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Muchaamba F, Stephan R. A Comprehensive Methodology for Microbial Strain Typing Using Fourier-Transform Infrared Spectroscopy. Methods Protoc 2024; 7:48. [PMID: 38921827 PMCID: PMC11207048 DOI: 10.3390/mps7030048] [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: 04/10/2024] [Revised: 05/29/2024] [Accepted: 06/04/2024] [Indexed: 06/27/2024] Open
Abstract
Timely and accurate detection and characterization of microbial threats is crucial for effective infection and outbreak management. Additionally, in food production, rapid microbe identification is indispensable for maintaining quality control and hygiene standards. Current methods for typing microbial strains often rely on labor-intensive, time-consuming, and expensive DNA- and sera-serotyping techniques, limiting their applicability in rapid-response scenarios. In this context, the IR Biotyper®, utilizing Fourier-transform infrared (FTIR) spectroscopy, offers a novel approach, providing specific spectra for fast strain typing within 3 h. This methodology article serves as a comprehensive resource for researchers and technicians aiming to utilize FTIR spectroscopy for microbial strain typing. It encompasses detailed guidelines on sample preparation, data acquisition, and analysis techniques, ensuring the generation of reliable and reproducible results. We highlight the IR Biotyper®'s rapid and accurate discrimination capabilities, showcasing its potential for real-time pathogen monitoring and source-tracking to enhance public health and food safety. We propose its integration as an early screening method, followed by more detailed analysis with whole-genome sequencing, to optimize detection accuracy and response efficiency in microbial surveillance systems.
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Affiliation(s)
- Francis Muchaamba
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 272, CH-8057 Zurich, Switzerland
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2
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McGalliard R, Muhamadali H, AlMasoud N, Haldenby S, Romero-Soriano V, Allman E, Xu Y, Roberts AP, Paterson S, Carrol ED, Goodacre R. Bacterial discrimination by Fourier transform infrared spectroscopy, MALDI-mass spectrometry and whole-genome sequencing. Future Microbiol 2024. [PMID: 38652264 DOI: 10.2217/fmb-2024-0043] [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] [Indexed: 04/25/2024] Open
Abstract
Aim: Proof-of-concept study, highlighting the clinical diagnostic ability of FT-IR compared with MALDI-TOF MS, combined with WGS. Materials & methods: 104 pathogenic isolates of Neisseria meningitidis, Streptococcus pneumoniae, Streptococcus pyogenes and Staphylococcus aureus were analyzed. Results: Overall prediction accuracy was 99.6% in FT-IR and 95.8% in MALDI-TOF-MS. Analysis of N. meningitidis serogroups was superior in FT-IR compared with MALDI-TOF-MS. Phylogenetic relationship of S. pyogenes was similar by FT-IR and WGS, but not S. aureus or S. pneumoniae. Clinical severity was associated with the zinc ABC transporter and DNA repair genes in S. pneumoniae and cell wall proteins (biofilm formation, antibiotic and complement permeability) in S. aureus via WGS. Conclusion: FT-IR warrants further clinical evaluation as a promising diagnostic tool.
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Affiliation(s)
- Rachel McGalliard
- Department of Clinical Infection, Microbiology & Immunology, University of Liverpool Institute of Infection, Veterinary & Ecological Sciences, Ronald Ross Building, 8 West Derby Street, Liverpool, UK
- Department of Infectious Diseases, Alder Hey Children's NHS Foundation Trust, Eaton Road, Liverpool, UK
| | - Howbeer Muhamadali
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
- center for Metabolomics Research, Department of Biochemistry, Cell & Systems Biology, Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool, UK
| | - Najla AlMasoud
- College of Science, Princess Nourah Bint Abdulrahman University, Department of Chemistry, Riyadh, 11671, Saudi Arabia
| | - Sam Haldenby
- center for Genomic Research, University of Liverpool, Mersey Bio Building, Crown Street, Liverpool, UK
| | - Valeria Romero-Soriano
- center for Genomic Research, University of Liverpool, Mersey Bio Building, Crown Street, Liverpool, UK
| | - Ellie Allman
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Yun Xu
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
- center for Metabolomics Research, Department of Biochemistry, Cell & Systems Biology, Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool, UK
| | - Adam P Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Steve Paterson
- center for Genomic Research, University of Liverpool, Mersey Bio Building, Crown Street, Liverpool, UK
| | - Enitan D Carrol
- Department of Clinical Infection, Microbiology & Immunology, University of Liverpool Institute of Infection, Veterinary & Ecological Sciences, Ronald Ross Building, 8 West Derby Street, Liverpool, UK
- Department of Infectious Diseases, Alder Hey Children's NHS Foundation Trust, Eaton Road, Liverpool, UK
| | - Royston Goodacre
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
- center for Metabolomics Research, Department of Biochemistry, Cell & Systems Biology, Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool, UK
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3
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Han M, Chae M, Lee S, No K, Han S. Strain typing and antimicrobial susceptibility of Salmonella enterica Albany isolates from duck farms in South Korea. Heliyon 2024; 10:e27402. [PMID: 38486745 PMCID: PMC10937681 DOI: 10.1016/j.heliyon.2024.e27402] [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: 08/30/2023] [Revised: 02/21/2024] [Accepted: 02/28/2024] [Indexed: 03/17/2024] Open
Abstract
Salmonella enterica is distributed worldwide and is a common cause of bacterial food poisoning in humans and a serious public health problem. Although duck meat consumption has recently increased in Korea, studies on the epidemiological relationship between S. enterica contamination in duck farms are scarce. Salmonella enterica serovar Albany isolates recovered from duck farms were analyzed using two typing methods - IR Biotyper® (IRBT) and multilocus variable-number tandem repeat analysis (MLVA). The clustering results were compared with the epidemiological survey findings and the antimicrobial resistance profiles. From April 2019 to October 2020, 20 individual feces per farm from 5-6-week-old ducks were collected repeatedly from 105 duck farms. Salmonella spp. isolated from duck feces were identified using PCR and multilocus sequence typing to investigate the prevalence and distribution of the Salmonella serovars. The prevalence of S. enterica was 19%, and S. enterica Albany was the predominantly recovered isolate. The S. enterica Albany isolates underwent antimicrobial susceptibility testing to determine the minimum inhibitory concentration. MLVA and IRBT methods established relatedness and diversity among the S. enterica Albany isolates. Multidrug-resistant S. enterica Albany was distributed in all the farms. Antimicrobial resistance profiles reflected the duck farm characteristics and isolates recovered from the same farm showed an identical profile. Isolates repeatedly recovered from the same farm also showed identical IRBT clusters and MLVA groups. These findings suggest that the isolates remained on the duck farm and re-infected new duck flocks. Thus, proper cleaning and disinfection is required before the farms are repopulated.
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Affiliation(s)
- Mina Han
- Institute of Chungbuk Provincial Veterinary Service and Research, Cheongju, South Korea
| | - Munhui Chae
- Institute of Chungbuk Provincial Veterinary Service and Research, Cheongju, South Korea
| | - Sangkab Lee
- Institute of Chungbuk Provincial Veterinary Service and Research, Cheongju, South Korea
| | - Kyongok No
- Institute of Chungbuk Provincial Veterinary Service and Research, Cheongju, South Korea
| | - Seongtae Han
- Institute of Chungbuk Provincial Veterinary Service and Research, Cheongju, South Korea
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Novais Â, Gonçalves AB, Ribeiro TG, Freitas AR, Méndez G, Mancera L, Read A, Alves V, López-Cerero L, Rodríguez-Baño J, Pascual Á, Peixe L. Development and validation of a quick, automated, and reproducible ATR FT-IR spectroscopy machine-learning model for Klebsiella pneumoniae typing. J Clin Microbiol 2024; 62:e0121123. [PMID: 38284762 PMCID: PMC10865814 DOI: 10.1128/jcm.01211-23] [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: 09/18/2023] [Accepted: 12/18/2023] [Indexed: 01/30/2024] Open
Abstract
The reliability of Fourier-transform infrared (FT-IR) spectroscopy for Klebsiella pneumoniae typing and outbreak control has been previously assessed, but issues remain in standardization and reproducibility. We developed and validated a reproducible FT-IR with attenuated total reflectance (ATR) workflow for the identification of K. pneumoniae lineages. We used 293 isolates representing multidrug-resistant K. pneumoniae lineages causing outbreaks worldwide (2002-2021) to train a random forest classification (RF) model based on capsular (KL)-type discrimination. This model was validated with 280 contemporaneous isolates (2021-2022), using wzi sequencing and whole-genome sequencing as references. Repeatability and reproducibility were tested in different culture media and instruments throughout time. Our RF model allowed the classification of 33 capsular (KL)-types and up to 36 clinically relevant K. pneumoniae lineages based on the discrimination of specific KL- and O-type combinations. We obtained high rates of accuracy (89%), sensitivity (88%), and specificity (92%), including from cultures obtained directly from the clinical sample, allowing to obtain typing information the same day bacteria are identified. The workflow was reproducible in different instruments throughout time (>98% correct predictions). Direct colony application, spectral acquisition, and automated KL prediction through Clover MS Data analysis software allow a short time-to-result (5 min/isolate). We demonstrated that FT-IR ATR spectroscopy provides meaningful, reproducible, and accurate information at a very early stage (as soon as bacterial identification) to support infection control and public health surveillance. The high robustness together with automated and flexible workflows for data analysis provide opportunities to consolidate real-time applications at a global level. IMPORTANCE We created and validated an automated and simple workflow for the identification of clinically relevant Klebsiella pneumoniae lineages by FT-IR spectroscopy and machine-learning, a method that can be extremely useful to provide quick and reliable typing information to support real-time decisions of outbreak management and infection control. This method and workflow is of interest to support clinical microbiology diagnostics and to aid public health surveillance.
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Affiliation(s)
- Ângela Novais
- UCIBIO, Applied Molecular Biosciences Unit, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Ana Beatriz Gonçalves
- UCIBIO, Applied Molecular Biosciences Unit, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Teresa G. Ribeiro
- UCIBIO, Applied Molecular Biosciences Unit, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- CCP, Culture Collection of Porto, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Ana R. Freitas
- UCIBIO, Applied Molecular Biosciences Unit, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- 1H-TOXRUN, One Health Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL, Gandra, Portugal
| | - Gema Méndez
- CLOVER Bioanalytical Software, Granada, Spain
| | | | - Antónia Read
- Clinical Microbiology Laboratory, Local Healthcare Unit, Matosinhos, Portugal
| | - Valquíria Alves
- Clinical Microbiology Laboratory, Local Healthcare Unit, Matosinhos, Portugal
| | - Lorena López-Cerero
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Vírgen Macarena, Instituto de Biomedicina de Sevilla (IBIS; CSIC/Hospital Virgen Macarena/Universidad de Sevilla), Sevilla, Spain
- Departamentos de Microbiología y Medicina, Universidad de Sevilla, Sevilla, Spain
| | - Jesús Rodríguez-Baño
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Vírgen Macarena, Instituto de Biomedicina de Sevilla (IBIS; CSIC/Hospital Virgen Macarena/Universidad de Sevilla), Sevilla, Spain
- Departamentos de Microbiología y Medicina, Universidad de Sevilla, Sevilla, Spain
| | - Álvaro Pascual
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Vírgen Macarena, Instituto de Biomedicina de Sevilla (IBIS; CSIC/Hospital Virgen Macarena/Universidad de Sevilla), Sevilla, Spain
- Departamentos de Microbiología y Medicina, Universidad de Sevilla, Sevilla, Spain
| | - Luísa Peixe
- UCIBIO, Applied Molecular Biosciences Unit, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- CCP, Culture Collection of Porto, Faculty of Pharmacy, University of Porto, Porto, Portugal
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5
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Manzulli V, Cordovana M, Serrecchia L, Rondinone V, Pace L, Farina D, Cipolletta D, Caruso M, Fraccalvieri R, Difato LM, Tolve F, Vetritto V, Galante D. Application of Fourier Transform Infrared Spectroscopy to Discriminate Two Closely Related Bacterial Species: Bacillus anthracis and Bacillus cereus Sensu Stricto. Microorganisms 2024; 12:183. [PMID: 38258007 PMCID: PMC10821103 DOI: 10.3390/microorganisms12010183] [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: 11/27/2023] [Revised: 12/29/2023] [Accepted: 01/12/2024] [Indexed: 01/24/2024] Open
Abstract
Fourier transform infrared spectroscopy (FTIRS) is a diagnostic technique historically used in the microbiological field for the characterization of bacterial strains in relation to the specific composition of their lipid, protein, and polysaccharide components. For each bacterial strain, it is possible to obtain a unique absorption spectrum that represents the fingerprint obtained based on the components of the outer cell membrane. In this study, FTIRS was applied for the first time as an experimental diagnostic tool for the discrimination of two pathogenic species belonging to the Bacillus cereus group, Bacillus anthracis and Bacillus cereus sensu stricto; these are two closely related species that are not so easy to differentiate using classical microbiological methods, representing an innovative technology in the field of animal health.
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Affiliation(s)
- Viviana Manzulli
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, 71121 Foggia, Italy; (L.S.); (V.R.); (L.P.); (D.F.); (D.C.); (M.C.); (R.F.); (L.M.D.); (F.T.); (V.V.); (D.G.)
| | | | - Luigina Serrecchia
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, 71121 Foggia, Italy; (L.S.); (V.R.); (L.P.); (D.F.); (D.C.); (M.C.); (R.F.); (L.M.D.); (F.T.); (V.V.); (D.G.)
| | - Valeria Rondinone
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, 71121 Foggia, Italy; (L.S.); (V.R.); (L.P.); (D.F.); (D.C.); (M.C.); (R.F.); (L.M.D.); (F.T.); (V.V.); (D.G.)
| | - Lorenzo Pace
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, 71121 Foggia, Italy; (L.S.); (V.R.); (L.P.); (D.F.); (D.C.); (M.C.); (R.F.); (L.M.D.); (F.T.); (V.V.); (D.G.)
| | - Donatella Farina
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, 71121 Foggia, Italy; (L.S.); (V.R.); (L.P.); (D.F.); (D.C.); (M.C.); (R.F.); (L.M.D.); (F.T.); (V.V.); (D.G.)
| | - Dora Cipolletta
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, 71121 Foggia, Italy; (L.S.); (V.R.); (L.P.); (D.F.); (D.C.); (M.C.); (R.F.); (L.M.D.); (F.T.); (V.V.); (D.G.)
| | - Marta Caruso
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, 71121 Foggia, Italy; (L.S.); (V.R.); (L.P.); (D.F.); (D.C.); (M.C.); (R.F.); (L.M.D.); (F.T.); (V.V.); (D.G.)
| | - Rosa Fraccalvieri
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, 71121 Foggia, Italy; (L.S.); (V.R.); (L.P.); (D.F.); (D.C.); (M.C.); (R.F.); (L.M.D.); (F.T.); (V.V.); (D.G.)
| | - Laura Maria Difato
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, 71121 Foggia, Italy; (L.S.); (V.R.); (L.P.); (D.F.); (D.C.); (M.C.); (R.F.); (L.M.D.); (F.T.); (V.V.); (D.G.)
| | - Francesco Tolve
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, 71121 Foggia, Italy; (L.S.); (V.R.); (L.P.); (D.F.); (D.C.); (M.C.); (R.F.); (L.M.D.); (F.T.); (V.V.); (D.G.)
| | - Valerio Vetritto
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, 71121 Foggia, Italy; (L.S.); (V.R.); (L.P.); (D.F.); (D.C.); (M.C.); (R.F.); (L.M.D.); (F.T.); (V.V.); (D.G.)
| | - Domenico Galante
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, 71121 Foggia, Italy; (L.S.); (V.R.); (L.P.); (D.F.); (D.C.); (M.C.); (R.F.); (L.M.D.); (F.T.); (V.V.); (D.G.)
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Raki H, Aalaila Y, Taktour A, Peluffo-Ordóñez DH. Combining AI Tools with Non-Destructive Technologies for Crop-Based Food Safety: A Comprehensive Review. Foods 2023; 13:11. [PMID: 38201039 PMCID: PMC10777928 DOI: 10.3390/foods13010011] [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: 10/24/2023] [Revised: 11/27/2023] [Accepted: 12/06/2023] [Indexed: 01/12/2024] Open
Abstract
On a global scale, food safety and security aspects entail consideration throughout the farm-to-fork continuum, considering food's supply chain. Generally, the agrifood system is a multiplex network of interconnected features and processes, with a hard predictive rate, where maintaining the food's safety is an indispensable element and is part of the Sustainable Development Goals (SDGs). It has led the scientific community to develop advanced applied analytical methods, such as machine learning (ML) and deep learning (DL) techniques applied for assessing foodborne diseases. The main objective of this paper is to contribute to the development of the consensus version of ongoing research about the application of Artificial Intelligence (AI) tools in the domain of food-crop safety from an analytical point of view. Writing a comprehensive review for a more specific topic can also be challenging, especially when searching within the literature. To our knowledge, this review is the first to address this issue. This work consisted of conducting a unique and exhaustive study of the literature, using our TriScope Keywords-based Synthesis methodology. All available literature related to our topic was investigated according to our criteria of inclusion and exclusion. The final count of data papers was subject to deep reading and analysis to extract the necessary information to answer our research questions. Although many studies have been conducted, limited attention has been paid to outlining the applications of AI tools combined with analytical strategies for crop-based food safety specifically.
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Affiliation(s)
- Hind Raki
- College of Computing, University Mohammed VI Polytechnic, Ben Guerir 43150, Morocco; (Y.A.); (D.H.P.-O.)
| | - Yahya Aalaila
- College of Computing, University Mohammed VI Polytechnic, Ben Guerir 43150, Morocco; (Y.A.); (D.H.P.-O.)
| | - Ayoub Taktour
- Materials Sciences and Nanotechnoloy (MSN), University Mohammed VI Polytechnic, Ben Guerir 43150, Morocco;
| | - Diego H. Peluffo-Ordóñez
- College of Computing, University Mohammed VI Polytechnic, Ben Guerir 43150, Morocco; (Y.A.); (D.H.P.-O.)
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7
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Phou S, Perez-Alvarez I, Morgan M, Contreras DA, Ben-Aderet M, Gaddam E, Paquette R, Vescio R, Pepkowitz SH, Gibb DR, Zabner R, Klapper EB. Successful autologous hematopoietic stem cell transplants using Salmonella positive products collected from asymptomatic donors. Transfusion 2023; 63:861-866. [PMID: 36880384 DOI: 10.1111/trf.17306] [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: 08/26/2022] [Revised: 12/19/2022] [Accepted: 12/26/2022] [Indexed: 03/08/2023]
Abstract
BACKGROUND Bacterial contamination of hematopoietic stem cell (HSC) products is most commonly due to normal skin flora. Salmonella in HSC products is rare, and to our knowledge safe administration of an autologous HSC product containing Salmonella has not been reported. STUDY DESIGN AND METHODS We describe two patients undergoing autologous HSC transplant: peripheral blood HSC collection was performed by leukapheresis, and samples were cultured according to standard institutional protocol. Subsequent microorganism identification was performed using MALDI-TOF (Bruker Biotyper). Strain-relatedness was investigated by infrared spectroscopy using the IR Biotyper (Bruker). RESULTS The patients were asymptomatic throughout the collection process; however, HSC products collected on two consecutive days from each patient were positive for Salmonella. Isolates from both cultures were further characterized as Salmonella enterica serovar Dublin by the local public health department. Antibiotic susceptibility testing revealed different sensitivity patterns for the two strains. IR Biotyper demonstrated significant discriminatory power among the clinically significant Salmonella enterica subspecies, serogroups B, C1, and D. The patient strains were similar as both belonged to Group D Salmonella enterica serovar Dublin but were not identical. The Salmonella positive autologous HSC products were infused to both patients following administration of empiric antibiotic therapy. Both patients successfully engrafted and did well. CONCLUSION Salmonella is rarely seen in cellular therapy products and positivity may be the result of asymptomatic bacteremia at the time of collection. We present two instances of autologous HSC products containing Salmonella that were infused, along with prophylactic antimicrobial therapy without significant adverse clinical effects.
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Affiliation(s)
- Samantha Phou
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Ingrid Perez-Alvarez
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Margie Morgan
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Deisy A Contreras
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Michael Ben-Aderet
- Department of Hospital Epidemiology, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Emily Gaddam
- Department of Hospital Epidemiology, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Ronald Paquette
- Division of Hematology and Cellular Therapy, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Robert Vescio
- Division of Hematology and Cellular Therapy, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Samuel H Pepkowitz
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - David R Gibb
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Rachel Zabner
- Department of Infectious Diseases, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Ellen B Klapper
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
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8
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Tata A, Marzoli F, Cordovana M, Tiengo A, Zacometti C, Massaro A, Barco L, Belluco S, Piro R. A multi-center validation study on the discrimination of Legionella pneumophila sg.1, Legionella pneumophila sg. 2-15 and Legionella non- pneumophila isolates from water by FT-IR spectroscopy. Front Microbiol 2023; 14:1150942. [PMID: 37125166 PMCID: PMC10133462 DOI: 10.3389/fmicb.2023.1150942] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 03/20/2023] [Indexed: 05/02/2023] Open
Abstract
This study developed and validated a method, based on the coupling of Fourier-transform infrared spectroscopy (FT-IR) and machine learning, for the automated serotyping of Legionella pneumophila serogroup 1, Legionella pneumophila serogroups 2-15 as well as their successful discrimination from Legionella non-pneumophila. As Legionella presents significant intra- and inter-species heterogeneities, careful data validation strategies were applied to minimize late-stage performance variations of the method across a large microbial population. A total of 244 isolates were analyzed. In details, the method was validated with a multi-centric approach with isolates from Italian thermal and drinking water (n = 82) as well as with samples from German, Italian, French, and British collections (n = 162). Specifically, robustness of the method was verified over the time-span of 1 year with multiple operators and two different FT-IR instruments located in Italy and Germany. Moreover, different production procedures for the solid culture medium (in-house or commercial) and different culture conditions (with and without 2.5% CO2) were tested. The method achieved an overall accuracy of 100, 98.5, and 93.9% on the Italian test set of Legionella, an independent batch of Legionella from multiple European culture collections, and an extra set of rare Legionella non-pneumophila, respectively.
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Affiliation(s)
- Alessandra Tata
- Laboratorio di Chimica Sperimentale, Istituto Zooprofilattico Sperimentale delle Venezie, Vicenza, Italy
- *Correspondence: Alessandra Tata,
| | - Filippo Marzoli
- Department of Food Safety, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | | | - Alessia Tiengo
- OIE Italian Reference Laboratory for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Padova, Italy
| | - Carmela Zacometti
- Laboratorio di Chimica Sperimentale, Istituto Zooprofilattico Sperimentale delle Venezie, Vicenza, Italy
| | - Andrea Massaro
- Laboratorio di Chimica Sperimentale, Istituto Zooprofilattico Sperimentale delle Venezie, Vicenza, Italy
| | - Lisa Barco
- OIE Italian Reference Laboratory for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Padova, Italy
| | - Simone Belluco
- Department of Food Safety, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Roberto Piro
- Laboratorio di Chimica Sperimentale, Istituto Zooprofilattico Sperimentale delle Venezie, Vicenza, Italy
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