1
|
Suniga PAP, Mantovani C, dos Santos MG, do Egito AA, Verbisck NV, dos Santos LR, Dávila AMR, Zimpel CK, Zerpa MCS, Chiebao DP, de Sá Guimarães AM, de Castro Nassar AF, de Araújo FR. Glanders Diagnosis in an Asymptomatic Mare from Brazil: Insights from Serology, Microbiological Culture, Mass Spectrometry, and Genome Sequencing. Pathogens 2023; 12:1250. [PMID: 37887766 PMCID: PMC10609850 DOI: 10.3390/pathogens12101250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/21/2023] [Accepted: 10/06/2023] [Indexed: 10/28/2023] Open
Abstract
This manuscript elucidates the occurrence of glanders in an asymptomatic mare from Brazil presenting positive Burkholderia mallei antibody titers. The diagnosis was established through a multi-pronged approach encompassing microbiological culture, mass spectrometry, and genome sequencing. The outbreak occurred in 2019 in Tatuí, São Paulo, Brazil, and the infected mare, despite displaying no clinical symptoms, had multiple miliary lesions in the liver, as well as intense catarrhal discharge in the trachea. Samples were collected from various organs and subjected to bacterial isolation, molecular detection, and identification. The strain was identified as B. mallei using PCR and confirmed by MALDI-TOF mass spectrometry. Whole-genome sequencing revealed a genome size of 5.51 Mb with a GC content of 65.8%, 5871 genes (including 4 rRNA and 53 tRNA genes), and 5583 coding DNA sequences (CDSs). Additionally, 227 predicted pseudogenes were detected. In silico analysis of different genomic loci that allow for differentiation with Burkholderia pseudomallei confirmed the identity of the isolate as B. mallei, in addition to the characteristic genome size. The BAC 86/19 strain was identified as lineage 3, sublineage 2, which includes other strains from Brazil, India, and Iran. The genome sequencing of this strain provides valuable information that can be used to better understand the pathogen and its epidemiology, as well as to develop diagnostic tools for glanders.
Collapse
Affiliation(s)
- Paula Adas Pereira Suniga
- Postgraduate Program in Animal Science, Faculty of Veterinary Medicine and Animal Science-FAMEZ/UFMS, Federal University of Mato Grosso Do Sul, Av. Senador Filinto Muller, 2443, Campo Grande 79074-460, MS, Brazil; (P.A.P.S.); (A.A.d.E.)
- MAI/DAI Scholarship, Federal University of Mato Grosso Do Sul, Cidade Universitária, Av. Costa E Silva, Campo Grande 79070-900, MS, Brazil
| | - Cynthia Mantovani
- Embrapa Beef Cattle/Ministry of Agriculture and Livestock Scholarship, Embrapa Beef Cattle, Av. Rádio Maia, 830, Campo Grande 79106-550, MS, Brazil;
| | | | - Andréa Alves do Egito
- Postgraduate Program in Animal Science, Faculty of Veterinary Medicine and Animal Science-FAMEZ/UFMS, Federal University of Mato Grosso Do Sul, Av. Senador Filinto Muller, 2443, Campo Grande 79074-460, MS, Brazil; (P.A.P.S.); (A.A.d.E.)
- Embrapa Beef Cattle, Campo Grande 79106-550, MS, Brazil; (M.G.d.S.); (N.V.V.); (F.R.d.A.)
| | | | | | - Alberto Martín Rivera Dávila
- Computational and Systems Biology Laboratory, Graduate Program in Biodiversity and Health, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil;
| | - Cristina Kraemer Zimpel
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA;
| | - Maria Carolina Sisco Zerpa
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, SP, Brazil; (M.C.S.Z.); (A.M.d.S.G.)
| | - Daniela Pontes Chiebao
- Animal Health Research Center, Biological Institute, Av. Conselheiro Rodrigues Alves, 1252, São Paulo 04014-002, SP, Brazil; (D.P.C.); (A.F.d.C.N.)
| | - Ana Márcia de Sá Guimarães
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, SP, Brazil; (M.C.S.Z.); (A.M.d.S.G.)
| | | | | |
Collapse
|
2
|
Bacanelli G, Araujo FR, Verbisck NV. Improved MALDI-TOF MS Identification of Mycobacterium tuberculosis by Use of an Enhanced Cell Disruption Protocol. Microorganisms 2023; 11:1692. [PMID: 37512865 PMCID: PMC10386467 DOI: 10.3390/microorganisms11071692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/22/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
Mycobacterium tuberculosis is the microorganism that causes tuberculosis, a disease affecting millions of people worldwide. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a fast, reliable, and cost-effective method for microorganism identification which has been used for the identification of Mycobacterium spp. isolates. However, the mycobacteria cell wall is rich in lipids, which makes it difficult to obtain proteins for MALDI-TOF MS analysis. In this study, two cell preparation protocols were compared: the MycoEx, recommended by MALDI-TOF instrument manufacturer Bruker Daltonics, and the MycoLyser protocol described herein, which used the MagNA Lyser instrument to enhance cell disruption with ethanol. Cell disruption and protein extraction steps with the two protocols were performed using the Mycobacterium tuberculosis H37Rv strain, and the MALDI-TOF MS results were compared. The MycoLyser protocol allowed for improved Biotyper identification of M. tuberculosis since the log(score) values obtained with this protocol were mostly ≥ 1.800 and significantly higher than that underwent MycoEx processing. The identification reliability was increased as well, considering the Bruker criteria. In view of these results, it is concluded that the MycoLyser protocol for mycobacterial cell disruption and protein extraction improves the MALDI-TOF MS method's efficacy for M. tuberculosis identification.
Collapse
Affiliation(s)
- Gisele Bacanelli
- Biotechnology and Biodiversity of the Central Western Region Postgraduate Program, Federal University of Mato Grosso do Sul, Campo Grande 79070-900, MS, Brazil
| | | | | |
Collapse
|
3
|
Gonzalo X, Yrah S, Broda A, Laurenson I, Claxton P, Kostrzewa M, Drobniewski F, Larrouy-Maumus G. Performance of lipid fingerprint by routine matrix-assisted laser desorption/ionization time of flight for the diagnosis of Mycobacterium tuberculosis complex species. Clin Microbiol Infect 2023; 29:387.e1-387.e6. [PMID: 36270589 DOI: 10.1016/j.cmi.2022.10.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 09/21/2022] [Accepted: 10/13/2022] [Indexed: 11/19/2022]
Abstract
OBJECTIVES Rapid detection of bacterial pathogens at species and sub-species levels is crucial for appropriate treatment, infection control, and public health management. Currently, one of the challenges in clinical microbiology is the discrimination of mycobacterial sub-species within the M. tuberculosis complex (MTBC). Our objective was to evaluate the ability of a biosafe mycobacterial lipid-based approach to identify MTBC cultures and sub-species. METHODS A blinded study was conducted using 90 mycobacterial clinical isolate strains comprising MTBC strains sub-cultured in Middlebrook 7H11 medium supplemented with 10% oleic-acid, dextrose, catalase growth supplement and incubated for up to 6 weeks at 37°C and using the following seven reference strains (M. tuberculosis H37Rv, M canettii, M. africanum, M. pinnipedii, M. caprae, M. bovis, and M. bovis BCG) grown under the same conditions, to set the reference lipid database and test it against the 90 MTBC clinical isolates. Cultured mycobacteria were heat-inactivated and loaded onto the matrix-assisted laser desorption/ionization target followed by the addition of the matrix. Acquisition of the data was performed using the positive ion mode. RESULTS Based on the identification of clear and defined lipid signatures from the seven reference strains, the method that we developed was fast (<10 minutes) and produced interpretable profiles for all but four isolates, caused by poor ionization giving an n = 86 with interpretable spectra. The sensitivity and specificity of the matrix-assisted laser desorption/ionization time of flight were 94.4 (95% CI, 86.4-98.5) and 94.4 (95% CI, 72.7-99.9), respectively. CONCLUSIONS Mycobacterial lipid profiling provides a means of rapid, safe, and accurate discrimination of species within the MTBC.
Collapse
Affiliation(s)
- Ximena Gonzalo
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Shih Yrah
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Agnieszka Broda
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Ian Laurenson
- Scottish Mycobacteria Reference Laboratory, Edinburgh, United Kingdom
| | - Pauline Claxton
- Scottish Mycobacteria Reference Laboratory, Edinburgh, United Kingdom
| | | | - Francis Drobniewski
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Gerald Larrouy-Maumus
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom.
| |
Collapse
|
4
|
Automatic Identification of MALDI-TOF MS Database Using Classical Bordetella Species Isolates. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:1679951. [PMID: 35756428 PMCID: PMC9217575 DOI: 10.1155/2022/1679951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/24/2022] [Accepted: 05/24/2022] [Indexed: 11/18/2022]
Abstract
Objective To evaluate and expand the automatic identification and clustering of clinical Bordetella species by MALDI-TOF MS. Methods Twenty-eight field isolated strains, identified by whole-gene sequencing analysis, were analyzed by MALDI-TOF MS, and the spectra obtained were used to replenish the internal database of the manufacturer. To evaluate and expand the robustness of the database, MALDI-TOF MS identified 91 clinical isolates (except those used for implementation). A distance tree based on mass spectrometry data is constructed to confirm similarity and clusters of each clinical Bordetella species by using the MALDI Biotyper 3.1 software. Results In this research, when we used the implemented Bruker Daltonics database in our laboratory, 91 clinical isolates were identified at the genus level (100%) and 93.4% were identified at the species level (85/91). We performed proteomics analysis and divided these 91 isolates into cluster I (2.2%) and cluster II (97.8%). The largest group is cluster II (n = 89 isolates), which has been divided into two subclusters. Trees created by analyzing the protein mass spectra of the three species of the clinical isolates reflected their classification. Conclusion MALDI-TOF MS may present an attractive alternative to automatically confirm and cluster the fastidious bacteria difficult to culture. Extension of identification of the MALDI-TOF MS database is viably fast, more efficient, and alternative to conventional methods in confirming the classical Bordetella species. This strategy could promote the epidemiological and taxonomic research of this important pathogen.
Collapse
|
5
|
Robinne S, Saad J, Morsli M, Hamidou ZH, Tazerart F, Drancourt M, Baron SA. Rapid Identification of Mycobacterium tuberculosis Complex Using Mass Spectrometry: A Proof of Concept. Front Microbiol 2022; 13:753969. [PMID: 35432257 PMCID: PMC9008353 DOI: 10.3389/fmicb.2022.753969] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 02/15/2022] [Indexed: 11/13/2022] Open
Abstract
Mycobacteria that form the Mycobacterium tuberculosis complex are responsible for deadly tuberculosis in animals and patients. Identification of these pathogens at the species level is of primary importance for treatment and source tracing and currently relies on DNA analysis, including whole genome sequencing (WGS), which requires a whole day. In this study, we report the unprecedented discrimination of M. tuberculosis complex species using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS), with WGS as the comparative reference standard. In the first step, optimized peptide extraction applied to 36 isolates otherwise identified in five of the 11 M. tuberculosis complex variants by WGS yielded 139 MALDI-TOF spectra, which were used to identify biomarkers of interest that facilitate differentiation between variants. In a second step, 70/80 (88%) other isolates were correctly classified by an algorithm based on specific peaks. This study is the first to report a MALDI-TOF-MS method for discriminating M. tuberculosis complex mycobacteria that is easily implemented in clinical microbiology laboratories.
Collapse
Affiliation(s)
- Simon Robinne
- Aix-Marseille-University, IRD, MEPHI, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Jamal Saad
- Aix-Marseille-University, IRD, MEPHI, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Madjid Morsli
- Aix-Marseille-University, IRD, MEPHI, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Zelika Harouna Hamidou
- Aix-Marseille-University, IRD, MEPHI, Marseille, France
- IHU Méditerranée Infection, Marseille, France
- Laboratoire National de Référence des IST/VIH et de la Tuberculose, Niamey, Niger
| | - Fatah Tazerart
- IHU Méditerranée Infection, Marseille, France
- Institut des Sciences Vétérinaires, Université de Blida 1, Blida, Algeria
| | - Michel Drancourt
- Aix-Marseille-University, IRD, MEPHI, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Sophie Alexandra Baron
- Aix-Marseille-University, IRD, MEPHI, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
- IHU Méditerranée Infection, Marseille, France
- *Correspondence: Sophie Alexandra Baron,
| |
Collapse
|
6
|
Lorente-Leal V, Liandris E, Bezos J, Pérez-Sancho M, Romero B, de Juan L. MALDI-TOF Mass Spectrometry as a Rapid Screening Alternative for Non-tuberculous Mycobacterial Species Identification in the Veterinary Laboratory. Front Vet Sci 2022; 9:827702. [PMID: 35155660 PMCID: PMC8831857 DOI: 10.3389/fvets.2022.827702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 01/03/2022] [Indexed: 11/30/2022] Open
Abstract
Non-tuberculous mycobacteria (NTM) are difficult to identify by biochemical and genetic methods due to their microbiological properties and complex taxonomy. The development of more efficient and rapid methods for species identification in the veterinary microbiological laboratory is, therefore, of great importance. Although MALDI-TOF Mass Spectrometry (MS) has become a promising tool for the identification of NTM species in human clinical practise, information regarding its performance on veterinary isolates is scarce. This study assesses the capacity of MALDI-TOF MS to identify NTM isolates (n = 75) obtained from different animal species. MALDI-TOF MS identified 76.0% (n = 57) and 4% (n = 3) of the isolates with high and low confidence, respectively, in agreement with the identification achieved by Sanger sequencing of housekeeping genes (16S rRNA, hsp65, and rpoB). Thirteen isolates (17.3%) were identified by Sanger sequencing to the complex level, indicating that these may belong to uncharacterised species. MALDI-TOF MS approximated low confidence identifications toward closely related mycobacterial groups, such as the M. avium or M. terrae complexes. Two isolates were misidentified due to a high similarity between species or due to the lack of spectra in the database. Our results suggest that MALDI-TOF MS can be used as an effective alternative for rapid screening of mycobacterial isolates in the veterinary laboratory and potentially for the detection of new NTM species. In turn, Sanger sequencing could be implemented as an additional method to improve identifications in species for which MALDI-TOF MS identification is limited or for further characterisation of NTM species.
Collapse
Affiliation(s)
- Víctor Lorente-Leal
- VISAVET Health Surveillance Center, Universidad Complutense de Madrid, Madrid, Spain
- Animal Health Department, Faculty of Veterinary Medicine, Universidad Complutense de Madrid, Madrid, Spain
| | - Emmanouil Liandris
- VISAVET Health Surveillance Center, Universidad Complutense de Madrid, Madrid, Spain
| | - Javier Bezos
- VISAVET Health Surveillance Center, Universidad Complutense de Madrid, Madrid, Spain
- Animal Health Department, Faculty of Veterinary Medicine, Universidad Complutense de Madrid, Madrid, Spain
| | - Marta Pérez-Sancho
- VISAVET Health Surveillance Center, Universidad Complutense de Madrid, Madrid, Spain
- Animal Health Department, Faculty of Veterinary Medicine, Universidad Complutense de Madrid, Madrid, Spain
| | - Beatriz Romero
- VISAVET Health Surveillance Center, Universidad Complutense de Madrid, Madrid, Spain
- Animal Health Department, Faculty of Veterinary Medicine, Universidad Complutense de Madrid, Madrid, Spain
- *Correspondence: Beatriz Romero
| | - Lucía de Juan
- VISAVET Health Surveillance Center, Universidad Complutense de Madrid, Madrid, Spain
- Animal Health Department, Faculty of Veterinary Medicine, Universidad Complutense de Madrid, Madrid, Spain
| |
Collapse
|
7
|
Djebala S, Evrard J, Moula N, Gille L, Bayrou C, Eppe J, Casalta H, Sartelet A, Bossaert P. Comparison between generalised peritonitis and parietal fibrinous peritonitis in cows after caesarean section. Vet Rec 2020; 187:e49. [PMID: 32591365 DOI: 10.1136/vr.105867] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 05/16/2020] [Accepted: 06/07/2020] [Indexed: 11/03/2022]
Abstract
BACKGROUND Parietal fibrinous peritonitis (PFP) and generalised peritonitis (GP) are two postoperative complications in cows, characterised by fluid and fibrin accumulation throughout the peritoneum (GP) or in an encapsulated cavity (PFP). Unlike GP, PFP is scarcely documented. METHODS Twenty-one GP cases and 12 PFP cases were confirmed by ultrasound in cows referred to the Veterinary Clinic (Liège University) for complications after caesarean section. All cows underwent a standardised examination protocol. Blood samples were analysed for metabolic and inflammatory markers. Bacteriology was performed on peritoneal fluid samples. Treatment consisted of surgical drainage of the abdominal cavity (GP) or the encapsulated cavity (PFP). Variables concerning anamnesis, clinical findings and treatment outcomes were compared. RESULTS Perioperative complications had occurred in 9/21 GP cows but 0/12 PFP cows (P<0.05). Biochemical analysis indicated pronounced inflammation and did not differ between groups. Peritoneal fluid samples of both groups were contaminated and contained similar bacteria (Trueperella pyogenes and Escherichia coli). While 11/12 PFP cows were discharged, all patients with GP died or were euthanased (P<0.05). CONCLUSIONS We hypothesise that PFP and GP are two different manifestations of perioperative peritoneal contamination. The severity and spread of the contamination determine the clinical presentation and the prognosis.
Collapse
Affiliation(s)
- Salem Djebala
- Clinical Department of Ruminant, University of Liege, Liege, Belgium
| | - Julien Evrard
- Gestion et Prévention de Santé, Regional Association of Health and Animal Identification, Ciney, Belgium
| | - Nassim Moula
- Department of Animal Production, University of Liege, Liege, Belgium
| | - Linde Gille
- Clinical Department of Ruminant, University of Liege, Liege, Belgium
| | - Calixte Bayrou
- Clinical Department of Ruminant, University of Liege, Liege, Belgium
| | - Justine Eppe
- Clinical Department of Ruminant, University of Liege, Liege, Belgium
| | - Hélène Casalta
- Clinical Department of Ruminant, University of Liege, Liege, Belgium
| | - Arnaud Sartelet
- Clinical Department of Ruminant, University of Liege, Liege, Belgium
| | - Philippe Bossaert
- Clinical Department of Ruminant, University of Liege, Liege, Belgium
| |
Collapse
|
8
|
Djebala S, Evrard J, Moula N, Sartelet A, Bossaert P. Atypical case of parietal fibrinous peritonitis in a Belgian Blue heifer without a history of laparotomy. VETERINARY RECORD CASE REPORTS 2020. [DOI: 10.1136/vetreccr-2020-001086] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Salem Djebala
- Clinical Department of RuminantUniversity of LiegeLiegeBelgium
| | - Julien Evrard
- Gestion et Prévention de SantéRegional Association of Health and Animal IdentificationCineyBelgium
| | - Nassim Moula
- Department of Animal ProductionUniversity of LiegeLiegeBelgium
| | - Arnaud Sartelet
- Clinical Department of RuminantUniversity of LiegeLiegeBelgium
| | | |
Collapse
|