Bacterial Molecular Genetics

This project refers to the search and characterization of targets involved in the modulation of virulence and resistance in MDR gram-negative pathogens. To address this general work plan, we combine methods of microbial genetics, comparative genomics, transcriptomic analysis, structural biology and bioinformatics within a pangenomic strategy. The main objectives addressed are: i) selection of "type strains" from phenotypic and genotypic data and subsequent sequencing and annotation of their genomes when they are not available; ii) comparative genomics and determination of shared proteomes and proteomes exclusive to the most extreme strains in terms of virulence and/or drug resistance (in collaboration with the Computational Biology group led by Xavier Daura); iii) molecular epidemiology and genotype-phenotype correlations; iv) study of the intrinsic physiological mechanisms involved in virulence/resistance through the generation of specific mutants and evaluation of their phenotypes and virulence in different alternative animal models (Caenorhabditis elegans and Galleria mellonella, and zebrafish in collaboration with the Evolutionary Immunology group led by Nerea Roher); and v) final selection and validation of candidate targets based on the previous results.

 

In nosocomial settings, although with a moderate incidence, S. maltophilia can cause serious infections, mainly in immunocompromised patients. Once in a human host, S. maltophilia is difficult to eradicate due to its ability to form biofilms and its natural arsenal of antibiotic resistance. Cell-to-cell signaling processes in S. maltophilia, controlled by quorum sensing (QS) systems, are believed to be fundamental in the regulation of several of these virulence and resistance factors. Our group aims to deepen the understanding of the QS networks of S. maltophilia at the functional and molecular levels and exploit this knowledge for the identification of targets for the development of an antimicrobial strategy based on quorum sensing quenching. Antimicrobial compounds against these targets could potentially be used to reduce the pathogenic capacity of the bacteria and/or enhance the activity of current antibiotics.

 

One of the antibiotics that the group has focused on in recent years has been colistin. Colistin (polymyxin E) is an antibiotic used as a last resort for MDR gram-negative pathogens. Colistin is a polycationic peptide that interacts with the bacterial lipopolysaccharide (LPS) of the outer membrane and through its hydrophobic portion disrupts bacterial cell membranes, causing cell lysis. The emergence of isolates resistant to colistin, as for other antibiotics, is considered a serious problem that requires special attention since it is a restricted use drug. Our group has recently alerted to the existence of adaptive resistance and heteroresistance to colistin in S. maltophilia. We are currently identifying the genetic determinants of colistin resistance and applying genomic sequencing and transcriptome analyses to reveal the mechanisms that govern these heterogeneous resistance phenomena. Furthermore, and in collaboration with the laboratories of Uwe Mamat and Nicolas Gisch at the Borstel Research Center (RCB, Germany), we are studying LPS modifications as a mechanism of colistin resistance in S. maltophilia.

 

In collaboration with the Computational Biology group of the IBB led by Xavier Daura, we work on the design of antibacterial impacts identified through virtual screening of chemical compounds against key targets of the pathogenesis and virulence processes. The drug discovery process and experimental validation of successful compounds includes: i) target proposal based on experimental evidence; ii) analysis of the intrinsic antimicrobial activity of selected compounds against the target and an extended panel of MDR gram-negative organisms; iii) the potentiating activity of the affected compounds in combination with known antibiotics; iv) determination of the inhibitory effect of the compounds on biofilm formation; v) efficacy assays based on the analysis of antimicrobial or antivirulence activity in vivo in different animal models; and vi) in vitro evaluation of the induction of drug resistance. In addition, we are evaluating, in collaboration with Timothy O'Sullivan at University College Cork (Ireland), molecules that interfere with the bacteria's native QS communication system and prevent them from producing biofilm.

 

QUORUM-SENSING-DEPENDENT RESPONSE REGULATORS IN STENOTROPHOMONAS MALTOPHILIA AS SOURCE OF NOVEL ANTIMICROBIAL AND ANTIBIOFILM STRATEGIES (STENORR). Convocatòria PID 2023; Ministerio de Ciencia e Innovación (MICINN). Execution: 1/09/24 → 31/08/27

QUORUM SENSING REGULATORY NETWORKS IN STENOTROPHOMONAS MALTOPHILIA AS TARGETS FOR THERAPEUTIC ALTERNATIVES TO CURRENT ANTIBIOTICS. Convocatòria PID2019; Ministeri de Ciència i Innovació (MICINN). Execution: 1/06/20 → 30/05/23

The Mla system and its role in maintaining outer membrane barrier function in Stenotrophomonas maltophilia. Front Cell Infect Microbiol. 2024 Feb 26;14:1346565. doi: 10.3389/fcimb.2024.1346565.

Synthesis and evaluation of aromatic BDSF bioisosteres on biofilm formation and colistin sensitivity in pathogenic bacteria. Eur J Med Chem. 2023 Dec 5;261:115819. doi: 10.1016/j.ejmech.2023.115819.

A Stenotrophomonas maltophilia TetR-Like Transcriptional Regulator Involved in Fatty Acid Metabolism Is Controlled by Quorum Sensing Signals. Appl Environ Microbiol. 2023 Jun 28;89(6):e0063523. doi: 10.1128/aem.00635-23.

Improved mini-Tn7 Delivery Plasmids for Fluorescent Labeling of Stenotrophomonas maltophilia. Appl Environ Microbiol. 2023 Jun 28;89(6):e0031723. doi: 10.1128/aem.00317-23.

Synthesis and evaluation of novel furanones as biofilm inhibitors in opportunistic human pathogens. Eur J Med Chem. 2022; 242:114678. doi: 10.1016/j.ejmech.2022.114678.

Strain-specific interspecies interactions between co-isolated pairs of Staphylococcus aureus and Pseudomonas aeruginosa from patients with tracheobronchitis or bronchial colonization. Sci Rep. 2022; 12(1):3374. doi: 10.1038/s41598-022-07018-5.

The Pseudomonas aeruginosa substrate-binding protein Ttg2D functions as a general glycerophospholipid transporter across the periplasm. Commun Biol. 2021; 4(1):448. doi: 10.1038/s42003-021-01968-8.

Antigen Discovery in Bacterial Panproteomes. Methods Mol Biol. 2021; 2183:43-62. doi: 10.1007/978-1-0716-0795-4_5.

Effects of cigarette smoke on the administration of isoniazid and rifampicin to macrophages infected with Mycobacterium tuberculosis. Exp Lung Res. 2021; 47(2):87-97. doi: 10.1080/01902148.2020.1854371.

Phenotypic and Transcriptomic Analyses of Seven Clinical Stenotrophomonas maltophilia Isolates Identify a Small Set of Shared and Commonly Regulated Genes Involved in the Biofilm Lifestyle. Appl Environ Microbiol. 2020; 86(24):e02038-20. doi: 10.1128/AEM.02038-20.

Genetic Variants of the DSF Quorum Sensing System in Stenotrophomonas maltophilia Influence Virulence and Resistance Phenotypes Among Genotypically Diverse Clinical Isolates. Front Microbiol. 2020; 11:1160. doi: 10.3389/fmicb.2020.01160.

The phylogenetic landscape and nosocomial spread of the multidrug-resistant opportunist Stenotrophomonas maltophilia. Nat Commun. 2020; 11(1):2044. doi: 10.1038/s41467-020-15123-0.

E-cigarettes: Effects in phagocytosis and cytokines response against Mycobacterium tuberculosis. PLoS One. 2020; 15(2):e0228919. doi: 10.1371/journal.pone.0228919.

Sulfonamide-based diffusible signal factor analogs interfere with quorum sensing in Stenotrophomonas maltophilia and Burkholderia cepacia. Future Med Chem. 2019 Jul;11(13):1565-1582. doi: 10.4155/fmc-2019-0015.

Heterogeneous Colistin-Resistance Phenotypes Coexisting in Stenotrophomonas maltophilia Isolates Influence Colistin Susceptibility Testing. Front Microbiol. 2018; 9:2871. doi: 10.3389/fmicb.2018.02871.

Quorum Sensing Signaling and Quenching in the Multidrug-Resistant Pathogen Stenotrophomonas maltophilia. Front Cell Infect Microbiol. 2018; 8:122. doi: 10.3389/fcimb.2018.00122.

Proteomic analysis of outer membrane proteins and vesicles of a clinical isolate and a collection strain of Stenotrophomonas maltophilia. J Proteomics. 2016; 142:122-9. doi: 10.1016/j.jprot.2016.05.001.

Triclosan-induced genes Rv1686c-Rv1687c and Rv3161c are not involved in triclosan resistance in Mycobacterium tuberculosis. Sci Rep. 2016; 6:26221. doi: 10.1038/srep26221.

Decoding the genetic and functional diversity of the DSF quorum-sensing system in Stenotrophomonas maltophilia. Front Microbiol. 2015; 6:761. doi: 10.3389/fmicb.2015.00761. eCollection 2015.

Draft Genome Sequence of Stenotrophomonas maltophilia Strain UV74 Reveals Extensive Variability within Its Genomic Group. Genome Announc. 2015; 3(3):e00611-15. doi: 10.1128/genomeA.00611-15.

Stenotrophomonas maltophilia responds to exogenous AHL signals through the LuxR solo SmoR (Smlt1839). Front Cell Infect Microbiol. 2015; 5:41. doi: 10.3389/fcimb.2015.00041.

Animals devoid of pulmonary system as infection models in the study of lung bacterial pathogens. Front Microbiol. 2015; 6:38. doi: 10.3389/fmicb.2015.00038.

Draft Genome Sequence of Stenotrophomonas maltophilia Strain M30, Isolated from a Chronic Pressure Ulcer in an Elderly Patient. Genome Announc. 2014; 2(3):e00576-14. doi: 10.1128/genomeA.00576-14.

Two different rpf clusters distributed among a population of Stenotrophomonas maltophilia clinical strains display differential diffusible signal factor production and virulence regulation. J Bacteriol. 2014; 196(13):2431-42. doi: 10.1128/JB.01540-14.

antibacTR: dynamic antibacterial-drug-target ranking integrating comparative genomics, structural analysis and experimental annotation. BMC Genomics. 2014; 15(1):36. doi: 10.1186/1471-2164-15-36.

Abundance of the Quorum-Sensing Factor Ax21 in Four Strains of Stenotrophomonas maltophilia Correlates with Mortality Rate in a New Zebrafish Model of Infection. PLoS One. 2013; 8(6):e67207. doi: 10.1371/journal.pone.0067207.