Evaluation of MinION nanopore sequencing for rapid enterovirus genotyping

Application of Nanopore Sequencing in the Detection of Foodborne Microorganisms

Foodborne pathogens have become the subject of intense interest because of their high incidence and mortality worldwide. In the past few decades, people have developed many methods to solve this challenge. At present, methods such as traditional microbial culture methods, nucleic acid or protein-based pathogen detection methods, and whole-genome analysis are widely used in the detection of pathogenic microorganisms in food. However, these methods are limited by time-consuming, cumbersome operations or high costs. The development of nanopore sequencing technology offers the possibility to address these shortcomings. Nanopore sequencing, a third-generation technology, has the advantages of simple operation, high sensitivity, real-time sequencing, and low turnaround time. It can be widely used in the rapid detection and serotyping of foodborne pathogens. This review article discusses foodborne diseases, the principle of nanopore sequencing technology, the application of nanopore sequencing technology in foodborne pathogens detection, as well as its development prospects.

Nanopore Amplicon Sequencing Reveals Molecular Convergence and Local Adaptation of Rhodopsin in Great Lakes Salmonids

Local adaptation can drive diversification of closely related species across environmental gradients and promote convergence of distantly related taxa that experience similar conditions. We examined a potential case of adaptation to novel visual environments in a species flock (Great Lakes salmonids, genus Coregonus) using a new amplicon genotyping protocol on the Oxford Nanopore Flongle and MinION. We sequenced five visual opsin genes for individuals of Coregonus artedi, Coregonus hoyi, Coregonus kiyi, and Coregonus zenithicus. Comparisons revealed species-specific differences in a key spectral tuning amino acid in rhodopsin (Tyr261Phe substitution), suggesting local adaptation of C. kiyi to the blue-shifted depths of Lake Superior. Ancestral state reconstruction demonstrates that parallel evolution and "toggling" at this amino acid residue has occurred several times across the fish tree of life, resulting in identical changes to the visual systems of distantly related taxa across replicated environmental gradients. Our results suggest that ecological differences and local adaptation to distinct visual environments are strong drivers of both evolutionary parallelism and diversification.

From the Pipeline to the Bedside: Advances and Challenges in Clinical Metagenomics

Next-generation sequencing (NGS) technologies have revolutionized multiple areas in the field of infectious diseases, from pathogen discovery to characterization of genes mediating drug resistance. Consequently, there is much anticipation that NGS technologies may be harnessed in the realm of diagnostic methods to complement or replace current culture-based and molecular microbiologic techniques. In this context, much consideration has been given to hypothesis-free, culture-independent tests that can be performed directly on primary clinical samples. The closest realizations of such universal diagnostic methods achieved to date are based on targeted amplicon and unbiased metagenomic shotgun NGS approaches. Depending on the exact details of implementation and analysis, these approaches have the potential to detect viruses, bacteria, fungi, parasites, and archaea, including organisms that were previously undiscovered and those that are uncultivatable. Shotgun metagenomics approaches additionally can provide information on the presence of virulence and resistance genetic elements. While many limitations to the use of NGS in clinical microbiology laboratories are being overcome with decreasing technology costs, expanding curated pathogen sequence databases, and better data analysis tools, there remain many challenges to the routine use and implementation of these methods. This review summarizes recent advances in applications of targeted amplicon and shotgun-based metagenomics approaches to infectious disease diagnostic methods. Technical and conceptual challenges are considered, along with expectations for future applications of these techniques.

Metagenomic water quality monitoring with a portable laboratory

We describe the technical feasibility of metagenomic water quality analysis using only portable equipment, for example mini-vacuum pumps and filtration units, mini-centrifuges, mini-PCR machines and the memory-stick sized MinION of Oxford Nanopore Technologies, for the library preparation and sequencing of 16S rRNA gene amplicons. Using this portable toolbox on site, we successfully characterized the microbiome of water samples collected from Birtley Sewage Treatment Plant, UK, and its environs. We also demonstrated the applicability of the portable metagenomics toolbox in a low-income country by surveying water samples from the Akaki River around Addis Ababa, Ethiopia. The 16S rRNA gene sequencing workflow, including DNA extraction, PCR amplification, sequencing library preparation, and sequencing was accomplished within one working day. The metagenomic data became available within 24-72 h, depending on internet speed. Metagenomic analysis clearly distinguished the microbiome of pristine samples from sewage influenced water samples. Metagenomic analysis identified the potential role of two bacterial genera not conventionally monitored, Arcobacter and Aeromonas, as predominant faecal pollution indicators/waterborne hazards. Subsequent quantitative PCR analysis validated the high Arcobacter butzleri abundances observed in the urban influenced Akaki River water samples by portable next generation sequencing with the MinION device. Overall, our field deployable metagenomics toolbox advances the capability of scientists to comprehensively monitor microbiomes anywhere in the world, including in the water, food and drinks industries, the health services, agriculture and beyond.

Rapid and Sensitive Direct Detection and Identification of Poliovirus from Stool and Environmental Surveillance Samples by Use of Nanopore Sequencing

Global poliovirus surveillance involves virus isolation from stool and environmental samples, intratypic differential (ITD) by PCR, and sequencing of the VP1 region to distinguish vaccine (Sabin), vaccine-derived, and wild-type polioviruses and to ensure an appropriate response. This cell culture algorithm takes 2 to 3 weeks on average between sample receipt and sequencing. Direct detection of viral RNA using PCR allows faster detection but has traditionally faced challenges related to poor sensitivity and difficulties in sequencing common samples containing poliovirus and enterovirus mixtures.

Global poliovirus surveillance involves virus isolation from stool and environmental samples, intratypic differential (ITD) by PCR, and sequencing of the VP1 region to distinguish vaccine (Sabin), vaccine-derived, and wild-type polioviruses and to ensure an appropriate response. This cell culture algorithm takes 2 to 3 weeks on average between sample receipt and sequencing. Direct detection of viral RNA using PCR allows faster detection but has traditionally faced challenges related to poor sensitivity and difficulties in sequencing common samples containing poliovirus and enterovirus mixtures. We present a nested PCR and nanopore sequencing protocol that allows rapid (<3 days) and sensitive direct detection and sequencing of polioviruses in stool and environmental samples. We developed barcoded primers and a real-time analysis platform that generate accurate VP1 consensus sequences from multiplexed samples. The sensitivity and specificity of our protocol compared with those of cell culture were 90.9% (95% confidence interval, 75.7% to 98.1%) and 99.2% (95.5% to 100.0%) for wild-type 1 poliovirus, 92.5% (79.6% to 98.4%) and 98.7% (95.4% to 99.8%) for vaccine and vaccine-derived serotype 2 poliovirus, and 88.3% (81.2% to 93.5%) and 93.2% (88.6% to 96.3%) for Sabin 1 and 3 poliovirus alone or in mixtures when tested on 155 stool samples in Pakistan. Variant analysis of sequencing reads also allowed the identification of polioviruses and enteroviruses in artificial mixtures and was able to distinguish complex mixtures of polioviruses in environmental samples. The median identity of consensus nanopore sequences with Sanger or Illumina sequences from the same samples was >99.9%. This novel method shows promise as a faster and safer alternative to cell culture for the detection and real-time sequencing of polioviruses in stool and environmental samples.

First genomic characterization of a Belgian Enterovirus C104 using sequence-independent Nanopore sequencing

Because of the enormous variation in their genome sequence, genotyping enteroviruses by standard methods can prove to be quite challenging. Nanopore sequencing offers the potential to overcome the limitations of older techniques, but thus far, only amplicon-based strategies have been used to sequence complete enterovirus genomes. By combining a sequence-independent, single primer amplification (SISPA) for cDNA generation with next-generation sequencing using the Oxford Nanopore MinION, complete enterovirus genomes can be obtained in an easy-to-use, sequence-independent manner. To demonstrate its usability, we applied this technique to determine the complete genome sequence of an enterovirus C104 strain, representing the first documented occurrence of this uncommon enterovirus strain in Belgium.

Evaluation of a portable nanopore-based sequencer for detection of viruses in water

The newly emerged nanopore sequencing technology such as MinION™ allows for real-time detection of long DNA/RNA fragments on a portable device, yet few have examined its performance for environmental viromes. Here we seeded one RNA virus bacteriophage MS2 and one DNA virus bacteriophage PhiX174 into 10 L well water at three levels ranging from 1 to 21,100 plaque-forming units (PFU)/mL. Two workflows were established to maximize the number of sequencing reads of RNA and DNA viruses using MinION™. With dead-end ultrafiltration, PEG precipitation, and random amplification, MinION™ was capable of detecting MS2 at 155 PFU/mL and PhiX174 at 1-2 PFU/mL. While the DNA workflow only detected PhiX174, the RNA workflow detected both MS2 and PhiX174. The virus concentration, or relative abundance of viral nucleic acids in total nucleic acids, is critical to the proportion of viral reads in sequencing results. Our findings also highlight the importance of including control samples in sequencing runs for environmental water samples with low virus abundance.

A comparative assessment of conventional and molecular methods, including MinION nanopore sequencing, for surveying water quality

Nucleic acid based techniques, such as quantitative PCR (qPCR) and next generation sequencing (NGS), provide new insights into microbial water quality, but considerable uncertainty remains around their correct interpretation. We demonstrate, for different water sources in informal settlements in the Kathmandu Valley, Nepal, significant Spearman rank correlations between conventional and molecular microbiology methods that indicate faecal contamination. At family and genera level, 16S rRNA amplicon sequencing results obtained with the low-cost, portable next generation sequencer MinION from Oxford Nanopore Technologies had significant Spearman rank correlations with Illumina MiSeq sequencing results. However, method validation by amplicon sequencing of a MOCK microbial community revealed the need to ascertain MinION sequencing results for putative pathogens at species level with complementary qPCR assays. Vibrio cholerae hazards were poorly associated with plate count faecal coliforms, but flagged up by the MinION screening method, and confirmed by a qPCR assay. Plate counting methods remain important to assess viability of faecal coliforms in disinfected water sources. We outline a systematic approach for data collection and interpretation of such complementary results. In the Kathmandu Valley, there is high variability of water quality from different sources, including for treated water samples, illustrating the importance of disinfection at the point of use.

A comparative assessment of conventional and molecular methods, including MinION nanopore sequencing, for surveying water quality

Nucleic acid based techniques, such as quantitative PCR (qPCR) and next generation sequencing (NGS), provide new insights into microbial water quality, but considerable uncertainty remains around their correct interpretation. We demonstrate, for different water sources in informal settlements in the Kathmandu Valley, Nepal, significant Spearman rank correlations between conventional and molecular microbiology methods that indicate faecal contamination. At family and genera level, 16S rRNA amplicon sequencing results obtained with the low-cost, portable next generation sequencer MinION from Oxford Nanopore Technologies had significant Spearman rank correlations with Illumina MiSeq sequencing results. However, method validation by amplicon sequencing of a MOCK microbial community revealed the need to ascertain MinION sequencing results for putative pathogens at species level with complementary qPCR assays. Vibrio cholerae hazards were poorly associated with plate count faecal coliforms, but flagged up by the MinION screening method, and confirmed by a qPCR assay. Plate counting methods remain important to assess viability of faecal coliforms in disinfected water sources. We outline a systematic approach for data collection and interpretation of such complementary results. In the Kathmandu Valley, there is high variability of water quality from different sources, including for treated water samples, illustrating the importance of disinfection at the point of use.

Increasing the accuracy of nanopore DNA sequencing using a time-varying cross membrane voltage

Nanopore DNA sequencing is limited by low base-calling accuracy. Improved base-calling accuracy has so far relied on specialized base-calling algorithms, different nanopores and motor enzymes, or biochemical methods to re-read DNA molecules. Two primary error modes hamper sequencing accuracy: enzyme mis-steps and sequences with indistinguishable signals. We vary the driving voltage from 100 to 200 mV, with a frequency of 200 Hz, across a Mycobacterium smegmatis porin A (MspA) nanopore, thus changing how the DNA strand moves through the nanopore. A DNA helicase moves the DNA through the nanopore in discrete steps, and the variable voltage moves the DNA continuously between these steps. The electronic signal produced with variable voltage is used to overcome the primary error modes in base calling. We found that single-passage de novo base-calling accuracy of 62.7 ± 0.5% with a constant driving voltage improves to 79.3 ± 0.3% with a variable driving voltage. The variable-voltage sequencing mode is complementary to other methods to boost the accuracy of nanopore sequencing and could be incorporated into any enzyme-actuated nanopore sequencing device.

MinION sequencing to genotype US strains of infectious laryngotracheitis virus

Over the last decade the US broiler industry has fought long-lasting outbreaks of infectious laryngotracheitis (ILTV). Previously, nine genotypes (I-IX) of ILTVs have been recognized using the polymerase chain reaction-restriction fragment length polymorphisms (PCR-RFLP) method with three viral alleles (gB, gM and UL47/gG). In this study, the genotyping system was simplified to six genotypes by amplicon sequencing and examining discriminating single nucleotide polymorphisms (SNPs) within these open reading frames. Using phylogenomic analysis of 27 full genomes of ILTV, a single allele (ORF A/ORF B) was identified containing SNPs that could differentiate ILTVs into genotypes congruent with the phylogenetic partitioning. The allelic variations allowed for the cataloging of the 27 strains into 5 genotypes: vaccinal TCO, vaccinal CEO, virulent CEO-like, virulent US and virulent US backyard flocks from 1980 to 1990, correlating with the PCR-RFLP genotypes I/ II/ III (TCO), IV (CEO), V (virulent CEO-like), VI (virulent US) and VII/VIII/IX (virulent US backyard flock isolates). With the unique capabilities of third generation sequencing, we investigated the application of Oxford Nanopore MinION technology for rapid sequencing of the amplicons generated in the single-allele assay. This technology was an improvement over Sanger-based sequencing of the single allele amplicons due to a booster amplification step in the MinION sequencing protocol. Overall, there was a 90% correlation between the genotyping results of the single-allele assay and the multi-allele assay. Surveillance of emerging ILTV strains could greatly benefit from real-time amplicon sequencing using the single-allele assay and MinION sequencing. RESEARCH HIGHLIGHTS A multi-allelic assay identified nine ILTV genotypes circulating in the US Single-allele genotyping is congruent with whole genome phylogenetic partitioning US ILTV strains can be grouped into five genotypes using the single-allele assay The single-allele assay can be done using MinION sequencing of barcoded amplicons.