Portable devices and mobile instruments for infectious diseases point-of-care testing

INTRODUCTION

Rapidity, simplicity, and portability are highly desirable characteristics of tests and devices designed for performing diagnostics at the point of care (POC), either near patients managed in healthcare facilities or to offer bioanalytical alternatives in external settings. By reducing the turnaround time of the diagnostic cycle, POC diagnostics can reduce the dissemination, morbidity, and mortality of infectious diseases and provide tools to control the global threat of antimicrobial resistance. Areas covered: A literature search of PubMed and Google Scholar, and extensive mining of specialized publications, Internet resources, and manufacturers' websites have been used to organize and write this overview of the challenges and requirements associated with the development of portable sample-to-answer diagnostics, and showcase relevant examples of handheld devices, portable instruments, and less mobile systems which may or could be operated at POC. Expert commentary: Rapid (<1 h) diagnostics can contribute to control infectious diseases and antimicrobial resistant pathogens. Portable devices or instruments enabling sample-to-answer bioanalysis can provide rapid, robust, and reproducible testing at the POC or close from it. Beyond testing, to realize some promises of personalized/precision medicine, it will be critical to connect instruments to healthcare data management systems, to efficiently link decentralized testing results to the electronic medical record of patients.

Testing the optimality properties of a dual antibiotic treatment in a two-locus, two-allele model

Mathematically speaking, it is self-evident that the optimal control of complex, dynamical systems with many interacting components cannot be achieved with 'non-responsive' control strategies that are constant through time. Although there are notable exceptions, this is usually how we design treatments with antimicrobial drugs when we give the same dose and the same antibiotic combination each day. Here, we use a frequency- and density-dependent pharmacogenetics mathematical model based on a standard, two-locus, two-allele representation of how bacteria resist antibiotics to probe the question of whether optimal antibiotic treatments might, in fact, be constant through time. The model describes the ecological and evolutionary dynamics of different sub-populations of the bacterium Escherichia coli that compete for a single limiting resource in a two-drug environment. We use in vitro evolutionary experiments to calibrate and test the model and show that antibiotic environments can support dynamically changing and heterogeneous population structures. We then demonstrate, theoretically and empirically, that the best treatment strategies should adapt through time and constant strategies are not optimal.

Severe community-acquired pneumonia: approach to therapy

Despite substantial progress in therapeutic options, severe community-acquired pneumonia (CAP) remains a significant cause of morbidity and mortality worldwide. Recognising the clinical importance of CAP over the past several years, different medical societies and health organisations in different countries have proposed specific guidelines for the management of CAP. Early and rapid initiation of antimicrobial therapy has been advocated for a favourable outcome. Treatment is empirical as the diagnostic yield for potential pathogens does not exceed 50%. Dual therapy is emerging as the preferred therapy for severe CAP. The regimen is based on an epidemiological approach with emphasis on covering both typical and atypical pathogens. Non-antimicrobial adjuvant therapies including non-invasive ventilation and immunomodulatory agents are emerging as promising area for future development.

The gene: the polymerase chain reaction and its clinical application

Chromosomal DNA transfers and stores information regarding the structure and function of the cell. Genetic information, encoded within sequences of nucleotides that compose DNA, is grouped into functional units called genes. Genetic diseases are caused by changes in the chromosomal DNA, leading to a change in the quantity or function of the protein gene product. In the past, genetic diagnosis was limited by the availability of sufficient quantity and quality of DNA and the absence of an efficient amplification procedure. The polymerase chain reaction (PCR), an inexpensive, rapid, and accurate means of amplifying DNA, is already making a major contribution to the diagnostic sciences. PCR techniques have been widely used in diverse applications, including molecular analysis of microbial pathogens, inheritable diseases and syndromes, and neoplasms. The purpose of this article is to 1) Review gene structure and function, 2) review principles of PCR technology and its applications in molecular biology, and 3) discuss an experimental clinical application of PCR to identify novel infectious agents responsible for odontogenic infections.

Integration of molecular characterization of microorganisms in a global antimicrobial resistance surveillance program

The SENTRY Antimicrobial Surveillance Program has incorporated molecular strain typing and resistance genotyping as a means of providing additional information that may be useful for understanding pathogenic microorganisms worldwide. Resistance phenotypes of interest include multidrug-resistant pathogens, extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae, methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant enterococci, and fluoroquinolone-resistant (FQR) strains of gram-negative bacilli and Streptococcus pneumoniae. Clusters of > or =2 isolates within a given resistance profile that are linked temporally and by hospital location are flagged for DNA fingerprinting. Further characterization of organisms with respect to resistance genotype is accomplished with use of polymerase chain reaction and DNA sequencing. This process has been highly successful in identifying clonal spread within clusters of multiresistant pathogens. Between 50% and 90% of MRSA clusters identified by phenotypic screening contained evidence of clonal spread. Among the Enterobacteriaceae, ESBL-producing strains of Escherichia coli and Klebsiella pneumoniae are the most common pathogens causing clusters of infection, and approximately 50% of recognized clusters demonstrate clonal spread. Clusters of Pseudomonas aeruginosa, Acinetobacter species, and Stenotrophomonas maltophilia have been noted with clonal spread among patients with urinary tract, respiratory, and bloodstream infections. Characterization of mutations in the FQR-determining region of phenotypically susceptible isolates of E. coli and S. pneumoniae has identified first-stage mutants among as many as 40% of isolates. The ability to characterize organisms phenotypically and genotypically is extremely powerful and provides unique information that is important in a global antimicrobial surveillance program.

Rapid diagnosis of bacteremia by universal amplification of 23S ribosomal DNA followed by hybridization to an oligonucleotide array

The rapid identification of bacteria in blood cultures and other clinical specimens is important for patient management and antimicrobial therapy. We describe a rapid (<4 h) detection and identification system that uses universal PCR primers to amplify a variable region of bacterial 23S ribosomal DNA, followed by reverse hybridization of the products to a panel of oligonucleotides. This procedure was successful in discriminating a range of bacteria in pure cultures. When this procedure was applied directly to 158 unselected positive blood culture broths on the day when growth was detected, 125 (79.7%) were correctly identified, including 4 with mixed cultures. Nine (7.2%) yielded bacteria for which no oligonucleotide targets were present in the oligonucleotide panel, and 16 culture-positive broths (10.3%) produced no PCR product. In seven of the remaining eight broths, streptococci were identified but not subsequently grown, and one isolate of Staphylococcus aureus was misidentified as a coagulase-negative staphylococcus. The accuracy, range, and discriminatory power of the assay can be continually extended by adding further oligonucleotides to the panel without significantly increasing complexity or cost.

Molecular epidemiology in the care of patients

Several different epidemiologic typing methods have been applied in studies of microbial pathogens. These methods include the more traditional nonmolecular approaches as well as the more sophisticated molecular typing methods. Application of traditional epidemiologic typing methods, such as antibiogram, serotyping, biotyping, and phage typing, have occasionally been useful in describing the epidemiology of infectious diseases. However, these methods have generally been considered to be too variable, labor intensive, and slow to be of practical value in epidemiologic investigations. In response to these limitations, several techniques have been adopted from the molecular biology field for use as epidemiologic typing methods and have been applied in studies of bacteria, fungi, viruses, and protozoa. The most widely used molecular typing methods are the DNA-based methods, such as plasmid profiling, restriction endonuclease analysis of plasmid and genomic DNA, Southern hybridization analysis using specific DNA probes, and chromosomal DNA profiling using either pulsed-field gel electrophoresis or polymerase chain reaction-based methods. The various molecular typing methods may be applied to the investigation of outbreaks of infections or may be used in the context of epidemiologic surveillance. For outbreak investigation, typing methods are used to compare isolates from a suspected outbreak to delineate clonally related and unrelated strains with the goal of short-term control of transmission. In the context of epidemiologic surveillance, molecular typing methods may be used to monitor geographic spread and prevalence shifts of epidemic and endemic clones with the goal of long-term evaluation of preventive strategies or for the detection and monitoring of emerging and reemerging infections. The specific typing method selected may vary with the task at hand; however, the typing studies must always be used to supplement, rather than replace, careful epidemiologic investigation.

Laboratory role in the management of hospital acquired infections

The microbiology laboratory has many important roles. It must collaborate with the infection control team on the investigations of outbreaks. During outbreaks, it must save relevant samples, look for reservoirs and undertake typing techniques, all of which should be timely. New technology should be available to detect, identify and characterize micro-organisms. Molecular biological techniques have enhanced the speed and sensitivity of detection methods and have allowed the laboratory to identify organisms that do not grow or grow slowly in culture. Molecular techniques also enable the microbiologist to identify antibiotic resistance genes and to 'fingerprint' hospital organisms, thereby facilitating studies of nosocomial transmission.

Managing community-acquired pneumonia. Factors to consider in outpatient care

Most patients with community-acquired pneumonia are treated as outpatients, and choice of therapy is usually empirical because the etiologic agent is unknown. Therapy should include coverage for both typical and atypical organisms. In geographic areas with highly resistant S pneumoniae, one of the newer fluoroquinolones should be considered, since resistance to penicillin is associated with cross-resistance to macrolides and tetracyclines. Once-daily dosing should be given strong preference because more frequent dosing results in poor compliance, which may lead to inadequate therapy and increased resistance. At present, the duration of therapy should probably be no less than 7 days. Patients should be categorized for mortality risk with objective scoring methods, and the need for hospitalization should be decided accordingly. Greater use of observational and intermediate-care beds is encouraged, as is improved utilization of pneumococcal vaccine.