenland. Despite the low genetic strain diversity, WGS data revealed several recent short-term transmission events in line with the increasing incidence in the region. Thus, the isolated setting and the uniformity of circulating Mtb strains indicated that the majority of East Greenlandic TB cases originated from one or few strains introduced within the last century. Thereby, the study shows the consequences of even short interruptions in TB control efforts in previously TB high incidence areas and demonstrates the potential role of WGS in detecting ongoing micro epidemics, thus guiding public health efforts in the future

Sub-Surface Geology, Petrology and Hydrothermal Alteration of the Menengai Geothermal Field, Kenya: Case Study of Wells MW-02, MW-04, MW-06 and MW-07

ABSTRACT Menengai is a trachytic central caldera volcano in the Kenya rift valley with abundant high-temperature geothermal activity. The field is currently in its initial stages of development for geothermal energy in Kenya following Olkaria and Eburru fields. Regional surface geology of Menengai is largely composed of late Quaternary volcanics. The building of a 200,000 year old trachyte shield volcano was followed by piecemeal subsidence through two paroxysmal eruptions 29,000 and 8,000 B.P to produce a caldera of about 84 km 2 in size that has subsequently been largely filled by recent trachyte lavas. Twenty four exploration and production wells, some of them hotter than 390 o C, have been drilled in Menengai caldera by Geothermal Development Company (GDC). The aim of this study is to reveal the evolutionary history of the Menengai volcano and to describe its igneous lithostratigraphy and secondary mineralization in order to characterize hydrothermal processes within the field. Analytical methods used include binocular microscope analysis, petrographic analysis, X-ray Diffractometer analysis and inductively coupled plasma (ICP-ES) analysis. Studies of drill cutting from wells MW-02, MW-04, MW-06 and MW-07 have provided information on the stratigraphy, hydrothermal alteration and present state of the geothermal system. Petrochemistry of these wells revealed subsurface lithostratigraphy that includes, consolidated pyroclastic tuff, pyroclastics, basalt, trachybasalt, phonolite, trachy-andesite, syenitic intrusive units, while trachyte constitutes over 90% of the total. Reaction of geothermal fluids with the host rocks has resulted in a progressive hydrothermal alteration with increasing depth. A number of studies have recognized characteristic alteration zones at Menengai based on distribution of key index alteration minerals. These zones, in order of increasing alteration grade, are zeolitesmectite, quartz-illite and wollastonite-actinolite zone. The study reveals that Menengai evolved a complex compositional variation with time as a result of magma fractionation, possibly in combination with crustal contamination and hydrothermal activities en route to the surface. The study defines the geology of the Menengai into, post-caldera, syn-caldera, upper and lower pre-caldera volcanics. Petrography and mineral chemistry of the basaltic and trachytic end members of the Menengai rocks indicate that two or more distinct magma types were involved in the formation of the volcano. This study reveals that magma exists beneath the caldera floor, at depth slightly over 2000 m within the summit area. This is evidenced by fresh glassy, quenched cuttings at these depths in wells MW-04 and MW-06. This implies that the thickness of the geothermal reservoir above the magma-containing domain may be no more than 1.5 km from the hydrostatic surface at ~400 m

Mycobacterium tuberculosis outbreak strain of Danish origin spreading at worrying rates among Greenland-born persons in Denmark and Greenland

Transmission of Mycobacterium tuberculosis continues at high rates among Greenland-born persons in Greenland and Denmark, with 203 and 450 notified cases per 10(5) population, respectively, in the year 2010. Here, we document that the predominant M. tuberculosis outbreak strain C2/1112-15 of Danish origin has been transmitted to Greenland-born persons in Denmark and subsequently to Greenland, where it is spreading at worrying rates and adding to the already heavy tuberculosis burden in this population group. It is now clear that the C2/1112-15 strain is able to gain new territories using a new population group as the “vehicle.” Thus, it might have the ability to spread even further, considering the potential clinical consequences of strain diversity such as that seen in the widely spread Beijing genotype. The introduction of the predominant M. tuberculosis outbreak strain C2/1112-15 into the Arctic circumpolar region is a worrying tendency which deserves attention. We need to monitor whether this strain already has, or will, spread to other countries

Direct DNA extraction from Mycobacterium tuberculosis frozen stocks as a reculture-independent approach to whole-genome sequencing

Culturing before DNA extraction represents a major time-consuming step in whole-genome sequencing of slow-growing bacteria, such as Mycobacterium tuberculosis. We report a workflow to extract DNA from frozen isolates without reculturing. Prepared libraries and sequence data were comparable with results from recultured aliquots of the same stocks