Tips from the journals of the American Society for Microbiology

Sequences of H5N1 virus from live bird markets in China matched sequences from patients who had recently visited the live bird markets, according to a paper in the December 2011 Journal of Virology. Live poultry markets have long been suspected of providing the reservoir of H5N1 responsible for human cases, but this is the first molecular evidence linking H5N1 in humans to these markets, the authors say.

"We collected 69 environmental samples—basically swabs from ditches, cages, floors, water, and so on—from the live bird markets, which six individual patients visited before disease onset," during the 2008-2009 flu season, says corresponding author Yuelong Shu. "Among these 69 samples, we isolated a total of 12 highly pathogenic H5N1 avian influenza viruses from four of the six live bird markets." In those cases, "the genetic sequence of the environmental and corresponding human isolates was similar [with a sequence identity of greater than 99 percent], demonstrating a solid link between human infection and live poultry markets," says Shu.

The investigators also analyzed 31 H5N1 highly pathogenic avian influenza viruses isolated from the 38 human H5N1 cases identified in China during the past five years, revealing "diverse genotypes… that were consistent with those identified in poultry outbreaks or in live poultry markets," according to the report.

The results of this investigation have important policy implications, says Shu. "Enhanced infection control measures are warranted in these markets, not only to reduce human H5N1 infection, but also to minimize the likelihood of coinfection with H5N1 and 2009 H1N1 viruses," the researchers write. "The sporadic cases of human H5N1 highly pathogenic avian influenza infection, the H5N1 outbreaks in birds, and the simultaneous circulation of the 2009 H1N1 pandemic virus in China raise concern that a deadly reassortment virus may emerge."

(X.-F. Wan, L. Dong, Y. Shu, et al. Indications that live poultry markets are a major source of human H5N1 influenza virus infection in China. J. Virol. 85:13432-13438.)

A compound that is abundant in apples and strawberries inhibits the highly pathogenic E. coli O157:H7 biofilms while sparing a beneficial strain of E. coli that also forms biofilms in the human gut, according to a paper in the December 2011 issue of the journal Infection and Immunology.

Transcriptome analysis revealed that the compound, called phloretin, suppresses toxin and other genes involved in O157:H7 pathology and biofilm formation. And in a rat model of colitis, phloretin, reduced colon inflammation and body weight loss. "Phloretin has a triple biological activity as an antioxidant compound, a biofilm inhibitor, and an anti-inflammatory agent," says corresponding author Jintae Lee of Yeungnam University, Gyeongsan, Korea.

E. coli O157:H7 causes hemorrhages in the intestine. To date, no effective therapy for O157:H7 biofilms has been found. Biofilms generally are notoriously resistant to antimicrobial therapy. So in the study, Lee screened a dozen flavonoids, including phloretin, for their ability to inhibit these biofilms. "We found that phloretin markedly reduced E. coli O157:H7 biofilm formation on abiotic surface and human colon epithelial cells, while phloretin did not harm commensal E. coli K-12 biofilms," says Lee. Commensal E. coli can actually fortify the human immune system, he says.

In addition to its anti- E. coli O157:H7 biofilm activity, phloretin "accounts in part for the antioxidant capacity of apples, and it also shows anti-inflammatory activity," says Lee. "This study suggests that phloretin in apples could reduce the risk of E. coli O157:H7 infection and intestinal inflammation."

"This study demonstrated for the first time that phloretin, a natural flavonoid, is a nontoxic inhibitor of enterohemorrhagic E. coli O157:H7 biofilms, but does not harm commensal E. coli K-12 biofilms," Lee writes. "Also, importantly, our results confirmed that phloretin shows anti-inflammatory properties in both the in vitro and in vivo inflammatory colitis models. The effect of phloretin was noticeably more pronounced than that of the conventional [inflammatory bowel disease] drug 5-aminosalicylic acid."

(J.-H. Lee, S.C. Regmi, J.-A. Kim, M.H. Cho, H. Yun, C.-S. Lee, and J. Lee, 2011. Apple flavonoid phloretin inhibits Escherichia coli O157:H7 biofilm formation and ameliorates colon inflammation in rats. Infect. Immun. 79:4819-4827.)

Microbes in human incubators, like those found in neonatal intensive care units, grow most robustly on cold spots when the relative humidity is at least 60 percent, according to a paper in the December 2011 issue of the journal Applied and Environmental Microbiology.

Two of the high humidity incubators tested in this study sustained contamination by Staphylococcus, "a reason for concern, since the vast majority of infections in preterm neonates are caused by… [staphylococci]," according to the report. Additionally, the researchers observed "slightly increased numbers of Gram-negative bacteria at the cold sites of neonatal incubators with high humidity levels," noting that infections with such "are known to have the highest neonatal death rates."

In this study, Hermie J.M. Harmsen and colleagues of the University of Groningen, The Netherlands, sampled cold and warm spots from 12 incubators with a relative humidity of at least 60 percent, and a temperature of at least 34 degrees C., and 11 incubators with a relative humidity of less than 60%, and a temperature of less than 34 degrees C. Most of the cold and warm spots from the latter incubators, as well as the warm spots from the former turned up negative for microbial contamination, but cold spots from the incubators with high relative humidity "had much higher colony forming unit counts on average than the other three groups," says Harmsen.

The research is important, says Harmsen, in order to reduce the incidence of microbial infection in neonates. "A direct relation between microbial growth in an incubator and infection has yet to be shown but common sense dictates it would be better if the temperature distribution within an incubator were as homogeneous as possible," he says.

Cold spots in warm, humid incubators and other closed environments are particularly vulnerable to contamination because the most important limiting factor for microbes in such environments is lack of moisture, and in such environments, the relative humidity is higher around cold spots, says Harmsen.

Interestingly, the research grew out of a project to create a risk assessment model for microbial growth on board the International Space Station, says Harmsen. "A neonatal incubator is not only a perfect model system for the International Space Station, as its average temperature and relative humidity are controlled and its inhabitants are both somewhat immune-compromised; this clinical setting is also very relevant itself as microbial infection and subsequent mortality in neonates are matters of great importance," says Harmsen. "Being able to predict which areas of an incubator might be more highly contaminated, based solely on the local temperature distribution, would facilitate improvement of hygiene in the incubator."

(M.C. de Goffau, K.A. Bergman, H.J. de Vries, N.E.L. Meessen, J.E. Degener, J.M. van Dijl, and H.J.M. Harmsen, 2011. Cold spots in neonatal incubators are hot spots for microbial contamination. Appl. Environ. Microbiol. 77:8568-8572.)

Concentrated animal feeding operations (CAFOs) on industrial animal factories can stink up an entire county, due to ammonia, and a smorgasbord of volatile organic compounds (VOCs). Jeppe Lund Nielsen of Aalborg University, Aalborg, Denmark, et al. report that biofiltration with microbial filters can remove most of the butyric acid, dimethyl disulfide, and ammonia from the exhaust air, along with other smelly compounds. The research is published in the December 2011 issue of the journal Applied and Environmental Microbiology.

The investigators mounted trickle biofilters directly on livestock facilities. These filters are stuffed with porous corrugated cellulose pads that serve the bacteria as soil does plants, and irrigated with water to support the active biofilm and wash away toxic waste.

"We hypothesized that the bacteria in these air filters would be highly specialized, with individual microbes targeting specific organic compounds in the smell, which consists of 200-300 compounds in total," says Nielsen. The study's main aim was to identify microorganisms involved in breaking down butyric acid and dimethyl disulfide, as well as to measure their performance. The filters removed 99.9 percent, 94 percent, and 90 percent of the butyric acid, dimethyl disulfide, and ammonia in the exhaust air, respectively, as well as reducing carboxylic acid concentrations by more than 70 percent, organic sulfur compounds by up to 50 percent, and various aromatic compounds by anywhere from 48 to 89 percent. The main community members breaking down dimethyl disulfide were Actinobacteria, followed by the betaproteobacterial ammonia-oxidizing bacteria, and bacteroidetes, as well as some fungi.

Nielsen adds that humans can smell some of these compounds at concentrations of less than a part per billion, and thus, that "only very specialized microbes [would] thrive at such low concentrations… This aspect of the filter environment was expected to select for a uniquely tolerant group of specialized microbes."

(Anja Kristiansen, Sabine Lindholst, Anders Feilberg, Per H. Nielsen, Josh D. Neufeld and Jeppe L. Nielsen, 2011. Butyric acid- and dimethyl disulfide-assimilating microorganisms in a biofilter treating air emissions from a livestock facility. Appl. Environ. Microbiol. 77:8595-8604.)

The American Society for Microbiology is the largest single life science society, composed of over 39,000 scientists and health professionals. ASM's mission is to advance the microbiological sciences as a vehicle for understanding life processes and to apply and communicate this knowledge for the improvement of health and environmental and economic well-being worldwide.