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Strakova N, Michova H, Shagieva E, Ovesna P, Karpiskova R, Demnerova K. Genotyping of Campylobacter jejuni and prediction tools of its antimicrobial resistance. Folia Microbiol (Praha) 2024; 69:207-219. [PMID: 37816942 PMCID: PMC10876727 DOI: 10.1007/s12223-023-01093-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 09/09/2023] [Indexed: 10/12/2023]
Abstract
Although Campylobacter jejuni is the pathogen responsible for the most common foodborne illness, tracing of the infection source remains challenging due to its highly variable genome. Therefore, one of the aim of the study was to compare three genotyping methods (MLST, PFGE, and mP-BIT) to determine the most effective genotyping tool. C. jejuni strains were divided into 4 clusters based on strain similarity in the cgMLST dendrogram. Subsequently, the dendrograms of the 3 tested methods were compared to determine the accuracy of each method compared to the reference cgMLST method. Moreover, a cost-benefit analysis has showed that MLST had the highest inverse discrimination index (97%) and required less workflow, time, fewer consumables, and low bacterial sample quantity. PFGE was shown to be obsolete both because of its low discriminatory power and the complexity of the procedure. Similarly, mP‑BIT showed low separation results, which was compensated by its high availability. Therefore, our data showed that MLST is the optimal tool for genotyping C. jejuni. Another aim was to compare the antimicrobial resistance to ciprofloxacin, erythromycin, and tetracycline in C. jejuni strains isolated from human, water, air, food, and animal samples by two gene sequence-based prediction methods and to compare them with the actual susceptibility of C. jejuni strains using the disc diffusion method. Both tools, ResFinder and RGI, synchronously predict the antimicrobial susceptibility of C. jejuni and either can be used.
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Affiliation(s)
- Nicol Strakova
- Veterinary Research Institute, Hudcova 296/70, Brno, Czech Republic.
| | - Hana Michova
- Laboratory of Food Microbiology, Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czech Republic
| | - Ekaterina Shagieva
- Laboratory of Food Microbiology, Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czech Republic
| | - Petra Ovesna
- Institute of Biostatistics and Analyses, Masaryk University, Brno, Czech Republic
| | - Renata Karpiskova
- Department of Public Health, Medical Faculty, Masaryk University, Brno, Czech Republic
| | - Katerina Demnerova
- Laboratory of Food Microbiology, Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czech Republic
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Reliability Evaluation of MALDI-TOF MS Associated with SARAMIS Software in Rapid Identification of Thermophilic Campylobacter Isolated from Food. FOOD ANAL METHOD 2019. [DOI: 10.1007/s12161-019-01447-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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3
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Lawton SJ, Weis AM, Byrne BA, Fritz H, Taff CC, Townsend AK, Weimer BC, Mete A, Wheeler S, Boyce WM. Comparative analysis of Campylobacter isolates from wild birds and chickens using MALDI-TOF MS, biochemical testing, and DNA sequencing. J Vet Diagn Invest 2018; 30:354-361. [PMID: 29528812 PMCID: PMC6505823 DOI: 10.1177/1040638718762562] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was compared to conventional biochemical testing methods and nucleic acid analyses (16S rDNA sequencing, hippurate hydrolysis gene testing, whole genome sequencing [WGS]) for species identification of Campylobacter isolates obtained from chickens ( Gallus gallus domesticus, n = 8), American crows ( Corvus brachyrhynchos, n = 17), a mallard duck ( Anas platyrhynchos, n = 1), and a western scrub-jay ( Aphelocoma californica, n = 1). The test results for all 27 isolates were in 100% agreement between MALDI-TOF MS, the combined results of 16S rDNA sequencing, and the hippurate hydrolysis gene PCR ( p = 0.0027, kappa = 1). Likewise, the identifications derived from WGS from a subset of 14 isolates were in 100% agreement with the MALDI-TOF MS identification. In contrast, biochemical testing misclassified 5 isolates of C. jejuni as C. coli, and 16S rDNA sequencing alone was not able to differentiate between C. coli and C. jejuni for 11 sequences ( p = 0.1573, kappa = 0.0857) when compared to MALDI-TOF MS and WGS. No agreement was observed between MALDI-TOF MS dendrograms and the phylogenetic relationships revealed by rDNA sequencing or WGS. Our results confirm that MALDI-TOF MS is a fast and reliable method for identifying Campylobacter isolates to the species level from wild birds and chickens, but not for elucidating phylogenetic relationships among Campylobacter isolates.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Walter M. Boyce
- Walter M. Boyce, Department
of Pathology, Microbiology and Immunology, University of California, Davis, 1
Shields Avenue, Davis, CA 95616.
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Woźniak-Biel A, Bugla-Płoskońska G, Kielsznia A, Korzekwa K, Tobiasz A, Korzeniowska-Kowal A, Wieliczko A. High Prevalence of Resistance to Fluoroquinolones and Tetracycline Campylobacter Spp. Isolated from Poultry in Poland. Microb Drug Resist 2018; 24:314-322. [PMID: 28628752 PMCID: PMC5905868 DOI: 10.1089/mdr.2016.0249] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Campylobacter spp. is a major cause of foodborne diseases in humans, particularly when transmitted by the handling or consumption of undercooked poultry meat. Most Campylobacter infections are self-limiting, but antimicrobial treatment (e.g., fluoroquinolones and macrolides) is necessary in severe or prolonged cases. The indiscriminate use of these drugs, both in clinical medicine and animal production, has a major impact on public health. The aim of the present study was to identify Campylobacter strains, isolated from turkey and broilers, using both PCR and the matrix-assisted laser desorption-ionization time-of-flight (MALDI-TOF) methods to reveal the accuracy of identification, as well to evaluate the antimicrobial and genetic resistance of the investigated strains. MALDI-TOF and PCR methods were used to show differences, if any, in the specificity of that test. In this study, MALDI-TOF mass spectrometry gave the same results as multiplex PCR, in all cases. The highest rate of resistance (i.e., 100% of turkey and broiler strains) was detected against ciprofloxacin, whereas 58.1% of turkey and 78.6% of broiler strains were resistant to tetracycline. Multidrug-resistant isolates were not found in the study. All ciprofloxacin-resistant strains had a mutation in the gyrA gene, at the Thr-86 position. The presence of the tetO gene was found in 71% of turkey and in 100% of broiler strains. All resistant to tetracycline strains included tetO gene. Additionally, in five turkey and three broiler strains, susceptible to tetracycline, tetO gene was present. These results indicate the high prevalence of Campylobacter strains, which are phenotypically and genetically resistant to fluoroquinolones and tetracycline.
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Affiliation(s)
- Anna Woźniak-Biel
- Department of Epizootiology with Clinic of Bird and Exotic Animals, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland
| | - Gabriela Bugla-Płoskońska
- Department of Microbiology, Institute of Genetics and Microbiology, University of Wroclaw, Wrocław, Poland
| | - Alicja Kielsznia
- Department of Microbiology, Institute of Genetics and Microbiology, University of Wroclaw, Wrocław, Poland
| | - Kamila Korzekwa
- Department of Microbiology, Institute of Genetics and Microbiology, University of Wroclaw, Wrocław, Poland
| | - Anna Tobiasz
- Department of Immunology of Infectious Diseases, Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Agnieszka Korzeniowska-Kowal
- Department of Immunology of Infectious Diseases, Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Alina Wieliczko
- Department of Epizootiology with Clinic of Bird and Exotic Animals, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland
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El-Bouri K, Johnston S, Rees E, Thomas I, Bome-Mannathoko N, Jones C, Reid M, Ben-Ismaeil B, Davies AP, Harris LG, Mack D. Comparison of bacterial identification by MALDI-TOF mass spectrometry and conventional diagnostic microbiology methods: agreement, speed and cost implications. Br J Biomed Sci 2018. [DOI: 10.1080/09674845.2012.12002436] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- K. El-Bouri
- Public Health Wales Microbiology Laboratory ABM Swansea, Singleton Hospital, Abertawe-Bro Morgannwg University Health Board, Swansea, United Kingdom
| | - S. Johnston
- Public Health Wales Microbiology Laboratory ABM Swansea, Singleton Hospital, Abertawe-Bro Morgannwg University Health Board, Swansea, United Kingdom
| | - E. Rees
- Public Health Wales Microbiology Laboratory ABM Swansea, Singleton Hospital, Abertawe-Bro Morgannwg University Health Board, Swansea, United Kingdom
| | - I. Thomas
- Public Health Wales Microbiology Laboratory ABM Swansea, Singleton Hospital, Abertawe-Bro Morgannwg University Health Board, Swansea, United Kingdom
| | - N. Bome-Mannathoko
- Medical Microbiology and Infectious Diseases, Institute of Life Science, School of Medicine, Swansea University, Swansea, United Kingdom
| | - C. Jones
- Medical Microbiology and Infectious Diseases, Institute of Life Science, School of Medicine, Swansea University, Swansea, United Kingdom
| | - M. Reid
- Public Health Wales Microbiology Laboratory ABM Swansea, Singleton Hospital, Abertawe-Bro Morgannwg University Health Board, Swansea, United Kingdom
- Medical Microbiology and Infectious Diseases, Institute of Life Science, School of Medicine, Swansea University, Swansea, United Kingdom
| | - B. Ben-Ismaeil
- Public Health Wales Microbiology Laboratory ABM Swansea, Singleton Hospital, Abertawe-Bro Morgannwg University Health Board, Swansea, United Kingdom
| | - A. P. Davies
- Public Health Wales Microbiology Laboratory ABM Swansea, Singleton Hospital, Abertawe-Bro Morgannwg University Health Board, Swansea, United Kingdom
- Medical Microbiology and Infectious Diseases, Institute of Life Science, School of Medicine, Swansea University, Swansea, United Kingdom
| | - L. G. Harris
- Medical Microbiology and Infectious Diseases, Institute of Life Science, School of Medicine, Swansea University, Swansea, United Kingdom
| | - D. Mack
- Public Health Wales Microbiology Laboratory ABM Swansea, Singleton Hospital, Abertawe-Bro Morgannwg University Health Board, Swansea, United Kingdom
- Medical Microbiology and Infectious Diseases, Institute of Life Science, School of Medicine, Swansea University, Swansea, United Kingdom
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Campylobacter jejuni Fatal Sepsis in a Patient with Non-Hodgkin's Lymphoma: Case Report and Literature Review of a Difficult Diagnosis. Int J Mol Sci 2016; 17:544. [PMID: 27077849 PMCID: PMC4849000 DOI: 10.3390/ijms17040544] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 04/02/2016] [Accepted: 04/07/2016] [Indexed: 02/06/2023] Open
Abstract
Campylobacter jejuni (C. jejuni) bacteremia is difficult to diagnose in individuals with hematological disorders undergoing chemotherapy. The cause can be attributed to the rarity of this infection, to the variable clinical presentation, and to the partial overlapping symptoms underlying the disease. Here, we report a case of a fatal sepsis caused by C. jejuni in a 76-year-old Caucasian man with non-Hodgkin’s lymphoma. After chemotherapeutic treatment, the patient experienced fever associated with severe neutropenia and thrombocytopenia without hemodynamic instability, abdominal pain, and diarrhea. The slow growth of C. jejuni in the blood culture systems and the difficulty in identifying it with conventional biochemical phenotyping methods contributed to the delay of administering a targeted antimicrobial treatment, leading to a fatal outcome. Early recognition and timely intervention are critical for the successful management of C. jejuni infection. Symptoms may be difficult to recognize in immunocompromised patients undergoing chemotherapy. Thus, it is important to increase physician awareness regarding the clinical manifestations of C. jejuni to improve therapeutic efficacy. Moreover, the use of more aggressive empirical antimicrobial treatments with aminoglycosides and/or carbapenems should be considered in immunosuppressed patients, in comparison to those currently indicated in the guidelines for cancer-related infections supporting the use of cephalosporins as monotherapy.
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Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry: A New Guide to Infectious Disease. ARCHIVES OF PEDIATRIC INFECTIOUS DISEASES 2016. [DOI: 10.5812/pedinfect.31816] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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8
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Muhamadali H, Weaver D, Subaihi A, AlMasoud N, Trivedi DK, Ellis DI, Linton D, Goodacre R. Chicken, beams, and Campylobacter: rapid differentiation of foodborne bacteria via vibrational spectroscopy and MALDI-mass spectrometry. Analyst 2015; 141:111-22. [PMID: 26523729 DOI: 10.1039/c5an01945a] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Campylobacter species are one of the main causes of food poisoning worldwide. Despite the availability of established culturing and molecular techniques, due to the fastidious nature of these microorganisms, simultaneous detection and species differentiation still remains challenging. This study focused on the differentiation of eleven Campylobacter strains from six species, using Fourier transform infrared (FT-IR) and Raman spectroscopies, together with matrix-assisted laser desorption ionisation-time of flight-mass spectrometry (MALDI-TOF-MS), as physicochemical approaches for generating biochemical fingerprints. Cluster analysis of data from each of the three analytical approaches provided clear differentiation of each Campylobacter species, which was generally in agreement with a phylogenetic tree based on 16S rRNA gene sequences. Notably, although C. fetus subspecies fetus and venerealis are phylogenetically very closely related, using FT-IR and MALDI-TOF-MS data these subspecies were readily differentiated based on differences in the lipid (2920 and 2851 cm(-1)) and fingerprint regions (1500-500 cm(-1)) of the FT-IR spectra, and the 500-2000 m/z region of the MALDI-TOF-MS data. A finding that was further investigated with targeted lipidomics using liquid chromatography-mass spectrometry (LC-MS). Our results demonstrate that such metabolomics approaches combined with molecular biology techniques may provide critical information and knowledge related to the risk factors, virulence, and understanding of the distribution and transmission routes associated with different strains of foodborne Campylobacter spp.
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Affiliation(s)
- Howbeer Muhamadali
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
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Matrix-assisted laser desorption ionization-time of flight mass spectrometry: a fundamental shift in the routine practice of clinical microbiology. Clin Microbiol Rev 2014; 26:547-603. [PMID: 23824373 DOI: 10.1128/cmr.00072-12] [Citation(s) in RCA: 514] [Impact Index Per Article: 51.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Within the past decade, clinical microbiology laboratories experienced revolutionary changes in the way in which microorganisms are identified, moving away from slow, traditional microbial identification algorithms toward rapid molecular methods and mass spectrometry (MS). Historically, MS was clinically utilized as a high-complexity method adapted for protein-centered analysis of samples in chemistry and hematology laboratories. Today, matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) MS is adapted for use in microbiology laboratories, where it serves as a paradigm-shifting, rapid, and robust method for accurate microbial identification. Multiple instrument platforms, marketed by well-established manufacturers, are beginning to displace automated phenotypic identification instruments and in some cases genetic sequence-based identification practices. This review summarizes the current position of MALDI-TOF MS in clinical research and in diagnostic clinical microbiology laboratories and serves as a primer to examine the "nuts and bolts" of MALDI-TOF MS, highlighting research associated with sample preparation, spectral analysis, and accuracy. Currently available MALDI-TOF MS hardware and software platforms that support the use of MALDI-TOF with direct and precultured specimens and integration of the technology into the laboratory workflow are also discussed. Finally, this review closes with a prospective view of the future of MALDI-TOF MS in the clinical microbiology laboratory to accelerate diagnosis and microbial identification to improve patient care.
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Zautner AE, Masanta WO, Tareen AM, Weig M, Lugert R, Groß U, Bader O. Discrimination of multilocus sequence typing-based Campylobacter jejuni subgroups by MALDI-TOF mass spectrometry. BMC Microbiol 2013; 13:247. [PMID: 24195572 PMCID: PMC4228279 DOI: 10.1186/1471-2180-13-247] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 10/30/2013] [Indexed: 11/26/2022] Open
Abstract
Background Campylobacter jejuni, the most common bacterial pathogen causing gastroenteritis, shows a wide genetic diversity. Previously, we demonstrated by the combination of multi locus sequence typing (MLST)-based UPGMA-clustering and analysis of 16 genetic markers that twelve different C. jejuni subgroups can be distinguished. Among these are two prominent subgroups. The first subgroup contains the majority of hyperinvasive strains and is characterized by a dimeric form of the chemotaxis-receptor Tlp7m+c. The second has an extended amino acid metabolism and is characterized by the presence of a periplasmic asparaginase (ansB) and gamma-glutamyl-transpeptidase (ggt). Results Phyloproteomic principal component analysis (PCA) hierarchical clustering of MALDI-TOF based intact cell mass spectrometry (ICMS) spectra was able to group particular C. jejuni subgroups of phylogenetic related isolates in distinct clusters. Especially the aforementioned Tlp7m+c+ and ansB+/ ggt+ subgroups could be discriminated by PCA. Overlay of ICMS spectra of all isolates led to the identification of characteristic biomarker ions for these specific C. jejuni subgroups. Thus, mass peak shifts can be used to identify the C. jejuni subgroup with an extended amino acid metabolism. Conclusions Although the PCA hierarchical clustering of ICMS-spectra groups the tested isolates into a different order as compared to MLST-based UPGMA-clustering, the isolates of the indicator-groups form predominantly coherent clusters. These clusters reflect phenotypic aspects better than phylogenetic clustering, indicating that the genes corresponding to the biomarker ions are phylogenetically coupled to the tested marker genes. Thus, PCA clustering could be an additional tool for analyzing the relatedness of bacterial isolates.
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Affiliation(s)
- Andreas Erich Zautner
- UMG-Labor/Institut für Medizinische Mikrobiologie, Universitätsmedizin Göttingen, Kreuzbergring 57, 37075, Göttingen, Germany.
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Mukhopadhya I, Hansen R, Nicholl CE, Alhaidan YA, Thomson JM, Berry SH, Pattinson C, Stead DA, Russell RK, El-Omar EM, Hold GL. A comprehensive evaluation of colonic mucosal isolates of Sutterella wadsworthensis from inflammatory bowel disease. PLoS One 2011; 6:e27076. [PMID: 22073125 PMCID: PMC3205041 DOI: 10.1371/journal.pone.0027076] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Accepted: 10/09/2011] [Indexed: 12/13/2022] Open
Abstract
Inflammatory bowel disease (IBD) arises in genetically susceptible individuals as a result of an unidentified environmental trigger, possibly a hitherto unknown bacterial pathogen. Twenty-six clinical isolates of Sutterella wadsworthensis were obtained from 134 adults and 61 pediatric patients undergoing colonoscopy, of whom 69 and 29 respectively had IBD. S. wadsworthensis was initially more frequently isolated from IBD subjects, hence this comprehensive study was undertaken to elucidate its role in IBD. Utilizing these samples, a newly designed PCR was developed, to study the prevalence of this bacterium in adult patients with ulcerative colitis (UC). Sutterella wadsworthensis was detected in 83.8% of adult patients with UC as opposed to 86.1% of control subjects (p = 0.64). Selected strains from IBD cases and controls were studied to elicit morphological, proteomic, genotypic and pathogenic differences. This study reports Scanning Electron Microscopy (SEM) appearances and characteristic MALDI-TOF MS protein profiles of S. wadsworthensis for the very first time. SEM showed that the bacterium is pleomorphic, existing in predominantly two morphological forms, long rods and coccobacilli. No differences were noted in the MALDI-TOF mass spectrometry proteomic analysis. There was no distinct clustering of strains identified from cases and controls on sequence analysis. Cytokine response after monocyte challenge with strains from patients with IBD and controls did not yield any significant differences. Our studies indicate that S. wadsworthensis is unlikely to play a role in the pathogenesis of IBD. Strains from cases of IBD could not be distinguished from those identified from controls.
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Affiliation(s)
- Indrani Mukhopadhya
- Gastrointestinal Research Group, Division of Applied Medicine, University of Aberdeen, Foresterhill, Aberdeen, United Kingdom
| | - Richard Hansen
- Gastrointestinal Research Group, Division of Applied Medicine, University of Aberdeen, Foresterhill, Aberdeen, United Kingdom
- Child Health, University of Aberdeen, Royal Aberdeen Children's Hospital, Foresterhill, Aberdeen, United Kingdom
| | - Charlotte E. Nicholl
- Gastrointestinal Research Group, Division of Applied Medicine, University of Aberdeen, Foresterhill, Aberdeen, United Kingdom
| | - Yazeid A. Alhaidan
- Gastrointestinal Research Group, Division of Applied Medicine, University of Aberdeen, Foresterhill, Aberdeen, United Kingdom
| | - John M. Thomson
- Gastrointestinal Research Group, Division of Applied Medicine, University of Aberdeen, Foresterhill, Aberdeen, United Kingdom
| | - Susan H. Berry
- Gastrointestinal Research Group, Division of Applied Medicine, University of Aberdeen, Foresterhill, Aberdeen, United Kingdom
| | - Craig Pattinson
- Aberdeen Proteomics Group, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, United Kingdom
| | - David A. Stead
- Aberdeen Proteomics Group, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, United Kingdom
| | - Richard K. Russell
- Department of Paediatric Gastroenterology, Royal Hospital for Sick Children, Glasgow, United Kingdom
| | - Emad M. El-Omar
- Gastrointestinal Research Group, Division of Applied Medicine, University of Aberdeen, Foresterhill, Aberdeen, United Kingdom
| | - Georgina L. Hold
- Gastrointestinal Research Group, Division of Applied Medicine, University of Aberdeen, Foresterhill, Aberdeen, United Kingdom
- * E-mail: .
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A comprehensive evaluation of colonic mucosal isolates of Sutterella wadsworthensis from inflammatory bowel disease. PLoS One 2011. [PMID: 22073125 DOI: 10.1371/journal.pone.0027076.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Inflammatory bowel disease (IBD) arises in genetically susceptible individuals as a result of an unidentified environmental trigger, possibly a hitherto unknown bacterial pathogen. Twenty-six clinical isolates of Sutterella wadsworthensis were obtained from 134 adults and 61 pediatric patients undergoing colonoscopy, of whom 69 and 29 respectively had IBD. S. wadsworthensis was initially more frequently isolated from IBD subjects, hence this comprehensive study was undertaken to elucidate its role in IBD. Utilizing these samples, a newly designed PCR was developed, to study the prevalence of this bacterium in adult patients with ulcerative colitis (UC). Sutterella wadsworthensis was detected in 83.8% of adult patients with UC as opposed to 86.1% of control subjects (p = 0.64). Selected strains from IBD cases and controls were studied to elicit morphological, proteomic, genotypic and pathogenic differences. This study reports Scanning Electron Microscopy (SEM) appearances and characteristic MALDI-TOF MS protein profiles of S. wadsworthensis for the very first time. SEM showed that the bacterium is pleomorphic, existing in predominantly two morphological forms, long rods and coccobacilli. No differences were noted in the MALDI-TOF mass spectrometry proteomic analysis. There was no distinct clustering of strains identified from cases and controls on sequence analysis. Cytokine response after monocyte challenge with strains from patients with IBD and controls did not yield any significant differences. Our studies indicate that S. wadsworthensis is unlikely to play a role in the pathogenesis of IBD. Strains from cases of IBD could not be distinguished from those identified from controls.
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13
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Matrix-assisted laser desorption ionization (MALDI)-time of flight mass spectrometry- and MALDI biotyper-based identification of cultured biphenyl-metabolizing bacteria from contaminated horseradish rhizosphere soil. Appl Environ Microbiol 2011; 77:6858-66. [PMID: 21821747 DOI: 10.1128/aem.05465-11] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacteria that are able to utilize biphenyl as a sole source of carbon were extracted and isolated from polychlorinated biphenyl (PCB)-contaminated soil vegetated by horseradish. Isolates were identified using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). The usage of MALDI Biotyper for the classification of isolates was evaluated and compared to 16S rRNA gene sequence analysis. A wide spectrum of bacteria was isolated, with Arthrobacter, Serratia, Rhodococcus, and Rhizobium being predominant. Arthrobacter isolates also represented the most diverse group. The use of MALDI Biotyper in many cases permitted the identification at the level of species, which was not achieved by 16S rRNA gene sequence analyses. However, some isolates had to be identified by 16S rRNA gene analyses if MALDI Biotyper-based identification was at the level of probable or not reliable identification, usually due to a lack of reference spectra included in the database. Overall, this study shows the possibility of using MALDI-TOF MS and MALDI Biotyper for the fast and relatively nonlaborious identification/classification of soil isolates. At the same time, it demonstrates the dominant role of employing 16S rRNA gene analyses for the identification of recently isolated strains that can later fill the gaps in the protein-based identification databases.
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Kiehntopf M, Melcher F, Hänel I, ElAdawy H, Tomaso H. Differentiation ofCampylobacterSpecies by Surface-Enhanced Laser Desorption/Ionization–Time-of-Flight Mass Spectrometry. Foodborne Pathog Dis 2011; 8:875-85. [DOI: 10.1089/fpd.2010.0775] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Michael Kiehntopf
- Institute of Clinical Chemistry and Laboratory Medicine, Jena University Hospital, Friedrich-Schiller-University Jena, Jena, Germany
| | - Franka Melcher
- Institute of Clinical Chemistry and Laboratory Medicine, Jena University Hospital, Friedrich-Schiller-University Jena, Jena, Germany
| | - Ingrid Hänel
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, Jena, Germany
| | - Hosny ElAdawy
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, Jena, Germany
| | - Herbert Tomaso
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, Jena, Germany
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Bessède E, Solecki O, Sifré E, Labadi L, Mégraud F. Identification of Campylobacter species and related organisms by matrix assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry. Clin Microbiol Infect 2011; 17:1735-9. [PMID: 21375659 DOI: 10.1111/j.1469-0691.2011.03468.x] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The identification of Campylobacter species and related organisms at the species level has always been difficult using phenotypic methods because of their low metabolic activity, whereas molecular methods are more reliable but time-consuming. In this study, 1007 different strains were identified using three different methods: conventional methods, molecular biology (real-time PCR and sequencing) and matrix assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry. Molecular methods were considered the gold standard. The accuracy of MALDI-TOF mass spectrometry reached 100% compared with the gold standard for all of the Campylobacter species, except Campylobacter jejuni (99.4%). The accuracy of conventional methods compared with the gold standard ranged from 0% to 100% depending on the species. However, MALDI-TOF mass spectrometry was not able to identify a mixture of two different species present in the same sample in four instances. Finally, MALDI-TOF mass spectrometry is highly recommended to identify Campylobacter spp. as only 0.4% discrepancy was found, whereas conventional methods led to 4.5% discrepancy.
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Affiliation(s)
- E Bessède
- Université Victor Segalen Bordeaux 2, Centre National de Référence des Campylobacters et Hélicobacters, Bordeaux Cedex, France
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Kolínská R, Dřevínek M, Aldová E, Zemličková H. Identification of Plesiomonas spp.: serological and MALDI-TOF MS methods. Folia Microbiol (Praha) 2011; 55:669-72. [PMID: 21253918 DOI: 10.1007/s12223-010-0109-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Indexed: 11/24/2022]
Abstract
Biochemical and serological profiles of isolates of Plesiomonas shigelloides were assayed using standard procedures in isolates from various clinical samples. Seventy-four isolates, including P. shigelloides type strain, were further characterized by MALDI-TOF MS using 3-methoxy-4-hydroxycinnamic acid as matrix. Multiple ions in the 3- to 12-kDa mass range were found in the spectra of each strain, from which the "species-identifying" unique biomarker ions were identified. After creating the species-specific patterns, a spectral database was generated for reliable, rapid, reproducible and accurate identification of Plesiomonas strains. The classical strain description (biochemical and serological) was thus complemented with the metabolic (proteomic) characterization.
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Affiliation(s)
- R Kolínská
- Czech National Collection of Type Cultures (CNCTC), National Institute of Public Health, 10042 Prague, Czech Republic.
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Seng P, Rolain JM, Fournier PE, La Scola B, Drancourt M, Raoult D. MALDI-TOF-mass spectrometry applications in clinical microbiology. Future Microbiol 2010; 5:1733-54. [DOI: 10.2217/fmb.10.127] [Citation(s) in RCA: 283] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
MALDI-TOF-mass spectrometry (MS) has been successfully adapted for the routine identification of microorganisms in clinical microbiology laboratories in the past 10 years. This revolutionary technique allows for easier and faster diagnosis of human pathogens than conventional phenotypic and molecular identification methods, with unquestionable reliability and cost–effectiveness. This article will review the application of MALDI-TOF-MS tools in routine clinical diagnosis, including the identification of bacteria at the species, subspecies, strain and lineage levels, and the identification of bacterial toxins and antibiotic-resistance type. We will also discuss the application of MALDI-TOF-MS tools in the identification of Archaea, eukaryotes and viruses. Pathogenic identification from colony-cultured, blood-cultured, urine and environmental samples is also reviewed.
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Affiliation(s)
- Piseth Seng
- Pôle des Maladies Infectieuses, Assistance Publique-Hôpitaux de Marseille et URMITE UMR CNRS-IRD 6236, IFR48, Faculté de Médecine, Université de la Méditerranée, Marseille, France: URMITE, Faculté de Médecine, 27 Boulevard Jean Moulin, 13385 Marseille cedex 5, France
| | - Jean-Marc Rolain
- Pôle des Maladies Infectieuses, Assistance Publique-Hôpitaux de Marseille et URMITE UMR CNRS-IRD 6236, IFR48, Faculté de Médecine, Université de la Méditerranée, Marseille, France: URMITE, Faculté de Médecine, 27 Boulevard Jean Moulin, 13385 Marseille cedex 5, France
| | - Pierre Edouard Fournier
- Pôle des Maladies Infectieuses, Assistance Publique-Hôpitaux de Marseille et URMITE UMR CNRS-IRD 6236, IFR48, Faculté de Médecine, Université de la Méditerranée, Marseille, France: URMITE, Faculté de Médecine, 27 Boulevard Jean Moulin, 13385 Marseille cedex 5, France
| | - Bernard La Scola
- Pôle des Maladies Infectieuses, Assistance Publique-Hôpitaux de Marseille et URMITE UMR CNRS-IRD 6236, IFR48, Faculté de Médecine, Université de la Méditerranée, Marseille, France: URMITE, Faculté de Médecine, 27 Boulevard Jean Moulin, 13385 Marseille cedex 5, France
| | - Michel Drancourt
- Pôle des Maladies Infectieuses, Assistance Publique-Hôpitaux de Marseille et URMITE UMR CNRS-IRD 6236, IFR48, Faculté de Médecine, Université de la Méditerranée, Marseille, France: URMITE, Faculté de Médecine, 27 Boulevard Jean Moulin, 13385 Marseille cedex 5, France
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18
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Murray P. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry: usefulness for taxonomy and epidemiology. Clin Microbiol Infect 2010; 16:1626-30. [DOI: 10.1111/j.1469-0691.2010.03364.x] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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19
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Susceptibility of Campylobacter jejuni to organic acids and monoacylglycerols. Folia Microbiol (Praha) 2010; 55:215-20. [DOI: 10.1007/s12223-010-0031-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2009] [Revised: 12/16/2009] [Indexed: 10/19/2022]
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Krutkiewicz A, Klimuszko D. Genotyping and PCR detection of potential virulence genes in Campylobacter jejuni and Campylobacter coli isolates from different sources in Poland. Folia Microbiol (Praha) 2010; 55:167-75. [DOI: 10.1007/s12223-010-0025-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2009] [Revised: 12/14/2010] [Indexed: 11/28/2022]
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21
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Species-specific identification and differentiation of Arcobacter, Helicobacter and Campylobacter by full-spectral matrix-associated laser desorption/ionization time of flight mass spectrometry analysis. J Med Microbiol 2010; 59:295-301. [DOI: 10.1099/jmm.0.016576-0] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Rapid and reliable identification of Arcobacter and Helicobacter species, and their distinction from phenotypically similar Campylobacter species, has become increasingly important, since many of them are now recognized as human and/or animal pathogens. Matrix-associated laser desorption/ionization–time of flight (MALDI-TOF) MS has been shown to be a rapid and sensitive method for characterization of micro-organisms. In this study, we therefore established a reference database of selected Arcobacter, Helicobacter and Campylobacter species for MALDI-TOF MS identification. Besides the species with significance as food-borne pathogens – Arcobacter butzleri, Helicobacter pullorum, Campylobacter jejuni and Campylobacter coli – several other members of these genera were included in the reference library to determine the species specificity of the designed MALDI Biotyper reference database library. Strains that made up the reference database library were grown on Columbia agar, and yielded reproducible and unique mass spectra profiles, which were compared with the Bruker Biotyper database, version 2. The database was used to identify 144 clinical isolates using whole spectral profiles. Furthermore, reproducibility of MALDI-TOF MS results was evaluated with respect to age and/or storage of bacteria and different growth media. It was found that correct identification could be obtained even if the bacteria were stored at room temperature or at 4 °C up to 9 days before being tested. In addition, bacteria were correctly identified when grown on Campylosel agar; however, they were not when grown on modified charcoal cefoperazone deoxycholate agar. These results indicate that MALDI-TOF MS fingerprinting is a fast and reliable method for the identification of Arcobacter and Helicobacter species, and their distinction from phenotypically similar Campylobacter species, with applications in clinical diagnostics.
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Moliner C, Ginevra C, Jarraud S, Flaudrops C, Bedotto M, Couderc C, Etienne J, Fournier PE. Rapid identification of Legionella species by mass spectrometry. J Med Microbiol 2009; 59:273-284. [PMID: 19926729 DOI: 10.1099/jmm.0.014100-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Legionella species are facultative, intracellular bacteria that infect macrophages and protozoa, with the latter acting as transmission vectors to humans. These fastidious bacteria mostly cause pulmonary tract infections and are routinely identified by various molecular methods, mainly PCR targeting the mip gene and sequencing, which are expensive and time-consuming. Recently, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) has emerged as a rapid and inexpensive method for identification of bacterial species. This study evaluated the use of MALDI-TOF-MS for rapid species and serogroup identification of 21 Legionella species recognized as human pathogens. To this end, a reference MS database was developed including 59 Legionella type strains, and a blind test was performed using 237 strains from various species. Two hundred and twenty-three of the 237 strains (94.1 %) were correctly identified at the species level, although ten (4.2 %) were identified with a score lower than 2.0. Fourteen strains (5.9 %) from eight species were misidentified at the species level, including seven (3.0 %) with a significant score, suggesting an intraspecific variability of protein profiles within some species. MALDI-TOF-MS was reproducible but could not identify Legionella strains at the serogroup level. When compared with mip gene sequencing, MALDI-TOF-MS exhibited a sensitivity of 99.2 and 89.9 % for the identification of Legionella strains at the genus and species level, respectively. This study demonstrated that MALDI-TOF-MS is a reliable tool for the rapid identification of Legionella strains at the species level.
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Affiliation(s)
- Claire Moliner
- URMITE CNRS-IRD UMR 6236, Faculté de Médecine, 27 boulevard Jean Moulin, 13385 Marseille Cedex 05, France
| | - Christophe Ginevra
- Hospices Civils de Lyon, Faculté de Médecine Lyon Est Claude Bernard, Lyon, France.,Université de Lyon, Lyon, France.,INSERM, U851, 21 avenue Tony Garnier, 69007 Lyon, France.,Université Lyon 1, IFR128, Lyon, France
| | - Sophie Jarraud
- Université Lyon 1, IFR128, Lyon, France.,Hospices Civils de Lyon, Faculté de Médecine Lyon Est Claude Bernard, Lyon, France.,Université de Lyon, Lyon, France.,INSERM, U851, 21 avenue Tony Garnier, 69007 Lyon, France
| | - Christophe Flaudrops
- Fédération de Microbiologie Clinique, Hôpital de la Timone, 264 rue Saint-Pierre, 13385 Marseille Cedex 05, France
| | - Marielle Bedotto
- Fédération de Microbiologie Clinique, Hôpital de la Timone, 264 rue Saint-Pierre, 13385 Marseille Cedex 05, France
| | - Carine Couderc
- Fédération de Microbiologie Clinique, Hôpital de la Timone, 264 rue Saint-Pierre, 13385 Marseille Cedex 05, France
| | - Jerome Etienne
- Université Lyon 1, IFR128, Lyon, France.,INSERM, U851, 21 avenue Tony Garnier, 69007 Lyon, France.,Université de Lyon, Lyon, France.,Hospices Civils de Lyon, Faculté de Médecine Lyon Est Claude Bernard, Lyon, France
| | - Pierre-Edouard Fournier
- Fédération de Microbiologie Clinique, Hôpital de la Timone, 264 rue Saint-Pierre, 13385 Marseille Cedex 05, France.,URMITE CNRS-IRD UMR 6236, Faculté de Médecine, 27 boulevard Jean Moulin, 13385 Marseille Cedex 05, France
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