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Frentzel H, Kraemer M, Kelner-Burgos Y, Uelze L, Bodi D. Cereulide production capacities and genetic properties of 31 emetic Bacillus cereus group strains. Int J Food Microbiol 2024; 417:110694. [PMID: 38614024 DOI: 10.1016/j.ijfoodmicro.2024.110694] [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: 11/28/2023] [Revised: 04/02/2024] [Accepted: 04/05/2024] [Indexed: 04/15/2024]
Abstract
The highly potent toxin cereulide is a frequent cause of foodborne intoxications. This extremely resistant toxin is produced by Bacillus cereus group strains carrying the plasmid encoded cesHPTABCD gene cluster. It is known that the capacities to produce cereulide vary greatly between different strains but the genetic background of these variations is not clear. In this study, cereulide production capacities were associated with genetic characteristics. For this, cereulide levels in cultures of 31 strains were determined after incubation in tryptic soy broth for 24 h at 24 °C, 30 °C and 37 °C. Whole genome sequencing based data were used for an in-depth characterization of gene sequences related to cereulide production. The taxonomy, population structure and phylogenetic relationships of the strains were evaluated based on average nucleotide identity, multi-locus sequence typing (MLST), core genome MLST and single nucleotide polymorphism analyses. Despite a limited strain number, the approach of a genome wide association study (GWAS) was tested to link genetic variation with cereulide quantities. Our study confirms strain-dependent differences in cereulide production. For most strains, these differences were not explainable by sequence variations in the cesHPTABCD gene cluster or the regulatory genes abrB, spo0A, codY and pagRBc. Likewise, the population structure and phylogeny of the tested strains did not comprehensively reflect the cereulide production capacities. GWAS yielded first hints for associated proteins, while their possible effect on cereulide synthesis remains to be further investigated.
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Affiliation(s)
- Hendrik Frentzel
- German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany.
| | - Marco Kraemer
- German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Ylanna Kelner-Burgos
- German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Laura Uelze
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Sequencing and Genotyping Service Unit, Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - Dorina Bodi
- German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
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Atienza MDLHG, González IG, De Artola DGM, Sánchez LÁI. Auritidibacter ignavus: an underestimated pathogen? Diagn Microbiol Infect Dis 2024; 109:116318. [PMID: 38744094 DOI: 10.1016/j.diagmicrobio.2024.116318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 04/18/2024] [Indexed: 05/16/2024]
Abstract
Auritidibacter ignavus is an emerging diagnosed microorganism associated with fulminant otitis, mastoiditis and recurrent otitis. Here we describe a clinical case in a little girl in La Gomera Island together with images of the bacteriological culture and whole genome sequencing.
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Affiliation(s)
| | - Isabel Gutiérrez González
- Departamento de microbiología, Hospital Universitario Nuestra Señora de la Candelaria, Tenerife, España
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Chew KL, Achik R, Osman NH, Octavia S, Teo JWP. Genomic epidemiology of human candidaemia isolates in a tertiary hospital. Microb Genom 2023; 9:mgen001047. [PMID: 37440287 PMCID: PMC10438824 DOI: 10.1099/mgen.0.001047] [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: 06/21/2022] [Accepted: 05/17/2023] [Indexed: 07/14/2023] Open
Abstract
Invasive candida infections are significant infections that may occur in vulnerable patients with high rates of mortality or morbidity. Drug-resistance rates also appear to be on the rise which further complicate treatment options and outcomes. The aims of this study were to describe the prevalence, molecular epidemiology, and genetic features of Candida bloodstream isolates in a hospital setting. The resistance mechanisms towards the two most commonly administered antifungals, fluconazole and anidulafungin, were determined. Blood culture isolates between 1 January 2018 and 30 June 2021 positive for Candida spp. were included. Susceptibility testing was performed using Etest. Whole-genome-sequencing was performed using Illumina NovaSeq with bioinformatics analysis performed. A total of 203 isolates were sequenced: 56 C. glabrata, 53 C. tropicalis, 44 C. albicans, 36 C. parapsilosis complex (consisting of C. parapsilosis, C. orthopsilosis, and C. metapsilosis), six C. krusei, five C. dubliniensis, and three C. auris. A single cluster of azole-resistant C. tropicalis, and four clusters of C. parapsilosis isolates were observed, suggesting possible transmission occurring over several years. We found 11.3%, and 52.7 % of C. tropicalis and C. parapsilosis, respectively, clustered with other isolates, suggesting exogenous sources may play a significant role of transmission, particularly for C. parapsilosis. The clusters spanned over several years suggesting the possibility of environmental reservoirs contributing to the spread. Limited clonality was seen for C. albicans. Several sequence types appeared to be dominant for C. glabrata, however the SNP differences varied widely, indicating absence of sustained transmission.
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Affiliation(s)
- Ka Lip Chew
- Department of Laboratory Medicine, National University Hospital, Singapore, Singapore
| | - Rosemini Achik
- Department of Laboratory Medicine, National University Hospital, Singapore, Singapore
| | - Nurul Hudaa Osman
- Environmental Health Institute, National Environment Agency, Singapore, Singapore
| | - Sophie Octavia
- Environmental Health Institute, National Environment Agency, Singapore, Singapore
| | - Jeanette W. P. Teo
- Department of Laboratory Medicine, National University Hospital, Singapore, Singapore
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Goldstein O, Gana-Weisz M, Banfi S, Nigro V, Bar-Shira A, Thaler A, Gurevich T, Mirelman A, Giladi N, Alcalay RN, Orr-Urtreger A. Novel variants in genes related to vesicle-mediated-transport modify Parkinson's disease risk. Mol Genet Metab 2023; 139:107608. [PMID: 37201419 DOI: 10.1016/j.ymgme.2023.107608] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/11/2023] [Accepted: 05/11/2023] [Indexed: 05/20/2023]
Abstract
OBJECTIVES VPS35 and VPS13 have been associated with Parkinson's disease (PD), and their shared phenotype in yeast when reduced in function is abnormal vacuolar transport. We aim to test if additional potentially deleterious variants in other genes that share this phenotype can modify the risk for PD. METHODS 77 VPS and VPS-related genes were analyzed using whole-genome-sequencing data from 202 PD patients of Ashkenazi Jewish (AJ) ancestry. Filtering was done based on quality and functionality scores. Ten variants in nine genes were further genotyped in 1200 consecutively recruited unrelated AJ-PD patients, and allele frequencies and odds ratio calculated compared to gnomAD-AJ-non-neuro database, in un-stratified (n = 1200) and stratified manner (LRRK2-G2019S-PD patients (n = 145), GBA-PD patients (n = 235), and non-carriers of these mutations (NC, n = 787)). RESULTS Five variants in PIK3C3, VPS11, AP1G2, HGS and VPS13D were significantly associated with PD-risk. PIK3C3-R768W showed a significant association in an un-stratified (all PDs) analysis, as well as in stratified (LRRK2, GBA, and NC) analyses (Odds ratios = 2.71, 5.32, 3.26. and 2.19 with p = 0.0015, 0.002, 0.0287, and 0.0447, respectively). AP1G2-R563W was significantly associated in LRRK2-carriers (OR = 3.69, p = 0.006) while VPS13D-D2932N was significantly associated in GBA-carriers (OR = 5.45, p = 0.0027). VPS11-C846G and HGS-S243Y were significantly associated in NC (OR = 2.48 and 2.06, with p = 0.022 and 0.0163, respectively). CONCLUSIONS Variants in genes involved in vesicle-mediated protein transport and recycling pathways, including autophagy and mitophagy, may differentially modify PD-risk in LRRK2-carriers, GBA carriers, or NC. Specifically, PIK3C3-R768W is a PD-risk allele, with the highest effect size in LRRK2-G2019S carriers. These results suggest oligogenic effect that may depends on the genetic background of the patient. An unbiased burden of mutations approach in these genes should be evaluated in additional PD and control groups. The mechanisms by which these novel variants interact and increase PD-risk should be researched in depth for better tailoring therapeutic intervention for PD prevention or slowing disease progression.
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Affiliation(s)
- Orly Goldstein
- Laboratory of Biomarkers and Genomics of Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Mali Gana-Weisz
- Laboratory of Biomarkers and Genomics of Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Sandro Banfi
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, NA, Italy; Medical Genetics, Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Vincenzo Nigro
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, NA, Italy; Medical Genetics, Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Anat Bar-Shira
- Laboratory of Biomarkers and Genomics of Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Avner Thaler
- Movement disorders Division, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Laboratory for Early Markers of Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Sackler Faculty of Medicine, and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Tanya Gurevich
- Movement disorders Division, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Sackler Faculty of Medicine, and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Anat Mirelman
- Movement disorders Division, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Laboratory for Early Markers of Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Sackler Faculty of Medicine, and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Nir Giladi
- Movement disorders Division, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Laboratory for Early Markers of Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Sackler Faculty of Medicine, and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Roy N Alcalay
- Laboratory of Biomarkers and Genomics of Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Movement disorders Division, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Avi Orr-Urtreger
- Laboratory of Biomarkers and Genomics of Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Sackler Faculty of Medicine, and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.
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Shani S, Goldstein O, Gana-Weisz M, Bar-Shira A, Thaler A, Gurevich T, Mirelman A, Giladi N, Alcalay RN, Orr-Urtreger A. Variants in PSMB9 and FGR differentially affect Parkinson's disease risk in GBA and LRRK2 mutation carriers. Parkinsonism Relat Disord 2023; 111:105398. [PMID: 37116292 DOI: 10.1016/j.parkreldis.2023.105398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/16/2023] [Accepted: 04/11/2023] [Indexed: 04/30/2023]
Abstract
INTRODUCTION Recent studies found an association between Parkinson's disease (PD) and alterations in the innate immune system. However, whether the involvement of this system in two of the known genetic forms of PD, GBA-PD and LRRK2-PD, and in patients who do not carry these mutations is different, is yet to be determined. We aimed to test if genetic variations in the innate immune genes are differentially associated with PD in these subgroups. METHODS Innate immune genes were identified and classified into sub-lists according to Reactome pathways. Whole-genome-sequencing (WGS) was performed on 201 unrelated Ashkenazi-Jewish (AJ) PD patients including 104 GBA-PD, 32 LRRK2-PD, and 65 non-carriers-PD (NC-PD). To identify genes with different burden between these subgroups of PD, gene-based Sequence kernel association optimal unified test (SKAT-O) analysis was performed on innate immune pathways. Candidate variants within the significant genes were further genotyped in a cohort of 1200 unrelated, consecutively recruited, AJ-PD patients, and to evaluate their association with PD-risk their allele frequencies were compared to AJ-non-neuro cases in gnomAD database, in a stratified and un-stratified manner. RESULTS SKAT-O analysis showed significantly different burden for PSMB9 (GBA-PD versus NC-PD) and FGR (GBA-PD versus LRRK2-PD). Two candidate variants in PSMB9 showed an association with GBA-PD-risk and NC-PD-risk while one FGR variant showed an association with LRRK2-PD-risk. CONCLUSION Our data supports differential involvement of innate immunity risk alleles in PD and emphasizes the differences between the GBA- and LRRK2-PD subgroups.
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Affiliation(s)
- Shachar Shani
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; The Laboratory of Biomarkers and Genomics of Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Orly Goldstein
- The Laboratory of Biomarkers and Genomics of Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.
| | - Mali Gana-Weisz
- The Laboratory of Biomarkers and Genomics of Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Anat Bar-Shira
- The Laboratory of Biomarkers and Genomics of Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Avner Thaler
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Movement Disorders Division, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Laboratory for Early Markers of Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Tanya Gurevich
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Movement Disorders Division, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Anat Mirelman
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Movement Disorders Division, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Laboratory for Early Markers of Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Nir Giladi
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel; Brain Division Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Roy N Alcalay
- The Laboratory of Biomarkers and Genomics of Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Movement Disorders Division, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Avi Orr-Urtreger
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; The Laboratory of Biomarkers and Genomics of Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
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Kling D, Phillips C, Kennett D, Tillmar A. Investigative genetic genealogy: Current methods, knowledge and practice. Forensic Sci Int Genet 2021; 52:102474. [PMID: 33592389 DOI: 10.1016/j.fsigen.2021.102474] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [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: 10/02/2020] [Revised: 01/12/2021] [Accepted: 01/27/2021] [Indexed: 12/15/2022]
Abstract
Investigative genetic genealogy (IGG) has emerged as a new, rapidly growing field of forensic science. We describe the process whereby dense SNP data, commonly comprising more than half a million markers, are employed to infer distant relationships. By distant we refer to degrees of relatedness exceeding that of first cousins. We review how methods of relationship matching and SNP analysis on an enlarged scale are used in a forensic setting to identify a suspect in a criminal investigation or a missing person. There is currently a strong need in forensic genetics not only to understand the underlying models to infer relatedness but also to fully explore the DNA technologies and data used in IGG. This review brings together many of the topics and examines their effectiveness and operational limits, while suggesting future directions for their forensic validation. We further investigated the methods used by the major direct-to-consumer (DTC) genetic ancestry testing companies as well as submitting a questionnaire where providers of forensic genetic genealogy summarized their operation/services. Although most of the DTC market, and genetic genealogy in general, has undisclosed, proprietary algorithms we review the current knowledge where information has been discussed and published more openly.
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Affiliation(s)
- Daniel Kling
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden; Department of Forensic Sciences, Oslo University Hospital, Oslo, Norway.
| | - Christopher Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain.
| | - Debbie Kennett
- Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Andreas Tillmar
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden; Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
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Chew KL, Octavia S, Teo JWP. Complete Genome Sequence of Candida theae from Hickman Line Infection in an Immunocompromised Child. Mycopathologia 2020; 185:727-9. [PMID: 32705414 DOI: 10.1007/s11046-020-00476-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 07/06/2020] [Indexed: 10/20/2022]
Abstract
We present the first whole-genome-sequencing data of a rare fungal species, Candida theae isolated in the context of a Hickman line infection in a patient with juvenile myelomonocytic leukaemia. To our knowledge, this is the first instance of publicly available genomic data for this species. Loci associated with antifungal resistance were referenced against its closely related members of the Candida parapsilosis complex.
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