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[bamboo2] 15/7/2024 19:26

Nanopore sequencing demonstrates identification of antibiotic-resistant pathogens hidden to traditional methods in new study

Rapid and accurate antibiotic resistance profiling with Oxford Nanopore sequencing demonstrates potential for clinical impact.

A new study published in Nature Communications has demonstrated the ability of real-time nanopore sequencing in identifying the antibiotic resistance of pathogens hidden to standard traditional methods, such as MALDI-TOF MS and VITEK 2, showcasing the potential for rapid nanopore sequencing to characterise drug resistant infections in a hospital setting.

Rosemary Sinclair Dokos, SVP for Product and Programme Management at Oxford Nanopore Technologies, said that the study “highlights the potential of real-time genomic technology to significantly enhance our understanding of antibiotic resistance,” adding, “by providing rapid and detailed insights, this technology has the potential to support timely and informed decision-making, and could lead to better outcomes in infectious disease and improved public health strategies."

The research, led by Ela Sauerborn under the supervision of Dr. Lara Urban and her team at Helmholtz Center Munich, was conducted in a research hospital and demonstrates how real-time genomics can offer rapid, precise insights that traditional methods might miss.

Antibiotic resistance is recognised as one of the top ten global health threats, increasing mortality and morbidity due to delayed or inappropriate therapy. The study emphasises the urgent need for rapid and accurate pathogen identification to combat this issue effectively. In terms of speed, the study showcases equivalence of nanopore sequencing to traditional methods. However, the biggest differentiator is that, within a similar timeframe to VITEK 2 and MALDI-TOF MS, real-time genomics uncovered plasmid-encoded resistance genes that these methods missed - identification of which is crucial for timely and appropriate therapy.

This point was demonstrated in a case study by Dr. Urban’s team that focused on a multi-drug resistant Klebsiella pneumoniae infection. This strain of bacteria has developed antibiotic resistance in some cases, and a decision was made to change antibiotic treatment from Meropenem to Ceftazidime-Avibactam (CAZ-AVI), the latter being recommended given the strain’s susceptibility to CAZ-AVI. However, traditional methods were unable to detect that the Klebsiella pneumoniae infection had developed resistance to CAZ-AVI itself.

In a recreation of the case study, Dr. Urban’s team used nanopore sequencing to accurately identify the presence of KPC-14 resistance genes, predicting antibiotic resistance accurately as opposed to established clinical diagnostics. This demonstrated that nanopore sequencing could have unveiled the CAZ-AVI resistance that other methods failed to detect, thereby influencing the therapeutic approach, such as the early administration of alternative antibiotics or combination therapy and potentially leading to positive outcomes. Further, this approach is cost-effective and suitable for global application in every clinical microbiology setting, while the accessibility of the platform enables low- and middle-income settings to adopt real-time genomic tools, particularly where there are barriers to the use of standard diagnostic machinery.

Dr. Lara Urban commented, "The fast, adaptive, and in situ nature of antibiotic resistance profiling by nanopore sequencing would have surpassed current clinical practice in accurately informing clinical management."

The study was conducted in collaboration with esteemed institutions, including the Technical University of Munich, Helmholtz Zentrum München, and the European Molecular Biology Laboratory European Bioinformatics Institute. This partnership underscores the global effort to advance genomic research and combat antibiotic resistance through innovative technology.

For more details, please visit the full study published in Nature Communications.


First author Ela Sauerborn will be discussing this research at the Nanopore Community Meeting 2024: Boston this September

[bamboo2] 08/7/2024 19:54

Nanopore is currently being installed in around 10 NHS hospitals as an extension of the original 2/3yr trial at Guys and St. Thomas' in London.

The workflow has been updated so that a single 'assay' can determine from a single sample, between different bacterial, fungal and virial infections. First reports are available in a little as 30mins.

It is the clinical market that will lead to a massive expansion in turnover.

"We are approaching the holy grail of infectious diseases diagnostics."

Clinicians in Sweden, New Zealand, Australia, France and the US are also working on various forms of ONT based diagnostics.

Plain language summary

Metagenomics is the analysis of genetic material from microbes such as bacteria and viruses in a sample. There are limitations with existing metagenomics methods, such as not being able to detect the full range of microbes present in a sample. This paper introduces an approach that identifies multiple types of microbes. This is accomplished through the mechanical disruption of human cells, which allows for an effective depletion of human genetic material. Our method demonstrates encouraging preliminary results within a 7 h process, achieving good sensitivity for the detection of bacteria and viruses. We demonstrate the identification of relevant microbes in samples from patients with respiratory infections. This technique holds promise for adoption in clinical settings, potentially enhancing our ability to diagnose respiratory infections quickly.

[kooba] 08/7/2024 08:59

The Times: The chief executive of Oxford Nanopore has warned that Britain's most promising companies will be 'snapped up' in takeovers or will move their listings to New York unless the new Labour government accelerates financial reforms begun under the Conservatives.

[ih_828197] 05/7/2024 16:05

Imo they are gonna disrupt ILMN just like AMD disrupted Intel.

[mszmu] 05/7/2024 12:15

rec2204 Jul '24 - 10:06 - 1474 of 1474

Why?

[ih_828197] 04/7/2024 10:06

the tide is turning if earnings and guidance are good this will see 200p in the short term, long term i truly believe ONT is a 100B company in the making, it feels like investing in AMD in 2014

[csalvage] 04/7/2024 09:51

Berenberg cuts Oxford Nanopore price target to 282 (350) pence - 'buy'

[bamboo2] 03/7/2024 16:24

Sequencing for a new generation.

With Apple silicon and Oxford Nanopore, sequencing becomes not just powerful but also more globally accessible...

[eeza] 28/6/2024 10:31

Circling the plughole, again.

[steeplejack] 27/6/2024 17:34

Chunky seller has been overhanging the price by all accounts rather than some prop. trader.Maybe the seller is finished.

[steeplejack] 26/6/2024 13:53

This has got the feel of a second liner being tossed hither and thither by some proprietary book looking to make his daily beer money.By the end of the year,the stock should garner greater respect for the various reasons mentioned previously.

It’s a far cry from those heady floatation days three years back.Another casualty of the ‘irrational exuberance’ that surrounded so many covid plays that benefitted,but were then subsequently plagued, by post covid rating trauma!

“Nanopore, a spin-off from Oxford University whose handheld genome-sequencing devices are being used to track emerging Covid-19 strains, launched with a value of £3.4 billion from shares priced at 425p.

Within an hour, the stock soared to 619.9p lifting its market cap to within a shade of £5 billion - double the implied valuation from a funding round in May.”

[seball] 26/6/2024 08:07

Almost half of Mcap is Cash. This drop is over done Price target £1.60 and some even higher.

On Monday, Barclays (LON:BARC) adjusted its price target on shares of Oxford Nanopore Technologies (ONT:LN) (OTC: ONTTF), reducing it to GBP1.60 from GBP1.85, while maintaining an Overweight rating on the stock. The revision reflects the firm's outlook for the company in light of recent market conditions and operational strategies.

The company faced challenges in the last two quarters, which have been a period of assessment for many firms in the sector. Despite these hurdles, Barclays anticipates some sequential improvements in Oxford Nanopore's end markets.

Oxford Nanopore's revenue composition is expected to be more heavily weighted towards the second half of the year. This projection is supported by several factors including new product launches, increased utilization of the company's offerings, and the timing of larger projects that are in the pipeline.

The firm highlights Oxford Nanopore's capital expenditure-light business model as a distinctive advantage. This approach could potentially set the company apart from competitors in the biotechnology and genomics industry, which often require significant upfront investments.

In summary, while the price target has been lowered, the Overweight rating suggests that Barclays continues to see Oxford Nanopore as a favorable investment, with positive developments anticipated in the latter half of the year.

[takeiteasy] 26/6/2024 07:56

There is no sign of things letting up if you even track just the last month - PACB being hurt equally atm. I cannot see any way to pick a specific share price just yet with any sense of certainty and think the rot share price drop wise will stop at this point.

[p1nkfish] 26/6/2024 07:44

Across the board.

[takeiteasy] 26/6/2024 06:13

I suggest that ONT must regret ever listing on such a dysfunctional UK stock exchange - yes agreed. But the other two are US listed so maybe a wider sector derating is going on atm?

[steeplejack] 24/6/2024 20:54

Yes technicals can be all important.Take Bitcoin.Strip away all the waffle about blockchain and in reality the movement of bitcoin is no more than a function of the weight of buyers and sellers and that is what chartism monitors.In the absence of meaningful functional research,the technicals are paramount.Looking at the ONT chart who can meaningfully predict the bottom with past apparent support levels being breached again and again.I suppose at some juncture,they’ll be press comment,bid rumour and things will turn but i suggest that ONT must regret ever listing on such a dysfunctional UK stock exchange.

[brucie5] 24/6/2024 18:49

Was always on the cards when 90p went. Now a question of how low, before it recovers. Yes, I'm afraid technicals are important.

[steeplejack] 24/6/2024 17:15

Well,luckily i have just put a very small toe in the water here but frankly,i can’t be bothered to make head or tail of this price collapse and buy more until there’s greater clarity.Looks like this is moved by technical analysis rather than fundamentals.The management who bought stock back in early March around 127p must be a wee bit bemused. i’m increasingly reluctant to buy UK stocks nowadays in any meaningful size and frankly wouldn’t bother at all if i wasn’t domiciled in the UK …..and born here…old habits die hard.

[seball] 24/6/2024 14:27

This is going to bounce as oversold, buyers will start to out number sellers. over £400m in cash. Those able to hold for the next few months on run up to October will be handsomely rewarded imo. Good luck all

[brucie5] 24/6/2024 10:45

Indeed. But I tend to think the second test of the 90 threshold is more telling.Last time it was in the 90s I bought quite heavily on hunch of likely support and sold in the 100s when momentum evaporated.

[steeplejack] 24/6/2024 09:31

I wouldn't read too much into the price movements of an esoteric second liner like ONT.the UK market remains in a malaise and the analytical coverage of companies like Oxford Nanophore remains anaemic.Namesake Oxford Biomedica provides a reasonable template i suspect.Slumping as low as 170p a few months back,the stock has now recovered to around 320p.As we move into the Autumn,bid speculation should see the stock begin to recover but for now its disinterest rather than insight that is depressing this stock.

[brucie5] 24/6/2024 08:52

Retesting historic support for the second time. Odd perhaps given imminent aforementioned discussion of LAT shares?

[bamboo2] 24/6/2024 08:08

An Analytical Eye on mRNA

How a new collaboration looks to improve analytical testing for mRNA products

[dawneyd] 21/6/2024 14:01

Thank you for doing that bamboo2, good to have it confirmed.
Now hoping for good news in the update next month.