No / The role of mutations in genes associated with phenotypic resistance to bedaquiline (BDQ) and delamanid (DLM) in Mycobacterium tuberculosis complex (MTBc) strains is poorly characterized. A clear understanding of the genetic variants' role is crucial to guide the development of molecular-based drug susceptibility testing (DST). In this work, we analyzed all mutations in candidate genomic regions associated with BDQ- and DLM-resistant phenotypes using a whole-genome sequencing (WGS) data set from a collection of 4,795 MTBc clinical isolates from six countries with a high burden of tuberculosis (TB). From WGS analysis, we identified 61 and 163 unique mutations in genomic regions potentially involved in BDQ- and DLM-resistant phenotypes, respectively. Importantly, all strains were isolated from patients who likely have never been exposed to these medicines. To characterize the role of mutations, we calculated the free energy variation upon mutations in the available protein structures of Ddn (DLM), Fgd1 (DLM), and Rv0678 (BDQ) and performed MIC assays on a subset of MTBc strains carrying mutations to assess their phenotypic effect. The combination of structural and phenotypic data allowed for cataloguing the mutations clearly associated with resistance to BDQ (n = 4) and DLM (n = 35), only two of which were previously described, as well as about a hundred genetic variants without any correlation with resistance. Significantly, these results show that both BDQ and DLM resistance-related mutations are diverse and distributed across the entire region of each gene target, which is of critical importance for the development of comprehensive molecular diagnostic tools.

La tuberculose est la neuvième cause de mortalité dans le monde. Les progrès pour contrôler cette maladies ont été ralentis par plusieurs facteurs, notamment la diffusion de souches de tuberculose à bacilles multirésistants aux antibiotiques (MDR). Le traitement de la tuberculose MDR est long, toxique, et souvent inefficace. Après plus de 40 ans de pénurie, deux nouveaux médicaments ont été approuvé pour le traitement de la tuberculose MDR : la bédaquiline et le delamanide. Globalement, il y eu des délais considérables dans l'introduction de ces nouveaux médicaments dans la pratique clinique, comme souligné par le faible nombre d'études présentes en littérature. Les études présentés dans ce travail ont décrit des cohortes de patients atteints de tuberculose MDR et traités par bédaquiline et/ou delamanide en France, en montrant d'abord une tolérance satisfaisante, même pour des durées prolongées de traitement et pour l'association des deux nouveaux médicaments. En outre, l'efficacité microbiologique de la bédaquiline apparait comparable à celle des fluoroquinolones, la classe d'antibiotiques la plus efficace pour la tuberculose MDR. Dans une autre étude, l'on a mis en évidence l'apparition rapide de la résistance à la bédaquiline en France, ce qui était inattendu, en particulier pour les cas de résistance primaire. Malgré les limitations méthodologiques associées aux études observationnelles et rétrospectives, ce travail a permis d'augmenter les connaissances sur la tolérance et l'efficacité du traitement avec les nouvelles molécules pour la tuberculose MDR. Une suite des recherches est envisagée avec la mise en place d'une cohorte national prospective des cas MDR. / Tuberculosis is the ninth leading cause of death worldwide. Progress in controlling this disease has been slowed down by multiple factors, including the emergence of multidrug-resistant (MDR) strains. MDR tuberculosis treatment is long, toxic, and often not effective. After more than 40 years of draught, two new drugs have been approved for the treatment of MDR tuberculosis: bedaquiline and delamanid. Globally, there have been considerable delays in the introduction of these new drugs in clinical practice, as shown by the little number of studies which are available in literature. The studies described in this manuscript have described cohorts of patients affected by MDR tuberculosis and treated with bedaquiline and/or delamanid in France: the main finding was a satisfying safety, even for prolonged treatment durations and for the association of the two new drugs. In addition, the microbiological efficacy of bedaquiline was shown to be comparable to the one of the fluoroquinolones, the most effective antibiotic class to treat MDR tuberculosis. In another study, we have shown the rapid appearance of bedaquiline resistance in France, an unexpected finding in particular for the cases of primary resistance. Notwithstanding the methodologic weaknesses associated with observational and retrospective studies, this work has increased the evidence on safety and efficacy of MDR tuberculosis treatment with the new drugs. The next step will be represented by the establishment of a prospective national research cohort of MDR tuberculosis cases.

Introduktion: tuberkulos går tillbaka ända till stenåldern och det var inte förrän på 1800-talet som Robert Koch upptäckte att det var Mycobacterium tuberculosis (M. tuberculosis) som orsakade tuberkulos. Idag drabbas cirka 10 miljoner årligen av tuberkulos och år 2017 uppstod cirka 600 000 nya fall av multiresistent tuberkulos (MDR-TB). M. tuberculosis är en bakterie med en unik cellvägg bestående av en hög koncentration av mykolsyra. Bakteriens fettrika cellvägg kan i sin tur fungera som en barriär mot läkemedel som behandlar tuberkulos, vilket gör sjukdomen svårbehandlad. Tuberkulos smittar via små luftburna droppar men det är bara cirka 10 % av alla som smittas som drabbas av sjukdomssymtom. Tuberkulos diagnosticeras vanligen med hjälp av sputumprover från de djupa luftvägarna och för att finna resistens för läkemedel görs bakterieodlingar i flytande eller fast medium. Tuberkulos behandlas med en kombination av flera olika läkemedel. Standardbehandlingen (HRZE) som används vid behandling av tuberkulos består av isoniazid, rifampicin, pyrazinamid och etambutol. Vid en felaktig eller ofullständig behandling med dessa läkemedel kan bakterien utveckla resistens och MDR-TB kan uppstå.  Vid MDR-TB är patienten vanligtvis resistent mot isoniazid och rifampicin vilket gör sjukdomen svår att behandla och en annan kombination av läkemedel behövs. Bedaquiline, delamanid och pretomanid är nyutvecklade läkemedel som förhoppningsvis ska kunna användas hos patienter med MDR-TB. Syfte: syftet med arbetet var att undersöka effekten och potentiella risker med bedaquiline, delamanid och pretomanid vid behandling av MDR-TB. Metod: artiklar till litteraturstudien erhölls från databaserna PubMed och ClinicalTrials där totalt 7 artiklar valdes ut för att granska effekten samt risken med bedaquiline, delamanid och pretomanid hos patienter med MDR-TB. Resultat: det erhållna resultatet från artiklarna erhölls genom att framförallt analysera den primära utkomsten. Alla artiklar tyder på att bedaquiline, delamanid samt pretomanid har en god effektiv baktericid effekt på M. tuberculosis och kan möjligtvis förkorta behandlingsperioden. Men alla läkemedel gav även ett flertal biverkningar så som, huvudvärk, illamående, yrsel, hyperurikemi och ett förlängt QT-intervall. Men biverkningarna klassades som milda till moderata. Diskussion: många biverkningar uppstod i studierna och endast ett fåtal deltagare deltog. Däremot observerads det att dessa nya kombinationer kan även minska utvecklingen av ytterligare resistens för läkemedel. Trots vissa avvikelser i studierna kan delamanid, bedaquiline och pretomanid vara nya alternativa behandlingar för MDR-TB. Men fler studier med en större studiepopulation behöver utföras för att säkerställa säkerheten samt effektiviteten av samtliga läkemedel. Men samtliga läkemedel visar lovande resultat i nuvarande studier för den framtida kampen mot MDR-TB. / Archeological findings of tuberculosis can be found way back to the Stone Age but it wasn’t before the 18th century that Robert Koch discovered that it was Mycobacterium tuberculosis (M. tuberculosis) who caused the disease tuberculosis. Current data indicates that approximately 10 million people are infected with tuberculosis each year and 600 000 new cases of multidrug resistance tuberculosis (MDR-TB) was observed in 2017.  Tuberculosis is a bacterium with a unique cell wall consisting of a high concentration of mycolic acid. The fatty cell wall of the bacteria can act as a barrier against antituberculotic drugs, making the disease difficult to treat. Tuberculosis is a disease who can be spread among people via airborne droplets but only about 10 % of all people who are infected are affected by disease symptoms.  Tuberculosis is usually diagnosed by spot-sputum samples from deep within the airways. Resistance to antituberculotic drugs are detected by culture growth of the bacteria on either a liquid or solid medium. Tuberculosis is treated with a combination of several different drugs such as isoniazide, rifampicine, pyrazinamide and ethambutol. Also called HRZE and is a standard regimen for tuberculosis. If treatment occurs incorrectly or is incomplete the bacteria can develop resistance to these drugs and MDR-TB can emerge. Patients with MDR-TB is usually resistant to either or both isoniazide and rifampicine which makes the disease difficult to treat and another combination of drugs is needed. Bedaquiline, delamanide and pretomanide are newly developed drugs that can hopefully be used in the treatment of MDR-TB. The purpose of the thesis was to analyze the efficacy and potential risks with bedaquiline, delamanide and pretomanide in the treatment of MDR-TB. The articles for this literature study were obtained from the two databases PubMed and ClinicalTrials. A total of 7 articles were chosen to analyze the efficacy and potential risks with bedaquiline, delamanide and pretomanid used in treatment in patients with MDR-TB. The result obtained from the articles was obtained by primarily analyzing the primary outcome from each article. All articles suggest that bedaquiline, delamanide and pretomanide have a favorable bactericidal efficacy against M. tuberculosis and may shorten the treatment period. However, all of the studied drugs produced numerous side effects such as headaches, nausea, dizziness, hyperuricemia and an extended QT interval. Although all the side effects that occurred in the studies were classified as mild to moderate. Many side effects occurred in the studies and only a few participants participated in each study. However, it was observed that the new combinations with bedaquiline, delamanide and pretomanide can reduce the development of additional drug resistance. Despite some deviations in the studies, bedaquiline, delamanide and pretomanid may be new alternative treatments for MDR-TB. But more studies with a larger study population is needed to ensure the safety profile and efficacy of all of the drugs above. However, bedaquiline, delamanide and pretomanid show promising results in current studies for the future fight against MDR-TB.