Class 2015
Grant: PD/BD/113629/2015
PhD thesis
Adaptation of Burkholderia cepacia complex bacteria to the cystic fibrosis lung: focus on lipopolysaccharide O-antigen and cell wall physical properties
Advisor
• Isabel Sá-Correia, Professor @ IST/ULisboa, PT
Collaborators
• Vaughn Cooper, Professor @ University of Pittsburgh, School of Medicine, USA
• Miguel Valvano, Professor @ Queen’s University of Belfast, UK
• Celeste Barreto, Luísa Pereira (Cystic Fibrosis Center), Luís Lito, JoséMelo Cristino (Clinical PathologyService), Hospital de Santa Maria, Lisboa, PT
PhD Degree complete: Discussion on January 28, 2020
THESIS ABSTRACT
The Burkholderia cepacia complex (Bcc) comprises 24 closely related opportunistic pathogenic species with high potential to cause serious chronic respiratory infections in cystic fibrosis (CF) patients. The CF lung is a hostile environment due to host immune responses, continuous antibiotic therapy, high levels of oxidative stress and low oxygen concentration. This thesis work contributed to the understanding of the adaptive strategies of Bcc bacteria to the CF lung at a genome-wide level and with a focus on the cell envelope. The genome sequences of twenty B. cenocepacia and B. multivorans clonal variants that co-inhabited the same CF patient-lung environment, for at least 3 years, were compared. Mutation rates were in the range of 2.08-2.27 SNPs/year leading to rapid genotypic and phenotypic diversification. The comparative genomic analysis indicated that the lipopolysaccharide O-antigen locus undergoes alterations during chronic infection. A novel hybrid O-antigen locus, encoding a novel O-antigen structure only present in the first B. cenocepacia isolate, was compared with the loci of 10 subsequent clonal variants that lack the O-antigen. A systematic retrospective longitudinal screening, including 357 isolates from 19 chronically infected patients, representing 21 strains of six Bcc species, was performed to know if the loss of the O-antigen during chronic infection can be considered a general phenomenon. Only isolates from the two most prevalent and feared species, B. cenocepacia and B multivorans, showed the referred tendency. To understand the role of long-term infection in B. cenocepacia cell surface properties, atomic force microscopy was used to study cell adhesion, cell morphology and mechanical properties. The ability of the early isolate to adhere to AFM Si3N4-tip was significantly higher compared with late variants that lack the O-antigen and exhibit identical adhesion values. A reduction of cell size and cell shape evolution from the rod form typical of the species to a coccoid–like form was also observed.
RESUMO DA TESE
O complexo Burkholderia cepacia (Bcc) inclui 24 espécies patogénicas oportunistas muito relacionadas, com elevado potencial de causar infeções respiratórias crónicas graves em pacientes com fibrose quística (CF). O pulmão de CF é um ambiente hostil devido às respostas imunes do hospedeiro, à terapia continuada com antibióticos, elevados níveis de stresse oxidativo e baixa concentração de oxigénio. Este trabalho de tese vem contribuir para a compreensão das estratégias adaptativas daquelas bactérias ao pulmão de CF, envolvendo todo o genoma e foco no envelope celular. Foram comparadas as sequências genómicas de vinte variantes clonais de B. cenocepacia e B. multivorans que cohabitaram o mesmo ambiente do pulmão de um doente com FQ, durante pelo menos três anos. As frequências de mutação encontravam-se na gama 2,08-2,27 SNPs/ano, levando à rápida diversificação genotípica e fenotípica. A análise genómica comparativa indicou que o locus do O-antigénio (OAg) do lipopolissacárido (LPS) sofre alterações durante a infeção crónica. Um novo locus híbrido para o OAg, codificando uma nova estrutura presente apenas no primeiro isolado de B de cenocepacia, foi comparado com os loci de 10 variantes clonais subsequentes que não possuem o OAg. Foi realizado um estudo longitudinal e retrospetivo que incluiu 357 isolados de 19 pacientes infetados cronicamente, representando 21 estirpes de seis espécies de Bcc, para saber se a perda do OAg durante a infeção crónica pode ser considerada um fenómeno geral. Somente os isolados das duas espécies mais prevalentes e temidas, B. cenocepacia e B. multivorans, apresentaram a tendência referida. Para entender o papel que a infeção crónica exerce nas propriedades da superfície celular de B. cenocepacia, foi usada a microscopia de força atómica (AFM) para estudar a adesão celular, morfologia celular e propriedades mecânicas. A capacidade de adesão do isolado inicial é significativamente superior à dos variantes tardios que não possuem o OAg e exibem valores de adesão idênticos. Também foi observada uma redução do tamanho das células e a sua evolução da forma bastonete típica da espécie para a forma cocóide.
PUBLICATIONS
Papers
Hassan, A.A., Dos Santos, S.C., Cooper, V.S., and Sa-Correia, I., Comparative Evolutionary Patterns of Burkholderia cenocepacia and B. multivorans During Chronic Co-infection of a Cystic Fibrosis Patient Lung. Frontiers in Microbiology 11, 574626, 2020.
Tavares, M., Kozak, M., Balola, A., Coutinho, C.P., Godinho, C.P., Hassan, A.A., Cooper, V.S., Sá-Correia, I., Adaptation and Survival of Burkholderia cepacia and B. contaminans During Long-Term Incubation in Saline Solutions Containing Benzalkonium Chloride. Frontiers in Bioengineering and Biotechnology 8(630), 2020.
Hassan, A.A., Coutinho, C.P., and Sá-Correia, I. Burkholderia cepacia complex species differ in the frequency of variation of the lipopolysaccharide O-antigen expression during cystic fibrosis chronic respiratory infection. Frontiers in Cellular and Infection Microbiology 9(273), 2019.
Hassan AA, Vitorino MV, Rodrigues MS, Sá-Correia I, Variation of Burkholderia cenocepacia cell wall morphology and mechanical properties during cystic fibrosis lung infection, assessed by atomic force microscopy, Scientific Reports. 9(1), 16118, 2018.
Hassan, A. A., Maldonado, R.F., dos Santos, S.C., Di Lorenzo, F., Silipo, A., Coutinho, C.P., Cooper, V.S., Molinaro, A., Valvano, M.A., Sá-Correia, I., Structure of O-Antigen and Hybrid Biosynthetic Locus in Burkholderia cenocepacia Clonal Variants Recovered from a Cystic Fibrosis Patient. Frontiers in Microbiology 8, 1027, 2017.
Oral Communications
Hassan AA, Vitorino MA, Rodrigues MS and Sá-Correia I, “Diversification of Burkholderia cenocepacia cell wall mechanical properties during cystic fibrosis chronic lung infection, assessed by atomic force microscopy”, 21st IBCWG, 2-5 May, 2018, Dublin, Ireland
Poster Communications
A Amir Hassan, Miguel V Vitorino, Carla P Coutinho, Mario S Rodrigues and Isabel Sá-Correia, “Comparison of the physical properties of Burkholderia cenocepacia clonal variants isolated during cystic fibrosis chronic lung infection, studied by atomic force microscopy”, MicroBiotec2017, December 7-8, 2017, Porto, Portugal
A. Amir Hassan, Sandra C. dos Santos, Rita F. Maldonado, Carla P. Coutinho, Flaviana Di Lorenzo, Robert Sebra, Marcus Dillon, Vaughn S. Cooper, Antonio Molinaro, Miguel Valvano and Isabel Sá-Correia. “Lipopolysaccharide O-antigen modification during long-term infection in cystic fibrosis: comparative genomic analysis of 11 Burkholderia cenocepacia sequential clonal variants, XIX National Congress of Biochemistry, December 8–10, 2016, Guimarães, Portugal
A. Amir Hassan, Carla P. Coutinho, Rita F. Maldonado and Isabel Sá-Correia, “Variation of O-antigen presence in Burkholderia cepacia complex bacteria lipopolysaccharide (LPS) during chronic lung infection: a 20-year retrospective study at a national cystic fibrosis (CF) center”, MicroBiotec2015, December 10-12, 2015, Évora, Portugal
DOCTORAL PROGRAM (36 ECTS)
• General Doctoral Training (6 ECTS)
• Advanced Experimental Techniques and methodologies (6 ECTS)
• Bioentrepreneurship (6 ECTS)
• Advanced Topics in Bioengineering and Biosciences (6 ECTS)
• Outreach and Teaching Skills (6 ECTS)
• Functional and Comparative Genomics (6 ECTS)
Advanced courses: Genome Assembly and Annotation Course, by Elixir, October 23-27, 2017, Instituto Gulbenkian Ciência, Oeiras, Portugal
Current position/address
Protein Research Unit, Laboratory of Microbiology,
Department Biochemistry and Microbiology Campus Ledeganck, KL
Faculty of Sciences, Gent University
Ledeganckstraat 35, B-9000 Ghent, Belgium