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Oğuz Ş, Andiç S. Isolation, identification, and characterization of thermophilic lactic acid bacteria isolated from whey of Kars Kashar cheeses. Antonie Van Leeuwenhoek 2024; 117:85. [PMID: 38811466 DOI: 10.1007/s10482-024-01982-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 05/18/2024] [Indexed: 05/31/2024]
Abstract
Kars Kashar cheese is an artisanal pasta-filata type cheese and geographically marked in Eastern Anatolia of Turkey. The aims of this research were to determine for the first time thermophilic lactic acid bacteria (LAB) of Kars Kashar cheese and characterize the technological properties of obtained isolates. In our research, a number of 15 samples of whey were collected from the different villages in Kars. These samples were incubated at 45 °C and used as the source material for isolating thermophilic LAB. A total of 250 colonies were isolated from thermophilic whey, and 217 of them were determined to be presumptive LAB based on their Gram staining and catalase test. A total of 170 isolates were characterized by their phenotypic properties and identified using the MALDI-TOF mass spectrometry method. Phenotypic identification of isolates displayed that Enterococcus and Lactobacillus were the predominant microbiota. According to MALDI-TOF MS identification, 89 isolates were identified as Enterococcus (52.35%), 57 isolates as Lactobacillus (33.53%), 23 isolates as Streptococcus (13.53%), and one isolate as Lactococcus (0.59%). All thermophilic LAB isolates were successfully identified to the species level and it has been observed that MALDI-TOF MS can be successfully used for the identification of selected LAB. The acidification and proteolytic activities of the isolated thermophilic LAB were examined, and the isolates designated for use as starter cultures were also genotypically defined.
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Affiliation(s)
- Şehriban Oğuz
- Department of Food Engineering, Faculty of Engineering, Van Yuzuncu Yil University, 65080, Van, Turkey.
| | - Seval Andiç
- Department of Food Engineering, Faculty of Engineering, Van Yuzuncu Yil University, 65080, Van, Turkey
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2
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Ahuja V, Singh A, Paul D, Dasgupta D, Urajová P, Ghosh S, Singh R, Sahoo G, Ewe D, Saurav K. Recent Advances in the Detection of Food Toxins Using Mass Spectrometry. Chem Res Toxicol 2023; 36:1834-1863. [PMID: 38059476 PMCID: PMC10731662 DOI: 10.1021/acs.chemrestox.3c00241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/30/2023] [Accepted: 11/08/2023] [Indexed: 12/08/2023]
Abstract
Edibles are the only source of nutrients and energy for humans. However, ingredients of edibles have undergone many physicochemical changes during preparation and storage. Aging, hydrolysis, oxidation, and rancidity are some of the major changes that not only change the native flavor, texture, and taste of food but also destroy the nutritive value and jeopardize public health. The major reasons for the production of harmful metabolites, chemicals, and toxins are poor processing, inappropriate storage, and microbial spoilage, which are lethal to consumers. In addition, the emergence of new pollutants has intensified the need for advanced and rapid food analysis techniques to detect such toxins. The issue with the detection of toxins in food samples is the nonvolatile nature and absence of detectable chromophores; hence, normal conventional techniques need additional derivatization. Mass spectrometry (MS) offers high sensitivity, selectivity, and capability to handle complex mixtures, making it an ideal analytical technique for the identification and quantification of food toxins. Recent technological advancements, such as high-resolution MS and tandem mass spectrometry (MS/MS), have significantly improved sensitivity, enabling the detection of food toxins at ultralow levels. Moreover, the emergence of ambient ionization techniques has facilitated rapid in situ analysis of samples with lower time and resources. Despite numerous advantages, the widespread adoption of MS in routine food safety monitoring faces certain challenges such as instrument cost, complexity, data analysis, and standardization of methods. Nevertheless, the continuous advancements in MS-technology and its integration with complementary techniques hold promising prospects for revolutionizing food safety monitoring. This review discusses the application of MS in detecting various food toxins including mycotoxins, marine biotoxins, and plant-derived toxins. It also explores the implementation of untargeted approaches, such as metabolomics and proteomics, for the discovery of novel and emerging food toxins, enhancing our understanding of potential hazards in the food supply chain.
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Affiliation(s)
- Vishal Ahuja
- University
Institute of Biotechnology, Chandigarh University, Mohali, Punjab 140413, India
- University
Centre for Research & Development, Chandigarh
University, Mohali, Punjab 140413, India
| | - Amanpreet Singh
- Department
of Chemistry, University Institute of Science, Chandigarh University, Mohali, Punjab 140413, India
| | - Debarati Paul
- Amity
Institute of Biotechnology, AUUP, Noida, Uttar Pradesh 201313, India
| | - Diptarka Dasgupta
- Material
Resource Efficiency Division, CSIR-Indian
Institute of Petroleum, Dehradun 248005, India
| | - Petra Urajová
- Laboratory
of Algal Biotechnology-Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, Třeboň 379
01, Czech Republic
| | - Sounak Ghosh
- Laboratory
of Algal Biotechnology-Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, Třeboň 379
01, Czech Republic
| | - Roshani Singh
- Laboratory
of Algal Biotechnology-Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, Třeboň 379
01, Czech Republic
| | - Gobardhan Sahoo
- Laboratory
of Algal Biotechnology-Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, Třeboň 379
01, Czech Republic
| | - Daniela Ewe
- Laboratory
of Algal Biotechnology-Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, Třeboň 379
01, Czech Republic
| | - Kumar Saurav
- Laboratory
of Algal Biotechnology-Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, Třeboň 379
01, Czech Republic
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3
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Kalın G, Alp E, Chouaikhi A, Roger C. Antimicrobial Multidrug Resistance: Clinical Implications for Infection Management in Critically Ill Patients. Microorganisms 2023; 11:2575. [PMID: 37894233 PMCID: PMC10609422 DOI: 10.3390/microorganisms11102575] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/05/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
The increasing incidence of antimicrobial resistance (AMR) worldwide represents a serious threat in the management of sepsis. Due to resistance to the most common antimicrobials prescribed, multidrug-resistant (MDR) pathogens have been associated with delays in adequate antimicrobial therapy leading to significant increases in mortality, along with prolonged hospital length of stay (LOS) and increases in healthcare costs. In response to MDR infections and the delay of microbiological results, broad-spectrum antibiotics are frequently used in empirical antimicrobial therapy. This can contribute to the overuse and misuse of antibiotics, further promoting the development of resistance. Multiple measures have been suggested to combat AMR. This review will focus on describing the epidemiology and trends concerning MDR pathogens. Additionally, it will explore the crucial aspects of identifying patients susceptible to MDR infections and optimizing antimicrobial drug dosing, which are both pivotal considerations in the fight against AMR. Expert commentary: The increasing AMR in ICUs worldwide makes the empirical antibiotic therapy challenging in septic patients. An AMR surveillance program together with improvements in MDR identification based on patient risk stratification and molecular rapid diagnostic tools may further help tailoring antimicrobial therapies and avoid unnecessary broad-spectrum antibiotics. Continuous infusions of antibiotics, therapeutic drug monitoring (TDM)-based dosing regimens and combination therapy may contribute to optimizing antimicrobial therapy and limiting the emergence of resistance.
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Affiliation(s)
- Gamze Kalın
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Erciyes University, Kayseri 38280, Türkiye
| | - Emine Alp
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Ankara Yıldırım Beyazıt University, Ankara 06760, Türkiye;
| | - Arthur Chouaikhi
- Department of Anesthesiology and Intensive Care, Pain and Emergency Medicine, Nîmes-Caremeau University Hospital, Place du Professeur Robert Debré, CEDEX 9, 30029 Nîmes, France;
| | - Claire Roger
- Department of Anesthesiology and Intensive Care, Pain and Emergency Medicine, Nîmes-Caremeau University Hospital, Place du Professeur Robert Debré, CEDEX 9, 30029 Nîmes, France;
- UR UM 103 IMAGINE, Faculty of Medicine, Montpellier University, Chemin du Carreau de Lanes, 30029 Nîmes, France
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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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Chen L, Gao W, Tan X, Han Y, Jiao F, Feng B, Xie J, Li B, Zhao H, Tu H, Yu S, Wang L. MALDI-TOF MS Is an Effective Technique To Classify Specific Microbiota. Microbiol Spectr 2023; 11:e0030723. [PMID: 37140390 PMCID: PMC10269913 DOI: 10.1128/spectrum.00307-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 04/11/2023] [Indexed: 05/05/2023] Open
Abstract
MALDI-TOF MS is well-recognized for single microbial identification and widely used in research and clinical fields due to its specificity, speed of analysis, and low cost of consumables. Multiple commercial platforms have been developed and approved by the U.S. Food and Drug Administration. Matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) has been used for microbial identification. However, microbes can present as a specific microbiota, and detection and classification remain a challenge. Here, we constructed several specific microbiotas and tried to classify them using MALDI-TOF MS. Different concentrations of nine bacterial strains (belonging to eight genera) constituted 20 specific microbiotas. Using MALDI-TOF MS, the overlap spectrum of each microbiota (MS spectra of nine bacterial strains with component percentages) could be classified by hierarchical clustering analysis (HCA). However, the real MS spectrum of a specific microbiota was different than that of the overlap spectrum of component bacteria. The MS spectra of specific microbiota showed excellent repeatability and were easier to classify by HCA, with an accuracy close to 90%. These results indicate that the widely used MALDI-TOF MS identification method for individual bacteria can be expanded to classification of microbiota. IMPORTANCE MALDI-TOF MS can be used to classify specific model microbiota. The actual MS spectrum of the model microbiota was not a simple superposition of every single bacterium in a certain proportion but had a specific spectral fingerprint. The specificity of this fingerprint can enhance the accuracy of microbiota classification.
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Affiliation(s)
- Liangqiang Chen
- Kweichow Moutai Group, Renhuai, Guizhou, People’s Republic of China
| | - Wenjing Gao
- Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, People’s Republic of China
| | - Xue Tan
- Kweichow Moutai Group, Renhuai, Guizhou, People’s Republic of China
| | - Ying Han
- Kweichow Moutai Group, Renhuai, Guizhou, People’s Republic of China
| | - Fu Jiao
- Kweichow Moutai Group, Renhuai, Guizhou, People’s Republic of China
| | - Bin Feng
- Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, People’s Republic of China
| | - Jinghang Xie
- Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, People’s Republic of China
| | - Bin Li
- Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, People’s Republic of China
| | - Huilin Zhao
- Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, People’s Republic of China
| | - Huabin Tu
- Kweichow Moutai Group, Renhuai, Guizhou, People’s Republic of China
| | - Shaoning Yu
- Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, People’s Republic of China
| | - Li Wang
- Kweichow Moutai Group, Renhuai, Guizhou, People’s Republic of China
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Shen SC, Chen KJ. Late-Onset Bleb-Related Endophthalmitis Caused by Moraxella nonliquefaciens: A Case Report. Antibiotics (Basel) 2023; 12:antibiotics12030607. [PMID: 36978474 PMCID: PMC10045099 DOI: 10.3390/antibiotics12030607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/15/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
Moraxella species are Gram-negative coccobacilli that typically colonize the flora of the human upper respiratory tract and have low pathogenic potential. There are limited case reports implicating the organisms as the cause of endocarditis, bacteremia, septic arthritis, ocular infection, and meningitis. In cases of keratitis and conjunctivitis, Moraxella nonliquefaciens is not commonly isolated from the ocular surface. We present a case of a diabetic patient who developed late-onset bleb-related endophthalmitis caused by M. nonliquefaciens 4 years after glaucoma filtering surgery. Within one day, the patient presented with an acutely fulminant course with sudden visual loss, redness, and ocular pain. Appropriate antibiotic treatment and early vitrectomy resulted in a favorable final visual acuity of 20/100, which was his vision prior to infection. The use of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass spectrometry (MALDI-TOF MS) enabled the rapid identification of the organism. Endophthalmitis caused by M. nonliquefaciens should be considered in patients who underwent glaucoma filtering surgery with antifibrotic agents.
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Affiliation(s)
- Su-Chin Shen
- Department of Ophthalmology, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
- College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
| | - Kuan-Jen Chen
- Department of Ophthalmology, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
- College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
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Boyaci Gunduz CP, Agirman B, Erten H. Identification of yeasts in fermented foods and beverages using MALDI-TOF MS. FEMS Yeast Res 2022; 22:6823700. [PMID: 36367538 DOI: 10.1093/femsyr/foac056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/21/2022] [Accepted: 11/09/2022] [Indexed: 11/13/2022] Open
Abstract
Yeasts are an important group of microorganisms and contribute to the fermentation of a broad range of foods and beverages spontaneously or as a starter culture. Rapid and reliable microbial species identification is essential to evaluate biodiversity in fermented foods and beverages. Nowadays, high-throughput omics technologies and bioinformatics tools produce large-scale molecular-level data in many fields. These omics technologies generate data at different expression levels and are used to identify microorganisms. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a powerful analytical technique in proteomic technology. It is a tool used to analyze the peptides or proteins of microorganisms for identification. MALDI-TOF MS has been used for the taxonomic identification of microorganisms as a fast, high-throughput, and cost-effective method. This review briefly discussed the application of MALDI-TOF MS in identifying yeasts in fermented foods and beverages.
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Affiliation(s)
- Cennet Pelin Boyaci Gunduz
- Department of Food Engineering, Faculty of Engineering, Cukurova University, TR-01330 Adana, Turkey.,Department of Food Engineering, Faculty of Engineering, Adana Alparslan Turkes Science and Technology University, Adana 01250, Turkey
| | - Bilal Agirman
- Department of Food Engineering, Faculty of Engineering, Cukurova University, TR-01330 Adana, Turkey
| | - Huseyin Erten
- Department of Food Engineering, Faculty of Engineering, Cukurova University, TR-01330 Adana, Turkey
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Argyropoulos CD, Skoulou V, Efthimiou G, Michopoulos AK. Airborne transmission of biological agents within the indoor built environment: a multidisciplinary review. AIR QUALITY, ATMOSPHERE, & HEALTH 2022; 16:477-533. [PMID: 36467894 PMCID: PMC9703444 DOI: 10.1007/s11869-022-01286-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/17/2022] [Indexed: 06/17/2023]
Abstract
The nature and airborne dispersion of the underestimated biological agents, monitoring, analysis and transmission among the human occupants into building environment is a major challenge of today. Those agents play a crucial role in ensuring comfortable, healthy and risk-free conditions into indoor working and leaving spaces. It is known that ventilation systems influence strongly the transmission of indoor air pollutants, with scarce information although to have been reported for biological agents until 2019. The biological agents' source release and the trajectory of airborne transmission are both important in terms of optimising the design of the heating, ventilation and air conditioning systems of the future. In addition, modelling via computational fluid dynamics (CFD) will become a more valuable tool in foreseeing risks and tackle hazards when pollutants and biological agents released into closed spaces. Promising results on the prediction of their dispersion routes and concentration levels, as well as the selection of the appropriate ventilation strategy, provide crucial information on risk minimisation of the airborne transmission among humans. Under this context, the present multidisciplinary review considers four interrelated aspects of the dispersion of biological agents in closed spaces, (a) the nature and airborne transmission route of the examined agents, (b) the biological origin and health effects of the major microbial pathogens on the human respiratory system, (c) the role of heating, ventilation and air-conditioning systems in the airborne transmission and (d) the associated computer modelling approaches. This adopted methodology allows the discussion of the existing findings, on-going research, identification of the main research gaps and future directions from a multidisciplinary point of view which will be helpful for substantial innovations in the field.
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Affiliation(s)
| | - Vasiliki Skoulou
- B3 Challenge Group, Chemical Engineering, School of Engineering, University of Hull, Cottingham Road, Hull, HU6 7RX UK
| | - Georgios Efthimiou
- Centre for Biomedicine, Hull York Medical School, University of Hull, Cottingham Road, Hull, HU6 7RX UK
| | - Apostolos K. Michopoulos
- Energy & Environmental Design of Buildings Research Laboratory, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
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Lecerf P, De Paepe R, Jazaeri Y, Normand AC, Martiny D, Packeu A. Evaluation of a Liquid Media MALDI-TOF MS Protocol for the Identification of Dermatophytes Isolated from Tinea capitis Infections. J Fungi (Basel) 2022; 8:jof8121248. [PMID: 36547581 PMCID: PMC9783569 DOI: 10.3390/jof8121248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 11/15/2022] [Accepted: 11/18/2022] [Indexed: 11/29/2022] Open
Abstract
One of the most common types of tinea is the superficial infection of the hair and scalp area known as tinea capitis. It is responsible for frequent outbreaks in nurseries and schools and represents a global health problem. Correct identification of the infection agent is essential in the determination of the infection source, epidemiological course, and treatment initiation. The conventional identification methods (direct exam, culture, DNA sequencing) are time-consuming, require experienced staff, are time-consuming, and the latter is expensive for routine identifications. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is gaining new ground for routine identification of filamentous fungi. The main advantages of MALDI-TOF MS are its rapid and accurate identification capability, relatively low cost, and easy integration into the laboratory routine. Its accuracy heavily depends on the quality of the reference spectra database. Identification of clinical isolates with MALDI-TOF MS protocol requires a sub-culturing step to ensure reliable identification. It can take days to weeks before fungal growth appears on solid medium. In this study, a unique MALDI-TOF MS protocol using liquid cultures of dermatophyte species was developed in order to shorten the turnaround time for the culture and identification of clinical isolates. Material and Method A standard MALDI-TOF MS protocol was adapted for liquid instead of solid cultures. Three different databases were tested. Results Using the liquid media MALDI-TOF MS protocol, a global rate of 62% correct identification (RCI) was obtained, compared with 87% for the protocol based on solid cultures. Trichophyton tonsurans was not correctly identified in all isolates using liquid cultures, with 88% of the isolates misidentified as Trichophyton interdigitale. The turnaround time for primary isolates for the solid and liquid protocols were respectively 11.7 and 11.6 days (no significant difference between both methods (p = 0.96)). Conclusions The newly designed liquid MALDI-TOF MS protocol did not lead to a significantly shorter turnaround time for the identification of dermatophytes isolated from tinea capitis infections. The turnaround time for the method with primary isolates was not significantly lower, and the rate of correct identification decreased remarkably, which emphasizes the need for a sub-culturing step. Using different database did not lead to improvement in turnaround time or rate of correct identification. This study highlights the importance of the medium and the reference database when performing MALDI-TOF MS.
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Affiliation(s)
- Pauline Lecerf
- Dermatology Department, University Hospital Brugmann & Saint-Pierre, Université Libre de Bruxelles, 1020 Brussels, Belgium
- Correspondence:
| | - Roelke De Paepe
- Mycology and Aerobiology Department, Sciensano, 1050 Brussels, Belgium
| | - Yasaman Jazaeri
- Dermatology Department, University Hospital Brugmann & Saint-Pierre, Université Libre de Bruxelles, 1020 Brussels, Belgium
| | - Anne-Cécile Normand
- Parasitology/Mycology Department AP-HP, Hôpitaux de Paris, 75013 Paris, France
| | - Delphine Martiny
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles Universitair Laboratorium Brussel (LHUB-ULB), Université Libre de Bruxelles (ULB), 1000 Brussels, Belgium
- Faculty of Medicine and Franco, University of Mons (UMONS), 7000 Mons, Belgium
| | - Ann Packeu
- Mycology and Aerobiology Department, Sciensano, 1050 Brussels, Belgium
- BCCM/IHEM Fungal Collection, Sciensano, Mycology and Aerobiology Section, 1050 Brussels, Belgium
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de Carvalho JA, Monteiro RC, Hagen F, de Camargo ZP, Rodrigues AM. Trends in Molecular Diagnostics and Genotyping Tools Applied for Emerging Sporothrix Species. J Fungi (Basel) 2022; 8:jof8080809. [PMID: 36012797 PMCID: PMC9409836 DOI: 10.3390/jof8080809] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/22/2022] [Accepted: 07/25/2022] [Indexed: 11/23/2022] Open
Abstract
Sporotrichosis is the most important subcutaneous mycosis that affects humans and animals worldwide. The mycosis is caused after a traumatic inoculation of fungal propagules into the host and may follow an animal or environmental transmission route. The main culprits of sporotrichosis are thermodimorphic Sporothrix species embedded in a clinical clade, including S. brasiliensis, S. schenckii, S. globosa, and S. luriei. Although sporotrichosis occurs worldwide, the etiological agents are not evenly distributed, as exemplified by ongoing outbreaks in Brazil and China, caused by S. brasiliensis and S. globosa, respectively. The gold standard for diagnosing sporotrichosis has been the isolation of the fungus in vitro. However, with the advance in molecular techniques, molecular assays have complemented and gradually replaced the classical mycological tests to quickly and accurately detect and/or differentiate molecular siblings in Sporothrix. Nearly all techniques available for molecular diagnosis of sporotrichosis involve PCR amplification, which is currently moving towards detecting Sporothrix DNA directly from clinical samples in multiplex qPCR assays. From an epidemiological perspective, genotyping is key to tracing back sources of Sporothrix infections, detecting diversity in outbreak areas, and thus uncovering finer-scale epidemiological patterns. Over the past decades, molecular epidemiological studies have provided essential information to policymakers regarding outbreak management. From high-to-low throughput genotyping methods, MLSA, AFLP, SSR, RAPD, PCR-RFLP, and WGS are available to assess the transmission dynamics and sporotrichosis expansion. This review discusses the trends in the molecular diagnosis of sporotrichosis, genotyping techniques applied in molecular epidemiological studies, and perspectives for the near future.
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Affiliation(s)
- Jamile Ambrósio de Carvalho
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil; (J.A.d.C.); (R.C.M.); (Z.P.d.C.)
| | - Ruan Campos Monteiro
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil; (J.A.d.C.); (R.C.M.); (Z.P.d.C.)
| | - Ferry Hagen
- Department of Medical Mycology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands;
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Sciencepark 904, 1098 XH Amsterdam, The Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Zoilo Pires de Camargo
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil; (J.A.d.C.); (R.C.M.); (Z.P.d.C.)
- Department of Medicine, Discipline of Infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil
| | - Anderson Messias Rodrigues
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil; (J.A.d.C.); (R.C.M.); (Z.P.d.C.)
- Department of Medicine, Discipline of Infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil
- Correspondence: ; Tel.: +55-1155764551 (ext. 1540)
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Rodrigues AM, Gonçalves SS, de Carvalho JA, Borba-Santos LP, Rozental S, de Camargo ZP. Current Progress on Epidemiology, Diagnosis, and Treatment of Sporotrichosis and Their Future Trends. J Fungi (Basel) 2022; 8:jof8080776. [PMID: 35893145 PMCID: PMC9331723 DOI: 10.3390/jof8080776] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/14/2022] [Accepted: 07/16/2022] [Indexed: 01/19/2023] Open
Abstract
Sporotrichosis, a human and animal disease caused by Sporothrix species, is the most important implantation mycosis worldwide. Sporothrix taxonomy has improved in recent years, allowing important advances in diagnosis, epidemiology, and treatment. Molecular epidemiology reveals that S. brasiliensis remains highly prevalent during the cat-transmitted sporotrichosis outbreaks in South America and that the spread of S. brasiliensis occurs through founder effects. Sporothrix globosa and S. schenckii are cosmopolitan on the move, causing major sapronoses in Asia and the Americas, respectively. In this emerging scenario, one-health approaches are required to develop a creative, effective, and sustainable response to tackle the spread of sporotrichosis. In the 21st century, it has become vital to speciate Sporothrix, and PCR is the main pillar of molecular diagnosis, aiming at the detection of the pathogen DNA from clinical samples through multiplex assays, whose sensitivity reaches remarkably three copies of the target. The treatment of sporotrichosis can be challenging, especially after the emergence of resistance to azoles and polyenes. Alternative drugs arising from discoveries or repositioning have entered the radar of basic research over the last decade and point to several molecules with antifungal potential, especially the hydrazone derivatives with great in vitro and in vivo activities. There are many promising developments for the near future, and in this review, we discuss how these trends can be applied to the Sporothrix-sporotrichosis system to mitigate the advance of an emerging and re-emerging disease.
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Affiliation(s)
- Anderson Messias Rodrigues
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), Sao Paulo 04023062, Brazil; (J.A.d.C.); (Z.P.d.C.)
- Department of Medicine, Discipline of Infectious Diseases, Federal University of São Paulo (UNIFESP), Sao Paulo 04023062, Brazil
- Correspondence: ; Tel.: +55-1155764551 (ext. 1540)
| | - Sarah Santos Gonçalves
- Infectious Diseases Postgraduate Program, Center for Research in Medical Mycology, Federal University of Espírito Santo (UFES), Vitoria 29043900, Brazil;
| | - Jamile Ambrósio de Carvalho
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), Sao Paulo 04023062, Brazil; (J.A.d.C.); (Z.P.d.C.)
- Department of Medicine, Discipline of Infectious Diseases, Federal University of São Paulo (UNIFESP), Sao Paulo 04023062, Brazil
| | - Luana P. Borba-Santos
- Cell Biology and Parasitology Program, Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941902, Brazil; (L.P.B.-S.); (S.R.)
| | - Sonia Rozental
- Cell Biology and Parasitology Program, Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941902, Brazil; (L.P.B.-S.); (S.R.)
| | - Zoilo Pires de Camargo
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), Sao Paulo 04023062, Brazil; (J.A.d.C.); (Z.P.d.C.)
- Department of Medicine, Discipline of Infectious Diseases, Federal University of São Paulo (UNIFESP), Sao Paulo 04023062, Brazil
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Lardinois B, Belkhir L, Verroken A. Helicobacter canis: A Review of Microbiological and Clinical Features. Front Microbiol 2022; 12:814944. [PMID: 35281304 PMCID: PMC8905544 DOI: 10.3389/fmicb.2021.814944] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 12/17/2021] [Indexed: 11/17/2022] Open
Abstract
Helicobacter canis, an enterohepatic Helicobacter, has proven its role in human diseases and has been rediscussed in recent years as its zoonotic potential is increasingly described. Routine microbiological detection of this pathogen is a difficult task as its culture may fail due to fastidious growth. It is therefore supposed that many clinical laboratories under-recognize H. canis infections. A review of all clinical and microbiological literature currently available from previous relevant H. canis human clinical cases, mainly bacteremia, added with a clinical case observed at the Cliniques universitaires Saint-Luc, was performed. Clinical features of H. canis reports show the presence of underlying clinical conditions in 89% of the cases, bacteremia in 83%, associated fever in 58%, and recent close contact with pets in 83%, especially dogs. The observed microbiological trends from 10 cases of bacteremia were a median of 4 days until positive blood culture bottle detection, subcultures showing a thin layer of small colonies under microaerophilic atmosphere at 35–42°C after 3–4 days of growth, and an identification requiring 16S rRNA sequencing given the difficulties observed with MALDI-TOF MS. Low MICs were observed for penicillins, amoxicillin/clavulanic acid, carbapenems, and metronidazole in opposition to high MICs for ciprofloxacin. A frequent association of H. canis and bacteremia in immunocompromised patients with recurrent fever in contact with pets, especially dogs, was identified. Considering the fastidious growing capacities, final identification from blood cultures may not be expected before 7 days. Intravenous ceftriaxone, oral doxycycline, or metronidazole has been suggested as efficient therapeutic choices.
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Affiliation(s)
- Benjamin Lardinois
- Department of Microbiology, Cliniques universitaires Saint-Luc, Université catholique de Louvain, Brussels, Belgium
| | - Leïla Belkhir
- Department of Internal Medicine and Infectious Diseases, Cliniques universitaires Saint-Luc, Université catholique de Louvain, Brussels, Belgium
| | - Alexia Verroken
- Department of Microbiology, Cliniques universitaires Saint-Luc, Université catholique de Louvain, Brussels, Belgium
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13
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Borotová P, Galovičová L, Vukovic NL, Vukic M, Tvrdá E, Kačániová M. Chemical and Biological Characterization of Melaleuca alternifolia Essential Oil. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11040558. [PMID: 35214891 PMCID: PMC8880210 DOI: 10.3390/plants11040558] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/14/2022] [Accepted: 02/18/2022] [Indexed: 06/12/2023]
Abstract
The essential oil of Melaleuca alternifolia, commonly known as tea tree oil, has many beneficial properties due to its bioactive compounds. The aim of this research was to characterize the tea tree essential oil (TTEO) from Slovakia and its biological properties, which are specific to the chemical composition of essential oil. Gas chromatography/mass spectroscopy revealed that terpinen-4-ol was dominant with a content of 40.3%. γ-Terpinene, 1,8-cineole, and p-cymene were identified in contents of 11.7%, 7.0%, and 6.2%, respectively. Antioxidant activity was determined at 41.6% radical inhibition, which was equivalent to 447 μg Trolox to 1 mL sample. Antimicrobial activity was observed by the disk diffusion method against Gram-positive (G+), Gram-negative (G-) bacteria and against yeasts, where the best antimicrobial activity was against Enterococcus faecalis and Candida albicans with an inhibition zone of 10.67 mm. The minimum inhibitory concentration showed better susceptibility by G+ and G- planktonic cells, while yeast species and biofilm-forming bacteria strains were more resistant. Antibiofilm activity was observed against Pseudomonas fluorescens and Salmonella enterica by MALDI-TOF, where degradation of the protein spectra after the addition of essential oil was obtained. Good biological properties of tea tree essential oil allow its use in the food industry or in medicine as an antioxidant and antimicrobial agent.
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Affiliation(s)
- Petra Borotová
- AgroBioTech Research Centre, Slovak University of Agriculture, Tr. A. Hlinku 2, 949 76 Nitra, Slovakia
- Faculty of Biotechnology and Food Sciences, Institute of Applied Biology, Slovak University of Agriculture, Tr. A. Hlinku 2, 949 76 Nitra, Slovakia;
| | - Lucia Galovičová
- Faculty of Horticulture and Landscape Engineering, Institute of Horticulture, Slovak University of Agriculture, Tr. A. Hlinku 2, 949 76 Nitra, Slovakia;
| | - Nenad L. Vukovic
- Department of Chemistry, Faculty of Science, University of Kragujevac, 34000 Kragujevac, Serbia; (N.L.V.); (M.V.)
| | - Milena Vukic
- Department of Chemistry, Faculty of Science, University of Kragujevac, 34000 Kragujevac, Serbia; (N.L.V.); (M.V.)
| | - Eva Tvrdá
- Faculty of Biotechnology and Food Sciences, Institute of Applied Biology, Slovak University of Agriculture, Tr. A. Hlinku 2, 949 76 Nitra, Slovakia;
| | - Miroslava Kačániová
- Faculty of Horticulture and Landscape Engineering, Institute of Horticulture, Slovak University of Agriculture, Tr. A. Hlinku 2, 949 76 Nitra, Slovakia;
- Department of Bioenergy, Food Technology and Microbiology, Institute of Food Technology and Nutrition, University of Rzeszow, 4 Zelwerowicza Str., 35-601 Rzeszow, Poland
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14
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Multicenter evaluation of attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy-based method for rapid identification of clinically relevant yeasts. J Clin Microbiol 2021; 60:e0139821. [PMID: 34669460 DOI: 10.1128/jcm.01398-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fourier transform infrared (FTIR) spectroscopy has demonstrated applicability as a reagent-free whole-organism fingerprinting technique for both microbial identification and strain typing. For routine application of this technique in microbiology laboratories, acquisition of FTIR spectra in the attenuated total reflectance (ATR) mode simplifies the FTIR spectroscopy workflow, providing results within minutes after initial culture without prior sample preparation. In our previous central work, 99.7% correct species identification of clinically relevant yeasts was achieved by employing an ATR-FTIR-based method and spectral database developed by our group. In this study, ATR-FTIR spectrometers were placed in 6 clinical microbiology laboratories over a 16-month period and were used to collect spectra of routine yeast isolates for on-site identification to the species level. The identification results were compared to those obtained from conventional biochemical tests and/or matrix-assisted laser desorption/ionization time of flight mass spectrometry. Isolates producing discordant results were reanalyzed by routine identification methods, ATR-FTIR spectroscopy and PCR gene sequencing of the D1/D2 and ITS regions. Among the 573 routine clinical yeast isolates collected and identified by the ATR-FTIR-based method, 564 isolates (98.4%) were correctly identified at the species level while the remaining isolates were inconclusive with no misidentifications. Due to the low prevalence of Candida auris in routine isolates, additional randomly selected C. auris (n = 24) isolates were obtained for evaluation and resulted in 100% correct identification. Overall, the data obtained in our multicenter evaluation study using multiple spectrometers and system operators indicate that ATR-FTIR spectroscopy is a reliable, cost-effective yeast identification technique that provides accurate and timely (∼3 minutes/sample) species identification promptly after the initial culture.
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15
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Ponnusamy A, Ajis AH, Tan YS, Chai LC. Dynamics of fungal and bacterial microbiome associated with green-mould contaminated sawdust substrate of Pleurotus pulmonarius (grey oyster mushroom). J Appl Microbiol 2021; 132:2131-2143. [PMID: 34637602 DOI: 10.1111/jam.15327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 08/11/2021] [Accepted: 10/07/2021] [Indexed: 11/27/2022]
Abstract
AIMS Green-mould contamination is identified as one of the challenges faced by mushroom cultivation industry globally which believed to be caused by Trichoderma spp. METHODS AND RESULTS To explore the dynamics of microbial population in mushroom substrate during commercial mushroom cultivation and how microbiota might play a role in green-mould contamination, we applied both culturing and targeted metagenomics approaches to identify microbiota in noncomposted sawdust substrates at different cultivation stages. The microbiological analysis showed that the green-mould contaminated substrates harboured higher total mesophilic bacteria count. The green-moulds isolated from the contaminated mushroom substrates were identified as Trichoderma pleurotum (n = 15; 93.8%) and Graphium penicillioides (n = 1; 6.3%). To our surprise, the targeted metagenomic analysis revealed that Graphium comprised 56.3% while Trichoderma consisted of only 36.1% of the total fungi population, suggesting that green-mould contamination might not be caused by Trichoderma alone, but also Graphium that grows very slowly in the laboratory. CONCLUSION It is worthwhile to note that G. penicillioides was also isolated in the early stages of mushroom cultivation, but not T. pleurotum. The results indicated that the structure and composition of the bacterial population in the mushroom substrate varied and the bacterial population shifted along the cultivation process. SIGNIFICANCE AND IMPACT OF STUDY This study revealed a possibility of G. penicillioides as an overlooked fungi causing green-mould contamination.
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Affiliation(s)
- Ameertha Ponnusamy
- Faculty of Science, Institute of Biological Sciences, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Ana Hazirah Ajis
- Faculty of Science, Institute of Biological Sciences, Universiti Malaya, Kuala Lumpur, Malaysia.,Mushroom Research Centre, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Yee Shin Tan
- Faculty of Science, Institute of Biological Sciences, Universiti Malaya, Kuala Lumpur, Malaysia.,Mushroom Research Centre, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Lay Ching Chai
- Faculty of Science, Institute of Biological Sciences, Universiti Malaya, Kuala Lumpur, Malaysia
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16
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Han SS, Jeong YS, Choi SK. Current Scenario and Challenges in the Direct Identification of Microorganisms Using MALDI TOF MS. Microorganisms 2021; 9:microorganisms9091917. [PMID: 34576812 PMCID: PMC8466008 DOI: 10.3390/microorganisms9091917] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/01/2021] [Accepted: 09/07/2021] [Indexed: 01/12/2023] Open
Abstract
MALDI TOF MS-based microbial identification significantly lowers the operational costs because of minimal requirements of substrates and reagents for extraction. Therefore, it has been widely used in varied applications such as clinical, food, military, and ecological research. However, the MALDI TOF MS method is laced with many challenges including its limitation of the reference spectrum. This review briefly introduces the background of MALDI TOF MS technology, including sample preparation and workflow. We have primarily discussed the application of MALDI TOF MS in the identification of microorganisms. Furthermore, we have discussed the current trends for bioaerosol detection using MALDI TOF MS and the limitations and challenges involved, and finally the approaches to overcome these challenges.
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Affiliation(s)
- Sang-Soo Han
- Advanced Defense Science & Technology Research Institute, Agency for Defense Development, Daejeon 34186, Korea;
| | - Young-Su Jeong
- Chem-Bio Technology Center, Agency for Defense Development, Daejeon 34186, Korea;
- Correspondence: ; Tel.: +82-42-821-4843; Fax: +82-42-823-3400
| | - Sun-Kyung Choi
- Chem-Bio Technology Center, Agency for Defense Development, Daejeon 34186, Korea;
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17
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Salvagno GL, Danese E, Lippi G. Mass spectrometry and total laboratory automation: opportunities and drawbacks. Clin Chem Lab Med 2021; 58:994-1001. [PMID: 32191622 DOI: 10.1515/cclm-2019-0723] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 02/14/2020] [Indexed: 11/15/2022]
Abstract
The diffusion of laboratory automation, initiated nearly 50 years ago with consolidation of preanalytical, clinical chemistry and immunochemistry workstations, is now also gradually embracing mass spectrometry (MS). As for other diagnostic disciplines, the automation of MS carries many advantages, such as efficient personnel management (i.e. improving working atmosphere by decreasing manual activities, lowering health risks, simplifying staff training), better organization (i.e. reducing workloads, improving inventory handling, increasing analytical process standardization) and the possibility to reduce the number of platforms. The development and integration of different technologies into automated MS analyzers will also generate technical and practical advantages, such as prepackaged and ready-to-use reagents, automated dispensing, incubation and measurement, automated sample processing (e.g. system fit for many models of laboratory automation, bar code readers), multiplex testing, automatic data processing, also including quality control assessment, and automated validation/interpretation (e.g. autoverification). A new generation of preanalytical workstations, which can be directly connected to MS systems, will allow the automation of manual extraction and elimination of time-consuming activities, such as tube labeling and capping/decapping. The use of automated liquid-handling platform for pipetting samples, along with addition of internal standards, may then enable the optimization of some steps of extraction and protein precipitation, thus decreasing turnaround time and increasing throughput in MS testing. Therefore, this focused review is aimed at providing a brief update on the importance of consolidation and integration of MS platforms in laboratory automation.
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Affiliation(s)
| | - Elisa Danese
- Section of Clinical Biochemistry, University of Verona, Verona, Italy
| | - Giuseppe Lippi
- Section of Clinical Biochemistry, University of Verona, Verona, Italy
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A Case of Nosocomial Outbreak of Pantoea agglomerans Related to Parenteral Nutrition Procedures. Healthcare (Basel) 2021; 9:healthcare9060684. [PMID: 34200170 PMCID: PMC8226852 DOI: 10.3390/healthcare9060684] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/01/2021] [Accepted: 06/01/2021] [Indexed: 11/17/2022] Open
Abstract
Pantoea agglomerans is a Gram-negative bacterium that infrequently infects humans. Most reports involving it are about infections in soft tissues or bone/joint infections caused by contamination from soil or penetrating trauma by vegetation, such as thorns and splinters. More frequently, it is found as an opportunistic pathogen in immunocompromised patients. It is not rare to find reports of bacteremia and sepsis from contamination of intravenous fluid, parenteral nutrition, blood products and anesthetic agents-that is, through contamination of medical devices and products. We reported a bacterial infection epidemic occurred in 2011 in a hospital in middle Italy which involved different hospital wards; Pantoea agglomerans was isolated from blood cultures of all infected patients and the source of infection was identified in contaminated parenteral nutrition prepared from the local pharmacy.
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19
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Chamberlain CA, Hatch M, Garrett TJ. Extracellular Vesicle Analysis by Paper Spray Ionization Mass Spectrometry. Metabolites 2021; 11:metabo11050308. [PMID: 34065030 PMCID: PMC8151837 DOI: 10.3390/metabo11050308] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/23/2021] [Accepted: 05/06/2021] [Indexed: 12/29/2022] Open
Abstract
Paper spray ionization mass spectrometry (PSI-MS) is a direct MS analysis technique with several reported bacterial metabolomics applications. As with most MS-based bacterial studies, all currently reported PSI-MS bacterial analyses have focused on the chemical signatures of the cellular unit. One dimension of the bacterial metabolome that is often lost in such analyses is the exometabolome (extracellular metabolome), including secreted metabolites, lipids, and peptides. A key component of the bacterial exometabolome that is gaining increased attention in the microbiology and biomedical communities is extracellular vesicles (EVs). These excreted structures, produced by cells in all domains of life, contain a variety of biomolecules responsible for a wide array of cellular functions, thus representing a core component of the bacterial secreted metabolome. Although previously examined using other MS approaches, no reports currently exist for a PSI-MS analysis of bacterial EVs, nor EVs from any other organism (exosomes, ectosomes, etc.). PSI-MS holds unique analytical strengths over other commonly used MS platforms and could thus provide an advantageous approach to EV metabolomics. To address this, we report a novel application representing, to our knowledge, the first PSI-MS analysis of EVs from any organism (using the human gut resident Oxalobacter formigenes as the experimental model, a bacterium whose EVs were never previously investigated). In this report, we show how we isolated and purified EVs from bacterial culture supernatant by EV-specific affinity chromatography, confirmed and characterized these vesicles by nanoparticle tracking analysis, analyzed the EV isolate by PSI-MS, and identified a panel of EV-derived metabolites, lipids, and peptides. This work serves as a pioneering study in the field of MS-based EV analysis and provides a new, rapid, sensitive, and economical approach to EV metabolomics.
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20
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Differentiation of Gastric Helicobacter Species Using MALDI-TOF Mass Spectrometry. Pathogens 2021; 10:pathogens10030366. [PMID: 33803832 PMCID: PMC8003121 DOI: 10.3390/pathogens10030366] [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: 03/04/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 02/07/2023] Open
Abstract
Gastric helicobacters (Helicobacter (H.) pylori and non-H. pylori Helicobacter species (NHPHs)) colonize the stomach of humans and/or animals. Helicobacter species identification is essential since many of them are recognized as human and/or animal pathogens. Currently, Helicobacter species can only be differentiated using molecular methods. Differentiation between NHPHs using MALDI-TOF MS has not been described before, probably because these species are poorly represented in current MALDI-TOF MS databases. Therefore, we identified 93 gastric Helicobacter isolates of 10 different Helicobacter species using MALDI-TOF MS in order to establish a more elaborate Helicobacter reference database. While the MALDI Biotyper database was not able to correctly identify any of the isolates, the in-house database correctly identified all individual mass spectra and resulted in 82% correct species identification based on the two highest log score matches (with log scores ≥2). In addition, a dendrogram was constructed using all newly created main spectrum profiles. Nine main clusters were formed, with some phylogenetically closely related Helicobacter species clustering closely together and well-defined subclusters being observed in specific species. Current results suggest that MALDI-TOF MS allows rapid differentiation between gastric Helicobacter species, provided that an extensive database is at hand and variation due to growth conditions and agar-medium-related peaks are taken into account.
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21
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Solntceva V, Kostrzewa M, Larrouy-Maumus G. Detection of Species-Specific Lipids by Routine MALDI TOF Mass Spectrometry to Unlock the Challenges of Microbial Identification and Antimicrobial Susceptibility Testing. Front Cell Infect Microbiol 2021; 10:621452. [PMID: 33634037 PMCID: PMC7902069 DOI: 10.3389/fcimb.2020.621452] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 12/18/2020] [Indexed: 12/16/2022] Open
Abstract
MALDI-TOF mass spectrometry has revolutionized clinical microbiology diagnostics by delivering accurate, fast, and reliable identification of microorganisms. It is conventionally based on the detection of intracellular molecules, mainly ribosomal proteins, for identification at the species-level and/or genus-level. Nevertheless, for some microorganisms (e.g., for mycobacteria) extensive protocols are necessary in order to extract intracellular proteins, and in some cases a protein-based approach cannot provide sufficient evidence to accurately identify the microorganisms within the same genus (e.g., Shigella sp. vs E. coli and the species of the M. tuberculosis complex). Consequently lipids, along with proteins are also molecules of interest. Lipids are ubiquitous, but their structural diversity delivers complementary information to the conventional protein-based clinical microbiology matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) based approaches currently used. Lipid modifications, such as the ones found on lipid A related to polymyxin resistance in Gram-negative pathogens (e.g., phosphoethanolamine and aminoarabinose), not only play a role in the detection of microorganisms by routine MALDI-TOF mass spectrometry but can also be used as a read-out of drug susceptibility. In this review, we will demonstrate that in combination with proteins, lipids are a game-changer in both the rapid detection of pathogens and the determination of their drug susceptibility using routine MALDI-TOF mass spectrometry systems.
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Affiliation(s)
- Vera Solntceva
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
| | | | - Gerald Larrouy-Maumus
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
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22
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Jadhav SR, Shah RM, Palombo EA. MALDI-ToF MS: A Rapid Methodology for Identifying and Subtyping Listeria monocytogenes. Methods Mol Biol 2021; 2220:17-29. [PMID: 32975763 DOI: 10.1007/978-1-0716-0982-8_2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Listeria monocytogenes is a major food-borne pathogen and causative agent of a fatal disease, listeriosis. Stringent regulatory guidelines and zero tolerance policy toward this bacterium necessitate rapid, accurate, and reliable methods of identification and subtyping. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF MS) has recently become a method of choice for routine identification of pathogens in clinical settings and has largely replaced biochemical assays. Identification relies on well-curated databases such as SARAMIS. Extensive use of SARAMIS to generate consensus mass spectra, in conjunction with statistical analysis, such as partial least square-discriminant analysis and hierarchical cluster analysis, is useful in subtyping bacteria. While MALDI-ToF MS has been extensively used for pathogen detection, its application in bacterial subtyping has been limited. The protocol describes a MALDI-ToF MS workflow as a single tool for simultaneous identification and subtyping of L. monocytogenes directly from solid culture medium.
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Affiliation(s)
- Snehal R Jadhav
- Centre for Advanced Sensory Science, School of Exercise and Nutrition Sciences, Deakin University, Melbourne, VIC, Australia.
- Department of Chemistry and Biotechnology, Swinburne University of Technology, Melbourne, VIC, Australia.
| | - Rohan M Shah
- Department of Chemistry and Biotechnology, Swinburne University of Technology, Melbourne, VIC, Australia
| | - Enzo A Palombo
- Department of Chemistry and Biotechnology, Swinburne University of Technology, Melbourne, VIC, Australia.
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23
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Petrucelli MF, de Abreu MH, Cantelli BAM, Segura GG, Nishimura FG, Bitencourt TA, Marins M, Fachin AL. Epidemiology and Diagnostic Perspectives of Dermatophytoses. J Fungi (Basel) 2020; 6:E310. [PMID: 33238603 PMCID: PMC7712040 DOI: 10.3390/jof6040310] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 10/27/2020] [Accepted: 11/02/2020] [Indexed: 12/12/2022] Open
Abstract
Dermatophytoses affect about 25% of the world population, and the filamentous fungus Trichophyton rubrum is the main causative agent of this group of diseases. Dermatomycoses are caused by pathogenic fungi that generally trigger superficial infections and that feed on keratinized substrates such as skin, hair, and nails. However, there are an increasing number of reports describing dermatophytes that invade deep layers such as the dermis and hypodermis and that can cause deep infections in diabetic and immunocompromised patients, as well as in individuals with immunodeficiency. Despite the high incidence and importance of dermatophytes in clinical mycology, the diagnosis of this type of infection is not always accurate. The conventional methods most commonly used for mycological diagnosis are based on the identification of microbiological and biochemical features. However, in view of the limitations of these conventional methods, molecular diagnostic techniques are increasingly being used because of their higher sensitivity, specificity and rapidity and have become more accessible. The most widely used molecular techniques are conventional PCR, quantitative PCR, multiplex PCR, nested, PCR, PCR-RFLP, and PCR-ELISA. Another promising technique for the identification of microorganisms is the analysis of protein profiles by MALDI-TOF MS. Molecular techniques are promising but it is necessary to improve the quality and availability of the information in genomic and proteomic databases in order to streamline the use of bioinformatics in the identification of dermatophytes of clinical interest.
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Affiliation(s)
- Monise Fazolin Petrucelli
- Biotechnology Unit, Unaerp, Av. Costábile Romano, 2201, Ribeirão Preto SP 14096-900, Brazil; (M.F.P.); (M.H.d.A.); (B.A.M.C.); (G.G.S.); (F.G.N.); (T.A.B.); (M.M.)
| | - Mariana Heinzen de Abreu
- Biotechnology Unit, Unaerp, Av. Costábile Romano, 2201, Ribeirão Preto SP 14096-900, Brazil; (M.F.P.); (M.H.d.A.); (B.A.M.C.); (G.G.S.); (F.G.N.); (T.A.B.); (M.M.)
| | - Bruna Aline Michelotto Cantelli
- Biotechnology Unit, Unaerp, Av. Costábile Romano, 2201, Ribeirão Preto SP 14096-900, Brazil; (M.F.P.); (M.H.d.A.); (B.A.M.C.); (G.G.S.); (F.G.N.); (T.A.B.); (M.M.)
| | - Gabriela Gonzalez Segura
- Biotechnology Unit, Unaerp, Av. Costábile Romano, 2201, Ribeirão Preto SP 14096-900, Brazil; (M.F.P.); (M.H.d.A.); (B.A.M.C.); (G.G.S.); (F.G.N.); (T.A.B.); (M.M.)
| | - Felipe Garcia Nishimura
- Biotechnology Unit, Unaerp, Av. Costábile Romano, 2201, Ribeirão Preto SP 14096-900, Brazil; (M.F.P.); (M.H.d.A.); (B.A.M.C.); (G.G.S.); (F.G.N.); (T.A.B.); (M.M.)
| | - Tamires Aparecida Bitencourt
- Biotechnology Unit, Unaerp, Av. Costábile Romano, 2201, Ribeirão Preto SP 14096-900, Brazil; (M.F.P.); (M.H.d.A.); (B.A.M.C.); (G.G.S.); (F.G.N.); (T.A.B.); (M.M.)
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto SP 14049-900, Brazil
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto SP 14049-900, Brazil
| | - Mozart Marins
- Biotechnology Unit, Unaerp, Av. Costábile Romano, 2201, Ribeirão Preto SP 14096-900, Brazil; (M.F.P.); (M.H.d.A.); (B.A.M.C.); (G.G.S.); (F.G.N.); (T.A.B.); (M.M.)
| | - Ana Lúcia Fachin
- Biotechnology Unit, Unaerp, Av. Costábile Romano, 2201, Ribeirão Preto SP 14096-900, Brazil; (M.F.P.); (M.H.d.A.); (B.A.M.C.); (G.G.S.); (F.G.N.); (T.A.B.); (M.M.)
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Drake MJ. Re: The Urethral Microbiota: A Missing Link in the Female Urinary Microbiota. Eur Urol 2020; 79:428. [PMID: 33143949 DOI: 10.1016/j.eururo.2020.10.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 10/15/2020] [Indexed: 10/23/2022]
Affiliation(s)
- Marcus J Drake
- Bristol Urological Institute, University of Bristol, Southmead Hospital, Bristol, UK.
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25
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Ko HM, Jo JH, Baek HG. Effective Identification of Ochrobactrum anthropi Isolated from Clinical Specimens. KOREAN JOURNAL OF CLINICAL LABORATORY SCIENCE 2020. [DOI: 10.15324/kjcls.2020.52.3.221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Hyun-Mi Ko
- Dental Science Research Institute, Department of Oral Anatomy, School of Dentistry, Chonnam National University, Gwangju, Korea
| | - Jun-Hyeon Jo
- Department of Laboratory Medicine, Kwangju Christian Hospital, Gwangju, Korea
| | - Hae-Gyeong Baek
- Department of Laboratory Medicine, Kwangju Christian Hospital, Gwangju, Korea
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26
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Iles RK, Zmuidinaite R, Iles JK, Carnell G, Sampson A, Heeney JL. Development of a Clinical MALDI-ToF Mass Spectrometry Assay for SARS-CoV-2: Rational Design and Multi-Disciplinary Team Work. Diagnostics (Basel) 2020; 10:E746. [PMID: 32987950 PMCID: PMC7600155 DOI: 10.3390/diagnostics10100746] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/22/2020] [Accepted: 09/22/2020] [Indexed: 12/14/2022] Open
Abstract
The COVID-19 pandemic caused by the SARS-CoV-2 coronavirus has stretched national testing capacities to breaking points in almost all countries of the world. The need to rapidly screen vast numbers of a country's population in order to control the spread of the infection is paramount. However, the logistical requirement for reagent supply (and associated cost) of RT-PCR based testing (the current front-line test) have been hugely problematic. Mass spectrometry-based methods using swab and gargle samples have been reported with promise, but have not approached the task from a systematic analysis of the entire diagnostic process. Here, the pipeline from sample processing, the biological characteristics of the pathogen in human biofluid, the downstream bio- and physical-chemistry and the all-important data processing with clinical interpretation and reporting, are carefully compiled into a single high-throughput and reproducible rapid process. Utilizing MALDI-ToF mass spectrometric detection to viral envelope glycoproteins in a systems biology-multidisciplinary team approach, we have achieved a multifaceted clinical MALDI ToF MS screening test, primarily (but not limited to) SARS-CoV-2, with direct application to other future epidemics/pandemics that may arise. The clinical information generated not only includes SARS-CoV-2 coronavirus detection-(Spike protein fragments S1, S2b, S2a peaks), but other respiratory viral infections detected as well as an assessment of generalised oral upper respiratory immune response (elevated total Ig light chain peak) and a measure of the viral immune response (elevated intensity of IgA heavy chain peak). The advantages of the method include; (1) ease of sampling, (2) speed of analysis, and much reduced cost of testing. These features reveal the diagnostic utility of MALDI-ToF mass spectrometry as a powerful and economically attractive global solution.
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Affiliation(s)
- Ray K. Iles
- MAPSciences the iLAB, Stannard Way, Bedford MK44 3RZ, UK; (R.Z.); (J.K.I.)
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, Cambridge University, Madingley Road, Cambridge CB3 0ES, UK; (G.C.); (A.S.); (J.L.H.)
- NISAD, Medicon Village, SE-223 81 Lund, Sweden
| | - Raminta Zmuidinaite
- MAPSciences the iLAB, Stannard Way, Bedford MK44 3RZ, UK; (R.Z.); (J.K.I.)
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, Cambridge University, Madingley Road, Cambridge CB3 0ES, UK; (G.C.); (A.S.); (J.L.H.)
| | - Jason K. Iles
- MAPSciences the iLAB, Stannard Way, Bedford MK44 3RZ, UK; (R.Z.); (J.K.I.)
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, Cambridge University, Madingley Road, Cambridge CB3 0ES, UK; (G.C.); (A.S.); (J.L.H.)
| | - George Carnell
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, Cambridge University, Madingley Road, Cambridge CB3 0ES, UK; (G.C.); (A.S.); (J.L.H.)
| | - Alex Sampson
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, Cambridge University, Madingley Road, Cambridge CB3 0ES, UK; (G.C.); (A.S.); (J.L.H.)
| | - Jonathan L. Heeney
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, Cambridge University, Madingley Road, Cambridge CB3 0ES, UK; (G.C.); (A.S.); (J.L.H.)
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27
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Dominguez DC. A profile of the Simplexa™ Bordetella Direct assay for the detection and differentiation of Bordetella pertussis and Bordetella parapertussis in nasopharyngeal swabs. Expert Rev Mol Diagn 2020; 20:889-894. [PMID: 32885709 DOI: 10.1080/14737159.2020.1819240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
INTRODUCTION Pertussis is a highly contagious respiratory infection caused by Bordetella pertussis and to minor extent B. parapertussis. Despite high vaccination coverage, epidemics persist worldwide. Laboratory testing with the capacity to support increasing demand and generate fast and accurate results is needed to promptly provide treatment to mitigate symptoms, prevent transmission, and thus impact infection control and disease surveillance. AREAS COVERED This review will describe the features of the Simplexa™ Bordetella Direct Assay and compare this technology with other existing assays. Unmet needs and future directions will be discussed. EXPERT COMMENTARY Resurgence of pertussis highlights the importance of reliable and accurate diagnosis. The Simplexa™ Bordetella Direct Assay provides an easy workflow, reduced hand-on time, less risk of contamination, and rapid turnaround time. The use of efficient molecular assays in routine clinical laboratory is valuable for increasing demand, improvement of infection control, and surveillance.
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Affiliation(s)
- Delfina C Dominguez
- Clinical Laboratory Science/Public Health Sciences, The University of Texas at El Paso , El Paso, TX, USA
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28
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Rcheulishvili N, Zhang Y, Papukashvili D, Deng YL. Survey and Evaluation of Spacecraft-Associated Aluminum-Degrading Microbes and Their Rapid Identification Methods. ASTROBIOLOGY 2020; 20:925-934. [PMID: 32783563 DOI: 10.1089/ast.2019.2078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Aluminum corrosion has become a major obstacle in spacecraft construction given that aluminum is used extensively throughout the construction process. Despite its many attributes in strength and durability, aluminum is susceptible to corrosion, in particular, corrosion due to microbial contamination. Scientists have encountered a number of problems with microbial aluminum corrosion within spacecraft components. Here, we summarize recent findings with regard to the phenomenon of microbiologically influenced corrosion (MIC) on space stations in the context of microbial strains isolated from the Mir space station (Mir) and the International Space Station (ISS). Given that strains found on spacecraft are of terrestrial origin, an understanding of the contribution of Al-corrosive microbes to corrosion and related risks to space travel and astronaut health is essential for implementation of prevention strategies. Accordingly, an efficient rapid identification method of microbes with the capability to degrade aluminum is proposed. In particular, onboard implementation of a matrix-assisted laser desorption/ionization-time of flight mass spectrometer (MALDI-TOF MS) is addressed. The use of a MALDI-TOF MS on board spacecraft will be crucial to future successes in space travel given that traditional methods of identifying corrosive species are far more time-consuming. Identification of microbes by way of a MALDI-TOF MS may also aid in the study of microbial corrosion and be a valuable asset for MIC prevention.
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Affiliation(s)
- Nino Rcheulishvili
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, Beijing Institute of Technology, Beijing, China
| | - Ying Zhang
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, Beijing Institute of Technology, Beijing, China
| | - Dimitri Papukashvili
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, Beijing Institute of Technology, Beijing, China
| | - Yu-Lin Deng
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, Beijing Institute of Technology, Beijing, China
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29
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Brummaier T, Hinfothong P, Soe NL, Tongmanakit J, Watthanaworawit W, Ling C. Brachybacterium nesterenkovii isolated from a human blood culture-a first report. New Microbes New Infect 2020; 36:100699. [PMID: 32566231 PMCID: PMC7296184 DOI: 10.1016/j.nmni.2020.100699] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/09/2020] [Accepted: 05/13/2020] [Indexed: 10/27/2022] Open
Abstract
Brachybacterium is a genus of Gram-positive bacteria that rarely causes infections in humans. Here we report the case of an 8-month-old infant who presented with an acute febrile illness. During the diagnostic process, a blood culture was positive with Gram-positive cocci that were identified as Brachybacterium nesterenkovii by MALDI-TOF. As a result of the unclear clinical significance of this isolate and the continuous febrile state, a second blood culture was taken and returned B. nesterenkovii once more. To our knowledge this is the first time that B. nesterenkovii has been isolated from human blood cultures during the course of a systemic infection.
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Affiliation(s)
- T Brummaier
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - P Hinfothong
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - N L Soe
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - J Tongmanakit
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - W Watthanaworawit
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - C Ling
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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30
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Saracino IM, Pavoni M, Saccomanno L, Fiorini G, Pesci V, Foschi C, Piccirilli G, Bernardini G, Holton J, Figura N, Lazzarotto T, Borghi C, Vaira B. Antimicrobial Efficacy of Five Probiotic Strains Against Helicobacter pylori. Antibiotics (Basel) 2020; 9:antibiotics9050244. [PMID: 32403331 PMCID: PMC7277513 DOI: 10.3390/antibiotics9050244] [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: 04/03/2020] [Revised: 05/06/2020] [Accepted: 05/09/2020] [Indexed: 12/19/2022] Open
Abstract
Treatment of Helicobacter pylori (H. pylori) infection is a challenge for clinicians. The large increase in drug-resistant strains makes the formulation of new therapeutic strategies fundamental. The frequent onset of side effects during antibiotic treatment (mainly due to intestinal dysbiosis) should not be underestimated as it may cause the interruption of treatment, failure of H. pylori eradication and clonal selection of resistant bacteria. Probiotic integration during antibiotic treatment can exert a dual function: a direct antagonistic effect on H. pylori and a balancing effect on dysbiosis. Therefore, it fulfills the definition of a new therapeutic strategy to successfully treat H. pylori infection. Data reported in literature give promising but discrepant results. Aim: To assess in vitro bacteriostatic and bactericidal activity of probiotic strains against H. pylori. Materials and methods: L. casei, L. paracasei, L. acidophilus, B. lactis and S. thermophilus strains were used. Agar well diffusion and time-kill curves were carried out to detect bacteriostatic and bactericidal activity, respectively. Results: All probiotic strains showed both bacteriostatic and bactericidal activity vs. H. pylori. Conclusions: Such findings prompted us to plan a protocol of treatment in which probiotics are given to infected patients in association with antibiotic therapy.
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Affiliation(s)
- Ilaria Maria Saracino
- Department of Surgical and Medical Sciences, University of Bologna, 40138 Bologna, Italy; (I.M.S.); (M.P.); (L.S.); (G.F.); (V.P.); (C.B.)
| | - Matteo Pavoni
- Department of Surgical and Medical Sciences, University of Bologna, 40138 Bologna, Italy; (I.M.S.); (M.P.); (L.S.); (G.F.); (V.P.); (C.B.)
| | - Laura Saccomanno
- Department of Surgical and Medical Sciences, University of Bologna, 40138 Bologna, Italy; (I.M.S.); (M.P.); (L.S.); (G.F.); (V.P.); (C.B.)
| | - Giulia Fiorini
- Department of Surgical and Medical Sciences, University of Bologna, 40138 Bologna, Italy; (I.M.S.); (M.P.); (L.S.); (G.F.); (V.P.); (C.B.)
| | - Valeria Pesci
- Department of Surgical and Medical Sciences, University of Bologna, 40138 Bologna, Italy; (I.M.S.); (M.P.); (L.S.); (G.F.); (V.P.); (C.B.)
| | - Claudio Foschi
- Microbiology and Clinical Microbiology, Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138 Bologna, Italy; (C.F.); (G.P.); (T.L.)
| | - Giulia Piccirilli
- Microbiology and Clinical Microbiology, Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138 Bologna, Italy; (C.F.); (G.P.); (T.L.)
| | - Giulia Bernardini
- Department of Biotechnology Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy; (G.B.); (N.F.)
| | - John Holton
- Department of Health & Social Sciences, University of Middlesex, London NW4 4HE, UK;
| | - Natale Figura
- Department of Biotechnology Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy; (G.B.); (N.F.)
| | - Tiziana Lazzarotto
- Microbiology and Clinical Microbiology, Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138 Bologna, Italy; (C.F.); (G.P.); (T.L.)
| | - Claudio Borghi
- Department of Surgical and Medical Sciences, University of Bologna, 40138 Bologna, Italy; (I.M.S.); (M.P.); (L.S.); (G.F.); (V.P.); (C.B.)
| | - Berardino Vaira
- Department of Surgical and Medical Sciences, University of Bologna, 40138 Bologna, Italy; (I.M.S.); (M.P.); (L.S.); (G.F.); (V.P.); (C.B.)
- Correspondence: ; Tel./Fax: +39-0512-144-140
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Mursalin MH, Livingston ET, Callegan MC. The cereus matter of Bacillus endophthalmitis. Exp Eye Res 2020; 193:107959. [PMID: 32032628 PMCID: PMC7113113 DOI: 10.1016/j.exer.2020.107959] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 01/06/2020] [Accepted: 02/03/2020] [Indexed: 02/06/2023]
Abstract
Bacillus cereus (B. cereus) endophthalmitis is a devastating intraocular infection primarily associated with post-traumatic injuries. The majority of these infections result in substantial vision loss, if not loss of the eye itself, within 12-48 h. Multifactorial mechanisms that lead to the innate intraocular inflammatory response during this disease include the combination of robust bacterial replication, migration of the organism throughout the eye, and toxin production by the organism. Therefore, the window of therapeutic intervention in B. cereus endophthalmitis is quite narrow compared to that of other pathogens which cause this disease. Understanding the interaction of bacterial and host factors is critical in understanding the disease and formulating more rational therapeutics for salvaging vision. In this review, we will discuss clinical and research findings related to B. cereus endophthalmitis in terms of the organism's virulence and inflammogenic potential, and strategies for improving of current therapeutic regimens for this blinding disease.
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Affiliation(s)
- Md Huzzatul Mursalin
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Erin T Livingston
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Michelle C Callegan
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Department of Ophthalmology, Dean McGee Eye Institute, Oklahoma City, OK, USA; Oklahoma Center for Neuroscience, Oklahoma City, OK, USA; Dean A. McGee Eye Institute, Oklahoma City, OK, USA.
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32
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Xu X, Xiao N, Yang M, Su Y, Guo Y. Discrimination of the microbial subspecies using the ribosomal protein spectra coupled with the metabolite high resolution mass spectra. Talanta 2020; 208:120361. [DOI: 10.1016/j.talanta.2019.120361] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 09/01/2019] [Accepted: 09/14/2019] [Indexed: 10/26/2022]
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33
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Zehnbauer BA. The Journal of Molecular Diagnostics: 20 Years Defining Professional Practice. J Mol Diagn 2019; 21:938-942. [PMID: 31635797 DOI: 10.1016/j.jmoldx.2019.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 09/09/2019] [Indexed: 01/09/2023] Open
Abstract
This editorial highlights 20 years of JMD defining professional practice.
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Affiliation(s)
- Barbara A Zehnbauer
- Department of Pathology, Emory University School of Medicine, Atlanta, Georgia (Editor-in-Chief).
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34
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Nguyen HQ, Lee D, Kim Y, Paek M, Kim M, Jang KS, Oh J, Lee YS, Yeon JE, Lubman DM, Kim J. Platelet Factor 4 as a Novel Exosome Marker in MALDI-MS Analysis of Exosomes from Human Serum. Anal Chem 2019; 91:13297-13305. [PMID: 31549806 DOI: 10.1021/acs.analchem.9b04198] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Exosomes are nanosized vesicles commonly found in biological fluids as a result of a secretion process involving endosomes and multivesicular bodies. The isolation and analysis of exosomes can be useful for noninvasive clinical diagnosis of a variety of human diseases. We investigated the utility of analyzing exosomal proteins, using matrix-assisted laser desorption/ionization combined with Fourier-transform ion cyclotron resonance mass spectrometry (MALDI-FTICR-MS), as a means of determining the presence of exosomes. MALDI-FTICR-MS analyses of exosomes enriched from human serum via centrifugation in a mass range of m/z 1000-20 000 yielded a distinctive protein around m/z 7766. The high mass accuracy and resolution of MALDI-FTICR-MS allowed for reliable comparisons against a protein database, through which the protein was identified as platelet factor 4 (PLF4), whose singly charged protein peak has an elemental composition of C341H577N96O101S4+, with a theoretical most abundant isotopic peak at m/z 7765.194 and a theoretical average peak at m/z 7766. The MALDI-TOF MS analysis of exosomes from the serum of 27 patients with different states of liver diseases provided the most abundant PLF4 peak for each mass spectrum, along with several additional minor peaks. In conclusion, MALDI-MS is suitable as an alternative exosome detection method, serving as a valuable confirmation tool, greatly decreasing the time and workload associated with exosome identification.
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Affiliation(s)
- Huu-Quang Nguyen
- Department of Chemistry , Chungnam National University , Daejeon , Republic of Korea
| | - Dabin Lee
- Department of Chemistry , Chungnam National University , Daejeon , Republic of Korea
| | - Yeoseon Kim
- Department of Chemistry , Chungnam National University , Daejeon , Republic of Korea
| | - Minseok Paek
- Department of Chemistry , Chungnam National University , Daejeon , Republic of Korea
| | - Minsun Kim
- Scientific Instruments Reliability Assessment Center , Korea Basic Science Institute , Daejeon , Republic of Korea
| | - Kyoung-Soon Jang
- Biomedical Omics Center , Korea Basic Science Institute , Cheongju , Republic of Korea
| | - Jooyeon Oh
- ASTA Corporation , Suwon-si , Gyeonggi-Do , Republic of Korea
| | - Young-Sun Lee
- Department of Internal Medicine , Korea University College of Medicine , Seoul , South Korea
| | - Jong Eun Yeon
- Department of Internal Medicine , Korea University College of Medicine , Seoul , South Korea
| | - David M Lubman
- Department of Surgery , University of Michigan Medical Center , Ann Arbor , Michigan 48109 , United States
| | - Jeongkwon Kim
- Department of Chemistry , Chungnam National University , Daejeon , Republic of Korea
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35
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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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36
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Shin DJ, Andini N, Hsieh K, Yang S, Wang TH. Emerging Analytical Techniques for Rapid Pathogen Identification and Susceptibility Testing. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2019; 12:41-67. [PMID: 30939033 PMCID: PMC7369001 DOI: 10.1146/annurev-anchem-061318-115529] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
In the face of looming threats from multi-drug resistant microorganisms, there is a growing need for technologies that will enable rapid identification and drug susceptibility profiling of these pathogens in health care settings. In particular, recent progress in microfluidics and nucleic acid amplification is pushing the boundaries of timescale for diagnosing bacterial infections. With a diverse range of techniques and parallel developments in the field of analytical chemistry, an integrative perspective is needed to understand the significance of these developments. This review examines the scope of new developments in assay technologies grouped by key enabling domains of research. First, we examine recent development in nucleic acid amplification assays for rapid identification and drug susceptibility testing in bacterial infections. Next, we examine advances in microfluidics that facilitate acceleration of diagnostic assays via integration and scale. Lastly, recentdevelopments in biosensor technologies are reviewed. We conclude this review with perspectives on the use of emerging concepts to develop paradigm-changing assays.
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Affiliation(s)
- Dong Jin Shin
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA;
| | - Nadya Andini
- Department of Emergency Medicine, Stanford University, Stanford, California 94305, USA;
| | - Kuangwen Hsieh
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA;
| | - Samuel Yang
- Department of Emergency Medicine, Stanford University, Stanford, California 94305, USA;
| | - Tza-Huei Wang
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA;
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Moraxella nonliquefaciens and M. osloensis Are Important Moraxella Species That Cause Ocular Infections. Microorganisms 2019; 7:microorganisms7060163. [PMID: 31167433 PMCID: PMC6616425 DOI: 10.3390/microorganisms7060163] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 05/31/2019] [Accepted: 05/31/2019] [Indexed: 01/29/2023] Open
Abstract
Moraxella is an ocular bacterial pathogen isolated in cases of keratitis, conjunctivitis, and endophthalmitis. Gram-negative brick-shaped diplobacilli from ocular specimens, and slow growth in culture, are early indications of Moraxella ocular infection; however, identifying Moraxella to species can be complex and inconsistent. In this study, bacteria consistent with Moraxella were identified to species using: (1) DNA sequencing coupled with vancomycin susceptibility, (2) MALDI-TOF mass spectrometry, and (3) the Biolog ID system. Study samples consisted of nine ATCC Moraxella controls, 82 isolates from keratitis, 21 isolates from conjunctivitis, and 4 isolates from endophthalmitis. The ATCC controls were correctly identified. For keratitis, 66 (80.5%) were identified as M. nonliquefaciens, 7 (9.0%) as M. lacunata, 5 (6%) as M. osloensis, 2 (2.5%) as Acinetobacter lwoffii, 1 (1.0%) as M. bovis/nonliquefaciens, and 1 (1.0%) as M. osloensis/nonliquefaciens. For conjunctivitis, 9 (43.0%) were identified as M. osloensis, 6 (29.0%) as M. nonliquefaciens, 3 (14.3%) as Roseomonas, 2 (9.5%) as Acinetobacter (parvus, junii), and 1 (4.5%) as M. catarrhalis/nonliquefaciens. From endophthalmitis, 3 of 4 of the isolates were M. nonliquefaciens. Overall, M. nonliquefaciens and M. osloensis were identified in 70% (75 of 107) and 13% (14 of 107) of cases, respectively, totaling 83% (89 of 107). M. nonliquefaciens and M. osloensis are important bacterial pathogens of the eye as determined by DNA sequencing, MALDI-TOF MS, and Biolog. Although Moraxella catarrhalis is a clinical pathogen, other species of Moraxella appear to have a prominent role in eye infections.
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Chamberlain CA, Rubio VY, Garrett TJ. Strain-Level Differentiation of Bacteria by Paper Spray Ionization Mass Spectrometry. Anal Chem 2019; 91:4964-4968. [PMID: 30888152 PMCID: PMC6537876 DOI: 10.1021/acs.analchem.9b00330] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Paper spray ionization mass spectrometry (PSI-MS) is a relatively new analytical technique allowing for rapid mass spectrometric analysis of biological samples with little or no sample preparation. The expeditious nature of the analysis and minimal requirement for sample preparation make PSI-MS a promising avenue for future clinical assays with one potential application in the identification of different types of bacteria. Although past PSI-MS studies have demonstrated the ability to distinguish between bacteria of different species and morphological classes, achieving within-species strain-level differentiation has never been performed. In this report, we demonstrate the first strain-level bacterial differentiation by PSI-MS with the mammalian intestinal bacterium Oxalobacter formigenes ( Oxf). This novel application holds promising clinical significance as it could be used to differentiate between pathogenic bacteria and their harmless, commensal relatives, saving time and money in clinical diagnostics. Both whole cells and cell lysates of Oxf strains HC1 and OxWR were analyzed using the Prosolia Velox 360TM PSI source coupled to a Thermo Scientific Q Exactive high-resolution mass spectrometer with a rapid 30 s analytical method. Multivariate statistical analysis followed by examination of significant features provided for and confirmed differentiation between Oxf HC1 and OxWR. We report a panel of strain-exclusive metabolites that could serve as potential strain-indicating biomarkers.
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Affiliation(s)
- Casey A. Chamberlain
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida 32610, United States
| | - Vanessa Y. Rubio
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Timothy J. Garrett
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida 32610, United States
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Arastehfar A, Daneshnia F, Farahyar S, Fang W, Salimi M, Salehi M, Hagen F, Weihua P, Roudbary M, Boekhout T. Incidence and spectrum of yeast species isolated from the oral cavity of Iranian patients suffering from hematological malignancies. J Oral Microbiol 2019; 11:1601061. [PMID: 31044032 PMCID: PMC6484487 DOI: 10.1080/20002297.2019.1601061] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 01/30/2019] [Accepted: 03/22/2019] [Indexed: 01/05/2023] Open
Abstract
Background: Oral candidiasis (OC) has a profound effect on the life quality of immunocompromised patients, such as those undergoing chemotherapy. Objective: Systematic investigation of clinical outcome and microbiological features of yeast isolates recovered from the oral cavity of 150 Iranian patients with hematological malignancies. Design: MALDI-TOF MS, 21-plex PCR, and rDNA sequencing were used for identification. Antifungal susceptibility testing (broth microdilution, CLSI M27-A3/S4) and genotypic diversity of yeast isolates (amplified fragment length polymorphism) were assessed. Results: Nystatin treatment resulted in 70% therapeutic failure and administration of 150 mg fluconazole (FLZ) + nystatin for patients with OC relapse showed 70% clinical failure. Previous history of OC was significantly correlated with FLZ treatment requirement and nystatin failure (P = 0.005, α < 0.05). Candida albicans (80.3%) and Kluyveromyces marxianus (C. kefyr) (12.7%) were the two most prevalent yeast species isolated. FLZ and AMB exhibited the highest geometric mean values. 21-PCR showed 98.9% agreement with MALDI-TOF MS. K. marxianus isolates had the same genotype, while C. albicans isolates grouped in 15 genotypes. Conclusions: Marked rate of therapeutic failure of nystatin necessitated OC treatment with systemic antifungals. K. marxianus was the second most prevalent yeast and 21-plex PCR could be considered as an inexpensive identification tool.
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Affiliation(s)
- Amir Arastehfar
- Department of Yeasts , Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands
| | - Farnaz Daneshnia
- Department of Yeasts , Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands
| | - Shirin Farahyar
- Department of Medical Mycology and Parasitology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.,Microbial Biotechnology Research Center (MBiRC), Iran University of Medical Sciences, Tehran, Iran
| | - Wenjie Fang
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Maryam Salimi
- Department of Medical Mycology and Parasitology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammadreza Salehi
- Department of infectious diseases and Tropical Medicine, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Ferry Hagen
- Department of Yeasts , Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands
| | - Pan Weihua
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Maryam Roudbary
- Department of Medical Mycology and Parasitology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Teun Boekhout
- Department of Yeasts , Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands.,Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, Netherlands
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Galata V, Backes C, Laczny CC, Hemmrich-Stanisak G, Li H, Smoot L, Posch AE, Schmolke S, Bischoff M, von Müller L, Plum A, Franke A, Keller A. Comparing genome versus proteome-based identification of clinical bacterial isolates. Brief Bioinform 2019; 19:495-505. [PMID: 28013236 DOI: 10.1093/bib/bbw122] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Indexed: 11/14/2022] Open
Abstract
Whole-genome sequencing (WGS) is gaining importance in the analysis of bacterial cultures derived from patients with infectious diseases. Existing computational tools for WGS-based identification have, however, been evaluated on previously defined data relying thereby unwarily on the available taxonomic information.Here, we newly sequenced 846 clinical gram-negative bacterial isolates representing multiple distinct genera and compared the performance of five tools (CLARK, Kaiju, Kraken, DIAMOND/MEGAN and TUIT). To establish a faithful 'gold standard', the expert-driven taxonomy was compared with identifications based on matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) analysis. Additionally, the tools were also evaluated using a data set of 200 Staphylococcus aureus isolates.CLARK and Kraken (with k =31) performed best with 626 (100%) and 193 (99.5%) correct species classifications for the gram-negative and S. aureus isolates, respectively. Moreover, CLARK and Kraken demonstrated highest mean F-measure values (85.5/87.9% and 94.4/94.7% for the two data sets, respectively) in comparison with DIAMOND/MEGAN (71 and 85.3%), Kaiju (41.8 and 18.9%) and TUIT (34.5 and 86.5%). Finally, CLARK, Kaiju and Kraken outperformed the other tools by a factor of 30 to 170 fold in terms of runtime.We conclude that the application of nucleotide-based tools using k-mers-e.g. CLARK or Kraken-allows for accurate and fast taxonomic characterization of bacterial isolates from WGS data. Hence, our results suggest WGS-based genotyping to be a promising alternative to the MS-based biotyping in clinical settings. Moreover, we suggest that complementary information should be used for the evaluation of taxonomic classification tools, as public databases may suffer from suboptimal annotations.
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Affiliation(s)
- Valentina Galata
- Chair for Clinical Bioinformatics, Saarland University, Campus Building E2.1, 66123 Saarbrücken, Germany
| | - Christina Backes
- Chair for Clinical Bioinformatics, Saarland University, Campus Building E2.1, 66123 Saarbrücken, Germany
| | - Cédric Christian Laczny
- Chair for Clinical Bioinformatics, Saarland University, Campus Building E2.1, 66123 Saarbrücken, Germany
| | - Georg Hemmrich-Stanisak
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Schittenhelmstr. 12, 24105 Kiel, Germany
| | - Howard Li
- Siemens Healthcare, R&D, 725 Potter Street, Berkeley, CA 94710, USA
| | - Laura Smoot
- Siemens Healthcare, R&D, 1584 Enterprise Blvd., West Sacramento, CA 95691, USA
| | - Andreas Emanuel Posch
- Siemens Healthcare GmbH, Strategy and Innovation, Hartmannstr. 16, 91052 Erlangen, Germany
| | - Susanne Schmolke
- Siemens Healthcare GmbH, Strategy and Innovation, Hartmannstr. 16, 91052 Erlangen, Germany
| | - Markus Bischoff
- Institute of Medical Microbiology and Hygiene, Saarland University, Kirrberger Straße, Campus Building 43, 66421 Homburg/Saar, Germany
| | - Lutz von Müller
- Institute of Medical Microbiology and Hygiene, Saarland University, Kirrberger Straße, Campus Building 43, 66421 Homburg/Saar, Germany
| | - Achim Plum
- Curetis GmbH, Max-Eyth-Str. 42, 71088 Holzgeringen, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Schittenhelmstr. 12, 24105 Kiel, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, Campus Building E2.1, 66123 Saarbrücken, Germany
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Pandey A, Jain R, Sharma A, Dhakar K, Kaira GS, Rahi P, Dhyani A, Pandey N, Adhikari P, Shouche YS. 16S rRNA gene sequencing and MALDI-TOF mass spectrometry based comparative assessment and bioprospection of psychrotolerant bacteria isolated from high altitudes under mountain ecosystem. SN APPLIED SCIENCES 2019. [DOI: 10.1007/s42452-019-0273-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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Ivanusa SY, Ivanov AM, Lazutkin MV, Chebotar AV. [Opportunities of modern laboratory diagnostics of infectious complications of acute pancreatitis (review).]. Klin Lab Diagn 2019; 64:145-152. [PMID: 31012552 DOI: 10.18821/0869-2084-2019-64-3-145-152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 03/04/2019] [Indexed: 06/09/2023]
Abstract
A systematic search of literary sources in the abstract databases Scopus, Web of Science, MedLine, the Cochrane Library, CyberLeninka, RSCI for 2010-2018. The search queries were: acute pancreatitis and complications, acute pancreatitis and diagnosis, acute pancreatitis and diagnosis and complications, acute pancreatitis and compications, and sepsis. The results of search and analysis of selected literature sources are presented. It was revealed that the currently used set of laboratory and instrumental methods of diagnosis of infectious complications of acute pancreatitis does not fully meet the needs of clinical practice. The most common of them are the determination of blood concentrations Of C-reactive protein and procalcitonin. At the same time, a number of disadvantages of these methods are noted. In the last decade, many new markers of systemic infection have been introduced into clinical practice. Some of them are currently being investigated in order to diagnose systemic infection in General and infectious complications of acute pancreatitis in particular. The most promising are such as presepsin, MID-regional Pro-adrenomedullinum, CD64 neutrophil index and some others.
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Affiliation(s)
- S Ya Ivanusa
- MGBUOBA, Military-medical Academy S.M. Kirov, 194044, St. Petersburg, Russian Federation
| | - A M Ivanov
- MGBUOBA, Military-medical Academy S.M. Kirov, 194044, St. Petersburg, Russian Federation
| | - M V Lazutkin
- MGBUOBA, Military-medical Academy S.M. Kirov, 194044, St. Petersburg, Russian Federation
| | - A V Chebotar
- MGBUOBA, Military-medical Academy S.M. Kirov, 194044, St. Petersburg, Russian Federation
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Validation of MALDI-TOF MS Biotyper database optimized for anaerobic bacteria: The ENRIA project. Anaerobe 2018; 54:224-230. [DOI: 10.1016/j.anaerobe.2018.03.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 03/06/2018] [Accepted: 03/09/2018] [Indexed: 12/25/2022]
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Khan LB, Swift S, Kamal T, Read HM. Simulation of MICROBACT Strip Assay Using Colored Liquids to Demonstrate Identification of Unknown Gram-Negative Organisms in Undergraduate Laboratory. JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION 2018; 19:19.2.76. [PMID: 29983847 PMCID: PMC6022772 DOI: 10.1128/jmbe.v19i2.1565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 04/20/2018] [Indexed: 06/08/2023]
Abstract
Identification of unknown microorganisms to the species level is an important component of a microbiology course. Modern technologies such as matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and 16S rRNA gene sequencing offer a rapid species level identification when compared to conventional phenotype-based methods, however they rely on a well-established taxonomy database and phenotypic assays can still play an important role in species determination. Another major limitation is the up-front cost of purchasing these modern specialized instruments and the requirement of skilled personnel to operate specialized equipment and software, which makes them unsuitable to use in the undergraduate teaching laboratory. Commercial biochemical identification systems such as the Oxoid Microbact™ GNB 12A/12E/24E kit is used for the identification of Enterobacteriaceae and other Gram negative bacteria in clinical and veterinary diagnostic laboratories, and food industries for disease control and treatment. In this article, we describe a method of reliably simulating this Microbact™ strip assay using artificial color liquids (which are affordable and easy to source) for the demonstration of phenotypic characterization of unknown Gram negative organisms while providing a safe teaching environment as no bacteria are used, familiarizing students with the concept of using Microbact™ 12A kit to identify a range of unknown Gram negative organisms.
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Affiliation(s)
- Latifa B. Khan
- Department of Molecular Medicine and Pathology, School of Medical Sciences, The University of Auckland, Auckland 1023, New Zealand
| | - Simon Swift
- Department of Molecular Medicine and Pathology, School of Medical Sciences, The University of Auckland, Auckland 1023, New Zealand
| | - Tania Kamal
- Department of Molecular Medicine and Pathology, School of Medical Sciences, The University of Auckland, Auckland 1023, New Zealand
- Auckland Cancer Society Research Centre, The University of Auckland, Auckland 1023, New Zealand
| | - Hannah M. Read
- Department of Molecular Medicine and Pathology, School of Medical Sciences, The University of Auckland, Auckland 1023, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland 1023, New Zealand
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45
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Gu M, Buckley M. Semi-supervised machine learning for automated species identification by collagen peptide mass fingerprinting. BMC Bioinformatics 2018; 19:241. [PMID: 29940843 PMCID: PMC6019507 DOI: 10.1186/s12859-018-2221-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Accepted: 05/28/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Biomolecular methods for species identification are increasingly being utilised in the study of changing environments, both at the microscopic and macroscopic levels. High-throughput peptide mass fingerprinting has been largely applied to bacterial identification, but increasingly used to identify archaeological and palaeontological skeletal material to yield information on past environments and human-animal interaction. However, as applications move away from predominantly domesticate and the more abundant wild fauna to a much wider range of less common taxa that do not yet have genetically-derived sequence information, robust methods of species identification and biomarker selection need to be determined. RESULTS Here we developed a supervised machine learning algorithm for classifying the species of ancient remains based on collagen fingerprinting. The aim was to minimise requirements on prior knowledge of known species while yielding satisfactory sensitivity and specificity. The algorithm uses iterations of a modified random forest classifier with a similarity scoring system to expand its identified samples. We tested it on a set of 6805 spectra and found that a high level of accuracy can be achieved with a training set of five identified specimens per taxon. CONCLUSIONS This method consistently achieves higher accuracy than two-dimensional principal component analysis and similar accuracy with hierarchical clustering using optimised parameters, which greatly reduces requirements for human input. Within the vertebrata, we demonstrate that this method was able to achieve the taxonomic resolution of family or sub-family level whereas the genus- or species-level identification may require manual interpretation or further experiments. In addition, it also identifies additional species biomarkers than those previously published.
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Affiliation(s)
- Muxin Gu
- Michael Smith Building, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PT, UK
| | - Michael Buckley
- Manchester Institute of Biotechnology, School of Earth and Environmental Sciences, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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Abstract
The increase in bacteria harboring antimicrobial resistance (AMR) is a global problem because there is a paucity of antibiotics available to treat multidrug-resistant bacterial infections in humans and animals. Detection of AMR present in bacteria that may pose a threat to veterinary and public health is routinely performed using standardized phenotypic methods. Molecular methods are often used in addition to phenotypic methods but are set to replace them in many laboratories due to the greater speed and accuracy they provide in detecting the underlying genetic mechanism(s) for AMR. In this article we describe some of the common molecular methods currently used for detection of AMR genes. These include PCR, DNA microarray, whole-genome sequencing and metagenomics, and matrix-assisted laser desorption ionization-time of flight mass spectrometry. The strengths and weaknesses of these methods are discussed, especially in the context of implementing them for routine surveillance activities on a global scale for mitigating the risk posed by AMR worldwide. Based on current popularity and ease of use, PCR and single-isolate whole-genome sequencing seem irreplaceable.
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48
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Ombelet S, Ronat JB, Walsh T, Yansouni CP, Cox J, Vlieghe E, Martiny D, Semret M, Vandenberg O, Jacobs J. Clinical bacteriology in low-resource settings: today's solutions. THE LANCET. INFECTIOUS DISEASES 2018. [PMID: 29519767 DOI: 10.1016/s1473-3099(18)30093-8] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Low-resource settings are disproportionately burdened by infectious diseases and antimicrobial resistance. Good quality clinical bacteriology through a well functioning reference laboratory network is necessary for effective resistance control, but low-resource settings face infrastructural, technical, and behavioural challenges in the implementation of clinical bacteriology. In this Personal View, we explore what constitutes successful implementation of clinical bacteriology in low-resource settings and describe a framework for implementation that is suitable for general referral hospitals in low-income and middle-income countries with a moderate infrastructure. Most microbiological techniques and equipment are not developed for the specific needs of such settings. Pending the arrival of a new generation diagnostics for these settings, we suggest focus on improving, adapting, and implementing conventional, culture-based techniques. Priorities in low-resource settings include harmonised, quality assured, and tropicalised equipment, consumables, and techniques, and rationalised bacterial identification and testing for antimicrobial resistance. Diagnostics should be integrated into clinical care and patient management; clinically relevant specimens must be appropriately selected and prioritised. Open-access training materials and information management tools should be developed. Also important is the need for onsite validation and field adoption of diagnostics in low-resource settings, with considerable shortening of the time between development and implementation of diagnostics. We argue that the implementation of clinical bacteriology in low-resource settings improves patient management, provides valuable surveillance for local antibiotic treatment guidelines and national policies, and supports containment of antimicrobial resistance and the prevention and control of hospital-acquired infections.
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Affiliation(s)
- Sien Ombelet
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium; Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium.
| | | | | | - Cedric P Yansouni
- JD MacLean Centre for Tropical Diseases, McGill University Health Centre, Montreal, QC, Canada
| | - Janneke Cox
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Erika Vlieghe
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium; Department of General Internal Medicine, Infectious and Tropical Diseases, Antwerp University Hospital, Antwerp, Belgium; Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Delphine Martiny
- Department of Microbiology, LHUB-ULB, Pôle Hospitalier Universitaire de Bruxelles, Brussels, Belgium
| | - Makeda Semret
- JD MacLean Centre for Tropical Diseases, McGill University Health Centre, Montreal, QC, Canada; St Mary's Hospital Centre, Montreal, QC, Canada
| | - Olivier Vandenberg
- Department of Microbiology, LHUB-ULB, Pôle Hospitalier Universitaire de Bruxelles, Brussels, Belgium; Center for Environmental Health and Occupational Health, Public Health School, Université Libre de Bruxelles, Brussels, Belgium
| | - Jan Jacobs
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium; Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
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Huang CH, Huang L. Rapid species- and subspecies-specific level classification and identification of Lactobacillus casei group members using MALDI Biotyper combined with ClinProTools. J Dairy Sci 2018; 101:979-991. [DOI: 10.3168/jds.2017-13642] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 09/30/2017] [Indexed: 12/16/2022]
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50
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Saviauk T, Kiiski JP, Nieminen MK, Tamminen NN, Roine AN, Kumpulainen PS, Hokkinen LJ, Karjalainen MT, Vuento RE, Aittoniemi JJ, Lehtimäki TJ, Oksala NK. Electronic Nose in the Detection of Wound Infection Bacteria from Bacterial Cultures: A Proof-of-Principle Study. Eur Surg Res 2018; 59:1-11. [PMID: 29320769 DOI: 10.1159/000485461] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 11/20/2017] [Indexed: 01/06/2023]
Abstract
BACKGROUND Soft tissue infections, including postoperative wound infections, result in a significant burden for modern society. Rapid diagnosis of wound infections is based on bacterial stains, cultures, and polymerase chain reaction assays, and the results are available earliest after several hours, but more often not until days after. Therefore, antibiotic treatment is often administered empirically without a specific diagnosis. METHODS We employed our electronic nose (eNose) system for this proof-of-concept study, aiming to differentiate the most relevant bacteria causing wound infections utilizing a set of clinical bacterial cultures on identical blood culture dishes, and established bacterial lines from the gaseous headspace. RESULTS Our eNose system was capable of differentiating both methicillin-sensitive Staphylococcus aureus (MSSA) and methicillin-resistant Staphylococcus aureus (MRSA), Streptococcus pyogenes, Escherichia coli, Pseudomonas aeruginosa, and Clostridium perfringens with an accuracy of 78% within minutes without prior sample preparation. Most importantly, the system was capable of differentiating MRSA from MSSA with a sensitivity of 83%, a specificity of 100%, and an overall accuracy of 91%. CONCLUSIONS Our results support the concept of rapid detection of the most relevant bacteria causing wound infections and ultimately differentiating MRSA from MSSA utilizing gaseous headspace sampling with an eNose.
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Affiliation(s)
- Taavi Saviauk
- School of Medicine, University of Tampere, Tampere, Finland
| | - Juha P Kiiski
- School of Medicine, University of Tampere, Tampere, Finland.,Department of Musculoskeletal Disease, Division of Plastic Surgery, Tampere University Hospital, Tampere, Finland
| | | | | | - Antti N Roine
- School of Medicine, University of Tampere, Tampere, Finland
| | - Pekka S Kumpulainen
- Department of Automation Science and Engineering, Tampere University of Technology, Tampere, Finland
| | | | - Markus T Karjalainen
- Department of Automation Science and Engineering, Tampere University of Technology, Tampere, Finland
| | - Risto E Vuento
- Department of Clinical Microbiology, Fimlab Laboratories, Tampere, Finland
| | - Janne J Aittoniemi
- Department of Clinical Microbiology, Fimlab Laboratories, Tampere, Finland
| | - Terho J Lehtimäki
- School of Medicine, University of Tampere, Tampere, Finland.,Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
| | - Niku K Oksala
- Department of Surgery, School of Medicine, University of Tampere, Tampere, Finland.,Department of Vascular Surgery, Tampere University Hospital, Tampere, Finland
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