Population genetics, taxonomy, phylogeny and evolution of Borrelia burgdorferi sensu lato

Abstract

In order to understand the population structure and dynamics of bacterial microorganisms, typing systems that accurately reflect the phylogenetic and evolutionary relationship of the agents are required. Over the past 15 years multilocus sequence typing schemes have replaced single locus approaches, giving novel insights into phylogenetic and evolutionary relationships of many bacterial species and facilitating taxonomy. Since 2004, several schemes using multiple loci have been developed to better understand the taxonomy, phylogeny and evolution of Lyme borreliosis spirochetes and in this paper we have reviewed and summarized the progress that has been made for this important group of vector-borne zoonotic bacteria.

Figure 1

Factors impacting the evolutionary ecology of LB spirochetes. Biotic factors are shown next to the host-vector-spirochete triangle. Abiotic factors (such as climate or landscape) act indirectly on LB spirochetes by impacting on host and vector populations. The contemporary picture is further compounded by the evolutionary and demographic history of hosts, vectors, and pathogens.

Figure 2

Bayesian phylogenetic inferences generated using MLST housekeeping genes (A) and ospC (B) sequences. Previously assigned species are color coded as follows: B. burgdorferi s.s. – ■, B. afzelii – , B. garinii – ●, B. bavariensis - , B. valaisiana – ⦿, and B. lusitaniae – ▼. The MLST tree was rooted with sequences of the relapsing fever spirochetes B. duttonii, B. hermsii, and B. turicatae. The branch length of the outgroup is not according to scale as indicated by slashes. While in the MLST tree LB species cluster monophyletically, this is not the case using ospC sequences (original figure A from Population Biology of Lyme Borreliosis Spirochetes; Kurtenbach et al [2010], DOI: 10.1002/9780470600122.ch12; Copyright (2010, John Wiley & Sons); reprinted with permission of John Wiley & Sons, Inc.; original figure B Margos et al. [2009], doi 10.1128/AEM.00116-09, reproduced and modified with permission from the American Society for Microbiology)

Figure 3

Multi Locus Sequence Typing. Targetted PCR is used to amplify several genes distributed throughout the genome exhibiting nearly neutral variation. Internal fragments, kept in-frame, of similar length for each gene are used. For each individual gene, fragments of identical length are aligned and compared to sequences in a ‘virtual strain collection centre’, a MLST database, and to each other permitting determination of an allelic profile for each strain. The allelic profile determines the sequence type (ST) and it can be used to infer relationships of descent within bacterial species based on models of clonal expansion and diversification. Concatenated sequences of all genes can be used for phylogenetic inferences. The accumulative nature of MLST database makes it an attrative instrument to understand intra- and inter-specific relationships of bacteria.

Figure 4

Map showing the global distribution of the LB species. The shaded areas show the distribution of tick vectors. Seven species of LB group spirochetes are found in North America, eight species in Europe, and eight species in Asia, two species overlap in the Old and New Worlds, three in Europe and Asia (see text for details).

Figure 5

goeBURST diagrams based on the multi-locus allelic profiles for B. garinii (A), B. valaisiana (B) and B. afzelii (C). Each coloured box represents an ST. The colour and size of the boxes corresponds to geographic region and the number of that ST found. STs unique to a particular country were coloured as follows: red England, blue France, yellow Germany, green Latvia, purple Scotland. Those STs that were found in more than one country are grey. STs connected by black or blue lines are single-locus variants (SLVs) and STs connected by grey or green lines are double-locus variants (DLVs) (original figure from Vollmer et al. [2011] Environmental Microbiology, doi:10.1111/j.1462-2920.2010.02319.x, reproduced with permission from John Wiley and Sons)

Figure 6

Proposed post-glacial migration routes for three small mammal species taken from Hewitt (1999) based on fossil and molecular data. (original figure from Hewitt [1999] Biological Journal of the Linnean Society, doi:10.1111/j.1095-8312.1999.tb01160.x, partially reproduced with permission from John Wiley and Sons).

Figure 7

A population snapshot of 244 samples of Borrelia burgdorferi found in Canada (166 samples) and the Unites States (78 samples) as determined by spatial analysis using spatialepidemiology.net. The figure reveals correspondence of sequence type and geographic distribution. Most ST were found either in the Northeast or the Midwest suggesting limited gene flow between populations.

Figure 8

Neighbour joining tree generated using concatenated sequences of MLSA housekeeping genes showing LB groups species. Black dots indicate species that occur in North America, circles indicate species that occur in Eurasia, grey dots indicate species that occur in the Old and New Worlds. The scale bar shows 1 % divergence. Branch confidence values calculated using a bootstrap procedure with 100 repeatitions (original figure from Margos et al. [2010] Ticks and Tick-borne Diseases, doi: 10.1016/j.ttbdis.2010.09.002, modified and reproduced with permission from Elsevier)

Figure 9

Graphic representation of the ‘time’ captured by various genetic elements used for typing of bacterial microorganisms. The highly conserved 16S locus reveals deep evolutionary relationships but is unable to capture recent events. Fast evolving genetic elements, such as loci under diversifying selection, microsatellits or variable number of tandem repeats (VNTR) may reveal very recent events but – due to saturation – are not able to ‘see’ ancient events. Intergenic spacer (IGS) regions are supposed to be selectively neutral and should therefore accumulate mutations indiscriminately and linear to time. IGS may be short and saturate quickly or may contain regulatory elements which might not permit all mutations to be fixed. Due to the slow evolution of housekeeping genes multilocus sequence typing captures the intermediate relationship of bacteria. Genome-wide SNPs provide the broadest ‘view’ on an organism past as these are able to capture recent as well as ancient events.