High-throughput identification of clinically important bacterial pathogens using DNA microarray

Solid and Suspension Microarrays for Microbial Diagnostics

Advancements in molecular technologies have provided new platforms that are being increasingly adopted for use in the clinical microbiology laboratory. Among these, microarray methods are particularly well suited for diagnostics as they allow multiplexing, or the ability to test for multiple targets simultaneously from the same specimen. Microarray technologies commonly used for the detection and identification of microbial targets include solid-state microarrays, electronic microarrays and bead suspension microarrays. Microarray methods have been applied to microbial detection, genotyping and antimicrobial resistance gene detection. Microarrays can offer a panel approach to diagnose specific patient presentations, such as respiratory or gastrointestinal infections, and can discriminate isolates by genotype for tracking epidemiology and outbreak investigations. And, as more information has become available on specific genes and pathways involved in antimicrobial resistance, we are beginning to be able to predict susceptibility patterns based on sequence detection for particular organisms. With further advances in automated microarray processing methods and genotype-phenotype prediction algorithms, these tests will become even more useful as an adjunct or replacement for conventional antimicrobial susceptibility testing, allowing for more rapid selection of targeted therapy for infectious diseases.

High prevalence and molecular analysis of macrolide-nonsusceptible Moraxella catarrhalis isolated from nasopharynx of healthy children in China

Three hundred eighty-three isolates of Moraxella catarrhalis were collected from healthy children aged less than 2 years in China and assessed for antimicrobial resistance. We found that 92.2% (n=353) produced a β-lactamase. Nonsusceptibility rates to erythromycin and azithromycin, determined using Clinical Laboratory Standards Institute (CLSI) breakpoints, were 40.3% and 22.5%, respectively; nonsusceptibility rates determined using pharmacokinetics/pharmacodynamics breakpoints, however, were 59% and 60.1%. The minimal inhibitory concentration (MIC)(90) values were >256 μg/ml. Nonsusceptibility rates varied by region from 9.7% in Dongguan to 75.9% in Jinan. Further, concomitant resistance to β-lactam antibiotics was also observed. Pulsed-field gel electrophoresis analysis of 27/37 high-level macrolide-resistant M. catarrhalis isolates showed that closely related pulsotypes dominated, with a total of 11 different pulsotypes being observed. The closely related pulsotypes were observed in isolates originating from all six Chinese cities investigated, possibly as a consequence of the mobility of the Chinese population. Sixteen patterns of 23S rRNA mutations were found among 97 selected isolates using polymerase chain reaction and sequencing, but no known ermA, ermB, mefA, or mefE genes could be detected. Mutations A2982T and A2796T in 23S rRNA were related to high-level macrolide resistance (MICs ranging from 24 to >256 μg/ml), while an A2983T mutation was associated with low-level macrolide resistance (MICs ranging from 0.19 to 16 μg/ml).

Application of phylogenetic microarrays to interrogation of human microbiota

Human-associated microbiota is recognized to play vital roles in maintaining host health, and it is implicated in many disease states. While the initial surge in the profiling of these microbial communities was achieved with Sanger and next-generation sequencing, many oligonucleotide microarrays have also been developed recently for this purpose. Containing probes complementary to small ribosomal subunit RNA gene sequences of community members, such phylogenetic arrays provide direct quantitative comparisons of microbiota composition among samples and between sample groups. Some of the developed microarrays including PhyloChip, Microbiota Array, and HITChip can simultaneously measure the presence and abundance of hundreds and thousands of phylotypes in a single sample. This review describes the currently available phylogenetic microarrays that can be used to analyze human microbiota, delineates the approaches for the optimization of microarray use, and provides examples of recent findings based on microarray interrogation of human-associated microbial communities.

Development of an up-converting phosphor technology-based 10-channel lateral flow assay for profiling antibodies against Yersinia pestis

In this study, a 10-channel up-converting phosphor technology-based lateral flow (TC-UPT-LF) assay was developed to profile antibodies against Yersinia pestis. Ten expressed Y. pestis proteins were covalently conjugated with an up-converting phosphor particle to develop double-antigen sandwich immunochromatographic strips to detect corresponding antibodies. After optimization one by one, each strip was integrated into a TC-UPT-LF disc for simultaneously detection of different antibodies. A scanning biosensor was also developed to acquire the results. The performance of the TC-UPT-LF assay was evaluated by using standard samples and plague monkey serum samples. Fifty-one patient serum samples were detected by the TC-UPT-LF assay. The TC-UPT-LF disc could be stable for 10 days at 37°C with an average CV of 10.3%. Its sensitivity and qualitative results are comparable to those of ELISA. Its linearity fitting coefficient of determination (R2) for different antibody detection is between 0.93 and 0.99. Besides F1 antibody, the LcrV and YopD antibodies also showed higher positive ratio than the other seven antibodies, as 100% (13/13) and 92% (12/13) in monkey sera and 86.3% (44/51) and 66.7% (34/51) in patient sera, respectively. It is suggested that the TC-UPT-LF assay has been successfully developed for multi-detection and LcrV and YopD can be the potential diagnostic markers of the plague.

Target amplification for broad spectrum microbial diagnostics and detection

Microarrays are massively parallel detection platforms that were first used extensively for gene expression studies, but have also been successfully applied to microbial detection in a number of diverse fields requiring broad-range microbial identification. This technology has enabled researchers to gain an insight into the microbial diversity of environmental samples, facilitated discovery of a number of new pathogens and enabled studies of multipathogen infections. In contrast to gene expression studies, the concentrations of targets in analyzed samples for microbial detection are usually much lower, and require the use of nucleic acid amplification techniques. The rapid advancement of manufacturing technologies has increased the content of the microarrays; thus, the required amplification is a challenging problem. The constant parallel improvements in both microarray and sample amplification techniques in the near future may lead to a radical progression in medical diagnostics and systems for efficient detection of microorganisms in the environment.

DNA microarray-based identification of bacterial and fungal pathogens in bloodstream infections

The accurate and rapid identification of pathogens in blood is a major challenge in clinical pathogen diagnostics because of the high mortality of sepsis. Here we report the development of DNA microarray for the identification of pathogens causing bloodstream infections. Species-specific and bacteria- and fungi-broad-ranged probes were designed to identify 50 bacteria and 7 fungi. The specificities and sensitivities of the selected probes were successfully validated by applying reference strains. To assess the performance of the DNA microarray in a clinical setting, blind tests were performed using 112 blood culture specimens that showed preliminary presence of pathogenic microorganisms by culture-based method, resulting in the correct identification of pathogens in 104 samples showing the sensitivity of 93%. In addition, closely-related species could be discriminated by the distinct hybridization patterns. This DNA microarray-based pathogen diagnosis takes approximately 10 h starting from a positive blood culture, considerably reducing time required to sufficiently identify pathogens by subsequent agar-culture and biochemical tests which requires altogether at least 1-3 days. Also, the amount of sample required for the identification of pathogens is much less than that required for biochemical assays. Thus, the DNA microarray reported here should be useful for the effective identification of microbial pathogens in blood cultures from septicemic patients.