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ASM 2013, Day 2: Clinical Microbiology and Agricultural Metagenomics

Mimi Padmabandu
| May 21, 2013

grapesTo kick off the discussion about clinical microbiology, Victor Nizet from the University of California San Diego spoke about his work on virulence factors using Staphylococcus aureus. He and his colleagues noted that the structure of the golden pigment molecule seen in S. aureus resembles the structure of beta carotene and other antioxidants. Experimental knockout of this pigment caused S. aureus to become more susceptible to host oxidative killing mechanisms, and introduction of this pigment gene increased the virulence of that strep strain. Nizet proposed that the golden pigment may be a potential target for drug therapy development.

Next, Sarah M. Fortune from the Harvard School of Public Health discussed strain-based differences in the evolution of drug resistance in Mycobacterium tuberculosis, and the potential for this rapid evolution of drug resistance to create “super bugs.” She explained that some patients with tuberculosis clear the infection with treatment while other patients fail to clear the infection because they acquire de novo drug-resistant organisms. To investigate the reasons for this de novo development of drug resistance, Fortune and colleagues used whole-genome sequencing and the macaque model to determine the mutation rate of M. tuberculosis. Contrary to expectations, they found that organisms acquired mutations at the same rate regardless of disease state—M. tuberculosis mutated at the same rate both per day and over time.

Fortune then collaborated with Jennifer Gardy of the British Columbia Centre for Disease Control to find the M. tuberculosis mutation rate in humans. With Gardy’s expertise in outbreak surveillance and genomic epidemiology, whole-genome sequencing of isolates from humans demonstrated that M. tuberculosis was acquiring mutations at the same rate in humans as in macaques. Fortune also found that when M. tuberculosis is killed by host mechanisms, the virus—specifically the genome—remains present for some time, so that bacterial burdens are the same whether or not the virus is viable. This finding led Fortune to conclude that a time-dependent factor, such as DNA damage, is the driver for genomic diversity in M. tuberculosis. Fortune and colleagues further identified a strong signature of oxidative DNA damage consistent with this hypothesis.

Jean-Laurent Casanova of Rockefeller University spoke about primary infection in childhood in the context of invasive pneumococcal disease (IPD). Some children with IPD lack a spleen at birth (isolated congenital asplenia, or ICA), and ICA has been correlated with a predisposition to bacterial infections. Using whole-exome sequencing, Casanova examined commonly mutated genes among 23 ICA exomes and identified the RPSA gene as a strong candidate for causing ICA. Further sequencing and analysis of RPSA mutations suggests that mutations in RPSA impair spleen development. Because RPSA is a ribosomal protein, this finding presents a case for epigenetic regulation of protein translation.

Robert Doms from the University of Pennsylvania, Chair and Pathologist-in-Chief at the Children’s Hospital of Pennsylvania, posed the question: Can we recreate the cure of HIV in the case of Timothy Brown by another method? Doms collaborated with Sangamo Biosciences to isolate T cells, genetically inactive the CCR5 coreceptor using zinc finger nucleases (which cleave the target sequence to case a double-stranded break), and then reintroduce the modified T cells. They identified the mutated CCR5 allele caused by zinc finger nucleases, and ongoing and future studies will explore methods for improving zinc finger nuclease cleavage efficiency and identifying these genomic rearrangements.

Metagenomics in Agriculture

There was also a trend at ASM this year of examining the role of microbes in food production. Andrew Benson of the University of Nebraska presented applications of high-throughput metagenome analyses in the pre- and post-harvest environments. As pre-harvest applications include human gut health, metagenome sequencing on HiSeq platforms identified microbial taxa and function in the gut, and also identified archaebacteria, which Benson noted would have been lost with standard 16S metagenomics. To examine applications in the post-harvest environment, Benson used Illumina bovine BeadChips to study genetic diversity in beef cattle, and he remarked that post-harvest applications of microbiome analysis are just beginning.

Presenting the “merlot microbiome,” Iratxe Zarraonaindia from the Argonne National Laboratory discussed the role that microbes play in plant health and productivity, remarking that “in order to understand what is happening in red wine, it’s not enough to just understand the grapes.” Zarraonaindia used sequencing with MiSeq and HiSeq systems to resolve differences in the microbial species composition of different plant tissues. In flowers, 98.6% of the microbes were gammaproteobacteria, whereas in grapes and leaves, alphaproteobacteria were abundant. Zarraonaindia also annotated the functional differences among roots and bulk soil, providing opportunities for future study of microbial interactions with plant hosts.

The Foundation for Discoveries and Applications of the Future

At the President’s Forum, Keith Yamamoto and Margaret McFall-Ngai spoke about the importance of curiosity-driven basic research for the future of science. McFall-Ngai of the University of Wisconsin-Madison used examples from hydra, zebrafish, the medicinal leech, and the Hawaiian bobtail squid to explain the mechanisms of host-microbe interactions. She presented a detailed look at the symbiosis between Vibrio fischeri and squid, as V. fischeri chemotaxes to the squid light organ by sensing chitobiose. An RNA-Seq experiment revealed that the host transcriptome is regulated by five V. fischeri cells in the aggregate, and that the chitotriosidase gene (which converts polymeric chitin into chitobiose) is robustly upregulated, providing insight into the mechanism of symbiosis.

Yamamoto, Vice Chancellor for Research at the University of California San Francisco, Executive Vice Dean of the School of Medicine, and Chair of the Coalition for Life Sciences, argued that biological research is at an inflection point. To move through this inflection point, Yamamoto maintained that integration, outreach and advocacy, and education are key. He contended that federally funded research is a public trust, and that advocacy is an important way for scientists to justify this trust and fight for good policies. The implications of this paradigm for the future of ASM, according to Yamamoto, are for ASM to maintain leadership in promoting microbiology research, engage the public and policymakers, and serve as the convening center for developing new education programs and practices. Both Yamamoto and Jeff F. Miller, president of ASM, remarked that they hope to see ASM on the list of collaborators in the Coalition for Life Sciences in the near future.