Unraveling Mycobacterium tuberculosis genomic diversity and evolution in Lisbon,Portugal, a highly drug resistant setting

Background

Multidrug- (MDR) and extensively drug resistant (XDR) tuberculosis (TB) presents a challenge to disease control and elimination goals. In Lisbon, Portugal, specific and successful XDR-TB strains have been found in circulation for almost two decades.

Results

In the present study we have genotyped and sequenced the genomes of 56 Mycobacterium tuberculosis isolates recovered mostly from Lisbon. The genotyping data revealed three major clusters associated with MDR-TB, two of which are associated with XDR-TB. Whilst the genomic data contributed to elucidate the phylogenetic positioning of circulating MDR-TB strains, showing a high predominance of a single SNP cluster group 5. Furthermore, a genome-wide phylogeny analysis from these strains, together with 19 publicly available genomes of Mycobacterium tuberculosis clinical isolates, revealed two major clades responsible for M/XDR-TB in the region: Lisboa3 and Q1 (LAM).The data presented by this study yielded insights on microevolution and identification of novel compensatory mutations associated with rifampicin resistance in rpoB and rpoC. The screening for other structural variations revealed putative clade-defining variants. One deletion in PPE41, found among Lisboa3 isolates, is proposed to contribute to immune evasion and as a selective advantage. Insertion sequence (IS) mapping has also demonstrated the role of IS6110 as a major driver in mycobacterial evolution by affecting gene integrity and regulation.

Conclusions

Globally, this study contributes with novel genome-wide phylogenetic data and has led to the identification of new genomic variants that support the notion of a growing genomic diversity facing both setting and host adaptation.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-991) contains supplementary material, which is available to authorized users.     

Mechanisms driving the specificity of a myrmecophyte–ant association

In the understory of pristine Guianese forests, the myrmecophyte Hirtella physophora almost exclusively shelters colonies of the plant-ant Allomerus decemarticulatus in its leaf pouches. We experimentally tested three non-mutually exclusive hypotheses concerning phenomena that can determine the species specificity of this association throughout the foundation stage of the colonies: (1) interspecific competition results in the overwhelming presence of A. decemarticulatus queens or incipient colonies; (2) exclusion filters prevent other ant species from entering the leaf pouches; and (3) host-recognition influences the choice of founding queens, especially A. decemarticulatus . Neither interspecific competition, nor the purported exclusion filters that we examined play a major role in maintaining the specificity of this association. Unexpectedly, the plant trichomes lining the domatia appear to serve as construction material during claustral foundation rather than as a filter. Finally, A. decemarticulatus queens are able to identify their host plant from a distance through chemical and/or visual cues, which is rarely demonstrated in studies on obligatory ant–plant associations. We discuss the possibility that this specific host-recognition ability could participate in shaping a compartmentalized plant-ant community where direct competition between ant symbionts is limited.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 97 , 90–97.     

The Iberian Peninsula: ancient history of a hot spot of mite harvestmen (Arachnida: Opiliones: Cyphophthalmi: Sironidae) diversity

The Iberian Peninsula represents a hot spot of cyphophthalmid (mite harvestman) disparity, with four of the eight genera currently recognized in the family Sironidae represented in the region – a generic diversity and morphological disparity not found in any other region of the World so far. From these, two genera (Iberosiro and Odontosiro) are monotypic, and are restricted to the western side of the peninsula. Parasiro is restricted to the north‐east region, from the Catalonian Coastal Ranges and both sides of the Eastern Pyrenees, in areas where the annual rainfall surpasses 1000 mm, and mostly restricted to areas with Paleozoic and Variscan rocks, with other species of the genus extending to Corsica, Sardinia, and the Italian Peninsula. A second species of the genus Paramiopsalis, Paramiopsalis eduardoi sp. nov. from Fragas do Eume, is described here along with a re‐diagnosis of the genus. Paramiopsalis species, together with Odontosiro, inhabit the north‐west corner of the Iberian Peninsula, an area with some of the highest recorded annual rainfall, and with Paleozoic rocks from the Iberian Massif or Variscan granitoid rocks. A phylogenetic analysis of the members of the family Sironidae using four molecular markers, despite not including all of the Iberian genera, clearly shows the non‐monophyly of the Iberian Cyphophthalmi, indicating that the Iberian Peninsula is home to multiple ancient lineages of mite harvestmen. The two Paramiopsalis species form a sister clade to the Balkan genus Cyphophthalmus, whereas Parasiro constitutes the first lineage of the sironids represented.     

Visualizing Cell-to-cell Transfer of HIV using Fluorescent Clones of HIV and Live Confocal Microscopy

By fusing the green fluorescent protein to their favorite proteins, biologists now have the ability to study living complex cellular processes using fluorescence video microscopy. To track the movements of the human immunodeficiency virus core protein during cell-to-cell transmission of human immunodeficiency virus, we have GFP-tagged the Gag protein in the context of an infectious molecular clone of HIV, called HIV Gag-iGFP. We study this viral clone using video confocal microscopy. In the following visualized experiment, we transfect a human T cell line with HIV Gag-iGFP, and we use fluorescently labeled uninfected CD4+ T cells to serve as target cells for the virus. Using the different fluorescent labels we can readily follow viral production and transport across intercellular structures called virological synapses. Simple gas permeable imaging chambers allow us to observe synapses with live confocal microscopy from minutes to days. These approaches can be used to track viral proteins as they move in from one cell to the next.Download video file.^{(80M, mov)}     

Developing a realistic sexual network model of chlamydia transmission in Britain

Background  

A national chlamydia screening programme is currently being rolled out in the UK and other countries. However, much of the epidemiology remains poorly understood. In this paper we present a stochastic, individual based, dynamic sexual network model of chlamydia transmission and its parameterisation. Mathematical models provide a theoretical framework for understanding the key epidemiological features of chlamydia: sexual behaviour, health care seeking and transmission dynamics.     

High risk of early sub-therapeutic penicillin concentrations after intramuscular benzathine penicillin G injections in Ethiopian children and adults with rheumatic heart disease

IntroductionIntramuscular benzathine penicillin G (BPG) injections are a cornerstone of secondary prophylaxis to prevent acute rheumatic fever (ARF) and rheumatic heart disease (RHD). Uncertainties regarding inter-ethnic and preparation variability, and target exposure profiles of BPG injection are key knowledge gaps for RHD control.MethodsTo evaluate BPG pharmacokinetics (PK) in patients receiving 4-weekly doses in Ethiopia, we conducted a prospective cohort study of ARF/RHD patients attending cardiology outpatient clinics. Serum samples were collected weekly for one month after injection and assayed with a liquid chromatography-mass spectroscopy assay. Concentration-time datasets for BPG were analyzed by nonlinear mixed effects modelling using NONMEM.ResultsA total of 190 penicillin concentration samples from 74 patients were included in the final PK model. The median age, weight, BMI was 21 years, 47 kg and 18 kg/m², respectively. When compared with estimates derived from Indigenous Australian patients, the estimate for median (95% confidence interval) volume of distribution (V/F) was lower (54.8 [43.9–66.3] l.70kg^-1) whilst the absorption half-life (t_1/2-abs2) was longer (12.0 [8.75–17.7] days). The median (IQR) percentage of time where the concentrations remained above 20 ng/mL and 10 ng/mL within the 28-day treatment cycle was 42.5% (27.5–60) and 73% (58.5–99), respectively.ConclusionsThe majority of Ethiopian patients receiving BPG as secondary prophylaxis to prevent RHD do not attain target concentrations for more than two weeks during each 4-weekly injection cycle, highlighting the limitations of current BPG strategies. Between-population variation, together with PK differences between different preparations may be important considerations for ARF/RHD control programs.     

Connectivity counts: disentangling effects of vegetation structure elements on the searching movement of a parasitoid

1. A heterogeneous habitat structure can have a profound impact on foraging carnivorous arthropods. In the present study, we examined which elements of complex vegetation structure influence the searching movement of a parasitoid model organism. 2. Previous field work showed that tall and dense vegetation reduces the parasitism success of the eulophid egg parasitoid Oomyzus galerucivorus while the probability of host egg deposition increased close to plant tips. 3. In laboratory bioassays, dried grass stems were arranged according to the natural situation in different setups. The wasps' walking time on stems increased with increasing stem height and density. High stem density decreased the walking time of the parasitoids on the ground and an increased stem height reduced the propensity to fly to the ground. Connectivity had a minor positive effect on the number of stem contacts, but considerably reduced the number of wasps reaching the upper part of grass stems by two‐thirds. 4. Thus, although enhanced vegetation complexity enhances walking activity of the parasitoids in the vegetation, laying eggs at the tip of long grass stems in dense vegetation can be an adaptive strategy for the host, as it maximises the number of connections between plant parts to cross by parasitoids before reaching the host. The connection points disorient the wasps, which lose time, reverse their direction or fly away.