Discrimination of bacteria using whole organism fingerprinting: the utility of modern physicochemical techniques for bacterial typing

AlMasoud, Najla; Muhamadali, Howbeer; Chisanga, Malama; AlRabiah, Haitham; Lima, Cássio; Goodacre, Royston

doi:10.1039/d0an01482f

Cited by 40 publications

(48 citation statements)

References 176 publications

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“…Prescribing the correct antibiotic treatment to patients, in time, is of paramount importance for this cause [5]. The routine microbiological techniques used in clinical laboratories require at least 48 h and up to 4 days to deliver results on pathogen resistance [6,7]. This leads physicians to use empirical treatment based on patient history and resistance rates of healthcare facilities.…”

Section: Introductionmentioning

confidence: 99%

Detection of multi-resistant clinical strains of E. coli with Raman spectroscopy

et al. 2022

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In recent years, we have seen a steady rise in the prevalence of antibiotic-resistant bacteria. This creates many challenges in treating patients who carry these infections, as well as stopping and preventing outbreaks. Identifying these resistant bacteria is critical for treatment decisions and epidemiological studies. However, current methods for identification of resistance either require long cultivation steps or expensive reagents. Raman spectroscopy has been shown in the past to enable the rapid identification of bacterial strains from single cells and cultures. In this study, Raman spectroscopy was applied for the differentiation of resistant and sensitive strains of Escherichia coli. Our focus was on clinical multi-resistant (extended-spectrum β-lactam and carbapenem-resistant) bacteria from hospital patients. The spectra were collected using both UV resonance Raman spectroscopy in bulk and single-cell Raman microspectroscopy, without exposure to antibiotics. We found resistant strains have a higher nucleic acid/protein ratio, and used the spectra to train a machine learning model that differentiates resistant and sensitive strains. In addition, we applied a majority of voting system to both improve the accuracy of our models and make them more applicable for a clinical setting. This method could allow rapid and accurate identification of antibiotic resistant bacteria, and thus improve public health. Graphical abstract

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Section: Introductionmentioning

confidence: 99%

Detection of multi-resistant clinical strains of E. coli with Raman spectroscopy

et al. 2022

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“…Vibrational spectroscopy is a technique that has been used for the analysis of various chemicals, and in recent years has been successfully adapted for microbial research, showing great promise in becoming a novel diagnostic system in this field [ 4 , 5 , 6 , 8 , 9 , 15 , 16 , 17 , 18 ].…”

Section: Introductionmentioning

confidence: 99%

“…Raman scattering happens when the excitation energy is not the same as that of the scattered energy post interaction with the analyte molecule. Due to the low emission rate of scattered photons, an integration time of minutes is required to obtain useful spectra, however, ways to enhance this intrinsic aspect have been developed [ 18 , 19 ].…”

Section: Introductionmentioning

confidence: 99%

“…This allows for shorter integration times and increased sensitivity compared to standard Raman spectroscopy. SERS is advantageous due to its potential as a low cost, rapid, low volume, non-destructive, broad information content, high specificity and sensitivity diagnostic method [ 1 , 9 , 10 , 18 , 20 , 22 ], also in part because analysis is easily performed in aqueous environments without interface [ 4 , 25 ]. In bacteriology, the efficacy of SERS was demonstrated with purified cultures, mixed and even single cell samples [ 6 , 7 , 8 , 9 , 13 , 15 , 20 ].…”

Section: Introductionmentioning

confidence: 99%

“…Despite the aforementioned advancements, the field is generally geared towards food and medical pathogen identification [ 1 , 2 , 6 , 7 , 8 , 9 , 10 , 12 , 14 , 18 , 20 , 22 , 27 , 28 ]. Furthermore, most experiments are conducted using well-studied species (ex.…”

Section: Introductionmentioning

confidence: 99%

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Differentiation of Closely Related Oak-Associated Gram-Negative Bacteria by Label-Free Surface Enhanced Raman Spectroscopy (SERS)

Vaitiekūnaite

Snitka

2021

Microorganisms

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Due to the harmful effects of chemical fertilizers and pesticides, the need for an eco-friendly solution to improve soil fertility has become a necessity, thus microbial biofertilizer research is on the rise. Plant endophytic bacteria inhabiting internal tissues represent a novel niche for research into new biofertilizer strains. However, the number of species and strains that need to be differentiated and identified to facilitate faster screening in future plant-bacteria interaction studies, is enormous. Surface enhanced Raman spectroscopy (SERS) may provide a platform for bacterial discrimination and identification, which, compared with the traditional methods, is relatively rapid, uncomplicated and ensures high specificity. In this study, we attempted to differentiate 18 bacterial isolates from two oaks via morphological, physiological, biochemical tests and SERS spectra analysis. Previous 16S rRNA gene fragment sequencing showed that three isolates belong to Paenibacillus, 3—to Pantoea and 12—to Pseudomonas genera. Additional tests were not able to further sort these bacteria into strain-specific groups. However, the obtained label-free SERS bacterial spectra along with the high-accuracy principal component (PCA) and discriminant function analyses (DFA) demonstrated the possibility to differentiate these bacteria into variant strains. Furthermore, we collected information about the biochemical characteristics of selected isolates. The results of this study suggest a promising application of SERS in combination with PCA/DFA as a rapid, non-expensive and sensitive method for the detection and identification of plant-associated bacteria.

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Rapid Identification of Species, Antimicrobial‐Resistance Genotypes and Phenotypes of Gram‐Positive Cocci Using Long Short‐Term Memory Raman Spectra Methods

Chen

Ling

et al. 2023

Advanced Intelligent Systems

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Bacterial infections are actually a major cause of high morbidity and mortality in a range of medical conditions including cancer and diabetes. The emergence of antibiotic resistance in gram-positive cocci, such as methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE), poses a worldwide threat to human health. In China, the proportion of hospital-acquired MRSA among all MRSA infections is as high as 50.4% according to the literature. [1] Linezolid (LZD), an oxazolidinone antibiotic first approved for clinical use in 2000, is effective against a variety of gram-positive pathogens and is considered as a last resort drug to treat severe types of infections (such as nosocomial and communityacquired pneumonia, and complicated skin and soft tissue infections) caused by multidrug-resistant Gram-positive pathogens including VRE and MRSA. [2] However, since the first linezolid-resistant (LR) enterococcus strain was isolated from a transplant patient in 2001, [3] LR strains have become prevalent worldwide, causing infection with few treatment options.

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Discrimination of bacteria using whole organism fingerprinting: the utility of modern physicochemical techniques for bacterial typing

Abstract: Rapid and accurate classification and discrimination of bacteria is an important task and the recent ongoing COVID-19 pandemic has highlighted that rapid diagnostics that give real-time results is vital. Coupled...

Cited by 40 publications

References 176 publications

Detection of multi-resistant clinical strains of E. coli with Raman spectroscopy

Detection of multi-resistant clinical strains of E. coli with Raman spectroscopy

Differentiation of Closely Related Oak-Associated Gram-Negative Bacteria by Label-Free Surface Enhanced Raman Spectroscopy (SERS)

Rapid Identification of Species, Antimicrobial‐Resistance Genotypes and Phenotypes of Gram‐Positive Cocci Using Long Short‐Term Memory Raman Spectra Methods

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