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Caitlin Pepperell

Picture of Caitlin PepperellAssistant Professor of Medicine and Medical Microbiology & Immunology
5301 Microbial Sciences Building
1550 Linden Drive
Office: (608) 262-5983
Laboratory: 262-6167
Email: pepperell@wisc.edu
Overview · Personnel · Publications · Lab Website
  • Mortimer TD, Weber AM, Pepperell CS (2018) Signatures of Selection at Drug Resistance Loci in . mSystems 3(1): (PMC5790871) View Abstract · Pubmed Record

    Tuberculosis (TB) is the leading cause of death by an infectious disease, and global TB control efforts are increasingly threatened by drug resistance in . Unlike most bacteria, where lateral gene transfer is an important mechanism of resistance acquisition, resistant arises solely by chromosomal mutation. Using whole-genome sequencing data from two natural populations of , we characterized the population genetics of known drug resistance loci using measures of diversity, population differentiation, and convergent evolution. We found resistant subpopulations to be less diverse than susceptible subpopulations, consistent with ongoing transmission of resistant . A subset of resistance genes ("sloppy targets") were characterized by high diversity and multiple rare variants; we posit that a large genetic target for resistance and relaxation of purifying selection contribute to high diversity at these loci. For "tight targets" of selection, the path to resistance appeared narrower, evidenced by single favored mutations that arose numerous times in the phylogeny and segregated at markedly different frequencies in resistant and susceptible subpopulations. These results suggest that diverse genetic architectures underlie drug resistance in and that combined approaches are needed to identify causal mutations. Extrapolating from patterns observed for well-characterized genes, we identified novel candidate variants involved in resistance. The approach outlined here can be extended to identify resistance variants for new drugs, to investigate the genetic architecture of resistance, and when phenotypic data are available, to find candidate genetic loci underlying other positively selected traits in clonal bacteria. , the causative agent of tuberculosis (TB), is a significant burden on global health. Antibiotic treatment imposes strong selective pressure on populations. Identifying the mutations that cause drug resistance in is important for guiding TB treatment and halting the spread of drug resistance. Whole-genome sequencing (WGS) of isolates can be used to identify novel mutations mediating drug resistance and to predict resistance patterns faster than traditional methods of drug susceptibility testing. We have used WGS from natural populations of drug-resistant to characterize effects of selection for advantageous mutations on patterns of diversity at genes involved in drug resistance. The methods developed here can be used to identify novel advantageous mutations, including new resistance loci, in and other clonal pathogens.

  • Mortimer TD, Annis DS, O'Neill MB, Bohr LL, Smith TM, Poinar HN, Mosher DF, Pepperell CS (2017) Adaptation in a Fibronectin Binding Autolysin of . mSphere 2(6): (PMC5705806) View Abstract · Pubmed Record

    Human-pathogenic bacteria are found in a variety of niches, including free-living, zoonotic, and microbiome environments. Identifying bacterial adaptations that enable invasive disease is an important means of gaining insight into the molecular basis of pathogenesis and understanding pathogen emergence. , a leading cause of urinary tract infections, can be found in the environment, food, animals, and the human microbiome. We identified a selective sweep in the gene encoding the Aas adhesin, a key virulence factor that binds host fibronectin. We hypothesize that the mutation under selection (_2206A>C) facilitates colonization of the urinary tract, an environment where bacteria are subject to strong shearing forces. The mutation appears to have enabled emergence and expansion of a human-pathogenic lineage of . These results demonstrate the power of evolutionary genomic approaches in discovering the genetic basis of virulence and emphasize the pleiotropy and adaptability of bacteria occupying diverse niches. is an important cause of urinary tract infections (UTI) in women; such UTI are common, can be severe, and are associated with significant impacts to public health. In addition to being a cause of human UTI, can be found in the environment, in food, and associated with animals. After discovering that UTI strains of are for the most part closely related to each other, we sought to determine whether these strains are specially adapted to cause disease in humans. We found evidence suggesting that a mutation in the gene is advantageous in the context of human infection. We hypothesize that the mutation allows to survive better in the human urinary tract. These results show how bacteria found in the environment can evolve to cause disease.

  • Mortimer TD, Weber AM, Pepperell CS (2017) Evolutionary Thrift: Mycobacteria Repurpose Plasmid Diversity during Adaptation of Type VII Secretion Systems. Genome Biol Evol 9(3):398-413 (PMC5381665) View Abstract · Pubmed Record

    Mycobacteria have a distinct secretion system, termed type VII (T7SS), which is encoded by paralogous chromosomal loci (ESX) and associated with pathogenesis, conjugation, and metal homeostasis. Evolution of paralogous gene families is of interest because duplication is an important mechanism by which novel genes evolve, but there are potential conflicts between adaptive forces that stabilize duplications and those that enable evolution of new functions. Our objective was to delineate the adaptive forces underlying diversification of T7SS. Plasmid-borne ESX were described recently, and we found evidence that the initial duplication and divergence of ESX systems occurred on plasmids and was driven by selection for advantageous mutations. Plasmid conjugation has been linked to T7SS and type IV secretion systems (T4SS) in mycobacteria, and we discovered that T7SS and T4SS genes evolved in concert on the plasmids. We hypothesize that differentiation of plasmid ESX helps to prevent conjugation among cells harboring incompatible plasmids. Plasmid ESX appear to have been repurposed following migration to the chromosome, and there is evidence of positive selection driving further differentiation of chromosomal ESX. We hypothesize that ESX loci were initially stabilized on the chromosome by mediating their own transfer. These results emphasize the diverse adaptive paths underlying evolution of novelty, which in this case involved plasmid duplications, selection for advantageous mutations in the mobile and core genomes, migration of the loci between plasmids and chromosomes, and lateral transfer among chromosomes. We discuss further implications for the choice of model organism to study ESX functions in Mycobacterium tuberculosis.

  • Devault AM, Mortimer TD, Kitchen A, Kiesewetter H, Enk JM, Golding GB, Southon J, Kuch M, Duggan AT, Aylward W, Gardner SN, Allen JE, King AM, Wright G, Kuroda M, Kato K, Briggs DE, Fornaciari G, Holmes EC, Poinar HN, Pepperell CS (2017) A molecular portrait of maternal sepsis from Byzantine Troy. Elife 6: (PMC5224923) View Abstract · Pubmed Record

    Pregnancy complications are poorly represented in the archeological record, despite their importance in contemporary and ancient societies. While excavating a Byzantine cemetery in Troy, we discovered calcified abscesses among a woman's remains. Scanning electron microscopy of the tissue revealed 'ghost cells', resulting from dystrophic calcification, which preserved ancient maternal, fetal and bacterial DNA of a severe infection, likely chorioamnionitis. and dominated the abscesses. Phylogenomic analyses of ancient, historical, and contemporary data showed that Troy fell within contemporary genetic diversity, whereas Troy belongs to a lineage that does not appear to be commonly associated with human disease today. We speculate that the ecology of infection may have differed in the ancient world as a result of close contacts between humans and domesticated animals. These results highlight the complex and dynamic interactions with our microbial milieu that underlie severe maternal infections.

  • Eldholm V, Pettersson JH, Brynildsrud OB, Kitchen A, Rasmussen EM, Lillebaek T, Rønning JO, Crudu V, Mengshoel AT, Debech N, Alfsnes K, Bohlin J, Pepperell CS, Balloux F (2016) Armed conflict and population displacement as drivers of the evolution and dispersal of Mycobacterium tuberculosis. Proc. Natl. Acad. Sci. U.S.A. 113(48):13881-13886 (PMC5137683) View Abstract · Pubmed Record

    The "Beijing" Mycobacterium tuberculosis (Mtb) lineage 2 (L2) is spreading globally and has been associated with accelerated disease progression and increased antibiotic resistance. Here we performed a phylodynamic reconstruction of one of the L2 sublineages, the central Asian clade (CAC), which has recently spread to western Europe. We find that recent historical events have contributed to the evolution and dispersal of the CAC. Our timing estimates indicate that the clade was likely introduced to Afghanistan during the 1979-1989 Soviet-Afghan war and spread further after population displacement in the wake of the American invasion in 2001. We also find that drug resistance mutations accumulated on a massive scale in Mtb isolates from former Soviet republics after the fall of the Soviet Union, a pattern that was not observed in CAC isolates from Afghanistan. Our results underscore the detrimental effects of political instability and population displacement on tuberculosis control and demonstrate the power of phylodynamic methods in exploring bacterial evolution in space and time.

  • Dang UJ, Devault AM, Mortimer TD, Pepperell CS, Poinar HN, Golding GB (2016) Estimation of Gene Insertion/Deletion Rates with Missing Data. Genetics 204(2):513-529 (PMC5068843) View Abstract · Pubmed Record

    Lateral gene transfer is an important mechanism for evolution among bacteria. Here, genome-wide gene insertion and deletion rates are modeled in a maximum-likelihood framework with the additional flexibility of modeling potential missing data. The performance of the models is illustrated using simulations and a data set on gene family phyletic patterns from Gardnerella vaginalis that includes an ancient taxon. A novel application involving pseudogenization/genome reduction magnitudes is also illustrated, using gene family data from Mycobacterium spp. Finally, an R package called indelmiss is available from the Comprehensive R Archive Network at https://cran.r-project.org/package=indelmiss, with support documentation and examples.

  • O'Neill MB, Mortimer TD, Pepperell CS (2015) Diversity of Mycobacterium tuberculosis across Evolutionary Scales. PLoS Pathog. 11(11):e1005257 (PMC4642946) View Abstract · Pubmed Record

    Tuberculosis (TB) is a global public health emergency. Increasingly drug resistant strains of Mycobacterium tuberculosis (M.tb) continue to emerge and spread, highlighting adaptability of this pathogen. Most studies of M.tb evolution have relied on 'between-host' samples, in which each person with TB is represented by a single M.tb isolate. However, individuals with TB commonly harbor populations of M.tb numbering in the billions. Here, we use analyses of M.tb genomic data from within and between hosts to gain insight into influences shaping genetic diversity of this pathogen. We find that the amount of M.tb genetic diversity harbored by individuals with TB can vary dramatically, likely as a function of disease severity. Surprisingly, we did not find an appreciable impact of TB treatment on M.tb diversity. In examining genomic data from M.tb samples within and between hosts with TB, we find that genes involved in the regulation, synthesis, and transportation of immunomodulatory cell envelope lipids appear repeatedly in the extremes of various statistical measures of diversity. Many of these genes have been identified as possible targets of selection in other studies employing different methods and data sets. Taken together, these observations suggest that M.tb cell envelope lipids are targets of selection within hosts. Many of these lipids are specific to pathogenic mycobacteria and, in some cases, human-pathogenic mycobacteria. We speculate that rapid adaptation of cell envelope lipids is facilitated by functional redundancy, flexibility in their metabolism, and their roles mediating interactions with the host.

  • Ackley SF, Liu F, Porco TC, Pepperell CS (2015) Modeling historical tuberculosis epidemics among Canadian First Nations: effects of malnutrition and genetic variation. PeerJ 3:e1237 (PMC4586807) View Abstract · Pubmed Record

    Late 19th century epidemics of tuberculosis (TB) in Western Canadian First Nations resulted in peak TB mortality rates more than six times the highest rates recorded in Europe. Using a mathematical modeling approach and historical TB mortality time series, we investigate potential causes of high TB mortality and rapid epidemic decline in First Nations from 1885 to 1940. We explore two potential causes of dramatic epidemic dynamics observed in this setting: first, we explore effects of famine prior to 1900 on both TB and population dynamics. Malnutrition is recognized as an individual-level risk factor for TB progression and mortality; its population-level effects on TB epidemics have not been explored previously. Second, we explore effects of heterogeneity in susceptibility to TB in two ways: modeling heterogeneity in susceptibility to infection, and heterogeneity in risk of developing disease once infected. Our results indicate that models lacking famine-related changes in TB parameters or heterogeneity result in an implausibly poor fit to both the TB mortality time series and census data; the inclusion of these features allows for the characteristic decline and rise in population observed in First Nations during this time period and confers improved fits to TB mortality data.

  • Mortimer TD, Pepperell CS (2014) Genomic signatures of distributive conjugal transfer among mycobacteria. Genome Biol Evol 6(9):2489-500 (PMC4202316) View Abstract · Pubmed Record

    Distributive conjugal transfer (DCT) is a newly described mechanism of lateral gene transfer (LGT) that results in a mosaic transconjugant structure, similar to the products of meiosis. We have tested popular LGT detection methods on whole-genome sequence data from experimental DCT transconjugants and used the best performing methods to compare genomic signatures of DCT with those of LGT through natural transformation, conjugative plasmids, and mobile genetic elements (MGE). We found that DCT results in transfer of larger chromosomal segments, that these segments are distributed more broadly around the chromosome, and that a greater proportion of the chromosome is affected by DCT than by other mechanisms of LGT. We used the best performing methods to characterize LGT in Mycobacterium canettii, the mycobacterial species most closely related to Mycobacterium tuberculosis. Patterns of LGT among M. canettii were highly distinctive. Gene flow appeared unidirectional, from lineages with minimal evidence of LGT to isolates with a substantial proportion (6-13%) of sites identified as recombinant. Among M. canettii isolates with evidence of LGT, recombinant fragments were larger and more evenly distributed relative to bacteria that undergo LGT through natural transformation, conjugative plasmids, and MGE. Spatial bias in M. canettii was also unusual in that patterns of recombinant fragment sharing mirrored overall phylogenetic structure. Based on the proportion of recombinant sites, the size of recombinant fragments, their spatial distribution and lack of association with MGE, as well as unidirectionality of DNA transfer, we conclude that DCT is the predominant mechanism of LGT among M. canettii.

  • de Haas DW, Pepperell C, Foley J (2014) Perspectives on greenhouse gas emission estimates based on Australian wastewater treatment plant operating data. Water Sci. Technol. 69(3):451-63 View Abstract · Pubmed Record

    Primary operating data were collected from forty-six wastewater treatment plants (WWTPs) located across three states within Australia. The size range of plants was indicatively from 500 to 900,000 person equivalents. Direct and indirect greenhouse gas emissions were calculated using a mass balance approach and default emission factors, based on Australia's National Greenhouse Energy Reporting (NGER) scheme and IPCC guidelines. A Monte Carlo-type combined uncertainty analysis was applied to the some of the key emission factors in order to study sensitivity. The results suggest that Scope 2 (indirect emissions due to electrical power purchased from the grid) dominate the emissions profile for most of the plants (indicatively half to three quarters of the average estimated total emissions). This is only offset for the relatively small number of plants (in this study) that have significant on-site power generation from biogas, or where the water utility purchases grid electricity generated from renewable sources. For plants with anaerobic digestion, inventory data issues around theoretical biogas generation, capture and measurement were sometimes encountered that can skew reportable emissions using the NGER methodology. Typically, nitrous oxide (N(2)O) emissions dominated the Scope 1 (direct) emissions. However, N(2)O still only accounted for approximately 10 to 37% of total emissions. This conservative estimate is based on the 'default' NGER steady-state emission factor, which amounts to 1% of nitrogen removed through biological nitrification-denitrification processing in the plant (or indicatively 0.7 to 0.8% of plant influent total nitrogen). Current research suggests that true N(2)O emissions may be much lower and certainly not steady-state. The results of this study help to place in context research work that is focused on direct emissions from WWTPs (including N(2)O, methane and carbon dioxide of non-biogenic origin). For example, whereas non-biogenic CO(2) contributions are relatively minor, it appears that opportunities to reduce indirect emissions as a result of modest savings in power consumption are at least in the same order as those from reducing N(2)O emissions. To avoid potentially high reportable emissions under NGER guidelines, particularly for methane, the onus is placed on WWTP managers to ensure that accurate plant monitoring operating records are kept.

  • Pepperell CS, Casto AM, Kitchen A, Granka JM, Cornejo OE, Holmes EC, Holmes EC, Birren B, Galagan J, Feldman MW (2013) The role of selection in shaping diversity of natural M. tuberculosis populations. PLoS Pathog. 9(8):e1003543 (PMC3744410) View Abstract · Pubmed Record

    Mycobacterium tuberculosis (M.tb), the cause of tuberculosis (TB), is estimated to infect a new host every second. While analyses of genetic data from natural populations of M.tb have emphasized the role of genetic drift in shaping patterns of diversity, the influence of natural selection on this successful pathogen is less well understood. We investigated the effects of natural selection on patterns of diversity in 63 globally extant genomes of M.tb and related pathogenic mycobacteria. We found evidence of strong purifying selection, with an estimated genome-wide selection coefficient equal to -9.5 × 10(-4) (95% CI -1.1 × 10(-3) to -6.8 × 10(-4)); this is several orders of magnitude higher than recent estimates for eukaryotic and prokaryotic organisms. We also identified different patterns of variation across categories of gene function. Genes involved in transport and metabolism of inorganic ions exhibited very low levels of non-synonymous polymorphism, equivalent to categories under strong purifying selection (essential and translation-associated genes). The highest levels of non-synonymous variation were seen in a group of transporter genes, likely due to either diversifying selection or local selective sweeps. In addition to selection, we identified other important influences on M.tb genetic diversity, such as a 25-fold expansion of global M.tb populations coincident with explosive growth in human populations (estimated timing 1684 C.E., 95% CI 1620-1713 C.E.). These results emphasize the parallel demographic histories of this obligate pathogen and its human host, and suggest that the dominant effect of selection on M.tb is removal of novel variants, with exceptions in an interesting group of genes involved in transportation and defense. We speculate that the hostile environment within a host imposes strict demands on M.tb physiology, and thus a substantial fitness cost for most new mutations. In this respect, obligate bacterial pathogens may differ from other host-associated microbes such as symbionts.

  • Pepperell CS, Casto AM, Kitchen A, Granka JM, Cornejo OE, Holmes EC, Birren B, Galagan J, Feldman MW (2013) Correction: The Role of Selection in Shaping Diversity of Natural M. tuberculosis Populations. PLoS Pathog. 9(8): View Abstract · Pubmed Record

    [This corrects the article on p. e1003543 in vol. 9.].

  • Pepperell C, Chang AH, Wobeser W, Parsonnet J, Hoeppner VH (2011) Local epidemic history as a predictor of tuberculosis incidence in Saskatchewan Aboriginal communities. Int. J. Tuberc. Lung Dis. 15(7):899-905 (PMC3292043) View Abstract · Pubmed Record

    Average tuberculosis (TB) incidence rates are high in Canadian Aboriginal communities, but there is significant variability within this group. To determine whether local history of post-contact TB epidemics is predictive of contemporary epidemiology among Aboriginal communities in Saskatchewan, Canada. TB incidence, age-specific morbidity patterns and rates of clustering of TB genotypes from 1986 to 2004 were compared between two groups of communities: Group 1, in which post-contact epidemics of TB were established around 1870, and Group 2, in which they were delayed until after 1920. Concomitant effects of socio-economic and geographic variables were explored with multivariate models. Group 2 communities were characterized by higher annual incidence of TB (median 431 per 100,000 population vs. 38/100,000). In multivariate models that included socio-economic and geographic variables, historical grouping remained a significant independent predictor of community incidence of TB. Clustering of TB genotypes was associated with Group 2 (OR 8.7, 95%CI 3.3-22.7) and age 10-34 years (OR 2.5, 95%CI 1.1-5.7). TB transmission dynamics can vary significantly as a function of a population's historical experience with TB. Populations at different stages along the epidemic trajectory may be amenable to different types of interventions.

  • Pepperell CS, Granka JM, Alexander DC, Behr MA, Chui L, Gordon J, Guthrie JL, Jamieson FB, Langlois-Klassen D, Long R, Nguyen D, Wobeser W, Feldman MW (2011) Dispersal of Mycobacterium tuberculosis via the Canadian fur trade. Proc. Natl. Acad. Sci. U.S.A. 108(16):6526-31 (PMC3080970) View Abstract · Pubmed Record

    Patterns of gene flow can have marked effects on the evolution of populations. To better understand the migration dynamics of Mycobacterium tuberculosis, we studied genetic data from European M. tuberculosis lineages currently circulating in Aboriginal and French Canadian communities. A single M. tuberculosis lineage, characterized by the DS6(Quebec) genomic deletion, is at highest frequency among Aboriginal populations in Ontario, Saskatchewan, and Alberta; this bacterial lineage is also dominant among tuberculosis (TB) cases in French Canadians resident in Quebec. Substantial contact between these human populations is limited to a specific historical era (1710-1870), during which individuals from these populations met to barter furs. Statistical analyses of extant M. tuberculosis minisatellite data are consistent with Quebec as a source population for M. tuberculosis gene flow into Aboriginal populations during the fur trade era. Historical and genetic analyses suggest that tiny M. tuberculosis populations persisted for ∼100 y among indigenous populations and subsequently expanded in the late 19th century after environmental changes favoring the pathogen. Our study suggests that spread of TB can occur by two asynchronous processes: (i) dispersal of M. tuberculosis by minimal numbers of human migrants, during which small pathogen populations are sustained by ongoing migration and slow disease dynamics, and (ii) expansion of the M. tuberculosis population facilitated by shifts in host ecology. If generalizable, these migration dynamics can help explain the low DNA sequence diversity observed among isolates of M. tuberculosis and the difficulties in global elimination of tuberculosis, as small, widely dispersed pathogen populations are difficult both to detect and to eradicate.

  • Pepperell C, Hoeppner VH, Lipatov M, Wobeser W, Schoolnik GK, Feldman MW (2010) Bacterial genetic signatures of human social phenomena among M. tuberculosis from an Aboriginal Canadian population. Mol. Biol. Evol. 27(2):427-40 (PMC2877553) View Abstract · Pubmed Record

    Despite a widespread global distribution and highly variable disease phenotype, there is little DNA sequence diversity among isolates of Mycobacterium tuberculosis. In addition, many regional population genetic surveys have revealed a stereotypical structure in which a single clone, lineage, or clade makes up the majority of the population. It is often assumed that dominant clones are highly adapted, that is, the overall structure of M. tuberculosis populations is the result of positive selection. In order to test this assumption, we analyzed genetic data from extant populations of bacteria circulating in Aboriginal communities in Saskatchewan, Canada. Demographic parameters of the bacterial population were estimated from archival epidemiological data collected over approximately 130 years since the onset of epidemic tuberculosis in the host communities. Bacterial genetic data were tested against neutral theory expectations and the local evolutionary history of M. tuberculosis investigated by phylogenetic analysis. Our findings are not consistent with positive selection on the bacterial population. Instead, we uncovered founder effects persisting over decades and barriers to gene flow within the bacterial population. Simulation experiments suggested that a combination of these neutral influences could result in the stereotypical structure of M. tuberculosis populations. Some aspects of population structure were suggestive of background selection, and data were on the whole consistent with combined effects of population bottlenecks, subdivision, and background selection. Neutral phenomena, namely, bottlenecks and partitions within populations, are prominent influences on the evolution of M. tuberculosis and likely contribute to restricted genetic diversity observed within this species. Given these influences, a complex evolutionary model will be required to define the relative fitness of different M. tuberculosis lineages and, ultimately, to uncover the genetic basis for its success as a pathogen.