Diagnosing Pneumocystis jirovecii pneumonia: A review of current methods and novel approaches.

Pneumocystis jirovecii can cause life-threatening pneumonia in immunocompromised patients. Traditional diagnostic testing has relied on staining and direct visualization of the life-forms in bronchoalveolar lavage fluid. This method has proven insensitive, and invasive procedures may be needed to obtain adequate samples. Molecular methods of detection such as polymerase chain reaction (PCR), loop-mediated isothermal amplification (LAMP), and antibody-antigen assays have been developed in an effort to solve these problems. These techniques are very sensitive and have the potential to detect Pneumocystis life-forms in noninvasive samples such as sputum, oral washes, nasopharyngeal aspirates, and serum. This review evaluates 100 studies that compare use of various diagnostic tests for Pneumocystis jirovecii pneumonia (PCP) in patient samples. Novel diagnostic methods have been widely used in the research setting but have faced barriers to clinical implementation including: interpretation of low fungal burdens, standardization of techniques, integration into resource-poor settings, poor understanding of the impact of host factors, geographic variations in the organism, heterogeneity of studies, and limited clinician recognition of PCP. Addressing these barriers will require identification of phenotypes that progress to PCP and diagnostic cut-offs for colonization, generation of life-form specific markers, comparison of commercial PCR assays, investigation of cost-effective point of care options, evaluation of host factors such as HIV status that may impact diagnosis, and identification of markers of genetic diversity that may be useful in diagnostic panels. Performing high-quality studies and educating physicians will be crucial to improve the rates of diagnosis of PCP and ultimately to improve patient outcomes.

[What place and what future for the pathology of infectious and tropical diseases in France?]. / Quelle place et quel avenir pour l'anatomo-cyto-pathologie des maladies infectieuses et tropicales en France?

The management of tissues and cellular samples by the pathologists in the infectious and tropical diseases pathology field in 2014 needs a strong knowledge of both morphological and molecular domains which includes the good control: (i) of the taxonomy of infectious and tropical diseases pathology leading to the pathogens identification and (ii) of the ancillary methods which can be used in fixed samples in order to detect or better identify these pathogens. There is a recent paradox in France concerning the frequency of infectious diseases to be diagnosed in pathology laboratories and the progressive loss of pathologist's expertise in this domain. Different reasons could explain this statement including the omnipresence of the tumour lesions to be managed in a pathology laboratory as well as the recent constraints associated with the different biomarkers that are mandatory to be detected by immunohistochemistry and/or by molecular biology. Even if the microbiologists play a pivotal role for identifying the different pathogens as well as for the assessment of their sensitivity to the anti-microbial drugs, a large number of infectious diseases can be diagnosed only on fixed tissue and/or cells by the pathologists. The purpose of this review is to describe the current and future issues of infectious and tropical diseases diagnoses in pathology laboratories, in particular in France.

Laboratory diagnosis of human rabies: recent advances.

Rabies, an acute progressive, fatal encephalomyelitis, transmitted most commonly through the bite of a rabid animal, is responsible for an estimated 61,000 human deaths worldwide. The true disease burden and public health impact due to rabies remain underestimated due to lack of sensitive laboratory diagnostic methods. Rapid diagnosis of rabies can help initiate prompt infection control and public health measures, obviate the need for unnecessary treatment/medical tests, and assist in timely administration of pre- or postexposure prophylactic vaccination to family members and medical staff. Antemortem diagnosis of human rabies provides an impetus for clinicians to attempt experimental therapeutic approaches in some patients, especially after the reported survival of a few cases of human rabies. Traditional methods for antemortem and postmortem rabies diagnosis have several limitations. Recent advances in technology have led to the improvement or development of several diagnostic assays which include methods for rabies viral antigen and antibody detection and assays for viral nucleic acid detection and identification of specific biomarkers. These assays which complement traditional methods have the potential to revolutionize rabies diagnosis in future.

[Consider the advantages and disadvantages of microbial examinations in a hospital, and ideal microbial laboratory].

The main benefit of carrying out microbial examinations in a hospital is that it rapidly yields information on infectious diseases. Microbiology technicians can easily communicate with the physicians and can carry out precise analyses. The disadvantages are the high costs of microbiological examinations, and the need for long training times for microbial laboratory technicians because of the highly technical nature of their duties. In-hospital microbial inspections will lead to: 1)improved rapid diagnostic tests for infectious diseases and evaluation of antibiotic treatment in the early stages of disease; 2) detection of the precise origin of microbes and confirmation of etiological factors; 3) antibiotic susceptibility testing and evaluation of combined effects of antibiotics against multiple drug-resistant bacteria; and 4)genetic analysis and epidemiological statistical analysis for the purpose of infection control in a hospital and surrounding areas.

Rapid detection, characterization, and enumeration of foodborne pathogens.

As food safety management further develops, microbiological testing will continue to play an important role in assessing whether Food Safety Objectives are achieved. However, traditional microbiological culture-based methods are limited, particularly in their ability to provide timely data. The present review discusses the reasons for the increasing interest in rapid methods, current developments in the field, the research needs, and the future trends. The advent of biotechnology has introduced new technologies that led to the emergence of rapid diagnostic methods and altered food testing practices. Rapid methods are comprised of many different detection technologies, including specialized enzyme substrates, antibodies and DNA, ranging from simple differential plating media to the use of sophisticated instruments. The use of non-invasive sampling techniques for live animals especially came into focus with the 1990s outbreak of bovine spongiform encephalopathy that was linked to the human outbreak of Creutzfeldt Jakob's Disease. Serology is still an important tool in preventing foodborne pathogens to enter the human food supply through meat and milk from animals. One of the primary uses of rapid methods is for fast screening of large number of samples, where most of them are expected to be test-negative, leading to faster product release for sale. This has been the main strength of rapid methods such as real-time Polymerase Chain Reaction (PCR). Enrichment PCR, where a primary culture broth is tested in PCR, is the most common approach in rapid testing. Recent reports show that it is possible both to enrich a sample and enumerate by pathogen-specific real-time PCR, if the enrichment time is short. This can be especially useful in situations where food producers ask for the level of pathogen in a contaminated product. Another key issue is automation, where the key drivers are miniaturization and multiple testing, which mean that not only one instrument is flexible enough to test for many pathogens but also many pathogens can be detected with one test. The review is mainly based on the author's scientific work that has contributed with the following new developments to this field: (i) serologic tests for large-scale screening, surveillance, or eradication programs, (ii) same-day detection of Salmonella that otherwise was considered as difficult to achieve, (iii) pathogen enumeration following a short log-phase enrichment, (iv) detection of foodborne pathogens in air samples, and finally (v) biotracing of pathogens based on mathematical modeling, even in the absence of isolate. Rapid methods are discussed in a broad global health perspective, international food supply, and for improvement of quantitative microbial risk assessments. The need for quantitative sample preparation techniques, culture-independent, metagenomic-based detection, online monitoring, a global validation infrastructure has been emphasized. The cost and ease of use of rapid assays remain challenging obstacles to surmount.

Diabetic foot infections: A need for innovative assessments.

Foot wounds are the most common diabetes-related cause of hospitalization and frequently result in amputation. Although generally diagnosed clinically based on signs and symptoms of inflammation, empirical antibiotic treatment should be based on tissue cultures until resolution of infection. Advances in molecular detection over the past decade, including rapid chromogenic agar and real-time polymerase chain reaction, have improved diagnostic capabilities. However, chronic wounds may host biofilm bacteria not adequately detected by current microbiological testing. Enhanced DNA testing is required to identify these pathogens as well as evolving and previously underdiagnosed bacteria. Two options, nucleic acid fluorescent in situ hybridization and rDNA sequencing, are on the horizon for clinical use. Wound biofilms also necessitate more complex clinical management including debridement, augmenting host defenses, suppression of biofilms, and wound closure. Adopting these advances in diagnosis and treatment may help with overall prognosis and reduce health care costs.

Top ten hot topics in parenteral science and technology.

Ten current "hot topics" in parenteral science and technology are reviewed to update the reader on current advances and challenges with each topic. Topics selected are formulation advances, packaging advances, extractables and leachables, analytical method advances for biopharmaceuticals, protein pharmaceutics, quality by design, manufacturing and equipment advances, aseptic processing advances, rapid microbial methods, and visual inspection of parenteral products.

New microbiology tools for public health and their implications.

The realm of diagnostic assays for detection of acute infections is rapidly changing from antibody detection to pathogen detection, from clinical laboratory based to point-of-care based, from single analyte detection to multiple analyte detection, and is more focused on detection using less invasive approaches for collecting biological samples. New assays are typically more sensitive than are conventional assays and have the capability of providing more information that characterizes the pathogen or the host response to the pathogen. From a public health perspective, the advent of molecular epidemiology, which allows tracking of pathogens based on unique genetic sequences or antigenic properties, has revolutionized how epidemiologists investigate and evaluate epidemics and assess endemic diseases. In addition, the use of point-of-care (POC) devices can impact the detection and surveillance of infections and will enhance our ability to accurately identify the causes of illnesses.

Controlling antimicrobial use and decreasing microbiological laboratory tests for urinary tract infections in spinal-cord-injury patients with chronic indwelling catheters.

PURPOSE: The effect of replacing the indwelling catheter of patients suspected of having a urinary tract infection (UTI) before collecting a urine sample on the number of organisms isolated in cultures and on drug and microbiology laboratory costs was studied. METHODS: Data were collected for all patients hospitalized in two spinal cord injury (SCI) units between October 2001 and March 2002 who had an indwelling catheter or suprapubic catheter and were suspected of having a UTI. Urine samples were obtained through a port of the indwelling catheter in one SCI unit, while the indwelling catheter was replaced immediately before each urine sample was obtained in the second SCI unit. Patient demographics, history of antimicrobial use, bacterial isolate sensitivity data, and current antimicrobial treatment were recorded. RESULTS: A total of 85 patients, 41 in the control group and 44 in the intervention group, were enrolled during the six-month study period. In the control and intervention groups, 93 and 79 organisms were isolated, respectively, with an average of 2 isolates per patient in the control group and 1 per patient in the intervention group. Patients in the control group had significantly more multidrug-resistant organisms in their urine, with 34 isolated from 26 patients (63%) (p < 0.001). Changing the indwelling catheter decreased antimicrobial and microbiology laboratory costs, resulting in a cost saving of $15.64 per patient. CONCLUSION: Replacement of the indwelling catheter before collecting a urine sample for culture and conducting susceptibility testing reduced the pathogens identified, the number of toxic antimicrobials prescribed to treat the infection, and the costs of antimicrobials and microbiology laboratory technician time.