The near-quantitative sampling of genomic DNA from various food-borne Eubacteria

A retrospective study of the detection of sepsis pathogens comparing blood culture and culture-independent digital PCR

Fast and precise identification of microorganisms in the early diagnosis of sepsis is crucial for enhancing patient outcomes. Digital PCR (dPCR) is a highly sensitive approach for absolute quantification that can be utilized as a culture-independent molecular technique for diagnosing sepsis pathogens. We performed a retrospective investigation on 69 ICU patients suspected of sepsis. Our findings showed that a multiplex dPCR diagnostic kit outperformed blood culture in detecting the 15 most frequent bacteria that cause sepsis. Ninety-two bacterial strains were identified using dPCR at concentrations varying from 34 copies/mL to 105,800 copies/mL. The detection rate of dPCR was much greater than that of BC, with 27.53% (19/69) versus 73.91% (51/69). The sensitivity of dPCR was 63.2%. Our research indicated that dPCR outperforms blood culture in the early detection of sepsis-causing microorganisms. The diagnostic kit can detect a greater variety of pathogens with quantitative data, including polymicrobial infections, and has a quicker processing time. DPCR is a valuable technique that could aid in the proper management of sepsis.

Validation of a Metagenomic Next-Generation Sequencing Assay for Lower Respiratory Pathogen Detection

Lower respiratory infection (LRI) is the most fatal communicable disease, with only a few pathogens identified. Metagenomic next-generation sequencing (mNGS), as an unbiased, hypothesis-free, and culture-independent method, theoretically enables the detection of all pathogens in a single test. In this study, we developed and validated a DNA-based mNGS method for the diagnosis of LRIs from bronchoalveolar lavage fluid (BALF). We prepared simulated in silico data sets and published raw data sets from patients to evaluate the performance of our in-house bioinformatics pipeline and compared it with the popular metagenomics pipeline Kraken2-Bracken. In addition, a series of biological microbial communities were used to comprehensively validate the performance of our mNGS assay. Sixty-nine clinical BALF samples were used for clinical validation to determine the accuracy. The in-house bioinformatics pipeline validation showed a recall of 88.03%, precision of 99.14%, and F1 score of 92.26% via single-genome simulated data. Mock in silico microbial community and clinical metagenomic data showed that the in-house pipeline has a stricter cutoff value than Kraken2-Bracken, which could prevent false-positive detection by the bioinformatics pipeline. The validation for the whole mNGS pipeline revealed that overwhelming human DNA, long-term storage at 4°C, and repeated freezing-thawing reduced the analytical sensitivity of the assay. The mNGS assay showed a sensitivity of 95.18% and specificity of 91.30% for pathogen detection from BALF samples. This study comprehensively demonstrated the analytical performance of this laboratory-developed mNGS assay for pathogen detection from BALF, which contributed to the standardization of this technology. IMPORTANCE To our knowledge, this study is the first to comprehensively validate the mNGS assay for the diagnosis of LRIs from BALF. This study exhibited a ready-made example for clinical laboratories to prepare reference materials and develop comprehensive validation schemes for their in-house mNGS assays, which would accelerate the standardization of mNGS testing.

Detection of virulence and extended spectrum β-lactamase genes in Salmonella by multiplex high-resolution melt curve real-time PCR assay

AIMS

Develop and standardize multiplex high-resolution melt curve (HRM) real-time PCR assays for simultaneous detection of Salmonella virulence and extended spectrum β-lactamase (ESBL) genes in food.

METHODS AND RESULTS

Two sets of multiplex real-time PCR assays targeting six virulence and three ESBL genes with internal amplification control were standardized. The first assay detected hilA, fimH, sipA, bla_TEM and bla_SHV, and the second detected invA, fimA, stn and bla_CMY . The PCR assays were validated with DNA samples from 77 different Salmonella strains. The assay specificity was tested with DNA from 47 non-Salmonella strains. Melt curve analyses showed distinct, well-separated melting peaks of each target gene detected by their respective melting temperatures (T_m ). Different food samples were spiked with 10, 10² and 10³  CFU/ml of Salmonella. The optimized assays were able to detect all target genes in concentrations of as low as 10 CFU/ml in 25 g foods within 10 h of enrichment.

CONCLUSIONS

Multiplex HRM real-time PCR assays can be used as rapid detection methods for detecting Salmonella in foods.

SIGNIFICANCE AND IMPACT OF STUDY

The assays developed in this study will allow for accurate detection of virulence and ESBL genes in Salmonella that are present in low concentrations in food samples.

The complex multicellular morphology of the food spoilage bacteria Brochothrix thermosphacta strains isolated from ground chicken

Herein we describe a highly structured, filamentous growth phenotype displayed by an isolate of the food spoilage microorganism Brochothrix thermosphacta. The growth morphology of this B. thermosphacta strain (strain BII) was dependent on environmental factors such as the growth media, incubation temperatures, and the inoculum concentration. Inoculation of cultures in highly dilute suspensions resulted in the formation of isolated, tight aggregates resembling fungal growth in liquid media. This same strain also formed stable, mesh-like structures in 6-well tissue culture plates under specific growth conditions. The complex growth phenotype does not appear to be unique to strain BII but was common among B. thermosphacta strains isolated from chicken. Light and electron micrographs showed that the filaments of multiple BII cells can organize into complex, tertiary structures resembling multistranded cables. Time-lapse microscopy was employed to monitor the development of such aggregates over 18 h and revealed growth originating from short filaments into compact ball-like clusters that appeared fuzzy due to protruding filaments or cables. This report is the first to document this complex filamentous growth phenotype in a wild-type bacterial isolate of B. thermosphacta.

Offline Next Generation Metagenomics Sequence Analysis Using MinION Detection Software (MINDS)

Field laboratories interested in using the MinION often need the internet to perform sample analysis. Thus, the lack of internet connectivity in resource-limited or remote locations renders downstream analysis problematic, resulting in a lack of sample identification in the field. Due to this dependency, field samples are generally transported back to the lab for analysis where internet availability for downstream analysis is available. These logistics problems and the time lost in sample characterization and identification, pose a significant problem for field scientists. To address this limitation, we have developed a stand-alone data analysis packet using open source tools developed by the Nanopore community that does not depend on internet availability. Like Oxford Nanopore Technologies’ (ONT) cloud-based What’s In My Pot (WIMP) software, we developed the offline MinION Detection Software (MINDS) based on the Centrifuge classification engine for rapid species identification. Several online bioinformatics applications have been developed surrounding ONT’s framework for analysis of long reads. We have developed and evaluated an offline real time classification application pipeline using open source tools developed by the Nanopore community that does not depend on internet availability. Our application has been tested on ATCC’s 20 strain even mix whole cell (ATCC MSA-2002) sample. Using the Rapid Sequencing Kit (SQK-RAD004), we were able to identify all 20 organisms at species level. The analysis was performed in 15 min using a Dell Precision 7720 laptop. Our offline downstream bioinformatics application provides a cost-effective option as well as quick turn-around time when analyzing samples in the field, thus enabling researchers to fully utilize ONT’s MinION portability, ease-of-use, and identification capability in remote locations.

Complete Genome Sequences of Two Strains of the Meat Spoilage Bacterium Brochothrix thermosphacta Isolated from Ground Chicken

Brochothrix thermosphacta is an important meat spoilage bacterium. Here we report the genome sequences of two strains of B. thermosphacta isolated from ground chicken. The genome sequences were determined using long-read PacBio single-molecule real-time (SMRT) technology and are the first complete genome sequences reported for B. thermosphacta.

Nucleic Acid Extraction from Synthetic Mars Analog Soils for in situ Life Detection

Biological informational polymers such as nucleic acids have the potential to provide unambiguous evidence of life beyond Earth. To this end, we are developing an automated in situ life-detection instrument that integrates nucleic acid extraction and nanopore sequencing: the Search for Extra-Terrestrial Genomes (SETG) instrument. Our goal is to isolate and determine the sequence of nucleic acids from extant or preserved life on Mars, if, for example, there is common ancestry to life on Mars and Earth. As is true of metagenomic analysis of terrestrial environmental samples, the SETG instrument must isolate nucleic acids from crude samples and then determine the DNA sequence of the unknown nucleic acids. Our initial DNA extraction experiments resulted in low to undetectable amounts of DNA due to soil chemistry-dependent soil-DNA interactions, namely adsorption to mineral surfaces, binding to divalent/trivalent cations, destruction by iron redox cycling, and acidic conditions. Subsequently, we developed soil-specific extraction protocols that increase DNA yields through a combination of desalting, utilization of competitive binders, and promotion of anaerobic conditions. Our results suggest that a combination of desalting and utilizing competitive binders may establish a "universal" nucleic acid extraction protocol suitable for analyzing samples from diverse soils on Mars. Key Words: Life-detection instruments-Nucleic acids-Mars-Panspermia. Astrobiology 17, 747-760.

Microbial community responses to soil tillage and crop rotation in a corn/soybean agroecosystem

The acreage planted in corn and soybean crops is vast, and these crops contribute substantially to the world economy. The agricultural practices employed for farming these crops have major effects on ecosystem health at a worldwide scale. The microbial communities living in agricultural soils significantly contribute to nutrient uptake and cycling and can have both positive and negative impacts on the crops growing with them. In this study, we examined the impact of the crop planted and soil tillage on nutrient levels, microbial communities, and the biochemical pathways present in the soil. We found that farming practice, that is conventional tillage versus no‐till, had a much greater impact on nearly everything measured compared to the crop planted. No‐till fields tended to have higher nutrient levels and distinct microbial communities. Moreover, no‐till fields had more DNA sequences associated with key nitrogen cycle processes, suggesting that the microbial communities were more active in cycling nitrogen. Our results indicate that tilling of agricultural soil may magnify the degree of nutrient waste and runoff by altering nutrient cycles through changes to microbial communities. Currently, a minority of acreage is maintained without tillage despite clear benefits to soil nutrient levels, and a decrease in nutrient runoff—both of which have ecosystem‐level effects and both direct and indirect effects on humans and other organisms.