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ASM 2013, Day 3: Diversity is King

Amy Cullinan and Mimi Padmabandu
| May 22, 2013

Diversity was a celebrated theme, which is fitting given the wide range of phylogenetic, environmental, and morphological variation associated with microbial species. Two standout talks in the morning of the final day of ASM had me running to the convention center at 8:15 AM in the rain, iced coffee in hand. Julian Parkhill from the Wellcome Trust Sanger Institute gave a fantastic presentation on studying microbial transmission on both local and global levels using genomic methods. Dr. Parkhill cited two examples of microbial transmission and how next-generation sequencing enabled high-resolution phylogenetic mapping.

The first example was the emergence of highly invasive non-typhoidal salmonella typhimurium in sub-Saharan African populations in Malawi and the Democratic Republic of Congo. Normally a gut-associated pathogen with known transmission routes, the question was whether or not this represented a unique strain with new abilities to infect the host, or whether there was something about the humans in this area that was influencing the pathogen, or some complex combination of these. Using data from next-generation sequencing, Parkhill’s group generated a robust phylogenetic tree revealing two very closely related strains that each carried a virulence plasmid, and one of the lineages had acquired resistance to chloramphenicol, allowing it an evolutionary advantage. Examining the detailed trees of these new typhimurium lineages also provided a rich source of pseudogenes, mutations, and deletions in areas of the genome important for transmission. This and other epidemiological evidence showed that salmonella infection strongly coincides with HIV infection, suggesting that the microbes were actually adapting to niches in the population.

Dr. Parkhill presented another story about Mycobacterium abcessus, normally an environmental bug, which was increasingly being isolated from the sputum of cystic fibrosis patients. Along with clustering of reported infections, evidence suggested a shift in transmission patterns. Using data from high-throughput sequencing and phylogenetic analysis, many interesting clusters, some differing only by a handful of SNPs, were revealed. Importantly, these patterns suggested a hospital transmission route, despite tight infection control procedeures for CF patients. Although there was insufficient evidence for patient-to-patient transmission, the genome information revealed dominant M. abcessus clones circulating in the patient population.

Later in the morning, Bart Weimer from University of California at Davis gave an update on the 100K Genomes project, which aims to sequence the entire genomes of 100,000 foodborne pathogens. Motivated by the world’s food safety challenges, which includes a burgeoning human population, increased distances from food production areas, and larger and more deadly outbreaks of food-borne illnesses, the 100K genomes project aims to provide a validated database for in-depth study of common pathogen genomes. Drawing from work on particularly tough Salmonella enterica serotypes, Dr. Weimer gave examples of how compared to a 16S approach, whole-genome sequencing gives more informative phylogenetic clusters and can help identify new genes. Researchers can send in samples, and the team at UC Davis will process and sequence it, then give it back to the researcher who then has a year to analyze the data before it goes public. Drawing on the considerable genome sequencing capabilities of the Beijing Genome Institute’s new facilities in a joint venture, the project will use short-read sequencing technologies such as Illumina, followed in a few cases by long read sequencing technologies. The highest possible indexing strategies on the HiSeq 2500 will be used to maximize throughput, allowing de novo sequencing of 300-400 viral genomes per lane. With this wealth of genome information, researchers can even look for epigenetic modifications. Dr. Weimer shared with the audience that the first release of 100 foodborne pathogen genomes happened yesterday.

Alison Ling from the University of Colorado Boulder investigated the effect of microbial communities on concrete erosion in sewer pipes. Using both Sanger methods and the MiSeq system, Ling performed 16S rRNA sequencing of species isolated from two manholes. Sequencing revealed bacterial succession patterns, demonstrating that the neutrophile species (predominantly Gammaproteobacteria) originally in the manhole were dominated by acidophile species over time, with a corresponding significant drop in pH. Ling’s research provides insights into the mechanisms of sewer pipe erosion, which is estimated to have a significant impact on infrastructure expenditure.

Natasha De Leon Rodriguez from the University of Georgia presented preliminary results regarding the metagenome of the trophosphere. In collaboration with NASA, De Leon-Rodriguez isolated bacterial species from the atmosphere and used Illumina sequencing technology to analyze the metagenome. She found that 17 taxa were present across samples from different regions, regardless of location or time of sampling. Comparative metagenomic analysis is ongoing, and further analysis is required to understand how bacteria reach the atmosphere and stay aloft.

Alison E. Murray of the Desert Research Institute gave an adventurous talk about her expeditions to Antarctica’s Lake Vida to investigate the abiotic and life-associated processes in an icy, briny, dark environment. Analysis of 3H-leucine incorporation revealed evidence for protein synthesis, but interestingly did not show signs of DNA replication. Murray found a phylogenetically diverse and metabolically active microbial community dominated by gammaproteobacteria. Evidence for rRNA was detected for two phyla, and cultivation efforts resulted in isolates from three phyla. Murray used MiSeq and HiSeq instruments for metatranscriptomic analysis, and functional distribution of metatranscriptome reads mapped to closely related bacterial genomes.

The emergence of human infections with avian influenza viruses (H7N9 and H5N1) and the high mortality rates resulting from these viruses have raised concerns about the potential for a future pandemic and human-to-human transmission. While vaccines are in development, our understanding of these viruses is still incomplete. Robert Webster from The St. Jude Children’s Research Hospital presented a historical look at the progression of H5 and H7 subtypes. These subtypes had low pathogenicity in wild bird reservoirs, spread to domestic birds, acquired changes at the cleavage site of hemagglutinin, and were then transmitted to humans via live poultry markets. Webster indicates that a new strain, H9N2, is the main candidate on the watch list for the future, as it contains the genetic “backbone” (6 gene segments) of H5N1 and H7N9 and is endemic across the Eurasian continent. Complementing Webster’s talk, Albert D. Osterhaus of the Erasmus Medical Center presented concerns for potential human-to-human transmission of H7N9, as H7N9 replication and pathological changes demonstrated in ferret lungs are comparable to those seen with H5N1.