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2021 ◽  
Author(s):  
Catharine Rose Carlin ◽  
Jingqiu Liao ◽  
Lauren K Hudson ◽  
Tracey L Peters ◽  
Thomas G Denes ◽  
...  

Soil samples collected in the Great Smoky Mountains National Park yielded a Listeria isolate that could not be classified to the species level. Whole-genome sequence-based average nucleotide identity BLAST and in silico DNA-DNA Hybridization analyses confirmed this isolate to be a novel Listeria sensu stricto species with the highest similarity to L. marthii (ANI=93.9%, isDDH=55.9%). Additional whole-genome-based analysis using the Genome Taxonomy Database Toolkit, an automated program for classifying bacterial genomes, further supported delineation as a novel Listeria sensu stricto species, as this tool failed to assign a species identification but identified L. marthii as the closest match. Phenotypic and genotypic characterization results indicate that this species is nonpathogenic. Specifically, the novel Listeria species described here is phenotypically (i) non-hemolytic and (ii) negative for phosphatidylinositol-specific phospholipase C activity; the draft genome lacks all virulence genes found in the Listeria pathogenicity island 1 (LIPI-1), as well as the internalin genes inlA and inlB. While the type strain for the new species is phenotypically catalase-negative (an unusual characteristic for Listeria sensu stricto species), its genome contained an apparently intact catalase gene (kat); hence assessment of this phenotype with future isolates will be important. Rapid species identification systems (Listeria API, VITEK 2, VITEK MS) misidentified this novel species as either L. monocytogenes, L. innocua, or L. marthii. We propose the name L. swaminathanii, and the type strain is FSL L7-0020T (=ATCC TSD-239T).


2021 ◽  
Vol 4 (2) ◽  
pp. 72
Author(s):  
Huyyirnah Huyyirnah ◽  
Rosmaniar R

Isolasi bakteri pendegradasi hidrokarbon memerlukan teknik yang baik dan nutrisi optimal untuk pertumbuhannya. Kendala dalam pembuatan medium dan pengamatan isolat bakteri yang mengandung hidrokarbon sering terjadi di laboratorium, sehingga dibutuhkan teknik pengembangan metode dalam proses isolasi bakteri pendegradasi hidrokarbon. Penelitian ini bertujuan untuk mengetahui dan membandingkan jumlah dan jenis koloni bakteri yang tumbuh dalam medium Zobell+saline-water soluble fraction (SSF) dibandingkan dengan medium Zobell+minyak bumi. Metode penelitian yaitu mengisolasi bakteri menggunakan medium Zobell+SSF 6 jam (A), 12 jam (B), 24 jam (C) dan sebagai kontrol adalah medium Zobell+1% v/v minyak bumi (K), perhitungan bakteri menggunakan metode TPC dan mengidentifikasi bakteri dengan alat VITEK-MS. Hasil penelitian memperlihatkan bahwa jumlah bakteri yang tumbuh pada medium Zobell+SSF 24 jam (C) adalah 6.9 x 108 CFU/ml, hal ini menunjukkan lebih baik dibandingkan dengan Zobell+1% v/v minyak bumi (K)=5.2 x 108 CFU/ml, medium Zobell+SSF 12 jam (B)=6.6 x 107 CFU/ml dan medium Zobell+SSF 6 jam (A)=1.8 x 107 CFU/ml.Kesimpulan penelitian ini adalah bahwa dari segi jumlah total bakteri medium modifikasi Zobell+SSF pengadukan selama 24 jam (C) lebih baik dalam menumbuhkan bakteri pendegradasi hidrokarbon dibandingkan dengan pengadukan 6 jam (A), 12 jam (B), dan medium Zobell+1% v/v minyak bumi (K). Sedangkan apabila berdasarkan dengan keragaman bakteri, didapatkan hasil bahwa strain bakteri yang terisolasi pada medium modifikasi Zobell+SSF perlakuan pengadukan 6, 12, 24 jam sama dengan strain bakteri yang tumbuh pada kontrol (medium Zobell +1% v/v minyak bumi. Bakteri yang teridentifikasi sebagai bakteri pendegaradsi hidrokarbon adalah bakteri Klebsiella pneumoniae, Enterobacter asburiae/Enterobacter cloacae dan Pseudomonas aeruginosa.


2021 ◽  
Vol 2021 ◽  
pp. 1-5
Author(s):  
Ândrea Celestino de Souza ◽  
Luciano Z. Goldani ◽  
Eliane Würdig Roesch ◽  
Larissa Lutz ◽  
Patricia Orlandi Barth ◽  
...  

Determination of the susceptibility profile of isolates of Candida from blood culture bottles is extremely important for correctly guiding patient pharmacotherapy. The aim of this study was to compare the results of analysis of Candida isolated directly from blood culture bottles by the VITEK MS MALDI-TOF identification system and the fluconazole disk diffusion assay with those of standard identification methods. Testing directly from the bottle allowed results 24 to 48 hours quicker than the standard method. There was a categorical agreement of 51.64% (47 of 91 samples) between the results of analysis directly from the bottle and analysis by the standard method. Regarding species identification, there was 96.15% agreement for Candida parapsilosis (25 of 26 samples). Categorical agreement between the rapid and standard disk diffusion methods was 95%, and the agreement between the rapid disk diffusion method and the broth microdilution method was 97%. Only minor errors in the rapid method were observed: 3 (5%) in the standard disk diffusion method and 2 (3%) in the broth microdilution method. Our study concluded that the rapid disk diffusion method for fluconazole is a fast, easy, reproducible, and consistent method. Its timely implementation for testing antifungal agents in the clinical microbiology laboratory can help reduce profile release times, thus helping to determine the most appropriate antifungal treatment.


2021 ◽  
Vol 8 (Supplement_1) ◽  
pp. S215-S215
Author(s):  
Jeremy Meeder ◽  
Derek Moates ◽  
Hannah Pierce ◽  
Jamie Hutchinson ◽  
Pia Cumagun ◽  
...  

Abstract Background The ePlex BCID Gram-Negative (GN) panel utilizes electrowetting technology to detect the most common causes of GN bacteremia (21 targets) and 6 antimicrobial resistance genes from positive blood culture bottles. Rapid detection of extended spectrum β-lactamases (ESBL; CTX-M), carbapenemases (KPC, NDM, IMP, VIM, OXA 23/48), and highly resistant bacteria such as Stenotrophomonas maltophilia enables early optimization of antimicrobial therapy. Methods In this prospective study, we evaluated the performance of the BCID-GN panel compared to traditional standard of care culture and susceptibility testing with organism identification using the BioMerieux Vitek MS Matrix Assisted Laser Desorption Ionization (MALDI) Time of Flight mass spectrometry. Samples submitted for standard of care testing in Biomerieux BacT/Alert resin FA/FN blood culture bottles on the BacT/Alert VIRTUO automated blood culture system with GN bacteria on direct exam (n=108) were included. Results All but two GN bacteria identified by MALDI were represented on the BCID-GN Panel (106/108, 98.1%) and most tests (107/108, 99.1%) yielded valid results. Discordant analyses revealed a positive percent agreement (PPA) of 102/105 (97.2%) with 3 false negatives (2 pan-susceptible Enterobacterales, 1 ESBL E.coli) and a negative percent agreement (NPA) of 105/105 (100%). Consistent with alternative resistance mechanisms, only 8/12 (66.7%) of Enterobacterales with resistance to 3rd generation cephalosporins harbored the CTX-M gene. In contrast, 8/8 (100%) of isolates from samples harboring the CTX-M gene were resistant to 3rd generation cephalosporins. Conclusion Detection of 1 S. maltophilia, 1 Acinetobacter baumannii expressing OXA 23/48, and 8 Enterobacterales expressing CTX-M represent opportunities for early optimization of antimicrobial therapy in 10/108 (9.3%) of samples. The BCID-GN Panel provides rapid accurate detection of resistant gram negative bacteria enabling high quality data driven optimization of antimicrobial therapy. Disclosures Todd P. McCarty, MD, Cidara (Grant/Research Support)GenMark (Grant/Research Support, Other Financial or Material Support, Honoraria for Research Presentation)T2 Biosystems (Consultant) Sixto M. Leal, Jr., MD, PhD, Abnova (Grant/Research Support)AltImmune (Grant/Research Support)Amplyx Pharmaceuticals (Grant/Research Support)Astellas Pharmaceuticals (Grant/Research Support)CNINE Dx (Grant/Research Support)GenMark Diagnostics (Grant/Research Support, Other Financial or Material Support, Honoraria- Research Presentation)IHMA (Grant/Research Support)IMMY Dx (Grant/Research Support)JMI/Sentry (Grant/Research Support)mFluiDx Dx (Grant/Research Support)SpeeDx Dx (Grant/Research Support)Tetraphase Pharmaceuticals (Grant/Research Support)


Author(s):  
D. V. Ul’shina ◽  
D. A. Kovalev ◽  
I. V. Kuznetsova ◽  
O. V. Bobrysheva ◽  
T. L. Krasovskaya ◽  
...  

The effectiveness of differentiation of bacterial pathogens using MALDI-TOF mass spectrometry depends on the quality of sample preparation, compliance with mass spectrometric analysis parameters and statistical approaches used, implemented by various modern software tools. The review provides a brief description of the most known software used in the processing and bioinformation analysis of time-of-flight mass spectrometry data. A list of computer platforms, programs and environments, both commercial and publicly available, is presented. The results of indication and identification of pathogens of particularly dangerous and natural-focal infections by MALDI-TOF mass spectrometry using publicly available software – programming language R, Mass-Up, MicrobeMS, licensed – MatLab, ClinProTools, as well as free web applications, including, Speclust, Ribopeaksare provided. The data on usage of such well-known platforms as MALDI BioTyper, SARAMIS Vitek-MS and Andromas (Andromas SAS, France) for inter- and intra-specific differentiation of closely related species are presented. Results of identification and differentiation of microorganisms applying MALDI-TOF mass spectrometry based on detection of specific proteins for cross-comparison – biomarkers – are given. The analysis shows that the programming language R environment is one of the publicly available universal platforms with an optimal combination of algorithms for processing and interpreting of a large array of mass spectrometric data.


Infectio ◽  
2021 ◽  
Vol 26 (1) ◽  
pp. 67
Author(s):  
Nahún R Plasencia-Dueñas ◽  
Cynthia A Zegarra-Rodríguez ◽  
Virgilio E Failoc-Rojas ◽  
Cristian Díaz-Vélez

Objetivo: describir el perfil microbiológico de las superficies inanimadas en contacto con el paciente en un hospital nivel III de la seguridad social de Chiclayo, Perú. Material y métodos: Se realizó un estudio transversal, con los datos de los informes del Control microbiológico cualitativo de ambientes físicos de 5 servicios de un Hospital de Chiclayo nivel III del Perú. El método para la identificación de microorganismos fue el sistema automatizado VITEK MS. Se presentan análisis descriptivos como frecuencias y porcentajes. Resultados: Se reportaron un total de 177 aislamientos, de los cuales 97,74% (173) fueron positivos, de estos, el 50,87% (88) estuvo conformado por bacilos gramnegativos, siendo el microorganismo más aislado Acinetobacter baumannii (17 muestras) seguido de Rhizobium radiobacter (16) y Sphingomonas paucimobilis13. Conclusiones: El ambiente hospitalario se encuentra altamente contaminado, siendo la mayoría microorganismos patógenos. Estos resultados guardarían relación con el prolongado tiempo de vida de los microorganismos en las superficies inertes y el proceso de limpieza y desinfección del ambiente hospitalario, por lo que la evaluación de su eficacia y el posible desarrollo de nuevas y mejores técnicas de limpieza deben ser motivo de investigación.


2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Wanitda Watthanaworawit ◽  
Tamalee Roberts ◽  
Jill Hopkins ◽  
Ian Gassiep ◽  
Robert Norton ◽  
...  

Abstract Background Burkholderia pseudomallei is the bacterial causative agent of melioidosis, a difficult disease to diagnose clinically with high mortality if not appropriately treated. Definitive diagnosis requires isolation and identification of the organism. With the increased adoption of MALDI-TOF MS for the identification of bacteria, we established a method for rapid identification of B. pseudomallei using the Vitek MS, a system that does not currently have B. pseudomallei in its in-vitro diagnostic database. Results A routine direct spotting method was employed to create spectra and SuperSpectra. An initial B. pseudomallei SuperSpectrum was created at Shoklo Malaria Research Unit (SMRU) from 17 reference isolates (46 spectra). When tested, this initial SMRU SuperSpectrum was able to identify 98.2 % (54/55) of Asian isolates, but just 46.7 % (35/75) of Australian isolates. Using spectra (430) from different reference and clinical isolates, two additional SMRU SuperSpectra were created. Using the combination of all SMRU SuperSpectra with seven existing SuperSpectra from Townsville, Australia 119 (100 %) Asian isolates and 31 (100 %) Australian isolates were correctly identified. In addition, no misidentifications were obtained when using these 11 SuperSpectra when tested with 34 isolates of other bacteria including the closely related species Burkholderia thailandensis and Burkholderia cepacia. Conclusions This study has established a method for identification of B. pseudomallei using Vitek MS, and highlights the impact of geographical differences between strains for identification using this technique.


Author(s):  
Ya-Ting Ning ◽  
Wen-Hang Yang ◽  
Wei Zhang ◽  
Meng Xiao ◽  
Yao Wang ◽  
...  

Filamentous fungi identification by Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been challenging due to the lack of simple and rapid protein extraction methods and insufficient species coverage in the database. In this study, we created two rapid protein extraction methods for filamentous fungi: a one-step zirconia-silica beads method (ZSB) and a focused-ultrasonication method (FUS). The identification accuracy of two methods were evaluated with the VITEK MS, as well as number of spectra peaks and signal-to-noise ratio (S/N) with M-Discover 100 MALDI-TOF MS compared to the routine method. The better method was applied to build a filamentous fungi in-house spectra library for the M-Discover 100 MS, and then another one and routine method were performed in parallel to verify the accuracy and commonality of the in-house library. Using the two optimized methods, the dedicated operating time before MALDI-TOF MS analysis was reduced from 30 min to 7 (ZSB) or 5 (FUS) min per sample, with only a few seconds added for each additional strain. And both two methods identified isolates from most mold types equal to or better than the routine method, and the total correct identification rate using VITEK MS was 79.67, 76.42, and 76.42%, respectively. On the other hand, the two rapid methods generally achieved higher maximum and minimum S/N ratios with these isolates tested as compared to the routine method. Besides, the ZSB method produced overall mean of maximum and minimum S/N ratio higher than that by FUS. An in-house library of M-Discover MS was successfully built from 135 isolates from 42 species belonging to 18 genera using the ZSB method. Analysis of 467 isolates resulted in 97.22% correctly identified isolates to the species level by the ZSB method versus 95.50% by the routine method. The two novel methods are time- and cost-effective and allow efficient identification of filamentous fungi while providing a simplified procedure to build an in-house library. Thus, more clinical laboratories may consider adopting MALDI-TOF MS for filamentous fungi identification in the future.


Author(s):  
Kimberly C. Claeys ◽  
Teri L. Hopkins ◽  
Kathryn Schlaffer ◽  
Stephanie Hitchcock ◽  
Yunyun Jiang ◽  
...  

Background: Decisions regarding which rapid diagnostic tests (RDT) for bloodstream infections to implement remains challenging given the diversity of organisms detected by different platforms. We used the Desirability of Outcome Ranking Management of Antimicrobial Therapy (DOOR-MAT) as a framework to compare two RDT platforms on potential desirability of antimicrobial therapy decisions. Methods: An observational study was performed at University of Maryland Medical System comparing Verigene Blood Culture (BC) to GenMark Dx ePlex Blood Culture ID (BCID) (Research Use Only) panels on blood cultures from adult patients. Positive percent agreement (PPA) between each RDT platform and Vitek MS was calculated for comparison of on-panel targets. Theoretical antimicrobial decisions were made based on RDT results, taking into consideration patient parameters, antimicrobial stewardship practices, and local infectious diseases epidemiology. DOOR-MAT with a partial credit scoring system was applied to these decisions and mean scores compared across platforms using paired t-test. Results: The study consisted of 160 unique patients. The Verigene BC PPA was 98.6% (95% CI 95.1, 99.8) and ePlex BCID PPA was 98% (95% CI 94.3, 99.6). Among the 31 organisms not on the Verigene BC panels, 61% were identified by the ePlex BCID Panels. The mean (standard deviation [SD]) DOOR-MAT score for Verigene BC was 86.8 (SD ± 28.5) versus ePlex BCID was 91.9 (SD ± 23.1), P = 0.01. Conclusion: Both RDT platforms had high PPA for on-panel targets. The ePlex BCID was able to identify more organisms than Verigene, resulting in higher mean DOOR-MAT scores.


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