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Jia B, Burnley H, Gardner IA, Saab ME, Doucet A, Hammell KL. Diagnosis of Renibacterium salmoninarum infection in harvested Atlantic salmon (Salmo salar L.) on the east coast of Canada: Clinical findings, sample collection methods and laboratory diagnostic tests. JOURNAL OF FISH DISEASES 2023; 46:575-589. [PMID: 36861304 DOI: 10.1111/jfd.13770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 02/09/2023] [Accepted: 02/11/2023] [Indexed: 06/18/2023]
Abstract
Chronic subclinical infection with the aetiological agent of bacterial kidney disease (BKD), Renibacterium salmoninarum, presents challenges for the clinical management of disease in farmed salmonids and for prevalence estimation. Harvested salmon sampled at processing plants provide the opportunity to describe subclinical outcomes of BKD using gross necropsy observations and diagnostic test results in farmed Atlantic salmon (Salmo salar L.) populations that are apparently healthy (i.e. alive at harvest) but naturally exposed to R. salmoninarum infection. Sampling of farmed salmon (Population A, n = 124 and Population B, n = 160) was performed immediately post-slaughter as fish were being processed at a plant in New Brunswick, Canada. Populations were selected based on planned harvests from sites with histories of recent exposure events related to clinical BKD as evidenced by the site veterinarian's diagnosis of mortality attributable to BKD: One site (Pop A) had recently increasing mortalities attributed to BKD, and the other site (Pop B) had ongoing low-level mortalities with BKD pathology. As expected with the different exposure histories, Pop A had a higher percentage (57.2%) of R. salmoninarum culture-positive kidney samples compared with similar fish samples in Pop B (17.5%). Diagnosis of R. salmoninarum by gross granulomatous lesions in internal visceral organs, bacterial culture and identification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) using different swab transport methods, and molecular detection methods (quantitative PCR, qPCR) were compared. Agreement of culture-positive percentages at the sample level was moderate (kappa: 0.61-0.75) among specimens collected using different kidney sampling methods in Pop A and Pop B. The highest proportion of R. salmoninarum-positive cultures occurred when kidney tissues were transported to the laboratory and inoculated directly onto agar using a swab (94% of cultures from Pop A and 82% from Pop B when fish were positive by any culture method). Fish with cumulative lesion scores (severity of granulomatous lesions in 3 different visceral organs) of >4 were all culture positive, and when compared with non-lesioned fish, had substantially higher odds of being culture positive: Pop A: odds ratio (OR) = 73, 95% confidence interval (CI) (7.91, 680.8); Pop B: OR = 66, 95% CI (6.12, 720.7). Our study found that onsite postmortem examinations with severity scores of gross granulomatous lesions were predictive of positive culture results for R. salmoninarum, and they were a useful proxy for assessing prevalence in apparently healthy populations with subclinical infection.
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Affiliation(s)
- Beibei Jia
- Department of Health Management, and Centre for Veterinary Epidemiological Research, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - Holly Burnley
- Department of Health Management, and Centre for Veterinary Epidemiological Research, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - Ian A Gardner
- Department of Health Management, and Centre for Veterinary Epidemiological Research, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - Matthew E Saab
- Department of Health Management, and Centre for Veterinary Epidemiological Research, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
- Aquatic Diagnostic Services, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - Adele Doucet
- Department of Health Management, and Centre for Veterinary Epidemiological Research, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
- Vet-Champlain Animal Care, Dieppe, New Brunswick, Canada
| | - K Larry Hammell
- Department of Health Management, and Centre for Veterinary Epidemiological Research, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
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Bigge R, Bunk B, Rudolph WW, Gunzer F, Coldewey SM, Riedel T, Schröttner P. Comparative Study of Different Diagnostic Routine Methods for the Identification of Acinetobacter radioresistens. Microorganisms 2022; 10:microorganisms10091767. [PMID: 36144369 PMCID: PMC9503985 DOI: 10.3390/microorganisms10091767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/19/2022] [Accepted: 08/29/2022] [Indexed: 11/16/2022] Open
Abstract
Recent publications indicate that A. radioresistens can cause infections in humans, even though it is rarely reported in routine diagnostics. However, the fact that it is infrequently detected may be explained by the misidentification of the species by conventional methods. It is also likely that A. radioresistens is not considered clinically relevant and therefore not consistently included in diagnostic results. To elucidate the medical significance of this probably clinically underestimated bacterial species, we created a well-documented reference strain collection of 21 strains collected in routine diagnostics. For further analysis of A. radioresistens, it is essential to know which methods can be used to achieve a trustworthy identification. We, therefore, compared three methods widely used in routine diagnostics (MALDI-TOF MS, VITEK 2, and sequencing of housekeeping genes) in terms of secure and reliable identification of A. radioresistens. As reference methods, whole genome-based approaches were applied. VITEK 2 led to misidentification for four strains. However, MALDI-TOF MS and sequencing of housekeeping genes led to reliable and robust identifications.
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Affiliation(s)
- Richard Bigge
- Institute for Microbiology and Virology, University Hospital Carl Gustav Carus, 01307 Dresden, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, 38124 Braunschweig, Germany
| | - Wolfram W. Rudolph
- Department of Hospital Infection Control, University Hospital Carl Gustav Carus, 01307 Dresden, Germany
| | - Florian Gunzer
- Department of Hospital Infection Control, University Hospital Carl Gustav Carus, 01307 Dresden, Germany
| | - Sina M. Coldewey
- Department of Anesthesiology and Intensive Care Medicine, Jena University Hospital, 07745 Jena, Germany
- Septomics Research Center, Jena University Hospital, 07747 Jena, Germany
- Center for Sepsis Control and Care, Jena University Hospital, 07747 Jena, Germany
| | - Thomas Riedel
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, 38124 Braunschweig, Germany
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Percy Schröttner
- Institute for Microbiology and Virology, University Hospital Carl Gustav Carus, 01307 Dresden, Germany
- Correspondence: ; Tel.: +49-(351)-458-16585
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Propionibacterium/Cutibacterium species-related positive samples, identification, clinical and resistance features: a 10-year survey in a French hospital. Eur J Clin Microbiol Infect Dis 2020; 39:1357-1364. [PMID: 32125556 DOI: 10.1007/s10096-020-03852-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 02/16/2020] [Indexed: 02/07/2023]
Abstract
A 10-year retrospective study of Propionibacterium/Cutibacterium-positive samples gathered from hospitalized patients was conducted at Nantes University hospital. A total of 2728 Propionibacterium/Cutibacterium-positive samples analyzed between 2007 and 2016 were included. Due to the implementation of MALDI-TOF identification in 2013, most non-Cutibacterium acnes isolates were identified a second time using this technology. Over that period, Cutibacterium acnes remained the most predominant species accounting for 91.5% (2497/2728) of the isolates, followed by Cutibacterium avidum (4.2%, 115/2728) and Cutibacterium granulosum (2.4%, 64/2728). Regarding the origin of samples, the orthopaedic department was the main Cutibacterium sample provider representing 51.9% (1415/2728) of all samples followed by the dermatology department (11.5%, 315/2728). Samples were recovered from various tissue locations: 31.5% (858/2728) from surgery-related samples such as shoulder, spine or hip replacement devices and 19.1% (520/2728) from skin samples. MALDI-TOF method revealed misidentification before 2013. Cutibacterium avidum was falsely identified as C. granulosum (n = 33). Consequently, MALDI-TOF technology using up-to-date databases should be preferred to biochemical identification in order to avoid biased species identification. Regarding antibiotic resistance, 14.7% (20/136) of C. acnes was resistant to erythromycin. 4.1% (41/1005) of C. acnes strains, 17.9% (12/67) of C. avidum strains and 3.6% (1/28) of C. granulosum strains were found resistant to clindamycin.
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Kozajda A, Jeżak K, Kapsa A. Airborne Staphylococcus aureus in different environments-a review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:34741-34753. [PMID: 31654301 PMCID: PMC6900272 DOI: 10.1007/s11356-019-06557-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 09/23/2019] [Indexed: 05/22/2023]
Abstract
The aim of the literature review was to describe the environments where the presence of airborne Staphylococcus aureus was confirmed and to catalogue the most often used methods and conditions of bioaerosol sampling to identify the bacteria. The basis for searching of studies on S. aureus in the bioaerosol in different environments was PubMed database resources from the years 1990-2019 (May). The review included studies which were carried on in selected environments: hospitals and other health care facilities, large-scale animal breeding, wastewater treatment plants, residential areas, educational institutions, and other public places. The highest concentrations and genetic diversity of identified S. aureus strains, including MRSA (methicillin-resistant S. aureus), have been shown in large-scale animal breeding. The role of the airborne transmission in dissemination of infection caused by these pathogens is empirically confirmed in environmental studies. Commonly available, well-described, and relatively inexpensive methods of sampling, identification, and subtyping guarantee a high reliability of results and allow to obtain fast and verifiable outcomes in environmental studies on air transmission routes of S. aureus strains.
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Affiliation(s)
- Anna Kozajda
- Nofer Institute of Occupational Medicine, 8 Teresy Str, 91-348, Łódź, Poland.
| | - Karolina Jeżak
- Nofer Institute of Occupational Medicine, 8 Teresy Str, 91-348, Łódź, Poland
| | - Agnieszka Kapsa
- Nofer Institute of Occupational Medicine, 8 Teresy Str, 91-348, Łódź, Poland
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Kostrzewa M, Nagy E, Schröttner P, Pranada AB. How MALDI-TOF mass spectrometry can aid the diagnosis of hard-to-identify pathogenic bacteria - the rare and the unknown. Expert Rev Mol Diagn 2019; 19:667-682. [PMID: 31303071 DOI: 10.1080/14737159.2019.1643238] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Introduction: Ten years after its introduction into clinical microbiology, MALDI-TOF mass spectrometry has become the standard routine identification tool for bacteria in most laboratories. The technology has accelerated analyses and improved the quality of results. The greatest significance has been observed for bacteria that were challenging to be identified by traditional methods. Areas covered: We searched in existing literature (Pubmed) for reports how MALDI-TOF MS has contributed to identification of rare and unknown bacteria from different groups. We describe how this has improved the diagnostics in different groups of bacteria. Reference patterns for strains which yet cannot be assigned to a known species even enable the search for related bacteria in studies as well as in routine diagnostics. MALDI-TOF MS can help to discover and investigate new species and their clinical relevance. It is a powerful tool in the elucidation of the bacterial composition of complex microbiota in culturomics studies. Expert opinion: MALDI-TOF MS has improved the diagnosis of bacterial infections. It also enables knowledge generation for prospective diagnostics. The term 'hard-to-identify' might only be rarely attributed to bacteria in the future. Novel applications are being developed, e.g. subspecies differentiation, typing, and antibiotic resistance testing which may further contribute to improved microbial diagnostics.
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Affiliation(s)
- Markus Kostrzewa
- Bioanalytical Development, Bruker Daltonik GmbH , Bremen , Germany
| | - Elisabeth Nagy
- Institute of Clinical Microbiology, University of Szeged , Szeged , Hungary
| | - Percy Schröttner
- Institut für Medizinische Mikrobiologie und Hygiene, Technische Universität Dresden , Dresden , Germany
| | - Arthur B Pranada
- Department of Medical Microbiology, MVZ Dr. Eberhard & Partner Dortmund (ÜBAG) , Dortmund , Germany
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Naugler C, Church DL. Clinical laboratory utilization management and improved healthcare performance. Crit Rev Clin Lab Sci 2019. [DOI: 10.1080/10408363.2018.1526164] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Christopher Naugler
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Canada
- Department of Family Medicine, University of Calgary, Calgary, Canada
- Department of Community Health Sciences, University of Calgary, Calgary, Canada
| | - Deirdre L. Church
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Canada
- Department of Medicine, University of Calgary, Calgary, Canada
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Cordovana M, Kostrzewa M, Sóki J, Witt E, Ambretti S, Pranada A. Bacteroides fragilis: A whole MALDI-based workflow from identification to confirmation of carbapenemase production for routine laboratories. Anaerobe 2018; 54:246-253. [DOI: 10.1016/j.anaerobe.2018.04.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 03/30/2018] [Accepted: 04/03/2018] [Indexed: 10/17/2022]
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Microbial Diversity: The Gap between the Estimated and the Known. DIVERSITY-BASEL 2018. [DOI: 10.3390/d10020046] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Shell WS, Sayed ML, Allah FMG, Gamal FEM, Khedr AA, Samy AA, Ali AHM. Matrix-assisted laser desorption-ionization-time-of-flight mass spectrometry as a reliable proteomic method for characterization of Escherichia coli and Salmonella isolates. Vet World 2017; 10:1083-1093. [PMID: 29062198 PMCID: PMC5639107 DOI: 10.14202/vetworld.2017.1083-1093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 08/10/2017] [Indexed: 11/16/2022] Open
Abstract
Aim: Identification of pathogenic clinical bacterial isolates is mainly dependent on
phenotypic and genotypic characteristics of the microorganisms. These conventional
methods are costive, time-consuming, and need special skills and training. An
alternative, mass spectral (proteomics) analysis method for identification of
clinical bacterial isolates has been recognized as a rapid, reliable, and
economical method for identification. This study was aimed to evaluate and compare
the performance, sensitivity and reliability of traditional bacteriology,
phenotypic methods and matrix-assisted laser desorption-ionization-time-of-flight
mass spectrometry (MALDI-TOF MS) in the identification of clinical
Escherichia coli and Salmonella isolates
recovered from chickens. Materials and Methods: A total of 110 samples (cloacal, liver, spleen, and/or gall bladder) were
collected from apparently healthy and diseased chickens showing clinical signs as
white chalky diarrhea, pasty vent, and decrease egg production as well as freshly
dead chickens which showing postmortem lesions as enlarged liver with congestion
and enlarged gall bladder from different poultry farms. Results: Depending on colonial characteristics and morphological characteristics,
E. coli and Salmonella isolates were
recovered and detected in only 42 and 35 samples, respectively. Biochemical
identification using API 20E identification system revealed that the suspected
E. coli isolates were 33 out of 42 of colonial and
morphological identified E. coli isolates where
Salmonella isolates were represented by 26 out of 35 of
colonial and morphological identified Salmonella isolates.
Serological identification of isolates revealed that the most predominant
E. coli serotypes were O1 and O78 while the most predominant
Salmonella serotype of Salmonella was
Salmonella Pullorum. All E. coli and
Salmonella isolates were examined using MALDI-TOF MS. In
agreement with traditional identification, MADI-TOF MS identified all clinical
bacterial samples with valid scores as E. coli and
Salmonella isolates except two E. coli
isolates recovered from apparently healthy and diseased birds, respectively, with
recovery rate of 93.9% and 2 Salmonella isolates recovered
from apparently healthy and dead birds, respectively, with recovery rate of
92.3%. Conclusion: Our study demonstrated that Bruker MALDI-TOF MS Biotyper is a reliable rapid and
economic tool for the identification of Gram-negative bacteria especially
E. coli and Salmonella which could be used as
an alternative diagnostic tool for routine identification and differentiation of
clinical isolates in the bacteriological laboratory. MALDI-TOF MS need more
validation and verification and more study on the performance of direct colony and
extraction methods to detect the most sensitive one and also need using more
samples to detect sensitivity, reliability, and performance of this type of
bacterial identification.
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Affiliation(s)
- Waleed S Shell
- Central Laboratory for Evaluation of Veterinary Biologics Abbasaia, Agriculture Research Center, Cairo, Egypt
| | - Mahmoud Lotfy Sayed
- Central Laboratory for Evaluation of Veterinary Biologics Abbasaia, Agriculture Research Center, Cairo, Egypt
| | - Fatma Mohamed Gad Allah
- Central Laboratory for Evaluation of Veterinary Biologics Abbasaia, Agriculture Research Center, Cairo, Egypt
| | | | - Afaf Ahmed Khedr
- Central Laboratory for Evaluation of Veterinary Biologics Abbasaia, Agriculture Research Center, Cairo, Egypt
| | - A A Samy
- Department of Microbiology and Immunology, National Research Center, Cairo, Egypt
| | - Abdel Hakam M Ali
- Central Laboratory for Evaluation of Veterinary Biologics Abbasaia, Agriculture Research Center, Cairo, Egypt
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S. Shell W, L. Sayed M, A. El-Geda A, M. El Sade G, A. Samy A, M.M. Ali A. Identification of Staphylococcus aureus Causing Bovine Mastitis using MALDI-TOF Fingerprinting. ACTA ACUST UNITED AC 2017. [DOI: 10.3923/ijds.2017.105.113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Kumaran S, Abdelhamid HN, Wu HF. Quantification analysis of protein and mycelium contents upon inhibition of melanin for Aspergillus niger: a study of matrix assisted laser desorption/ionization mass spectrometry (MALDI-MS). RSC Adv 2017. [DOI: 10.1039/c7ra03741d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Mass spectrometry (MS) provides a simple discrimination method for microorganisms.
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Affiliation(s)
- Sekar Kumaran
- Department of Chemistry and Center for Nanoscience and Nanotechnology
- National Sun Yat-Sen University
- Kaohsiung
- Taiwan
- School of Pharmacy
| | - Hani Nasser Abdelhamid
- Department of Chemistry and Center for Nanoscience and Nanotechnology
- National Sun Yat-Sen University
- Kaohsiung
- Taiwan
- School of Pharmacy
| | - Hui-Fen Wu
- Department of Chemistry and Center for Nanoscience and Nanotechnology
- National Sun Yat-Sen University
- Kaohsiung
- Taiwan
- School of Pharmacy
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