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Al-Marzooq F, Ghazawi A, Alshamsi M, Alzaabi A, Aleissaee O, Almansoori H, Alsaadi A, Aldhaheri R, Ahli H, Daoud L, Ahmad A, Collyns T, Oommen S. Genomic approach to evaluate the intrinsic antibacterial activity of novel diazabicyclooctanes (zidebactam and nacubactam) against clinical Escherichia coli isolates from diverse clonal lineages in the United Arab Emirates. J Infect Public Health 2025; 18:102761. [PMID: 40120434 DOI: 10.1016/j.jiph.2025.102761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2024] [Revised: 03/09/2025] [Accepted: 03/13/2025] [Indexed: 03/25/2025] Open
Abstract
BACKGROUND The spiking rise in the prevalence of multidrug-resistant (MDR) pathogens necessitates discovering new antimicrobial agents. This study aims to investigate the intrinsic activity of two novel diazabicyclooctane (DBO) β-lactamase inhibitors, zidebactam and nacubactam, against diverse MDR Escherichia coli isolates from the United Arab Emirates. We aimed to correlate their antibacterial efficacy with the genomic characteristics of the strains. METHODS This study investigated 73 E. coli strains and tested them for susceptibility to different antibiotics, including DBOs. PCR screening for carbapenemase and major β-lactamase genes was done. The strains were then grouped according to phenotypic and genotypic profiles. Whole-genome sequencing was employed to characterize the genetic landscape and clonality of selected 32 strains. Additionally, time-kill studies were conducted to confirm the bactericidal activity of DBOs. RESULTS Zidebactam demonstrated superior efficacy compared to nacubactam, primarily due to its higher affinity for penicillin-binding protein 2 (PBP2). Notably, zidebactam alone exhibited the most potent in vitro activity, outperforming both traditional β-lactams and novel antibiotics like cefiderocol. DBOs maintained effectiveness against strains harboring various resistance determinants, including NDM-5, OXA-181, CTX-M-15, SHV-12, CMY, and DHA. Genomic analysis revealed multiple mutations in PBP1-3, with PBP2 mutations correlating with DBO susceptibility variations. Importantly, DBOs remained highly effective against isolates with PBP mutations, even those belonging to high-risk clonal lineages (ST167, ST410, ST131). Time-kill studies confirmed the bactericidal activity of DBOs, with only one strain showing reduced susceptibility (MIC: 4 µg/ml). CONCLUSIONS This study provides compelling evidence for the potential of DBOs, particularly zidebactam, as novel antibacterial agents. Their unique characteristics and broad-spectrum activity position them as promising candidates for future antibiotic development. While the inclusion of DBO therapies in the antibiotic arsenal could significantly impact MDR pathogen treatment, realizing their full potential requires further research, clinical evaluation, and vigilant monitoring of resistance mechanisms through integrated genomic approaches.
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Affiliation(s)
- Farah Al-Marzooq
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates.
| | - Akela Ghazawi
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Maitha Alshamsi
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates; Tawam Hospital, Al-Ain, United Arab Emirates
| | - Abdulrahman Alzaabi
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Omar Aleissaee
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Hamad Almansoori
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Abdullah Alsaadi
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Rauda Aldhaheri
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Hafsa Ahli
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Lana Daoud
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Amna Ahmad
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | | | - Seema Oommen
- Burjeel Medical City/coLAB, Abu Dhabi, United Arab Emirates
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Bighi NMS, Fonseca ÉL, Freitas FS, Morgado SM, Vicente ACP. Pandemic ST131 Escherichia coli presenting the UPEC/EAEC and ExPEC/EAEC hybrid pathotypes recovered from extraintestinal infections in a clinical setting of the Brazilian Amazon region. Mem Inst Oswaldo Cruz 2025; 120:e240204. [PMID: 40243867 PMCID: PMC11984961 DOI: 10.1590/0074-02760240204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2024] [Accepted: 12/06/2024] [Indexed: 04/18/2025] Open
Abstract
BACKGROUND Escherichia coli is a commensal organism but may become pathogenic by the acquisition of virulence factors involved with intestinal (IPEC) or extraintestinal (ExPEC) infections. Some strains, known as hybrids, may harbour virulence determinants of both IPEC and ExPEC pathotypes, increasing their virulence potential. Reports of hybrid E. coli in Brazil are rare, and the associated lineages were poorly explored. OBJECTIVES This study characterised ExPEC E. coli strains focusing on the occurrence of hybrid pathotypes. METHODS Fifteen clinical ExPEC strains were submitted to multilocus sequence typing (MLST), susceptibility test, and polymerase chain reaction (PCR) targeting IEC/ExPEC virulence markers. FINDINGS All strains were multidrug-resistant, and 11 STs were determined among the 15 ExPEC strains, including local/new and pandemic lineages, such as ST69 and ST131. Twelve/15 isolates were classified as hybrids, due to the presence of virulence markers of both Enteroaggregative E. coli (EAEC) and ExPEC or UPEC pathotypes. These UPEC/EAEC (n = 10) and ExPEC/EAEC (n = 2) hybrid strains were found among distinct phylogroups and lineages, including new STs. Interestingly, most hybrids belonged to the pandemic ST131 lineage, and this genotype had never been previously reported in the ST131 circulating in Brazil. MAIN CONCLUSIONS Therefore, this study provides new information on the epidemiological scenario of hybrid E. coli, contributing to a better understanding of the occurrence and pathogenic potential of these organisms.
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Affiliation(s)
- Nathália MS Bighi
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Genética Molecular de Microrganismos, Rio de Janeiro, RJ, Brasil
| | - Érica Lourenço Fonseca
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Genética Molecular de Microrganismos, Rio de Janeiro, RJ, Brasil
| | - Fernanda S Freitas
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Genética Molecular de Microrganismos, Rio de Janeiro, RJ, Brasil
| | - Sergio Mascarenhas Morgado
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Genética Molecular de Microrganismos, Rio de Janeiro, RJ, Brasil
| | - Ana Carolina Paulo Vicente
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Genética Molecular de Microrganismos, Rio de Janeiro, RJ, Brasil
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Pitout JDD, Peirano G, Matsumura Y, DeVinney R, Chen L. Escherichia coli sequence type 410 with carbapenemases: a paradigm shift within E. coli toward multidrug resistance. Antimicrob Agents Chemother 2024; 68:e0133923. [PMID: 38193668 PMCID: PMC10869336 DOI: 10.1128/aac.01339-23] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024] Open
Abstract
Escherichia coli sequence type ST410 is an emerging carbapenemase-producing multidrug-resistant (MDR) high-risk One-Health clone with the potential to significantly increase carbapenem resistance among E. coli. ST410 belongs to two clades (ST410-A and ST410-B) and three subclades (ST410-B1, ST410-B2, and ST410-B3). After a fimH switch between clades ST410-A and ST410-B1, ST410-B2 and ST410-B3 subclades showed a stepwise progression toward developing MDR. (i) ST410-B2 initially acquired fluoroquinolone resistance (via homologous recombination) in the 1980s. (ii) ST410-B2 then obtained CMY-2, CTX-M-15, and OXA-181 genes on different plasmid platforms during the 1990s. (iii) This was followed by the chromosomal integration of blaCMY-2, fstl YRIN insertion, and ompC/ompF mutations during the 2000s to create the ST410-B3 subclade. (iv) An IncF plasmid "replacement" scenario happened when ST410-B2 transformed into ST410-B3: F36:31:A4:B1 plasmids were replaced by F1:A1:B49 plasmids (both containing blaCTX-M-15) followed by blaNDM-5 incorporation during the 2010s. User-friendly cost-effective methods for the rapid identification of ST410 isolates and clades are needed because limited data are available about the frequencies and global distribution of ST410 clades. Basic mechanistic, evolutionary, surveillance, and clinical studies are urgently required to investigate the success of ST410 (including the ability to acquire successive MDR determinants). Such information will aid with management and prevention strategies to curb the spread of carbapenem-resistant E. coli. The medical community can ill afford to ignore the spread of a global E. coli clone with the potential to end the carbapenem era.
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Affiliation(s)
- Johann D. D. Pitout
- Cummings School of Medicine, Calcary, Alberta, Canada
- University of Calgary, Alberta Precision Laboratories, Calgary, Alberta, Canada
- University of Pretoria, Pretoria, Gauteng, South Africa
| | - Gisele Peirano
- Cummings School of Medicine, Calcary, Alberta, Canada
- University of Calgary, Alberta Precision Laboratories, Calgary, Alberta, Canada
| | - Yasufumi Matsumura
- Kyoto University Graduate School of Medicine, Pretoria, Gauteng, South Africa
| | | | - Liang Chen
- Meridian Health Center for Discovery and Innovation, Kyoto, Japan
- Hackensack Meridian School of Medicine at Seton Hall University, Nutley, New Jersey, USA
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Sumbana JJ, Santona A, Abdelmalek N, Fiamma M, Deligios M, Manjate A, Sacarlal J, Rubino S, Paglietti B. Polyclonal Multidrug ESBL-Producing Klebsiella pneumoniae and Emergence of Susceptible Hypervirulent Klebsiella pneumoniae ST23 Isolates in Mozambique. Antibiotics (Basel) 2023; 12:1439. [PMID: 37760735 PMCID: PMC10525843 DOI: 10.3390/antibiotics12091439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 08/30/2023] [Accepted: 09/09/2023] [Indexed: 09/29/2023] Open
Abstract
Globally, antibiotic-resistant Klebsiella spp. cause healthcare-associated infections with high mortality rates, and the rise of hypervirulent Klebsiella pneumoniae (hvKp) poses a significant threat to human health linked to community-acquired infections and increasing non-susceptibility. We investigated the phenotypic and genetic features of 36 Klebsiella isolates recovered from invasive infections at Hospital Central of Maputo in Mozambique during one year. The majority of the isolates displayed multidrug resistance (MDR) (29/36) to cephalosporins, gentamicin, ciprofloxacin, and trimethoprim-sulfamethoxazole but retained susceptibility to amikacin, carbapenems, and colistin. Most isolates were ESBLs-producing (28/36), predominantly carrying the blaCTX-M-15 and other beta-lactamase genes (blaSHV, blaTEM-1, and blaOXA-1). Among the 16 genomes sequenced, multiple resistance genes from different antibiotic classes were identified, with blaCTX-M-15, mostly in the ISEcp1-blaCTX-M-15-orf477 genetic environment, co-existing with blaTEM-1 and aac(3)-IIa in five isolates. Our results highlight the presence of polyclonal MDR ESBL-producing K. pneumoniae from eight sequence types (ST), mostly harbouring distinct yersiniabactin within the conjugative integrative element (ICE). Further, we identified susceptible hvKp ST23, O1-K1-type isolates carrying yersiniabactin (ybt1/ICEKp10), colibactin, salmochelin, aerobactin, and hypermucoid locus (rmpADC), associated with severe infections in humans. These findings are worrying and underline the importance of implementing surveillance strategies to avoid the risk of the emergence of the most threatening MDR hvKp.
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Affiliation(s)
- José João Sumbana
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (J.J.S.); (A.S.)
- Department of Microbiology, Faculty of Medicine, Eduardo Mondlane University, Maputo P.O. Box 257, Mozambique
| | - Antonella Santona
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (J.J.S.); (A.S.)
| | - Nader Abdelmalek
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (J.J.S.); (A.S.)
| | - Maura Fiamma
- Clinical-Chemical Analysis and Microbiology Laboratory, San Francesco Hospital, 08100 Nuoro, Italy
| | - Massimo Deligios
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (J.J.S.); (A.S.)
| | - Alice Manjate
- Department of Microbiology, Faculty of Medicine, Eduardo Mondlane University, Maputo P.O. Box 257, Mozambique
| | - Jahit Sacarlal
- Department of Microbiology, Faculty of Medicine, Eduardo Mondlane University, Maputo P.O. Box 257, Mozambique
| | - Salvatore Rubino
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (J.J.S.); (A.S.)
| | - Bianca Paglietti
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (J.J.S.); (A.S.)
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Wiethoff JP, Sandmann S, Theiler T, Nze Nkogue C, Akomo-Okoue EF, Varghese J, Kreidenweiss A, Mellmann A, Lell B, Adegnika AA, Held J, Schaumburg F. Pharyngeal Communities and Antimicrobial Resistance in Pangolins in Gabon. Microbiol Spectr 2023; 11:e0066423. [PMID: 37338382 PMCID: PMC10434165 DOI: 10.1128/spectrum.00664-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 06/05/2023] [Indexed: 06/21/2023] Open
Abstract
Wildlife can be a reservoir and source of zoonotic pathogens for humans. For instance, pangolins were considered one of the potential animal reservoirs of SARS-CoV-2. The aim of this study was to assess the prevalence of antimicrobial-resistant species (e.g., extended-spectrum β-lactamase [ESBL]-producing Enterobacterales) and Staphylococcus aureus-related complex and to describe the bacterial community in wild Gabonese pangolins. The pharyngeal colonization of pangolins sold in Gabon (n = 89, 2021 to 2022) was analyzed using culture media selective for ESBL-producing Enterobacterales, S. aureus-related complex, Gram-positive bacteria and nonfermenters. Phylogenetic analyses of ESBL-producing Enterobacterales was done using core-genome multilocus sequence typing (cgMLST) and compared with publicly available genomes. Patterns of cooccurring species were detected by network analysis. Of the 439 bacterial isolates, the majority of species belonged to the genus Pseudomonas (n = 170), followed by Stenotrophomonas (n = 113) and Achromobacter (n = 37). Three Klebsiella pneumoniae isolates and one Escherichia coli isolate were ESBL-producers, which clustered with human isolates from Nigeria (MLST sequence type 1788 [ST1788]) and Gabon (ST38), respectively. Network analysis revealed a frequent cooccurrence of Stenotrophomonas maltophilia with Pseudomonas putida and Pseudomonas aeruginosa. In conclusion, pangolins can be colonized with human-related ESBL-producing K. pneumoniae and E. coli. Unlike in other African wildlife, S. aureus-related complex was not detected in pangolins. IMPORTANCE There is an ongoing debate if pangolins are a relevant reservoir for viruses such as SARS-CoV-2. Here, we wanted to know if African pangolins are colonized with bacteria that are relevant for human health. A wildlife reservoir of antimicrobial resistance would be of medical relevance in regions were consumption of so-called bushmeat is common. In 89 pangolins, we found three ESBL-producing Klebsiella pneumoniae strains and one ESBL-producing Escherichia coli strains, which were closely related to isolates from humans in Africa. This points toward either a transmission between pangolins and humans or a common source from which both humans and pangolins became colonized.
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Affiliation(s)
- Johanna P. Wiethoff
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Tübingen, Germany
| | - Sarah Sandmann
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - Tom Theiler
- Institute of Medical Microbiology, University of Münster, Münster, Germany
| | | | | | - Julian Varghese
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - Andrea Kreidenweiss
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Tübingen, Germany
| | | | - Bertrand Lell
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Tübingen, Germany
| | - Ayôla A. Adegnika
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Tübingen, Germany
| | - Jana Held
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Tübingen, Germany
| | - Frieder Schaumburg
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
- Institute of Medical Microbiology, University of Münster, Münster, Germany
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Mhaya A, Trabelsi R, Aillerie S, M’Zali F, Bégu D, Tounsi S, Gdoura R, Arpin C. Detection of Clones B2-ST131-C2 and A-ST617 in Escherichia coli Producing Both CTX-M-15 and CTX-M-27 from Tunisian Community Patients. Antibiotics (Basel) 2022; 11:antibiotics11101329. [PMID: 36289987 PMCID: PMC9598323 DOI: 10.3390/antibiotics11101329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/25/2022] [Accepted: 09/26/2022] [Indexed: 01/18/2023] Open
Abstract
During a two-month period (2017–2018), 336 urine samples positive for Escherichia coli were collected from Tunisian patients. Of the 336 samples, 266 were collected from community patients and 70 from hospital settings. In all, 15 ESBL producers were identified (8 and 7, respectively) and assigned to 13 pulsotypes, including four ESBL-producing E. coli (ESBL-E) with E1 and E2 profiles (2 isolates each) from community patients. The two strains E1 were identified as B2-ST131 subclade C2 and the two isolates E2, A-ST617. The four strains carrying both CTX-M-15 and CTX-M-27, exhibited the multireplicon IncFII/F1A/F1B with the same formula F31:A4:B1. Two isolates with patterns E3 and E4 (Dice coefficient, 78.7%) isolated from community and hospital settings of two geographic areas were assigned to the emerging ST131 C1-M27 subclade and contained the replicon F1:A-:B20. The remaining ESBL-E divided into different sequence types/associated CTX-M: 2 ST131-C2/CTX-M-15 and ST744/CTX-M-55, ST617/CTM-15, ST2973/CTX-M-55, ST6448/CTX-M-15, ST224/CTX-M-15, ST1431/CTX-M-15, and ST38/CTX-M-27, one isolate each. Our study reports for the first time the presence in the Tunisian community of two clones of E. coli, including the virulent clone ST131-C2 harboring both CTX-M-15 and CTX-M-27, and confirms the spread of the emergent clone ST131-C1-M-27, notably in community urinary tract infections.
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Affiliation(s)
- Amel Mhaya
- University of Bordeaux, Department of Biological and Medical Sciences, UMR CNRS 5234, 146 Rue Léo Saignat, 33076 Bordeaux, France
- Centre of Biotechnology of Sfax, Laboratory of Biopesticides, Road of Sidi Mansour Km 6, 3018 Sfax, Tunisia
| | - Rahma Trabelsi
- University of Sfax, Department of Life Science, Research Laboratory of Environmental Toxicology-Microbiology and Health, Road of Soukra Km 3.5, 3000 Sfax, Tunisia
| | - Sabine Aillerie
- University of Bordeaux, Department of Biological and Medical Sciences, UMR CNRS 5234, 146 Rue Léo Saignat, 33076 Bordeaux, France
| | - Fatima M’Zali
- University of Bordeaux, Aquitaine Microbiologie, 146 Rue Léo Saignat, 33076 Bordeaux, France
| | - Dominique Bégu
- University of Bordeaux, Department of Biological and Medical Sciences, UMR CNRS 5234, 146 Rue Léo Saignat, 33076 Bordeaux, France
| | - Slim Tounsi
- Centre of Biotechnology of Sfax, Laboratory of Biopesticides, Road of Sidi Mansour Km 6, 3018 Sfax, Tunisia
| | - Radhouane Gdoura
- University of Sfax, Department of Life Science, Research Laboratory of Environmental Toxicology-Microbiology and Health, Road of Soukra Km 3.5, 3000 Sfax, Tunisia
| | - Corinne Arpin
- University of Bordeaux, Department of Biological and Medical Sciences, UMR CNRS 5234, 146 Rue Léo Saignat, 33076 Bordeaux, France
- Correspondence:
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