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Wetzstein N, Diricks M, Andres S, Kuhns M, Marschall L, Biciusca T, Smaczny C, Friesen I, Niemann S, Wichelhaus TA. Genomic diversity and clinical relevance of Mycobacterium simiae. ERJ Open Res 2024; 10:00773-2023. [PMID: 38500796 PMCID: PMC10945383 DOI: 10.1183/23120541.00773-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 01/23/2024] [Indexed: 03/20/2024] Open
Abstract
Introduction Mycobacterium simiae is a slow-growing non-tuberculous mycobacterium that can cause non-tuberculous mycobacterium (NTM) pulmonary disease and extrapulmonary infections. Until now, detailed genomic and clinical characteristics, as well as possible transmission routes of this rare pathogen remain largely unknown. Methods We conducted whole genome sequencing of available M. simiae isolates collected at a tertiary care centre in Central Germany from 2006 to 2020 and set them into context with publicly available M. simiae complex sequences through phylogenetic analysis. Resistance, virulence and stress genes, as well as known Mycobacteriaceae plasmid sequences were detected in whole genome raw reads. Clinical data and course were retrieved and correlated with genomic data. Results We included 33 M. simiae sensu stricto isolates from seven patients. M. simiae showed low clinical relevance with only two patients fulfilling American Thoracic Society (ATS) criteria in our cohort and three receiving NTM-effective therapy. The bacterial populations were highly stable over time periods of up to 14 years, and no instances of mixed or re-infections with other strains of M. simiae were observed. Clustering with <12 single nucleotide polymorphisms distance was evident among isolates from different patients; however, proof for human-to-human transmission could not be established from epidemiological data. Conclusion Overall, the available sequence data for M. simiae complex was significantly extended and new insights into its pathogenomic traits were obtained. We demonstrate high longitudinal genomic stability within single patients. Although we cannot exclude human-to-human transmission, we consider it unlikely in the light of available epidemiological data.
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Affiliation(s)
- Nils Wetzstein
- Goethe University Frankfurt, University Hospital, Department of Internal Medicine, Infectious Diseases, Frankfurt am Main, Germany
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- These authors contributed equally as first authors
| | - Margo Diricks
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- These authors contributed equally as first authors
| | - Sönke Andres
- National and WHO Supranational Reference Laboratory for Mycobacteria, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Martin Kuhns
- National and WHO Supranational Reference Laboratory for Mycobacteria, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Lisa Marschall
- Goethe University Frankfurt, University Hospital, Department of Internal Medicine, Infectious Diseases, Frankfurt am Main, Germany
| | - Teodora Biciusca
- Goethe University Frankfurt, University Hospital, Department of Radiology, Frankfurt am Main, Germany
| | - Christina Smaczny
- Goethe University Frankfurt, University Hospital, Department of Internal Medicine, Pneumology, Frankfurt am Main, Germany
| | - Inna Friesen
- National and WHO Supranational Reference Laboratory for Mycobacteria, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- National and WHO Supranational Reference Laboratory for Mycobacteria, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
- These authors contributed equally as senior authors
| | - Thomas A. Wichelhaus
- Goethe University Frankfurt, University Hospital, Institute of Medical Microbiology and Infection Control, Frankfurt am Main, Germany
- These authors contributed equally as senior authors
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Wetzstein N, Kohl TA, Diricks M, Mas-Peiro S, Holubec T, Kessel J, Graf C, Koch B, Herrmann E, Vehreschild MJGT, Hogardt M, Niemann S, Stephan C, Wichelhaus TA. Clinical characteristics and outcome of Mycobacterium chimaera infections after cardiac surgery: systematic review and meta-analysis of 180 heater-cooler unit-associated cases. Clin Microbiol Infect 2023; 29:1008-1014. [PMID: 36918144 DOI: 10.1016/j.cmi.2023.03.005] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 02/13/2023] [Accepted: 03/05/2023] [Indexed: 03/14/2023]
Abstract
OBJECTIVES Since 2013, heater-cooler unit (HCU) associated Mycobacterium chimaera infections linked to a global outbreak have been described. These infections were characterised by high morbidity and mortality due to delayed diagnosis, as well as challenges in antimycobacterial and surgical therapy. This study aimed to investigate the clinical characteristics and outcome of published cases of HCU-associated M. chimaera infections. METHODS We searched PubMed and the Web of Science until 15 June 2022 for case reports, case series, and cohort studies, without language restriction, on patients with M. chimaera infection and a prior history of cardiac surgery. In this systematic review of case reports, no risk of bias assessment could be performed. Clinical, microbiological, and radiological features were recorded. Logistic regression and time-to-event analyses were performed to identify the potential factors associated with better survival. RESULTS One hundred eighty patients from 54 publications were included. Most patients underwent surgical aortic valve (67.0%; 118/176 of patients with available data) or combined aortic valve and root replacement (15.3%; 27/176). The median period between the time point of surgery and the first symptoms was 17 months (interquartile range 13-26 months). The overall case fatality rate was 45.5% (80/176), with a median survival of 24 months after the initiation of antimycobacterial therapy or diagnosis. A reoperation (including the removal or exchange of foreign material) was associated with better survival in multivariate logistic regression (OR 0.32 for lethal events; 95% CI 0.12-0.79; p 0.015) and in time-to-event analysis (p 0.0094). DISCUSSION This systematic review and meta-analysis confirm the high overall mortality of HCU -associated disseminated M. chimaera infections after cardiac surgery. A reoperation seems to be associated with better survival. Physicians have to stay aware of this infection, as patients might still be present today due to the long latency period.
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Affiliation(s)
- Nils Wetzstein
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany.
| | - Thomas A Kohl
- The German Centre for Infection Research (DZIF), partner site Hamburg-Lübeck-Borstel-Riems, Germany; Molecular and Experimental Mycobacteriology, Research Centre Borstel, Borstel, Germany
| | - Margo Diricks
- The German Centre for Infection Research (DZIF), partner site Hamburg-Lübeck-Borstel-Riems, Germany; Molecular and Experimental Mycobacteriology, Research Centre Borstel, Borstel, Germany
| | - Silvia Mas-Peiro
- Department of Internal Medicine, Cardiology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Tomas Holubec
- Department of Cardiovascular Surgery, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Johanna Kessel
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Christiana Graf
- Department of Internal Medicine, Gastroenterology and Hepatology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Benjamin Koch
- Department of Internal Medicine, Nephrology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Eva Herrmann
- Institute of Biostatistics and Mathematical Modelling, Goethe University, Frankfurt am Main, Germany
| | - Maria J G T Vehreschild
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Michael Hogardt
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Stefan Niemann
- The German Centre for Infection Research (DZIF), partner site Hamburg-Lübeck-Borstel-Riems, Germany; Molecular and Experimental Mycobacteriology, Research Centre Borstel, Borstel, Germany
| | - Christoph Stephan
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Thomas A Wichelhaus
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
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Wetzstein N, Diricks M, Kohl TA, Wichelhaus TA, Andres S, Paulowski L, Schwarz C, Lewin A, Kehrmann J, Kahl BC, Dichtl K, Hügel C, Eickmeier O, Smaczny C, Schmidt A, Zimmermann S, Nährlich L, Hafkemeyer S, Niemann S, Maurer FP, Hogardt M. Molecular Epidemiology of Mycobacterium abscessus Isolates Recovered from German Cystic Fibrosis Patients. Microbiol Spectr 2022; 10:e0171422. [PMID: 35938728 PMCID: PMC9431180 DOI: 10.1128/spectrum.01714-22] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 07/17/2022] [Indexed: 11/20/2022] Open
Abstract
Infections due to Mycobacterium abscessus are a major cause of mortality and morbidity in cystic fibrosis (CF) patients. Furthermore, M. abscessus has been suspected to be involved in person-to-person transmissions. In 2016, dominant global clonal complexes (DCCs) that occur worldwide among CF patients have been described. To elucidate the epidemiological situation of M. abscessus among CF patients in Germany and to put these data into a global context, we performed whole-genome sequencing of a set of 154 M. abscessus isolates from 123 German patients treated in 14 CF centers. We used MTBseq pipeline to identify clusters of closely related isolates and correlate those with global findings. Genotypic drug susceptibility for macrolides and aminoglycosides was assessed by characterization of the erm(41), rrl, and rrs genes. By this approach, we could identify representatives of all major DCCs (Absc 1, Absc 2, and Mass 1) in our cohort. Intrapersonal isolates showed higher genetic relatedness than interpersonal isolates (median 3 SNPs versus 16 SNPs; P < 0.001). We further identified four clusters with German patients from same centers clustering with less than 25 SNPs distance (range 3 to 18 SNPs) but did not find any hint for in-hospital person-to-person transmission. This is the largest study investigating phylogenetic relations of M. abscessus isolates in Germany. We identified representatives of all reported DCCs but evidence for nosocomial transmission remained inconclusive. Thus, the occurrence of genetically closely related isolates of M. abscessus has to be interpreted with care, as a direct interhuman transmission cannot be directly deduced. IMPORTANCE Mycobacterium abscessus is a major respiratory pathogen in cystic fibrosis (CF) patients. Recently it has been shown that dominant global clonal complexes (DCCs) have spread worldwide among CF patients. This study investigated the epidemiological situation of M. abscessus among CF patients in Germany by performing whole-genome sequencing (WGS) of a set of 154 M. abscessus from 123 German patients treated in 14 CF centers. This is the largest study investigating the phylogenetic relationship of M. abscessus CF isolates in Germany.
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Affiliation(s)
- Nils Wetzstein
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Margo Diricks
- German Center for Infection Research (DZIF), partner site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Thomas A. Kohl
- German Center for Infection Research (DZIF), partner site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Thomas A. Wichelhaus
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Sönke Andres
- German Center for Infection Research (DZIF), partner site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
- National and WHO Supranational Reference Laboratory for Mycobacteria, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Laura Paulowski
- German Center for Infection Research (DZIF), partner site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
- National and WHO Supranational Reference Laboratory for Mycobacteria, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Carsten Schwarz
- Division of Cystic Fibrosis, Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Division of Cystic Fibrosis, CF Center Westbrandenburg, Campus Potsdam, Klinikum Potsdam, Potsdam, Germany
| | - Astrid Lewin
- Unit Mycotic and Parasitic Agents and Mycobacteria, Robert Koch Institute, Berlin, Germany
| | - Jan Kehrmann
- Institute of Medical Microbiology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Barbara C. Kahl
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - Karl Dichtl
- Max von Pettenkofer Institut, Institute of Medical Microbiology and Hygiene, Medizinische Fakultät, Ludwig-Maximilians-Universität, Munich, Germany
| | - Christian Hügel
- Department of Respiratory Medicine and Allergology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
- Christiane Herzog CF Center, Medical Clinic, Department of Respiratory Medicine and Allergology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Olaf Eickmeier
- Division for Allergy, Pneumology and Cystic Fibrosis, Department for Children and Adolescence, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Christina Smaczny
- Department of Respiratory Medicine and Allergology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
- Christiane Herzog CF Center, Medical Clinic, Department of Respiratory Medicine and Allergology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Annika Schmidt
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Insitute for Medical Microbiology and Hygiene, University Hospital Tübingen, Tübingen, Germany
| | - Stefan Zimmermann
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Heidelberg, Germany
| | - Lutz Nährlich
- Department of Pediatrics, Justus-Liebig-University Giessen, Giessen, Germany
| | - Sylvia Hafkemeyer
- Mukoviszidose Institut, gemeinnützige Gesellschaft für Forschung und Therapieentwicklung mbH, Bonn, Germany
| | - Stefan Niemann
- German Center for Infection Research (DZIF), partner site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Florian P. Maurer
- German Center for Infection Research (DZIF), partner site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
- National and WHO Supranational Reference Laboratory for Mycobacteria, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
- Institute of Medical Microbiology, Virology and Hospital Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Michael Hogardt
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
- German National Consiliary Laboratory on Cystic Fibrosis Bacteriology, Frankfurt am Main, Germany
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Akwani WC, van Vliet AH, Joel JO, Andres S, Diricks M, Maurer FP, Chambers MA, Hingley-Wilson SM. The Use of Comparative Genomic Analysis for the Development of Subspecies-Specific PCR Assays for Mycobacterium abscessus. Front Cell Infect Microbiol 2022; 12:816615. [PMID: 35419298 PMCID: PMC8995789 DOI: 10.3389/fcimb.2022.816615] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 03/07/2022] [Indexed: 01/21/2023] Open
Abstract
Mycobacterium abscessus complex (MABC) is an important pathogen of immunocompromised patients. Accurate and rapid determination of MABC at the subspecies level is vital for optimal antibiotic therapy. Here we have used comparative genomics to design MABC subspecies-specific PCR assays. Analysis of single nucleotide polymorphisms and core genome multilocus sequence typing showed clustering of genomes into three distinct clusters representing the MABC subspecies M. abscessus, M. bolletii and M. massiliense. Pangenome analysis of 318 MABC genomes from the three subspecies allowed for the identification of 15 MABC subspecies-specific genes. In silico testing of primer sets against 1,663 publicly available MABC genomes and 66 other closely related Mycobacterium genomes showed that all assays had >97% sensitivity and >98% specificity. Subsequent experimental validation of two subspecies-specific genes each showed the PCR assays worked well in individual and multiplex format with no false-positivity with 5 other mycobacteria of clinical importance. In conclusion, we have developed a rapid, accurate, multiplex PCR-assay for discriminating MABC subspecies that could improve their detection, diagnosis and inform correct treatment choice.
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Affiliation(s)
- Winifred C. Akwani
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Arnoud H.M. van Vliet
- Department of Pathology and Infectious Diseases, School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Jordan O. Joel
- Department of Pathology and Infectious Diseases, School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Sönke Andres
- National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Margo Diricks
- National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Florian P. Maurer
- National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- Institute of Medical Microbiology, Virology, and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Mark A. Chambers
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
- Department of Pathology and Infectious Diseases, School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Suzanne M. Hingley-Wilson
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
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Diricks M, Kohl TA, Käding N, Leshchinskiy V, Hauswaldt S, Vázquez OJ, Utpatel C, Niemann S, Rupp J, Merker M. Correction to: Whole genome sequencing-based classifcation of human-related Haemophilus species and detection of antimicrobial resistance genes. Genome Med 2022; 14:22. [PMID: 35209955 PMCID: PMC8867676 DOI: 10.1186/s13073-022-01028-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Margo Diricks
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Thomas A Kohl
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Nadja Käding
- Department of Infectious Diseases and Microbiology, University Hospital Schleswig-Holstein, Lübeck, Germany.,German Center for Infection Research (DZIF), TTU HAARBI, Lübeck, Germany
| | - Vladislav Leshchinskiy
- Department of Infectious Diseases and Microbiology, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Susanne Hauswaldt
- Department of Infectious Diseases and Microbiology, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Omar Jiménez Vázquez
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Jan Rupp
- Department of Infectious Diseases and Microbiology, University Hospital Schleswig-Holstein, Lübeck, Germany.,German Center for Infection Research (DZIF), TTU HAARBI, Lübeck, Germany
| | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany. .,German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany. .,Evolution of the Resistome, Research Center Borstel, Borstel, Germany.
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Diricks M, Kohl TA, Käding N, Leshchinskiy V, Hauswaldt S, Jiménez Vázquez O, Utpatel C, Niemann S, Rupp J, Merker M. Whole genome sequencing-based classification of human-related Haemophilus species and detection of antimicrobial resistance genes. Genome Med 2022; 14:13. [PMID: 35139905 PMCID: PMC8830169 DOI: 10.1186/s13073-022-01017-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 05/31/2021] [Accepted: 01/24/2022] [Indexed: 12/31/2022] Open
Abstract
Background Bacteria belonging to the genus Haemophilus cause a wide range of diseases in humans. Recently, H. influenzae was classified by the WHO as priority pathogen due to the wide spread of ampicillin resistant strains. However, other Haemophilus spp. are often misclassified as H. influenzae. Therefore, we established an accurate and rapid whole genome sequencing (WGS) based classification and serotyping algorithm and combined it with the detection of resistance genes. Methods A gene presence/absence-based classification algorithm was developed, which employs the open-source gene-detection tool SRST2 and a new classification database comprising 36 genes, including capsule loci for serotyping. These genes were identified using a comparative genome analysis of 215 strains belonging to ten human-related Haemophilus (sub)species (training dataset). The algorithm was evaluated on 1329 public short read datasets (evaluation dataset) and used to reclassify 262 clinical Haemophilus spp. isolates from 250 patients (German cohort). In addition, the presence of antibiotic resistance genes within the German dataset was evaluated with SRST2 and correlated with results of traditional phenotyping assays. Results The newly developed algorithm can differentiate between clinically relevant Haemophilus species including, but not limited to, H. influenzae, H. haemolyticus, and H. parainfluenzae. It can also identify putative haemin-independent H. haemolyticus strains and determine the serotype of typeable Haemophilus strains. The algorithm performed excellently in the evaluation dataset (99.6% concordance with reported species classification and 99.5% with reported serotype) and revealed several misclassifications. Additionally, 83 out of 262 (31.7%) suspected H. influenzae strains from the German cohort were in fact H. haemolyticus strains, some of which associated with mouth abscesses and lower respiratory tract infections. Resistance genes were detected in 16 out of 262 datasets from the German cohort. Prediction of ampicillin resistance, associated with blaTEM-1D, and tetracycline resistance, associated with tetB, correlated well with available phenotypic data. Conclusions Our new classification database and algorithm have the potential to improve diagnosis and surveillance of Haemophilus spp. and can easily be coupled with other public genotyping and antimicrobial resistance databases. Our data also point towards a possible pathogenic role of H. haemolyticus strains, which needs to be further investigated. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-022-01017-x.
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Affiliation(s)
- Margo Diricks
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Thomas A Kohl
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Nadja Käding
- Department of Infectious Diseases and Microbiology, University Hospital Schleswig-Holstein, Lübeck, Germany.,German Center for Infection Research (DZIF), TTU HAARBI, Lübeck, Germany
| | - Vladislav Leshchinskiy
- Department of Infectious Diseases and Microbiology, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Susanne Hauswaldt
- Department of Infectious Diseases and Microbiology, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Omar Jiménez Vázquez
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Jan Rupp
- Department of Infectious Diseases and Microbiology, University Hospital Schleswig-Holstein, Lübeck, Germany.,German Center for Infection Research (DZIF), TTU HAARBI, Lübeck, Germany
| | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany. .,German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany. .,Evolution of the Resistome, Research Center Borstel, Borstel, Germany.
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Nambiar R, Tornheim JA, Diricks M, De Bruyne K, Sadani M, Shetty A, Rodrigues C. Linezolid resistance in Mycobacterium tuberculosis isolates at a tertiary care centre in Mumbai, India. Indian J Med Res 2021; 154:85-89. [PMID: 34782533 PMCID: PMC8715694 DOI: 10.4103/ijmr.ijmr_1168_19] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Background & objectives: Linezolid (LZD) is increasingly being used in tuberculosis (TB) treatment. However, LZD resistance has already been reported, which is highly alarming, given its critical therapeutic role. This study was aimed to phenotypically and genotypically assess LZD resistance in Mycobacterium tuberculosis (MTB) isolates at a laboratory in a tertiary care centre in Mumbai, India. Methods: A sample of 32 consecutive LZD-resistant MTB isolates identified by liquid culture susceptibility testing was subjected to whole-genome sequencing (WGS) on the Illumina NextSeq platform. Sequences were analyzed using BioNumerics software to predict resistance for 12 antibiotics within 15 min. Results: Sixty eight of the 2179 isolates tested for LZD resistance by MGIT-based susceptibility testing (June 2015 to June 2016) were LZD-resistant. Thirty two consecutive LZD-resistant isolates were analyzed by WGS to screen for known mutations conferring LZD resistance. WGS of 32 phenotypically LZD-resistant isolates showed that C154R in the rplC gene and G2814T in the rrl gene were the major resistance determinants. Interpretation & conclusions: LZD resistance poses an important risk to the success of treatment regimens, especially those designed for resistant isolates; such regimens are extensively used in India. As LZD-containing regimens increase in prominence, it is important to support clinical decision-making with an improved understanding of the common mutations conferring LZD resistance and their frequency in different settings.
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Affiliation(s)
- Remya Nambiar
- Department of Microbiology, PD Hinduja Hospital & MRC, Mumbai, Maharashtra, India
| | - Jeffrey A Tornheim
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Margo Diricks
- Department of Data Analytics, Applied Maths NV, BioMérieux, 9830 Sint-Martens-Latem, Belgium
| | - Katrien De Bruyne
- Department of Data Analytics, Applied Maths NV, BioMérieux, 9830 Sint-Martens-Latem, Belgium
| | - Meeta Sadani
- Department of Microbiology, PD Hinduja Hospital & MRC, Mumbai, Maharashtra, India
| | - Anjali Shetty
- Department of Microbiology, PD Hinduja Hospital & MRC, Mumbai, Maharashtra, India
| | - Camilla Rodrigues
- Department of Microbiology, PD Hinduja Hospital & MRC, Mumbai, Maharashtra, India
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8
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Steindor M, Stehling F, Olivier M, Kehrmann J, Diricks M, Maurer FP, Horn PA, Straßburg S, Welsner M, Sutharsan S, Lindemann M. Species-Specific Interferon-Gamma Release Assay for the Diagnosis of Mycobacterium abscessus Complex Infection. Front Microbiol 2021; 12:692395. [PMID: 34322105 PMCID: PMC8312262 DOI: 10.3389/fmicb.2021.692395] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 06/14/2021] [Indexed: 11/13/2022] Open
Abstract
Mycobacterium abscessus complex (MABC) infection has a devastating impact on the course of cystic fibrosis (CF) and non-CF lung disease. Diagnosis of MABC pulmonary disease is challenging, and current diagnostic approaches lack accuracy, especially in CF. In this study, we aimed to establish an MABC-specific interferon-γ release assay to detect host immune responses to MABC and improve diagnostics of MABC infection by the detection of antigen-specific T cells. Four species-specific proteins of MABC were overexpressed in an Escherichia coli expression system. Purified proteins were used to stimulate peripheral blood mononuclear cells of study subjects in an ELISpot assay. Interferon-γ response of 12 subjects with established diagnosis of MABC infection (10 CF and two non-CF) was compared with 35 controls (22 CF and 13 non-CF) distributed to three control groups, 17 CF subjects without NTM infection, nine subjects with NTM infection other than MABC, and nine subjects with tuberculosis. Cellular in vitro responses in the MABC group were stronger than in the control groups, especially toward the protein MAB_0405c (39 vs. 4 spots per 300,000 PBMC, p = 0.004; data represent mean values) in all patients and also in the subgroup of CF subjects (39 spots vs. 1 spot, p = 0.003). Receiver operating characteristic curve analysis indicated that spot numbers of at least 20 were highly predictive of MABC infection (all patients: area under curve 0.773, sensitivity 58%, and specificity 94%; CF patients: area under curve 0.818, sensitivity 60%, and specificity 100%). In conclusion, we identified MAB_0405c as a protein that may stimulate MABC-specific interferon-γ secretion and may add to the diagnosis of MABC infection in affected patients.
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Affiliation(s)
- Mathis Steindor
- Pediatric Pulmonology and Sleep Medicine, Children's University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Florian Stehling
- Pediatric Pulmonology and Sleep Medicine, Children's University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Margarete Olivier
- Pediatric Pulmonology and Sleep Medicine, Children's University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Jan Kehrmann
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Margo Diricks
- Molecular and Experimental Mycobacteriology, Research Center Borstel - Leibniz Lung Center, Borstel, Germany.,National and WHO Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Florian P Maurer
- National and WHO Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany.,Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Peter A Horn
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Svenja Straßburg
- Department of Pulmonary Medicine, Adult Cystic Fibrosis Center, University Hospital Essen - Ruhrlandklinik, University of Duisburg-Essen, Essen, Germany
| | - Matthias Welsner
- Department of Pulmonary Medicine, Adult Cystic Fibrosis Center, University Hospital Essen - Ruhrlandklinik, University of Duisburg-Essen, Essen, Germany
| | - Sivagurunathan Sutharsan
- Department of Pulmonary Medicine, Adult Cystic Fibrosis Center, University Hospital Essen - Ruhrlandklinik, University of Duisburg-Essen, Essen, Germany
| | - Monika Lindemann
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
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9
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Papić B, Diricks M, Kušar D. Analysis of the Global Population Structure of Paenibacillus larvae and Outbreak Investigation of American Foulbrood Using a Stable wgMLST Scheme. Front Vet Sci 2021; 8:582677. [PMID: 33718463 PMCID: PMC7952629 DOI: 10.3389/fvets.2021.582677] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 07/27/2020] [Accepted: 02/05/2021] [Indexed: 12/12/2022] Open
Abstract
Paenibacillus larvae causes the American foulbrood (AFB), a highly contagious and devastating disease of honeybees. Whole-genome sequencing (WGS) has been increasingly used in bacterial pathogen typing, but rarely applied to study the epidemiology of P. larvae. To this end, we used 125 P. larvae genomes representative of a species-wide diversity to construct a stable whole-genome multilocus sequence typing (wgMLST) scheme consisting of 5745 loci. A total of 51 P. larvae isolates originating from AFB outbreaks in Slovenia were used to assess the epidemiological applicability of the developed wgMLST scheme. In addition, wgMLST was compared with the core-genome MLST (cgMLST) and whole-genome single nucleotide polymorphism (wgSNP) analyses. All three approaches successfully identified clusters of outbreak-associated strains, which were clearly separated from the epidemiologically unlinked isolates. High levels of backward comparability of WGS-based analyses with conventional typing methods (ERIC-PCR and MLST) were revealed; however, both conventional methods lacked sufficient discriminatory power to separate the outbreak clusters. The developed wgMLST scheme provides an improved understanding of the intra- and inter-outbreak genetic diversity of P. larvae and represents an important progress in unraveling the genomic epidemiology of this important honeybee pathogen.
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Affiliation(s)
- Bojan Papić
- Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Margo Diricks
- bioMérieux, Applied Maths NV, Sint-Martens-Latem, Belgium
| | - Darja Kušar
- Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia
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10
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Gröschel MI, Meehan CJ, Barilar I, Diricks M, Gonzaga A, Steglich M, Conchillo-Solé O, Scherer IC, Mamat U, Luz CF, De Bruyne K, Utpatel C, Yero D, Gibert I, Daura X, Kampmeier S, Rahman NA, Kresken M, van der Werf TS, Alio I, Streit WR, Zhou K, Schwartz T, Rossen JWA, Farhat MR, Schaible UE, Nübel U, Rupp J, Steinmann J, Niemann S, Kohl TA. The phylogenetic landscape and nosocomial spread of the multidrug-resistant opportunist Stenotrophomonas maltophilia. Nat Commun 2020; 11:2044. [PMID: 32341346 PMCID: PMC7184733 DOI: 10.1038/s41467-020-15123-0] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [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: 08/13/2019] [Accepted: 02/15/2020] [Indexed: 02/06/2023] Open
Abstract
Recent studies portend a rising global spread and adaptation of human- or healthcare-associated pathogens. Here, we analyse an international collection of the emerging, multidrug-resistant, opportunistic pathogen Stenotrophomonas maltophilia from 22 countries to infer population structure and clonality at a global level. We show that the S. maltophilia complex is divided into 23 monophyletic lineages, most of which harbour strains of all degrees of human virulence. Lineage Sm6 comprises the highest rate of human-associated strains, linked to key virulence and resistance genes. Transmission analysis identifies potential outbreak events of genetically closely related strains isolated within days or weeks in the same hospitals. Multidrug resistance of the opportunistic pathogen Stenotrophomonas maltophilia is an increasing problem. Here, analyzing strains from 22 countries, the authors show that the S. maltophilia complex is divided into 23 monophyletic lineages and find evidence for intra-hospital transmission.
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Affiliation(s)
- Matthias I Gröschel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,Department of Pulmonary Diseases & Tuberculosis, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Conor J Meehan
- School of Chemistry and Bioscience, University of Bradford, Bradford, United Kingdom
| | - Ivan Barilar
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Margo Diricks
- bioMérieux, Applied Maths NV, Keistraat 120, 9830, St-Martens-Latem, Belgium
| | - Aitor Gonzaga
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Matthias Steglich
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Oscar Conchillo-Solé
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Barcelona, Spain.,Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Isabell-Christin Scherer
- Department of Infectious Diseases and Microbiology, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Uwe Mamat
- Cellular Microbiology, Research Center Borstel, Borstel, Germany
| | - Christian F Luz
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Katrien De Bruyne
- bioMérieux, Applied Maths NV, Keistraat 120, 9830, St-Martens-Latem, Belgium
| | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Daniel Yero
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Barcelona, Spain.,Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Isidre Gibert
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Barcelona, Spain.,Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Xavier Daura
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Barcelona, Spain.,Catalan Institution for Research and Advanced Studies, Barcelona, Spain
| | | | | | - Michael Kresken
- Antiinfectives Intelligence GmbH, Rheinbach, Germany.,Rheinische Fachhochschule Köln gGmbH, Cologne, Germany
| | - Tjip S van der Werf
- Department of Pulmonary Diseases & Tuberculosis, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Ifey Alio
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Kai Zhou
- Shenzhen Institute of Respiratory Diseases, the First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China.,Second Clinical Medical College, Jinan University, Shenzhen, China
| | - Thomas Schwartz
- Karlsruhe Institute of Technology, Institute of Functional Interfaces, Eggenstein- Leopoldshafen, Germany
| | - John W A Rossen
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Maha R Farhat
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.,Division of Pulmonary and Critical Care, Massachusetts General Hospital, Boston, MA, USA
| | - Ulrich E Schaible
- Cellular Microbiology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research (DZIF), partner site Hamburg - Lübeck - Borstel - Riems, Cologne, Germany.,Leibniz Research Alliance INFECTIONS'21, Cologne, Germany
| | - Ulrich Nübel
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,Leibniz Research Alliance INFECTIONS'21, Cologne, Germany.,Germany Center for Infection Research (DZIF), partner site Hannover - Braunschweig, Cologne, Germany.,Braunschweig Integrated Center of Systems Biology (BRICS), Technical University, Braunschweig, Germany
| | - Jan Rupp
- Department of Infectious Diseases and Microbiology, University Hospital Schleswig-Holstein, Lübeck, Germany.,German Center for Infection Research (DZIF), partner site Hamburg - Lübeck - Borstel - Riems, Cologne, Germany
| | - Joerg Steinmann
- Institute of Medical Microbiology, University Medical Center Essen, Essen, Germany.,Medical Microbiology and Infection Prevention, Institute of Clinical Hygiene, Paracelsus Medical Private University, Klinikum Nürnberg, Nuremberg, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany. .,German Center for Infection Research (DZIF), partner site Hamburg - Lübeck - Borstel - Riems, Cologne, Germany. .,Leibniz Research Alliance INFECTIONS'21, Cologne, Germany.
| | - Thomas A Kohl
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research (DZIF), partner site Hamburg - Lübeck - Borstel - Riems, Cologne, Germany
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11
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Gutmann A, Lepak A, Diricks M, Desmet T, Nidetzky B. Glycosyltransferase cascades for natural product glycosylation: Use of plant instead of bacterial sucrose synthases improves the UDP-glucose recycling from sucrose and UDP. Biotechnol J 2017; 12. [PMID: 28429856 DOI: 10.1002/biot.201600557] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [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: 12/22/2016] [Revised: 04/14/2017] [Accepted: 04/20/2017] [Indexed: 02/02/2023]
Abstract
Natural product glycosylations by Leloir glycosyltransferases (GTs) require expensive nucleotide-activated sugars as substrates. Sucrose synthase (SuSy) converts sucrose and uridine 5'-diphosphate (UDP) into UDP-glucose. Coupling of SuSy and GT reactions in one-pot cascade transformations creates a UDP cycle, which regenerates the UDP-glucose continuously and so makes it an expedient donor for glucoside production. Here we compare SuSys with divergent kinetic characteristics for UDP-glucose recycling in the synthesis of the natural C-glucoside nothofagin. Development of a fast reversed-phase ion-pairing HPLC method, quantifying all relevant reactants from the coupled conversion in a single run, was key to dissect the main factors of recycling efficiency. Limitations due to high KM , both for UDP and sucrose, were revealed for the bacterial SuSy from Acidithiobacillus caldus. The L637M-T640V double mutant of this SuSy with a 60-fold reduced KM for UDP substantially improved UDP-glucose recycling. The SuSy from Glycine max (soybean) was nevertheless the most active enzyme at the UDP (≤ 0.5 mM) and sucrose (≤ 1 M) concentrations used. It was also unexpectedly stable at up to 50°C where spontaneous decomposition of UDP-glucose started to become problematic. The herein gained in-depth understanding of requirements for UDP-glucose regeneration supports development of efficient GT-SuSy cascades.
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Affiliation(s)
- Alexander Gutmann
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Graz, Austria
| | - Alexander Lepak
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Graz, Austria
| | - Margo Diricks
- Centre for Industrial Biotechnology and Biocatalysis, Department of Biochemical and Microbial Technology, Ghent University, Ghent, Belgium
| | - Tom Desmet
- Centre for Industrial Biotechnology and Biocatalysis, Department of Biochemical and Microbial Technology, Ghent University, Ghent, Belgium
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Graz, Austria
- Austrian Centre of Industrial Biotechnology, Graz, Austria
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12
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Diricks M, Gutmann A, Debacker S, Dewitte G, Nidetzky B, Desmet T. Sequence determinants of nucleotide binding in Sucrose Synthase: improving the affinity of a bacterial Sucrose Synthase for UDP by introducing plant residues. Protein Eng Des Sel 2017; 30:141-148. [PMID: 27590052 DOI: 10.1093/protein/gzw048] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 08/04/2016] [Indexed: 11/13/2022] Open
Abstract
Sucrose Synthase (SuSy) catalyzes the reversible conversion of sucrose and a nucleoside diphosphate (NDP) into NDP-glucose and fructose. Biochemical characterization of several plant and bacterial SuSys has revealed that the eukaryotic enzymes preferentially use UDP whereas prokaryotic SuSys prefer ADP as acceptor. In this study, SuSy from the bacterium Acidithiobacillus caldus, which has a higher affinity for ADP as reflected by the 25-fold lower Km value compared to UDP, was used as a test case to scrutinize the effect of introducing plant residues at positions in a putative nucleotide binding motif surrounding the nucleobase ring of NDP. All eight single to sextuple mutants had similar activities as the wild-type enzyme but significantly reduced Km values for UDP (up to 60 times). In addition, we recognized that substrate inhibition by UDP is introduced by a methionine at position 637. The affinity for ADP also increased for all but one variant, although the improvement was much smaller compared to UDP. Further characterization of a double mutant also revealed more than 2-fold reduction in Km values for CDP and GDP. This demonstrates the general impact of the motif on nucleotide binding. Furthermore, this research also led to the establishment of a bacterial SuSy variant that is suitable for the recycling of UDP during glycosylation reactions. The latter was successfully demonstrated by combining this variant with a glycosyltransferase in a one-pot reaction for the production of the C-glucoside nothofagin, a health-promoting flavonoid naturally found in rooibos (tea).
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Affiliation(s)
- Margo Diricks
- Department of Biochemical and Microbial Technology, Centre for Industrial Biotechnology and Biocatalysis, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Alexander Gutmann
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, 8010 Graz, Austria
| | - Simon Debacker
- Department of Biochemical and Microbial Technology, Centre for Industrial Biotechnology and Biocatalysis, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Griet Dewitte
- Department of Biochemical and Microbial Technology, Centre for Industrial Biotechnology and Biocatalysis, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, 8010 Graz, Austria.,Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria
| | - Tom Desmet
- Department of Biochemical and Microbial Technology, Centre for Industrial Biotechnology and Biocatalysis, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
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13
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Dewitte G, Walmagh M, Diricks M, Lepak A, Gutmann A, Nidetzky B, Desmet T. Screening of recombinant glycosyltransferases reveals the broad acceptor specificity of stevia UGT-76G1. J Biotechnol 2016; 233:49-55. [DOI: 10.1016/j.jbiotec.2016.06.034] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 06/21/2016] [Accepted: 06/30/2016] [Indexed: 12/23/2022]
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14
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Schmölzer K, Gutmann A, Diricks M, Desmet T, Nidetzky B. Sucrose synthase: A unique glycosyltransferase for biocatalytic glycosylation process development. Biotechnol Adv 2015; 34:88-111. [PMID: 26657050 DOI: 10.1016/j.biotechadv.2015.11.003] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [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: 09/22/2015] [Revised: 11/18/2015] [Accepted: 11/24/2015] [Indexed: 01/24/2023]
Abstract
Sucrose synthase (SuSy, EC 2.4.1.13) is a glycosyltransferase (GT) long known from plants and more recently discovered in bacteria. The enzyme catalyzes the reversible transfer of a glucosyl moiety between fructose and a nucleoside diphosphate (NDP) (sucrose+NDP↔NDP-glucose+fructose). The equilibrium for sucrose conversion is pH dependent, and pH values between 5.5 and 7.5 promote NDP-glucose formation. The conversion of a bulk chemical to high-priced NDP-glucose in a one-step reaction provides the key aspect for industrial interest. NDP-sugars are important as such and as key intermediates for glycosylation reactions by highly selective Leloir GTs. SuSy has gained renewed interest as industrially attractive biocatalyst, due to substantial scientific progresses achieved in the last few years. These include biochemical characterization of bacterial SuSys, overproduction of recombinant SuSys, structural information useful for design of tailor-made catalysts, and development of one-pot SuSy-GT cascade reactions for production of several relevant glycosides. These advances could pave the way for the application of Leloir GTs to be used in cost-effective processes. This review provides a framework for application requirements, focusing on catalytic properties, heterologous enzyme production and reaction engineering. The potential of SuSy biocatalysis will be presented based on various biotechnological applications: NDP-sugar synthesis; sucrose analog synthesis; glycoside synthesis by SuSy-GT cascade reactions.
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Affiliation(s)
- Katharina Schmölzer
- Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria.
| | - Alexander Gutmann
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12/I, 8010 Graz, Austria.
| | - Margo Diricks
- Centre for Industrial Biotechnology and Biocatalysis, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium.
| | - Tom Desmet
- Centre for Industrial Biotechnology and Biocatalysis, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium.
| | - Bernd Nidetzky
- Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria; Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12/I, 8010 Graz, Austria.
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15
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Diricks M, De Bruyn F, Van Daele P, Walmagh M, Desmet T. Identification of sucrose synthase in nonphotosynthetic bacteria and characterization of the recombinant enzymes. Appl Microbiol Biotechnol 2015; 99:8465-74. [PMID: 25846332 DOI: 10.1007/s00253-015-6548-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [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: 12/17/2014] [Revised: 03/09/2015] [Accepted: 03/15/2015] [Indexed: 10/23/2022]
Abstract
Sucrose synthase (SuSy) catalyzes the reversible conversion of sucrose and a nucleoside diphosphate into fructose and nucleotide (NDP)-glucose. To date, only SuSy's from plants and cyanobacteria, both photosynthetic organisms, have been characterized. Here, four prokaryotic SuSy enzymes from the nonphotosynthetic organisms Nitrosomonas Europaea (SuSyNe), Acidithiobacillus caldus (SuSyAc), Denitrovibrio acetiphilus (SusyDa), and Melioribacter roseus (SuSyMr) were recombinantly expressed in Escherichia coli and thoroughly characterized. The purified enzymes were found to display high-temperature optima (up to 80 °C), high activities (up to 125 U/mg), and high thermostability (up to 15 min at 60 °C). Furthermore, SuSyAc, SuSyNe, and SuSyDa showed a clear preference for ADP as nucleotide, as opposed to plant SuSy's which prefer UDP. A structural and mutational analysis was performed to elucidate the difference in NDP preference between eukaryotic and prokaryotic SuSy's. Finally, the physiological relevance of this enzyme specificity is discussed in the context of metabolic pathways and genomic organization.
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Affiliation(s)
- Margo Diricks
- Centre for Industrial Biotechnology and Biocatalysis, Department of Biochemical and Microbial Technology, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Frederik De Bruyn
- Centre for Industrial Biotechnology and Biocatalysis, Department of Biochemical and Microbial Technology, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Paul Van Daele
- Centre for Industrial Biotechnology and Biocatalysis, Department of Biochemical and Microbial Technology, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Maarten Walmagh
- Centre for Industrial Biotechnology and Biocatalysis, Department of Biochemical and Microbial Technology, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Tom Desmet
- Centre for Industrial Biotechnology and Biocatalysis, Department of Biochemical and Microbial Technology, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
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