SemiRaman: A self-supervised contrastive representation learning-based framework for semi-supervised Raman spectral identification of pathogenic bacteria.

Previous articleNext article No AccessNew Biological BooksDiagnostic Bacteriology. A Textbook for the Isolation and Identification of Pathogenic Bacteria. Isabelle Gilbert Schaub , M. Kathleen Foley Walter C. TobieWalter C. Tobie Search for more articles by this author PDFPDF PLUS Add to favoritesDownload CitationTrack CitationsPermissionsReprints Share onFacebookTwitterLinkedInRedditEmail SectionsMoreDetailsFiguresReferencesCited by The Quarterly Review of Biology Volume 28, Number 1Mar., 1953 Published in association with Stony Brook University Article DOIhttps://doi.org/10.1086/399454 Views: 1Total views on this site PDF download Crossref reports no articles citing this article.

Fast and reliable identification of pathogenic bacteria is of upmost importance to human health and safety. Methods that are currently used in clinical practice are often time consuming, require expensive equipment, trained personnel, and therefore have limited applications in low resource environments. Molecular identification methods address some of these shortcomings. At the same time, they often use antibodies, their fragments, or other biomolecules as recognition units, which makes such tests specific to a particular target. In contrast, array-based methods use a combination of reporters that are not specific to a single pathogen. These methods provide a more data-rich and universal response that can be used for identification of a variety of bacteria of interest. In this report, we demonstrate the application of the excitation–emission spectroscopy of an environmentally sensitive fluorescent dye for identification of pathogenic bacterial species. 2-(4′-Dimethylamino)-3-hydroxyflavone (DMAF) interacts with the bacterial cell envelope resulting in a distinct spectral response that is unique to each bacterial species. The dynamics of dye–bacteria interaction were thoroughly investigated, and the limits of detection and identification were determined. Neural network classification algorithm was used for pattern recognition analysis and classification of spectral data. The sensor successfully discriminated between eight representative pathogenic bacteria, achieving a classification accuracy of 85.8% at the species level and 98.3% at the Gram status level. The proposed method based on excitation–emission spectroscopy of an environmentally sensitive fluorescent dye is a powerful and versatile diagnostic tool with high accuracy in identification of bacterial pathogens.

A method is described for fast identification of bacteria by combining (a) the enrichment of bacterial cells by using magnetite (Fe3O4) magnetic beads modified with human IgG (IgG@Fe3O4) and (b) MALDI-TOF MS analysis. IgG has affinity to protein A, protein G, protein L and glycans on the surface of bacterial cells, and IgG@Fe3O4. Ittherefore is applicable to the preconcentration of a range of bacterial species. The feasibility of the method has been demonstrated by collecting six species of pathogenic bacteria (Gram-positives: Staphylococcus aureus and Kocuria rosea; Gram-negatives: Klebsiella pneumoniae, Klebsiella oxytoca, Enterobacter cloacae and Pseudomonas aeruginosa). Bacteria with concentrations as low as 10CFU·mL-1 in spiked water samples were extracted by this sorbent with recovery rates of >50%. After enrichment, bacteria on the IgG@Fe3O4 sorbent were further identified by MALDI-TOF MS. Bacteria in concentrations as low as 105CFU in 100μL of human whole blood can be identified by the method. Compared to other blood culture based tests, the culture time is shortened by 40% (from ~10h to ~6h), and the plate culture procedure (overnight) is avoided. After short blood culture, the enrichment and identification can be finished in one hour. The IgG@Fe3O4 is of practical value in clinical diagnosis and may be combined with other identification methods, e.g. PCR, Raman spectroscopy, infrared spectroscopy, etc. Graphical abstract A non-targeted, fast and sensitive assay for bacterial identification from human blood has been developed based on the enrichment of bacteria by IgG@Fe3O4 and identification by MALDI-TOF MS.

Use of volatile compounds as a diagnostic tool for the detection of pathogenic bacteria

According to the course character and training objective, we analyzed the necessity of the experiment teaching reform of microbiology examination. The modules of employable Skills(MES) was applied to the experiment teaching of microbiology examination tentatively. On the basis of the needs of microbiology laboratory jobs, the contents of experimental course were integrated and optimized to skills module, comprehensive training module and application module, which include fourteen study units such as basic techniques of identification of bacteria, the separation and identifi-cation of pathogenic bacteria, microbiology examination of clinical specimen etc. Intensive teaching and multiplex teaching methods were applied to each module according to the module's characteristic, teaching objectives and cognitive rules of students. This teaching reform has achieved initial results. Key words: Microbiology examination; Experiment teaching reform; Modules of Employ-able Skills

Detection and identification of pathogenic bacteria and their protein toxins play a crucial role in a proper response to natural or terrorist-caused outbreaks of infectious diseases. The recent availability of whole genome sequences of priority bacterial pathogens opens new diagnostic possibilities for identification of bacteria by retrieving their genomic or proteomic information. We describe a method for identification of bacteria based on tandem mass spectrometric (MS/MS) analysis of peptides derived from bacterial proteins. This method involves bacterial cell protein extraction, trypsin digestion, liquid chromatography MS/MS analysis of the resulting peptides, and a statistical scoring algorithm to rank MS/MS spectral matching results for bacterial identification. To facilitate spectral data searching, a proteome database was constructed by translating genomes of bacteria of interest with fully or partially determined sequences. In this work, a prototype database was constructed by the automated analysis of 87 publicly available, fully sequenced bacterial genomes with the GLIMMER gene finding software. MS/MS peptide spectral matching for peptide sequence assignment against this proteome database was done by SEQUEST. To gauge the relative significance of the SEQUEST-generated matching parameters for correct peptide assignment, discriminant function (DF) analysis of these parameters was applied and DF scores were used to calculate probabilities of correct MS/MS spectra assignment to peptide sequences in the database. The peptides with DF scores exceeding a threshold value determined by the probability of correct peptide assignment were accepted and matched to the bacterial proteomes represented in the database. Sequence filtering or removal of degenerate peptides matched with multiple bacteria was then performed to further improve identification. It is demonstrated that using a preset criterion with known distributions of discriminant function scores and probabilities of correct peptide sequence assignments, a test bacterium within the 87 database microorganisms can be unambiguously identified.

RamanCluster: A deep clustering-based framework for unsupervised Raman spectral identification of pathogenic bacteria

Background: Blood infections are an extensive range of disorders that can vary from limited bacteremia to fatal septicemia. Bac- teremia refers to the transient presence of a bacterium in the bloodstream. A delay in the diagnosis and treatment of sepsis can cause mortality, with a 20% - 50% prevalence rate. Objectives: Due to the changing patterns of antibiotic resistance, as well as dierences in patterns over time in dierent settings, we decided to identify infectious agents and their antibiotic resistance patterns in blood cultures. Materials and Methods: This study was conducted at Shahid Beheshti hospital, Hamadan, Iran, during a one-year period (March 21, 2014, to March 22, 2015). From patients with suspected bloodstream infections, 5-10 mL of blood was collected three times and inoculated into culture bottles. After identifying the types of microorganisms, susceptibility testing was performed according to CLSI standards, and the results were analyzed with statistical software. Results: In the present study, 2,130 blood cultures were obtained from 710 patients (384 females and 326 males). Of these cultures, 232 (18.9%) were positive; 107 (46%) and 125 (54%) were from females and males, respectively. Most of the positive cultures were re- lated to the internal medicine and hematology wards, which had 132 cases (56.9%), and the ICU, with 37 cases (16%). The most frequent isolates were Pseudomonas aeruginosa, Escherichia coli, Acinetobacter baumannii, and coagulase-negative Staphylococcus aureus, with prevalence rates of 18.2%, 24.1%, 10.3%, and 10.3%, respectively. The most eective antibiotic against Gram-positive isolates was van- comycin. Conclusions: This study revealed that the most eective antibiotics against two Gram-negative and Gram-positive groups were amikacin and norfloxacin, so it is recommended that these antibiotics be used empirically, at least in the setting where this study was conducted, before performing the culturing and antibiogram process.

Engineering the bacteriophage 80 alpha endolysin as a fast and ultrasensitive detection toolbox against Staphylococcus aureus

Milk and milk powders are very rich in several nutrients and relished by everybody throughout the world. The present study was undertaken with the aim of investigating the bacteriological quality of locally available dry powder milk in Bangladesh. A total number of eight powder milk samples were collected from Gazipur city and its surrounding areas during the period from January 2017 to February 2017. The analysis comprised of enumeration of total viable bacterial count (TVBC), isolation of bacterial isolates and identification of pathogenic bacteria. Almost all the powder milk samples showed the total aerobic heterotrophic bacterial (TAHB) level above the standard acceptable range (>104 CFU/g). Both gram positive and gram negative pathogenic bacteria viz. Staphylococcus aureus, Staphylococcus epidermidis, Bacillus, pseudomonas sp. and Enterobacter sp. were isolated from studied samples through morphological and biochemical characteristics. Pseudomonas sp. were confirmed by API 20E. These results highlighted the necessity to maintain appropriate sanitary and hygienic measures at each critical point in order to safeguard consumers from food borne pathogens.Asian J. Med. Biol. Res. September 2018, 4(3): 267-273

Pathogenic bacteria that are part of the natural microflora can be found in aquaculture products. Microbial pathogens associated with fish can be transmitted to humans who consume or handle the fish. This study aimed to isolate human pathogenic bacteria present in the gills, intestine and skin of apparently healthy and spoil fishes. Tilapia (Oreochromisniloticus) and Cat fish (Clariaslazera) were collected from Wukari old market and Yam market of Wukari Nigeria. Bacteria were isolated from the fish gill, intestine and skin. The growth properties of distinct isolates on specific culture media were used to differentiate and characterize them. Pathogenic bacteria were recovered from various fish species that appeared with different features. The following human pathogenic bacteria were isolated; Escherichia coli and Staphylococcus aureus. The total bacteria count value ranges between 0.12 x 105 to 3.52 x 105 for the tilapia fish and 0.12 x 105 to 3.96 x 105 cfu/ml for cat fish. The identification revealed that Staphylococcus aureus and Escherichia coli was the most abundant pathogenic bacteria and also present in the initial water samples collected. Presence of Staphylococcus aureus and Eshcherichia coli is attributed to contamination of the fish samples by man through handling and processing. These enteric bacteria in fish serve as indicator organisms of faecal contamination and or water pollution. Their presence also represents a potential hazard to humans’ life. The isolates were higher from Yam market samples compared to Wukari old market.

Koto Masjid Village is the largest production center in striped catfish fish farming activities in Riau Province. One of the inhibiting factors is the disease caused by bacteria, this study aims to determine the types of pathogenic bacteria that have the potential to infect striped catfish. This research was conducted in August - November 2019, samples of striped catfish used in the study amounted to 15 tails with an average length of 15-25 cm taken from 5 ponds in Kampung II, Koto Masjid Village, XIII Koto Kampar Subdistrict, and then identified bacteria by Conventional Laboratory in Fish Parasites and Diseases, Faculty of Fisheries and Marine, Riau University, Pekanbaru. This study uses a survey method that is by taking samples from the field in Pu and then the isolation of bacteria is carried out from the kidney organ in the TSB media then purified on the TSA media. The results of the study found 3 types of pathogenic bacteria namely Aeromonas sp., Edwardsiella sp., and Pseudomonas sp. Water quality during the study was pH 6.6-70, DO 4.05-4.35 mg/L, NH3 0.035-0.2 mg/L and Temperature 28-300C.

Identification of pathogenic bacteria and antimicrobial susceptibility pattern of isolates from under nails

Enumeration and Identification of Pathogenic Bacteria from Sewage in Kuwait

BackgroundUnfortunately, many COPD patients continue to exacerbate despite good adherence to GOLD Class D recommended therapy. Acute exacerbations lead to an increase in symptoms, decline in lung function and increased mortality rate. The purpose of this review is to do a literature search for any prophylactic anti-microbial treatment trials in GOLD class D patients who ‘failed’ recommended therapy and discuss the role of COPD phenotypes, lung and gut microbiota and co-morbidities in developing a tailored approach to anti-microbial therapies for high frequency exacerbators.Main textThere is a paucity of large, well-conducted studies in the published literature to date. Factors such as single-centre, study design, lack of well-defined controls, insufficient patient numbers enrolled and short follow-up periods were significant limiting factors in numerous studies. One placebo-controlled study involving more than 1000 patients, who had 2 or more moderate exacerbations in the previous year, demonstrated a non-significant reduction in exacerbations of 19% with 5 day course of moxifloxacillin repeated at 8 week intervals. In Pseudomonas aeruginosa (Pa) colonised COPD patients, inhaled antimicrobial therapy using tobramycin, colistin and gentamicin resulted in significant reductions in exacerbation frequency. Viruses were found to frequently cause acute exacerbations in COPD (AECOPD), either as the primary infecting agent or as a co-factor. However, other, than the influenza vaccination, there were no trials of anti-viral therapies that resulted in a positive effect on reducing AECOPD. Identifying clinical phenotypes and co-existing conditions that impact on exacerbation frequency and severity is essential to provide individualised treatment with targeted therapies. The role of the lung and gut microbiome is increasingly recognised and identification of pathogenic bacteria will likely play an important role in personalised antimicrobial therapies.ConclusionAntimicrobial therapeutic options in patients who continue to exacerbate despite adherence to guidelines-directed therapy are limited. Phenotyping patients, identification of co-existing conditions and assessment of the microbiome is key to individualising antimicrobial therapy. Given the impact of viruses on AECOPD, anti-viral therapeutic agents and targeted anti-viral vaccinations should be the focus of future research studies.