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Feucherolles M. Integrating MALDI-TOF Mass Spectrometry with Machine Learning Techniques for Rapid Antimicrobial Resistance Screening of Foodborne Bacterial Pathogens. Methods Mol Biol 2025; 2852:85-103. [PMID: 39235738 DOI: 10.1007/978-1-0716-4100-2_6] [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] [Indexed: 09/06/2024]
Abstract
Although MALDI-TOF mass spectrometry (MS) is considered as the gold standard for rapid and cost-effective identification of microorganisms in routine laboratory practices, its capability for antimicrobial resistance (AMR) detection has received limited focus. Nevertheless, recent studies explored the predictive performance of MALDI-TOF MS for detecting AMR in clinical pathogens when machine learning techniques are applied. This chapter describes a routine MALDI-TOF MS workflow for the rapid screening of AMR in foodborne pathogens, with Campylobacter spp. as a study model.
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Affiliation(s)
- Maureen Feucherolles
- Molecular and Thermal Analysis Platform, Luxembourg Institute of Science and Technology, Belvaux, Luxembourg.
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2
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Kim JK, Yun HY, Kim JS, Kim W, Lee CS, Kim BG, Jeong HJ. Development of fluorescence-linked immunosorbent assay for rapid detection of Staphylococcus aureus. Appl Microbiol Biotechnol 2024; 108:2. [PMID: 38153552 DOI: 10.1007/s00253-023-12836-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 09/22/2023] [Accepted: 09/30/2023] [Indexed: 12/29/2023]
Abstract
Staphylococcus aureus is a major pathogen that causes infections and life-threatening diseases. Although antibiotics, such as methicillin, have been used, methicillin-resistant S. aureus (MRSA) causes high morbidity and mortality rates, and conventional detection methods are difficult to be used because of time-consuming process. To control the spread of S. aureus, a development of a rapid and simple detection method is required. In this study, we generated a fluorescent anti-S. aureus antibody, and established a novel fluorescence-linked immunosorbent assay (FLISA)-based S. aureus detection method. The method showed high sensitivity and low limit of detection toward MRSA detection. The assay time for FLISA was 5 h, which was faster than that of conventional enzyme-linked immunosorbent assay (ELISA) or rapid ELISA. Moreover, the FLISA-based detection method was applied to diagnose clinically isolated MRSA samples that required only 5.3 h of preincubation. The FLISA method developed in this study can be widely applied as a useful tool for convenient S. aureus detection. KEY POINTS: • A fluorescence-linked immunosorbent assay-based S. aureus detection method • Simultaneous quantification of a maximum of 96 samples within 5 h • Application of the novel system to diagnosis clinical isolates.
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Affiliation(s)
- Joo-Kyung Kim
- Interdisciplinary Program for Biochemical Engineering and Biotechnology, Seoul National University, Seoul, 08826, South Korea
| | - Hyun-Young Yun
- Department of Biological and Chemical Engineering, Hongik University, Sejong, 30016, South Korea
| | - Jae-Seok Kim
- Department of Laboratory Medicine, Kangdong Sacred Heart Hospital, Hallym University College of Medicine, Seoul, 05355, South Korea
| | - Wooseong Kim
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, 03760, South Korea
| | - Chang-Soo Lee
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon, 34134, South Korea
| | - Byung-Gee Kim
- Interdisciplinary Program for Biochemical Engineering and Biotechnology, Seoul National University, Seoul, 08826, South Korea
| | - Hee-Jin Jeong
- Department of Biological and Chemical Engineering, Hongik University, Sejong, 30016, South Korea.
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3
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Chen FH, Cheng CY, Chou SW, Yang CH, Lu IC, Yeh ML. High-Resolution Intact Protein Analysis via Phase-Modulated, Stepwise Frequency Scan Ion Trap Mass Spectrometry. Anal Chem 2024. [PMID: 39238447 DOI: 10.1021/acs.analchem.4c02775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2024]
Abstract
Mass spectrometry (MS) using an electron multiplier for intact protein analysis remains limited. Because of the massive size and complex structure of proteins, the slow flight speed of their ions results in few secondary electrons and thus low detection sensitivity and poor spectral resolution. Thus, we present a compact ion trap-mass spectrometry approach to directly detect ion packets and obtain the high-resolution molecular signature of proteins. The disturbances causing deviations of ion motion and mass conversion have been clarified in advance. The radio frequency waveform used to manipulate ions is proposed to be a sequence of constant-frequency steps, interconnected by short time-outs, resulting in least dispersive distortion. Furthermore, more such constant-phase conjunctions are arranged in each step to compensate for fluctuations resulting from defects in the system and operation. In addition, two auxiliary pulses are generated in the right phase of each step to select ions of a specific secular state to detect one clean and sharp spectral line.This study demonstrates a top-down approach for the MS measurement of cytochrome C molecules, resulting in a spectral profile of the protein in its natural state at a resolution of 20 Da. Additionally, quick MS scans of other proteins were performed.
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Affiliation(s)
- Fang-Hsu Chen
- Department of Biomedical Engineering, National Cheng Kung University, Tainan City 701, Taiwan
| | - Chun-Yen Cheng
- Department of Biomedical Engineering, National Cheng Kung University, Tainan City 701, Taiwan
- AcroMass Technologies Inc., Hukou, Hsinchu 30352, Taiwan
| | - Szu-Wei Chou
- AcroMass Technologies Inc., Hukou, Hsinchu 30352, Taiwan
| | - Cheng-Han Yang
- Department of Chemistry, National Chung Hsing University, Taichung City 40227, Taiwan
| | - I-Chung Lu
- Department of Chemistry, National Chung Hsing University, Taichung City 40227, Taiwan
| | - Ming-Long Yeh
- Department of Biomedical Engineering, National Cheng Kung University, Tainan City 701, Taiwan
- Medical Device Innovation Center, National Cheng Kung University, Tainan City, 701, Taiwan
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Zrelli M, Ferjani A, Nouira M, Hammami S, Ghithia N, Mouelhi L, Debbeche R, Raoult D, Boutiba Ben Boubaker I. Diversity in gut microbiota among colorectal cancer patients: findings from a case-control study conducted at a Tunisian University Hospital. Discov Oncol 2024; 15:402. [PMID: 39225843 PMCID: PMC11372012 DOI: 10.1007/s12672-024-01232-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 08/12/2024] [Indexed: 09/04/2024] Open
Abstract
PURPOSE Globally, colorectal cancer (CRC) is among the most prevalent cancers. One distinctive feature of colorectal cancer is its close relationship to the gut microbiota, which is a crucial component of the tumor microenvironment. Over the last ten years, research has demonstrated that colorectal cancer is accompanied with dysbiosis of gut bacteria, fungi, viruses, and Archaea, and that these alterations may be causal. OBJECTIVES This study aimed to evaluate the disruption of the microorganism composition in the intestine, especially bacteria and to determine their relationship with colorectal cancer. METHODS An evaluation system for determining colorectal cancer (CRC) risk and prognosis can be established more easily with the help of accurate gut microbiota profiling. Stool samples from 14 CRC patients and 13 controls were collected and the flora relative abundance was measured using targeted quantitative PCR (qPCR) assays to evaluate diagnostic potential of selected biomarkers: Streptococcus gallolyticus and Enterococcus faecalis. Culture and MALDI-TOF mass spectrometry were coupled to identify the gut microbiota in both colorectal cancer and control groups. RESULTS Compared with controls, the gut microbiota of CRC patients showed an increase in the abundance of Enterococcus, Fusobacterium and Streptococcus. At the species level, the CRC enriched bacterium including Escherichia coli, Enterococcus faecalis, Fusobacterium nucleatum, Streptococcus gallolyticus, Flavoni fractorplautii and Eggerthella lenta acted as promising biomarkers for early detection of CRC. CONCLUSION This study highlights the potential of gut microbiota biomarkers as a promising non-invasive tool for the accurate detection and distinction of individuals with CRC.
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Affiliation(s)
- Mariem Zrelli
- Faculty of Medicine of Tunis, Research Laboratory ''Antimicrobial Resistance'' LR99ES09, University of Tunis El Manar, 1007, Tunis, Tunisia.
- Laboratory of Microbiology, Charles Nicolle Hospital, 1006, Tunis, Tunisia.
| | - Asma Ferjani
- Faculty of Medicine of Tunis, Research Laboratory ''Antimicrobial Resistance'' LR99ES09, University of Tunis El Manar, 1007, Tunis, Tunisia
- Laboratory of Microbiology, Charles Nicolle Hospital, 1006, Tunis, Tunisia
| | - Mariem Nouira
- Epidemiology Department, Charles Nicolle Hospital, Faculty of Medicine of Tunis, University of Tunis El Manar, 1006, Tunis, Tunisia
| | - Sirine Hammami
- Department of Gastroenterology, Charles Nicolle Hospital, 1006, Tunis, Tunisia
| | - Nadine Ghithia
- Department of Gastroenterology, Charles Nicolle Hospital, 1006, Tunis, Tunisia
| | - Leila Mouelhi
- Department of Gastroenterology, Charles Nicolle Hospital, 1006, Tunis, Tunisia
| | - Radhouane Debbeche
- Department of Gastroenterology, Charles Nicolle Hospital, 1006, Tunis, Tunisia
| | - Didier Raoult
- IRD, APHM, MEPHI, Aix Marseille Univ, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.
- IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.
| | - Ilhem Boutiba Ben Boubaker
- Faculty of Medicine of Tunis, Research Laboratory ''Antimicrobial Resistance'' LR99ES09, University of Tunis El Manar, 1007, Tunis, Tunisia
- Laboratory of Microbiology, Charles Nicolle Hospital, 1006, Tunis, Tunisia
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Anedda E, Alexa EA, Farrell ML, Croffie M, Madigan G, Morris D, Burgess CM. Comparison of antimicrobial resistant Enterobacterales isolates from the dairy production environment in low and high zinc containing regions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 953:175905. [PMID: 39218095 DOI: 10.1016/j.scitotenv.2024.175905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Revised: 08/21/2024] [Accepted: 08/28/2024] [Indexed: 09/04/2024]
Abstract
Heavy metals occur naturally in the environment, and their concentration varies in soil across different regions. However, the presence of heavy metals may influence the antimicrobial resistance (AMR) in bacterial populations. Therefore, the objective of this study was to investigate and characterise the antimicrobial resistance profiles of Enterobacterales in soil and bovine milk filters from high and low zinc-containing regions in Ireland. In total, 50 soil samples and 29 milk filters were collected from two geographic locations with varying soil zinc concentrations. Samples were cultured for the enumeration and detection of Enterobacterales. Specifically, extended-spectrum beta-lactamase-producing Enterobacterales, carbapenem-resistant Enterobacterales and ciprofloxacin-resistant Enterobacterales were isolated using selective media. Species identification was performed using MALDI-TOF. The phenotypic resistance profiles of selected Enterobacterales were determined by disk diffusion testing, following EUCAST and CLSI criteria; while, the genotypic resistance profiles of the same isolates were determined by whole genome sequencing (WGS). Heavy metal concentrations were also measured for all soil samples. A total of 40 antimicrobial resistant Enterobacterales were identified in soil (n = 31) and milk filters (n = 9). The predominant species detected in the high zinc-containing region was Escherichia coli in both sample types (soil n = 10, milk filters n = 2), while in the low zinc-containing region Serratia fonticola was predominant in soil samples (n = 8) and E. coli in milk filters (n = 4). Ten E. coli isolates identified from soil samples in the high zinc-containing region were multidrug resistant, showing resistance to all the antimicrobials tested, except for carbapenems. The WGS findings confirmed the phenotypic resistance results. Moreover, zinc resistance-associated genes and genes encoding for efflux pumps were identified. The current study revealed distinct phenotypic resistance profiles of Enterobacterales in low and high zinc-containing regions, and highlighted the benefit of utilising milk filters for AMR surveillance in dairy production.
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Affiliation(s)
- E Anedda
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Ireland; Food Safety Department, Teagasc Food Research Centre Ashtown, Dublin, Ireland
| | - E A Alexa
- School of Food Science and Environmental Health, Technological University Dublin, Dublin, Ireland
| | - M L Farrell
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Ireland; School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - M Croffie
- Environment, Soils and Land Use Department, Teagasc Johnstown Castle Research Centre, Wexford, Ireland
| | - G Madigan
- Bacteriology/Parasitology Division, Department of Agriculture, Food and the Marine, Backweston Complex, Celbridge, Ireland
| | - D Morris
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Ireland.
| | - C M Burgess
- Food Safety Department, Teagasc Food Research Centre Ashtown, Dublin, Ireland.
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Galletti MFBM, Hecht JA, McQuiston JR, Gartin J, Cochran J, Blocher BH, Ayres BN, Allerdice MEJ, Beati L, Nicholson WL, Snellgrove AN, Paddock CD. Applying MALDI-TOF MS to resolve morphologic and genetic similarities between two Dermacentor tick species of public health importance. Sci Rep 2024; 14:19834. [PMID: 39191821 DOI: 10.1038/s41598-024-69768-8] [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: 03/07/2024] [Accepted: 08/08/2024] [Indexed: 08/29/2024] Open
Abstract
Hard ticks (Acari: Ixodidae) have been historically identified by morphological methods which require highly specialized expertise and more recently by DNA-based molecular assays that involve high costs. Although both approaches provide complementary data for tick identification, each method has limitations which restrict their use on large-scale settings such as regional or national tick surveillance programs. To overcome those obstacles, the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been introduced as a cost-efficient method for the identification of various organisms, as it balances performance, speed, and high data output. Here we describe the use of this technology to validate the distinction of two closely related Dermacentor tick species based on the development of the first nationwide MALDI-TOF MS reference database described to date. The dataset obtained from this protein-based approach confirms that tick specimens collected from United States regions west of the Rocky Mountains and identified previously as Dermacentor variabilis are the recently described species, Dermacentor similis. Therefore, we propose that this integrative taxonomic tool can facilitate vector and vector-borne pathogen surveillance programs in the United States and elsewhere.
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Affiliation(s)
- Maria F B M Galletti
- Rickettsial Zoonoses Branch, Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, USA.
| | - Joy A Hecht
- Rickettsial Zoonoses Branch, Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, USA
| | - John R McQuiston
- Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, USA
| | - Jarrett Gartin
- Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, USA
| | - Jake Cochran
- Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, USA
| | - Bessie H Blocher
- Rickettsial Zoonoses Branch, Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, USA
| | - Bryan N Ayres
- Rickettsial Zoonoses Branch, Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, USA
| | - Michelle E J Allerdice
- Rickettsial Zoonoses Branch, Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, USA
| | - Lorenza Beati
- United States National Tick Collection, Institute for Coastal Plain Science, Georgia Southern University, Statesboro, USA
| | - William L Nicholson
- Rickettsial Zoonoses Branch, Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, USA
| | - Alyssa N Snellgrove
- Rickettsial Zoonoses Branch, Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, USA
| | - Christopher D Paddock
- Rickettsial Zoonoses Branch, Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, USA
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Sonalio K, Boyen F, Devriendt B, Chantziaras I, Beuckelaere L, Biebaut E, Haesebrouck F, Santamarta I, de Oliveira LG, Maes D. Rationalizing the use of common parameters and technological tools to follow up Mycoplasma hyopneumoniae infections in pigs. Porcine Health Manag 2024; 10:31. [PMID: 39180129 PMCID: PMC11342468 DOI: 10.1186/s40813-024-00381-x] [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: 01/05/2024] [Accepted: 08/05/2024] [Indexed: 08/26/2024] Open
Abstract
BACKGROUND Mycoplasma (M.) hyopneumoniae is associated with respiratory disease in pigs and is the primary agent of enzootic pneumonia. Quantification of M. hyopneumoniae-related outcome parameters can be difficult, expensive, and time-consuming, in both research and field settings. In addition to well-established methods, technological tools are becoming available to monitor various aspects of relevant animal- and environment-related features, often in real-time. Therefore, this study aimed to assess whether certain parameters, such as animal movement and body temperature using microchips (IMT), correlate with established parameters and whether the currently used parameters can be rationalized. RESULTS The percentage of movement was significantly reduced by M. hyopneumoniae infection in pigs (p < 0.05), where the M. hyopneumoniae-infected group showed a lower percentage of movement (1.9%) when compared to the negative control group (6.9%). On the other hand, macroscopic (MLCL) and microscopic (MLL) lung lesions, respiratory disease score (RDS), M. hyopneumoniae-DNA load, and anti-M. hyopneumoniae antibody levels increased significantly in the M. hyopneumoniae-infected group 28 days post-inoculation (p < 0.05). Moderate (r > 0.30) to very strong correlations (> 0.80) were observed between the abovementioned parameters (p < 0.05), except for IMT. A significant and moderate correlation was reported between IMT and rectal temperature (r = 0.49; p < 0.05). Last, the average daily weight gain and the percentage of air in the lung were not affected by M. hyopneumoniae infection (p > 0.05). CONCLUSIONS M. hyopneumoniae infection significantly reduced the movement of piglets and increased lung lesions, M. hyopneumoniae-DNA load, and anti-M. hyopneumoniae antibody levels; and, good correlations were observed between most parameters, indicating a direct relationship between them. Thus, we suggest that changes in movement might be a reliable indicator of M. hyopneumoniae infection in pigs, and that a selected group of parameters-specifically RDS, MLCL, MLL, M. hyopneumoniae-DNA load, anti-M. hyopneumoniae antibody levels, and movement-are optimal to assess M. hyopneumoniae infection under experimental conditions.
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Affiliation(s)
- Karina Sonalio
- Department of Internal Medicine, Reproduction and Population Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium.
- Department of Veterinary Clinic and Surgery, School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal, Brazil.
| | - Filip Boyen
- Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Bert Devriendt
- Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Ilias Chantziaras
- Department of Internal Medicine, Reproduction and Population Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Lisa Beuckelaere
- Department of Internal Medicine, Reproduction and Population Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Evelien Biebaut
- Department of Internal Medicine, Reproduction and Population Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Freddy Haesebrouck
- Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | | | - Luís Guilherme de Oliveira
- Department of Veterinary Clinic and Surgery, School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal, Brazil
| | - Dominiek Maes
- Department of Internal Medicine, Reproduction and Population Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
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Abdelaziz MNS, Zayda MG, Maung AT, El-Telbany M, Mohammadi TN, Lwin SZC, Linn KZ, Wang C, Yuan L, Masuda Y, Honjoh KI, Miyamoto T. Genetic Characterization, Antibiotic Resistance, and Virulence Genes Profiling of Bacillus cereus Strains from Various Foods in Japan. Antibiotics (Basel) 2024; 13:774. [PMID: 39200074 PMCID: PMC11351997 DOI: 10.3390/antibiotics13080774] [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: 07/19/2024] [Revised: 08/12/2024] [Accepted: 08/14/2024] [Indexed: 09/01/2024] Open
Abstract
Bacillus cereus sensu stricto is a foodborne pathogen that causes food poisoning. Their spore and biofilm-forming abilities persist in various environments and foods. This study investigated the prevalence, virulence, antibiotic resistance, and genetic diversity of B. cereus s. s. strains isolated from various food samples. Of 179 samples, 22.34% were positive for B. cereus s. s., with significantly high detection rates in milk products and raw chicken meat. Forty strains were isolated from positive samples. Matrix-assisted laser desorption ionization/time of flight mass spectrometry analysis revealed nine distinct clusters and multi-locus sequence typing revealed 34 sequence types including 23 novel sequences, demonstrating high genetic diversity among the isolates. PCR analysis revealed that all the strains contained at least one toxin gene, but none contained the cytK gene. Antibiotic resistance tests revealed that all isolates were classified as multidrug-resistant, with high resistance levels, particularly to β-lactam antibiotics and vancomycin, but were susceptible to gentamicin. All isolates showed variations in biofilm formation. This study highlights the significant public health risk due to B. cereus s. s. and underscores the need for stringent monitoring and control measures in food production to manage antimicrobial resistance and ensure food safety.
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Affiliation(s)
- Marwa Nabil Sayed Abdelaziz
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan; (M.N.S.A.); (A.T.M.); (M.E.-T.); (S.Z.C.L.); (K.Z.L.); (C.W.); (L.Y.); (Y.M.); (K.-i.H.)
- Department of Food Hygiene, Animal Health Research Institute (AHRI), Agriculture Research Center (ARC), Giza 12618, Egypt
| | - Mahmoud Gamaleldin Zayda
- Department of Food Hygiene, Faculty of Veterinary Medicine, University of Sadat City, Sadat City 32897, Egypt;
| | - Aye Thida Maung
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan; (M.N.S.A.); (A.T.M.); (M.E.-T.); (S.Z.C.L.); (K.Z.L.); (C.W.); (L.Y.); (Y.M.); (K.-i.H.)
| | - Mohamed El-Telbany
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan; (M.N.S.A.); (A.T.M.); (M.E.-T.); (S.Z.C.L.); (K.Z.L.); (C.W.); (L.Y.); (Y.M.); (K.-i.H.)
| | | | - Su Zar Chi Lwin
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan; (M.N.S.A.); (A.T.M.); (M.E.-T.); (S.Z.C.L.); (K.Z.L.); (C.W.); (L.Y.); (Y.M.); (K.-i.H.)
| | - Khin Zar Linn
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan; (M.N.S.A.); (A.T.M.); (M.E.-T.); (S.Z.C.L.); (K.Z.L.); (C.W.); (L.Y.); (Y.M.); (K.-i.H.)
| | - Chen Wang
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan; (M.N.S.A.); (A.T.M.); (M.E.-T.); (S.Z.C.L.); (K.Z.L.); (C.W.); (L.Y.); (Y.M.); (K.-i.H.)
| | - Lu Yuan
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan; (M.N.S.A.); (A.T.M.); (M.E.-T.); (S.Z.C.L.); (K.Z.L.); (C.W.); (L.Y.); (Y.M.); (K.-i.H.)
| | - Yoshimitsu Masuda
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan; (M.N.S.A.); (A.T.M.); (M.E.-T.); (S.Z.C.L.); (K.Z.L.); (C.W.); (L.Y.); (Y.M.); (K.-i.H.)
| | - Ken-ichi Honjoh
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan; (M.N.S.A.); (A.T.M.); (M.E.-T.); (S.Z.C.L.); (K.Z.L.); (C.W.); (L.Y.); (Y.M.); (K.-i.H.)
| | - Takahisa Miyamoto
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan; (M.N.S.A.); (A.T.M.); (M.E.-T.); (S.Z.C.L.); (K.Z.L.); (C.W.); (L.Y.); (Y.M.); (K.-i.H.)
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9
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Talim J, Martins I, Messias C, Sabino H, Oliveira L, Pinto T, Albuquerque J, Cerqueira A, Dolores Í, Moreira B, Silveira R, Neves F, Rabello R. Multidrug-Resistant Staphylococcus aureus Colonizing Pigs and Farm Workers in Rio de Janeiro State, Brazil: Potential Interspecies Transmission of Livestock-Associated MRSA (LA-MRSA) ST398. Antibiotics (Basel) 2024; 13:767. [PMID: 39200067 PMCID: PMC11350785 DOI: 10.3390/antibiotics13080767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 08/08/2024] [Accepted: 08/11/2024] [Indexed: 09/01/2024] Open
Abstract
Multidrug-resistant (MDR) Staphylococcus aureus has been increasingly isolated from pigs and people in close contact with them, especially livestock-associated methicillin-resistant S. aureus (LA-MRSA). In this cross-sectional study, we investigated S. aureus colonization in pigs and farm workers, their resistance profile, and genetic background to estimate interspecies transmission potential within farms from Rio de Janeiro state, Brazil, between 2014 and 2019. We collected nasal swabs from 230 pigs and 27 workers from 16 and 10 farms, respectively. Five MDR strains were subjected to whole genome sequencing. Fourteen (6.1%) pigs and seven (25.9%) humans were colonized with S. aureus, mostly (64-71%) MDR strains. Resistance to clindamycin, erythromycin, penicillin, and tetracycline was the most common among the pig and human strains investigated. MDR strains shared several resistance genes [blaZ, dfrG, fexA, lsa(E), and tet(M)]. Pig and human strains recovered from the same farm shared the same genetic background and antimicrobial resistance profile. LA-MRSA ST398-SCCmecV-t011 was isolated from pigs in two farms and from a farm worker in one of them, suggesting interspecies transmission. The association between pig management practices and MDR S. aureus colonization might be investigated in additional studies.
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Affiliation(s)
- Joana Talim
- Department of Microbiology and Parasitology, Instituto Biomédico, Universidade Federal Fluminense, Niterói 24020-150, RJ, Brazil; (J.T.); (H.S.); (J.A.); (A.C.); (F.N.)
| | - Ianick Martins
- Faculty of Medicine, Universidade Federal Fluminense, Niterói 24033-900, RJ, Brazil;
| | - Cassio Messias
- Centro de Ciências Biológicas e da Natureza, Universidade Federal do Acre, Rio Branco 69915-900, AC, Brazil;
| | - Hellen Sabino
- Department of Microbiology and Parasitology, Instituto Biomédico, Universidade Federal Fluminense, Niterói 24020-150, RJ, Brazil; (J.T.); (H.S.); (J.A.); (A.C.); (F.N.)
| | - Laura Oliveira
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil; (L.O.); (T.P.); (B.M.)
| | - Tatiana Pinto
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil; (L.O.); (T.P.); (B.M.)
| | - Julia Albuquerque
- Department of Microbiology and Parasitology, Instituto Biomédico, Universidade Federal Fluminense, Niterói 24020-150, RJ, Brazil; (J.T.); (H.S.); (J.A.); (A.C.); (F.N.)
| | - Aloysio Cerqueira
- Department of Microbiology and Parasitology, Instituto Biomédico, Universidade Federal Fluminense, Niterói 24020-150, RJ, Brazil; (J.T.); (H.S.); (J.A.); (A.C.); (F.N.)
| | - Ítalo Dolores
- Departament of Clinical Medicine, Faculty of Medicine, Universidade de São Paulo, São Paulo 01246-903, SP, Brazil;
| | - Beatriz Moreira
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil; (L.O.); (T.P.); (B.M.)
| | - Renato Silveira
- Department of Morphology, Instituto Biomédico, Universidade Federal Fluminense, Niterói 24210-130, RJ, Brazil;
| | - Felipe Neves
- Department of Microbiology and Parasitology, Instituto Biomédico, Universidade Federal Fluminense, Niterói 24020-150, RJ, Brazil; (J.T.); (H.S.); (J.A.); (A.C.); (F.N.)
| | - Renata Rabello
- Department of Microbiology and Parasitology, Instituto Biomédico, Universidade Federal Fluminense, Niterói 24020-150, RJ, Brazil; (J.T.); (H.S.); (J.A.); (A.C.); (F.N.)
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10
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Kowalczyk K, Coraça-Huber DC, Wille-Kollmar W, Berktold M, Nagl M. Activity of N-Chlorotaurine against Periodontal Pathogens. Int J Mol Sci 2024; 25:8357. [PMID: 39125925 PMCID: PMC11313407 DOI: 10.3390/ijms25158357] [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: 06/27/2024] [Revised: 07/24/2024] [Accepted: 07/29/2024] [Indexed: 08/12/2024] Open
Abstract
Dental plaque bacteria play an important role in the pathogenicity of periodontitis and peri-implantitis. Therefore, antimicrobial agents are one means of treatment. N-chlorotaurine (NCT) as an endogenous well-tolerated topical antiseptic could be of advantage for this purpose. Accordingly, its microbicidal activity against some dental plaque bacteria was investigated at therapeutic concentrations in vitro. In quantitative killing assays, the activity of NCT against planktonic bacteria and against biofilms grown for 48 h on implantation screws was tested. Electron microscopy was used to demonstrate the formation of biofilm and its morphological changes. The killing of planktonic bacteria of all tested species, namely Streptococcus sanguinis, Streptococcus salivarius, Streptococcus oralis, Streptococcus cristatus, Rothia aeria, and Capnocytophaga ochracea, was shown within 10-20 min by 1% NCT in 0.01 M phosphate-buffered saline at 37 °C. Bacteria grown on screws for 24 h were inactivated by 1% NCT after 15-20 min as well, but the formation of biofilm on the screws was visible in electron microscopy not before 48 h. The killing of biofilms by 1% NCT was demonstrated after 30 min (streptococci) and 40 min (R. aeria). As expected, NCT has broad activity against dental plaque bacteria as well and should be further investigated on its clinical efficacy in periodontitis and peri-implantitis.
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Affiliation(s)
- Kacper Kowalczyk
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (K.K.); (M.B.)
| | - Débora C. Coraça-Huber
- Research Laboratory for Biofilms and Implant Associated Infections (BIOFILM LAB), University Hospital for Orthopaedics and Traumatology, Medical University of Innsbruck, A-6020 Innsbruck, Austria;
| | | | - Michael Berktold
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (K.K.); (M.B.)
| | - Markus Nagl
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (K.K.); (M.B.)
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11
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Koumaki D, Maraki S, Evangelou G, Rovithi E, Petrou D, Apokidou ES, Gregoriou S, Koumaki V, Ioannou P, Zografaki K, Doxastaki A, Papadopoulou K, Stafylaki D, Mavromanolaki VE, Krasagakis K. Clinical Significance and Microbiological Characteristics of Staphylococcus lugdunensis in Cutaneous Infections. J Clin Med 2024; 13:4327. [PMID: 39124594 PMCID: PMC11312498 DOI: 10.3390/jcm13154327] [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: 06/23/2024] [Revised: 07/21/2024] [Accepted: 07/23/2024] [Indexed: 08/12/2024] Open
Abstract
Background/Objectives:Staphylococcus lugdunensis is a coagulase-negative staphylococcus (CoNS) commonly found on human skin. Unlike other CoNS, S. lugdunensis has a notable potential to cause severe infections comparable to Staphylococcus aureus. This study aimed to characterize the clinical and microbiological profile of patients with S. lugdunensis skin infections at a single center. Methods: We conducted a retrospective analysis of patient records from the Dermatology Department of the University Hospital of Heraklion, Greece, covering the period from January 2014 to January 2024. Patients' clinical presentations, demographics, infection sites, comorbidities, prior infections, antimicrobial treatments, and therapeutic responses were examined. Specimens were collected, transported, and processed according to standardized microbiological protocols. Bacterial identification and antibiotic susceptibility testing were performed using the Vitek 2 automated system and MALDI-TOF MS, with results interpreted according to Clinical and Laboratory Standards Institute (CLSI) criteria. Results: A total of 123 skin specimens positive for S. lugdunensis were analyzed. The cohort comprised 62 males (50.4%) and 61 females (49.6%), with a mean age of 40.24 ± 20.14 years. Most specimens were collected from pus (84%), primarily from below the waist (66.7%). Hidradenitis suppurativa (26%) was the most common condition associated with S. lugdunensis, followed by folliculitis, abscesses, ulcers, cellulitis, and acne. Co-infections with other bacteria were noted in 49.6% of cases, and 25.2% of infections were nosocomially acquired. The majority of patients (65%) received systemic antibiotics, predominantly amoxicillin/clavulanic acid, cefuroxime axetil, and doxycycline, with a cure rate of 100%. All isolates were susceptible to several antibiotics, though resistance to penicillin (28.5%) and clindamycin (36%) was observed. Conclusions:S. lugdunensis is a significant pathogen in skin infections, capable of causing severe disease. The high cure rate demonstrates the effectiveness of appropriate antibiotic therapy. Continued monitoring and antimicrobial stewardship are essential to manage resistance and ensure effective treatment.
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Affiliation(s)
- Dimitra Koumaki
- Dermatology Department, University Hospital of Heraklion, 71110 Heraklion, Greece; (G.E.); (E.R.); (D.P.); (K.Z.); (A.D.); (K.K.)
| | - Sofia Maraki
- Department of Clinical Microbiology, University Hospital of Heraklion, 71110 Heraklion, Greece; (S.M.); (D.S.)
| | - Georgios Evangelou
- Dermatology Department, University Hospital of Heraklion, 71110 Heraklion, Greece; (G.E.); (E.R.); (D.P.); (K.Z.); (A.D.); (K.K.)
| | - Evangelia Rovithi
- Dermatology Department, University Hospital of Heraklion, 71110 Heraklion, Greece; (G.E.); (E.R.); (D.P.); (K.Z.); (A.D.); (K.K.)
| | - Danae Petrou
- Dermatology Department, University Hospital of Heraklion, 71110 Heraklion, Greece; (G.E.); (E.R.); (D.P.); (K.Z.); (A.D.); (K.K.)
| | - Erato Solia Apokidou
- Department of Internal Medicine, Agios Nikolaos General Hospital, Knosou 4, 72100 Agios Nikolaos, Greece;
| | - Stamatios Gregoriou
- 1st Department of Dermatology and Venereology, Medical School of Athens, National and Kapodistrian University of Athens, Andreas Sygros Hospital, I. Dragoumi 5, 16121 Athens, Greece;
| | - Vasiliki Koumaki
- Department of Medical Microbiology, Medical School of Athens, National and Kapodistrian University of Athens, 75 Mikras Asias Str., Goudi, 11527 Athens, Greece;
| | - Petros Ioannou
- Department of Internal Medicine, University Hospital of Heraklion, 71110 Heraklion, Greece
- School of Medicine, University of Crete, 70003 Heraklion, Greece
| | - Kyriaki Zografaki
- Dermatology Department, University Hospital of Heraklion, 71110 Heraklion, Greece; (G.E.); (E.R.); (D.P.); (K.Z.); (A.D.); (K.K.)
| | - Aikaterini Doxastaki
- Dermatology Department, University Hospital of Heraklion, 71110 Heraklion, Greece; (G.E.); (E.R.); (D.P.); (K.Z.); (A.D.); (K.K.)
| | - Kalliopi Papadopoulou
- 2nd Department of Internal Medicine, General Hospital of Venizeleio, Knossou Avenue 44, 71409 Heraklion, Greece;
| | - Dimitra Stafylaki
- Department of Clinical Microbiology, University Hospital of Heraklion, 71110 Heraklion, Greece; (S.M.); (D.S.)
| | | | - Konstantinos Krasagakis
- Dermatology Department, University Hospital of Heraklion, 71110 Heraklion, Greece; (G.E.); (E.R.); (D.P.); (K.Z.); (A.D.); (K.K.)
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12
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Konadu AB, Ampofo PC, Akyeh ML, Hewlett SA, Osei-Tutu K, Nyako EA. Comparative evaluation of selected concentrations of sodium hypochlorite on the outcome of endodontic therapy among Ghanaians. PLoS One 2024; 19:e0306693. [PMID: 38976717 PMCID: PMC11230539 DOI: 10.1371/journal.pone.0306693] [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: 03/13/2024] [Accepted: 06/21/2024] [Indexed: 07/10/2024] Open
Abstract
BACKGROUND Endodontic treatment is one of the main dental treatments to manage inflamed or infected root canal systems of teeth. The success of endodontic treatment principally depends on eradicating microorganisms in the root canal by chemo-mechanical debridement with irrigation solutions like sodium hypochlorite (NaOCl). NaOCl has been used in concentrations ranging from 0.5% to 5.25%. This study determined the antimicrobial effectiveness of selected concentrations (0.5%, 1.0%, 2.6%, and 5.2%) of NaOCl in endodontic treatment. METHODS The study sites were the University of Ghana Dental School (UGDS) and Noguchi Memorial Institute for Medical Research (NMIMR). Sixty infected single-rooted single-canal teeth were used. Before (S1) and after (S2), root canal samples during the endodontic treatment with the selected concentrations of NaOCl were examined via anaerobic and aerobic cultures. The isolates were identified using Matrix Assisted Laser Desorption Ionization-Time Of Flight Mass Spectrometry (MALDI-TOF MS). RESULTS All S1 samples were positive for cultivable bacteria. Fifty-three (53) different microbial species belonging to 20 different microbial genera were isolated. Streptococcus viridans was the most frequently isolated microbe. There were zero isolates in the root canals irrigated with 2.6% and 5.2% NaOCl. Two teeth had isolates in the groups irrigated with the lower concentrations (0.5% and 1.0%) of NaOCl. The persistent bacteria were one species each of Streptococcus mitis and Streptococcus oralis, respectively. CONCLUSION Root canal treatments using chemo-mechanical preparation with the selected concentrations (0.5%, 1.0%, 2.6%, and 5.2%) of NaOCl were effective in significantly reducing the microbial load, and for the 5.2% and 2.6% concentrations, in eliminating all the microorganisms.
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Affiliation(s)
- Akua B. Konadu
- Department of Restorative Dentistry, University of Ghana Dental School, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Patrick C. Ampofo
- Department of Restorative Dentistry, University of Ghana Dental School, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Moses L. Akyeh
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Sandra A. Hewlett
- Department of Restorative Dentistry, University of Ghana Dental School, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Kofi Osei-Tutu
- Dental Department, the Trust Specialist Hospital, Accra, Ghana
| | - Ebenezer A. Nyako
- Department of Restorative Dentistry, University of Ghana Dental School, College of Health Sciences, University of Ghana, Accra, Ghana
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13
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Avery EG, Zeppa JJ, Duncan DB, Barker KR, Fattouh R, Matukas LM, Rutherford C, Cabrera A, Sheth PM, Tran V, Goneau L, Katz K, Li XX, Kozak R. Evaluation of the utility and cost of secondary confirmatory testing for Neisseria gonorrhoeae identification from culture. Diagn Microbiol Infect Dis 2024; 109:116336. [PMID: 38723452 DOI: 10.1016/j.diagmicrobio.2024.116336] [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: 02/10/2024] [Revised: 04/17/2024] [Accepted: 04/27/2024] [Indexed: 05/28/2024]
Abstract
Current guideline recommends the use of two identification methods for Neisseria gonorrhoeae. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) is now used for primary identification and may be sufficient for definitive identification of N. gonorrhoeae. The performance of three secondary tests (BactiCard, RapID NH and NET test) were compared using 45 bacterial isolates, including 37 Neisseria species. These secondary tests demonstrated diminished specificity (67% - 88%) for N. gonorrhoeae compared with MALDI-TOF. Additionally, data from six clinical microbiology laboratories was used to compare confirmatory test costs and the agreement of results with MALDI-TOF. Discrepancies were documented for 9.4% of isolates, though all isolates (n= 288) identified by MALDI-TOF as N. gonorrhoeae were confirmed by the reference laboratory. These data demonstrate that MALDI-TOF alone is sufficient for N. gonorrhoeae identification, as secondary did not add diagnostic value but do add costs to the testing process.
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Affiliation(s)
- Ellen G Avery
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Joseph J Zeppa
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Donald Brody Duncan
- Division of Medical Microbiology, Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada; Hamilton Regional Laboratory Medicine Program, Hamilton, ON, Canada
| | - Kevin R Barker
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada; Division of Microbiology, Department of Laboratory Medicine and Genetics, Trillium Health Partners, Mississauga, ON, Canada; Institute for Better Health, Trillium Health Partners, Mississauga, Ontario, Canada
| | - Ramzi Fattouh
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada; Division of Microbiology, Department of Laboratory Medicine, St. Michael's Hospital, Unity Health Toronto, Toronto, ON, Canada
| | - Larissa M Matukas
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada; Division of Microbiology, Department of Laboratory Medicine, St. Michael's Hospital, Unity Health Toronto, Toronto, ON, Canada
| | - Candy Rutherford
- Hamilton Regional Laboratory Medicine Program, Hamilton, ON, Canada
| | - Ana Cabrera
- Pathology and Laboratory Medicine Department, London Health Sciences Centre, London, ON, Canada; Pathology and Laboratory Medicine Department, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada; Microbiology and Immunology Department, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Prameet M Sheth
- Division of Microbiology and Infectious Diseases, Kingston Health Sciences Center, Kingston, ON, Canada; Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada
| | - Vanessa Tran
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada; Public Health Ontario, Toronto, ON, Canada
| | - Lee Goneau
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada; Dynacare Laboratory, Brampton, ON, Canada
| | - Kevin Katz
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada; Shared Hospital Laboratory, Toronto, ON, Canada; Laboratory Medicine and Molecular Diagnostics, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Xena X Li
- Shared Hospital Laboratory, Toronto, ON, Canada; Laboratory Medicine and Molecular Diagnostics, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Robert Kozak
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada; Shared Hospital Laboratory, Toronto, ON, Canada; Laboratory Medicine and Molecular Diagnostics, Sunnybrook Health Sciences Centre, Toronto, ON, Canada.
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14
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Zhou C, Schwee C, Matovu RE, Wiley JD, Wiley MR, Berning BJ, Iwen PC, Fey PD. Eubacterium callanderi bacteremia: A case report. IDCases 2024; 36:e01989. [PMID: 38774153 PMCID: PMC11107343 DOI: 10.1016/j.idcr.2024.e01989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/06/2024] [Accepted: 05/07/2024] [Indexed: 05/24/2024] Open
Abstract
Eubacterium species are a group of obligated anaerobic gram-positive bacilli that are recognized as commensals of the gastrointestinal tract flora. Cases of bacteremia mediated by Eubacterium are rare. This report describes a case of bacteremia caused by Eubacterium callanderi in an 82-year-old female with a history of a cecal perforation secondary to an obstructing sigmoid stricture. The results showed the utility of using whole genome sequencing to identify the causative agent and underlined the significance to identify anaerobic organisms in diagnostic microbiology practice and to perform antimicrobial susceptibility testing to guide therapy and enhance patient outcomes.
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Affiliation(s)
- Chunyi Zhou
- Department of Pathology, Microbiology, and Immunology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Casey Schwee
- Department of Pathology, Microbiology, and Immunology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Ronald E. Matovu
- Clinical Microbiology Laboratory, Nebraska Medicine, Omaha, NE 68105, USA
| | | | - Michael R. Wiley
- Department of Pathology, Microbiology, and Immunology, University of Nebraska Medical Center, Omaha, NE 68198, USA
- PraesensBio, LLC, Omaha, NE 68124, USA
- Nebraska Public Health Laboratory, Omaha, NE 68198, USA
| | - Bennett J. Berning
- Division of Acute Care Surgery, Department of Surgery, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Peter C. Iwen
- Department of Pathology, Microbiology, and Immunology, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Nebraska Public Health Laboratory, Omaha, NE 68198, USA
| | - Paul D. Fey
- Department of Pathology, Microbiology, and Immunology, University of Nebraska Medical Center, Omaha, NE 68198, USA
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15
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Marzouk E, Abalkhail A, ALqahtani J, Alsowat K, Alanazi M, Alzaben F, Alnasser A, Alasmari A, Rawway M, Draz A, Abu-Okail A, Altwijery A, Moussa I, Alsughayyir S, Alamri S, Althagafi M, Almaliki A, Elmanssury AE, Elbehiry A. Proteome analysis, genetic characterization, and antibiotic resistance patterns of Klebsiella pneumoniae clinical isolates. AMB Express 2024; 14:54. [PMID: 38722429 PMCID: PMC11082098 DOI: 10.1186/s13568-024-01710-7] [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: 02/10/2024] [Accepted: 04/22/2024] [Indexed: 05/12/2024] Open
Abstract
Klebsiella pneumoniae (K. pneumoniae) is a member of the ESKAPE group and is responsible for severe community and healthcare-associated infections. Certain Klebsiella species have very similar phenotypes, which presents a challenge in identifying K. pneumoniae. Multidrug-resistant K. pneumoniae is also a serious global problem that needs to be addressed. A total of 190 isolates were isolated from urine (n = 69), respiratory (n = 52), wound (n = 48) and blood (n = 21) samples collected from various hospitals in the Al-Qassim, Saudi Arabia, between March 2021 and October 2022. Our study aimed to rapidly and accurately detect K. pneumoniae using the Peptide Mass Fingerprinting (PMF) technique, confirmed by real-time PCR. Additionally, screening for antibiotic susceptibility and resistance was conducted. The primary methods for identifying K. pneumoniae isolates were culture, Gram staining, and the Vitek® 2 ID Compact system. An automated MALDI Biotyper (MBT) instrument was used for proteome identification, which was subsequently confirmed using SYBR green real-time polymerase chain reaction (real-time PCR) and microfluidic electrophoresis assays. Vitek® 2 AST-GN66 cards were utilized to evaluate the antimicrobial sensitivity of K. pneumoniae isolates. According to our results, Vitek® 2 Compact accurately identified 178 out of 190 (93.68%) K. pneumoniae isolates, while the PMF technique correctly detected 188 out of 190 (98.95%) isolates with a score value of 2.00 or higher. Principal component analysis was conducted using MBT Compass software to classify K. pneumoniae isolates based on their structure. Based on the analysis of the single peak intensities generated by MBT, the highest peak values were found at 3444, 5022, 5525, 6847, and 7537 m/z. K. pneumoniae gene testing confirmed the PMF results, with 90.53% detecting entrobactin, 70% detecting 16 S rRNA, and 32.63% detecting ferric iron uptake. The resistance of the K. pneumoniae isolates to antibiotics was as follows: 64.75% for cefazolin, 62.63% for trimethoprim/sulfamethoxazole, 59.45% for ampicillin, 58.42% for cefoxitin, 57.37% for ceftriaxone, 53.68% for cefepime, 52.11% for ampicillin-sulbactam, 50.53% for ceftazidime, 52.11% for ertapenem, and 49.47% for imipenem. Based on the results of the double-disk synergy test, 93 out of 190 (48.95%) K. pneumoniae isolates were extended-spectrum beta-lactamase. In conclusion, PMF is a powerful analytical technique used to identify K. pneumoniae isolates from clinical samples based on their proteomic characteristics. K. pneumoniae isolates have shown increasing resistance to antibiotics from different classes, including carbapenem, which poses a significant threat to human health as these infections may become difficult to treat.
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Affiliation(s)
- Eman Marzouk
- Department of Public Health, College of Applied Medical Sciences, Qassim University, Buraydah, 51452 , P.O. Box 6666, Saudi Arabia.
| | - Adil Abalkhail
- Department of Public Health, College of Applied Medical Sciences, Qassim University, Buraydah, 51452 , P.O. Box 6666, Saudi Arabia
| | - Jamaan ALqahtani
- Family Medicine Department, King Fahad Armed Hospital, 23311, Jeddah, Saudi Arabia
| | - Khalid Alsowat
- Pharmacy Department, Prince Sultan Armed Forces Hospital, 42375, Medina, Saudi Arabia
| | - Menwer Alanazi
- Dental Department, King Salman Armed Forces Hospital, 47521, Tabuk, Saudi Arabia
| | - Feras Alzaben
- Department of Food Service, King Fahad Armed Forces Hospital, 23311, Jeddah, Saudi Arabia
| | - Abdulaziz Alnasser
- Psychiatry Department, Prince Sultan Military Medical City, 11632, Riyadh, Saudi Arabia
| | - Anas Alasmari
- Neurology department, king Fahad military hospital, 23311, Jeddah, Saudi Arabia
| | - Mohammed Rawway
- Biology Department, College of Science, Jouf University, 42421, Sakaka, Saudi Arabia
- Botany and Microbiology Department, Faculty of Science, Al-Azhar University, 71524, Assiut, Egypt
| | - Abdelmaged Draz
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, Qassim University, 52571, Buraydah, Saudi Arabia
| | - Akram Abu-Okail
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, Qassim University, 52571, Buraydah, Saudi Arabia
| | | | - Ihab Moussa
- Department of Botany and Microbiology, College of Science, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Sulaiman Alsughayyir
- Medical Administration, Armed Forces Medical Services, 12426, Riyadh, Saudi Arabia
| | - Saleh Alamri
- Prince Sultan Military Medical City, 13525, Riyadh, Saudi Arabia
| | - Mohammed Althagafi
- Laboratory Department, Armed Forces Center for Health Rehabilitation, 21944, Taif, Saudi Arabia
| | - Abdulrahman Almaliki
- Physiotherapy Department, Armed Forces Center for Health Rehabilitation, 21944, Taif, Saudi Arabia
| | - Ahmed Elnadif Elmanssury
- Department of Public Health, College of Applied Medical Sciences, Qassim University, Buraydah, 51452 , P.O. Box 6666, Saudi Arabia
| | - Ayman Elbehiry
- Department of Public Health, College of Applied Medical Sciences, Qassim University, Buraydah, 51452 , P.O. Box 6666, Saudi Arabia
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16
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Hortin GL. Does Increased Regulation of Laboratory-Developed Tests (LDTs) Make Sense? The Harms of Over-Regulation. J Appl Lab Med 2024; 9:646-650. [PMID: 38332567 DOI: 10.1093/jalm/jfad131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 12/11/2023] [Indexed: 02/10/2024]
Affiliation(s)
- Glen L Hortin
- Department of Pathology, Moffitt Cancer Center, Tampa, FL, United States
- Department of Oncologic Science, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
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17
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de Oliveira LMA, Simões LC, Crestani C, Costa NS, Pantoja JCDF, Rabello RF, Teixeira LM, Khan UB, Bentley S, Jamrozy D, Pinto TDCA, Zadoks RN. Long-Term Co-Circulation of Host-Specialist and Host-Generalist Lineages of Group B Streptococcus in Brazilian Dairy Cattle with Heterogeneous Antimicrobial Resistance Profiles. Antibiotics (Basel) 2024; 13:389. [PMID: 38786118 PMCID: PMC11117364 DOI: 10.3390/antibiotics13050389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 04/20/2024] [Accepted: 04/23/2024] [Indexed: 05/25/2024] Open
Abstract
Group B Streptococcus (GBS) is a major cause of contagious bovine mastitis (CBM) in Brazil. The GBS population is composed of host-generalist and host-specialist lineages, which may differ in antimicrobial resistance (AMR) and zoonotic potential, and the surveillance of bovine GBS is crucial to developing effective CBM control and prevention measures. Here, we investigated bovine GBS isolates (n = 156) collected in Brazil between 1987 and 2021 using phenotypic testing and whole-genome sequencing to uncover the molecular epidemiology of bovine GBS. Clonal complex (CC) 61/67 was the predominant clade in the 20th century; however, it was replaced by CC91, with which it shares a most common recent ancestor, in the 21st century, despite the higher prevalence of AMR in CC61/67 than in CC91, and high selection pressure for AMR from indiscriminate antimicrobial use in the Brazilian dairy industry. CC103 also emerged as a dominant CC in the 21st century, and a considerable proportion of herds had two or more GBS strains, suggesting poor biosecurity and within-herd evolution due to the chronic nature of CBM problems. The majority of bovine GBS belonged to serotype Ia or III, which was strongly correlated with CCs. Ninety-three isolates were resistant to tetracycline (≥8 μg/mL; tetO = 57, tetM = 34 or both = 2) and forty-four were resistant to erythromycin (2.0 to >4 μg/mL; ermA = 1, ermB = 38, mechanism unidentified n = 5). Only three isolates were non-susceptible to penicillin (≥8.0 μg/mL), providing opportunities for improved antimicrobial stewardship through the use of narrow-spectrum antimicrobials for the treatment of dairy cattle. The common bovine GBS clades detected in this study have rarely been reported in humans, suggesting limited risk of interspecies transmission of GBS in Brazil. This study provides new data to support improvements to CBM and AMR control, bovine GBS vaccine design, and the management of public health risks posed by bovine GBS in Brazil.
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Affiliation(s)
- Laura Maria Andrade de Oliveira
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (L.C.S.); (N.S.C.); (L.M.T.); (T.d.C.A.P.)
| | - Leandro Correia Simões
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (L.C.S.); (N.S.C.); (L.M.T.); (T.d.C.A.P.)
| | | | - Natália Silva Costa
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (L.C.S.); (N.S.C.); (L.M.T.); (T.d.C.A.P.)
| | | | | | - Lucia Martins Teixeira
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (L.C.S.); (N.S.C.); (L.M.T.); (T.d.C.A.P.)
| | - Uzma Basit Khan
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK; (U.B.K.); (S.B.); (D.J.)
| | - Stephen Bentley
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK; (U.B.K.); (S.B.); (D.J.)
| | - Dorota Jamrozy
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK; (U.B.K.); (S.B.); (D.J.)
| | - Tatiana de Castro Abreu Pinto
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (L.C.S.); (N.S.C.); (L.M.T.); (T.d.C.A.P.)
| | - Ruth N. Zadoks
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Camden, NSW 2570, Australia
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18
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Cruz S, Abreu D, Gomes R, Martins-Oliveira I, Silva-Dias A, Perez-Viso B, Cantón R, Pina-Vaz C. An improved protocol for bacteria identification by MALDI-TOF MS directly from positive blood cultures. Eur J Clin Microbiol Infect Dis 2024; 43:605-610. [PMID: 38112967 PMCID: PMC10917851 DOI: 10.1007/s10096-023-04725-3] [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: 09/25/2023] [Accepted: 11/20/2023] [Indexed: 12/21/2023]
Abstract
FASTinov® developed a rapid antimicrobial susceptibility test that includes the purification of a bacterial suspension directly from positive blood cultures (BC). In order to streamline laboratory workflow, the use of the bacterial suspension obtained through FASTinov® sample prep was tested for identification (ID) by matrix absorption laser deionization-time of flight mass spectrometry (MALDI-TOF MS) (Bruker) in 364 positive BC, and its accuracy assessed comparing with the MALDI-TOF MS ID of the next-day subcultured colonies. FASTinov sample prep was highly reliable for rapid ID directly from BC with proportion of agreement of 94.9% for Gram-positive and 96.3% for Gram-negative bacteria.
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Affiliation(s)
- Sara Cruz
- Division of Microbiology, Department of Pathology, Faculty of Medicine, University of Porto, Porto, Portugal
| | | | | | | | - Ana Silva-Dias
- FASTinov SA, Porto, Porto, Portugal
- CINTESIS-Center for Health Technology and Services Research, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Blanca Perez-Viso
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Rafael Cantón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Cidália Pina-Vaz
- Division of Microbiology, Department of Pathology, Faculty of Medicine, University of Porto, Porto, Portugal.
- FASTinov SA, Porto, Porto, Portugal.
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19
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Kale R, Chaturvedi D, Dandekar P, Jain R. Analytical techniques for screening of cannabis and derivatives from human hair specimens. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:1133-1149. [PMID: 38314866 DOI: 10.1039/d3ay00786c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Cannabis and associated substances are some of the most frequently abused drugs across the globe, mainly due to their anxiolytic and euphorigenic properties. Nowadays, the analysis of hair samples has been given high importance in forensic and analytical sciences and in clinical studies because they are associated with a low risk of infection, do not require complicated storage conditions, and offer a broad window of non-invasive detection. Analysis of hair samples is very easy compared to the analysis of blood, urine, and saliva samples. This review places particular emphasis on methodologies of analyzing hair samples containing cannabis, with a special focus on the preparation of samples for analysis, which involves screening and extraction techniques, followed by confirmatory assays. Through this manuscript, we have presented an overview of the available literature on the screening of cannabis using mass spectroscopy techniques. We have presented a detailed overview of the advantages and disadvantages of this technique, to establish it as a suitable method for the analysis of cannabis from hair samples.
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Affiliation(s)
- Rohit Kale
- Department of Biological Sciences and Biotechnology, Institute of Chemical Technology, Mumbai 400019, India.
| | - Deepa Chaturvedi
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai 400019, India.
| | - Prajakta Dandekar
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai 400019, India.
| | - Ratnesh Jain
- Department of Biological Sciences and Biotechnology, Institute of Chemical Technology, Mumbai 400019, India.
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20
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Xu Z, Yu K, Zhang M, Ju Y, He J, Jiang Y, Li Y, Jiang J. Accurate Clinical Detection of Vitamin D by Mass Spectrometry: A Review. Crit Rev Anal Chem 2024:1-25. [PMID: 38376891 DOI: 10.1080/10408347.2024.2316237] [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: 02/21/2024]
Abstract
Vitamin D deficiency is thought to be associated with a wide range of diseases, including diabetes, cancer, depression, neurodegenerative diseases, and cardiovascular and cerebrovascular diseases. This vitamin D deficiency is a global epidemic affecting both developing and developed countries and therefore qualitative and quantitative analysis of vitamin D in a clinical context is essential. Mass spectrometry has played an increasingly important role in the clinical analysis of vitamin D because of its accuracy, sensitivity, specificity, and the ability to detect multiple substances at the same time. Despite their many advantages, mass spectrometry-based methods are not without analytical challenges. Front-end and back-end challenges such as protein precipitation, analyte extraction, derivatization, mass spectrometer functionality, must be carefully considered to provide accurate and robust analysis of vitamin D through a well-designed approach with continuous control by internal and external quality control. Therefore, the aim of this review is to provide a comprehensive overview of the development of mass spectrometry methods for vitamin D accurate analysis, including emphasis on status markers, deleterious effects of biological matrices, derivatization reactions, effects of ionization sources, contribution of epimers, standardization of assays between laboratories.
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Affiliation(s)
- Zhilong Xu
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai, China
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
| | - Kai Yu
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai, China
| | - Meng Zhang
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai, China
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
| | - Yun Ju
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai, China
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
| | - Jing He
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai, China
| | - Yanxiao Jiang
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai, China
| | - Yunuo Li
- College of Natural Resources and Environment, Northwest A&F University, Yangling, China
| | - Jie Jiang
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai, China
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
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21
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Brouwer C, Boekhout T, Alwasel S, Rahman M, Janga R, Welling MM. Screening sensibility and antifungal activity after topical application of a synthetic lactoferrin-derived antimicrobial peptide. Am J Transl Res 2024; 16:669-680. [PMID: 38463589 PMCID: PMC10918136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 02/15/2024] [Indexed: 03/12/2024]
Abstract
OBJECTIVE Onychomycosis is the most common disease of the nails and constitutes about half of all nail abnormalities. Onychomycosis is usually caused by dermatophytes and incomparably less frequently by yeast-like fungi and non-dermatophyte molds. Current treatment options for onychomycosis are ineffective. METHODS This study evaluated the performance of a commercial and CE-registered product containing antimicrobial peptide hLF1-11 in vitro for treating toenail onychomycosis. In a case-control setting, nail samples from 59 volunteers were obtained before and after treatment by a pedicurist and investigated for the presence of fungi by culturing, barcode sequencing, and MALDI-TOF-MS. RESULTS Of 89 samples, T. rubrum (19%) and C. parapsilosis (17%) were cultured. In total, 47 samples (53%) were positive for culture. MALDI-TOF-MS could identify 28, but 19 remained unidentified; those species were not included in the commercial MALDI-TOF reference database library. A positive effect of treatment by the hLF1-11 product on 41 volunteers (1 placebo, 18 low doses, 22 high doses) was observed. No adverse effects of the peptide were observed or reported by the pedicurist or any of the participants. CONCLUSIONS This study showed a positive therapeutic effect of a commercial product containing hLF1-11 in the case of 88.9% of the patients with onychomycosis. The present formulation of hLF1-11 into PBS is stable enough to permit storage at room temperature for at least two years.
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Affiliation(s)
| | - Teun Boekhout
- College of Sciences, King Saud UniversityRiyadh, Saudi Arabia
| | - Saleh Alwasel
- College of Sciences, King Saud UniversityRiyadh, Saudi Arabia
| | | | - Ruth Janga
- Dushi Pia Medical PedicureIJsselstein, The Netherlands
| | - Mick M Welling
- Interventional Molecular Imaging Laboratory, Department of Radiology, Leiden University Medical CenterLeiden, The Netherlands
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22
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Elbehiry A, Al Shoaibi M, Alzahrani H, Ibrahem M, Moussa I, Alzaben F, Alsubki RA, Hemeg HA, Almutairi D, Althobaiti S, Alanazi F, Alotaibi SA, Almutairi H, Alzahrani A, Abu-Okail A. Enterobacter cloacae from urinary tract infections: frequency, protein analysis, and antimicrobial resistance. AMB Express 2024; 14:17. [PMID: 38329626 PMCID: PMC10853136 DOI: 10.1186/s13568-024-01675-7] [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: 11/23/2023] [Accepted: 01/27/2024] [Indexed: 02/09/2024] Open
Abstract
The genus Enterobacter belongs to the ESKAPE group, which includes Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. This group is characterized by the development of resistance to various antibiotics. In recent years, Enterobacter cloacae (E. cloacae) has emerged as a clinically important pathogen responsible for a wide range of healthcare-associated illnesses. Identifying Enterobacter species can be challenging due to their similar phenotypic characteristics. The emergence of multidrug-resistant E. cloacae is also a significant problem in healthcare settings. Therefore, our study aimed to identify and differentiate E. cloacae using Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) as a fast and precise proteomic analytical technique. We also tested hospital-acquired E. cloacae isolates that produce Extended-spectrum beta-lactamases (ESBL) against commonly used antibiotics for treating urinary tract infections (UTIs). We used a total of 189 E. cloacae isolates from 2300 urine samples of patients with UTIs in our investigation. We employed culturing techniques, as well as the BD Phoenix™ automated identification system (Becton, Dickinson) and Analytical Profile Index (API) system for the biochemical identification of E. cloacae isolates. We used the MALDI Biotyper (MBT) device for peptide mass fingerprinting analysis of all isolates. We utilized the single peak intensities and Principal Component Analysis (PCA) created by MBT Compass software to discriminate and cluster the E. cloacae isolates. Additionally, we evaluated the sensitivity and resistance of ESBL-E. cloacae isolates using the Kirby Bauer method. Out of the 189 E. cloacae isolates, the BD Phoenix system correctly identified 180 (95.24%) isolates, while the API system correctly identified 165 (87.30%) isolates. However, the MBT accurately identified 185 (98.95%) isolates with a score of 2.00 or higher. PCA positively discriminated the identified E. cloacae isolates into one group, and prominent peaks were noticed between 4230 mass-to-charge ratio (m/z) and 8500 m/z. The ESBL-E. cloacae isolates exhibited a higher degree of resistance to ampicillin, amoxicillin-clavulanate, cephalothin, cefuroxime, and cefoxitin. Several isolates were susceptible to carbapenems (meropenem, imipenem, and ertapenem); however, potential future resistance against carbapenems should be taken into consideration. In conclusion, MALDI-TOF MS is a powerful and precise technology that can be routinely used to recognize and differentiate various pathogens in clinical samples. Additionally, the growing antimicrobial resistance of this bacterium may pose a significant risk to human health.
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Affiliation(s)
- Ayman Elbehiry
- Department of Public Health, College of Public Health and Health Informatics, Qassim University, 52741, Al Bukayriyah, Saudi Arabia.
| | - Mansor Al Shoaibi
- Department of Support Service, King Fahad Armed Hospital, 23311, Jeddah, Saudi Arabia
| | - Hamzah Alzahrani
- Department of Preventive Medicine, King Fahad Armed Hospital, 23311, Jeddah, Saudi Arabia
| | - Mai Ibrahem
- Department of Public Health, College of Applied Medical Science, King Khalid University, 61421, Abha, Saudi Arabia
| | - Ihab Moussa
- Department of Botany and Microbiology, College of Science, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Feras Alzaben
- Department of Food Service, King Fahad Armed Forces Hospital, 23311, Jeddah, Saudi Arabia
| | - Rousa A Alsubki
- Department of Clinical Laboratory Science, College of Applied Science, King Saud University, Riyadh, Saudi Arabia
| | - Hassan A Hemeg
- Department of Medical Laboratory Technology, College of Applied Medical Sciences, Taibah University, Madinah, Saudi Arabia
| | - Dakheel Almutairi
- Medical Transportation Administration of Prince Sultan Military Medical City, 12233, Riyadh, Saudi Arabia
| | - Saleh Althobaiti
- Pharmacy Department, Armed Forces Hospital in Jubail, 35517, Jubail, Saudi Arabia
| | - Fawaz Alanazi
- Supply Administration, Armed Forces Hospital, King Abdul Aziz Naval Base in Jubail, 35517, Jubail, Saudi Arabia
| | - Sultan A Alotaibi
- Medical Administration, Armed Forces Hospital, King Abdul Aziz Naval Base in Jubail, 35517, Jubail, Saudi Arabia
| | - Hamoud Almutairi
- Aviation Medicine, King Abdulaziz Medical City of National Guard, 14611, Riyadh, Saudi Arabia
| | - Ali Alzahrani
- Department of Preventive Medicine, King Fahad Armed Hospital, 23311, Jeddah, Saudi Arabia
| | - Akram Abu-Okail
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, 52571, Buraydah, Saudi Arabia
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23
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Calderaro A, Chezzi C. MALDI-TOF MS: A Reliable Tool in the Real Life of the Clinical Microbiology Laboratory. Microorganisms 2024; 12:322. [PMID: 38399726 PMCID: PMC10892259 DOI: 10.3390/microorganisms12020322] [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: 01/14/2024] [Revised: 01/28/2024] [Accepted: 02/01/2024] [Indexed: 02/25/2024] Open
Abstract
Matrix-Assisted Desorption/Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) in the last decade has revealed itself as a valid support in the workflow in the clinical microbiology laboratory for the identification of bacteria and fungi, demonstrating high reliability and effectiveness in this application. Its use has reduced, by 24 h, the time to obtain a microbiological diagnosis compared to conventional biochemical automatic systems. MALDI-TOF MS application to the detection of pathogens directly in clinical samples was proposed but requires a deeper investigation, whereas its application to positive blood cultures for the identification of microorganisms and the detection of antimicrobial resistance are now the most useful applications. Thanks to its rapidity, accuracy, and low price in reagents and consumables, MALDI-TOF MS has also been applied to different fields of clinical microbiology, such as the detection of antibiotic susceptibility/resistance biomarkers, the identification of aminoacidic sequences and the chemical structure of protein terminal groups, and as an emerging method in microbial typing. Some of these applications are waiting for an extensive evaluation before confirming a transfer to the routine. MALDI-TOF MS has not yet been used for the routine identification of parasites; nevertheless, studies have been reported in the last few years on its use in the identification of intestinal protozoa, Plasmodium falciparum, or ectoparasites. Innovative applications of MALDI-TOF MS to viruses' identification were also reported, seeking further studies before adapting this tool to the virus's diagnostic. This mini-review is focused on the MALDI-TOF MS application in the real life of the diagnostic microbiology laboratory.
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Affiliation(s)
- Adriana Calderaro
- Department of Medicine and Surgery, University of Parma, Viale A. Gramsci 14, 43126 Parma, Italy;
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24
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Correia JL, Fiuza JG, Ferreira G, Almeida MD, Moreira D, Neto VD. Embolic stroke and misidentification candida species endocarditis: Case presentation and literature review. Diagn Microbiol Infect Dis 2024; 108:116133. [PMID: 37984110 DOI: 10.1016/j.diagmicrobio.2023.116133] [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: 08/04/2023] [Revised: 11/09/2023] [Accepted: 11/11/2023] [Indexed: 11/22/2023]
Abstract
Fungal endocarditis is a rare but serious form of infective endocarditis associated with high morbidity and mortality. Among fungal pathogens, Candida species are the most frequently isolated and commonly found in individuals with predisposing factors, such as prosthetic heart valves. The clinical presentation of endocarditis is highly variable and nonspecific, often including symptoms and signs of embolization. In this paper, we present a case of fungal prosthetic valve endocarditis in which the initial presentation was an acute ischemic stroke. The initial misidentification of Candida famata was attributed to limitations in the presumptive methodology used through selective chromogenic culture identification. However, the surgical specimen underwent mass spectrometry, leading to the correct identification of Candida guilliermondii instead of Candida famata. Furthermore, we conducted a non-systematic narrative review of the literature on Candida endocarditis. Our findings underscore the importance of considering fungal endocarditis in the differential diagnosis of patients with possible extracardiac complications, particularly those with a history of heart valve replacement. Early diagnosis and a comprehensive treatment strategy tailored by species identification and antifungal susceptibility testing are crucial in improving patient outcomes.
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Affiliation(s)
| | | | | | | | | | - Vanda Devesa Neto
- Tondela-Viseu Hospital Center, Viseu, Portugal; Faculty of Health Sciences - University of Beira Interior, Covilhã, Portugal
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Abou Chacra L, Drouet H, Ly C, Bretelle F, Fenollar F. Evaluation of Various Diagnostic Strategies for Bacterial Vaginosis, Including a New Approach Based on MALDI-TOF Mass Spectrometry. Microorganisms 2024; 12:111. [PMID: 38257938 PMCID: PMC10821145 DOI: 10.3390/microorganisms12010111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 12/19/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024] Open
Abstract
Bacterial vaginosis (BV) is a common dysbiosis of unclear etiology but with potential consequences representing a public health problem. The diagnostic strategies vary widely. The Amsel criteria and Nugent score have obvious limitations, while molecular biology techniques are expensive and not yet widespread. We set out to evaluate different diagnostic strategies from vaginal samples using (1) a combination of abnormal vaginal discharge and vaginal pH > 4.5; (2) the Amsel-like criteria (replacing the "whiff test" with "malodorous discharge"); (3) the Nugent score; (4) the molecular quantification of Fannyhessea vaginae and Gardnerella vaginalis (qPCR); (5) and MALDI-TOF mass spectrometry (we also refer to it as "VAGI-TOF"). Overall, 54/129 patients (42%) were diagnosed with BV using the combination of vaginal discharge and pH, 46/118 (39%) using the Amsel-like criteria, 31/130 (24%) using qPCR, 32/130 (25%) using "VAGI-TOF", and 23/84 (27%) using the Nugent score (not including the 26 (31%) with intermediate flora). Of the 84 women for whom the five diagnostic strategies were performed, the diagnosis of BV was considered for 38% using the combination of vaginal discharge and pH, 34.5% using the Amsel-like criteria, 27% using the Nugent score, 25% using qPCR, and 25% using "VAGI-TOF". When qPCR was considered as the reference, the sensitivity rate for BV was 76.2% for the combination of vaginal discharge and pH, 90.5% for the Amsel-like criteria, 95.2% for the Nugent score, and 90.5% for "VAGI-TOF", while the specificity rates were 74.6%, 84.1%, 95.3%, and 95.3%, respectively. When the Nugent score was considered as the reference, the sensitivity for BV was 69.6% for the combination of vaginal discharge and pH, 82.6% for the Amsel-like criteria, 87% for qPCR, and 78.7% for "VAGI-TOF", while the specificity rates were 80%, 94.3%, 100%, and 97.1%, respectively. Overall, the use of qPCR and "VAGI-TOF" provided a consistent diagnosis of BV, followed by the Nugent score. If qPCR seems tedious and for some costly, "VAGI-TOF" could be an inexpensive, practical, and less time-consuming alternative.
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Affiliation(s)
- Linda Abou Chacra
- Campus Santé Timone, Aix-Marseille University, IRD, AP-HM, SSA, VITROME, 13005 Marseille, France; (L.A.C.); (H.D.); (C.L.)
- IHU-Méditerranée Infection, 13005 Marseille, France
| | - Hortense Drouet
- Campus Santé Timone, Aix-Marseille University, IRD, AP-HM, SSA, VITROME, 13005 Marseille, France; (L.A.C.); (H.D.); (C.L.)
- IHU-Méditerranée Infection, 13005 Marseille, France
| | - Claudia Ly
- Campus Santé Timone, Aix-Marseille University, IRD, AP-HM, SSA, VITROME, 13005 Marseille, France; (L.A.C.); (H.D.); (C.L.)
- IHU-Méditerranée Infection, 13005 Marseille, France
| | - Florence Bretelle
- Campus Santé Timone, Aix-Marseille University, IRD, AP-HM, MEPHI, 13005 Marseille, France;
- Department of Gynaecology and Obstetrics, Gynépole, La Conception, AP-HM, 13005 Marseille, France
| | - Florence Fenollar
- Campus Santé Timone, Aix-Marseille University, IRD, AP-HM, SSA, VITROME, 13005 Marseille, France; (L.A.C.); (H.D.); (C.L.)
- IHU-Méditerranée Infection, 13005 Marseille, France
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26
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Pham ML, Van Horn K, Zarate E, Pickering E, Murphy C, Bryant K. A multicenter evaluation of Copan's Colibrí™, an automated instrument for MALDI TOF MS target application for bacterial identification. Diagn Microbiol Infect Dis 2024; 108:116098. [PMID: 37890307 DOI: 10.1016/j.diagmicrobio.2023.116098] [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: 07/20/2023] [Revised: 08/24/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023]
Abstract
The Colibrí™ is a new instrument that automates picking and placement of colonies on target plates for MALDI identification. This study compared the performance of the Colibrí™ to standard manual spotting using the VITEK® MS for bacterial identification. Colonies were selected from cultures of urine, wound, respiratory, and positive blood cultures. The Colibrí™ sampled the colonies, transferred them to a MALDI target slide, and overlayed each spot with matrix. Manual spotting was then performed using the same or similar colonies. A total of 444 bacteria were compared. Identification was achieved with both methods for 432 organisms with only 2 discrepant results, overall agreement of 99.54%. Twelve organisms (2.70%) gave no identification using Colibrí™. The Colibrí™ provides automation to a manual process with a high accuracy. Use of the Colibrí™ instrumentation provides an opportunity to reallocate technologist time to more complicated tasks and provides complete traceability from plating to organism identification.
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Affiliation(s)
- My Lien Pham
- Kaiser Permanente, Southern California Permanente Medical Group, Regional Reference Laboratories, Chino Hills, CA, USA
| | - Kenneth Van Horn
- Kaiser Permanente, Southern California Permanente Medical Group, Regional Reference Laboratories, Chino Hills, CA, USA.
| | | | | | | | - Kendall Bryant
- Kaiser Permanente, Airport Way Regional Laboratory, Portland, OR, USA
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Raslan MA, Raslan SA, Shehata EM, Mahmoud AS, Viana MVC, Aburjaile F, Barh D, Sabri NA, Azevedo V. Mass Spectrometry Applications to Study Human Microbiome. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1443:87-101. [PMID: 38409417 DOI: 10.1007/978-3-031-50624-6_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Microbiotas are an adaptable component of ecosystems, including human ecology. Microorganisms influence the chemistry of their specialized niche, such as the human gut, as well as the chemistry of distant surroundings, such as other areas of the body. Metabolomics based on mass spectrometry (MS) is one of the primary methods for detecting and identifying small compounds generated by the human microbiota, as well as understanding the functional significance of these microbial metabolites. This book chapter gives basic knowledge on the kinds of untargeted mass spectrometry as well as the data types that may be generated in the context of microbiome study. While data analysis remains a barrier, the emphasis is on data analysis methodologies and integrative analysis, particularly the integration of microbiome sequencing data. Mass spectrometry (MS)-based techniques have resurrected culture methods for studying the human gut microbiota, filling in the gaps left by high-throughput sequencing methods in terms of culturing minor populations.
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Affiliation(s)
| | | | | | - Amr S Mahmoud
- Department of Obstetrics and Gynecology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Marcus Vinicius Canário Viana
- Laboratório de Genética Celular e Molecular, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Flávia Aburjaile
- Preventive Veterinary Medicine Departament, Veterinary School, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Debmalya Barh
- Laboratório de Genética Celular e Molecular, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Institute of Integrative Omics and Applied Biotechnology, Nonakuri, Purba Medinipur, West Bengal, India
| | - Nagwa A Sabri
- Department of Clinical Pharmacy, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt.
| | - Vasco Azevedo
- Laboratório de Genética Celular e Molecular, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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Won EJ, Park SJ, Jo U, Sung H, Choi EJ, Kim MN. Phaeohyphomycosis due to Pleurostomophora richardsiae in a Patient with a Hematological Malignancy. MYCOBIOLOGY 2023; 51:468-470. [PMID: 38179113 PMCID: PMC10763908 DOI: 10.1080/12298093.2023.2275500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 10/20/2023] [Indexed: 01/06/2024]
Affiliation(s)
- Eun Jeong Won
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Sook-Ja Park
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Uiree Jo
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Heungsup Sung
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Eun-Ji Choi
- Department of Hematology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Mi-Na Kim
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
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Kebabonye K, Jongman M, Loeto D, Moyo S, Choga W, Kasvosve I. Determining Potential Link between Environmental and Clinical Isolates of Cryptococcus neoformans/Cryptococcus gattii Species Complexes Using Phenotypic and Genotypic Characterisation. MYCOBIOLOGY 2023; 51:452-462. [PMID: 38179115 PMCID: PMC10763847 DOI: 10.1080/12298093.2023.2272380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 10/10/2023] [Indexed: 01/06/2024]
Abstract
Opportunistic infections due to Cryptococcus neoformans and C. gattii species complexes continue to rise unabated among HIV/AIDS patients, despite improved antifungal therapies. Here, we collected a total of 20 environmental and 25 presumptive clinical cryptococcal isolates from cerebrospinal fluid (CSF) samples of 175 patients enrolled in an ongoing clinical trial Ambition 1 Project (Botswana-Harvard Partnership). Identity confirmation of the isolates was done using MALDI-TOF MS and PCR. We describe the diversity of the isolates by PCR fingerprinting and sequencing (Oxford Nanopore Technology) of the intergenic spacer region. Mating types of the isolates were determined by amplification of the MAT locus. We report an unusual prevalence of 42.1% of C. neoformans x C. deneoformans hybrids Serotype AD (n = 16), followed by 39.5% of C. neoformans Serotype A (n = 15), 5.3% of C. deneoformans, Serotype D (n = 2), 7.9% of C. gattii (n = 3), and 5.3% of C. tetragattii (n = 2) in 38 representative isolates that have been characterized. Mating type-specific PCR performed on 38 representative environmental and clinical isolates revealed that 16 (42.1%) were MATa/MATα hybrids, 17 (44.7%) were MATα, and five (13.2%) possessed MATa mating type. We used conventional and NGS platforms to demonstrate a potential link between environmental and clinical isolates and lay a foundation to further describe mating patterns/history in Botswana.
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Affiliation(s)
- Kenosi Kebabonye
- School of Health Allied Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Mosimanegape Jongman
- Department of Biological Sciences, Faculty of Science, University of Botswana, Gaborone, Botswana
- Research Laboratory, Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Daniel Loeto
- Department of Biological Sciences, Faculty of Science, University of Botswana, Gaborone, Botswana
| | - Sikhulile Moyo
- School of Health Allied Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
- Research Laboratory, Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Division of Medical Virology, Stellenbosch University, Cape Town, South Africa
- School of Health Systems of Public Health, University of Pretoria, Pretoria, South Africa
| | - Wonderful Choga
- Research Laboratory, Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Ishmael Kasvosve
- School of Health Allied Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
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Kim N, Kim YH, Jo G, Yoo J, Park SM, Jun BH, Yeo WS. Efficient Analysis of Small Molecules via Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (LDI-TOF MS) Using Gold Nanoshells with Nanogaps. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 14:25. [PMID: 38202480 PMCID: PMC10781185 DOI: 10.3390/nano14010025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/27/2023] [Accepted: 12/12/2023] [Indexed: 01/12/2024]
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a commonly used technique for analyzing large biomolecules. However, the utilization of organic matrices limits the small-molecule analysis because of the interferences in the low-mass region and the reproducibility issues. To overcome these limitations, a surface-assisted laser desorption/ionization (SALDI), which utilizes nanostructured metallic surfaces, has been developed. Herein, a novel approach for SALDI-MS was proposed using silica@gold core-shell hybrid materials with a nanogap-rich shell (SiO2@Au NGS), which is an emerging material due to its excellent heat-generating capabilities. The gold shell thickness was controlled by adjusting the concentration of gold precursor for the growth of gold nanoparticles. SALDI-MS measurements were performed on a layer formed by drop-casting a mixture of SiO2@Au NGS and analytes. At the optimized process, the gold shell thickness was observed to be 17.2 nm, which showed the highest absorbance. Based on the enhanced SALDI capability, SiO2@Au NGS was utilized to detect various small molecules, including amino acids, sugars, and flavonoids, and the ionization softness was confirmed with a survival yield upon fragmentation. The limits of detection, reproducibility, and salt tolerance of SiO2@Au NGS demonstrate its potential as an effective and reliable SALDI material for small-molecule analyses.
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Affiliation(s)
- Noori Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea; (N.K.); (Y.-H.K.); (G.J.); (J.Y.)
| | - Yoon-Hee Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea; (N.K.); (Y.-H.K.); (G.J.); (J.Y.)
| | - Gaon Jo
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea; (N.K.); (Y.-H.K.); (G.J.); (J.Y.)
| | - Jin Yoo
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea; (N.K.); (Y.-H.K.); (G.J.); (J.Y.)
| | - Seung-min Park
- Department of Urology, Stanford University School of Medicine, Stanford, CA 94305, USA;
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore 639798
| | - Bong-Hyun Jun
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea; (N.K.); (Y.-H.K.); (G.J.); (J.Y.)
| | - Woon-Seok Yeo
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea; (N.K.); (Y.-H.K.); (G.J.); (J.Y.)
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Coenye T. Biofilm antimicrobial susceptibility testing: where are we and where could we be going? Clin Microbiol Rev 2023; 36:e0002423. [PMID: 37812003 PMCID: PMC10732061 DOI: 10.1128/cmr.00024-23] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 07/27/2023] [Indexed: 10/10/2023] Open
Abstract
Our knowledge about the fundamental aspects of biofilm biology, including the mechanisms behind the reduced antimicrobial susceptibility of biofilms, has increased drastically over the last decades. However, this knowledge has so far not been translated into major changes in clinical practice. While the biofilm concept is increasingly on the radar of clinical microbiologists, physicians, and healthcare professionals in general, the standardized tools to study biofilms in the clinical microbiology laboratory are still lacking; one area in which this is particularly obvious is that of antimicrobial susceptibility testing (AST). It is generally accepted that the biofilm lifestyle has a tremendous impact on antibiotic susceptibility, yet AST is typically still carried out with planktonic cells. On top of that, the microenvironment at the site of infection is an important driver for microbial physiology and hence susceptibility; but this is poorly reflected in current AST methods. The goal of this review is to provide an overview of the state of the art concerning biofilm AST and highlight the knowledge gaps in this area. Subsequently, potential ways to improve biofilm-based AST will be discussed. Finally, bottlenecks currently preventing the use of biofilm AST in clinical practice, as well as the steps needed to get past these bottlenecks, will be discussed.
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Affiliation(s)
- Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
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Hong H, Ximing Y, Jinghan M, Al-danakh A, Shujuan P, Ying L, Yuting Y, Yuehong L, Xingwei Y. Candida auris infection; diagnosis, and resistance mechanism using high-throughput sequencing technology: a case report and literature review. Front Cell Infect Microbiol 2023; 13:1211626. [PMID: 38145050 PMCID: PMC10739385 DOI: 10.3389/fcimb.2023.1211626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 10/30/2023] [Indexed: 12/26/2023] Open
Abstract
Background Candida auris (C. auris), a recently developing fungal disease with high virulence, easy transmission, and substantial medication resistance in hospitals, poses a growing danger to human health. In 2009, the initial documentation of this disease was made when it was discovered in the ear canal of an elderly Japanese patient. Since its initial isolation, the presence of C. auris across six continents has been a cause for severe concern among medical professionals and scientists. According to recent findings, C. auris is connected with five geographically different lineages and significant rates of antifungal resistance. Furthermore, C. auris infections in healthcare settings lack appropriate treatment options and standardized strategies for prevention and control. This results in many treatment failures and hinders the elimination of C. auris in healthcare institutions. To examine the drug resistance mechanism of C. auris and to aid in clinical therapy, we provide a case of C. auris infection along with a short review of the relevant literature. Clinical presentation An 81-year-old female with cerebral hemorrhage was admitted to the hospital and diagnosed with a urinary catheter-related C. auris. The sample was evaluated and reported in terms of culture, identification, drug sensitivity, and gene sequencing. We also evaluated the relationship between the morphology of the isolated strains and their drug resistance. Whole-genome sequencing yielded the genes ERG11-Y132F, CDR1-E709D, TAC1B-Q503E, and TAC1B-A583S; however, no additional loci included alterations of concern, according to our results. ERG11-Y132F and TAC1B-A583S are drug-resistant gene loci, whereas CDR1-E709D and TAC1B-Q503E are unidentified variants. Conclusion We discover a C. auris case of specific a strain in an old female that has some drug-resistant genes, and some genes may be different from already reported gene sites. Gene locus, mutation, and drug resistance mechanism studies may contribute to the creation of innovative drugs and therapeutic treatments. Clinicians and microbiologists must be aware of this globally spreading yeast, which poses substantial hospital diagnostic, treatment, and infection control challenges. Future multicenter research must be performed to uncover this health threat and provide new, effective treatments.
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Affiliation(s)
- He Hong
- Department of Clinical Laboratory, Dongzhimen Hospital of Beijing University of Chinese Medicine, Beijing, China
| | - Yang Ximing
- Department of Clinical Laboratory, Dongzhimen Hospital of Beijing University of Chinese Medicine, Beijing, China
| | - Ma Jinghan
- Department of Clinical Laboratory, Dongzhimen Hospital of Beijing University of Chinese Medicine, Beijing, China
| | - Abdullah Al-danakh
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Pan Shujuan
- Department of Clinical Laboratory, Dongzhimen Hospital of Beijing University of Chinese Medicine, Beijing, China
| | - Lin Ying
- Department of Clinical Laboratory, Dongzhimen Hospital of Beijing University of Chinese Medicine, Beijing, China
| | - Yang Yuting
- Department of Clinical Laboratory, Dongzhimen Hospital of Beijing University of Chinese Medicine, Beijing, China
| | - Liu Yuehong
- Department of Clinical Laboratory, Dongzhimen Hospital of Beijing University of Chinese Medicine, Beijing, China
| | - Yao Xingwei
- Department of Clinical Laboratory, Dongzhimen Hospital of Beijing University of Chinese Medicine, Beijing, China
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Iskender S, Heydarov S, Yalcin M, Faydaci C, Kurt O, Surme S, Kucukbasmaci O. Rapid determination of colistin resistance in Klebsiella pneumoniae by MALDI-TOF peak based machine learning algorithm with MATLAB. Diagn Microbiol Infect Dis 2023; 107:116052. [PMID: 37769565 DOI: 10.1016/j.diagmicrobio.2023.116052] [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: 03/13/2023] [Revised: 07/05/2023] [Accepted: 08/05/2023] [Indexed: 10/03/2023]
Abstract
INTRODUCTION To date, limited data exist on demonstrating the usefulness of machine learning (ML) algorithms applied to MALDI-TOF in determining colistin resistance among Klebsiella pneumoniae. We aimed to detect colistin resistance in K. pneumoniae using MATLAB on MALDI-TOF database. MATERIALS AND METHODS A total of 260 K. pneumoniae isolates were collected. Three ML models, namely, linear discriminant analysis (LDA), support vector machine, and Ensemble were used as ML algorithms and applied to training data set. RESULTS The accuracies for the training phase with 200 isolates were found to be 99.3%, 93.1%, and 88.3% for LDA, support vector machine, and Ensemble models, respectively. Accuracy, sensitivity, specificity, and precision values for LDA in the application test set with 60 K. pneumoniae isolates were 81.6%, 66.7%, 91.7%, and 84.2%, respectively. CONCLUSION This study provides a rapid and accurate MALDI-TOF MS screening assay for clinical practice in identifying colistin resistance in K. pneumoniae.
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Affiliation(s)
- Secil Iskender
- Department of Medical Microbiology, Istanbul University-Cerrahpasa, Cerrahpasa Medical Faculty, Istanbul, Turkey
| | - Saddam Heydarov
- Electronics Technologies, Istanbul Gelisim University, Istanbul, Turkey
| | - Metin Yalcin
- Department of Medical Microbiology, Istanbul University-Cerrahpasa, Cerrahpasa Medical Faculty, Istanbul, Turkey
| | - Cagri Faydaci
- Electronics Technologies, Istanbul Gelisim University, Istanbul, Turkey
| | - Ozge Kurt
- Department of Medical Microbiology, Istanbul University-Cerrahpasa, Cerrahpasa Medical Faculty, Istanbul, Turkey
| | - Serkan Surme
- Department of Medical Microbiology, Istanbul University-Cerrahpasa, Cerrahpasa Medical Faculty, Istanbul, Turkey
| | - Omer Kucukbasmaci
- Department of Medical Microbiology, Istanbul University-Cerrahpasa, Cerrahpasa Medical Faculty, Istanbul, Turkey.
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Esposito F, Cardoso B, Sellera FP, Sano E, Fuentes-Castillo D, Fontana H, Fuga B, Moura Q, Sato MI, Brandão CJ, Lincopan N. Expansion of healthcare-associated hypervirulent KPC-2-producing Klebsiella pneumoniae ST11/KL64 beyond hospital settings. One Health 2023; 17:100594. [PMID: 37448770 PMCID: PMC10336671 DOI: 10.1016/j.onehlt.2023.100594] [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: 12/20/2022] [Revised: 06/21/2023] [Accepted: 06/24/2023] [Indexed: 07/15/2023] Open
Abstract
The spread of carbapenemase-producing Klebsiella pneumoniae beyond hospital settings is a global critical issue within a public health and One Health perspective. Another worrisome concern is the convergence of virulence and resistance in healthcare-associated lineages of K. pneumoniae leading to unfavorable clinical outcomes. During a surveillance study of WHO critical priority pathogens circulating in an impacted urban river in São Paulo, Brazil, we isolate two hypermucoviscous and multidrug-resistant K. pneumoniae strains (PINH-4250 and PINH-4900) from two different locations near to medical centers. Genomic investigation revealed that both strains belonged to the global high-risk sequence type (ST) ST11, carrying the blaKPC-2 carbapenemase gene, besides other medically important antimicrobial resistance determinants. A broad virulome was predicted and associated with hypervirulent behavior in the Galleria mellonella infection model. Comparative phylogenomic analysis of PINH-4250 and PINH-4900 along to an international collection of publicly available genomes of K. pneumoniae ST11 revealed that both environmental strains were closely related to hospital-associated K. pneumoniae strains recovered from clinical samples between 2006 and 2018, in São Paulo city. Our findings support that healthcare-associated KPC-2-positive K. pneumoniae of ST11 clone has successfully expanded beyond hospital settings. In summary, aquatic environments can become potential sources of international clones of K. pneumoniae displaying carbapenem resistance and hypervirulent behaviors, which is a critical issue within a One Health perspective.
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Affiliation(s)
- Fernanda Esposito
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
- One Health Brazilian Resistance Project (OneBR), Brazil
| | - Brenda Cardoso
- One Health Brazilian Resistance Project (OneBR), Brazil
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Fábio P. Sellera
- One Health Brazilian Resistance Project (OneBR), Brazil
- Department of Internal Medicine, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
- School of Veterinary Medicine, Metropolitan University of Santos, Santos, Brazil
| | - Elder Sano
- One Health Brazilian Resistance Project (OneBR), Brazil
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Danny Fuentes-Castillo
- One Health Brazilian Resistance Project (OneBR), Brazil
- Departamento de Patología y Medicina Preventiva, Facultad de Ciencias Veterinarias, Universidad de Concepción, Chillán, Chile
| | - Herrison Fontana
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
- One Health Brazilian Resistance Project (OneBR), Brazil
| | - Bruna Fuga
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
- One Health Brazilian Resistance Project (OneBR), Brazil
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Quézia Moura
- Federal Institute of Education Science and Technology of Espírito Santo, Vila Velha, Brazil
| | - Maria I.Z. Sato
- Environmental Company of São Paulo State (CETESB), São Paulo, Brazil
| | - Carlos J. Brandão
- Environmental Company of São Paulo State (CETESB), São Paulo, Brazil
| | - Nilton Lincopan
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
- One Health Brazilian Resistance Project (OneBR), Brazil
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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Kim HJ, Jung Y, Kim MJ, Kim HY. Novel Heptaplex PCR-Based Diagnostics for Enteric Fever Caused by Typhoidal Salmonella Serovars and Its Applicability in Clinical Blood Culture. J Microbiol Biotechnol 2023; 33:1457-1466. [PMID: 37674393 DOI: 10.4014/jmb.2307.07031] [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: 07/24/2023] [Revised: 08/12/2023] [Accepted: 08/14/2023] [Indexed: 09/08/2023]
Abstract
Enteric fever is caused by typhoidal Salmonella serovars (Typhi, Paratyphi A, Paratyphi B, and Paratyphi C). Owing to the importance of Salmonella serovars in clinics and public hygiene, reliable diagnostics for typhoidal serovars are crucial. This study aimed to develop a novel diagnostic tool for typhoidal Salmonella serovars and evaluate the use of human blood for clinically diagnosing enteric fever. Five genes were selected to produce specific PCR results against typhoidal Salmonella serovars based on the genes of Salmonella Typhi. Heptaplex PCR, including genetic markers of generic Salmonella, Salmonella enterica subsp. enterica, and typhoidal Salmonella serovars, was developed. Typhoidal Salmonella heptaplex PCR using genomic DNAs from 200 Salmonella strains (112 serovars) provided specifically amplified PCR products for each typhoidal Salmonella serovar. These results suggest that heptaplex PCR can sufficiently discriminate between typhoidal and nontyphoidal Salmonella serovars. Heptaplex PCR was applied to Salmonella-spiked blood cultures directly and provided diagnostic results after 12- or 13.5-h blood culture. Additionally, it demonstrated diagnostic performance with colonies recovered from a 6-h blood culture. This study provides a reliable DNA-based tool for diagnosing typhoidal Salmonella serovars that may be useful in clinical microbiology and epidemiology.
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Affiliation(s)
- Hyun-Joong Kim
- Department of Food Engineering, Mokpo National University, Muan 58554, Republic of Korea
| | - Younsik Jung
- Institute of Life Sciences and Resources and the Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104 Republic of Korea
| | - Mi-Ju Kim
- Institute of Life Sciences and Resources and the Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104 Republic of Korea
| | - Hae-Yeong Kim
- Institute of Life Sciences and Resources and the Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104 Republic of Korea
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Wataradee S, Samngamnim S, Boonserm T, Ajariyakhajorn K. Genotypic and antimicrobial susceptibility of Streptococcus agalactiae causing bovine mastitis in the central region of Thailand. Front Vet Sci 2023; 10:1250436. [PMID: 38026633 PMCID: PMC10666187 DOI: 10.3389/fvets.2023.1250436] [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: 07/20/2023] [Accepted: 10/27/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction Streptococcus agalactiae is a highly contagious pathogen that causes bovine mastitis, leading to significant economic losses. This study aimed to (1) identify and characterize S. agalactiae strains responsible for bovine mastitis by examining their phenotypic and genotypic characteristics in Thai dairy-intensive farming areas and (2) determine their susceptibility profiles to antimicrobial agents. Material and methods In total, 100 S. agalactiae isolates obtained from clinical and subclinical mastitis cases from 13 dairy herds located in the central region of Thailand were examined. To confirm the identity of the bacterial pathogens, conventional microbiological procedures recommended by the National Mastitis Council (NMC) and the VITEK® 2 system were employed. Results All 100 isolates were successfully identified as S. agalactiae using the NMC procedure, whereas 94 isolates were identified as S. agalactiae using the VITEK® 2 system. Finally, the S. agalactiae-specific gene dlt S was identified in all the examined isolates using polymerase chain reaction. Capsular polysaccharide (CPS) typing revealed that all strains belonged to CPS type Ia. Multilocus sequence typing identified 33 selected isolates as sequence type 103. Random amplified polymorphic DNA (RAPD) typing yielded 43 RAPD types, with 6 RAPD clusters identified. These results demonstrated a high level of genetic diversity among S. agalactiae within the studied herds. RAPD analysis suggested that specific S. agalactiae strains could persist in dairy farms for 2-12 months. Furthermore, antimicrobial susceptibility testing was performed using the broth microdilution method. Most strains demonstrated susceptibility to ampicillin, penicillin, penicillin/novobiocin, cephalothin, oxacillin, ceftiofur, and erythromycin. Discussion This study revealed the phenotypic and genotypic characteristics of S. agalactiae isolates responsible for bovine mastitis in the central region of Thailand. The rapid identification of S. agalactiae and application of molecular typing methods can provide valuable epidemiological information regarding S. agalactiae causing mastitis in dairy farms. The antimicrobial susceptibility of S. agalactiae indicates that antimicrobial treatment for control and eradication could be a successful protocol. Our findings revealed that a single clonal strain of S. agalactiae affected the 13 studied farms. Further research is needed to explore the feasibility of vaccine development and application.
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Gao W, Han Y, Chen L, Tan X, Liu J, Xie J, Li B, Zhao H, Yu S, Tu H, Feng B, Yang F. Fusion data from FT-IR and MALDI-TOF MS result in more accurate classification of specific microbiota. Analyst 2023; 148:5650-5657. [PMID: 37800908 DOI: 10.1039/d3an01108a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/07/2023]
Abstract
Microbes are usually present as a specific microbiota, and their classification remains a challenge. MALDI-TOF MS is particularly successful in library-based microbial identification at the species level as it analyzes the molecular weight of peptides and ribosomal proteins. FT-IR allows more accurate classification of bacteria at the subspecies level due to the high sensitivity, specificity and repeatability of FT-IR signals from bacteria, which is not achievable with MALDI-TOF MS. Previous studies have shown that more accurate identification results can be obtained by the fusion of FT-IR and MALDI-TOF MS spectral data. Here, we constructed 20 groups of model microbiota samples and used FT-IR, MALDI-TOF MS, and their fusion data to classify them. Hierarchical clustering analysis (HCA) showed that the classification accuracy of FT-IR, MALDI-TOF MS, and the fusion data was 85%, 90%, and 100%, respectively. These results indicate that both FT-IR and MALDI-TOF MS can effectively classify specific microbiota, and the fusion of their spectral data could improve the classification accuracy. The FT-IR and MALDI-TOF MS data fusion strategy may be a promising technology for specific microbiota classification.
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Affiliation(s)
- Wenjing Gao
- Institute of Mass Spectrometry, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Ying Han
- Kweichow Moutai Group, Renhuai, Guizhou 564501, China.
| | | | - Xue Tan
- Kweichow Moutai Group, Renhuai, Guizhou 564501, China.
| | - Jieyou Liu
- Zhuhai DL Biotech Co., Ltd, Zhuhai, Guangdong 519041, China
| | - Jinghang Xie
- Institute of Mass Spectrometry, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Bin Li
- Institute of Mass Spectrometry, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Huilin Zhao
- Institute of Mass Spectrometry, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Shaoning Yu
- Institute of Mass Spectrometry, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Huabin Tu
- Kweichow Moutai Group, Renhuai, Guizhou 564501, China.
| | - Bin Feng
- Institute of Mass Spectrometry, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Fan Yang
- Kweichow Moutai Group, Renhuai, Guizhou 564501, China.
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Zhang H, Yang Y, Jiang Y, Zhang M, Xu Z, Wang X, Jiang J. Mass Spectrometry Analysis for Clinical Applications: A Review. Crit Rev Anal Chem 2023:1-20. [PMID: 37910438 DOI: 10.1080/10408347.2023.2274039] [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: 11/03/2023]
Abstract
Mass spectrometry (MS) has become an attractive analytical method in clinical analysis due to its comprehensive advantages of high sensitivity, high specificity and high throughput. Separation techniques coupled MS detection (e.g., LC-MS/MS) have shown unique advantages over immunoassay and have developed as golden criterion for many clinical applications. This review summarizes the characteristics and applications of MS, and emphasizes the high efficiency of MS in clinical research. In addition, this review also put forward further prospects for the future of mass spectrometry technology, including the introduction of miniature MS instruments, point-of-care detection and high-throughput analysis, to achieve better development of MS technology in various fields of clinical application. Moreover, as ambient ionization mass spectrometry (AIMS) requires little or no sample pretreatment and improves the flux of MS, this review also summarizes its potential applications in clinic.
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Affiliation(s)
- Hong Zhang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, P. R. China
| | - Yali Yang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, P. R. China
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, P. R. China
| | - Yanxiao Jiang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, P. R. China
| | - Meng Zhang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, P. R. China
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, P. R. China
| | - Zhilong Xu
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, P. R. China
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, P. R. China
| | - Xiaofei Wang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, P. R. China
| | - Jie Jiang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, P. R. China
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, P. R. China
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Chang YH, Huang YC, Chen HC, Ma DHK, Yeh LK, Hung KH, Hsiao CH. Molecular and Phenotypic Characterization of Ocular Methicillin-Resistant Staphylococcus epidermidis Isolates in Taiwan. Invest Ophthalmol Vis Sci 2023; 64:33. [PMID: 37862027 PMCID: PMC10599164 DOI: 10.1167/iovs.64.13.33] [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: 08/13/2023] [Accepted: 10/01/2023] [Indexed: 10/21/2023] Open
Abstract
Purpose Staphylococcus epidermidis, a commensal, has emerged as an important opportunistic pathogen, particularly methicillin-resistant S. epidermidis (MRSE). The mechanism behind this transformation remains unclear. This study aimed to investigate the molecular and phenotypic characteristics of MRSE isolated from healthy conjunctiva and ocular infections. Methods We collected MRSE isolates from two groups: healthy conjunctiva from patients undergoing cataract surgeries and ocular infections at our hospital. Genotypic analysis included pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), staphylococcal cassette chromosome mec (SCCmec), and biofilm-related genes (icaA, aap, and bhp). Additionally, phenotypic data on biofilm production and antibiotic susceptibility were recorded. Results A total of 86 isolates, including 42 from healthy conjunctiva and 44 from ocular infections, were analyzed. MLST identified 21 sequence types (STs), with ST59 being the most frequent (n = 33, 39.5%), followed by ST130 (n = 10, 11.6%), ST57 (n = 6, 7.0%), and ST2 (n = 6, 7.0%). All isolates were categorized in 23 PFGE types, and SCCmec IV was the most prevalent SCCmec type (n = 52, 60.5%). The two sources of isolates exhibited overlapping molecular types and phenotypic traits, although the ocular infection isolates exhibited significantly higher multidrug resistance compared to healthy conjunctiva isolates (P = 0.032). When contrasting ST59 with non-ST59, ST59 displayed a significantly higher presence of aap (100%) and bhp (69.7%) while lacking icaA (0%). ST59 also showed lower susceptibility to fluoroquinolones compared to non-ST59 (42.4%-54.5% vs. 75.5%-83.0%; P < 0.01). Conclusions MRSE isolates from healthy conjunctiva and ocular infections demonstrated a degree of resemblance. Specific strains, notably ST59, exhibited distinctive characterizations.
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Affiliation(s)
- Yin-Hsi Chang
- Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
- College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Yhu-Chering Huang
- College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Hung-Chi Chen
- Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
- College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - David H. K. Ma
- Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
- College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Lung-Kun Yeh
- Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
- College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Kuo-Hsuan Hung
- Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
- College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Ching-Hsi Hsiao
- Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
- College of Medicine, Chang Gung University, Taoyuan, Taiwan
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Nellessen CM, Nehl DB. An easy adjustment of instrument settings ('Peak MALDI') improves identification of organisms by MALDI-ToF mass spectrometry. Sci Rep 2023; 13:15018. [PMID: 37700004 PMCID: PMC10497524 DOI: 10.1038/s41598-023-42328-2] [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: 06/06/2023] [Accepted: 09/08/2023] [Indexed: 09/14/2023] Open
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF MS) is a mature technolaogy with 'auto-execute' instrument settings and peak processing parameters tailored for rapid bacterial identification. Adoption for other organisms has been problematic, with optimisation efforts focusing on sample preparation. Using the Bruker MALDI Biotyper, we demonstrate 'Peak MALDI': easily-applied settings that immediately enhance sensitivity, improve spectrum quality, and increase identification confidence for any target, establishing its potential value for all MALDI-ToF MS systems.
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Affiliation(s)
| | - David B Nehl
- Department of Agriculture, Fisheries and Forestry, Sydney, Australia
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Kaushal S, Priyadarshi N, Garg P, Singhal NK, Lim DK. Nano-Biotechnology for Bacteria Identification and Potent Anti-bacterial Properties: A Review of Current State of the Art. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:2529. [PMID: 37764558 PMCID: PMC10536455 DOI: 10.3390/nano13182529] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 08/26/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023]
Abstract
Sepsis is a critical disease caused by the abrupt increase of bacteria in human blood, which subsequently causes a cytokine storm. Early identification of bacteria is critical to treating a patient with proper antibiotics to avoid sepsis. However, conventional culture-based identification takes a long time. Polymerase chain reaction (PCR) is not so successful because of the complexity and similarity in the genome sequence of some bacterial species, making it difficult to design primers and thus less suitable for rapid bacterial identification. To address these issues, several new technologies have been developed. Recent advances in nanotechnology have shown great potential for fast and accurate bacterial identification. The most promising strategy in nanotechnology involves the use of nanoparticles, which has led to the advancement of highly specific and sensitive biosensors capable of detecting and identifying bacteria even at low concentrations in very little time. The primary drawback of conventional antibiotics is the potential for antimicrobial resistance, which can lead to the development of superbacteria, making them difficult to treat. The incorporation of diverse nanomaterials and designs of nanomaterials has been utilized to kill bacteria efficiently. Nanomaterials with distinct physicochemical properties, such as optical and magnetic properties, including plasmonic and magnetic nanoparticles, have been extensively studied for their potential to efficiently kill bacteria. In this review, we are emphasizing the recent advances in nano-biotechnologies for bacterial identification and anti-bacterial properties. The basic principles of new technologies, as well as their future challenges, have been discussed.
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Affiliation(s)
- Shimayali Kaushal
- KU-KIST Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea;
| | - Nitesh Priyadarshi
- National Agri-Food Biotechnology Institute (NABI), Sector-81, Mohali 140306, India; (N.P.); (P.G.)
| | - Priyanka Garg
- National Agri-Food Biotechnology Institute (NABI), Sector-81, Mohali 140306, India; (N.P.); (P.G.)
| | - Nitin Kumar Singhal
- National Agri-Food Biotechnology Institute (NABI), Sector-81, Mohali 140306, India; (N.P.); (P.G.)
| | - Dong-Kwon Lim
- KU-KIST Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea;
- Department of Integrative Energy Engineering, College of Engineering, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
- Brain Science Institute, Korea Institute of Science and Technology (KIST), 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea
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Pławińska-Czarnak J, Wódz K, Strzałkowska Z, Żychska M, Nowak T, Kwieciński A, Kwieciński P, Bielecki W, Rodo A, Rzewuska M, Kłosińska D, Anusz K, Orłowska B. Comparison of automatic methods MALDI-TOF, VITEK2 and manual methods for the identification of intestinal microbial communities on the example of samples from alpacas ( Vicugna pacos). J Vet Res 2023; 67:361-372. [PMID: 37786852 PMCID: PMC10541665 DOI: 10.2478/jvetres-2023-0051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 08/22/2023] [Indexed: 10/04/2023] Open
Abstract
Introduction Universally, in microbiological diagnostics the detection of live bacteria is essential. Rapid identification of pathogens enables appropriate remedial measures to be taken. The identification of many bacteria simultaneously facilitates the determination of the characteristics of the accompanying microbiota and/or the microbiological complexity of a given environment. Material and Methods The effectiveness of the VITEK2 Compact automated microbial identification system and matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS), analytical profile index (API) and Remel RapID tests were compared in identification of bacteria isolated from the alpaca gastrointestinal tract. Results Most isolates were Gram-positive, such as Bacillus cereus, Bacillus flexus, Bacillus licheniformis, Bacillus pumilus and Bacillus subtilis; Enterococcus faecium, Enterococcus gallinarum, Enterococcus hirae and Enterococcus casseliflavus; Staphylococcus aureus, Staphylococcus equorum, Staphylococcus lentus, Staphylococcus pseudintermedius and Staphylococcus sciuri; Paenibacillus amylolyticus; Cellulosimicrobium cellulans; Leuconostoc mesenteroides; Clostridium perfringens; Corynebacterium stationis, Corynebacterium xerosis, and Corynebacterium diphtheriae (the last only isolated manually by API Coryne and the VITEK2 system and Corynebacteria (CBC) card). Corynebacterium diphtheriae was misidentified by MALDI-TOF MS as Candida lipolytica (currently Yarrowia lipolytica). Gram-positive and Gram-variable Micrococcus luteus were also isolated. Gram-negative Enterobacter cloacae, Enterobacter gergoviae, Enterobacter hormaechei and Enterobacter ludwigii; E. coli; Klebsiella pneumoniae subsp. pneumoniae; Citrobacter braakii and Citrobacter freundii; Serratia liquefaciens, Serratia odorifera and Serratia marcescens; Morganella morganii subsp. morganii; Providencia alcalifaciens; Pseudomonas aeruginosa; Stenotrophomonas maltophilia; Moraxella osloensis; and Ochrobactrum intermedium were also found. The yeasts Candida albicans, Candida haemulonii and Candida ciferrii were also present. Conclusion MALDI-TOF MS enabled the identification of pathogens and opportunistic pathogens from the alpaca gut which may represent a high risk to human and animal health.
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Affiliation(s)
| | - Karolina Wódz
- Laboratory of Molecular Biology, Vet-Lab Brudzew, 62-720Brudzew, Poland
| | | | - Monika Żychska
- Laboratory of Veterinary Epidemiology and Economic, Institute of Veterinary Medicine, Warsaw University of Life Sciences, 02-786Warsaw, Poland
| | - Tomasz Nowak
- Laboratory of Molecular Biology, Vet-Lab Brudzew, 62-720Brudzew, Poland
| | - Adam Kwieciński
- Laboratory of Molecular Biology, Vet-Lab Brudzew, 62-720Brudzew, Poland
| | - Piotr Kwieciński
- Laboratory of Molecular Biology, Vet-Lab Brudzew, 62-720Brudzew, Poland
| | - Wojciech Bielecki
- Department of Pathology and Veterinary Diagnostics, Institute of Veterinary Medicine, Warsaw University of Life Sciences, 02-776Warsaw, Poland
| | - Anna Rodo
- Department of Pathology and Veterinary Diagnostics, Institute of Veterinary Medicine, Warsaw University of Life Sciences, 02-776Warsaw, Poland
| | - Magdalena Rzewuska
- Department of Preclinical Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences, 02-787Warsaw, Poland
| | - Daria Kłosińska
- Division of Histology and Embryology, Department of Morphological Sciences, Faculty of Veterinary Medicine, Warsaw University of Life Sciences, 02-776Warsaw, Poland
| | - Krzysztof Anusz
- Department of Food Hygiene and Public Health Protection, Warsaw, Poland
| | - Blanka Orłowska
- Department of Food Hygiene and Public Health Protection, Warsaw, Poland
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Uvarova YE, Demenkov PS, Kuzmicheva IN, Venzel AS, Mischenko EL, Ivanisenko TV, Efimov VM, Bannikova SV, Vasilieva AR, Ivanisenko VA, Peltek SE. Accurate noise-robust classification of Bacillus species from MALDI-TOF MS spectra using a denoising autoencoder. J Integr Bioinform 2023; 20:jib-2023-0017. [PMID: 37978847 PMCID: PMC10757077 DOI: 10.1515/jib-2023-0017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 07/10/2023] [Indexed: 11/19/2023] Open
Abstract
Bacillus strains are ubiquitous in the environment and are widely used in the microbiological industry as valuable enzyme sources, as well as in agriculture to stimulate plant growth. The Bacillus genus comprises several closely related groups of species. The rapid classification of these remains challenging using existing methods. Techniques based on MALDI-TOF MS data analysis hold significant promise for fast and precise microbial strains classification at both the genus and species levels. In previous work, we proposed a geometric approach to Bacillus strain classification based on mass spectra analysis via the centroid method (CM). One limitation of such methods is the noise in MS spectra. In this study, we used a denoising autoencoder (DAE) to improve bacteria classification accuracy under noisy MS spectra conditions. We employed a denoising autoencoder approach to convert noisy MS spectra into latent variables representing molecular patterns in the original MS data, and the Random Forest method to classify bacterial strains by latent variables. Comparison of the DAE-RF with the CM method using the artificially noisy test samples showed that DAE-RF offers higher noise robustness. Hence, the DAE-RF method could be utilized for noise-robust, fast, and neat classification of Bacillus species according to MALDI-TOF MS data.
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Affiliation(s)
- Yulia E. Uvarova
- Federal Research Center Institute of Cytology and Genetics SB RAS, 630090Novosibirsk, Russia
| | - Pavel S. Demenkov
- Federal Research Center Institute of Cytology and Genetics SB RAS, 630090Novosibirsk, Russia
- Kurchatov Center for Genome Research, Institute of Cytology and Genetics SB RAS, 630090Novosibirsk, Russia
- Novosibirsk State University, 630090Novosibirsk, Russia
| | | | - Artur S. Venzel
- Federal Research Center Institute of Cytology and Genetics SB RAS, 630090Novosibirsk, Russia
- Novosibirsk State University, 630090Novosibirsk, Russia
| | - Elena L. Mischenko
- Federal Research Center Institute of Cytology and Genetics SB RAS, 630090Novosibirsk, Russia
| | - Timofey V. Ivanisenko
- Federal Research Center Institute of Cytology and Genetics SB RAS, 630090Novosibirsk, Russia
- Kurchatov Center for Genome Research, Institute of Cytology and Genetics SB RAS, 630090Novosibirsk, Russia
| | - Vadim M. Efimov
- Federal Research Center Institute of Cytology and Genetics SB RAS, 630090Novosibirsk, Russia
| | - Svetlana V. Bannikova
- Federal Research Center Institute of Cytology and Genetics SB RAS, 630090Novosibirsk, Russia
| | - Asya R. Vasilieva
- Federal Research Center Institute of Cytology and Genetics SB RAS, 630090Novosibirsk, Russia
| | - Vladimir A. Ivanisenko
- Federal Research Center Institute of Cytology and Genetics SB RAS, 630090Novosibirsk, Russia
- Kurchatov Center for Genome Research, Institute of Cytology and Genetics SB RAS, 630090Novosibirsk, Russia
- Novosibirsk State University, 630090Novosibirsk, Russia
| | - Sergey E. Peltek
- Federal Research Center Institute of Cytology and Genetics SB RAS, 630090Novosibirsk, Russia
- Kurchatov Center for Genome Research, Institute of Cytology and Genetics SB RAS, 630090Novosibirsk, Russia
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Birhanu AG. Mass spectrometry-based proteomics as an emerging tool in clinical laboratories. Clin Proteomics 2023; 20:32. [PMID: 37633929 PMCID: PMC10464495 DOI: 10.1186/s12014-023-09424-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 08/03/2023] [Indexed: 08/28/2023] Open
Abstract
Mass spectrometry (MS)-based proteomics have been increasingly implemented in various disciplines of laboratory medicine to identify and quantify biomolecules in a variety of biological specimens. MS-based proteomics is continuously expanding and widely applied in biomarker discovery for early detection, prognosis and markers for treatment response prediction and monitoring. Furthermore, making these advanced tests more accessible and affordable will have the greatest healthcare benefit.This review article highlights the new paradigms MS-based clinical proteomics has created in microbiology laboratories, cancer research and diagnosis of metabolic disorders. The technique is preferred over conventional methods in disease detection and therapy monitoring for its combined advantages in multiplexing capacity, remarkable analytical specificity and sensitivity and low turnaround time.Despite the achievements in the development and adoption of a number of MS-based clinical proteomics practices, more are expected to undergo transition from bench to bedside in the near future. The review provides insights from early trials and recent progresses (mainly covering literature from the NCBI database) in the application of proteomics in clinical laboratories.
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Idelevich EA, Nedow B, Vollmer M, Becker K. Evaluation of a Novel Benchtop Tool for Acceleration of Sample Preparation for MALDI-TOF Mass Spectrometry. J Clin Microbiol 2023; 61:e0021223. [PMID: 37493547 PMCID: PMC10446855 DOI: 10.1128/jcm.00212-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 06/27/2023] [Indexed: 07/27/2023] Open
Abstract
During the past decade, MALDI-TOF mass spectrometry (MS) has become a standard method for identification of bacteria and yeasts. Nonetheless, further optimization of the identification process is important to streamline workflows and save resources. This study evaluated the application of a multipurpose benchtop tool, MBT FAST Shuttle IVD, for accelerated drying of liquid assay components (matrix, formic acid, and/or sample) on a MALDI target. A total of 50 bacterial and fungal isolates were subjected to three different sample preparation procedures prior to the identification by MALDI-TOF MS: direct transfer (DT), extended direct transfer (eDT), and protein extraction (PE). Compared to conventional drying at room temperature, the preparation was performed with standardized heating of the MALDI target on the MBT FAST Shuttle. During DT, eDT, and PE, 56.7% (P < 0.001), 56.8% (P < 0.001), and 52.8% (P < 0.001) of time for matrix drying were saved by using the MBT FAST Shuttle, respectively. Applying the MBT FAST Shuttle, 57.5% (P < 0.001) of time for drying of formic acid were saved for eDT and 57.5% (P < 0.001) of time for sample drying were saved for PE. A significant improvement of the identification rates and scores was observed with MBT FAST Shuttle for eDT (P = 0.001) and PE (P = 0.008) methods, while the effect on identification quality for DT was not statistically significant (P = 0.16). In conclusion, the use of the MBT FAST Shuttle shortened the drying time of assay components by about a half for all preparation methods. Moreover, positive effect on identification success was observed.
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Affiliation(s)
- Evgeny A. Idelevich
- Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - Betty Nedow
- Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| | - Marcus Vollmer
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Karsten Becker
- Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
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Ikeda H, Tokonami A, Nishii S, Shan X, Yamamoto Y, Sadanaga Y, Chen Z, Shiigi H. Evaluation of Bacterial Activity Based on the Electrochemical Properties of Tetrazolium Salts. Anal Chem 2023; 95:12358-12364. [PMID: 37605797 DOI: 10.1021/acs.analchem.3c01871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
This study focused on the electrochemical properties of tetrazolium salts to develop a simple method for evaluating viable bacterial counts, which are indicators of hygiene control at food and pharmaceutical manufacturing sites. Given that the oxidized form of 3-(4,5-di-methylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), which has excellent cell membrane permeability, changes to the insoluble reduced form of formazan inside the cell, the number of viable cells was estimated by focusing on the reduction current of MTT remaining in the suspension. Dissolved oxygen is an important substance for bacterial activity; however, it interferes with the electrochemical response of MTT. We investigated the electrochemical properties of MTT to obtain a potential-selective current response that was not affected by dissolved oxygen. Real-time observation of viable bacteria in suspension revealed that uptake of MTT into bacteria was completed within 10 min, including the lag period. In addition, we observed that the current response depends on viable cell density regardless of the bacterial species present. Our method enables a rapid estimation of the number of viable bacteria, making it possible to confirm the safety of food products before they are shipped from the factory and thereby prevent food poisoning.
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Affiliation(s)
- Hikaru Ikeda
- Department of Applied Chemistry, Osaka Metropolitan University, 1-2 Gakuen, Naka, Sakai 599-8570, Osaka, Japan
| | - Akira Tokonami
- Department of Applied Chemistry, Osaka Metropolitan University, 1-2 Gakuen, Naka, Sakai 599-8570, Osaka, Japan
| | - Shigeki Nishii
- Department of Applied Chemistry, Osaka Metropolitan University, 1-2 Gakuen, Naka, Sakai 599-8570, Osaka, Japan
| | - Xueling Shan
- Jiangsu Key Laboratory of Advanced Catalytic Materials and Technology, Changzhou University, Changzhou 213164, China
| | - Yojiro Yamamoto
- Department of Applied Chemistry, Osaka Metropolitan University, 1-2 Gakuen, Naka, Sakai 599-8570, Osaka, Japan
| | - Yasuhiro Sadanaga
- Department of Applied Chemistry, Osaka Metropolitan University, 1-2 Gakuen, Naka, Sakai 599-8570, Osaka, Japan
| | - Zhidong Chen
- Jiangsu Key Laboratory of Advanced Catalytic Materials and Technology, Changzhou University, Changzhou 213164, China
| | - Hiroshi Shiigi
- Department of Applied Chemistry, Osaka Metropolitan University, 1-2 Gakuen, Naka, Sakai 599-8570, Osaka, Japan
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Bacanelli G, Araujo FR, Verbisck NV. Improved MALDI-TOF MS Identification of Mycobacterium tuberculosis by Use of an Enhanced Cell Disruption Protocol. Microorganisms 2023; 11:1692. [PMID: 37512865 PMCID: PMC10386467 DOI: 10.3390/microorganisms11071692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/22/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
Mycobacterium tuberculosis is the microorganism that causes tuberculosis, a disease affecting millions of people worldwide. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a fast, reliable, and cost-effective method for microorganism identification which has been used for the identification of Mycobacterium spp. isolates. However, the mycobacteria cell wall is rich in lipids, which makes it difficult to obtain proteins for MALDI-TOF MS analysis. In this study, two cell preparation protocols were compared: the MycoEx, recommended by MALDI-TOF instrument manufacturer Bruker Daltonics, and the MycoLyser protocol described herein, which used the MagNA Lyser instrument to enhance cell disruption with ethanol. Cell disruption and protein extraction steps with the two protocols were performed using the Mycobacterium tuberculosis H37Rv strain, and the MALDI-TOF MS results were compared. The MycoLyser protocol allowed for improved Biotyper identification of M. tuberculosis since the log(score) values obtained with this protocol were mostly ≥ 1.800 and significantly higher than that underwent MycoEx processing. The identification reliability was increased as well, considering the Bruker criteria. In view of these results, it is concluded that the MycoLyser protocol for mycobacterial cell disruption and protein extraction improves the MALDI-TOF MS method's efficacy for M. tuberculosis identification.
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Affiliation(s)
- Gisele Bacanelli
- Biotechnology and Biodiversity of the Central Western Region Postgraduate Program, Federal University of Mato Grosso do Sul, Campo Grande 79070-900, MS, Brazil
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Tsekleves E, de Souza D, Pickup R, Ahorlu C, Darby A. Developing home cleaning intervention through community engagement to reduce infections and antimicrobial resistance in Ghanaian homes. Sci Rep 2023; 13:10505. [PMID: 37380793 DOI: 10.1038/s41598-023-37317-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 06/20/2023] [Indexed: 06/30/2023] Open
Abstract
Globally Antimicrobial Resistance (AMR) constitutes a health crisis, particularly in developing countries, where infectious disease are commonly fatal. There is clear evidence for microbial exposure and infection transmission within the home. Personal and environmental hygiene are the best ways of reducing household infections thus decreasing the need for antibiotics and consequently diminishing AMR. Despite this being an obvious step, research efforts to understand the home environment and its impact on AMR, cleaning and possible interventions on household cleaning are limited. We combined design and microbiology methods in an innovative mixed-method approach. A traditional survey design (n = 240), a design ethnography (n = 12), a co-design workshop and a pre-intervention microbiological dust sample analysis was undertaken to provide insights for codesign workshops in which new cleaning practices might be developed to minimise any AMR bacteria present in the household environments located in the Greater Accra Region of Ghana. Microbiological analysis of household dust showed that 36.6% of bacterial isolates detected were found to carry at least one resistance to the panel of antibiotics tested. Four scenarios were generated from an economic segmentation of the survey data. 50 ethnographic insights were 'presented' and descriptions of 12 bacteria species that showed resistance to one or more antibiotics (representing 176 bacterial isolates that showed resistance to one or more antibiotics found in the dust samples) were presented to the participants in a codesign workshop. An intervention, a new regime of cleaning practices agreed through the co-design workshop and practiced for thirty days, was made in (n = 7) households. The high prevalence of multidrug resistance observed in this study indicate the need for antibiotics surveillance program, not only in hospital settings but also in the household environment. There is, thus, an urgent need for targeting of interventions at the household level. Activating knowledge through community engagement in the research helps in increasing public perception and breaking down the scientist-public barrier.
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Affiliation(s)
| | - Dziedzom de Souza
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Roger Pickup
- Biomedical and Life Sciences, Lancaster University, Lancaster, UK
| | - Collins Ahorlu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Andy Darby
- ImaginationLancaster, Lancaster University, Lancaster, UK
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Costa A, Figueroa-Espinosa R, Martínez JA, Fernández-Canigia L, Maldonado MI, Bergese SA, Schneider AE, Vay C, Rodriguez CH, Nastro M, Gutkind GO, Di Conza JA. MALDI-TOF MS-Based KPC Direct Detection from Patients' Positive Blood Culture Bottles, Short-Term Cultures, and Colonies at the Hospital. Pathogens 2023; 12:865. [PMID: 37513712 PMCID: PMC10385308 DOI: 10.3390/pathogens12070865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/15/2023] [Accepted: 06/19/2023] [Indexed: 07/30/2023] Open
Abstract
Carbapenemase resistance in Enterobacterales is a global public health problem and rapid and effective methods for detecting these resistance mechanisms are needed urgently. Our aim was to evaluate the performance of a MALDI-TOF MS-based "Klebsiella pneumoniae carbapenemase" (KPC) detection protocol from patients' positive blood cultures, short-term cultures, and colonies in healthcare settings. Bacterial identification and KPC detection were achieved after protein extraction with organic solvents and target spot loading with suitable organic matrices. The confirmation of KPC production was performed using susceptibility tests and blaKPC amplification using PCR and sequencing. The KPC direct detection (KPC peak at approximately 28.681 Da) from patients' positive blood cultures, short-term cultures, and colonies, once bacterial identification was achieved, showed an overall sensibility and specificity of 100% (CI95: [95%, 100%] and CI95: [99%, 100%], respectively). The concordance between hospital routine bacterial identification protocol and identification using this new methodology from the same extract used for KPC detection was ≥92%. This study represents the pioneering effort to directly detect KPC using MALDI-TOF MS technology, conducted on patient-derived samples obtained from hospitals for validation purposes, in a multi-resistance global context that requires concrete actions to preserve the available therapeutic options and reduce the spread of antibiotic resistance markers.
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Affiliation(s)
- Agustina Costa
- Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires 1113, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires 1033, Argentina
| | - Roque Figueroa-Espinosa
- Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires 1113, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires 1033, Argentina
| | - Jerson A Martínez
- Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires 1113, Argentina
| | | | | | | | - Ana E Schneider
- Hospital Alemán de Buenos Aires, Buenos Aires 1113, Argentina
| | - Carlos Vay
- Hospital de Clínicas "José de San Martín", Universidad de Buenos Aires, Buenos Aires 1118, Argentina
| | - Carlos H Rodriguez
- Hospital de Clínicas "José de San Martín", Universidad de Buenos Aires, Buenos Aires 1118, Argentina
| | - Marcela Nastro
- Hospital de Clínicas "José de San Martín", Universidad de Buenos Aires, Buenos Aires 1118, Argentina
| | - Gabriel O Gutkind
- Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires 1113, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires 1033, Argentina
| | - José A Di Conza
- Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires 1113, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires 1033, Argentina
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50
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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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