scholarly journals Laboratory Analysis of an Outbreak of Candida auris in New York from 2016 to 2018-Impact and Lessons Learned

2019 ◽  
Author(s):  
YanChun Zhu ◽  
Brittany O’Brien ◽  
Lynn Leach ◽  
Alexandra Clark ◽  
Marian Bates ◽  
...  
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Antifungal Susceptibility ◽  
Clinical Isolates ◽  
Rapid Screening ◽  
Care Hospital ◽  
Environmental Surveillance ◽  
Intrinsic Resistance ◽  
Candida Auris ◽  
Healthcare Facilities

ABSTRACTCandida auris is a multidrug-resistant yeast which has emerged in healthcare facilities worldwide, however little is known about identification methods, patient colonization, spread, environmental survival, and drug resistance. Colonization on both biotic and abiotic surfaces, along with travel, appear to be the major factors for the spread of this pathogen across the globe. In this investigation, we present laboratory findings from an ongoing C. auris outbreak in NY from August 2016 through 2018. A total of 540 clinical isolates, 11,035 patient surveillance specimens, and 3,672 environmental surveillance samples were analyzed. Laboratory methods included matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for yeast isolate identification, real-time PCR for rapid surveillance sample screening, culture on selective/non-selective media for recovery of C. auris and other yeasts from surveillance samples, antifungal susceptibility testing to determine the C. auris resistance profile, and Sanger sequencing of ribosomal genes for C. auris genotyping. Results included: a) identification and confirmation of C. auris in 413 clinical isolates and 931 patient surveillance isolates, as well as identification of 277 clinical cases and 350 colonized cases from 151 healthcare facilities including 59 hospitals, 92 nursing homes, 1 long-term acute care hospital (LTACH), and 2 hospices, b) successful utilization of an in-house developed C. auris real-time PCR assay for the rapid screening of patient and environmental surveillance samples, c) demonstration of relatively heavier colonization of C. auris in nares compared to the axilla/groin, and d) predominance of the South Asia Clade I with intrinsic resistance to fluconazole and elevated minimum inhibitory concentration (MIC) to voriconazole (81%), amphotericin B (61%), 5-FC (3%) and echinocandins (1%). These findings reflect greater regional prevalence and incidence of C. auris and the deployment of better detection tools in an unprecedented outbreak.

scholarly journals Laboratory Analysis of an Outbreak of Candida auris in New York from 2016 to 2018: Impact and Lessons Learned

2019 ◽  
Vol 58 (4) ◽  
Author(s):  
YanChun Zhu ◽  
Brittany O’Brien ◽  
Lynn Leach ◽  
Alexandra Clarke ◽  
Marian Bates ◽  
...  
Keyword(s):  
Health Care ◽  
New York ◽  
Real Time ◽  
Real Time Pcr ◽  
Health Care Facilities ◽  
Clinical Isolates ◽  
Environmental Surveillance ◽  
Candida Auris ◽  
Content Type ◽  
Care Facilities

ABSTRACT Candida auris is a multidrug-resistant yeast which has emerged in health care facilities worldwide; however, little is known about identification methods, patient colonization, environmental survival, spread, and drug resistance. Colonization on both biotic (patients) and abiotic (health care objects) surfaces, along with travel, appear to be the major factors for the spread of this pathogen across the globe. In this investigation, we present laboratory findings from an ongoing C. auris outbreak in New York (NY) from August 2016 through 2018. A total of 540 clinical isolates, 11,035 patient surveillance specimens, and 3,672 environmental surveillance samples were analyzed. Laboratory methods included matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) for yeast isolate identification, real-time PCR for rapid surveillance sample screening, culture on selective/nonselective media for recovery of C. auris and other yeasts from surveillance samples, antifungal susceptibility testing to determine the C. auris resistance profile, and Sanger sequencing of the internal transcribed spacer (ITS) and D1/D2 regions of the ribosomal gene for C. auris genotyping. Results included (a) identification and confirmation of C. auris in 413 clinical isolates and 931 patient surveillance isolates as well as identification of 277 clinical cases and 350 colonized cases from 151 health care facilities, including 59 hospitals, 92 nursing homes, 1 long-term acute care hospital (LTACH), and 2 hospices, (b) successful utilization of an in-house developed C. auris real-time PCR assay for the rapid screening of patient and environmental surveillance samples, (c) demonstration of relatively heavier colonization of C. auris in nares than in the axilla/groin, and (d) predominance of the South Asia clade I with intrinsic resistance to fluconazole and elevated MIC to voriconazole (81%), amphotericin B (61%), flucytosine (5FC) (3%), and echinocandins (1%). These findings reflect greater regional prevalence and incidence of C. auris and the deployment of better detection tools in an unprecedented outbreak.

scholarly journals Development of Rapid Screening of Campylobacter spp. and the GyrA Mutants Using PCR-DNA Strip and Real-Time PCR

2016 ◽  
Vol 33 (1) ◽  
pp. 12-18
Author(s):  
Chiaki KOJIMA ◽  
Michiru KISHIMOTO ◽  
Machiko MIYATA ◽  
Sayumi NOMURA ◽  
Takayuki EZAKI
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Rapid Screening

Molecular epidemiology and carbapenem resistance of Pseudomonas aeruginosa isolated from patients with burns

2021 ◽  
Vol 30 (2) ◽  
pp. 135-141 ◽  
Author(s):  
Younes Khalili ◽  
Mohammad Yousef Memar ◽  
Safar Farajnia ◽  
Khosro Adibkia ◽  
Hossein Samadi Kafil ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Molecular Epidemiology ◽  
Real Time ◽  
Real Time Pcr ◽  
Random Amplified Polymorphic Dna ◽  
Carbapenem Resistance ◽  
Efflux Pumps ◽  
Common Mechanism ◽  
Care Hospital ◽  
Burn Care

Objective: The aim of this study was to investigate the molecular epidemiology and carbapenem resistance mechanisms of Pseudomonas aeruginosa isolated from patients with burns in Azerbaijan, Iran. Method: Pseudomonas aeruginosa was isolated from 38 patients with burns. Disk diffusion and agar dilution methods were used to determine antibiotic susceptibility patterns. The overproduction of AmpC β-lactamase and efflux pumps were detected by phenotypic methods. The presence of carbapenemase-encoding genes was detected by multiplex polymerase chain reaction (PCR). Expression of the OprD gene and MexAB efflux pumps were also evaluated with real-time PCR. Random amplified polymorphic DNA typing (RAPD-PCR) was used for genotyping of carbapenem-resistant Pseudomonas aeruginosa (CRPA). Results: Minimum inhibitory concentration (MIC) assays demonstrated high levels of resistance to all classes of antibiotics except colistin and polymyxin B. The initial screening by carbapenem disks indicated 24 isolates (63.15%) as CRPA. Different mechanisms of carbapenem resistance were observed, including carbapenemase production (8.4%), overexpression of AmpC (25%) and decreased expression of OprD (75%). The overexpression of MexAB efflux pumps was detected in 19 (79.1%) isolates by phenotypic assay or real-time PCR. The resistance to carbapenem was multifactorial in most cases (58.3%). The RAPD genotyping revealed different patterns with nine clusters. Conclusion: According to our results, the prevalence of CRPA is at an alarming level. Our results did not demonstrate an epidemic clone. The most common mechanism of carbapenem resistance was decreased expression of OprD. Therefore, we suggest a reconsideration in the management of CRPA infections of patients in our burn care hospital in Azerbaijan, Iran.

scholarly journals A Real-Time PCR Screening Assay for Rapid Detection of Listeria Monocytogenes Outbreak Strains

Foods ◽  
2020 ◽  
Vol 9 (1) ◽  
pp. 67 ◽  
Author(s):  
Marina Torresi ◽  
Anna Ruolo ◽  
Vicdalia Aniela Acciari ◽  
Massimo Ancora ◽  
Giuliana Blasi ◽  
...  
Keyword(s):  
Listeria Monocytogenes ◽  
Real Time ◽  
Real Time Pcr ◽  
Human Case ◽  
Outbreak Investigation ◽  
Rapid Screening ◽  
Reference Laboratory ◽  
Screening Assay ◽  
Pcr Screening ◽  
Umbria Region

From January 2015 to March 2016, an outbreak of 23 human cases of listeriosis in the Marche region and one human case in the Umbria region of Italy was caused by Listeria monocytogenes strains showing a new pulsotype never described before in Italy. A total of 37 clinical strains isolated from patients exhibiting listeriosis symptoms and 1374 strains correlated to the outbreak were received by the Italian National Reference Laboratory for L. monocytogenes (It NRL Lm) of Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise (IZSAM) for outbreak investigation. A real-time PCR assay was purposely designed for a rapid screening of the strains related to the outbreak. PCR-positive strains were successively typed through molecular serogrouping, pulsed field gel electrophoresis (PFGE), and Next Generation Sequencing (NGS). Applying the described strategy, based on real-time PCR screening, we were able to considerably reduce time and costs during the outbreak investigation activities.

scholarly journals Real-Time PCR Assay for Detection of blaZ Genes in Staphylococcus aureus Clinical Isolates

2014 ◽  
Vol 52 (4) ◽  
pp. 1259-1261 ◽  
Author(s):  
L. A. Pereira ◽  
G. B. Harnett ◽  
M. M. Hodge ◽  
J. A. Cattell ◽  
D. J. Speers
Keyword(s):  
Staphylococcus Aureus ◽  
Real Time ◽  
Real Time Pcr ◽  
Clinical Isolates ◽  
Pcr Assay

Development of real-time PCR to detect oral vaccine-like poliovirus and its application to environmental surveillance

2014 ◽  
Vol 195 ◽  
pp. 148-155 ◽  
Author(s):  
Masae Iwai-Itamochi ◽  
Hiromu Yoshida ◽  
Mayumi Obara-Nagoya ◽  
Eiji Horimoto ◽  
Takeshi Kurata ◽  
...  
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Oral Vaccine ◽  
Environmental Surveillance

Rapid Screening of Leukemia Fusion Transcripts in Acute Leukemia by Real-time PCR

2002 ◽  
Vol 43 (12) ◽  
pp. 2291-2299 ◽  
Author(s):  
Kazuoki Osumi ◽  
Takafumi Fukui ◽  
Hitoshi Kiyoi ◽  
Masanobu Kasai ◽  
Yoshihisa Kodera ◽  
...  
Keyword(s):  
Acute Leukemia ◽  
Real Time ◽  
Real Time Pcr ◽  
Rapid Screening ◽  
Fusion Transcripts

Improved diagnostic and real-time pcr in rapid screening for Salmonella in the poultry food chain

2006 ◽  
Vol 54 (3) ◽  
pp. 297-312 ◽  
Author(s):  
Annamária Szmolka ◽  
Éva Kaszanyitzky ◽  
B. Nagy
Keyword(s):  
Real Time ◽  
Food Chain ◽  
Real Time Pcr ◽  
Culture Method ◽  
Rapid Screening ◽  
Poultry Feed ◽  
Broiler Chicks ◽  
Diagnostic Pcr ◽  
Enrichment Cultures ◽  
Specific Pcr

The goal of this study was to improve the diagnostic applicability of genus- and serovar- (S. Enteritidis and S. Typhimurium) specific PCR systems in screening faecal and caecal samples of poultry, poultry feed and poultrymeat for Salmonella, by keeping the opportunity to obtain Salmonella cultures from positive samples. Peptone broth pre-enrichment cultures of the samples were tested by PCR. In faecal and caecal samples from broiler chicks a strong inhibitory action was frequently observed. This could be reduced markedly by the addition of bovine serum albumin (BSA) acting as amplification facilitator. The results of testing pre-enrichment cultures from artificially contaminated faecal, poultry feed and poultrymeat samples (using S. Enteritidis, S. Typhimurium and S. Hadar as contaminants) suggest that the sensitivity of the above systems is 101-102 CFU g-1 sample. The testing of 95 caecal samples from slaughtered chicks resulted in 49% culture-positive and 76% PCR-positive samples. The suitability of a generic real-time PCR for testing faecal samples of poultry was also studied. Its detection limit for these samples was found to be lower than that of the diagnostic PCR system. Both methods reduced the time required for Salmonella detection to 24-30 h, and the advantage of the real-time PCR was its increased sensitivity. We have established a diagnostic and a real-time PCR system for rapid and reliable genus- and serovar- (S. Enteritidis and S. Typhimurium) specific detection of Salmonella for monitoring purposes in the poultry food chain. Sensitivity is equal to, or higher than, that of the standard bacterial culture method, and the method still provides the Salmonella culture if needed.

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