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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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Ibik YE, Ejder N, Sevim E, Rakici E, Tanriverdi ES, Copur Cicek A. Evaluating molecular epidemiology of carbapenem non-susceptible Klebsiella pneumoniae isolates with MLST, MALDI-TOF MS, PFGE. Ann Clin Microbiol Antimicrob 2023; 22:93. [PMID: 37891628 PMCID: PMC10612262 DOI: 10.1186/s12941-023-00640-9] [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: 02/27/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND This study aimed to evaluate antibiotic resistance genes and virulence genes and the clonal relationship of the carbapenem-nonsusceptible Klebsiella pneumoniae strains by molecular methods which are isolated from various clinical specimens from patients treated in tertiary care hospital in Turkey. METHODS Identification of 32 carbapenem non-susceptible K. pneumoniae were determined by VITEK-2 (BioMérieux, France) automated system. Thirteen colistin-resistant strains were tested with the broth microdilution method. Various antibiotic resistance genes and virulence genes frequently seen in carbapenem-resistant strains were screened by PCR. Immunochromatographic tests used in the rapid diagnosis of carbapenemases were compared with PCR results. In addition, PFGE, MLST and MALDI-TOF MS methods were used to determine the clonal relationship among these strains. RESULTS PCR demonstrated that 31 of the strains carried at least one of the carbapenemase genes. In one strain, the coexistence of blaOXA-48+NDM was shown. The most common resistance genes were determined as blaSHV (84.3%), blaCTX-M-1 (46.8%), blaOXA-48 (40.6%), blaKPC (40.6%), blaTEM (31.2%), blaNDM (18.8%) respectively. Among the virulence genes; magA (68.7%) was the most common, followed by kpn (59.3%) and K2 (9.3%). Immunochromatographic tests were found to be 100% compatible with PCR results. All colistin-resistant isolates were also found to be resistant by colistin broth microdilution. In PFGE analysis, 25 different genotypes were determined and clustering isolates were collected in 5 different clusters and the clustering rate was 35.4%. In MLST analysis, ST101 type was determined as the most common ST type with a rate of 29%. ST101 is followed by ST16, ST307, ST14, ST147, ST309, ST377, ST395 and ST2096, respectively. The compatibility rate between MALDI-TOF MS and VITEK-2 was found 94.3%, in bacterial identification. In MALDI-TOF MS typing, the maximum similarity between the strains was less than 70% and clustering not shown. CONCLUSION In addition to OXA-48, which is endemic in our country, it has been determined that KPC, which is more common in the world, is becoming increasingly common in our region. ST101 type was determined as the most common type between the strains. To the best of our knowledge, this is the first study that compares these three methods in our country. There may be differences between bacterial identifications made with VITEK-2 and MALDI-TOF MS. In this study, it was observed that MALDI-TOF MS analyses were not compatible with the typing of strains according to PFGE and MLST analysis results.
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Affiliation(s)
- Yunus Emre Ibik
- Microbiology Laboratory, Ordu University Training and Research Hospital, Ordu, 52000, Turkey.
- Department of Medical Microbiology, Faculty of Medicine, Recep Tayyip Erdogan University, Rize, Turkey.
| | - Nebahat Ejder
- Department of Medical Microbiology, Faculty of Medicine, Recep Tayyip Erdogan University, Rize, Turkey
| | - Elif Sevim
- Department of Medical Biology, Faculty of Medicine, Ahi Evran University, Kırşehir, Turkey
| | - Erva Rakici
- Department of Medical Microbiology, Faculty of Medicine, Recep Tayyip Erdogan University, Rize, Turkey
| | | | - Aysegül Copur Cicek
- Department of Medical Microbiology, Faculty of Medicine, Recep Tayyip Erdogan University, Rize, Turkey
- Department of Medical Microbiology, School of Medicine, Istanbul Medipol University, Istanbul, Turkey
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Zhang LY, Tian B, Huang YH, Gu B, Ju P, Luo Y, Tang J, Wang L. Classification and prediction of Klebsiella pneumoniae strains with different MLST allelic profiles via SERS spectral analysis. PeerJ 2023; 11:e16161. [PMID: 37780376 PMCID: PMC10538299 DOI: 10.7717/peerj.16161] [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: 06/01/2023] [Accepted: 09/01/2023] [Indexed: 10/03/2023] Open
Abstract
The Gram-negative non-motile Klebsiella pneuomoniae is currently a major cause of hospital-acquired (HA) and community-acquired (CA) infections, leading to great public health concern globally, while rapid identification and accurate tracing of the pathogenic bacterium is essential in facilitating monitoring and controlling of K. pneumoniae outbreak and dissemination. Multi-locus sequence typing (MLST) is a commonly used typing approach with low cost that is able to distinguish bacterial isolates based on the allelic profiles of several housekeeping genes, despite low resolution and labor intensity of the method. Core-genome MLST scheme (cgMLST) is recently proposed to sub-type and monitor outbreaks of bacterial strains with high resolution and reliability, which uses hundreds or thousands of genes conserved in all or most members of the species. However, the method is complex and requires whole genome sequencing of bacterial strains with high costs. Therefore, it is urgently needed to develop novel methods with high resolution and low cost for bacterial typing. Surface enhanced Raman spectroscopy (SERS) is a rapid, sensitive and cheap method for bacterial identification. Previous studies confirmed that classification and prediction of bacterial strains via SERS spectral analysis correlated well with MLST typing results. However, there is currently no similar comparative analysis in K. pneumoniae strains. In this pilot study, 16 K. pneumoniae strains with different sequencing typings (STs) were selected and a phylogenetic tree was constructed based on core genome analysis. SERS spectra (N = 45/each strain) were generated for all the K. pneumoniae strains, which were then comparatively classified and predicted via six representative machine learning (ML) algorithms. According to the results, SERS technique coupled with the ML algorithm support vector machine (SVM) could achieve the highest accuracy (5-Fold Cross Validation = 100%) in terms of differentiating and predicting all the K. pneumoniae strains that were consistent to corresponding MLSTs. In sum, we show in this pilot study that the SERS-SVM based method is able to accurately predict K. pneumoniae MLST types, which has the application potential in clinical settings for tracing dissemination and controlling outbreak of K. pneumoniae in hospitals and communities with low costs and high rapidity.
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Affiliation(s)
- Li-Yan Zhang
- Laboratory Medicine, Ganzhou Municipal Hospital, Guangdong Provincial People’s Hospital Ganzhou Hospital, Ganzhou, Guangdong Province, China
- Laboratory Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong Province, China
| | - Benshun Tian
- Laboratory Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong Province, China
| | - Yuan-Hong Huang
- Laboratory Medicine, Ganzhou Municipal Hospital, Guangdong Provincial People’s Hospital Ganzhou Hospital, Ganzhou, Guangdong Province, China
| | - Bin Gu
- Laboratory Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong Province, China
| | - Pei Ju
- School of Life Sciences, Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - Yanfei Luo
- Laboratory Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong Province, China
| | - Jiawei Tang
- Laboratory Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong Province, China
| | - Liang Wang
- Laboratory Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong Province, China
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Vitorino R, Barros AS, Guedes S, Caixeta DC, Sabino-Silva R. Diagnostic and monitoring applications using Near infrared (NIR) Spectroscopy in cancer and other diseases. Photodiagnosis Photodyn Ther 2023:103633. [PMID: 37245681 DOI: 10.1016/j.pdpdt.2023.103633] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/19/2023] [Accepted: 05/23/2023] [Indexed: 05/30/2023]
Abstract
Early cancer diagnosis plays a critical role in improving treatment outcomes and increasing survival rates for certain cancers. NIR spectroscopy offers a rapid and cost-effective approach to evaluate the optical properties of tissues at the microvessel level and provides valuable molecular insights. The integration of NIR spectroscopy with advanced data-driven algorithms in portable instruments has made it a cutting-edge technology for medical applications. NIR spectroscopy is a simple, non-invasive and affordable analytical tool that complements expensive imaging modalities such as functional magnetic resonance imaging, positron emission tomography and computed tomography. By examining tissue absorption, scattering, and concentrations of oxygen, water, and lipids, NIR spectroscopy can reveal inherent differences between tumor and normal tissue, often revealing specific patterns that help stratify disease. In addition, the ability of NIR spectroscopy to assess tumor blood flow, oxygenation, and oxygen metabolism provides a key paradigm for its application in cancer diagnosis. This review evaluates the effectiveness of NIR spectroscopy in the detection and characterization of disease, particularly in cancer, with or without the incorporation of chemometrics and machine learning algorithms. The report highlights the potential of NIR spectroscopy technology to significantly improve discrimination between benign and malignant tumors and accurately predict treatment outcomes. In addition, as more medical applications are studied in large patient cohorts, consistent advances in clinical implementation can be expected, making NIR spectroscopy a valuable adjunct technology for cancer therapy management. Ultimately, the integration of NIR spectroscopy into cancer diagnostics promises to improve prognosis by providing critical new insights into cancer patterns and physiology.
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Affiliation(s)
- Rui Vitorino
- Institute of Biomedicine-iBiMED, Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal; UnIC@RISE, Department of Surgery and Physiology, Faculty of Medicine of the University of Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal; LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal.
| | - António S Barros
- UnIC@RISE, Department of Surgery and Physiology, Faculty of Medicine of the University of Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Sofia Guedes
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Douglas C Caixeta
- Innovation Center in Salivary Diagnostics and Nanobiotechnology, Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Minas Gerais, Brazil
| | - Robinson Sabino-Silva
- Innovation Center in Salivary Diagnostics and Nanobiotechnology, Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Minas Gerais, Brazil
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Chen Y, Zhang HL, Zhang L, Nizamani MM, Zhou T, Zhang H, Liu T. Genetic diversity assessment of Hopea hainanensis in Hainan Island. FRONTIERS IN PLANT SCIENCE 2022; 13:1075102. [PMID: 36570896 PMCID: PMC9767952 DOI: 10.3389/fpls.2022.1075102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 11/18/2022] [Indexed: 06/17/2023]
Abstract
Hopea hainanensis (Dipterocarpaceae) is an endangered tree species restricted to Hainan Island, China, and a small part of Northern Vietnam. On Hainan Island, it is an important indicator species for tropical forests. The wood of Hopea hainanensis has a very high utilization value in nature since it is compact in structure, hard in texture, not easily deformed after drying, durable, and resistant to sunlight and water. As a result of its high quality, it has been felled and mined by humans without restraint, resulting in a reduction of its population size, severe habitat fragmentation, and a sharp decline in its population. Therefore, its conservation biology needs to be researched urgently. Researchers are currently focusing on the ecological factors and seed germination in the habitat of Hopea hainanensis to determine its endangered status. In the literature, there are no systematic analyses of the endangered mechanism of Hopea hainanensis in terms of genetic diversity. It focuses especially on the systematic genetic diversity of Hopea hainanensis in fragmented habitats. Using single nucleotide polymorphism (SNP) and genotyping-by-sequencing (GBS) technology, 42 samples from seven different cohabitation groups were genotyped. The results showed that the average heterozygosity of the six populations of Hopea hainanensis was 19.77%, which indicated that the genetic diversity of Hopea hainanensis was low. Genetic diversity research is essential for rare and endangered plant protection research. We can find a scientific basis for protecting endangered plants on slope bases by analyzing genetic differences and relationships among populations.
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Affiliation(s)
- Yukai Chen
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Hai-Li Zhang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, School of Life Sciences, Hainan University, Haikou, China
| | - Li Zhang
- Guizhou Normal University Museum, Guizhou Normal University, Guizhou, China
| | - Mir Muhammad Nizamani
- Department of Plant Pathology, Agricultural College, Guizhou University, Guiyang, China
| | - Taoxiu Zhou
- College of Biological Science and Technology, Yangzhou University, Yangzhou, China
| | - Haiyang Zhang
- College of International Studies, Sichuan University, Chengdu, China
| | - Tingting Liu
- Guizhou Normal University Museum, Guizhou Normal University, Guizhou, China
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Pistiki A, Salbreiter M, Sultan S, Rösch P, Popp J. Application of Raman spectroscopy in the hospital environment. TRANSLATIONAL BIOPHOTONICS 2022. [DOI: 10.1002/tbio.202200011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Aikaterini Pistiki
- Leibniz‐Institute of Photonic Technology Member of the Leibniz Research Alliance–Leibniz Health Technologies Jena Germany
- InfectoGnostics Research Campus Jena Center of Applied Research Jena Germany
| | - Markus Salbreiter
- InfectoGnostics Research Campus Jena Center of Applied Research Jena Germany
- Institute of Physical Chemistry and Abbe Center of Photonics Friedrich Schiller University Jena Germany
| | - Salwa Sultan
- InfectoGnostics Research Campus Jena Center of Applied Research Jena Germany
- Institute of Physical Chemistry and Abbe Center of Photonics Friedrich Schiller University Jena Germany
| | - Petra Rösch
- InfectoGnostics Research Campus Jena Center of Applied Research Jena Germany
- Institute of Physical Chemistry and Abbe Center of Photonics Friedrich Schiller University Jena Germany
| | - Jürgen Popp
- Leibniz‐Institute of Photonic Technology Member of the Leibniz Research Alliance–Leibniz Health Technologies Jena Germany
- InfectoGnostics Research Campus Jena Center of Applied Research Jena Germany
- Institute of Physical Chemistry and Abbe Center of Photonics Friedrich Schiller University Jena Germany
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Stewart J, Judd LM, Jenney A, Holt KE, Wyres KL, Hawkey J. Epidemiology and genomic analysis of Klebsiella oxytoca from a single hospital network in Australia. BMC Infect Dis 2022; 22:704. [PMID: 36002802 PMCID: PMC9400251 DOI: 10.1186/s12879-022-07687-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/17/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Infections caused by Klebsiella oxytoca are the second most common cause of Klebsiella infections in humans. Most studies have focused on K. oxytoca outbreaks and few have examined the broader clinical context of K. oxytoca. METHODS Here, we collected all clinical isolates identified as K. oxytoca in a hospital microbiological diagnostic lab across a 15-month period (n = 239). Whole genome sequencing was performed on a subset of 92 isolates (all invasive, third-generation cephalosporin resistant (3GCR) and non-urinary isolates collected > 48 h after admission), including long-read sequencing on a further six isolates with extended-spectrum beta-lactamase or carbapenemase genes. RESULTS The majority of isolates were sensitive to antimicrobials, however 22 isolates were 3GCR, of which five were also carbapenem resistant. Genomic analyses showed those identified as K. oxytoca by the clinical laboratory actually encompassed four distinct species (K. oxytoca, Klebsiella michiganensis, Klebsiella grimontii and Klebsiella pasteurii), referred to as the K. oxytoca species complex (KoSC). There was significant diversity within the population, with only 10/67 multi-locus sequence types (STs) represented by more than one isolate. Strain transmission was rare, with only one likely event identified. Six isolates had extended spectrum beta-lactamase (blaSHV-12 and/or blaCTX-M-9) or carbapenemase (blaIMP-4) genes. One pair of K. michiganensis and K. pasteurii genomes carried identical blaIMP-4 IncL/M plasmids, indicative of plasmid transmission. CONCLUSION Whilst antimicrobial resistance was rare, the resistance plasmids were similar to those found in other Enterobacterales, demonstrating that KoSC has access to the same plasmid reservoir and thus there is potential for multi-drug resistance. Further genomic studies are required to improve our understanding of the KoSC population and facilitate investigation into the attributes of successful nosocomial isolates.
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Affiliation(s)
- James Stewart
- grid.413210.50000 0004 4669 2727Department of Infectious Diseases, Cairns Hospital, Cairns, QLD 4870 Australia
| | - Louise M. Judd
- grid.1002.30000 0004 1936 7857Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC 3004 Australia
| | - Adam Jenney
- grid.1002.30000 0004 1936 7857Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC 3004 Australia ,grid.1623.60000 0004 0432 511XMicrobiology Unit, Alfred Pathology Service, The Alfred Hospital Melbourne, Melbourne, VIC 3004 Australia
| | - Kathryn E. Holt
- grid.1002.30000 0004 1936 7857Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC 3004 Australia ,grid.8991.90000 0004 0425 469XDepartment of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT UK
| | - Kelly L. Wyres
- grid.1002.30000 0004 1936 7857Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC 3004 Australia
| | - Jane Hawkey
- grid.1002.30000 0004 1936 7857Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC 3004 Australia
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Li X, Zhu L, Wang X, Li J, Tang B. Evaluation of IR Biotyper for Lactiplantibacillus plantarum Typing and Its Application Potential in Probiotic Preliminary Screening. Front Microbiol 2022; 13:823120. [PMID: 35401469 PMCID: PMC8988154 DOI: 10.3389/fmicb.2022.823120] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 02/24/2022] [Indexed: 12/25/2022] Open
Abstract
IR Biotyper (IRBT), which is a spectroscopic system for microorganism typing based on Fourier transform infrared (FTIR) technology, has been used to detect the spread of clones in clinical microbiology laboratories. However, the use of IRBT to detect probiotics has rarely been reported. Herein, we evaluated the discriminatory power of IRBT to type Lactiplantibacillus plantarum isolates at the strain level and explored its application potential in probiotic preliminary selection. Twenty Lactiplantibacillus isolates collected from pickled radishes during successive fermentation were used to test the robustness of IRBT at the strain level. IRBT was then compared with genotyping methods such as whole-genome sequencing (WGS), pulsed-field gel electrophoresis (PFGE), and multilocus sequence typing (MLST) to evaluate its discrimination power. IRBT distributed the 20 isolates into five clusters, with L. argentoratensis isolate C7-83 being the most distant from the other isolates, which belonged to L. plantarum. IRBT showed good reproducibility, although deviation in the discriminative power of IRBT was found at the strain level across laboratories, probably due to technical variance. All examined methods allowed bacterial identification at the strain level, but IRBT had higher discriminatory power than MLST and was comparable to the WGS and PFGE. In the phenotypic comparison study, we observed that the clustering results of probiotic physiological attributes (e.g., sensitivity to acid and bile salts, hydrophobicity of the cell surface, and resistance to antibiotics) were consistent with the typing results of IRBT. Our results indicated that IRBT is a robust tool for L. plantarum strain typing that could improve the efficiency of probiotic identification and preliminary screening, and can potentially be applied in probiotic traceability and quality control.
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Affiliation(s)
- Xiaoqiong Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Food Sciences, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Liying Zhu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Food Sciences, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xin Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Food Sciences, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jinjun Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Food Sciences, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- *Correspondence: Jinjun Li,
| | - Biao Tang
- Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Biao Tang,
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Deidda F, Bozzi Cionci N, Cordovana M, Campedelli I, Fracchetti F, Di Gioia D, Ambretti S, Pane M. Bifidobacteria Strain Typing by Fourier Transform Infrared Spectroscopy. Front Microbiol 2021; 12:692975. [PMID: 34589064 PMCID: PMC8473902 DOI: 10.3389/fmicb.2021.692975] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 08/09/2021] [Indexed: 11/13/2022] Open
Abstract
Fourier transform infrared (FTIR) spectroscopy, a technology traditionally used in chemistry to determine the molecular composition of a wide range of sample types, has gained growing interest in microbial typing. It is based on the different vibrational modes of the covalent bonds between atoms of a given sample, as bacterial cells, induced by the absorption of infrared radiation. This technique has been largely used for the study of pathogenic species, especially in the clinical field, and has been proposed also for the typing at different subspecies levels. The high throughput, speed, low cost, and simplicity make FTIR spectroscopy an attractive technique also for industrial applications, in particular, for probiotics. The aim of this study was to compare FTIR spectroscopy with established genotyping methods, pulsed-field gel electrophoresis (PFGE), whole-genome sequencing (WGS), and multilocus sequence typing (MLST), in order to highlight the FTIR spectroscopy potential discriminatory power at strain level. Our study focused on bifidobacteria, an important group of intestinal commensals generally recognized as probiotics. For their properties in promoting and maintaining health, bifidobacteria are largely marketed by the pharmaceutical, food, and dairy industries. Strains belonging to Bifidobacterium longum subsp. longum and Bifidobacterium animalis subsp. lactis were taken into consideration together with some additional type strains. For B. longum subsp. longum, it was possible to discriminate the strains with all the methods used. Although two isolates were shown to be strictly phylogenetically related, constituting a unique cluster, based on PFGE, WGS, and MLST, no clustering was observed with FTIR. For B. animalis subsp. lactis group, PFGE, WGS, and MLST were non-discriminatory, and only one strain was easily distinguished. On the other hand, FTIR discriminated all the isolates one by one, and no clustering was observed. According to these results, FTIR analysis is not only equivalent to PFGE, WGS, and MLST, but also for some strains, in particular, for B. animalis subsp. lactis group, more informative, being able to differentiate strains not discernible with the other two methods based on phenotypic variations likely deriving from certain genetic changes. Fourier transform infrared spectroscopy has highlighted the possibility of using the cell surface as a kind of barcode making tracing strains possible, representing an important aspect in probiotic applications. Furthermore, this work constitutes the first investigation on bifidobacterial strain typing using FTIR spectroscopy.
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Affiliation(s)
| | - Nicole Bozzi Cionci
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | | | | | | | - Diana Di Gioia
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Simone Ambretti
- Microbiology Unit-University Hospital of Bologna Policlinico Sant'Orsola-Malpighi, Bologna, Italy
| | - Marco Pane
- Probiotical Research S.r.L., Novara, Italy
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Efflux Pump Overexpression Profiling in Acinetobacter baumannii and Study of New 1-(1-Naphthylmethyl)-Piperazine Analogs as Potential Efflux Inhibitors. Antimicrob Agents Chemother 2021; 65:e0071021. [PMID: 34097483 DOI: 10.1128/aac.00710-21] [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: 11/20/2022] Open
Abstract
Overexpression of efflux pumps extruding antibiotics currently used for the treatment of Acinetobacter baumannii infections has been described as an important mechanism causing antibiotic resistance. The first aim of this work was to phenotypically evaluate the overexpression of efflux pumps on a collection of 124 ciprofloxacin-resistant A. baumannii strains. An overexpression of genes encoding one or more efflux pumps was obtained for 19 out of the 34 strains with a positive phenotypic efflux (56%). The most frequent genes overexpressed were those belonging to the RND family, with adeJ being the most prevalent (50%). Interestingly, efflux pump genes coding for MATE and MFS families were also overexpressed quite frequently: abeM (32%) and abaQ (26%). The second aim was to synthesize 1-(1-naphthylmethyl)-piperazine analogs as potential new efflux pump inhibitors and biologically evaluate them against strains with a positive phenotypic efflux. Quinoline and pyridine analogs were found to be more effective than their parent compound, 1-(1-naphthyl methyl)-piperazine. Stereochemistry also played an important part in the inhibitory activity, as quinoline derivative (R)-3a was identified as being the most effective and less cytotoxic. Its inhibitory activity was also correlated with the number of efflux pumps expressed by a strain. The results obtained in this work suggest that quinoline analogs of 1-(1-naphthylmethyl)-piperazine are promising leads in the development of new anti-Acinetobacter baumannii therapeutic alternatives in combination with antibiotics for which an efflux-mediated resistance is suspected.
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11
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Pruss A, Kwiatkowski P, Łopusiewicz Ł, Masiuk H, Sobolewski P, Fijałkowski K, Sienkiewicz M, Smolak A, Giedrys-Kalemba S, Dołęgowska B. Evaluation of Chemical Changes in Laboratory-Induced Colistin-Resistant Klebsiella pneumoniae. Int J Mol Sci 2021; 22:ijms22137104. [PMID: 34281159 PMCID: PMC8268070 DOI: 10.3390/ijms22137104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 12/03/2022] Open
Abstract
This study evaluates the electrical potential and chemical alterations in laboratory-induced colistin-resistant Klebsiella pneumoniae, as compared to the susceptible strain using spectroscopic analyses. The minimal inhibitory concentration (MIC) of colistin, ζ-potential and chemical composition analysis of K. pneumoniae strains are determined. The results obtained for the K. pneumoniaeCol-R with induced high-level colistin resistance (MIC = 16.0 ± 0.0 mg/L) are compared with the K. pneumoniaeCol-S strain susceptible to colistin (MIC = 0.25 ± 0.0 mg/L). Fourier transform infrared (FTIR) and Raman spectroscopic studies revealed differences in bacterial cell wall structures and lipopolysaccharide (LPS) of K. pneumoniaeCol-R and K. pneumoniaeCol-S strains. In the beginning, we assumed that the obtained results could relate to a negative charge of the bacterial surface and different electrostatic interactions with cationic antibiotic molecules, reducing the affinity of colistin and leading to its lower penetration into K. pneumoniaeCol-R cell. However, no significant differences in the ζ-potential between the K. pneumoniaeCol-R and K. pneumoniaeCol-S strains are noticed. In conclusion, this mechanism is most probably associated with recognisable changes in the chemical composition of the K. pneumoniaeCol-R cell wall (especially in LPS) when compared to the susceptible strain.
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Affiliation(s)
- Agata Pruss
- Department of Laboratory Medicine, Chair of Microbiology, Immunology and Laboratory Medicine, Pomeranian Medical University in Szczecin, Powstańców Wielkopolskich 72, 70-111 Szczecin, Poland; (A.P.); (B.D.)
| | - Paweł Kwiatkowski
- Department of Diagnostic Immunology, Chair of Microbiology, Immunology and Laboratory Medicine, Pomeranian Medical University in Szczecin, Powstańców Wielkopolskich 72, 70-111 Szczecin, Poland
- Correspondence: ; Tel.: +48-91-466-1659
| | - Łukasz Łopusiewicz
- Center of Bioimmobilisation and Innovative Packaging Materials, Faculty of Food Sciences and Fisheries, West Pomeranian University of Technology Szczecin, Janickiego 35, 71-270 Szczecin, Poland;
| | - Helena Masiuk
- Department of Medical Microbiology, Chair of Microbiology, Immunology and Laboratory Medicine, Pomeranian Medical University in Szczecin, Powstańców Wielkopolskich 72, 70-111 Szczecin, Poland; (H.M.); (S.G.-K.)
| | - Peter Sobolewski
- Department of Polymer and Biomaterials Science, Faculty of Chemical Technology and Engineering, West Pomeranian University of Technology Szczecin, Piastów 45, 70-311 Szczecin, Poland;
| | - Karol Fijałkowski
- Department of Microbiology and Biotechnology, West Pomeranian University of Technology Szczecin, Piastów 45, 70-311 Szczecin, Poland;
| | - Monika Sienkiewicz
- Department of Allergology and Respiratory Rehabilitation, Medical University of Łódź, Żeligowskiego 7/9, 90-752 Łódź, Poland;
| | - Adam Smolak
- Microbiological Laboratory, Independent Public Clinical Hospital No. 1 in Szczecin, Unii Lubelskiej 1, 71-252 Szczecin, Poland;
| | - Stefania Giedrys-Kalemba
- Department of Medical Microbiology, Chair of Microbiology, Immunology and Laboratory Medicine, Pomeranian Medical University in Szczecin, Powstańców Wielkopolskich 72, 70-111 Szczecin, Poland; (H.M.); (S.G.-K.)
| | - Barbara Dołęgowska
- Department of Laboratory Medicine, Chair of Microbiology, Immunology and Laboratory Medicine, Pomeranian Medical University in Szczecin, Powstańców Wielkopolskich 72, 70-111 Szczecin, Poland; (A.P.); (B.D.)
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12
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Costa FSL, Bezerra CCR, Neto RM, Morais CLM, Lima KMG. Identification of resistance in Escherichia coli and Klebsiella pneumoniae using excitation-emission matrix fluorescence spectroscopy and multivariate analysis. Sci Rep 2020; 10:12994. [PMID: 32747745 PMCID: PMC7400627 DOI: 10.1038/s41598-020-70033-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 06/09/2020] [Indexed: 11/08/2022] Open
Abstract
Klebsiella pneumoniae and Escherichia coli are part of the Enterobacteriaceae family, being common sources of community and hospital infections and having high antimicrobial resistance. This resistance profile has become the main problem of public health infections. Determining whether a bacterium has resistance is critical to the correct treatment of the patient. Currently the method for determination of bacterial resistance used in laboratory routine is the antibiogram, whose time to obtain the results can vary from 1 to 3 days. An alternative method to perform this determination faster is excitation-emission matrix (EEM) fluorescence spectroscopy combined with multivariate classification methods. In this paper, Linear Discriminant Analysis (LDA), Quadratic Discriminant Analysis (QDA) and Support Vector Machines (SVM), coupled with dimensionality reduction and variable selection algorithms: Principal Component Analysis (PCA), Genetic Algorithm (GA), and the Successive Projections Algorithm (SPA) were used. The most satisfactory models achieved sensitivity and specificity rates of 100% for all classes, both for E. coli and for K. pneumoniae. This finding demonstrates that the proposed methodology has promising potential in routine analyzes, streamlining the results and increasing the chances of treatment efficiency.
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Affiliation(s)
- Fernanda S L Costa
- Institute of Chemistry, Biological Chemistry and Chemometrics, Federal University of Rio Grande do Norte, Natal, RN, 59072-970, Brazil
| | - Caio C R Bezerra
- Laboratory of Mycobateria, Department of Microbiology and Parasitology, Federal University of Rio Grande do Norte, Natal, RN, 59072-970, Brazil
| | - Renato M Neto
- Laboratory of Mycobateria, Department of Microbiology and Parasitology, Federal University of Rio Grande do Norte, Natal, RN, 59072-970, Brazil
| | - Camilo L M Morais
- Lancashire Teaching Hospitals NHS Trust, Fulwood, Preston, PR2 9HT, UK
| | - Kássio M G Lima
- Institute of Chemistry, Biological Chemistry and Chemometrics, Federal University of Rio Grande do Norte, Natal, RN, 59072-970, Brazil.
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13
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Cunningham-Oakes E, Weiser R, Pointon T, Mahenthiralingam E. Understanding the challenges of non-food industrial product contamination. FEMS Microbiol Lett 2020; 366:5707401. [PMID: 31977006 PMCID: PMC6986549 DOI: 10.1093/femsle/fnaa010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 01/14/2020] [Indexed: 12/14/2022] Open
Abstract
Preventing microbial contamination of non-food products is a major area of industrial microbiology where preservatives are used to stop microbial growth. However, microorganisms occasionally overcome product preservation, causing recalls and the implementation of multiple procedures to prevent further contamination. Correct reporting of microbial contamination in non-food industrial products is vital, especially if spoilage organisms are antimicrobial resistant and pose a health threat. Gram-negative bacteria such as Pseudomonas, Burkholderia and Enterobacteriaceae are frequently reported as non-food product contaminants, including species that overlap current antimicrobial resistance priorities. Historical analysis of recall databases highlighted that for greater than 15% of contamination incidents, the causative microbial agents are reported as unidentified. Here we review the current antimicrobial resistant bacterial species associated with non-food product contamination and evaluate recall reporting in Europe from 2005 to 2018. Our review shows that 49% of microbial contaminants are reported as unidentified despite frequent detection of antimicrobial resistant pathogens; in contrast, 98% of food-related microbial contaminants are classified. Recommendations to fill this microbial identification gap in non-food product recalls are made. Overall, reporting standards for microbial contamination in non-food products must be improved to enable surveillance and for understanding the risks associated with antimicrobial resistant microorganisms.
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Affiliation(s)
- Edward Cunningham-Oakes
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Park Place, Cardiff, UK, Wales CF10 3AX, UK
| | - Rebecca Weiser
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Park Place, Cardiff, UK, Wales CF10 3AX, UK
| | - Tom Pointon
- Unilever Research and Development, Port Sunlight, Wirral, CH62 4ZD, UK
| | - Eshwar Mahenthiralingam
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Park Place, Cardiff, UK, Wales CF10 3AX, UK
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14
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Vogt S, Löffler K, Dinkelacker AG, Bader B, Autenrieth IB, Peter S, Liese J. Fourier-Transform Infrared (FTIR) Spectroscopy for Typing of Clinical Enterobacter cloacae Complex Isolates. Front Microbiol 2019; 10:2582. [PMID: 31781074 PMCID: PMC6851243 DOI: 10.3389/fmicb.2019.02582] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 10/24/2019] [Indexed: 12/24/2022] Open
Abstract
Members of the Enterobacter (E.) cloacae complex have emerged as important pathogens frequently encountered in nosocomial infections. Several outbreaks with E. cloacae complex have been reported in recent years, especially in neonatal units. Fast and reliable strain typing methods are crucial for real-time surveillance and outbreak analysis to detect pathogen reservoirs and transmission routes. The aim of this study was to evaluate the performance of Fourier-transform infrared (FTIR) spectroscopy as a fast method for typing of clinical E. cloacae complex isolates, when whole genome sequencing (WGS) analysis was used as reference. First, the technique was used retrospectively on 24 first isolates of E. cloacae complex strains from neonatal patients and showed good concordance with SNP-based clustering [adjusted rand index (ARI) = 0.818] and with the sequence type (ST) (ARI = 0.801). 29 consecutive isolates from the same patients were shown by WGS analysis to almost always belong to the same SNP cluster as the first isolates, which was only inconsistently recognized by FTIR spectroscopy. Training of an artificial neural network (ANN) with all FTIR spectra from sequenced strains markedly improved the recognition of related and unrelated isolate spectra. In a second step, FTIR spectroscopy was applied on 14 strains during an outbreak with E. cloacae complex and provided fast typing results that were confirmed by WGS analysis. In conclusion, FTIR spectroscopy is a promising tool for strain typing of clinical E. cloacae complex strains. Discriminatory power can be improved by implementing an ANN for spectrum analysis. Due to its low costs and fast turnaround times, the method presents a valuable tool for real-time surveillance as well as outbreak analysis.
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Affiliation(s)
- Sophia Vogt
- Institute of Medical Microbiology and Hygiene, University Hospital Tübingen, Tübingen, Germany.,German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Kim Löffler
- Institute of Medical Microbiology and Hygiene, University Hospital Tübingen, Tübingen, Germany.,German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Ariane G Dinkelacker
- Institute of Medical Microbiology and Hygiene, University Hospital Tübingen, Tübingen, Germany.,German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Baris Bader
- Institute of Medical Microbiology and Hygiene, University Hospital Tübingen, Tübingen, Germany.,German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Ingo B Autenrieth
- Institute of Medical Microbiology and Hygiene, University Hospital Tübingen, Tübingen, Germany.,German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Silke Peter
- Institute of Medical Microbiology and Hygiene, University Hospital Tübingen, Tübingen, Germany.,German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Jan Liese
- Institute of Medical Microbiology and Hygiene, University Hospital Tübingen, Tübingen, Germany.,German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
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15
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Martak D, Valot B, Sauget M, Cholley P, Thouverez M, Bertrand X, Hocquet D. Fourier-Transform InfraRed Spectroscopy Can Quickly Type Gram-Negative Bacilli Responsible for Hospital Outbreaks. Front Microbiol 2019; 10:1440. [PMID: 31293559 PMCID: PMC6606786 DOI: 10.3389/fmicb.2019.01440] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 06/07/2019] [Indexed: 12/19/2022] Open
Abstract
The typing of epidemic bacterial pathogens in hospitals relies on DNA-based, expensive, and time-consuming techniques, that are often limited to retrospective studies. However, the quick identification of epidemic pathogens in the routine of the microbiology laboratories would expedite infection control procedures that limit the contamination of new patients. IR Biotyper (Bruker Daltonics GmbH) is a new typing machine based on Fourier-transform infrared (FTIR) spectroscopy which generates spectra, aiming at typing the micro-organisms within 3 h. This technique discriminates the isolates by exploring the differences of the surface cell polysaccharides. In this work, we evaluated the ability of the FTIR spectroscopy to recognize Gram-negative bacilli clones responsible for hospital outbreaks. Isolates of Pseudomonas aeruginosa (n = 100), Klebsiella pneumoniae (n = 16), Enterobacter cloacae (n = 23), and Acinetobacter baumannii (n = 20) were typed by the reference methods Multi-Locus Sequence Typing (defining sequence types – STs) along with or without pulsed field gel electrophoresis (PFGE) (defining pulsotypes), and by FTIR spectroscopy. The congruence of FTIR spectroscopy clustering was compared to those of MLST and PFGE by Adjusted Rand index and Adjusted Wallace coefficient. We found that FTIR spectroscopy accurately clustered P. aeruginosa, K. pneumoniae, and E. cloacae isolates belonging to the same ST. The performance of the FTIR spectroscopy was slightly lower for A. baumannii. Furthermore, FTIR spectroscopy also correctly clustered P. aeruginosa isolates having a similar pulsotype. Overall, the IR Biotyper can quickly (in less than 3 h) detect the spread of clones of P. aeruginosa, K. pneumoniae, E. cloacae, and A. baumannii. The use of this technique by clinical microbiology laboratories may help to tackle the spread of epidemic clones by the quick implementation of infection control measures.
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Affiliation(s)
- Daniel Martak
- Laboratoire d'Hygiène Hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France.,UMR 6249, Laboratoire Chrono-Environnement, Centre National de la Recherche Scientifique-Université de Franche-Comté, Besançon, France
| | - Benoît Valot
- UMR 6249, Laboratoire Chrono-Environnement, Centre National de la Recherche Scientifique-Université de Franche-Comté, Besançon, France
| | - Marlène Sauget
- Laboratoire d'Hygiène Hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France.,UMR 6249, Laboratoire Chrono-Environnement, Centre National de la Recherche Scientifique-Université de Franche-Comté, Besançon, France.,Centre de Ressources Biologiques - Filière Microbiologique de Besançon, Centre Hospitalier Régional Universitaire, Besançon, France
| | - Pascal Cholley
- Laboratoire d'Hygiène Hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France.,UMR 6249, Laboratoire Chrono-Environnement, Centre National de la Recherche Scientifique-Université de Franche-Comté, Besançon, France
| | - Michelle Thouverez
- Laboratoire d'Hygiène Hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France.,UMR 6249, Laboratoire Chrono-Environnement, Centre National de la Recherche Scientifique-Université de Franche-Comté, Besançon, France
| | - Xavier Bertrand
- Laboratoire d'Hygiène Hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France.,UMR 6249, Laboratoire Chrono-Environnement, Centre National de la Recherche Scientifique-Université de Franche-Comté, Besançon, France
| | - Didier Hocquet
- Laboratoire d'Hygiène Hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France.,UMR 6249, Laboratoire Chrono-Environnement, Centre National de la Recherche Scientifique-Université de Franche-Comté, Besançon, France.,Centre de Ressources Biologiques - Filière Microbiologique de Besançon, Centre Hospitalier Régional Universitaire, Besançon, France
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16
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Vincze S, Al Dahouk S, Dieckmann R. Microbiological Safety of Non-Food Products: What Can We Learn from the RAPEX Database? INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16091599. [PMID: 31067693 PMCID: PMC6538994 DOI: 10.3390/ijerph16091599] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 05/03/2019] [Accepted: 05/03/2019] [Indexed: 01/04/2023]
Abstract
For consumer protection across borders, the European Union has established the rapid alert system for dangerous non-food products (RAPEX), with the overarching goal of preventing or limiting the sale and use of non-food products that present a serious risk for the health and safety of consumers. In our study, we comprehensively analyzed RAPEX notifications associated with products posing a microbiological risk from 2005 through 2017. Additional information was retrieved from national laboratory reports. A total of 243 microbiologically harmful consumer products triggered notifications in 23 out of 31 participating countries. About half of the products were reported by Spain, Germany, and Italy. Notifications mainly included contaminated toys, cosmetics, and chemical products. Depending on the notifying country, measures taken to prevent the spread of dangerous products were predominantly ordered either by public authorities or economic operators. The interval between microbiological diagnosis and the date of RAPEX notifications considerably varied between RAPEX member states, ranging between a few days and 82 weeks. The nature and extent of RAPEX usage substantially differed among member states, calling for harmonization and optimization. Slight modifications to RAPEX could help to systematically record microbiological hazards, which may improve the assessment of potential health risks due to contaminated non-food products.
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Affiliation(s)
- Szilvia Vincze
- Department of Biological Safety, German Federal Institute for Risk Assessment, 10589 Berlin, Germany.
| | - Sascha Al Dahouk
- Department of Biological Safety, German Federal Institute for Risk Assessment, 10589 Berlin, Germany.
| | - Ralf Dieckmann
- Department of Biological Safety, German Federal Institute for Risk Assessment, 10589 Berlin, Germany.
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17
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Novais Â, Freitas AR, Rodrigues C, Peixe L. Fourier transform infrared spectroscopy: unlocking fundamentals and prospects for bacterial strain typing. Eur J Clin Microbiol Infect Dis 2018; 38:427-448. [DOI: 10.1007/s10096-018-3431-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 11/11/2018] [Indexed: 01/25/2023]
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18
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Typing and Species Identification of Clinical Klebsiella Isolates by Fourier Transform Infrared Spectroscopy and Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry. J Clin Microbiol 2018; 56:JCM.00843-18. [PMID: 30135233 DOI: 10.1128/jcm.00843-18] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 08/19/2018] [Indexed: 12/18/2022] Open
Abstract
Klebsiella pneumoniae and related species are frequent causes of nosocomial infections and outbreaks. Therefore, quick and reliable strain typing is crucial for the detection of transmission routes in the hospital. The aim of this study was to evaluate Fourier transform infrared spectroscopy (FTIR) and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) as rapid methods for typing clinical Klebsiella isolates in comparison to whole-genome sequencing (WGS), which was considered the gold standard for typing and identification. Here, 68 clinical Klebsiella strains were analyzed by WGS, FTIR, and MALDI-TOF MS. FTIR showed high discriminatory power in comparison to the WGS reference, whereas MALDI-TOF MS exhibited a low ability to type the isolates. MALDI-TOF mass spectra were further analyzed for peaks that showed high specificity for different Klebsiella species. Phylogenetic analysis revealed that the Klebsiella isolates comprised three different species: K. pneumoniae, K. variicola, and K. quasipneumoniae Genome analysis showed that MALDI-TOF MS can be used to distinguish K. pneumoniae from K. variicola due to shifts of certain mass peaks. The peaks were tentatively identified as three ribosomal proteins (S15p, L28p, L31p) and one stress response protein (YjbJ), which exhibit amino acid differences between the two species. Overall, FTIR has high discriminatory power to recognize the clonal relationship of isolates, thus representing a valuable tool for rapid outbreak analysis and for the detection of transmission events due to fast turnaround times and low costs per sample. Furthermore, specific amino acid substitutions allow the discrimination of K. pneumoniae and K. variicola by MALDI-TOF MS.
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19
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Lasch P, Stämmler M, Zhang M, Baranska M, Bosch A, Majzner K. FT-IR Hyperspectral Imaging and Artificial Neural Network Analysis for Identification of Pathogenic Bacteria. Anal Chem 2018; 90:8896-8904. [DOI: 10.1021/acs.analchem.8b01024] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Peter Lasch
- ZBS6 Proteomics and Spectroscopy, Robert Koch-Institute, Seestrasse 10, Berlin, D-13353, Germany
| | - Maren Stämmler
- ZBS6 Proteomics and Spectroscopy, Robert Koch-Institute, Seestrasse 10, Berlin, D-13353, Germany
| | - Miao Zhang
- ZBS6 Proteomics and Spectroscopy, Robert Koch-Institute, Seestrasse 10, Berlin, D-13353, Germany
| | - Malgorzata Baranska
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-060 Krakow, Poland
| | - Alejandra Bosch
- CINDEFI,
CONICET-CCT
La Plata, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, 1900 La Plata, Buenos Aires, Argentina
| | - Katarzyna Majzner
- ZBS6 Proteomics and Spectroscopy, Robert Koch-Institute, Seestrasse 10, Berlin, D-13353, Germany
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-060 Krakow, Poland
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20
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Giacometti F, Piva S, Vranckx K, De Bruyne K, Drigo I, Lucchi A, Manfreda G, Serraino A. Application of MALDI-TOF MS for the subtyping of Arcobacter butzleri strains and comparison with their MLST and PFGE types. Int J Food Microbiol 2018; 277:50-57. [PMID: 29684765 DOI: 10.1016/j.ijfoodmicro.2018.04.026] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 04/05/2018] [Accepted: 04/13/2018] [Indexed: 12/19/2022]
Abstract
For the first time, this study evaluated the use of MALDI-TOF as a typing tool for Arcobacter butzleri. A total of 104 A. butzleri strains isolated from different sources in an artisanal dairy plant in Italy were identified and typed using MALDI-TOF and compared with their multilocus sequence typing (MLST) and pulsed field gel electrophoresis (PFGE) profiles found in previous studies. MALDI-TOF correctly identified all the isolates to species level. No clearly delineated clusters appeared on dendrograms based on either the complete spectra or the significant peaks, but nine clusters were defined using the cophenetic correlation. Interestingly, MALDI-TOF proved able to discriminate A. butzleri strains below species level, confirming its potential use for epidemiological surveys. As expected, the comparative analysis with PFGE and MLST showed that the discriminatory index was lower for MALDI-TOF but roughly comparable to sequence types and pulsotypes. MALDI-TOF appears to be a relatively low cost answer to the urgent need for more rapid, less expensive typing tools suitable for source attribution studies, readily allowing multiple typing methods to be combined. This study provides insights into MALDI-TOF as potential epidemiological tool. Its application in healthcare surveillance systems awaits further exploration to encourage interaction and convergence studies between primary care in humans and animal and food veterinary authorities as part of the One Health concept.
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Affiliation(s)
- Federica Giacometti
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano dell'Emilia, Italy.
| | - Silvia Piva
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano dell'Emilia, Italy.
| | | | | | - Ilenia Drigo
- Istituto Zooprofilattico Sperimentale delle Venezie, Villorba, Treviso, Italy.
| | - Alex Lucchi
- Department of Agricultural and Food Sciences, University of Bologna, Ozzano dell'Emilia, Italy.
| | - Gerardo Manfreda
- Department of Agricultural and Food Sciences, University of Bologna, Ozzano dell'Emilia, Italy.
| | - Andrea Serraino
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano dell'Emilia, Italy.
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21
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Quintelas C, Ferreira EC, Lopes JA, Sousa C. An Overview of the Evolution of Infrared Spectroscopy Applied to Bacterial Typing. Biotechnol J 2017; 13. [DOI: 10.1002/biot.201700449] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 10/18/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Cristina Quintelas
- Dr. C. Quintelas, Dr. E. C. Ferreira; CEB − Centro de Engenharia Biológica; Universidade do Minho; Braga Portugal
| | - Eugénio C. Ferreira
- Dr. C. Quintelas, Dr. E. C. Ferreira; CEB − Centro de Engenharia Biológica; Universidade do Minho; Braga Portugal
| | - João A. Lopes
- Dr. J. A. Lopes; Research Institute for Medicines (iMed.ULisboa); Faculdade de Farmácia; Universidade de Lisboa; Lisboa Portugal
| | - Clara Sousa
- Dr. C. Sousa; LAQV/REQUIMTE; Departamento de Ciências Químicas Faculdade de Farmácia; Universidade do Porto; Rua Jorge Viterbo Ferreira, 228 4050-313 Porto Portugal
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