Emerging Options for the Diagnosis of Bacterial Infections and the Characterization of Antimicrobial Resistance

Abstract

Precise and rapid identification and characterization of pathogens and antimicrobial resistance patterns are critical for the adequate treatment of infections, which represent an increasing problem in intensive care medicine. The current situation remains far from satisfactory in terms of turnaround times and overall efficacy. Application of an ineffective antimicrobial agent or the unnecessary use of broad-spectrum antibiotics worsens the patient prognosis and further accelerates the generation of resistant mutants. Here, we provide an overview that includes an evaluation and comparison of existing tools used to diagnose bacterial infections, together with a consideration of the underlying molecular principles and technologies. Special emphasis is placed on emerging developments that may lead to significant improvements in point of care detection and diagnosis of multi-resistant pathogens, and new directions that may be used to guide antibiotic therapy.

Sample Preparation and Diagnostic Methods for a Variety of Settings: A Comprehensive Review

“…In addition to the usual hurdles that sample preparation presents in analytical processes, the process of diagnostic testing in particular often requires other factors to be taken into consideration, such as the effects of collecting analytical samples on a patient, the clinical utility of the testing methodology being chosen, the cost of testing to the patient, and whether the same testing procedure will need to be repeated in the future [ 16 , 17 , 18 , 19 ]. Additionally, in the case of infectious diseases, diagnostic methods with adequate specificity and detail are important for preventing established pathogens from acquiring antimicrobial resistance due to prescribing broad-spectrum rather than targeted antimicrobial drugs, identifying newly emerging and reemerging infectious diseases, and properly monitoring for outbreaks of infectious diseases [ 19 , 20 , 21 ]. Infectious diseases, in particular, tend to have these difficulties due to the nature of the agents that cause them, their transmissibility compared with chronic and lifestyle-associated diseases, and the broad range of methods of diagnosing the diseases caused by them that have been developed, which can range from clinical diagnosis based on signs and symptoms being exhibited to molecular methods of laboratory diagnosis that identify the exact strain of the pathogen [ 20 , 22 , 23 , 24 ].…”

“…As shown in Figure 3 , the sample preparation for gold standard or culture-based methods of diagnosing infectious diseases in a traditional laboratory setting generally involves preparing growth media for pathogens, staining them with Gram’s method, extracting genetic material or other biomarkers, separating target analytes for sequencing or other identifications, and exposing of pathogens on growth media to antibiotics in order to determine antimicrobial resistance [ 21 , 24 , 25 , 26 , 27 , 28 , 29 , 40 ]. Since much of this sample preparation process is either impractical for use in POCT methods or has a much longer turnaround time as well as less sensitivity and specificity than biochemical or molecular diagnostic laboratory methods, many of the methods developed over the past decade have focused on either making the extraction and separation steps compatible with POC platforms or increasing the sample throughput of biochemical and molecular diagnostic methods used in clinical laboratory platforms [ 21 , 24 , 25 , 26 , 27 , 28 , 29 , 38 , 39 , 41 , 46 , 66 , 70 ]. As previously mentioned, the large number of advances in areas such as microfluidics, advanced materials, and biosensors, as well as the growing ubiquity of smartphones, has greatly supplemented this process for POC devices and methods while advances in laboratory automation, extractions and separations, and high-throughput assay platforms, such as microplates, have analogously supplemented the process for centralized laboratory methods, as shown in Figure 4 [ 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 ,…”

“…For molecular methods, including NAATs in particular, the greatest bottleneck in this process usually consists of extracting the target biomarkers by lysing the pathogens in a collected sample and separating or purifying the target analytes in order to proceed to amplification or detection [ 26 , 37 , 53 , 58 , 67 ]. In response to this, a great number of extraction/lysis methods have been developed for use in tandem with diagnostic methods utilizing nucleic acids as the target biomarkers, as they are both simple to apply to POC settings while maintaining sensitivity and specificity and are amenable to scaling up for high-throughput clinical laboratory testing for a large number of pathogens [ 21 , 26 , 74 , 75 , 76 , 77 , 78 ]. Similarly, many separation methodologies have been developed to complement the number of extraction methods for use with analytical setups in various settings and sizes [ 76 , 77 , 79 , 80 , 81 , 82 ].…”

Prevalence and Antimicrobial Resistance Pattern of Community Acquired Staphylococcus aureus in Patients Received at the Traumatology Unit of a Secondary Referral Health Setting in the Western Cameroon

“…Conjugative transfer of the vanA gene from vancomycin-resistant Enterococcus feacalis to MRSA [19] as well as the thickening of the bacterial cell wall due to a large accumulation of peptidoglycan [20] are major contributors to the resistance of S. aureus to vancomycin. A range of existing diagnostic methods and others undergoing development are available for a point of care and accurate detection of pathogenic bacteria and their resistance profile [21].…”

Antimicrobial Activity and Toxicity of Analogs of Wasp Venom EMP Peptides. Potential Influence of Oxidized Methionine

“…One of the major current problems in medicine is the growing resistance of pathogenic organisms to traditional treatments. The situation is made worse by the abuse of antibiotics and the rapid selection of resistance variants [1][2][3]. It is therefore important to find new active compounds that not only have anti-microbial activity but also have mechanisms of action against which resistance is slower to evolve.…”