Tips from the journals of the American Society for Microbiology

Feed Likely Source of Salmonella Contamination on Pig Farms

Commercial feed appears to be a source of Salmonella contamination in commercial swine production units, according to a paper in the November 2010 issue of the journal Applied and Environmental Microbiology. Moreover, nearly half of isolates found in pigs were multidrug resistant. The findings suggest that pork could be a source of human infection. They also strongly question the conventional wisdom that processed feed is not a source of contamination. Heat treatment during processing has been thought to kill any bacterial contaminants.

The research team, led by Wondwossen A. Gebreyes of the College of Veterinary Medicine, The Ohio State University, tested samples collected from feed bins prior to exposure to the barn environment, as well as fecal samples and environmental samples from the barns. They found contaminated feed in eight of 36 barns tested, with a sample prevalence of 3.6%. These isolates fell into five different genotypes. In four of the five cases, they found that fecal samples they tested from a given barn and time point matched the feed samples from the same barn and time period, suggesting that the feed was indeed the contamination source.

“These genotypic clusters also shared similar antimicrobial resistance profiles and serogroups,” says Gebreyes. That provides additional support for both the genotypic findings, confirming the hypothesis that the contamination originated in the feed.

Gebreyes says that the source of feed contamination is most likely the feed ingredients, but that feed could be contaminated via handling, after processing.

“Although we cannot ascertain 100% that the feed was the source of contamination that was transmitted to the fecal samples, the findings strongly imply that fact,” says Gebreyes. “The other alternative is that the feed was contaminated after it was introduced into the barn. Regardless, the findings strongly imply that salmonella can be maintained and easily disseminated in a population of food animals.”

(B. Molla, A.Sterman, J. Mathews, V. Artuso-Ponte, M. Abley, W. Farmer, P. Rajala-Schultz, W. E. Morgan Morrow, W. A. Gebreyes. 2010. Salmonella enterica in Commercial Swine Feed and Subsequent Isolation of Phenotypically and Genotypically Related Strains from Fecal Samples. Applied and Environmental Microbiology; 76.21: 7188-7193.)

New, Much Faster, More Accurate Diagnostic for Influenza and Respiratory Syncytial Virus

A new, fully automated system is much quicker, and more accurate in diagnosing influenza A and B, and respiratory syncytial virus (RSV) A and B than conventional alternatives, according to a paper in the November Journal of Clinical Microbiology. The new technology promises faster and more appropriate treatment of patients.

“Instead of relying on insensitive but rapid influenza tests for diagnosis in the clinic, or waiting 24 hours or more for molecular results to come back, we can now provide molecular level sensitivity in less than three hours,” says principal investigator Nathan A. Ledeboer of the Medical College of Wisconsin, and Dynacare Laboratories, Milwaukee.

“This will mean that hospitalized patients with influenza and RSV infections will be isolated faster, which will decrease the risk of transmission to other patients in the hospital,” says Ledeboer. The faster turnaround also means that “fewer patients will be placed on empiric therapy, which will decrease costs and decrease the risk of an adverse event caused by medication.” In the study, the assay, a microarray, was tested on 720 patient samples collected throughout the US.

The new technology, called Respiratory Virus Nucleic Acid Test SP” (RVNATsp), is 98 percent sensitive (meaning that 98 percent of positive results are accurate) and 96 percent specific, meaning that 96 percent of negative results are accurate). By comparison, the conventional alternative, culture, is nearly 100 percent specific, but only 70 percent sensitive.

Influenza virus infects millions annually. It is typically associated with infections of the upper respiratory tract and can cause mild to severe illness. RSV can cause severe symptoms in infants, young children, and immunocompromised individuals, and is the leading cause of hospitalization of children under five years of age. In the most vulnerable individuals, children less than six months old, people with chronic lung disease, and immunocompromised individuals, RSV can migrate from the initial site of infection in the upper airway to the smaller bronchioles of the lower airway, where it can cause life-threatening bronchiolitis or pneumonia.

(P. J. Jannetto, B.W. Buchan, K. A. Vaughan, J. S. Ledford, D. K. Anderson, D. C. Henley, N. B. Quigley, N. A. Ledeboer. 2010. Real-Time Detection of Influenza A, Influenza B, and Respiratory Syncytial Virus A and B in Respiratory Specimens by Use of Nanoparticle Probes. Journal of Clinical Microbiology; 48.11: 3997-4002.)

Upending Conventional Wisdom, Certain Virus Families are Ancient

Certain families of single-stranded DNA virus are more than 40 to 50 million years old, according to investigators from the Institute for Advanced Study, Princeton, NJ, and the Fox Chase Cancer Center, Philadelphia. The investigators found remnants of circoviruses and parvoviruses in the genomes of diverse vertebrates from fishes to birds and mammals that had been integrated into their genomes at different times from the recent past to more than 50 million years ago. The research upends the conventional wisdom that most virus families are of very recent origin, and is published in the December Journal of Virology.

“Until recently, age estimates for all viruses except retroviruses were in the thousands of years, and nobody expected to be able to trace viruses beyond that time frame due to high mutation rates of the most commonly circulating viruses,” says Anna Marie Skalka of Fox Chase. “We showed that several families have been around for tens of millions of years, and have barely changed over that time frame.”

Viruses have long been speculated to be a source of novel animal genes, yet little evidence, except from retroviruses, has supported this idea. The team’s motivation included the desire to search for such evidence in other viruses.

“We first scanned all published vertebrate genomes for traces of single stranded RNA (ssRNA) viruses other than retroviruses,” says Skalka. The team then used a variety of techniques to devise a new method for determining the age of DNA sequences. “To our amazement, we discovered ancient fossils [viral sequences] in 19 vertebrate species that are related to certain currently circulating RNA viruses,” notably the deadly Ebolaviruses, and the Bornaviruses, she says. These results, published earlier this year, encouraged these investigators to look for ancient fossils derived from ssDNA viruses.

“Once again we were amazed to find sequences from replication (rep) and capsid genes from ancient viruses related to the Parvovirus and Circovirus families in 31 of the 49 vertebrate genomes we tested,” says Skalka.

While rep proteins from the circoviruses were already known — some of them selectively kill tumor cells — the relevant codes were certainly not known to have existed in vertebrates almost as far back as when the dinosaurs roamed earth. Skalka notes that there is no evidence yet that those coding sequences are expressed. “But should a beneficial role for these integrations be found, such as control of cancer progression, it may explain why these viruses were selected for over millions of years of vertebrate evolution.”

One additional notable finding is that the timeframe of the viral fossils’ appearance, 40-60 million years ago, was a time of rapid accumulation of exogenous and other elements into the genome, including multiple families of viruses, so-called “short interspersed elements” and pseudogenes. That’s a curious phenomenon which merits investigating, says first author Vladimir A. Belyi.

(V.A. Belyi, A J. Levine, A. Skalka. 2010. Sequences from Ancestral Single-Stranded DNA Viruses in Vertebrate Genomes: the Parvoviridae and Circoviridae Are More than 40 to 50 Million Years Old. Journal of Virology; 84.23: 12458-12462.)

Cellular Protein Hobbles HIV-1

A cellular protein called BST-2 had already been known to interfere with the spread of human immunodeficiency virus type 1 (HIV-1), by inhibiting the release of its progeny particles from infected cells. Now a team from McGill University, Montreal, shows that in addition, each progeny virion’s ability to cause infection is severely impaired.

“BST-2 may exert a more potent inhibition effect on HIV-1 transmission than previously thought,” says coauthor Chen Liang. The research is published in the December Journal of Virology.

BST-2 appears to attenuate infectivity of progeny particles by interfering with their maturation. Normally, during synthesis of new virus particles, a protein called PR55Gag is cleaved into three major structural proteins of HIV. “This cleavage process transforms HIV-1 from an immature and non-infectious virion into a mature and infectious virion,” says Chen. The protease inhibitors, drugs given to AIDS patients to contain the disease, block this step. Similarly, BST-2 seems to interfere with this step, because in the study, its presence was associated with accumulation of uncleaved Gag precursor and intermediate products. The mechanism of that interference has yet to be elucidated.

BST-2 (bone marrow stromal cell antigen-2), also known as tetherin, is a cellular protein which has been shown to restrict production of enveloped viruses besides HIV-1, including HIV-2, simian immunodeficiency virus, Kaposi’s sarcoma herpes virus, Lassa virus, Marburg virus, and Ebola virus. It interferes with release of new virus particles by anchoring one end of itself in the plasma membrane of the infected cell while the other end becomes inserted into the viral envelope.

Different viruses have evolved various countermeasures. For example, in the case of HIV-1, the viral protein Vpu downregulates BST-2 from the cell surface, removing it from virus budding sites.

“The antiviral function of BST-2 has been extensively studied by a number of groups besides ours,” says Chen. “Our hope is that the results of all of these studies can eventually be used to develop a BST-2 based anti-HIV-1 therapy.”

(J. Zhang, C. Liang. 2010. BST-2 Diminishes HIV-1 Infectivity. Journal of Virology; 84.23: 12336-12343.)

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