Posts filed under ‘Biología Molecular’

Rapid and Accurate Molecular Identification of the Emerging Multidrug-Resistant Pathogen Candida auris

Journal of Clinical Microbiology August 2017 V.55 N.8 P.2445-2452

Milena Kordalewska, Yanan Zhao, Shawn R. Lockhart, Anuradha Chowdhary, Indira Berrio, and David S. Perlin

aPublic Health Research Institute, Rutgers Biomedical and Health Sciences, Newark, New Jersey, USA

bMycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA

cDepartment of Medical Mycology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India

dClínica El Rosario, Medellín, Colombia

eMedical and Experimental Mycology Group, Corporación para Investigaciones Biológicas (CIB), Medellín, Colombia

fHospital General de Medellin Luz Castro de Gutiérrez ESE, Medellín, Colombia

Candida auris is an emerging multidrug-resistant fungal pathogen causing nosocomial and invasive infections associated with high mortality. C. auris is commonly misidentified as several different yeast species by commercially available phenotypic identification platforms. Thus, there is an urgent need for a reliable diagnostic method. In this paper, we present fast, robust, easy-to-perform and interpret PCR and real-time PCR assays to identify C. auris and related species: Candida duobushaemulonii, Candida haemulonii, and Candida lusitaniae. Targeting rDNA region nucleotide sequences, primers specific for C. auris only or C. auris and related species were designed. A panel of 140 clinical fungal isolates was used in both PCR and real-time PCR assays followed by electrophoresis or melting temperature analysis, respectively. The identification results from the assays were 100% concordant with DNA sequencing results. These molecular assays overcome the deficiencies of existing phenotypic tests to identify C. auris and related species.

PDF

http://jcm.asm.org/content/55/8/2445.full.pdf+html

July 26, 2017 at 9:29 am

Molecular Diagnosis of Orthopedic-Device-Related Infection Directly from Sonication Fluid by Metagenomic Sequencing

Journal of Clinical Microbiology August 2017 V.55 N.8 P.2334-2347

Teresa L. Street, Nicholas D. Sanderson, Bridget L. Atkins, Andrew J. Brent, Kevin Cole, Dona Foster, Martin A. McNally, Sarah Oakley, Leon Peto, Adrian Taylor, Tim E. A. Peto, Derrick W. Crook, and David W. Eyre

aNuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom

bBone Infection Unit, Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom

cMicrobiology Laboratory, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom

dDepartment of Infectious Diseases and Microbiology, Royal Sussex County Hospital, Brighton, United Kingdom

ePublic Health England, Microbiology, Royal Sussex County Hospital, Brighton, United Kingdom

fNational Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom

Culture of multiple periprosthetic tissue samples is the current gold standard for microbiological diagnosis of prosthetic joint infections (PJI). Additional diagnostic information may be obtained through culture of sonication fluid from explants. However, current techniques can have relatively low sensitivity, with prior antimicrobial therapy and infection by fastidious organisms influencing results. We assessed if metagenomic sequencing of total DNA extracts obtained direct from sonication fluid can provide an alternative rapid and sensitive tool for diagnosis of PJI. We compared metagenomic sequencing with standard aerobic and anaerobic culture in 97 sonication fluid samples from prosthetic joint and other orthopedic device infections. Reads from Illumina MiSeq sequencing were taxonomically classified using Kraken. Using 50 derivation samples, we determined optimal thresholds for the number and proportion of bacterial reads required to identify an infection and confirmed our findings in 47 independent validation samples. Compared to results from sonication fluid culture, the species-level sensitivity of metagenomic sequencing was 61/69 (88%; 95% confidence interval [CI], 77 to 94%; for derivation samples 35/38 [92%; 95% CI, 79 to 98%]; for validation samples, 26/31 [84%; 95% CI, 66 to 95%]), and genus-level sensitivity was 64/69 (93%; 95% CI, 84 to 98%). Species-level specificity, adjusting for plausible fastidious causes of infection, species found in concurrently obtained tissue samples, and prior antibiotics, was 85/97 (88%; 95% CI, 79 to 93%; for derivation samples, 43/50 [86%; 95% CI, 73 to 94%]; for validation samples, 42/47 [89%; 95% CI, 77 to 96%]). High levels of human DNA contamination were seen despite the use of laboratory methods to remove it. Rigorous laboratory good practice was required to minimize bacterial DNA contamination. We demonstrate that metagenomic sequencing can provide accurate diagnostic information in PJI. Our findings, combined with the increasing availability of portable, random-access sequencing technology, offer the potential to translate metagenomic sequencing into a rapid diagnostic tool in PJI.

PDF

http://jcm.asm.org/content/55/8/2334.full.pdf+html

July 26, 2017 at 9:27 am

Recent advances in understanding Epstein-Barr virus.

F1000Res. 2017 Mar 29;6:386.

Stanfield BA1, Luftig MA1.

Author information

1 Department of Molecular Genetics and Microbiology, Duke Center for Virology, Duke University Medical Center, Durham, NC, USA.

Abstract

Epstein-Barr virus (EBV) is a common human herpes virus known to infect the majority of the world population.

Infection with EBV is often asymptomatic but can manifest in a range of pathologies from infectious mononucleosis to severe cancers of epithelial and lymphocytic origin. Indeed, in the past decade, EBV has been linked to nearly 10% of all gastric cancers.

Furthermore, recent advances in high-throughput next-generation sequencing and the development of humanized mice, which effectively model EBV pathogenesis, have led to a wealth of knowledge pertaining to strain variation and host-pathogen interaction.

This review highlights some recent advances in our understanding of EBV biology, focusing on new findings on the early events of infection, the role EBV plays in gastric cancer, new strain variation, and humanized mouse models of EBV infection.

PDF

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5373418/pdf/f1000research-6-11413.pdf

July 25, 2017 at 7:50 pm

Infectious Mononucleosis.

Curr Top Microbiol Immunol. 2015;390(Pt 1):211-40.

Dunmire SK1, Hogquist KA2, Balfour HH3.

Author information

1 Center for Immunology, University of Minnesota, Minneapolis, MN, 55455, USA. dunmi002@umn.edu.

2 Center for Immunology, University of Minnesota, Minneapolis, MN, 55455, USA. hogqu001@umn.edu.

3 Department of Laboratory Medicine and Pathology, Department of Pediatrics, University of Minnesota, University of Minnesota Medical School, Minneapolis, MN, 55455, USA. balfo001@umn.edu.

Abstract

Infectious mononucleosis is a clinical entity characterized by sore throat, cervical lymph node enlargement, fatigue, and fever most often seen in adolescents and young adults and lasting several weeks.

It can be caused by a number of pathogens, but this chapter only discusses infectious mononucleosis due to primary Epstein-Barr virus (EBV) infection. EBV is a γ-herpesvirus that infects at least 90% of the population worldwide.

The virus is spread by intimate oral contact among teenagers and young adults. How preadolescents acquire the virus is not known.

A typical clinical picture with a positive heterophile test is usually sufficient to make the diagnosis, but heterophile antibodies are not specific and do not develop in some patients. EBV-specific antibody profiles are the best choice for staging EBV infection.

In addition to causing acute illness, there can also be long-term consequences as the result of acquisition of the virus.

Several EBV-related illnesses occur including certain cancers and autoimmune diseases, as well as complications of primary immunodeficiency in persons with the certain genetic mutations.

A major obstacle to understanding these sequelae has been the lack of an efficient animal model for EBV infection, although progress in primate and mouse models has recently been made. Key future challenges are to develop protective vaccines and effective treatment regimens.

PDF

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4670567/pdf/nihms741628.pdf

July 25, 2017 at 7:48 pm

The Active Component of Aspirin, Salicylic Acid, Promotes Staphylococcus aureus Biofilm Formation in a PIA-dependent Manner

Front. Microbiol. 23 January 2017   

Cristian Dotto1, Andrea Lombarte Serrat1, Natalia Cattelan2, María S. Barbagelata1†, Osvaldo M. Yantorno2, Daniel O. Sordelli1, Monika Ehling-Schulz3, Tom Grunert3 and Fernanda R. Buzzola1*

1 Departamento de Microbiología, Parasitología e Inmunología, Facultad de Medicina, Instituto de Investigaciones en Microbiología y Parasitología Médica, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad de Buenos Aires, Buenos Aires, Argentina

2 Facultad de Ciencias Exactas, Centro de Investigación y Desarrollo de Fermentaciones Industriales (CINDEFI), Centro Científico Technológico Consejo Nacional de Investigaciones Científicas y Tócnicas (CTT CONICET La Plata), Universidad Nacional de La Plata, La Plata, Argentina

3 Functional Microbiology, Institute for Microbiology, University of Veterinary Medicine, Vienna, Austria

Aspirin has provided clear benefits to human health. But salicylic acid (SAL) -the main aspirin biometabolite- exerts several effects on eukaryote and prokaryote cells. SAL can affect, for instance, the expression of Staphylococcus aureus virulence factors.

SAL can also form complexes with iron cations and it has been shown that different iron chelating molecules diminished the formation of S. aureus biofilm. The aim of this study was to elucidate whether the iron content limitation caused by SAL can modify the S. aureus metabolism and/or metabolic regulators thus changing the expression of the main polysaccharides involved in biofilm formation.

The exposure of biofilm to 2 mM SAL induced a 27% reduction in the intracellular free Fe2+ concentration compared with the controls. In addition, SAL depleted 23% of the available free Fe2+ cation in culture media. These moderate iron-limited conditions promoted …

FULL TEXT

https://doi.org/10.3389/fmicb.2017.00004

 

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July 19, 2017 at 6:53 pm

Pneumocystis jiroveci pneumonia: comparative study of cases in HIV-infected patients and immunocompromised non-HIV-infected patients.

Rev Chilena Infectol. August 2014 V.31 N.4 P.417-24.

[Article in Spanish]

Cerón I, Rabagliati R, Langhaus J, Silva F, Guzmán AM, Lagos M.

Abstract

BACKGROUND:

Although P. jiroveci pneumonia affects immunocompromised (IC) patients of any etiology, clinical features and prognostic outcomes are different depending if they are patients with HIV infection or other causes of IC.

OBJECTIVES:

To compare clinical and laboratory features as well as outcomes of P. jiroveci pneumonia in HIV versus non-HIV patients.

METHODS:

Retrospective review of clinical records of HIV and non-HIV patients with P. jiroveci pneumonia managed at the Hospital Clínico Universidad Católica in Santiago, Chile, between 2005 and 2007.

RESULTS:

We included 28 HIV and 45 non-HIV patients with confirmed P. jiroveci pneumonia. The non-HIV population was older (65 vs 36,2 years, p < 0,01), had shorter duration of symptoms (7 [1-21] vs 14 [2-45] days, p < 0,01), required more invasive techniques (60 vs 21%, p < 0,01) and RT-PCR to confirm the diagnosis (93 vs 68%, p < 0,01), were more frequently treated at intensive care units (58 vs. 25%, p < 0,01) requiring artificial ventilation (56 vs 11%, p < 0,01), and had a higher attributable mortality (33% vs 0%, p < 0,01).

CONCLUSIONS:

Our study confirmed that P. jiroveci pneumonia in non-HIV IC patients is more severe, more difficult to diagnose and has higher mortality that in HIV patients. Therefore, it is mandatory to optimize diagnostic and therapeutic strategies for this patients group

PDF

http://www.scielo.cl/pdf/rci/v31n4/art07.pdf

July 18, 2017 at 3:44 pm

Pneumocystis pneumonia in hospitalized patients: a detailed examination of symptoms, management, and outcomes in human immunodeficiency virus (HIV)-infected and HIV-uninfected persons.

Transpl Infect Dis. 2012 Oct;14(5):510-8.

McKinnell JA1, Cannella AP, Kunz DF, Hook EW 3rd, Moser SA, Miller LG, Baddley JW, Pappas PG.

Author information

1 Division of Infectious Diseases, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA.

Abstract

BACKGROUND:

Pneumocystis jirovecii pneumonia (PCP) is a life-threatening infection for immunocompromised individuals. Robust data and clear guidelines are available for prophylaxis and treatment of human immunodeficiency virus (HIV)-related PCP (HIV-PCP), yet few data and no guidelines are available for non-HIV-related PCP (NH-PCP). We postulated that prevention and inpatient management of HIV-PCP differed from NH-PCP.

METHODS:

We performed a retrospective case review of all pathologically confirmed cases of PCP seen at the University of Alabama Medical Center from 1996 to 2008. Data on clinical presentation, hospital course, and outcome were collected using a standardized data collection instrument. Bivariate analysis compared prophylaxis, adjunctive corticosteroids, and clinical outcomes between patients with HIV-PCP and NH-PCP.

RESULTS:

Our analysis of the cohort included 97 cases of PCP; 65 HIV and 32 non-HIV cases. Non-HIV cases rarely received primary prophylaxis (4% vs. 38%, P = 0.01) and received appropriate antibiotics later in the course of hospitalization (5.2 days vs. 1.1 days, P < 0.005). Among transplant patients, NH-PCP was diagnosed a mean of 1066 days after transplantation and most patients were on low-dose corticosteroids (87%) at the time of disease onset. No significant differences in adjunctive corticosteroid use (69% vs. 77%, P = 0.39) and 90-day mortality (41% vs. 28%, P = 0.20) were detected.

CONCLUSIONS:

Patients who have undergone organ or stem cell transplant remain at risk for PCP for many years after transplantation. In our cohort, patients who developed NH-PCP were rarely given prophylaxis, and initiation of appropriate antibiotics was significantly delayed compared to cases of HIV-PCP. Medical providers should be aware of the ongoing risk for NH-PCP, even late after transplantation, and consider more aggressive approaches to both prophylaxis and earlier empirical therapy for PCP.

PDF

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3889465/pdf/nihms-536426.pdf

July 18, 2017 at 3:43 pm

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