Sampling challenges in diagnosis of chronic bacterial infections

Abstract

In recent decades there has been an increase in knowledge of the distribution, species diversity and growth patterns of bacteria in human chronic infections. This has challenged standard diagnostic methods, which have undergone a development to both increase the accuracy of testing as well as to decrease the occurrence of contamination. In particular, the introduction of new technologies based on molecular techniques into the clinical diagnostic process has increased detection and identification of infectious pathogens. Sampling is the first step in the diagnostic process, making it crucial for obtaining a successful outcome. However, sampling methods have not developed at the same speed as molecular identification. The heterogeneous distribution and potentially small number of pathogenic bacterial cells in chronic infected tissue makes sampling a complicated task, and samples must be collected judiciously and handled with care. Clinical sampling is a step in the diagnostic process that may benefit from innovative methods based on current knowledge of bacteria present in chronic infections. In the present review, we describe and discuss different aspects that complicate sampling of chronic infections. The purpose is to survey representative scientific work investigating the presence and distribution of bacteria in chronic infections in relation to various clinical sampling methods.

Surface Topography-Adaptive Robotic Superstructures for Biofilm Removal and Pathogen Detection on Human Teeth

“…In addition, we also demonstrate that human coronavirus OC43 (HCoV-OC43) in biofilms can be also retrieved for viability detection (Figure S18), allowing interkingdom detection of bacteria, fungi, and viruses as well as their byproducts. The data indicate feasibility of applying STARS for diagnostic sampling of disease-causing biofilms, achieving localized sample retrieval for detection of infective agents and virulence-associated biomolecules, which would provide invaluable guidance for precise and personalized therapies. ,, Together, STARS may lead to simultaneous therapeutic and diagnostic applications that combine autonomous, tether-free biofilm removal with concomitant data collection functionality.…”

“…This feature enables precise retrieval of biofilm contents with high spatial precision at the submillimeter level (Figure A, close-up). The heterogeneous distribution and non-uniform location of biofilms associated with human chronic infections make accurate sampling difficult, which would be particularly important for hard-to-reach biofilms such as those formed in the interdental space . A key challenge is to collect samples in targeted locations and in sufficient quantities that can be used to detect pathogens and biomolecules using currently available technologies.…”

“…Biofilms are composed of microbial cells enmeshed in an extracellular matrix that are firmly attached on a variety of surfaces. − A major challenge is targeting biofilms formed on surfaces with arbitrary orientations and complex topographical features like crevices . Such complex, biofilm-covered surfaces pervade health care and industry causing chronic infections and costly contaminations. ,,, Furthermore, the ability to sample biofilm contents could inform more effective treatment and ultimately enable precision medicine to increase successful clinical outcomes. , However, while methods to molecularly identify pathogens have advanced dramatically, sampling methods, the first step in a diagnostics process, have not advanced at the same pace. − Sampling is particularly challenging due to the heterogeneous distribution of diverse pathogens, − requiring biofilm disruption and collection, often from within crevices or grooves. To address these needs, we develop a microrobotic system to access and remove adhesive biofilms and perform sampling for pathogen detection using iron oxide nanoparticles (IONP), a versatile class of materials with catalytic and magnetic properties. − …”

Dynamics of skin microbiota in shoulder surgery infections

“…The causing microorganisms in an operational wound are often heterogeneously distributed [101]. For this reason, it is recommended to collect 5 or more specimens from different sites of the surgical wound and implant [102]. Tissue biopsies have been found to be more reliable than aspiration of synovial fluid in diagnosis of a bacterial infection.…”

Recent Advances in the Use of Mesoporous Silica Nanoparticles for the Diagnosis of Bacterial Infections

“… 8 Bacterial infection can occur in any part of the body; therefore, vast sampling matrices with heterogeneous distribution of pathogenic bacteria in infected tissue make the isolation of bacteria and diagnosis process challenging. 9 Isolation of the pathogenic bacteria is critical to elucidate bacterial pathogenicity and assessing potential effects on the patient. 10 The isolation of bacteria from complex sampling media and enrichment of the target organism is commonly performed by physical separation techniques, which decreases the recovery of target bacteria due to a series of steps containing washing and replications.…”