scholarly journals Laboratory diagnosis of pneumonia in the molecular age

2016 ◽  
Vol 48 (6) ◽  
pp. 1764-1778 ◽  
Author(s):  
Antoni Torres ◽  
Nelson Lee ◽  
Catia Cilloniz ◽  
Jordi Vila ◽  
Menno Van der Eerden
Keyword(s):  
Laboratory Diagnosis ◽  
High Rate ◽  
Microbial Pathogens ◽  
Molecular Diagnostic ◽  
Respiratory Pathogens ◽  
Major Advance ◽  
Lung Microbiome ◽  
Microbiological Methods ◽  
New Knowledge ◽  
Diagnostic Technology

Pneumonia remains a worldwide health problem with a high rate of morbidity and mortality. Identification of microbial pathogens which cause pneumonia is an important area for optimum clinical management of pneumonia patients and is a big challenge for conventional microbiological methods. The development and implementation of molecular diagnostic tests for pneumonia has been a major advance in the microbiological diagnosis of respiratory pathogens in recent years. However, with new knowledge regarding the microbiome, together with the recognition that the lungs are a dynamic microbiological ecosystem, our current concept of pneumonia is not totally realistic as this new concept of pneumonia involves a dysbiosis or alteration of the lung microbiome. A new challenge for microbiologists and clinicians has therefore arisen. There is much to learn regarding the information provided by this new diagnostic technology, which will lead to improvements in the time to antibiotic therapy, targeted antibiotic selection and more effective de-escalation and improved stewardship for pneumonia patients. This article provides an overview of current methods of laboratory diagnosis of pneumonia in the molecular age.

Microbiome in Chronic Obstructive Pulmonary Disease: Role of Natural Products Against Microbial Pathogens

2020 ◽  
Vol 27 (18) ◽  
pp. 2931-2948
Author(s):  
Alessia Santoro ◽  
Carlo Tomino ◽  
Giulia Prinzi ◽  
Vittorio Cardaci ◽  
Massimo Fini ◽  
...  
Keyword(s):  
Chronic Obstructive Pulmonary Disease ◽  
Microbial Communities ◽  
Pulmonary Disease ◽  
Bacterial Infections ◽  
Microbial Pathogens ◽  
Resistant Bacteria ◽  
Chronic Obstructive ◽  
Detection Rates ◽  
Obstructive Pulmonary Disease ◽  
Lung Microbiome

The “microbiome” is the operative term to refer to a collection of all taxa constituting microbial communities, such as bacteria, archaea, fungi and protists (originally microbiota). The microbiome consists of the indigenous microbial communities and of the host environment that they inhabit. Actually, it has been shown that there is a close relationship between the microbiome and human health and disease condition. Although, initially, the lung was considered sterile, actually, the existence of a healthy lung microbiome is usually accepted. Lung microbiome changes are reported in Chronic Obstructive Pulmonary Disease (COPD) and in its exacerbation. Viral and bacterial infections of the respiratory system are a major cause of COPD exacerbations (AECOPD) leading to increased local and systemic inflammation. Detection rates of virus in AECOPD are variable between 25-62% according to the detection method. The study of human airway and lung disease virome is quite recent and still very limited. The purpose of this review is to summarize recent findings on the lung microbiome composition with a special emphasis on virome in COPD and in AECOPD. Some drugs of natural origins active against resistant bacteria and virus are described.

scholarly journals A ten-year follow-up of human leptospirosis in Uruguay: an unresolved health problem

2012 ◽  
Vol 54 (2) ◽  
pp. 69-76 ◽  
Author(s):  
Felipe Schelotto ◽  
Elba Hernández ◽  
Sabina González ◽  
Alicia Del Monte ◽  
Silvana Ifran ◽  
...  
Keyword(s):  
Young Male ◽  
Standard Technique ◽  
Signs And Symptoms ◽  
Complete Recovery ◽  
Laboratory Diagnosis ◽  
Diagnostic Techniques ◽  
Clinical Feature ◽  
Serum Samples ◽  
Microbiological Methods ◽  
Major Factors

Leptospira spp. are delicate bacteria that cannot be studied by usual microbiological methods. They cause leptospirosis, a zoonotic disease transmitted to humans through infected urine of wild or domestic animals. We studied the incidence of this disease in the Uruguayan population, its epidemiologic and clinical features, and compared diagnostic techniques. After examining 6,778 suspect cases, we estimated that about 15 infections/100,000 inhabitants occurred yearly, affecting mainly young male rural workers. Awareness about leptospirosis has grown among health professionals, and its lethality has consequently decreased. Bovine infections were probably the principal source of human disease. Rainfall volumes and floods were major factors of varying incidence. Most patients had fever, asthenia, myalgias or cephalalgia, with at least one additional abnormal clinical feature. 30-40% of confirmed cases presented abdominal signs and symptoms, conjunctival suffusion and altered renal or urinary function. Jaundice was more frequent in patients aged > 40 years. Clinical infections followed an acute pattern and their usual outcome was complete recovery. Laboratory diagnosis was based on indirect micro-agglutination standard technique (MAT). Second serum samples were difficult to obtain, often impairing completion of diagnosis. Immunofluorescence was useful as a screening test and for early detection of probable infections.

scholarly journals Trends in Antibiotic Resistance of Major Uropathogens

2020 ◽  
Author(s):  
Falah Hasan Obayes AL-Khikani
Keyword(s):  
Urinary Tract Infection ◽  
Urinary Tract ◽  
Tract Infection ◽  
Antimicrobial Susceptibility ◽  
Bacterial Species ◽  
High Rate ◽  
Control Group ◽  
Microbiological Methods ◽  
Antimicrobial Susceptibility Tests ◽  
Susceptibility Tests

Around the world, there is no population clear from urinary tract infection (UTI), particularly among women. UTI is considered the most predominant bacterial infection. This study aimed to detect the incidence of the most common major uropathogens in patients severe from urinary tract infection with antibiotic sensitivity tests that assist urologist doctors for appropriate antimicrobial empirical therapy.Methods: This study was carried in a private laboratory in Babil city, Iraq from May 2019 to May 2020. Totally 70 individuals suffering from clear symptoms of UTI, as well as, 20 healthy persons participated in this study as a control group. Then, the standard microbiological methods carried out to isolate and identify bacterial species. Antimicrobial susceptibility tests were performed using different antimicrobial discs by applying the Kirby–Bauer disc diffusion method.Results: Totally, 90 specimens were obtained from them 20 control group, 19 with no growth, and 51 patients with bacterial growth distributed as 43 (83%) females and 8 (17%) males. E. coli were the most common predominant organisms. All isolates were showed a high rate of resistance to evaluated cephalosporins 100% and 82% to cefotaxime and ceftriaxone respectively, while very low resistance recorded in Aminoglycosides 20% and 13% to Gentamicin and amikacin respectively. Most age group infected with UTI was 21-40 years old.Conclusion: The current study showed an increasing burden of urinary tract infection caused by various bacteria implicated in UTI that causes changeable sensitivity to various antimicrobial agents. Therefore, in clinical use appropriate medications should be selected based on the data obtained from antimicrobial susceptibility tests.

scholarly journals Respiratory Tularemia: Francisella Tularensis and Microarray Probe Designing

2016 ◽  
Vol 10 (1) ◽  
pp. 176-182 ◽  
Author(s):  
Reza Ranjbar ◽  
Payam Behzadi ◽  
Caterina Mammina
Keyword(s):  
Dna Microarray ◽  
Francisella Tularensis ◽  
High Specificity ◽  
Cost Effective ◽  
High Rate ◽  
Molecular Diagnostic ◽  
Microarray Technology ◽  
Microarray Probe ◽  
Specificity And Sensitivity ◽  
Oligo Microarray

Background:Francisella tularensis(F. tularensis) is the etiological microorganism for tularemia. There are different forms of tularemia such as respiratory tularemia. Respiratory tularemia is the most severe form of tularemia with a high rate of mortality; if not treated. Therefore, traditional microbiological tools and Polymerase Chain Reaction (PCR) are not useful for a rapid, reliable, accurate, sensitive and specific diagnosis. But, DNA microarray technology does. DNA microarray technology needs to appropriate microarray probe designing.Objective:The main goal of this original article was to design suitable long oligo microarray probes for detection and identification ofF. tularensis.Method:For performing this research, the complete genomes ofF. tularensissubsp.tularensisFSC198,F. tularensissubsp.holarcticaLVS,F. tularensissubsp.mediasiatica,F. tularensissubsp.novicida(F. novicidaU112), andF. philomiragiasubsp.philomiragiaATCC 25017 were studiedviaNCBI BLAST tool, GView and PanSeq Servers and finally the microarray probes were produced and processedviaAlleleID 7.7 software and Oligoanalyzer tool, respectively.Results:In thisin silicoinvestigation, a number of long oligo microarray probes were designed for detecting and identifyingF. tularensis. Among these probes, 15 probes were recognized as the best candidates for microarray chip designing.Conclusion:Calibrated microarray probes reduce the biasis of DNA microarray technology as an advanced, rapid, accurate and cost-effective molecular diagnostic tool with high specificity and sensitivity. Professional microarray probe designing provides us with much more facility and flexibility regarding preparation of a microarray diagnostic chip.

Diagnosis of melioidosis: the role of molecular techniques

2021 ◽  
Vol 16 (4) ◽  
pp. 271-288
Author(s):  
Ian Gassiep ◽  
Delaney Burnard ◽  
Michelle J Bauer ◽  
Robert E Norton ◽  
Patrick N Harris
Keyword(s):  
Laboratory Diagnosis ◽  
Diagnostic Techniques ◽  
Molecular Techniques ◽  
Molecular Diagnostic ◽  
Clinical Samples ◽  
Molecular Diagnostic Techniques ◽  
Detection And Identification ◽  
Life Years ◽  
Culture Independent ◽  
Future Utility

Melioidosis is an emerging infectious disease with an estimated global burden of 4.64 million disability-adjusted life years per year. A major determinant related to poor disease outcomes is delay to diagnosis due to the fact that identification of the causative agent Burkholderia pseudomallei may be challenging. Over the last 25 years, advances in molecular diagnostic techniques have resulted in the potential for rapid and accurate organism detection and identification direct from clinical samples. While these methods are not yet routine in clinical practice, laboratory diagnosis of infectious diseases is transitioning to culture-independent techniques. This review article aims to evaluate molecular methods for melioidosis diagnosis direct from clinical samples and discuss current and future utility and limitations.

Frequency of molecular detection of equine coronavirus in faeces and nasal secretions in 277 horses with acute onset of fever

2019 ◽  
Vol 184 (12) ◽  
pp. 385-385 ◽  
Author(s):  
Nicola Pusterla ◽  
Kaitlyn James ◽  
Samantha Mapes ◽  
Farifield Bain
Keyword(s):  
Clinical Signs ◽  
Acute Onset ◽  
Molecular Diagnostic ◽  
Nasal Discharge ◽  
Respiratory Pathogens ◽  
Sample Collection ◽  
Diagnostic Laboratory ◽  
Study Results ◽  
Streptococcus Equi ◽  
Nasal Secretions

ContextDue to the inconsistent development of enteric signs associated with ECoV infection in adult horses, many practitioners collect nasal secretions rather than feces for the molecular diagnostic work-up of such horses.Main conclusionECoV infection should be considered in horses presenting with acute onset of fever, especially when nasal discharge is absent as one of the cardinal clinical sign.ApproachA total of 277 adult horses with acute onset of fever were enrolled in this study. Feces were tested for ECoV and nasal secretions for common respiratory pathogens (equine herpesvirus (EHV)-1, EHV-4, equine influenza virus (EIV), equine rhinitis viruses (ERVs) and Streptococcus equi ss. equi) and ECoV by qPCR. Each submission was accompanied by a questionnaire requesting information pertaining to signalment, use, recent transportation, number of affected horses on the premise and presence of clinical signs at the time of sample collection.ResultsThe total number of horses testing qPCR-positive for ECoV in feces was 20 (7.2%), 4 of which also tested qPCR-positive for ECoV in nasal secretions. In the same population 9.0% of horses tested qPCR-positive for EHV-4, 6.1% for EIV, 4.3% for Streptococcus equi ss. equi, 3.2% for ERVs and 0.7% for EHV-1. Draft horses, pleasure use, multiple horses affected on a premise and lack of nasal discharge were significantly associated with ECoV qPCR-positive horses.InterpretationThe present study results showed that 7.2% of horses with acute onset of fever tested qPCR-positive for ECoV in feces, highlighting the importance of testing such horses for ECoV in feces. The various prevalence factors associated with ECoV qPCR-positive status likely relate to the high infectious nature of ECoV and breed-specific differences in management and husbandry practices.Significance of findingsECoV infection should be suspected and tested for in horses presenting with acute onset of fever, lethargy and anorexia with no respiratory signs. A two-step approach should be consider in which respiratory secretions and feces should be collected from such horses and submitted to a diagnostic laboratory. If the respiratory secretions test negative by qPCR for a panel of respiratory pathogens, feces already submitted to the laboratory should be tested for ECoV.

scholarly journals Are Staphylococcus intermedius Infections in Humans Cases of Mistaken Identity? A Case Series and Literature Review

2015 ◽  
Vol 2 (3) ◽  
Author(s):  
Roberto Viau ◽  
Andrea M. Hujer ◽  
Kristine M. Hujer ◽  
Robert A. Bonomo ◽  
Robin L.P. Jump
Keyword(s):  
Literature Review ◽  
Molecular Diagnostics ◽  
Case Series ◽  
Molecular Diagnostic ◽  
Diagnostic Tools ◽  
Human Pathogen ◽  
Detailed Review ◽  
Mistaken Identity ◽  
Staphylococcus Intermedius ◽  
Microbiological Methods

Abstract Staphylococcus intermedius and Staphylococcus pseudintermedius are difficult to distinguish using conventional microbiological methods. Molecular diagnostic tools change our understanding of the epidemiology of these 2 organisms. In this study, we present (1) a detailed review of the current literature on molecular diagnostics and (2) a case series in which misidentification was proven in 1 case. We conclude that S pseudintermedius is a more common human pathogen than previously recognized.

scholarly journals Emergence of Rapid Methods for Identifying Microbial Pathogens in Foods

1996 ◽  
Vol 79 (3) ◽  
pp. 809-812 ◽  
Author(s):  
Peter Feng
Keyword(s):  
Food Analysis ◽  
Food Microbiology ◽  
Microbial Pathogens ◽  
Bacterial Cells ◽  
Culture Methods ◽  
Rapid Methods ◽  
Microbiological Methods ◽  
Assay Time ◽  
Short Time ◽  
Microbiological Procedures

Abstract Because of the complexities of food analysis, conventional microbiological methods must use timeconsuming enrichment steps for culturing viable bacterial cells in foods. With rapid advancements in technology, however, numerous so-called rapid methods were introduced into the field of food microbiology in a relatively short time. Culture methods that were once used to obtain profiles for bacterial identification were simplified or automated. Many microbiological procedures were also streamlined or automated to reduce assay time, labor, and materials. Nucleic acid-based assays are used to identify gene sequences in foodborne bacteria, and antibody-based assays are used in numerous formats to detect bacterial pathogens and toxins in foods. The difficulties of analyzing food, however, remain challenging, and rapid methods need to be evaluated thoroughly before they are used for routine food analysis.

scholarly journals Toll-like receptor 9 inhibition reduces mortality in polymicrobial sepsis

2008 ◽  
Vol 205 (6) ◽  
pp. 1277-1283 ◽  
Author(s):  
George Plitas ◽  
Bryan M. Burt ◽  
Hoang M. Nguyen ◽  
Zubin M. Bamboat ◽  
Ronald P. DeMatteo
Keyword(s):  
Immune Response ◽  
Critical Role ◽  
Cecal Ligation ◽  
High Rate ◽  
Microbial Pathogens ◽  
Lower Serum ◽  
Human Sepsis ◽  
Cytokine Levels ◽  
Potential Strategy

The high rate of mortality in patients with sepsis results from an inappropriately amplified systemic inflammatory response to infection. Toll-like receptors (TLRs) are important for the activation of innate immunity against microbial pathogens. We demonstrate a critical role of TLR9 in the dysregulated immune response and death associated with sepsis. Compared with wild-type (WT) mice, TLR9−/− mice exhibited lower serum inflammatory cytokine levels, higher bacterial clearance, and greater survival after experimental peritonitis induced by cecal ligation and puncture (CLP). Protection of TLR9−/− mice after CLP was associated with a greater number of peritoneal dendritic cells (DCs) and granulocytes than in WT controls. Adoptive transfer of TLR9−/− DCs was sufficient to protect WT mice from CLP and increased the influx of peritoneal granulocytes. Subsequent experiments with a depleting antibody revealed that granulocytes were required for survival in TLR9−/− mice. Remarkably, a single injection of an inhibitory CpG sequence that blocks TLR9 protected WT mice, even when administered as late as 12 h after CLP. Our findings demonstrate that the detrimental immune response to bacterial sepsis occurs via TLR9 stimulation. TLR9 blockade is a potential strategy for the treatment of human sepsis.

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