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Le développement de la réponse immunitaire innée de l’hôte au cours des infections respiratoires nécessite la mise en place rapide d'un réseau moléculaire et cellulaire relativement complexe ayant pour but de contrôler la croissance microbienne ainsi que permettre son éradication. Dans certaines circonstances, et malgré l’existence de vaccins et d'antibiotiques efficaces, l’infection par Streptococcus pneumoniae peut aboutir à des pathologies graves telles qu'une pneumonie, une méningite et/ou une septicémie. Ainsi, à l'heure actuelle, les maladies associées au pneumocoque sont encore loin d'être sous contrôle. Dans ce contexte, une meilleure compréhension de la réponse immunitaire innée de l’hôte contre ce pathogène est nécessaire.Mes travaux de thèse ont permis pour la première fois de mettre en évidence la fonctionnalité et la relevance biologique de l’inflammasome NLRP3 au sein des neutrophiles pulmonaires in vivo dans un modèle d’infection respiratoire par S. pneumoniae.Ainsi, de façon inattendue, les neutrophiles jouent un rôle accessoire original à des temps précoces de l’infection via leur capacité à produire de l’IL-1β. Cette synthèse protéique est possible grâce à la combinaison de 2 signaux à la fois dérivés de l’hôte (TNF-α des macrophages alvéolaires) et de la bactérie (toxine). Ces deux signaux permettent l’assemblage et l’activation de l’inflammasome NLRP3 neutrophilique. D’un point de vue translationnel, nous avons été capables de démontrer un mécanisme similaire avec des neutrophiles humains.Cette production d’IL-1β par les neutrophiles participe à l’activation des lymphocytes T γδ producteurs d’IL-17; une cytokine essentielle dans le contrôle de l’infection bactérienne via sa capacité à induire rapidement le recrutement d’une deuxième vague de neutrophiles participant directement à l’élimination et la clairance bactérienne.Sur la base de ces travaux fondamentaux, nous avons émis l’hypothèse qu’une augmentation du pool de cellules innées sécrétrices d’IL-17A pourrait avoir un effet bénéfique sur le contrôle d’une infection respiratoire à pneumocoque. Ainsi via l’administration prophylactique et locale d’IL-7, nous avons été capables d’augmenter la fréquence et le nombre de lymphocytes innés producteurs d’IL-17A résultant en un meilleur contrôle de la charge bactérienne pathogène associée à une augmentation du recrutement neutrophilique. A ce stade, ces résultats encourageants, nous pousse à mieux comprendre les mécanismes moléculaires et cellulaires associés à cet effet dans l’éventualité de proposer à terme une nouvelle approche thérapeutique dans le contrôle des infections respiratoires pulmonaires basée sur la manipulation de la biologie de l’IL-7. / The mounting of an appropriate host innate immune response in the lungs requires the rapid establishment of a complex cellular and molecular networking that allows the containment and clearance of pathogens during respiratory infections. Both neutrophils and γδT cells are central players in the host response during mucosal infections. Using a model of invasive pneumococcal disease, we illustrated a role for Interleukin-17A in controlling neutrophil recruitment, bacterial loads and survival. Following Streptococcus pneumoniae infection, we defined pulmonary γδT cells, especially the lung resident Vγ6Vδ1+ subset, as the primary source of IL-17A in an IL-23/IL- 1β-dependent manner. Using gene-targeted mice, we demonstrated that γδT cells largely contributed to neutrophilia and to the control of the pathology. Furthermore, we now defined a second and unexpected early role for neutrophils as accessory cells in γδT17 cell activation through IL-1β secretion. Neutrophil-derived IL-1β was dependent on NLRP3 inflammasome activity and required alveolar macrophage-secreted TNF-α for priming and bacterial pneumolysin for NLRP3- dependent caspase-1 activation. This report thus brings to light the sequential molecular/cellular events leading to γδT17 cell activation and highlights the existence of a biologically relevant and fully functional NLRP3 inflammasome in pulmonary neutrophils that regulates a key immune axis in the development of protective innate response to respiratory bacterial infection.Based on these observations, we hypothesized that an increase in the pool of IL-17A-producing innate-like T lymphocytes might play a protective role during pneumococcal infection. As recently suggested, we demonstrated that intranasal IL-7/M25 complex administration into naïve mice allowed the expansion of the cellular pool of innate immune cells presenting a Th17-like phenotype in the lungs especially T cells. Moreover, we showed during S. pneumoniae infection that prophylactic IL-7/M25 treatment increased the capacity of Vγ6Vδ1+ T cells to produce IL-17A. Interestingly, this phenotype led to higher neutrophil recruitment and a better control of bacterial burden in the lungs as well as systemic dissemination. Thus, we report a critical role of IL-7 in creating an IL-17-enriched microenvironment which improves the early development of host innate immune response to respiratory bacterial infection. This observation might pave the way to the development of future innovative cytokine/cell-based strategies against Streptococcus pneumoniae.

Abstract The aims of this work were to study the carriage of respiratory bacteria and to identify risk factors affecting pharyngeal colonisation by these pathogens among young Finnish men during military service, and also to investigate the role of mannose-binding lectin (MBL) concentrations and MBL2 gene polymorphisms in the carriage of respiratory bacteria. A total of 892 military recruits entering the Kainuu Brigade, including 224 men with asthma, were followed up prospectively to the end of their military service. Carriage of Streptococcus pneumoniae, Neisseria meningitidis and beta-haemolytic streptococci appeared to be higher during and at the end of military service than at the beginning. Smoking was found to be a significant risk factor for colonisation by these bacteria. S.pneumoniae was more common in the asthmatic than military conscripts in the non-asthmatic ones at the beginning of military service. A low MBL level increased the risk of carrying N. meningitidis and beta-haemolytic streptococci during military service among non-smokers but not among smokers. Low MBL levels producing MBL2 haplotypes seemed to be associated with the carriage of N. meningitidis and S. pneumoniae. Characterisation of all the oropharyngeal N.meningitidis isolates obtained (n=215) by phenotypic and genotypic methods showed that most of them belonged to the carriage-associated ST-60 clonal complex. Clonal complexes ST-41/44, ST-32, and ST-23, which have previously been associated with disease, also accounted for a third of the carriage strains. Furthermore, a significant association was indicated between an acute upper respiratory infection and oropharyngeal carriage of the virulent meningococcal ST-23 clone. In conclusion, the results reported here show a significant increase in bacterial carriage during military service and provide new information on the association between MBL and carriage of respiratory bacteria. These findings also highlight the importance of smoking cessation, especially among military conscripts, who have been found to be a risk group for invasive bacterial diseases, and they also point to the importance of meningococcal vaccination for military recruits and the need for an efficacious vaccine against serogroup B meningococci. / Tiivistelmä Hengitystieinfektiot ovat yleisiä varusmiespalvelun aikana. Myös oireeton bakteerien nielukantajuus on lisääntynyt. Useimmiten infektiot ovat lieviä virusinfektioita, mutta bakteerien nielukantajuus voi johtaa myös vaikeisiin bakteeritulehduksiin. Tämän väitöskirjatyön tarkoituksena oli tutkia bakteerien nielukantajuutta varusmiespalveluksen alkaessa ja päättyessä sekä mahdollisten hengitystieinfektioiden aikana ja näin saada uutta tietoa bakteerien nielukantajuuteen vaikuttavista tekijöistä. Lisäksi tavoitteena oli selvittää mannoosia sitovan lektiinin (MBL) sekä MBL2-geenin polymorfismien yhteyttä bakteerien nielukantajuuteen. Työn tarkoituksena oli myös feno- ja genotyypittää varusmiehiltä palveluksen aikana eristetyt meningokokkikannat ja verrata niitä vastaavana ajankohtana invasiivista tautia sairastaneista henkilöistä eristettyihin meningokokkikantoihin. Tutkimuksessa seurattiin prospektiivisesti 892 varusmiestä, jotka suorittivat asepalveluksen Kainuun Prikaatissa vuosina 2004–2006. Tutkimukseen osallistuneista varusmiehistä 224:llä oli astma. Tutkimuksessa havaittiin, että oireeton bakteerien nielukantajuus lisääntyy merkitsevästi varusmiespalveluksen aikana. Lisäksi havaittiin, että tupakointi oli merkittävä itsenäinen riskitekijä pneumokokin, meningokokin sekä beta-hemolyyttisten streptokokkien nielukantajuudelle varusmiespalveluksen aikana. Astmaatikkojen pneumokokin nielukantajuus varusmiespalveluksen alussa oli yleisempi kuin terveiden varusmiesten. Tutkimuksessa osoitettiin myös pienen seerumin MBL-pitoisuuden sekä MBL2-geenin polymorfismin eksoni 1:n alueella ja geenin säätelyalueella olevan riskitekijöitä meningokokin, pneumokokin sekä beta-hemolyyttisten streptokokkien nielukantajuudelle tupakoimattomilla varusmiehillä. Meningokokin nielukannoista jopa kolmasosa kuului genotyyppiryhmään, jonka on aiemmissa tutkimuksissa havaittu liittyvän invasiiviseen tautiin. Tutkimuksessa osoitettiin myös tietyn hyperinvasiivisen meningokokin genotyypin (ST-23) liittyvän hengitystieinfektioepisodeihin. Tässä väitöskirjatyössä osoitettiin, että bakteerien nielukantajuus lisääntyy merkitsevästi varusmiespalveluksen aikana ja että oireettomilla varusmiehillä tavataan myös hyperinvasiivisia meningokokkikantoja. Tutkimus antoi myös uutta tietoa hyperinvasiivisten meningokokin genotyyppien liittymisestä hengitystieinfektioihin sekä MBL:n vaikutuksesta bakteerien nielukantajuuteen. Tutkimushavainnot tukevat tupakoimattomuuden edistämisen tärkeyttä myös varusmiespalveluksen aikana.

Sortases are cell-membrane associated cysteine transpeptidases that are essential for the assembly and covalent anchoring of certain surface proteins to the cell wall in Gram-positive bacteria. Thus, they play critical roles in virulence, infection and colonization by pathogens. Sortases have been classified as type A, B, C, D, E and F based on their phylogeny and the target-protein motifs that they recognize. Sortase A (SrtA) enzymes participate in cell wall anchoring of proteins involved in bacterial adhesion, immune evasion, internalization, and phage recognition and in some cases pili formation. SrtA substrates are characterised by the presence of a C-terminal cell wall sorting signal as LPXTG motif, followed by a stretch of hydrophobic residues and a positively charged tail. Experimental and bioinformatics studies show that class A sortases are housekeeping as well as virulence determining proteins. Hence, Sortase A enzymes are considered as promising antibacterial drug targets, particularly because many organisms are developing multi-drug resistance behaviour. SrtA adopts an eight-stranded β-barrel structure and the overall fold is conserved among the sortase isoforms, with some modifications. The thesis candidate has determined the three dimensional (3D) crystal structures of wild-type and active site mutant of Sortase A from Streptococcus pneumoniae R6 strain by using X-ray diffraction method. The wild-type enzyme crystallized in P21 space group whereas active site cysteine mutant crystallized in C2 space group. In both the cases, N-terminal 81 residue deletion constructs (ΔN81) were used for crystallization. Uncommonly, both the structures showed a phenomenon of domain-swapping which resulted in the protein adopting a domain-swapped dimeric form. Two such dimers in wild-type protein and three dimers in mutant protein were observed in the asymmetric unit. To the best of our knowledge, our work reveals for the first time the occurrence of domain-swapping in sortase superfamily. Experimental techniques like size-exclusion chromatography, native-PAGE, analytical centrifugation and thiol cross-linking (carried out in our collaborator’s laboratory at National Institute of Immunology (NII), New Delhi, India) of functionally active wild-type SrtA from S. pneumoniae showed dimerization as well as domain-swapping in solution state. These results support the possibility that the protein indeed exists in a domain-swapped dimeric form and the determined structure is not the result of crystal packing artifact but is physiologically relevant as well. The work done by the thesis candidate covering crystallization of both, the active and inactive protein constructs, their structure determination using molecular replacement method, detailed structural analyses, structural comparisons with known SrtA structures and new structural findings are described in from Chapter 2 to Chapter 4. Based on the SrtA crystal structure the author of the thesis has also proposed various point mutations which are likely to disrupt domain– swapping and result in loss of dimer formation. In addition, as a part of the ongoing project in our laboratory, molecular dynamics studies of these domain-swapped dimers containing two sets of active site residues facing each other in a very compact volume have been initiated to understand substrate binding, which in future could lead to inhibitor design. Apart from the crystal structure analyses of SrtA structures, the author of the thesis has also carried out systematic crystal structure investigation of dipeptides and pentapeptides containing non-standard amino acids (ΔPhe, Aib and β-amino acids) along with computational studies. Conformationally restricted α,β-dehydrophenylalanine residue (ΔF) and α-aminoisobutyric acid (Aib) have been incorporated in highly amyloidogenic human Islet Amyloid Polypeptide (hIAPP) fragments. Amyloid deposits, observed in a vast majority of Type 2 diabetic patients, are primarily on account of misfolding and aggregation into fibrils of hIAPP, a 37 residue endocrine hormone secreted by pancreatic β-cells. It has been suggested that intermediates produced in the process of fibrillization are toxic to insulin producing β-cells. Hence, the inhibition of misfolding of hIAPP that involves structural transition from its native state (coil and/or helical and/or transient helical conformation) to β-sheet conformation, could be a possible strategy to mitigate Type 2 Diabetes Mellitus (T2DM). All the peptides discussed in this thesis were synthesized in our collaborator, Prof. V. S. Chauhan’s laboratory at the International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India. In this work, author of the thesis has designed short peptides containing helicogenic residue, α,β-dehydrophenylalanine (ΔF) and determined their 3D crystal structures. It was found that pentapeptides, FGA∆FL and FGA∆FI act as inhibitors of hIAPP fibrillization. As revealed by crystal structure analysis, both the peptides have similar backbone conformation consisting of a ‘nest’ motif, which is an anion receptor. Molecular docking suggested that both the pentapeptides interact with the hIAPP20-27 segment, stabilizing the hIAPP in helical form by shielding the core aggregation initiation region. This reduces the possibility of oligomerization, formation of toxic intermediates and subsequently the transition to β-structure and fibrillization. Thus, the crystal structures of pentapeptide inhibitors together with computational docking studies suggest an atomic level model of the possible mode of action by which the FGAΔF(L/I) peptides manifest their fibrillization inhibition activity and this could be of value in the design of a new class of amyloid inhibitors. In another peptide design, L→U (Aib) mutation was done in core fibrillization region ANFLV i.e. hIAPP13-17. The resulting mutant peptide ANFUV as well as native fragment ANFLV was crystallized and their 3D crystal structures were determined. ANFLV crystallized in two space groups C2 and P2 adopting extended conformation. Crystal packing of ANFLV in both the crystals shows parallel beta sheet arrangement which is favoured and strengthened by hydrogen bonding between asparagine side chains of Asn-Asn pair each located in neighbouring parallel beta-strands. Hydrogen bonded Asn-Asn residue pairing in parallel beta-strands suggests its significant contribution during hIAPP fibril formation. The substitution L→U abolished its fibrillization property and the structure of ANFUV was solved by direct methods in P21 space group. The occurrence of β-bulge in ANFUV induced by Aib, as observed in crystal packing, suggests that Aib acts as a β-breaker through β-bulge inducing property in the highly amyloidogenic hIAPP segment. β-bulge forming property, an attribute of Aib as β-breaker may be responsible for the curtailment of fibrillization potential of the peptide in which the residue was incorporated. The aim of the anti-amyloid work is to design potent anti-fibrillization peptides and the work is important to design peptide based drugs to fight type II diabetes. The utilization of ΔPhe in the molecular self-assembly offers an added benefit in terms of variety and stability. Taking advantage of the conformation constraining property of ΔPhe residue, its incorporation in dipeptide molecules has been probed. The author has studied nanotube formation through molecular self-assembly, involving two classes of non¬standard amino acids i.e. ΔF and β-amino acids. FΔF in D-form, L-form and DL-mixture crystallized in different space groups forming rectangular/hexagonal channels constituting different channel dimensions. Recently, the application of FΔF nanotubes have been demonstrated in controlled drug delivery, showing the relevance of the work in health care. Another class of dipeptides containing β-amino acids (β-FF, β-FΔF, β-AΔF, β-VΔF, β¬LΔF, β-IΔF, and β-LF) was also explored for the self-assembled nanotube formation. These β-peptides were crystallized and their 3D structures were determined solely by the author of the thesis. Except the β-AΔF & β-LΔF, these peptides self-assemble and form rectangular/ hexagonal channels. Structures of ΔF and β-amino acid containing dipeptides forming ordered nanotubes through self-assembly are detailed in Chapters 8 and 9 in the thesis. Overall, the author of the thesis has crystallized and determined structures of more than twenty peptides. Experimentally, β-peptide nanotubes were observed to encapsulate drug molecules and thus might be useful as a drug delivery system. In the present thesis crystal structures of the following designed peptide sequences (including one natural sequence ANFLV) are reported in detail. Table 1 Peptide sequence Representation Length Discussed in 1. Phe-Gly-Ala-ΔPhe-Leu FGAΔFL 5 Chapter 6 2. Phe-Gly-Ala-ΔPhe-Ile FGAΔFI 5 Chapter 6 3. Ala-Asn-Phe-Leu-Val (2 forms) ANFLV_P2, ANFLV_C2 5 Chapter 7 4. Ala-Asn-Phe-Aib-Val ANFUV 5 Chapter 7 5. LPhe-ΔPhe (2 forms) LFΔF1 , LFΔF2 2 Chapter 8 6. DPhe-ΔPhe DFΔF 2 Chapter 8 7. DLPhe-ΔPhe DLFΔF 2 Chapter 8 8. LTyr-ΔPhe LYΔF 2 Chapter 8 9. LSer-ΔPhe LSΔF 2 Chapter 8 10. Boc-D,LPhe-ΔPhe Boc-DLFΔF 2 Chapter 8 11. Cbz-D,LPhe-ΔPhe Z-DLFΔF 2 Chapter 8 12. D,LMet-ΔPhe DLMΔF 2 Chapter 8 13. β-Phe-ΔPhe β-FΔF 2 Chapter 9 14. β-Phe-Phe β-FF 2 Chapter 9 15. β-Val-ΔPhe β-VΔF 2 Chapter 9 16. β-Ile-ΔPhe β-IΔF 2 Chapter 9 17. β-Leu-ΔPhe β-LΔF 2 Chapter 9 18. β-Leu-Phe β-LF 2 Chapter 9 19. β-Ala-ΔPhe β-AΔF 2 Chapter 9 20. Cyclo(Phe-ΔPhe) DKP-FΔF 2 Appendix C 21. Cyclo(Ile-ΔPhe) DKP-IΔF 2 Appendix C 22. Cyclo(Cha-Cha) DKP-ChaCha 2 Appendix C 23. Cyclo(Cha-Phe) DKP-ChaF 2 Appendix C 24. Cyclo(Cha-ΔPhe) DKP-ChaΔF 2 Appendix C 25. Cyclo(S-tritylCys-ΔPhe) DKP-CΔF 2 Appendix C Most of the dipeptides, except the N-terminal protected dipeptides, cyclic dipeptides (i.e. DKPs) and LSΔF, were found in the zwitterionic conformation and out of these, ten dipeptides resulted in tubular structures of dimensions in the nanoscale range. The thesis is organized into nine chapters and five appendices. Chapter 1 is an introduction to the work presented in the thesis, while Chapter 2, Chapter 3 and Chapter 4 describe the crystallographic work on the protein Sortase A. Chapter 5 is an introduction to the non-standard amino acids used for peptide designs and Chapter 6, Chapter 7, Chapter 8, Chapter 9 and Appendix C describe the crystallographic work on peptides. Chapter 1 starts with a general introduction to the Gram-positive bacteria containing sortase enzymes, and the bacterial cell-wall where sortase catalyzed proteins get attached for implicating their virulence during host-pathogen interactions. Pneumococcal diseases mostly affect children and their count has been observed to be higher than the combined total cases of malaria, AIDS and tuberculosis in child population worldwide. The chapter describes different virulence factors of S. pneumoniae out of which many are proteins. Among these, LPXTG containing proteins, which are the prime substrates of the sortase enzymes, are discussed in detail. Sortase enzymes, their classification and their structural studies with conserved ‘Sortase fold’ are discussed elaborately. A brief mention is made about the enzymatic activity of Sortase A to understand the transpeptidation mechanism. To appreciate the biomedical and biotechnological importance of the sortase enzyme, some potential applications of Sortase A are detailed in this chapter. A section is dedicated to describe the protein in the present study 'Sortase A from Streptococcus pneumoniae'. At the end, the scope of the present work, comprising of both protein and peptide crystallography, is presented. Chapter 2 begins with a brief account of the sequence analysis of Sortase A from S. pneumoniae and phylogenetic analysis of the sortase superfamily enzymes, followed by the details of protein purification & crystallization of two different constructs, wild-type SrtA from S. pneumoniae (Spn-∆N59SrtAWT and Spn-∆N81SrtAWT) as well as that of an active site cysteine mutant (Spn-∆N81SrtAC207A). This chapter includes X-ray intensity data collection of both types of crystals and data processing. Sortases are membrane anchored enzymes and therefore their expression as a full-length protein is a difficult task. Hence, the deletion of N-terminal transmembrane region from the enzyme is crucial for expression in its soluble form and is important for its successful crystallization. Thus, two wild-type constructs of S. pneumoniae sortase A, ∆N59SrtAWT (N-terminal 59 residue deletion) and ∆N81SrtAWT (N-terminal 81 residue deletion), and one active site mutant ∆N81SrtAC207A (N-terminal 81 residue deletion & active site Cys207 to Ala mutation) were cloned, expressed and purified. Cloning, expression and purification of the protein were done at the laboratory of our collaborator Prof. Rajendra P. Roy, Cell biology lab-II, National Institute of Immunology (NII), New Delhi, India. Crystallization of Spn-∆N59SrtAWT (~23 kDa) construct was initiated by manual screening using sparse matrix conditions from Hampton research. Initial trials were set up by following hanging-drop vapour diffusion method. Spn-∆N59SrtAWT construct crystallized in diamond, needle, rod and wedge-shaped crystal forms in more than one crystallization condition but they failed to diffract. Further trials were set up in microbatch plates that resulted in diamond-shaped crystals again, which diffracted up to a maximum of 4.0 Å resolution. Sequence comparison of the present construct was performed to modify the construct to achieve better diffraction. Thus, we made modifications in the Spn¬∆N59SrtAWT construct by deleting additional 22 residues at the N-terminal (i.e. total 81 residues deletion in the original sequence from the N-terminal) similar to SrtA from S. pyogenes. Hence, Spn-∆N81SrtAWT construct was prepared. For further crystallization experiments, we used the new construct Spn-∆N81SrtAWT. Similar to Spn-∆N59SrtAWT construct, crystallization set up for Spn-∆N81SrtAWT were done in microbatch plates at 293 K by using the Hampton conditions. During the crystallization set up, protein concentration was varied from 6-30 mg/ml. Notably, the protein crystals grown with 25 mg/ml protein concentration diffracted very well. Thus increasing the protein concentration helped to improve diffraction quality. Crystals obtained in Index-88 condition (0.2 M tri-ammonium citrate and 20% (w/v) PEG 3350, pH 7.0) diffracted up to 2.9 Å. Additive screen was used to improve its diffraction quality. This time many diffracting crystals were obtained and the best rod-shaped crystals grown in additive screen-79 (40% v/v (±)-1,3-butanediol) diffracted well up to 2.70 Å at home source. Thus, Spn-ΔN81SrtAWT crystallized at protein concentration of 25 mg ml-1 (in 10 mM Tris buffer, pH 7.5; 2 mM β-mercaptoethanol) with a condition containing 0.2 M tri-ammonium citrate and 20% (w/v) PEG 3350, pH 7.0, along with 40% v/v (±)¬1,3-butanediol as an additive agent by using microbatch-under-oil crystallization method. The chapter also includes crystallization of active site mutant Cys207Ala of ∆N81SrtAWT from S. pneumoniae (Spn-∆N81SrtAC207A). Spn-∆N81SrtAC207A mutant crystallized as a beautiful rectangular block type crystal (with a diffraction up to 2.7 Å at home source and up to 2.48 Å at synchrotron) at protein concentration of 25 mg ml-1 (in 10 mM Tris buffer, pH 7.5; 2 mM β-mercaptoethanol) with a condition containing 0.2 M tri-ammonium citrate and 20% (w/v) PEG 3350, pH 7.0, along with 1.0 M guanidine hydrochloride as an additive agent by using microbatch-under-oil crystallization method. Data collection was done on home-source diffraction facility for both the crystals however; mutant data in better resolution was collected by the author of the thesis at BM-14 beamline at ESRF, Grenoble, France. Thus, two crystals of SrtA, wild-type (Spn-∆N81SrtAWT) and its C207A mutant (Spn-∆N81SrtAC207A) were indexed satisfactorily in two space groups and their cell parameters are given in the following table 2. Table 2 Protein Space group a (Å) b (Å) c (Å) β (°) X-ray source Spn-∆N81SrtAWT P21 66.94 103.45 74.87 115.65 Home source Spn-∆N81SrtAC207A C2 155.57 113.33 81.34 90.80 Synchrotron The quality of both the data sets was assessed by SFCHECK and none of them showed twinning. Thus, the data sets collected were found appropriate and useful for structure determination as discussed in Chapter 3. Chapter 3 details the structure determination of Sortase A from S. pneumoniae for a wild-type construct (Spn-ΔN81SrtAWT) and for an active site cysteine mutant construct (Spn-ΔN81SrtAC207A). Sortase A from S. pyogenes was used as a search model in the molecular replacement (MR) method and a single solution for each data set was obtained through PHASER program. It resulted in four-molecules in wild-type sortase structure and six-molecules in the mutant structure in the respective crystal asymmetric unit. Iterative model building and structure refinement revealed a clear case of domain-swapping as observed in the electron density map. Finally, in the asymmetric unit of wild-type structure and in mutant protein structure two and three domain-swapped dimers were located, respectively. Simulated annealing and TLS refinement resulted in the protein structure with best refinement statistics. All these are elaborately discussed in Chapter 3. The last round of refinement of Spn-ΔN81SrtAWT converged to Rwork = 18.10% and Rfree = 23.39 % for 25152 unique reflections in the resolution range 30.7-2.7 Å whereas for Spn¬ΔN81SrtAC207A structure these parameters converged to Rwork = 18.25% and Rfree = 22.39% for 50010 unique reflections in the resolution range 47.15-2.48 Å. Chapter 4 describes the wild-type (Spn-ΔN81SrtAWT) as well as mutant (Spn¬ΔN81SrtAC207A) structures of Sortase A. The structure of Sortase A is not found in its commonly observed monomeric form but occur in a domain-swapped dimeric form. There are two dimers in Spn-ΔN81SrtAWT and three in Spn-ΔN81SrtAC207A as observed in the asymmetric unit. Each dimer contains two characteristic 8-stranded beta-barrel folds i.e. ‘sortase fold’ which is unique to the sortase superfamily. Unlike the structure of SrtA from other organisms known so far, the monomer does not form the 8-stranded beta-barrel all by itself. One monomer exchanges the β7 and β8 strands with the other monomer having β1 to β6 strands, thereby forming a complete 8-stranded β-barrel fold and such kind of two complete folds are present in each dimer. Because of the mutual swapping of strands between two monomers in a dimer, the dimer thus formed is defined as a domain-swapped dimer. This is the first time we have observed Sortase A structure in the domain-swapped dimeric form and is also the first example of domain-swapping in the sortase superfamily. Interestingly, all the catalytic residues (His141, Cys207 and Arg215) in each sortase fold in the swapped dimer lie at the secondary interface (open interface) generated by domain-swapping. Catalytic R215 (in one fold) interacts with D209 residue (in other fold of same dimer) through salt bridge interactions. Each dimer contains two pairs of such residues at the secondary interface but only one pair shows this kind of interaction. R215 (B-chain) interacts with D209 (A-chain) in AB dimer whereas R215 (D-chain) interacts with D209 (C-chain) in CD dimer. Asymmetry in the catalytic residues for their orientations and observed interactions at the secondary interface was evidenced. These active site residues were seen buried to a great extent except Arg215 which is slightly better exposed. It was difficult to find the exact substrate-binding pocket to approach the catalytic Cys207. However, biochemical and biophysical analyses (done at NII, New Delhi) provided strong evidence for the existence of the swapped-dimeric form at physiological pH as well. The enzyme exists with an equilibrium between its monomeric and dimeric forms, and the dimeric population is the most active species of the functionally active enzyme. An important role of Glu208 (in all the chains of two dimers; e.g. Chain A) was seen in the catalytic site where its side chain wobbles between His141 and H142 (both in Chain B) residues for interaction. Due to such kind of interactions the backbone conformation between C207-E208 (Chain B) shows variability, and coordinates the distance between His141 (ND1, Chain A) and Cys207 (SG, Chain B) each belonging to opposite chains in a swapped-dimer. The nature of side chain conformations of Glu208 in all the four sets of active site residues (in wild-type as well as in cysteine mutant structure) indicates that its movement presumably regulates thiolate-imidazolium acid-base pair formation which is a crucial condition for the sortase function where cysteine thiolate acts as nucleophile. Based on the crystal structure, the thesis candidate has suggested several mutants which might disrupt domain-swapping pointing to future studies on the system. Domain movement analyses by using HingeProt and DynDom servers indicate that the two-sortase folds joined with hinge loops in each dimer may show twist movement around the hinge axis. Possibly, such motion will affect the secondary interface covering active site residues and may allow increasing the exposure of the catalytic residues to perform catalysis. Presumably, such kind of domain movements may play a key role for the unique kind of regulatory mechanism for transpeptidase activity in sortase enzymes. However, more study has to be done to explore the role of these possibilities, if any, in the enzyme function and its regulation. Chapter 5 provides an introduction to non-standard amino acids, their sources and their uses in de novo peptide design; this is followed by a description of outcomes of structural investigations of modified peptides and their applications in various fields of medical and material science. Specifically, α, β-dehydrophenylalanine (ΔPhe), α-aminoisobutyric acid (Aib) and β-amino acids are discussed and their structures and conformational preferences are highlighted for their use in naturally occurring peptides or peptide fragments. Chapter 6 begins with an introduction to the human Islet Amyloid Polypeptide (hIAPP), which is an amyloidogenic protein and considered to be an important protein constituent of the amyloid plaques in pancreatic beta-cells in Type 2 diabetes patients. Therefore, fibrillization inhibition of hIAPP is considered as an important therapeutic approach to combat Type 2 Diabetes Mellitus (T2DM). In this chapter, the author of the thesis describes an approach to design peptide based inhibitors of hIAPP fibrillization using non¬standard amino acid ΔPhe (α,β-dehydrophenylalanine) residue. The first designed inhibitor has the sequence origin from hIAPP23-27 and it was developed by replacing I→ΔF (i.e. β¬favouring residue to helical conformation favouring) which resulted in FGAΔFL peptide. Fibrillization inhibition studies were done by co-incubation of hIAPP and FGAΔFL in 1:5 molar ratio and monitored by electron microscopy and thioflavin T binding assay that showed ~75% fibrillization inhibition. It suggested that the inhibitor is working effectively and thus the author determined its crystal structure by X-ray diffraction method. Peptide synthesis and experimental studies like electron microscopy and Thioflavin T binding assay were done in our collaborator’s laboratory at ICGEB, New Delhi, India. Subsequently a sequence similar peptide FGAΔFI was also designed by mutating L→I in the first inhibitor sequence. The resulting peptide FGAΔFI showed ~70% fibrillization inhibition. Following this success, crystal structures of both peptides were determined. FGAΔFL crystallized in P212121 space group whereas FGAΔFI crystallized in P21 space group. Though it was not anticipated, crystal structure analysis revealed that FGAΔFL and its analogue FGAΔFI harbour the anion receptor ‘nest’ motif. Both peptides dock with the helical form of hIAPP which may contribute to the inhibitory function of the peptides through their interaction with hIAPP in the core fibrillization region. These peptides effectively inhibit hIAPP fibrillization in vitro and it seems that these are unique examples of ‘nest-motif’ containing peptides that inhibit fibrillization. We also propose a model for fibrillization inhibition by these peptides; this has been published in Chemical Communications, a journal published by the Royal Society of Chemistry (RSC) and its reprint is enclosed within the thesis. In general, the approach described in the chapter may be applicable to target helices or helical intermediates and could be utilized in developing inhibitors useful, apart from T2DM, in other amyloid diseases including Alzheimer’s disease and Parkinson’s disease. Table 3 Peptide Crystal system and space group Unit cell details X-ray data Structure solution and refinement Agreement factor FGAΔFL Orthorhombic, P212121 a=8.9951 (9) Åb=13.0144 (12) Åc=27.7521 (24) ÅV=3248.82 (5) Å3 Z=4 Mo Kα(λ=0.71073Å) 4703 Unique reflections 2581 [|Fo| > 4σ (|Fo|)] Direct methods: SHELXS97 & SHELXL97 5.95 % for [|Fo| > 4σ (|Fo|)] FGAΔFI Monoclinic, P21 a=8.9951 (9) Åb=13.0144 (12) Åc=27.7521 (24) Å β=92.637 (2)°V=935.59 (2) Å3 Z=2 Mo Kα(λ=0.71073Å) 4024 Unique reflections 2612 [|Fo| > 4σ (|Fo|)] Direct methods: SHELXS97 & SHELXL97 5.02 % for [|Fo| > 4σ (|Fo|)] Chapter 7 describes another important but less studied core fibrillization fragment of hIAPP (hIAPP13-17) different than the hIAPP23-27 discussed in the previous chapter. It also discusses the development of fibrillization inhibitor design from this segment. The fragment hIAPP13-17 i.e. ANFLV crystallized in two space groups; C2 with one molecule in the asymmetric unit and P2 with two molecules in the asymmetric unit. In these structures, ANFLV peptide shows fully extended conformation i.e. a β-conformation. Crystal packing shows parallel β-sheet arrangement with the involvement of dry ‘steric-zippers’. The peptide prefers cross-strand Asn-Asn residue pair by side chain hydrogen bonding and is discussed in comparison with a few crystal structures of hIAPP fragments, solved by Eisenberg’s group, containing Asn residue in their sequence. It is observed that if the Asn is located in the sequence between two terminal residues the peptide will arrange itself in parallel beta sheet. This supports a structural model of hIAPP fibril in parallel beta sheet arrangement as the hIAPP sequence contains several Asn residues. To develop an inhibitor from ANFLV, a partial success was achieved where the Leu → Aib mutant i.e. ANFUV was developed. ThT (Thioflavin T) and TEM (Transmission electron microscopy) results show that the mutant peptide does not fibrilize on its own. This strongly supports the fact that the native peptide (ANFLV) lost its inherent fibrillization characteristic with the introduction of Aib in place of Leu i.e. the resultant mutant ANFUV is a non-fibrillizing peptide. The logic behind the development was to retain ANF in the same extended conformation and then break the β-strand with β-breaker residues. The structure of ANFLV showed parallel beta-sheets along with the additional side chain-side chain hydrogen bonding in the same direction as the fibril axis. Thus, we retained the ANF region to keep the sticky segment in the design and then Leu was mutated to Aib, a known β-breaker, to alter backbone conformation. The crystal structure of the peptide ANFUV resulted in the similar ANF region in beta conformation and Aib in helical conformation. Interestingly, in this situation the conformation of Aib develops a beta-bulge observed in the crystal packing and this bulge structure probably turned the peptide to have non-fibrillizing characteristics. These results will be useful in designing peptide inhibitors by using U as a beta breaker to inhibit hIAPP fibrillization. Table 4 Peptide Crystal system and space group Unit cell details X-ray data Structure solution and refinement Agreement factor ANFLV1 Monoclinic, C2 a=36.1350 (20) Åb=4.8050 (10) Åc=19.4190 (20) Å β=98.644 (5)°V=3333.40 (27) Å3 Z=4 Synchrotron (λ=0.77490 Å) 1982 Unique reflections 1825 [|Fo| > 4σ (|Fo|)] Direct methods: Sir92 & SHELXL97 11.71% for [|Fo| > 4σ (|Fo|)] ANFLV2 Monoclinic, P2 a=18.7940 (80) Åb=4.7970 (10) Åc=35.4160 (50) Å β=103.929 (10)°V=3099.03 (81) Å3 Z=4 Synchrotron (λ=0.77490 Å) 2651 Unique reflections 2580 [|Fo| > 4σ (|Fo|)] Direct methods: Sir92 & SHELXL97 15.39% for [|Fo| > 4σ (|Fo|)] ANFUV Monoclinic, P21 a=10.8140 (22) Åb=9.1330 (18) Åc=16.7540 (34) Å β=107.960 (30)°V=1574.07 (161) Å3 Z=2 Synchrotron (λ=0.97918 Å) 1426 Unique reflections 1398 [|Fo| > 4σ (|Fo|)] Direct methods: SHELXS97 & SHELXL97 5.45% for [|Fo| > 4σ (|Fo|)] Chapter 8 elaborates the self-assembly of α-dipeptides containing conformationally constrained achiral amino acid, α,β-dehydrophenylalanine (ΔF). The structural polymorphism in LFΔF peptide and the resulting self-assembly are discussed. Its D-isomer (DF∆F) and its racemic mixture (DLF∆F) are also discussed as these peptides self-assemble to give channel-forming assemblies. In addition to LFΔF, crystal structures of LYΔF, DLMΔF and LSΔF peptides and their self-assemblies are presented as well. Except DLMΔF xi and N-terminal protected DLFΔF (Boc-DLF∆F and Z-DLF∆F) peptides, the other dipeptides discussed in this chapter resulted in tubular structures of nanoscale dimensions through molecular self-aggregation. Table 5 Peptide Crystal system and space group Unit cell details X-ray data Structure solution and refinement Agreement factor LFΔF1 Hexagonal, P65 a=23.1873(24) Åb=23.1873(24) Åc=5.5260(8) ÅV=2573.01(5) Å3 Z=6 Mo Kα(λ=0.71073Å) 3489 Unique reflections 2915 [|Fo| > 4σ (|Fo|)] Direct methods: SHELXS97 & SHELXL97 6.19% for [|Fo| > 4σ (|Fo|)] LFΔF2 Monoclinic, P21 a=5.5739(2) Åb=13.1383(4) Åc=13.5816(4) Å β=96.137(2)°V=988.90(2) Å3 Z=2 Mo Kα(λ=0.71073Å) 4865 Unique reflections 3402 [|Fo| > 4σ (|Fo|)] Direct methods: SHELXS97 & SHELXL97 4.35% for [|Fo| > 4σ (|Fo|)] DFΔF Orthorhombic, P21212 a=13.1690(21) Åb=25.3673(40) Åc=5.5622(9) ÅV=1858.12(5) Å3 Z=4 Mo Kα(λ=0.71073Å) 4370 Unique reflections 3426 [|Fo| > 4σ (|Fo|)] Direct methods: SHELXS97 & SHELXL97 4.44% for [|Fo| > 4σ (|Fo|)] DLFΔF Monoclinic, P21/c a=5.5392(14) Åb=26.0376(55) Åc=13.1839(27) Å β=90.278(16)°V=1901.46(8) Å3 Z=4 Mo Kα(λ=0.71073Å) 2051 Unique reflections 1264 [|Fo| > 4σ (|Fo|)] Direct methods: SHELXS97 & SHELXL97 7.08% for [|Fo| > 4σ (|Fo|)] LYΔF Hexagonal, P65 a=23.5523(4) Åb=23.5523(4) Åc=5.5183(1) ÅV=2650.96(1) Å3 Z=6 Mo Kα(λ=0.71073Å) 2746 Unique reflections 1871 [|Fo| > 4σ (|Fo|)] Direct methods: SHELXS97 & SHELXL97 3.91% for [|Fo| > 4σ (|Fo|)] LSΔF Monoclinic, P21 a=5.2998(20) Åb=9.6732(30) Åc=14.1827(57) Å β=95.604(27)°V=723.62(20) Å3 Z=2 Mo Kα(λ=0.71073Å) 1978 Unique reflections 1558 [|Fo| > 4σ (|Fo|)] Direct methods: SHELXS97 & SHELXL97 13.59% for [|Fo| > 4σ (|Fo|)] DLMΔF Monoclinic, P21/c a=9.9032(5) Åb=8.6675(4) Åc=34.0283(18) Å β=90.088(3)°V=29

La Broncho-Pneumopathie Chronique Obstructive (BPCO) est une maladie pulmonaire inflammatoire consécutive à l'exposition chronique à la pollution atmosphérique et surtout au tabagisme dans environ 90% des cas. Cette maladie se caractérise par une obstruction des bronches due à une hypersécrétion de mucus, une hypertrophie des muscles lisses, ainsi qu’une destruction de la paroi des alvéoles respiratoires amenant le patient à l’emphysème. Le stress induit par la fumée de cigarette provoque une activation de la barrière épithéliale pulmonaire associée à une altération de la réponse immunitaire responsable d’une susceptibilité accrue aux infections pulmonaires. De ce fait, les patients atteints de cette maladie développent des exacerbations principalement liées à ces infections bactériennes en particulier à Non-Typable Haemophilus influenza (NTHi) et Streptoccocus pneumoniae (Sp).La cytokine IL-22 est un acteur très important des défenses antibactériennes et du maintien de la barrière épithéliale. Cette cytokine appartient à la grande famille de l’IL-10, et à la sous-famille des cytokines IL-20 composée de l’IL-19, l’IL-20 et l’IL-24. L’IL-22 se lie au récepteur formé par les sous-unités IL-10Rb et IL-22Ra, tandis que les cytokines IL-19, IL-20 et IL-24 utilisent deux récepteurs associant l’IL-20Rb avec l’IL-20Ra ou l’IL-22Ra. Il a été démontré que les cytokines de la famille IL-20 (IL-19, IL-20, IL-24) agissent sur la clairance bactérienne au cours d’une infection cutanée par Staphylococcus aureus (Myles et al., 2013), en inhibant la production des cytokines IL-17 et IL-22. De plus, des précédents travaux au laboratoire, ont montré un défaut de l’expression des cytokines IL-17 et IL-22 qui participaient à la susceptibilité à l’infection chez les souris atteintes de BPCO (Pichavant et al., 2015). Enfin, nos données actuelles montrent que l'exposition à la fumée de cigarette augmente l'expression des cytokines de la famille IL-20 et que l'inhibition de cette voie permet de bloquer le développement d'épisodes d'exacerbation chez des souris BPCO.L'objectif de cette thèse est de préciser le rôle des cytokines IL-20 dans la réponse à l'infection bactérienne (Sp, NTHi) tant dans un contexte physiologique qu'au cours d’un contexte mimant la BPCO. Pour cela, nous nous focaliserons sur le rôle de l’épithélium pulmonaire tant dans la production que dans la fonction de ces cytokines en contexte infectieux.Pour répondre à ces questions, nous avons analysé l’expression des cytokines IL-20 par l’épithélium pulmonaire in vitro et ex vivo dans un modèle murin mimant l’exacerbation de la BPCO ainsi que dans des biopsies pulmonaires de patients fumeurs atteints ou non de BPCO. Dans un second temps nous avons évalué la modulation par un anticorps bloquant le récepteur des cytokines IL-20 (anti-IL-20Rb) au cours de la réponse anti-infectieuse de l'épithélium dans nos modèles in vivo (souris infectées par Sp) et in vitro (cellules épithéliales de trachées murines). Nous avons en parallèle évalué l'implication des cytokines IL-20 dans la réparation épithéliale.L’ensemble des résultats acquis au cours de la thèse nous a permis de démontrer l'implication des cytokines IL-20 et de préciser leur rôle sur l’épithélium pulmonaire au cours de l'infection bactérienne ainsi que dans la pathologie de la BPCO. De plus, les résultats obtenus avec l’anticorps neutralisant anti-IL-20Rb dans ces contextes d’infections et de BPCO, font de celui-ci une potentielle piste thérapeutique pour le traitement des lésions dues à l’infection. / Chronic Obstructive Pulmonary Disease (COPD) is an inflammatory lung disease due to chronic exposure to air pollution and especially to cigarette smoke exposure in approximately 90% of the cases. This disease is characterized by obstruction of the bronchi due to hypersecretion of mucus, hypertrophy of the smooth muscles, and destruction of the alveolar wall leading the patient to emphysema. The stress induced by cigarette smoke exposure causes activation of resident cells including pulmonary epithelial cells and an alteration of the immune system responsible for an increased susceptibility to pulmonary infections. As a result, patients with this disease develop exacerbations especially du to Non-Typable Haemophilus influenza (NTHi) and Streptoccocus pneumoniae (Sp).The IL-22 cytokine plays a key role in antibacterial defenses and maintenance of the epithelial barrier. This cytokine belongs to the large IL-10 family, and to the IL-20 cytokine subfamily also including IL-19, IL-20 and IL-24. IL-22 binds to the receptor formed by the IL-10Rb and IL-22Ra subunits, while the IL-19, IL-20 and IL-24 cytokines binds to IL-20Rb associated with either IL-20Ra or IL-22Ra subunits. IL-20 cytokines (IL-19, IL-20, IL-24) have been shown to impair bacterial clearance during cutaneous infection with Staphylococcus aureus (Myles et al., 2013), by inhibiting the production of IL-17 and IL-22 cytokines. In addition, previous work in the laboratory showed a defect in the expression of IL-17 and IL-22 cytokines contributing to the susceptibility to infection in COPD mice (Pichavant et al., 2015). In fact, our current data show that exposure to cigarette smoke increases cytokine expression of the IL-20 family and that inhibition of this pathway blocks the development of exacerbation episodes in COPD mice.The aim of this thesis is to clarify the role of IL-20 cytokines in the response to bacterial infections (Sp, NTHi) both in a physiological context and in a context mimicking COPD. To do so, we will focus on the role of pulmonary epithelium both in the production and function of these cytokines in infectious context.To answer these questions, we analyzed the expression of IL-20 cytokines by pulmonary epithelium in vitro and ex vivo in a mouse model mimicking the COPD exacerbation as well as in pulmonary biopsies of smokers and non-smokers patients and of COPD patients. In a second step we evaluated the modulation by an IL-20 receptor blocking antibody (anti-IL-20Rb) of the anti-infectious response in our in vitro (murine tracheal epithelial cells) and in vivo models (Sp-infected mice). In parallel, we evaluated the involvement of IL-20 cytokines in the epithelial repair.All the results acquired during the thesis allowed us to demonstrate the expression of IL-20 cytokines and to demonstrate their role on the pulmonary epithelium during bacterial infection as well as in COPD. In addition, the results obtained with the anti-IL-20Rb neutralizing antibody in these contexts of infections and COPD, suggests a potential therapeutic application for respiratory infection.

No description available.

Analysis of signaling cascade of protein kinase StkP in Streptococcus pneumoniae Streptococcus pneumoniae is not only an important human pathogen but also an appropriate model organism to investigate cell division in ovoid bacteria. This bacterium lacks both, NO and Min systems for selection of cell division site. Thus, the mechanism which determines the site of cell division is unknown. Additionally, the genome of S. pneumoniae encodes a single gene for eukaryotic-like serine/threonine protein kinase StkP and a single gene for eukaryotic-like serine/threonine protein phosphatase of PP2C type called PhpP. StkP is one of the main regulators of cell division. Cell division is probably affected by the phosphorylation of its substrates, which include, among others, cell division proteins FtsZ, FtsA, DivIVA, MacP, Jag/KhpB/EloR, and LocZ/MapZ. The aim of the first project of this dissertation thesis is determination of the function of protein LocZ in the cell division. In summary, locZ is not essential, however, it is involved in proper septum placement in S. pneumoniae and our data suggest that it is a positive regulator of Z-ring placement. Cells lacking LocZ are able to form Z-ring, but the Z-ring is spatially misplaced resulting in cell division defects, shape deformation, and generation of unequally sized,...

Inflammaging is a hallmark of human aging. Defined as low-grade, chronic inflammation, it is characterized by heightened proinflammatory cytokines in the blood and tissues and predicts morbidity and mortality. Despite this, the etiology of inflammaging and its role in infection have remained elusive, an issue this thesis addressed. First, we provided a comprehensive overview of an intranasal Streptococcus pneumoniae colonization model (Chapter 2). We described in detail the colonization technique, and demonstrated how to isolate and phenotype recruited cells, quantify bacterial load and measure production of immune mediators in the nasopharynx. Since both myeloid cell recruitment and tumour necrosis factor (TNF) production were increased following S. pneumoniae colonization with age, we investigated whether TNF directly augmented monocyte frequency (Chapter 3). TNF increased CCR2 expression on monocytes in old mice, leading to their enhanced egress from the bone marrow, resulting in enrichment of this population in the circulation. Monocyte numbers directly influenced plasma IL-6 levels, and this negatively impacted anti-bacterial responses, as monocyte blockade improved pneumococcal clearance in old mice. Lastly, to better understand the fundamental source of inflammaging, we studied the impact of the host microbiome on its development. This work was rooted in Elie Metchnikoff’s early predictions that leakage of intestinal bacterial products could dysregulate macrophage function, resulting in inflammation that would progress aging (Chapter 4). We showed that old mice had increased intestinal permeability, aberrant expression of cellular junction genes and increased microbial translocation from the gut to the blood. Germ-free mice lived longer than their conventionally colonized counterparts, and were protected from the development of inflammaging and defective macrophage function. Together, these studies resolve a major disparity in the field by demonstrating that systemic TNF production is initiated by increased levels of circulating bacterial products, driving functional defects in myeloid cells, which ultimately impairs anti-bacterial immunity. / Thesis / Candidate in Philosophy

Made available in DSpace on 2014-07-29T15:26:24Z (GMT). No. of bitstreams: 1 tese caritas medicina tropical.pdf: 1784866 bytes, checksum: b85c7ab5508fd90ff809159f179430cc (MD5) Previous issue date: 2009-02-17 / Objectives: (i) to identify risk factors for S. pneumoniae penicillin nonsusceptible isolates (PNSp) in children attending day-care centers (DCCs) in Goiânia, Brazil and to assess the genetic patterns of pneumococcal isolates; (ii) to estimate the coverage for carriage serotypes for the 7-valente (PCV7) pneumococcal conjugate vaccine, and for the investigational 10 (PCV10) and 13-valent (PCV13) vaccines; (iii) to assess the genetic relatedeness between isolates expressing capsular type 14 and those non(sero)- typeable isolates (NTPn); (iv) to investigate if carriage isolates match genetically to any international pneumococcal clone (PMEN network). Methods: A cross-sectional survey of carriage PNSp was conducted among 1.192 children, 2 months to 5 years of age, attending 62 DCCs in Central Brazil. Capsular typing was performed in PNSp isolates (CLSI, 2007) and in a sample of isolates susceptible to penicillin (PSSp) matched to PNSp and DCCs whenever possible. Serotyping was performed by Quellung reactions and confirmed by multibead assay. NTPn isolates and serotype 14 were tested by PCR for capsule genes. Odds ratio for PNSp carriage and respective 95% confidence interval (95%CI) were assessed by logistic regression. Pulsed field gel electrophoresis (PFGE) was applied to assess the genetic similarity between PNSp serotype 14 and NTPn isolates. PCR was performed for the presence of pneumococcal capsule gene locus. For comparison purpose we also evaluated the genetic profile of PNSp serotype 14 invasive strains derived from the current pneumococcal invasive disease surveillance for the same pediatric population. Isolates were epidemiologically related if they shared &#8805;80% similarity on the dendrogram (Dice coefficient). A cluster was defined as three or more related isolates. Results: A total of 686 pneumococci were isolated for a colonization rate of 57.6% and 178 (25.8%) were PNSp. Among the PNSp isolates the usual common types were found: 14 (53%), 23F (10.2%), 6B (6%), 19F (4.8%) and 19A (4.2%). PSSp isolates displayed 30 different serotypes although serotype 14 was the most common. Overall a high prevalence of NTPn (11.1%) was observed with 62.9% PNSp. Serotypes coverage xvi for the PCV7, PCV10 and PCV13 vaccines were 55.2%, 55.9% and 65.1%, respectively. Being less than 24 months of age (OR=1.79; p=0.006), hospitalization in the previous three months (OR=2.19; p=0.025), and recurrent acute otitis media (OR=2.89; p=0.013) were independently associated with PNSp in a multivariate model. Among the 123 PNSp submitted to PFGE (106/carriage and 17/ invasive isolates) a major group of 34 serotype 14 strains (8 invasive and 26 carriage) was identified and found to be genetically related to the global pneumococcal clone Spain 9V-3 (82.7% similarity). All NTPn presented capsule gene locus and 10 (45.4%) of them presented capsule gene locus to type 14. Conclusions: (i) DCC attendees with history of recurrent AOM could significantly contribute to the spread of nasopharyngeal PNSp strains into the community; (ii) epidemiologic and molecular evidences support the findings that pneumococcal nonypeable carriage isolates are genetically similar to carriage and invasive isolates expressing capsular type 14; (iii) carriage and invasive isolates circulating in Goiânia belong to a serotype 14 variant of the Spain 9V -3 clone and play a critical role in the spread of PNSp strains to the entire pediatric community of Goiânia / Objetivo: (i) identificar fatores associados à colonização nasofaríngea por S. pneumoniae não suscetíveis à penicilina em crianças que frequentam creches no município de Goiânia-GO e caracterizar geneticamente as cepas não suscetíveis; (ii) determinar a cobertura das vacinas conjugadas pneumocócicas 7, 10 e 13 valente; (iii) avaliar o relacionamento genético entre cepas do sorotipo 14 e pneumococos não tipáveis (PnNT); (iv) identificar a presença de cepas colonizadoras relacionadas geneticamente aos clones internacionais de S. pneumoniae. Metodologia: Um estudo de prevalência de portador de pneumococo não suscetível à penicilina (SpNP) foi conduzido de agosto a dezembro de 2005, em 1192 crianças de dois a 59 meses de idade, atendidas em 62 creches em Goiânia. Os testes de suscetibilidade antimicrobiana seguiram as recomendações do CLSI de 2007 e a sorotipagem foi realizada pela reação de Quellung e confirmada por ensaio multibead. Isolados PnNT e do sorotipo 14 foram analisados por reação de PCR. Odds ratio para portador de SpNP e respectivos intervalos de 95% de confiança foram estimados por regressão logística. Para avaliar a similaridade genética entre os isolados de portador (sorotipo 14 e PnNT) e isolados invasivos (sorotipo 14) obtidos de crianças de Goiânia utilizou-se amostras de isolados invasivos de um estudo maior de vigilância populacional que vem sendo conduzido desde 2007. Assim, eletroforese em campo pulsado (PFGE) foi utilizada para a tipagem molecular. Definiu-se como linhagem a presença de três ou mais cepas resistentes com similaridade genética &#8805; 80%. Resultados: S. pneumoniae foi isolado de 686 (57,6%) crianças das creches e 178 (25,9%) dessas eram portadoras de SpNS. Sorotipo 14 (53%), 23F (10,2%), 6B (6%), 19F (4,8%) e 19A (4,2%) estavam presentes em 78,2% dos PnNS. Detectou-se alta prevalência (11,1%) de isolados não tipáveis, dos quais 62.9% eram resistentes à penicilina. A cobertura dos sorotipos colonizadores para as vacinas 7-valente, 10- valente e 13-valente foi respectivamente 55,2%, 55,9% e 65,1%. Crianças menores de 24 meses de idade (OR=1,79; p=0,006), hospitalização nos últimos três meses (OR=2,19; p=0,025), e otite média aguda recorrente (OR=2,89; p=0,013) foram fatores xiv independentemente associados com SpNS na análise multivariada. Entre os 123 isolados submetidos à PFGE, 106 eram de nasofaringe de crianças das creches, dos quais 84 expressavam a cápsula tipo 14 e 22 eram isolados PnNT. Todas as cepas invasivas eram sorotipo 14. A maior linhagem agrupou 34 pneumococos do sorotipo 14, com 82,7% de similaridade, os quais foram geneticamente relacionados ao clone Spain 9V-3. Todas as cepas PnNT apresentaram locus para o gene da cápsula para o tipo 14. Houve uma diferença estatisticamente significante entre os valores da CIM para a penicilina entre as três principais linhagens (Krukal-Wallis, p<0,001). Conclusões: (i) crianças com otite média recorrente podem exercer papel importante na disseminação de pneumococos resistentes para a comunidade; (ii) Evidências genéticas apóiam os achados de que cepas de pneumococo não tipáveis assemelham-se ao genótipo das cepas do sorotipo 14; (iii) isolados de portadores e invasivos que circulam em Goiânia pertencem a um sorotipo 14 variante do clone Spain9V-3, responsável pela disseminação da resistência do pneumococo na população pediátrica de Goiânia

No description available.