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Part 2 outlines how water used as a raw material or for cleaning purposes in the manufacture of cosmetic products should be tested in microbiological control studies to ensure that it meets the microbiological quality requirements. For this purpose, samples must be taken from the water treatment system. Samples should be taken according to a defined sampling plan, based on the history of results in terms of number of samples and sampling frequency, at different points in the plant. Sampling points must allow adequate sampling. Sample quantities should be sufficient for the chosen method of analysis. Requirements for transport and storage of samples must be fulfilled. Samples must be analysed by specified appropriate methods, e.g. based on the methods of the Drinking Water Ordinance (German). The methods should be selected in such a way that it is possible to determine the number of bacteria (quantitative) and also to identify the species of microorganisms found (qualitative) and to evaluate the results with regard to the quality requirements. [ABSTRACT FROM AUTHOR]

Copyright of Veterinarska Stanica is the property of Croatian Veterinary Institute and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

This study compared the EXS 2600 system with the MALDI Biotyper for identifying microorganisms in dairy samples. Of the 196 bacterial isolates from milk, whey, buttermilk, cream, and dairy wastewater, the species and genus consistent identification between two systems showed 74% and 99%, respectively. However, the level of species identification rate exhibited a difference, which was higher in Zybio than in Bruker—76.0% and 66.8%, respectively. Notably, the EXS 2600 system performed better with certain yeast species and H. alvei, while the Biotyper excelled with Pseudomonas bacteria. Unique microbial compositions were found in 85% of dairy samples, with whey and buttermilk having the highest diversity. This research highlights the EXS 2600's potential as a reliable dairy microbial identification tool and underscores the need for a more diverse and comprehensive spectral database, despite the database's focus on clinical applications (as announced). [ABSTRACT FROM AUTHOR]

Background: Milk-borne bacteria cause degradation of milk products and constitute a significant risk to public health. Aim: The objectives of present study are to determine the microbiological quality of dairy products and to investigate pathogenic microorganisms. Methods: A total of 60 samples of raw milk, homemade cheese and yogurt were randomly selected from different retail marketplaces in Basrah. The bacteriological and biochemical tests were utilised to identify the pathogens in dairy samples, as well as the molecular technique was used as accurate diagnostic test. Results: The prevalence of contamination milk products with various isolates was estimated as 50% (95% Cl: 36.8-63.2). The mean of total bacteria count (TBC) for cheese was 7.29±2.70, raw milk 4.62±2.86, and yogurt 2.87±1.05, with significant p-value (P=0.001). The mean count of aerobic spore-forming (ASF) contaminated raw milk was analysed as 3.77±1.18 and less contamination detected in the yogurt samples with mean of ASF was estimated as 2.52±1.47 SD log 10 CFU/ml. A range of important microorganisms to human health were identified through employing the VITEK_2 system and sequencing 16S rDNA gene, including Staphylococcus aureus, Escherichia coli, Pseudomonas aerogenosa, and Bacillus cereus. Conclusion: The study indicates that there is a high level of bacterial contamination in the dairy products with different bacteria species, which is medically important. Therefore, food safety management must be implemented to reduce biological risk carried by dairy products and ensure healthy food for consumers. [Open Vet J 2024; 14(3.000): 779-786]

Background: Milk-borne bacteria cause degradation of milk products and constitute a significant risk to public health. Aim: The objectives of the present study are to determine the microbiological quality of dairy products and to investigate pathogenic microorganisms. Methods: A total of 60 samples of raw milk, homemade cheese, and yogurt were randomly selected from different retail marketplaces in Basrah. The bacteriological and biochemical tests were utilized to identify the pathogens in dairy samples, as well as the molecular technique was used as an accurate diagnostic test. Results: The prevalence of contamination of milk products with various isolates was estimated as 50% (95% Cl: 36.8-63.2). The mean of total bacteria count for cheese was 7.29 ± 2.70, raw milk 4.62 ± 2.86, and yogurt 2.87 ± 1.05, with a significant p-value (p = 0.001). The mean count of aerobic spore-forming (ASF) contaminated raw milk was analyzed as 3.77 ± 1.18 and less contamination detected in the yogurt samples with mean of ASF was estimated as 2.52 ± 1.47 SD log 10 CFU/ml. A range of important microorganisms to human health were identified by employing the VITEK_2 system and sequencing 16S rDNA gene, including Staphylococcus aureus, Escherichia coli, Pseudomonas aerogenosa, and Bacillus cereus. Conclusion: The study indicates that there is a high level of bacterial contamination in dairy products with different bacteria species, which is medically important. Therefore, food safety management must be implemented to reduce biological risks carried by dairy products and ensure healthy food for consumers. [ABSTRACT FROM AUTHOR]

Although many user-friendly workflows exist for identifications of peptides and proteins in mass-spectrometry-based proteomics, there is a need of easy to use, fast, and accurate workflows for identifications of microorganisms, antimicrobial resistant proteins, and biomass estimation. Identification of microorganisms is a computationally demanding task that requires querying thousands of MS/MS spectra in a database containing thousands to tens of thousands of microorganisms. Existing software can't handle such a task in a time efficient manner, taking hours to process a single MS/MS experiment. Another paramount factor to consider is the necessity of accurate statistical significance to properly control the proportion of false discoveries among the identified microorganisms, and antimicrobial-resistant proteins, and to provide robust biomass estimation. Recently, we have developed Microorganism Classification and Identification (MiCId) workflow that assigns accurate statistical significance to identified microorganisms, antimicrobial-resistant proteins, and biomass estimation. MiCId's workflow is also computationally efficient, taking about 6–17 minutes to process a tandem mass-spectrometry (MS/MS) experiment using computer resources that are available in most laptop and desktop computers, making it a portable workflow. To make data analysis accessible to a broader range of users, beyond users familiar with the Linux environment, we have developed a graphical user interface (GUI) for MiCId's workflow. The GUI brings to users all the functionality of MiCId's workflow in a friendly interface along with tools for data analysis, visualization, and to export results. [ABSTRACT FROM AUTHOR]

Copyright of Revista Española de Quimioterapia is the property of Sociedad Espanola de Quimioterapia and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Matrix-assisted laser desorption ionization-time-of-flight (MALDI-TOF) mass spectrometry (MS) has become a valuable laboratory tool for rapid diagnostics, research, and exploration in veterinary medicine. While instrument acquisition costs are high for the technology, cost per sample is very low, the method requires minimal sample preparation, and analysis is easily conducted by end-users requiring minimal training. Matrix-assisted laser desorption ionization-time-of-flight MS has found widespread application for the rapid identification of microorganisms, diagnosis of dermatophytes and parasites, protein/lipid profiling, molecular diagnostics, and the technique demonstrates significant promise for 2D chemical mapping of tissue sections collected postmortem. In this review, an overview of the MALDI-TOF technique will be reported and manuscripts outlining current uses of the technology for veterinary science since 2019 will be summarized. The article concludes by discussing gaps in knowledge and areas of future growth.

A lack of rapid and dependable microbial identification platforms, as well as insufficient or overdue microbiological surveillance and corresponding resolutions implemented in clinical diagnosis and treatment, agricultural production, and the food industry, can seriously harm human health and reduce productivity in the food industry. Here, a two-dimensional Ni–Co bimetallic metal–organic framework nanozyme (2D-NCM) is prepared for the rapid and efficient discrimination of microbes including clinical pathogens and brewing fungi. The nanozyme 2D-NCM, which is synthesized via a facile layered double hydroxide in situ transformation strategy, exhibits enhanced peroxidase-like activity. The biocatalytic activity of 2D-NCM could be altered to different degrees via different interactions between 2D-NCM and microbes. By selection of diverse compositions of absorbance at different time points, the sensing unit, 2D-NCM, could provide multichannel information for microbial identification. The nanozyme-based platform prevents the tedious synthesis of multiple biosensing receptors and the demand for complicated operation/precise devices, resulting in lower cost, quicker response (within 0.5 h), higher throughput, and simpler handling without washing procedures. This study provides an alternative strategy to construct practicable, facile, and flexible MOF nanozyme based biosensing arrays for the identification of microbes, making an active contribution toward precision medicine, food safety, and environmental protection. [ABSTRACT FROM AUTHOR]

DNA extraction is a crucial step in all nucleic acid-based protocols to identify microorganisms. Lactic acid bacteria are a significant part of healthy microbiota in the human gastrointestinal tract. These gram-positive bacteria have several layers of peptidoglycan in the cell walls. These structures cause difficulties in the cell lysis and obtaining reliable protocols for DNA isolations . The purpose of this study was to assess the autoclave and lysozyme-based DNA purification approaches for achieving the high-quality genomic DNAs of Lactobacillus acidophilus bacteria. DNA concentrations and qualities were also compared with the commercial kit. The results showed that the proper DNA isolation methods were various, according to the downstream applications. Protocols that included lysozyme produced a higher amount of DNA than the autoclave method. Lysozyme treatment combined with silica -guanidinethiocyanate procedure was the efficient protocol with affordable cost for routine lysis of L. acidophilus bacteria. Appropriate DNA concentration and quality were obtained through this method comparable to those of the commercial kit. Inversely, autoclave treatment had little effect on the breakage of the cell walls indicating low concentrations of extracted DNAs. This method could not completely break down all the bacterial cell walls. However, the breakage of low numbers of cell walls was microscopically observed in the supernatant of the autoclaved cell suspension. The quality of this protocol was found to be adequate for performing direct polymerase chain reaction (PCR) assay on samples with large amounts of lactobacilli. These conclusions suggest attentively selecting the DNA extraction method based on the planned downstream analysis of PCR products. [ABSTRACT FROM AUTHOR]

The identification of microorganisms using single-temperatures pyrolysis gas chromatography (ST-PyGC) has limitations, for example, the risk of missing characteristic peaks that are essential to the chemotaxonomic interpretation. In this paper, we proposed a new multi-temperature PyGC (MT-PyGC) method as an alternative to ST-PyGC, without sacrificing its speed and quality. Six bacteria (three Gram-positive and three Gram-negative), one micro-fungus and one archaeon, representing microorganisms from different domains, were analyzed by MT-PyGC. It is found that MT pyrograms cover a more complete range of characteristic peaks than ST. Coupling with thermogravimetric analysis, chemotaxonomic information extracted from pyrograms by MT-PyGC have the potential for the differentiation of microorganisms from environments including deep subterranean reservoirs and biomass conversion/biofuel production. [ABSTRACT FROM AUTHOR]

Matrix-assisted laser desorption ionization-time-of-flight (MALDI-TOF) mass spectrometry (MS) has become a valuable laboratory tool for rapid diagnostics, research, and exploration in veterinary medicine. While instrument acquisition costs are high for the technology, cost per sample is very low, the method requires minimal sample preparation, and analysis is easily conducted by end-users requiring minimal training. Matrix-assisted laser desorption ionization-time-of-flight MS has found widespread application for the rapid identification of microorganisms, diagnosis of dermatophytes and parasites, protein/lipid profiling, molecular diagnostics, and the technique demonstrates significant promise for 2D chemical mapping of tissue sections collected postmortem. In this review, an overview of the MALDI-TOF technique will be reported and manuscripts outlining current uses of the technology for veterinary science since 2019 will be summarized. This review concludes by discussing gaps in knowledge and areas of future growth. [ABSTRACT FROM AUTHOR]

Bloodstream infections are a leading cause of morbidity and mortality. The rapid diagnostic testing of positive blood cultures (PBCs) shortens times to effective therapy and the de-escalation of broad-spectrum empiric therapy. This is the first study examining the Qvella FASTTM System for the rapid (~20 min) purification of microorganisms directly from PBCs using BacT/Alert® FA/FAN bottles in the bioMérieux Virtuo instrument. We compared the performance of the FASTTM System Liquid ColonyTM (LC), for immediate downstream ID and phenotypic AST, to standard workflow involving colonies obtained by overnight subculture. The LC yielded a concordant species ID by VITEK MS in 121/138 (87.7%) samples, identifying 32 different Gram-positive and Gram-negative species with 3/123 (2.6%) discordances. Compared to standard workflow, direct AST of the LC using VITEK® 2 yielded 98.4% categorical agreement and 98.0% essential agreement. Very major error, major error, and minor error rates were 1.0%, 0.0%, and 1.8%, respectively, for Gram-negative organisms; and 1.9%, 0.2%, and 1.2%, respectively, for Gram-positive organisms. The median times from positive blood culture flag to results by FASTTM System for ID and AST were 7.8 h and 15.7 h, respectively, versus 22.4 h and 36.6 h for standard workflow, respectively. In conclusion, the FASTTM System provides reliable results for direct ID and AST from PBCs with significantly decreased turnaround times. [ABSTRACT FROM AUTHOR]

One of the biggest threats to human health today is the emergence of resistance among the most significant bacterial diseases. To identify outbreaks and the transmission of clinically important resistance genes and the genetic components associated with them in human infections, there is a need for genomic surveillance of antimicrobial resistance genes. The objective of this study is to evaluate the phenotype and genotype of antimicrobial resistance in clinically isolated gramnegative microorganism strains, as well as their molecular characterization. Microbiological identification was done using the automatic microbiological analyzer and GN ID REF21341 cards. The isolates' susceptibility to antimicrobials was evaluated using conventional disc diffusion. Using particular primers, resistance genes were amplified through PCR (applied biosystems). The identities of all 1470 isolates, including Escherichia coli (28%), Klebsiella pneumoniae (21%), Acinetobactor baumanii (7%), Serratia marcescens (6%), Enterobacter cloacae (6%), Proteus mirabilis (6%), Pseudomonas aeruginosa (5%), Citrobacter freundii (5%), Citrobacter braakii, Acinetobacter lwoffi, Enterobacter aerogenes and Proteus vulgaris (4%). All of these isolates exhibited multidrug resistance (MDR) to several kinds of antimicrobial medicines. Nine Carbapenem-resistant gramnegative bacilli strains were identified to be positive for blaNDM and blaOXA-1. Our study found a concerning association between these diseases' antimicrobial resistance and the routinely prescribed antibiotics. This discovery compromises the medical field's therapeutic options and encourages the use of specialists who have less potent antimicrobial effects. [ABSTRACT FROM AUTHOR]

Infections triggered by fungi of the genus Candida are widely known, although the high incidence and mortality factors are still unclear. The classic methods of identifying Candida species are subject to errors, requiring new techniques with faster and more accurate performance. We present a study for identifying fungi species by analyzing volatile organic compounds of cultures acquired and interpreted using Electronic Nose and Artificial Intelligence methods. The proposed approach contributes to establishing an agile and appropriate treatment, reducing the complications of the disease and the number of deaths. We perform experiments with three species of Candida obtaining accuracy above 90% in the fungi identification. Therefore, future works are encouraged to deal with more types of fungi to help create a new identification methodology faster and more reliable using artificial intelligence methods. [ABSTRACT FROM AUTHOR]

Background and objective: Infective endocarditis (IE) is an infection with a poor prognosis, and an associated in-hospital mortality of at least 25%. Optimal therapy of IE requires long-term effective antibiotic therapy and valve surgery in many cases. The aim of this study was to review the demographics, bacteriology, and outcomes of patients with IE admitted to a tertiary referral center in Mexico City, over a 10-year period. Methods: Retrospective cohort study of patients admitted at Instituto Nacional Salvador Zubiran with a new diagnosis of IE over a 10-year period, from January 2009 to January 2019. Patients who met the definition for definitive diagnosis of infective endocarditis according to the modified Duke criteria were included in the study. Results: There were 62 patients (50.85 ± 17.46 years, 40.3% females) with IE. The culprit microorganism was identified in all cases, with Staphylococcus aureus being the most frequently found (34%). Valve surgery was performed in 58.1%, while 41.9% only received medical treatment. The mortality rate was 25.8% at 30 days and 41.9% at 12 months. Comparing the surgical and medical treatment groups, we found that 50% and 36% in each group, respectively, had died within 12 months of admission. Conclusions: Our center has a high prevalence of health care-associated endocarditis, mostly related to the presence of intravascular access devices. Most of the patients had a surgical indication. Patients with type 2 diabetes mellitus and decreased right ventricular systolic function had an increased mortality rate at 12 months. [ABSTRACT FROM AUTHOR]

Copyright of Journal of Chinese Institute of Food Science & Technology is the property of Journal of Chinese Institute of Food Science & Technology Periodical Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

The identification of microorganisms using single-temperatures pyrolysis gas chromatography (ST-PyGC) has limitations, for example, the risk of missing characteristic peaks that are essential to the chemotaxonomic interpretation. In this paper, we proposed a new multi-temperature PyGC (MT-PyGC) method as an alternative to ST-PyGC, without sacrificing its speed and quality. Six bacteria (three Gram-positive and three Gram-negative), one micro-fungus and one archaeon, representing microorganisms from different domains, were analyzed by MT-PyGC. It is found that MT pyrograms cover a more complete range of characteristic peaks than ST. Coupling with thermogravimetric analysis, chemotaxonomic information extracted from pyrograms by MT-PyGC have the potential for the differentiation of microorganisms from environments including deep subterranean reservoirs and biomass conversion/biofuel production.

Urinary tract infections (UTIs), which can lead to pyelonephritis, urosepsis, and even death, are among the most prevalent infectious diseases worldwide, with a notable increase in treatment costs due to the emergence of drug-resistant pathogens. Current diagnostic strategies for UTIs, such as urine culture and flow cytometry, require time-consuming protocols and expensive equipment. We present here a machine learning-assisted colorimetric sensor array based on recognition of ligand-functionalized Fe single-atom nanozymes (SANs) for the identification of microorganisms at the order, genus, and species levels. Colorimetric sensor arrays are built from the SAN Fe 1 -NC functionalized with four types of recognition ligands, generating unique microbial identification fingerprints. By integrating the colorimetric sensor arrays with a trained computational classification model, the platform can identify more than 10 microorganisms in UTI urine samples within 1 h. Diagnostic accuracy of up to 97% was achieved in 60 UTI clinical samples, holding great potential for translation into clinical practice applications.

Bloodstream infections are a leading cause of morbidity and mortality. The rapid diagnostic testing of positive blood cultures (PBCs) shortens times to effective therapy and the de-escalation of broad-spectrum empiric therapy. This is the first study examining the Qvella FASTTM System for the rapid (~20 min) purification of microorganisms directly from PBCs using BacT/Alert® FA/FAN bottles in the bioMérieux Virtuo instrument. We compared the performance of the FASTTM System Liquid ColonyTM (LC), for immediate downstream ID and phenotypic AST, to standard workflow involving colonies obtained by overnight subculture. The LC yielded a concordant species ID by VITEK MS in 121/138 (87.7%) samples, identifying 32 different Gram-positive and Gram-negative species with 3/123 (2.6%) discordances. Compared to standard workflow, direct AST of the LC using VITEK® 2 yielded 98.4% categorical agreement and 98.0% essential agreement. Very major error, major error, and minor error rates were 1.0%, 0.0%, and 1.8%, respectively, for Gram-negative organisms; and 1.9%, 0.2%, and 1.2%, respectively, for Gram-positive organisms. The median times from positive blood culture flag to results by FASTTM System for ID and AST were 7.8 h and 15.7 h, respectively, versus 22.4 h and 36.6 h for standard workflow, respectively. In conclusion, the FASTTM System provides reliable results for direct ID and AST from PBCs with significantly decreased turnaround times.

The present study aimed to evaluate the diagnostic performance specificity (Sp), sensitivity (Se), positive predictive value (PPV), negative predictive value (NPV), and accuracy (Acc) of two chromogenic culture media for rapid identification of Gram-positive bacteria causing subclinical mastitis (SCM) in dairy cows. For this, the performance of chromogenic culture media Gram-positive (GP) and Staphylococcus (Staph) (CHROMagar ™, Paris—France) was evaluated in milk samples collected from: (1) lactating cows with SCM (n = 504), and (2) cows in the post-partum period (PP) (7 ± 3 days post-partum; n = 536). Rapid identification of Gram-positive bacteria in chromogenic media was performed by visual inspection of colony colors after 24 h of incubation at 37°C. Bacterial identification by MALDI-TOF mass spectrometry was considered the reference methodology for calculating: Acc, Se, Sp, PPV, NPV, and Cohen's Kappa coefficient of agreement (k). The chromogenic media GP showed high Acc for Strep. agalactiae/dysgalactiae identification in both samples of SCM (Se: 89.1%; Sp: 96.3% and Acc: 95.6%) and of cows in PP (Se: 100%; Sp: 99.0% and Acc: 99.1%). Similar results were observed for Strep. uberis/Enterococcus spp. identification (Se: 90.5%; Sp: 92.5% and Acc: 92.3%) in SCM samples and Se: 100%; Sp: 99.6% and Acc: 99.6% in samples of PP cows using the GP media. However, the GP chromogenic media showed low Se (25.0% in SCM samples and 50.0% in samples of cows in PP) for Staph. aureus identification, despite Sp and Acc were high (Sp: 98.3% and Acc: 95.4% in SCM and Sp samples: 99.4% and Acc: 98.9% in PP cow samples). Staph culture media showed high Acc for Staph. aureus identification (Se: 80.0%; Sp: 98.8% and Acc: 98.0% in SCM samples and Se: 66.7%; Sp: 100% and Acc: 99.6% in PP cow samples), although the low prevalence of Staph. epidermidis and Staph. saprophyticus limit inferences about the performance of identifying these pathogens in Staph media. In conclusion, despite the limitation of the GP media for identification of Staph. aureus, GP, and Staph chromogenic media obtained satisfactory diagnostic performance results for the rapid identification of the main Gram-positive pathogens associated with SCM.

Mammalian orthoreovirus (MRV), a non-enveloped virus with a ten-segmented double-stranded RNA genome, infects virtually all mammals, including humans. Human infection with MRV seems to be common in early childhood, but is rarely symptomatic. Despite the ubiquitous presence of MRV in mammals as well as in environmental waters, the molecular characterisation of the MRV genome remains to be fully elucidated. In this study, two novel strains, MRV-2 THK0325 and MRV-1 THK0617, were unintentionally isolated from wastewater in Japan via an environmental surveillance of enteric viruses. Homology and phylogenetic analysis demonstrated that all the segments of THK0325 were closely related to the MRV-2 Osaka strains, which were recently proposed to have existed for at least two decades in Japan. Most of the segments in THK0617 also showed a close relationship with the MRV-2 Osaka strains, but the M2, S1, and S3 segments belong to another MRV cluster. According to the S1 sequence, the determinant of serotype THK0617 was classified as MRV-1, and both the M2 and S3 segments were closely related to MRV-1 and -3 from the tree shrew in China. These results suggest that the MRV-2 Osaka-like strain spread widely throughout Japan, accompanied by intertypic reassortment occurring in East Asia. [ABSTRACT FROM AUTHOR]

Urinary tract infection is one of the most common bacterial infections leading to increased morbidity, mortality and societal costs. Current diagnostics exacerbate this problem due to an inability to provide timely pathogen identification. Surface enhanced Raman spectroscopy (SERS) has the potential to overcome these issues by providing immediate bacterial classification. To date, achieving accurate classification has required technically complicated processes to capture pathogens, which has precluded the integration of SERS into rapid diagnostics. This work demonstrates that gold-coated membrane filters capture and aggregate bacteria, separating them from urine, while also providing Raman signal enhancement. An optimal gold coating thickness of 50 nm was demonstrated, and the diagnostic performance of the SERS-active filters was assessed using phantom urine infection samples at clinically relevant concentrations (105 CFU/ml). Infected and uninfected (control) samples were identified with an accuracy of 91.1%. Amongst infected samples only, classification of three bacteria (Escherichia coli, Enterococcus faecalis, Klebsiella pneumoniae) was achieved at a rate of 91.6%. [ABSTRACT FROM AUTHOR]

Efficient and accurate identification of microorganisms throughout the food chain can potentially allow the identification of sources of contamination and the timely implementation of control measures. High throughput DNA sequencing represents a potential means through which microbial monitoring can be enhanced. While Illumina sequencing platforms are most typically used, newer portable platforms, such as the Oxford Nanopore Technologies (ONT) MinION, offer the potential for rapid analysis of food chain microbiomes. Initial assessment of the ability of rapid MinION-based sequencing to identify microbes within a simple mock metagenomic mixture is performed. Subsequently, we compare the performance of both ONT and Illumina sequencing for environmental monitoring of an active food processing facility. Overall, ONT MinION sequencing provides accurate classification to species level, comparable to Illumina-derived outputs. However, while the MinION-based approach provides a means of easy library preparations and portability, the high concentrations of DNA needed is a limiting factor. [ABSTRACT FROM AUTHOR]

Among the advantages of an electrowetting-on-dielectric (EWOD) chip are its uncomplicated fabrication and low cost; one of its greatest strengths that might be applied in the field of biomedical technology is that it can accurately control volume and reduces the amount of samples and reagents. We present an EWOD for the biochemical identification of microorganisms, which is required to confirm the source of microbial contamination or quality inspection of product-added bacteria, etc. The traditional kit we used existed in the market; the detection results are judged by the pattern of color change after incubation. After a preliminary study, we confirmed that an image-processing tool (ImageJ) provides a suitable method of analysis, and that, when the concentration of the sugar reagent is 38 µg/µL, the best operating parameters for the EWOD chip in silicone oil are 40 V and 1.5 kHz. Additionally, we completed the biochemical identification of five bacterial species on the EWOD chip at the required concentration of the kit. Next, we found a decreased duration of reaction and that the least number of bacteria that were identifiable on the chip lies between 100 and 1000 CFU per droplet. Because the number of bacteria required on the chip is much smaller than for the kit, we tested whether a single colony can be used for identification, which provided a positive result. Finally, we designed an experimental flow to simulate an actual sample in an unclean environment, in which we divided the various processed samples into four groups to conduct experiments on the chip.

The current study was intended to study the rotavirus infection occurring in camels in south of Iraq. In the beginning, 470 camel calves (CCs) were general-health-based investigated. The current work included 175 diarrheic and non-diarrheic CCs (DCCs) and (NDCCs), respectively, located in middle and south Iraq. Fifty fecal samples from DCCs and NDCCs were collected from different animal farms and sales locations of some provinces. One-step Rotavirus rapid test (OSRRT) and enzyme-linked immunosorbent assay (ELISA) were performed. The results for the rapid test showed higher positive rates of the diarrheic camel calves (DCCs), 35% and 37.1%, in both males and females, respectively, than those in non-diarrheic camel calves (NDCCs), 9.6% and 8.3%, in both males and females, respectively. The results indicated higher positive rates of the DCCs of age at >30 days, 22 (56.4%), than those in the NDCCs of age at >30 days and DCCs and NDCCs of age at d"30 days, 7 (14%), 5 (13.8%) and 2 (4%), respectively. For the highest infection rates, the results in March revealed 90% and 44.44% for both DCCs and NDCCs, respectively. For the highest infection rates, the results Mothana revealed 66.67% and 25% for both DCCs and NDCCs, respectively. For the ELISA, the results indicated higher positive rates 31.42% and 4.17%, of DCCs and NDCCs, respectively, in females than those from male calves 30% and 3.85%, respectively. The results indicated a higher positive rate 51.28% of the DCCs of age at >30 days than those in the NDCCs of age at >30 days and DCCs and NDCCs of age at d"30 days, 8%, 8.83% and 0%, respectively. For the highest infection rates, the results in March uncovered 80% and 33.33% for both DCCs and NDCCs, respectively. For the highest infection rates, the results Mothana revealed, 50% and 16.67%, for both DCCs and NDCCs, respectively. The study improves the presence of the rotavirus in the camel calves in the tested cities from Iraq. [ABSTRACT FROM AUTHOR]

Effective management of infectious osteomyelitis relies on timely microorganism identification and appropriate antibiotic therapy. Extracellular vesicles (EVs) carry protein and genetic information accumulated rapidly in the circulation upon infection. Rat osteomyelitis models infected by Staphylococcus aureus, Staphylococcus epidermidis, Pseudomonas aeruginosa, and Escherichia coli were established for the present study. Serum EVs were isolated 3 days after infection. The size and number of serum EVs from infected rats were significantly higher than those from controls. In addition, bacterial aggregation assay showed that the S. aureus and E. coli formed large aggregates in response to the stimulation of serum EVs from S. aureus-infected and E. coli-infected rats, respectively. Treatment of EVs-S. epidermidis led to large aggregates of S. epidermidis and E. coli, whereas stimulation of EVs-P. aeruginosa to large aggregates of S. aureus and P. aeruginosa. To evaluate the changes in EVs in osteomyelitis patients, 28 patients including 5 S. aureus ones and 21 controls were enrolled. Results showed that the size and number of serum EVs from S. aureus osteomyelitis patients were higher than those from controls. Further analysis using receiver operating characteristic curves revealed that only the particle size might be a potential diagnostic marker for osteomyelitis. Strikingly, serum EVs from S. aureus osteomyelitis patients induced significantly stronger aggregation of S. aureus and a cross-reaction with P. aeruginosa. Together, these findings indicate that the size and number of serum EVs may help in the diagnosis of potential infection and that EVs-bacteria aggregation assay may be a quick test to identify infectious microorganisms for osteomyelitis patients.

Effective management of infectious osteomyelitis relies on timely microorganism identification and appropriate antibiotic therapy. Extracellular vesicles (EVs) carry protein and genetic information accumulated rapidly in the circulation upon infection. Rat osteomyelitis models infected by Staphylococcus aureus, Staphylococcus epidermidis, Pseudomonas aeruginosa , and Escherichia coli were established for the present study. Serum EVs were isolated 3 days after infection. The size and number of serum EVs from infected rats were significantly higher than those from controls. In addition, bacterial aggregation assay showed that the S. aureus and E. coli formed large aggregates in response to the stimulation of serum EVs from S. aureus -infected and E. coli -infected rats, respectively. Treatment of EVs- S. epidermidis led to large aggregates of S. epidermidis and E. coli , whereas stimulation of EVs- P. aeruginosa to large aggregates of S. aureus and P. aeruginosa. To evaluate the changes in EVs in osteomyelitis patients, 28 patients including 5 S. aureus ones and 21 controls were enrolled. Results showed that the size and number of serum EVs from S. aureus osteomyelitis patients were higher than those from controls. Further analysis using receiver operating characteristic curves revealed that only the particle size might be a potential diagnostic marker for osteomyelitis. Strikingly, serum EVs from S. aureus osteomyelitis patients induced significantly stronger aggregation of S. aureus and a cross-reaction with P. aeruginosa. Together, these findings indicate that the size and number of serum EVs may help in the diagnosis of potential infection and that EVs-bacteria aggregation assay may be a quick test to identify infectious microorganisms for osteomyelitis patients. [ABSTRACT FROM AUTHOR]

Abortion in small ruminants is a significant problem in Iraq and causes severe economic losses in sheep farms. Chlamydia abortus causes enzootic abortion in ewes and is associated with reproductive problems in sheep in Sulaimani province - Northern Iraq. During a lambing season in 2017, abortion was widespread among several sheep flocks in different regions of Sulaimani (Kalar, Said Sadiq, and Chamchamal), and C. abortus was one of the causes. Accordingly, we carried out this study to isolate and identify C. abortus in aborted ewes in these regions. We collected 30 samples of aborted fetuses from five herds in which abortions had been observed. The pathogen isolation was done by inoculation into embryonated chicken eggs and conventional PCR was used to identify C. abortus in clinical specimens. C. abortus was identified in one of the 30 aborted fetuses (3.33%) from the Kalar district, and all the remaining 29 samples (96.66%) were found positive to Brucella abortus. The gene ompA encoding the outer membrane protein of C. abortus was sequenced and got the accession number MK643153 in NCBI GenBank. The sequence was named C. abortus strain Sul/2017. Our isolate showed 99.79% homology with Sul/014 (accession No. KY399850) and differed from the latter by two amino acid substitutions at E115K and K259N. The topology of the phylogenetic tree based on the ompA gene showed that the isolate belongs to C. abortus and has a common ancestor with isolates of sheep in Iraq and Tunisia with accession numbers KY399850 and HQ62243, respectively. [ABSTRACT FROM AUTHOR]

The aim of our study was to describe microorganisms which occur in the traditional Slovak cheese „Bryndza". There were a total of 60 cheese samples collected from ten different farms during May 2019. The microbiota studies included the total bacterial count, coliforms, enterococci, lactic acid bacteria, yeasts and microscopic fungi. The total bacterial counts were cultivated on plate count agar at 30 °C in aerobic conditions, lactic acid bacteria on MRS at 37 °C in anaerobic conditions, coliform on VRBL and VRBG at 37 °C in aerobic condition, yeasts and microscopic fungi on MEA at 25 °C under aerobic condition. Gram-positive, Gram-negative and yeasts isolates were identified with MALDI-TOF MS Biotyper. Totally, a number of 1175 isolates of G-, G+ and yeast were identified with score higher than 2 and moulds. Escherichia coli and Stenotrophomonas maltophilia were the most frequently identified species of Gram-negative and Leuconostoc mesenteroides ssp. mesenteroides and Lactococcus lactis ssp. lactis from Gram-positive bacteria. Yarrowia lipolitica and Kluyveromyces lactis were the most distributed yeasts. Lactic acid bacteria group was represented by Lactobacillus, Lactococcus, Leuconostoc and Pediococcus. The most abundant genera of lactic acid bacteria were Lactobacillus with 11 species. This study describes the indigenous microbiota of the traditional ewe's milk cheeses from Slovakia. [ABSTRACT FROM AUTHOR]

Mass spectrometry (MS) is a type of analysis used to determine what molecules make up a sample, based on the mass spectrum that are created by the ions. Mass spectrometers are able to perform traditional target analyte identification and quantitation; however, they may also be used within a clinical setting for the rapid identification of bacteria. The causative agent in sepsis is changed over time, and clinical decisions affecting the management of infections are often based on the outcomes of bacterial identification. Therefore, it is essential that such identifications are performed quickly and interpreted correctly. Matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometer is one of the most popular MS instruments used in biology, due to its rapid and precise identification of genus and species of an extensive range of Gram-negative and -positive bacteria. Microorganism identification by Mass spectrometry is based on identifying a characteristic spectrum of each species and then matched with a large database within the instrument. The present review gives a contemporary perspective on the challenges and opportunities for bacterial identification as well as a written report of how technological innovation has advanced MS. Future clinical applications will also be addressed, particularly the use of MALDI-TOF MS in the field of microbiology for the identification and the analysis of antibiotic resistance. [ABSTRACT FROM AUTHOR]

The implementation of MALDI-TOF MS in medical microbiology laboratories has revolutionized practices and significantly reduced turnaround times of identification processes. However, although bacteriology quickly benefited from the contributions of this technique, adjustments were necessary to accommodate the specific characteristics of fungi. MALDI-TOF MS is now an indispensable tool in clinical mycology laboratories, both for the identification of yeasts and filamentous fungi, and other innovative uses are gradually emerging. Based on the practical experience of our medical mycology laboratory, this review will present the current uses of MALDI-TOF MS and the adaptations we implemented, to allow their practical execution in a daily routine. We will also introduce some less mainstream applications, like those for fungemia, or even still under development, as is the case for the determination of sensitivity to antifungal agents or typing methods.

Ornithobacterium rhinotracheale is one of the most important bacterial agents of respiratory diseases in poultry. For correct identification and characterization of this fastidious bacterium, reliable diagnostic tools are essential. Still, phenotypic tests are used to identify O. rhinotracheale and serotyping is the most common method for characterization, despite known drawbacks and disadvantages such as divergent results, cross-reactivity between strains, or the non-typeability of strains. The intention of the present study was to evaluate MALDI-TOF MS and whole genome sequencing for the identification and characterization of O. rhinotracheale. For this purpose, a selection of 59 well-defined reference strains and 47 field strains derived from outbreaks on Austrian turkey farms were investigated by MALDI-TOF MS. The field strains originated from different geographical areas in Austria with some of the isolates derived from multiple outbreaks on farms within a year, or recurrent outbreaks over several years. MALDI-TOF MS proved a suitable method for identification of O. rhinotracheale to genus or species level except for 3 strains representing serotypes M, K and F. Phylogenetic analysis showed that most strains grouped within one cluster even though they were comprised of different serotypes, while serotypes F, K, and M clearly formed a different cluster. All field isolates from turkey farms clustered together, independent of the origin of the isolates, e.g., geographical area, multiple outbreaks within a year or recurrent outbreaks over several years. Whole genome sequencing of serotype M, K and F strains confirmed the extraordinary status and deviation from known fully-sequenced strains due to a lack of sequence similarity. This was further confirmed by alignments of single genes (16S-RNA and rpoB) and multilocus sequence typing although the demarcation was less obvious. Altogether, the results indicate that these three serotypes belong to a different species than O. rhinotracheale, and might even be members of multiple new species.

Fermentation is an essential process step to develop precursor compounds for aroma and flavour characteristics of chocolate, as well as preventing germination of the cocoa bean. Despite the importance of the role of microorganisms during the chocolate production, to date, there are some discrepancies of the "cocobiota" community found during fermentation and the impact of starter culture in fermented cocoa beans. This review provides both a detailed overview of the starter cultures used in fermented cocoa beans and the microbial diversity involved during this process, and an in-depth discussion of the methods used to identify these microorganisms. In this review, we included only published articles from 2008 to 2018 in English language. A total of forty-seven studies contributed to the description of the cocobiota from 13 different countries. In detail, we observed that the most common fermentation method used is the wooden box, followed by heap. Interestingly, 37% of the studies cited in this review did not mention the type of cocoa variety studied. Most of the techniques used to identify the microbiota are fingerprinting based (DGGE); however, few studies have been using next-generation technologies to elucidate the possible functions and interactions among microbes. Our results showed a greater diversity of yeasts if compared with bacterial involved in the fermentation. This review will help researchers seeking to design starter cultures to drive cocoa bean fermentation, and thus achieve a homogenous mass of fermented cocoa beans as well as serve as a guide for assessing methodologies for the identification of microorganisms. • The ecology of fermented cocoa is influenced by intrinsic and extrinsic factors. • Saccharomyces, Lactobacillus and Acetobacter are the main taxa in cocoa fermentation. • Several studies focus on the identification of " cocobiota". • Needed to correct identification and characterisation of starter cultures • Cocoa fermentation must standardise according regions and variety cultivated. [ABSTRACT FROM AUTHOR]

While some microbial eukaryotes can improve effluent quality in wastewater treatment plants (WWTPs), eukaryotic waterborne pathogens are a threat to public health. This study aimed to identify Eukarya, particularly faecal pathogens including Cryptosporidium , in different treatment stages (influent, intermediate and effluent) from four WWTPs in Western Australia (WA). Three WWTPs that utilise stabilisation ponds and one WWTP that uses activated sludge (oxidation ditch) treatment technologies were sampled. Eukaryotic 18S rRNA (18S) was targeted in the wastewater samples (n = 26) for next-generation sequencing (NGS), and a mammalian-blocking primer was used to reduce the amplification of mammalian DNA. Overall, bioinformatics analyses revealed 49 eukaryotic phyla in WWTP samples, and three of these phyla contained human intestinal parasites, which were primarily detected in the influent. These human intestinal parasites either had a low percent sequence composition or were not detected in the intermediate and effluent stages and included the amoebozoans Endolimax sp., Entamoeba sp. and Iodamoeba sp., the human pinworm Enterobius vermicularis (Nematoda), and Blastocystis sp. subtypes (Sarcomastigophora). Six Blastocystis subtypes and four Entamoeba species were identified by eukaryotic 18S NGS, however, Cryptosporidium sp. and Giardia sp. were not detected. Real-time polymerase chain reaction (PCR) also failed to detect Giardia , but Cryptosporidium -specific NGS detected Cryptosporidium in all WWTPs, and a total of nine species were identified, including five zoonotic pathogens. Although eukaryotic 18S NGS was able to identify some faecal pathogens, this study has demonstrated that more specific NGS approaches for pathogen detection are more sensitive and should be applied to future wastewater pathogen assessments. Image 1 • Western Australian WWTPs were studied for faecal pathogens with eukaryotic 18S NGS. • Stabilisation ponds and activated sludge treatment technologies were assessed. • Influent had the highest percent compositions of intestinal parasites. • Six Blastocystis subtypes and four Entamoeba species were identified. • Nine Cryptosporidium species/genotypes were only detected by Cryptosporidium -specific NGS. [ABSTRACT FROM AUTHOR]

The matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) technique is increasingly used in hospital laboratories for routine identification of microorganisms. However, its performance is variable, particularly for highly variable species such as Neisseria meningitidis. Reliable identification of N. meningitidis is crucial for the management of invasive meningococcal disease by rapid implementation of treatment and preventive measures among close contacts. We assessed and improved N. meningitidis identification by MALDI-TOF MS by enriching the databases with reference strains identified using whole genome sequencing (WGS) as a reference standard. We first built a collection of 24 strains from several species of the Neisseria genus that we characterized by WGS. This collection was added to the available database to test by MALDI-TOF MS another collection of 32 clinical isolates received between 2015 and 2017 at the French National Reference Laboratory for Meningococci. Using the commercially available library of mass spectrometry profiles, only 67% (95% confidence interval (CI), 47–82) concordance was observed at the species level between MALDI-TOF MS and WGS characterization. However, when the new enriched reference collection was used on the second subset of isolates, the identification of N. meningitidis was significantly improved (p 0.0016), showing 92% (95% CI, 75–98) specificity while that of the manufacturer's database alone was 52% (95% CI, 34–70). Our data highlight the need to update the available MALDI-TOF MS database with high-quality references to enhance the identification of N. meningitidis and avoid unwarranted preventive measures or missing identification. [ABSTRACT FROM AUTHOR]

BACKGROUND Methanol vapors, broadly emitted by industry, can be cost‐effectively treated by biofiltration. However, long‐term operation under high concentrations regularly encountered in the pulp and paper industry (> 5 g m−3) has been barely studied. RESULTS: Methanol concentrations between 1.6 and 14 g m−3 were treated in a biofilter. Complete methanol removal was obtained for concentrations up to 3.5 g m−3, for an empty bed retention time (EBRT) of 60 s. A higher EBRT (160 s) was necessary to eliminate all methanol for concentrations up to 7 g m−3. For higher concentrations, a maximum elimination capacity (ECmax) of 343.8 g m−3 h−1 was achieved. The main challenge encountered during the biofiltration of high methanol concentrations was excessive biomass buildup (with a performance drop due to clogging occurring every 2 weeks). Under high methanol concentrations, 11 bacteria, three fungi, and one yeast prevailed in the biofilm. Flies and fly larvae were detected when no biofilter clogging was observed, regulating biomass excess. CONCLUSIONS: High methanol concentrations trigger biomass growth and clogging. Diptera represent a research opportunity to control such phenomena. © 2019 Society of Chemical Industry [ABSTRACT FROM AUTHOR]

Background: Early detection of bacteria and their antibiotic susceptibility patterns are critical to guide therapeutic decision-making for optimal care of septic patients. The current gold standard, blood culturing followed by subculture on agar plates for subsequent identification, is too slow leading to excessive use of broad-spectrum antibiotic with harmful consequences for the patient and, in the long run, the public health. The aim of the present study was to assess the performance of two commercial assays, QuickFISH® (OpGen) and Maldi Sepsityper™ (Bruker Daltonics) for early and accurate identification of microorganisms directly from positive blood cultures. Materials and methods: During two substudies of positive blood cultures, the two commercial assays were assessed against the routine method used at the clinical microbiology laboratory, Unilabs AB, at Skaraborg Hospital, Sweden. Results: The Maldi Sepsityper™ assay enabled earlier microorganism identification. Using the cut-off for definite species identification according to the reference method (>2.0), sufficiently accurate species identification was achieved, but only among Gram-negative bacteria. The QuickFISH® assay was time-saving and showed high concordance with the reference method, 94.8% (95% CI 88.4–98.3), when the causative agent was covered by the QuickFISH® assay. Conclusions: The use of the commercial assays may shorten the time to identification of causative agents in bloodstream infections and can be a good complement to the current clinical routine diagnostics. Nevertheless, the performance of the commercial assays is considerably affected by the characteristics of the causative agents. [ABSTRACT FROM AUTHOR]

Introduction: Enterobacteria are the main group causing infections in humans. The aim of this review is to present the new genera and the taxonomic changes that the Enterobacteriacea family has experienced in recent years. Methodology: a systematic search of papers published in databases from January 2000 to July 2018 was done. Additionally, the bibliographic references of each document were reviewed and each paper citing the article was reviewed in search of clinical cases. Results: Nineteen new genera of Enterobacteria have been described since 2000. The genera Yersinia, Morganella and Erwinia do not belong to the family Enterobacteriacea anymore. Conclusions: for an adequate clinical and epidemiological interpretation, it is advisable to update the libraries of the commercial systems used for the identification of the microorganisms, as well as to train the staff in the taxonomic changes of microorganisms. [ABSTRACT FROM AUTHOR]

The use of petroleum-based synthetic plastics has led to a deleterious solid waste management especially in the form of marine debris and presents a major growing global pollution problem. In response to these issues, the application of biobased and biodegradable polymers as an alternative to synthetic plastics has been proposed. Polyhydroxyalkanoates (PHA) is a biodegradable microbial polymer. In this study, the biodegradation of this PHA both in soil and lake environment was evaluated. The percentage of degradation of the PHAs with various monomers such as poly (3-hydroxybutrate) [P(3HB)] and its copolymers poly(3-hydroxybutyrate-co-4-hydroxybutyrate) [P(3HB-co-4HB] in soil and lake was carried out. Besides, the modifications of these biopolymers into salt-leached films were also tested. Based on the results obtained, P(3HB-co-4HB) films showed the highest rate of degradation for both lake and soil environment. Also the degradation of PHA, mainly caused by microbial activity, isolation and identification microorganisms capable of degrading PHA was also carried out. Based on the degradation index, Pseudomonas species and Acidovorax species were isolated. [ABSTRACT FROM AUTHOR]

Several non-culture molecular (multiplex polymerase chain reaction assays, DNA microarrays, massive parallel DNA sequencing, in situ hybridization, microbiome profiling, and molecular typing of pathogens) and analytical (electrophoresis, gel electrophoresis, surface-enhanced Raman scattering, and mass spectrometry) tools have been developed in recent years for the identification of bacteria and diagnosis of bacterial infections from clinical samples. Among mass spectrometric techniques, electrospray ionization (ESI) and rapid evaporative ionization (REI) mass spectrometric (MS) techniques have attracted much attention in the identification of microorganisms (bacteria, fungi, and viruses), and in the diagnosis of various bacterial infections. This review highlights the developed ESI-MS-based methods, including polymerase chain reaction (PCR) combined with ESI-MS and capillary electrophoresis (CE) and liquid chromatography (LC)-ESI-MS, for the identification of microorganisms (pathogenic bacteria, fungi, and viruses) in various samples. Recent applications of ESI- and REI-MS in identifying pathogenic bacteria are depicted in tables, and some significant findings are summarized. [ABSTRACT FROM AUTHOR]

MALDI fingerprinting was first described two decades ago as a technique to identify microbial cell lines. Microbial fingerprinting has since evolved into an automated platform for microorganism identification and classification, which is now routinely used in clinical and environmental sectors. The extension of fingerprinting to mammalian cells has yet to progress partly due to compartmentalization of eukaryotic cells and overall higher cellular complexity. A number of publications on mammalian whole cell fingerprinting suggest that the method could be useful for classification of different cell types, cell states, and monitoring cell differentiation. We report the optimization of MALDI fingerprinting workflow parameters for mammalian cells and its application for differential profiling of mammalian cell lines and two-component cell line mixtures. Murine fallopian tube cells and high-grade ovarian carcinoma cell lines and their mixtures are used as model mammalian cell lines. Two-component cell mixtures serve to determine the method's feasibility for complex biological samples as the ability to detect cancer cells in a mixed cell population. The level of detection of cancer cells in the two-component mixture by principle component analysis (PCA) starts to deteriorate at 5% but with application of a different statistical approach, Wilcoxon rank sum test, the level of detection was determined to be 1%. The ability to differentiate heterogeneous cell mixtures will help further extend whole cell MALDI fingerprinting to complex biological systems.Graphical Abstract [ABSTRACT FROM AUTHOR]

Rapid and correct identification of microorganisms is an essential part of pharmaceutical analysis. Several phenotypic, genotypic, and proteotypic methods, each of which has its own advantages and limitations, are currently used to identify microorganisms. The aim of the present work was to reveal features and validate the operation of a Vitek 2 Compact 30 bacteriological analyzer (bioMerieux, France), which was based on determining the biochemical properties of microorganisms. The applicability of this method was determined using accuracy, precision, and robustness. Correct results were found in 86% of 396 cases. Results obtained under repeatability and intermediate precision conditions showed no differences. Approaches to molecular and genetic identification of microorganisms isolated from preparations in addition to automated biochemical identification were discussed. [ABSTRACT FROM AUTHOR]

The impact on time to results (TTR) and clinical decisions was evaluated for mono-microbial positive blood cultures (BC) processed using the BD Kiestra Work Cell Automation (WCA) system. Positive BC were processed by the WCA system by full-automatic subculture on solid media and digital imaging after 8 h of incubation (8-h method) followed by identification (ID) and antimicrobial susceptibility testing (AST). To evaluate the accuracy of the 8-h method, ID and AST from 8-h and overnight incubated colonies were compared for the same organisms. To evaluate its clinical impact, results from 102 BC processed by the 8-h method (cases) were compared with those from 100 BC processed by overnight incubation method (controls) in a comparable period. Identification after 8-h and overnight incubation gave concordant results in 101/102 (99.0%) isolates. Among a total of 1379 microorganism-antimicrobial combinations, categorical agreement was 99.4% (1371/1379); no very major error, 7 major errors, and one minor error were observed. TTR in cases (32.8 h ± 8.3 h) was significantly (p < 0.001) shorter than in controls (55.4 h ± 13.3 h). A significant reduction was observed for duration of empirical therapy (cases 54.8 h ± 23.3 h vs controls 86.9 h ± 34.1 h, p < 0.001) and 30-day crude mortality rate (cases 16.7% vs controls 29.0%, p < 0.037). Automation and 8-h digital reading of plates from positive BC, followed by ID and AST, greatly reduce TTR and shorten the duration of antimicrobial empiric therapy, possibly improving outcome in patients with mono-microbial bloodstream infections. [ABSTRACT FROM AUTHOR]

For patients with bloodstream infections, rapid initiation of the appropriate antimicrobial therapy is essential in reducing mortality and morbidity. New developments and automation in clinical microbiology labs speed up the identification and susceptibility results but are expensive. To gain insight in the added value of the new workflows, we simulated the possible impact of rapid identification and susceptibility tests on a real-life cohort of 158 positive blood culture episodes. Our routine workflow was theoretically challenged against two new workflows, one based on rapid identification with MALDI-TOF MS and one based on molecular testing. First, we observed an important role of the rapid communication of the gram stain results, as about one third of patients needed an adaptation of the antimicrobial therapy based on these results. Antibiotic adaptation based on the microorganism identification was necessary in 10% and in another 25% of cases after the availability of the susceptibility results. The added value of the newer workflow methods lies mainly in the field of the rapid identification and was rather limited in our cohort. In conclusion, for optimizing the blood culture workflow, each microbiology lab should critically scan its own workflow and know its own blood culture epidemiology, before investing in expensive or time-consuming processes. [ABSTRACT FROM AUTHOR]