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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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2
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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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3
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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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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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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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6
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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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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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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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9
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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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10
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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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11
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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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12
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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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13
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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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14
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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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15
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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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16
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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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18
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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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19
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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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20
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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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21
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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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22
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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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23
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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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25
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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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26
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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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27
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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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28
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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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29
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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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30
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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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31
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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: 0] [Impact Index Per Article: 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: 6] [Impact Index Per Article: 6.0] [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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38
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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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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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Sivanesan I, Gopal J, Hasan N, Muthu M. A systematic assessment of matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) application for rapid identification of pathogenic microbes that affect food crops: delivered and future deliverables. RSC Adv 2023; 13:17297-17314. [PMID: 37304772 PMCID: PMC10251190 DOI: 10.1039/d3ra01633a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/20/2023] [Indexed: 06/13/2023] Open
Abstract
MALDI-TOF MS has decades of experience in the detection and identification of microbial pathogens. This has now become a valuable analytical tool when it comes to the identification and detection of clinical microbial pathogens. This review gives a brief synopsis of what has been achieved using MALDI-TOF MS in clinical microbiology. The major focus, however, is on summarizing and highlighting the effectiveness of MALDI-TOF MS as a novel tool for rapid identification of food crop microbial pathogens. The methods used and the sample preparation methodologies reported thus far have been highlighted and the challenges and gaps and recommendations for fine tuning the technique have been put forth. In an era where anything close to the health and welfare of humanity has been considered as the top priority, this review pitches on one such relevant research topics.
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Affiliation(s)
- Iyyakkannu Sivanesan
- Department of Bioresources and Food Science, Institute of Natural Science and Agriculture, Konkuk University 1 Hwayang-dong, Gwangjin-gu Seoul 05029 Korea
| | - Judy Gopal
- Department of Research and Innovation, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS) Thandalam Chennai 602105 Tamil Nadu India +91 44 2681 1009 +91 44 66726677
| | - Nazim Hasan
- Department of Chemistry, Faculty of Science, Jazan University P.O. Box 114 Jazan Saudi Arabia
| | - Manikandan Muthu
- Department of Research and Innovation, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS) Thandalam Chennai 602105 Tamil Nadu India +91 44 2681 1009 +91 44 66726677
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Becker K, Lupetti A. Editorial: MALDI-TOF MS in microbiological diagnostics: future applications beyond identification. Front Microbiol 2023; 14:1204452. [PMID: 37180259 PMCID: PMC10167274 DOI: 10.3389/fmicb.2023.1204452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 04/12/2023] [Indexed: 05/16/2023] Open
Affiliation(s)
- Karsten Becker
- Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| | - Antonella Lupetti
- Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, Pisa, Italy
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Ledesma M, Poodts D, Amoia S, Hajos S, Fundia A, Vay C, Pibuel M, Lompardía S. Discrimination of the chemotherapy resistance status of human leukemia and glioblastoma cell lines by MALDI-TOF-MS profiling. Sci Rep 2023; 13:5596. [PMID: 37019937 PMCID: PMC10076308 DOI: 10.1038/s41598-023-32608-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/30/2023] [Indexed: 04/07/2023] Open
Abstract
Chemotherapy mistreatment is partially due to a lack of rapid and reliable tools to discriminate between sensitive and resistant phenotypes. In many cases, the resistance mechanism is not fully understood, contributing to the diagnostic tools' absence. This work aims to determine the capacity of MALDI-TOF-MS profiling to discriminate between chemotherapy-resistant and sensitive phenotypes in leukemia and glioblastoma cells. A multivariate analysis of two therapy-resistant leukemia cell lines (Ki562 and Kv562) and two TMZ-resistant glioblastoma cell lines (U251-R and LN229-R) and their sensitive counterparts was performed. In this work, we first show MALDI-TOF-MS patterns analysis ability to differentiate these cancer cell lines by their chemotherapy-resistant status. We present a rapid and inexpensive tool that would guide and complement the therapeutic decision.
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Affiliation(s)
- Martín Ledesma
- Unidad de Conocimiento Traslacional, Hospital de Alta Complejidad del Bicentenario Esteban Echeverría, San Martín 504, B1842, Monte Grande, Provincia de Buenos Aires, Argentina
| | - Daniela Poodts
- Cátedra de Inmunología, Departamento de Microbiología, Inmunología, Biotecnología y Genética, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires (UBA), Junín 956, C1113, Buenos Aires, Argentina
| | - Sofía Amoia
- Cátedra de Inmunología, Departamento de Microbiología, Inmunología, Biotecnología y Genética, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires (UBA), Junín 956, C1113, Buenos Aires, Argentina
| | - Silvia Hajos
- Cátedra de Inmunología, Departamento de Microbiología, Inmunología, Biotecnología y Genética, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires (UBA), Junín 956, C1113, Buenos Aires, Argentina
- Instituto de Estudios de la Inmunidad Humoral (IDEHU), UBA-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Junín 956, C1113, Buenos Aires, Argentina
| | - Ariela Fundia
- Instituto de Medicina Experimental (IMEX)-CONICET, Academia Nacional de Medicina, José Andrés Pacheco de Melo 3081, C1425, Buenos Aires, Argentina
| | - Carlos Vay
- Laboratorio de Bacteriología, Departamento de Bioquímica Clínica, Facultad de Farmacia y Bioquímica, Hospital de Clínicas "José de San Martín", UBA, Av. Córdoba 2351, C1120, Buenos Aires, Argentina
| | - Matías Pibuel
- Cátedra de Inmunología, Departamento de Microbiología, Inmunología, Biotecnología y Genética, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires (UBA), Junín 956, C1113, Buenos Aires, Argentina.
- Instituto de Estudios de la Inmunidad Humoral (IDEHU), UBA-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Junín 956, C1113, Buenos Aires, Argentina.
| | - Silvina Lompardía
- Cátedra de Inmunología, Departamento de Microbiología, Inmunología, Biotecnología y Genética, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires (UBA), Junín 956, C1113, Buenos Aires, Argentina.
- Instituto de Estudios de la Inmunidad Humoral (IDEHU), UBA-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Junín 956, C1113, Buenos Aires, Argentina.
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Prakash O, Dodsworth JA, Dong X, Ferry JG, L'Haridon S, Imachi H, Kamagata Y, Rhee SK, Sagar I, Shcherbakova V, Wagner D, Whitman WB. Proposed minimal standards for description of methanogenic archaea. Int J Syst Evol Microbiol 2023; 73. [PMID: 37097839 DOI: 10.1099/ijsem.0.005500] [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: 04/26/2023] Open
Abstract
Methanogenic archaea are a diverse, polyphyletic group of strictly anaerobic prokaryotes capable of producing methane as their primary metabolic product. It has been over three decades since minimal standards for their taxonomic description have been proposed. In light of advancements in technology and amendments in systematic microbiology, revision of the older criteria for taxonomic description is essential. Most of the previously recommended minimum standards regarding phenotypic characterization of pure cultures are maintained. Electron microscopy and chemotaxonomic methods like whole-cell protein and lipid analysis are desirable but not required. Because of advancements in DNA sequencing technologies, obtaining a complete or draft whole genome sequence for type strains and its deposition in a public database are now mandatory. Genomic data should be used for rigorous comparison to close relatives using overall genome related indices such as average nucleotide identity and digital DNA-DNA hybridization. Phylogenetic analysis of the 16S rRNA gene is also required and can be supplemented by phylogenies of the mcrA gene and phylogenomic analysis using multiple conserved, single-copy marker genes. Additionally, it is now established that culture purity is not essential for studying prokaryotes, and description of Candidatus methanogenic taxa using single-cell or metagenomics along with other appropriate criteria is a viable alternative. The revisions to the minimal criteria proposed here by the members of the Subcommittee on the Taxonomy of Methanogenic Archaea of the International Committee on Systematics of Prokaryotes should allow for rigorous yet practical taxonomic description of these important and diverse microbes.
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Affiliation(s)
- Om Prakash
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science, Ganeshkhind, Pune, 411007, Maharashtra, India
- Symbiosis Centre for Climate Change and Sustainability, Symbiosis International (Deemed University), Lavale, Pune-412115, Maharashtra, India
| | - Jeremy A Dodsworth
- Department of Biology, California State University, San Bernardino, CA 92407, USA
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - James G Ferry
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Stephane L'Haridon
- CNRS, IFREMER, Laboratoire de Microbiologie des Environnements Extrêmes, University of Brest, F-29280, Plouzané, France
| | - Hiroyuki Imachi
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Yoichi Kamagata
- Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8560, Japan
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, Chungdae-ro 1, Cheongju 28644, Republic of Korea
| | - Isita Sagar
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science, Ganeshkhind, Pune, 411007, Maharashtra, India
| | - Viktoria Shcherbakova
- Laboratory of Anaerobic Microorganisms, All-Russian Collection of Microorganisms (VKM), Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center Pushchino Center for Biological Research of the Russian Academy of Sciences, Prospect Nauki 3, Pushchino, Moscow, 142290, Russian Federation
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg A71-359, 14473 Potsdam, Germany
- Institut of Geosciences, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - William B Whitman
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
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Gupta A, Agarwal J, Singh V, Das A, Sen M. Matrix-Assisted Laser Desorption Ionization Time of Flight (MALDI-TOF) as an Indispensable Tool in Diagnostic Bacteriology: A Comparative Analysis With Conventional Technique. Cureus 2023; 15:e36984. [PMID: 37139282 PMCID: PMC10149887 DOI: 10.7759/cureus.36984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/31/2023] [Indexed: 04/03/2023] Open
Abstract
INTRODUCTION Owing to its accurate diagnosis, rapid turnaround time, cost effectivity, and less rates of error, Matrix-assisted Laser Desorption Ionization Time of Flight (MALDI-TOF) has replaced most of the phenotypic methods of identification. Thus, the objective of this study was to compare and evaluate MALDI-TOF MS to conventional biochemical-to identify bacterial microorganisms. METHODS Different bacterial species isolated from 2010 to 2018 (pre-MALDI-TOF era), using routine bio-chemicals were compared to bacterial species isolated from 2019 to August 2021 (post MALDI-TOF), using MALDI-TOF, in the microbiology laboratory of a tertiary care hospital in North India. Chi-Square test (χ2) was used for the evaluation of bacterial identification between biochemical tests and MALDI-TOF MS association with a 95% confidence interval, considering wrong identification in genera or at a species level. RESULTS Many different and new genera and species of bacteria could be identified using MALDI-TOF, which was not possible using only routine manual bio-chemicals like Kocuria rhizophilus, Rothia mucilaginosa, Enterococcus casseliflavus, Enterococcus gallinarum, Leuconostoc, Leclercia adecarboxylata, Raoultella ornithological, Cryseobacterium indologenes. Conclusion: Each of the newly identified bacteria played an important role in deciding treatment. Wide use of the MALDI-TOF system will not only strengthen diagnostic stewardship but also encourage antimicrobial stewardship programs.
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Jarzembowski T, Piechowicz L, Bronk M, Pałubicka A, Naumiuk Ł. Changes in the Protein Profile in Staphylococcal Strains from Patients Infected with the SARS-CoV-2 Virus. Pol J Microbiol 2023; 72:93-99. [PMID: 36803915 DOI: 10.33073/pjm-2023-001] [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: 09/23/2022] [Accepted: 12/03/2022] [Indexed: 02/22/2023] Open
Abstract
Staphylococcus aureus strains are particularly often isolated from patients with SARS-CoV-2 infection. The aim of the current research was to determine whether the SARS-CoV-2 virus infection affects the protein profile of S. aureus. Bacteria were isolated from the forty swabs collected from the patients in the hospitals of the Pomeranian region. MALDI-TOF MS spectra were obtained using a Microflex LT instrument. Twenty-nine peaks were identified. The peak (2,430) is described here for the first time and was unique for the isolates from patients infected with the SARS-CoV-2 virus. These results support the hypothesis of bacterial adaptation to the conditions caused by viral infection.
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Affiliation(s)
- Tomasz Jarzembowski
- 1Department of Medical of Microbiology, Medical Faculty, Medical University of Gdansk, Gdansk, Poland
| | - Lidia Piechowicz
- 1Department of Medical of Microbiology, Medical Faculty, Medical University of Gdansk, Gdansk, Poland
| | - Marek Bronk
- 2Department of Clinical Microbiology, Hospital of the Medical University of Gdansk, Gdansk, Poland
| | - Anna Pałubicka
- 3Specialist Hospital in Koscierzyna Sp. z o.o., Department of Laboratory and Microbiological Diagnostics, Koscierzyna, Poland
| | - Łukasz Naumiuk
- 2Department of Clinical Microbiology, Hospital of the Medical University of Gdansk, Gdansk, Poland
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Salam MA, Al-Amin MY, Pawar JS, Akhter N, Lucy IB. Conventional methods and future trends in antimicrobial susceptibility testing. Saudi J Biol Sci 2023; 30:103582. [PMID: 36852413 PMCID: PMC9958398 DOI: 10.1016/j.sjbs.2023.103582] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 01/07/2023] [Accepted: 01/29/2023] [Indexed: 02/12/2023] Open
Abstract
Antimicrobial susceptibility testing is an essential task for selecting appropriate antimicrobial agents to treat infectious diseases. Constant evolution has been observed in methods used in the diagnostic microbiology laboratories. Disc diffusion or broth microdilution are classical and conventional phenotypic methods with long turnaround time and labour-intensive but still widely practiced as gold-standard. Scientists are striving to develop innovative, novel and faster methods of antimicrobial susceptibility testing to be applicable for routine microbiological laboratory practice and research. To meet the requirements, there is an increasing trend towards automation, genotypic and micro/nano technology-based innovations. Automation in detection systems and integration of computers for online data analysis and data sharing are giant leaps towards versatile nature of automated methods currently in use. Genotypic methods detect a specific genetic marker associated with resistant phenotypes using molecular amplification techniques and genome sequencing. Microfluidics and microdroplets are recent addition in the continuous advancement of methods that show great promises with regards to safety and speed and have the prospect to identify and monitor resistance mechanisms. Although genotypic and microfluidics methods have many exciting features, however, their applications into routine clinical laboratory practice warrant extensive validation. The main impetus behind the evolution of methods in antimicrobial susceptibility testing is to shorten the overall turnaround time in obtaining the results and to enhance the ease of sample processing. This comprehensive narrative review summarises major conventional phenotypic methods and automated systems currently in use, and highlights principles of some of the emerging genotypic and micro/nanotechnology-based methods in antimicrobial susceptibility testing.
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Key Words
- ADR, Adverse drug reaction
- AMR, Antimicrobial resistance
- AST, Antimicrobial susceptibility testing
- ATCC, American Type Culture Collection
- Advantages and disadvantages
- Antimicrobial susceptibility testing
- Automations
- CFU, Colony forming units
- CLSI, Clinical & Laboratory Standards Institute
- Conventional methods
- DOT-MGA, Direct-On-Target Microdroplet Growth Assay
- EUCAST, European Committee on Antimicrobial Susceptibility Testing
- Etest, Epsilometer testing
- Genotypic methods
- ID, Identification
- MALDI-TOF MS, Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry
- MBC, Minimum bactericidal concentration
- MDR, Multi drug resistant
- MHA, Muller Hinton Agar
- MIC, Minimum inhibitory concentration
- Micro/nanotechnology-based techniques
- NAAT, Nucleic Acid Amplification Test
- PCR, Polymerase chain reaction
- PMF, Peptide mass fingerprint
- POC, Point of care
- WGS, Whole Genome Sequencing
- ZOI, Zone of inhibition
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Affiliation(s)
- Md. Abdus Salam
- Department of Basic Medical Sciences, Kulliyyah of Medicine, International Islamic University, Malaysia
| | - Md. Yusuf Al-Amin
- Purdue University Interdisciplinary Life Sciences Graduate Program, Purdue University, West Lafayette, IN, USA,Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - Jogendra Singh Pawar
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - Naseem Akhter
- Department of Neurology, Henry Ford Health System, Detroit, MI 48202, USA
| | - Irine Banu Lucy
- Department of Physics, University of Rajshahi, Rajshahi 6205, Bangladesh,Corresponding author at: Department of Physics, University of Rajshahi, Rajshahi 6205, Bangladesh.
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Castro AE, De Ungria MCA. Methods used in microbial forensics and epidemiological investigations for stronger health systems. Forensic Sci Res 2023; 7:650-661. [PMID: 36817258 PMCID: PMC9930754 DOI: 10.1080/20961790.2021.2023272] [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] [Indexed: 10/18/2022] Open
Abstract
This review discusses microbial forensics as an emerging science that finds application in protecting human health. It is important to distinguish naturally acquired infections from those caused by the intentional release of microorganisms to the environment. This information is crucial in formulating procedures against the spread of infectious diseases and prosecuting persons who may be involved in acts of biocrime, bioterrorism, or biowarfare. A comparison between epidemiological investigations and microbial forensic investigations is provided. In addition, a discussion on how microbial forensics strengthens health systems is included in this review. Microbial forensic investigations and epidemiologic examinations employ similar concepts and involve identifying and characterising the microbe of interest. Both fields require formulating an appropriate case definition, determining a pathogen's mode of transmission, and identifying the source(s) of infection. However, the two subdisciplines differ in their objectives. An epidemiological investigation aims to identify the pathogen's source to prevent the spread of the disease. Microbial forensics focuses on source-tracking to facilitate the prosecution of persons responsible for the spread of a pathogen. Both fields use molecular techniques in analysing and comparing DNA, gene products, and biomolecules to identify and characterise the microorganisms of interest. We included case studies to show methods used in microbial forensic investigations, a brief discussion of the public significance of microbial forensic systems, and a roadmap for establishing a system at a national level. This system is expected to strengthen a country's capacity to respond to public health emergencies. Several factors must be considered in establishing national microbial forensic systems. First is the inherent ubiquity, diversity, and adaptability of microorganisms that warrants the use of robust and accurate molecular typing systems. Second, the availability of facilities and scientists who have been trained in epidemiology, molecular biology, bioinformatics, and data analytics. Human resources and infrastructure are critical requirements because formulating strategies and allocating resources in times of infectious disease outbreaks must be data-driven. Establishing and maintaining a national microbial forensic system to strengthen capacities in conducting forensic and epidemiological investigations should be prioritised by all countries, accompanied by a national policy that sets the legislative framework and provides for the system's financial requirements.
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Affiliation(s)
- Arizaldo E. Castro
- Microbial Ecology of Terrestrial and Aquatic Systems Laboratory, Institute of Biology, University of the Philippines Diliman, Quezon City, Philippines,CONTACT Arizaldo E. Castro
| | - Maria Corazon A. De Ungria
- DNA Analysis Laboratory, Natural Sciences Research Institute, University of the Philippines Diliman, Quezon City, Philippines,Program on Biodiversity, Ethnicity, and Forensics, Philippine Genome Center, University of the Philippines Diliman, Quezon City, Philippines
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Semi-supervised learning for MALDI–TOF mass spectrometry data classification: an application in the salmon industry. Neural Comput Appl 2023. [DOI: 10.1007/s00521-023-08333-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
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Torrico MC, Fernández-Arévalo A, Ballart C, Solano M, Rojas E, Abras A, Gonzales F, Arnau A, Tebar S, Llovet T, Lozano D, Ariza-Vioque E, Gascón J, Picado A, Torrico F, Muñoz C, Gállego M. Usefulness of Matrix-Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry in the Characterization of Leishmania Strains Causing Tegumentary Leishmaniasis in Bolivia versus hsp70 Gene Sequencing. Microbiol Spectr 2023; 11:e0347722. [PMID: 36633426 PMCID: PMC9927355 DOI: 10.1128/spectrum.03477-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 11/23/2022] [Indexed: 01/13/2023] Open
Abstract
Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) is a proteomic technique with proven efficiency in the identification of microorganisms, such as bacteria, fungi, and parasites. The present study aimed to evaluate the usefulness of MALDI-TOF MS for the characterization of Leishmania species circulating in Bolivia using hsp70 gene sequencing as a reference technique. 55 Leishmania strains that were isolated from patients with tegumentary leishmaniasis were analyzed. MALDI-TOF MS identified two species of the L. braziliensis complex (L. braziliensis, n = 26; L. braziliensis outlier, n = 18), one species of the L. guyanensis complex (L. guyanensis, n = 1), one species of the L. lainsoni complex (L. lainsoni, n = 2), and two species of the L. mexicana complex (L. amazonensis, n = 5; and L. garnhami, n = 3). All of the strains were correctly identified at the subgenus, genus, and complex level, but 10 of them (18%) were misidentified as other species within the same complex by the hsp70 gene sequencing, with 7 of these corresponding to possible hybrids. Thus, one L. braziliensis corresponded to L. peruviana, two L. braziliensis corresponded to L. braziliensis/L. peruviana possible hybrids, two L. amazonensis corresponded to L. mexicana, and three L. garnhami and two L. amazonensis corresponded to L. mexicana/L. amazonensis possible hybrids. Accordingly, MALDI-TOF MS could be used as an alternative to molecular techniques for the identification of Leishmania spp., as it is low cost, simple to apply, and able to quickly produce results. In Bolivia, its application would allow for the improvement of the management of patient follow-ups, the updating of the epidemiological data of the Leishmania species, and a contribution to the control of tegumentary leishmaniasis. IMPORTANCE The objective of the study was to evaluate the usefulness of MALDI-TOF MS for the characterization of Leishmania species circulating in Bolivia, in comparison with the sequencing of the hsp70 gene. In our study, all of the isolates could be identified, and no misidentifications were observed at the complex level. Although the equipment implies a high initial investment in our context, MALDI-TOF MS can be used in different areas of microbiology and significantly reduces the cost of testing. Once the parasite culture is obtained, the technique quickly yields information by accessing a free database that is available online. This would allow for the improvement of the management of patients and follow-ups, the updating of the epidemiological data of the species, and a contribution to the control of tegumentary leishmaniasis in Bolivia. Likewise, it can be used to determine a specific treatment to be given, according to the causal species of Leishmania, when there are protocols in this regard in the area.
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Affiliation(s)
- Mary Cruz Torrico
- Facultad de Medicina, Universidad Mayor de San Simón, Cochabamba, Bolivia
- Fundación CEADES y Medio Ambiente, Cochabamba, Bolivia
- Secció de Parasitologia, Departament de Biologia, Sanitat i Medi Ambient, Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona, Barcelona, Spain
| | - Anna Fernández-Arévalo
- Secció de Parasitologia, Departament de Biologia, Sanitat i Medi Ambient, Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona, Barcelona, Spain
| | - Cristina Ballart
- Secció de Parasitologia, Departament de Biologia, Sanitat i Medi Ambient, Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona, Barcelona, Spain
- Instituto de Salud Global de Barcelona (ISGlobal), Barcelona, Spain
| | - Marco Solano
- Facultad de Medicina, Universidad Mayor de San Simón, Cochabamba, Bolivia
| | - Ernesto Rojas
- Facultad de Medicina, Universidad Mayor de San Simón, Cochabamba, Bolivia
| | - Alba Abras
- Departament de Biologia, Universitat de Girona, Girona, Spain
| | - Fabiola Gonzales
- Facultad de Medicina, Universidad Mayor de San Simón, Cochabamba, Bolivia
| | - Albert Arnau
- Secció de Parasitologia, Departament de Biologia, Sanitat i Medi Ambient, Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona, Barcelona, Spain
- Departament de Biologia, Universitat de Girona, Girona, Spain
| | - Silvia Tebar
- Secció de Parasitologia, Departament de Biologia, Sanitat i Medi Ambient, Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona, Barcelona, Spain
| | - Teresa Llovet
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau Barcelona, Barcelona, Spain
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Daniel Lozano
- Facultad de Medicina, Universidad Mayor de San Simón, Cochabamba, Bolivia
- Fundación CEADES y Medio Ambiente, Cochabamba, Bolivia
| | - Eva Ariza-Vioque
- Secció de Parasitologia, Departament de Biologia, Sanitat i Medi Ambient, Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona, Barcelona, Spain
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Joaquim Gascón
- Instituto de Salud Global de Barcelona (ISGlobal), Barcelona, Spain
- CIBERINFEC, ISCIII-CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III
| | - Albert Picado
- Instituto de Salud Global de Barcelona (ISGlobal), Barcelona, Spain
| | - Faustino Torrico
- Facultad de Medicina, Universidad Mayor de San Simón, Cochabamba, Bolivia
- Fundación CEADES y Medio Ambiente, Cochabamba, Bolivia
| | - Carmen Muñoz
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau Barcelona, Barcelona, Spain
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Spain
- Institut de Recerca Biomèdica Sant Pau, Barcelona, Spain
| | - Montserrat Gállego
- Secció de Parasitologia, Departament de Biologia, Sanitat i Medi Ambient, Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona, Barcelona, Spain
- Instituto de Salud Global de Barcelona (ISGlobal), Barcelona, Spain
- CIBERINFEC, ISCIII-CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III
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