Auto-Brewery Syndrome

A Case Study of Gut Fermentation Syndrome (Auto-Brewery) with Saccharomyces cerevisiae as the Causative Organism,
International Journal of Clinical Medicine, Vol. 4 No. 7, 2013, pp. 309-312.

Gut Fermentation Syndrome also known as Auto-Brewery Syndrome is a relatively unknown phenomenon in modern medicine. Very few articles have been written on the syndrome and most of them are anecdotal. This article presents a case study of a 61 years old male with a well documented case of Gut Fermentation Syndrome verified with glucose and carbohydrate challenges. Stool cultures demonstrated the causative organism as Saccharomyces cerevisiae.
The patient was treated with antifungals and a low carbohydrate diet and the syndrome resolved.
Helicobacter pylori was also found and could have been a possible confounding variable although the symptoms resolved post-treatment of the S. cerevisiae.
Auto-Brewey, Yeast, Fermentation, Gut Fermentation Syndrome

journalistic version:

Ultrarapid pathogen identification by NGS assays

A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples
Genome Res. 2014 Jul;24(7):1180-92.
Samia N. Naccache, et al.

Unbiased next-generation sequencing (NGS) approaches enable comprehensive pathogen detection in the clinical microbiology laboratory and have numerous applications for public health surveillance, outbreak investigation, and the diagnosis of infectious diseases. However, practical deployment of the technology is hindered by the bioinformatics challenge of analyzing results accurately and in a clinically relevant timeframe. Here we describe SURPI (“sequence-based ultrarapid pathogen identification”), a computational pipeline for pathogen identification from complex metagenomic NGS data generated from clinical samples, and demonstrate use of the pipeline in the analysis of 237 clinical samples comprising more than 1.1 billion sequences. Deployable on both cloud-based and standalone servers, SURPI leverages two state-of-the-art aligners for accelerated analyses, SNAP and RAPSearch, which are as accurate as existing bioinformatics tools but orders of magnitude faster in performance. In fast mode, SURPI detects viruses and bacteria by scanning data sets of 7-500 million reads in 11 min to 5 h, while in comprehensive mode, all known microorganisms are identified, followed by de novo assembly and protein homology searches for divergent viruses in 50 min to 16 h. SURPI has also directly contributed to real-time microbial diagnosis in acutely ill patients, underscoring its potential key role in the development of unbiased NGS-based clinical assays in infectious diseases that demand rapid turnaround times.

NGS assays for pathogen diagnosis

journalistic version:

Jazz pianist recovered from AIDS-related dementia

Fred Hersch Floats On, With A Dynamic Trio In Tow
July 19, 2014

The last time Fred Hersch was featured on Weekend Edition Saturday, the headline read, “Back On Stage By No Small Miracle.” It was 2009, and scarcely a year earlier, the jazz pianist had suffered AIDS-related dementia and fallen into a coma for several months.
Since recovering, Hersch has come roaring back to music, releasing a string of live albums to critical success.

A new studio recording by Hersch’s trio came out earlier this month; it’s called Floating.
This week, a review in The New York Times said that while Hersch has been putting out great trio albums for 30 years, “He hasn’t made one better than this.”


Chikun-What? A New Mosquito-Borne Virus Lands In The U.S.
July 03, 2014

Pediatrician Jennifer Halverson will never forget her 36th birthday.

The St. Paul native was volunteering at a maternity clinic in Port-au-Prince, Haiti. She felt great — she went to her job that day and then out to dinner with friends.

But when she got home and went to sleep that night in May, something didn’t feel right.

“Then I woke up at 3 in the morning,” she says, “and what struck me the most was that my shoulders were on fire. It was like I was being stabbed in both shoulders.”

The pain quickly spread to all of Halverson’s joints — her hips, her knees and elbows. Even her fingers and toes hurt.

Halverson also had a fever, a rash and painful sores in her mouth. When she flew home to Minnesota, the doctors confirmed what she thought might be true: chikungunya. Though the rash and sores quickly faded, and the illness is rarely fatal, the joint pain it causes can last for months. Halverson is still hurting — she says she still can’t open jars.

A year ago, chikungunya didn’t even exist in the Western Hemisphere. It was only found in Africa and Asia.
But in October, the mosquito-borne illness cropped up on the island of St. Martin. Then it spread like wildfire.

The Pan American Health Organization reported Monday that over the past seven months, chikungunya has sickened more than a quarter-million people in the Caribbean.

GWAS explains only a small proportion of the total heritability

By exploiting allied phenotypic data, it is possible to examine the genetic contribution to such aspects of disease biology (including prognosis) by comparing the genetic profiles of patients with contrasting clinical phenotypes—a so-called ‘within-cases’ analysis.

Prognosis in autoimmune and infectious disease: new insights from genetics
Clinical & Translational Immunology (2014) 3, e15
James C Lee, et al.

Keywords: autoimmunity; FOXO3; genetics; infection; prognosis

despite the apparent success, GWAS results have only explained a relatively small proportion of the total heritability of each disease.[3]
Work is now underway to try to identify the ‘missing heritability’ through a variety of complementary methods, including:

  • whole-genome sequencing (to identify rare variants that may have larger effect sizes) and
  • studies to examine interactions between a given gene and other genes (epistasis) and
  • between genes and the environment.


Measles Outbreak In Ohio Amish

Measles Outbreak In Ohio Leads Amish To Reconsider Vaccines   
June 24, 2014

A nurse in Knox County for nearly three decades, Fletcher had never seen the illness, but she knew the symptoms.
“The rash. They had the conjunctivitis in the eyes, their eyes were red,” she says. “They don’t want the light, they sit in the darkened room, wear dark glasses. I mean they were just miserable. High temperatures, 103, 104 temps. So this was the measles.”

The largest outbreak of measles in recent U.S. history is underway. Ohio has the majority of these cases — 341 confirmed and eight hospitalizations. The virus has spread quickly among the largely unvaccinated Amish communities in the center of the state.

Zoster Sine Herpete

Herpesvirus infections of the nervous system
Donald H Gilden, et al.
Nature Clinical Practice Neurology (2007) 3, 82-94

VZV-associated viremia and lymphotropism have been documented during varicella, herpes zoster, PHN and zoster sine herpete, and even in normal healthy adults.

The detection of VZV DNA [40, 41] and VZV-specific proteins42 in blood MNCs of some patients with PHN and zoster sine herpete, [43, 44, 45] as well as in tissue of patients with chronic VZV ganglionitis, [46] might reflect low-level productive infection in ganglia—a hypothesis that is supported by favorable clinical responses in some PHN patients treated with antiviral agents. [47, 48]

After varicella, the varicella zoster virus (VZV) becomes latent in ganglia along the entire neuraxis; its reactivation can lead to herpes zoster, vasculopathy, myelitis, necrotizing retinitis or zoster sine herpete

see also:
Zoster sine herpete
It would be rash to ignore it
Neurology February 1, 2011   vol. 76  no. 5  416-417

6. Varicella-Zoster Virus Infection
Donald H. Gilden
University of Colorado Health Sciences Center
2003. pp 10

A case of neuropathic brachioradial pruritus caused by cervical disc herniation

Molecular mechanisms of varicella zoster virus pathogenesis
Nature Reviews Microbiology 12, 197–210 (2014)

The Invisible Universe Of The Human Microbiome

The Invisible Universe Of The Human Microbiome
NPR. Nov 5, 2013

The next time you look in a mirror, think about this: In many ways you’re more microbe than human.
There are 10 times more cells from microorganisms like bacteria and fungi in and on our bodies than there are human cells.
But these tiny compatriots are invisible to the naked eye.
So we asked artist Ben Arthur to give us a guided tour of the rich universe of the human microbiome.

associated article:

Washington University

Myths And Stigma Stoke TB Epidemic In Tajikistan

Myths And Stigma Stoke TB Epidemic In Tajikistan
July 02, 2013

The difficulty with treating tuberculosis is that it takes months of antibiotics, sometimes even years, to drive the bacteria out of a person’s body. Orion’s grandmoth er has been on and off TB treatment for years, and Martin has just confirmed that she still has active, infectious TB.

The grandmoth er insists that TB comes from the cold, and that Orion got it from swimming in the cold river. “He likes fish,” Abdulloeva says of her grandson. “So he was saying, “Fish, fish” and going to the river. That’s why he got the TB.”

Martin insists to the Abdulloeva that TB is spread through the air.
The 66-year-old woman flatly dismisses the nurse’s explanation. “No, its from cold,” Abdulloeva says.

Orion’s grandfather, Mahmadaly Qurbonaliev, next suggests that a local clergyman may have put a spell on the boy, and that’s why he still cannot walk.

Some people even think the coughing and wasting away is a genetic condition, Martin says.
“Father has TB, daughter has TB, granddaughter has TB — you can understand in a way why they believe it’s genetic.”


A Boston Family’s Struggle With TB Reveals A Stubborn Foe
June 03, 2013

Thanks to gold-standard tuberculosis treatment and prevention programs, cases of TB in the United States have declined every year for the past two decades — to the lowest level ever.

One-third of the human race is infected with tuberculosis, a persistent public health problem that kills 1.4 million people a year.

She should have been quarantined at a TB treatment center until she was no longer contagious.
But she was discharged over Martin Luther King weekend 2011, and public health officials didn’t get notified in time.
They had the legal power to require her to stay in the hospital for treatment.


Man Immune To HIV Helped Scientists Fight Virus

Stephen Crohn, a New York artist and editor, carried a genetic mutation that protected him against HIV.

In Life, Man Immune To HIV Helped Scientists Fight Virus
September 21, 2013

Scientists ultimately figured out that one of those receptors on Stephen Crohn’s cells was shortened and not accessible to the virus. Without the receptor, HIV could’t infect his cells.

This genetic change is called the delta 32 mutation.
Its discovery has helped researchers develop the anti-viral drug maraviroc and devise the first experimental strategy for curing HIV.

Stephen Crohn’s death was tragic. It was a suicide. And his sister has said that he may have been overwhelmed by survivor’s guilt.

It is very traumatic.
I think he told me once that he had lost 80 or 90 good friends.
Week after week, you’re going to memorials, you’re going to funerals.
That’s just daunting. That’s a daunting task.

see also:
A human ‘knockout’ confers resistance to HIV infection
Chemokine receptors: multifaceted therapeutic targets
Nature Reviews Immunology 2, 106-115 (February 2002)
The annual tab for Truvada ranges from about $11,000 to $14,000.