Rapid and accurate identification of newly emerging infectious pathogens using bio-optical sensor in clinical specimens (Conference Presentation)

2020 ◽  
Author(s):  
Bonhan Koo ◽  
Yong Shin
Keyword(s):  
Optical Sensor ◽  
Accurate Identification ◽  
Clinical Specimens

scholarly journals Virulence Factors and Antifungal Susceptibility Profile of C. tropicalis Isolated from Various Clinical Specimens in Alexandria, Egypt

2021 ◽  
Vol 7 (5) ◽  
pp. 351
Author(s):  
Mohammed A. El-Kholy ◽  
Ghada F. Helaly ◽  
Ebtisam F. El Ghazzawi ◽  
Gamal El-Sawaf ◽  
Sherine M. Shawky
Keyword(s):  
Virulence Factors ◽  
Biofilm Formation ◽  
Antifungal Susceptibility ◽  
Accurate Identification ◽  
Icu Patients ◽  
Clinical Specimens ◽  
High Incidence ◽  
Invasive Infections ◽  
Vitek 2 ◽  
Urinary Isolates

Background: The incidence of candidiasis caused by non-albicans Candida (NAC) species is increasing. Candida tropicalis has emerged as one of the most important NAC species. This study aims to examine the antifungal susceptibility profile and some virulence factors of C. tropicalis isolated from various clinical specimens. Methods: A total of 71 C. tropicalis isolates from various clinical specimens (69.01%, 18.31%, 9.86%, and 2.82% of isolates were collected from urine, respiratory samples, blood, and skin and soft tissue infections, respectively) from ICU patients in Alexandria, Egypt. The isolates were identified at species level by CHROMagar Candida and VITEK 2 compact system. Furthermore, the antifungal susceptibility was determined using the VITEK 2 system AST-YS07 card containing different antifungals. Hemolysin, phospholipase, and proteinase activity and biofilm formation were also tested as virulence factors. Results: Only 30 isolates (42.25%) were non-susceptible (MIC ≥ 4 µg/mL) to fluconazole, of which 28 isolates showed non-susceptibility (MIC ≥ 0.25 µg/mL) to voriconazole. All isolates showed both hemolysin and proteinase activities, while only 9 isolates (12.68%) showed phospholipase production and 70 isolates (98.59%) demonstrated biofilm formation. Strong biofilm production was observed among the blood culture isolates (85.71%), followed by the respiratory and urinary isolates (61.54% and 46.94%, respectively). Conclusions: This study sought to provide useful data on the antifungal susceptibility of C. tropicalis isolates from ICU patients suffering from invasive infections with an increased trend towards elevated MICs levels of both fluconazole and voriconazole. Due to the high incidence of systemic candidiasis and antifungal resistance, C. tropicalis is emerging as a serious root of infections. Therefore, early and accurate identification of Candida species along with susceptibility testing is of utmost importance.

Detection of NDM-1 and VIM Genes in Carbapenem-Resistant Klebsiella pneumoniae Isolates from a Tertiary Health-Care Center in Kathmandu, Nepal

Chemotherapy ◽  
2021 ◽  
pp. 1-11
Author(s):  
Sabita Thapa ◽  
Nabaraj Adhikari ◽  
Anil Kumar Shah ◽  
Ishworiya Lamichhane ◽  
Binod Dhungel ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Bacterial Infections ◽  
Care Center ◽  
Diffusion Method ◽  
Accurate Identification ◽  
Clinical Specimens ◽  
Health Care Center ◽  
Carbapenem Resistant ◽  
Resistant Genes ◽  
Specificity And Sensitivity

<b><i>Background:</i></b> <i>Klebsiella pneumoniae</i> is one of the leading causes of nosocomial infections. Carbapenems are used as the last resort for the treatment of multidrug resistant Gram-negative bacterial infections. In recent years, resistance to these lifesaving drugs has been increasingly reported due to the production of carbapenemase. The main objective of this study was to detect the carbapenem-resistant genes <i>bla</i><sub>NDM-1</sub> and <i>bla</i><sub>VIM</sub> in <i>K. pneumoniae</i> isolated from different clinical specimens. <b><i>Methods:</i></b> A total of 585 clinical specimens (urine, pus, sputum, blood, catheter tips, and others) from human subjects attended at Annapurna Neurological Institute and Allied Sciences, Kathmandu were obtained in the period between July 2018 and January 2019. The specimens were isolated and identified for <i>K. pneumoniae</i>. All <i>K</i>. <i>pneumoniae</i> isolates were processed for antimicrobial susceptibility testing (AST) using the disk diffusion method. The isolates were further phenotypically confirmed for carbapenemase production by the modified Hodge test (MHT) using imipenem (10 μg) and meropenem (10 μg) discs. Thus, confirmed carbapenemase-producing isolates were further screened for the production of <i>bla</i><sub>NDM-1</sub> and <i>bla</i><sub>VIM</sub> using conventional polymerase chain reaction (PCR). <b><i>Results:</i></b> Among the clinical isolates tested, culture positivity was 38.29% (224/585), and the prevalence of <i>K. pneumoniae</i> was 25.89% (58/224). On AST, <i>K. pneumoniae</i> exhibited resistance toward carbapenems including ertapenem, meropenem, and imipenem, while it showed the highest susceptibility rate against to tigecycline (93.1%; 54/58). Overall, AST detected 60.34% (35/58) carbapenem-resistant isolates, while the MHT phenotypically confirmed 51.72% (30/58) isolates as carbapenemase-producers and 48.28% (28/58) as carbapenemase nonproducers. On subsequent screening for resistant genes among carbapenemase-producers by PCR assay, 80% (24/30) and 3.33% (1/30) isolates were found to be positive for <i>bla</i><sub>NDM-1</sub> and <i>bla</i><sub>VIM</sub>, respectively. In the same assay among 28 carbapenem nonproducing isolates, 9 (32.14%) isolates were positive for <i>bla</i><sub>NDM-1</sub> gene while none of them were tested positive for <i>bla</i><sub>VIM</sub> gene. <b><i>Conclusions:</i></b> Molecular detection of resistant genes provides greater specificity and sensitivity than those with conventional techniques, thus aiding in accurate identification of antimicrobial resistance and clinical management of the disease.

scholarly journals Rapid and Accurate Identification of SARS-CoV-2 Omicron Variants Using Droplet Digital PCR (RT-ddPCR)

2022 ◽  
Author(s):  
Margaret Mills ◽  
Pooneh Hajian ◽  
Shah Mohamed Bakhash ◽  
Hong Xie ◽  
Derrek Mantzke ◽  
...  
Keyword(s):  
Digital Pcr ◽  
Washington State ◽  
Genome Sequences ◽  
Accurate Identification ◽  
Clinical Specimens ◽  
Public Health Professionals ◽  
Variant Detection ◽  
Ngs Data ◽  
Rna Concentration ◽  
Selection Of

Background Mutations in the receptor binding domain of the SARS-CoV-2 Spike protein are associated with increased transmission or substantial reductions in vaccine efficacy, including in the recently described Omicron variant. The changing frequencies of these mutations combined with their differing susceptibility to available therapies have posed significant problems for clinicians and public health professionals. Objective To develop an assay capable of rapidly and accurately identifying variants including Omicron in clinical specimens to enable case tracking and/or selection of appropriate clinical treatment. Study Design Using three duplex RT-ddPCR reactions targeting four amino acids, we tested 419 positive clinical specimens from February to December 2021 during a period of rapidly shifting variant prevalences and compared genotyping results to genome sequences for each sample, determining the sensitivity and specificity of the assay for each variant. Results Mutation determinations for 99.7% of detected samples agree with NGS data for those samples, and are accurate despite wide variation in RNA concentration and potential confounding factors like transport medium, presence of additional respiratory viruses, and additional mutations in primer and probe sequences. The assay accurately identified the first 15 Omicron variants in our laboratory including the first Omicron in Washington State and discriminated against S-gene dropout Delta specimen. Conclusion We describe an accurate, precise, and specific RT-ddPCR assay for variant detection that remains robust despite being designed prior the emergence of Delta and Omicron variants. The assay can quickly identify mutations in current and past SARS-CoV-2 variants, and can be adapted to future mutations.

scholarly journals Diagnostic Identification and Differentiation of Microfilariae

2019 ◽  
Vol 57 (10) ◽  
Author(s):  
Blaine A. Mathison ◽  
Marc Roger Couturier ◽  
Bobbi S. Pritt
Keyword(s):  
Human Infection ◽  
Accurate Identification ◽  
Clinical Specimens ◽  
Clinical Laboratories ◽  
Filarial Nematodes ◽  
Medical Technologists ◽  
Diagnostic Capabilities

ABSTRACT The morphologic similarities of the microfilariae and their infrequency in clinical specimens in settings of endemicity present challenges to clinical laboratories in maintaining competence for accurate identification and differentiation. We present here a review of the primary filarial nematodes causing human infection, including an illustrated key, which we hope will improve the diagnostic capabilities of hematologists, microbiologists, medical technologists, and similarly qualified laboratorians.

scholarly journals Melioidosis – A Serious Emerging Threat in Bangladesh

2014 ◽  
Vol 14 (2) ◽  
pp. 164-173
Author(s):  
Aparna Das ◽  
H A M Nazmul Ahasan ◽  
Baharul Minnat ◽  
Chayan Kumar Singha
Keyword(s):  
Chronic Disease ◽  
Chronic Infection ◽  
Laboratory Diagnosis ◽  
Definitive Diagnosis ◽  
Selective Isolation ◽  
Accurate Identification ◽  
Clinical Specimens ◽  
Pyogenic Infection ◽  
Laboratory Facilities

Melioidosis, a pyogenic infection that presents acutely or as a chronic infection, is caused by the soilassociated bacterium Burkholderiapseudomallei. Infection is acquired by inoculation or inhalation and is more common in patients with underlying chronic disease. It is endemic in the tropical belt. Although Bangladesh is not considered as a country where melioidosis is endemic, an increasing number of cases have been reported recently. Definitive diagnosis requires the isolation of B. pseudomalleiin culture from clinical specimens. However, the laboratory diagnosis of melioidosis in Bangladesh and other under-resourced countries is limited by a lack of familiarity with the bacterium and a lack of facilities to accurately confirm the identity of the isolate. It is highly likely that melioidosis is underdiagnosed in this country. There is a need to increase awareness of this infection among clinicians and clinical microbiologists and improve laboratory facilities for the selective isolation and accurate identification of B. pseudomallei. Melioidosis has a notoriously protracted course; cure is difficult without a prolonged course of appropriate antibiotics.DOI: http://dx.doi.org/10.3329/jom.v14i2.19669 J Medicine 2013, 14(2): 164-173

A rapid bio-optical sensor for diagnosing Q fever in clinical specimens

2018 ◽  
Vol 11 (4) ◽  
pp. e201700167 ◽  
Author(s):  
Bonhan Koo ◽  
Choong Eun Jin ◽  
Se Yoon Park ◽  
Tae Yoon Lee ◽  
Jeonghun Nam ◽  
...  
Keyword(s):  
Optical Sensor ◽  
Q Fever ◽  
Clinical Specimens

Immunolabelling of glomerular deposits in kidney biopsies routinely fixed in glutaraldehyde

1989 ◽  
Vol 47 ◽  
pp. 910-911
Author(s):  
Ś Lhoták ◽  
I. Alexopoulou ◽  
G. T. Simon
Keyword(s):  
Uv Light ◽  
Kidney Diseases ◽  
Light Chains ◽  
Microscopical Level ◽  
Accurate Identification ◽  
Light Microscopical Level ◽  
Dense Deposits ◽  
Cacodylate Buffer ◽  
Glomerular Deposits ◽  
Prognostic Importance

Various kidney diseases are characterized by the presence of dense deposits in the glomeruli. The type(s) of immunoglobulins (Igs) present in the dense deposits are characteristic of the disease. The accurate Identification of the deposits is therefore of utmost diagnostic and prognostic importance. Immunofluorescence (IF) used routinely at the light microscopical level is unable to detect and characterize small deposits found in early stages of glomerulonephritis. Although conventional TEM is able to localize such deposits, it is not capable of determining their nature. It was therefore attempted to immunolabel at EM level IgG, IgA IgM, C3, fibrinogen and kappa and lambda Ig light chains commonly found in glomerular deposits on routinely fixed ( 2% glutaraldehyde (GA) in 0.1M cacodylate buffer) kidney biopsies.The unosmicated tissue was embedded in LR White resin polymerized by UV light at -10°C. A postembedding immunogold technique was employed

A combined pseudoreplica-immunocytochemical technique for research and diagnostic virology

1990 ◽  
Vol 48 (3) ◽  
pp. 900-901
Author(s):  
Blayne Fritz ◽  
Stanley J. Naides ◽  
Kenneth Moore
Keyword(s):  
Phosphotungstic Acid ◽  
Immunogold Labelling ◽  
Uranyl Acetate ◽  
Distilled Water ◽  
Clinical Specimens ◽  
Tissue Sections ◽  
Specimen Retrieval ◽  
Transmission Electron ◽  
Viral Particles ◽  
Diagnostic Virology

The pseudoreplica method of staining viral particles for visualization by transmission electron microscopy is a very popular technique. The ability to concentrate clinical specimens while semi-embedding viral particles makes it especially well suited for morphologic and diagnostic virology. Immunolabelling viral particles with colloidal gold is a technique frequently employed by both research and diagnostic virologists. We have characterized a procedure which provides the advantage of both by modifying and combining pseudoreplica staining and immunogold labelling.Modification of specimen retrieval and delay of staining allows us to utilize pseudoreplica processed specimens within our standard immunogold labelling protocol. In brief, we absorbed samples onto 2% agarose, added.25% Formvar and wicked dry. We then floated the Formvar-virus film onto double distilled water, added grids and retrieved with parafilm. The Formvar-virus specimens were then treated as thin tissue sections within our standard two stage immunolabelling protocol. Following completion of immunogold labelling; each grid was negatively stained with phosphotungstic acid or uranyl acetate contrast stains.

Project BRAIN: Working Together to Improve Educational Outcomes for Students With Traumatic Brain Injury

2012 ◽  
Vol 22 (3) ◽  
pp. 106-118 ◽  
Author(s):  
Paula Denslow ◽  
Jean Doster ◽  
Kristin King ◽  
Jennifer Rayman
Keyword(s):  
Traumatic Brain Injury ◽  
At Risk ◽  
Brain Injury ◽  
Educational Outcomes ◽  
School Personnel ◽  
Department Of Education ◽  
Health Providers ◽  
Accurate Identification ◽  
Transition Intervention ◽  
Working Together

Children and youth who sustain traumatic brain injury (TBI) are at risk for being unidentified or misidentified and, even if appropriately identified, are at risk of encountering professionals who are ill-equipped to address their unique needs. A comparison of the number of people in Tennessee ages 3–21 years incurring brain injury compared to the number of students ages 3–21 years being categorized and served as TBI by the Department of Education (DOE) motivated us to create this program. Identified needs addressed by the program include the following: (a) accurate identification of students with TBI; (b) training of school personnel; (c) development of linkages and training of hospital personnel; and (d) hospital-school transition intervention. Funded by Health Services and Resources Administration (HRSA) grants with support from the Tennessee DOE, Project BRAIN focuses on improving educational outcomes for students with TBI through the provision of specialized group training and ongoing education for educators, families, and health professionals who support students with TBI. The program seeks to link families, hospitals, and community health providers with school professionals such as speech-language pathologists (SLPs) to identify and address the needs of students with brain injury.

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