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Gruszecka J, Filip R. Epidemiological Study of Pathogens in Spontaneous Bacterial Peritonitis in 2017-2024-A Preliminary Report of the University Hospital in South-Eastern Poland. Microorganisms 2024; 12:1008. [PMID: 38792837 PMCID: PMC11123777 DOI: 10.3390/microorganisms12051008] [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: 04/15/2024] [Revised: 05/13/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
Spontaneous Bacterial Peritonitis (SBP) is a serious complication and a common cause of death in patients with liver cirrhosis. Between January 2017 and March 2024, a retrospective study was conducted involving 302 patients (>18 years old) with ascites treated at a tertiary referral center in south-eastern Poland. Microbiological analysis of the ascitic fluids was performed in all patients. The presence of microorganisms was found in samples from 17 patients, and 21 pathogens were isolated, including 15 Gram-positive bacteria and 6 Gram-negative bacteria. Staphylococcus epidermidis, MRCNS (methicillin-resistant coagulase-negative staphylococci, resistant to all beta-lactam antibiotics: penicillins, penicillins with beta-lactamase inhibitor, cephalosporins and carbapenems) was the main pathogen detected (19.05%, 4/21), followed by Enterococcus faecalis (9.52%, 2/21), Enterococcus faecium (9.52%, 2/21), Staphylococcus haemolyticus, MRCNS (4.76%, 1/21), Streptococcus mitis (9.52%, 2/21), Streptococcus parasanguinis (9.52%, 2/21), Micrococcus luteus (4.76%, 1/21) and Bacillus spp. (4.76%, 1/21). The following Gram-negative bacteria were also found in the specimens examined: Escherichia coli, ESBL (extended-spectrum β-lactamase producing E. coli) (4.76%, 1/21), Escherichia coli (4.76%, 1/21), Pseudomonas aeruginosa (4.76%, 1/21), Klebsiella oxytoca (9.52%, 2/21) and Sphingomonas paucimobilis (4.76%, 1/21). Gram-positive bacteria caused nosocomial infections in nine patients with SBP, Gram-negative bacteria caused nosocomial infections in two patients. In six patients with SBP, community-acquired infections caused by Gram-negative bacteria were found in three cases, Gram-positive bacteria in two cases, and in one case, community-acquired infection was caused by mixed Gram-positive and Gram-negative. Bacteria isolated from patients with hospital-acquired SBP showed higher drug resistance than those found in patients with non-hospital SBP. Bacterial infections in cirrhotic patients with complications may be responsible for their deteriorating health. Prompt intervention is critical to reducing mortality.
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Affiliation(s)
- Jolanta Gruszecka
- Institute of Health Sciences, Medical College of Rzeszow University, 35-310 Rzeszow, Poland;
- Department of Clinical Microbiology, Clinical Hospital No. 2, 35-301 Rzeszow, Poland
| | - Rafał Filip
- Faculty of Medicine, Medical College of Rzeszow University, 35-959 Rzeszow, Poland
- IBD Unit, Department of Gastroenterology, Clinical Hospital No. 2, 35-301 Rzeszow, Poland
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Lee H, Koo J, Oh J, Cho SI, Lee H, Lee HJ, Sung GH, Kim J. Clinical Evaluation of VITEK MS PRIME with PICKME Pen for Bacteria and Yeasts, and RUO Database for Filamentous Fungi. Microorganisms 2024; 12:964. [PMID: 38792793 PMCID: PMC11124449 DOI: 10.3390/microorganisms12050964] [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: 04/04/2024] [Revised: 05/01/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
The VITEK MS PRIME (bioMérieux, Marcy-l'Étoile, France), a newly developed matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) system, alongside the VITEK PICKME pen (PICKME), offers easy sample preparation for bacteria and yeasts. The VITEK MS PRIME also offers two software platforms for filamentous fungi: the IVD database and the RUO database. Our study evaluated its identification agreement on 320 clinical isolates of bacteria and yeasts, comparing PICKME and traditional wooden toothpick sampling techniques against MicroIDSys Elite (ASTA) results. Additionally, we assessed the IVD (v3.2) and SARAMIS (v4.16) RUO databases on 289 filamentous fungi against molecular sequencing. The concordance rates for species-level identification of bacteria and yeasts were about 89.4% (286/320) between the PICKME and wooden toothpick, and about 83.4-85.3% between the VITEK MS PRIME and ASTA MicroIDSys Elite. Retesting with PICKME improved concordance to 91.9%. For filamentous fungi, species-level identification reached 71.3% with the IVD database and 85.8% with RUO, which significantly enhanced basidiomycetes' identification from 35.3% to 100%. Some strains in the IVD database, like Aspergillus versicolor, Exophiala xenobiotica, and Nannizzia gypsea, failed to be identified. The VITEK MS PRIME with PICKME offers reliable and efficient microorganism identification. For filamentous fungi, combined use of the RUO database can be beneficial, especially for basidiomycetes.
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Affiliation(s)
- Hyeyoung Lee
- Department of Laboratory Medicine, International St. Mary’s Hospital, College of Medicine, Catholic Kwandong University, Incheon 22711, Republic of Korea; (H.L.); (J.K.); (S.-I.C.); (H.L.); (H.J.L.)
| | - Jehyun Koo
- Department of Laboratory Medicine, International St. Mary’s Hospital, College of Medicine, Catholic Kwandong University, Incheon 22711, Republic of Korea; (H.L.); (J.K.); (S.-I.C.); (H.L.); (H.J.L.)
| | - Junsang Oh
- Biomedical Institute of Mycological Resource, International St. Mary’s Hospital, College of Medicine, Catholic Kwandong University, Incheon 22711, Republic of Korea;
- Department of Convergence Science, College of Medicine, Catholic Kwandong University, Gangneung 25601, Republic of Korea
| | - Sung-Il Cho
- Department of Laboratory Medicine, International St. Mary’s Hospital, College of Medicine, Catholic Kwandong University, Incheon 22711, Republic of Korea; (H.L.); (J.K.); (S.-I.C.); (H.L.); (H.J.L.)
| | - Hyunjoo Lee
- Department of Laboratory Medicine, International St. Mary’s Hospital, College of Medicine, Catholic Kwandong University, Incheon 22711, Republic of Korea; (H.L.); (J.K.); (S.-I.C.); (H.L.); (H.J.L.)
| | - Hyun Ji Lee
- Department of Laboratory Medicine, International St. Mary’s Hospital, College of Medicine, Catholic Kwandong University, Incheon 22711, Republic of Korea; (H.L.); (J.K.); (S.-I.C.); (H.L.); (H.J.L.)
| | - Gi-Ho Sung
- Biomedical Institute of Mycological Resource, International St. Mary’s Hospital, College of Medicine, Catholic Kwandong University, Incheon 22711, Republic of Korea;
- Department of Convergence Science, College of Medicine, Catholic Kwandong University, Gangneung 25601, Republic of Korea
| | - Jayoung Kim
- Department of Laboratory Medicine, International St. Mary’s Hospital, College of Medicine, Catholic Kwandong University, Incheon 22711, Republic of Korea; (H.L.); (J.K.); (S.-I.C.); (H.L.); (H.J.L.)
- Biomedical Institute of Mycological Resource, International St. Mary’s Hospital, College of Medicine, Catholic Kwandong University, Incheon 22711, Republic of Korea;
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Sibińska E, Arendowski A, Fijałkowski P, Gabryś D, Pomastowski P. Comparison of the Bruker Microflex LT and Zybio EXS2600 MALDI TOF MS systems for the identification of clinical microorganisms. Diagn Microbiol Infect Dis 2024; 108:116150. [PMID: 38035652 DOI: 10.1016/j.diagmicrobio.2023.116150] [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: 06/20/2023] [Revised: 11/16/2023] [Accepted: 11/24/2023] [Indexed: 12/02/2023]
Abstract
The emergence of Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry (MALDI TOF MS) technology has expanded the capabilities for identifying microorganisms in clinical labs, replacing traditional biochemical testing with a proteomic approach. In the present study, we compared results between the two commercial MALDI TOF MS systems, Bruker Microflex LT Biotyper and Zybio EXS2600 Ex-Accuspec, for the identification of 1979 urinary isolates by direct extraction method. Current study found that both systems identified a high percentage of isolates to at least the genus level - Bruker 95.6 % of isolates, Zybio 92.4 %. In the case of 89.5 % of all analyzed spectra, the identification results were consistent between the used devices. The highest score values and the highest percentage of spectra identified to species were obtained for gram-negative bacteria. The results show that both systems are equally good choices in terms of analytical performance for routine microbiological diagnostic procedures.
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Affiliation(s)
- Ewelina Sibińska
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4 Str., Toruń 87-100, Poland
| | - Adrian Arendowski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4 Str., Toruń 87-100, Poland.
| | - Piotr Fijałkowski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4 Str., Toruń 87-100, Poland
| | - Dorota Gabryś
- Radiotherapy Department, Maria Sklodowska-Curie National Research Institute of Oncology, Wybrzeże Armii Krajowej 15 Str., Gliwice 44-102, Poland
| | - Paweł Pomastowski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4 Str., Toruń 87-100, Poland
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Yun SY, Lee Y, Hong J, Kim DC, Lee H, Yong D, Lim YK, Kook JK, Lee K. Identification of Fusobacterium Species Using Matrix-Assisted Laser Desorption/Ionization-Time-of-Flight Mass Spectrometry by Updating ASTA CoreDB. Yonsei Med J 2022; 63:1138-1143. [PMID: 36444550 PMCID: PMC9760896 DOI: 10.3349/ymj.2022.0271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 10/14/2022] [Accepted: 10/20/2022] [Indexed: 11/22/2022] Open
Abstract
PURPOSE Fusobacterium species can cause infections, and associations with cancer are being increasingly reported. As their clinical significance differs, accurate identification of individual species is important. However, matrix-assisted laser desorption/ionization-time of flight mass spectrometry has not been found to be effective in identifying Fusobacterium species in previous studies. In this study, we aimed to improve the accuracy and efficacy of identifying Fusobacterium species in clinical laboratories. MATERIALS AND METHODS In total, 229 Fusobacterium isolates were included in this study. All isolates were identified at the species level based on nucleotide sequences of the 16S ribosomal RNA gene and/or DNA-dependent RNA polymerase β-subunit gene (rpoB). Where necessary, isolates were identified based on whole genome sequences. Among them, 47 isolates were used for updating the ASTA database, and 182 isolates were used for the validation of Fusobacterium spp. identification. RESULTS Fusobacterium isolates used for validation (182/182) were correctly identified at the genus level, and most (180/182) were correctly identified at the species level using the ASTA MicroIDSys system. Most of the F. nucleatum isolates (74/75) were correctly identified at the subspecies level. CONCLUSION The updated ASTA MicroIDSys system can identify nine species of Fusobacterium and four subspecies of F. nucleatum in good agreement. This tool can be routinely used in clinical microbiology laboratories to identify Fusobacterium species and serve as a springboard for future research.
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Affiliation(s)
- Shin Young Yun
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - Yunhee Lee
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - Juwon Hong
- R&D Center, NOSQUEST Inc., Yongin, Korea
| | | | - Hyukmin Lee
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea.
| | - Dongeun Yong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - Yun Kyong Lim
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Korea
| | - Joong-Ki Kook
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Korea.
| | - Kyungwon Lee
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
- Seoul Clinical Laboratories Academy, Yongin, Korea
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Ko YJ, Lee OJ, Lee SB, Kim CM, Lee J, Kook JK, Park SN, Shin JH, Kim SH, Won EJ, Park G, Kang SH, Jang SJ. Accuracy of ASTA MicroIDSys, a New Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry System, for the Identification of Korean Reference and Clinical Bacterial and Yeast Strains. Diagn Microbiol Infect Dis 2022; 103:115658. [DOI: 10.1016/j.diagmicrobio.2022.115658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 01/17/2022] [Accepted: 01/22/2022] [Indexed: 11/03/2022]
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Comparative Evaluation of Bruker Biotyper and ASTA MicroIDSys for Species Identification in a Clinical Microbiology Laboratory. Diagnostics (Basel) 2021; 11:diagnostics11091683. [PMID: 34574024 PMCID: PMC8470862 DOI: 10.3390/diagnostics11091683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 08/27/2021] [Accepted: 09/14/2021] [Indexed: 11/17/2022] Open
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI–TOF MS) has been widely used for microbial identification, because of its speed and accuracy, since its introduction to clinical microbiology laboratories. In this study, we evaluated the performance of ASTA MicroIDSys, a newly developed MALDI–TOF, and compared it with the widely used Bruker Biotyper. Microbial identification with the Bruker Biotyper system was performed by using a direct smear method and the Bruker Biotyper database (reference library version 6.0.0.0). The isolates were also tested in parallel, using the ASTA MicroIDSys system with a direct smear method and the MicroIDSys database, CoreDB v1.26. A total of 914 clinical isolates were recovered from the clinical specimens. Identical results with confidence scores (≥2.0, for the Bruker Biotyper) and acceptable scores (≥140 for the ASTA MicroIDSys) were obtained for 840 (91.9%) isolates. The minor errors were defined as misidentification at the species level, and the rate was 1.1% (9/792) for Bruker Biotyper and 1.6% (13/792) for ASTA MicroIDSys. Major errors were defined as misidentification at the genus level, and the rate was 0.3% (2/792) for both Bruker Biotyper and ASTA MicroIDSys. ASTA MicroIDSys showed reliable performance for microbial identification, which was comparable to that of the Bruker Biotyper. Therefore, ASTA MicroIDSys can be applied for the identification of microorganisms in clinical microbiology laboratories.
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Lee OJ, Ko YJ, Lee SB, Kim CM, Jang SJ, Kook JK, Lim YK, Shin JH, Shin MG, Kee SJ, Jeong SH, Kang SH, Park G. Performance assessment of ASTA MicroIDSys, a new matrix assisted laser desorption ionization-time of flight mass spectrometry system, for identification of viridans group streptococci. Microbiol Immunol 2021; 65:566-574. [PMID: 34516008 DOI: 10.1111/1348-0421.12942] [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: 06/21/2021] [Revised: 08/30/2021] [Accepted: 09/10/2021] [Indexed: 11/29/2022]
Abstract
The performance of the ASTA MicroIDSys system (ASTA, Suwon, South Korea), a new matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) system, was evaluated for the identification of viridans group streptococci (VGS) and compared with the results obtained with the Bruker Biotyper system (Bruker Daltonics, Hamburg, Germany). A total of 106 Streptococcus reference strains belonging to 24 species from the bacterial strain bank was analyzed using the two MALDI-TOF MS systems. Of the 106 reference strains tested, ASTA MicroIDSys and Bruker Biotyper correctly identified 84.9% and 81.1% at the species level, 100% and 97.2% at the group level and 100% and 98.1% at the genus level, respectively. The difference between the two systems was not statistically significant (P = 0.289). Out of 24 species, 13 species were accurately identified to the species level with 100% accurate identification rates with both systems. The accurate identification rates at the species level of ASTA MicroIDSys and Bruker Biotyper were 100% and 87.5% for the S. anginosus group; 78.4% and 73.5% for the S. mitis group; 91.7% and 91.7% for the S. mutans group; and 100% and 100% for the S. salivarius group, respectively. The ASTA MicroIDSys showed an identification performance equivalent to that of the Bruker Biotyper for VGS. Therefore, it would be useful for the identification of VGS strains in clinical microbiology laboratories. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- O-Jin Lee
- Department of Laboratory Medicine, Green Cross Laboratories, Yongin, Republic of Korea
| | - Young Jin Ko
- Department of Laboratory Medicine, School of Medicine, Chosun University, Gwangju, Republic of Korea
| | - Seul-Bi Lee
- Department of Laboratory Medicine, School of Medicine, Chosun University, Gwangju, Republic of Korea
| | - Choon Mee Kim
- Premedical Science, College of Medicine, Chosun University, Gwangju, Republic of Korea
| | - Sook-Jin Jang
- Department of Laboratory Medicine, School of Medicine, Chosun University, Gwangju, Republic of Korea
| | - Joong-Ki Kook
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, College of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Yun Kyong Lim
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, College of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Jong Hee Shin
- Department of Laboratory Medicine, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Myung Geun Shin
- Department of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Republic of Korea
| | - Seung Jung Kee
- Department of Laboratory Medicine, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Seok Hoon Jeong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Republic of Korea
| | - Seong-Ho Kang
- Department of Laboratory Medicine, School of Medicine, Chosun University, Gwangju, Republic of Korea
| | - Geon Park
- Department of Laboratory Medicine, School of Medicine, Chosun University, Gwangju, Republic of Korea
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Multilaboratory Evaluation of the MALDI-TOF Mass Spectrometry System, MicroIDSys Elite, for the Identification of Medically Important Filamentous Fungi. Mycopathologia 2020; 186:15-26. [PMID: 33180204 DOI: 10.1007/s11046-020-00507-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 10/30/2020] [Indexed: 12/17/2022]
Abstract
With the increasing number of fungal infections and immunocompromised patients, rapid and accurate fungal identification is required in clinical microbiology laboratories. We evaluated the applicability of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) system, MicroIDSys Elite (ASTA Corp., South Korea) for the identification of medically important filamentous fungi. A total of 505 strains comprising 37 genera and 90 species collected from 11 Korean hospitals were sent to the microbiology laboratory of International St. Mary's Hospital. All isolates were tested using MicroIDSys Elite, and data were analyzed using the MoldDB v.1.22 database (ASTA). Correct identification rates were compared with the multigene sequencing results. MicroIDSys Elite correctly identified 86.5% (437/505) and 88.9% (449/505) of all tested isolates at the species and genus level, respectively. About 98.2% of Aspergillus isolates were identified at the species level, including cryptic and rare species of A. calidoustus, A. tamarii, A. lentulus, A. versicolor and A. aculeatus. MicroIDSys Elite identified 75.0% of basidiomycetes, including Schizophyllum commune, and 84.3% of the dermatophytes. It also distinguished Sprothrix globosa at the species level. The mean scores of total isolates corresponding to correct species identification were significantly higher than those obtained for genus-level identification (253.5 ± 50.7 vs. 168.6 ± 30.3, P < 0.001). MicroIDSys Elite showed high accuracy for the identification of filamentous fungi, including cryptic and rare Aspergillus species. It is suitable for use in clinical laboratories as a rapid and efficient tool for clinical mold identification. Further evaluations are recommended for MicroIDSys Elite as a rapid and efficient tool for the identification of medically important filamentous fungi.
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