My research focuses on microbial population genomics and evolution. I was trained at the University of the Philippines (B.S.), Binghamton University (M.S.), University of Connecticut (Ph.D.), Cornell University (Postdoc) and the Harvard School of Public Health (Postdoc).
Current work in my lab aims to elucidate the evolutionary processes and ecological factors that drive the diversification and adaptation of microorganisms in different environments. Specifically, we study the genomic differences between strains and species, with implications to the evolution of antibiotic resistance, emergence of virulent lineages, host adaptation, gene flow, geographical distribution and spread. Using an inter-disciplinary approach combining next-generation sequencing (genomics), population genetics, phylogenetics and lab-based assays, we ask the questions:
(1) How extensive are the genomic differences within a species? How did they arise and to which extent are they neutral or adaptive?
(2) How do perturbations, such as antibiotic use or environmental change, alter the genomic diversity and population structure of microbes?
(3) What is the genetic basis of host adaptation and host switching?
(4) How is resistance maintained and distributed in bacterial populations, and what are the mechanisms that promote the emergence and dissemination of super-fit multidrug resistant clones?
(5) How can we use genomic data to identify co-circulating, independent transmission chains and unsuspected “cryptic” transmission events?
We study different species of bacterial pathogens. My lab works closely with the New Hampshire Veterinary Diagnostic Laboratory (NHVDL) to study the emergence of antibiotic resistance in multiple Staphylococcus species and enteric bacteria from pets, livestock and wildlife. We also work with NH state health and agriculture agencies to study the genome dynamics and evolution of bacterial pathogens such as Salmonella enterica, Campylobacter jejuni and Staphylococcus aureus infecting humans and animals. We also use publicly available genomes to further explore the nature of microbial species and the different evolutionary processes that contribute to their diversification and adaptation.
Within-species variation: Bacterial and archaeal populations are remarkably heterogeneous. They may be clonal, but microbial populations are often composed of multiple co-circulating lineages distinguished by phenotypic and genetic differences, the latter originating from both allelic variation and gene content variation. While puzzling, within-species heterogeneity in microbes is not uncommon, but the underlying factors that drive this variation remain unclear. We are interested in understanding the processes that contribute to the generation and maintenance of this variation within a species. To address this, we study "populations of genomes" that represent clusters of close relatives within and between environments or hosts.
Horizontal gene transfer (HGT) and recombination: The acquisition of genetic material between two organisms that do not share a direct ancestor-descendant relationship is an important mechanism that contributes to the rapid creation of biological novelty that otherwise might have taken millions of years to occur. This is particularly pervasive across microbial lineages, creating phenotypic and genetic variation that can take bewilderingly complex forms even between closely related lineages. HGT enables organisms to acquire pre-existing adaptive characters from other organisms, regardless of phylogenetic distance. Thus, instead of genetic traits within lineages always emerging gradually through successive mutations and selection, evolution is accelerated as a parallel process, where inventions made in different lineages can come together in a single cell through HGT. In microbial populations, HGT and recombination (the acquisition of genetic material through genetic exchange of similar DNA sequences) are important proc
Ph.D., Microbiology, University of Connecticut
M.S., Biology/Biological Sciences, State University of New York at Binghamton
B.S., Forestry, University of The Phillipines
Ecology and Population
BMS 503: General Microbiology
BMS 504: General Microbiology Lab
BMS 703: Infectious Disease and Health
GEN 713: Microbial Ecology & Evolution
INCO 790: Adv Rsrch Exp/MCBS
MESB 999: Doctoral Research
Smith, M. M., Park, C. J., Andam, C. P., & Aber, J. D. (2018). Utilization of Low Grade Wood for Use as Animal Bedding: A Case Study of Eastern Hemlock. Journal of Forestry, 116(6), 520-528. doi:10.1093/jofore/fvy040
Chang, Q., Abuelaish, I., Biber, A., Jaber, H., Callendrello, A., Andam, C. P., . . . Hanage, W. P. (2018). Genomic epidemiology of meticillin-resistant Staphylococcus aureus ST22 widespread in communities of the Gaza Strip, 2009. Eurosurveillance, 23(34). doi:10.2807/1560-7917.es.2018.23.34.17-00592
Chang, Q., Abuelaish, I., Biber, A., Jaber, H., Callendrello, A., Andam, C. P., . . . Hanage, W. P. (2018). Genomic epidemiology of meticillin-resistant Staphylococcus aureus ST22 widespread in communities of the Gaza Strip, 2009. Eurosurveillance, 23(34). doi:10.2807/1560-7917.es.2018.23.34.1700592
McGill, C. M., Tomco, P. L., Ondrasik, R. M., Belknap, K. C., Dwyer, G. K., Quinlan, D. J., . . . Barth, B. M. (2018). Therapeutic effect of Northern Labrador tea extracts for acute myeloid leukemia. Phytotherapy Research, 32(8), 1636-1641. doi:10.1002/ptr.6091
Chaguza, C., Cornick, J. E., Andam, C. P., Gladstone, R. A., Alaerts, M., Musicha, P., . . . Everett, D. B. (2017). Population genetic structure, antibiotic resistance, capsule switching and evolution of invasive pneumococci before conjugate vaccination in Malawi. Vaccine, 35(35), 4594-4602. doi:10.1016/j.vaccine.2017.07.009
Andam, C. P., Fournier, G. P., & Gogarten, J. P. (2011). Multilevel populations and the evolution of antibiotic resistance through horizontal gene transfer. FEMS Microbiology Reviews, 35(5), 756-767. doi:10.1111/j.1574-6976.2011.00274.x
Andam, C. P., & Gogarten, J. P. (2011). Biased gene transfer in microbial evolution. Nature Reviews Microbiology, 9(7), 543-555. doi:10.1038/nrmicro2593
Williams, D., Fournier, G. P., Lapierre, P., Swithers, K. S., Green, A. G., Andam, C. P., & Gogarten, J. P. (2011). A Rooted Net of Life. Biology Direct, 6(1), 45. doi:10.1186/1745-6150-6-45
Andam, C. P., Williams, D., & Gogarten, J. P. (2010). Biased gene transfer mimics patterns created through shared ancestry. Proceedings of the National Academy of Sciences, 107(23), 10679-10684. doi:10.1073/pnas.1001418107
Andam, C. P., Mondo, S. J., & Parker, M. A. (2007). Monophyly of nodA and nifH Genes across Texan and Costa Rican Populations of Cupriavidus Nodule Symbionts. Applied and Environmental Microbiology, 73(14), 4686-4690. doi:10.1128/aem.00160-07