Microbial Identification Methods Research Articles

Development of a Rapid and Accurate Nanopore-based Sequencing Platform for on-Field Identification of Beer-Spoilage Bacteria in the Breweries

When a beer is contaminated with unknown microorganisms, rapid and accurate identification of the contaminants and risk assessment of their spoilage capability are of critical importance for proper corrective actions. Molecular-based identification techniques have been used for years to identify beer-spoilage bacteria in the breweries. However, these techniques require expensive, advanced analytical instruments (e.g., DNA sequencer, MALDI-TOF MS, etc.), and advanced skills, hindering their practical use for routine microbiological testing in the field. Thus, the evaluation and development of alternative methods for microbial identification that are low-cost, but rapid and provide the same level of accuracy, are a necessity. One particular technology is the nanopore-based sequencer, MinION, developed by Oxford Nanopore Technologies (ONT). MinION is a low cost, portable real-time device for DNA and RNA sequencing. We developed and evaluated a MinION sequencer-based platform for beer-spoilage bacterial identification. The near full length 16S rRNA gene of a wide variety of beer-spoilage bacteria and those commonly found in the brewery environment, were sequenced using three different sequencing kits and analyzed using the EPI2ME cloud-based analysis platform and a consensus sequence-based approach. The methods successfully rapidly identified test-microorganisms at a species level, (approx. 3.5 h from DNA extraction to data analysis) and with a high accuracy, similar to Sanger sequencing (average per. identity > 98.5%). The MinION sequencer-based microbial identification platform was shown to be a powerful tool for on-field rapid and accurate beer-spoilage bacterial identification, which could revolutionize the way microbial identification is performed in a brewery QC laboratory.

CHEMICAL AND BIOLOGICAL INDICATORS FOR EVALUATION OF ARCTIC SOIL DEGRADATION AND ITS POTENTIAL TO REMEDIATION

In recent years, significant efforts have been made to accelerate the economic development of the Arctic zone, leading to intense environmental pollution of this region, accompanied by the significant impact of accumulated environmental damage in the region. The solution to these problems is difficult due to the remoteness of these areas and severe climatic conditions. Therefore, it is important to evaluate the potential for restoration of arctic soils. For this purpose, various indicators are used, including biological ones. In the analyzed arctic soil samples, high concentrations of petroleum hydrocarbons (up to 47,000 mg/kg) and chloride-ions (0.10–0.14 wt %) were established. Microbioassay demonstrated a presence of hydrocarbon-oxidizing microorganisms: Penicillium, Azotobacter chroococcum, Bacillus subtilis, Pseudomonas oleovorans. A low enzymatic activity and specific Arctic climate point out a low self-restoration ability of the soil, demonstrated the need for its remediation. The microbioassay with microbial strains identification and soil remediation methods suitable for the Arctic zone were recommended.

Progress Report: Next-Generation Sequencing, Multiplex Polymerase Chain Reaction, and Broad-Range Molecular Assays as Diagnostic Tools for Fever of Unknown Origin Investigations in Adults.

Even well into the 21st century, infectious diseases still account for most causes of fever of unknown origin (FUO). Advances in molecular technologies, including broad-range polymerase chain reaction (PCR) of the 16S ribosomal RNA gene followed by Sanger sequencing, multiplex PCR assays, and more recently, next-generation sequencing applications, have transitioned from research methods to more commonplace in some clinical microbiology laboratories. They have the potential to supplant traditional microbial identification methods and antimicrobial susceptibility testing. Despite the remaining challenges with these technologies, publications in the past decade justify excitement about the potential to transform FUO investigations. We discuss available evidence using these molecular methods for FUO evaluations, including potential cost-benefits and future directions.

ПЕРСПЕКТИВНЫЕ НАПРАВЛЕНИЯ В ПИЩЕВОЙ МИКРОБИОЛОГИИ. МЕТОДЫ ВЫЯВЛЕНИЯ И ИДЕНТИФИКАЦИИ МИКРООРГАНИЗМОВ

Foodborne pathogens pose a serious problem for human health. Fast and accurate analytical methods are needed to ensure food quality and safety. This article analyzes promising methods for the detection and identification of microorganisms in food microbiology. The choice of analytical method depends on the available technology, the pathogens detected, the complexity of sampling and sample averaging, the urgency of the test, and the expected microbial load. Having analyzed the various methods of microbial detection and identification in food microbiology, it can be concluded that all methods have both advantages and disadvantages and, therefore, the gap between sophisticated technology, research advances and the specific application of developed methods in routine analysis needs to be filled. The creation of a fast, cheap and non-labor-intensive method will serve as a breakthrough in food microbiology and will allow laboratories to quickly and qualitatively conduct research to ensure food safety

Rapid identification of microbial contaminants in pharmaceutical products using a PCA/LDA-based FTIR-ATR method

Microbiological quality of pharmaceuticals is fundamental in ensuring efficacy and safety of medicines. Conventional methods for microbial identification in non-sterile drugs are widely used; however they can be time-consuming and laborious. The aim of this paper was to develop a chemometric-based rapid microbiological method (RMM) for identifying contaminants in pharmaceutical products using Fourier transform infrared with attenuated total reflectance spectrometry (FTIR-ATR). Principal components analysis (PCA) and linear discriminant analysis (LDA) were used to obtain a predictive model capable of distinguishing Bacillus subtilis (ATCC 6633), Candida albicans (ATCC 10231), Enterococcus faecium (ATCC 8459), Escherichia coli (ATCC 8739), Micrococcus luteus (ATCC 10240), Pseudomonas aeruginosa (ATCC 9027), Salmonella typhimurium (ATCC 14028), Staphylococcus aureus (ATCC 6538), and Staphylococcus epidermidis (ATCC 12228) microbial growth. FTIR-ATR spectra provide data on proteins, DNA/RNA, lipids, and carbohydrates constitution of microbial growth. Microbial identification provided by PCA/LDA based on FTIR-ATR method were compatible with those obtained using traditional microbiological methods. The chemometric-based FTIR-ATR method for rapid identification of microbial contaminants in pharmaceutical products was validated by assessing the sensitivity (93.5%), specificity (83.3%), and limit of detection (17-23 CFU/mL of sample). Therefore, we propose that FTIR-ATR spectroscopy may be used for rapid identification of microbial contaminants in pharmaceutical products and taking into account the samples studied

Annotation of Ribosomal Protein Mass Peaks in MALDI-TOF Mass Spectra of Bacterial Species and Their Phylogenetic Significance

Although MALDI-TOF mass spectrometry based microbial identification has achieved a level of accuracy that facilitate its use in classifying microbes to the species and strain level, questions remain on the identities of the mass peaks profiled from individual microbial species. Specifically, in the popular approach of comparing the mass spectrum of known and unknown microbes for identification purposes, the identities of the mass peaks were not taken into consideration. This study sought to determine if ribosomal proteins could account for some of the mass peaks profiled in MALDI-TOF mass spectra of different bacterial species. Using calculated molecular mass of ribosomal proteins for annotating mass peaks in bacterial species’ MALDITOF mass spectra downloaded from the SpectraBank database, this study revealed that ribosomal proteins could account for the low molecular weight mass peaks of <10000 Da. However, contrary to published reports, ribosomal proteins could not account for most of the mass peaks profiled. In particular, the data revealed that between 1 and 6 ribosomal protein mass peaks could be annotated in each mass spectrum. Annotated ribosomal proteins were S16, S17, S18, S20 and S21 from the small ribosome subunit, and L27, L28, L29, L30, L31, L31 Type B, L32, L33, L34, L35 and L36 from the large ribosome subunit. The ribosomal proteins with the most number of mass peak annotations were L36 and L29, with L34, L33, and L31 completing the list of ribosomal proteins with large number of annotations. Given the highly conserved nature of most ribosomal proteins, possible phylogenetic significance of the annotated ribosomal proteins were investigated through reconstruction of maximum likelihood phylogenetic trees. Results revealed that except for ribosomal protein L34, L31, L36 and S18, all annotated ribosomal proteins hold phylogenetic significance under the criteria of recapitulation of phylogenetic cluster groups present in the phylogeny of 16S rRNA. Phylogenetic significance of the annotated ribosomal proteins was further verified by the phylogenetic tree constructed based on the concatenated amino acid sequence of L29, S16, S20, S17, L27 and L35. Finally, analysis of the structure of the annotated ribosomal proteins did not reveal a high conservation of structure of the ribosomal proteins. Collectively, small low molecular weight (<10000 Da) ribosomal proteins could annotate some of the mass peaks in MALDI-TOF mass spectra of various bacterial species, and most of the ribosomal proteins hold phylogenetic significance. However, structural analysis did not identify a conserved structure for the annotated ribosomal proteins. Annotation of ribosomal protein mass peaks in MALDI-TOF mass spectra highlighted the deep biological basis inherent in the mass spectrometry-based microbial identification method.

Identification of Microorganisms by Liquid Chromatography-Mass Spectrometry (LC-MS1) and in Silico Peptide Mass Libraries

Over the past decade, modern methods of MS (MS) have emerged that allow reliable, fast and cost-effective identification of pathogenic microorganisms. Although MALDI-TOF MS has already revolutionized the way microorganisms are identified, recent years have witnessed also substantial progress in the development of liquid chromatography (LC)-MS based proteomics for microbiological applications. For example, LC-tandem MS (LC-MS2) has been proposed for microbial characterization by means of multiple discriminative peptides that enable identification at the species, or sometimes at the strain level. However, such investigations can be laborious and time-consuming, especially if the experimental LC-MS2 data are tested against sequence databases covering a broad panel of different microbiological taxa. In this proof of concept study, we present an alternative bottom-up proteomics method for microbial identification. The proposed approach involves efficient extraction of proteins from cultivated microbial cells, digestion by trypsin and LC-MS measurements. Peptide masses are then extracted from MS1 data and systematically tested against an in silico library of all possible peptide mass data compiled in-house. The library has been computed from the UniProt Knowledgebase covering Swiss-Prot and TrEMBL databases and comprises more than 12,000 strain-specific in silico profiles, each containing tens of thousands of peptide mass entries. Identification analysis involves computation of score values derived from correlation coefficients between experimental and strain-specific in silico peptide mass profiles and compilation of score ranking lists. The taxonomic positions of the microbial samples are then determined by using the best-matching database entries. The suggested method is computationally efficient - less than 2 mins per sample - and has been successfully tested by a test set of 39 LC-MS1 peak lists obtained from 19 different microbial pathogens. The proposed method is rapid, simple and automatable and we foresee wide application potential for future microbiological applications.

Assessment of Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF- MS) for Accurate Bacterial Identification in Clinical Labs

Abstract Introduction/Objective On behalf of the diagnostic Medical Laboratory rapid, and accurate identification of bacteria with their one-to-one anti-microbial susceptibility outlines is of ultimate importance for the management of infected patients. Contemporary microbial identification methods employed in routine clinical diagnostic laboratories relies on the use of conventional phenotypic methods. Phenotypic methods are time consuming with minimum turn-around times of at least 24 hrs and in many occurrences of 48hrs. With the intention of accelerate laboratory processes the MALDI-TOF MS was familiarized. MALDI-TOF MS is established on proteomic profiling and permits for rapid identification of bacteria. This technology has not been widely used in Egypt, but has been regularly used in Europe for the past few years. Methods Two hundred forty three positive non duplicate blood cultures were accrued over a period of six months. Experimental aliquots were taken from excess sample material that was collected as part of routine clinical care. 105 were positive for Gram negative bacilli, 123 were positive for Gram positive cocci, 3 positive for Gram positive bacilli, and 7 were positive for yeast. MALDI-TOF identification was compared to conventional identification. Conventional identification consisted of a combination of MALDI-TOF identification of a subcultures colony by direct smear, biochemical reactions, Vitek 2, and molecular identification. Results Ninety seven of the one hundred and five blood cultures positive for Gram negative bacilli were monomicrobial. The majority of these were identified as Escherichia coli by conventional methods, followed by Klebsiella pneumoniae and Pseudomonas aeruginosa. Eighty-four of these monomicrobial cultures were identified by MALDI-TOF to the species level. Eighty-one of the eighty-four were concordant with the conventional identification (96.4%). Conclusion The MALDI-TOF proved to be useful for the rapid and reliable identification of g-ve bacteria from the clinical specimens. The difference in turnaround time for bacterial identification was significant between MALDI-TOF MS and VITEK 2 with minimal preparation for the blood cultures.

Bioinformatics in the identification of microorganisms

Rapid and accurate identification of microorganisms can be of great value for clinical management. For many fastidious and slow-growing microorganisms, the conventional method used for detection is time-consuming, costly and labour-intensive. Hence, the development of new and improved microbial identification methods are necessary to overcome this bottleneck. Current trend has shifted towards the use of new molecular technologies in genomics and proteomics for bacterial identification and characterization. This mini review will focus on summarizing different types of genotypic and proteomics identification methods, as well as bioinformatics tools used for rapid identification and characterization of microorganisms from various specimens.

Microbial detection and identification methods: Bench top assays to omics approaches.

Rapid detection of foodborne pathogens, spoilage microbes, and other biological contaminants in complex food matrices is essential to maintain food quality and ensure consumer safety. Traditional methods involve culturing microbes using a range of nonselective and selective enrichment methods, followed by biochemical confirmation among others. The time-to-detection is a key limitation when testing foods, particularly those with short shelf lives, such as fresh meat, fish, dairy products, and vegetables. Some recent detection methods developed include the use of spectroscopic techniques, such as matrix-assisted laser desorption ionization-time of flight along with hyperspectral imaging protocols.This review presents a comprehensive overview comparing insights into the principles, characteristics, and applications of newer and emerging techniques methods applied to the detection and identification of microbes in food matrices, to more traditional benchtop approaches. The content has been developed to provide specialist scientists a broad view of bacterial identification methods available in terms of their benefits and limitations, which may be useful in the development of future experimental design. The case is also made for incorporating some of these emerging methods into the mainstream, for example, underutilized potential of spectroscopic techniques and hyperspectral imaging.

Assessing Gram-stain error rates within the pharmaceutical microbiology laboratory

Gram-staining remains the fundamental method for determinative bacteriology, dividing bacteria into Gram-positive and Gram-negative organisms. This test provides information as to the origin of any contamination and is a pre-requisite for many microbial identification methods. Despite the longevity of the test, the test is highly reliant upon analyst technique and therefore errors occur. While there are a few studies looking at errors in the clinical context, research has not been extended to the pharmaceutical microbiology laboratory context. In this study, we present a review of over 6,000 Gram-stains and establish an error rate of around 3%, with the most common reason for error being an over-decolourisation step resulting in organisms that should be Gram-positive appearing as Gram-negative. The analysis enables others to benchmark their facilities against.

Impact of rapid microbial identification on clinical outcomes in bloodstream infection: the RAPIDO randomized trial

ObjectivesBloodstream infection has a high mortality rate. It is not clear whether laboratory-based rapid identification of the organisms involved would improve outcome. MethodsThe RAPIDO trial was an open parallel-group multicentre randomized controlled trial. We tested all positive blood cultures from hospitalized adults by conventional methods of microbial identification and those from patients randomized (1:1) to rapid diagnosis in addition to matrix-assisted desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) performed directly on positive blood cultures. The only primary outcome was 28-day mortality. Clinical advice on patient management was provided to members of both groups by infection specialists. ResultsFirst positive blood culture samples from 8628 patients were randomized, 4312 into rapid diagnosis and 4136 into conventional diagnosis. After prespecified postrandomization exclusions, 2740 in the rapid diagnosis arm and 2810 in the conventional arm were included in the mortality analysis. There was no significant difference in 28-day survival (81.5% 2233/2740 rapid vs. 82.3% 2313/2810 conventional; hazard ratio 1.05, 95% confidence interval 0.93–1.19, p 0.42). Microbial identification was quicker in the rapid diagnosis group (median (interquartile range) 38.5 (26.7–50.3) hours after blood sampling vs. 50.3 (47.1–72.9) hours after blood sampling, p < 0.01), but times to effective antimicrobial therapy were no shorter (respectively median (interquartile range) 24 (2–78) hours vs. 13 (2–69) hours). There were no significant differences in 7-day mortality or total antibiotic consumption; times to resolution of fever, discharge from hospital or de-escalation of broad-spectrum therapy or 28-day Clostridioides difficile incidence. ConclusionsRapid identification of bloodstream pathogens by MALDI-TOF MS in this trial did not reduce patient mortality despite delivering laboratory data to clinicians sooner.

Utilização da espectrometria de massa MALDI-TOF para avaliação microbiológica de leite e derivados

Leite e seus derivados são alimentos que se destacam pelo elevado teor nutritivo. Essa característica permite que seja encontrada uma grande diversidade de micro-organismos nesses produtos, incluindo aqueles considerados desejáveis e indesejáveis. Associado a isso, um elevado volume de leite tem sido produzido mundialmente, demandando que métodos mais práticos e acurados, como a espectrometria de massa MALDI-TOF, sejam aplicados para avaliação microbiológica de produtos lácteos. Essa metodologia se baseia na ionização e dessorção de proteínas microbianas, que em seguida são aceleradas em um tubo a vácuo. De acordo com o tempo de voo ao longo do tubo das diferentes partículas ionizadas que compunham a amostra, são formados espectros característicos que podem ser comparados aos espectros presentes no banco de dados do aparelho, permitindo uma identificação do micro-organismo. Muitos estudos científicos têm demonstrado que a identificação por MALDI-TOF de distintos micro-organismos isolados de produtos lácteos (leite fluido, queijos e leites fermentados) foi compatível com o resultado obtido por métodos de sequenciamento genético (gene rRNA 16S), que é considerado o padrão-ouro para identificação microbiana. Apesar de ser um método novo e que demanda um considerável investimento para aquisição do aparelho, seu desempenho tem sido satisfatório e promissor. Portanto, há uma grande perspectiva futura para sua utilização de forma mais efetiva na identificação de micro-organismos provenientes de produtos lácteos.

Study on Odor Detection and Microbial Identification Method in Closed Water Area of Jiangxi Province

Study on Odor Detection and Microbial Identification Method in Closed Water Area of Jiangxi Province

Application of colony BOXA2R-PCR for the differentiation and identification of lactic acid COCCI

Repetitive-PCR (rep-PCR) is a well-established genetic method for bacterial strain fingerprinting that is used mostly with REP, ERIC, (GTG)5, BOXA1R and occasionally BOXA2R repetitive primers. In this study, it was demonstrated that BOXA2R-PCR could effectively discriminate between Lactococcus lactis, Leuconostoc mesenteroides and Streptococcus thermophilus; differentiate Lactococcus lactis strains and subspeciate them into lactis and cremoris in a single reaction; generate unique strain fingerprints of various lactic acid bacteria (LAB species) commonly isolated from fermented dairy products, including occasional spoilage bacteria and yeasts. Furthermore, using direct colony PCR a reproducible and rapid method was developed for the differentiation and identification of lactic acid cocci. The simplicity and speed of this microbial identification method has potential practical value for dairy microbiologists, which was demonstrated through a microbiota investigation of select Australian retail dairy products.

Methods of Microbial Identification During Drug Quality Analysis and Applicability Assessment

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.

Application of matrix-assisted laser desorption ionization time-of-flight mass spectrometry for rapid and accurate identification of Ralstonia solanacearum and Ralstonia pseudosolanacearum

Ralstonia solanacearum “species complex” (RSSC) represents soil-borne plant pathogenic bacteria, consisting of diverse and widespread strains that cause bacterial wilt on a wide range of host plants. A recent polyphasic taxonomic study has divided the RSSC into three bacterial species; Ralstonia pseudosolanacearum (phylotypes I and III), Ralstonia solanacearum (phylotype II) and Ralstonia syzygii (phylotype IV). Currently, standard identification of RSSC in plant health laboratories mainly relies on performance of two tests that are based on a different principle. However, these tests are inadequate to precisely discriminate among the three bacterial species in the RSSC. The accurate identification of each of the three bacterial species in the RSSC requires additional molecular tests, including a phylotype determination. These methodologies are labor-intensive, time consuming and rather impractical for routine identification purposes in a plant health laboratory. We explored the potential for an accurate identification of R. pseudosolanacearum (phylotypes I and III) and R. solanacearum (phylotype II) in RSSC, upon implementation of the MALDI-TOF MS tool, and after the creation and validation of an in-house database supplementing the commercial database and covering the entire known genetic diversity in RSSC. MALDI-TOF MS is an emerging approach for identification of bacterial plant pathogens and has been shown to be robust and reproducible. Additionally, when compared to the conventional microbial identification methods it is shown to be less laborious and less expensive. Validation data demonstrated that our in-house database (Mass Spectra Profiles, MSPs) was very specific resulting in the rapid and accurate identification of Ralstonia solanacearum (phylotype II), and Ralstonia pseudosolanacearum (phylotypes I and III). Additionally, no false positive results were obtained with our in-house database for other related Ralstonia sp., such as the R. picketii isolate PD 3286, or for the Pseudomonas syringae and Pseudomonas spp. isolates.

A universal PCR method and its application in sequence-based identification of microorganisms in dairy

To resolve problems with dairy product quality related to microbial contamination, it is necessary to be able to identify microorganisms in those dairy products quickly and accurately. With traditional PCR-based methods for microbial identification, specific primers need to be designed for the different microorganisms. In this study, we developed a universal PCR method with two semi-random primers to amplify microbial genomic DNA without considering the gene sequence of the test microorganism. The sequence obtained using this method was specific and could be used to identify the microorganism. The DNA sequences of known microorganisms related to dairy were amplified and identified to the species level, confirming the validity of this method. The DNA sequences of unknown common microorganisms were then amplified directly without culturing, and these microorganisms could also be identified to the species level. Compared with the common rRNA sequencing methods, this new method has high universality and resolution.

Simple Sample Preparation Method for Direct Microbial Identification and Susceptibility Testing From Positive Blood Cultures.

Rapid identification and determination of the antibiotic susceptibility profiles of the infectious agents in patients with bloodstream infections are critical steps in choosing an effective targeted antibiotic for treatment. However, there has been minimal effort focused on developing combined methods for the simultaneous direct identification and antibiotic susceptibility determination of bacteria in positive blood cultures. In this study, we constructed a lysis-centrifugation-wash procedure to prepare a bacterial pellet from positive blood cultures, which can be used directly for identification by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) and antibiotic susceptibility testing by the Vitek 2 system. The method was evaluated using a total of 129 clinical bacteria-positive blood cultures. The whole sample preparation process could be completed in <15 min. The correct rate of direct MALDI-TOF MS identification was 96.49% for gram-negative bacteria and 97.22% for gram-positive bacteria. Vitek 2 antimicrobial susceptibility testing of gram-negative bacteria showed an agreement rate of antimicrobial categories of 96.89% with a minor error, major error, and very major error rate of 2.63, 0.24, and 0.24%, respectively. Category agreement of antimicrobials against gram-positive bacteria was 92.81%, with a minor error, major error, and very major error rate of 4.51, 1.22, and 1.46%, respectively. These results indicated that our direct antibiotic susceptibility analysis method worked well compared to the conventional culture-dependent laboratory method. Overall, this fast, easy, and accurate method can facilitate the direct identification and antibiotic susceptibility testing of bacteria in positive blood cultures.

A simple method for rapid microbial identification from positive monomicrobial blood culture bottles through matrix-assisted laser desorption ionization time-of-flight mass spectrometry.

Rapid identification of microbes in the bloodstream is crucial in managing septicemia because of its high disease severity, and direct identification from positive blood culture bottles through matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) can shorten the turnaround time. Therefore, we developed a simple method for rapid microbiological identification from positive blood cultures by using MALDI-TOF MS. We modified previously developed methods to propose a faster, simpler and more economical method, which includes centrifugation and hemolysis. Specifically, our method comprises two-stage centrifugation with gravitational acceleration (g) at 600g and 3000g, followed by the addition of a lysis buffer and another 3000g centrifugation. In total, 324 monomicrobial bacterial cultures were identified. The success rate of species identification was 81.8%, which is comparable with other complex methods. Theidentification success rate was the highest for Gram-negative aerobes (85%), followed by Gram-positive aerobes (78.2%) and anaerobes (67%). The proposed method requires less than 10min, costs less than US$0.2 per usage, and facilitates batch processing. We conclude that this method is feasible for clinical use in microbiology laboratories, and can serve as a reference for treatments or further complementary diagnostic testing.