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Lima A, Rowe L, Silbert S. Validation of a new extraction-free real-time PCR test to detect MPOX virus. Diagn Microbiol Infect Dis 2024; 109:116265. [PMID: 38520832 DOI: 10.1016/j.diagmicrobio.2024.116265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 03/05/2024] [Accepted: 03/12/2024] [Indexed: 03/25/2024]
Abstract
The monkeypox (Mpox) virus has raised significant concerns given its recent spread with an increasing number of confirmed cases worldwide. In this study, we evaluated the performance of a laboratory developed test (LDT) using BioGX Xfree hMPXV/OPXV reagents for the qualitative detection of non-variola Orthopoxviruses and Mpox virus DNA, in swabs from human pustular or vesicular rash specimens. Analytical and clinical testing analysis were carried out on two different platforms: the BD MAX™ System (BD Diagnostics) and the new pixl.16 Real-Time PCR Platform (BioGX), using a synthetic Mpox virus DNA (ATCC VR-3270SD) and residual clinical samples previously identified with an EUA approved Mpox real-time PCR assay. In the end, the Xfree hMPXV/OPXV LDT proved to be a sensitive, specific, and reproducible test for the detection of Mpox on both platforms evaluated with the pixl.16 having an advantage of a small footprint and providing faster TAT facilitated by an extraction-free workflow.
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Affiliation(s)
- Amorce Lima
- Esoteric Testing/R&D Laboratory, Tampa General Hospital, 1 Tampa General Circle, Tampa, FL 33606, USA.
| | - Laura Rowe
- Esoteric Testing/R&D Laboratory, Tampa General Hospital, 1 Tampa General Circle, Tampa, FL 33606, USA
| | - Suzane Silbert
- Esoteric Testing/R&D Laboratory, Tampa General Hospital, 1 Tampa General Circle, Tampa, FL 33606, USA
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2
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Knoth C, Humphries R, Johnson JK, Patel A, Lima A, Silbert S, Vinjé J. Multicenter evaluation of BioCode GPP for syndromic molecular detection of gastrointestinal pathogens from stool specimens. J Clin Microbiol 2024; 62:e0154523. [PMID: 38329337 PMCID: PMC10935640 DOI: 10.1128/jcm.01545-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 01/02/2024] [Indexed: 02/09/2024] Open
Abstract
Acute gastroenteritis (AGE) is a leading cause of morbidity and mortality worldwide across all age groups that disproportionally affects young children in low- and middle-income countries and immunocompromised patients in high-income countries. Regional outbreaks of AGE are typically detected by traditional microbiological detection methods that target limited organisms and are associated with low sensitivity and lengthy time-to-results. Combined, these may result in repeat testing, imprecise or delayed treatment, and delayed recognition of outbreaks. We conducted a multi-site prospective study comparing the BioCode Gastrointestinal Pathogen Panel (BioCode GPP) for the detection of 17 common bacterial, viral, and protozoan causes of gastroenteritis with reference methods, including stool culture, enzyme immunoassays, pathogen-specific PCR assays, and sequencing. One thousand five hundred fifty-eight residual, de-identified stool samples (unpreserved stool and stool in Cary-Blair transport medium) were enrolled and tested for 11 bacterial, 3 viral, and 3 protozoan pathogens. BioCode GPP and reference methods were positive for 392 (25.2%) and 283 (18.2%) samples, respectively (P < 0.0001). In this study, the BioCode GPP and reference methods detected 69 and 65 specimens positive for Clostridioides difficile, 51 and 48 for enteroaggregative Escherichia coli, 33 and 27 for enterotoxigenic E. coli, 50 and 47 for norovirus GI/GII, and 30 and 22 for rotavirus A, respectively. The BioCode GPP showed good positive and negative agreements for each pathogen ranging from 89.5% to 100%, with overall sensitivity and specificity of 96.1% and 99.7%, post adjudication. The BioCode GPP detected >1 pathogens in 49 samples, representing 12.5% of the total 392 positive specimens. IMPORTANCE This study highlights performance of a novel technology for timely and accurate detection and differentiation of 17 common bacterial, viral, and protozoan causes of gastroenteritis. Utilizing molecular tests such as the BioCode Gastrointestinal Pathogen Panel may improve the detection of gastrointestinal pathogens and provide actionable results, particularly for patient populations at most risk.
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Affiliation(s)
| | - Romney Humphries
- University of California Los Angeles Medical Center, Los Angeles, California, USA
| | - J. Kristie Johnson
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Anami Patel
- Le Bonheur Children’s Hospital, Memphis, Tennessee, USA
| | | | | | - Jan Vinjé
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Lima A, Uy D, Kostera J, Silbert S. Comparative Clinical Evaluation of the Alinity m STI Multiplex PCR Assay for Diagnosis and Surveillance of Chlamydia trachomatis, Neisseria gonorrhea, Trichomonas vaginalis, and Mycoplasma genitalium. Sex Transm Dis 2024:00007435-990000000-00336. [PMID: 38465972 DOI: 10.1097/olq.0000000000001964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
BACKGROUND Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) are routinely tested and reported; however, Trichomonas vaginalis (TV) is the most common STI in the US and the prevalence of Mycoplasma genitalium (MG) infections is likely higher than estimated. We examined the clinical performance of the Alinity m STI assay for detection and surveillance of CT/NG/TV/MG in urine specimens from patients at a large academic medical center. METHODS Urine specimen from 198 patients were tested in this evaluation. Alinity m STI and Aptima Combo 2 CT/NG and TV assay (Panther System) results were compared, with discrepant results run on the cobas 6800 CT/NG, TV/MG assays. Analyzer turnaround times (TAT), time from loading the specimen on the analyzer to results reporting, were determined for Alinity m and Panther systems. RESULTS Overall percent agreement of the Alinity m in comparison with the Aptima and cobas assays for CT, NG, TV, and MG were respectively: 99.5% (97.2, 99.9%), 99.5% (97.2, 99.9%), 98.4% (95.5, 99.5%), and 86.4% (66.7, 95.3). There were 5 discrepant samples (CT = 1, NG = 1, TV = 3) between the Alinity m and the Aptima assays, and 3 MG discrepant samples between the Alinity m STI and cobas 6800. Two of the five Aptima and Alinity m discrepant samples were resolved as they yielded similar results on both Alinity m and cobas 6800. TV and MG infections comprised 54% of the positive samples and were more often asymptomatic than CT and NG infections. Analyzer TAT was 3 hours 25 minutes for the Aptima CT/NG, 3 hours 25 minutes for Aptima TV, and 1 hour 55 minutes for Alinity m STI assay. CONCLUSIONS The Alinity m STI assay allows for fast and simultaneous detection of the four major STI pathogens, which can facilitate surveillance and provide accurate results to help clinicians diagnose for initiation of appropriate treatment.
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Jackson JK, Kennedy SJ, Felton EA, Cella E, Lima A, Becker D, Silbert S, Kim K, Azarian T, Shaw LN. Draft genome sequence of a highly proteolytic Staphylococcus aureus USA300 isolate from human urine. Microbiol Resour Announc 2023; 12:e0067923. [PMID: 37933968 PMCID: PMC10720404 DOI: 10.1128/mra.00679-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 09/29/2023] [Indexed: 11/08/2023] Open
Abstract
The secreted proteases of Staphylococcus aureus have been shown to be critical during infection. Here, we present the draft genome sequence of S. aureus TGH337, a hyper-proteolytic USA300 strain isolated from human urine.
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Affiliation(s)
- Jessica K. Jackson
- Department of Molecular Biosciences, University of South Florida, Tampa, Florida, USA
| | - Sarah J. Kennedy
- Department of Molecular Biosciences, University of South Florida, Tampa, Florida, USA
| | - Emily A. Felton
- Department of Molecular Biosciences, University of South Florida, Tampa, Florida, USA
| | - Eleonora Cella
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida, USA
| | - Amorce Lima
- Esoteric Testing/R&D Laboratory, Tampa General Hospital, Tampa, Florida, USA
| | - Deanna Becker
- Esoteric Testing/R&D Laboratory, Tampa General Hospital, Tampa, Florida, USA
| | - Suzane Silbert
- Esoteric Testing/R&D Laboratory, Tampa General Hospital, Tampa, Florida, USA
| | - Kami Kim
- Division of Infectious Disease and Internal Medicine, University of South Florida, Tampa, Florida, USA
- Center for Global Health Infectious Diseases Research, University of South Florida, Tampa, Florida, USA
- Global Emerging Diseases Institute, Tampa General Hospital, Tampa, Florida, USA
| | - Taj Azarian
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida, USA
| | - Lindsey N. Shaw
- Department of Molecular Biosciences, University of South Florida, Tampa, Florida, USA
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Zhang X, Knoth C, Pham A, Lima A, Dominguez R, Ibarra-Flores I, Lopez JC, Uy D, Silbert S, Patel A, Aye M, Tang YW, Dien Bard J. The Clinical Performance of the BioCode Respiratory Pathogen Panel for the Detection of Viruses and Bacteria from Nasopharyngeal Swabs. Microbiol Spectr 2023; 11:e0404422. [PMID: 37039708 PMCID: PMC10269715 DOI: 10.1128/spectrum.04044-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 03/21/2023] [Indexed: 04/12/2023] Open
Abstract
Early detection of microbial pathogens causing respiratory tract infection plays a crucial role in clinical management. The BioCode Respiratory Pathogen Panel (BioCode RPP) utilizes reverse transcriptase PCR (RT-PCR) in combination with barcoded magnetic beads to amplify, detect, and identify respiratory pathogens. This panel qualitatively detects and identifies 14 viruses, including influenza virus A with H1 pdm09, H1, and H3 subtyping; influenza B; respiratory syncytial virus (RSV); human metapneumovirus; parainfluenza virus 1; parainfluenza virus 2; parainfluenza virus 3; parainfluenza virus 4; coronavirus (229E, NL63, OC43, and HKU1); adenovirus; and human rhinovirus/enterovirus, and 3 bacteria, including Chlamydia pneumoniae, Mycoplasma pneumoniae, and Bordetella pertussis. Reproducibility, which was assessed with contrived specimens containing 12 targets at 3 clinical sites, with 2 operators at each site for 5 days, was 99.4% for Flu A H3 and Flu B, 98.9% for RSV, and 100% for the remaining 9 targets assayed. A multicenter clinical trial evaluated the performance of the BioCode RPP with 2,647 nasopharyngeal swab specimens from 5 geographically distinct sites and revealed comparable performance between the BioCode RPP and FilmArray Respiratory Panel (FA-RP). Specifically, the positive percent agreements (PPAs) for various pathogens ranged between 80.8% and 100% compared with the FA-RP (1.7 and 2.0). Negative percent agreement ranged from 98.4% to 100% for BioCode RPP. The BioCode RPP also offers scalable automated testing capability of up to 96 specimens in a single run with total sample-to-result time under 5 h. The invalid rate of the BioCode RPP on initial testing was 1.0% (26/2,649). IMPORTANCE Early detection of microbial pathogens causing respiratory tract infection plays a crucial role in clinical management. The BioCode Respiratory Pathogen Panel (BioCode RPP) is a high-throughput test that utilizes RT-PCR in combination with barcoded magnetic beads to amplify, detect, and identify 17 respiratory pathogens, including 14 viruses and 3 bacteria. This study summarizes data generated from a multicenter clinical trial evaluating the performance of the BioCode RPP on 2,647 nasopharyngeal swab specimens from five geographically distinct sites.
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Affiliation(s)
- Xin Zhang
- Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Sichuan Academy of Medicine & Sichuan Provincial People’s Hospital, Chengdu, China
| | - Colleen Knoth
- Applied BioCode Inc., Santa Fe Springs, California, USA
| | - Anh Pham
- Applied BioCode Inc., Santa Fe Springs, California, USA
| | | | - Rosario Dominguez
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
| | - Irvin Ibarra-Flores
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
| | - Juan C. Lopez
- Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Dominic Uy
- Tampa General Hospital, Tampa, Florida, USA
| | | | | | - Michael Aye
- Applied BioCode Inc., Santa Fe Springs, California, USA
| | - Yi-Wei Tang
- Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jennifer Dien Bard
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
- Keck School of Medicine, University of Southern California, Los Angeles, California, USA
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Lima A, Healer V, Rowe L, Silbert S. Performance evaluation of the Aptima CMV quant assay using plasma and non-plasma samples. J Clin Virol 2023; 164:105467. [PMID: 37126896 DOI: 10.1016/j.jcv.2023.105467] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND Cytomegalovirus (CMV) infection has a major negative impact on transplantation and is associated with increased morbidity and mortality in this patient population. Quantitation of CMV infections using a molecular test is the preferred method for monitoring patients post-transplant. For this analysis, we compared the Aptima CMV Quant Assay (Aptima CMV) on the Panther system to the ELITech MGB Alert® CMV 3.0 ASR (MGB CMV) run on the ELITe InGenius®. METHODS The analytical performance of the assay was assessed using commercially available CMV reference panels that meet the 1st WHO International Standard for Human Cytomegalovirus for nucleic acid amplification techniques. The clinical performance of the assay was determined using 249 plasma and non-plasma samples. RESULTS The 95% LOD of the Aptima assay was determined to be 50 IU/mL and 200 IU/mL for the MGB CMV assay. A strong linear correlation with the reference panel (R2 = 0.9945), excellent reproducibility, and accuracy (R2 = 0.986) over the detection range of the assay was observed. Of the 249 clinical samples tested, only 17 (6.8%) yielded discordant results which were at or near the lower limit of quantification of the assays. Although the Aptima CMV assay demonstrated excellent concordance of qualitative results to the MGB CMV assay for all samples, the MGB CMV quantified CMV DNA at an average of 0.5 Log IU/mL higher than Aptima CMV. CONCLUSION The Aptima CMV assay is both sensitive and accurate in quantifying CMV in both plasma and non-plasma specimens on the fully automated Panther system.
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Affiliation(s)
- Amorce Lima
- Esoteric Testing Laboratory, Pathology Department, Tampa General Hospital, Tampa, FL, United States of America.
| | - Vicki Healer
- Esoteric Testing Laboratory, Pathology Department, Tampa General Hospital, Tampa, FL, United States of America
| | - Laura Rowe
- Esoteric Testing Laboratory, Pathology Department, Tampa General Hospital, Tampa, FL, United States of America
| | - Suzane Silbert
- Esoteric Testing Laboratory, Pathology Department, Tampa General Hospital, Tampa, FL, United States of America
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Goos J, Neff C, Holmberg K, Lyons A, Monroe N, Selvarangan R, Banerjee D, Hueschen LA, Chapin K, Tansarli G, Silbert S, Lima A, Connor BA, Rogova M, Steele M, Stubbs AM, Bard JD, Flores-Vazquez J, Andjelic C. 531. Clinical Evaluation of the BioFire® FilmArray® Gastrointestinal (GI) Panel for use with Rectal Swab Specimens in Cary-Blair Media. Open Forum Infect Dis 2022. [DOI: 10.1093/ofid/ofac492.586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Abstract
Background
The BioFire® FilmArray® Gastrointestinal (GI) Panel provides results for 22 bacterial, viral, and protozoan pathogens responsible for GI infection in about an hour. This test is indicated for use with stool specimens in Cary-Blair media (SCB) as a specimen type. For many patients, a stool sample can be difficult to provide during a single clinic visit, potentially delaying diagnosis and treatment. Rectal swabs in Cary-Blair (RSCB; an off-label sample type) are a more convenient and faster specimen type to collect, as collection can occur during a patient’s healthcare visit. The purpose of this study was to assess the performance of the GI Panel when testing RSCB compared to SCB.
Methods
Paired SCB and RSCB specimens were collected from outpatient subjects with signs of GI infection and tested in parallel using the GI Panel. All detections were confirmed using culture (for some bacterial analytes) and PCR/sequencing. Performance of the GI Panel in RSCB versus SCB specimen types was assessed using the ratios (RSCB/SCB) of sensitivities and false positive rates (FPR). Positive percent agreement (PPA) and negative percent agreement (NPA) for the GI Panel test in RSCB compared to SCB were also evaluated.
Results
A total of 299 paired SCB and RSCB specimens were collected and tested with the GI Panel. Detections for 17 of the 22 analytes on the GI Panel were observed in both specimen types. When comparing results from RSCB and SCB specimen types, the overall ratio of sensitivity was 0.86 and the overall ratio of FPR was 0.31. Further, overall PPA was 76.6% and overall NPA was 99.8%.
Conclusion
Overall, the GI Panel is sensitive and specific for the rapid detection of many of the organisms responsible for GI infection when using either specimen type, however RSCB specimens have a lower diagnostic yield (i.e. fewer detections) compared to SCB. As a result, GI Panel performance for the RSCB is characterized as less sensitive compared to performance for SCB specimens. Acknowledging these limitations, the convenience and time-to-result benefits of the RSCB specimen type may aid in the effective diagnosis and management of GI infection in outpatient settings.
The BioFire FilmArray GI Panel is not cleared or approved for use with rectal swabs in Cary-Blair.
Disclosures
Jared Goos, PhD, bioMerieux: Employee|bioMerieux: Stocks/Bonds Crissy Neff, n/a, bioMerieux: Employee|bioMerieux: Stocks/Bonds Kristen Holmberg, n/a, bioMerieux: Employee Annie Lyons, n/a, bioMerieux: Employee Nicole Monroe, Dr. sc. nat., bioMerieux: Employee Rangaraj Selvarangan, BVSc, PhD, D(ABMM), FIDSA, F(AAM), BioFire: Grant/Research Support|Luminex: Grant/Research Support Kimberle Chapin, MD, Cepheid: Employee Bradley A. Connor, MD, BioMerieux: Advisor/Consultant Cynthia Andjelic, PhD, bioMerieux: Employee.
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Affiliation(s)
| | | | | | | | | | | | | | - Leslie A Hueschen
- Children's Mercy Hospital/University of Missouri-Kansas City , KANSAS CITY, Missouri
| | | | | | | | | | - Bradley A Connor
- New York Center for Travel and Tropical Medicine , New York, New York
| | - Marina Rogova
- New York Center for Travel and Tropical Medicine , New York, New York
| | - Mark Steele
- University Health Truman Medical Center , Kansas City, Missouri
| | - Amy M Stubbs
- University Health-TMC/University of Missouri-Kansas City , FAIRWAY, Kansas
| | - Jennifer Dien Bard
- Children's Hospital Los Angeles; University of Southern California , Los Angeles, CA
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Piccicacco N, Zeitler K, Ing A, Montero J, Faughn J, Silbert S, Kim K. Real-world effectiveness of early remdesivir and sotrovimab in the highest-risk COVID-19 outpatients during the Omicron surge. J Antimicrob Chemother 2022; 77:2693-2700. [PMID: 35913836 PMCID: PMC9384598 DOI: 10.1093/jac/dkac256] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 07/06/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Remdesivir and sotrovimab both have clinical trial data in the outpatient setting demonstrating reduction in the risk of hospitalizations and emergency department (ED) visits related to COVID-19. OBJECTIVES To evaluate the effectiveness of remdesivir in comparison with sotrovimab and matched high-risk control patients in preventing COVID-19-related hospitalizations and ED visits during the Omicron B.1.1.529 surge. PATIENTS AND METHODS This retrospective cohort study included outpatients positive for SARS-CoV-2, with non-severe symptoms for ≤7 days and deemed high-risk for severe COVID-19 by an internal scoring matrix. Patients who received remdesivir or sotrovimab from 27/12/2021 to 04/02/2022 were included (n = 82 and n = 88, respectively). These were compared with a control cohort of high-risk COVID-19 outpatients who did not receive therapy (n = 90). The primary outcome was a composite of 29 day COVID-19-related hospitalizations and/or ED visits. Pre-specified secondary outcomes included components of the primary endpoint, 29 day all-cause mortality and serious adverse drug events. RESULTS Patients treated with remdesivir were significantly less likely to be hospitalized or visit the ED within 29 days from symptom onset (11% versus 23.3%; OR = 0.41, 95% CI = 0.17-0.95). Patients receiving sotrovimab were also less likely to be hospitalized or visit the ED (8% versus 23.3%; OR = 0.28, 95% CI = 0.11-0.71). There was no difference in the incidence of hospitalizations/ED visits between sotrovimab and remdesivir. CONCLUSIONS Our highest-risk outpatients with Omicron-related COVID-19 who received early sotrovimab or remdesivir had significantly lower likelihoods of a hospitalization and/or ED visit.
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Affiliation(s)
| | - Kristen Zeitler
- Department of Pharmacy, Tampa General Hospital, Tampa, FL, USA
| | - Austin Ing
- Department of Pharmacy, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jose Montero
- Division of Infectious Diseases, Department of Internal Medicine, University of South Florida Morsani College of Medicine, Tampa, FL, USA
| | - Jonathan Faughn
- Esoteric Testing/R&D and Microbiology Laboratories, Tampa General Hospital, Tampa, FL, USA
| | - Suzane Silbert
- Esoteric Testing/R&D and Microbiology Laboratories, Tampa General Hospital, Tampa, FL, USA
| | - Kami Kim
- Division of Infectious Diseases, Department of Internal Medicine, University of South Florida Morsani College of Medicine, Tampa, FL, USA.,Global Emerging Diseases Institute, Tampa General Hospital, Tampa, FL, USA
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Berry GJ, Zhen W, Smith E, Manji R, Silbert S, Lima A, Harington A, McKinley K, Kensinger B, Neff C, Lu D. Multicenter Evaluation of the BioFire Respiratory Panel 2.1 (RP2.1) for Detection of SARS-CoV-2 in Nasopharyngeal Swab Samples. J Clin Microbiol 2022; 60:e0006622. [PMID: 35387475 PMCID: PMC9116161 DOI: 10.1128/jcm.00066-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/10/2022] [Indexed: 11/20/2022] Open
Abstract
As the incidence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) begins to overlap with the traditional respiratory season in the Northern Hemisphere, simultaneous testing for SARS-CoV-2 and the other common causes of respiratory infections is imperative. This has led to the development of multiplex respiratory assays that include SARS-CoV-2 as a target. One such assay is the BioFire respiratory panel 2.1 (RP2.1), which is an expansion of the original BioFire FilmArray respiratory panel 2 (RP2) to include SARS-CoV-2. In this multicenter evaluation, we assessed the performance characteristics of the BioFire RP2.1 for the detection of SARS-CoV-2. One or more targets on the panel were detected in 19.3% (101/524) of specimens tested, with SARS-CoV-2 detected in 12.6% (66/524) of specimens. Human rhinovirus/enterovirus was also detected in 32.7% (33/101) and adenovirus in 3.0% (3/101) of positive specimens, with one dual positive for both SARS-CoV-2 and adenovirus being detected. A further breakdown of pathogens by age revealed a 4-fold predominance of human rhinovirus/enterovirus in subjects 0 to 18 years of age, whereas in all other age groups, SARS-CoV-2 was clearly the predominant pathogen. Overall, SARS-CoV-2 results obtained from the BioFire RP2.1 were highly concordant with the composite result, exhibiting 98.4% (61/62) positive percent agreement (95% confidence interval [CI], 91.4 to 99.7%) and 98.9% (457/462) negative percent agreement (95% CI, 97.5 to 99.5%) with further analysis of discordant results suggesting that the concentration of SARS-CoV-2 in the specimens was near the limit of detection (LoD) for both the BioFire RP2.1 and the comparator assays. Overall, the BioFire RP2.1 exhibited excellent performance in the detection of SARS-CoV-2.
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Affiliation(s)
- Gregory J. Berry
- Infectious Disease Diagnostics, Northwell Health Laboratories, Lake Success, New York, USA
- Department of Pathology and Laboratory Medicine, The Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York, USA
| | - Wei Zhen
- Infectious Disease Diagnostics, Northwell Health Laboratories, Lake Success, New York, USA
| | - Elizabeth Smith
- Infectious Disease Diagnostics, Northwell Health Laboratories, Lake Success, New York, USA
| | - Ryhana Manji
- Infectious Disease Diagnostics, Northwell Health Laboratories, Lake Success, New York, USA
| | | | | | | | | | | | - Crissy Neff
- BioFire Diagnostics, LLC, Salt Lake City, Utah, USA
| | - Daisy Lu
- BioFire Diagnostics, LLC, Salt Lake City, Utah, USA
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Bruzek S, Vestal G, Lasher A, Lima A, Silbert S. Bacterial Whole Genome Sequencing on the Illumina iSeq 100 for Clinical and Public Health Laboratories. J Mol Diagn 2020; 22:1419-1429. [DOI: 10.1016/j.jmoldx.2020.09.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 08/12/2020] [Accepted: 09/10/2020] [Indexed: 12/30/2022] Open
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11
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Lima A, Healer V, Vendrone E, Silbert S. Validation of a modified CDC assay and performance comparison with the NeuMoDx™ and DiaSorin® automated assays for rapid detection of SARS-CoV-2 in respiratory specimens. J Clin Virol 2020; 133:104688. [PMID: 33220549 PMCID: PMC7657030 DOI: 10.1016/j.jcv.2020.104688] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 10/20/2020] [Accepted: 11/07/2020] [Indexed: 12/25/2022]
Abstract
COVID-19 cases are rising in the US, Brazil and India with no apparent end in sight. The validated modified CDC assay performs well but its testing capacity is limited. Laboratories need to acquire multiple assays to meet SARS-CoV-2 testing demand. NeuMoDx has the highest throughput and shortest TAT than the other assays tested.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019 (COVID-19), has spread rapidly around the globe since it was first identified in December of 2019 in Wuhan, China. In a race to contain the infection, researchers and healthcare officials have developed several assays to help diagnose individuals with COVID-19. To help laboratories decide what assay to bring into testing lines, factors such as assay availability, cost, throughput, and TAT should be considered. Here we validated a modified version of the CDC assay and used it as a reference to evaluate the performance of the NeuMoDxTM SARS-CoV-2 and DiaSorin SimplexaTM Covid-19 Direct assays. In silico analysis and clinical sample testing showed that the primers/probes designed by the CDC were specific to the SARS-CoV-2 as they accurately detected all reactive samples with an assay LoD of 200 copies/mL. The performance of the three assays were analyzed using 159 nasopharyngeal swabs specimen tested within 1–5 days after routine testing. A 100 % agreement was observed between the commercial assays and the modified CDC SARS-CoV-2 assay. A deeper look at the Ct values showed no significant difference between NeuMoDx and the modified CDC SARS-CoV-2 assay, whereas DiaSorin had lower overall Ct values than the modified CDC SARS-CoV-2 assay. NeuMoDx and DiaSorin workflows were much easier to perform. NeuMoDx has the highest throughput and shortest TAT, whereas although the modified CDC SARS-CoV-2 assay has comparable throughput to DiaSorin, it has the longest hands-on time and highest TAT.
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Affiliation(s)
- Amorce Lima
- Esoteric Testing/R&D Laboratory, Tampa General Hospital, 1 Tampa General Cir, Tampa, FL, United States.
| | - Vicki Healer
- Esoteric Testing/R&D Laboratory, Tampa General Hospital, 1 Tampa General Cir, Tampa, FL, United States
| | - Elaine Vendrone
- Esoteric Testing/R&D Laboratory, Tampa General Hospital, 1 Tampa General Cir, Tampa, FL, United States
| | - Suzane Silbert
- Esoteric Testing/R&D Laboratory, Tampa General Hospital, 1 Tampa General Cir, Tampa, FL, United States
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Decker SJ, Goldstein TA, Ford JM, Teng MN, Pugliese RS, Berry GJ, Pettengill M, Silbert S, Hazelton TR, Wilson JW, Shine K, Wang ZX, Hutchinson M, Castagnaro J, Bloom OE, Breining DA, Goldsmith BM, Sinnott JT, O'Donnell DG, Crawford JM, Lockwood CJ, Kim K. 3D Printed Alternative to the Standard Synthetic Flocked Nasopharyngeal Swabs Used for COVID-19 testing. Clin Infect Dis 2020; 73:e3027-e3032. [PMID: 32910817 PMCID: PMC7499529 DOI: 10.1093/cid/ciaa1366] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Indexed: 11/17/2022] Open
Abstract
Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, can be detected in respiratory samples by Real-time Reverse Transcriptase (RT)-PCR or other molecular methods. Accessibility of diagnostic testing for COVID-19 has been limited by intermittent shortages of supplies required for testing, including flocked nasopharyngeal (FLNP) swabs. Methods We developed a 3D-printed nasopharyngeal (3DP) swab as a replacement of the FLNP swab. The performance of 3DP and FLNP swabs were compared in a clinical trial of symptomatic patients at three clinical sites (n=291) using three SARS-CoV-2 EUA tests: a modified version of the CDC Real-time Reverse Transcriptase (RT)-PCR Diagnostic Panel and two commercial automated formats, Roche Cobas and NeuMoDx. Results The cycle threshold (C(t)) values from the gene targets and the RNase P gene control in the CDC assay showed no significant differences between swabs for both gene targets (p=0.152 and p=0.092), with the RNase P target performing significantly better in the 3DP swabs (p & 0.001). The C(t) values showed no significant differences between swabs for both viral gene targets in the Roche cobas assay (p=0.05 and p=0.05) as well as the NeuMoDx assay (p=0.401 and p=0.484). The overall clinical correlation of COVID-19 diagnosis between all methods was 95.88% (Kappa 0.901). Conclusions 3DP swabs were equivalent to standard FLNP in three testing platforms for SARS-CoV-2. Given the need for widespread testing, 3DP swabs printed on-site are an alternate to FLNP that can rapidly scale in response to acute needs when supply chain disruptions affect availability of collection kits.
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Affiliation(s)
- Summer J Decker
- University of South Florida, Morsani College of Medicine, Tampa, FL
| | | | - Jonathan M Ford
- University of South Florida, Morsani College of Medicine, Tampa, FL
| | - Michael N Teng
- University of South Florida, Morsani College of Medicine, Tampa, FL
| | | | - Gregory J Berry
- Northwell Health System.,Department of Pathology and Laboratory Medicine, Donald and Barbara Zucker School of Medicine at Hofstra / Northwell
| | | | | | - Todd R Hazelton
- University of South Florida, Morsani College of Medicine, Tampa, FL
| | - Jason W Wilson
- University of South Florida, Morsani College of Medicine, Tampa, FL
| | - Kristy Shine
- Thomas Jefferson University, Sidney Kimmel Medical College
| | - Zi-Xuan Wang
- Thomas Jefferson University and Thomas Jefferson University Hospital
| | | | | | | | - Dwayne A Breining
- Northwell Health System.,Department of Pathology and Laboratory Medicine, Donald and Barbara Zucker School of Medicine at Hofstra / Northwell
| | | | - John T Sinnott
- University of South Florida, Morsani College of Medicine, Tampa, FL
| | | | - James M Crawford
- Northwell Health System.,Department of Pathology and Laboratory Medicine, Donald and Barbara Zucker School of Medicine at Hofstra / Northwell
| | | | - Kami Kim
- University of South Florida, Morsani College of Medicine, Tampa, FL
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Rojas HF, Lima A, Kubasek C, Gostnell A, Silbert S. Evaluation of Copan FecalSwab™ preserved stool specimens with the BD MAX™ Enteric Bacterial Panel and the BD MAX™ Extended Enteric Bacterial Panel. Diagn Microbiol Infect Dis 2020; 97:115055. [DOI: 10.1016/j.diagmicrobio.2020.115055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 04/01/2020] [Accepted: 04/01/2020] [Indexed: 11/25/2022]
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Voigt C, Silbert S, Widen RH, Marturano JE, Lowery TJ, Ashcraft D, Pankey G. The T2Bacteria Assay Is a Sensitive and Rapid Detector of Bacteremia That Can Be Initiated in the Emergency Department and Has Potential to Favorably Influence Subsequent Therapy. J Emerg Med 2020; 58:785-796. [DOI: 10.1016/j.jemermed.2019.11.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 10/01/2019] [Accepted: 11/23/2019] [Indexed: 11/25/2022]
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15
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Pancholi P, Young S, Widen R, Silbert S, Schmitt B, Dunn R, Drain A, Weissfeld S. A multicenter evaluation of a sample to answer real-time PCR assay for toxigenic C. difficile in symptomatic subjects. Diagn Microbiol Infect Dis 2020; 96:114920. [DOI: 10.1016/j.diagmicrobio.2019.114920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 09/05/2019] [Accepted: 10/17/2019] [Indexed: 11/24/2022]
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Rocchetti TT, Silbert S, Gostnell A, Kubasek C, Jerris R, Vong J, Widen R. Rapid detection of four non-fermenting Gram-negative bacteria directly from cystic fibrosis patient's respiratory samples on the BD MAX™ system. Pract Lab Med 2018; 12:e00102. [PMID: 30009245 PMCID: PMC6041425 DOI: 10.1016/j.plabm.2018.e00102] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 03/13/2018] [Accepted: 05/23/2018] [Indexed: 12/30/2022] Open
Abstract
The aim of this study was to develop a multiplex PCR test to detect Achromobacter xylosoxidans (AX), Burkholderia cepacia (BC), Pseudomonas aeruginosa (PSA) and Stenotrophomonas maltophilia (SM) directly from CF patient's respiratory samples using the open mode of the BD MAX™ System. A total of 402 CF respiratory samples were evaluated by culture and PCR. Specific sets of primers and probes for each target were designed in-house. Out of 402 samples tested, 196 were identified as negative and 206 as positive by culture for AX, PSA, BC and SM. Among culture positive samples, PCR detected 21/27 AX, 4/5 BC, 138/140 PSA and 29/34 SM. In addition, PCR assay identified 35 samples as positive that were initially negative by culture for those 4 targets. The CF BDM test proved to be an excellent tool to detect AX, BC, PSA and SM by real-time PCR on an automated platform.
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Affiliation(s)
- Talita T. Rocchetti
- Esoteric Testing Laboratory, Pathology Department, Tampa General Hospital, Tampa, FL, USA
- Laboratório Especial de Microbiologia Clínica (LEMC), Federal University of São Paulo/UNIFESP, São Paulo, SP, Brazil
| | - Suzane Silbert
- Esoteric Testing Laboratory, Pathology Department, Tampa General Hospital, Tampa, FL, USA
- Correspondence to: Esoteric Testing Laboratory, Tampa General Hospital, 1 Tampa General Circle, Tampa, FL 33606-3571, USA.
| | - Alicia Gostnell
- Esoteric Testing Laboratory, Pathology Department, Tampa General Hospital, Tampa, FL, USA
| | - Carly Kubasek
- Esoteric Testing Laboratory, Pathology Department, Tampa General Hospital, Tampa, FL, USA
| | | | | | - Raymond Widen
- Esoteric Testing Laboratory, Pathology Department, Tampa General Hospital, Tampa, FL, USA
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Ramos AC, Gales AC, Monteiro J, Silbert S, Chagas-Neto T, Machado AMO, Carvalhaes CG. Evaluation of a rapid immunochromatographic test for detection of distinct variants of Klebsiella pneumoniae carbapenemase (KPC) in Enterobacteriaceae. J Microbiol Methods 2017; 142:1-3. [PMID: 28844719 DOI: 10.1016/j.mimet.2017.08.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 08/23/2017] [Accepted: 08/23/2017] [Indexed: 10/19/2022]
Abstract
The rapid detection of KPC-producing Enterobacteriaceae by microbiology laboratories has been required for infectious control programs. Herein we evaluated the performance of a novel immunochromatographic test for detecting KPC-2-, KPC-3-, KPC-4-, KPC-6-, KPC-7-, KPC-8-, and KPC-11-producing isolates and the influence of different growth media on the test performance.
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Affiliation(s)
- Ana C Ramos
- Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo, São Paulo, Brazil.
| | - Ana C Gales
- Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo, São Paulo, Brazil
| | - Jussimara Monteiro
- Associação Fundo de Incentivo à Pesquisa, AFIP Medicina Diagnóstica, São Paulo, Brazil
| | - Suzane Silbert
- Esoteric Testing Laboratory, Pathology Department, Tampa General Hospital, Tampa, United States
| | - Thomás Chagas-Neto
- Laboratório Central, Hospital São Paulo, Division of Laboratory Medicine, Departament of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo, São Paulo, Brazil
| | - Antonia M O Machado
- Laboratório Central, Hospital São Paulo, Division of Laboratory Medicine, Departament of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo, São Paulo, Brazil
| | - Cecilia G Carvalhaes
- Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo, São Paulo, Brazil; Laboratório Central, Hospital São Paulo, Division of Laboratory Medicine, Departament of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo, São Paulo, Brazil
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Rocchetti TT, Silbert S, Gostnell A, Kubasek C, Campos Pignatari AC, Widen R. Detection of Mycobacterium chelonae, Mycobacterium abscessus Group, and Mycobacterium fortuitum Complex by a Multiplex Real-Time PCR Directly from Clinical Samples Using the BD MAX System. J Mol Diagn 2017; 19:295-302. [DOI: 10.1016/j.jmoldx.2016.10.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 10/03/2016] [Accepted: 10/07/2016] [Indexed: 11/16/2022] Open
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Silbert S, Pfaller MA, Hollis RJ, Barth AL, Sader HS. Evaluation of Three Molecular Typing Techniques for Nonfermentative Gram-Negative Bacilli. Infect Control Hosp Epidemiol 2015; 25:847-51. [PMID: 15518027 DOI: 10.1086/502307] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
AbstractObjective:To evaluate three different DNA techniques for typing nonfermentative gram-negative bacilli isolated from Latin American hospitals.Design:One hundred twenty-six nonfermentative gram-negative bacilli were typed.Participants:Pseudomonas aeruginosa(n = 64) andAcinetobacter baumannii(n = 42) samples were obtained from blood cultures of patients admitted to 10 medical centers in Latin America during 1998 andStenotrophomonas maltophilia(n = 20) samples were obtained from patients admitted to the Hospital São Paulo between 1999 and 2001.Methods:All samples were typed using automated ribotyping, PFGE, and ERIC-PCR. The discriminatory power for each technique was calculated using Hunter's generalized formula.Results:All strains could be typed by automated ribotyping and ERIC-PCR, but two strains (1.6%) were not typeable by PFGE. All three techniques showed 100% reproducibility. The time to obtain the results was shorter for automated ribotyping and ERIC-PCR compared with PFGE. Likewise, the costs for ERIC-PCR and PFGE were lower than those for automated ribotyping. The interpretation of results was more complicated and more difficult with ERIC-PCR than with both PFGE and automated ribotyping. All techniques presented excellent discriminatory power forP. aeruginosa(0.98). PFGE presented the highest discriminatory power (0.94) forA. baumannii,and both PFGE and ERIC-PCR showed higher discriminatory power (0.90 for both) than automated ribotyping (0.82) for S.maltophilia.Conclusions:PFGE showed the highest discriminatory power for typing these nonfermentative gram-negative bacilli. However, automated ribotyping and ERIC-PCR can provide results in a shorter time period with similar discriminatory power.
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Affiliation(s)
- Suzane Silbert
- Laboratório Especial de Microbiologia Clínica, Disciplina de Doenças Infecciosas e Parasitárias, Universidade Federal de São Paulo, São Paulo, Brasil
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Monteiro J, Widen RH, Pignatari AC, Kubasek C, Silbert S. Differentiation of Klebsiella pneumoniae carbapenemase (KPC) variants by pyrosequencing. J Microbiol Methods 2014; 100:42-5. [DOI: 10.1016/j.mimet.2014.02.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 02/26/2014] [Accepted: 02/26/2014] [Indexed: 10/25/2022]
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Monteiro J, Widen RH, Pignatari ACC, Kubasek C, Silbert S. Rapid detection of carbapenemase genes by multiplex real-time PCR. J Antimicrob Chemother 2012; 67:906-9. [PMID: 22232516 DOI: 10.1093/jac/dkr563] [Citation(s) in RCA: 218] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
OBJECTIVES To develop a single multiplex real-time PCR assay to detect six different genetic types of carbapenemases already identified in Enterobacteriaceae (KPC, GES, NDM, IMP, VIM and OXA-48). METHODS A total of 58 bacterial isolates were tested. Thirty were previously characterized as resistant to carbapenems and documented by PCR and sequencing analysis to carry the following genes: bla(KPC) type, bla(GES) type, bla(IMP) type, bla(VIM) type, bla(OXA-48) and bla(NDM-1). These positive strains included 21 Enterobacteriaceae, 1 Acinetobacter baumannii and 8 Pseudomonas aeruginosa isolates. The remaining 28 isolates previously tested susceptible to carbapenems and were negative for these genes. Bacterial DNA was extracted using the easyMag extractor (bioMérieux, France). The real-time PCR was performed using the Rotor-Gene 6000 instrument (Corbett Life Science, Australia) and specific primers for each carbapenemase target were designed using the DNAStar software (Madison, WI, USA). RESULTS Each one of the six carbapenemase genes tested presented a different melting curve after PCR amplification. The melting temperature (T(m)) analysis of the amplicons identified was as follows: bla(IMP) type (T(m) 80.1°C), bla(OXA-48) (T(m) 81.6°C), bla(NDM-1) (T(m) 84°C), bla(GES) type (T(m) 88.6°C), bla(VIM) type (T(m) 90.3°C) and bla(KPC) type (T(m) 91.6°C). No amplification was detected among the negative samples. The results showed 100% concordance with the genotypes previously identified. CONCLUSIONS The new assay was able to detect the presence of six different carbapenemase gene types in a single 3 h PCR.
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Affiliation(s)
- Jussimara Monteiro
- Esoteric Testing Laboratory, Pathology Department, Tampa General Hospital, Tampa, FL, USA
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22
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Silva FM, Carmo MS, Silbert S, Gales AC. SPM-1-ProducingPseudomonas aeruginosa: Analysis of the Ancestor Relationship Using Multilocus Sequence Typing, Pulsed-Field Gel Electrophoresis, and Automated Ribotyping. Microb Drug Resist 2011; 17:215-20. [DOI: 10.1089/mdr.2010.0140] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Fernanda M. Silva
- Laboratório Especial de Microbiologia Clínica, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Mirian S. Carmo
- Laboratório Especial de Microbiologia Clínica, Universidade Federal de São Paulo, São Paulo, Brazil
- Centro Universitário FIEO—UNIFIEO, São Paulo, Brazil
| | - Suzane Silbert
- Esoteric Testing Laboratory, Tampa General Hospital, Tampa, Florida
| | - Ana C. Gales
- Laboratório Especial de Microbiologia Clínica, Universidade Federal de São Paulo, São Paulo, Brazil
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d'Azevedo PA, Furtado GH, Medeiros EA, Santiago KA, Silbert S, Pignatari AC. Molecular characterization of vancomycin-resistant Enterococci strains eight years apart from its first isolation in São Paulo, Brazil. Rev Inst Med Trop Sao Paulo 2008; 50:195-8. [DOI: 10.1590/s0036-46652008000400001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2007] [Accepted: 06/30/2008] [Indexed: 11/21/2022] Open
Abstract
E. faecium was the first reported VRE species, carrying the vanA gene in Brazil. In spite of this, vancomycin-resistant E. faecalis has become the predominant species in Brazilian hospitals. The aim of this study was to evaluate the genetic relatedness of VREs isolated in a Brazilian teaching hospital eight years apart from its first isolation. We analyzed 38 VRE strains obtained from 81 surveillance cultures of patients admitted to the four largest intensive care units in Hospital São Paulo in February, 2006. Presence of the vanA gene was assayed by PCR and PFGE analysis was used for molecular characterization. All VRE strains carried the vanA gene. Two distinct clonal groups were observed among vancomycin-resistant E. faecalis. Vancomycin-resistant E. faecium belonged to five distinct clones were demonstrated by molecular typing. All of these clones were different from the first vancomycin-resistant enterococci clone isolated eight years ago in our hospital.
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Affiliation(s)
- Pedro Alves d'Azevedo
- Universidade Federal de São Paulo, Brasil; Fundação Faculdade Federal de Porto Alegre, Brasil
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Sitnik R, Sette Jr H, Santana R, Menezes L, Graça C, Dastoli G, Silbert S, Pinho J. Hepatitis B virus genotype E detected in Brazil in an African patient who is a frequent traveler. Braz J Med Biol Res 2007; 40:1689-92. [DOI: 10.1590/s0100-879x2006005000185] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2007] [Accepted: 07/10/2007] [Indexed: 01/04/2023] Open
Affiliation(s)
- R Sitnik
- Hospital Israelita Albert Einstein, Brasil
| | | | | | | | | | | | - S Silbert
- Hospital Israelita Albert Einstein, Brasil; Universidade Federal de São Paulo, Brasil
| | - J.R.R Pinho
- Hospital Israelita Albert Einstein, Brasil; Universidade de São Paulo, Brasil
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Zavascki AP, Soares FC, Superti SV, Silbert S, Silva FM, Barth AL. Stable carbapenem susceptibility rates among multidrug-resistant Acinetobacter spp. strains in a setting of high prevalence of carbapenem-resistant Pseudomonas aeruginosa. Int J Antimicrob Agents 2007; 30:187-9. [PMID: 17452093 DOI: 10.1016/j.ijantimicag.2007.03.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2007] [Accepted: 03/08/2007] [Indexed: 11/27/2022]
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Almeida FP, Martino MDV, Silva M, Lamblet LC, Corrêa L, Silbert S, Vallone C. Vancomycin-resistant enterococci outbreak in an intensive care unit: prevention and control. Crit Care 2007. [PMCID: PMC3301160 DOI: 10.1186/cc5820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Almeida MTG, Rubio FG, Garcia DO, Pavarino-Bertelli ÉC, Rossit ARB, Bando SY, Silbert S, Goloni-Bertollo EM, Soares MMCN, Martinez MB. Genetic relatedness among clinical strains of Stenotrophomonas maltophilia in tertiary care hospital settings in São Paulo State, Brazil. Braz J Microbiol 2007. [DOI: 10.1590/s1517-83822007000200017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Ribeiro J, Mendes RE, Domingos R, França E, Silbert S, Jones RN, Sader HS. Microbiological and epidemiological characterization of imipenem-resistant Pseudomonas aeruginosa strains from a Brazilian tertiary hospital: report from the SENTRY Antimicrobial Surveillance Program. J Chemother 2007; 18:461-7. [PMID: 17127220 DOI: 10.1179/joc.2006.18.5.461] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
OBJECTIVES To evaluate the antimicrobial susceptibility profile, the genetic similarity, and the mechanisms of carbapenem resistance among imipenem-resistant Pseudomonas aeruginosa isolates collected from a Brazilian tertiary teaching hospital. METHODS Seventy-eight consecutive samples of P. aeruginosa were evaluated during 2000 and 2001. The antimicrobial susceptibility was evaluated by reference broth microdilution methods and the imipenem-resistant isolates were screened for metallo-beta-lactamase (MbetaL) production throughout disc approximation test and MbetaL Etest strips and isolates with positive screen test result were submitted to PCR assays using primers blaIMP-1, bla VIM-1, blaVIM-2 e blaSPM-1. The genetic similarity of MbetaL-producing strains was evaluated by automated ribotyping for epidemiological typing purpose. RESULTS Resistance rates were high to the majority of antimicrobial agents tested except polymyxin B, which inhibited all samples at the Clinical and Laboratory Standards Institute breakpoint (< or = 2 microg/ml). Twenty-nine (37.2%) isolates were resistant to imipenem and these isolates showed great genomic variability. MbetaL production was demonstrated in two imipenem-resistant isolates, which were detected using blaSPM-1 and blaIMP-2-specific primers. Sequence analysis revealed the presence of blaSPM-1 and a novel blaIMP-type gene, blaIMP-16. CONCLUSION The results of this study showed high resistance rates to the majority of antimicrobial agents among P. aeruginosa samples. High imipenem resistance rates were probably due to continuous selection of resistant mutants. The production of MbetaL did not represent a frequent mechanism of carbapenem resistance in this medical center; but a novel MbetaL was identified. Continued antimicrobial surveillance and infection control measures should be emphasized to minimize the emergence and dissemination of antimicrobial resistance.
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Affiliation(s)
- J Ribeiro
- Infection Control Committee, Hospital de Base do Distrito Federal, Brasília, DF, Brazil.
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Freitas MCS, Pacheco-Silva A, Barbosa D, Silbert S, Sader H, Sesso R, Camargo LFA. Prevalence of vancomycin-resistant Enterococcus fecal colonization among kidney transplant patients. BMC Infect Dis 2006; 6:133. [PMID: 16923193 PMCID: PMC1559694 DOI: 10.1186/1471-2334-6-133] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2006] [Accepted: 08/22/2006] [Indexed: 11/18/2022] Open
Abstract
Background End stage renal disease patients are at risk of Vancomycin-Resistant Enterococcus (VRE) infections. The first reports of VRE isolation were from hemodialysis patients. However, to date, VRE fecal colonization rates as well as associated risk factors in kidney transplant patients have not yet been established in prospective studies. Methods We collected one or two stool samples from 280 kidney transplant patients and analysed the prevalence of VRE and its associated risk factors. Patients were evaluated according to the post-transplant period: group 1, less than 30 days after transplantation (102 patients), group 2, one to 6 months after transplantation (73 patients) and group 3, more than 6 months after transplantation (105 patients). Results The overall prevalence rate of fecal VRE colonization was 13.6% (38/280), respectively 13.7% for Group 1, 15.1% for group 2 and 12.4% for group 3. E. faecium and E. faecalis comprised 50% of all VRE isolates. No immunologic variables were clearly correlated with VRE colonization and no infections related to VRE colonization were reported. Conclusion Fecal VRE colonization rates in kidney transplant patients were as high as those reported for other high-risk groups, such as critical care and hemodialysis patients. This high rate of VRE colonization observed in kidney transplant recipients may have clinical relevance in infectious complications.
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Affiliation(s)
- Maria Cecília S Freitas
- Department of Medicine, Division of Nephrology, Universidade Federal de São Paulo (UNIFESP), Hospital do Rim e Hipertensão, Brazil
- Department of Medicine, Division of Nephrology and Infectious Diseases, Universidade Federal de São Paulo, Hospital do Rim e Hipertensão, SP, Brazil
| | - Alvaro Pacheco-Silva
- Department of Medicine, Division of Nephrology, Universidade Federal de São Paulo (UNIFESP), Hospital do Rim e Hipertensão, Brazil
- Department of Medicine, Division of Nephrology and Infectious Diseases, Universidade Federal de São Paulo, Hospital do Rim e Hipertensão, SP, Brazil
| | - Dulce Barbosa
- Department of Medicine, Division of Nephrology, Universidade Federal de São Paulo (UNIFESP), Hospital do Rim e Hipertensão, Brazil
- Department of Medicine, Division of Nephrology and Infectious Diseases, Universidade Federal de São Paulo, Hospital do Rim e Hipertensão, SP, Brazil
| | - Suzane Silbert
- Department of Medicine, Division of Nephrology, Universidade Federal de São Paulo (UNIFESP), Hospital do Rim e Hipertensão, Brazil
- Special Clinical Microbiology Laboratory (LEMC), Division of Infectious Diseases-UNIFESP, Brazil
- Department of Medicine, Division of Nephrology and Infectious Diseases, Universidade Federal de São Paulo, Hospital do Rim e Hipertensão, SP, Brazil
| | - Hélio Sader
- Special Clinical Microbiology Laboratory (LEMC), Division of Infectious Diseases-UNIFESP, Brazil
- Department of Medicine, Division of Nephrology and Infectious Diseases, Universidade Federal de São Paulo, Hospital do Rim e Hipertensão, SP, Brazil
| | - Ricardo Sesso
- Department of Medicine, Division of Nephrology, Universidade Federal de São Paulo (UNIFESP), Hospital do Rim e Hipertensão, Brazil
- Department of Medicine, Division of Nephrology and Infectious Diseases, Universidade Federal de São Paulo, Hospital do Rim e Hipertensão, SP, Brazil
| | - Luis Fernando A Camargo
- Infectious Diseases Unit, Hospital do Rim e Hipertensão, Universidade Federal de São Paulo, Brazil
- Department of Medicine, Division of Nephrology and Infectious Diseases, Universidade Federal de São Paulo, Hospital do Rim e Hipertensão, SP, Brazil
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Tognim MCB, Gales AC, Penteado AP, Silbert S, Sader HS. Dissemination of IMP-1 metallo- beta -lactamase-producing Acinetobacter species in a Brazilian teaching hospital. Infect Control Hosp Epidemiol 2006; 27:742-7. [PMID: 16807851 DOI: 10.1086/504356] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2004] [Accepted: 02/07/2005] [Indexed: 01/23/2023]
Abstract
OBJECTIVE To evaluate the emergence and dissemination of metallo- beta -lactamase (MBL)-producing Acinetobacter species. DESIGN All carbapenem-resistant Acinetobacter strains (1 strain per patient) collected during the period 1993-2001 were evaluated. SETTING A Brazilian tertiary care teaching hospital (Hospital Sao Paulo, Sao Paulo). METHODS Seventy-three strains of carbapenem-resistant Acinetobacter species were recovered from the organism bank of the hospital. All isolates were tested for antimicrobial susceptibility by broth microdilution methods, and the production of MBL was initially assessed by phenotypic tests (MBL Etest strip and a disk approximation test). The MBL enzymes were identified by polymerase chain reaction using primers for bla(IMP), bla(VIM), and bla(SPM), followed by gene sequencing. Genetic similarity among the carbapenem-resistant strains was evaluated by automated ribotyping. RESULTS Only colistin and ampicillin-sulbactam showed reasonable in vitro activity against carbapenem-resistant isolates (97% and 74% of isolates susceptible, respectively). More than half of the isolates (55%) had a positive MBL phenotypic test result and a positive polymerase chain reaction result for bla(IMP-1). The proportion of IMP-1-producing Acinetobacter isolates among carbapenem-resistant strains increased from 0% in the 1993-1997 period to 29% in 1998 and 100% in the 1999-2001 period. No carbapenem-resistant Acinetobacter isolates that harbored bla(VIM) or bla(SPM) were detected. Molecular typing results revealed 20 ribogroups among carbapenem-resistant isolates. During the study period of 1994-2001, we identified 2 major ribogroups, 52-1 (MBL-negative and MBL-positive strains) and 60-7 (MBL-positive strains), that had a coefficient of similarity of 0.85 or higher. CONCLUSIONS Our results indicate that IMP-1-producing strains of Acinetobacter emerged in our institution in 1998. Since then, production of this MBL was detected not only in the major ribogroups of carbapenem-resistant Acinetobacter species but also among isolates that belonged to 17 distinct ribogroups, indicating that this important mechanism of antimicrobial resistance was disseminated among distinct clones.
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Affiliation(s)
- Maria C B Tognim
- Division of Infectious Diseases, Universidade Federal de São Paulo, São Paulo, Brazil
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Sader HS, Reis AO, Silbert S, Gales AC. IMPs, VIMs and SPMs: the diversity of metallo-beta-lactamases produced by carbapenem-resistant Pseudomonas aeruginosa in a Brazilian hospital. Clin Microbiol Infect 2005; 11:73-6. [PMID: 15649310 DOI: 10.1111/j.1469-0691.2004.01031.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Pseudomonas aeruginosa isolates (n=183), collected from bacteraemic patients hospitalised in Sao Paulo Hospital (Brazil) during 2000-2001, were screened for susceptibility to antimicrobial agents. The polymyxins were the most active compounds (100% susceptibility), followed by amikacin and cefepime (59.0%), meropenem (57.4%), and imipenem and gentamicin (55.2%). Imipenem-resistant isolates were ribotyped and screened for production of metallo-beta-lactamases (MBLs) by PCR with primers for bla(IMP), bla(VIM) and bla(SPM). MBL production was detected in 36 isolates (19.7% of the entire collection; 43.9% of the imipenem-resistant isolates) and the MBLs included SPM-1-like (55.6%), VIM-2-like (30.6%) and IMP-1-like (8.3%) enzymes.
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Affiliation(s)
- H S Sader
- Laboratorio Alerta e Laboratorio Especial de Microbiologia Clínica, Disciplina de Doenças Infecciosas e Parasitárias, Universidade Federal de São Paulo, São Paulo, Brazil.
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Barbosa D, Lima L, Silbert S, Sader H, Cendoroglo M, Draibe S, Camargo L, Vianna L, Belasco A, Sesso R. Evaluation of the prevalence and risk factors for colonization by vancomycin-resistant Enterococcus among patients on dialysis. Am J Kidney Dis 2005; 44:337-43. [PMID: 15264193 DOI: 10.1053/j.ajkd.2004.04.038] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
BACKGROUND Vancomycin-resistant Enterococcus (VRE) has been reported among long-term dialysis patients, although risk factors for VRE colonization are not well defined. This study aims to appraise the prevalence and risk factors for VRE colonization among patients on long-term dialysis therapy, as well as the mechanisms for dissemination of vancomycin resistance. METHODS This is a cross-sectional survey of 320 patients on long-term dialysis therapy at 2 hospitals of the Federal University of São Paulo from June 2001 to March 2003. Fecal samples were collected from each patient once a week for 1 month. Samples with positive test results for VRE were submitted to molecular typing through automated ribotyping. RESULTS VRE prevalence was 14.4%. There were significant associations between VRE and dialysis type (hemodialysis, P = 0.04), number of hospitalizations (P = 0.03), low hemoglobin level (P = 0.03), and leukocytosis (P = 0.05). Among samples with VRE (n = 56), 25% were Enterococcus faecium; 10.7%, Enterococcus casseliflavus; 57.1%, Enterococcus gallinarum; and 3.6%, Enterococcus faecalis. All samples isolated were sensitive to teicoplanin, except for E faecium samples, which were strongly resistant, although 9 of 14 patients with this isolate presented the same ribogroup (111-S-4). Typing of 6 samples from 8 dialysis patients with E gallinarum was performed, showing a predominant ribogroup (112-S-4). CONCLUSION Hospital environment, hemodialysis, anemia, and leukocytosis appear to be associated with VRE colonization. These results suggest that dissemination of these bacteria among patients on long-term dialysis therapy may be taking place.
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Affiliation(s)
- Dulce Barbosa
- Department of Nursing, Division of Nursing in Infectology, Federal University of São Paulo, Escola Paulista de Medicina, São Paulo, Brazil.
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Tognim MCB, Andrade SS, Silbert S, Gales AC, Jones RN, Sader HS. Resistance trends of Acinetobacter spp. in Latin America and characterization of international dissemination of multi-drug resistant strains: five-year report of the SENTRY Antimicrobial Surveillance Program. Int J Infect Dis 2004; 8:284-91. [PMID: 15325597 DOI: 10.1016/j.ijid.2003.11.009] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2003] [Revised: 11/10/2003] [Accepted: 11/11/2003] [Indexed: 02/06/2023] Open
Abstract
OBJECTIVES To analyze the antimicrobial susceptibility of Acinetobacter spp. isolates collected from Latin American medical centers as part of the SENTRY Antimicrobial Surveillance Program and also to evaluate the dissemination of multi-drug resistant Acinetobacter spp. strains in the region. METHODS A total of 826 isolates of Acinetobacter spp. from multiple infection sites were collected from January 1997 to December 2001 in ten medical centers and susceptibility tested to >25 selected agents by broth microdilution. Multi-drug resistant Acinetobacter spp. isolates were molecular typed. RESULTS Resistance rates to carbapenems varied significantly among countries. A continued annual increase occurred in the Argentinean medical centers. In contrast, carbapenem resistance was rare in Chilean centers, and decreased significantly in the Brazilian institutions. Acinetobacter spp. isolates recovered from lower respiratory tract and bloodstream infections were associated with lower antimicrobial susceptibility rates. Resistance rates to imipenem were higher among isolates collected from intensive care units (13.5%) than among isolates from other units. A major ribogroup pattern (521-1) was detected among eight Acinetobacter spp. strains isolated from three distinct Latin American countries. CONCLUSIONS This study found that antimicrobial resistance is still a major issue among Acinetobacter spp. isolates collected from some Latin American countries. The dissemination of a major bacterial cluster in different regions reinforces the importance of longitudinal surveillance programs, such as SENTRY, as valuable tools for monitoring antimicrobial susceptibility rates and guiding local interventions.
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Affiliation(s)
- Maria Cristina Bronharo Tognim
- Laboratório Especial de Microbiologia Clínica, Disciplina de Doenças Infecciosas e Parasitárias, Universidade Federal de São Paulo-SP, CEP 04025-010, Brazil
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Abstract
The antimicrobial susceptibility patterns of 73 glycopeptide-resistant Enterococcus faecalis isolates from nine hospitals in Brazil were analysed by the disk diffusion method and Etests. Isolates were typed by pulsed-field gel electrophoresis (PFGE), and vancomycin resistance genes were detected by PCR. The isolates shared a single major PFGE pattern, with six subtypes, and all were positive for vanA. These results indicate the occurrence of inter-hospital dissemination of glycopeptide-resistant E. faecalis in São Paulo, and raise concerns about the rapid dissemination of this pathogen throughout Brazil.
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Affiliation(s)
- J C R Cordeiro
- Laboratório Especial de Microbiologia Clínica, Disciplina de Doenças Infecciosas e Parasitárias, Universidade Federal de São Paulo, Brazil
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Silbert S, Boyken L, Hollis RJ, Pfaller MA. Improving typeability of multiple bacterial species using pulsed-field gel electrophoresis and thiourea. Diagn Microbiol Infect Dis 2004; 47:619-21. [PMID: 14711485 DOI: 10.1016/s0732-8893(03)00164-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Although pulsed-field gel electrophoresis is considered the "gold standard" technique for molecular typing, typeability may not be excellent for some bacterial species because of DNA degradation. Previous reports suggest that the addition of thiourea in the gel buffer can improved the typeability for some species. In the present study, 66 Gram-negative strains (seven species) known to be affected by DNA degradation and four control strains were evaluated by PFGE with and without the addition of 50 microg/M of thiourea to the buffer used in the electrophoresis. Macrorestriction patterns were obtained for all K. pneumoniae, S. marcescens, P. aeruginosa, and Salmonella spp., for 95.4% of E. coli, and for 50% of E. cloacae strains from the gels performed in the buffer with throurea. However, typeability was not improved for Acinetobacter spp. The range of non-typeable species for which thiourea can limit the problem of DNA degradation is considerably wider than described in previous publications.
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Affiliation(s)
- Suzane Silbert
- Laboratório Especial de Microbiologia Clínica, Disciplina de Doenças Infecciosas e Parasitárias, Universidade Federal de São Paulo, Rua Leandro Dupret, 188. CEP, São Paulo, Brazil.
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Castanheira M, Jones RN, Silbert S, Brandileone MCC, Sader HS. Typing and Molecular Characterization ofStreptococcus pneumoniaewith Reduced Susceptibility to Cefotaxime Isolated in Latin America. Microb Drug Resist 2003; 9:345-51. [PMID: 15000740 DOI: 10.1089/107662903322762770] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The treatment of systemic infections, especially meningitis, caused by Streptococcus pneumoniae nonsusceptible to third-generation cephalosporins, is extremely difficult due to the paucity of therapeutic options. The main objective of this study was to characterize isolates of S. pneumoniae with reduced susceptibility to cefotaxime (MICs, > or = 1 microg/ml) by different typing methods and to evaluate whether clonal dissemination of this pathogen had occurred among Latin American medical centers. A total of 46 isolates collected from respiratory tract specimens, blood cultures, cerebrospinal fluid, eye, and other sources were analyzed. The isolates were collected from Latin American medical centers located in Argentina, Brazil, Chile, Colombia, Mexico, and Uruguay through two multicenter surveillance programs, in 1997 and 1998. Isolates were serotyped and molecular typed by pulsed-field gel electrophoresis (PFGE) and automated ribotyping. Antimicrobial susceptibilities were determined to 19 drugs by reference broth microdilution methods. Ten isolates (21.7%) had cefotaxime MICs > or = 2 microg/ml, whereas 36 (78.3%) had cefotaxime MIC results at 1 microg/ml. All isolates were susceptible to gatifloxacin, levofloxacin, and vancomycin. The isolates were distributed among five major serotypes (%): 23F (39.1%), 14 (32.6%), 19F (23.9%), 9V (2.2%), and 6B (2.2%). However, distinct molecular patterns were detected among isolates with a unique serotype. Six and four PFGE patterns were identified among isolates with serotype 23F and 19F, respectively. When PFGE and automated ribotyping analyses were combined, four clusters were identified. The largest cluster (10 isolates) was represented by isolates with ribotype 18-2, major PFGE pattern I, and serotype 14. ATCC 700671 (international clone Spain 9V-3) also showed ribotype 18-2. This clone was detected in four countries: Argentina, Brazil, Chile, and Uruguay. A second cluster (8 isolates) were characterized by isolates with ribotype 17-4, PFGE type D, and serotype 23F, similar to ATCC 700669 (international clone Spain23F-1). Isolates from this cluster were identified in three countries: Brazil, Chile, and Mexico. Our results indicated that clonal dissemination of S. pneumoniae with reduced susceptibility to cefotaxime has occurred in Latin America mainly among serogroups 14, 19F, and 23F.
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Affiliation(s)
- Mariana Castanheira
- Laboratório Especial de Microbiologia Clínica, Disciplina de Doenças Infecciosas e Parasitárias, Universidade Federal de São Paulo, Brazil
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Tosin I, Silbert S, Sader HS. The use of molecular typing to evaluate the dissemination of antimicrobial resistance among gram-negative rods in Brazilian hospitals. Braz J Infect Dis 2003; 7:360-9. [PMID: 14636474 DOI: 10.1590/s1413-86702003000600002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Antimicrobial resistance has increased rapidly in Brazil and worldwide during the past few years, giving rise to a growing necessity for antimicrobial resistance surveillance programs. These programs have been instituted in order to monitor bacterial resistance in various regions, and to guide empirical antimicrobial therapy. We evaluated the use of molecular typing in multicenter surveillance programs. We also studied the dissemination modes of selected resistance profiles. Antimicrobial susceptibility to various antimicrobial agents was evaluated by the reference broth microdilution method. Bacterial isolates with selected susceptibility patterns were characterized by pulsed field-gel electrophoresis (PFGE). A total of 119 Gram-negative bacteria were molecularly typed, including 22 imipenem-resistant Pseudomonas aeruginosa, 26 ESBL-producing Escherichia coli, 27 cefoxitin-resistant-ESBL-producing Klebsiella pneumoniae, 33 Enterobacter spp., 8 Citrobacter spp., and 3 S. marcescens isolates resistant to ceftazidime. The isolates were from clinically apparent bacteremia of patients hospitalized in medical centers located in 13 cities of 11 Brazilian states. Our molecular typing results revealed a great genetic diversity among isolates of the same species. However, some major PFGE patterns were found in more than one isolate. All repeated PFGE patterns were detected in only 2 isolates, which were isolated within the same institutions or in different medical centers. We conclude that the ability to characterize organisms phenotypically and genotypically is a powerful epidemiologic tool and it provides unique information that is very important for multicenter surveillance programs.
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Affiliation(s)
- Iraci Tosin
- Federal University of São Paulo, Special Laboratory of Clinical Microbiology, Florianápolis, SC, Brazil
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Gales AC, Menezes LC, Silbert S, Sader HS. Dissemination in distinct Brazilian regions of an epidemic carbapenem-resistant Pseudomonas aeruginosa producing SPM metallo-beta-lactamase. J Antimicrob Chemother 2003; 52:699-702. [PMID: 12951331 DOI: 10.1093/jac/dkg416] [Citation(s) in RCA: 155] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND In Brazil, carbapenem use has been limited by high carbapenem-resistance rates among Pseudomonas aeruginosa isolates. OBJECTIVE The main objective of this study was to evaluate the presence of an epidemic P. aeruginosa strain in unrelated Brazilian hospitals. We also aimed to search for the gene blaSPM, which encodes production of SPM, a novel metallo-beta-lactamase (MBL). METHODS A reference broth microdilution method was used for antimicrobial susceptibility testing. The isolates were typed by ribotyping and pulsed-field gel electrophoresis (PFGE). A disc-approximation test using MBL inhibitors was employed to screen isolates for MBL production. PCR was used to search for the gene blaSPM. RESULTS A total of 43 clinical isolates of carbapenem-resistant P. aeruginosa were collected from 12 hospitals. Colistin retained greatest activity in vitro. A single ribogroup included 17 P. aeruginosa isolates (39.5%) collected from seven unrelated hospitals located in five Brazilian states. Sixteen of these isolates showed an identical PFGE pattern, and 15 produced an SPM-1-like MBL. The remaining 26 isolates were grouped into 25 diverse ribogroups; none were MBL producers. CONCLUSIONS The emergence and dissemination of an epidemic clone has contributed to the high carbapenem resistance rates among P. aeruginosa isolates in Brazil. In addition, the production of SPM MBL has an important role in carbapenem resistance in this region. This is the first report of dissemination of an SPM-1-like-MBL-producing strain of P. aeruginosa among unrelated Brazilian hospitals.
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Affiliation(s)
- Ana C Gales
- Laboratório Alerta, Universidade Federal de São Paulo, SP, Brazil.
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Sejas LM, Silbert S, Reis AO, Sader HS. Avaliação da qualidade dos discos com antimicrobianos para testes de disco-difusão disponíveis comercialmente no Brasil. J Bras Patol Med Lab 2003. [DOI: 10.1590/s1676-24442003000100006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Cereda RF, Gales AC, Silbert S, Jones RN, Sader HS. Molecular typing and antimicrobial susceptibility of vancomycin-resistant Enterococcus faecium in Brazil. Infect Control Hosp Epidemiol 2002; 23:19-22. [PMID: 11868887 DOI: 10.1086/501962] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
OBJECTIVES To characterize vancomycin-resistant enterococci (VRE) isolates and to evaluate the mode of dissemination of this pathogen in Brazil. DESIGN We collected 22 vancomycin-resistant Enterococcus faecium isolates from 6 medical centers in Sao Paulo, Brazil, and 1 isolate from a medical center in Curitiba, Brazil. PARTICIPANTS All Brazilian hospitals that had identified vancomycin-resistant E. faecium up to the beginning of this study (late 1999) contributed isolates to the study. METHODS The isolates were susceptibility tested using the broth microdilution method and the E-test. The presence of vancomycin resistance genes (vanA, vanB, vanC1, vanC2-3, and vanD) was evaluated by polymerase chain reaction; molecular typing was performed by pulsed-field gel electrophoresis (PFGE). RESULTS The vanA gene was demonstrated in all vancomycin-resistant E. faecium, except for 1 isolate. None of the vancomycin resistance genes cited above was detected in the isolate from Curitiba, which was the first vancomycin-resistant E. faecium described in Brazil. All isolates were resistant to ampicillin and teicoplanin. The main clone remains susceptible to doxycycline and chloramphenicol, but intermediate to quinupristin-dalfopristin. PFGE analysis demonstrated 7 major PFGE patterns. A unique PFGE pattern with 4 subtypes was detected in 17 isolates from 4 different hospitals. CONCLUSION The results of our study indicate the occurrence of intra- and interhospital dissemination of VRE in Sao Paulo, Brazil.
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Affiliation(s)
- Rosangela F Cereda
- Division of Infectious Diseases, Universidade Federal Sao Paulo, Sao Paulo, Brazil
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Abstract
The aim of this study was to assess the diversity and genomic variability of Pseudomonas aeruginosa isolates from cystic fibrosis (CF) patients being treated at a university hospital in Brazil. Ninety-seven isolates of P. aeruginosa from 43 CF patients were characterized by macrorestriction analysis of chromosomal DNA by pulsed-field gel electrophoresis (PFGE) and tested for susceptibility to 20 antimicrobial agents by broth microdilution. It was possible to evaluate single isolates from 20 patients and multiple isolates (two to seven) from 23 patients collected during a 22-month period. Among all of the unrelated patients, we detected only one pair of patients sharing a common strain. Among the 77 isolates from 23 patients who had multiple isolates analyzed, we identified 37 major types by PFGE, and five different colonization patterns were recognized. The isolates were susceptible to several antimicrobial agents, although consecutive isolates from the same patient may display differences in their susceptibilities. Mucoid isolates were more resistant (P < 0.001) than nonmucoid isolates to five antibiotics. Our results indicate that CF patients remain colonized by more than one strain of P. aeruginosa for long periods of time. In addition, the finding of several different genotypes in the same patient suggests that the colonizing strain may occasionally be replaced.
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Affiliation(s)
- S Silbert
- Laboratório Especial de Microbiologia Clínica, Disciplina de Doenças Infecciosas e Parasitárias, Universidade Federal de São Paulo, São Paulo, Brazil.
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Roland RK, Mendes RE, Silbert S, Bolsoni AP, Sader HS. In vitro antimicrobial activity of piperacillin/tazobactam in comparison with other broad-spectrum beta-lactams. Braz J Infect Dis 2000; 4:226-35. [PMID: 11063554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023] Open
Abstract
Combining tazobactam, a beta-lactamase inhibitor, with the ureidopenicillin, piperacillin, successfully restores the activity of piperacillin against beta-lactamase producing bacteria. Thus, piperacillin/tazobactam is highly active against most clinically important species of Gram-negative and Gram-positive bacteria, including anaerobes. We evaluated the in vitro activity of piperacillin/tazobactam against clinical isolates from a tertiary university hospital located in Sao Paulo, Brazil. Its activity was compared to that of ticarcillin/clavulanic acid, ampicillin/sulbactam, ceftazidime, ceftriaxone, cefotaxime, cefoxitin, aztreonam, and imipenem against 820 isolates (608 Gram-negative and 212 Gram-positive) collected from hospitalized patients in 1999. The most frequent species tested were Pseudomonas aeruginosa (168/20%), Escherichia coli (139/17%), Acinetobacter spp. (131/16%), and Staphylococcus aureus (76/9%). Of the isolates studied, 30% were from the bloodstream, 16% from the lower respiratory tract, and 11% from surgical wounds or soft tissue. The isolates were susceptibility tested by the broth microdilution method according to NCCLS procedures. The isolates tested were highly resistant to most antimicrobial agents evaluated. Imipenem resistance was not verified among Enterobacteriaceae, and piperacillin/tazobactam was the second most active beta-lactams against this group of bacteria (80.0% susceptibility). Extended-spectrum beta-lactamase production was very high among E. coli (approximately 20%) and Klebsiella pneumoniae (approximately 40%). Imipenem was uniformly active against these species (100% susceptibility) and piperacillin/tazobactam was the second most active compound inhibiting 84.4% of isolates. Pseudomonas aeruginosa was highly resistant to all beta-lactams evaluated and piperacillin/tazobactam was the most active compound against this species. Our results demonstrate an extremely high level of antimicrobial resistance in the hospital evaluated, especially among non-enteric Gram-negative bacilli. Due to this high level of resistance, piperacillin/tazobactam represents an important contribution to the treatment of nosocomial infections.
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Affiliation(s)
- R K Roland
- Laboratory of Microbiology, Division of Infectious Diseases, Federal University of São Paulo, SP, Brazil
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Sprinz E, Mallman R, Barcellos S, Silbert S, Schestatsky G, Bem David D. AIDS-related cryptosporidial diarrhoea: an open study with roxithromycin. J Antimicrob Chemother 1998; 41 Suppl B:85-91. [PMID: 9579719 DOI: 10.1093/jac/41.suppl_2.85] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
In immunocompromised patients, cryptosporidial diarrhoea is a debilitating and potentially life-threatening infection for which no effective specific therapy exists. In an uncontrolled study of 24 AIDS patients with diarrhoea exclusively due to Cryptosporidium spp., treatment with roxithromycin, 300 mg bd for 4 weeks, produced symptomatic improvement of diarrhoea in 79% of cases, with 50% of patients achieving complete response. The response rate was 100% in a subgroup of five patients with no previous or concomitant opportunistic infections. In complete responders, improvement was rapid, occurring within 3-5 days, and the duration of response was at least 6 months. Response did not appear to be correlated with the degree of immunodeficiency. The most limiting adverse effects were abdominal pain (two patients), elevated hepatic enzymes (two patients) and abdominal pain with elevated hepatic enzymes (one patient). Minor symptoms, such as gastrointestinal upset, occurred in nine patients. We conclude that roxithromycin is relatively well tolerated and effective against cryptosporidial diarrhoea in AIDS patients. Further studies to optimize dosing regimens are required.
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Affiliation(s)
- E Sprinz
- Department of Internal Medicine, Hospital de Clinicas de Porto Alegre, Universidade Federal Do Rio Grande do Sul, Brazil
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Silbert S, Rosa DD, Matte U, Goldim JR, Barcellos SH, Procianoy RS. [Coagulase-negative Staphylococcus sp. in blood cultures from infants less than 60 days old: infection versus contamination]. J Pediatr (Rio J) 1997; 73:161-5. [PMID: 14685410 DOI: 10.2223/jped.524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
OBJECTIVE The aim of this study was to determine the prevalence of infection versus the prevalence of contamination in infants less than 60 days old who had blood cultures positive for CoNS. MATERIAL AND METHODS Between February and June - 1993, a number of 45 blood cultures positive for CoNS from 41 patients were studied. Patients were classified in three groups according to their clinical and laboratorial data: I- infected patients, II- non-infected patients and III- dubious. RESULTS The results showed that 11 patients (26.8%) were included in group I, 25 (61%) in group II (contaminated blood cultures), and 5 (12.2%) in group III. CONCLUSION It is suggested that more than one blood culture should be requested before treatment with antimicrobials, avoiding unnecessary administration of antibiotics.
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Affiliation(s)
- S Silbert
- Bióloga da Unidade de Microbiologia do Hospital de Clínicas de Porto Alegre.
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Silbert S, Michel T, Lee R, Neer EJ. Differential degradation rates of the G protein alpha o in cultured cardiac and pituitary cells. J Biol Chem 1990; 265:3102-5. [PMID: 2105942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Signal transduction in biological membranes is modulated by a family of GTP-binding proteins termed G proteins. Differences in the tissue-specific expression of G protein subtypes suggest that the levels of individual G proteins may be an important determinant of the hormonal response in a given cell type. We have used a polyclonal antibody raised against the purified G protein, alpha o to study alpha o in the rat pituitary cell line GH4 and in primary rat cardiocytes in culture by quantitative immunoprecipitation. Biosynthetic labeling and specific immunoprecipitation of alpha o in pulse-chase experiments demonstrated that the t1/2 for alpha o degradation is 28 +/- 7 h (n = 4) in GH4 pituitary cells and is greater than 72 h (n = 4) in cardiocytes. The steady-state level of alpha o protein is similar in both cell types as measured by Western blots. Northern blots of poly(A)-selected mRNA from these two cell types were probed with labeled alpha o cDNA and showed they have similar alpha o mRNA levels. The observation of different degradation rates, but similar steady-state protein levels, suggests that the rate of alpha o synthesis is different in GH4 cells and cardiocytes. Since mRNA levels are approximately equal in both, our studies imply that protein translation controls may be important determinants of G protein alpha subunit concentrations in biological membranes.
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Affiliation(s)
- S Silbert
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115
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Silbert S, Michel T, Lee R, Neer EJ. Differential degradation rates of the G protein alpha o in cultured cardiac and pituitary cells. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(19)39739-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Abstract
Two siblings with facio-scapulo-humeral dystrophy (FSH) had muscle biopsy with light microscopy and histochemistry performed. Rapid disease progression resulted in the death of one child at age 5 years. Such an outcome has not been previously reported.
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Abstract
An infundibulum at the origin of the posterior communicating artery is observed to such an extent that it provokes little interest or comment. Although considered preaneurysmal by some, no serious consideration is given to its surgical removal. We present a patient with a subarachnoid hemorrhage, a middle cerebral artery aneurysm, and bilateral posterior communicating artery infundibula to draw attention to the importance of the infundibulum in certain circumstances.
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