Whole genome sequencing for M/XDR tuberculosis surveillance and for resistance testing

Whole genome sequencing (WGS) can help to relate Mycobacterium tuberculosis genomes to one another to assess genetic relatedness and infer the likelihood of transmission between cases. The same sequence data are now increasingly being used to predict drug resistance and susceptibility. Controlling the spread of tuberculosis and providing patients with the correct treatment are central to the World Health Organization's target to 'End TB' by 2035, for which the global prevalence of drug-resistant tuberculosis remains one of the main obstacles to success. So far, WGS has been applied largely to drug-susceptible strains for the purposes of understanding transmission, leaving a number of analytical considerations before transferring what has been learnt from drug-susceptible disease to drug-resistant tuberculosis. We discuss these potential problems here, alongside some of the challenges to characterizing the Mycobacterium tuberculosis 'resistome'-the optimal knowledge-base required for WGS-based assays to successfully direct individualized treatment regimens through the prediction of drug resistance and susceptibility in the future.

Tracing Mycobacterium tuberculosis 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.

Perspectives for personalized therapy for patients with multidrug-resistant tuberculosis

According to the World Health Organization (WHO), tuberculosis is the leading cause of death attributed to a single microbial pathogen worldwide. In addition to the large number of patients affected by tuberculosis, the emergence of Mycobacterium tuberculosis drug-resistance is complicating tuberculosis control in many high-burden countries. During the past 5 years, the global number of patients identified with multidrug-resistant tuberculosis (MDR-TB), defined as bacillary resistance at least against rifampicin and isoniazid, the two most active drugs in a treatment regimen, has increased by more than 20% annually. Today we experience a historical peak in the number of patients affected by MDR-TB. The management of MDR-TB is characterized by delayed diagnosis, uncertainty of the extent of bacillary drug-resistance, imprecise standardized drug regimens and dosages, very long duration of therapy and high frequency of adverse events which all translate into a poor prognosis for many of the affected patients. Major scientific and technological advances in recent years provide new perspectives through treatment regimens tailor-made to individual needs. Where available, such personalized treatment has major implications on the treatment outcomes of patients with MDR-TB. The challenge now is to bring these adances to those patients that need them most.

Isolation of rabbit pulmonary microvascular endothelial cells and characterization of their angiotensin converting enzyme activity

An in vitro model using cultured rabbit pulmonary endothelial cells of microvascular origin was developed to define the luminal surface membrane characteristics of microvascular endothelium. Endothelial cells were isolated from peripheral lung segments and sorted after preferential uptake of a fluorescent derivative, diiodoindocarbo cyanine acetylated-LDL. Cells were further characterized by demonstrating angiotensin converting enzyme (ACE) on their surface by means of indirect immunofluorescence. ACE activity and its pharmacologic modification were then studied as functional assays of cell activity. Hydrolysis of Benz-phe-ala-pro (BPAP), a synthetic substrate for ACE was saturable over a concentration range of 1 to 100 microns. Thus, BPAP hydrolysis in cultured microvascular endothelial cells behaves overall in a manner similar to that seen in large resistance vessels except that a portion of the hydrolysis is not inhibited by captopril, an ACE-specific inhibitor, indicating the presence of another protease capable of BPAP hydrolysis. Accordingly, this system can be used to compare ACE and other protease kinetics in microvessel cells with those of large vessel endothelium or perfused lungs.

In situ iodination of angiotensin-converting enzyme and other pulmonary endothelial membrane proteins

Biochemical responses of endothelial cells in culture to pharmacological or physiological stimuli are often extrapolated to define the behavior of the vascular endothelium in vivo. However, culture conditions cannot recreate the environment of endothelial cells in vivo. To compare cell functions in vivo and in vitro, we iodinated endothelial membrane proteins of both the perfused rabbit lung and cultured rabbit lung endothelial cells. Endothelial cell protein 125I-labeling in the perfused intact lung was catalyzed by lactoperoxidase and glucose oxidase immobilized on 3-10 microns polyacrylamide beads (Enzymobeads, Bio-Rad). Changes in 5-hydroxytryptamine uptake, angiotensin converting enzyme activity and perfusion pressure made before, during and/or after iodination were small, suggesting that the procedure does not grossly injury the lung. As confirmed by tissue autoradiography, iodination was confined to the vascular space. A subcellular "membrane" fraction of the whole homogenate was enriched for several iodinated proteins. Lectin binding further purified a library of putative iodinated endothelial membranes proteins, one of which was angiotensin-converting enzyme as shown by immunoprecipitation with goat anti-rabbit antibody to angiotensin-converting enzyme. Iodinated proteins of similar molecular weights were also isolated from cultured rabbit lung endothelium iodinated under the same conditions, thus confirming the endothelial lineage of proteins iodinated in the intact lung. We conclude that this technique labels endothelial surface proteins in the intact lung without causing observable tissue injury and thus should be valuable in the study of the physiology and pathophysiology of the vascular lining in vivo.

Endotoxin-induced exposure of pulmonary glycoproteins in an intact animal

A method has been developed to radioiodinate luminally disposed endothelial proteins in an in situ perfused lung system without causing obvious vascular changes. The spectrum of endothelial cell proteins labeled in control animals and those treated with endotoxin for 45 min were compared. No changes in gross tissue morphology or in the distribution of radiolabel (125I-s-SHPP) were detected in control or treated lungs. Lectin affinity purification was applied to a lung membrane fraction to isolate labeled proteins, which were in turn resolved by gel electrophoresis and autoradiography. Comparisons of gel autoradiographs from control and treated lungs identified eight glycoproteins, the labeling of which was enhanced in endotoxin-treated animals. A similar lectin affinity analysis of radiolabeled effluent blood cells from the lungs identified only two proteins, neither of which were consistently changed by endotoxin pretreatment. A glycoprotein response can, therefore, be measured at the pulmonary endothelial surface on endotoxin administration to the whole animal without causing obvious lung injury.