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Landman WJM, van Eck JHH, Heuvelink AE. Interference between Escherichia coli genotypes from the E. coli peritonitis syndrome given simultaneously to productive SPF White Leghorn hens by intratracheal inoculation. Avian Pathol 2024; 53:359-367. [PMID: 38516984 DOI: 10.1080/03079457.2024.2334683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/17/2024] [Accepted: 03/19/2024] [Indexed: 03/23/2024]
Abstract
The purpose of the present study was to examine if potentiation of mortality occurred after simultaneous administration of several Escherichia coli genotypes, each capable of inducing the E. coli peritonitis syndrome, in comparison with single genotype application. Five groups of productive specified pathogen free White Leghorn hens were housed in isolators. Groups 1-4 consisted of 32 hens each, group 5 of 10 hens. At 32 weeks of age all groups were inoculated intratracheally. Groups 1 and 2 were inoculated with a mix of four E. coli genotypes and groups 3 and 4 with a mix of four other genotypes. Groups 1 and 3 were given 1 median lethal dose (LD50) of each genotype per hen and groups 2 and 4 had a dose of 0.1 LD50 per genotype per hen; group 5 was mock inoculated. The experiment ended one week after inoculations. In Group 5, no mortality occurred and gross lesions were absent at post-mortem examination. Mortality in groups 1 and 3 was 84% and 81%, respectively; in groups 2 and 4 59% and 66%, respectively. Although mortality in groups 1 and 3 exceeded the expected 50%, this could not be due to potentiation as cluster analysis of reisolates showed that in individual hens only one genotype was found, indicating interference between E. coli genotypes. In groups all four or only two genotypes were recovered, showing that not all genotypes will induce colibacillosis in all experimental groups. Therefore, broad protection can be best assessed by challenging with various single genotypes.RESEARCH HIGHLIGHTS All four or only two E. coli genotypes were found in groups of hens given mixes of four genotypes.In contrast, only one genotype was found in individual hens.E. coli genotypes interfere with each other in hens after given as a mix.Interference is likely based on a random process.Broad protection can best be assessed by challenging with single genotypes.
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Affiliation(s)
| | - J H H van Eck
- Department of Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
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2
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Genath A, Hackmann C, Denkel L, Weber A, Maechler F, Kola A, Schwarz S, Gastmeier P, Leistner R. The genetic relationship between human and pet isolates: a core genome multilocus sequence analysis of multidrug-resistant bacteria. Antimicrob Resist Infect Control 2024; 13:107. [PMID: 39304920 DOI: 10.1186/s13756-024-01457-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 08/25/2024] [Indexed: 09/22/2024] Open
Abstract
INTRODUCTION The global increase of multidrug-resistant organisms (MDROs) is one of the most urgent public health threats affecting both humans and animals. The One Health concept emphasizes the interconnectedness of human, animal and environmental health and highlights the need for integrated approaches to combat antimicrobial resistance (AMR). Although the sharing of environments and antimicrobial agents between companion animals and humans poses a risk for MDRO transmission, companion animals have been studied to a lesser extent than livestock animals. This study therefore used core genome multilocus sequence typing (cgMLST) to investigate the genetic relationships and putative transmission of MDROs between humans and pets. METHODS This descriptive integrated typing study included 252 human isolates, 53 dog isolates and 10 cat isolates collected from 2019 to 2022 at the Charité University Hospital in Berlin, Germany. CgMLST was performed to characterize methicillin-resistant Staphylococcus aureus, vancomycin-resistant enterococci and multidrug-resistant gram-negative bacteria. The genetic diversity of the MDROs of the different host populations was determined and compared based on sequence type and core genome complex type. RESULTS Within this study the majority of samples from pets and humans was genetically distinct. However, for some isolates, the number of allelic differences identified by cgMLST was low. Two cases of putative household transmission or shared source of VR E. faecium and MDR E. coli between humans and pets were documented. CONCLUSIONS The interaction between humans and their pets appears to play a minor role in the spread of the MDROs studied. However, further research is needed. This study emphasizes the importance of comprehensive molecular surveillance and a multidisciplinary One Health approach to understand and contain the spread of MDROs in human and animal populations. TRIAL REGISTRATION The study is registered with the German Clinical Trials Register (DRKS00030009).
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Affiliation(s)
- Antonia Genath
- Institute of Hygiene and Environmental Medicine, Charité University Medicine Berlin, Berlin, Germany.
- Berlin School of Public Health, Charité University Medicine Berlin, Berlin, Germany.
| | - Carolin Hackmann
- Institute of Hygiene and Environmental Medicine, Charité University Medicine Berlin, Berlin, Germany
- Unit 36, Respiratory Infection, Department of Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Luisa Denkel
- Institute of Hygiene and Environmental Medicine, Charité University Medicine Berlin, Berlin, Germany
| | - Anna Weber
- Institute of Hygiene and Environmental Medicine, Charité University Medicine Berlin, Berlin, Germany
| | - Friederike Maechler
- Institute of Hygiene and Environmental Medicine, Charité University Medicine Berlin, Berlin, Germany
| | - Axel Kola
- Institute of Hygiene and Environmental Medicine, Charité University Medicine Berlin, Berlin, Germany
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre of Infection Medicine, School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Petra Gastmeier
- Institute of Hygiene and Environmental Medicine, Charité University Medicine Berlin, Berlin, Germany
| | - Rasmus Leistner
- Institute of Hygiene and Environmental Medicine, Charité University Medicine Berlin, Berlin, Germany
- Division Gastroenterology, Infectious Diseases and Rheumatology, Medical Department, Charité University Medicine Berlin, Berlin, Germany
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3
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Barrera Patiño CP, Soares JM, Blanco KC, Bagnato VS. Machine Learning in FTIR Spectrum for the Identification of Antibiotic Resistance: A Demonstration with Different Species of Microorganisms. Antibiotics (Basel) 2024; 13:821. [PMID: 39334995 PMCID: PMC11428736 DOI: 10.3390/antibiotics13090821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 07/22/2024] [Accepted: 08/26/2024] [Indexed: 09/30/2024] Open
Abstract
Recent studies introduced the importance of using machine learning algorithms in research focused on the identification of antibiotic resistance. In this study, we highlight the importance of building solid machine learning foundations to differentiate antimicrobial resistance among microorganisms. Using advanced machine learning algorithms, we established a methodology capable of analyzing the FTIR structural profile of the samples of Streptococcus pyogenes and Streptococcus mutans (Gram-positive), as well as Escherichia coli and Klebsiella pneumoniae (Gram-negative), demonstrating cross-sectional applicability in this focus on different microorganisms. The analysis focuses on specific biomolecules-Carbohydrates, Fatty Acids, and Proteins-in FTIR spectra, providing a multidimensional database that transcends microbial variability. The results highlight the ability of the method to consistently identify resistance patterns, regardless of the Gram classification of the bacteria and the species involved, reinforcing the premise that the structural characteristics identified are universal among the microorganisms tested. By validating this approach in four distinct species, our study proves the versatility and precision of the methodology used, in addition to bringing support to the development of an innovative protocol for the rapid and safe identification of antimicrobial resistance. This advance is crucial for optimizing treatment strategies and avoiding the spread of resistance. This emphasizes the relevance of specialized machine learning bases in effectively differentiating between resistance profiles in Gram-negative and Gram-positive bacteria to be implemented in the identification of antibiotic resistance. The obtained result has a high potential to be applied to clinical procedures.
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Affiliation(s)
- Claudia Patricia Barrera Patiño
- São Carlos Institute of Physics, University of São Paulo, Avenida Trabalhador São-Carlense No. 400, Parque Arnold Schimidt, São Carlos CEP 13566-590, SP, Brazil
| | - Jennifer Machado Soares
- São Carlos Institute of Physics, University of São Paulo, Avenida Trabalhador São-Carlense No. 400, Parque Arnold Schimidt, São Carlos CEP 13566-590, SP, Brazil
| | - Kate Cristina Blanco
- São Carlos Institute of Physics, University of São Paulo, Avenida Trabalhador São-Carlense No. 400, Parque Arnold Schimidt, São Carlos CEP 13566-590, SP, Brazil
| | - Vanderlei Salvador Bagnato
- São Carlos Institute of Physics, University of São Paulo, Avenida Trabalhador São-Carlense No. 400, Parque Arnold Schimidt, São Carlos CEP 13566-590, SP, Brazil
- Biomedical Engineering, Texas A&M University, 400 Bizzell St., College Station, TX 77843, USA
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Nakajima N, Jinnai M, Izumiyama S, Kuroki T. Evaluating Fourier-transform infrared spectroscopy with IR Biotyper as a faster and simpler method for investigating the sources of an outbreak of legionellosis. Eur J Clin Microbiol Infect Dis 2024; 43:991-997. [PMID: 38379053 DOI: 10.1007/s10096-024-04781-3] [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: 11/13/2023] [Accepted: 02/09/2024] [Indexed: 02/22/2024]
Abstract
Fourier-transform infrared (FTIR) spectroscopy using the IR Biotyper and core genome single nucleotide polymorphism (cgSNP) analysis were performed on 12 Legionella isolates associated with an outbreak at a spa house in Kanagawa Prefecture, Japan, and 3 non-outbreak isolates. The discriminative power of FTIR spectroscopy for 48-h incubation conditions of L. pneumophila in this outbreak was lower than cgSNP-based typing but higher than serogroup typing. FTIR spectroscopy could screen outbreak isolates from a group of genetically related isolates and may be useful as an initial typing method in Legionella outbreak investigations.
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Affiliation(s)
- Naoki Nakajima
- Department of Microbiology, Kanagawa Prefectural Institute of Public Health, 1-3-1 Shimomachiya, Chigasaki, Kanagawa, 253-0087, Japan.
| | - Michio Jinnai
- Department of Microbiology, Kanagawa Prefectural Institute of Public Health, 1-3-1 Shimomachiya, Chigasaki, Kanagawa, 253-0087, Japan
| | - Shinji Izumiyama
- Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Toshiro Kuroki
- Faculty of Veterinary Medicine, Okayama University of Science, Okayama, Japan
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Aranega-Bou P, Cornbill C, Rodger G, Bird M, Moore G, Roohi A, Hopkins KL, Hopkins S, Ribeca P, Stoesser N, Lipworth SI. WITHDRAWN: Evaluation of Fourier Transform Infrared spectroscopy (IR Biotyper) as a complement to Whole genome sequencing (WGS) to characterise Enterobacter cloacae , Citrobacter freundii and Klebsiella pneumoniae isolates recovered from hospital sinks. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.04.24.23289028. [PMID: 37214917 PMCID: PMC10193520 DOI: 10.1101/2023.04.24.23289028] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The authors have withdrawn their manuscript due to becoming aware of methodology issues related to the curation of the training set used to determine cut-off values for Biotyper cluster assignation and lack of replicate measurements on different days for the isolates analysed. It is therefore unclear whether the conclusions of the manuscript are founded and no further work is possible to correct these issues as the instrument is no longer available to the authors. If you have any questions, please contact the corresponding author.
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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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Zendri F, Schmidt V, Mauder N, Loeffler A, Jepson RE, Isgren C, Pinchbeck G, Haldenby S, Timofte D. Rapid typing of Klebsiella pneumoniae and Pseudomonas aeruginosa by Fourier-transform Infrared spectroscopy informs infection control in veterinary settings. Front Microbiol 2024; 15:1334268. [PMID: 38371930 PMCID: PMC10869444 DOI: 10.3389/fmicb.2024.1334268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 01/09/2024] [Indexed: 02/20/2024] Open
Abstract
Introduction The emergence of multi-drug resistant (MDR) pathogens linked to healthcare-associated infections (HCAIs) is an increasing concern in modern veterinary practice. Thus, rapid bacterial typing for real-time tracking of MDR hospital dissemination is still much needed to inform best infection control practices in a clinically relevant timeframe. To this end, the IR Biotyper using Fourier-Transform InfraRed (FTIR) spectroscopy has the potential to provide fast cluster analysis of potentially related organisms with substantial cost and turnaround time benefits. Materials and methods A collection of MDR bacterial isolates (n = 199, comprising 92 Klebsiella pneumoniae and 107 Pseudomonas aeruginosa) obtained from companion animal (i.e., dogs, cats and horses) clinical investigations, faecal and environmental screening from four veterinary facilities between 2012 and 2019 was analysed retrospectively by FTIR spectroscopy. Its performance was compared against MLST extracted from whole genomes of a subset of clustering isolates (proportionally to cluster size) for investigation of potential nosocomial transmission between patients and the surrounding hospital environments. Results Concordance between the FTIR and MLST types was overall high for K. pneumoniae (Adjusted Rand Index [ARI] of 0.958) and poor for P. aeruginosa (ARI of 0.313). FTIR K. pneumoniae clusters (n = 7) accurately segregated into their respective veterinary facility with evidence of intra-hospital spread of K. pneumoniae between patients and environmental surfaces. Notably, K. pneumoniae ST147 intensely circulated at one Small Animal Hospital ICU. Conversely, Pseudomonas aeruginosa FTIR clusters (n = 18) commonly contained isolates of diversified hospital source and heterogeneous genetic background (as also genetically related isolates spread across different clusters); nonetheless, dissemination of some clones, such as P. aeruginosa ST2644 in the equine hospital, was apparent. Importantly, FTIR clustering of clinical, colonisation and/or environmental isolates sharing genomically similar backgrounds was seen for both MDR organisms, highlighting likely cross-contamination events that led to clonal dissemination within settings. Conclusion FTIR spectroscopy has high discriminatory power for hospital epidemiological surveillance of veterinary K. pneumoniae and could provide sufficient information to support early detection of clonal dissemination, facilitating implementation of appropriate infection control measures. Further work and careful optimisation need to be carried out to improve its performance for typing of P. aeruginosa veterinary isolates.
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Affiliation(s)
- Flavia Zendri
- Department of Veterinary Anatomy, Physiology and Pathology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Neston, United Kingdom
| | - Vanessa Schmidt
- Department of Small Animal Clinical Science, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Neston, United Kingdom
| | | | - Anette Loeffler
- Western Counties Equine Hospital Ltd., Culmstock, United Kingdom
| | | | - Cajsa Isgren
- Department of Livestock and One Health, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Neston, United Kingdom
| | - Gina Pinchbeck
- Centre for Genomic Research, University of Liverpool, Liverpool, United Kingdom
| | - Sam Haldenby
- Centre for Genomic Research, University of Liverpool, Liverpool, United Kingdom
| | - Dorina Timofte
- Department of Veterinary Anatomy, Physiology and Pathology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Neston, United Kingdom
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8
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Uribe G, Salipante SJ, Curtis L, Lieberman JA, Kurosawa K, Cookson BT, Hoogestraat D, Stewart MK, Olmstead T, Bourassa L. Evaluation of Fourier transform-infrared spectroscopy (FT-IR) as a control measure for nosocomial outbreak investigations. J Clin Microbiol 2023; 61:e0034723. [PMID: 37787542 PMCID: PMC10595069 DOI: 10.1128/jcm.00347-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 06/29/2023] [Indexed: 10/04/2023] Open
Abstract
Whole-genome sequencing (WGS) provides greater resolution than other molecular epidemiology strategies and is emerging as a new gold standard approach for microbial strain typing. The Bruker IR Biotyper is designed as a screening tool to identify bacterial isolates that require WGS to establish accurate relationships, but its performance and utility in nosocomial outbreak investigations have not been thoroughly investigated. Here, we evaluated the IR Biotyper by retrospectively examining isolates tested by WGS during investigations of potential nosocomial transmission events or outbreaks. Ninety-eight clinical isolates from 14 different outbreak investigations were examined: three collections of Acinetobacter baumannii (n = 2, n = 9, n = 5 isolates in each collection), one of Escherichia coli (n = 16), two of Pseudomonas aeruginosa (n = 2 and n = 5), two of Serratia marcescens (n = 9 and n = 7), five of Staphylococcus aureus (n = 8, n = 4, n = 3, n = 3, n = 17), and one of Stenotrophomonas maltophilia (n = 8). Linear regression demonstrated a weak, positive correlation between the number of pairwise genome-wide single-nucleotide polymorphisms (SNPs) and IR Biotyper spectral distance values for Gram-positive (r = 0.43, P ≤ 0.0001), Gram-negative (r = 0.1554, P = 0.0639), and all organisms combined (r = 0.342, P ≤ 0.0001). Overall, the IR Biotyper had a positive predictive value (PPV) of 55.81% for identifying strains that were closely related by genomic identity, but a negative predictive value (NPV) of 86.79% for identifying unrelated isolates. When experimentally adjusted cut-offs were applied to A. baumannii, P. aeruginosa, and E. coli, the PPV was 62% for identifying strains that were closely related and the NPV was 100% for identifying unrelated isolates. Implementation of the IR Biotyper as a screening tool in this cohort would have reduced the number of Gram-negative isolates requiring further WGS analysis by 50% and would reduce the number of S. aureus isolates needing WGS resolution by 48%.
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Affiliation(s)
- Gabriela Uribe
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Stephen J. Salipante
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Lauren Curtis
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Joshua A. Lieberman
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Kyoko Kurosawa
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Brad T. Cookson
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Daniel Hoogestraat
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Mary K. Stewart
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Tessa Olmstead
- Department of Psychiatry and Behavioral Sciences, University of New Mexico, Albuquerque, New Mexico, USA
| | - Lori Bourassa
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
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Yamin D, Uskoković V, Wakil AM, Goni MD, Shamsuddin SH, Mustafa FH, Alfouzan WA, Alissa M, Alshengeti A, Almaghrabi RH, Fares MAA, Garout M, Al Kaabi NA, Alshehri AA, Ali HM, Rabaan AA, Aldubisi FA, Yean CY, Yusof NY. Current and Future Technologies for the Detection of Antibiotic-Resistant Bacteria. Diagnostics (Basel) 2023; 13:3246. [PMID: 37892067 PMCID: PMC10606640 DOI: 10.3390/diagnostics13203246] [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: 09/30/2023] [Revised: 10/14/2023] [Accepted: 10/15/2023] [Indexed: 10/29/2023] Open
Abstract
Antibiotic resistance is a global public health concern, posing a significant threat to the effectiveness of antibiotics in treating bacterial infections. The accurate and timely detection of antibiotic-resistant bacteria is crucial for implementing appropriate treatment strategies and preventing the spread of resistant strains. This manuscript provides an overview of the current and emerging technologies used for the detection of antibiotic-resistant bacteria. We discuss traditional culture-based methods, molecular techniques, and innovative approaches, highlighting their advantages, limitations, and potential future applications. By understanding the strengths and limitations of these technologies, researchers and healthcare professionals can make informed decisions in combating antibiotic resistance and improving patient outcomes.
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Affiliation(s)
- Dina Yamin
- Al-Karak Public Hospital, Karak 61210, Jordan;
- Institute for Research in Molecular Medicine, University Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia
- Department of Veterinary Clinical Studies, Faculty of Veterinary Medicine, University Malaysia Kelantan, Kota Bharu 16100, Kelantan, Malaysia;
| | - Vuk Uskoković
- TardigradeNano LLC., Irvine, CA 92604, USA;
- Department of Mechanical Engineering, San Diego State University, San Diego, CA 92182, USA
| | - Abubakar Muhammad Wakil
- Department of Veterinary Clinical Studies, Faculty of Veterinary Medicine, University Malaysia Kelantan, Kota Bharu 16100, Kelantan, Malaysia;
- Department of Veterinary Physiology and Biochemistry, Faculty of Veterinary Medicine, University of Maiduguri, Maiduguri 600104, Borno, Nigeria
| | - Mohammed Dauda Goni
- Public Health and Zoonoses Research Group, Faculty of Veterinary Medicine, University Malaysia Kelantan, Pengkalan Chepa 16100, Kelantan, Malaysia;
| | - Shazana Hilda Shamsuddin
- Department of Pathology, School of Medical Sciences, University Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia;
| | - Fatin Hamimi Mustafa
- Department of Electronic & Computer Engineering, Faculty of Electrical Engineering, University Teknologi Malaysia, Johor Bharu 81310, Johor, Malaysia;
| | - Wadha A. Alfouzan
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat 13110, Kuwait;
- Microbiology Unit, Department of Laboratories, Farwania Hospital, Farwania 85000, Kuwait
| | - Mohammed Alissa
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia;
| | - Amer Alshengeti
- Department of Pediatrics, College of Medicine, Taibah University, Al-Madinah 41491, Saudi Arabia;
- Department of Infection Prevention and Control, Prince Mohammad Bin Abdulaziz Hospital, National Guard Health Affairs, Al-Madinah 41491, Saudi Arabia
| | - Rana H. Almaghrabi
- Pediatric Department, Prince Sultan Medical Military City, Riyadh 12233, Saudi Arabia;
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia;
| | - Mona A. Al Fares
- Department of Internal Medicine, King Abdulaziz University Hospital, Jeddah 21589, Saudi Arabia;
| | - Mohammed Garout
- Department of Community Medicine and Health Care for Pilgrims, Faculty of Medicine, Umm Al-Qura University, Makkah 21955, Saudi Arabia;
| | - Nawal A. Al Kaabi
- College of Medicine and Health Science, Khalifa University, Abu Dhabi 127788, United Arab Emirates;
- Sheikh Khalifa Medical City, Abu Dhabi Health Services Company (SEHA), Abu Dhabi 51900, United Arab Emirates
| | - Ahmad A. Alshehri
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia;
| | - Hamza M. Ali
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Taibah University, Madinah 41411, Saudi Arabia;
| | - Ali A. Rabaan
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia;
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia
- Department of Public Health and Nutrition, The University of Haripur, Haripur 22610, Pakistan
| | | | - Chan Yean Yean
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, University Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Nik Yusnoraini Yusof
- Institute for Research in Molecular Medicine, University Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia
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10
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Scheier TC, Franz J, Boumasmoud M, Andreoni F, Chakrakodi B, Duvnjak B, Egli A, Zingg W, Ramette A, Wolfensberger A, Kouyos RD, Brugger SD. Fourier-transform infrared spectroscopy for typing of vancomycin-resistant Enterococcus faecium: performance analysis and outbreak investigation. Microbiol Spectr 2023; 11:e0098423. [PMID: 37737606 PMCID: PMC10581122 DOI: 10.1128/spectrum.00984-23] [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: 03/09/2023] [Accepted: 08/01/2023] [Indexed: 09/23/2023] Open
Abstract
Vancomycin-resistant Enterococci, mainly Enterococcus faecium (VREfm), are causing nosocomial infections and outbreaks. Bacterial typing methods are used to assist in outbreak investigations. Most of them, especially genotypic methods like multi-locus sequence typing (MLST), whole genome sequencing (WGS), or pulsed-field gel electrophoresis, are quite expensive and time-consuming. Fourier-transform infrared (FT-IR) spectroscopy assesses the biochemical composition of bacteria, such as carboxyl groups in polysaccharides. It is an affordable technique and has a faster turnaround time. Thus, the aim of this study was to evaluate FT-IR spectroscopy for VREfm outbreak investigations. Basic performance requirements like reproducibility and the effects of incubation time were assessed in distinct sample sets. After determining a FT-IR spectroscopy cut-off range, the clustering agreement between FT-IR and WGS within a retrospective (n: 92 isolates) and a prospective outbreak (n: 15 isolates) was investigated. For WGS an average nucleotide identity (ANI) cut-off score of 0.999 was used. Basic performance analysis showed reproducible results. Moreover, FT-IR spectroscopy readouts showed a high agreement with WGS-ANI analysis in clinical outbreak investigations (V-measure 0.772 for the retrospective and 1.000 for the prospective outbreak). FT-IR spectroscopy had a higher discriminatory power than MLST in the outbreak investigations. After determining cut-off values to achieve optimal resolution, FT-IR spectroscopy is a promising technique to assist in outbreak investigation as an affordable, easy-to-use tool with a turnaround time of less than one day. IMPORTANCE Vancomycin-resistant Enterococci, mainly Enterococcus faecium (VREfm), are a frequent cause of nosocomial outbreaks. Several bacterial typing methods are used to track transmissions and investigate outbreaks, whereby genome-based techniques are used as a gold standard. Current methods are either expensive, time-consuming, or both. Additionally, often, specifically trained staff needs to be available. This study provides insight into the use of Fourier-transform infrared (FT-IR) spectroscopy, an affordable, easy-to-use tool with a short turnaround time as a typing method for VREfm. By assessing clinical samples, this work demonstrates promising results for species discrimination and reproducibility. FT-IR spectrosopy shows a high level of agreement in the analysis of VREfm outbreaks in comparison with whole genome sequencing-based methods.
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Affiliation(s)
- T. C. Scheier
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zurich, Zurich, Switzerland
| | - J. Franz
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zurich, Zurich, Switzerland
| | - M. Boumasmoud
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zurich, Zurich, Switzerland
- Institute of Integrative Biology, ETH Zürich, Zurich, Switzerland
| | - F. Andreoni
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zurich, Zurich, Switzerland
| | - B. Chakrakodi
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zurich, Zurich, Switzerland
| | - B. Duvnjak
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zurich, Zurich, Switzerland
| | - A. Egli
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - W. Zingg
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zurich, Zurich, Switzerland
| | - A. Ramette
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - A. Wolfensberger
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zurich, Zurich, Switzerland
| | - R. D. Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zurich, Zurich, Switzerland
| | - S. D. Brugger
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zurich, Zurich, Switzerland
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11
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Kumbhar S, Khairate R, Bhatia M, Choudhari P, Gaikwad V. Evaluation of curcumin-loaded chitosan nanoparticles for wound healing activity. ADMET AND DMPK 2023; 11:601-613. [PMID: 37937244 PMCID: PMC10626514 DOI: 10.5599/admet.1897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 08/14/2023] [Indexed: 11/09/2023] Open
Abstract
Background and purpose Wound healing is a biological process that can be difficult to manage clinically. In skin wound healing, the interaction of many cells, growth factors, and cytokines reveals an outstanding biological function mechanism. Wound healing that occurs naturally restores tissue integrity, however, it is usually restricted to wound repair. Curcumin synthesised in a chitosan matrix can be used to heal skin sores. Experimental approach The ionotropic gelation procedure required crosslinking chitosan with a tripolyphosphate (TPP) crosslinker to generate curcumin nanoparticles encapsulated in chitosan. Key results The nanoparticles were between 200 and 400 nm in size, with a strong positive surface charge and good entrapment efficacy, according to SEM and TEM investigations. Curcumin and chitosan compatibility was investigated using FTIR spectroscopy. All batches showed consistent drug release, with the F5 batch having the highest curcumin release, at 75% after 16 hours. On L929 cells, scratch assays were utilised to assess wound healing. Wound closure with widths of 59 and 65 mm with curcumin and 45 and 78 mm with curcumin-loaded chitosan nanoparticles was seen after 24 and 48 hours of examination. Conclusions According to the findings, prepared curcumin chitosan nanoparticles are beneficial in healing skin damage.
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Affiliation(s)
- Smita Kumbhar
- Department of Pharmaceutical Analysis, DSTS Mandal’s College of Pharmacy, Solapur, India
| | - Rupali Khairate
- Department of Pharmaceutical Analysis, DSTS Mandal’s College of Pharmacy, Solapur, India
| | - Manish Bhatia
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, India
| | - Prafulla Choudhari
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, India
| | - Vinod Gaikwad
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER), Hajipur, India
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12
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Bhunia AK, Singh AK, Parker K, Applegate BM. Petri-plate, bacteria, and laser optical scattering sensor. Front Cell Infect Microbiol 2022; 12:1087074. [PMID: 36619754 PMCID: PMC9813400 DOI: 10.3389/fcimb.2022.1087074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
Classical microbiology has paved the path forward for the development of modern biotechnology and microbial biosensing platforms. Microbial culturing and isolation using the Petri plate revolutionized the field of microbiology. In 1887, Julius Richard Petri invented possibly the most important tool in microbiology, the Petri plate, which continues to have a profound impact not only on reliably isolating, identifying, and studying microorganisms but also manipulating a microbe to study gene expression, virulence properties, antibiotic resistance, and production of drugs, enzymes, and foods. Before the recent advances in gene sequencing, microbial identification for diagnosis relied upon the hierarchal testing of a pure culture isolate. Direct detection and identification of isolated bacterial colonies on a Petri plate with a sensing device has the potential for revolutionizing further development in microbiology including gene sequencing, pathogenicity study, antibiotic susceptibility testing , and for characterizing industrially beneficial traits. An optical scattering sensor designated BARDOT (bacterial rapid detection using optical scattering technology) that uses a red-diode laser, developed at the beginning of the 21st century at Purdue University, some 220 years after the Petri-plate discovery can identify and study bacteria directly on the plate as a diagnostic tool akin to Raman scattering and hyperspectral imaging systems for application in clinical and food microbiology laboratories.
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Affiliation(s)
- Arun K. Bhunia
- Molecular Food Microbiology Laboratory, Department of Food Science, Purdue University, West Lafayette, IN, United States,Purdue University, Purdue University Interdisciplinary Life Science Program (PULSe), West Lafayette, IN, United States,Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, United States,Department of Comparative Pathobiology, Purdue University, West Lafayette, IN, United States,*Correspondence: Arun K. Bhunia,
| | - Atul K. Singh
- Molecular Food Microbiology Laboratory, Department of Food Science, Purdue University, West Lafayette, IN, United States,Clear Labs, San Carlos, CA, United States
| | - Kyle Parker
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
| | - Bruce M. Applegate
- Molecular Food Microbiology Laboratory, Department of Food Science, Purdue University, West Lafayette, IN, United States,Purdue University, Purdue University Interdisciplinary Life Science Program (PULSe), West Lafayette, IN, United States,Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, United States,Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
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13
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Wang P, Sun H, Yang W, Fang Y. Optical Methods for Label-Free Detection of Bacteria. BIOSENSORS 2022; 12:bios12121171. [PMID: 36551138 PMCID: PMC9775963 DOI: 10.3390/bios12121171] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 12/06/2022] [Accepted: 12/13/2022] [Indexed: 05/27/2023]
Abstract
Pathogenic bacteria are the leading causes of food-borne and water-borne infections, and one of the most serious public threats. Traditional bacterial detection techniques, including plate culture, polymerase chain reaction, and enzyme-linked immunosorbent assay are time-consuming, while hindering precise therapy initiation. Thus, rapid detection of bacteria is of vital clinical importance in reducing the misuse of antibiotics. Among the most recently developed methods, the label-free optical approach is one of the most promising methods that is able to address this challenge due to its rapidity, simplicity, and relatively low-cost. This paper reviews optical methods such as surface-enhanced Raman scattering spectroscopy, surface plasmon resonance, and dark-field microscopic imaging techniques for the rapid detection of pathogenic bacteria in a label-free manner. The advantages and disadvantages of these label-free technologies for bacterial detection are summarized in order to promote their application for rapid bacterial detection in source-limited environments and for drug resistance assessments.
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Affiliation(s)
- Pengcheng Wang
- Jiangsu Province Key Laboratory of Anesthesiology, Xuzhou Medical University, Xuzhou 221004, China
| | - Hao Sun
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Wei Yang
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Yimin Fang
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
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14
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Recent Studies on Advance Spectroscopic Techniques for the Identification of Microorganisms: A Review. ARAB J CHEM 2022. [DOI: 10.1016/j.arabjc.2022.104521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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15
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Wendel AF, Peter D, Mattner F, Weiss M, Hoppenz M, Wolf S, Bader B, Peter S, Liese J. Surveillance of Enterobacter cloacae complex colonization and comparative analysis of different typing methods on a neonatal intensive care unit in Germany. Antimicrob Resist Infect Control 2022; 11:54. [PMID: 35365217 PMCID: PMC8973561 DOI: 10.1186/s13756-022-01094-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 03/13/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Enterobacter cloacae complex is a group of common opportunistic pathogens on neonatal intensive care units. Active microbiological screening to guide empirical antimicrobial treatment or to detect transmission events is recommended in high-risk preterm neonates. A rise in colonization with E. cloacae complex was observed in a German perinatal centre. The aim of this study was to evaluate the performance of different typing techniques using whole genome sequencing (WGS) as a reference.
Methods
Enterobacter cloacae complex isolates from clinical and screening specimens with an epidemiological link to the neonatal intensive care units were further assessed. Identification and antibiotic susceptibility testing was performed by a combination of VITEK2 (bioMérieux) and MALDI-TOF (Bruker Daltonics), followed by RAPD/rep-PCR and PFGE (XbaI). Retrospectively, all isolates were analyzed by Fourier-transform infrared (FTIR) spectroscopy (IR Biotyper, Bruker Daltonics). Whole genome sequencing with SNP-based clustering was used as the reference method. Furthermore, resistome analysis, sequence type and species identification were derived from the WGS data. Transmission analysis was based on epidemiological and typing data.
Results
Between September 2017 and March 2018 32 mostly preterm neonates were found to be colonized with E. cloacae complex and 32 isolates from 24 patients were available for further typing. RAPD/rep-PCR and PFGE showed good concordance with WGS whereas FTIR displayed mediocre results [adjusted rand index (ARI) = 0.436]. A polyclonal increase and two dominant and overlapping clonal clusters of two different E. hormaechei subspecies were detected. Overall, four different species were identified. Genotyping confirmed third-generation cephalosporin resistance development in isolates of the same patient. During the six-month period several infection prevention interventions were performed and no E. cloacae complex isolates were observed during the following months.
Conclusions
Interpretation of the microbiological results alone to detect transmission events is often challenging and bacterial typing is of utmost importance to implement targeted infection control measures in an epidemic occurrence of E. cloacae complex. WGS is the most discriminatory method. However, traditional methods such as PFGE or RAPD/rep-PCR can provide reliable and quicker results in many settings. Furthermore, research is needed to quickly identify E. cloacae complex to the species level in the microbiological laboratory.
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16
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Azrad M, Matok LA, Leshem T, Peretz A. Comparison of FT-IR with whole-genome sequencing for identification of maternal-to‑neonate transmission of antibiotic-resistant bacteria. J Microbiol Methods 2022; 202:106603. [DOI: 10.1016/j.mimet.2022.106603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 10/18/2022] [Accepted: 10/18/2022] [Indexed: 12/27/2022]
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17
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Cozma AP, Rimbu CM, Zendri F, Maciuca IE, Timofte D. Clonal Dissemination of Extended-Spectrum Cephalosporin-Resistant Enterobacterales between Dogs and Humans in Households and Animal Shelters of Romania. Antibiotics (Basel) 2022; 11:antibiotics11091242. [PMID: 36140020 PMCID: PMC9495119 DOI: 10.3390/antibiotics11091242] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 11/16/2022] Open
Abstract
Faecal carriage of extended-spectrum cephalosporin-resistant (ESC-R) Enterobacterales in healthy pets is a concerning issue. This study aimed to determine the prevalence, genetic background, and potential for interspecies transmission of these bacteria between dogs and humans within the same household (HH) or shelter environment in Romania. Faecal samples (n = 263) collected from healthy dogs (n = 102), their owners (n = 32), as well as dogs (n = 110) and staff (n = 19) from dog shelters, were screened for ESC-R carriage. Clonal relatedness of canine and human Escherichia coli isolates was established using Fourier Transform Infrared Spectroscopy (FTIR), followed by Illumina WGS of selected isolates. The highest prevalence of ESC-R Enterobacterales faecal carriage was identified in staff working at dog shelters (78.9%), followed by dogs from households (44.11%), dog owners (43.7%), and dogs from shelters (27%). FTIR identified 15 clusters of closely related E. coli isolates, including dog and human isolates from the same environment. Co-carriage of ESC-R isolates in both the dog and owner was identified in 12 HHs (37.5%), with two HHs (6%) having both the owner and dog carrying isolates with identical FTIR spectra, phylogroup, resistance genes, and Inc plasmids. Major ExPEC lineages such as ST127, ST10, ST155, and ST88 were detected in human and dog isolates. Our study revealed a high prevalence of faecal ESC-R E. coli carriage in both dogs and humans from Romanian households and shelters, where bidirectional clonal transmission between humans and dogs is likely. Furthermore, we identified ESC-R Enterobacterales co-carriage in people and dogs sharing the same environment using FTIR, demonstrating its value in AMR surveillance for humans and animals.
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Affiliation(s)
- Andreea Paula Cozma
- Department of Exact Sciences, Faculty of Horticulture, University of Life Sciences, 700490 Iasi, Romania
| | - Cristina Mihaela Rimbu
- Department of Public Health, Faculty of Veterinary Medicine, University of Life Sciences, 700490 Iasi, Romania
| | - Flavia Zendri
- Institute of Infection, Veterinary and Ecological Sciences, Department of Veterinary Anatomy, Physiology and Pathology, Leahurst Campus, University of Liverpool, Neston CH64 7TE, UK
| | - Iuliana Elena Maciuca
- Institute of Infection, Veterinary and Ecological Sciences, Department of Veterinary Anatomy, Physiology and Pathology, Leahurst Campus, University of Liverpool, Neston CH64 7TE, UK
| | - Dorina Timofte
- Department of Public Health, Faculty of Veterinary Medicine, University of Life Sciences, 700490 Iasi, Romania
- Institute of Infection, Veterinary and Ecological Sciences, Department of Veterinary Anatomy, Physiology and Pathology, Leahurst Campus, University of Liverpool, Neston CH64 7TE, UK
- Correspondence:
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18
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Machine learning-based typing of Salmonella enterica O-serogroups by the Fourier-Transform Infrared (FTIR) Spectroscopy-based IR Biotyper system. METHODS IN MICROBIOLOGY 2022; 201:106564. [PMID: 36084763 DOI: 10.1016/j.mimet.2022.106564] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/30/2022] [Accepted: 08/30/2022] [Indexed: 11/24/2022]
Abstract
BACKGROUND Salmonella enterica is among the major burdens for public health at global level. Typing of salmonellae below the species level is fundamental for different purposes, but traditional methods are expensive, technically demanding, and time-consuming, and therefore limited to reference centers. Fourier transform infrared (FTIR) spectroscopy is an alternative method for bacterial typing, successfully applied for classification at different infra-species levels. AIM This study aimed to address the challenge of subtyping Salmonella enterica at O-serogroup level by using FTIR spectroscopy. We applied machine learning to develop a novel approach for S. enterica typing, using the FTIR-based IR Biotyper® system (IRBT; Bruker Daltonics GmbH & Co. KG, Germany). We investigated a multicentric collection of isolates, and we compared the novel approach with classical serotyping-based and molecular methods. METHODS A total of 958 well characterized Salmonella isolates (25 serogroups, 138 serovars), collected in 11 different centers (in Europe and Japan), from clinical, environmental and food samples were included in this study and analyzed by IRBT. Infrared absorption spectra were acquired from water-ethanol bacterial suspensions, from culture isolates grown on seven different agar media. In the first part of the study, the discriminatory potential of the IRBT system was evaluated by comparison with reference typing method/s. In the second part of the study, the artificial intelligence capabilities of the IRBT software were applied to develop a classifier for Salmonella isolates at serogroup level. Different machine learning algorithms were investigated (artificial neural networks and support vector machine). A subset of 88 pre-characterized isolates (corresponding to 25 serogroups and 53 serovars) were included in the training set. The remaining 870 samples were used as validation set. The classifiers were evaluated in terms of accuracy, error rate and failed classification rate. RESULTS The classifier that provided the highest accuracy in the cross-validation was selected to be tested with four external testing sets. Considering all the testing sites, accuracy ranged from 97.0% to 99.2% for non-selective media, and from 94.7% to 96.4% for selective media. CONCLUSIONS The IRBT system proved to be a very promising, user-friendly, and cost-effective tool for Salmonella typing at serogroup level. The application of machine learning algorithms proved to enable a novel approach for typing, which relies on automated analysis and result interpretation, and it is therefore free of potential human biases. The system demonstrated a high robustness and adaptability to routine workflows, without the need of highly trained personnel, and proving to be suitable to be applied with isolates grown on different agar media, both selective and unselective. Further tests with currently circulating clinical, food and environmental isolates would be necessary before implementing it as a potentially stand-alone standard method for routine use.
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19
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Alafeef M, Pan D. Diagnostic Approaches For COVID-19: Lessons Learned and the Path Forward. ACS NANO 2022; 16:11545-11576. [PMID: 35921264 PMCID: PMC9364978 DOI: 10.1021/acsnano.2c01697] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 07/12/2022] [Indexed: 05/17/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is a transmitted respiratory disease caused by the infection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although humankind has experienced several outbreaks of infectious diseases, the COVID-19 pandemic has the highest rate of infection and has had high levels of social and economic repercussions. The current COVID-19 pandemic has highlighted the limitations of existing virological tests, which have failed to be adopted at a rate to properly slow the rapid spread of SARS-CoV-2. Pandemic preparedness has developed as a focus of many governments around the world in the event of a future outbreak. Despite the largely widespread availability of vaccines, the importance of testing has not diminished to monitor the evolution of the virus and the resulting stages of the pandemic. Therefore, developing diagnostic technology that serves as a line of defense has become imperative. In particular, that test should satisfy three criteria to be widely adopted: simplicity, economic feasibility, and accessibility. At the heart of it all, it must enable early diagnosis in the course of infection to reduce spread. However, diagnostic manufacturers need guidance on the optimal characteristics of a virological test to ensure pandemic preparedness and to aid in the effective treatment of viral infections. Nanomaterials are a decisive element in developing COVID-19 diagnostic kits as well as a key contributor to enhance the performance of existing tests. Our objective is to develop a profile of the criteria that should be available in a platform as the target product. In this work, virus detection tests were evaluated from the perspective of the COVID-19 pandemic, and then we generalized the requirements to develop a target product profile for a platform for virus detection.
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Affiliation(s)
- Maha Alafeef
- Department of Chemical, Biochemical and Environmental
Engineering, University of Maryland Baltimore County, Interdisciplinary
Health Sciences Facility, 1000 Hilltop Circle, Baltimore, Maryland 21250,
United States
- Departments of Diagnostic Radiology and Nuclear
Medicine and Pediatrics, Center for Blood Oxygen Transport and Hemostasis,
University of Maryland Baltimore School of Medicine, Health Sciences
Research Facility III, 670 W Baltimore Street, Baltimore, Maryland 21201,
United States
- Department of Bioengineering, the
University of Illinois at Urbana−Champaign, Urbana, Illinois 61801,
United States
- Biomedical Engineering Department, Jordan
University of Science and Technology, Irbid 22110,
Jordan
| | - Dipanjan Pan
- Department of Chemical, Biochemical and Environmental
Engineering, University of Maryland Baltimore County, Interdisciplinary
Health Sciences Facility, 1000 Hilltop Circle, Baltimore, Maryland 21250,
United States
- Departments of Diagnostic Radiology and Nuclear
Medicine and Pediatrics, Center for Blood Oxygen Transport and Hemostasis,
University of Maryland Baltimore School of Medicine, Health Sciences
Research Facility III, 670 W Baltimore Street, Baltimore, Maryland 21201,
United States
- Department of Bioengineering, the
University of Illinois at Urbana−Champaign, Urbana, Illinois 61801,
United States
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20
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Comparison of fast Fourier transform infrared spectroscopy biotyping with whole genome sequencing-based genotyping in common nosocomial pathogens. Anal Bioanal Chem 2022; 414:7179-7189. [PMID: 35962141 PMCID: PMC9482911 DOI: 10.1007/s00216-022-04270-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/28/2022] [Accepted: 08/08/2022] [Indexed: 11/28/2022]
Abstract
Early detection of bacterial transmission and outbreaks in hospitals is important because nosocomial infections can result in health complications and longer hospitalization. Current practice to detect outbreaks uses genotyping methods amplified fragment length polymorphism (AFLP) and whole genome sequencing (WGS), which are not suitable methods for real-time transmission screening of both susceptible and resistant bacteria. The aim was to assess the typing technique Fourier transform infrared (FTIR) spectroscopy as real-time screening method to discriminate large amounts of susceptible and resistant bacteria at strain level when there is no evident outbreak in comparison with the WGS reference. Isolates of past hospital outbreak strains of Acinetobacter baumannii/calcoaceticus complex (n = 25), Escherichia coli (n = 31), Enterococcus faecium (n = 22), Staphylococcus aureus (n = 37) and Pseudomonas aeruginosa (n = 30) were used for validation of FTIR. Subsequently, Enterococcus faecalis (n = 106) and Enterococcus faecium (n = 104) isolates from weekly routine screening samples when no potential outbreak was present were analysed. FTIR showed reproducibility and congruence of cluster composition with WGS for A. baumannii/calcoaceticus complex and E. faecium outbreak isolates. The FTIR results of E. faecalis and E. faecium isolates from routine samples showed reproducibility, but the congruence of cluster composition with WGS was low. For A. baumannii/calcoaceticus complex and E. faecium outbreak isolates, FTIR appears to be a discriminatory typing tool. However, our study shows the discriminatory power is too low to screen real-time for transmission of E. faecium and E. faecalis at patient wards based on isolates acquired in routine surveillance cultures when there is no clear suspicion of an ongoing outbreak.
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21
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Wang-Wang JH, Bordoy AE, Martró E, Quesada MD, Pérez-Vázquez M, Guerrero-Murillo M, Tiburcio A, Navarro M, Castellà L, Sopena N, Casas I, Saludes V, Giménez M, Cardona PJ. Evaluation of Fourier Transform Infrared Spectroscopy as a First-Line Typing Tool for the Identification of Extended-Spectrum β-Lactamase-Producing Klebsiella pneumoniae Outbreaks in the Hospital Setting. Front Microbiol 2022; 13:897161. [PMID: 35756036 PMCID: PMC9218594 DOI: 10.3389/fmicb.2022.897161] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/19/2022] [Indexed: 12/20/2022] Open
Abstract
Early detection of pathogen cross-transmission events and environmental reservoirs is needed to control derived nosocomial outbreaks. Whole-genome sequencing (WGS) is considered the gold standard for outbreak confirmation, but, in most cases, it is time-consuming and has elevated costs. Consequently, the timely incorporation of WGS results to conventional epidemiology (CE) investigations for rapid outbreak detection is scarce. Fourier transform infrared spectroscopy (FTIR) is a rapid technique that establishes similarity among bacteria based on the comparison of infrared light absorption patterns of bacterial polysaccharides and has been used as a typing tool in recent studies. The aim of the present study was to evaluate the performance of the FTIR as a first-line typing tool for the identification of extended-spectrum β-lactamase-producing Klebsiella pneumoniae (ESBL-Kp) outbreaks in the hospital setting in comparison with CE investigations using WGS as the gold standard method. Sixty-three isolates of ESBL-Kp collected from 2018 to 2021 and classified according to CE were typed by both FTIR and WGS. Concordance was measured using the Adjusted Rand index (AR) and the Adjusted Wallace coefficient (AW) for both CE and FTIR clustering considering WGS as the reference method. Both AR and AW were significantly higher for FTIR clustering than CE clustering (0.475 vs. 0.134, p = 0.01, and 0.521 vs. 0.134, p = 0.009, respectively). Accordingly, FTIR inferred more true clustering relationships than CE (38/42 vs. 24/42, p = 0.001). However, a similar proportion of genomic singletons was detected by both FTIR and CE (13/21 vs. 12/21, p = 1). This study demonstrates the utility of the FTIR method as a quick, low-cost, first-line tool for the detection of ESBL-Kp outbreaks, while WGS analyses are being performed for outbreak confirmation and isolate characterization. Thus, clinical microbiology laboratories would benefit from integrating the FTIR method into CE investigations for infection control measures in the hospital setting.
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Affiliation(s)
- Jun Hao Wang-Wang
- Microbiology Department, Laboratori Clínic Metropolitana Nord, Germans Trias i Pujol University Hospital, Badalona, Spain.,Genetics and Microbiology Department, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Antoni E Bordoy
- Microbiology Department, Laboratori Clínic Metropolitana Nord, Germans Trias i Pujol University Hospital, Badalona, Spain.,Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
| | - Elisa Martró
- Microbiology Department, Laboratori Clínic Metropolitana Nord, Germans Trias i Pujol University Hospital, Badalona, Spain.,Genetics and Microbiology Department, Universitat Autònoma de Barcelona, Bellaterra, Spain.,Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain.,Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - María Dolores Quesada
- Microbiology Department, Laboratori Clínic Metropolitana Nord, Germans Trias i Pujol University Hospital, Badalona, Spain.,Genetics and Microbiology Department, Universitat Autònoma de Barcelona, Bellaterra, Spain.,Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - María Pérez-Vázquez
- Reference and Research Laboratory for Antibiotic Resistance and Health Care Infections, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Madrid, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Mercedes Guerrero-Murillo
- Clinical Genomics Research Unit, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, Badalona, Spain.,Clinical Genomics Unit, Clinical Genetics Service, Laboratori Clínic Metropolitana Nord, Germans Trias i Pujol University Hospital, Can Ruti Campus, Badalona, Spain
| | - Andrea Tiburcio
- Microbiology Department, Laboratori Clínic Metropolitana Nord, Germans Trias i Pujol University Hospital, Badalona, Spain
| | - Marina Navarro
- Microbiology Department, Laboratori Clínic Metropolitana Nord, Germans Trias i Pujol University Hospital, Badalona, Spain
| | - Laia Castellà
- Enfermería Control de Infección, Dirección Enfermería, Germans Trias i Pujol University Hospital, Badalona, Spain
| | - Nieves Sopena
- Infectious Diseases Department, Germans Trias i Pujol University Hospital, Badalona, Spain
| | - Irma Casas
- Preventive Medicine Department, Germans Trias i Pujol University Hospital, Badalona, Spain
| | - Verónica Saludes
- Microbiology Department, Laboratori Clínic Metropolitana Nord, Germans Trias i Pujol University Hospital, Badalona, Spain.,Genetics and Microbiology Department, Universitat Autònoma de Barcelona, Bellaterra, Spain.,Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain.,Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Montserrat Giménez
- Microbiology Department, Laboratori Clínic Metropolitana Nord, Germans Trias i Pujol University Hospital, Badalona, Spain.,Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Pere-Joan Cardona
- Microbiology Department, Laboratori Clínic Metropolitana Nord, Germans Trias i Pujol University Hospital, Badalona, Spain.,Genetics and Microbiology Department, Universitat Autònoma de Barcelona, Bellaterra, Spain.,Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
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22
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Validation of Fourier Transform Infrared Spectroscopy for Serotyping of Streptococcus pneumoniae. J Clin Microbiol 2022; 60:e0032522. [PMID: 35699436 PMCID: PMC9297836 DOI: 10.1128/jcm.00325-22] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Fourier transform infrared (FT-IR) spectroscopy (IR Biotyper; Bruker) allows highly discriminatory fingerprinting of closely related bacterial strains. In this study, FT-IR spectroscopy-based capsular typing of Streptococcus pneumoniae was validated as a rapid, cost-effective, and medium-throughput alternative to the classical phenotypic techniques. A training set of 233 strains was defined, comprising 34 different serotypes and including all 24 vaccine types (VTs) and 10 non-vaccine types (NVTs). The acquired spectra were used to (i) create a dendrogram where strains clustered together according to their serotypes and (ii) train an artificial neural network (ANN) model to predict unknown pneumococcal serotypes. During validation using 153 additional strains, we reached 98.0% accuracy for determining serotypes represented in the training set. Next, the performance of the IR Biotyper was assessed using 124 strains representing 59 non-training set serotypes. In this setting, 42 of 59 serotypes (71.1%) could be accurately categorized as being non-training set serotypes. Furthermore, it was observed that comparability of spectra was affected by the source of the Columbia medium used to grow the pneumococci and that this complicated the robustness and standardization potential of FT-IR spectroscopy. A rigorous laboratory workflow in combination with specific ANN models that account for environmental noise parameters can be applied to overcome this issue in the near future. The IR Biotyper has the potential to be used as a fast, cost-effective, and accurate phenotypic serotyping tool for S. pneumoniae.
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23
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Analysis of four carbapenem-resistant Acinetobacter baumannii outbreaks using Fourier-transform infrared spectroscopy. Infect Control Hosp Epidemiol 2022:1-3. [PMID: 35535742 DOI: 10.1017/ice.2022.109] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We used Fourier-transform infrared (FTIR) spectroscopy to analyze 4 carbapenem-resistant Acinetobacter baumannii outbreaks. FTIR distinguished between isolates from different hospitals and uncovered the relatedness between isolates from acute-care hospitals and a post-acute-care hospital. Using higher cutoffs reveals more distant relationships and lower cutoffs support analyses of recent events.
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24
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Pai S, Hebbar A, Selvaraj S. A critical look at challenges and future scopes of bioactive compounds and their incorporations in the food, energy, and pharmaceutical sector. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:35518-35541. [PMID: 35233673 PMCID: PMC9079019 DOI: 10.1007/s11356-022-19423-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 02/21/2022] [Indexed: 05/27/2023]
Abstract
Bioactive compounds refer to secondary metabolites extracted from plants, fungi, microbes, or animals. Besides having pharmacological or toxicological effects on organisms leading to utilization in food and pharmaceutical industries, the discovery of novel properties of such compounds has led to the diversification of their applications, ranging from cosmetics and functionalized biomaterials to bioremediation and alternate fuels. Conventional time-consuming and solvent-intensive methods of extraction are increasingly being replaced by green solvents such as ionic liquids, supercritical fluids, and deep eutectic solvents, as well as non-conventional methods of extraction assisted by microwaves, pulse electric fields, enzymes, ultrasound, or pressure. These methods, along with advances in characterization and optimization strategies, have boosted the commercial viability of extraction especially from agrowastes and organic residues, promoting a sustainable circular economy. Further development of microfluidics, optimization models, nanoencapsulation, and metabolic engineering are expected to overcome certain limitations that restrict the growth of this field, in the context of improving screening, extraction, and economy of processes, as well as retaining biodiversity and enhancing the stability and functionality of such compounds. This review is a compilation of the various extraction and characterization methods employed for bioactive compounds and covers major applications in food, pharmacy, chemicals, energy, and bioremediation. Major limitations and scope of improvement are also discussed.
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Affiliation(s)
- Sanidhya Pai
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education (MAHE), Manipal, 576104, India
| | - Akshatha Hebbar
- Department of Chemical Engineering, Manipal Institute of Technology, Manipal Academy of Higher Education (MAHE), Manipal, 576104, India
| | - Subbalaxmi Selvaraj
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education (MAHE), Manipal, 576104, India.
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25
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Su W, Wu L, Liang Q, Lin X, Xu X, Yu S, Lin Y, Zhou J, Fu Y, Gao X, Zhang B, Li L, Li D, Yin Y, Song G. Extraction Optimization, Structural Characterization, and Anti-Hepatoma Activity of Acidic Polysaccharides From Scutellaria barbata D. Don. Front Pharmacol 2022; 13:827782. [PMID: 35444545 PMCID: PMC9014130 DOI: 10.3389/fphar.2022.827782] [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: 12/02/2021] [Accepted: 03/07/2022] [Indexed: 11/13/2022] Open
Abstract
The Chinese medicinal herb Scutellaria barbata D. Don has antitumour effects and is used to treat liver cancer in the clinic. S. barbata polysaccharide (SBP), one of the main active components extracted from S. barbata D. Don, exhibits antitumour activity. However, there is still a lack of research on the extraction optimization, structural characterization, and anti-hepatoma activity of acidic polysaccharides from S. barbata D. Don. In this study, the optimal extraction conditions for SBP were determined by response surface methodology (RSM): the material-liquid ratio was 1:25, the extraction time was 2 h, and the extraction temperature was 90°C. Under these conditions, the average extraction efficiency was 3.85 ± 0.13%. Two water-soluble polysaccharides were isolated from S. barbata D. Don, namely, SBP-1A and SBP-2A, these homogeneous acidic polysaccharide components with average molecular weights of 1.15 × 105 Da and 1.4 × 105 Da, respectively, were obtained at high purity. The results showed that the monosaccharide constituents of the two components were fucose, galactosamine hydrochloride, rhamnose, arabinose, glucosamine hydrochloride, galactose, glucose, xylose, and mannose; the molar ratio of these constituents in SBP-1A was 0.6:0.3:0.6:30.6:3.3:38.4:16.1:8:1.4, and that in SBP-2A was 0.6:0.5:0.8:36.3:4.4:42.7:9.2:3.6:0.7. In addition, SBP-1A and SBP-2A contained uronic acid and β-glucan, and the residue on the polysaccharide was mainly pyranose. The in vitro results showed that the anti-hepatoma activity of SBP-2A was better than that of SBP-1A and SBP. In addition, SBP-2A significantly enhanced HepG2 cell death, as cell viability was decreased, and SBP-2A induced HepG2 cell apoptosis and blocked the G1 phase. This phenomenon was coupled with the upregulated expression of P53 and Bax/Bcl-2 ratio, as well as the downregulated expression of the cell cycle-regulating protein cyclinD1, CDK4, and Bcl-2 in this study. Further analysis showed that 50 mg/kg SBP-2A inhibited the tumour growth in H22 tumour-bearing mice, with an average inhibition rate of 40.33%. Taken together, SBP-2A, isolated and purified from S. barbata showed good antitumour activity in vivo and in vitro, and SBP-2A may be a candidate drug for further evaluation in cancer prevention. This study provides insight for further research on the molecular mechanism of the anti-hepatoma activity of S. barbata polysaccharide.
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Affiliation(s)
- Wenwen Su
- Department of Biochemistry and Molecular Biology, Mudanjiang Medical University, Mudanjiang, China
| | - Leilei Wu
- Collage of Pharmacology, Mudanjiang Medical University, Mudanjiang, China
| | - Qichao Liang
- Collage of Pharmacology, Mudanjiang Medical University, Mudanjiang, China
| | - Xiaoyue Lin
- The First Clinical College of Medicine, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Xiaoyi Xu
- The First Clinical College of Medicine, Mudanjiang Medical University, Mudanjiang, China
| | - Shikai Yu
- Collage of Basic Medicine, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Yitong Lin
- Department of Biochemistry and Molecular Biology, Mudanjiang Medical University, Mudanjiang, China
| | - Jiadong Zhou
- Collage of Basic Medicine, Mudanjiang Medical University, Mudanjiang, China
| | - Yang Fu
- Department of Biochemistry and Molecular Biology, Mudanjiang Medical University, Mudanjiang, China
| | - Xiaoyan Gao
- Department of Biochemistry and Molecular Biology, Mudanjiang Medical University, Mudanjiang, China
| | - Bo Zhang
- Department of Oncology, Mudanjiang Cancer Hospital, Mudanjiang, China
| | - Li Li
- Collage of Basic Medicine, Mudanjiang Medical University, Mudanjiang, China
| | - Dan Li
- Department of Biochemistry and Molecular Biology, Mudanjiang Medical University, Mudanjiang, China
| | - Yongkui Yin
- College of Life Sciences, Mudanjiang Medical University, Mudanjiang, China
| | - Gaochen Song
- Department of Biochemistry and Molecular Biology, Mudanjiang Medical University, Mudanjiang, China
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26
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Rebrosova K, Samek O, Kizovsky M, Bernatova S, Hola V, Ruzicka F. Raman Spectroscopy-A Novel Method for Identification and Characterization of Microbes on a Single-Cell Level in Clinical Settings. Front Cell Infect Microbiol 2022; 12:866463. [PMID: 35531343 PMCID: PMC9072635 DOI: 10.3389/fcimb.2022.866463] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/07/2022] [Indexed: 12/02/2022] Open
Abstract
Rapid and accurate identification of pathogens causing infections is one of the biggest challenges in medicine. Timely identification of causative agents and their antimicrobial resistance profile can significantly improve the management of infection, lower costs for healthcare, mitigate ever-growing antimicrobial resistance and in many cases, save lives. Raman spectroscopy was shown to be a useful-quick, non-invasive, and non-destructive -tool for identifying microbes from solid and liquid media. Modifications of Raman spectroscopy and/or pretreatment of samples allow single-cell analyses and identification of microbes from various samples. It was shown that those non-culture-based approaches could also detect antimicrobial resistance. Moreover, recent studies suggest that a combination of Raman spectroscopy with optical tweezers has the potential to identify microbes directly from human body fluids. This review aims to summarize recent advances in non-culture-based approaches of identification of microbes and their virulence factors, including antimicrobial resistance, using methods based on Raman spectroscopy in the context of possible use in the future point-of-care diagnostic process.
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Affiliation(s)
- Katarina Rebrosova
- Department of Microbiology, Faculty of Medicine of Masaryk University and St. Anne’s University Hospital, Brno, Czechia
| | - Ota Samek
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czechia
| | - Martin Kizovsky
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czechia
| | - Silvie Bernatova
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czechia
| | - Veronika Hola
- Department of Microbiology, Faculty of Medicine of Masaryk University and St. Anne’s University Hospital, Brno, Czechia
| | - Filip Ruzicka
- Department of Microbiology, Faculty of Medicine of Masaryk University and St. Anne’s University Hospital, Brno, Czechia
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27
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Theakstone A, Brennan PM, Ashton K, Czeiter E, Jenkinson M, Syed K, Reed M, Baker M. Vibrational spectroscopy for the triage of traumatic brain injury CT priority and hospital admissions. J Neurotrauma 2022; 39:773-783. [PMID: 35236121 PMCID: PMC9225408 DOI: 10.1089/neu.2021.0410] [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] [Indexed: 11/12/2022] Open
Abstract
Computed Tomogram (CT) brain imaging is routinely used to support clinical decision-making in patients with traumatic brain injury (TBI). However, only 7% of scans demonstrate evidence of TBI. The other 93% of scans contribute a significant cost to the healthcare system and a radiation risk to patients. There may be better strategies to identify which patients, particularly those with mild TBI, are at risk of deterioration and require hospital admission. We introduce a blood serum liquid biopsy that utilises attenuated total reflectance (ATR)-Fourier transform infrared (FTIR) spectroscopy with machine learning algorithms as a decision-making tool to identify which mild TBI patients will most benefit from CT brain imaging. Serum samples were obtained from (n=298) patients who had acquired a TBI and were enrolled in CENTER-TBI, and from asymptomatic control patients (n=87). Injury patients (all severities) were stratified against non-injury controls. The mild TBI cohort was further examined by stratifying those who had at least one CT abnormality against those who had no CT abnormalities. The test performed exceptionally well in classifications of mild injury patients versus non-injury controls (sensitivity = 96.4% and specificity = 98.0%) and also provided a sensitivity of 80.2% when stratifying mild patients with at least one CT abnormality against those without. The results provided illustrate the test ability to identify 4 out of every 5 CT abnormalities and shows great promise to be introduced as a triage tool for CT priority in mild TBI patients.
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Affiliation(s)
- Ashton Theakstone
- University of Strathclyde, 3527, 99 George Street, Glasgow, United Kingdom of Great Britain and Northern Ireland, G1 1RD;
| | - Paul M Brennan
- The University of Edinburgh Centre for Clinical Brain Sciences, 439257, Translational Neurosurgery, Edinburgh, Edinburgh, United Kingdom of Great Britain and Northern Ireland;
| | - Katherine Ashton
- Lancashire Teaching Hospitals NHS Foundation Trust, 6724, Neuropathology, Preston, Lancashire, United Kingdom of Great Britain and Northern Ireland;
| | - Endre Czeiter
- University of Pecs Medical School, 37657, Department of Neurosurgery, Pecs, Hungary.,University of Pecs, 37656, Neurotrauma Research Group, Szentágothai Research Centre, Pecs, Hungary.,University of Pecs, 37656, MTA-PTE Clinical Neuroscience MR Research Group, Pecs, Hungary;
| | - Michael Jenkinson
- The Walton Centre NHS Foundation Trust, 195157, Liverpool, Liverpool, United Kingdom of Great Britain and Northern Ireland.,University of Liverpool, 4591, Department of Pharmacology & Therapeutics, Liverpool, Merseyside, United Kingdom of Great Britain and Northern Ireland;
| | - Khaja Syed
- The Walton Centre NHS Foundation Trust, 195157, Liverpool, Liverpool, United Kingdom of Great Britain and Northern Ireland;
| | - Matthew Reed
- Royal Infirmary of Edinburgh, 59843, Department of Emergency Medicine, Edinburgh, Edinburgh, United Kingdom of Great Britain and Northern Ireland;
| | - Matthew Baker
- Dxcover Limited, Glasgow, United Kingdom of Great Britain and Northern Ireland;
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28
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Abu-Aqil G, Sharaha U, Suleiman M, Riesenberg K, Lapidot I, Salman A, Huleihel M. Culture-independent susceptibility determination of E. coli isolated directly from patients’ urine using FTIR and machine-learning. Analyst 2022; 147:4815-4823. [DOI: 10.1039/d2an01253g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
One of the most common human bacterial infections is the urinary tract infection (UTI).
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Affiliation(s)
- George Abu-Aqil
- Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Uraib Sharaha
- Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Manal Suleiman
- Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Klaris Riesenberg
- Director of Microbiology Laboratory, Soroka University Medical Center, Beer-Sheva 84105, Israel
| | - Itshak Lapidot
- Department of Electrical and Electronics Engineering, ACLP-Afeka Center for Language Processing, Afeka Tel-Aviv Academic College of Engineering, Tel-Aviv 69107, Israel
| | - Ahmad Salman
- Department of Physics, SCE - Shamoon College of Engineering, Beer-Sheva 84100, Israel
| | - Mahmoud Huleihel
- Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
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29
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Fourier Transform Infrared Spectroscopy for Typing Burkholderia cenocepacia ET12 Isolates. Microbiol Spectr 2021; 9:e0183121. [PMID: 34878338 PMCID: PMC8653821 DOI: 10.1128/spectrum.01831-21] [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] [Indexed: 11/23/2022] Open
Abstract
The IR Biotyper and matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) using ClinProTools software (MALDI-TOF MS–ClinProTools) are two novel typing methods that rely on the analysis of carbohydrate and peptide residues in intact bacterial cells. These two methods have shown promising results in the rapid and accurate typing of bacteria. In this study, we evaluated these novel typing methods in comparison with genotypic typing for cluster analysis of Burkholderia cenocepacia epidemic strain ET12, isolated from adult cystic fibrosis patients. Sixty-six isolates of B. cenocepacia were used in this study, 35 of which were identified as the ET12 strain and 31 as non-ET12 strains by repetitive-element PCR (rep-PCR). Twelve isolates were used for the creation of typing models using IR Biotyper and MALDI-TOF MS–ClinProTools, and 54 isolates were used for external validation of the typing models. The IR Biotyper linear discriminant analysis (LDA) model had a diagnostic sensitivity of 84.6% for typing the epidemic strain, ET12. At a cutoff of 70%, MALDI-TOF MS–ClinProTools had 87.5% diagnostic sensitivity in detecting the ET12 strain (P = 1.00). Both methods had a diagnostic specificity of ≥80% for detecting the ET12 strain. In conclusion, IR Biotyper and MALDI-TOF MS–ClinProTools offer rapid typing using proteomics and analysis of small cellular molecules with a low running cost. Our pilot study showed suboptimal accuracy of both methods for typing outbreak strains of B. cenocepacia. Extending the spectral region analyzed by the IR Biotyper can improve the accuracy and has the potential of improving the generalizability of this technique for typing other organisms. IMPORTANCE Respiratory infections due to Burkholderia cenocepacia, particularly the ET12 epidemic strain, are considered sentinel events for persons with cystic fibrosis, as they are often associated with person-to-person transmission and accelerated decline in lung function and early mortality. Current typing methods are generally only available at reference centers, with long turn-around-times, which can affect the identification of outbreaks and critical patient triage. This pilot study aims to add to the growing literature illustrating the potential utility of Fourier transform infrared spectroscopy (FTIR), a novel rapid method, for the successful typing of clinically significant bacteria. In this study, we evaluated its utility to discriminate between the ET12 clone and non-ET12 isolates of B. cenocepacia and compared it to proteomics cluster analysis using MALDI-TOF MS and ClinProTools software. Both methods had encouraging but suboptimal accuracy (≥85% sensitivity and ≥83% specificity), which will likely be improved by extending the spectral region analyzed by the IR Biotyper with updated software.
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30
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Mullié C, Lemonnier D, Adjidé CC, Maizel J, Mismacque G, Cappe A, Carles T, Pierson-Marchandise M, Zerbib Y. Nosocomial outbreak of monoclonal VIM carbapenemase-producing Enterobacter cloacae complex in an intensive care unit during the COVID-19 pandemic: an integrated approach. J Hosp Infect 2021; 120:48-56. [PMID: 34861315 PMCID: PMC8631059 DOI: 10.1016/j.jhin.2021.11.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 11/24/2021] [Accepted: 11/24/2021] [Indexed: 01/18/2023]
Abstract
Background An outbreak of VIM carbapenemase-expressing Enterobacter cloacae complex occurred between March and October 2020 in an intensive care unit (ICU) of a tertiary care and teaching hospital in France. At the same time, the hospital was facing the COVID-19 first wave. Aim To describe the management of an outbreak caused by a VIM-producing Enterobacter cloacae complex strain during the COVID-19 pandemic in an ICU and to show the importance of an integrated approach. Methods A multi-focal investigation was conducted including descriptive and molecular epidemiology, environmental screening, and assessment of infection prevention and control measures. Findings A total of 14 cases were identified in this outbreak with a high attributable mortality rate (85.7%). The outbreak management was coordinated by a crisis cell, and involved the implementation of multi-disciplinary actions such as: enhanced hygiene measures, microbiological and molecular analysis of patients and environmental E. cloacae complex strains, and simulation-based teaching. All 23 E. cloacae complex strains isolated from patients and environment samples belonged to multi-locus sequence type ST78 and carried bla-VIM4 gene. Using Fourier transform infrared spectroscopy, all but two isolates were also found to belong to a single cluster. Although the source of this outbreak could not be pinpointed, the spread of the strain was controlled thanks to this multi-focal approach and multi-disciplinary implementation. Conclusion This investigation highlighted the usefulness of Fourier transform infra-red spectroscopy in the rapid typing of outbreak strains as well as the importance of an integrated approach to successfully fight against multidrug-resistant micro-organism dissemination and healthcare-associated infections.
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Affiliation(s)
- C Mullié
- Laboratoire Hygiène Risque Biologique & Environnement, CHU Amiens Picardie, Amiens, France; Laboratoire AGIR UR UPJV 4294, Université de Picardie Jules Verne, Amiens, France.
| | - D Lemonnier
- Unité d'Hygiène et d'Epidémiologie Hospitalière, CHU Amiens Picardie, Amiens, France.
| | - C C Adjidé
- Laboratoire Hygiène Risque Biologique & Environnement, CHU Amiens Picardie, Amiens, France
| | - J Maizel
- Service de Médecine Intensive et Réanimation, CHU Amiens Picardie, Amiens, France
| | - G Mismacque
- Unité d'Hygiène et d'Epidémiologie Hospitalière, CHU Amiens Picardie, Amiens, France
| | - A Cappe
- Département de Pharmacie Clinique, CHU Amiens Picardie, Amiens, France
| | - T Carles
- Département de Pharmacie Clinique, CHU Amiens Picardie, Amiens, France
| | - M Pierson-Marchandise
- Service Prévention, Evaluations, Vigilances et Amélioration des Pratiques, CHU Amiens Picardie, Amiens, France
| | - Y Zerbib
- Service de Médecine Intensive et Réanimation, CHU Amiens Picardie, Amiens, France
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31
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Salim YS, Rashid NA, Halim SIA, Chan CH, Ong CH, Harun MK. Fourier transform infrared (
FTIR)
authentication and batch‐to‐batch consistency for different types of paints using benchtop and handheld
FTIR
spectrophotometers for oil and gas industry. POLYM ENG SCI 2021. [DOI: 10.1002/pen.25746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Yoga Sugama Salim
- Faculty of Applied Sciences Universiti Teknologi MARA Shah Alam Selangor Malaysia
| | | | | | - Chin Han Chan
- Faculty of Applied Sciences Universiti Teknologi MARA Shah Alam Selangor Malaysia
| | - Chong Hup Ong
- Norimax Sdn Bhd Taman Perindustrian Puchong Puchong Selangor Malaysia
| | - Mohamad Kamal Harun
- Faculty of Applied Sciences Universiti Teknologi MARA Shah Alam Selangor Malaysia
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32
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Figoli CB, Garcea M, Bisioli C, Tafintseva V, Shapaval V, Gómez Peña M, Gibbons L, Althabe F, Yantorno OM, Horton M, Schmitt J, Lasch P, Kohler A, Bosch A. A robust metabolomics approach for the evaluation of human embryos from in vitro fertilization. Analyst 2021; 146:6156-6169. [PMID: 34515271 DOI: 10.1039/d1an01191j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The identification of the most competent embryos for transfer to the uterus constitutes the main challenge of in vitro fertilization (IVF). We established a metabolomic-based approach by applying Fourier transform infrared (FTIR) spectroscopy on 130 samples of 3-day embryo culture supernatants from 26 embryos that implanted and 104 embryos that failed. On examining the internal structure of the data by unsupervised multivariate analysis, we found that the supernatant spectra of nonimplanted embryos constituted a highly heterogeneous group. Whereas ∼40% of these supernatants were spectroscopically indistinguishable from those of successfully implanted embryos, ∼60% exhibited diverse, heterogeneous metabolic fingerprints. This observation proved to be the direct result of pregnancy's multifactorial nature, involving both intrinsic embryonic traits and external characteristics. Our data analysis strategy thus involved one-class modelling techniques employing soft independent modelling of class analogy that identified deviant fingerprints as unsuitable for implantation. From these findings, we could develop a noninvasive Fourier-transform-infrared-spectroscopy-based approach that represents a shift in the fundamental paradigm for data modelling applied in assisted-fertilization technologies.
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Affiliation(s)
- Cecilia Beatriz Figoli
- Laboratorio de Bioespectrosocpia, CINDEFI-CONICET, CCT La Plata, Facultad de Ciencias Exactas, UNLP, 1900 La Plata, Argentina.
| | - Marcelo Garcea
- PREGNA Medicina Reproductiva, C1425 AYV Ciudad Autónoma de Buenos Aires, Argentina
| | - Claudio Bisioli
- PREGNA Medicina Reproductiva, C1425 AYV Ciudad Autónoma de Buenos Aires, Argentina
| | - Valeria Tafintseva
- Faculty of Science and Technology, Norwegian University of Life Sciences, 1432 Ås, Norway.
| | - Volha Shapaval
- Faculty of Science and Technology, Norwegian University of Life Sciences, 1432 Ås, Norway.
| | - Mariana Gómez Peña
- PREGNA Medicina Reproductiva, C1425 AYV Ciudad Autónoma de Buenos Aires, Argentina
| | - Luz Gibbons
- IECS, Instituto de Efectividad Clínica y Sanitaria, C1414 Ciudad Autónoma de Buenos Aires, Argentina
| | - Fernando Althabe
- IECS, Instituto de Efectividad Clínica y Sanitaria, C1414 Ciudad Autónoma de Buenos Aires, Argentina
| | - Osvaldo Miguel Yantorno
- Laboratorio de Bioespectrosocpia, CINDEFI-CONICET, CCT La Plata, Facultad de Ciencias Exactas, UNLP, 1900 La Plata, Argentina.
| | - Marcos Horton
- PREGNA Medicina Reproductiva, C1425 AYV Ciudad Autónoma de Buenos Aires, Argentina
| | | | - Peter Lasch
- Centre for Biological Threats and Special Pathogens (ZBS) Proteomics and Spectroscopy Unit, Robert Koch-Institut, 13353 Berlin, Germany
| | - Achim Kohler
- Faculty of Science and Technology, Norwegian University of Life Sciences, 1432 Ås, Norway.
| | - Alejandra Bosch
- Laboratorio de Bioespectrosocpia, CINDEFI-CONICET, CCT La Plata, Facultad de Ciencias Exactas, UNLP, 1900 La Plata, Argentina.
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Wijesinghe HGS, Hare DJ, Mohamed A, Shah AK, Harris PNA, Hill MM. Detecting antimicrobial resistance in Escherichia coli using benchtop attenuated total reflectance-Fourier transform infrared spectroscopy and machine learning. Analyst 2021; 146:6211-6219. [PMID: 34522918 DOI: 10.1039/d1an00546d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The widespread dissemination of resistance to third-generation cephalosporins in the Enterobacterales through the production of extended-spectrum β-lactamase (ESBL) is considered a critical global crisis requiring urgent attention of clinicians and scientists alike. Rapid diagnostic methods that can identify microbial resistance profiles closer to the point of care are crucial to minimize the overuse of antimicrobial agents and improve patient outcomes. Although Fourier transform infrared (FTIR) microscopy has shown promise in distinguishing between bacterial species, the high cost and technical requirements of the IR microscope may limit broad clinical use. To address the practical needs of a clinical microbiology laboratory, here, we examine the ability of a lower cost portable benchtop attenuated total reflectance (ATR)-FTIR spectrometer to achieve antimicrobial resistance detection, using a simple, clinically aligned sampling protocol. The technical reproducibility was confirmed through multi-day analysis of an Escherichia coli type strain, which serves as quality control. We generated a dataset of 100 E. coli clinical bloodstream isolates with 63 ceftriaxone resistant blaCTX-M ESBL gene variant strains and developed a classifier for blaCTX-M genotype detection. After assessing 35 machine learning methods using the training set (n = 71), four methods were further optimised, and the best performing method was evaluated using the held-out testing set (n = 29). A tuned support vector machine model with a polynomial kernel, using the 700-1500 cm-1 range achieved a sensitivity of 89.2%, and specificity of 66.7% for detecting blaCTX-M in independent testing, approaching the reported performance of FTIR microscopy. With further algorithm improvement, these data suggest the potential deployment of a portable FTIR spectrometer as a rapid antimicrobial susceptibility prediction platform to enable the efficient use of antimicrobials.
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Affiliation(s)
- Hewa G S Wijesinghe
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, QLD, 4006, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4067, Australia
| | - Dominic J Hare
- Atomic Medicine Initiative, University of Technology Sydney, Broadway, NSW, 2007, Australia
| | - Ahmed Mohamed
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, QLD, 4006, Australia.
| | - Alok K Shah
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, QLD, 4006, Australia.
| | - Patrick N A Harris
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, QLD, 4006, Australia.,Herston Infectious Disease Institute, Royal Brisbane & Women's Hospital, Herston, QLD, 4029, Australia.,Central Microbiology, Pathology Queensland, Royal Brisbane & Women's Hospital, Herston, QLD, 4029, Australia
| | - Michelle M Hill
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, QLD, 4006, Australia.,QIMR Berghofer Medical Research Institute, Herston, Brisbane, QLD, 4006, Australia.
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Theakstone AG, Brennan PM, Jenkinson MD, Mills SJ, Syed K, Rinaldi C, Xu Y, Goodacre R, Butler HJ, Palmer DS, Smith BR, Baker MJ. Rapid Spectroscopic Liquid Biopsy for the Universal Detection of Brain Tumours. Cancers (Basel) 2021; 13:cancers13153851. [PMID: 34359751 PMCID: PMC8345395 DOI: 10.3390/cancers13153851] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/22/2021] [Accepted: 07/29/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Due to the non-specific symptoms of brain cancer (e.g., headaches or memory changes), gliomas will often remain undetected until they are larger or at a higher grade, reducing the patient’s likelihood of a good clinical outcome. Earlier detection and diagnosis of brain tumours is vital to improve patient outcomes, leading to safer surgeries and earlier treatments. A liquid biopsy for brain tumour would prove revolutionary however in order to detect disease earlier the liquid biopsy needs to be able to detect smaller tumours; and current liquid biopsies perform worse when detecting smaller or earlier stage tumours. Here, for the first time, we confirm the applicability of a validated spectroscopic liquid biopsy approach to detect both small and low-grade gliomas proving that the spectroscopic liquid biopsy approach is insensitive to tumour volume unlike other liquid biopsies. Abstract Background: To support the early detection and diagnosis of brain tumours we have developed a rapid, cost-effective and easy to use spectroscopic liquid biopsy based on the absorbance of infrared radiation. We have previously reported highly sensitive results of our approach which can discriminate patients with a recent brain tumour diagnosis and asymptomatic controls. Other liquid biopsy approaches (e.g., based on tumour genetic material) report a lower classification accuracy for early-stage tumours. In this manuscript we present an investigation into the link between brain tumour volume and liquid biopsy test performance. Methods: In a cohort of 177 patients (90 patients with high-grade glioma (glioblastoma (GBM) or anaplastic astrocytoma), or low-grade glioma (astrocytoma, oligoastrocytoma and oligodendroglioma)) tumour volumes were calculated from magnetic resonance imaging (MRI) investigations and patients were split into two groups depending on MRI parameters (T1 with contrast enhancement or T2/FLAIR (fluid-attenuated inversion recovery)). Using attenuated total reflection (ATR)-Fourier transform infrared (FTIR) spectroscopy coupled with supervised learning methods and machine learning algorithms, 90 tumour patients were stratified against 87 control patients who displayed no symptomatic indications of cancer, and were classified as either glioma or non-glioma. Results: Sensitivities, specificities and balanced accuracies were all greater than 88%, the area under the curve (AUC) was 0.98, and cancer patients with tumour volumes as small as 0.2 cm3 were correctly identified. Conclusions: Our spectroscopic liquid biopsy approach can identify gliomas that are both small and low-grade showing great promise for deployment of this technique for early detection and diagnosis.
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Affiliation(s)
- Ashton G. Theakstone
- Technology and Innovation Centre, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1RD, UK;
- Correspondence: (A.G.T.); (M.J.B.); Tel.: +44-141-444-7343 (A.G.T.); +44-141-548-4700 (M.J.B.)
| | - Paul M. Brennan
- Translational Neurosurgery, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK;
| | - Michael D. Jenkinson
- The Walton Centre NHS Foundation Trust, Lower Lane, Liverpool L9 7LJ, UK; (M.D.J.); (S.J.M.); (K.S.)
- Department of Pharmacology & Therapeutics, Institute of System, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Samantha J. Mills
- The Walton Centre NHS Foundation Trust, Lower Lane, Liverpool L9 7LJ, UK; (M.D.J.); (S.J.M.); (K.S.)
| | - Khaja Syed
- The Walton Centre NHS Foundation Trust, Lower Lane, Liverpool L9 7LJ, UK; (M.D.J.); (S.J.M.); (K.S.)
| | - Christopher Rinaldi
- Technology and Innovation Centre, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1RD, UK;
| | - Yun Xu
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK; (Y.X.); (R.G.)
| | - Royston Goodacre
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK; (Y.X.); (R.G.)
| | - Holly J. Butler
- Dxcover Limited, 204 George Street, Glasgow G1 1XW, UK; (H.J.B.); (D.S.P.); (B.R.S.)
| | - David S. Palmer
- Dxcover Limited, 204 George Street, Glasgow G1 1XW, UK; (H.J.B.); (D.S.P.); (B.R.S.)
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, Glasgow G1 1XL, UK
| | - Benjamin R. Smith
- Dxcover Limited, 204 George Street, Glasgow G1 1XW, UK; (H.J.B.); (D.S.P.); (B.R.S.)
| | - Matthew J. Baker
- Dxcover Limited, 204 George Street, Glasgow G1 1XW, UK; (H.J.B.); (D.S.P.); (B.R.S.)
- Correspondence: (A.G.T.); (M.J.B.); Tel.: +44-141-444-7343 (A.G.T.); +44-141-548-4700 (M.J.B.)
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Ribeiro S, Mourão J, Novais Â, Campos J, Peixe L, Antunes P. From farm to fork: Colistin voluntary withdrawal in Portuguese farms reflected in decreasing occurrence of mcr-1-carrying Enterobacteriaceae from chicken meat. Environ Microbiol 2021; 23:7563-7577. [PMID: 34327794 DOI: 10.1111/1462-2920.15689] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 07/27/2021] [Indexed: 11/27/2022]
Abstract
Expansion of mcr-carrying Enterobacteriaceae (MCR-E) is a well-recognized problem affecting animals, humans and the environment. Ongoing global control actions involve colistin restrictions among food-animal production, but their impact on poultry-derived products is largely unknown, justifying comprehensive farm-to-fork studies. Occurrence of MCR-E among 53 chicken-meat batches supplied from 29 Portuguese farms shortly after colistin withdrawal was evaluated. Strains (FT-IR/MLST/WGS), mcr plasmids and their adaptive features were characterized by cultural, molecular and genomic approaches. We found high rates of chicken-meat batches (80%-100% - 4 months; 12% - the last month) with multiple MDR + mcr-1-carrying Escherichia coli (Ec-including ST117 and ST648-Cplx) and Klebsiella pneumoniae (Kp-ST147-O5:K35) clones, some of them persisting over time. The mcr-1 was located in the chromosome (Ec-ST297/16-farms) or dispersed IncX4 (Ec-ST602/ST6469/5-farms), IncHI2-ST2/ST4 (Ec-ST533/ST6469/5 farms and Kp-ST147/6-farms) or IncI2 (Ec-ST117/1-farm) plasmids. WGS revealed high load and diversity in virulence, antibiotic resistance and metal tolerance genes. This study supports colistin withdrawal potential efficacy in poultry production and highlights both poultry-production chain as a source of mcr-1 and the risk of foodborne transmission to poultry-meat consumers. Finally, in the antibiotic reduction/replacement context, other potential co-selective pressures (e.g., metals-Cu as feed additives) need to be further understood to guide concerted, effective and durable actions under 'One Health' perspective.
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Affiliation(s)
- Sofia Ribeiro
- UCIBIO - Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, 4050-313, Portugal
| | - Joana Mourão
- UCIBIO - Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, 4050-313, Portugal.,Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Ângela Novais
- UCIBIO - Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, 4050-313, Portugal.,Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, 4050-313, Portugal
| | - Joana Campos
- UCIBIO - Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, 4050-313, Portugal.,INEB-Institute of Biomedical Engineering, i3S-Institute for Research & Innovation in Health, University of Porto, Porto, Portugal
| | - Luísa Peixe
- UCIBIO - Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, 4050-313, Portugal.,Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, 4050-313, Portugal
| | - Patrícia Antunes
- UCIBIO - Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, 4050-313, Portugal.,Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, 4050-313, Portugal.,Faculty of Nutrition and Food Sciences, University of Porto, Porto, 4150-180, Portugal
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Mooranian A, Jones M, Ionescu CM, Walker D, Wagle SR, Kovacevic B, Chester J, Foster T, Johnston E, Mikov M, Al-Salami H. Advancements in Assessments of Bio-Tissue Engineering and Viable Cell Delivery Matrices Using Bile Acid-Based Pharmacological Biotechnologies. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:1861. [PMID: 34361247 PMCID: PMC8308343 DOI: 10.3390/nano11071861] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/07/2021] [Accepted: 07/14/2021] [Indexed: 12/18/2022]
Abstract
The utilisation of bioartificial organs is of significant interest to many due to their versatility in treating a wide range of disorders. Microencapsulation has a potentially significant role in such organs. In order to utilise microcapsules, accurate characterisation and analysis is required to assess their properties and suitability. Bioartificial organs or transplantable microdevices must also account for immunogenic considerations, which will be discussed in detail. One of the most characterized cases is the investigation into a bioartificial pancreas, including using microencapsulation of islets or other cells, and will be the focus subject of this review. Overall, this review will discuss the traditional and modern technologies which are necessary for the characterisation of properties for transplantable microdevices or organs, summarizing analysis of the microcapsule itself, cells and finally a working organ. Furthermore, immunogenic considerations of such organs are another important aspect which is addressed within this review. The various techniques, methodologies, advantages, and disadvantages will all be discussed. Hence, the purpose of this review is providing an updated examination of all processes for the analysis of a working, biocompatible artificial organ.
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Affiliation(s)
- Armin Mooranian
- The Biotechnology and Drug Development Research Laboratory, Curtin Medical School, Curtin Health Innovation Research Institute, Curtin University, Bentley, Perth, WA 6102, Australia; (A.M.); (M.J.); (C.M.I.); (D.W.); (S.R.W.); (B.K.); (J.C.); (T.F.); (E.J.)
- Hearing Therapeutics, Ear Science Institute Australia, Queen Elizabeth II Medical Centre, Nedlands, Perth, WA 6009, Australia
| | - Melissa Jones
- The Biotechnology and Drug Development Research Laboratory, Curtin Medical School, Curtin Health Innovation Research Institute, Curtin University, Bentley, Perth, WA 6102, Australia; (A.M.); (M.J.); (C.M.I.); (D.W.); (S.R.W.); (B.K.); (J.C.); (T.F.); (E.J.)
- Hearing Therapeutics, Ear Science Institute Australia, Queen Elizabeth II Medical Centre, Nedlands, Perth, WA 6009, Australia
| | - Corina Mihaela Ionescu
- The Biotechnology and Drug Development Research Laboratory, Curtin Medical School, Curtin Health Innovation Research Institute, Curtin University, Bentley, Perth, WA 6102, Australia; (A.M.); (M.J.); (C.M.I.); (D.W.); (S.R.W.); (B.K.); (J.C.); (T.F.); (E.J.)
- Hearing Therapeutics, Ear Science Institute Australia, Queen Elizabeth II Medical Centre, Nedlands, Perth, WA 6009, Australia
| | - Daniel Walker
- The Biotechnology and Drug Development Research Laboratory, Curtin Medical School, Curtin Health Innovation Research Institute, Curtin University, Bentley, Perth, WA 6102, Australia; (A.M.); (M.J.); (C.M.I.); (D.W.); (S.R.W.); (B.K.); (J.C.); (T.F.); (E.J.)
- Hearing Therapeutics, Ear Science Institute Australia, Queen Elizabeth II Medical Centre, Nedlands, Perth, WA 6009, Australia
| | - Susbin Raj Wagle
- The Biotechnology and Drug Development Research Laboratory, Curtin Medical School, Curtin Health Innovation Research Institute, Curtin University, Bentley, Perth, WA 6102, Australia; (A.M.); (M.J.); (C.M.I.); (D.W.); (S.R.W.); (B.K.); (J.C.); (T.F.); (E.J.)
- Hearing Therapeutics, Ear Science Institute Australia, Queen Elizabeth II Medical Centre, Nedlands, Perth, WA 6009, Australia
| | - Bozica Kovacevic
- The Biotechnology and Drug Development Research Laboratory, Curtin Medical School, Curtin Health Innovation Research Institute, Curtin University, Bentley, Perth, WA 6102, Australia; (A.M.); (M.J.); (C.M.I.); (D.W.); (S.R.W.); (B.K.); (J.C.); (T.F.); (E.J.)
- Hearing Therapeutics, Ear Science Institute Australia, Queen Elizabeth II Medical Centre, Nedlands, Perth, WA 6009, Australia
| | - Jacqueline Chester
- The Biotechnology and Drug Development Research Laboratory, Curtin Medical School, Curtin Health Innovation Research Institute, Curtin University, Bentley, Perth, WA 6102, Australia; (A.M.); (M.J.); (C.M.I.); (D.W.); (S.R.W.); (B.K.); (J.C.); (T.F.); (E.J.)
- Hearing Therapeutics, Ear Science Institute Australia, Queen Elizabeth II Medical Centre, Nedlands, Perth, WA 6009, Australia
| | - Thomas Foster
- The Biotechnology and Drug Development Research Laboratory, Curtin Medical School, Curtin Health Innovation Research Institute, Curtin University, Bentley, Perth, WA 6102, Australia; (A.M.); (M.J.); (C.M.I.); (D.W.); (S.R.W.); (B.K.); (J.C.); (T.F.); (E.J.)
- Hearing Therapeutics, Ear Science Institute Australia, Queen Elizabeth II Medical Centre, Nedlands, Perth, WA 6009, Australia
| | - Edan Johnston
- The Biotechnology and Drug Development Research Laboratory, Curtin Medical School, Curtin Health Innovation Research Institute, Curtin University, Bentley, Perth, WA 6102, Australia; (A.M.); (M.J.); (C.M.I.); (D.W.); (S.R.W.); (B.K.); (J.C.); (T.F.); (E.J.)
- Hearing Therapeutics, Ear Science Institute Australia, Queen Elizabeth II Medical Centre, Nedlands, Perth, WA 6009, Australia
| | - Momir Mikov
- Department of Pharmacology, Toxicology and Clinical Pharmacology, Faculty of Medicine, University of Novi Sad, Hajduk Veljkova 3, 21101 Novi Sad, Serbia;
| | - Hani Al-Salami
- The Biotechnology and Drug Development Research Laboratory, Curtin Medical School, Curtin Health Innovation Research Institute, Curtin University, Bentley, Perth, WA 6102, Australia; (A.M.); (M.J.); (C.M.I.); (D.W.); (S.R.W.); (B.K.); (J.C.); (T.F.); (E.J.)
- Hearing Therapeutics, Ear Science Institute Australia, Queen Elizabeth II Medical Centre, Nedlands, Perth, WA 6009, Australia
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Dizaji AN, Ozek NS, Yilmaz A, Aysin F, Yilmaz M. Gold nanorod arrays enable highly sensitive bacterial detection via surface-enhanced infrared absorption (SEIRA) spectroscopy. Colloids Surf B Biointerfaces 2021; 206:111939. [PMID: 34186307 DOI: 10.1016/j.colsurfb.2021.111939] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/18/2021] [Accepted: 06/22/2021] [Indexed: 12/26/2022]
Abstract
Infrared (IR) spectroscopy is a unique and powerful method in the identification, characterization, and classification of chemical and biological molecules. However, the low absorbance of biological molecules has arisen as a major bottleneck and inhibits the application of IR in practical applications. To overcome this limitation, in the last four decades, surface-enhanced IR absorption (SEIRA) spectroscopy has been proposed and has become the focus of interest in various applications. In this study, for the first time, we proposed the employment of 3D anisotropic gold nanorod arrays (GNAs) as a highly active SEIRA platform in bacterial detection. For this, GNA platforms were fabricated through an oblique angle deposition (OAD) approach by using a physical vapor deposition (PVD) system. OAD of gold at proper deposition angle (10°) created closely-packed and columnar gold nanorod structures onto the glass slides in a well-controlled manner. GNA platform was tested as a SEIRA system in three different species of bacteria (Escherichia coli, Staphylococcus aureus, and Bacillus subtilis) by collecting IR spectra of each bacteria from different parts of GNA. The employment of GNA provided robust IR spectra with high reproducibility and signal-to-noise ratio. For the comparison, IR spectra of each bacteria were collected from aluminum foil and a smooth gold surface (SGS). No or very low IR spectra were observed in comparison to the GNA platform for these substrates. Unsupervised (PCA, HCA) and supervised (SIMCA, LDA, and SVM classification) machine learning analysis of bacteria spectra obtained from GNA substrate indicated that all bacteria samples can be detected and identified without using a label-containing biosensor, in a fast and simple manner.
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Affiliation(s)
- Araz Norouz Dizaji
- Department of Chemical Engineering, Ataturk University, 25240 Erzurum, Turkey; East Anatolia High Technology Application and Research Center (DAYTAM), Ataturk University, 25240 Erzurum, Turkey
| | - Nihal Simsek Ozek
- East Anatolia High Technology Application and Research Center (DAYTAM), Ataturk University, 25240 Erzurum, Turkey; Department of Biology, Ataturk University, 25240 Erzurum, Turkey
| | - Asli Yilmaz
- East Anatolia High Technology Application and Research Center (DAYTAM), Ataturk University, 25240 Erzurum, Turkey; Department of Molecular Biology and Genetics, Ataturk University, 25240 Erzurum, Turkey
| | - Ferhunde Aysin
- East Anatolia High Technology Application and Research Center (DAYTAM), Ataturk University, 25240 Erzurum, Turkey; Department of Biology, Ataturk University, 25240 Erzurum, Turkey
| | - Mehmet Yilmaz
- Department of Chemical Engineering, Ataturk University, 25240 Erzurum, Turkey; East Anatolia High Technology Application and Research Center (DAYTAM), Ataturk University, 25240 Erzurum, Turkey; Department of Nanoscience and Nanoengineering, Ataturk University, 25240 Erzurum, Turkey.
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Cordovana M, Mauder N, Kostrzewa M, Wille A, Rojak S, Hagen RM, Ambretti S, Pongolini S, Soliani L, Justesen US, Holt HM, Join-Lambert O, Le Hello S, Auzou M, Veloo AC, May J, Frickmann H, Dekker D. Classification of Salmonella enterica of the (Para-)Typhoid Fever Group by Fourier-Transform Infrared (FTIR) Spectroscopy. Microorganisms 2021; 9:microorganisms9040853. [PMID: 33921159 PMCID: PMC8071548 DOI: 10.3390/microorganisms9040853] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/05/2021] [Accepted: 04/07/2021] [Indexed: 12/31/2022] Open
Abstract
Typhoidal and para-typhoidal Salmonella are major causes of bacteraemia in resource-limited countries. Diagnostic alternatives to laborious and resource-demanding serotyping are essential. Fourier transform infrared spectroscopy (FTIRS) is a rapidly developing and simple bacterial typing technology. In this study, we assessed the discriminatory power of the FTIRS-based IR Biotyper (Bruker Daltonik GmbH, Bremen, Germany), for the rapid and reliable identification of biochemically confirmed typhoid and paratyphoid fever-associated Salmonella isolates. In total, 359 isolates, comprising 30 S. Typhi, 23 S. Paratyphi A, 23 S. Paratyphi B, and 7 S. Paratyphi C, respectively and other phylogenetically closely related Salmonella serovars belonging to the serogroups O:2, O:4, O:7 and O:9 were tested. The strains were derived from clinical, environmental and food samples collected at different European sites. Applying artificial neural networks, specific automated classifiers were built to discriminate typhoidal serovars from non-typhoidal serovars within each of the four serogroups. The accuracy of the classifiers was 99.9%, 87.0%, 99.5% and 99.0% for Salmonella Typhi, Salmonella Paratyphi A, B and Salmonella Paratyphi C, respectively. The IR Biotyper is a promising tool for fast and reliable detection of typhoidal Salmonella. Hence, IR biotyping may serve as a suitable alternative to conventional approaches for surveillance and diagnostic purposes.
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Affiliation(s)
- Miriam Cordovana
- Bruker Daltonik GmbH, 28359 Bremen, Germany; (M.C.); (N.M.); (M.K.)
| | - Norman Mauder
- Bruker Daltonik GmbH, 28359 Bremen, Germany; (M.C.); (N.M.); (M.K.)
| | - Markus Kostrzewa
- Bruker Daltonik GmbH, 28359 Bremen, Germany; (M.C.); (N.M.); (M.K.)
| | - Andreas Wille
- Institute for Hygiene and Environment, 20539 Hamburg, Germany;
| | - Sandra Rojak
- Department of Microbiology and Hospital Hygiene, Bundeswehr Central Hospital Koblenz, 56070 Koblenz, Germany; (S.R.); (R.M.H.)
| | - Ralf Matthias Hagen
- Department of Microbiology and Hospital Hygiene, Bundeswehr Central Hospital Koblenz, 56070 Koblenz, Germany; (S.R.); (R.M.H.)
| | - Simone Ambretti
- Operative Unit of Microbiology, IRCCS-Azienda Ospedaliero Policlinico Sant’Orsola-Universitaria di Bologna, 40138 Bologna, Italy;
| | - Stefano Pongolini
- Risk Analysis and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale Della Lombardia e dell’Emilia-Romagna, 43126 Parma, Italy; (S.P.); (L.S.)
| | - Laura Soliani
- Risk Analysis and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale Della Lombardia e dell’Emilia-Romagna, 43126 Parma, Italy; (S.P.); (L.S.)
| | - Ulrik S. Justesen
- Department of Clinical Microbiology, Odense University Hospital, 5000 Odense C, Denmark; (U.S.J.); (H.M.H.)
| | - Hanne M. Holt
- Department of Clinical Microbiology, Odense University Hospital, 5000 Odense C, Denmark; (U.S.J.); (H.M.H.)
| | - Olivier Join-Lambert
- Department of Microbiology, Université de Caen, Normandie, CEDEX 5, 14032 Caen, France; (O.J.-L.); (S.L.H.); (M.A.)
| | - Simon Le Hello
- Department of Microbiology, Université de Caen, Normandie, CEDEX 5, 14032 Caen, France; (O.J.-L.); (S.L.H.); (M.A.)
| | - Michel Auzou
- Department of Microbiology, Université de Caen, Normandie, CEDEX 5, 14032 Caen, France; (O.J.-L.); (S.L.H.); (M.A.)
| | - Alida C. Veloo
- University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, University of Groningen, 9700 AB Groningen, The Netherlands;
| | - Jürgen May
- Infectious Disease Department, Bernhard Nocht Institute for Tropical Medicine Hamburg, 20359 Hamburg, Germany; or
- University Medical Center Hamburg-Eppendorf (UKE), Tropical Medicine II Hamburg, 20359 Hamburg, Germany
| | - Hagen Frickmann
- Department of Microbiology and Hospital Hygiene, Bundeswehr Hospital Hamburg, 20359 Hamburg, Germany; or
- Institute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock, 18057 Rostock, Germany
| | - Denise Dekker
- Infectious Disease Department, Bernhard Nocht Institute for Tropical Medicine Hamburg, 20359 Hamburg, Germany; or
- German Centre for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, 38124 Braunschweig, Germany
- Correspondence:
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Kaprou GD, Bergšpica I, Alexa EA, Alvarez-Ordóñez A, Prieto M. Rapid Methods for Antimicrobial Resistance Diagnostics. Antibiotics (Basel) 2021; 10:209. [PMID: 33672677 PMCID: PMC7924329 DOI: 10.3390/antibiotics10020209] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/09/2021] [Accepted: 02/13/2021] [Indexed: 02/06/2023] Open
Abstract
Antimicrobial resistance (AMR) is one of the most challenging threats in public health; thus, there is a growing demand for methods and technologies that enable rapid antimicrobial susceptibility testing (AST). The conventional methods and technologies addressing AMR diagnostics and AST employed in clinical microbiology are tedious, with high turnaround times (TAT), and are usually expensive. As a result, empirical antimicrobial therapies are prescribed leading to AMR spread, which in turn causes higher mortality rates and increased healthcare costs. This review describes the developments in current cutting-edge methods and technologies, organized by key enabling research domains, towards fighting the looming AMR menace by employing recent advances in AMR diagnostic tools. First, we summarize the conventional methods addressing AMR detection, surveillance, and AST. Thereafter, we examine more recent non-conventional methods and the advancements in each field, including whole genome sequencing (WGS), matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) spectrometry, Fourier transform infrared (FTIR) spectroscopy, and microfluidics technology. Following, we provide examples of commercially available diagnostic platforms for AST. Finally, perspectives on the implementation of emerging concepts towards developing paradigm-changing technologies and methodologies for AMR diagnostics are discussed.
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Affiliation(s)
- Georgia D. Kaprou
- Department of Food Hygiene and Technology, University of León, 24071 León, Spain; (I.B.); (E.A.A.); (A.A.-O.); (M.P.)
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367 Belvaux, Luxembourg
| | - Ieva Bergšpica
- Department of Food Hygiene and Technology, University of León, 24071 León, Spain; (I.B.); (E.A.A.); (A.A.-O.); (M.P.)
- Institute of Food Safety, Animal Health and Environment BIOR, LV-1076 Riga, Latvia
| | - Elena A. Alexa
- Department of Food Hygiene and Technology, University of León, 24071 León, Spain; (I.B.); (E.A.A.); (A.A.-O.); (M.P.)
| | - Avelino Alvarez-Ordóñez
- Department of Food Hygiene and Technology, University of León, 24071 León, Spain; (I.B.); (E.A.A.); (A.A.-O.); (M.P.)
- Institute of Food Science and Technology, University of León, 24071 León, Spain
| | - Miguel Prieto
- Department of Food Hygiene and Technology, University of León, 24071 León, Spain; (I.B.); (E.A.A.); (A.A.-O.); (M.P.)
- Institute of Food Science and Technology, University of León, 24071 León, Spain
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Locke A, Fitzgerald S, Mahadevan-Jansen A. Advances in Optical Detection of Human-Associated Pathogenic Bacteria. Molecules 2020; 25:E5256. [PMID: 33187331 PMCID: PMC7696695 DOI: 10.3390/molecules25225256] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 11/04/2020] [Accepted: 11/06/2020] [Indexed: 02/06/2023] Open
Abstract
Bacterial infection is a global burden that results in numerous hospital visits and deaths annually. The rise of multi-drug resistant bacteria has dramatically increased this burden. Therefore, there is a clinical need to detect and identify bacteria rapidly and accurately in their native state or a culture-free environment. Current diagnostic techniques lack speed and effectiveness in detecting bacteria that are culture-negative, as well as options for in vivo detection. The optical detection of bacteria offers the potential to overcome these obstacles by providing various platforms that can detect bacteria rapidly, with minimum sample preparation, and, in some cases, culture-free directly from patient fluids or even in vivo. These modalities include infrared, Raman, and fluorescence spectroscopy, along with optical coherence tomography, interference, polarization, and laser speckle. However, these techniques are not without their own set of limitations. This review summarizes the strengths and weaknesses of utilizing each of these optical tools for rapid bacteria detection and identification.
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Affiliation(s)
- Andrea Locke
- Vanderbilt Biophotonics Center, Nashville, TN 37232, USA; (A.L.); (S.F.)
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37232, USA
| | - Sean Fitzgerald
- Vanderbilt Biophotonics Center, Nashville, TN 37232, USA; (A.L.); (S.F.)
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37232, USA
| | - Anita Mahadevan-Jansen
- Vanderbilt Biophotonics Center, Nashville, TN 37232, USA; (A.L.); (S.F.)
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37232, USA
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Fourier Transform Infrared Spectroscopy Is a New Option for Outbreak Investigation: a Retrospective Analysis of an Extended-Spectrum-Beta-Lactamase-Producing Klebsiella pneumoniae Outbreak in a Neonatal Intensive Care Unit. J Clin Microbiol 2020; 58:JCM.00098-20. [PMID: 32161093 DOI: 10.1128/jcm.00098-20] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 02/28/2020] [Indexed: 12/13/2022] Open
Abstract
The IR Biotyper is a new automated typing system based on Fourier-transform infrared (FT-IR) spectroscopy that gives results within 4 h. We aimed (i) to use the IR Biotyper to retrospectively analyze an outbreak of extended-spectrum beta-lactamase-producing Klebsiella pneumoniae (ESBL-KP) in a neonatal intensive care unit and to compare results to BOX-PCR and whole-genome sequencing (WGS) results as the gold standard and (ii) to assess how the cutoff values used to define clusters affect the discriminatory power of the IR Biotyper. The sample consisted of 18 isolates from 14 patients. Specimens were analyzed in the IR Biotyper using the default analysis settings, and spectra were analyzed using OPUS 7.5 software. The software contains a feature that automatically proposes a cutoff value to define clusters; the cutoff value defines up to which distance the spectra are considered to be in the same cluster. Based on FT-IR, the outbreak represented 1 dominant clone, 1 secondary clone, and several unrelated clones. FT-IR results, using the cutoff value generated by the accompanying software after 4 replicates, were concordant with WGS for all but 1 isolate. BOX-PCR was underdiscriminatory compared to the other two methods. Using the cutoff value generated after 12 replicates, the results of FT-IR and WGS were completely concordant. The IR Biotyper can achieve the same typeability and discriminatory power as genome-based methods. However, to attain this high performance requires either previous, strain-dependent knowledge about the optimal technical parameters to be used or validation by a second method.
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