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Mwandira W, Mavroulidou M, Satheesh A, Gunn MJ, Gray C, Purchase D, Garelick J. An electrokinetic-biocementation study for clay stabilisation using carbonic anhydrase-producing bacteria. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:104916-104931. [PMID: 37702861 PMCID: PMC10567949 DOI: 10.1007/s11356-023-29817-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 09/06/2023] [Indexed: 09/14/2023]
Abstract
This study investigates the feasibility of biocementing clay soil underneath a railway embankment of the UK rail network via carbonic anhydrase (CA) biocementation, implementing the treatments electrokinetically. Compared to previous biocementation studies using the ureolytic route, the CA pathway is attractive as CA-producing bacteria can sequester CO2 to produce biocement. Clay soil samples were treated electrokinetically using biostimulation and bioaugmentation conditions to induce biocementation. The effects of the treatment were assessed in terms of undrained shear strength using the cone penetration test, moisture content, and calcium carbonate content measurements. Scanning electron microscopy (SEM) analyses were also conducted on soil samples before and after treatment to evaluate the reaction products. The results showed that upon biostimulation, the undrained shear strength of the soil increased uniformly throughout the soil, from 17.6 kPa (in the natural untreated state) to 106.6 kPa. SEM micrographs also showed a clear change in the soil structure upon biostimulation. Unlike biostimulation, bioaugmentation did not have the same performance, although a high amount of CaCO3 precipitates was detected, and bacteria were observed to have entered the soil. The prospects are exciting, as it was shown that it is possible to achieve a considerable strength increase by the biostimulation of native bacteria capturing CO2 while improving the soil strength, thus having the potential to contribute both to the resilience of existing railway infrastructure and to climate change mitigation.
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Affiliation(s)
- Wilson Mwandira
- Division of Civil and Building Services Engineering, London South Bank University, London, UK
| | - Maria Mavroulidou
- Division of Civil and Building Services Engineering, London South Bank University, London, UK.
| | - Anjali Satheesh
- Division of Civil and Building Services Engineering, London South Bank University, London, UK
| | - Michael John Gunn
- Division of Civil and Building Services Engineering, London South Bank University, London, UK
| | | | - Diane Purchase
- Faculty of Science and Technology, Middlesex University, London, UK
| | - Jonathan Garelick
- Network Rail-Eastern Region, One Stratford Place, Stratford City, London, E20, UK
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Sivanesan I, Gopal J, Hasan N, Muthu M. A systematic assessment of matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) application for rapid identification of pathogenic microbes that affect food crops: delivered and future deliverables. RSC Adv 2023; 13:17297-17314. [PMID: 37304772 PMCID: PMC10251190 DOI: 10.1039/d3ra01633a] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/20/2023] [Indexed: 06/13/2023] Open
Abstract
MALDI-TOF MS has decades of experience in the detection and identification of microbial pathogens. This has now become a valuable analytical tool when it comes to the identification and detection of clinical microbial pathogens. This review gives a brief synopsis of what has been achieved using MALDI-TOF MS in clinical microbiology. The major focus, however, is on summarizing and highlighting the effectiveness of MALDI-TOF MS as a novel tool for rapid identification of food crop microbial pathogens. The methods used and the sample preparation methodologies reported thus far have been highlighted and the challenges and gaps and recommendations for fine tuning the technique have been put forth. In an era where anything close to the health and welfare of humanity has been considered as the top priority, this review pitches on one such relevant research topics.
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Affiliation(s)
- Iyyakkannu Sivanesan
- Department of Bioresources and Food Science, Institute of Natural Science and Agriculture, Konkuk University 1 Hwayang-dong, Gwangjin-gu Seoul 05029 Korea
| | - Judy Gopal
- Department of Research and Innovation, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS) Thandalam Chennai 602105 Tamil Nadu India +91 44 2681 1009 +91 44 66726677
| | - Nazim Hasan
- Department of Chemistry, Faculty of Science, Jazan University P.O. Box 114 Jazan Saudi Arabia
| | - Manikandan Muthu
- Department of Research and Innovation, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS) Thandalam Chennai 602105 Tamil Nadu India +91 44 2681 1009 +91 44 66726677
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Milligan EG, Calarco J, Davis BC, Keenum IM, Liguori K, Pruden A, Harwood VJ. A Systematic Review of Culture-Based Methods for Monitoring Antibiotic-Resistant Acinetobacter, Aeromonas, and Pseudomonas as Environmentally Relevant Pathogens in Wastewater and Surface Water. Curr Environ Health Rep 2023:10.1007/s40572-023-00393-9. [PMID: 36821031 DOI: 10.1007/s40572-023-00393-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/11/2023] [Indexed: 02/24/2023]
Abstract
PURPOSE OF REVIEW Mounting evidence indicates that habitats such as wastewater and environmental waters are pathways for the spread of antibiotic-resistant bacteria (ARB) and mobile antibiotic resistance genes (ARGs). We identified antibiotic-resistant members of the genera Acinetobacter, Aeromonas, and Pseudomonas as key opportunistic pathogens that grow or persist in built (e.g., wastewater) or natural aquatic environments. Effective methods for monitoring these ARB in the environment are needed to understand their influence on dissemination of ARB and ARGs, but standard methods have not been developed. This systematic review considers peer-reviewed papers where the ARB above were cultured from wastewater or surface water, focusing on the accuracy of current methodologies. RECENT FINDINGS Recent studies suggest that many clinically important ARGs were originally acquired from environmental microorganisms. Acinetobacter, Aeromonas, and Pseudomonas species are of interest because their ability to persist and grow in the environment provides opportunities to engage in horizontal gene transfer with other environmental bacteria. Pathogenic strains of these organisms resistant to multiple, clinically relevant drug classes have been identified as an urgent threat. However, culture methods for these bacteria were generally developed for clinical samples and are not well-vetted for environmental samples. The search criteria yielded 60 peer-reviewed articles over the past 20 years, which reported a wide variety of methods for isolation, confirmation, and antibiotic resistance assays. Based on a systematic comparison of the reported methods, we suggest a path forward for standardizing methodologies for monitoring antibiotic resistant strains of these bacteria in water environments.
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Affiliation(s)
- Erin G Milligan
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, 24061, USA.,Center for Emerging, Zoonotic, and Arthropod-Borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Jeanette Calarco
- Department of Integrative Biology, University of South Florida, Tampa, FL, 33620, USA
| | - Benjamin C Davis
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Ishi M Keenum
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Krista Liguori
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Amy Pruden
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, 24061, USA. .,Center for Emerging, Zoonotic, and Arthropod-Borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA.
| | - Valerie J Harwood
- Department of Integrative Biology, University of South Florida, Tampa, FL, 33620, USA.
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Vilcarromero S, Small M, Lizarzaburu A, Rivadeneyra-Rodriguez A. Pleural empyema by Parvimonas micra in an immunocompetent patient: a case report. Rev Peru Med Exp Salud Publica 2023; 40:99-104. [PMID: 37377244 PMCID: PMC10953646 DOI: 10.17843/rpmesp.2023.401.11956] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 11/30/2022] [Indexed: 06/29/2023] Open
Abstract
We present the case of a young immunocompetent patient, with a history of pulmonary tuberculosis, who attended the hospital with a subacute clinical picture of persistent fever, weight loss, dyspnea and abolition of vesicular murmur. Chest CT scan showed an extensive empyema in the left hemithorax. Samples were taken for detection of common germs. Then, a chest drainage tube was placed and antibiotic therapy started. The MALDI-TOF MS test identified Parvimonas micra, an anaerobic bacterium, commensal to the oral flora, associated with severe periodontitis, but rarely reported in cases of pleural empyema, especially in immunocompetent patients. Gingivitis and pericoronaritis of the third molar were diagnosed during oral evaluation. The patient progressed favorably. Parvimonas micra should be considered as a possible etiological agent in cases of subacute or chronic pleural empyema, in addition to mycobacteria. Tests such as MALDI-TOF MS or 16S rRNA sequencing, chest tube placement, empirical antibiotic coverage and an adequate oral evaluation should be considered in these cases.
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Affiliation(s)
- Stalin Vilcarromero
- Infectious Diseases Service of the Hospital Edgardo Rebagliati Martins, EsSalud, Lima, Peru.nfectious Diseases Service of the Hospital Edgardo Rebagliati MartinsEsSaludLimaPeru
| | - Max Small
- Pneumology Service of the Hospital Edgardo Rebagliati Martins , EsSalud, Lima, Peru.Servicio de Neumología del Hospital Edgardo Rebagliati MartinsEsSaludLimaPeru
| | - Alexis Lizarzaburu
- Pneumology Service of the Hospital Edgardo Rebagliati Martins , EsSalud, Lima, Peru.Servicio de Neumología del Hospital Edgardo Rebagliati MartinsEsSaludLimaPeru
| | - Abel Rivadeneyra-Rodriguez
- Odontostomatology Service of the Hospital Edgardo Rebagliati Martins, EsSalud, Lima, Peru.Odontostomatology Service of the Hospital Edgardo Rebagliati MartinsEsSaludLimaPeru
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Kitagawa D, Suzuki Y, Abe N, Ui K, Suzuki K, Yamashita T, Sakaguchi A, Suzuki S, Masuo K, Nakano A, Nakano R, Sato M, Koichi M, Nakamura F, Yano H. Comparison of MALDI-TOF mass spectrometry and rpoB gene sequencing for the identification of clinical isolates of Aeromonas spp. Heliyon 2022; 8:e11585. [PMID: 36406716 PMCID: PMC9668526 DOI: 10.1016/j.heliyon.2022.e11585] [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: 01/25/2022] [Revised: 02/09/2022] [Accepted: 11/07/2022] [Indexed: 11/15/2022] Open
Abstract
Aeromonas spp., widely present in rivers and soil, cause mild gastroenteritis, severe septicemia, and soft tissue infections in humans. Treatment of these infections require accurate identification of pathogenic Aeromonas spp. However, identification at the species level using conventional methods is highly challenging. In this study, we aimed to compare the accuracy of two different approaches developed for bacterial identification: (i) housekeeping gene sequencing (rpoB) in conjunction with phylogenetic analysis and (ii) matrix-assisted laser desorption ionization mass spectrometry-time of flight (MALDI-TOF MS) (MALDI Biotyper and VITEK MS), for differentiating Aeromonas spp. We analyzed 58 Aeromonas isolates recovered from patients at different medical institutions in Japan using both identification methods. The rpoB sequencing method was the most accurate, identifying all Aeromonas isolates at the species level. Meanwhile, the MALDI Biotyper system correctly identified 53 (91.4%) isolates at the genus level and an additional 30 (51.7%) at the species level. The VITEK MS system correctly identified 58 (100%) isolates at the genus level and an additional 34 (58.6%) at the species level. Thus, MALDI Biotyper and VITEK MS accurately identified isolates at the genus level, but differences were found in the accuracy of identification of species. However, the low cost and ease of analysis make MALDI-TOF MS-based methods strong candidates for use in clinical laboratories that require easy-to-use identification methods. Mass spectrometry (MS)-based methods evaluated for Aeromonas spp. identification. Housekeeping gene rpoB sequencing most accurately identified Aeromonas species. MALDI Biotyper and VITEK MS differed in accuracy depending on the species. Database extension will help improve identification accuracy of MS-based methods.
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Mursalim MF, Budiyansah H, Raharjo HM, Debnath PP, Sakulworakan R, Chokmangmeepisarn P, Yindee J, Piasomboon P, Elayaraja S, Rodkhum C. Diversity and antimicrobial susceptibility profiles of Aeromonas spp. isolated from diseased freshwater fishes in Thailand. JOURNAL OF FISH DISEASES 2022; 45:1149-1163. [PMID: 35598068 DOI: 10.1111/jfd.13650] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/07/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
Motile Aeromonas septicemia (MAS), a disease caused by Aeromonas spp., is recognized as a major disease in freshwater aquaculture. This study aimed to investigate the distribution and diversity of Aeromonas spp. and their antimicrobial susceptibility patterns. A total of 86 isolates of Aeromonas spp. were recovered from diseased freshwater fishes from 13 farms in Thailand. All isolates were identified using biochemical characteristics, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), polymerase chain reaction assays, and the gyrB gene sequence analysis. The result of MALDI-TOF MS showed 100% (86 isolates) accuracy at genus-level identification, and 88.4% (76 isolates) accuracy at species-level identification. Six species of Aeromonas were confirmed through nucleotide sequencing and phylogenetic analysis of the gyrB gene Aeromonas veronii (72.1%), Aeromonas jandaei (11.6%), Aeromonas schubertii (9.3%), Aeromonas diversa (3.5%), Aeromonas hydrophila (2.3%), and Aeromonas punctata (1.2%). Antimicrobial susceptibility tests for all isolates revealed resistance against amoxicillin (99%), ampicillin (98%), oxolinic acid (81.4%), oxytetracycline (77%), trimethoprim-sulfamethoxazole (24%), and enrofloxacin (21%). The multiple antibiotic resistance (MAR) index varied between 0.14 and 0.86, with MAR values more than 0.2 in 99% of isolates. Furthermore, four diverse multidrug-resistant (MDR) patterns were found among Aeromonas isolates. Our finding show that A. veronii is the most abundant species in Thai cultured freshwater fish with the highest MDR patterns.
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Affiliation(s)
- Muhammad Fadhlullah Mursalim
- Center of Excellence in Fish Infectious Diseases Research Unit (CE FID), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- The International Graduate Course of Veterinary Science and Technology (VST), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Veterinary Study Program, Faculty of Medicine, Hasanuddin University, Makassar, Indonesia
| | - Hendri Budiyansah
- Center of Excellence in Fish Infectious Diseases Research Unit (CE FID), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- The International Graduate Course of Veterinary Science and Technology (VST), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Hartanto Mulyo Raharjo
- Center of Excellence in Fish Infectious Diseases Research Unit (CE FID), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- The International Graduate Course of Veterinary Science and Technology (VST), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Partho Pratim Debnath
- Center of Excellence in Fish Infectious Diseases Research Unit (CE FID), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Rungnapa Sakulworakan
- Center of Excellence in Fish Infectious Diseases Research Unit (CE FID), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- The International Graduate Course of Veterinary Science and Technology (VST), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Putita Chokmangmeepisarn
- Center of Excellence in Fish Infectious Diseases Research Unit (CE FID), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- The International Graduate Course of Veterinary Science and Technology (VST), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Jitrapa Yindee
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Patharapol Piasomboon
- Department of Veterinary Medicine, Faculty of Veterinary Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Sivaramasamy Elayaraja
- Center of Excellence in Fish Infectious Diseases Research Unit (CE FID), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Channarong Rodkhum
- Center of Excellence in Fish Infectious Diseases Research Unit (CE FID), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
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Pessoa RBG, de Oliveira WF, Correia MTDS, Fontes A, Coelho LCBB. Aeromonas and Human Health Disorders: Clinical Approaches. Front Microbiol 2022; 13:868890. [PMID: 35711774 PMCID: PMC9195132 DOI: 10.3389/fmicb.2022.868890] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 03/23/2022] [Indexed: 11/16/2022] Open
Abstract
The genus Aeromonas comprises more than 30 Gram-negative bacterial species and naturally inhabitants from aquatic environments. These microorganisms, commonly regarded as pathogens of fish and several other animals, have been gaining prominence on medical trial due to its ability to colonize and infect human beings. Besides water, Aeromonas are widely spreaded on most varied sources like soil, vegetables, and food; Although its opportunistic nature, they are able to cause infections on immunocompromised or immunocompetent patients. Aeromonas species regarded as potential human pathogens are usually A. hydrophila, A. caviae, and A. veronii biovar sobria. The main clinical manifestations are gastrointestinal tract disorders, wound, and soft tissue infections, as well as septicemia. Regarding to antibiotic responses, the bacteria present a diversified susceptibility profile and show inherence resistance to ampicillin. Aeromonas, as an ascending genus in microbiology, has been carefully studied aiming comprehension and development of methods for detection and medical intervention of infectious processes, not fully elucidated in medicine. This review focuses on current clinical knowledge related to human health disorders caused by Aeromonas to contribute on development of efficient approaches able to recognize and impair the pathological processes.
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Affiliation(s)
| | - Weslley Felix de Oliveira
- Departamento de Bioquímica, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Brazil
| | | | - Adriana Fontes
- Departamento de Biofísica e Radiobiologia, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Brazil
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Kosikowska U, Stec J, Andrzejczuk S, Mendrycka M, Pietras-Ożga D, Stępień-Pyśniak D. Plasmid-Mediated Fluoroquinolone Resistance Genes in Quinolone-Susceptible Aeromonas spp. Phenotypes Isolated From Recreational Surface Freshwater Reservoir. Front Cell Infect Microbiol 2022; 12:885360. [PMID: 35646727 PMCID: PMC9132129 DOI: 10.3389/fcimb.2022.885360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 03/24/2022] [Indexed: 11/13/2022] Open
Abstract
Aeromonas spp. are recognized as opportunistic pathogens causing diseases. Infections in humans can result mainly in gastrointestinal and wound diseases with or without progression to septicemia. Although Aeromonas spp. are not known uropathogens and they rarely cause urinary tract infection, we hypothesize that the presence of these bacteria in the water and the contact during, e.g., recreational and bathing activity can create the conditions for the colonization of the human body and may result to diseases in various locations, including the urinary tract. Our study presents the occurrence of aeromonad fluoroquinolone-susceptible phenotypes with the presence of plasmid-mediated fluoroquinolone resistance (PMQR) genes in a natural freshwater reservoir occasionally used for recreational activities. Sixty-nine isolates collected during the bathing period were identified by mass spectrometry and screened for the presence of fluoroquinolone-resistant phenotypes and genotypes. Fluoroquinolone susceptibility was determined as minimal inhibitory concentration values. PMQR qnr genes were detected by PCR. Isolates comprising eight species, namely, mainly Aeromonas veronii (50.7% isolates) and Aeromonas media (24.6% isolates) and rarely Aeromonas eucrenophila, Aeromonas caviae, Aeromonas bestiarum, Aeromonas ichthiosmia, and Aeromonas hydrophila, were selected. All isolates were phenotypically susceptible either to ciprofloxacin or levofloxacin. Unexpectedly, at least one to three of the PMQR genes were detected in 42.0% of the fluoroquinolone-susceptible Aeromonas spp. phenotypes. Mainly the qnrS (34.8% isolates) and qnrA (14.5% isolates) determinants were detected. In conclusion, the freshwater reservoir occasionally used for bathing was tainted with aeromonads, with a high occurrence of opportunistic pathogens such as A. veronii and A. media. MALDI‐TOF MS is a powerful technique for aeromonad identification. Our data reveals the mismatch phenomenon between fluoroquinolone-susceptible aeromonad phenotypes and the presence of plasmid-mediated qnr resistance genes. It suggests that phenotypically susceptible bacteria might be a potential source for the storage and transmission of these genes. The exposure during, e.g., a recreational activity may create the potential risk for causing infections, both diagnostically and therapeutically difficult, after expressing the resistance genes and quinolone-resistant strain selection.
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Affiliation(s)
- Urszula Kosikowska
- Department of Pharmaceutical Microbiology, Medical University of Lublin, Lublin, Poland
- *Correspondence: Urszula Kosikowska,
| | - Joanna Stec
- Department of Pharmaceutical Microbiology, Medical University of Lublin, Lublin, Poland
| | - Sylwia Andrzejczuk
- Department of Pharmaceutical Microbiology, Medical University of Lublin, Lublin, Poland
| | - Mariola Mendrycka
- Faculty of Medical Sciences and Health Sciences, Kazimierz Pulaski University of Technology and Humanities in Radom, Radom, Poland
| | - Dorota Pietras-Ożga
- Department of Epizootiology and Clinic of Infectious Diseases, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Lublin, Poland
| | - Dagmara Stępień-Pyśniak
- Department of Veterinary Prevention and Avian Diseases, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Lublin, Poland
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Ashfaq MY, Da'na DA, Al-Ghouti MA. Application of MALDI-TOF MS for identification of environmental bacteria: A review. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 305:114359. [PMID: 34959061 DOI: 10.1016/j.jenvman.2021.114359] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 12/07/2021] [Accepted: 12/18/2021] [Indexed: 05/22/2023]
Abstract
Bacteria play a variety of roles in the environment. They maintain the balance in the ecosystem and provide different ecosystem services such as in biogeochemical cycling of nutrients, biodegradation of toxic pollutants, and others. Therefore, isolation and identification of different environmental bacteria are important to most environmental research. Due to the high cost and time associated with the conventional molecular techniques, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has gained considerable attention for routine identification of bacteria. This review aims to provide an overview of the application of MALDI-TOF MS in various environmental studies through bibliometric analysis and literature review. The bibliometric analysis helped to understand the time-variable application of MALDI-TOF MS in various environmental studies. The categorical literature review covers various environmental studies comprising areas like ecology, food microbiology, environmental biotechnology, agriculture, and plant sciences, which show the application of the technique for identification and characterization of pollutant-degrading, plant-associated, disease-causing, soil-beneficial, and other environmental bacteria. Further research should focus on bridging the gap between the phylogenetic identity of bacteria and their specific environmental functions or metabolic traits that can help in rapid advancements in environmental research, thereby, improving time and cost savings.
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Affiliation(s)
- Mohammad Y Ashfaq
- Environmental Science program, Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, P.O. Box 2713, Doha, Qatar
| | - Dana A Da'na
- Environmental Science program, Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, P.O. Box 2713, Doha, Qatar
| | - Mohammad A Al-Ghouti
- Environmental Science program, Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, P.O. Box 2713, Doha, Qatar.
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Topić Popović N, Kazazić SP, Bojanić K, Strunjak-Perović I, Čož-Rakovac R. Sample preparation and culture condition effects on MALDI-TOF MS identification of bacteria: A review. MASS SPECTROMETRY REVIEWS 2021. [PMID: 34642960 DOI: 10.1002/mas.21739] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is an excellent tool for bacterial identification. It allows high throughput, sensitive and specific applications in clinical diagnostics and environmental research. Currently, there is no optimal standardized protocol for sample preparation and culture conditions to profile bacteria. The performance of MALDI-TOF MS is affected by several variables, such as sample preparation, culture media and culture conditions, incubation time/growth stage, incubation temperature, high salt content, blood in the culture media, and others. This review thus aims to clarify why a uniformed protocol is not plausible, to assess the effects these factors have on MALDI-TOF MS identification score, and discuss possible optimizations for its methodology, in relation to specific bacterial representatives and strain requirements.
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Affiliation(s)
- Natalija Topić Popović
- Laboratory for Aquaculture Biotechnology, Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
- Centre of Excellence for Marine Bioprospecting-BioProCro, Ruđer Bošković Institute, Zagreb, Croatia
| | - Snježana P Kazazić
- Laboratory for Mass Spectrometry and Functional Proteomics, Ruđer Bošković Institute, Zagreb, Croatia
| | - Krunoslav Bojanić
- Laboratory for Aquaculture Biotechnology, Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
- Centre of Excellence for Marine Bioprospecting-BioProCro, Ruđer Bošković Institute, Zagreb, Croatia
| | - Ivančica Strunjak-Perović
- Laboratory for Aquaculture Biotechnology, Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
- Centre of Excellence for Marine Bioprospecting-BioProCro, Ruđer Bošković Institute, Zagreb, Croatia
| | - Rozelindra Čož-Rakovac
- Laboratory for Aquaculture Biotechnology, Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
- Centre of Excellence for Marine Bioprospecting-BioProCro, Ruđer Bošković Institute, Zagreb, Croatia
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11
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Taxonomic Identification of Different Species of the Genus Aeromonas by Whole-Genome Sequencing and Use of Their Species-Specific β-Lactamases as Phylogenetic Markers. Antibiotics (Basel) 2021; 10:antibiotics10040354. [PMID: 33800590 PMCID: PMC8065696 DOI: 10.3390/antibiotics10040354] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 03/10/2021] [Accepted: 03/18/2021] [Indexed: 12/04/2022] Open
Abstract
Some Aeromonas species, potentially pathogenic for humans, are known to express up to three different classes of chromosomal β-lactamases, which may become hyperproduced and cause treatment failure. The aim of this study was to assess the utility of these species-specific β-lactamase genes as phylogenetic markers using whole-genome sequencing data. Core-genome alignments were generated for 36 Aeromonas genomes from seven different species and scanned for antimicrobial resistance genes. Core-genome alignment confirmed the MALDI-TOF identification of most of the isolates and re-identified an A. hydrophila isolate as A. dhakensis. Three (B, C and D) of the four Ambler classes of β-lactamase genes were found in A. sobria, A. allosacharophila, A. hydrophila and A. dhakensis (blaCphA, blaAmpC and blaOXA). A. veronii only showed class-B- and class-D-like matches (blaCphA and blaOXA), whereas those for A. media, A. rivipollensis and A. caviae were class C and D (blaCMY, blaMOX and blaOXA427). The phylogenetic tree derived from concatenated sequences of β-lactamase genes successfully clustered each species. Some isolates also had resistance to sulfonamides, quinolones and aminoglycosides. Whole-genome sequencing proved to be a useful method to identify Aeromonas at the species level, which led to the unexpected identification of A. dhakensis and A.rivipollensis and revealed the resistome of each isolate.
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Du X, Wang M, Zhou H, Li Z, Xu J, Li Z, Kan B, Chen D, Wang X, Jin Y, Ren Y, Ma Y, Liu J, Luan Y, Cui Z, Lu X. Comparison of the Multiple Platforms to Identify Various Aeromonas Species. Front Microbiol 2021; 11:625961. [PMID: 33537023 PMCID: PMC7848130 DOI: 10.3389/fmicb.2020.625961] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 12/18/2020] [Indexed: 12/02/2022] Open
Abstract
We compared several identification methods for Aeromonas genus members, including traditional biochemical testing, multiplex-PCR amplification, mass spectrometry identification, whole-genome sequencing, multilocus phylogenetic analysis (MLPA), and rpoD, gyrA, and rpoD-gyrA gene sequencing. Isolates (n = 62) belonging to the Aeromonas genus, which were came from the bacterial bank in the laboratory, were used to assess the identification accuracy of the different methods. Whole-genome sequencing showed that the Aeromonas spp. isolates comprised A. caviae (n = 21), A. veronii (n = 18), A. dhakensis (n = 8), A. hydrophila (n = 7), A. jandaei (n = 5), A. enteropelogenes (n = 2), and A. media (n = 1). Using the whole-genome sequencing results as the standard, the consistency of the other methods was compared with them. The results were 46.77% (29/62) for biochemical identification, 83.87% (52/62) for mass spectrometric identification, 67.74% (42/62) for multiplex-PCR, 100% (62/62) for MLPA typing, 72.58% for gyrA, and 59.68% for rpoD and gyrA-rpoD. MLPA was the most consistent, followed by mass spectrometry. Therefore, in the public health laboratory, both MLPA and whole-genome sequencing methods can be used to identify various Aeromonas species. However, rapid and relatively accurate mass spectrometry is recommended for clinical lab.
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Affiliation(s)
- Xiaoli Du
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Mengyu Wang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,School of Public Health, Nanchang University, Nanchang, Jiangxi, China.,Jiangxi Provincial Key Laboratory of Preventive Medicine, Nanchang University, Nanchang, China
| | - Haijian Zhou
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhenpeng Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jialiang Xu
- School of Light Industry, Beijing Technology and Business University, Beijing, China
| | - Zhe Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Biao Kan
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Daoli Chen
- Department of Microbiology Laboratory, Maanshan Center for Disease Control and Prevention of Anhui Province, Maanshan, China
| | - Xiaoli Wang
- Shijiazhuang Center for Disease Control and Prevention, Shijiazhuang, China
| | - Yujuan Jin
- Longgang Center for Disease Control and Prevention, Shenzhen, China
| | - Yan Ren
- LongHua District Center for Disease Control and Prevention, Shenzhen, China
| | - Yanping Ma
- Nanshan Center for Disease Control and Prevention, Shenzhen, China
| | - Jiuyin Liu
- Liaocheng Center for Disease Control and Prevention, Liaocheng, China
| | - Yang Luan
- Xi'an Center for Disease Control and Prevention, Xi'an, China
| | - Zhigang Cui
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xin Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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de Melo BST, Mendes-Marques CL, Campos TDL, Almeida AMPD, Leal NC, Xavier DE. High-resolution genome-wide analysis is essential for the identification of ambiguous Aeromonas strains. FEMS Microbiol Lett 2020; 366:5658690. [PMID: 31804685 DOI: 10.1093/femsle/fnz245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 12/04/2019] [Indexed: 11/13/2022] Open
Abstract
Aeromonads are mainly opportunistic pathogens; however, many species are emerging as important human pathogens. Therefore, monitoring these bacteria and their accurate characterization of its species is highly important. Aeromonas Aer593 strain was recovered from a diarrhoea outbreak and did not group with any previously described Aeromonas species by housekeeping gene sequencing. To clarify the taxonomic position of Aer593, its genome was sequenced and analysed by multilocus phylogenetic analysis (MLPA), in silico DNA-DNA hybridization (isDDH), average nucleotide identity (ANI) and core genome-based phylogenetic analyzes. The MLPA with the housekeeping genes gyrB, rpoD, recA, dnaJ, gyrA and dnaX ranked the Aer593 isolate into an independent branch suggesting that it could represent a new species. However, the identity percentages of Aer593 to A. caviae strains using robust genomic analysis by isDDH and ANI were at least 81.3% and 97.8%, respectively, defining Aer593 as A. caviae. Multilocus sequence typing (MLST) presented an exact match against only a single allele (groL96) and the novel ST648 was assigned for this strain. The core genome-based phylogenetic analyses with a total of 863 orthologous genes also grouped the Aer593 isolate with A. caviae reference strains. These findings warn about the possibility of misidentification of some Aeromonas strains by MLPA and show that high-resolution genome-wide analysis is essential for the correct identification of ambiguous Aeromonas strains.
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Affiliation(s)
- Beatriz Souza Toscano de Melo
- Departamento de Microbiologia, Instituto Aggeu Magalhães - FIOCRUZ, Av. Prof. Moraes Rego, Cidade Universitária, Recife - PE, 50670-420, Brazil
| | - Carina Lucena Mendes-Marques
- Departamento de Microbiologia, Instituto Aggeu Magalhães - FIOCRUZ, Av. Prof. Moraes Rego, Cidade Universitária, Recife - PE, 50670-420, Brazil
| | - Túlio de Lima Campos
- Departamento de Microbiologia, Instituto Aggeu Magalhães - FIOCRUZ, Av. Prof. Moraes Rego, Cidade Universitária, Recife - PE, 50670-420, Brazil
| | - Alzira Maria Paiva de Almeida
- Departamento de Microbiologia, Instituto Aggeu Magalhães - FIOCRUZ, Av. Prof. Moraes Rego, Cidade Universitária, Recife - PE, 50670-420, Brazil
| | - Nilma Cintra Leal
- Departamento de Microbiologia, Instituto Aggeu Magalhães - FIOCRUZ, Av. Prof. Moraes Rego, Cidade Universitária, Recife - PE, 50670-420, Brazil
| | - Danilo Elias Xavier
- Departamento de Microbiologia, Instituto Aggeu Magalhães - FIOCRUZ, Av. Prof. Moraes Rego, Cidade Universitária, Recife - PE, 50670-420, Brazil
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Lian Z, Bai J, Hu X, Lü A, Sun J, Guo Y, Song Y. Detection and characterization of Aeromonas salmonicida subsp. salmonicida infection in crucian carp Carassius auratus. Vet Res Commun 2020; 44:61-72. [PMID: 32472344 DOI: 10.1007/s11259-020-09773-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 04/29/2020] [Accepted: 04/30/2020] [Indexed: 10/24/2022]
Abstract
Aeromonas salmonicida is one of the most important pathogens in salmonids and non-salmonids species. Nevertheless, very little was reported in cyprinids about A. salmonicida infection. Hence, a pathogenic A. salmonicida subsp. salmonicida, namely isolate GCA-518, was isolated from diseased crucian carp Carassius auratus. Its optimal growth conditions were at 28 °C, pH 7.0 and 1.5% NaCl. Furthermore, the quantitative real-time PCR (qPCR) targeting serine protease (aspA) gene was established for rapid detection of the lowest limit of 5.6 × 102 copies per reaction. The pathogenicity was confirmed in crucian carp by intraperitoneal infection. Histopathologic examination displayed multifocal necrosis and infiltration of inflammatory cells in gill, liver, kidney and intestine. This is the first report on typical A. salmonicida infection in cultured crucian carp.
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Affiliation(s)
- Zhengyi Lian
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, 300384, China
| | - Jie Bai
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, 300384, China
| | - Xiucai Hu
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, 300384, China
| | - Aijun Lü
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, 300384, China.
| | - Jingfeng Sun
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, 300384, China
| | - Yongjun Guo
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, 300384, China
| | - Yajiao Song
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, 300384, China
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15
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Piamsomboon P, Jaresitthikunchai J, Hung TQ, Roytrakul S, Wongtavatchai J. Identification of bacterial pathogens in cultured fish with a custom peptide database constructed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). BMC Vet Res 2020; 16:52. [PMID: 32046727 PMCID: PMC7014616 DOI: 10.1186/s12917-020-2274-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 02/04/2020] [Indexed: 12/19/2022] Open
Abstract
Background The majority of infectious diseases of cultured fish is caused by bacteria. Rapid identification of bacterial pathogens is necessary for immediate management. The present study developed a custom Main Spectra Profile (MSP) database and validate the method using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for rapid identification of fish bacterial pathogens. Streptococcus agalactiae, Streptococcus iniae, Aeromonas hydrophila, Aeromonas veronii, and Edwardsiella tarda obtained from diseased fish were used as representative bacterial pathogens in this study. Bacterial peptides were extracted to create a Main Spectra Profile (MSP), and the MSPs of each bacterial species was added into the MALDI Biotyper database. Fifteen additional isolates of each bacterial species were tested to validate the utilized technique. Results The MSPs of all field isolates were clearly distinguishable, and the MSPs of the same species were clustered together. The identification methodology was validated with 75 bacterial isolates. The reliability and specificity of the method were determined with MALDI Biotyper log score values and matching results with 16 s rDNA sequencing. The species identification using the public MALDI Biotyper library (Bruker MALDI Biotyper) showed unreliable results (log score < 2.000) with 42.67% matching result with the reference method. In contrast, accurate identification was obtained when using the custom-made database, giving log score > 2.115, and a 100% matching result. Conclusion This study demonstrates an effective identification of fish bacterial pathogens when a complete custom-made MSP database is applied. Further applications require a broad, well-established database to accommodate prudent identification of many fish bacterial pathogens by MALDI-TOF MS.
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Affiliation(s)
- Patharapol Piamsomboon
- Department of Veterinary Medicine, Faculty of Veterinary Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Janthima Jaresitthikunchai
- Proteomics Research Laboratory, National Center for Genetic Engineering and Biotechnology, Pathum Thani, Thailand
| | - Tran Quang Hung
- University of South Bohemia in Ceske Budejovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Zátiší 728/II, 389 25, Vodňany, Czech Republic
| | - Sittiruk Roytrakul
- Proteomics Research Laboratory, National Center for Genetic Engineering and Biotechnology, Pathum Thani, Thailand
| | - Janenuj Wongtavatchai
- Department of Veterinary Medicine, Faculty of Veterinary Sciences, Chulalongkorn University, Bangkok, Thailand.
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16
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Kostas J, Parker KC. Using Matrix-Assisted Laser Desorption/Ionization Time of Flight Spectra To Elucidate Species Boundaries by Matching to Translated DNA Databases. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:73-84. [PMID: 32881510 DOI: 10.1021/jasms.9b00031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A method has been established to map a bacterial colony to the ever-expanding database of publicly available bacterial genomes by means of matrix-assisted laser desorption/ionization (MALDI) spectra. To accomplish this, spectra are mapped to the predicted masses of ∼65 families of mostly ribosomal proteins. Each of the ∼40 000 bacterial strains in the database receives scores, together with tables listing identified protein sequences and how the highest ranking strains are related to one another. The approach was first confirmed with 16 distinct species of bacteria from the Vibrionales whose genome had been sequenced. Identifications of a few species of bacteria from environmental samples from compost, lakes, and streams in Massachusetts are also reported. Most of these organisms map to known species in the Gammaproteobacteria and Firmicutes. The clades of bacteria deducible from shared ribosomal protein sequences do not always correspond well to named bacterial species. Instead, the identifications made by this methodology indicate groupings of organisms that can readily be distinguished by MALDI-TOF and indicate which polymorphisms in highly conserved proteins demarcate the groupings. Successful identifications highlight organism interrelationships that can be deduced from the available genomes, sorting together genomes into new proposed clades typically consistent with relationships deduced from DNA sequence analysis. In contrast, if for a high-quality spectrum from a fresh colony, no group of related organisms receives high scores, one might infer that no closely related genome has yet been deposited into the database.
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Affiliation(s)
- James Kostas
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Kenneth C Parker
- Virgin Instruments, 261 Cedar Hill Street, Suite 100, Marlborough, Massachusetts 01752, United States
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17
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Velichko NV, Pinevich AV. Classification and Identification Tasks in Microbiology: Mass Spectrometric Methods Coming to the Aid. Microbiology (Reading) 2019. [DOI: 10.1134/s0026261719050151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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18
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Pečur Kazazić S, Topić Popović N, Strunjak-Perović I, Florio D, Fioravanti M, Babić S, Čož-Rakovac R. Fish photobacteriosis-The importance of rapid and accurate identification of Photobacterium damselae subsp. piscicida. JOURNAL OF FISH DISEASES 2019; 42:1201-1209. [PMID: 31192462 DOI: 10.1111/jfd.13022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 04/24/2019] [Accepted: 04/25/2019] [Indexed: 06/09/2023]
Abstract
MALDI-TOF MS was tested for the identification of Photobacterium damselae subsp. piscicida on isolates grown on two media, cultured at three incubation times and applied on the target plate by the direct sample spotting (DS), by the on-target extraction (OTE) and by the full extraction (FE) method, in triplicates. The identification of samples grown on blood agar (BA) outperformed identification on tryptic soya agar (TSA) by 0.64% for DS and OTE. The OTE gave the highest scores in both culture media, all incubation times and replicates. Reliable 24-hr species identification was 61.54%, 84.61% and 53.85% for samples grown on TSA and identified by DS, OTE and FE, respectively. For isolates grown on BA, they were 76.92%, 96.15% and 30.77%, respectively. When identified by OTE, the 48-hr identification was 93.58%, but for 72 hr declined to 71.79%. The reliable identification with the highest score from the first measurement was 100% only for OTE from BA (24 hr), whereas OTE from TSA gave 84.61% (24 hr), 76.92% (48 hr) and 84.61% (72 hr). The reliable MALDI-TOF MS identification of Ph. damselae subsp. piscicida is incubation time, media, target plate preparation and replicate-dependent.
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Affiliation(s)
- Snježana Pečur Kazazić
- Laboratory for Mass Spectrometry and Functional Proteomics, Rudjer Bošković Institute, Zagreb, Croatia
| | - Natalija Topić Popović
- Laboratory for Aquaculture Biotechnology, Rudjer Bošković Institute, Zagreb, Croatia
- Centre of Excellence for Marine Bioprospecting-BioProCro, Rudjer Bošković Institute, Zagreb, Croatia
| | - Ivančica Strunjak-Perović
- Laboratory for Aquaculture Biotechnology, Rudjer Bošković Institute, Zagreb, Croatia
- Centre of Excellence for Marine Bioprospecting-BioProCro, Rudjer Bošković Institute, Zagreb, Croatia
| | - Daniela Florio
- Department of Veterinary Medical Sciences, Alma Mater Studiorum Università di Bologna, Ozzano Emilia, Italy
| | - Maria Fioravanti
- Department of Veterinary Medical Sciences, Alma Mater Studiorum Università di Bologna, Ozzano Emilia, Italy
| | - Sanja Babić
- Laboratory for Aquaculture Biotechnology, Rudjer Bošković Institute, Zagreb, Croatia
- Centre of Excellence for Marine Bioprospecting-BioProCro, Rudjer Bošković Institute, Zagreb, Croatia
| | - Rozelindra Čož-Rakovac
- Laboratory for Aquaculture Biotechnology, Rudjer Bošković Institute, Zagreb, Croatia
- Centre of Excellence for Marine Bioprospecting-BioProCro, Rudjer Bošković Institute, Zagreb, Croatia
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Jung-Schroers V, Jung A, Ryll M, Bauer J, Teitge F, Steinhagen D. Diagnostic methods for identifying different Aeromonas species and examining their pathogenicity factors, their correlation to cytotoxicity and adherence to fish mucus. JOURNAL OF FISH DISEASES 2019; 42:189-219. [PMID: 30521094 DOI: 10.1111/jfd.12917] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/28/2018] [Accepted: 09/28/2018] [Indexed: 06/09/2023]
Abstract
Aeromonas spp. are ubiquitous in the aquatic environment, acting as facultative or obligate pathogens for fish. Identifying Aeromonas spp. is important for pathogenesis and prognosis in diagnostic cases but can be difficult because of their close relationship. Forty-four already characterized isolates of Aeromonas spp. were analysed by 16S rRNA gene sequencing, by gyrase B sequencing, by analysing their fatty acid profiles, by biochemical reactions and by MALDI-TOF MS. To determine their pathogenicity, cytotoxicity, adhesion to mucus and the expression of 12 virulence factors were tested. The susceptibility of the isolates towards 13 different antibiotics was determined. MALDI-TOF MS was found to be an acceptable identification method for Aeromonas spp. Although the method does not detect all species correctly, it is time-effective and entails relatively low costs and no other methods achieved better results. A high prevalence of virulence-related gene fragments was detected in almost all examined Aeromonas spp., especially in A. hydrophila and A. salmonicida, and most isolates exhibited a cytotoxic effect. Single isolates of A. hydrophila and A. salmonicida showed multiple resistance to antibiotics. These results might indicate the potentially pathogenic capacity of Aeromonas spp., suggesting a risk for aquatic animals and even humans, given their ubiquitous nature.
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Affiliation(s)
- Verena Jung-Schroers
- Fish Disease Research Unit, University of Veterinary Medicine, Hannover, Germany
| | - Arne Jung
- Clinic for Poultry, University of Veterinary Medicine, Hannover, Germany
| | - Martin Ryll
- Clinic for Poultry, University of Veterinary Medicine, Hannover, Germany
| | - Julia Bauer
- Fish Disease Research Unit, University of Veterinary Medicine, Hannover, Germany
| | - Felix Teitge
- Fish Disease Research Unit, University of Veterinary Medicine, Hannover, Germany
| | - Dieter Steinhagen
- Fish Disease Research Unit, University of Veterinary Medicine, Hannover, Germany
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20
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Elbehiry A, Marzouk E, Abdeen E, Al-Dubaib M, Alsayeqh A, Ibrahem M, Hamada M, Alenzi A, Moussa I, Hemeg HA. Proteomic characterization and discrimination of Aeromonas species recovered from meat and water samples with a spotlight on the antimicrobial resistance of Aeromonas hydrophila. Microbiologyopen 2019; 8:e782. [PMID: 30614207 PMCID: PMC6854848 DOI: 10.1002/mbo3.782] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 11/17/2018] [Accepted: 11/20/2018] [Indexed: 02/06/2023] Open
Abstract
Aeromonas is recognized as a human pathogen following ingestion of contaminated food and water. One major problem in Aeromonas identification is that certain species are phenotypically very similar. The antimicrobial resistance is another significant challenge worldwide. We therefore aimed to use mass spectrometry technology for identification and discrimination of Aeromonas species and to screen the antimicrobial resistance of Aeromonas hydrophila (A. hydrophila). A total of 150 chicken meat and water samples were cultured, and then, the isolates were identified biochemically by the Vitek® 2 Compact system. Proteomic identification was performed by MALDI‐TOF MS and confirmed by a microchannel fluidics electrophoresis assay. Principal component analysis (PCA) and single‐peak analysis created by MALDI were also used to discriminate the Aeromonas species. The antimicrobial resistance of the A. hydrophila isolates was determined by Vitek® 2 AST cards. In total, 43 samples were positive for Aeromonas and comprised 22 A. hydrophila, 12 Aeromonas caviae (A. caviae), and 9 Aeromonas sobria (A. sobria) isolates. Thirty‐nine out of 43 (90.69%) Aeromonas isolates were identified by the Vitek® 2 Compact system, whereas 100% of the Aeromonas isolates were correctly identified by MALDI‐TOF MS with a score value ≥2.00. PCA successfully separated A. hydrophila, A. caviae and A. sobria isolates into two groups. Single‐peak analysis revealed four discriminating peaks that separated A. hydrophila from A. caviae and A. sobria isolates. The resistance of A. hydrophila to antibiotics was 95.46% for ampicillin, 50% for cefotaxime, 45.45% for norfloxacin and pefloxacin, 36.36% for ceftazidime and ciprofloxacin, 31.81% for ofloxacin and 27.27% for nalidixic acid and tobramycin. In conclusion, chicken meat and water were tainted with Aeromonas spp., with a high occurrence of A. hydrophila. MALDI‐TOF MS is a powerful technique for characterizing aeromonads at the genus and species levels. Future studies should investigate the resistance of A. hydrophila to various antimicrobial agents.
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Affiliation(s)
- Ayman Elbehiry
- Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, University of Sadat City, Sadat City, Egypt.,Department of Public Health, College of Public Health and Health Informatics, Qassim University, Buraidah, Saudi Arabia
| | - Eman Marzouk
- Department of Medical laboratories, College of Applied Medical Science, Qassim University, Buraidah, Saudi Arabia
| | - Eman Abdeen
- Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, University of Sadat City, Sadat City, Egypt
| | - Musaad Al-Dubaib
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, Buraidah, Saudi Arabia
| | - Abdullah Alsayeqh
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, Buraidah, Saudi Arabia
| | - Mai Ibrahem
- Department of Public Health, College of Applied Medical Science, King Khalid University, Abha, Saudi Arabia.,Department of Fish Diseases and Management, Faculty of Veterinary Medicine, Cairo University, Cairo, Egypt
| | - Mohamed Hamada
- Department of Food Hygiene & Control, Faculty of Veterinary Medicine, University of Sadat City, Sadat City, Egypt
| | - Afrah Alenzi
- Department of Medical laboratories, College of Applied Medical Science, Qassim University, Buraidah, Saudi Arabia
| | - Ihab Moussa
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia.,Department of Microbiology, Faculty of Veterinary Medicine, Cairo University, Cairo, Egypt
| | - Hassan A Hemeg
- Department of Medical Technology/Microbiology, College of Applied Medical Sciences, Taibah University, Madinah, Saudi Arabia
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21
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Pérez-Sancho M, Cerdá I, Fernández-Bravo A, Domínguez L, Figueras MJ, Fernández-Garayzábal JF, Vela AI. Limited performance of MALDI-TOF for identification of fish Aeromonas isolates at species level. JOURNAL OF FISH DISEASES 2018; 41:1485-1493. [PMID: 30105821 DOI: 10.1111/jfd.12837] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 05/11/2018] [Accepted: 05/11/2018] [Indexed: 06/08/2023]
Abstract
The aim of this study was to evaluate the usefulness of the MALDI-TOF MS to identify 151 isolates of Aeromonas obtained mostly from diseased fish. MALDI-TOF MS correctly identified all isolates to the genus level but important differences in the percentage of isolates correctly identified depending on the species were observed. Considering exclusively the first identification option, Aeromonas bestiarum, Aeromonas hydrophila, Aeromonas salmonicida, Aeromonas veronii and Aeromonas sobria were the best identified with results >95%. However, considering the first and second identification options, the only species that showed values >90% was A. hydrophila. Overall, when the database was supplemented with 14 new spectra, the number of accurate identifications increased (41% vs. 55%) and the number of inconclusive identifications decreased (45% vs. 29%), but great differences in the success of species-level identifications were found. Species-distinctive mass peaks were identified only for A. hydrophila and A. bestiarum (5003 and 7360 m/z in 95.5% and 94.1% of their isolates, respectively). This work demonstrates the utility of MALDI-TOF MS for Aeromonas identification to the genus level, but there is no consistency for the accurate identification of some of the most prevalent species implicated in fish disease.
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Affiliation(s)
- M Pérez-Sancho
- VISAVET Health Surveillance Centre, Universidad Complutense Madrid, Madrid, Spain
| | - I Cerdá
- VISAVET Health Surveillance Centre, Universidad Complutense Madrid, Madrid, Spain
| | - A Fernández-Bravo
- Facultad de Medicina y Ciencias de la Salud, Unidad de Microbiología, IVSPV, Universitat Rovira i Virgili, Reus, Spain
| | - L Domínguez
- VISAVET Health Surveillance Centre, Universidad Complutense Madrid, Madrid, Spain
- Faculty of Veterinary Medicine, Animal Health Department, Universidad Complutense Madrid, Madrid, Spain
| | - M J Figueras
- Facultad de Medicina y Ciencias de la Salud, Unidad de Microbiología, IVSPV, Universitat Rovira i Virgili, Reus, Spain
| | - J F Fernández-Garayzábal
- VISAVET Health Surveillance Centre, Universidad Complutense Madrid, Madrid, Spain
- Faculty of Veterinary Medicine, Animal Health Department, Universidad Complutense Madrid, Madrid, Spain
| | - A I Vela
- VISAVET Health Surveillance Centre, Universidad Complutense Madrid, Madrid, Spain
- Faculty of Veterinary Medicine, Animal Health Department, Universidad Complutense Madrid, Madrid, Spain
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Bronzato GF, Oliva MS, Alvin MG, Pribul BR, Rodrigues DP, Coelho SM, Coelho IS, Souza MM. MALDI-TOF MS as a tool for the identification of Vibrio alginolyticus from Perna perna mussels (Linnaeus, 1758). PESQUISA VETERINARIA BRASILEIRA 2018. [DOI: 10.1590/1678-5150-pvb-5233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
ABSTRACT: Vibrio species are ubiquitous in aquatic environments, including coastal and marine habitats. Vibrio alginolyticus is an opportunistic pathogen for fish, crustaceans and mussels and their identification by biochemical tests may be impaired due their nutritional requirements. The study used Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) to identify 49 Vibrio spp. isolates associated with mussels (Perna perna) from different locations along the Rio de Janeiro coast. The rpoA gene was used as a genus-specific marker of Vibrio spp. and was positive in all 209 isolates. MALDI-TOF MS confirmed 87.8% of V. alginolyticus when compared to the results of the biochemical tests. Four isolates were identified as Shewanella putrefaciens (8.16%) and one was identified as V. parahaemolyticus (2.0%). Just one isolate was not identified by this technique (2.0%). The pyrH sequencing confirmed 75% of the proteomic technique results. MALDI-TOF MS is an excellent option for characterization of bacterial species, as it is efficient, fast and easy to apply. In addition, our study confirms its high specificity and sensitivity in these marine bacteria identification.
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Fernández-Álvarez C, Torres-Corral Y, Santos Y. Use of ribosomal proteins as biomarkers for identification of Flavobacterium psychrophilum by MALDI-TOF mass spectrometry. J Proteomics 2018; 170:59-69. [DOI: 10.1016/j.jprot.2017.09.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 09/08/2017] [Accepted: 09/14/2017] [Indexed: 10/18/2022]
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24
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Fernández-Álvarez C, Torres-Corral Y, Saltos-Rosero N, Santos Y. MALDI-TOF mass spectrometry for rapid differentiation of Tenacibaculum species pathogenic for fish. Appl Microbiol Biotechnol 2017; 101:5377-5390. [DOI: 10.1007/s00253-017-8324-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 03/29/2017] [Accepted: 04/29/2017] [Indexed: 11/24/2022]
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Characterization of genetic determinants involved in antibiotic resistance in Aeromonas spp. and fecal coliforms isolated from different aquatic environments. Res Microbiol 2017; 168:461-471. [PMID: 28263906 DOI: 10.1016/j.resmic.2017.02.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 02/07/2017] [Accepted: 02/15/2017] [Indexed: 12/14/2022]
Abstract
Aeromonas spp. and fecal coliforms, two abundant and cultivable bacterial populations that can be found in water ecosystems, might substantially contribute to the spread of antibiotic resistance. We investigated the presence and spread of transposons (elements that can move from one location to another in the genome), integrons (structures able to capture and incorporate gene cassettes) and resistance plasmids in strains isolated from polluted and unpolluted water. We recovered 231 Aeromonas and 250 fecal coliforms from water samplings with different degrees of pollution (hospital sewage, activated sludge of a wastewater treatment plant, river water before and after treatment and water from an alpine lake). Sixteen Aeromonas spp. and 22 fecal coliforms carried intI, coding for the site-specific integrase of class 1 integrons, while 22 Aeromonas spp. and 14 fecal coliforms carried tnpA, the transposase gene of the Tn3-family of replicative transposons. The majority of intI and tnpA-positive strains were phenotypically resistant to at least four antibiotics. Integrons and transposons were mainly located on mobilizable plasmids. Our results did not detect common mobile structures in the two populations and therefore relativize the role played by Aeromonas spp. as vectors of antimicrobial resistance determinants between water and commensal gut bacteria.
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26
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Popović NT, Kazazić SP, Strunjak-Perović I, Čož-Rakovac R. Differentiation of environmental aquatic bacterial isolates by MALDI-TOF MS. ENVIRONMENTAL RESEARCH 2017; 152:7-16. [PMID: 27741451 DOI: 10.1016/j.envres.2016.09.020] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 09/20/2016] [Accepted: 09/24/2016] [Indexed: 05/20/2023]
Abstract
Identification of bacteria in aquatic and environmental applications, for monitoring purposes and research, for health assessments and therapy considerations of farmed and free-living aquatic organisms, still relies on conventional phenotypic and biochemical protocols. Although molecular techniques based on DNA amplification and sequencing are finding ways into diagnostic laboratories, they are time-consuming, costly and difficult in the case of multiplex assays. Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) is a rapid and accurate proteomic method reliable for identification of unknown bacteria to the genus and species level. Upon extension of databases, it will certainly find its position in environmental sciences. The paper presents an overview of the principle of the method, its effectiveness in comparison with conventional and molecular identification procedures, and applicability on environmental and aquatic isolates, discussing its advantages and shortcomings, as well as possible future implementations.
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Affiliation(s)
- Natalija Topić Popović
- Laboratory for Aquaculture Biotechnology, Division of Materials Chemistry, Rudjer Bošković Institute, Bijenička cesta 54, 10002 Zagreb, Croatia
| | - Snježana P Kazazić
- Laboratory for Mass Spectrometry, Division of Physical Chemistry, Rudjer Bošković Institute, Bijenička cesta 54, 10002 Zagreb, Croatia.
| | - Ivančica Strunjak-Perović
- Laboratory for Aquaculture Biotechnology, Division of Materials Chemistry, Rudjer Bošković Institute, Bijenička cesta 54, 10002 Zagreb, Croatia
| | - Rozelindra Čož-Rakovac
- Laboratory for Aquaculture Biotechnology, Division of Materials Chemistry, Rudjer Bošković Institute, Bijenička cesta 54, 10002 Zagreb, Croatia
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27
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Rahi P, Prakash O, Shouche YS. Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass-Spectrometry (MALDI-TOF MS) Based Microbial Identifications: Challenges and Scopes for Microbial Ecologists. Front Microbiol 2016; 7:1359. [PMID: 27625644 PMCID: PMC5003876 DOI: 10.3389/fmicb.2016.01359] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 08/17/2016] [Indexed: 12/29/2022] Open
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass-spectrometry (MALDI-TOF MS) based biotyping is an emerging technique for high-throughput and rapid microbial identification. Due to its relatively higher accuracy, comprehensive database of clinically important microorganisms and low-cost compared to other microbial identification methods, MALDI-TOF MS has started replacing existing practices prevalent in clinical diagnosis. However, applicability of MALDI-TOF MS in the area of microbial ecology research is still limited mainly due to the lack of data on non-clinical microorganisms. Intense research activities on cultivation of microbial diversity by conventional as well as by innovative and high-throughput methods has substantially increased the number of microbial species known today. This important area of research is in urgent need of rapid and reliable method(s) for characterization and de-replication of microorganisms from various ecosystems. MALDI-TOF MS based characterization, in our opinion, appears to be the most suitable technique for such studies. Reliability of MALDI-TOF MS based identification method depends mainly on accuracy and width of reference databases, which need continuous expansion and improvement. In this review, we propose a common strategy to generate MALDI-TOF MS spectral database and advocated its sharing, and also discuss the role of MALDI-TOF MS based high-throughput microbial identification in microbial ecology studies.
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Affiliation(s)
- Praveen Rahi
- Microbial Culture Collection, National Centre for Cell Science Pune, India
| | - Om Prakash
- Microbial Culture Collection, National Centre for Cell Science Pune, India
| | - Yogesh S Shouche
- Microbial Culture Collection, National Centre for Cell Science Pune, India
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Menanteau-Ledouble S, Kumar G, Saleh M, El-Matbouli M. Aeromonas salmonicida: updates on an old acquaintance. DISEASES OF AQUATIC ORGANISMS 2016; 120:49-68. [PMID: 27304870 DOI: 10.3354/dao03006] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Aeromonas salmonicida is the oldest known infectious agent to be linked to fish disease and constitutes a major bacterial pathogen of fish, in particular of salmonids. This bacterium can be found almost worldwide in both marine and freshwater environments and has been divided into several sub-species. In this review, we present the most recent developments concerning our understanding of this pathogen, including how the characterization of new isolates from non-salmonid hosts suggests a more nuanced picture of the importance of the so‑called 'atypical isolates'. We also describe the clinical presentation regarding the infection across several fish species and discuss what is known about the virulence of A. salmonicida and, in particular, the role that the type 3 secretion system might play in suppressing the immune response of its hosts. Finally, isolates have displayed varied levels of antibiotic resistance. Hence, we review a number of solutions that have been developed both to prevent outbreaks and to treat them once they occur, including the application of pre- and probiotic supplements.
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Affiliation(s)
- Simon Menanteau-Ledouble
- Clinical Division of Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
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29
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Ruiz-Castillo A, Lepe-Jiménez JA, Torres-Sánchez MJ, Artacho-Reinoso MJ, Aznar-Martín J. Influencia de la correcta identificación en la interpretación de las pruebas de sensibilidad en aislados de Aeromonas spp. productoras de bacteriemia. Enferm Infecc Microbiol Clin 2016; 34:96-100. [DOI: 10.1016/j.eimc.2015.02.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 02/26/2015] [Accepted: 02/27/2015] [Indexed: 10/23/2022]
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30
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Sala-Comorera L, Vilaró C, Galofré B, Blanch AR, García-Aljaro C. Use of matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry for bacterial monitoring in routine analysis at a drinking water treatment plant. Int J Hyg Environ Health 2016; 219:577-584. [PMID: 26809219 DOI: 10.1016/j.ijheh.2016.01.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Revised: 01/08/2016] [Accepted: 01/11/2016] [Indexed: 11/28/2022]
Abstract
The study of bacterial communities throughout a drinking water treatment plant could provide a basic understanding of the effects of water processing that could then be used to improve the management of such plants. However, it is necessary to develop new analytical techniques that are sufficiently efficient, robust and fast for their effective and useful application in routine analysis. The aim of this study is therefore to assess the performance of matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), as compared to the PhenePlate™ system, for routine analysis in a drinking water treatment plant. To this end we studied a total of 277 colonies isolated in different seasons and from different points throughout the water treatment process, including: raw water, sand filtration, ultrafiltration, reverse osmosis and chlorination. The colonies were analysed using MALDI-TOF MS by direct deposition of the cells on the plate. The colonies were also biochemically fingerprinted using the PhenePlate™ system, clustered according to their similarity and a representative strain was selected for 16S rRNA gene sequencing and API® gallery-based identification. The use of MALDI-TOF MS was reliable compared to the PhenePlate™ system and has the advantage of being faster and relatively cheap. Bacteria typing by MALDI-TOF MS is therefore a promising method to replace conventional routine phenotypic methods for the identification of bacteria in drinking water laboratories, thanks to its robustness. The major limiting factor for MALDI-TOF MS is the lack of a suitable mass spectra database; although each laboratory can develop its own library. This methodology will provide a tracking tool for companies to use in risk management and the detection of possible failures in both the water treatment processes and the distribution network, as well as offering characterization of the intrinsic microbial populations.
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Affiliation(s)
- Laura Sala-Comorera
- Department of Microbiology, Faculty of Biology, University of Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain
| | - Carles Vilaró
- Aigües de Barcelona, EMGCIA, C/General Batet 1-7, 08028 Barcelona, Spain
| | - Belén Galofré
- Aigües de Barcelona, EMGCIA, C/General Batet 1-7, 08028 Barcelona, Spain
| | - Anicet R Blanch
- Department of Microbiology, Faculty of Biology, University of Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain
| | - Cristina García-Aljaro
- Department of Microbiology, Faculty of Biology, University of Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain.
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31
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Yu WS, Lee KM, Hwang KJ. Taxonomic Identification of BacillusSpecies Using Matrix-Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry. ANNALS OF CLINICAL MICROBIOLOGY 2016. [DOI: 10.5145/acm.2016.19.4.110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Won Seon Yu
- Pathogen Resource TF, Center for Infectious Diseases, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, Cheongju, Korea
| | - Kyeong Min Lee
- Pathogen Resource TF, Center for Infectious Diseases, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, Cheongju, Korea
| | - Kyu Jam Hwang
- Pathogen Resource TF, Center for Infectious Diseases, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, Cheongju, Korea
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32
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Ojima-Kato T, Yamamoto N, Iijima Y, Tamura H. Assessing the performance of novel software Strain Solution on automated discrimination of Escherichia coli serotypes and their mixtures using matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Microbiol Methods 2015; 119:233-8. [DOI: 10.1016/j.mimet.2015.11.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 11/05/2015] [Accepted: 11/07/2015] [Indexed: 11/26/2022]
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33
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Topic Popovic N, Kazazic SP, Strunjak-Perovic I, Barisic J, Sauerborn Klobucar R, Kepec S, Coz-Rakovac R. Detection and diversity of aeromonads from treated wastewater and fish inhabiting effluent and downstream waters. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2015; 120:235-242. [PMID: 26092555 DOI: 10.1016/j.ecoenv.2015.06.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 05/27/2015] [Accepted: 06/08/2015] [Indexed: 06/04/2023]
Abstract
A two-season investigation of the wastewater treatment plant (WWTP) effluent, of related waters, sludge and fish across a wide area and 11 stations, with emphasis on Aeromonas spp. was conducted. Aeromonas veronii was the prevailing aeromonad isolated by MALDI TOF MS in the summer period. A rise of Aeromonas hydrophila was observed in summer in raw sewage, treated wastewater and effluent-carrying canal. The ratio of aeromonad species retrieved from fish tissues did not correspond with the water and sludge findings, as in spring in the effluent-carrying canal fish carried Aeromonas salmonicida ssp. salmonicida and Aeromonas bestiarum, while in summer mainly A. veronii and Acinetobacter johnsonii were isolated from fish tissues in the same location. No correlation was established between fecal coliforms/enterococci and aeromonad occurrence. All retrieved Aeromonas species demonstrated a distinct spectral pattern, with peaks showing unique mass distribution ranging from 4000 to 10,000Da. Hierarchical clustering separated aeromonads of all isolated species and clustered closely related strains together. Resistance was determined towards amoxicillin, and frequently towards sulfamethoxazole and erythromycin. In summer, a high proportion of water and sludge Aeromonas species demonstrated multiple resistance patterns towards five or more antimicrobials. The quinolone resistance of water aeromonads was mostly related to A. veronii. There are potential health concerns regarding aeromonad exposure amongst recreational fishermen who come into contact with fish inhabiting waters downstream from the WWTP, and WWTP workers who are occupationally exposed to wastewaters and their aerosols.
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Affiliation(s)
- Natalija Topic Popovic
- Laboratory for Ichthyopathology-Biological Materials, Rudjer Boskovic Institute, Zagreb, Croatia.
| | - Snjezana P Kazazic
- Laboratory for Chemical Kinetics and Atmospheric Chemistry, Rudjer Boskovic Institute, Zagreb, Croatia
| | | | - Josip Barisic
- Laboratory for Ichthyopathology-Biological Materials, Rudjer Boskovic Institute, Zagreb, Croatia
| | | | - Slavko Kepec
- Virkom d.o.o., Public Water Supply and Wastewater Services, Virovitica, Croatia
| | - Rozelinda Coz-Rakovac
- Laboratory for Ichthyopathology-Biological Materials, Rudjer Boskovic Institute, Zagreb, Croatia
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Practical Guidance for Clinical Microbiology Laboratories: Diagnosis of Bacterial Gastroenteritis. Clin Microbiol Rev 2015; 28:3-31. [PMID: 25567220 DOI: 10.1128/cmr.00073-14] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Bacterial gastroenteritis is a disease that is pervasive in both the developing and developed worlds. While for the most part bacterial gastroenteritis is self-limiting, identification of an etiological agent by bacterial stool culture is required for the management of patients with severe or prolonged diarrhea, symptoms consistent with invasive disease, or a history that may predict a complicated course of disease. Importantly, characterization of bacterial enteropathogens from stool cultures in clinical laboratories is one of the primary means by which public health officials identify and track outbreaks of bacterial gastroenteritis. This article provides guidance for clinical microbiology laboratories that perform stool cultures. The general characteristics, epidemiology, and clinical manifestations of key bacterial enteropathogens are summarized. Information regarding optimal specimen collection, transport, and processing and current diagnostic tests and testing algorithms is provided. This article is an update of Cumitech 12A (P. H. Gilligan, J. M. Janda, M. A. Karmali, and J. M. Miller, Cumitech 12A, Laboratory diagnosis of bacterial diarrhea, 1992).
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35
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Kudirkiene E, Welker M, Knudsen NR, Bojesen AM. Rapid and accurate identification of Streptococcus equi subspecies by MALDI-TOF MS. Syst Appl Microbiol 2015; 38:315-22. [PMID: 25944783 DOI: 10.1016/j.syapm.2015.02.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 02/26/2015] [Accepted: 02/27/2015] [Indexed: 11/16/2022]
Abstract
Streptococcus equi includes very important animal and human pathogens. S. equi subsp. equi (SEE) is a highly pathogenic equine specific subspecies, while S. equi subsp. zooepidemicus (SEZ) and S. equi subsp. ruminatorum are opportunistic pathogens of various animal species and humans. Due to great phenotypic and sequence similarity between three subspecies their discrimination remains difficult. In this study, we aimed to design and validate a novel, Superspectra based, MALDI-TOF MS approach for reliable, rapid and cost-effective identification of SEE and SEZ, the most frequent S. equi subspecies in horses. Superspectra created in this study enabled correct identification of 86 strains belonging to different subspecies of S. equi, isolated from various hosts, infection sites and years. In general, higher average identification accuracy was achieved for SEE (99.0±3.0%) than for SEZ (93.3±7.5%). This result may be attributed to the highly clonal population structure of SEE, as opposed to the diversity of SEZ seen in horses. Importantly strains with atypical colony appearance both within SEE and SEZ did not affect correct identification of the strains by MALDI-TOF MS. Atypical colony variants are often associated with a higher persistence or virulence of S. equi, thus their correct identification using the current method strengthens its potential use in routine clinical diagnostics. In conclusion, reliable identification of S. equi subspecies was achieved by combining a MALDI-TOF MS method with spectra analyses using the SARAMIS database. Additionally, first results on subtyping of SEZ indicated that a more refined discrimination, for example for epidemiological surveys, may be possible.
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Affiliation(s)
- Egle Kudirkiene
- Department of Veterinary Disease Biology, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg C, Denmark
| | - Martin Welker
- BioMérieux SA, Unit Microbiology, R&D Microbiology, La Balme Les Grottes 38390, France
| | - Nanna R Knudsen
- Department of Veterinary Disease Biology, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg C, Denmark
| | - Anders M Bojesen
- Department of Veterinary Disease Biology, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg C, Denmark.
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Shin HB, Yoon J, Lee Y, Kim MS, Lee K. Comparison of MALDI-TOF MS, housekeeping gene sequencing, and 16S rRNA gene sequencing for identification of Aeromonas clinical isolates. Yonsei Med J 2015; 56:550-5. [PMID: 25684008 PMCID: PMC4329371 DOI: 10.3349/ymj.2015.56.2.550] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
PURPOSE The genus Aeromonas is a pathogen that is well known to cause severe clinical illnesses, ranging from gastroenteritis to sepsis. Accurate identification of A. hydrophila, A. caviae, and A. veronii is important for the care of patients. However, species identification remains difficult using conventional methods. The aim of this study was to compare the accuracy of different methods of identifying Aeromonas at the species level: a biochemical method, matrix-assisted laser desorption ionization mass spectrometry-time of flight (MALDI-TOF MS), 16S rRNA sequencing, and housekeeping gene sequencing (gyrB, rpoB). MATERIALS AND METHODS We analyzed 65 Aeromonas isolates recovered from patients at a university hospital in Korea between 1996 and 2012. The isolates were recovered from frozen states and tested using the following four methods: a conventional biochemical method, 16S rRNA sequencing, housekeeping gene sequencing with phylogenetic analysis, and MALDI-TOF MS. RESULTS The conventional biochemical method and 16S rRNA sequencing identified Aeromonas at the genus level very accurately, although species level identification was unsatisfactory. MALDI-TOF MS system correctly identified 60 (92.3%) isolates at the species level and an additional four (6.2%) at the genus level. Overall, housekeeping gene sequencing with phylogenetic analysis was found to be the most accurate in identifying Aeromonas at the species level. CONCLUSION The most accurate method of identification of Aeromonas to species level is by housekeeping gene sequencing, although high cost and technical difficulty hinder its usage in clinical settings. An easy-to-use identification method is needed for clinical laboratories, for which MALDI-TOF MS could be a strong candidate.
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Affiliation(s)
- Hee Bong Shin
- Department of Laboratory Medicine and Genetics, Soonchunhyang University College of Medicine, Cheonan, Korea
| | - Jihoon Yoon
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - Yangsoon Lee
- Department of Laboratory Medicine, Hanyang University College of Medicine, Hanyang University Seoul Hospital, Seoul, Korea
| | - Myung Sook Kim
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - Kyungwon Lee
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea.
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Zhang L, Vranckx K, Janssens K, Sandrin TR. Use of MALDI-TOF mass spectrometry and a custom database to characterize bacteria indigenous to a unique cave environment (Kartchner Caverns, AZ, USA). J Vis Exp 2015:e52064. [PMID: 25590854 DOI: 10.3791/52064] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
MALDI-TOF mass spectrometry has been shown to be a rapid and reliable tool for identification of bacteria at the genus and species, and in some cases, strain levels. Commercially available and open source software tools have been developed to facilitate identification; however, no universal/standardized data analysis pipeline has been described in the literature. Here, we provide a comprehensive and detailed demonstration of bacterial identification procedures using a MALDI-TOF mass spectrometer. Mass spectra were collected from 15 diverse bacteria isolated from Kartchner Caverns, AZ, USA, and identified by 16S rDNA sequencing. Databases were constructed in BioNumerics 7.1. Follow-up analyses of mass spectra were performed, including cluster analyses, peak matching, and statistical analyses. Identification was performed using blind-coded samples randomly selected from these 15 bacteria. Two identification methods are presented: similarity coefficient-based and biomarker-based methods. Results show that both identification methods can identify the bacteria to the species level.
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Affiliation(s)
- Lin Zhang
- School of Mathematical and Natural Sciences, Arizona State University
| | | | | | - Todd R Sandrin
- School of Mathematical and Natural Sciences, Arizona State University;
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Lobatón T, Hoffman I, Vermeire S, Ferrante M, Verhaegen J, Van Assche G. Aeromonas species: an opportunistic enteropathogen in patients with inflammatory bowel diseases? A single center cohort study. Inflamm Bowel Dis 2015; 21:71-8. [PMID: 25517595 DOI: 10.1097/mib.0000000000000247] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
BACKGROUND The role of Aeromonas species as an enteropathogen in patients with and without inflammatory bowel disease (IBD) is still debated. The aim was to explore the significance of positive Aeromonas stool cultures in IBD and patients without IBD. METHODS Observational retrospective study including all patients with a stool culture positive for Aeromonas between January 2011 and October 2013 at the Leuven University Hospitals. Demographics, clinical, and endoscopic outcomes and laboratory results were analyzed. RESULTS A total of 77 patients (11 IBD) were identified. In 37 cases, Aeromonas caused a mild self-limited gastrointestinal infection. Among the 40 patients needing antibiotics, 22 presented a mild-to-moderate gastrointestinal infection; 4 suffered from extraintestinal complications; and 4 were coinfected by Campylobacter spp. A. veronii caused more frequently severe infection than the other species (25% versus 5%; P = 0.046). In 2 patients with ulcerative colitis, Aeromonas triggered a moderate-to-severe flare and 2 cases appeared in the context of de novo Crohn's disease. In contrast, in 1 patient with ulcerative colitis and 2 patients with Crohn's disease, Aeromonas caused a mild gastrointestinal infection not worsening the disease activity and in 4 patients with Crohn's disease, it presented in the context of active disease with no clear pathogenic role. Patients with IBD were treated more often with antibiotics (82 versus 41%, P = 0.012) and had more complications (46 versus 14%, P = 0.024). CONCLUSIONS Aeromonas caused mostly mild infections but also moderate and severe infections. A. veronii was more prevalent in patients with IBD and was associated with worse clinical outcomes. Aeromonas caused milder infections in patients without IBD. Other risk factors for severe infection were not found.
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Affiliation(s)
- Triana Lobatón
- Departments of *Gastroenterology; †Pediatrics; and ‡Microbiology, University Hospital Leuven, Leuven, Belgium
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39
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Vávrová A, Balážová T, Sedláček I, Tvrzová L, Šedo O. Evaluation of the MALDI-TOF MS profiling for identification of newly described Aeromonas spp. Folia Microbiol (Praha) 2014; 60:375-83. [DOI: 10.1007/s12223-014-0369-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 12/02/2014] [Indexed: 11/29/2022]
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40
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Ojima-Kato T, Yamamoto N, Suzuki M, Fukunaga T, Tamura H. Discrimination of Escherichia coli O157, O26 and O111 from other serovars by MALDI-TOF MS based on the S10-GERMS method. PLoS One 2014; 9:e113458. [PMID: 25411793 PMCID: PMC4239071 DOI: 10.1371/journal.pone.0113458] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Accepted: 10/26/2014] [Indexed: 11/23/2022] Open
Abstract
Enterohemorrhagic Escherichia coli (EHEC), causes a potentially life-threatening infection in humans worldwide. Serovar O157:H7, and to a lesser extent serovars O26 and O111, are the most commonly reported EHEC serovars responsible for a large number of outbreaks. We have established a rapid discrimination method for E. coli serovars O157, O26 and O111 from other E. coli serovars, based on the pattern matching of mass spectrometry (MS) differences and the presence/absence of biomarker proteins detected in matrix-assisted laser desorption/ionization time-of-flight MS (MALDI-TOF MS). Three biomarkers, ribosomal proteins S15 and L25, and acid stress chaperone HdeB, with MS m/z peaks at 10138.6/10166.6, 10676.4/10694.4 and 9066.2, respectively, were identified as effective biomarkers for O157 discrimination. To distinguish serovars O26 and O111 from the others, DNA-binding protein H-NS, with an MS peak at m/z 15409.4/15425.4 was identified. Sequence analysis of the O157 biomarkers revealed that amino acid changes: Q80R in S15, M50I in L25 and one mutation within the start codon ATG to ATA in the encoded HdeB protein, contributed to the specific peak pattern in O157. We demonstrated semi-automated pattern matching using these biomarkers and successfully discriminated total 57 O157 strains, 20 O26 strains and 6 O111 strains with 100% reliability by conventional MALDI-TOF MS analysis, regardless of the sample conditions. Our simple strategy, based on the S10-spc-alpha operon gene-encoded ribosomal protein mass spectrum (S10-GERMS) method, therefore allows for the rapid and reliable detection of this pathogen and may prove to be an invaluable tool both clinically and in the food industry.
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Affiliation(s)
- Teruyo Ojima-Kato
- Hub of Knowledge Aichi, Aichi Science and Technology Foundation, Yakusa, Toyota, Aichi, Japan
- * E-mail: (TO); (HT)
| | - Naomi Yamamoto
- School of Agriculture, Meijo University, Shiogamaguchi, Tenpaku-ku, Nagoya, Aichi, Japan
| | - Mayumi Suzuki
- School of Agriculture, Meijo University, Shiogamaguchi, Tenpaku-ku, Nagoya, Aichi, Japan
| | - Tomohiro Fukunaga
- Japan Food Research Laboratories, Osu, Naka-ku, Nagoya, Aichi, Japan
| | - Hiroto Tamura
- School of Agriculture, Meijo University, Shiogamaguchi, Tenpaku-ku, Nagoya, Aichi, Japan
- * E-mail: (TO); (HT)
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41
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Erler R, Wichels A, Heinemeyer EA, Hauk G, Hippelein M, Reyes NT, Gerdts G. VibrioBase: A MALDI-TOF MS database for fast identification of Vibrio spp. that are potentially pathogenic in humans. Syst Appl Microbiol 2014; 38:16-25. [PMID: 25466918 DOI: 10.1016/j.syapm.2014.10.009] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Revised: 10/20/2014] [Accepted: 10/27/2014] [Indexed: 11/17/2022]
Abstract
Mesophilic marine bacteria of the family Vibrionaceae, specifically V. cholerae, V. parahaemolyticus and V. vulnificus, are considered to cause severe illness in humans. Due to climate-change-driven temperature increases, higher Vibrio abundances and infections are predicted for Northern Europe, which in turn necessitates environmental surveillance programs to evaluate this risk. We propose that whole-cell matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) profiling is a promising tool for the fast and reliable species classification of environmental isolates. Because the reference database does not contain sufficient Vibrio spectra we generated the VibrioBase database in this study. Mass spectrometric data were generated from 997 largely environmental strains and filed in this new database. MALDI-TOF MS clusters were assigned based on the species classification obtained by analysis of partial rpoB (RNA polymerase beta-subunit) sequences. The affiliation of strains to species-specific clusters was consistent in 97% of all cases using both approaches, and the extended VibrioBase generated more specific species identifications with higher matching scores compared to the commercially available database. Therefore, we have made the VibrioBase database freely accessible, which paves the way for detailed risk assessment studies of potentially pathogenic Vibrio spp. from marine environments.
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Affiliation(s)
- René Erler
- Alfred Wegener Institute for Polar and Marine Research, Biologische Anstalt Helgoland, Kurpromenade 201, 27498 Helgoland, Germany.
| | - Antje Wichels
- Alfred Wegener Institute for Polar and Marine Research, Biologische Anstalt Helgoland, Kurpromenade 201, 27498 Helgoland, Germany
| | - Ernst-August Heinemeyer
- Governmental Institute of Public Health of Lower Saxony, Lüchtenburger Weg 24, 26603 Aurich, Germany
| | - Gerhard Hauk
- Regional Office for Health and Social Affairs of Mecklenburg-Western Pomerania, Gertrudenstraße 11, 18057 Rostock, Germany
| | - Martin Hippelein
- University Medical Center Schleswig-Holstein, Central Facility: Medical Investigation Office and Hygiene, Brunswiker Straße 4, 24105 Kiel, Germany
| | - Nadja Torres Reyes
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Telegrafenberg, 14473 Potsdam, Germany
| | - Gunnar Gerdts
- Alfred Wegener Institute for Polar and Marine Research, Biologische Anstalt Helgoland, Kurpromenade 201, 27498 Helgoland, Germany
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42
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Lim YL, Ee R, Yin WF, Chan KG. Quorum sensing activity of Aeromonas caviae strain YL12, a bacterium isolated from compost. SENSORS 2014; 14:7026-40. [PMID: 24759107 PMCID: PMC4029632 DOI: 10.3390/s140407026] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 04/06/2014] [Accepted: 04/10/2014] [Indexed: 11/26/2022]
Abstract
Quorum sensing is a well-studied cell-to-cell communication method that involves a cell-density dependent regulation of genes expression mediated by signalling molecules. In this study, a bacterium isolated from a plant material compost pile was found to possess quorum sensing activity based on bioassay screening. Isolate YL12 was identified using matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry and molecular typing using rpoD gene which identified the isolate as Aeromonas caviae. High resolution tandem mass spectrometry was subsequently employed to identify the N-acyl homoserine lactone profile of Aeromonas caviae YL12 and confirmed that this isolate produced two short chain N-acyl homoserine lactones, namely C4-HSL and C6, and the production was observed to be cell density-dependent. Using the thin layer chromatography (TLC) bioassay, both AHLs were found to activate C. violaceum CV026, whereas only C6-HSL was revealed to induce bioluminescence expression of E. coli [pSB401]. The data presented in this study will be the leading steps in understanding the role of quorum sensing in Aeromonas caviae strain YL12.
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Affiliation(s)
- Yan-Lue Lim
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia.
| | - Robson Ee
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia.
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia.
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia.
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43
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Zhang L, Borror CM, Sandrin TR. A designed experiments approach to optimization of automated data acquisition during characterization of bacteria with MALDI-TOF mass spectrometry. PLoS One 2014; 9:e92720. [PMID: 24662978 PMCID: PMC3963954 DOI: 10.1371/journal.pone.0092720] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 02/24/2014] [Indexed: 01/27/2023] Open
Abstract
MALDI-TOF MS has been shown capable of rapidly and accurately characterizing bacteria. Highly reproducible spectra are required to ensure reliable characterization. Prior work has shown that spectra acquired manually can have higher reproducibility than those acquired automatically. For this reason, the objective of this study was to optimize automated data acquisition to yield spectra with reproducibility comparable to those acquired manually. Fractional factorial design was used to design experiments for robust optimization of settings, in which values of five parameters (peak selection mass range, signal to noise ratio (S:N), base peak intensity, minimum resolution and number of shots summed) commonly used to facilitate automated data acquisition were varied. Pseudomonas aeruginosa was used as a model bacterium in the designed experiments, and spectra were acquired using an intact cell sample preparation method. Optimum automated data acquisition settings (i.e., those settings yielding the highest reproducibility of replicate mass spectra) were obtained based on statistical analysis of spectra of P. aeruginosa. Finally, spectrum quality and reproducibility obtained from non-optimized and optimized automated data acquisition settings were compared for P. aeruginosa, as well as for two other bacteria, Klebsiella pneumoniae and Serratia marcescens. Results indicated that reproducibility increased from 90% to 97% (p-value[Formula: see text]0.002) for P. aeruginosa when more shots were summed and, interestingly, decreased from 95% to 92% (p-value [Formula: see text] 0.013) with increased threshold minimum resolution. With regard to spectrum quality, highly reproducible spectra were more likely to have high spectrum quality as measured by several quality metrics, except for base peak resolution. Interaction plots suggest that, in cases of low threshold minimum resolution, high reproducibility can be achieved with fewer shots. Optimization yielded more reproducible spectra than non-optimized settings for all three bacteria.
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Affiliation(s)
- Lin Zhang
- School of Mathematical and Natural Sciences, Arizona State University, Phoenix, Arizona, United States of America
| | - Connie M. Borror
- School of Mathematical and Natural Sciences, Arizona State University, Phoenix, Arizona, United States of America
| | - Todd R. Sandrin
- School of Mathematical and Natural Sciences, Arizona State University, Phoenix, Arizona, United States of America
- * E-mail:
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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: 524] [Impact Index Per Article: 52.4] [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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45
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Manji R, Bythrow M, Branda JA, Burnham CAD, Ferraro MJ, Garner OB, Jennemann R, Lewinski MA, Mochon AB, Procop GW, Richter SS, Rychert JA, Sercia L, Westblade LF, Ginocchio CC. Multi-center evaluation of the VITEK® MS system for mass spectrometric identification of non-Enterobacteriaceae Gram-negative bacilli. Eur J Clin Microbiol Infect Dis 2013; 33:337-46. [PMID: 24019163 DOI: 10.1007/s10096-013-1961-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 08/13/2013] [Indexed: 12/17/2022]
Abstract
Studies have demonstrated that matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a rapid, accurate method for the identification of clinically relevant bacteria. The purpose of this study was to evaluate the performance of the VITEK MS v2.0 system (bioMérieux) for the identification of the non-Enterobacteriaceae Gram-negative bacilli (NEGNB). This multi-center study tested 558 unique NEGNB clinical isolates, representing 18 genera and 33 species. Results obtained with the VITEK MS v2.0 were compared with reference 16S rRNA gene sequencing and when indicated recA sequencing and phenotypic analysis. VITEK MS v2.0 provided an identification for 92.5 % of the NEGNB isolates (516 out of 558). VITEK MS v2.0 correctly identified 90.9 % of NEGNB (507 out of 558), 77.8 % to species level and 13.1 % to genus level with multiple species. There were four isolates (0.7 %) incorrectly identified to genus level and five isolates (0.9 %), with one incorrect identification to species level. The remaining 42 isolates (7.5 %) were either reported as no identification (5.0 %) or called "mixed genera" (2.5 %) since two or more different genera were identified as possible identifications for the test organism. These findings demonstrate that the VITEK MS v2.0 system provides accurate results for the identification of a challenging and diverse group of Gram-negative bacteria.
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Affiliation(s)
- R Manji
- Department of Pathology and Laboratory Medicine, North Shore-LIJ Health System Laboratories, 10 Nevada Drive, Lake Success, NY, 11042, USA
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Martino ME, Fasolato L, Montemurro F, Novelli E, Cardazzo B. Aeromonasspp.: ubiquitous or specialized bugs? Environ Microbiol 2013; 16:1005-18. [DOI: 10.1111/1462-2920.12215] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 07/10/2013] [Accepted: 07/10/2013] [Indexed: 11/27/2022]
Affiliation(s)
- Maria Elena Martino
- Department of Comparative Biomedicine and Food Science; University of Padova; Legnaro 35020 Italy
| | - Luca Fasolato
- Department of Comparative Biomedicine and Food Science; University of Padova; Legnaro 35020 Italy
| | - Filomena Montemurro
- Department of Comparative Biomedicine and Food Science; University of Padova; Legnaro 35020 Italy
| | - Enrico Novelli
- Department of Comparative Biomedicine and Food Science; University of Padova; Legnaro 35020 Italy
| | - Barbara Cardazzo
- Department of Comparative Biomedicine and Food Science; University of Padova; Legnaro 35020 Italy
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