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Shi H, Newton DP, Nguyen TH, Estrela S, Sanchez J, Tu M, Ho PY, Zeng Q, DeFelice B, Sonnenburg J, Huang KC. Nutrient competition predicts gut microbiome restructuring under drug perturbations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.06.606863. [PMID: 39211277 PMCID: PMC11360974 DOI: 10.1101/2024.08.06.606863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Human gut commensal bacteria are routinely exposed to various stresses, including therapeutic drugs, and collateral effects are difficult to predict. To systematically interrogate community-level effects of drug perturbations, we screened stool-derived in vitro communities with 707 clinically relevant small molecules. Across ∼5,000 community-drug interaction conditions, compositional and metabolomic responses were predictably impacted by nutrient competition, with certain species exhibiting improved growth due to adverse impacts on competitors. Changes to community composition were generally reversed by reseeding with the original community, although occasionally species promotion was long-lasting, due to higher-order interactions, even when the competitor was reseeded. Despite strong selection pressures, emergence of resistance within communities was infrequent. Finally, while qualitative species responses to drug perturbations were conserved across community contexts, nutrient competition quantitatively affected their abundances, consistent with predictions of consumer-resource models. Our study reveals that quantitative understanding of the interaction landscape, particularly nutrient competition, can be used to anticipate and potentially mitigate side effects of drug treatment on the gut microbiota.
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Gough AM, Parker AC, O'Bryan PJ, Whitehead TR, Roy S, Garcia BL, Hoffman PS, Jeffrey Smith C, Rocha ER. New functions of pirin proteins and a 2-ketoglutarate: Ferredoxin oxidoreductase ortholog in Bacteroides fragilis metabolism and their impact on antimicrobial susceptibility to metronidazole and amixicile. Microbiologyopen 2024; 13:e1429. [PMID: 39109824 PMCID: PMC11304471 DOI: 10.1002/mbo3.1429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 07/05/2024] [Accepted: 07/12/2024] [Indexed: 08/10/2024] Open
Abstract
The understanding of how central metabolism and fermentation pathways regulate antimicrobial susceptibility in the anaerobic pathogen Bacteroides fragilis is still incomplete. Our study reveals that B. fragilis encodes two iron-dependent, redox-sensitive regulatory pirin protein genes, pir1 and pir2. The mRNA expression of these genes increases when exposed to oxygen and during growth in iron-limiting conditions. These proteins, Pir1 and Pir2, influence the production of short-chain fatty acids and modify the susceptibility to metronidazole and amixicile, a new inhibitor of pyruvate: ferredoxin oxidoreductase in anaerobes. We have demonstrated that Pir1 and Pir2 interact directly with this oxidoreductase, as confirmed by two-hybrid system assays. Furthermore, structural analysis using AlphaFold2 predicts that Pir1 and Pir2 interact stably with several central metabolism enzymes, including the 2-ketoglutarate:ferredoxin oxidoreductases Kor1AB and Kor2CDAEBG. We used a series of metabolic mutants and electron transport chain inhibitors to demonstrate the extensive impact of bacterial metabolism on metronidazole and amixicile susceptibility. We also show that amixicile is an effective antimicrobial against B. fragilis in an experimental model of intra-abdominal infection. Our investigation led to the discovery that the kor2AEBG genes are essential for growth and have dual functions, including the formation of 2-ketoglutarate via the reverse TCA cycle. However, the metabolic activity that bypasses the function of Kor2AEBG following the addition of phospholipids or fatty acids remains undefined. Overall, our study provides new insights into the central metabolism of B. fragilis and its regulation by pirin proteins, which could be exploited for the development of new narrow-spectrum antimicrobials in the future.
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Affiliation(s)
- Andrea M. Gough
- Department of Microbiology and ImmunologyBrody School of Medicine at East Carolina UniversityGreenvilleNorth CarolinaUSA
| | - Anita C. Parker
- Department of Microbiology and ImmunologyBrody School of Medicine at East Carolina UniversityGreenvilleNorth CarolinaUSA
| | | | | | - Sourav Roy
- Department of Microbiology and ImmunologyBrody School of Medicine at East Carolina UniversityGreenvilleNorth CarolinaUSA
| | - Brandon L. Garcia
- Department of Microbiology and ImmunologyBrody School of Medicine at East Carolina UniversityGreenvilleNorth CarolinaUSA
| | - Paul S. Hoffman
- Department of Medicine, Division of Infectious Diseases and International HealthUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - C. Jeffrey Smith
- Department of Microbiology and ImmunologyBrody School of Medicine at East Carolina UniversityGreenvilleNorth CarolinaUSA
| | - Edson R. Rocha
- Department of Microbiology and ImmunologyBrody School of Medicine at East Carolina UniversityGreenvilleNorth CarolinaUSA
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Mahmood B, Paunkov A, Kupc M, Burián K, Nagy E, Leitsch D, Sóki J. Proteomics-Based RT-qPCR and Functional Analysis of 18 Genes in Metronidazole Resistance of Bacteroides fragilis. Antibiotics (Basel) 2024; 13:207. [PMID: 38534642 DOI: 10.3390/antibiotics13030207] [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: 01/16/2024] [Revised: 02/17/2024] [Accepted: 02/20/2024] [Indexed: 03/28/2024] Open
Abstract
Previously, we reported that metronidazole MICs are not dependent on the expression levels of nim genes in B. fragilis strains and we compared the proteomes of metronidazole-resistant laboratory B. fragilis strains to those of their susceptible parent strains. Here, we used RT-qPCR to correlate the expression levels of 18 candidate genes in a panel of selected, clinical nim gene-positive and -negative B. fragilis strains to their metronidazole MICs. Metronidazole MICs were correlated with the expression of certain tested genes. Specifically, lactate dehydrogenase expression correlated positively, whereas cytochrome fumarate reductase/succinate dehydrogenase, malate dehydrogenase, phosphoglycerate kinase redox and gat (GCN5-like acetyltransferase), and relA (stringent response) regulatory gene expressions correlated negatively with metronidazole MICs. This result provides evidence for the involvement of carbohydrate catabolic enzymes in metronidazole resistance in B. fragilis. This result was supported by direct substrate utilization tests. However, the exact roles of these genes/proteins should be determined in deletion-complementation tests. Moreover, the exact redox cofactor(s) participating in metronidazole activation need to be identified.
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Affiliation(s)
- Bakhtiyar Mahmood
- Institute of Medical Microbiology, Albert Szent-Györgyi Medical School, University of Szeged, 6725 Szeged, Hungary
- Department of Biology, University of Garmian, Kalar 2562, Kurdistan Region, Iraq
| | - Ana Paunkov
- Institute of Specific Prophylaxis and Tropical Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Malgorzata Kupc
- Institute of Specific Prophylaxis and Tropical Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Katalin Burián
- Institute of Medical Microbiology, Albert Szent-Györgyi Medical School, University of Szeged, 6725 Szeged, Hungary
| | - Elisabeth Nagy
- Institute of Medical Microbiology, Albert Szent-Györgyi Medical School, University of Szeged, 6725 Szeged, Hungary
| | - David Leitsch
- Institute of Specific Prophylaxis and Tropical Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - József Sóki
- Institute of Medical Microbiology, Albert Szent-Györgyi Medical School, University of Szeged, 6725 Szeged, Hungary
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Mahmood B, Juhász H, Leitsch D, Sóki J. The effects of identical nim gene-insertion sequence combinations on the expression of the nim genes and metronidazole resistance in Bacteroides fragilis strains. Anaerobe 2023; 81:102739. [PMID: 37209770 DOI: 10.1016/j.anaerobe.2023.102739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 05/13/2023] [Accepted: 05/15/2023] [Indexed: 05/22/2023]
Abstract
In this study we examined whether the same nim gene-insertion sequence (IS) element combinations give rise to the same expression levels as they harbor shared IS element-borne promoters. From our quantitative analysis, we found that the expressions of the nimB and nimE genes with their cognate IS elements were similar, but the metronidazole resistance of these strains were more diverse.
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Affiliation(s)
- Bakhtiyar Mahmood
- Institute of Medical Microbiology, Albert Szent-Györgyi Health Centre and Medical School, University of Szeged, Szeged, Hungary; Department of Biology, University of Garmian, Kalar, Kurdistan Region, Iraq
| | - Hajnalka Juhász
- Institute of Medical Microbiology, Albert Szent-Györgyi Health Centre and Medical School, University of Szeged, Szeged, Hungary
| | - David Leitsch
- Institute of Specific Prophylaxis and Tropical Medicine, Medical University of Vienna, Vienna, Austria
| | - József Sóki
- Institute of Medical Microbiology, Albert Szent-Györgyi Health Centre and Medical School, University of Szeged, Szeged, Hungary.
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Paunkov A, Hummel K, Strasser D, Sóki J, Leitsch D. Proteomic analysis of metronidazole resistance in the human facultative pathogen Bacteroides fragilis. Front Microbiol 2023; 14:1158086. [PMID: 37065137 PMCID: PMC10102347 DOI: 10.3389/fmicb.2023.1158086] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/14/2023] [Indexed: 04/03/2023] Open
Abstract
The anaerobic gut bacteria and opportunistic pathogen Bacteroides fragilis can cause life-threatening infections when leaving its niche and reaching body sites outside of the gut. The antimicrobial metronidazole is a mainstay in the treatment of anaerobic infections and also highly effective against Bacteroides spp. Although resistance rates have remained low in general, metronidazole resistance does occur in B. fragilis and can favor fatal disease outcomes. Most metronidazole-resistant Bacteroides isolates harbor nim genes, commonly believed to encode for nitroreductases which deactivate metronidazole. Recent research, however, suggests that the mode of resistance mediated by Nim proteins might be more complex than anticipated because they affect the cellular metabolism, e.g., by increasing the activity of pyruvate:ferredoxin oxidoreductase (PFOR). Moreover, although nim genes confer only low-level metronidazole resistance to Bacteroides, high-level resistance can be much easier induced in the laboratory in the presence of a nim gene than without. Due to these observations, we hypothesized that nim genes might induce changes in the B. fragilis proteome and performed comparative mass-spectrometric analyses with B. fragilis 638R, either with or without the nimA gene. Further, we compared protein expression profiles in both strains after induction of high-level metronidazole resistance. Interestingly, only few proteins were repeatedly found to be differentially expressed in strain 638R with the nimA gene, one of them being the flavodiiron protein FprA, an enzyme involved in oxygen scavenging. After induction of metronidazole resistance, a far higher number of proteins were found to be differentially expressed in 638R without nimA than in 638R with nimA. In the former, factors for the import of hemin were strongly downregulated, indicating impaired iron import, whereas in the latter, the observed changes were not only less numerous but also less specific. Both resistant strains, however, displayed a reduced capability of scavenging oxygen. Susceptibility to metronidazole could be widely restored in resistant 638R without nimA by supplementing growth media with ferrous iron sulfate, but not so in resistant 638R with the nimA gene. Finally, based on the results of this study, we present a novel hypothetic model of metronidazole resistance and NimA function.
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Affiliation(s)
- Ana Paunkov
- Institute for Specific Prophylaxis and Tropical Medicine, Center for Pathophysiology, Infectiology, and Immunology, Medical University of Vienna, Vienna, Austria
| | - Karin Hummel
- VetCore Facility for Research, University of Veterinary Medicine, Vienna, Austria
| | - Doris Strasser
- Institute for Specific Prophylaxis and Tropical Medicine, Center for Pathophysiology, Infectiology, and Immunology, Medical University of Vienna, Vienna, Austria
| | - József Sóki
- Faculty of Medicine, Institute of Medical Microbiology, University of Szeged, Szeged, Hungary
| | - David Leitsch
- Institute for Specific Prophylaxis and Tropical Medicine, Center for Pathophysiology, Infectiology, and Immunology, Medical University of Vienna, Vienna, Austria
- *Correspondence: David Leitsch,
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Eribo OA, Naidoo CC, Theron G, Walzl G, du Plessis N, Chegou NN. An Archetypical Model for Engrafting Bacteroides fragilis into Conventional Mice Following Reproducible Antibiotic Conditioning of the Gut Microbiota. Microorganisms 2023; 11:microorganisms11020451. [PMID: 36838416 PMCID: PMC9966493 DOI: 10.3390/microorganisms11020451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 02/15/2023] Open
Abstract
Bacteroides fragilis is a commonly investigated commensal bacterium for its protective role in host diseases. Here, we aimed to develop a reproducible antibiotic-based model for conditioning the gut microbiota and engrafting B. fragilis into a conventional murine host. Initially, we selected different combinations of antibiotics, including metronidazole, imipenem, and clindamycin, and investigated their efficacy in depleting the mouse Bacteroides population. We performed 16S rRNA sequencing of DNA isolated from fecal samples at different time points. The α-diversity was similar in mice treated with metronidazole (MET) and differed only at weeks 1 (p = 0.001) and 3 (p = 0.009) during metronidazole/imipenem (MI) treatment. Bacteroides compositions, during the MET and MI exposures, were similar to the pre-antibiotic exposure states. Clindamycin supplementation added to MET or MI regimens eliminated the Bacteroides population. We next repeated metronidazole/clindamycin (MC) treatment in two additional independent experiments, followed by a B. fragilis transplant. MC consistently and reproducibly eliminated the Bacteroides population. The depleted Bacteroides did not recover in a convalescence period of six weeks post-MC treatment. Finally, B. fragilis was enriched for ten days following engraftment into Bacteroides-depleted mice. Our model has potential use in gut microbiota studies that selectively investigate Bacteroides' role in diseases of interest.
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Affiliation(s)
- Osagie A. Eribo
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 8000, South Africa
| | - Charissa C. Naidoo
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 8000, South Africa
- African Microbiome Institute, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 8000, South Africa
| | - Grant Theron
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 8000, South Africa
- African Microbiome Institute, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 8000, South Africa
| | - Gerhard Walzl
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 8000, South Africa
| | - Nelita du Plessis
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 8000, South Africa
| | - Novel N. Chegou
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 8000, South Africa
- Correspondence:
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Kupc M, Paunkov A, Strasser D, Sóki J, Leitsch D. Initial expression levels of nimA are decisive for protection against metronidazole in Bacteroides fragilis. Anaerobe 2022; 77:102630. [PMID: 36028117 DOI: 10.1016/j.anaerobe.2022.102630] [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: 06/14/2022] [Revised: 08/17/2022] [Accepted: 08/19/2022] [Indexed: 11/19/2022]
Abstract
OBJECTIVES In the genus Bacteroides, the nim genes are resistance determinants for metronidazole, a nitroimidazole drug widely used against anaerobic pathogens. The Nim proteins are considered to act as nitroreductases. However, data from several studies suggest that the expression levels of Nim do not increase with increasing resistance which is conflicting with this notion. The impact of Nim protein levels on low-level metronidazole resistance, however, representing the early stage of induced resistance in the laboratory, has not been assessed as yet. METHODS The nimA gene was cloned into two different plasmids and introduced into B. fragilis strain 638R. Expression levels of nimA mRNA were measured by RT-qPCR and compared to those in strain 638R harbouring plasmid pI417, the original clinical plasmid harbouring IS element IS1168 with the nimA gene. Further, metronidazole susceptibility was assessed by Etest and the activity of pyruvate:ferredoxin oxidoreductase (PFOR) was measured in all strains after induction of high-level metronidazole resistance. RESULTS The level of protection against metronidazole by nimA correleated with the level of expression of nimA mRNA. Further, the activity of PFOR in highly-resistant B. fragilis 638R was only preserved when expression levels of nimA were high. CONCLUSIONS Although the development of high-level metronidazole resistance in B. fragilis strains with a nimA gene is not caused by an increase of nimA expression as compared to the less resistant parent strains, nimA expression levels might be of decisive importance in the early stage of resistance development. This has potential implications for metronidazole resistance in clinical isolates.
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Affiliation(s)
- Małgorzata Kupc
- Institute for Specific Prophylaxis and Tropical Medicine Center for Pathophysiology, Infectiology, and Immunology, Medical University of Vienna, Kinderspitalgasse 15, A-1090, Vienna, Austria
| | - Ana Paunkov
- Institute for Specific Prophylaxis and Tropical Medicine Center for Pathophysiology, Infectiology, and Immunology, Medical University of Vienna, Kinderspitalgasse 15, A-1090, Vienna, Austria
| | - Doris Strasser
- Institute for Specific Prophylaxis and Tropical Medicine Center for Pathophysiology, Infectiology, and Immunology, Medical University of Vienna, Kinderspitalgasse 15, A-1090, Vienna, Austria
| | - József Sóki
- Institute of Medical Microbiology, Faculty of Medicine, University of Szeged, 10 Dóm Square, H-6720, Szeged, Hungary
| | - David Leitsch
- Institute for Specific Prophylaxis and Tropical Medicine Center for Pathophysiology, Infectiology, and Immunology, Medical University of Vienna, Kinderspitalgasse 15, A-1090, Vienna, Austria.
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Paunkov A, Sóki J, Leitsch D. Modulation of Iron Import and Metronidazole Resistance in Bacteroides fragilis Harboring a nimA Gene. Front Microbiol 2022; 13:898453. [PMID: 35756037 PMCID: PMC9218692 DOI: 10.3389/fmicb.2022.898453] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/09/2022] [Indexed: 11/13/2022] Open
Abstract
Bacteroides fragilis is a commensal of the human gut but can also cause severe infections when reaching other body sites, especially after surgery or intestinal trauma. Bacteroides fragilis is an anaerobe innately susceptible to metronidazole, a 5-nitroimidazole drug that is prescribed against the majority of infections caused by anaerobic bacteria. In most of the cases, metronidazole treatment is effective but a fraction of B. fragilis is resistant to even very high doses of metronidazole. Metronidazole resistance is still poorly understood, but the so-called nim genes have been described as resistance determinants. They have been suggested to encode nitroreductases which reduce the nitro group of metronidazole to a non-toxic aminoimidazole. More recent research, however, showed that expression levels of nim genes are widely independent of the degree of resistance observed. In the search for an alternative model for nim-mediated metronidazole resistance, we screened a strain carrying an episomal nimA gene and its parental strain 638R without a nim gene for physiological differences. Indeed, the 638R daughter strain with the nimA gene had a far higher pyruvate-ferredoxin oxidoreductase (PFOR) activity than the parental strain. High PFOR activity was also observed in metronidazole-resistant clinical isolates, either with or without a nim gene. Moreover, the strain carrying a nimA gene fully retained PFOR activity and other enzyme activities such as thioredoxin reductase (TrxR) after resistance had been induced. In the parental strain 638R, these were lost or very strongly downregulated during the development of resistance. Further, after induction of high-level metronidazole resistance, parental strain 638R was highly susceptible to oxygen whereas the daughter strain with a nimA gene was hardly affected. Ensuing RT-qPCR measurements showed that a pathway for iron import via hemin uptake is downregulated in 638R with induced resistance but not in the resistant nimA daughter strain. We propose that nimA primes B. fragilis toward an alternative pathway of metronidazole resistance by enabling the preservation of normal iron levels in the cell.
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Affiliation(s)
- Ana Paunkov
- Institute for Specific Prophylaxis and Tropical Medicine Center for Pathophysiology, Infectiology, and Immunology, Medical University of Vienna, Vienna, Austria
| | - József Sóki
- Faculty of Medicine, Institute of Medical Microbiology, University of Szeged, Szeged, Hungary
| | - David Leitsch
- Institute for Specific Prophylaxis and Tropical Medicine Center for Pathophysiology, Infectiology, and Immunology, Medical University of Vienna, Vienna, Austria
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