scholarly journals Isolation of Elizabethkingia anophelis From COVID-19 Swab Kits

2022 ◽  
Vol 12 ◽  
Author(s):  
Liangcai Xu ◽  
Bo Peng ◽  
Yuxiang He ◽  
Yujun Cui ◽  
Qinghua Hu ◽  
...  
Keyword(s):  
Heat Resistance ◽  
Dna Sequence ◽  
Identification System ◽  
Metagenomic Sequencing ◽  
Bacterial Strains ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Definitive Method ◽  
Tof Ms ◽  
Control Samples

Purpose: To investigate and characterize the putative Elizabethkingia anophelis contaminant isolated from throat and anal swab samples of patients from three fever epidemic clusters, which were not COVID-19 related, in Shenzhen, China, during COVID-19 pandemic.Methods: Bacteria were cultured from throat (n = 28) and anal (n = 3) swab samples from 28 fever adolescent patients. The isolated bacterial strains were identified using matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF/MS) and the VITEK2 automated identification system. Nucleic acids were extracted from the patient samples (n = 31), unopened virus collection kits from the same manufacturer as the patient samples (n = 35, blank samples) and from unopened throat swab collection kits of two other manufacturers (n = 22, control samples). Metagenomic sequencing and quantitative real-time PCR (qPCR) detection were performed. Blood serum collected from patients (n = 13) was assessed for the presence of antibodies to E. anophelis. The genomic characteristics, antibiotic susceptibility, and heat resistance of E. anophelis isolates (n = 31) were analyzed.Results: The isolates were identified by MALDI-TOF/MS and VITEK2 as Elizabethkingia meningoseptica. DNA sequence analysis confirmed isolates to be E. anophelis. The patients’ samples and blank samples were positive for E. anophelis. Control samples were negative for E. anophelis. The sera from a sub-sample of 13 patients were antibody-negative for isolated E. anophelis. Most of the isolates were highly homologous and carried multiple β-lactamase genes (blaB, blaGOB, and blaCME). The isolates displayed resistance to nitrofurans, penicillins, and most β-lactam drugs. The bacteria survived heating at 56°C for 30 min.Conclusion: The unopened commercial virus collection kits from the same manufacturer as those used to swab patients were contaminated with E. anophelis. Patients were not infected with E. anophelis and the causative agent for the fevers remains unidentified. The relevant authorities were swiftly notified of this discovery and subsequent collection kits were not contaminated. DNA sequence-based techniques are the definitive method for Elizabethkingia species identification. The E. anophelis isolates were multidrug-resistant, with partial heat resistance, making them difficult to eradicate from contaminated surfaces. Such resistance indicates that more attention should be paid to disinfection protocols, especially in hospitals, to avoid outbreaks of E. anophelis infection.

scholarly journals Evaluation of the performance of MALDI-TOF MS and DNA sequence analysis in the identification of mycobacteria species

2018 ◽  
Vol 48 (6) ◽  
pp. 1351-357 ◽  
Author(s):  
Işın AKYAR ◽  
Cengiz ÇAVUŞOĞLU ◽  
Meltem AYAŞ ◽  
Süheyla SÜRÜCÜOĞLU ◽  
Arzu İLKİ ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Dna Sequence ◽  
Dna Sequence Analysis ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Tof Ms

scholarly journals The use of Principle Component Analysis and MALDI-TOF MS for the differentiation of mineral forming Virgibacillus and Bacillus species isolated from Sabkhas

2020 ◽  
Author(s):  
Rim Abdel Samad ◽  
Zulfa Al Disi ◽  
Mohammad Ashfaq ◽  
Nabil Zouari
Keyword(s):  
Clustering Analysis ◽  
Potential Role ◽  
Protein Profiling ◽  
Bacillus Species ◽  
Pca Analysis ◽  
Bacterial Strains ◽  
Protein Biomarkers ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Tof Ms

Occurrence of mineral forming and other bacteria in mats is well demonstrated. However, their high diversity shown by ribotyping was not explained, although it could explain the diversity of formed minerals. Common biomarkers as well as phylogenic relationships are useful tools to clustering the isolates and predict their potential role in the natural niche. In this study, combination of MALDI-TOF MS with PCA was shown a powerful tool to categorize 35 mineral forming bacterial strains isolated from Dohat Fshaikh sabkha, at northwest of Qatar (23 from decaying mats and 12 from living ones). 23 strains from decaying mats belong to Virgibacillus genus as identified by ribotyping and are shown highly involved in formation of protodolomite and a diversity of minerals. They were used as internal references in categorization of sabkha bacteria. Combination of isolation of bacteria on selective mineral forming media, their MALDI TOF MS protein profiling and PCA analysis established their relationship in a phyloproteomic based on protein biomarkers including m/z 4905, 3265, 5240, 6430, 7765, and 9815. PCA analysis clustered the studied strains into 3 major clusters, showing strong correspondence to the 3 phyloproteiomic groups that were established by the dendrogram. Both clustering analysis means have evidently demonstrated a relationship between known Virgibacillus strains and other related bacteria based on profiling of their synthesized proteins. Thus, larger populations of bacteria in mats can be easily screened for their potential to exhibit certain activities, which is of ecological, environmental and biotechnological significance.

scholarly journals Efficacy of MALDI-TOF mass spectrometry as well as genotypic and phenotypic methods in identification of staphylococci other than Staphylococcus aureus isolated from intramammary infections in dairy cows in Poland

2019 ◽  
Vol 31 (4) ◽  
pp. 523-530 ◽  
Author(s):  
Anna Wanecka ◽  
Jarosław Król ◽  
Jan Twardoń ◽  
Jacek Mrowiec ◽  
Agnieszka Korzeniowska-Kowal ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
16S Rrna ◽  
Species Level ◽  
Confirmatory Test ◽  
Identification System ◽  
Maldi Tof Ms ◽  
Intramammary Infections ◽  
Maldi Tof ◽  
Staphylococcus Spp ◽  
Tof Ms

We compared the effectiveness of various methods for the identification of Staphylococcus spp. other than S. aureus isolated from intramammary infections of cows on 3 dairy farms in Lower Silesia, Poland. A total of 131 isolates belonging to 18 Staphylococcus species were identified by sequence analysis of the 16S rRNA and dnaJ genes, as well using a commercial identification system (ID 32 STAPH; bioMérieux) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS; Bruker Daltonics). Sequencing of the 16S rRNA gene was found to have low discriminatory value because only 43% of isolates were recognized unequivocally. Much better results were obtained with the dnaJ gene (all isolates were correctly identified at the species level). However, some of these isolates achieved a low similarity level (<97%) and required a confirmatory test (sequencing of the rpoB gene). The performance of ID 32 STAPH was poor. Regardless of the probability level used (80% or 90%), the commercial system obtained identification rates <40%. Using MALDI-TOF MS and the commercial Bruker database, 67% of isolates were identified correctly with scores ≥2.0 (acceptable species-level identification) but this number increased to 97% after the database was expanded. The definitive identification of Staphylococcus spp. other than S. aureus causing intramammary infections in cattle often requires a combination of different procedures, and the existing databases should be updated.

scholarly journals Rapid differentiation of Staphylococcus aureus subspecies based on MALDI-TOF MS profiles

2018 ◽  
Vol 30 (6) ◽  
pp. 813-820 ◽  
Author(s):  
Marta Pérez-Sancho ◽  
Ana I. Vela ◽  
Pilar Horcajo ◽  
María Ugarte-Ruiz ◽  
Lucas Domínguez ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Rapid Identification ◽  
Automatic Identification ◽  
Identification System ◽  
Ionization Time ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Flight Mass Spectrometry ◽  
Different Origins ◽  
Tof Ms

Staphylococcus aureus encompasses 2 subspecies ( aureus and anaerobius) with significant differences in their epidemiology and pathogenicity. We evaluated the suitability of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for the rapid identification of both subspecies using a panel of 52 S. aureus isolates (30 subsp. anaerobius and 22 subsp. aureus) recovered from different origins, countries, and years. The on-board library identification system correctly identified 42 of 52 (81%) S. aureus isolates at the species level with score values >2.0. Limited performance was observed for differentiation of S. aureus subspecies (particularly subsp. anaerobius). Visual inspection of MALDI-TOF MS profiles identified 5 subspecies-specific mass peaks ( m/ z 3430 and 6861 in S. aureus subsp. anaerobius, and m/ z 4046, 6890, and 8093 in S. aureus subsp. aureus) with 100% sensitivity and specificity values, which is potentially useful for differentiating these subspecies. The suitability of 3 models, Genetic Analysis (GA), Quick Classifier (QC), and Supervised Neural Network, for automatic identification of both subspecies was evaluated using the Recognition Capability (RC) and Cross Validation (CV) values provided by the on-board ClinProTools software. The GA and QC models reached RC and CV values of 100%. Both models were externally validated using a panel of 26 S. aureus isolates of both subspecies, with both models correctly classifying all isolates of both subspecies. MALDI-TOF MS coupled with ClinProTools software represents a rapid and simple approach for S. aureus subspecies discrimination.

A comparison of Api 20A vs MALDI-TOF MS for routine identification of clinically significant anaerobic bacterial strains to the species level

2013 ◽  
Vol 92 (2) ◽  
pp. 209-212 ◽  
Author(s):  
Marta Kierzkowska ◽  
Anna Majewska ◽  
Robert T. Kuthan ◽  
Anna Sawicka-Grzelak ◽  
Grażyna Młynarczyk
Keyword(s):  
Species Level ◽  
Bacterial Strains ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Routine Identification ◽  
Clinically Significant ◽  
Tof Ms

scholarly journals Identification of airborne bacteria by 16S rDNA sequencing, MALDI-TOF MS and the MIDI microbial identification system

Aerobiologia ◽  
2015 ◽  
Vol 31 (3) ◽  
pp. 271-281 ◽  
Author(s):  
Else Marie Fykse ◽  
Torbjörn Tjärnhage ◽  
Tarmo Humppi ◽  
Vilde Sørvik Eggen ◽  
Andre Ingebretsen ◽  
...  
Keyword(s):  
16S Rdna ◽  
Identification System ◽  
Airborne Bacteria ◽  
16S Rdna Sequencing ◽  
Maldi Tof Ms ◽  
Microbial Identification ◽  
Maldi Tof ◽  
Rdna Sequencing ◽  
Microbial Identification System ◽  
Tof Ms

MALDI TOF MS – new possibilities in routine microbiological diagnostics

2019 ◽  
Vol 54 (2) ◽  
pp. 99-104
Author(s):  
Justyna Cieślik ◽  
Marta Wróblewska
Keyword(s):  
Multidrug Resistant ◽  
Modern Medicine ◽  
Correct Identification ◽  
Bacterial Strains ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Flight Mass Spectrometry ◽  
Short Period ◽  
Resistant Strains ◽  
Tof Ms

One of the problems of modern medicine is diagnosis, treatment and prophylaxis of infections caused by multidrug-resistant strains of bacteria. Fast and correct identification of these pathogens is of utmost importance, as it enables early implementation of effective therapy. Therefore, rapid, modern and affordable methods are of outstanding value as they make it possible to conduct a reliable analysis in a very short period of time. One of such techniques is matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), which in recent years is increasingly used in clinical microbiological laboratories. This method enables cheap, fast and reliable identification of microorganisms based on their protein profiles. At present the possibilities of use of MALDI-TOF MS method become more broad, e.g. for identification of microorganisms directly in positive blood culture samples, typing of bacterial strains in epidemiological investigation of an outbreak as well as detection of multidrug-resistant strains, including producers of carbapenemases.

scholarly journals Identification and Phylogenetic Analysis of Enterococcus Isolates Using MALDI-TOF MS, VITEK 2, and 16S rRNA Sequencing

2020 ◽  
Author(s):  
Se-Hyung Kim ◽  
Jung-Whan Chon ◽  
Hyo-Won Jeong ◽  
Kwang-Young Song ◽  
Dong-Hyeon Kim ◽  
...  
Keyword(s):  
16S Rrna ◽  
Phylogenetic Trees ◽  
Bacterial Species ◽  
Assay Method ◽  
Identification System ◽  
Rrna Gene ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Vitek 2 ◽  
Tof Ms

Abstract The bacterial genus Enterococcus encompasses 38 species. Two of the most common species are E. faecalis and E. faecium. Recently, however, there has been an increase in clinical reports concerning less prevalent Enterococcus species, such as E. durans, E. hirae, and E. gallinarum. Rapid and accurate laboratory methods are needed to facilitate the identification of all these bacterial species. In the present study, we compared the relative accuracy of matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS), VITEK 2, and 16S rRNA gene sequencing using 39 enterococci isolates from dairy samples, and compared the resultant phylogenetic trees. We found that MALDI-TOF MS correctly identified all isolates at the species level except for one, whereas the VITEK 2 system, which is an automated identification system using biochemical characteristics of species, misidentified ten isolates. However, phylogenetic trees constructed from both methods showed all isolates in similar positions. Our results clearly showed that MALDI-TOF MS is a reliable and rapid tool for identifying Enterococcus species with greater discriminatory power than the biochemical assay method of VITEK 2.

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