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van Kleef-van Koeveringe S, Matheeussen V, Schuermans A, De Koster S, Perales Selva N, Jansens H, De Coninck D, De Bruyne K, Mensaert K, Kluytmans-van den Bergh M, Kluytmans J, Goossens H, Dhaeze W, Leroux-Roels I. Epidemiology and molecular typing of multidrug-resistant bacteria in tertiary hospitals and nursing homes in Flanders, Belgium. Eur J Clin Microbiol Infect Dis 2024; 43:187-194. [PMID: 37971537 PMCID: PMC10774642 DOI: 10.1007/s10096-023-04699-2] [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: 12/14/2022] [Accepted: 10/31/2023] [Indexed: 11/19/2023]
Abstract
This study aimed to map MDRO carriage and potential transmission within and between three Flemish tertiary care hospitals and their neighbouring nursing homes. A cross-sectional MDRO prevalence survey was organized between October 2017 and February 2019. Perianal swabs were cultured for detection of MDRO. Determination of clonal relatedness based on wgMLST allelic profiles was performed. The prevalence of MDRO in Belgian hospitals and NHs is on the rise, compared to previous studies, and transmission in and between institutions is observed. These results re-emphasize the need for a healthcare network-wide infection prevention strategy in which WGS of MDRO strains can be supportive.
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Affiliation(s)
- Stefanie van Kleef-van Koeveringe
- Laboratory of Medical Microbiology, University Hospital Antwerp, Edegem, Belgium.
- Department of Medical Microbiology, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Wilrijk, Belgium.
| | - Veerle Matheeussen
- Laboratory of Medical Microbiology, University Hospital Antwerp, Edegem, Belgium
- Department of Medical Microbiology, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Wilrijk, Belgium
| | - Annette Schuermans
- Department of Infection Control and Epidemiology, University Hospital Leuven, Leuven, Belgium
| | - Sien De Koster
- Department of Medical Microbiology, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Wilrijk, Belgium
| | | | - Hilde Jansens
- Department of Infection Control, University Hospital Antwerp, Edegem, Belgium
| | - Dieter De Coninck
- bioMérieux, Augmented Diagnostics, Industrial Microbiology, Applied Maths NV, Sint-Martens-Latem, Belgium
| | - Katrien De Bruyne
- bioMérieux, Augmented Diagnostics, Industrial Microbiology, Applied Maths NV, Sint-Martens-Latem, Belgium
| | - Klaas Mensaert
- bioMérieux, Augmented Diagnostics, Industrial Microbiology, Applied Maths NV, Sint-Martens-Latem, Belgium
| | - Marjolein Kluytmans-van den Bergh
- Department of Infection Control, Amphia Hospital, Breda, The Netherlands
- Julius Center for Health Sciences and Primary Care, UMC Utrecht, Utrecht, The Netherlands
| | - Jan Kluytmans
- Microvida Laboratory for Microbiology, Amphia Hospital, Breda, and Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Herman Goossens
- Laboratory of Medical Microbiology, University Hospital Antwerp, Edegem, Belgium
- Department of Medical Microbiology, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Wilrijk, Belgium
| | - Wouter Dhaeze
- Department prevention, Agentschap Zorg en Gezondheid, Leuven, Belgium
| | - Isabel Leroux-Roels
- Laboratory of Medical Microbiology, University Hospital Ghent, Ghent, Belgium
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van Kleef – van Koeveringe S, Matheeussen V, Jansens H, Perales Selva N, De Coninck D, De Bruyne K, Mensaert K, Kluytmans - van den Bergh M, Kluytmans J, Goossens H, Dhaeze W. Epidemiology and molecular typing of multidrug-resistant bacteria in day care centres in Flanders, Belgium. Epidemiol Infect 2023; 151:e156. [PMID: 37711023 PMCID: PMC10548538 DOI: 10.1017/s0950268823001528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/28/2023] [Accepted: 08/29/2023] [Indexed: 09/16/2023] Open
Abstract
The global prevalence and spread of multidrug-resistant organisms (MDROs) represent an emerging public health threat. Day care centre (DCC) attendance is a risk factor for MDRO carriage in children and their environment. This study aimed to map the epidemiology of carriage and potential transmission of these organisms within 18 Flemish DDCs (Belgium). An MDRO prevalence survey was organised between November 2018 and February 2019 among children attending the centres. Selective chromogenic culture media were used for the detection of extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-E), carbapenemase-producing Enterobacterales (CPE), and vancomycin-resistant Enterococci (VRE) in faecal swabs obtained from diapers or jars (n = 448). All isolated MDROs were subjected to resistance gene sequencing. A total of 71 of 448 samples (15.8%) yielded isolates of ESBL-E with a predominance of Escherichia coli (92.2% of ESBL-E) and ESBL resistance gene blaCTX-M-15 (50.7% of ESBL coding genes in E. coli). ESBL-E prevalence varied between DCCs, ranging from 0 to 50%. Transmission, based on the clonal relatedness of ESBL-E strains, was observed. CPE was identified in only one child carrying an E. coli with an OXA-244 gene. VRE was absent from all samples. The observed prevalence of ESBL-E in Flemish DCCs is high compared with previous studies, and our findings re-emphasise the need for rigorous hygiene measures within such centres to control the further spread of MDROs in the community.
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Affiliation(s)
- Stefanie van Kleef – van Koeveringe
- Laboratory of Medical Microbiology, University Hospital Antwerp, Edegem, Belgium
- Department of Medical Microbiology, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Wilrijk, Belgium
| | - Veerle Matheeussen
- Laboratory of Medical Microbiology, University Hospital Antwerp, Edegem, Belgium
- Department of Medical Microbiology, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Wilrijk, Belgium
| | - Hilde Jansens
- Laboratory of Medical Microbiology, University Hospital Antwerp, Edegem, Belgium
- Department of Infection Control, University Hospital Antwerp, Edegem, Belgium
| | | | - Dieter De Coninck
- bioMérieux, Augmented Diagnostics, Industrial Microbiology, Applied Maths NV, Sint-Martens-Latem, Belgium
| | - Katrien De Bruyne
- bioMérieux, Augmented Diagnostics, Industrial Microbiology, Applied Maths NV, Sint-Martens-Latem, Belgium
| | - Klaas Mensaert
- bioMérieux, Augmented Diagnostics, Industrial Microbiology, Applied Maths NV, Sint-Martens-Latem, Belgium
| | - Marjolein Kluytmans - van den Bergh
- Department of Infection Control, Amphia Hospital, Breda, the Netherlands
- Julius Center for Health Sciences and Primary Care, UMC Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Jan Kluytmans
- Microvida Laboratory for Microbiology, Amphia Hospital, Breda, and Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Herman Goossens
- Laboratory of Medical Microbiology, University Hospital Antwerp, Edegem, Belgium
- Department of Medical Microbiology, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Wilrijk, Belgium
| | - Wouter Dhaeze
- Department Prevention, Agency for Care and Health, Leuven, Belgium
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De Koster S, Ringenier M, Xavier BB, Lammens C, De Coninck D, De Bruyne K, Mensaert K, Kluytmans-van den Bergh M, Kluytmans J, Dewulf J, Goossens H. Genetic characterization of ESBL-producing and ciprofloxacin-resistant Escherichia coli from Belgian broilers and pigs. Front Microbiol 2023; 14:1150470. [PMID: 37089550 PMCID: PMC10116946 DOI: 10.3389/fmicb.2023.1150470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 03/15/2023] [Indexed: 04/08/2023] Open
Abstract
BackgroundThe increasing number of infections caused by Escherichia coli resistant to clinically important antibiotics is a global concern for human and animal health. High overall levels of extended-spectrum beta-lactamase (ESBL)-producing and ciprofloxacin-resistant (ciproR) Escherichia coli in livestock are reported in Belgium. This cross-sectional study aimed to genotypically characterize and trace ESBL-and ciproR-E. coli of Belgian food-producing animals.MethodsA total of 798 fecal samples were collected in a stratified-random sampling design from Belgian broilers and sows. Consequently, 77 ESBL-E. coli and 84 ciproR-E. coli were sequenced using Illumina MiSeq. Minimum inhibitory concentration (MIC) for fluoroquinolones and cephalosporins were determined. Molecular in silico typing, resistance and virulence gene determination, and plasmid identification was performed. Scaffolds harboring ESBL or plasmid-mediated quinolone resistance (PMQR) genes were analyzed to detect mobile genetic elements (MGEs) and plasmid origins. Core genome allelic distances were used to determine genetic relationships among isolates.ResultsA variety of E. coli sequence types (ST) (n = 63), resistance genes and virulence profiles was detected. ST10 was the most frequently encountered ST (8.1%, n = 13). The pandemic multidrug-resistant clone ST131 was not detected. Most farms harbored more than one ESBL type, with blaCTX-M-1 (41.6% of ESBL-E. coli) being the most prevalent and blaCTX M-15 (n = 3) being the least prevalent. PMQR genes (15.5%, n = 13) played a limited role in the occurrence of ciproR-E. coli. More importantly, sequential acquisition of mutations in quinolone resistance-determining regions (QRDR) of gyrA and parC led to increasing MICs for fluoroquinolones. GyrA S83L, D87N and ParC S80I mutations were strongly associated with high-level fluoroquinolone resistance. Genetically related isolates identified within the farms or among different farms highlight transmission of resistant E. coli or the presence of a common reservoir. IncI1-I(alpha) replicon type plasmids carried different ESBL genes (blaCTX-M-1, blaCTX-M-32 and blaTEM-52C). In addition, the detection of plasmid replicons with associated insertion sequence (IS) elements and ESBL/PMQR genes in different farms and among several STs (e.g., IncI1-I(alpha)/IncX3) underline that plasmid transmission could be another important contributor to transmission of resistance in these farms.ConclusionOur findings reveal a multifaceted narrative of transmission pathways. These findings could be relevant in understanding and battling the problem of antibiotic resistance in farms.
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Affiliation(s)
- Sien De Koster
- Laboratory of Medical Microbiology, Vaccine and Infectious Diseases Institute, University of Antwerp, Antwerp, Belgium
| | - Moniek Ringenier
- Veterinary Epidemiology Unit, Department of Reproduction, Obstetrics and Herd Health, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Basil Britto Xavier
- Laboratory of Medical Microbiology, Vaccine and Infectious Diseases Institute, University of Antwerp, Antwerp, Belgium
- HIV/STI Unit, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Hospital Outbreak Support Team-HOST, ZNA Middelheim, Antwerp, Belgium
- Hospital Outbreak Support Team-HOST, GZA Ziekenhuizen, Wilrijk, Belgium
| | - Christine Lammens
- Laboratory of Medical Microbiology, Vaccine and Infectious Diseases Institute, University of Antwerp, Antwerp, Belgium
| | | | | | | | - Marjolein Kluytmans-van den Bergh
- Department of Infection Control, Amphia Hospital, Breda, Netherlands
- Julius Center for Health Sciences and Primary Care, UMC Utrecht, University of Utrecht, CG Utrecht, Netherlands
- Amphia Academy Infectious Disease Foundation, Amphia Hospital, CK Breda, Netherlands
| | - Jan Kluytmans
- Julius Center for Health Sciences and Primary Care, UMC Utrecht, University of Utrecht, CG Utrecht, Netherlands
- Microvida Laboratory for Microbiology, Amphia Hospital, Breda, Netherlands
| | - Jeroen Dewulf
- Veterinary Epidemiology Unit, Department of Reproduction, Obstetrics and Herd Health, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Herman Goossens
- Laboratory of Medical Microbiology, Vaccine and Infectious Diseases Institute, University of Antwerp, Antwerp, Belgium
- *Correspondence: Herman Goossens,
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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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5
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Goyal M, De Bruyne K, van Belkum A, West B. Different SARS-CoV-2 haplotypes associate with geographic origin and case fatality rates of COVID-19 patients. Infect Genet Evol 2021; 90:104730. [PMID: 33513449 PMCID: PMC7837616 DOI: 10.1016/j.meegid.2021.104730] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 01/18/2021] [Accepted: 01/20/2021] [Indexed: 02/06/2023]
Abstract
The current pandemic of COVID-19 is caused by the SARS-CoV-2 virus for which many variants at the Single Nucleotide Polymorphism (SNP) level have now been identified. We show here that different allelic variants among 692 SARS-CoV-2 genome sequences display a statistically significant association with geographic origin (p < 0.000001) and COVID-19 case severity (p = 0.016). Geographic variation in itself is associated with both case severity and allelic variation especially in strains from Indian origin (p < 0.000001). Using an new alternative bioinformatics approach we were able to confirm that the presence of the D614G mutation correlates with increased case severity in a sample of 127 sequences from a shared geographic origin in the US (p = 0.018). While leaving open the question on the pathogenesis mechanism involved, this suggests that in specific geographic locales certain genotypes of the virus are more pathogenic than others. We here show that viral genome polymorphisms may have an effect on case severity when other factors are controlled for, but that this effect is swamped out by these other factors when comparing cases across different geographic regions.
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Affiliation(s)
- Manisha Goyal
- bioMérieux, Open Innovation and Partnerships, 3 Route de Port Michaud, 38390 La Balme Les Grottes, France
| | - Katrien De Bruyne
- bioMérieux, Applied Maths, Keistraat 120, B-9830 Sint-Martens-Latem, Belgium
| | - Alex van Belkum
- bioMérieux, Open Innovation and Partnerships, 3 Route de Port Michaud, 38390 La Balme Les Grottes, France
| | - Brian West
- bioMérieux, Applied Maths, 13809 Research Blvd., Suite 645, Austin, Texas 78750, USA.
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6
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Goyal M, Hauben L, Pouseele H, Jaillard M, De Bruyne K, van Belkum A, Goering R. Retrospective Definition of Clostridioides difficile PCR Ribotypes on the Basis of Whole Genome Polymorphisms: A Proof of Principle Study. Diagnostics (Basel) 2020; 10:diagnostics10121078. [PMID: 33322677 PMCID: PMC7764247 DOI: 10.3390/diagnostics10121078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/08/2020] [Accepted: 12/10/2020] [Indexed: 12/18/2022] Open
Abstract
Clostridioides difficile is a cause of health care-associated infections. The epidemiological study of C. difficile infection (CDI) traditionally involves PCR ribotyping. However, ribotyping will be increasingly replaced by whole genome sequencing (WGS). This implies that WGS types need correlation with classical ribotypes (RTs) in order to perform retrospective clinical studies. Here, we selected genomes of hyper-virulent C. difficile strains of RT001, RT017, RT027, RT078, and RT106 to try and identify new discriminatory markers using in silico ribotyping PCR and De Bruijn graph-based Genome Wide Association Studies (DBGWAS). First, in silico ribotyping PCR was performed using reference primer sequences and 30 C. difficile genomes of the five different RTs identified above. Second, discriminatory genomic markers were sought with DBGWAS using a set of 160 independent C. difficile genomes (14 ribotypes). RT-specific genetic polymorphisms were annotated and validated for their specificity and sensitivity against a larger dataset of 2425 C. difficile genomes covering 132 different RTs. In silico PCR ribotyping was unsuccessful due to non-specific or missing theoretical RT PCR fragments. More successfully, DBGWAS discovered a total of 47 new markers (13 in RT017, 12 in RT078, 9 in RT106, 7 in RT027, and 6 in RT001) with minimum q-values of 0 to 7.40 × 10-5, indicating excellent marker selectivity. The specificity and sensitivity of individual markers ranged between 0.92 and 1.0 but increased to 1 by combining two markers, hence providing undisputed RT identification based on a single genome sequence. Markers were scattered throughout the C. difficile genome in intra- and intergenic regions. We propose here a set of new genomic polymorphisms that efficiently identify five hyper-virulent RTs utilizing WGS data only. Further studies need to show whether this initial proof-of-principle observation can be extended to all 600 existing RTs.
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Affiliation(s)
- Manisha Goyal
- BioMérieux, Open Innovation and Partnerships, 3 Route du Port Michaud, 38390 La Balme Les Grottes, France;
| | - Lysiane Hauben
- BioMérieux, Applied Maths NV, 9830 Sint-Martens-Latem, Belgium; (L.H.); (K.D.B.)
| | | | | | - Katrien De Bruyne
- BioMérieux, Applied Maths NV, 9830 Sint-Martens-Latem, Belgium; (L.H.); (K.D.B.)
| | - Alex van Belkum
- BioMérieux, Open Innovation and Partnerships, 3 Route du Port Michaud, 38390 La Balme Les Grottes, France;
- Correspondence: ; Tel.: +33-609-487-905
| | - Richard Goering
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, 2500 California Plaza, Omaha, NE 68178, USA;
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7
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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: 64] [Impact Index Per Article: 16.0] [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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8
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Petronella N, Kundra P, Auclair O, Hébert K, Rao M, Kingsley K, De Bruyne K, Banerjee S, Gill A, Pagotto F, Tamber S, Ronholm J. Changes detected in the genome sequences of Escherichia coli, Listeria monocytogenes, Vibrio parahaemolyticus, and Salmonella enterica after serial subculturing. Can J Microbiol 2019; 65:842-850. [PMID: 31356758 DOI: 10.1139/cjm-2019-0235] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Whole genome sequencing (WGS) is rapidly replacing other molecular techniques for identifying and subtyping bacterial isolates. The resolution or discrimination offered by WGS is significantly higher than that offered by other molecular techniques, and WGS readily allows infrequent differences that occur between 2 closely related strains to be found. In this investigation, WGS was used to identify the changes that occurred in the genomes of 13 strains of bacterial foodborne pathogens after 100 serial subcultures. Pure cultures of Shiga-toxin-producing Escherichia coli, Salmonella enterica, Listeria monocytogenes, and Vibrio parahaemolyticus were subcultured daily for 100 successive days. The 1st and 100th subcultures were whole-genome sequenced using short-read sequencing. Single nucleotide polymorphisms (SNPs) were identified between the 1st and final culture using 2 different approaches, and multilocus sequence typing of the whole genome was also performed to detect any changes at the allelic level. The number of observed genomic changes varied by strain, species, and the SNP caller used. This study provides insight into the genomic variation that can be detected using next-generation sequencing and analysis methods after repeated subculturing of 4 important bacterial pathogens.
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Affiliation(s)
- Nicholas Petronella
- Biostatistics and Modeling Division, Bureau of Food Surveillance and Science Integration, Food Directorate, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, Ontario, Canada
| | - Palni Kundra
- Department of Food Science and Agricultural Chemistry, Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Olivia Auclair
- Department of Food Science and Agricultural Chemistry, Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Karine Hébert
- Bureau of Microbial Hazards, Food Directorate, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, Ontario, Canada.,Listeriosis Reference Service, Bureau of Microbial Hazards, Food Directorate, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, Ontario, Canada
| | - Mary Rao
- Bureau of Microbial Hazards, Food Directorate, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, Ontario, Canada
| | - Kyle Kingsley
- Applied Maths, Data Analytics Unit, bioMérieux, Austin, Texas, USA
| | | | - Swapan Banerjee
- Bureau of Microbial Hazards, Food Directorate, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, Ontario, Canada
| | - Alexander Gill
- Bureau of Microbial Hazards, Food Directorate, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, Ontario, Canada
| | - Franco Pagotto
- Bureau of Microbial Hazards, Food Directorate, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, Ontario, Canada.,Listeriosis Reference Service, Bureau of Microbial Hazards, Food Directorate, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, Ontario, Canada
| | - Sandeep Tamber
- Bureau of Microbial Hazards, Food Directorate, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, Ontario, Canada
| | - Jennifer Ronholm
- Department of Food Science and Agricultural Chemistry, Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, Quebec, Canada.,Department of Animal Science, Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, Quebec, Canada
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9
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Heinrichs A, Argudín MA, De Mendonça R, Deplano A, Roisin S, Dodémont M, Coussement J, Filippin L, Dombrecht J, De Bruyne K, Huang TD, Supply P, Byl B, Glupczynski Y, Denis O. An Outpatient Clinic as a Potential Site of Transmission for an Outbreak of New Delhi Metallo-β-Lactamase–producing Klebsiella pneumoniae Sequence Type 716: A Study Using Whole-genome Sequencing. Clin Infect Dis 2018; 68:993-1000. [DOI: 10.1093/cid/ciy581] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 07/11/2018] [Indexed: 12/20/2022] Open
Affiliation(s)
- Amélie Heinrichs
- Laboratoire de Microbiologie, CUB-Hôpital Erasme, Université Libre de Bruxelles, Brussels
| | - Maria Angeles Argudín
- Laboratoire de Microbiologie, CUB-Hôpital Erasme, Université Libre de Bruxelles, Brussels
| | - Ricardo De Mendonça
- Laboratoire de Microbiologie, CUB-Hôpital Erasme, Université Libre de Bruxelles, Brussels
| | - Ariane Deplano
- Laboratoire de Microbiologie, CUB-Hôpital Erasme, Université Libre de Bruxelles, Brussels
| | - Sandrine Roisin
- Laboratoire de Microbiologie, CUB-Hôpital Erasme, Université Libre de Bruxelles, Brussels
| | - Magali Dodémont
- Laboratoire de Microbiologie, CUB-Hôpital Erasme, Université Libre de Bruxelles, Brussels
| | - Julien Coussement
- Laboratoire de Microbiologie, CUB-Hôpital Erasme, Université Libre de Bruxelles, Brussels
| | | | | | | | - Te-Din Huang
- Laboratory of Clinical Microbiology, Belgian National Reference Center for Monitoring Antimicrobial Resistance in Gram-negative Bacteria, CHU UCL Namur, Yvoir, Belgium
| | - Philip Supply
- INSERM U1019, CNRS-UMR 8204, Center for Infection and Immunity of Lille, Institut Pasteur de Lille, Université de Lille, Lille, France
| | - Baudouin Byl
- Ecole de Santé Publique, Université Libre de Bruxelles
- Clinique d’Epidémiologie et d’Hygiène Hospitalière, CUB-Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Youri Glupczynski
- Laboratory of Clinical Microbiology, Belgian National Reference Center for Monitoring Antimicrobial Resistance in Gram-negative Bacteria, CHU UCL Namur, Yvoir, Belgium
| | - Olivier Denis
- Laboratoire de Microbiologie, CUB-Hôpital Erasme, Université Libre de Bruxelles, Brussels
- Ecole de Santé Publique, Université Libre de Bruxelles
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10
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Giacometti F, Piva S, Vranckx K, De Bruyne K, Drigo I, Lucchi A, Manfreda G, Serraino A. Application of MALDI-TOF MS for the subtyping of Arcobacter butzleri strains and comparison with their MLST and PFGE types. Int J Food Microbiol 2018; 277:50-57. [PMID: 29684765 DOI: 10.1016/j.ijfoodmicro.2018.04.026] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [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: 10/10/2017] [Revised: 04/05/2018] [Accepted: 04/13/2018] [Indexed: 12/19/2022]
Abstract
For the first time, this study evaluated the use of MALDI-TOF as a typing tool for Arcobacter butzleri. A total of 104 A. butzleri strains isolated from different sources in an artisanal dairy plant in Italy were identified and typed using MALDI-TOF and compared with their multilocus sequence typing (MLST) and pulsed field gel electrophoresis (PFGE) profiles found in previous studies. MALDI-TOF correctly identified all the isolates to species level. No clearly delineated clusters appeared on dendrograms based on either the complete spectra or the significant peaks, but nine clusters were defined using the cophenetic correlation. Interestingly, MALDI-TOF proved able to discriminate A. butzleri strains below species level, confirming its potential use for epidemiological surveys. As expected, the comparative analysis with PFGE and MLST showed that the discriminatory index was lower for MALDI-TOF but roughly comparable to sequence types and pulsotypes. MALDI-TOF appears to be a relatively low cost answer to the urgent need for more rapid, less expensive typing tools suitable for source attribution studies, readily allowing multiple typing methods to be combined. This study provides insights into MALDI-TOF as potential epidemiological tool. Its application in healthcare surveillance systems awaits further exploration to encourage interaction and convergence studies between primary care in humans and animal and food veterinary authorities as part of the One Health concept.
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Affiliation(s)
- Federica Giacometti
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano dell'Emilia, Italy.
| | - Silvia Piva
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano dell'Emilia, Italy.
| | | | | | - Ilenia Drigo
- Istituto Zooprofilattico Sperimentale delle Venezie, Villorba, Treviso, Italy.
| | - Alex Lucchi
- Department of Agricultural and Food Sciences, University of Bologna, Ozzano dell'Emilia, Italy.
| | - Gerardo Manfreda
- Department of Agricultural and Food Sciences, University of Bologna, Ozzano dell'Emilia, Italy.
| | - Andrea Serraino
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano dell'Emilia, Italy.
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11
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Kluytmans–van den Bergh MF, Huizinga P, Bonten MJ, Bos M, De Bruyne K, Friedrich AW, Rossen JW, Savelkoul PH, Kluytmans JA. Presence of mcr-1-positive Enterobacteriaceae in retail chicken meat but not in humans in the Netherlands since 2009. Euro Surveill 2016; 21:30149. [DOI: 10.2807/1560-7917.es.2016.21.9.30149] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 02/01/2016] [Indexed: 11/20/2022] Open
Abstract
Recently, the plasmid-mediated colistin resistance gene mcr-1 was found in Enterobacteriaceae from humans, pigs and retail meat in China. Several reports have documented global presence of the gene in Enterobacteriaceae from humans, food animals and food since. We screened several well-characterised strain collections of Enterobacteriaceae, obtained from retail chicken meat and hospitalised patients in the Netherlands between 2009 and 2015, for presence of colistin resistance and the mcr-1 gene. A total of 2,471 Enterobacteriaceae isolates, from surveys in retail chicken meat (196 isolates), prevalence surveys in hospitalised patients (1,247 isolates), clinical cultures (813 isolates) and outbreaks in healthcare settings (215 isolates), were analysed. The mcr-1 gene was identified in three (1.5%) of 196 extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli isolates from retail chicken meat samples in 2009 and 2014. Two isolates were obtained from the same batch of meat samples, most likely representing contamination from a common source. No mcr-1-positive isolates were identified among 2,275 human isolates tested. All mcr-1-positive isolates were colistin-resistant (minimum inhibitory concentration (MIC) > 2 mg/L). Our findings indicate that mcr-1-based colistin-resistance currently poses no threat to healthcare in the Netherlands. They indicate however that continued monitoring of colistin resistance and its underlying mechanisms in humans, livestock and food is needed.
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Affiliation(s)
- Marjolein F Kluytmans–van den Bergh
- Julius Centre for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
- Amphia Academy Infectious Disease Foundation, Amphia Hospital, Breda, The Netherlands
| | - Pepijn Huizinga
- Laboratory for Microbiology and Infection Control, Amphia Hospital, Breda, The Netherlands
| | - Marc J Bonten
- Julius Centre for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | | | - Alexander W Friedrich
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - John W Rossen
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Paul H Savelkoul
- Department of Medical Microbiology, Maastricht University Medical Centre, Maastricht, The Netherlands
- Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands
| | - Jan A Kluytmans
- Julius Centre for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
- Laboratory for Microbiology and Infection Control, Amphia Hospital, Breda, The Netherlands
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12
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Wieme AD, Spitaels F, Aerts M, De Bruyne K, Van Landschoot A, Vandamme P. Identification of beer-spoilage bacteria using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Int J Food Microbiol 2014; 185:41-50. [PMID: 24929682 DOI: 10.1016/j.ijfoodmicro.2014.05.003] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [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: 01/10/2014] [Revised: 04/22/2014] [Accepted: 05/04/2014] [Indexed: 11/26/2022]
Abstract
Applicability of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for identification of beer-spoilage bacteria was examined. To achieve this, an extensive identification database was constructed comprising more than 4200 mass spectra, including biological and technical replicates derived from 273 acetic acid bacteria (AAB) and lactic acid bacteria (LAB), covering a total of 52 species, grown on at least three growth media. Sequence analysis of protein coding genes was used to verify aberrant MALDI-TOF MS identification results and confirmed the earlier misidentification of 34 AAB and LAB strains. In total, 348 isolates were collected from culture media inoculated with 14 spoiled beer and brewery samples. Peak-based numerical analysis of MALDI-TOF MS spectra allowed a straightforward species identification of 327 (94.0%) isolates. The remaining isolates clustered separately and were assigned through sequence analysis of protein coding genes either to species not known as beer-spoilage bacteria, and thus not present in the database, or to novel AAB species. An alternative, classifier-based approach for the identification of spoilage bacteria was evaluated by combining the identification results obtained through peak-based cluster analysis and sequence analysis of protein coding genes as a standard. In total, 263 out of 348 isolates (75.6%) were correctly identified at species level and 24 isolates (6.9%) were misidentified. In addition, the identification results of 50 isolates (14.4%) were considered unreliable, and 11 isolates (3.2%) could not be identified. The present study demonstrated that MALDI-TOF MS is well-suited for the rapid, high-throughput and accurate identification of bacteria isolated from spoiled beer and brewery samples, which makes the technique appropriate for routine microbial quality control in the brewing industry.
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Affiliation(s)
- Anneleen D Wieme
- Laboratory of Biochemistry and Brewing, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, B-9000 Ghent, Belgium; Laboratory of Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Freek Spitaels
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Maarten Aerts
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Katrien De Bruyne
- Applied Maths N.V., Keistraat 120, B-9830 Sint-Martens-Latem, Belgium
| | - Anita Van Landschoot
- Laboratory of Biochemistry and Brewing, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, B-9000 Ghent, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium.
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13
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Rahkila R, De Bruyne K, Johansson P, Vandamme P, Björkroth J. Reclassification of Leuconostoc gasicomitatum as Leuconostoc gelidum subsp. gasicomitatum comb. nov., description of Leuconostoc gelidum subsp. aenigmaticum subsp. nov., designation of Leuconostoc gelidum subsp. gelidum subsp. nov. and emended description of Leuconostoc gelidum. Int J Syst Evol Microbiol 2014; 64:1290-1295. [PMID: 24431060 DOI: 10.1099/ijs.0.058263-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In the present study we investigated the taxonomic status of 20 lactic acid bacteria (LAB) originating from packaged meat. On the basis of 16S rRNA gene sequence similarity, these strains were shown to belong to the genus Leuconostoc with Leuconostoc gelidum, Leuconostoc inhae and Leuconostoc gasicomitatum as the closest phylogenetic relatives. The novel strains shared more than 70 % DNA-DNA relatedness with type and reference strains of both L. gelidum and L. gasicomitatum. The DNA-DNA relatedness values between L. gelidum type and reference strains and L. gasicomitatum type and reference strains were also above 70 %, showing that all these strains belonged to the same species. Sequence analyses of concatenated atpA, pheS, and rpoA genes demonstrated that the novel strains as well as type and reference strains of L. gelidum and L. gasicomitatum are phylogenetically closely related, but form three clearly separated subgroups. Numerical analysis of HindIII ribopatterns and phenotypic tests supported this subdivision. Based on the data presented in this study, we propose to reclassify Leuconostoc gasicomitatum as Leuconostoc gelidum subsp. gasicomitatum comb. nov. (type strain, LMG 18811(T) = DSM 15947(T)). The novel strains isolated in the present study represent a novel subspecies, for which the name Leuconostoc gelidum subsp. aenigmaticum subsp. nov. is proposed, with POUF4d(T) ( = LMG 27840(T) = DSM 19375(T)) as the type strain. The proposal of these two novel subspecies automatically creates the subspecies Leuconostoc gelidum subsp. gelidum subsp. nov. (type strain, NCFB 2775(T) = DSM 5578(T)). An emended description of Leuconostoc gelidum is also provided.
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Affiliation(s)
- Riitta Rahkila
- Department of Food Hygiene and Environmental Health, University of Helsinki, Helsinki, Finland
| | - Katrien De Bruyne
- Laboratory of Microbiology, Ghent University, Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Per Johansson
- Department of Food Hygiene and Environmental Health, University of Helsinki, Helsinki, Finland
| | - Peter Vandamme
- Laboratory of Microbiology, Ghent University, Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Johanna Björkroth
- Department of Food Hygiene and Environmental Health, University of Helsinki, Helsinki, Finland
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14
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Huch M, De Bruyne K, Cleenwerck I, Bub A, Cho GS, Watzl B, Snauwaert I, Franz CMAP, Vandamme P. Streptococcus rubneri sp. nov., isolated from the human throat. Int J Syst Evol Microbiol 2013; 63:4026-4032. [PMID: 23749274 DOI: 10.1099/ijs.0.048538-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The novel, Gram-stain-positive, ovoid, lactic acid bacterial isolates LMG 27205, LMG 27206, LMG 27207(T) and MRI-F 18 were obtained from throat samples of healthy humans. 16S rRNA gene sequence analyses indicated that these isolates belong to the genus Streptococcus, specifically the Streptococcus mitis group, with Streptococcus australis and Streptococcus mitis as the nearest neighbours (99.45 and 98.56 % 16S rRNA gene sequence similarity to the respective type strains). Genotypic fingerprinting by fluorescent amplified fragment length polymorphism (FAFLP) and pulsed-field gel electrophoresis (PFGE), DNA-DNA hybridizations, comparative sequence analysis of pheS, rpoA and atpA and physiological and biochemical tests revealed that these bacteria formed a taxon well separated from its nearest neighbours and other species of the genus Streptococcus with validly published names and, therefore, represent a novel species, for which the name Streptococcus rubneri sp. nov. is proposed, with LMG 27207(T) ( = DSM 26920(T)) as the type strain.
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Affiliation(s)
- Melanie Huch
- Max Rubner-Institut, Federal Research Institute for Nutrition and Food, Department of Safety and Quality of Fruit and Vegetables, Haid-und-Neu-Straße 9, 76131 Karlsruhe, Germany
| | - Katrien De Bruyne
- Laboratory of Microbiology, Ghent University, Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Ilse Cleenwerck
- BCCM/LMG Bacteria Collection, Ghent University, Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Achim Bub
- Max Rubner-Institut, Federal Research Institute for Nutrition and Food, Department of Physiology and Biochemistry of Nutrition, Haid-und-Neu-Straße 9, 76131 Karlsruhe, Germany
| | - Gyu-Sung Cho
- Max Rubner-Institut, Federal Research Institute for Nutrition and Food, Department of Safety and Quality of Fruit and Vegetables, Haid-und-Neu-Straße 9, 76131 Karlsruhe, Germany
| | - Bernhard Watzl
- Max Rubner-Institut, Federal Research Institute for Nutrition and Food, Department of Physiology and Biochemistry of Nutrition, Haid-und-Neu-Straße 9, 76131 Karlsruhe, Germany
| | - Isabel Snauwaert
- Laboratory of Microbiology, Ghent University, Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Charles M A P Franz
- Max Rubner-Institut, Federal Research Institute for Nutrition and Food, Department of Safety and Quality of Fruit and Vegetables, Haid-und-Neu-Straße 9, 76131 Karlsruhe, Germany
| | - Peter Vandamme
- Laboratory of Microbiology, Ghent University, Ledeganckstraat 35, B-9000 Ghent, Belgium
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15
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Nguyen DTL, Van Hoorde K, Cnockaert M, De Brandt E, De Bruyne K, Le BT, Vandamme P. A culture-dependent and -independent approach for the identification of lactic acid bacteria associated with the production of nem chua, a Vietnamese fermented meat product. Food Res Int 2013. [DOI: 10.1016/j.foodres.2012.09.029] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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16
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Snauwaert I, Hoste B, De Bruyne K, Peeters K, De Vuyst L, Willems A, Vandamme P. Carnobacterium iners sp. nov., a psychrophilic, lactic acid-producing bacterium from the littoral zone of an Antarctic pond. Int J Syst Evol Microbiol 2012; 63:1370-1375. [PMID: 22798642 DOI: 10.1099/ijs.0.042861-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two lactic acid-producing, Gram-stain-positive rods were isolated from a microbial mat actively growing in the littoral zone of an Antarctic lake (Forlidas Pond) in the Pensacola mountains and studied using a polyphasic taxonomic approach. The isolates were examined by phylogenetic analysis of the 16S rRNA gene, multilocus sequence analysis of pheS, rpoA and atpA, and biochemical and genotypic characteristics. One strain, designated LMG 26641, belonged to Carnobacterium alterfunditum and the other strain, designated LMG 26642(T), could be assigned to a novel species, with Carnobacterium funditum DSM 5970(T) as its closest phylogenetic neighbour (99.2 % 16S rRNA gene sequence similarity). Carnobacterium iners sp. nov. could be distinguished biochemically from other members of the genus Carnobacterium by the lack of acid production from carbohydrates. DNA-DNA relatedness confirmed that strain LMG 26642(T) represented a novel species, for which we propose the name Carnobacterium iners sp. nov. (type strain is LMG 26642(T) = CCUG 62000(T)).
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Affiliation(s)
- Isabel Snauwaert
- Laboratory of Microbiology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Bart Hoste
- Laboratory of Microbiology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | | | - Karolien Peeters
- Laboratory of Microbiology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Anne Willems
- Laboratory of Microbiology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
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17
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Abstract
Two lactic acid bacteria, strains 257T and 252, were isolated from traditional heap fermentations of Ghanaian cocoa beans. 16S rRNA gene sequence analysis of these strains allocated them to the genus Weissella, showing 99.5 % 16S rRNA gene sequence similarity towards Weissella ghanensis LMG 24286T. Whole-cell protein electrophoresis, fluorescent amplified fragment length polymorphism fingerprinting of whole genomes and biochemical tests confirmed their unique taxonomic position. DNA–DNA hybridization experiments towards their nearest phylogenetic neighbour demonstrated that the two strains represent a novel species, for which we propose the name Weissella fabaria sp. nov., with strain 257T (=LMG 24289T =DSM 21416T) as the type strain. Additional sequence analysis using pheS gene sequences proved useful for identification of all Weissella–Leuconostoc–Oenococcus species and for the recognition of the novel species.
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Affiliation(s)
- Katrien De Bruyne
- Laboratory of Microbiology, Ghent University, Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Nicholas Camu
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Department of Applied Biological Sciences and Engineering, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Department of Applied Biological Sciences and Engineering, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Ghent University, Ledeganckstraat 35, B-9000 Ghent, Belgium
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18
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De Bruyne K, Franz CMAP, Vancanneyt M, Schillinger U, Mozzi F, de Valdez GF, De Vuyst L, Vandamme P. Pediococcus argentinicus sp. nov. from Argentinean fermented wheat flour and identification of Pediococcus species by pheS, rpoA and atpA sequence analysis. Int J Syst Evol Microbiol 2009; 58:2909-16. [PMID: 19060081 DOI: 10.1099/ijs.0.65833-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-positive, small coccus-shaped lactic acid bacterium, strain LMG 23999(T), was isolated from Argentinean wheat flour. 16S rRNA gene sequence analysis revealed that the phylogenetic position of the novel strain was within the genus Pediococcus, with Pediococcus stilesii, Pediococcus pentosaceus and Pediococcus acidilactici as its closest relatives (97.7, 97.3 and 96.9 % gene sequence similarity, respectively). Fluorescent amplified fragment length polymorphism fingerprinting of whole genomes and whole-cell protein electrophoresis confirmed the unique taxonomic status of the novel strain. DNA-DNA hybridizations, DNA G+C content determination, comparative sequence analysis of the pheS, rpoA and atpA genes and physiological and biochemical characterization demonstrated that strain LMG 23999(T) (=CCUG 54535(T)=CRL 776(T)) represents a novel species for which the name Pediococcus argentinicus sp. nov. is proposed. Multi-locus sequence analysis based on pheS, rpoA and atpA genes was found to be a suitable method for the identification of species of the genus Pediococcus.
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De Bruyne K, Camu N, Lefebvre K, De Vuyst L, Vandamme P. Weissella ghanensis sp. nov., isolated from a Ghanaian cocoa fermentation. Int J Syst Evol Microbiol 2009; 58:2721-5. [PMID: 19060047 DOI: 10.1099/ijs.0.65853-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During a study on lactic acid bacteria (and their species diversity) in spontaneous heap fermentations of Ghanaian cocoa beans, two strains, designated 215(T) and 194B, were isolated. A phylogenetic analysis based on 16S rRNA gene sequences demonstrated that these strains represented a distinct lineage close to the genus Weissella and showing only 92.1 % 16S rRNA gene sequence similarity with respect to their closest neighbour, Weissella soli LMG 20113(T). Whole-cell protein electrophoresis, fluorescent amplified fragment length polymorphism fingerprinting of whole genomes and physiological and biochemical tests confirmed the unique taxonomic position of the two novel isolates. On the basis of the results of the morphological and biochemical tests and 16S rRNA gene sequence analysis, strains 215(T) and 194B represent the most peripheral lineage of the genus Weissella, for which we propose the name Weissella ghanensis sp. nov. The type strain is 215(T) (=LMG 24286(T)=DSM 19935(T)).
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Affiliation(s)
- Katrien De Bruyne
- Laboratory of Microbiology and BCCM/LMG Bacteria Collection, Ghent University, Ghent, Belgium
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De Bruyne K, Schillinger U, Caroline L, Boehringer B, Cleenwerck I, Vancanneyt M, De Vuyst L, Franz CMAP, Vandamme P. Leuconostoc holzapfelii sp. nov., isolated from Ethiopian coffee fermentation and assessment of sequence analysis of housekeeping genes for delineation of Leuconostoc species. Int J Syst Evol Microbiol 2008; 57:2952-2959. [PMID: 18048756 DOI: 10.1099/ijs.0.65292-0] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-positive, ovoid lactic acid bacterium, strain LMG 23990(T), was isolated from Ethiopian coffee fermentation. 16S rRNA gene sequence analysis indicated that the novel strain belongs to the genus Leuconostoc, with Leuconostoc citreum and Leuconostoc lactis as the closest neighbours (99.6 and 99.0 % 16S rRNA gene sequence similarity, respectively). Genotypic fingerprinting by fluorescent amplified fragment length polymorphism, whole-cell protein electrophoresis, DNA-DNA hybridizations, comparative sequence analysis of pheS, rpoA, atpA, and physiological and biochemical tests allowed us to differentiate strain LMG 23990(T) from all established Leuconostoc species. Strain LMG 23990(T) (=CCUG 54536(T)) therefore represents a novel species, for which the name Leuconostoc holzapfelii sp. nov. is proposed.
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Affiliation(s)
- Katrien De Bruyne
- Laboratory of Microbiology, Ghent University, Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Ulrich Schillinger
- Federal Research Centre for Nutrition and Food, Institute of Hygiene and Toxicology, Haid-und-Neu-Strasse 9, D-76131 Karlsruhe, Germany
| | - Lily Caroline
- Federal Research Centre for Nutrition and Food, Institute of Hygiene and Toxicology, Haid-und-Neu-Strasse 9, D-76131 Karlsruhe, Germany
| | - Benjamin Boehringer
- Federal Research Centre for Nutrition and Food, Institute of Hygiene and Toxicology, Haid-und-Neu-Strasse 9, D-76131 Karlsruhe, Germany
| | - Ilse Cleenwerck
- BCCM/LMG Bacteria Collection, Ghent University, Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Marc Vancanneyt
- BCCM/LMG Bacteria Collection, Ghent University, Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Department of Applied Biological Sciences and Engineering, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Charles M A P Franz
- Federal Research Centre for Nutrition and Food, Institute of Hygiene and Toxicology, Haid-und-Neu-Strasse 9, D-76131 Karlsruhe, Germany
| | - Peter Vandamme
- Laboratory of Microbiology, Ghent University, Ledeganckstraat 35, B-9000 Ghent, Belgium
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