Identifying a deadly foodborne bacteria: What’s virus got to do with it?

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--A recent study uses a new approach to investigate the shiga toxin producing bacteria responsible for a serious disease outbreak in Germany in 2011. The real culprits behind the outbreak are the viruses that carry the gene for shiga toxin and transfer it to otherwise harmless bacteria  --

            What’s harder than finding a needle in a haystack? Finding the bacterial genome you’re looking for in a diarrhea sample. A recent study published on April 10, 2013 in the Journal of the American Medical Associaton (JAMA) made this task seem relatively easy. The bacteria being searched for was a  rare shiga toxin producing bacteria that causes bloody diarrhea and other severe complications in humans upon infection. This study was done by an international team of researchers coordinated by Mark J. Pallen who recently became the head of Warwick Medical School’s new Division of Microbiology and Infection. The bacterial strain that caused an outbreak in Germany was especially rare making it hard to identify. Because of this, researchers employed a new method to identify the genome sequence of this highly pathogenic bacteria. Their method of detection was to sequence all the genetic material present in fecal samples from patients with diarrhea during the outbreak and sort through this genetic information to find the sequence of the disease causing strain.

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            The source of the outbreak in Germany during the summer of 2011 is believed to be from the consumpton of raw sprouts contaminated with the dangerous bacteria strain (2). This outbreak affected thousands of people in a wealthy, modern, industrialized society, causing more than 50 deaths (4). In times like this, quick identification of the causative pathogen (in this case a shiga toxin producing bacterial strain) is critical for the management of the outbreak. Traditionally, the standard for identifying pathogens in clinical samples is to isolate the disease causing bacteria from other microbiota in the samples and then sequence it once it is in pure culture. This study's approach is different becuase they directly sequenced the mixed communities of bacteria and anything else present within the feces sample and then analyzed the sequence data to find the disease causing bacteria. The sequencing of mixed microbial communities is called metagenomics and allows identification independent of laboratory isolation and culture of the causative bacteria.

Bacterial Infection? ...Have a dose of virus.

            When you go to a hospital, you typically expect it to make you better, not get you sicker. Unfortunately, hospitals are filled with bacteria, many of which ‘prey’ on patients with weakened immune systems and preexisting health issues. One such bacterium is klebsiella, a genus of Enterobacteriaceae. This bacteria is estimated to cause nearly 8% of all nosocomial (hospital-acquired) infections each year (Podschun, 1998). Klebsiella pneumoniae is normally found growing in places such as the mouth and on skin, but it can create health issues if it enters the lungs, causing inflammation, hemorrhaging, and necrosis of lung tissue. It is especially dangerous if bacteria have developed antibiotic resistance, as an increasing number of hospital-acquired infections have done.

            This resistance is coded for in plasmids (small, circular, transferrable bits of DNA) that the bacteria pick up. A common protein that causes antibiotic resistance is beta-lactamase. This enzyme, breaks open the beta-lactam ring in antibiotic molecules containing this structure, thereby deactivating them. Penicillin is one such beta-lactam-based antibiotic. It is widely used to treat bacterial infections, and resistant bacterial strains are a large reason for concern. While there are other antibiotics that can be used, some of these bacteria have extended-spectrum beta-lactamase genes, which makes them even more efficient at denaturing a wider range of beta-lactam antibiotics. In poorer areas, where less common antibiotics are harder to come by, this is even more of an issue. In 2003, over half of the antibiotics in use were beta-lactam compounds (Elander, 2003).

            These infections add time to hospital stays. Not only is this an inconvenience, but it is also an economic drain on the hospitalized individual. These types of infection are also prominent in intensive care units, where patients are already suffering from depressed immune systems, and an added infection without the help of antibiotics can kill a patient.

            For this reason, the search for alternate antimicrobials is a high priority. Bacteriophages (viruses that only infect bacteria) hold great promise in this area, but to be effective, they must be able to infect a wide host of bacteria. There are four types of host resistance mechanisms to bacteriophage infection: adsorption inhibition, blocking of DNA injection, restriction-modification, and abortive infection (Weinbauer, 2004). The host restriction system is one of the best-studied parts of this system. In “Characterizing the biology of novel lytic bacteriophages infecting multidrug resistant Klebsiella pneumoniae,” Kesik-Szeloch et al. culture and screen a number of bacteriophages for the pathogenicity in Klebsiella, and their abilities to resist host restriction-modification mechanisms.