from the “Bad Bug Book,” Center for Safety
and Applied Nutrition, US FDA (Food and Drug Administration) at
There are 2 points to be emphasized:
- that vibrios are normal flora in warm saltwater (not indicative of any sewage contamination) and that
- most of the life-threatening illnesses occur in individuals with
underlying medical illnesses, including immunocompromised states, chronic liver disease, and diabetes. So-called normal individuals often just get gastroenteritis. The range of disease due to V. vulnificus can involve more northern geographical areas if the area is affected by a substantial heat wave.
The genomic code: inferring Vibrionaceae niche specialization
Nature Reviews Microbiology 4, 697-704 (September 2006)
Long-term measles-induced immunomodulation increases overall childhood infectious disease mortality
Science 8 May 2015: Vol. 348 no. 6235 pp. 694-699
Michael J. Mina, et al.
Immunosuppression after measles is known to predispose people to opportunistic infections for a period of several weeks to months. Using population-level data, we show that measles has a more prolonged effect on host resistance, extending over 2 to 3 years. We find that nonmeasles infectious disease mortality in high-income countries is tightly coupled to measles incidence at this lag, in both the pre- and post-vaccine eras. We conclude that long-term immunologic sequelae of measles drive interannual fluctuations in nonmeasles deaths. This is consistent with recent experimental work that attributes the immunosuppressive effects of measles to depletion of B and T lymphocytes. Our data provide an explanation for the long-term benefits of measles vaccination in preventing all-cause infectious disease. By preventing measles-associated immune memory loss, vaccination protects polymicrobial herd immunity.
Bad Flu Season Overshadows Other Winter Miseries
January 17, 2013
Dr. Beth Zeeman says she can spot a case of influenza from 20 paces. It’s not like a common cold.
“People think they’ve had the flu when they’ve had colds,” Zeeman, an emergency room specialist at MetroWest Medical Center in Framingham, Mass., tells Shots. “People use the word ‘flu’ for everything. But having influenza is really a different thing. It hits you like a ton of bricks.”
Joachim Santos, a carpenter from Brazil in a nearby examining room, says he’s never been as sick in all his 57 years. “I worry that it’s going to get more serious and I could die,” he says.
Dr. Andrew Pavia, an infectious disease specialist at the University of Utah, says flu has certain hallmarks. “A classic case of flu starts off suddenly with high fever, maybe shaking chills, severe muscle and body aches,” he says. “It’s not uncommon for people to say their hair hurts, they hurt so badly.”
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
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
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.