EditorialNovel Microbial Diagnostic Methods for Clinical,Environmental, and Food Samples
Pratik Banerjee,1 IrshadM. Sulaiman,2 György Schneider,3
Udayan Ray,4 and Bala Jagadeesan5
1Division of Epidemiology, Biostatistics, and Environmental Health Science, School of Public Health, University of Memphis,Memphis, TN, USA2Southeast Regional Laboratory, U.S. Food and Drug Administration, Atlanta, GA, USA3Department of Medical Microbiology and Immunology, University of Pecs, Pecs, Hungary4Royal Hobart Hospital, University of Tasmania School of Medicine, Hobart, TAS, Australia5Nestle Research Center, Lausanne, Switzerland
Correspondence should be addressed to Pratik Banerjee; [email protected]
Received 3 July 2017; Accepted 4 July 2017; Published 31 July 2017
The field of molecular diagnostics has experienced a remark-able growth and advancement in recent years resulting insignificant improvement in disease diagnosis and interven-tion. Rapid, sensitive, and accurate detection and identifi-cation of microbial entities are critical issues for ensuringtimeliness of clinical, environmental, and food safety inter-ventions. With the advent of new technologies in the fieldof biomedical sciences, the resolution of microbial detectionmethods has improved tremendously. Currently, most ofthe advanced microbial detection methods involve multi-disciplinary expertise (such as biology, chemistry, physics,engineering, material science, genomics, statistics, and bioin-formatics). The advancement of rapid microbial diagnos-tics fueled by these disciplines along with the growth ofclosely associated fields like nanotechnology and “omics” hasbrought opportunities as well as an immense challenge forresearchers and practitioners to adopt appropriate methodsconducive to their respective applications and sample types.
The methods and approaches of microbial detection mayvary quite significantly depending on the type of microbesand the nature of the sample or specimen under investigation.It is intuitive that “one size” does not fit all microbial diag-nostics strategies. As a result, the proper choice of diagnosticmodality is very important. Several new strategies of micro-bial detection have emerged in recent years with improvedsensitivity, discriminatory power, and most importantly, a
higher degree of accuracy. The clinical, environmental, andfood samples often confer hostile environments to microbes.Therefore, the microorganisms inhabiting in these matricesmay become injured or dead. In certain scenarios, microbialcells attain a viable but not culturable state in these matrices.Moreover, they may undergo additional stress during sampletransport and subsequent preparations. All these factors mayultimately pose a significant challenge for proper microbialdiagnosis if the detection methods are solely dependent onthe ability of the target organisms to grow under laboratoryor test conditions. Some molecular diagnostic techniquessuch as PCR and gene sequencing/metagenomics can beused in a culture independent manner and seems to addresssome of the long standing limitations (as described above)of microbial detection by growth-based (culture-dependent)methods.
This special issue provides a platform for sharing recentscientific advancements to researchers and practitionersworking in the broader public health area, including clinicaldiagnostics, environmental scientists, and food scientistsworking in food safety and food microbiology area. Thearticles included in this special issue include both originalscientific studies and review papers focused on microbialdetection and characterization methods and application inclinical, food, agriculture, and environmental fields. Articlesdealing with sample preparation, various human and animal
HindawiBioMed Research InternationalVolume 2017, Article ID 3942801, 3 pageshttps://doi.org/10.1155/2017/3942801
disease diagnosis methods, gut microbiota, biotechnologicalapplication ofmicrobes in foodproduction, and environmen-tal monitoring are included in this issue.
Appropriateness of sample preparation is one of the mostessential prerequisites of efficient detection of microbial enti-ties from complex sample matrices. Application of magneticseparation methods has emerged as a powerful techniquefor separation of biological entities (including intact cells orDNA) from clinical, food, or environmental samples. In theirreview article, M. Husakova et al. provide an overview ofavailable information regardingMycobacterium avium subsp.paratuberculosis (MAP) cells and DNA isolation methodsbased onmagnetic separation procedures for the detection ofMAP from a broad range of matrices including feces, blood,cheese, milk, and so on.
Several original research and review articles publishedin this issue highlight methods improvement as well asnovel diagnostic method development. The potential useof Treponema pallidum recombinant antigens for diagnos-tic purposes was summarized in the review paper by A.Kubanov et al. The paper gives an overview of candidatesurface-exposed proteins, adhesins, periplasmic, and flagellarproteins that could potentially be utilized for improvedsyphilis serological tests. Also, the authors highlight the factthat differentiation of early and late syphilis stages can becarried out by using these recombinant antigens. T. Matareet al. report an alternative method for testing the germ tubeformation ofCandida species.This approach is comparable tothe one that uses the human serum for this purpose. Authorsfound that bicarbonate and trismaleate can induce germtube formation. The optimal concentration of bicarbonatewas found to be 20mM at pH 5.5–6.5. The results alsodemonstrate that addition of 5–10% CO
2to the incubation
atmosphere increased the rate of germ tube formation.Optochin susceptibility is important parameters that
differentiate between Streptococcus pneumonia and otherstreptococci. Although it is a frequently used method, asignificant methodological discrepancy can be found in theliterature due to the lack of a standardized method. By study-ing different factors (strain, agar, and serotype) I. Burckhardtet al. used statistical methods to evaluate an ideal readingtime after inoculation, and their result suggests shorten-ing the incubation time from 24 h to 12 h.
Rapid and sensitive detection of human and animalprion diseases is crucial to prevent potential morbidity andmortality inflicted by this pathogenic agent. The diagnosticmodalities of prions are significantly different from otherpathogenic microbes such as bacteria, viruses, and fungiowing to the differences in biological properties and modeof host-pathogen interactions. The review article by H.-E.Kang et al. summarizes aspects of prion biology and theassay principle, performance, and conditions of contempo-rary methods of diagnosis with particular emphasis on thereal-time quaking-induced conversion (RT-QuIC) methodin both human and animal specimens. In another paper, aprotocol for evaluating the prevalence ofmultidrug resistancemutations in people with HIV-1 infection is suggested byS. Gupta et al. Their research focuses on patients with lowviremia and targets the protease and reverse transcriptase
regions ofHIV-1.Thewell-optimized protocol is sensitive andreproducible for different HIV-1 subtypes and overcomes thelimitations of narrow HIV subtype coverage.
Microbial community composition and diversity of ahost or host-derived sample may be implicated with variousoutcomes including disease status, the spread of pathogens,fermentation profiles in foods, and so on. With the adventof high-throughput sequencing technologies, the resolutionof microbial diagnostics has improved considerably. A vastmajority of nonculturable microbes can be detected by NextGeneration Sequencing (NGS) methods. Additionally, theNGS-metagenomics approach sheds light to shift ofmicrobialcommunity structure andmay reveal changes in the diversityof the constituent microbiota at different taxonomic levels.This information may become important to understanddisease pathology or even identify “biomarker” microbes. L.Cui et al. report the probable association of coronary heartdisease (CHD) with an altered diversity and compositionof gut microbiota. They evaluated the gut microbiome ofCHD patients and compared that with healthy volunteersby using high-throughput sequencing of 16S ribosomal RNAgenes. The results show that the diversity and composi-tion of gut flora were different between CHD patients andhealthy controls. For example, at phylum level Firmicutesand Fusobacteria were found to be higher in CHD patientscompared with the controls. The results of this study suggestthat an alteration of gut microbiota may be associated withthe incidence of CHD.
Survival and persistence of pathogens in the environ-ment may increase the risk of subsequent transmission tohumans.Ascaris lumbricoides is a leading cause of helminthicdiseases globally. The presence of parasitic helminth eggs isan indicator of sanitary risk and water quality. Therefore,rapid and sensitive detection of parasitic helminth egg iscritical for risk assessment of water supply and sanitation.In their article, L. A. Soto et al. describe the applicabilityof two molecular techniques, quantitative PCR (qPCR) anddigital PCR (dPCR), for detection of A. lumbricoides eggs inreclaimed water. The authors also report the development oftwo new DNA extraction protocols for the PCR assays. Theirresults reveal that both qPCR and dPCR can be utilized todetect DNA from A. lumbricoides eggs in reclaimed waterwith the limits of detection of conforming to the WorldHealth Organization’s recommended parameters.
In their paper, A. Abdelazez et al. examined differentfactors affecting survival and activity of Bifidobacteriumspecies in themanufacturing of frozen yogurt under differentconditions. They also evaluated the effect of storage temper-atures on their viability in frozen yogurt, physicochemical,rheological, and the sensory parameters of the product.The results of this study show that the Bifidobacterium spp.can grow well in simulated intestinal conditions and canbe used to manufacture frozen yogurt with this probioticbacteria. They also demonstrate that the supplementation ofBifidobacterium has no adverse effect on the shelf life, flavor,or compositional characteristics of the frozen yogurt product.
Environmental parameters such as temperature mayaffect the growth, biological, and physiological activities ofmicroorganisms and may also affect their detection. In their
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article, Y. Xu et al. reported the capability of a novel hypother-mia aerobic nitrite-denitrifying bacterium, Pseudomonasputida strain Y-9 (a common inhabitant of long-term floodedpaddy soil), to perform heterotrophic nitrification withammonium and aerobic denitrification with nitrate or nitriteat low temperature (15∘C). According to the results presentedin this study, the denitrification ability of P. putida Y-9 maypotentially be utilized for wastewater treatment to reducenitrogen pollution under cold temperature conditions.
In summary, this editorial provides a snapshot of thearticles published in this special issue. We hope the articlescontained in this special issue will advance our knowledgeand understanding of microbial detection field, and thereaders of this special issue will find some information ofinterest to their respective area of scientific investigations.
Acknowledgments
We extend our sincere thanks to the reviewers for theircontribution to the peer-review process and for providingconstructive critiques.We also express our appreciation to allthe authors for their interest in selecting this special issue asa venue for their scholarly work dissemination.
