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Sibińska E, Arendowski A, Fijałkowski P, Gabryś D, Pomastowski P. Comparison of the Bruker Microflex LT and Zybio EXS2600 MALDI TOF MS systems for the identification of clinical microorganisms. Diagn Microbiol Infect Dis 2024; 108:116150. [PMID: 38035652 DOI: 10.1016/j.diagmicrobio.2023.116150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 11/16/2023] [Accepted: 11/24/2023] [Indexed: 12/02/2023]
Abstract
The emergence of Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry (MALDI TOF MS) technology has expanded the capabilities for identifying microorganisms in clinical labs, replacing traditional biochemical testing with a proteomic approach. In the present study, we compared results between the two commercial MALDI TOF MS systems, Bruker Microflex LT Biotyper and Zybio EXS2600 Ex-Accuspec, for the identification of 1979 urinary isolates by direct extraction method. Current study found that both systems identified a high percentage of isolates to at least the genus level - Bruker 95.6 % of isolates, Zybio 92.4 %. In the case of 89.5 % of all analyzed spectra, the identification results were consistent between the used devices. The highest score values and the highest percentage of spectra identified to species were obtained for gram-negative bacteria. The results show that both systems are equally good choices in terms of analytical performance for routine microbiological diagnostic procedures.
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Affiliation(s)
- Ewelina Sibińska
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4 Str., Toruń 87-100, Poland
| | - Adrian Arendowski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4 Str., Toruń 87-100, Poland.
| | - Piotr Fijałkowski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4 Str., Toruń 87-100, Poland
| | - Dorota Gabryś
- Radiotherapy Department, Maria Sklodowska-Curie National Research Institute of Oncology, Wybrzeże Armii Krajowej 15 Str., Gliwice 44-102, Poland
| | - Paweł Pomastowski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4 Str., Toruń 87-100, Poland
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2
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Epididymo-Orchitis Caused by POM-1 Metallo-β-Lactamase-Producing Pseudomonas otitidis in an Immunocompetent Patient: Case Report and Molecular Characterization. Pathogens 2022; 11:pathogens11121475. [PMID: 36558809 PMCID: PMC9783037 DOI: 10.3390/pathogens11121475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/28/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
Pseudomonas otitidis is a rare and unique species among the Pseudomonas genus that has not been previously reported as a cause of male genitourinary tract infection. In this report, we describe a case of a 20-year-old immunocompetent male who presented with recurrent epididymo-orchitis, which was initially misidentified as Vibrio vulnificus and treated successfully. The causative agent could not be identified appropriately using the available routine methods, but a final identification was established using 16S rRNA targeted sequencing followed by whole-genome sequencing.
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Shi ZY, Huang PH, Chen YC, Huang HM, Chen YF, Chen IC, Sheen YJ, Shen CH, Hon JS, Huang CY. Sustaining Improvements of Surgical Site Infections by Six Sigma DMAIC Approach. Healthcare (Basel) 2022; 10:2291. [PMID: 36421615 PMCID: PMC9690239 DOI: 10.3390/healthcare10112291] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/11/2022] [Accepted: 11/12/2022] [Indexed: 02/22/2024] Open
Abstract
SSIs (surgical site infections) are associated with increased rates of morbidity and mortality. The traditional quality improvement strategies focusing on individual performance did not achieve sustainable improvement. This study aimed to implement the Six Sigma DMAIC method to reduce SSIs and to sustain improvements in surgical quality. The surgical procedures, clinical data, and surgical site infections were collected among 42,233 hospitalized surgical patients from 1 January 2019 to 31 December 2020. Following strengthening leadership and empowering a multidisciplinary SSI prevention team, DMAIC (Define, Measure, Analyze, Improve, and Control) was used as the performance improvement model. An evidence-based prevention bundle for reduction of SSI was adopted as performance measures. Environmental monitoring and antimicrobial stewardship programs were strengthened to prevent the transmission of multi-drug resistant microorganisms. Process change was integrated into a clinical pathway information system. Improvement cycles by corrective actions for the risk events of SSIs were implemented to ensure sustaining improvements. We have reached the targets of the prevention bundle elements in the post-intervention period in 2020. The carbapenem resistance rates of Enterobacteriaceae and P. aeruginosa were lower than 10%. A significant 22.2% decline in SSI rates has been achieved, from 0.9% for the pre-intervention period in 2019 to 0.7% for the post-intervention period in 2020 (p = 0.004). Application of the Six Sigma DMAIC approach could significantly reduce the SSI rates. It also could help hospital administrators and quality management personnel to create a culture of patient safety.
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Affiliation(s)
- Zhi-Yuan Shi
- Infection Control Center, Taichung Veterans General Hospital, Taichung 407219, Taiwan
- College of Medicine, National Chung Hsing University, Taichung 40227, Taiwan
- Department of Industrial Engineering & Enterprise Information, Tunghai University, Taichung 407224, Taiwan
| | - Pei-Hsuan Huang
- Infection Control Center, Taichung Veterans General Hospital, Taichung 407219, Taiwan
| | - Ying-Chun Chen
- Infection Control Center, Taichung Veterans General Hospital, Taichung 407219, Taiwan
| | - Hui-Mei Huang
- Nursing Department, Taichung Veterans General Hospital, Taichung 407219, Taiwan
| | - Yuh-Feng Chen
- Infection Control Center, Taichung Veterans General Hospital, Taichung 407219, Taiwan
| | - I-Chen Chen
- Department of Surgery, Taichung Veterans General Hospital, Taichung 407219, Taiwan
| | - Yi-Jing Sheen
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung 407219, Taiwan
| | - Ching-Hui Shen
- College of Medicine, National Chung Hsing University, Taichung 40227, Taiwan
- Department of Anesthesiology, Taichung Veterans General Hospital, Taichung 407219, Taiwan
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
| | - Jau-Shin Hon
- Department of Industrial Engineering & Enterprise Information, Tunghai University, Taichung 407224, Taiwan
| | - Chin-Yin Huang
- Department of Industrial Engineering & Enterprise Information, Tunghai University, Taichung 407224, Taiwan
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4
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Decarli A, Nascimento LV, Hiromi Sayama Esteves L, Arenas Rocha P, Yuki VMG, Cieslinski J, Telles JP, Ribeiro VST, Tuon FF. The impact of VITEK 2 implementation for identification and susceptibility testing of microbial isolates in a Brazilian public hospital. J Med Microbiol 2022; 71. [PMID: 35671205 DOI: 10.1099/jmm.0.001543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction. The use of automated systems in identification and susceptibility tests can improve antimicrobial therapy, and positively impact clinical outcomes with a decrease in antimicrobial resistance, hospitalization time, costs, and mortality.Aim. The aim of this study was to evaluate the clinical impact of an automated method for identification and susceptibility testing of microbial isolates.Methodology. This was a retrospective cross-sectional study aimed to analyse the results before and after the implementation period of a VITEK 2 system in a Brazilian university hospital. Based on data from medical records, patients with a positive culture of clinical samples from January to July 2017 (conventional method) and from August to December 2017 (automated method) were included in this study. Demographic data, hospitalization time, time interval between culture collection and results, culture results and site, susceptibility profile, minimum inhibitory concentration, and outcome data were evaluated. Chi-square and Fischer's tests were used in the analysis.Results. Of the total samples, 836 were considered valid by the inclusion criteria, with 219 patients before VITEK 2 system implementation group and 545 in the post-implementation group. The comparison between the two periods showed a reduction of 25 % of the time to culture reports, a decrease of 33.5 to 17.0 days of hospitalization, and a reduction in mortality from 44.3-31.0 %, respectively.Conclusion. The VITEK 2 system provided early access to appropriate antimicrobial therapy for patients and effected a positive clinical impact with a reduction in mortality and hospitalization time.
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Affiliation(s)
- Ariadne Decarli
- School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba, Paraná 80.215-901, Brazil
| | - Laís Vieira Nascimento
- School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba, Paraná 80.215-901, Brazil
| | | | - Patrícia Arenas Rocha
- School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba, Paraná 80.215-901, Brazil
| | | | - Juliette Cieslinski
- Laboratory of Emerging Infectious Diseases, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba, Paraná 80.215-901, Brazil
| | - João Paulo Telles
- School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba, Paraná 80.215-901, Brazil.,Laboratory of Emerging Infectious Diseases, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba, Paraná 80.215-901, Brazil.,Infectious Diseases Department, AC Camargo Cancer Center, São Paulo, Brazil
| | - Victoria Stadler Tasca Ribeiro
- School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba, Paraná 80.215-901, Brazil.,Laboratory of Emerging Infectious Diseases, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba, Paraná 80.215-901, Brazil
| | - Felipe Francisco Tuon
- School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba, Paraná 80.215-901, Brazil.,Laboratory of Emerging Infectious Diseases, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba, Paraná 80.215-901, Brazil
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An 18-Year Dataset on the Clinical Incidence and MICs to Antibiotics of Achromobacter spp. (Labeled Biochemically or by MAL-DI-TOF MS as A. xylosoxidans), Largely in Patient Groups Other than Those with CF. Antibiotics (Basel) 2022; 11:antibiotics11030311. [PMID: 35326774 PMCID: PMC8944543 DOI: 10.3390/antibiotics11030311] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/21/2022] [Accepted: 02/23/2022] [Indexed: 11/17/2022] Open
Abstract
Achromobacter spp. are intrinsically multidrug-resistant environmental microorganisms which are known to cause opportunistic, nosocomial, and sometimes chronic infections. The existing literature yields scarcely any larger datasets, especially with regard to the incidence in patient groups other than those with cystic fibrosis. The aim of this study was to fill this gap. We present a retrospective analysis of 314 clinical and 130 screening isolates detected in our diagnostic unit between 2004 and 2021, combined with patients’ demographic and clinical information (ward type and length of hospitalization), and the results of routine diagnostic antibiotic MIC determination. We found the apparent increase in prevalence in our diagnostic unit, in which cystic fibrosis patients are an underrepresented group, in large part to be attributable to an overall increase in the number of samples and, more importantly, changes in the diagnostic setting, such as the introduction of rigorous screening for Gram-negative multidrug-resistant pathogens. We found these Achromobacter spp. to be most commonly detected in urine, stool, wounds and airway samples, and found the resistance rates to vary strongly between different sample types. Intestinal carriage is frequently not investigated, and its frequency is likely underestimated. Isolates resistant to meropenem can hardly be treated.
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Dos Reis CMF, Ramos GLDPA, Pereira RDCL, Vallim DC, Costa LEDO. Evaluation of VITEK® 2 and MALDI-TOF/MS automated methodologies in the identification of atypical Listeria spp. isolated from food in different regions of Brazil. METHODS IN MICROBIOLOGY 2022; 194:106434. [PMID: 35176354 DOI: 10.1016/j.mimet.2022.106434] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 02/09/2022] [Accepted: 02/10/2022] [Indexed: 10/19/2022]
Abstract
Listeria monocytogenes is a pathogen responsible for listeriosis, a foodborne disease with high mortality rates (20-30%). It mainly affects the elderly, pregnant women, and immunocompromised people. Although not pathogenic, the isolation and identification of Listeria innocua are critical since they can indicate L. monocytogenes' presence as they are closely related and widely distributed in the environment and food processing plants. The objective of this study was to evaluate the effectiveness of the automated methods VITEK® 2 and MALDI-TOF/MS in identifying 94 strains of the genus Listeria with atypical identification profile. The resulting identification by Polymerase Chain Reaction (PCR), using specific primers for the most common species of Listeria, was considered the correct identification and presented a total of 31 strains identified as Listeria innocua (LI), 54 as L. monocytogenes (LM), 8 as Listeria welshimeri (LW) and 1 as Listeria grayi (LG). The VITEK® 2 automated system correctly identified, on average, 79% of the LI strains, 16% of the LM strains, and 88.0% of the LW strains. In the analysis by MALDI-TOF/MS, on average, 73% of LM strains were correctly identified, few LW strains were correctly identified, and all LI strains were incorrectly identified. Both VITEK® 2 and MALDI-TOF/MS correctly identified the LG strain in both analyzes. The results demonstrate that automated methodologies could not discriminate atypical strains of the Listeria genus and point to the need for the use of complementary tests, such as PCR and chromogenic media, for the correct identification of these strains.
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Affiliation(s)
- Cristhiane M F Dos Reis
- Federal Institute of Education, Science, and Technology of Rio de Janeiro (IFRJ), Food Department, 20270-021 Rio de Janeiro, Brazil; Laboratory of Bacterial Zoonoses, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (Fiocruz), 21040-360 Rio de Janeiro, Brazil
| | - Gustavo Luis de P A Ramos
- Federal Institute of Education, Science, and Technology of Rio de Janeiro (IFRJ), Food Department, 20270-021 Rio de Janeiro, Brazil; Fluminense Federal University (UFF), Faculty of Veterinary Medicine, 24230-340, Niterói, Rio de Janeiro, Brazil.
| | | | - Deyse Christina Vallim
- Laboratory of Bacterial Zoonoses, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (Fiocruz), 21040-360 Rio de Janeiro, Brazil
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Putney S, Theiss AH, Rajan NK, Deak E, Buie C, Ngo Y, Shah H, Yuan V, Botbol-Ponte E, Hoyos-Urias A, Knopfmacher O, Hogan CA, Banaei N, Herget MS. Novel electronic biosensor for automated inoculum preparation to accelerate antimicrobial susceptibility testing. Sci Rep 2021; 11:11360. [PMID: 34059754 PMCID: PMC8166823 DOI: 10.1038/s41598-021-90830-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 05/17/2021] [Indexed: 12/05/2022] Open
Abstract
A key predictor of morbidity and mortality for patients with a bloodstream infection is time to appropriate antimicrobial therapy. Accelerating antimicrobial susceptibility testing from positive blood cultures is therefore key to improving patient outcomes, yet traditional laboratory approaches can require 2–4 days for actionable results. The eQUANT—a novel instrument utilizing electrical biosensors—produces a standardized inoculum equivalent to a 0.5 McFarland directly from positive blood cultures. This proof-of-concept study demonstrates that eQUANT inocula prepared from clinically significant species of Enterobacterales were comparable to 0.5 McF inocula generated from bacterial colonies in both CFU/ml concentration and performance in antimicrobial susceptibility testing, with ≥ 95% essential and categorical agreement for VITEK2 and disk diffusion. The eQUANT, combined with a rapid, direct from positive blood culture identification technique, can allow the clinical laboratory to begin antimicrobial susceptibility testing using a standardized inoculum approximately 2–3 h after a blood culture flags positive. This has the potential to improve clinical practice by accelerating conventional antimicrobial susceptibility testing and the resulting targeted antibiotic therapy.
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Affiliation(s)
- Suzanne Putney
- Avails Medical Inc., 1455 Adams Drive, Menlo Park, CA, 94025, USA
| | - Andrew H Theiss
- Avails Medical Inc., 1455 Adams Drive, Menlo Park, CA, 94025, USA
| | - Nitin K Rajan
- Avails Medical Inc., 1455 Adams Drive, Menlo Park, CA, 94025, USA
| | - Eszter Deak
- Avails Medical Inc., 1455 Adams Drive, Menlo Park, CA, 94025, USA
| | - Creighton Buie
- Avails Medical Inc., 1455 Adams Drive, Menlo Park, CA, 94025, USA
| | - Yvonne Ngo
- Avails Medical Inc., 1455 Adams Drive, Menlo Park, CA, 94025, USA
| | - Hima Shah
- Avails Medical Inc., 1455 Adams Drive, Menlo Park, CA, 94025, USA
| | - Victoria Yuan
- Avails Medical Inc., 1455 Adams Drive, Menlo Park, CA, 94025, USA
| | | | | | - Oren Knopfmacher
- Avails Medical Inc., 1455 Adams Drive, Menlo Park, CA, 94025, USA
| | - Catherine A Hogan
- Stanford University School of Medicine, 3375 Hillview Ave, Palo Alto, CA, 94304, USA
| | - Niaz Banaei
- Stanford University School of Medicine, 3375 Hillview Ave, Palo Alto, CA, 94304, USA
| | - Meike S Herget
- Avails Medical Inc., 1455 Adams Drive, Menlo Park, CA, 94025, USA.
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Nazzal L, Soiefer L, Chang M, Tamizuddin F, Schatoff D, Cofer L, Aguero-Rosenfeld ME, Matalon A, Meijers B, Holzman R, Lowenstein J. Effect of Vancomycin on the Gut Microbiome and Plasma Concentrations of Gut-Derived Uremic Solutes. Kidney Int Rep 2021; 6:2122-2133. [PMID: 34386661 PMCID: PMC8343810 DOI: 10.1016/j.ekir.2021.05.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 05/03/2021] [Accepted: 05/10/2021] [Indexed: 12/12/2022] Open
Abstract
Introduction Declining renal function results in the accumulation of solutes normally excreted by healthy kidneys. Data suggest that some of the protein-bound solutes mediate accelerated cardiovascular disease. Many of the poorly dialyzable protein-bound uremic retention solutes are products of gut bacterial metabolism. Methods We performed a blinded-randomized controlled trial comparing the changes in plasma concentrations of a panel of protein-bound solutes and microbiome structure in response to the once-weekly oral administration of 250 mg of vancomycin or placebo over a period of 12 weeks in a cohort of stable patients with end-stage kidney disease. We also examined the pattern of recovery of the solutes and gut microbiome over 12 weeks of placebo administration following vancomycin. Results We enrolled 15 subjects. Ten subjects provided sufficient plasma and stool samples to permit us to examine the effect of vancomycin on plasma solute levels. We showed that a weekly dose of vancomycin resulted in a reduction in the plasma concentration of 7 colon-derived solutes. We described a significant effect of vancomycin on the microbiome structure with a decrease in alpha diversity and change in beta diversity. Multiple taxa decreased with vancomycin including genera Clostridium and Bacteroides. We demonstrated microbiome recovery after stopping vancomycin. However, recovery in the solutes was highly variable between subjects. Conclusions We demonstrated that microbiome suppression using vancomycin resulted in changes in multiple gut-derived uremic solutes. Future studies are needed to address whether reduction in those uremic solutes results in improvement of cardiovascular outcomes in ESKD patients.
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Affiliation(s)
- Lama Nazzal
- Department of Medicine, New York University School of Medicine, New York, New York, USA
| | - Leland Soiefer
- Department of Medicine, New York-Presbyterian/Weill Cornell, New York, New York, USA
| | - Michelle Chang
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Farah Tamizuddin
- Department of Radiology, New York University School of Medicine, New York, New York, USA
| | - Daria Schatoff
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Lucas Cofer
- Department of Medicine, New York University School of Medicine, New York, New York, USA
| | | | - Albert Matalon
- Department of Medicine, New York University School of Medicine, New York, New York, USA
| | - Bjorn Meijers
- Department of Nephrology and Renal Transplantation, University Hospitals Leuven, Leuven, Belgium
| | - Robert Holzman
- Department of Medicine, New York University School of Medicine, New York, New York, USA
| | - Jerome Lowenstein
- Department of Medicine, New York University School of Medicine, New York, New York, USA
- Correspondence: Jerome Lowenstein, Department of Medicine, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA.
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Kosecka-Strojek M, Wolska M, Żabicka D, Sadowy E, Międzobrodzki J. Identification of Clinically Relevant Streptococcus and Enterococcus Species Based on Biochemical Methods and 16S rRNA, sodA, tuf, rpoB, and recA Gene Sequencing. Pathogens 2020; 9:pathogens9110939. [PMID: 33187333 PMCID: PMC7696602 DOI: 10.3390/pathogens9110939] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/06/2020] [Accepted: 11/09/2020] [Indexed: 12/20/2022] Open
Abstract
Streptococci and enterococci are significant opportunistic pathogens in epidemiology and infectious medicine. High genetic and taxonomic similarities and several reclassifications within genera are the most challenging in species identification. The aim of this study was to identify Streptococcus and Enterococcus species using genetic and phenotypic methods and to determine the most discriminatory identification method. Thirty strains recovered from clinical samples representing 15 streptococcal species, five enterococcal species, and four nonstreptococcal species were subjected to bacterial identification by the Vitek® 2 system and Sanger-based sequencing methods targeting the 16S rRNA, sodA, tuf, rpoB, and recA genes. Phenotypic methods allowed the identification of 10 streptococcal strains, five enterococcal strains, and four nonstreptococcal strains (Leuconostoc, Granulicatella, and Globicatella genera). The combination of sequencing methods allowed the identification of 21 streptococcal strains, five enterococcal strains, and four nonstreptococcal strains. The 16S rRNA and rpoB genes had the highest identification potential. Only a combination of several molecular methods was sufficient for unambiguous confirmation of species identity. This study will be useful for comparison of several identification methods, both those used as a first choice in routine microbiology and those used for final confirmation.
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Affiliation(s)
- Maja Kosecka-Strojek
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland; (M.W.); (J.M.)
- Correspondence: ; Tel.: +48-12-664-6365
| | - Mariola Wolska
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland; (M.W.); (J.M.)
| | - Dorota Żabicka
- Department of Molecular Microbiology, National Medicines Institute, 00-725 Warsaw, Poland;
| | - Ewa Sadowy
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, 00-725 Warsaw, Poland;
| | - Jacek Międzobrodzki
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland; (M.W.); (J.M.)
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Price EP, Soler Arango V, Kidd TJ, Fraser TA, Nguyen TK, Bell SC, Sarovich DS. Duplex real-time PCR assay for the simultaneous detection of Achromobacter xylosoxidans and Achromobacter spp. Microb Genom 2020; 6:mgen000406. [PMID: 32667877 PMCID: PMC7478622 DOI: 10.1099/mgen.0.000406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 06/26/2020] [Indexed: 01/10/2023] Open
Abstract
Several members of the Gram-negative environmental bacterial genus Achromobacter are associated with serious infections, with Achromobacter xylosoxidans being the most common. Despite their pathogenic potential, little is understood about these intrinsically drug-resistant bacteria and their role in disease, leading to suboptimal diagnosis and management. Here, we performed comparative genomics for 158 Achromobacter spp. genomes to robustly identify species boundaries, reassign several incorrectly speciated taxa and identify genetic sequences specific for the genus Achromobacter and for A. xylosoxidans. Next, we developed a Black Hole Quencher probe-based duplex real-time PCR assay, Ac-Ax, for the rapid and simultaneous detection of Achromobacter spp. and A. xylosoxidans from both purified colonies and polymicrobial clinical specimens. Ac-Ax was tested on 119 isolates identified as Achromobacter spp. using phenotypic or genotypic methods. In comparison to these routine diagnostic methods, the duplex assay showed superior identification of Achromobacter spp. and A. xylosoxidans, with five Achromobacter isolates failing to amplify with Ac-Ax confirmed to be different genera according to 16S rRNA gene sequencing. Ac-Ax quantified both Achromobacter spp. and A. xylosoxidans down to ~110 genome equivalents and detected down to ~12 and ~1 genome equivalent(s), respectively. Extensive in silico analysis, and laboratory testing of 34 non-Achromobacter isolates and 38 adult cystic fibrosis sputa, confirmed duplex assay specificity and sensitivity. We demonstrate that the Ac-Ax duplex assay provides a robust, sensitive and cost-effective method for the simultaneous detection of all Achromobacter spp. and A. xylosoxidans and will facilitate the rapid and accurate diagnosis of this important group of pathogens.
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Affiliation(s)
- Erin P. Price
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia
| | - Valentina Soler Arango
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia
| | - Timothy J. Kidd
- School of Chemistry and Molecular Biosciences, Faculty of Science, The University of Queensland, St Lucia, Queensland, Australia
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
- Faculty of Medicine, The University of Queensland, Herston, Queensland, Australia
| | - Tamieka A. Fraser
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia
| | - Thuy-Khanh Nguyen
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Scott C. Bell
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
- Faculty of Medicine, The University of Queensland, Herston, Queensland, Australia
- Adult Cystic Fibrosis Centre, The Prince Charles Hospital, Chermside, Queensland, Australia
| | - Derek S. Sarovich
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia
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Rosa NM, Agnoletti F, Lollai S, Tola S. Comparison of PCR-RFLP, API® 20 Strep and MALDI-TOF MS for identification of Streptococcus spp. collected from sheep and goat milk samples. Small Rumin Res 2019. [DOI: 10.1016/j.smallrumres.2019.09.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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12
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Furlan JPR, Pitondo-Silva A, Braz VS, Gallo IFL, Stehling EG. Evaluation of different molecular and phenotypic methods for identification of environmental Burkholderia cepacia complex. World J Microbiol Biotechnol 2019; 35:39. [PMID: 30739255 DOI: 10.1007/s11274-019-2614-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 02/05/2019] [Indexed: 12/01/2022]
Abstract
The correct identification of different genera and bacterial species is essential, especially when these bacteria cause infections and appropriate therapies need to be chosen. Bacteria belonging to the Burkholderia cepacia complex are considered important opportunistic pathogens, causing different types of infections in immunocompromised, principally in patients with cystic fibrosis. Twenty-one isolates were obtained from different soil samples and identified by sequencing of 16S rRNA, 23S rRNA, recA gene, MLST and by VITEK 2 and MALDI-TOF MS systems. Then, statistical analyses were performed. VITEK 2 and MALDI-TOF MS systems showed different bacterial genera. Sequencing of the 16S rRNA, 23S rRNA gene and amplification of recA gene showed that all the isolates belong to the B. cepacia complex. Sequencing of the recA gene showed a predominance of B. cenocepacia. The PCR of the recA gene showed a high specificity when it is necessary to identify the bacteria belonging to the B. cepacia complex in comparison with 16S and 23S rRNA genes sequencing. MLST analyzes showed a diversity of STs, which have not yet been correlated to the species. Phenotypic identification was not suitable for the identification of these pathogens since in many cases different genera have been reported, including identification by using MALDI-TOF MS.
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Affiliation(s)
- João Pedro Rueda Furlan
- Department of Clinical Analysis, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (USP), Av. do Café S/N. Monte Alegre, Ribeirão Preto, SP, 14040-903, Brazil
| | - André Pitondo-Silva
- Department of Clinical Analysis, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (USP), Av. do Café S/N. Monte Alegre, Ribeirão Preto, SP, 14040-903, Brazil.,School of Dentistry, University of Ribeirao Preto (UNAERP), Ribeirão Preto, Brazil
| | - Vânia Santos Braz
- Department of Clinical Analysis, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (USP), Av. do Café S/N. Monte Alegre, Ribeirão Preto, SP, 14040-903, Brazil
| | - Inara Fernanda Lage Gallo
- Department of Clinical Analysis, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (USP), Av. do Café S/N. Monte Alegre, Ribeirão Preto, SP, 14040-903, Brazil
| | - Eliana Guedes Stehling
- Department of Clinical Analysis, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (USP), Av. do Café S/N. Monte Alegre, Ribeirão Preto, SP, 14040-903, Brazil.
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13
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Wu S, Xu J, Qiu C, Xu L, Chen Q, Wang X. Direct antimicrobial susceptibility tests of bacteria and yeasts from positive blood cultures by using serum separator gel tubes and MALDI-TOF MS. J Microbiol Methods 2018; 157:16-20. [PMID: 30557587 DOI: 10.1016/j.mimet.2018.12.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 12/12/2018] [Accepted: 12/13/2018] [Indexed: 12/25/2022]
Abstract
Early and appropriate antimicrobial treatment can effectively reduce the mortality rate caused by bloodstream infections (BSIs) and is critical for favorable patient outcomes. In general, >90% of positive blood cultures will show positive results within 48 h after incubation in the BACTECTM FX system. However, an additional 6-8 h are required to obtain clones of the bacterium and another 10-24 h to obtain antimicrobial susceptibility test (AST) results. In this study, direct ASTs of bacteria and yeasts from positive blood cultures were performed by using serum separator gel tubes and matrix-assisted laser desorption ionization-time of flight mass spectrometry(MALDI-TOF MS). 153 BSI cases were caused by a single pathogen. The coincidence rates of genus and species identification between the direct method (from positive blood cultures) and reference method (from subcultured clones) were 86.9% and 83%, respectively. On average, 98.6% of the direct ASTs in 88 Gram-negative bacteria tested had an accurate result compared to the reference method. In Gram- positive bacteria and yeasts, the accuracy rates were 99.2% and 100%, respectively. MALDI-TOF MS combined with serum separator gel tubes can be used for rapidly identifying and performing ASTs on positive blood cultures.
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Affiliation(s)
- Shenghai Wu
- Department of Laboratory, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Zhejiang, China
| | - Jie Xu
- Department of Laboratory, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Zhejiang, China
| | - Chunning Qiu
- Department of Laboratory, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Zhejiang, China
| | - Lihui Xu
- Department of Laboratory, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Zhejiang, China
| | - Qiong Chen
- Department of Laboratory, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Zhejiang, China
| | - Xianjun Wang
- Department of Laboratory, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Zhejiang, China.
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14
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Rodio DM, Bressan A, Ambrosi C, Scribano D, Tolli R, Mansour W, Speziale F, Antonelli G, Trancassini M, Pietropaolo V. Yersinia enterocolitica in Italy: A Case of Septicemia and Abdominal Aortic Aneurysm Infection. Front Med (Lausanne) 2018; 5:156. [PMID: 29881725 PMCID: PMC5978273 DOI: 10.3389/fmed.2018.00156] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 05/04/2018] [Indexed: 11/13/2022] Open
Abstract
We report a case of Yersinia enterocolitica septicemia in a 63-year-old patient admitted to the Vascular Surgery Department of Umberto I Hospital (Rome, Italy) for an abdominal aortic aneurysm. The microorganism, recovered from both peripheral blood cultures and aneurysmatic aortic wall specimens, was identified as Y. enterocolitica using matrix-assisted laser desorption ionization-time of flight analysis (MALDI-TOF MS) and 16S rDNA gene sequencing. The isolate responsible for septicemia belonged to the O:9 serotype (biogroup 2). A genetic screening of the isolate made it possible to detect the presence of both the yst and ail genes, encoding a heat-stable enterotoxin and a protein involved in invasion/adherence and serum resistance, respectively. Our case contributes in enriching epidemiological data concerning Y. enterocolitica infections, which might represent severe complications in patients suffering from cardiovascular diseases. Moreover, this study, together with the others, should be regarded as valuable and useful tools for monitoring the rate of infections worldwide.
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Affiliation(s)
- Donatella M. Rodio
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Alessia Bressan
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Cecilia Ambrosi
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
- Dani Di Giò Foundation–Onlus, Rome, Italy
| | - Daniela Scribano
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Rita Tolli
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana Mariano Aleandri, Rome, Italy
| | - Wassim Mansour
- Vascular and Endovascular Surgery Division, Department of Surgery Paride Stefanini, Policlinico Umberto I, Sapienza University of Rome, Rome, Italy
| | - Francesco Speziale
- Vascular and Endovascular Surgery Division, Department of Surgery Paride Stefanini, Policlinico Umberto I, Sapienza University of Rome, Rome, Italy
| | - Guido Antonelli
- Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Maria Trancassini
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Valeria Pietropaolo
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
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