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García-López M, Hernández P, Megias D, Ferrándiz MJ, de la Campa AG. Physiologic and Transcriptomic Effects Triggered by Overexpression of Wild Type and Mutant DNA Topoisomerase I in Streptococcus pneumoniae. Int J Mol Sci 2023; 24:15800. [PMID: 37958782 PMCID: PMC10648598 DOI: 10.3390/ijms242115800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/20/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
Topoisomerase I (TopoI) in Streptococcus pneumoniae, encoded by topA, is a suitable target for drug development. Seconeolitsine (SCN) is a new antibiotic that specifically blocks this enzyme. We obtained the topARA mutant, which encodes an enzyme less active than the wild type (topAWT) and more resistant to SCN inhibition. Likely due to the essentiality of TopoI, we were unable to replace the topAWT allele by the mutant topARA version. We compared the in vivo activity of TopoIRA and TopoIWT using regulated overexpression strains, whose genes were either under the control of a moderately (PZn) or a highly active promoter (PMal). Overproduction of TopoIRA impaired growth, increased SCN resistance and, in the presence of the gyrase inhibitor novobiocin (NOV), caused lower relaxation than TopoIWT. Differential transcriptomes were observed when the topAWT and topARA expression levels were increased about 5-fold. However, higher increases (10-15 times), produced a similar transcriptome, affecting about 52% of the genome, and correlating with a high DNA relaxation level with most responsive genes locating in topological domains. These results confirmed that TopoI is indeed the target of SCN in S. pneumoniae and show the important role of TopoI in global transcription, supporting its suitability as an antibiotic target.
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Affiliation(s)
- Miriam García-López
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain;
| | - Pablo Hernández
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain;
| | - Diego Megias
- Unidad de Microscopía Confocal, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain;
| | - María-José Ferrándiz
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain;
| | - Adela G. de la Campa
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain;
- Presidencia, Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain
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de Vasconcelos Junior AA, Tirado-Vélez JM, Martín-Galiano AJ, Megias D, Ferrándiz MJ, Hernández P, Amblar M, de la Campa AG. StaR Is a Positive Regulator of Topoisomerase I Activity Involved in Supercoiling Maintenance in Streptococcus pneumoniae. Int J Mol Sci 2023; 24:ijms24065973. [PMID: 36983048 PMCID: PMC10053502 DOI: 10.3390/ijms24065973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/16/2023] [Accepted: 03/18/2023] [Indexed: 03/30/2023] Open
Abstract
The DNA topoisomerases gyrase and topoisomerase I as well as the nucleoid-associated protein HU maintain supercoiling levels in Streptococcus pneumoniae, a main human pathogen. Here, we characterized, for the first time, a topoisomerase I regulator protein (StaR). In the presence of sub-inhibitory novobiocin concentrations, which inhibit gyrase activity, higher doubling times were observed in a strain lacking staR, and in two strains in which StaR was over-expressed either under the control of the ZnSO4-inducible PZn promoter (strain ΔstaRPZnstaR) or of the maltose-inducible PMal promoter (strain ΔstaRpLS1ROMstaR). These results suggest that StaR has a direct role in novobiocin susceptibility and that the StaR level needs to be maintained within a narrow range. Treatment of ΔstaRPZnstaR with inhibitory novobiocin concentrations resulted in a change of the negative DNA supercoiling density (σ) in vivo, which was higher in the absence of StaR (σ = -0.049) than when StaR was overproduced (σ = -0.045). We have located this protein in the nucleoid by using super-resolution confocal microscopy. Through in vitro activity assays, we demonstrated that StaR stimulates TopoI relaxation activity, while it has no effect on gyrase activity. Interaction between TopoI and StaR was detected both in vitro and in vivo by co-immunoprecipitation. No alteration of the transcriptome was associated with StaR amount variation. The results suggest that StaR is a new streptococcal nucleoid-associated protein that activates topoisomerase I activity by direct protein-protein interaction.
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Affiliation(s)
| | - Jose M Tirado-Vélez
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain
| | - Antonio J Martín-Galiano
- Unidades Centrales Científico-Técnicas, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain
| | - Diego Megias
- Unidad de Microscopía Confocal, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain
| | - María-José Ferrándiz
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain
| | - Pablo Hernández
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain
| | - Mónica Amblar
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain
| | - Adela G de la Campa
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain
- Presidencia, Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain
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García-López M, Megias D, Ferrándiz MJ, de la Campa AG. The balance between gyrase and topoisomerase I activities determines levels of supercoiling, nucleoid compaction, and viability in bacteria. Front Microbiol 2023; 13:1094692. [PMID: 36713152 PMCID: PMC9875019 DOI: 10.3389/fmicb.2022.1094692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 12/23/2022] [Indexed: 01/13/2023] Open
Abstract
Two enzymes are responsible for maintaining supercoiling in the human pathogen Streptococcus pneumoniae, gyrase (GyrA2GyrB2) and topoisomerase I. To attain diverse levels of topoisomerase I (TopoI, encoded by topA), two isogenic strains derived from wild-type strain R6 were constructed: PZn topA, carrying an ectopic topA copy under the control of the ZnSO4-regulated PZn promoter and its derivative ΔtopAPZn topA, which carries a topA deletion at its native chromosomal location. We estimated the number of TopoI and GyrA molecules per cell by using Western-blot and CFUs counting, and correlated these values with supercoiling levels. Supercoiling was estimated in two ways. We used classical 2D-agarose gel electrophoresis of plasmid topoisomers to determine supercoiling density (σ) and we measured compaction of nucleoids using for the first time super-resolution confocal microscopy. Notably, we observed a good correlation between both supercoiling calculations. In R6, with σ = -0.057, the average number of GyrA molecules per cell (2,184) was higher than that of TopoI (1,432), being the GyrA:TopoI proportion of 1:0.65. In ΔtopAPZn topA, the number of TopoI molecules depended, as expected, on ZnSO4 concentration in the culture media, being the proportions of GyrA:TopoI molecules in 75, 150, and 300 μM ZnSO4 of 1:0.43, 1:0.47, and 1:0.63, respectively, which allowed normal supercoiling and growth. However, in the absence of ZnSO4, a higher GyrA:TopoI ratio (1:0.09) caused hyper-supercoiling (σ = -0.086) and lethality. Likewise, growth of ΔtopAPZn topA in the absence of ZnSO4 was restored when gyrase was inhibited with novobiocin, coincidentally with the resolution of hyper-supercoiling (σ change from -0.080 to -0.068). Given that TopoI is a monomer and two molecules of GyrA are present in the gyrase heterotetramer, the gyrase:TopoI enzymes proportion would be 1:1.30 (wild type R6) or of 1:1.26-0.86 (ΔtopAPZn topA under viable conditions). Higher proportions, such as 1:0.18 observed in ΔtopAPZn topA in the absence of ZnSO4 yielded to hyper-supercoiling and lethality. These results support a role of the equilibrium between gyrase and TopoI activities in supercoiling maintenance, nucleoid compaction, and viability. Our results shed new light on the mechanism of action of topoisomerase-targeting antibiotics, paving the way for the use of combination therapies.
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Affiliation(s)
- Míriam García-López
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Diego Megias
- Unidad de Microscopía Confocal, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - María-José Ferrándiz
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain,*Correspondence: María-José Ferrándiz, ✉
| | - Adela G. de la Campa
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain,Presidencia, Consejo Superior de Investigaciones Científicas, Madrid, Spain,Adela G. de la Campa, ✉
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Amblar M, Zaballos Á, de la Campa AG. Role of PatAB Transporter in Efflux of Levofloxacin in Streptococcus pneumoniae. Antibiotics (Basel) 2022; 11:antibiotics11121837. [PMID: 36551495 PMCID: PMC9774293 DOI: 10.3390/antibiotics11121837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/13/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
PatAB is an ABC bacterial transporter that facilitates the export of antibiotics and dyes. The overexpression of patAB genes conferring efflux-mediated fluoroquinolone resistance has been observed in several laboratory strains and clinical isolates of Streptococcus pneumoniae. Using transformation and whole-genome sequencing, we characterized the fluoroquinolone-resistance mechanism of one S. pneumoniae clinical isolate without mutations in the DNA topoisomerase genes. We identified the PatAB fluoroquinolone efflux-pump as the mechanism conferring a low-level resistance to ciprofloxacin (8 µg/mL) and levofloxacin (4 µg/mL). Genetic transformation experiments with different amplimers revealed that the entire patA plus the 5'-terminus of patB are required for levofloxacin-efflux. By contrast, only the upstream region of the patAB operon, plus the region coding the N-terminus of PatA containing the G39D, T43A, V48A and D100N amino acid changes, are sufficient to confer a ciprofloxacin-efflux phenotype, thus suggesting differences between fluoroquinolones in their binding and/or translocation pathways. In addition, we identified a novel single mutation responsible for the constitutive and ciprofloxacin-inducible upregulation of patAB. This mutation is predicted to destabilize the putative rho-independent transcriptional terminator located upstream of patA, increasing transcription of downstream genes. This is the first report demonstrating the role of the PatAB transporter in levofloxacin-efflux in a pneumoccocal clinical isolate.
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Affiliation(s)
- Mónica Amblar
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Ctra Majadahonda-Pozuelo Km 2.200, Majadahonda, 28220 Madrid, Spain
- Correspondence: (M.A.); (A.G.d.l.C.); Tel.: +34-91448283 (M.A.); +34-91448944 (A.G.d.l.C.)
| | - Ángel Zaballos
- Unidades Centrales Científico Técnicas, Instituto de Salud Carlos III, Ctra Majadahonda-Pozuelo Km 2.200, Majadahonda, 28220 Madrid, Spain
| | - Adela G de la Campa
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Ctra Majadahonda-Pozuelo Km 2.200, Majadahonda, 28220 Madrid, Spain
- Presidencia, Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain
- Correspondence: (M.A.); (A.G.d.l.C.); Tel.: +34-91448283 (M.A.); +34-91448944 (A.G.d.l.C.)
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Tirado-Vélez JM, Carreño D, Sevillano D, Alou L, Yuste J, de la Campa AG. Seconeolitsine, the Novel Inhibitor of DNA Topoisomerase I, Protects against Invasive Pneumococcal Disease Caused by Fluoroquinolone-Resistant Strains. Antibiotics (Basel) 2021; 10:antibiotics10050573. [PMID: 34068007 PMCID: PMC8152265 DOI: 10.3390/antibiotics10050573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/07/2021] [Accepted: 05/09/2021] [Indexed: 11/16/2022] Open
Abstract
Antibiotic resistance in Streptococcus pneumoniae has increased worldwide, making fluoroquinolones an alternative therapeutic option. Fluoroquinolones inhibit the type II DNA topoisomerases (topoisomerase IV and gyrase). In this study we have evaluated the in vivo activity of seconeolitsine, an inhibitor of topoisomerase I. Levofloxacin (12.5 to 50 mg/kg) or seconeolitsine (5 to 40 mg/kg) were administered every 12 h during two days in mice infected with a serotype 8-resistant strain. At 48 h, a 70% protection was obtained with seconeolitsine (40 mg/kg; p < 0.001). However, survival with levofloxacin was 20%, regardless of the dose. In addition, seconeolitsine decreased bacteremia efficiently. Levofloxacin had higher levels in serum than seconeolitsine (Cmax of 14.7 vs. 1.6; p < 0.01) and higher values of area under the serum concentration-time curve (AUC0-12h of 17.3 vs. 5; p < 0.01). However, seconeolitsine showed higher levels of time to peak concentration and elimination half-life. This is consistent with the higher binding of seconeolitsine to plasma proteins (40% and 80% when used at 1 µg/mL and 50 µg/mL, respectively) in comparison to levofloxacin (12% at 5 µg/mL and 33% at 50 µg/mL). Our results suggest that seconeolitsine would be a promising therapeutic alternative against pneumococcal isolates with high fluoroquinolone resistance levels.
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Affiliation(s)
- Jose Manuel Tirado-Vélez
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain; (J.M.T.-V.); (D.C.)
| | - David Carreño
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain; (J.M.T.-V.); (D.C.)
| | - David Sevillano
- Microbiology Division-Department of Medicine, Universidad Complutense de Madrid, 28040 Madrid, Spain; (D.S.); (L.A.)
| | - Luis Alou
- Microbiology Division-Department of Medicine, Universidad Complutense de Madrid, 28040 Madrid, Spain; (D.S.); (L.A.)
| | - José Yuste
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain; (J.M.T.-V.); (D.C.)
- CIBER de Enfermedades Respiratorias, 28029 Madrid, Spain
- Correspondence: (J.Y.); (A.G.d.l.C.); Tel.: +34-918-223-620 (J.Y.); +34-918-223-944 (A.G.d.l.C.)
| | - Adela G. de la Campa
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain; (J.M.T.-V.); (D.C.)
- Presidencia, Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain
- Correspondence: (J.Y.); (A.G.d.l.C.); Tel.: +34-918-223-620 (J.Y.); +34-918-223-944 (A.G.d.l.C.)
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Ferrándiz MJ, Hernández P, de la Campa AG. Genome-wide proximity between RNA polymerase and DNA topoisomerase I supports transcription in Streptococcus pneumoniae. PLoS Genet 2021; 17:e1009542. [PMID: 33930020 PMCID: PMC8115823 DOI: 10.1371/journal.pgen.1009542] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 05/12/2021] [Accepted: 04/10/2021] [Indexed: 02/02/2023] Open
Abstract
Streptococcus pneumoniae is a major cause of disease and death that develops resistance to multiple antibiotics. DNA topoisomerase I (TopoI) is a novel pneumococcal drug target. TopoI is the sole type-I pneumococcal topoisomerase that regulates supercoiling homeostasis in this bacterium. In this study, a direct in vitro interaction between TopoI and RNA polymerase (RNAP) was detected by surface plasmon resonance. To understand the interplay between transcription and supercoiling regulation in vivo, genome-wide association of RNAP and TopoI was studied by ChIP-Seq. RNAP and TopoI were enriched at the promoters of 435 and 356 genes, respectively. Higher levels of expression were consistently measured in those genes whose promoters recruit both RNAP and TopoI, in contrast with those enriched in only one of them. Both enzymes occupied a narrow region close to the ATG codon. In addition, RNAP displayed a regular distribution throughout the coding regions. Likewise, the summits of peaks called with MACS tool, mapped around the ATG codon in both cases. However, RNAP showed a broader distribution towards ATG-downstream positions. Remarkably, inhibition of RNAP with rifampicin prevented the localization of TopoI at promoters and, vice versa, inhibition of TopoI with seconeolitsine prevented the binding of RNAP to promoters. This indicates a functional interplay between RNAP and TopoI. To determine the molecular factors responsible for RNAP and TopoI co-recruitment, we looked for DNA sequence motifs. We identified a motif corresponding to a -10-extended promoter for TopoI and for RNAP. Furthermore, RNAP was preferentially recruited to genes co-directionally oriented with replication, while TopoI was more abundant in head-on genes. TopoI was located in the intergenic regions of divergent genes pairs, near the promoter of the head-on gene of the pair. These results suggest a role for TopoI in the formation/stability of the RNAP-DNA complex at the promoter and during transcript elongation. Streptococcus pneumoniae is a main cause of pneumonia, meningitis and sepsis. Antibiotic resistance in this bacterium has spread worldwide, compromising medical treatment. Therefore, the development of new drugs directed to novel targets is necessary. DNA topology is essential for the regulation of replication and gene expression. Topology is regulated and maintained by DNA topoisomerases, carrying out nicking-closing reactions. Type I and type II topoisomerases act on single-stranded and double-stranded DNA, respectively. Although type II topoisomerases are the target of clinically used antibiotics, there are no clinical antibiotics directed against type I topoisomerases. Seconeolitsine, a new drug targeting topoisomerase I, is effective against bacteria that have a single type I topoisomerase, such as Streptococcus pneumoniae and Mycobacterium tuberculosis. In this report, we studied the role of topoisomerase I in transcription. We found that topoisomerase I and RNA polymerase physically interact in vitro and co-localize at gene promoters in vivo. Binding of each of these enzymes to promoters was prevented by the specific inhibition of the other enzyme, supporting a role for topoisomerase I in RNA polymerase transcription.
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Affiliation(s)
- María-José Ferrándiz
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Pablo Hernández
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Adela G. de la Campa
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
- Presidencia, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- * E-mail:
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Martín-Galiano AJ, Escolano-Martínez MS, Corsini B, de la Campa AG, Yuste J. Immunization with SP_1992 (DiiA) Protein of Streptococcus pneumoniae Reduces Nasopharyngeal Colonization and Protects against Invasive Disease in Mice. Vaccines (Basel) 2021; 9:vaccines9030187. [PMID: 33668195 PMCID: PMC7995960 DOI: 10.3390/vaccines9030187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/19/2021] [Accepted: 02/19/2021] [Indexed: 11/16/2022] Open
Abstract
Knowledge-based vaccinology can reveal uncharacterized antigen candidates for a new generation of protein-based anti-pneumococcal vaccines. DiiA, encoded by the sp_1992 locus, is a surface protein containing either one or two repeats of a 37mer N-terminal motif that exhibits low interstrain variability. DiiA belongs to the core proteome, contains several conserved B-cell epitopes, and is associated with colonization and pathogenesis. Immunization with DiiA protein via the intraperitoneal route induced a strong IgG response, including different IgG subtypes. Vaccination with DiiA increased bacterial clearance and induced protection against sepsis, conferring 70% increased survival at 48 h post-infection when compared to the adjuvant control. The immunogenic response and survival rates in mice immunized with a truncated DiiA version lacking 119 N-terminal residues were remarkably lower, confirming the relevance of the repeat zone in the immunoprotection by DiiA. Intranasal immunization of mice with the entire recombinant protein elicited mucosal IgG and IgA responses that reduced bacterial colonization of the nasopharynx, confirming that this protein might be a vaccine candidate for reducing the carrier rate. DiiA constitutes an example of how functionally unannotated proteins may still represent promising candidates that can be used in prophylactic strategies against the pneumococcal carrier state and invasive disease.
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Affiliation(s)
- Antonio J. Martín-Galiano
- Centro Nacional de Microbiología, Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain; (M.S.E.-M.); (B.C.); (A.G.d.l.C.)
- Correspondence: (A.J.M.-G.); (J.Y.); Tel.: +34-918223976 (A.J.M.-G.); +34-918223620 (J.Y.)
| | - María S. Escolano-Martínez
- Centro Nacional de Microbiología, Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain; (M.S.E.-M.); (B.C.); (A.G.d.l.C.)
| | - Bruno Corsini
- Centro Nacional de Microbiología, Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain; (M.S.E.-M.); (B.C.); (A.G.d.l.C.)
| | - Adela G. de la Campa
- Centro Nacional de Microbiología, Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain; (M.S.E.-M.); (B.C.); (A.G.d.l.C.)
- Presidencia Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain
| | - José Yuste
- Centro Nacional de Microbiología, Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain; (M.S.E.-M.); (B.C.); (A.G.d.l.C.)
- CIBER de Enfermedades Respiratorias (CIBERES), 28029 Madrid, Spain
- Correspondence: (A.J.M.-G.); (J.Y.); Tel.: +34-918223976 (A.J.M.-G.); +34-918223620 (J.Y.)
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Valenzuela MV, Domenech M, Mateos-Martínez P, González-Camacho F, de la Campa AG, García MT. Antibacterial activity of a DNA topoisomerase I inhibitor versus fluoroquinolones in Streptococcus pneumoniae. PLoS One 2020; 15:e0241780. [PMID: 33141832 PMCID: PMC7608930 DOI: 10.1371/journal.pone.0241780] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 10/20/2020] [Indexed: 12/23/2022] Open
Abstract
The DNA topoisomerase complement of Streptococcus pneumoniae is constituted by two type II enzymes (topoisomerase IV and gyrase), and a single type I enzyme (topoisomerase I). These enzymes maintain the DNA topology, which is essential for replication and transcription. While fluoroquinolones target the type II enzymes, seconeolitsine, a new antimicrobial agent, targets topoisomerase I. We compared for the first time the in vitro effect of inhibition of topoisomerase I by seconeolitsine and of the type II topoisomerases by the fluoroquinolones levofloxacin and moxifloxacin. We used three isogenic non-encapsulated strains and five non-vaccine serotypes isolates belonging to two circulating pneumococcal clones, ST638 (2 strains) and ST1569V (3 strains). Each group contained strains with diverse susceptibility to fluoroquinolones. Minimal inhibitory concentrations, killing curves and postantibiotic effects were determined. Seconeolitsine demonstrated the fastest and highest bactericidal activity against planktonic bacteria and biofilms. When fluoroquinolone-susceptible planktonic bacteria were considered, seconeolitsine induced postantibiotic effects (1.00−1.87 h) similar than levofloxacin (1.00−2.22 h), but longer than moxifloxacin (0.39−1.71 h). The same effect was observed in sessile bacteria forming biofilms. Seconeolitsine induced postantibiotic effects (0.84−2.31 h) that were similar to those of levofloxacin (0.99−3.32 h) but longer than those of moxifloxacin (0.89−1.91 h). The greatest effect was observed in the viability and adherence of bacteria in the postantibiotic phase. Seconeolitsine greatly reduced the thickness of the biofilms formed in comparison with fluoroquinolones: 2.91 ± 0.43 μm (seconeolitsine), 7.18 ± 0.58 μm (levofloxacin), 17.08 ± 1.02 μm (moxifloxacin). When fluoroquinolone-resistant bacteria were considered, postantibiotic effects induced by levofloxacin and moxifloxacin, but not by seconeolitsine, were shorter, decreasing up to 5-fold (levofloxacin) or 2-fold (moxifloxacin) in planktonic cells, and up to 1.7 (levofloxacin) or 1.4-fold (moxifloxacin) during biofilm formation. Therefore, topoisomerase I inhibitors could be an alternative for the treatment of pneumococcal diseases, including those caused by fluoroquinolone-resistant isolates.
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Affiliation(s)
- Myriam V. Valenzuela
- Departamento de Genética, Unidad de Microbiología, Fisiología y Microbiología, Universidad Complutense, Madrid, Spain
| | - Mirian Domenech
- Unidad de Neumococos, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid; Spain
| | - Patricia Mateos-Martínez
- Departamento de Genética, Unidad de Microbiología, Fisiología y Microbiología, Universidad Complutense, Madrid, Spain
| | - Fernando González-Camacho
- Unidad de Neumococos, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid; Spain
| | - Adela G. de la Campa
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid; Spain
- Presidencia, Consejo Superior de Investigaciones Científicas, Madrid, Spain
- * E-mail: (MTG); (AGC)
| | - Maria Teresa García
- Departamento de Genética, Unidad de Microbiología, Fisiología y Microbiología, Universidad Complutense, Madrid, Spain
- * E-mail: (MTG); (AGC)
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Sánchez-Tarjuelo R, Cortegano I, Manosalva J, Rodríguez M, Ruíz C, Alía M, Prado MC, Cano EM, Ferrándiz MJ, de la Campa AG, Gaspar ML, de Andrés B. The TLR4-MyD88 Signaling Axis Regulates Lung Monocyte Differentiation Pathways in Response to Streptococcus pneumoniae. Front Immunol 2020; 11:2120. [PMID: 33042124 PMCID: PMC7525032 DOI: 10.3389/fimmu.2020.02120] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 08/05/2020] [Indexed: 12/20/2022] Open
Abstract
Streptococcus pneumoniae is the main cause of bacterial pneumonia, a condition that currently produces significant global morbidity and mortality. The initial immune response to this bacterium occurs when the innate system recognizes common motifs expressed by many pathogens, events driven by pattern recognition receptors like the Toll-like family receptors (TLRs). In this study, lung myeloid-cell populations responsible for the innate immune response (IIR) against S. pneumoniae, and their dependence on the TLR4-signaling axis, were analyzed in TLR4-/- and Myeloid-Differentiation factor-88 deficient (MyD88-/-) mice. Neutrophils and monocyte-derived cells were recruited in infected mice 3-days post-infection. Compared to wild-type mice, there was an increased bacterial load in both these deficient mouse strains and an altered IIR, although TLR4-/- mice were more susceptible to bacterial infection. These mice also developed fewer alveolar macrophages, weaker neutrophil infiltration, less Ly6Chigh monocyte differentiation and a disrupted classical and non-classical monocyte profile. The pro-inflammatory cytokine profile (CXCL1, TNF-α, IL-6, and IL-1β) was also severely affected by the lack of TLR4 and no induction of Th1 was observed in these mice. The respiratory burst (ROS production) after infection was profoundly dampened in TLR4-/- and MyD88-/- mice. These data demonstrate the complex dynamics of myeloid populations and a key role of the TLR4-signaling axis in the IIR to S. pneumoniae, which involves both the MyD88 and TRIF (Toll/IL-1R domain-containing adaptor-inducing IFN-β) dependent pathways.
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Affiliation(s)
| | - Isabel Cortegano
- Immunobiology Department, Carlos III Health Institute, Madrid, Spain
| | - Juliana Manosalva
- Immunobiology Department, Carlos III Health Institute, Madrid, Spain
| | | | - Carolina Ruíz
- Immunobiology Department, Carlos III Health Institute, Madrid, Spain
| | - Mario Alía
- Immunobiology Department, Carlos III Health Institute, Madrid, Spain
| | | | - Eva M. Cano
- Chronic Disease Programme, Carlos III Health Institute, Madrid, Spain
| | | | - Adela G. de la Campa
- Bacterial Genetics Department, Carlos III Health Institute, Madrid, Spain
- Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | | | - Belén de Andrés
- Immunobiology Department, Carlos III Health Institute, Madrid, Spain
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10
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Ferrándiz MJ, Cercenado MI, Domenech M, Tirado-Vélez JM, Escolano-Martínez MS, Yuste J, García E, de la Campa AG, Martín-Galiano AJ. An Uncharacterized Member of the Gls24 Protein Superfamily Is a Putative Sensor of Essential Amino Acid Availability in Streptococcus pneumoniae. Microb Ecol 2019; 77:471-487. [PMID: 29978356 DOI: 10.1007/s00248-018-1218-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 06/03/2018] [Indexed: 06/08/2023]
Abstract
Proteins belonging to the Gls24 superfamily are involved in survival of pathogenic Gram-positive cocci under oligotrophic conditions and other types of stress, by a still unknown molecular mechanism. In Firmicutes, this superfamily includes three different valine-rich orthologal families (Gls24A, B, C) with different potential interactive partners. Whereas the Streptococcus pneumoniae Δgls24A deletion mutant experienced a general long growth delay, the Δgls24B mutant grew as the parental strain in the semisynthetic AGCH medium but failed to grow in the complex Todd-Hewitt medium. Bovine seroalbumin (BSA) was the component responsible for this phenotype. The effect of BSA on growth was concentration-dependent and was maintained when the protein was proteolyzed but not when heat-denatured, suggesting that BSA dependence was related to oligopeptide supplementation. Global transcriptional analyses of the knockout mutant revealed catabolic derepression and induction of chaperone and oligopeptide transport genes. This mutant also showed increased sensibility to cadmium and high temperature. The Δgls24B mutant behaved as a poor colonizer in the nasopharynx of mice and showed 20-fold competence impairment. Experimental data suggest that Gls24B plays a central role as a sensor of amino acid availability and its connection to sugar catabolism. This metabolic rewiring can be compensated in vitro, at the expenses of external oligopeptide supplementation, but reduce important bacteria skills prior to efficiently address systemic virulence traits. This is an example of how metabolic factors conserved in enterococci, streptococci, and staphylococci can be essential for survival in poor oligopeptide environments prior to infection progression.
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Affiliation(s)
- María J Ferrándiz
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - María I Cercenado
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Miriam Domenech
- Centro de Investigaciones Biológicas (CIB-CSIC), Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - José M Tirado-Vélez
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | | | - Jose Yuste
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Ernesto García
- Centro de Investigaciones Biológicas (CIB-CSIC), Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Adela G de la Campa
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
- Presidencia, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
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11
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García MT, Carreño D, Tirado-Vélez JM, Ferrándiz MJ, Rodrigues L, Gracia B, Amblar M, Ainsa JA, de la Campa AG. Boldine-Derived Alkaloids Inhibit the Activity of DNA Topoisomerase I and Growth of Mycobacterium tuberculosis. Front Microbiol 2018; 9:1659. [PMID: 30087665 PMCID: PMC6066988 DOI: 10.3389/fmicb.2018.01659] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 07/04/2018] [Indexed: 11/13/2022] Open
Abstract
The spread of multidrug-resistant isolates of Mycobacterium tuberculosis requires the discovery of new drugs directed to new targets. In this study, we investigated the activity of two boldine-derived alkaloids, seconeolitsine (SCN) and N-methyl-seconeolitsine (N-SCN), against M. tuberculosis. These compounds have been shown to target DNA topoisomerase I enzyme and inhibit growth of Streptococcus pneumoniae. Both SCN and N-SCN inhibited M. tuberculosis growth at 1.95-15.6 μM, depending on the strain. In M. smegmatis this inhibitory effect correlated with the amount of topoisomerase I in the cell, hence demonstrating that this enzyme is the target for these alkaloids in mycobacteria. The gene coding for topoisomerase I of strain H37Rv (MtbTopoI) was cloned into pQE1 plasmid of Escherichia coli. MtbTopoI was overexpressed with an N-terminal 6-His-tag and purified by affinity chromatography. In vitro inhibition of MtbTopoI activity by SCN and N-SCN was tested using a plasmid relaxation assay. Both SCN and N-SCN inhibited 50% of the enzymatic activity at 5.6 and 8.4 μM, respectively. Cleavage of single-stranded DNA was also inhibited with SCN. The effects on DNA supercoiling were also evaluated in vivo in plasmid-containing cultures of M. tuberculosis. Plasmid supercoiling densities were -0.060 in cells untreated or treated with boldine, and -0.072 in 1 × MIC N-SCN treated cells, respectively, indicating that the plasmid became hypernegatively supercoiled in the presence of N-SCN. Altogether, these results demonstrate that the M. tuberculosis topoisomerase I enzyme is an attractive drug target, and that SCN and N-SCN are promising lead compounds for drug development.
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Affiliation(s)
- María T. García
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - David Carreño
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - José M. Tirado-Vélez
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - María J. Ferrándiz
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Liliana Rodrigues
- CIBER de Enfermedades Respiratorias, Madrid, Spain
- Departamento de Microbiología, Medicina Preventiva y Salud Pública, Facultad de Medicina, Universidad de Zaragoza, Zaragoza, Spain
- Fundación Agencia Aragonesa para la Investigación y el Desarrollo, Zaragoza, Spain
| | - Begoña Gracia
- CIBER de Enfermedades Respiratorias, Madrid, Spain
- Departamento de Microbiología, Medicina Preventiva y Salud Pública, Facultad de Medicina, Universidad de Zaragoza, Zaragoza, Spain
| | - Mónica Amblar
- Unidad de Patología Molecular de Neumococo, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - José A. Ainsa
- CIBER de Enfermedades Respiratorias, Madrid, Spain
- Departamento de Microbiología, Medicina Preventiva y Salud Pública, Facultad de Medicina, Universidad de Zaragoza, Zaragoza, Spain
| | - Adela G. de la Campa
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
- Presidencia, Consejo Superior de Investigaciones Científicas, Madrid, Spain
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12
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Martín-Galiano AJ, Ferrándiz MJ, de la Campa AG. Bridging Chromosomal Architecture and Pathophysiology of Streptococcus pneumoniae. Genome Biol Evol 2018; 9:350-361. [PMID: 28158485 PMCID: PMC5381641 DOI: 10.1093/gbe/evw299] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/22/2016] [Indexed: 11/14/2022] Open
Abstract
The chromosome of Streptococcus pneumoniae is organized into topological domains based on its transcriptional response to DNA relaxation: Up-regulated (UP), down-regulated (DOWN), nonregulated (NR), and AT-rich. In the present work, NR genes found to have highly conserved chromosomal locations (17% of the genome) were categorized as members of position-conserved nonregulated (pcNR) domains, while NR genes with a variable position (36% of the genome) were classified as members of position-variable nonregulated (pvNR) domains. On average, pcNR domains showed high transcription rates, optimized codon usage, and were found to contain only a small number of RUP/BOX/SPLICE repeats. They were also poor in exogenous genes but enriched in leading strand genes that code for proteins involved in primary metabolism with central roles within the interactome. In contrast, pvNR genes coding for cell wall proteins, paralogs, virulence factors and immunogenic candidates for protein-based vaccines were found to be overrepresented. DOWN domains were enriched in genes essential for infection. Many UP and DOWN domain genes were seen to be activated during different stages of competence, whereas pcNR genes tended to be repressed until the competence was switched off. Pneumococcal genes appear to be subject to a topology-driven selection pressure that defines the chromosomal location of genes involved in metabolism, virulence and competence. The pcNR domains are interleaved between UP and DOWN domains according to a pattern that suggests the existence of macrodomain entities. The term “topogenomics” is here proposed to describe the study of the topological rules of genomes and their relationship with physiology.
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Affiliation(s)
- Antonio J Martín-Galiano
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Majadahonda, Spain
| | - María J Ferrándiz
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Majadahonda, Spain
| | - Adela G de la Campa
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Majadahonda, Spain.,Unidad de Genética Bacteriana, Presidencia, Consejo Superior de Investigaciones Científicas, Madrid, Spain
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13
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Ferrándiz MJ, Carreño D, Ayora S, de la Campa AG. HU of Streptococcus pneumoniae Is Essential for the Preservation of DNA Supercoiling. Front Microbiol 2018; 9:493. [PMID: 29662473 PMCID: PMC5890176 DOI: 10.3389/fmicb.2018.00493] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 03/02/2018] [Indexed: 01/11/2023] Open
Abstract
The histone-like protein HU is a conserved nucleoid-associated protein that is involved in the maintenance of the bacterial chromosome architecture. It is the only known nucleoid-associated protein in Streptococcus pneumoniae, but it has not been studied. The pneumococcal gene encoding this protein, hlp, is shown herein to be essential for cell viability. Its disruption was only possible either when it was duplicated in the chromosome and its expression induced from the P Zn promoter, or when hlp was cloned into a plasmid under the control of the inducible P mal promoter. In vitro assays indicated that pneumococcal HU shows a preference for binding to supercoiled DNA rather than to linear or nicked DNA. In vivo experiments in which the amount of HU was manipulated showed a relationship between the amount of HU and the level of DNA supercoiling. A twofold reduction in the amount of HU triggered a 21% increase in DNA relaxation in untreated cells. However, in cells treated with novobiocin, a drug that relaxes DNA by inhibiting DNA gyrase, a 35% increase in DNA relaxation was observed, instead of the expected 20% in cells with a constitutive HU amount. Conversely, a fourfold HU increase caused only 14% of DNA relaxation in the presence of novobiocin. Taken together, these results support an essential role for HU in the maintenance of DNA supercoiling in S. pneumoniae.
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Affiliation(s)
- María-José Ferrándiz
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - David Carreño
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Silvia Ayora
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Adela G de la Campa
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain.,Presidencia, Consejo Superior de Investigaciones Científicas, Madrid, Spain
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14
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Alvarado M, Martín-Galiano AJ, Ferrándiz MJ, Zaballos Á, de la Campa AG. Upregulation of the PatAB Transporter Confers Fluoroquinolone Resistance to Streptococcus pseudopneumoniae. Front Microbiol 2017; 8:2074. [PMID: 29123510 PMCID: PMC5662624 DOI: 10.3389/fmicb.2017.02074] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 10/10/2017] [Indexed: 11/27/2022] Open
Abstract
We characterized the mechanism of fluoroquinolone-resistance in two isolates of Streptococcus pseudopneumoniae having fluoroquinolone-efflux as unique mechanism of resistance. Whole genome sequencing and genetic transformation experiments were performed together with phenotypic determinations of the efflux mechanism. The PatAB pump was identified as responsible for efflux of ciprofloxacin (MIC of 4 μg/ml), ethidium bromide (MICs of 8-16 μg/ml) and acriflavine (MICs of 4-8 μg/ml) in both isolates. These MICs were at least 8-fold lower in the presence of the efflux inhibitor reserpine. Complete genome sequencing indicated that the sequence located between the promoter of the patAB operon and the initiation codon of patA, which putatively forms an RNA stem-loop structure, may be responsible for the efflux phenotype. RT-qPCR determinations performed on RNAs of cultures treated or not treated with subinhibitory ciprofloxacin concentrations were performed. While no significant changes were observed in wild-type Streptococcus pneumoniae R6 strain, increases in transcription were detected in the ciprofloxacin-efflux transformants obtained with DNA from efflux-positive isolates, in the ranges of 1.4 to 3.4-fold (patA) and 2.1 to 2.9-fold (patB). Ciprofloxacin-induction was related with a lower predicted free energy for the stem-loop structure in the RNA of S. pseudopneumoniae isolates (-13.81 and -8.58) than for R6 (-15.32 kcal/mol), which may ease transcription. The presence of these regulatory variations in commensal S. pseudopneumoniae isolates, and the possibility of its transfer to Streptococcus pneumoniae by genetic transformation, could increase fluoroquinolone resistance in this important pathogen.
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Affiliation(s)
- María Alvarado
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Antonio J. Martín-Galiano
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - María J. Ferrándiz
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Ángel Zaballos
- Unidad de Genómica, Instituto de Salud Carlos III, Madrid, Spain
| | - Adela G. de la Campa
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
- Presidencia, Consejo Superior de Investigaciones Científicas, Madrid, Spain
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15
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de la Campa AG, Ferrándiz MJ, Martín-Galiano AJ, García MT, Tirado-Vélez JM. The Transcriptome of Streptococcus pneumoniae Induced by Local and Global Changes in Supercoiling. Front Microbiol 2017; 8:1447. [PMID: 28824578 PMCID: PMC5534458 DOI: 10.3389/fmicb.2017.01447] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 07/17/2017] [Indexed: 01/28/2023] Open
Abstract
The bacterial chromosome is compacted in a manner optimal for DNA transactions to occur. The degree of compaction results from the level of DNA-supercoiling and the presence of nucleoid-binding proteins. DNA-supercoiling is homeostatically maintained by the opposing activities of relaxing DNA topoisomerases and negative supercoil-inducing DNA gyrase. DNA-supercoiling acts as a general cis regulator of transcription, which can be superimposed upon other types of more specific trans regulatory mechanism. Transcriptomic studies on the human pathogen Streptococcus pneumoniae, which has a relatively small genome (∼2 Mb) and few nucleoid-binding proteins, have been performed under conditions of local and global changes in supercoiling. The response to local changes induced by fluoroquinolone antibiotics, which target DNA gyrase subunit A and/or topoisomerase IV, involves an increase in oxygen radicals which reduces cell viability, while the induction of global supercoiling changes by novobiocin (a DNA gyrase subunit B inhibitor), or by seconeolitsine (a topoisomerase I inhibitor), has revealed the existence of topological domains that specifically respond to such changes. The control of DNA-supercoiling in S. pneumoniae occurs mainly via the regulation of topoisomerase gene transcription: relaxation triggers the up-regulation of gyrase and the down-regulation of topoisomerases I and IV, while hypernegative supercoiling down-regulates the expression of topoisomerase I. Relaxation affects 13% of the genome, with the majority of the genes affected located in 15 domains. Hypernegative supercoiling affects 10% of the genome, with one quarter of the genes affected located in 12 domains. However, all the above domains overlap, suggesting that the chromosome is organized into topological domains with fixed locations. Based on its response to relaxation, the pneumococcal chromosome can be said to be organized into five types of domain: up-regulated, down-regulated, position-conserved non-regulated, position-variable non-regulated, and AT-rich. The AT content is higher in the up-regulated than in the down-regulated domains. Genes within the different domains share structural and functional characteristics. It would seem that a topology-driven selection pressure has defined the chromosomal location of the metabolism, virulence and competence genes, which suggests the existence of topological rules that aim to improve bacterial fitness.
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Affiliation(s)
- Adela G de la Campa
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos IIIMadrid, Spain.,Presidencia, Consejo Superior de Investigaciones CientíficasMadrid, Spain
| | - María J Ferrándiz
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos IIIMadrid, Spain
| | - Antonio J Martín-Galiano
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos IIIMadrid, Spain
| | - María T García
- Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad ComplutenseMadrid, Spain
| | - Jose M Tirado-Vélez
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos IIIMadrid, Spain
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Brito L, Wilton J, Ferrándiz MJ, Gómez-Sanz A, de la Campa AG, Amblar M. Absence of tmRNA Has a Protective Effect against Fluoroquinolones in Streptococcus pneumoniae. Front Microbiol 2017; 7:2164. [PMID: 28119681 PMCID: PMC5222879 DOI: 10.3389/fmicb.2016.02164] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 12/23/2016] [Indexed: 11/13/2022] Open
Abstract
The transfer messenger RNA (tmRNA), encoded by the ssrA gene, is a small non-coding RNA involved in trans-translation that contributes to the recycling of ribosomes stalled on aberrant mRNAs. In most bacteria, its inactivation has been related to a decreased ability to respond to and recover from a variety of stress conditions. In this report, we investigated the role of tmRNA in stress adaptation in the human pathogen Streptococcus pneumoniae. We constructed a tmRNA deletion mutant and analyzed its response to several lethal stresses. The ΔssrA strain grew slower than the wild type, indicating that, although not essential, tmRNA is important for normal pneumococcal growth. Moreover, deletion of tmRNA increased susceptibility to UV irradiation, to exogenous hydrogen peroxide and to antibiotics that inhibit protein synthesis and transcription. However, the ΔssrA strain was more resistant to fluoroquinolones, showing twofold higher MIC values and up to 1000-fold higher survival rates than the wild type. Deletion of SmpB, the other partner in trans-translation, also reduced survival to levofloxacin in a similar extent. Accumulation of intracellular reactive oxygen species associated to moxifloxacin and levofloxacin treatment was also highly reduced (∼100-fold). Nevertheless, the ΔssrA strain showed higher intracellular accumulation of ethidium bromide and levofloxacin than the wild type, suggesting that tmRNA deficiency protects pneumococcal cells from fluoroquinolone-mediated killing. In fact, analysis of chromosome integrity revealed that deletion of tmRNA prevented the fragmentation of the chromosome associated to levofloxacin treatment. Moreover, such protective effect appears to relay mainly on inhibition of protein synthesis, since a similar effect was observed with antibiotics that inhibit that process. The emergence and spread of drug-resistant pneumococci is a matter of concern and these results contribute to a better comprehension of the mechanisms underlying fluoroquinolones action.
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Affiliation(s)
- Liliana Brito
- Unidad de Patología Molecular del Neumococo, Centro Nacional de Microbiología, Instituto de Salud Carlos III Madrid, Spain
| | - Joana Wilton
- Unidad de Patología Molecular del Neumococo, Centro Nacional de Microbiología, Instituto de Salud Carlos III Madrid, Spain
| | - María J Ferrándiz
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III Madrid, Spain
| | - Alicia Gómez-Sanz
- Unidad de Patología Molecular del Neumococo, Centro Nacional de Microbiología, Instituto de Salud Carlos III Madrid, Spain
| | - Adela G de la Campa
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos IIIMadrid, Spain; Presidencia, Consejo Superior de Investigaciones CientíficasMadrid, Spain
| | - Mónica Amblar
- Unidad de Patología Molecular del Neumococo, Centro Nacional de Microbiología, Instituto de Salud Carlos III Madrid, Spain
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17
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Ferrándiz MJ, Martín-Galiano AJ, Arnanz C, Camacho-Soguero I, Tirado-Vélez JM, de la Campa AG. An increase in negative supercoiling in bacteria reveals topology-reacting gene clusters and a homeostatic response mediated by the DNA topoisomerase I gene. Nucleic Acids Res 2016; 44:7292-303. [PMID: 27378778 PMCID: PMC5009749 DOI: 10.1093/nar/gkw602] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 06/24/2016] [Indexed: 12/31/2022] Open
Abstract
We studied the transcriptional response to an increase in DNA supercoiling in Streptococcus pneumoniae by using seconeolitsine, a new topoisomerase I inhibitor. A homeostatic response allowing recovery of supercoiling was observed in cells treated with subinhibitory seconeolitsine concentrations. Supercoiling increases of 40.7% (6 μM) and 72.9% (8 μM) were lowered to 8.5% and 44.1%, respectively. Likewise, drug removal facilitated the recovery of cell viability and DNA-supercoiling. Transcription of topoisomerase I depended on the supercoiling level. Also specific binding of topoisomerase I to the gyrase A gene promoter was detected by chromatin-immunoprecipitation. The transcriptomic response to 8 μM seconeolitsine had two stages. An early stage, associated to an increase in supercoiling, affected 10% of the genome. A late stage, manifested by supercoiling recovery, affected 2% of the genome. Nearly 25% of the early responsive genes formed 12 clusters with a coordinated transcription. Clusters were 6.7–31.4 kb in length and included 9–22 responsive genes. These clusters partially overlapped with those observed under DNA relaxation, suggesting that bacteria manage supercoiling stress using pathways with common components. This is the first report of a coordinated global transcriptomic response that is triggered by an increase in DNA supercoiling in bacteria.
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Affiliation(s)
- María-José Ferrándiz
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain
| | - Antonio J Martín-Galiano
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain
| | - Cristina Arnanz
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain
| | - Isabel Camacho-Soguero
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain
| | - José-Manuel Tirado-Vélez
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain
| | - Adela G de la Campa
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain Presidencia. Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain
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Escolano-Martínez MS, Domenech A, Yuste J, Cercenado MI, Ardanuy C, Liñares J, de la Campa AG, Martin-Galiano AJ. DiiA is a novel dimorphic cell wall protein of Streptococcus pneumoniae involved in invasive disease. J Infect 2016; 73:71-81. [PMID: 27105656 DOI: 10.1016/j.jinf.2016.04.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 04/06/2016] [Accepted: 04/11/2016] [Indexed: 12/16/2022]
Abstract
OBJECTIVES Many outer multidomain proteins play fundamental virulent roles in an allele-dependent manner. We aimed to investigate the influence of the outer SP1992 protein, here renamed DiiA (Dimorphic invasion-involved A), in pneumococcal disease. METHODS The presence and type of diiA allele was screened by PCR in 560 clinical isolates. Isogenic mutants carrying progressive diiA deletions were constructed and checked in mouse models of infection. DiiA binding to human molecules was carried out by surface plasmon resonance. RESULTS The diiA gene is exclusive of Streptococcus pneumoniae and included in the core genome. DiiA variants contain one or two imperfect repeats (R1 and R2), an unstructured region and a cell-wall anchor domain. Clonal complexes carrying both repeats were associated with invasive disease, while those carrying R2 preferentially caused non-invasive syndromes in patients with underlying risk factors. Mutants lacking both repeats were less efficient in nasopharyngeal colonization and dissemination from lungs. Moreover, the ΔdiiA defective strain suffered a severe impairment in bacterial proliferation in blood. Purified DiiA bound to collagen and lactoferrin with high affinity. CONCLUSIONS DiiA is a distinctive pneumococcal virulence factor contributing to colonization and long-term invasion in this pathogen.
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Affiliation(s)
- María S Escolano-Martínez
- Instituto de Salud Carlos III, Centro Nacional de Microbiología, Carretera a Pozuelo, km 2.2, Majadahonda, 28220 Madrid, Spain
| | - Arnau Domenech
- CIBER de Enfermedades Respiratorias (CIBERES), Spain; Servicio de Microbiología, Hospital Universitari de Bellvitge, Universitat de Barcelona, IDIBELL, Feixa Llarga, sn. L'Hospitalet de Llobregat, 08907 Barcelona, Spain
| | - José Yuste
- Instituto de Salud Carlos III, Centro Nacional de Microbiología, Carretera a Pozuelo, km 2.2, Majadahonda, 28220 Madrid, Spain; CIBER de Enfermedades Respiratorias (CIBERES), Spain
| | - María I Cercenado
- Instituto de Salud Carlos III, Centro Nacional de Microbiología, Carretera a Pozuelo, km 2.2, Majadahonda, 28220 Madrid, Spain
| | - Carmen Ardanuy
- CIBER de Enfermedades Respiratorias (CIBERES), Spain; Servicio de Microbiología, Hospital Universitari de Bellvitge, Universitat de Barcelona, IDIBELL, Feixa Llarga, sn. L'Hospitalet de Llobregat, 08907 Barcelona, Spain
| | - Josefina Liñares
- CIBER de Enfermedades Respiratorias (CIBERES), Spain; Servicio de Microbiología, Hospital Universitari de Bellvitge, Universitat de Barcelona, IDIBELL, Feixa Llarga, sn. L'Hospitalet de Llobregat, 08907 Barcelona, Spain
| | - Adela G de la Campa
- Instituto de Salud Carlos III, Centro Nacional de Microbiología, Carretera a Pozuelo, km 2.2, Majadahonda, 28220 Madrid, Spain; Presidencia, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Antonio J Martin-Galiano
- Instituto de Salud Carlos III, Centro Nacional de Microbiología, Carretera a Pozuelo, km 2.2, Majadahonda, 28220 Madrid, Spain.
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Domenech A, Moreno J, Ardanuy C, Liñares J, de la Campa AG, Martin-Galiano AJ. A Novel Typing Method for Streptococcus pneumoniae Using Selected Surface Proteins. Front Microbiol 2016; 7:420. [PMID: 27064593 PMCID: PMC4815138 DOI: 10.3389/fmicb.2016.00420] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 03/16/2016] [Indexed: 11/15/2022] Open
Abstract
The diverse pneumococcal diseases are associated with different pneumococcal lineages, or clonal complexes. Nevertheless, intra-clonal genomic variability, which influences pathogenicity, has been reported for surface virulence factors. These factors constitute the communication interface between the pathogen and its host and their corresponding genes are subjected to strong selective pressures affecting functionality and immunogenicity. First, the presence and allelic dispersion of 97 outer protein families were screened in 19 complete pneumococcal genomes. Seventeen families were deemed variable and were then examined in 216 draft genomes. This procedure allowed the generation of binary vectors with 17 positions and the classification of strains into surfotypes. They represent the outer protein subsets with the highest inter-strain discriminative power. A total of 116 non-redundant surfotypes were identified. Those sharing a critical number of common protein features were hierarchically clustered into 18 surfogroups. Most clonal complexes with comparable epidemiological characteristics belonged to the same or similar surfogroups. However, the very large CC156 clonal complex was dispersed over several surfogroups. In order to establish a relationship between surfogroup and pathogenicity, the surfotypes of 95 clinical isolates with different serogroup/serotype combinations were analyzed. We found a significant correlation between surfogroup and type of pathogenic behavior (primary invasive, opportunistic invasive, and non-invasive). We conclude that the virulent behavior of S. pneumoniae is related to the activity of collections of, rather than individual, surface virulence factors. Since surfotypes evolve faster than MLSTs and directly reflect virulence potential, this novel typing protocol is appropriate for the identification of emerging clones.
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Affiliation(s)
- Arnau Domenech
- Servicio de Microbiología, Hospital Universitari de Bellvitge, Universitat de Barcelona, IDIBELLBarcelona, Spain; CIBER de Enfermedades RespiratoriasMadrid, Spain
| | - Javier Moreno
- Servicio de Microbiología, Hospital Universitari de Bellvitge, Universitat de Barcelona, IDIBELLBarcelona, Spain; CIBER de Enfermedades RespiratoriasMadrid, Spain
| | - Carmen Ardanuy
- Servicio de Microbiología, Hospital Universitari de Bellvitge, Universitat de Barcelona, IDIBELLBarcelona, Spain; CIBER de Enfermedades RespiratoriasMadrid, Spain
| | - Josefina Liñares
- Servicio de Microbiología, Hospital Universitari de Bellvitge, Universitat de Barcelona, IDIBELLBarcelona, Spain; CIBER de Enfermedades RespiratoriasMadrid, Spain
| | - Adela G de la Campa
- Bacterial Genetics, Centro Nacional de Microbiología, Instituto de Salud Carlos IIIMajadahonda, Spain; Presidencia, Consejo Superior de Investigaciones CientíficasMadrid, Spain
| | - Antonio J Martin-Galiano
- Bacterial Genetics, Centro Nacional de Microbiología, Instituto de Salud Carlos III Majadahonda, Spain
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Marti S, Puig C, de la Campa AG, Tirado-Velez JM, Tubau F, Domenech A, Calatayud L, Garcia-Somoza D, Ayats J, Liñares J, Ardanuy C. Identification of Haemophilus haemolyticus in clinical samples and characterization of their mechanisms of antimicrobial resistance. J Antimicrob Chemother 2015; 71:80-4. [PMID: 26472767 DOI: 10.1093/jac/dkv307] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 08/28/2015] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES The objectives of this study were to establish the frequency of Haemophilus haemolyticus in clinical samples, to determine the antimicrobial resistance rate and to identify the mechanisms of resistance to β-lactams and quinolones. METHODS An updated database was used to differentiate between MALDI-TOF MS results for Haemophilus influenzae and H. haemolyticus. Antimicrobial susceptibility was studied by microdilution, following EUCAST criteria. The β-lactamase types were identified by PCR analysis of isolates that tested positive for nitrocefin hydrolysis. Mutations in the ftsI gene were identified in isolates with ampicillin MICs ≥0.25 mg/L. Mutations in the quinolone resistance-determining region (QRDR) were identified in isolates with ciprofloxacin MICs ≥0.5 mg/L. RESULTS Overall, we identified 69 H. haemolyticus isolates from 1706 clinical isolates of Haemophilus spp. from respiratory, genital, invasive, and other infection sources. The frequency of H. haemolyticus was low in respiratory samples compared with that of H. influenzae, but in genital-related samples, the frequency was similar to that of H. influenzae. We found low antimicrobial resistance rates among H. haemolyticus isolates, with 8.7% for ampicillin, 8.7% for co-trimoxazole, 7.2% for tetracycline and 4.3% for ciprofloxacin. Mutations in the ftsI gene classified the isolates into four groups, including the newly described Group Hhae IV, which presents mutations in the ftsI gene not identified in H. influenzae and H. haemolyticus type strains. Three ciprofloxacin-resistant H. haemolyticus isolates with mutations affecting GyrA and ParC were identified. CONCLUSIONS The frequency of H. haemolyticus was low, especially in respiratory samples, where H. influenzae is the main pathogen of this genus. Although antimicrobial resistance rates were low, three ciprofloxacin-resistant H. haemolyticus clinical isolates have been identified for the first time.
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Affiliation(s)
- Sara Marti
- Microbiology Department, Hospital Universitari de Bellvitge, Universitat de Barcelona-IDIBELL, Barcelona, Spain CIBER de Enfermedades Respiratorias (CIBERes), Instituto de Salud Carlos III, Madrid, Spain
| | - Carmen Puig
- Microbiology Department, Hospital Universitari de Bellvitge, Universitat de Barcelona-IDIBELL, Barcelona, Spain CIBER de Enfermedades Respiratorias (CIBERes), Instituto de Salud Carlos III, Madrid, Spain
| | - Adela G de la Campa
- CIBER de Enfermedades Respiratorias (CIBERes), Instituto de Salud Carlos III, Madrid, Spain Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - José Manuel Tirado-Velez
- CIBER de Enfermedades Respiratorias (CIBERes), Instituto de Salud Carlos III, Madrid, Spain Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Fe Tubau
- Microbiology Department, Hospital Universitari de Bellvitge, Universitat de Barcelona-IDIBELL, Barcelona, Spain CIBER de Enfermedades Respiratorias (CIBERes), Instituto de Salud Carlos III, Madrid, Spain
| | - Arnau Domenech
- Microbiology Department, Hospital Universitari de Bellvitge, Universitat de Barcelona-IDIBELL, Barcelona, Spain CIBER de Enfermedades Respiratorias (CIBERes), Instituto de Salud Carlos III, Madrid, Spain
| | - Laura Calatayud
- Microbiology Department, Hospital Universitari de Bellvitge, Universitat de Barcelona-IDIBELL, Barcelona, Spain CIBER de Enfermedades Respiratorias (CIBERes), Instituto de Salud Carlos III, Madrid, Spain
| | - Dolors Garcia-Somoza
- Microbiology Department, Hospital Universitari de Bellvitge, Universitat de Barcelona-IDIBELL, Barcelona, Spain CIBER de Enfermedades Respiratorias (CIBERes), Instituto de Salud Carlos III, Madrid, Spain
| | - Josefina Ayats
- Microbiology Department, Hospital Universitari de Bellvitge, Universitat de Barcelona-IDIBELL, Barcelona, Spain CIBER de Enfermedades Respiratorias (CIBERes), Instituto de Salud Carlos III, Madrid, Spain
| | - Josefina Liñares
- Microbiology Department, Hospital Universitari de Bellvitge, Universitat de Barcelona-IDIBELL, Barcelona, Spain CIBER de Enfermedades Respiratorias (CIBERes), Instituto de Salud Carlos III, Madrid, Spain
| | - Carmen Ardanuy
- Microbiology Department, Hospital Universitari de Bellvitge, Universitat de Barcelona-IDIBELL, Barcelona, Spain CIBER de Enfermedades Respiratorias (CIBERes), Instituto de Salud Carlos III, Madrid, Spain
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Ardanuy C, de la Campa AG, García E, Fenoll A, Calatayud L, Cercenado E, Pérez-Trallero E, Bouza E, Liñares J. Spread of Streptococcus pneumoniae serotype 8-ST63 multidrug-resistant recombinant Clone, Spain. Emerg Infect Dis 2015; 20:1848-56. [PMID: 25340616 PMCID: PMC4214286 DOI: 10.3201/eid2011.131215] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
This clone has spread throughout this country and caused invasive pneumococcal disease. Since 2004, a total of 131 isolates of Streptococcus pneumoniae multidrug-resistant invasive serotype 8 have been detected in Spain. These isolates showed resistance to erythromycin, clindamycin, tetracycline, and ciprofloxacin. All isolates were obtained from adult patients and shared a common genotype (sequence type [ST]63; penicillin-binding protein 1a [pbp1a], pbp2b, and pbp2x gene profiles; ermB and tetM genes; and a ParC-S79F change). Sixty-eight isolates that required a ciprofloxacin MIC ≥16 μg/mL had additional gyrA gene changes. Serotype 8-ST63 pbp2x sequences were identical with those of antimicrobial drug–susceptible serotype 8-ST53 isolates. Serotype 8-ST63 pbp2b sequences were identical with those of the multidrug-resistant Sweden 15A-ST63 clone. Recombination between the capsular locus and flanking regions of an ST53 isolate (donor) and an ST63 pneumococcus (recipient) generated the novel 15A-ST63 clone. One recombination point was upstream of pbp2x and another was within pbp1a. A serotype 8-ST63 clone was identified as a cause of invasive disease in Spain.
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Martín-Galiano AJ, Yuste J, Cercenado MI, de la Campa AG. Inspecting the potential physiological and biomedical value of 44 conserved uncharacterised proteins of Streptococcus pneumoniae. BMC Genomics 2014; 15:652. [PMID: 25096389 PMCID: PMC4143570 DOI: 10.1186/1471-2164-15-652] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 07/21/2014] [Indexed: 12/15/2022] Open
Abstract
Background The major Gram-positive coccoid pathogens cause similar invasive diseases and show high rates of antimicrobial resistance. Uncharacterised proteins shared by these organisms may be involved in virulence or be targets for antimicrobial therapy. Results Forty four uncharacterised proteins from Streptococcus pneumoniae with homologues in Enterococcus faecalis and/or Staphylococcus aureus were selected for analysis. These proteins showed differences in terms of sequence conservation and number of interacting partners. Twenty eight of these proteins were monodomain proteins and 16 were modular, involving domain combinations and, in many cases, predicted unstructured regions. The genes coding for four of these 44 proteins were essential. Genomic and structural studies showed one of the four essential genes to code for a promising antibacterial target. The strongest impact of gene removal was on monodomain proteins showing high sequence conservation and/or interactions with many other proteins. Eleven out of 40 knockouts (one for each gene) showed growth delay and 10 knockouts presented a chaining phenotype. Five of these chaining mutants showed a lack of putative DNA-binding proteins. This suggest this phenotype results from a loss of overall transcription regulation. Five knockouts showed defective autolysis in response to penicillin and vancomycin, and attenuated virulence in an animal model of sepsis. Conclusions Uncharacterised proteins make up a reservoir of polypeptides of different physiological importance and biomedical potential. A promising antibacterial target was identified. Five of the 44 examined proteins seemed to be virulence factors. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-652) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Antonio J Martín-Galiano
- Centro Nacional de Microbiología and CIBERES (CIBER de Enfermedades Respiratorias), Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.
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Ferrándiz MJ, Arnanz C, Martín-Galiano AJ, Rodríguez-Martín C, de la Campa AG. Role of global and local topology in the regulation of gene expression in Streptococcus pneumoniae. PLoS One 2014; 9:e101574. [PMID: 25019515 PMCID: PMC4096756 DOI: 10.1371/journal.pone.0101574] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 06/09/2014] [Indexed: 11/19/2022] Open
Abstract
The most basic level of transcription regulation in Streptococcus pneumoniae is the organization of its chromosome in topological domains. In response to drugs that caused DNA-relaxation, a global transcriptional response was observed. Several chromosomal domains were identified based on the transcriptional response of their genes: up-regulated (U), down-regulated (D), non-regulated (N), and flanking (F). We show that these distinct domains have different expression and conservation characteristics. Microarray fluorescence units under non-relaxation conditions were used as a measure of gene transcriptional level. Fluorescence units were significantly lower in F genes than in the other domains with a similar AT content. The transcriptional level of the domains categorized them was D>U>F. In addition, a comparison of 12 S. pneumoniae genome sequences showed a conservation of gene composition within U and D domains, and an extensive gene interchange in F domains. We tested the organization of chromosomal domains by measuring the relaxation-mediated transcription of eight insertions of a heterologous Ptccat cassette, two in each type of domain, showing that transcription depended on their chromosomal location. Moreover, transcription from the four promoters directing the five genes involved in supercoiling homeostasis, located either in U (gyrB), D (topA), or N (gyrA and parEC) domains was analyzed both in their chromosomal locations and in a replicating plasmid. Although expression from the chromosomal PgyrB and PtopA showed the expected domain regulation, their expression was down-regulated in the plasmid, which behaved as a D domain. However, both PparE and PgyrA carried their own regulatory signals, their topology-dependent expression being equivalent in the plasmid or in the chromosome. In PgyrA a DNA bend acted as a DNA supercoiling sensor. These results revealed that DNA topology functions as a general transcriptional regulator, superimposed upon other more specific regulatory mechanisms.
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Affiliation(s)
- María-José Ferrándiz
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III and CIBER Enfermedades Respiratorias, Madrid, Spain
| | - Cristina Arnanz
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III and CIBER Enfermedades Respiratorias, Madrid, Spain
| | - Antonio J. Martín-Galiano
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III and CIBER Enfermedades Respiratorias, Madrid, Spain
| | - Carlos Rodríguez-Martín
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III and CIBER Enfermedades Respiratorias, Madrid, Spain
| | - Adela G. de la Campa
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III and CIBER Enfermedades Respiratorias, Madrid, Spain
- Consejo Superior de Investigaciones Científicas, Madrid, Spain
- * E-mail:
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López E, Domenech A, Ferrándiz MJ, Frias MJ, Ardanuy C, Ramirez M, García E, Liñares J, de la Campa AG. Induction of prophages by fluoroquinolones in Streptococcus pneumoniae: implications for emergence of resistance in genetically-related clones. PLoS One 2014; 9:e94358. [PMID: 24718595 PMCID: PMC3981806 DOI: 10.1371/journal.pone.0094358] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 03/13/2014] [Indexed: 11/29/2022] Open
Abstract
Antibiotic resistance in Streptococcus pneumoniae has increased worldwide by the spread of a few clones. Fluoroquinolone resistance occurs mainly by alteration of their intracellular targets, the type II DNA topoisomerases, which is acquired either by point mutation or by recombination. Increase in fluoroquinolone-resistance may depend on the balance between antibiotic consumption and the cost that resistance imposes to bacterial fitness. In addition, pneumococcal prophages could play an important role. Prophage induction by fluoroquinolones was confirmed in 4 clinical isolates by using Southern blot hybridization. Clinical isolates (105 fluoroquinolone-resistant and 160 fluoroquinolone-susceptible) were tested for lysogeny by using a PCR assay and functional prophage carriage was studied by mitomycin C induction. Fluoroquinolone-resistant strains harbored fewer inducible prophages (17/43) than fluoroquinolone-susceptible strains (49/70) (P = 0.0018). In addition, isolates of clones associated with fluoroquinolone resistance [CC156 (3/25); CC63 (2/20), and CC81 (1/19)], had lower frequency of functional prophages than isolates of clones with low incidence of fluoroquinolone resistance [CC30 (4/21), CC230 (5/20), CC62 (9/21), and CC180 (21/30)]. Likewise, persistent strains from patients with chronic respiratory diseases subjected to fluoroquinolone treatment had a low frequency of inducible prophages (1/11). Development of ciprofloxacin resistance was tested with two isogenic strains, one lysogenic and the other non-lysogenic: emergence of resistance was only observed in the non-lysogenic strain. These results are compatible with the lysis of lysogenic isolates receiving fluoroquinolones before the development of resistance and explain the inverse relation between presence of inducible prophages and fluoroquinolone-resistance.
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Affiliation(s)
- Elena López
- Centro Nacional de Microbiología, ISCIII (Instituto de Salud Carlos III), Majadahonda, Madrid, Spain
- Ciber de Enfermedades Respiratorias, ISCIII, Madrid, Spain
| | - Arnau Domenech
- Ciber de Enfermedades Respiratorias, ISCIII, Madrid, Spain
- Microbiology Department, Hospital Universitari de Bellvitge-IDIBELL- Barcelona University, Barcelona, Spain
| | - María-José Ferrándiz
- Centro Nacional de Microbiología, ISCIII (Instituto de Salud Carlos III), Majadahonda, Madrid, Spain
- Ciber de Enfermedades Respiratorias, ISCIII, Madrid, Spain
| | - Maria João Frias
- Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Carmen Ardanuy
- Ciber de Enfermedades Respiratorias, ISCIII, Madrid, Spain
- Microbiology Department, Hospital Universitari de Bellvitge-IDIBELL- Barcelona University, Barcelona, Spain
| | - Mario Ramirez
- Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Ernesto García
- Ciber de Enfermedades Respiratorias, ISCIII, Madrid, Spain
- Centro de Investigaciones Biológicas, CSIC (Consejo Superior de Investigaciones Científicas), Madrid, Spain
| | - Josefina Liñares
- Ciber de Enfermedades Respiratorias, ISCIII, Madrid, Spain
- Microbiology Department, Hospital Universitari de Bellvitge-IDIBELL- Barcelona University, Barcelona, Spain
| | - Adela G. de la Campa
- Centro Nacional de Microbiología, ISCIII (Instituto de Salud Carlos III), Majadahonda, Madrid, Spain
- Ciber de Enfermedades Respiratorias, ISCIII, Madrid, Spain
- Presidencia, CSIC, Madrid, Spain
- * E-mail:
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García MT, Blázquez MA, Ferrándiz MJ, Sanz MJ, Silva-Martín N, Hermoso JA, de la Campa AG. New alkaloid antibiotics that target the DNA topoisomerase I of Streptococcus pneumoniae. J Biol Chem 2011; 286:6402-13. [PMID: 21169356 PMCID: PMC3057782 DOI: 10.1074/jbc.m110.148148] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Revised: 12/15/2010] [Indexed: 11/06/2022] Open
Abstract
Streptococcus pneumoniae has two type II DNA-topoisomerases (DNA-gyrase and DNA topoisomerase IV) and a single type I enzyme (DNA-topoisomerase I, TopA), as demonstrated here. Although fluoroquinolones target type II enzymes, antibiotics efficiently targeting TopA have not yet been reported. Eighteen alkaloids (seven aporphine and 11 phenanthrenes) were semisynthesized from boldine and used to test inhibition both of TopA activity and of cell growth. Two phenanthrenes (seconeolitsine and N-methyl-seconeolitsine) effectively inhibited both TopA activity and cell growth at equivalent concentrations (∼17 μM). Evidence for in vivo TopA targeting by seconeolitsine was provided by the protection of growth inhibition in a S. pneumoniae culture in which the enzyme was overproduced. Additionally, hypernegative supercoiling was observed in an internal plasmid after drug treatment. Furthermore, a model of pneumococcal TopA was made based on the crystal structure of Escherichia coli TopA. Docking calculations indicated strong interactions of the alkaloids with the nucleotide-binding site in the closed protein conformation, which correlated with their inhibitory effect. Finally, although seconeolitsine and N-methyl-seconeolitsine inhibited TopA and bacterial growth, they did not affect human cell viability. Therefore, these new alkaloids can be envisaged as new therapeutic candidates for the treatment of S. pneumoniae infections resistant to other antibiotics.
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Affiliation(s)
- María Teresa García
- From the Unidad de Genética Bacteriana, Centro Nacional de Microbiología and CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid
| | - María Amparo Blázquez
- the Departamento de Farmacología, Facultat de Farmàcia, Universitat de València, Vicent Andrés Estellés s/n. 46100 Burjasot, Valencia, and
| | - María José Ferrándiz
- From the Unidad de Genética Bacteriana, Centro Nacional de Microbiología and CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid
| | - María Jesús Sanz
- the Departamento de Farmacología, Facultat de Farmàcia, Universitat de València, Vicent Andrés Estellés s/n. 46100 Burjasot, Valencia, and
| | - Noella Silva-Martín
- the Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto de Química-Física “Rocasolano”, CSIC, Serrano 119, 28006 Madrid, Spain
| | - Juan A. Hermoso
- the Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto de Química-Física “Rocasolano”, CSIC, Serrano 119, 28006 Madrid, Spain
| | - Adela G. de la Campa
- From the Unidad de Genética Bacteriana, Centro Nacional de Microbiología and CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid
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Nieto C, Sadowy E, de la Campa AG, Hryniewicz W, Espinosa M. The relBE2Spn toxin-antitoxin system of Streptococcus pneumoniae: role in antibiotic tolerance and functional conservation in clinical isolates. PLoS One 2010; 5:e11289. [PMID: 20585658 PMCID: PMC2890582 DOI: 10.1371/journal.pone.0011289] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2010] [Accepted: 05/21/2010] [Indexed: 01/24/2023] Open
Abstract
Type II (proteic) chromosomal toxin-antitoxin systems (TAS) are widespread in Bacteria and Archaea but their precise function is known only for a limited number of them. Out of the many TAS described, the relBE family is one of the most abundant, being present in the three first sequenced strains of Streptococcus pneumoniae (D39, TIGR4 and R6). To address the function of the pneumococcal relBE2Spn TAS in the bacterial physiology, we have compared the response of the R6-relBE2Spn wild type strain with that of an isogenic derivative, Delta relB2Spn under different stress conditions such as carbon and amino acid starvation and antibiotic exposure. Differences on viability between the wild type and mutant strains were found only when treatment directly impaired protein synthesis. As a criterion for the permanence of this locus in a variety of clinical strains, we checked whether the relBE2Spn locus was conserved in around 100 pneumococcal strains, including clinical isolates and strains with known genomes. All strains, although having various types of polymorphisms at the vicinity of the TA region, contained a functional relBE2Spn locus and the type of its structure correlated with the multilocus sequence type. Functionality of this TAS was maintained even in cases where severe rearrangements around the relBE2Spn region were found. We conclude that even though the relBE2Spn TAS is not essential for pneumococcus, it may provide additional advantages to the bacteria for colonization and/or infection.
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Affiliation(s)
- Concha Nieto
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Ewa Sadowy
- National Medicines Institute, Warsaw, Poland
| | - Adela G. de la Campa
- Centro Nacional de Microbiología and CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Majadahonda, Spain
| | | | - Manuel Espinosa
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
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Ferrándiz MJ, Martín-Galiano AJ, Schvartzman JB, de la Campa AG. The genome of Streptococcus pneumoniae is organized in topology-reacting gene clusters. Nucleic Acids Res 2010; 38:3570-81. [PMID: 20176571 PMCID: PMC2887967 DOI: 10.1093/nar/gkq106] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The transcriptional response of Streptococcus pneumoniae was examined after exposure to the GyrB-inhibitor novobiocin. Topoisomer distributions of an internal plasmid confirmed DNA relaxation and recovery of the native level of supercoiling at low novobiocin concentrations. This was due to the up-regulation of DNA gyrase and the down-regulation of topoisomerases I and IV. In addition, >13% of the genome exhibited relaxation-dependent transcription. The majority of the responsive genes (>68%) fell into 15 physical clusters (14.6–85.6 kb) that underwent coordinated regulation, independently of operon organization. These genomic clusters correlated with AT content and codon composition, showing the chromosome to be organized into topology-reacting gene clusters that respond to DNA supercoiling. In particular, down-regulated clusters were flanked by 11–40 kb AT-rich zones that might have a putative structural function. This is the first case where genes responding to changes in the level of supercoiling in a coordinated manner were found organized as functional clusters. Such an organization revealed DNA supercoiling as a general feature that controls gene expression superimposed on other kinds of more specific regulatory mechanisms.
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Affiliation(s)
- María-José Ferrándiz
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III and CIBER Enfermedades Respiratorias, 28220 Majadahonda, Madrid, Spain
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de la Campa AG, Ardanuy C, Balsalobre L, Pérez-Trallero E, Marimón JM, Fenoll A, Liñares J. Changes in fluoroquinolone-resistant Streptococcus pneumoniae after 7-valent conjugate vaccination, Spain. Emerg Infect Dis 2009; 15:905-11. [PMID: 19523289 PMCID: PMC2727337 DOI: 10.3201/eid1506.080684] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Among 4,215 Streptococcus pneumoniae isolates obtained in Spain during 2006, 98 (2.3%) were ciprofloxacin resistant (3.6% from adults and 0.14% from children). In comparison with findings from a 2002 study, global resistance remained stable. Low-level resistance (30 isolates with MIC 4-8 microg/mL) was caused by a reserpine-sensitive efflux phenotype (n = 4) or single topoisomerase IV (parC [n = 24] or parE [n = 1]) changes. One isolate did not show reserpine-sensitive efflux or mutations. High-level resistance (68 isolates with MIC >or=16 microg/mL) was caused by changes in gyrase (gyrA) and parC or parE. New changes in parC (S80P) and gyrA (S81V, E85G) were shown to be involved in resistance by genetic transformation. Although 49 genotypes were observed, clones Spain9V-ST156 and Sweden15A-ST63 accounted for 34.7% of drug-resistant isolates. In comparison with findings from the 2002 study, clones Spain14-ST17, Spain23F-ST81, and ST8819F decreased and 4 new genotypes (ST9710A, ST57016, ST43322, and ST71733) appeared in 2006.
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Escudero JA, San Millan A, Catalan A, de la Campa AG, Rivero E, Lopez G, Dominguez L, Moreno MA, Gonzalez-Zorn B. First characterization of fluoroquinolone resistance in Streptococcus suis. Antimicrob Agents Chemother 2006; 51:777-82. [PMID: 17116660 PMCID: PMC1797769 DOI: 10.1128/aac.00972-06] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have identified and sequenced the genes encoding the quinolone-resistance determining region (QRDR) of ParC and GyrA in fluoroquinolone-susceptible and -resistant Streptococcus suis clinical isolates. Resistance is the consequence of single point mutations in the QRDRs of ParC and GyrA and is not due to clonal spread of resistant strains or horizontal gene transfer with other bacteria.
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Affiliation(s)
- Jose Antonio Escudero
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040 Madrid, Spain
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Balsalobre L, Hernández-Madrid A, Llull D, Martín-Galiano AJ, García E, Fenoll A, de la Campa AG. Molecular characterization of disease-associated streptococci of the mitis group that are optochin susceptible. J Clin Microbiol 2006; 44:4163-71. [PMID: 16971639 PMCID: PMC1698351 DOI: 10.1128/jcm.01137-06] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2006] [Revised: 08/16/2006] [Accepted: 09/06/2006] [Indexed: 11/20/2022] Open
Abstract
Eight optochin-susceptible (Opt(s)) alpha-hemolytic (viridans) streptococcus isolates were characterized at the molecular level. These isolates showed phenotypic characteristics typical of both viridans streptococci and Streptococcus pneumoniae. Comparison of the sequence of housekeeping genes from these isolates with those of S. pneumoniae, Streptococcus mitis, Streptococcus oralis, and Streptococcus pseudopneumoniae suggested that the Opt(s) isolates corresponded to streptococci of the mitis group. Besides, the Opt(s) streptococci were negative by a Gen-Probe AccuProbe pneumococcus test and hybridized with specific pneumococcal probes (lytA and ply) but also with ant, a gene not present in most S. pneumoniae strains. Moreover, the isolates were insoluble in 1% sodium deoxycholate but completely dissolved in 0.1% deoxycholate. Sequence analysis of the lytA gene revealed that the Opt(s) streptococci carried lytA alleles characteristic of those present in nonpneumococcal streptococci of the mitis group. The determination of the partial nucleotide sequence embracing the atp operon encoding the F(o)F(1) H(+)-ATPase indicated that the optochin susceptibility of the isolates was due to the acquisition of atpC, atpA, and part of atpB from S. pneumoniae by horizontal gene transfer.
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Affiliation(s)
- Luz Balsalobre
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain
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Martín-Galiano AJ, Overweg K, Ferrándiz MJ, Reuter M, Wells JM, de la Campa AG. Transcriptional analysis of the acid tolerance response in Streptococcus pneumoniae. Microbiology (Reading) 2005; 151:3935-3946. [PMID: 16339938 DOI: 10.1099/mic.0.28238-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Streptococcus pneumoniae, one of the major causes of morbidity and mortality in humans, faces a range of potentially acidic conditions in the middle and late stages of growthin vitro, in diverse human fluids during the infection process, and in biofilms present in the nasopharynx of carriers.S. pneumoniaewas shown to develop a weak acid tolerance response (ATR), where cells previously exposed to sublethal pHs (5·8–6·6) showed an increased survival rate of up to one order of magnitude after challenge at the lethal pH (4·4, survival rate of 10−4). Moreover, the survival after challenge of stationary phase cells at pH 4·4 was three orders of magnitude higher than that of cells taken from the exponential phase, due to the production of lactic acid during growth and increasing acidification of the growth medium until stationary phase. Global expression analysis after short-term (5, 15 and 30 min, the adaptation phase) and long-term (the maintenance phase) acidic shock (pH 6·0) was performed by microarray experiments, and the results were validated by real-time RT-PCR. Out of a total of 126 genes responding to acidification, 59 and 37 were specific to the adaptation phase and maintenance phase, respectively, and 30 were common to both periods. In the adaptation phase, both up- and down-regulation of gene transcripts was observed (38 and 21 genes, respectively), whereas in the maintenance phase most of the affected genes were down-regulated (34 out of 37). Genes involved in protein fate (including those involved in the protection of the protein native structure) and transport (including transporters of manganese and iron) were overrepresented among the genes affected by acidification, 8·7 and 24·6 % of the acid-responsive genes compared to 2·8 % and 9·6 % of the genome complement, respectively. Cross-regulation with the response to oxidative and osmotic stress was observed. Potential regulatory motifs involved in the ATR were identified in the promoter regions of some of the regulated genes.
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Affiliation(s)
- Antonio J Martín-Galiano
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220, Majadahonda, Madrid, Spain
| | - Karin Overweg
- Bacterial Infection and Immunity Group, Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK
| | - Maria J Ferrándiz
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220, Majadahonda, Madrid, Spain
| | - Mark Reuter
- Bacterial Infection and Immunity Group, Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK
| | - Jerry M Wells
- Bacterial Infection and Immunity Group, Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK
| | - Adela G de la Campa
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220, Majadahonda, Madrid, Spain
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Ferrándiz MJ, Ardanuy C, Liñares J, García-Arenzana JM, Cercenado E, Fleites A, de la Campa AG. New mutations and horizontal transfer of rpoB among rifampin-resistant Streptococcus pneumoniae from four Spanish hospitals. Antimicrob Agents Chemother 2005; 49:2237-45. [PMID: 15917517 PMCID: PMC1140543 DOI: 10.1128/aac.49.6.2237-2245.2005] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A total of 103 (0.7%) of 14,236 Streptococcus pneumoniae isolates collected in four Spanish hospitals from 1989 to 2003 were resistant to rifampin (MICs, 4 to 512 microg/ml). Only sixty-one (59.2%) of these isolates were available for molecular characterization. Resistance was mostly related to human immunodeficiency virus (HIV) infection in adult patients and to conjunctivitis in children. Thirty-six different pulsed-field gel electrophoresis patterns were identified among resistant isolates, five of which were related to international clones (Spain23F-1, Spain6B-2, Spain9V-3, Spain14-5, and clone C of serotype 19F), and accounted for 49.2% of resistant isolates. Single sense mutations at cluster N or I of the rpoB gene were found in 39 isolates, while double mutations, either at cluster I, at clusters I and II, or at clusters N and III, were found in 14 isolates. The involvement of the mutations in rifampin resistance was confirmed by genetic transformation. Single mutations at clusters N and I conferred MICs of 2 microg/ml and 4 to 32 microg/ml, respectively. Eight isolates showed high degrees of nucleotide sequence variations (2.3 to 10.8%) in rpoB, suggesting a recombinational origin for these isolates, for which viridans group streptococci are their potential gene donors. Although the majority of rifampin-resistant isolates were isolated from individual patients without temporal or geographical relationships, the clonal dissemination of rifampin-resistant isolates was observed among 12 HIV-infected patients in the two hospitals with higher rates of resistance.
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Affiliation(s)
- María José Ferrándiz
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain
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de la Campa AG, Balsalobre L, Ardanuy C, Fenoll A, Pérez-Trallero E, Liñares J. Fluoroquinolone resistance in penicillin-resistant Streptococcus pneumoniae clones, Spain. Emerg Infect Dis 2004; 10:1751-9. [PMID: 15504260 PMCID: PMC3323274 DOI: 10.3201/eid1010.040382] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Among 2,882 Streptococcus pneumoniae sent to the Spanish Reference Laboratory during 2002, 75 (2.6%) were ciprofloxacin-resistant. Resistance was associated with older patients (3.9% in adults and 7.2% in patients > or =65 years of age), with isolation from noninvasive sites (4.3% vs. 1.0%), and with penicillin and macrolide resistance. Among 14 low-level resistant (MIC 4-8 microg/mL) strains, 1 had a fluoroquinolone efflux phenotype, and 13 showed single ParC changes. The 61 high-level ciprofloxacin-resistant (MIC > or =16 microg/mL) strains showed either two or three changes at ParC, ParE, and GyrA. Resistance was acquired either by point mutation (70 strains) or by recombination with viridans streptococci (4 strains) at the topoisomerase II genes. Although 36 pulsed-field gel electrophoresis patterns were observed, 5 international multiresistant clones (Spain23F-1, Spain6B-2, Spain9V-3, Spain14-5 and Sweden15A-25) accounted for 35 (46.7%) of the ciprofloxacin-resistant strains. Continuous surveillance is needed to prevent the dissemination of these clones.
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Affiliation(s)
- Adela G de la Campa
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain.
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Martín-Galiano AJ, Wells JM, de la Campa AG. Relationship between codon biased genes, microarray expression values and physiological characteristics of Streptococcus pneumoniae. Microbiology (Reading) 2004; 150:2313-2325. [PMID: 15256573 DOI: 10.1099/mic.0.27097-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A codon-profile strategy was used to predict gene expression levels in Streptococcus pneumoniae. Predicted highly expressed (PHE) genes included those encoding glycolytic and fermentative enzymes, sugar-conversion systems and carbohydrate-transporters. Additionally, some genes required for infection that are involved in oxidative metabolism and hydrogen peroxide production were PHE. Low expression values were predicted for genes encoding specific regulatory proteins like two-component systems and competence genes. Correspondence analysis localized 484 ORFs which shared a distinctive codon profile in the right horn. These genes had a mean G+C content (33·4 %) that was lower than the bulk of the genome coding sequences (39·7 %), suggesting that many of them were acquired by horizontal transfer. Half of these genes (242) were pseudogenes, ORFs shorter than 80 codons or without assigned function. The remaining genes included several virulence factors, such as capsular genes, iga, lytB, nanB, pspA, choline-binding proteins, and functions related to DNA acquisition, such as restriction-modification systems and comDE. In order to compare predicted translation rate with the relative amounts of mRNA for each gene, the codon adaptation index (CAI) values were compared with microarray fluorescence intensity values following hybridization of labelled RNA from laboratory-grown cultures. High mRNA amounts were observed in 32·5 % of PHE genes and in 64 % of the 25 genes with the highest CAI values. However, high relative amounts of RNA were also detected in 10·4 % of non-PHE genes, such as those encoding fatty acid metabolism enzymes and proteases, suggesting that their expression might also be regulated at the level of transcription or mRNA stability under the conditions tested. The effects of codon bias and mRNA amount on different gene groups in S. pneumoniae are discussed.
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Affiliation(s)
- Antonio J Martín-Galiano
- Unidad de Genética Bacteriana (CSIC), Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220, Majadahonda, Madrid, Spain
| | - Jerry M Wells
- Bacterial Infection and Immunity Group, Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK
| | - Adela G de la Campa
- Unidad de Genética Bacteriana (CSIC), Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220, Majadahonda, Madrid, Spain
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Bastida T, Pérez-Vázquez M, Campos J, Cortés-Lletget MC, Román F, Tubau F, de la Campa AG, Alonso-Tarrés C. Levofloxacin Treatment Failure inHaemophilus influenzaePneumonia. Emerg Infect Dis 2003; 9:1475-8. [PMID: 14718097 DOI: 10.3201/eid0911.030176] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We describe the first case of failure of oral levofloxacin treatment of community-acquired pneumonia caused by Haemophilus influenzae. The strain showed cross-resistance to fluoroquinolones and carried four mutations in quinolone resistance-determining regions of DNA gyrase and topoisomerase IV genes.
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Affiliation(s)
- Teresa Bastida
- Hospital de l'Esperit Sant, Santa Coloma de Gramenet, Barcelona, Spain
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Martín-Galiano AJ, Balsalobre L, Fenoll A, de la Campa AG. Genetic characterization of optochin-susceptible viridans group streptococci. Antimicrob Agents Chemother 2003; 47:3187-94. [PMID: 14506029 PMCID: PMC201122 DOI: 10.1128/aac.47.10.3187-3194.2003] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2003] [Revised: 04/07/2003] [Accepted: 06/20/2003] [Indexed: 11/20/2022] Open
Abstract
Two clinical isolates of viridans group streptococci (VS) with different degrees of susceptibility to optochin (OPT), i.e., fully OPT-susceptible (Opt(s)) VS strain 1162/99 (for which the MIC was equal to that for Streptococcus pneumoniae, 0.75 micro g/ml) and intermediate Opt(s) VS strain 1174/97 (MIC, 6 micro g/ml) were studied. Besides being OPT susceptible, they showed characteristics typical of VS, such as bile insolubility; lack of reaction with pneumococcal capsular antibodies; and lack of hybridization with rRNA (AccuProbe)-, lytA-, and pnl-specific pneumococcal probes. However, these VS Opt(s) strains and VS type strains hybridized with ant, a gene not present in S. pneumoniae. A detailed characterization of the genes encoding the 16S rRNA and SodA classified isolates 1162/99 and 1174/97 as Streptococcus mitis. Analysis of the atpCAB region, which encodes the c, a, and b subunits of the F(0)F(1) H(+)-ATPase, the target of optochin, revealed high degrees of similarity between S. mitis 1162/99 and S. pneumoniae in atpC, atpA, and the N terminus of atpB. Moreover, amino acid identity between S. mitis 1174/97 and S. pneumoniae was found in alpha helix 5 of the a subunit. The organization of the chromosomal region containing the atp operon of the two Opt(s) VS and VS type strains was spr1284-atpC, with spr1284 being located 296 to 556 bp from atpC, whereas in S. pneumoniae this distance was longer than 68 kb. In addition, the gene order in S. pneumoniae was IS1239-74 bp-atpC. The results suggest that the full OPT susceptibility of S. mitis 1162/99 is due to the acquisition of atpC, atpA, and part of atpB from S. pneumoniae and that the intermediate OPT susceptibility of S. mitis 1174/97 correlates with the amino acid composition of its a subunit.
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Affiliation(s)
- Antonio J Martín-Galiano
- Unidad de Genética Bacteriana (Consejo Superior de Investigaciones Científicas), Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
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Balsalobre L, Ferrándiz MJ, Liñares J, Tubau F, de la Campa AG. Viridans group streptococci are donors in horizontal transfer of topoisomerase IV genes to Streptococcus pneumoniae. Antimicrob Agents Chemother 2003; 47:2072-81. [PMID: 12821449 PMCID: PMC161831 DOI: 10.1128/aac.47.7.2072-2081.2003] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A total of 46 ciprofloxacin-resistant (Cip(r)) Streptococcus pneumoniae strains were isolated from 1991 to 2001 at the Hospital of Bellvitge. Five of these strains showed unexpectedly high rates of nucleotide variations in the quinolone resistance-determining regions (QRDRs) of their parC, parE, and gyrA genes. The nucleotide sequence of the full-length parC, parE, and gyrA genes of one of these isolates revealed a mosaic structure compatible with an interspecific recombination origin. Southern blot analysis and nucleotide sequence determinations showed the presence of an ant-like gene in the intergenic parE-parC regions of the S. pneumoniae Cip(r) isolates with high rates of variations in their parE and parC QRDRs. The ant-like gene was absent from typical S. pneumoniae strains, whereas it was present in the intergenic parE-parC regions of the viridans group streptococci (Streptococcus mitis and Streptococcus oralis). These results suggest that the viridans group streptococci are acting as donors in the horizontal transfer of fluoroquinolone resistance genes to S. pneumoniae.
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Affiliation(s)
- Luz Balsalobre
- Unidad de Genética Bacteriana (Consejo Superior de Investigaciones Científicas), Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain
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de la Campa AG, Ferrandiz MJ, Tubau F, Pallarés R, Manresa F, Liñares J. Genetic characterization of fluoroquinolone-resistant Streptococcus pneumoniae strains isolated during ciprofloxacin therapy from a patient with bronchiectasis. Antimicrob Agents Chemother 2003; 47:1419-22. [PMID: 12654682 PMCID: PMC152524 DOI: 10.1128/aac.47.4.1419-1422.2003] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Five Spain(9V-3) Streptococcus pneumoniae strains were isolated from a patient with bronchiectasis who had received long-term ciprofloxacin therapy. One ciprofloxacin-susceptible strain was isolated before treatment, and four ciprofloxacin-resistant strains were isolated during treatment. The resistant strains were derived from the susceptible strain either by a parC mutation (low-level resistance) or by parC and gyrA mutations (high-level resistance). This study shows that ciprofloxacin therapy in a patient colonized by susceptible S. pneumoniae may select fluoroquinolone-resistant mutants.
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Affiliation(s)
- Adela G de la Campa
- Unidad de Genética Bacteriana (Consejo Superior de Investigaciones Científicas), Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.
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Martín-Galiano AJ, de la Campa AG. High-efficiency generation of antibiotic-resistant strains of Streptococcus pneumoniae by PCR and transformation. Antimicrob Agents Chemother 2003; 47:1257-61. [PMID: 12654655 PMCID: PMC152537 DOI: 10.1128/aac.47.4.1257-1261.2003] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
We designed a method by which to generate antibiotic-resistant strains of Streptococcus pneumoniae at frequencies 4 orders of magnitude greater than the spontaneous mutation rate. The method is based on the natural ability of this organism to be genetically transformed with PCR products carrying sequences homologous to its chromosome. The genes encoding the targets of ciprofloxacin (parC, encoding the ParC subunit of DNA topoisomerase IV), rifampin (rpoB, encoding the beta subunit of RNA polymerase), and streptomycin (rpsL, encoding the S12 ribosomal protein) from susceptible laboratory strain R6 were amplified by PCR and used to transform the same strain. Resistant mutants were obtained with a frequency of 10(-4) to 10(-5), depending on the fidelity of the DNA polymerase used for PCR amplifications. Ciprofloxacin-resistant mutants, for which the MICs were four-to eightfold higher than that for R6, carried a single mutation of a residue in the quinolone resistance-determining region: S79 (change to A, F, or Y) or D83 (change to N or V). Rifampin-resistant strains, for which the MICs were at least 133-fold higher than that for R6, contained a single mutation within cluster I of rpoB: S482 (change to P), Q486 (change to L), D489 (change to V), or H499 (change to L or Y). Streptomycin-resistant mutants, for which the MICs were at least 64-fold higher than that for R6, carried a mutation at either K56 (change to I, R, or T) or K101 (change to E). PCR products obtained from the mutants were able to transform R6 to resistance with high efficiency (>10(4)). This method could be used to efficiently obtain resistant mutants for any drug whose target is known.
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Affiliation(s)
- Antonio J Martín-Galiano
- Unidad de Genética Bacteriana (Consejo Superior de Investigaciones Científicas), Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain
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Abstract
Genetic studies aimed at eliminating expression of the atp operon (F(0)F(1) H(+)-ATPase) of Streptococcus pneumoniae by genetic disruption of atpC, the first gene of the operon, with a chloramphenicol-resistance cassette were performed. Resistant transformants were obtained only when the recipient strain had a duplication of atpC, recombination occurring in such a way that transcription of the operon from its own promoter was allowed. These results imply that the atp operon is essential for the viability of the cells.
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Affiliation(s)
- María José Ferrándiz
- Unidad de Genética Bacteriana (Consejo Superior de Investigaciones Científicas), Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain
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Martín-Galiano AJ, Gorgojo B, Kunin CM, de la Campa AG. Mefloquine and new related compounds target the F(0) complex of the F(0)F(1) H(+)-ATPase of Streptococcus pneumoniae. Antimicrob Agents Chemother 2002; 46:1680-7. [PMID: 12019076 PMCID: PMC127268 DOI: 10.1128/aac.46.6.1680-1687.2002] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The activities of mefloquine (MFL) and related compounds against previously characterized Streptococcus pneumoniae strains carrying defined amino acid substitutions in the c subunit of the F(0)F(1) H(+)-ATPase were studied. In addition, a series of MFL-resistant (Mfl(r)) strains were isolated and characterized. A good correlation was observed between inhibition of growth and inhibition of the membrane-associated F(0)F(1) H(+)-ATPase activity. MFL was about 10-fold more active than optochin and about 200-fold more active than quinine in inhibiting both the growth and the ATPase activities of laboratory pneumococcal strain R6. Mutant strains were inhibited by the different compounds to different degrees, depending on their specific mutations in the c subunit. The resistant strains studied had point mutations that changed amino acid residues in either the c subunit or the a subunit of the F(0) complex. Changes in the c subunit were located in one of the two transmembrane alpha helices: residues M13, G14, G20, M23, and N24 of helix 1 and residues M44, G47, V48, A49, and V57 of helix 2. Changes in the a subunit were also found in either of the transmembrane alpha helices, helix 5 or 6: residue L186 of helix 5 and residues W206, F209, and S214 of helix 6. These results suggest that the transmembrane helices of the c and a subunits interact and that the mutated residues are important for the structure of the F(0) complex and proton translocation.
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Affiliation(s)
- Antonio Javier Martín-Galiano
- Unidad de Genética Bacteriana (Consejo Superior de Investigaciones Científicas), Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain
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