Mycobacterium tuberculosis (Mtb) is the pathogen causing tuberculosis (TB), a disease most often affecting the lung. 1.5 million people die annually due to TB, mainly in low-income countries. Usually considered a disease of the poor, also developed nations recently put TB back on their agenda, fueled by the HIV epidemic and the global emergence of drug-resistant Mtb strains. HIV-coinfection is a predisposing factor for TB, and infection with multi-drug resistant and extremely drug resistant strains significantly impedes and lengthens antibiotic treatment, and increases fatality. Mtb is transmitted from a sick individual via coughing, and resident macrophages are the first cells to encounter the bacterium upon inhalation. These cells phagocytose intruders and subject them to a range of destructive mechanisms, aiming at killing pathogens and protecting the host. Mtb, however, has evolved to cope with host pressures, and has developed mechanisms to submerge macrophage defenses. Among these, inhibition of phagosomal maturation and adaptation to the intracellular environment are important features. Mtb profoundly alters its phenotype inside host cells, characterized by altered metabolism and slower growth. These adaptations contribute to the ability of Mtb to remain dormant inside a host during latent TB infection, a state that can last for decades. According to recent estimates, one third of the world’s population is latently infected with Mtb, which represents a huge reservoir for active TB disease. Mtb is also intrinsically tolerant to many antibiotics, and adaptation to host pressures enhances tolerance to first-line TB drugs. Therefore, TB antibiotic therapy takes 6 to 9 months, and current treatment regimens involve a combination of several antibiotics. Patient noncompliance due to therapeutic side effects as well as insufficient penetration of drugs into TB lesions are reasons for treatment failure and can lead to the rise of drug-resistant populations. In view of the global spread of drug-resistant strains, new antibiotics and treatment strategies are urgently needed. In this thesis, we studied the interplay of the primary host cell of Mtb, human macrophages, and different Mtb phenotypes. A low-burden infection resulted in restriction of Mtb replication via phagolysosomal effectors and the maintenance of an inactive Mtb phenotype reminiscent of dormant bacteria. Macrophages remained viable for up to 14 days, and profiling of secreted cytokines mirrored a silent infection. On the contrary, higher bacterial numbers inside macrophages could not be controlled by phagolysosomal functions, and intracellular Mtb shifted their phenotype towards active replication. Although slowed mycobacterial replication is believed to render Mtb tolerant to antibiotics, we did not observe such an effect. Mtb-induced macrophage cell death is dependent on ESAT6, a small mycobacterial virulence factor involved in host cell necrosis and the spread of the pathogen. Although well-studied, the fate of ESAT6 inside infected macrophages has been enigmatic. Cultivation of Mtb is commonly carried out in broth containing detergent to avoid aggregation of bacilli due to their waxy cell wall. Altering cultivation conditions revealed the presence of a mycobacterial capsule, and ESAT6 situated on the mycobacterial surface. Infection of macrophages with this encapsulated Mtb phenotype resulted in rapid ESAT6-dependent host cell death, and ESAT6 staining was lost as bacilli were ingested by macrophages. These observations could reflect the earlier reported integration of ESAT6 into membranes followed by membrane rupture and host cell death. In conclusion, the work presented in this thesis shows that the phenotype of Mtb has a significant impact on the struggle between the pathogen and human macrophages. Taking the bacterial phenotype into account can lead to the development of drugs active against altered bacterial populations that are not targeted by conventional antibiotics. Furthermore, deeper knowledge on Mtb virulence factors can inform the development of virulence blockers, a new class of antibiotics with great therapeutic potential.

<p><em>Streptococcus pneumoniae</em> (pneumokok) je&nbsp; jedan&nbsp; od&nbsp; vodećih&nbsp; uzroka morbiditeta i mortaliteta &scaron;irom sveta, kada su u pitanju infektivne bolesti. Pretežno izaziva infekcije gornjih respiratornih puteva (sinuzitis, otitis) i konjunktivitis. Vodeći je uzročnih vanbolničkih pneumonija, bakterijskog meningitisa i sepse. Lekovi izbora u terapiji pneumokoknih bolesti su beta laktamski antibiotici i makrolidi. Iako se makrolidni antibiotici uveliko koriste u lečenju pneumokoknih infekcija &scaron;irom sveta, porast rezistencije na makrolide&nbsp; bi&nbsp; mogao&nbsp; da&nbsp; kompromituje&nbsp; njihovu&nbsp; upotrebu. Rezistencija pneumokoka na makrolide je posredovana putem dva glavna mehanizma: modifikacija ciljnog mesta delovanja leka&nbsp; i aktivni efluks leka. Metilaciju 23S ribozomalne ribonukleinske kiseline (rRNK) obavlja enzim metilaza, čiju sintezu kodira<em> ermB</em> gen. Kod ovog tipa rezistencije dolazi do ukr&scaron;tene rezistencije na makrolide (M), linkozamide (L) i streptogramine B (Sb). Ovakav vid rezistencije se ispoljava kao MLS_b - fenotip i karakteri&scaron;e ga visok nivo rezistencije. Može se javiti kao konstitutivni (cMLS) i inducibilni (iMLS). Drugi mehanizam rezistencije na makrolide je aktivni efluks leka, kodiran od strane <em>mefA</em>&nbsp; gena. Efluks antibiotik a determini&scaron;e rezistenciju samo na 14-člane i 15-člane makrolide, bez ukr&scaron;tene rezistencije. Ispoljava se kao M-fenotip, a karakteri&scaron;e ga niži stepen rezistencije. Cilj ove studije je bio&nbsp; da&nbsp; se&nbsp; odredi u čestalost&nbsp; makrolidne&nbsp; rezistencije <em>Streptococcus pneumoniae</em> među invazivnim i neinvazivnim izolatima kod dece i odraslih, da se odrediti u čestalost korezistencije i multiple rezistencije kod makrolid rezistentnih sojeva&nbsp; <em>Streptococcus pneumoniae</em>, da se fenotipski odredi tip rezistencije na makrolide i da se ispita genska osnova makrolidne rezistencije (detektovati prisustvo <em>ermB</em> i <em>mefA</em> gena). Analizirani su podaci o 326 sojeva <em>Streptococcus pneumoniae</em> rezistentnih na makrolide (MRSP) sakupljenih &scaron;irom&nbsp; Srbije&nbsp; u&nbsp; periodu&nbsp; od&nbsp; januara&nbsp; 2010.&nbsp; do&nbsp; decembra&nbsp; 2012.&nbsp; godine. Sakupljeni&nbsp; MRSP&nbsp; izolati&nbsp; su&nbsp; transportovani&nbsp; u&nbsp; Nacionalnu&nbsp; referentnu laboratoriju za streptokok radi daljih ispitivanja. Identifikacija je vr&scaron;ena na osnovu mikroskopskih, kulturelnih i biohemijskih osobina. Konzervacija je vr&scaron;ena u moždano-srčanom bujonu sa 10% sadržajem glicerola na -80&deg;C. Dvostruki&nbsp; disk&nbsp; difuzioni&nbsp; test,&nbsp; kombinovani&nbsp; difuzion odilucioni&nbsp; test&nbsp; i automatizovani VITEK 2 sistem su kori&scaron;ćeni za određivanje fenotipova rezistencije na makrolide. Geni koji kodiraju rezistenciju na makrolide su detektovani PCR metodom. Ukupna rezistencija sojeva <em>S.pneumoniae</em> na makrolide u Srbiji je iznosila 34%. Sojevi <em>S.pneumoniae</em> rezistentni na makrolide su če&scaron;će bili izolovani kod dece (36%) u odnosu na odrasle (29%) osobe, i če&scaron;će su izolovani iz neinvazivnih (35,5%) u odnosu na invazivne (27,4%) materijale. Dominantan fenotip rezistencije na makrolide je bio MLS_b fenotip (78,5%). Konstitutivan MLS fenotip je bio zastupljen kod 73,9%, a inducibilan MLS kod 4,6% MRSP izolata. Potvrđena je udruženost <em>mefA</em>&nbsp; gena i M fenotipa; <em>ermB</em> gena i iMLS fenotipa, kao i <em>ermB</em> gena i cMLS fenotipa. Prisustvo oba ermB i mefA gena rezistencije je potvrđeno kod 43,9 % izolata. Svi izolati sa koji su imali oba gena rezistencije su ispoljili&nbsp; MLS_b fenotip.&nbsp; Istovremena&nbsp; neosetljivost&nbsp; na&nbsp; penicilin&nbsp; je bila zastupljena kod 16% MRSP sojeva. Visok nivo rezistencije na penicilin je imalo svega 5,8% MRSP izolata. Među MRSP sojevima je bio prisutan visok nivo&nbsp; rezistencije&nbsp; na&nbsp; tetraciklin&nbsp; (81,3%)&nbsp; i&nbsp; trimetoprim-sulfametoksazol (74,3%). Multirezistenti sojevi, koji su bili rezistentni na tetracikline i trimetoprim-sulfametoksazol su predstavljali dve trećine (66,1%) MRSP izolata.&nbsp; Zastupljenost&nbsp; udružene&nbsp; rezistencije&nbsp; MRSP&nbsp; na&nbsp; tetraciklin i trimetoprim-sulfametoksazol je bila veća kod sojeva sa MLS fenotipom (73,1%)&nbsp; u&nbsp; odnosu&nbsp; na&nbsp; sojeve&nbsp; sa&nbsp; M&nbsp; fenotipom&nbsp; (36,7%). Zastupljenost istovremene rezistencije na makrolide i druge antibiotike među kojima su penicilin, amoksicilin, cefotaksim, tetraciklin, trimetoprim-sulfametoksazol, kao&nbsp; i&nbsp; multirezistentnih&nbsp; sojeva&nbsp; je&nbsp; bila&nbsp; veća&nbsp; kod pedijatrijskih&nbsp; izolata pneumokoka&nbsp; u&nbsp; odnosu&nbsp; na&nbsp; sojeve&nbsp; dobijene&nbsp; kod&nbsp; odraslih.&nbsp; U čestalost istovremene rezistencije na makrolide i druge antibiotike među kojima su tetraciklin i ofloksacin je bila vi&scaron;e prisutna među neinvazivnim u odnosu na invazivne MRSP izolate. Invazivni MRSP izolati iz likvora su pokazivali veću rezistenciju na beta laktamske antibiotike u odnosu neinvazivne sojeve. MRSP sojevi su pokazali veoma visok nivo osetljivosti na levofloksacin (99,6), telitromicin (98,4%), cefotaksim (93,5%), i mipenem (97,3%). MRSP sojevi su u potpunosti bili osetljivi na vankomicin, linezolid, moksifloksacin, sparfloksacin, rifampicin&nbsp; i&nbsp; pristinamicin.&nbsp; Među&nbsp; invazivnim&nbsp; sojevima <em>S.pneumoniae</em> rezistentnim na makrolide je nađeno 12 različitih serotipova. Polovina izolata je pripadala serotipovima 19F (25%) i 14 (23%), dok su sledeći po učestalosti bili 6A (10,4%) i 23F (8,3%). Istovremena rezistencija na makrolide, penicilin, tetracikline i trimetoprim-sulfametoksazol je nađena kod serotipova 19F, 14 i 23F, dok su serotpovi 12F i 31 bili neosetljivi samo na makrolide. Na&scaron;e istraživanje predstavlja prvu detaljnu analizu fenotipskih i&nbsp; genotipskih&nbsp; osobina&nbsp; sojeva&nbsp; pneumokoka&nbsp; rezistentnih&nbsp; na&nbsp; makrolidne antibiotike u Srbiji. Dobijeni rezultati ukazuju na&nbsp; potrebu za aktivnim nadzorom nad pneumokoknim infekcijama u Srbiji.</p> / <p><em>Streptococcus pneumoniae</em> (pneumococcus) is one of the leading morbidity and&nbsp; mortality&nbsp; causes&nbsp; all&nbsp; over&nbsp; the&nbsp; world&nbsp; with&nbsp; respect&nbsp; to&nbsp; infectious&nbsp; diseases. <em>Streptococcus&nbsp; pneumoniae</em> is&nbsp; a&nbsp; leading&nbsp; cause&nbsp; of upper&nbsp; respiratory&nbsp; tract infections&nbsp; (&nbsp; sinusitis,&nbsp; otitis)&nbsp; and&nbsp; conjunctivitis. It&nbsp; is&nbsp; also&nbsp; the&nbsp; most&nbsp; common cause&nbsp; of&nbsp; community-acquired&nbsp; pneumonia, bacterial&nbsp; meningitis&nbsp; and&nbsp; sepsis. Beta lactam and&nbsp; macrolide antibiotics remained a first choice for empirical treatment of pneumococcal infections. Although macrolides are widely used for&nbsp;&nbsp; treatment&nbsp;&nbsp; of&nbsp;&nbsp; pneumococcal&nbsp;&nbsp; infections, an&nbsp;&nbsp; increase&nbsp;&nbsp; in&nbsp;&nbsp; macrolide resistance&nbsp; might compromise&nbsp; their use. Pneumococcal&nbsp; macrolide resistance is&nbsp; mediated&nbsp; by&nbsp; two&nbsp; major&nbsp; mechanisms:&nbsp; target&nbsp; site&nbsp; modification&nbsp; and&nbsp; active drug&nbsp; efflux.&nbsp; Methylation&nbsp; of&nbsp; the&nbsp; 23S&nbsp; ribosomal&nbsp; ribonucleic&nbsp; acid&nbsp; (rRNA)&nbsp; is performed&nbsp;&nbsp; by&nbsp;&nbsp; the&nbsp;&nbsp; enzyme&nbsp;&nbsp; methylase,&nbsp;&nbsp; encoded&nbsp;&nbsp; by&nbsp;&nbsp; the<em> ermB </em>gene. Modification&nbsp; of&nbsp; ribosomal&nbsp; targets&nbsp; leads&nbsp; to&nbsp; cross-resistance to&nbsp; macrolides (M),&nbsp; lincosamides&nbsp; (L)&nbsp; and&nbsp; streptogramins&nbsp; B&nbsp; (Sb). It&nbsp; is&nbsp; expressed&nbsp; as&nbsp; the MLS_b &ndash;phenotype,&nbsp; which&nbsp; confers&nbsp; a&nbsp; high-level&nbsp; resistance. This&nbsp; phenotype&nbsp; can&nbsp;&nbsp; be&nbsp;&nbsp; either&nbsp;&nbsp; constitutively&nbsp;&nbsp; (cMLS)&nbsp;&nbsp; or&nbsp;&nbsp; inducibly&nbsp;&nbsp; (iMLS). expressed. Another macrolide resistance mechanism is the active drug efflux, encoded by&nbsp; the <em>mefA&nbsp;</em> gene.&nbsp; The&nbsp; drug&nbsp; efflux&nbsp; confers&nbsp; resistance&nbsp; to&nbsp; 14-&nbsp; and&nbsp; 15-membered&nbsp; macrolides&nbsp; only,&nbsp; with&nbsp; no&nbsp; cross-resistance.&nbsp; It&nbsp; is&nbsp; expressed&nbsp; as&nbsp; the M-phenotype,&nbsp; which&nbsp; confers&nbsp; low-level&nbsp; resistance.&nbsp; The&nbsp; objective of&nbsp; this study&nbsp;&nbsp; was&nbsp;&nbsp; :&nbsp;&nbsp; 1) to&nbsp;&nbsp; examine&nbsp;&nbsp; the&nbsp;&nbsp; prevalence of&nbsp;&nbsp; macrolide&nbsp;&nbsp; resistant <em>Streptococcus&nbsp;&nbsp; pneumoniae </em>(MRSP) among&nbsp;&nbsp; invasive&nbsp;&nbsp; and&nbsp;&nbsp; noninvasive isolates in children and adults, 2) to examine the prevalence of coresistance and multiple-resistance among MRSP strains, 3) to examine the prevalence of&nbsp; macrolide&nbsp; resistant&nbsp; phenotypes,&nbsp; and&nbsp; 4)&nbsp; to&nbsp; examine&nbsp; the&nbsp; prevalence&nbsp; of macrolide&nbsp; resistant&nbsp; genotypes&nbsp; (detect&nbsp; the&nbsp; presence of&nbsp; the <em>ermB</em>&nbsp;&nbsp; and <em>mefA</em> gene).&nbsp; A&nbsp; total&nbsp; of&nbsp;&nbsp; 326&nbsp; MRSP&nbsp; strains&nbsp; were&nbsp; analyzed,&nbsp; which&nbsp; were&nbsp; collecte dall&nbsp; over&nbsp; Serbia&nbsp; in&nbsp; the&nbsp; period&nbsp; from&nbsp; January,&nbsp; 2010&nbsp; - December,&nbsp; 2012.&nbsp; The collected&nbsp;&nbsp; MRSP&nbsp;&nbsp; isolates&nbsp;&nbsp; were&nbsp;&nbsp; referred&nbsp;&nbsp; to&nbsp;&nbsp; the&nbsp;&nbsp; National&nbsp; Reference Laboratory&nbsp; for&nbsp; streptococci&nbsp; and&nbsp; pneumococci for&nbsp; further&nbsp; investigation. Identification based on microscopic, culture and biochemical features of the isolates. Conservation was performed in the brain-heart infusion broth with a&nbsp; 10%&nbsp; glycerol&nbsp; content&nbsp; at&nbsp; -80&deg;C.&nbsp; Macrolide&nbsp; resistance&nbsp; phenotypes&nbsp; were determined by a double disc diffusion test, combine d diffusion-dilution test and&nbsp;&nbsp; automatized&nbsp;&nbsp; VITEK&nbsp; 2 system. Macrolide&nbsp;&nbsp; resistance&nbsp;&nbsp; genes&nbsp;&nbsp; were&nbsp; determined by PCR. Overall, macrolide nonsusceptibility rate in Serbia was 34%.&nbsp; MRSP&nbsp; isolates&nbsp; were&nbsp; more&nbsp; prevale nt&nbsp; among&nbsp; children&nbsp; (36%)&nbsp; than adults&nbsp; (29%),&nbsp; and&nbsp; were&nbsp; more&nbsp; prevalent&nbsp; among&nbsp;&nbsp; noninvasive&nbsp; (35.5%)&nbsp; than invasive&nbsp; (27.4%)&nbsp; samples.&nbsp; Predominant&nbsp; macrolide&nbsp; resistance&nbsp; phenotype was&nbsp; the&nbsp; MLS b&nbsp; phenotype&nbsp; (78.5%),&nbsp; from&nbsp; which&nbsp; 73.9 %&nbsp; belonged&nbsp; to&nbsp; cMLS and&nbsp; 4.6%&nbsp; to&nbsp; iMLS&nbsp; phenotype.&nbsp; All&nbsp; the&nbsp; strains&nbsp; assigne d&nbsp; to&nbsp; the&nbsp; MLS_b phenotype harbored<em> ermB</em> gene, while all the strains with M phenotype had the mefA gene.&nbsp; The&nbsp; presence&nbsp; of&nbsp; both ermB and mefA resistance&nbsp; genes&nbsp; was confirmed&nbsp; in&nbsp; 43.9&nbsp; %&nbsp; of&nbsp; isolates. All&nbsp; the&nbsp; isolates&nbsp; which&nbsp; harbored&nbsp; both resistance genes expressed the MLS_b phenotype. Among macrolide resistant strains,&nbsp; penicillin&nbsp; nonsusceptiblility&nbsp; was&nbsp; observed&nbsp;&nbsp; in&nbsp; 16% .&nbsp; A&nbsp; high&nbsp; level resistance was confirmed in 5. 8% of MRSP isolates. MRSP strains showed high&nbsp; resistance rates to tetracyclin&nbsp; (81.3%) and&nbsp; trimethoprim-sulfamethoxazole&nbsp; (74.3%).&nbsp; Multiresistant&nbsp; strains,&nbsp; resistant&nbsp; to&nbsp; tetracyclines and&nbsp; trimethoprim-sulfamethoxazole,&nbsp; made&nbsp; two&nbsp; thirds&nbsp; (66.1&nbsp; %)&nbsp; of&nbsp; MRSP isolates.&nbsp; Among&nbsp; MRSP,&nbsp; co-resistance&nbsp; to&nbsp; tetracycline&nbsp; and&nbsp; trimethoprim-sulfamethoxazole&nbsp; was&nbsp; more&nbsp; prevalent&nbsp; among&nbsp; MLS&nbsp; phenotypes&nbsp; (73.1%) than&nbsp; M&nbsp; phenotypes&nbsp; (36.7%).&nbsp; Co-resistance&nbsp; strains&nbsp; to&nbsp; macrolides&nbsp; and&nbsp; other antibiotics including&nbsp;&nbsp;&nbsp; penicillin,&nbsp;&nbsp; amoxicillin,&nbsp;&nbsp;&nbsp; cefotaxime,&nbsp; tetracyclin, trimethoprim-sulfamethoxazole and multiresistant&nbsp; strains&nbsp; were more prevalent among children than adult. Coresistance to macrolides and other antibiotics&nbsp; including&nbsp; tetracycline&nbsp; and&nbsp; ofloxacin&nbsp; was&nbsp; more&nbsp; prevalent&nbsp; among noninvasive&nbsp;&nbsp; than&nbsp;&nbsp; invasive&nbsp;&nbsp; strains.&nbsp;&nbsp; Invasive&nbsp;&nbsp; MRSP&nbsp;&nbsp; isolates&nbsp;&nbsp; from&nbsp;&nbsp; the cerebrospinal fluid showed a higher resistance rate to beta lactam antibiotics than&nbsp; noninvasive&nbsp; strains.&nbsp; MRSP&nbsp; strains&nbsp; had&nbsp; a&nbsp; high&nbsp; susceptibility&nbsp; rates&nbsp; to levofloxacin&nbsp;&nbsp; (99.6),&nbsp;&nbsp; telithromycin&nbsp;&nbsp; (98.4%),&nbsp;&nbsp; cefotak sime&nbsp;&nbsp; (93.5%)&nbsp;&nbsp; and imipenem&nbsp; (97.3%).&nbsp; MRSP&nbsp; strains&nbsp; were&nbsp; fully&nbsp; susceptible&nbsp; to&nbsp; vancomycin, linezolid, moxifloxacin, sparfloxacin, rifampicin a nd pristinamycin. Among macrolide&nbsp;&nbsp; resistant <em>S.pneumoniae</em> strains,&nbsp;&nbsp; 12 different&nbsp;&nbsp; serotypes&nbsp;&nbsp; were identified.&nbsp; One&nbsp; half&nbsp; of&nbsp; these&nbsp; isolates&nbsp; belonged&nbsp; to the&nbsp; 19F&nbsp; (27.1%)&nbsp; and&nbsp; 14 (22.&nbsp; 9%)&nbsp; serotype,&nbsp; followed&nbsp; in&nbsp; frequency&nbsp; by&nbsp; the&nbsp; 6A&nbsp; (10.41%)&nbsp; and&nbsp; 23F (8.3%)&nbsp; serotype .&nbsp; Multiresistant&nbsp; strains&nbsp; (macrolides,&nbsp; penicillin,&nbsp; tetracyclines and&nbsp; trimethoprim-sulfamethoxazole)&nbsp; belonged&nbsp; to&nbsp; serotypes 19F,&nbsp; 14&nbsp; and 23F, while the 12F and 31 serotype were resistant to macrolides only. This in vestigation&nbsp;&nbsp; represents&nbsp;&nbsp; the&nbsp;&nbsp; first&nbsp;&nbsp; detailed&nbsp;&nbsp; analysis of&nbsp;&nbsp; phenotypes&nbsp;&nbsp; and genotypes&nbsp; of&nbsp; macrolide&nbsp; resistant&nbsp; pneumococcal&nbsp; strains&nbsp; in&nbsp; Serbia.&nbsp; The obtained&nbsp; results suggest&nbsp; the need for an active surveillance&nbsp; of pneumococcal infections in Serbia.</p>