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Archive for category: Editors’ Picks

Editors’ Picks

In major breakthrough, scientists complete first gapless sequence of a human genome, reveal hidden regions

, 1 April 2022/in Editors' Picks, Featured Articles /by panglobal
Karen Miga

Karen Miga, assistant professor of biomolecular engineering at UC Santa Cruz, co-led the Telomere-to-Telomere (T2T) Consortium, which has released the first complete, gapless assembly of a human genome sequence. (Photo by Carolyn Lagattuta)

 

The first truly complete sequence of a human genome, covering each chromosome from end to end with no gaps and unprecedented accuracy, is now accessible through the UCSC Genome Browser and is described in six papers published March 31 in Science.

Since the first working draft of a human genome sequence was assembled at UC Santa Cruz in 2000, genomics research has led to enormous advances in our understanding of human biology and disease. Nevertheless, crucial regions accounting for some 8% of the human genome have remained hidden from scientists for over 20 years due to the limitations of DNA sequencing technologies.

“Ever since we had the first draft human genome sequence, determining the exact sequence of complex genomic regions has been challenging,” said Evan Eichler, Ph.D., researcher at the University of Washington School of Medicine and T2T consortium co-chair. “I am thrilled that we got the job done. The complete blueprint is going to revolutionize the way we think about human genomic variation, disease and evolution.”

Telomere-to-Telomere Consortium

The sequencing and analysis were performed by a team of more than 100 people, the so-called Telemere-to-Telomere Consortium, or T2T, named for the telomeres that cap the ends of all chromosomes. T2T was initially set up in 2019 by Karen Miga, assistant professor of biomolecular engineering at UC Santa Cruz, and Adam Phillippy at the National Human Genome Research Institute (NHGRI).

The consortium’s gapless version of all 22 autosomes and the X sex chromosome is composed of 3.055 billion base pairs, the units from which chromosomes and our genes are built, and 19,969 protein-coding genes.

The new reference genome, called T2T-CHM13, adds nearly 200 million base pairs of novel DNA sequences, including 99 genes likely to code for proteins and nearly 2,000 candidate genes that need further study. It also corrects thousands of structural errors in the current reference sequence.

genetic structure

Complete sequence of a Y chromosome

The researchers also released this week the complete sequence of a Y chromosome from a different source, which took nearly as long to assemble as the rest of the genome combined, said Nicolas Altemose, a postdoctoral fellow at the University of California, Berkeley, and a co-author of four new papers about the completed genome. The analysis of this new Y chromosome sequence will appear in a future publication.

“In the future, when someone has their genome sequenced, we will be able to identify all of the variants in their DNA and use that information to better guide their health care,” said Phillippy, one of the leaders of T2T and a senior investigator at NHGRI. “Truly finishing the human genome sequence was like putting on a new pair of glasses. Now that we can clearly see everything, we are one step closer to understanding what it all means.”

The gaps now filled by the new sequence include the entire short arms of five human chromosomes and cover some of the most complex regions of the genome. These include highly repetitive DNA sequences found in and around important chromosomal structures such as the telomeres at the ends of chromosomes and the centromeres that coordinate the separation of replicated chromosomes during cell division.

New discoveries

The new DNA sequences reveal never-before-seen detail about the region around the centromere. Variability within this region may also provide new evidence of how our human ancestors evolved in Africa.

“Uncovering the complete sequence of these formerly missing regions of the genome told us so much about how they’re organized, which was totally unknown for many chromosomes,” said Altemose. “Before, we just had the blurriest picture of what was there, and now it’s crystal clear down to single base pair resolution.”

The new sequence also reveals previously undetected segmental duplications, long stretches of DNA that are duplicated in the genome and are known to play important roles in evolution and disease.

“These parts of the human genome that we haven’t been able to study for 20-plus years are important to our understanding of how the genome works, genetic diseases, and human diversity and evolution,” Miga said.

Many of the newly revealed regions have important functions in the genome even if they do not include active genes.

human chromosomes

 

What they found in and around the centromeres were layers of new sequences overlaying layers of older sequences, as if through evolution new centromere regions have been laid down repeatedly to bind to the kinetochore. The older regions are characterized by more random mutations and deletions, indicating they’re no longer used by the cell. The newer sequences where the kinetochore binds are much less variable, and also less methylated. The addition of a methyl group is an epigenetic tag that tends to silence genes.

All of the layers in and around the centromere are composed of repetitive lengths of DNA, based on a unit about 171 base pairs long, which is roughly the length of DNA that wraps around a group of proteins to form a nucleosome, keeping the DNA packaged and compact. These 171 base pair units form even larger repeat structures that are duplicated many times in tandem, building up a large region of repetitive sequences around the centromere.

DNA sequences around the centromere could also be used to trace human lineages back to our common ape ancestors, he noted.

“As you move away from the site of the active centromere, you get more and more degraded sequence, to the point where if you go out to the furthest shores of this sea of repetitive sequences, you start to see the ancient centromere that, perhaps, our distant primate ancestors used to bind to the kinetochore,” Altemose said. “It’s almost like layers of fossils.”

Seeing the whole genome as a complete system for the first time

“There is a profound advantage to seeing the whole genome as a complete system. It puts us in a position to unravel how that system works,” said David Haussler, director of the UC Santa Cruz Genomics Institute. “We’ve gotten an enormous understanding of human biology and disease from having roughly 90 percent of the human genome, but there were many important aspects that lay hidden, out of view of science, because we did not have the technology to read those portions of the genome. Now we can stand at the top of the mountain and see all of the landscape below and get a complete picture of our human genetic heritage.”

The T2T genome sequence, representing the finished CHM13 genome plus the recently finished T2T Y chromosome (CHM13 includes an X but not a Y chromosome), is now a new reference genome in the UCSC Genome Browser. The T2T sequence is fully annotated in the browser, providing an efficient way for scientists to access and visualize a wealth of information associated with genes and other elements of the genome.

“We wanted to put the information out in a way that is accessible and familiar to researchers so they can begin to build on it and use all the tools and resources the browser provides,” Miga explained.

Genome Reference Consortium

The new T2T reference genome will complement the standard human reference genome, known as Genome Reference Consortium build 38 (GRCh38), which had its origins in the publicly funded Human Genome Project and has been continually updated since the first draft in 2000.

“We’re adding a second complete genome, and then there will be more,” explained Haussler. “The next phase is to think about the reference for humanity’s genome as not being a single genome sequence. This is a profound transition, the harbinger of a new era in which we will eventually capture human diversity in an unbiased way.”

Human Pangenome Reference Consortium

The T2T Consortium has now joined with the Human Pangenome Reference Consortium, which aims to create a new “human pangenome reference” based on the complete genome sequences of 350 individuals.

“Pangenomics is about capturing the diversity of the human population, and it’s also about ensuring we’ve captured the whole genome properly,” said Benedict Paten, associate professor of biomolecular engineering at UCSC’s Baskin School of Engineering, a coauthor of the T2T papers, and a leader of the pangenomics effort. “Without having a map of these difficult-to-sequence regions of the genome across multiple individuals, then we’re missing a huge amount of the variation present in our population. T2T sets us up to look across hundreds of genomes from telomere to telomere. It’s going to be great!”

The standard reference genome (GRCh38) does not represent any one individual but was assembled from multiple donors. Merging them into one linear sequence created artificial structures in the sequence. The Human Pangenome Project will make it possible to compare newly sequenced genomes to multiple complete genomes representing a range of human ancestries.

More accurate assessments of genetic variants

An important outcome of the new T2T sequence is enabling more accurate assessments of genetic variants. When human genomes are sequenced for clinical studies to understand the role of genetic variants in disease or to study genetic diversity within and between human populations, they are nearly always analyzed by aligning the sequencing results with the reference genome for comparison. The T2T variant team documented major improvements in identifying and interpreting genetic variants using the new T2T sequence compared to the standard human reference genome.

“The new human genome is incredibly accurate at the base level, allowing us to flag hundreds of thousands of variants that had been misinterpreted by mapping them to the standard reference. Many of these new variants are in genes known to contribute to disease. We can now spot those because we have a more complete and accurate reference genome,” Miga said.

Miga’s research has focused on satellite DNA, the long stretches of repetitive DNA sequences found mostly in and around telomeres and centromeres. The centromeres separate each chromosome into a short arm and a long arm and hold duplicated chromosomes together prior to cell division.

“The centromeres play a critical role in how chromosomes segregate properly during cell division, and we’ve known for some time now that they are misregulated in all kinds of human diseases. But we’ve never been able to study them at the sequence level,” Miga said. “By far the largest portion of new sequences added to the reference are centromere satellite DNAs. For the first time, we can study ‘base-by-base’ the sequences that define the centromere and can start to understand how it works.”

Long-read sequencing a game changer

The T2T’s success is due to improved techniques for sequencing long stretches of DNA at once, which helps when determining the order of highly repetitive stretches of DNA. Among these are PacBio’s HiFi sequencing, which can read lengths of more than 20,000 base pairs with high accuracy. Technology developed by Oxford Nanopore Technologies, on the other hand, can read up to several million base pairs in sequence, though with less fidelity. For comparison, so-called next-generation sequencing by Illumina is limited to hundreds of base pairs.

“These new long-read DNA sequencing technologies are just incredible; they’re such game changers, not only for this repetitive DNA world, but because they allow you to sequence single long molecules of DNA,” Altemose said. “You can begin to ask questions at a level of resolution that just wasn’t possible before, not even with short-read sequencing methods.”

———

Karen Miga

Miga is a co-corresponding author of the main Science paper along with Adam Phillippy at NHGRI and Evan Eichler at the University of Washington:

  • The complete sequence of a human genome

She is also a co-corresponding author of the papers on:

  • Complete genomic and epigenetic maps of human centromeres
  • Epigenetic patterns in a complete human genome

and a coauthor of the papers on:

  • Segmental duplications and their variation in a complete human genome
  • A complete reference genome improves analysis of human genetic variation
  • From telomere to telomere: the transcriptional and epigenetic state of human repeat elements

 

—————-

The t2t working group

https://sites.google.com/ucsc.edu/t2tworkinggroup

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Harald Huber

Interview: International Hospital speaks to PENTAX Medical about their new focus on ‘Power of Choice’

, 15 March 2022/in Editors' Picks, Featured Articles /by panglobal
Harald Huber

Harald Huber, Global VP for Product and Category Management at Pentax Medical

International Hospital’s Twan Heesakkers speaks to Harald Huber, Global VP for Product and Category Management at PENTAX Medical, about the company’s new single-use bronchoscope, what they are focusing on this year and the ‘Power of Choice’.

Twan Heesakkers: What new products are you bringing to the market this year?
Harald Huber: This year we will bring a couple of new things to the market. We would like to put more emphasis on the [PENTAX Medical] ONE Pulmo, by creating more public awareness of the product. The ONE Pulmo is a single-use bronchoscope, our first product in the single-use area. We also have the PlasmaTYPHOON+, our unique solution for endoscope drying and storage, which we will also push forward. Furthermore, we are working very hard on providing innovative solutions, instead of following the traditional way the endoscope business was set up, which was more into products and endoscopic processors. We want to bring our way of thinking forward, which is more focussed on developing solutions rather than pure product business. So we want to interconnect these things, for example the PlasmaTYPHOON+ is part of our hygiene commitment. We are calling this the ‘Power of Choice’. This Power of Choice will also apply to our single-use endoscopes and has a compelling advantage for our customers. The idea behind ‘Power of Choice’ is that we do not want to dictate to our customers what kind of procedure they have to do. We want to allow them the highest possible freedom to pick the right equipment for their procedure. That’s why we want to offer as many solutions as possible in different areas and move away from the traditional thinking about products.

The PENTAX Medical ONE Pulmo

The PENTAX Medical ONE Pulmo single-use bronchoscope.

 

TH: You mentioned the single-use bronchoscope – the PENTAX Medical ONE Pulmo for which you received the CE mark last year? Can you tell us a little more about this product; what sets it apart from similar competitors’ products?

HH: When we came up with this solution we thought, ‘if we, as PENTAX Medical, come up with a single-use bronchoscope how will it be different?’ As you know, our company produces reusable products and everybody will ask, why are we coming up with a single-use bronchoscope? And that’s again in line with our idea of providing the Power of Choice. So the difference, I think, to other single-use bronchoscopes that you see on the market is that this is probably the first one that is purely developed by an endoscope company. So, with our expertise in image development we were able to develop a camera in such a way that on one side its  single-use, while on the other side it can provide comparable image quality to our reusable scopes. This is kind of the red line throughout the whole design process and differentiates us from the competition. It also continues with the design of the control body, with the handle actually. We want to provide a real Power of Choice. Doctors should not have to care if they use the single-use scope or the reusable one. They want to have the same familiar touch and feel that they are used to when doing an endoscopy procedure. That’s why we mimic the reusable scope, so it has the same properties of a reusable scope, and we develop it in such a way that it can be offered as a single-use solution.

PENTAX Medical ONE Pulmo

The PENTAX Medical ONE Pulmo is a single-use bronchoscope with superior suction power and HD image quality. The sterile-packed scopes are ready to use. Manoeuvrability and device insertion are easy and intuitive, creating a seamless user experience.

 

TH: Besides offering the ‘Power of Choice’, what other reasons are behind PENTAX Medical choosing to develop a single-use disposable bronchoscope?

HH: ‘Choice’ is an important factor as to why we did this. The other thing is that there is of course concern about contamination. There are special patient populations where it definitely makes sense to go for a single-use scope. We know that it does not make sense for all patient populations. Also, you have the sustainability factor, you have the cost of cleaning, pricing of the product, etc. There are multiple factors which tell you that single-use doesn’t make sense for all patients. However, it makes sense for a certain population – for example patients who are immunocompromised. Imagine somebody who has a very high health risk if somehow cross infected with a germ that is transmitted during the procedure. For this patient do we go with a reusable cope or will we take a single-use scope? And that’s the doctor’s decision, but what we want to make sure  as a provider/manufacturer  that there is little difference in the choice of scope so the same quality of care can be provided to the patient. Because if you do it the other way around and you are a pure single-use provider you cannot offer this choice.

The PENTAX Medical Video Duodenoscopes ED32-i10

The PENTAX Medical Video Duodenoscopes ED32-i10 and ED34-i10T2 combine a sterile disposable elevator cap (DEC™) for single-patient use and simple disposal that advances cleaning capability of the duodenoscope to help reduce the risk of cross-contamination and improve patient care with High-Definition image quality for detailed endoscopic visualization during ERCP procedures.

 

Distal end of the PENTAX Medical Video Duodenoscope ED32-i10

Distal end of the PENTAX Medical Video Duodenoscope ED32-i10

 

TH: PENTAX Medical is leading the collaborative i-scan imaging processing project. Can you explain what this project is about and the purpose of it.

HH: “i-scan is one part of our general solutions approach. For i-scan there are different modalities which support doctors in each step of the diagnostic process. These i-scan modalities include SE – or Surface Enhancing mode – that improves detection, particularly of the shadowed parts of the lesion. There is TE – or Tone Enhancement – which helps in the characterization of the lesion by amplifying the colours so the doctors understand better what they are seeing and can make an informed medical decision. Then we have OE – or Optical Enhancement – an optical filter which helps in demarcation, to understand the actual size of the lesion in the macule that the doctor sees.

This is an example of how we support doctors each step of the way and that’s part of our solution-driven thinking. We are also involved with many physicians for the i-scan project all across Europe and some parts from the US. They add to the project by sharing their insights on how they can benefit from i-scan in their medical procedures. We also use this as part of our learning initiative. Whenever they have tricky images they have identified, they bring them to a forum where they can be discussed.

TH: PENTAX Medical has developed their own data management and software solutions for their medical imaging devices. Can you tell us more about these solutions?

HH: We are deprioritizing data management and hospital software solutions. We are now more focussed on a solutions approach by combining our products and services.

 

TH: PENTAX Medical’s latest image and video processor is the Optivista Plus. I understand it can also be used as an educational platform with its “TwinMode” setting. Can you tell us more about this device?

HH: The TwinMode is an interesting feature! As part of the educational setting, it is possible to show a previously recorded image on the screen so the doctor, or the students in training, can compare these images with the current ones they are seeing. So, for example with the i-scan project, images enhanced with one of the modalities can be compared to the same image without any enhancements. That’s how students learn when they can compare.

 

TH: What else is in the pipeline for PENTAX Medical?
HH:
Our focus is set in the hygiene cosmos, where we have initiatives such as Power of Choice. We also have our World of Intelligence initiative that is focussed on the digital arena, like AI, which supports our solutions-driven approach. We ask the question, what kind of solution can we provide with our different products if you, the customer, combine them together. We have the processors and we have the scopes, we have the single-use scope, we have the semi disposable scopes, we have different image modalities which can be used in different combinations in order to provide the right solution for their particular case. So all that comes together with us being able to provide this choice for doctors.

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The International Hospital Federation issues statement in support of Ukraine

, 14 March 2022/in E-News, Editors' Picks /by panglobal

International Hospital Federation

The IHF stands with hospitals during conflict, calls on members to provide support

 

The situation in Ukraine is a major concern for all of us, and the escalation of violence that has been reported on many different channels is alarming.

On 25 February, we released a message of solidarity with the people and the healthcare community in Ukraine.

The escalation of violence impacting hospitals and healthcare personnel is being reported by many authorities including:

  • World Health Organization (WHO) (here).
  • WHO Director General, Dr Tedros Adhanom Ghebreyesus (here and here).
  • WHO Europe (here).
  • UN Office for the Coordination of Humanitarian Affairs (UNOCHA) (here).
  • International Committee of the Red Cross (ICRC) (here).

Attacks on hospitals, healthcare workers, and ambulances are not acceptable. No matter the context. No matter the reasons. It is a violation of International Humanitarian Law, and we firmly stand against it.

Many international organizations and local actors are working hard, both inside Ukraine and in the neighbouring countries, such as Poland, Hungary, Slovakia, Moldova, and Romania to support refugees, mainly women and children. The UN Refugee Agency (UNHCR) has issued an alert that the number of refugees could reach 4 million rapidly.

IHF Members want to help, but the Ukrainians have limited logistical capacity to manage donations. We are recommending to the IHF community to get involved (either with financial or supplies support) through organizations acting in the field in neighbouring countries, or to the headquarters of these organizations. These trusted organizations have the capacity to redistribute the donations in a strategic manner.

Many organizations are providing emergency assistance in the region. The IHF would suggest supporting the following:

  • International Committee of the Red Cross (ICRC)
  • National Societies for the Red Cross
  • Swiss Solidarity
  • Médecins Sans Frontières / Doctors Without Borders (MSF)
  • Care International
  • UN Refugee Agency (UNHCR)
  • World Health Organization (WHO)

There are also initiatives that our members and partners have shared with us that we believe you will be interested to discover and support. For example:

  • The Polish Hospital Federation is cooperating with the Polish Medical Mission (PMM) to provide direct support to the hospitals in Ukraine, as well as in the Polish hospitals located near the Ukraine border (read more here).
    Direct financial donations can be made via the PMM website.
  • Teladoc Health is supporting hospitals in Ukraine through the Ukrainian Government (offering technology and doctors) and is helping refugees in Poland by providing virtual medical care.

    If you are a healthcare professional who wants to volunteer, or if you want more information, you can contact Rafael Gotsens, International Medical Director, Teladoc Health, Inc. (rgotsens@teladochealth.com).

 

 

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We need a people’s vaccine

, 6 May 2021/in Editors' Picks, Featured Articles /by panglobal

As vaccine nationalism and inequitable distribution continue to plague the global rollout of COVID-19 vaccines, epidemiologists from leading academic institutes around world have issued a stark warning that so-called ‘variants of concern’ to SARS-CoV-2, the virus that causes COVID-19, could render current vaccines ineffective in less than a year. Callan Emery reports.

Read more
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Reducing costs, improving outcomes with AI in a radiology practice

, 26 February 2021/in Editors' Picks, Featured Articles /by 3wmedia

A study published in the Journal of Digital Imaging (2019) [1] looked at whether Artificial Intelligence (AI)-based, computer-aided detection (CAD) software can be used to reduce false positives per image (FPPI) on mammograms as compared to an FDA-approved conventional CAD. The study showed a 69% decrease in FPPI which, the researchers said, could also potentially […]

Read more
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Superbugs and failing drugs

, 26 August 2020/in Corona News, E-News, Editors' Picks /by 3wmedia

Bacteria that develop resistance to antibiotic drugs – superbugs – pose a major global health threat to humanity. In a concerted effort to stave off this threat, several global programmes have been established and numerous new research initiatives are being carried out. Whether they are successful is yet to be seen. International Hospital reports.
Antimicrobial or antibiotic resistance is a major emerging global health threat which continues to escalate around the world. In the EU it is responsible for around 33,000 deaths each year according to the European Commission [1] and is estimated to cost the EU EUR 1.5 billion per year in healthcare costs and productivity losses.
In the United States, the Centers for Disease Control and Prevention (CDC) estimates that more than 2.8 million antibiotic-resistant infections occur in the country each year, and more than 35,000 people die as a result [2].
In the CDC’s 2019 Antimicrobial Resistance Threats Report, Robert R. Redfield, M.D., Director of the CDC, emphasises that we should stop referring to a coming post-antibiotic era. “It’s already here,” he says. “You and I are living in a time when some miracle drugs no longer perform miracles and families are being ripped apart by a microscopic enemy. The time for action is now and we can be part of the solution.”
So, what exactly is antimicrobial resistance (AMR)? Simply put, antimicrobial resistance occurs when microorganisms – such as bacteria, viruses, fungi, protozoa and helminths (worm-like parasites) – mutate or develop a resistance gene when they are exposed to antimicrobial drugs, such as antibiotics, antifungals, antivirals, antimalarials, and antihelminthics. As a result, the drugs become ineffective and infections persist in the body, increasing the risk of morbidity and mortality as well as the spread of the disease to others.
The issue is of such global importance that a political declaration was endorsed by Heads of State at the United Nations General Assembly in New York in September 2016 signalling the world’s commitment to taking a broad, coordinated approach to address the root causes of antimicrobial resistance across multiple sectors, especially human health, animal health and agriculture.
In 2015, the World Health Organization (WHO) established the Global Antimicrobial Resistance and Use Surveillance System (GLASS) [3]. The system calls on countries to monitor and report on antibiotic resistance. The WHO noted in a report published June 1 this year, that in the past three years, participation has grown exponentially. GLASS now aggregates data from more than 64,000 surveillance sites with more than 2 million patients enrolled from 66 countries across the world. In 2018 the number of surveillance sites was 729 across 22 countries.
Hanan Balkhy, Assistant Director-General for antimicrobial resistance at WHO, explained: “The enormous expansion of countries, facilities and patients covered by the new AMR surveillance system allows us to better document the emerging public health threat of AMR.”
On the back of this data, the Organization notes that high rates of resistance among antimicrobials frequently used to treat common infections, such as urinary tract infections or some forms of diarrhoea, indicate that the world is running out of effective ways to tackle these diseases. For instance, the rate of resistance to ciprofloxacin, an antimicrobial frequently used to treat urinary tract infections, varied from 8.4% to 92.9% in 33 reporting countries.
In addition, the WHO expressed concern that the trend will further be fuelled by the inappropriate use of antibiotics during the COVID-19 pandemic. The Organization points out that evidence shows that only a small proportion of COVID-19 patients need antibiotics to treat subsequent bacterial infections and, as such, has issued guidance [4] not to provide antibiotic therapy or prophylaxis to patients with mild COVID-19 or to patients with suspected or confirmed moderate COVID-19 illness unless there is a clinical indication to do so.
Solutions
What can be done to counter AMR? Although antimicrobial resistance occurs naturally over time, usually through genetic changes, there are a number of countermeasures. Primarily, healthcare practitioners should reduce the misuse and overuse of antimicrobials which are accelerating AMR. The WHO notes, for example, that in many places, antibiotics are overused and misused in people and animals, and often given without professional oversight. Examples of misuse include when they are taken by people with viral infections like colds and flu, and when they are given as growth promoters in animals or used to prevent diseases in healthy animals.

CDC’s 2019 Antimicrobial Resistant Threats Report

The CDC’s 2019 AR Threats Report lists 18 antibiotic-resistant bacteria and fungi in three categories based on the level of concern to human health – urgent, serious, and concerning. The ‘urgent’ list includes the following five threats:
Carbapenem-resistant Acinetobacter
Carbapenem-resistant Acinetobacter cause pneumonia and wound, bloodstream, and urinary tract infections. Nearly all these infections happen in patients who recently received care in a healthcare facility. They are estimated to have caused 700 deaths in the US in 2017.
Candida auris
C. auris is an emerging multidrug-resistant yeast. It can cause severe infections and spreads easily between hospitalized patients and nursing home residents.
Clostridioides difficile
C. difficile causes life-threatening diarrhoea and colitis (an inflammation of the colon), mostly in people who have had both recent medical care and antibiotics. Estimated death per year in the US: 12,800.
Carbapenem-resistant Enterobacteriaceae (CRE)
CRE are a major concern for patients in healthcare facilities. Some Enterobacteriaceae are resistant to nearly all antibiotics, leaving more toxic or less effective treatment options. Estimated deaths in the US in 2017: 1,100.
Drug-resistant Neisseria gonorrhoeae
N. gonorrhoeae causes the sexually transmitted disease gonorrhoeae that can result in life-threatening ectopic pregnancy and infertility, and can increase the risk of getting and giving HIV.
See the report for the complete list. https://www.cdc.gov/drugresistance/pdf/threats-report/2019-ar-threats-report-508.pdf

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THE COVID-19 THREAT

, 26 August 2020/in Corona News, Editors' Picks, Featured Articles /by 3wmedia

As the threat of a COVID-19 pandemic stares us in the face, it may be opportune to consider some scenarios ahead, especially in light of lessons from other, similar outbreaks in recent decades.
The first problem is sporadic bursts of public concern, alternating with periods of denial. Managing both requires measured doses of reliable information from authoritative sources. Such measurement is a delicate art at the best of times. During a crisis, media hype can mutate it easily into mass misinformation.
Similarly, the threat of terrorism has close parallels with each of the above aspects.

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The challenge of sepsis: new approaches to old scourge

, 26 August 2020/in Editors' Picks, Featured Articles /by 3wmedia

Sepsis is a potentially fatal condition after the immune system over-reacts to an infection, leading to shock and organ failure. It is most frequently provoked by commonplace bacteria. Globally, over 30 million people develop sepsis each year. Some 6 million die as a result. Although there has been progress in controlling deaths from sepsis in recent decades, the challenge is still a major one. Indeed, in industrialized countries, the incidence of sepsis is higher than that of new cases of cancer.

Unpredictable and terrifying
Sepsis is frequently encountered in a hospital setting. It is also a leading cause for hospital readmission. In the US, studies estimate that one of 3 people who die in hospital have sepsis.
One of the biggest challenges for clinicians is that sepsis occurs unpredictably and progresses at terrifying speed. This makes timely diagnosis a tough call.
Definitions of sepsis have also tended to vary. In 2018, a working group of 19 specialists, convened by the Society of Critical Care Medicine in the US and the European Society of Intensive Care Medicine (ESICM), updated the clinical definitions and criteria for sepsis and septic shock. The taskforce recommended defining sepsis as “life- threatening organ dysfunction caused by an inappropriate host response to infection.” It also concluded that the term ‘ severe sepsis ‘ was redundant. 

Rory’s Regulations
Nevertheless, there has been some progress in recent years in understanding sepsis and standardizing approaches to diagnose, manage and treat the condition.
In 2012, Rory Staunton, a healthy 12-year-old from New York, died due to the fact that his sepsis was not diagnosed. In the wake of this, the government of New York State mandated all hospitals to comply with protocols to improve the early diagnosis and treatment of sepsis and septic shock, and made it compulsory for reporting all sepsis cases to the Department of Health.
The New York Sepsis Initiative, which the media called Rory’s Regulations after the young victim, essentially consist of two treatment bundles.
The first is a 3-hour bundle, and is indicated for patients with severe sepsis and needs to be activated within three hours of a patient’s arrival at hospital. It includes blood culturing to determine choice of antibiotics, starting antibiotic treatment and assessing blood lactate levels – an important marker for sepsis.
The second, 6-hour bundle, is earmarked for patients with septic shock and needs to be carried out within six hours of their arrival at hospital. It includes administration of intravenous fluid, vasopressors to contract blood vessels and a follow-up check on lactate levels.
Assessing the New York Sepsis Initiative
The New York Sepsis Initiative was assessed earlier this year by a team from Warren Alpert Medical School at Brown University. They studied data from 91,357 patients, treated over a period of 27 months at 183 hospitals.
The findings were encouraging. The two sepsis bundles were used in 81.3 percent of patients. After implementation of the protocols, compliance steadily increased across hospitals in the State. The study’s most important finding, however, was that patients administered the bundles saw a reduction in mortality risk over 4 percentage points, at 24.4 percent. The mortality risk in those who did not receive the bundles was 28.8 percent. In addition, hospitals complying with the protocols saw a significant reduction in average length of stay.

Limits to fighting sepsis
While the New York State initiative provides strong evidence of the potential for standardizing sepsis-fighting measures, another study this year shows there may be limits to its scope. The study, by researchers from Brigham and Women’s Hospital in Massachusetts, was published in March by ‘JAMA Network Open’. It sought to investigate the precise role of sepsis in hospital deaths and estimate how many were preventable.
The researchers studied records of 568 people from six acute care hospitals for the years 2014 and 2015, who had died in the hospital or after discharge to hospice care. Using a 6-point Likert scale, ranging from “definitely preventable” to “definitely not preventable,” they concluded that some 90 percent of deaths were not preventable in a hospital setting. On the other side, 1 in 8 sepsis-related deaths were deemed “potentially preventable with better hospital-based care.”
The key reason for such a prognosis was that most sepsis fatalities occur in medically complex, older patients with severe co-morbidities, including chronic conditions such as cancer, heart and lung disease. In the few cases of death due to sub-optimal care, the most common causes included late antibiotic administration.
The lead author of the study, Dr. Chanu Rhee, called for more “innovation in the prevention of underlying conditions” to reduce sepsis mortality by a significant margin.

Long term decline in sepsis death rates

Although the challenge of sepsis remains serious, there has been significant progress over recent decades. In October 2018, the annual meeting of ESICM (the European Society of Intensive Care Medicine) was presented with an analysis of 30-year trends in sepsis deaths. Using World Health Organization figures, researchers from Harvard Medical School and Imperial College London (ICL) found that the average death rate from sepsis in Europe, North America and Australasia fell from 36.2 per 100,000 men in 1985 to 27.1 in 2015, and for women, from 23.2 per 100,000 women to 19.6.
Countries which managed to reduce death rates most significantly were Finland, Iceland and Ireland, while increased rates were noted in both Denmark and Lithuania.
Prospects for managing and treating sepsis in future years is likely to improve due to several new weapons, ranging from targeted drug development to artificial intelligence. Growing interest in this field is indicated by more than 200 sepsis biomarkers approved by the US Food and Drug Administration (FDA), among them interleukins, C-reactive protein and procalcitonin.

MIT’s IL-6 sensor system
It is known that interleukin-6 (IL-6), a protein produced in response to inflammation, begins to increase a few hours prior to other sepsis symptoms. IL-6 levels have not been strong enough to be detected by traditional tests. However, new sensor technologies appear to offer promise.
Researchers at the Massachussets Institute of Technology (MIT) have developed a small microfluidic sensor which can reportedly detect sepsis in a small blood sample (such as that obtained from a finger prick) within 25 minutes. The system uses antibody-laced magnetic microbeads in one fluid channel, which mixes with the blood sample and identifies the IL-6 biomarker. Meanwhile, another channel attaches the biomarked beads to an electrode. When a current is run through the electrode, a signal is produced each time an IL-6 bead passes through.
The magnetic detection system is far less expensive than the high-end optics required by conventional assays, and requires far less blood. The MIT researchers state that they will eventually be able to detect minute increases in IL-6 during the test itself. They are now continuing work on researching other proteins which act as early markers for sepsis detection and would reinforce diagnostic accuracy.

Early warning sepsis indicator
A new hematological biomarker, introduced in 2018 by Beckman Coulter as the Early Sepsis Indicator, is reported as part of a routine complete blood count (CBC) and measures morphological changes in monocytes, cells which play a role in the dysregulated immune response to sepsis. A positive result alerts clinicians to a higher probability of sepsis at an early stage

Thermography tools
Another novel diagnostic technique is based on the fact that abnormal body temperature patterns accompany the earliest stages of sepsis. University of Missouri researchers have proposed using infrared thermography to measure the difference between body extremities and a patient’s core temperature. The team have developed an automatic real-time system which calculates this, based on a frontal and lateral infrared thermogram of the face. Writing in a recent edition of the ‘International Journal of Data Mining and Bioinformatics’, they state the system works successfully, irrespective of the angle of the head relative to the imager and differences in backgrounds.

Targeting enzymes
Other efforts involve new drugs. One priority consists of signalling pathways which control immune cell behaviour during sepsis. So far, most research on inflammation has focused on kinases, the enzymes which transfer phosphate groups to specific substrates.
In August 2019, researchers from the University of California San Diego (UCSD) School of Medicine discovered a wholly new target area – the enzymes which remove them. In particular, they focused on PHLPP1, an enzyme which impacts upon inflammation by removing phosphates from the transcription factor known as STAT1, which controls inflammatory genes.
Using a mouse model, the researchers administered live E. coli bacteria and lipopolysaccharide (LPS), to both PHLPP1-deficient and normal mice. They found that the former fared far better, with half surviving infection-induced sepsis after 5 days – compared to zero for normal mice. The UCSD researchers believe that inhibiting PHLPP1 might form the basis for new sepsis treatments in humans, offering the means to control the dangerous inflammation of sepsis while maintaining the critical bactericidal properties of white blood cells.

Non-antibiotic drugs against sepsis
Researchers at the Royal College of Surgeons in Ireland (RCSI) have tested a compound called cilengitide (brandname InnovoSep) in a preclinical trial. A key feature of InnovoSep is that it is not an antibiotic, and does not face the limitations associated with the latter – namely, the need for rapid identification of causative bacteria and growing resistance to antibiotics.
Cilengitide is an antagonist of alpha-v beta-3, the key endothelial cell integrin which mediates the adhesion of cells to the extracellular matrix. In everyday terms, the drug prevents bacteria “from getting into the bloodstream from the site of infection by stabilizing the blood vessels so that they cannot leak bacteria and infect the major organs,” according to Steven Kerrigan of the RCSI.

Artificial intelligence
To some, however, artificial intelligence (AI) is seen as potentially the most exciting frontier in the fight against sepsis. In 2018, the journal ‘Nature Medicine’ featured an AI system developed by scientists at Imperial College London, which proved to be more reliable predicting the best treatment for sepsis, as compared to human doctors. This was after it had ‘learned’ from an analysis of 100,000 patient records and clinical decisions in intensive care units about sepsis over a 15-year period.
Another promising AI system against sepsis has been developed by Sentara Healthcare in the US. Sentara’s sepsis prediction tool is based on identifying at-risk patients by using an algorithm to spot patterns from some 4,500 pieces of data in an electronic record. These focus on metrics such as body temperature, heart rate, blood tests, gender, medical history, etc.. Sentara had previously developed a ‘sepsis sniffer’ which detected when a patient had just begun to have sepsis. The current system goes further, and does not wait until a patient has already developed the disease.

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How artificial intelligence will change the role of doctors

, 26 August 2020/in Editors' Picks, Featured Articles /by 3wmedia

The term “artificial intelligence”, defined in the Oxford Dictionary as “the capacity of a machine to simulate or surpass intelligent human behaviour”, was first used in the 1950s, but the idea that the human brain, or at least parts of it, could somehow be ‘copied’ or ‘imitated’ using a series of mechanical networks has been part of myth and literature for centuries, as far back as, for example, the automatons of Hephaestus and Daedalus.

by Prof Jean-Louis Vincent

Artificial intelligence is an umbrella term that covers multiple tools and technologies. In recent years, huge advances in machine learning algorithms, neural networks, deep learning, facial recognition, computing power and statistical techniques have increased the potential applications of artificial intelligence across multiple aspects of everyday life. In terms of medicine, artificial intelligence is already beginning to find a place in disease prediction and diagnosis, clinical decision support and therapeutic guidance, prognostication, and remote follow-up and monitoring.

So, what do these new developments mean for the medical profession – is this ever advancing technology going to decrease the need for doctors? To some extent, the answer is of course yes, perhaps particularly in the field of diagnostics. Using machine learning, computerized systems are able to study and develop pattern recognition from millions of test results over a very short period of time, whereas a doctor can only see and process a limited number of events throughout a whole professional career. The vast amounts of data becoming available as increasing numbers of patients have electronic health records and are managed with electronic monitoring systems are providing the input needed for artificial intelligence to develop, while also reducing the administrative load on doctors and other healthcare staff, a common source of complaint. Machine-based interpretation of visual data is now more accurate, effective, and rapid than the human eye and associated with less risk of error. Interpretation of X-rays and other medical images will become increasingly automated, reducing the need for radiologists to perform this role. Similarly, electrocardiograms are already read automatically; many of the reports are still validated by a cardiologist, but is this really necessary? In ophthalmology, examination of the fundus for many diagnoses, including diabetic retinopathy and macular degeneration, can be performed more accurately by computerized algorithms than by most experienced ophthalmologists. Application of deep learning to a database of eye CT-scans at a London hospital has enabled more than 50 ocular diseases to be recognized by the system. Non-image-based diagnosis is also possible. A pilot system developed in California that applied machine learning to electronic health record data has been used to diagnose common pediatric problems and shown to perform better than junior doctors.

Although artificial intelligence may therefore indeed reduce the need for doctors in some areas, this is not necessarily a bad thing; it should not be seen as the enemy, but rather as a means of improving medical practice and patient care. More rapid, accurate diagnosis can only be positive. Another important example of how artificial intelligence can be beneficial is in predictive medicine. Natural language processing of data from electronic medical records was able to more accurately predict postoperative complications in patients undergoing major surgery than were patient safety indicators. Machine learning-based sepsis prediction has been associated with reduced mortality rates. Indeed, early identification of patients with an increased risk of sepsis raises awareness and facilitates early investigation and management by sepsis-trained physicians in a condition where rapid diagnosis and treatment are crucial to maximize chances of survival. More broadly, identification of patients at risk of deterioration on the general floor or after surgery will enable appropriate monitoring systems to be offered to a selection of patients in an environment where it is not feasible, financially or practically, to monitor every hospitalized patient.

Another example is the field of therapeutics. Machine-learning can identity the most effective therapeutic algorithms for individual patients, with the most appropriate evaluation and follow-up. These algorithms are being incorporated into closed-loop systems enabling appropriate treatments to be administered and doses adjusted in real-time for individual patients according to continual personal data provision. Just some of many examples include implantable cardioversion defibrillators, diabetes management with implantable glucose monitors and insulin pumps, and use of vasopressors to prevent hypotension during surgery. 

Artificial intelligence can thus be used to provide continually adjusted, up-to-date, patient-relevant information on the best therapeutic options for a specific patient much more rapidly and accurately than doctors can. Doctors can currently assimilate only a small portion of the information available on which to base such decisions. By configuring the huge amounts of patient data now available into predictive models, machine learning can provide physicians with recommendations regarding the optimum treatment schedule for a specific patient with a specific condition(s). Doctors are still needed to interpret the recommendation, explain them to the patient and their family, and initiate the chosen treatment course. Using artificial intelligence, doctors will be more enabled to select the optimum treatment regimens for individual patients, rather than the one-treatment-fits-all packages that are still used for many conditions today. Moreover, doctors will have greater access to accurate statistics to inform discussions with patients and their families, both about the likely outcomes from different treatment options, but also about likely prognosis if treatment is refused or withdrawn. The role of doctors in this situation will increasingly be one of advisor as patients become ever more involved in their own healthcare decisions.

Artificial intelligence is going to continue to invade every aspect of daily life, including medicine, and needs to be carefully developed and validated. Although currently very much associated with rich economies of the developed world, artificial intelligence could play a large role in improving healthcare in countries where qualified doctors are less widely available. These new technologies could therefore help to decrease inequalities in the health sector. Even in low income countries, the combination of artificial intelligence with telemedicine can help increase access to high quality medicine. Wherever it is employed, it will not entirely replace doctors but rather make them more efficient, provide more time for one-to-one patient contact and help provide care best adapted to individual patients, with reduced errors. People often raise the question of associated costs. But costs may not be very high, especially as the technology becomes more widely used. Indeed, artificial intelligence may even help reduce global healthcare costs by increasing efficiency.

Doctors should not fear this technology, but learn to accept and embrace it, determining and directing how it can best be incorporated into medical practice to improve patient care.
The author
Jean-Louis Vincent, MD, PhD
Dept of Intensive Care, Erasme Hospital, Université libre de Bruxelles, Brussels, Belgium

Suggested reading:
Darcy AM, Louie AK, Roberts LW. Machine learning and the profession of medicine. JAMA 2016;315:551-2.
De Fauw J, Ledsam JR, Romera-Paredes B, et al. Clinically applicable deep learning for diagnosis and referral in retinal disease. Nat Med 2018;24:1342-1350.
Joosten A, Alexander B, Duranteau J, et al. Feasibility of closed-loop titration of norepinephrine infusion in patients undergoing moderate- and high-risk surgery. Br J Anaesth 2019 Jun 26. doi: 10.1016/j.bja.2019.04.064129
Kilbride MK, Joffe S. The new age of patient autonomy implications for the patient-physician relationship. JAMA 2018;320:1973-1974
Liang H, Tsui BY, Ni H, et al. Evaluation and accurate diagnoses of pediatric diseases using artificial intelligence. Nat Med 2019;25:433-438.
McCoy A, Das R. Reducing patient mortality, length of stay and readmissions through machine learning-based sepsis prediction in the emergency department, intensive care unit and hospital floor units. BMJ Open Qual 2017;6:e000158
Murff HJ, FitzHenry F, Matheny ME, et al. Automated identification of postoperative complications within an electronic medical record using natural language processing. JAMA 2011;306:848–855. 
Topol EJ. High-performance medicine: the convergence of human and artificial intelligence. Nat Med 2019;25:44-56
Vincent JL, Creteur J. Big data are here to stay! Anaesth Crit Care Pain Med 2019;38:339-340.
Vincent JL, Einav S, Pearse R, et al. Improving detection of patient deterioration in the general hospital ward environment. Eur J Anaesthesiol 2018;35:325–333.

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