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Introduction

Genomic data coupled with phylogenetic methods have enhanced the ability to track infectious disease epidemics through space and time (Baker, Hanage & Holt, 2010). For example, studies have tracked and characterized epidemics occurring at different geographic scales, across local, regional, global, and even historical scales; investigating multidrug-resistant Staphylococcus aureus in hospital settings (Kos et al., 2012; Köser et al., 2012), inferring continental origins of food pathogens (Goss et al., 2014), explaining seasonal influenza dynamics (Lemey et al., 2014), and ancient oral pathogens (Warinner et al., 2014), respectively. Such studies provide valuable information regarding migration rates, directionalities of spread, unique variants, genetic diversity, and drug resistance, as well as informing policy-makers about infection patterns associated with human activities (Bos et al., 2011; Morelli et al., 2010; Zhang et al., 2010). Accordingly, applications of analytical tools to large datasets are abundant in clinical pathology, bioforensics, biosurveillance, and molecular epidemiology (Reimer et al., 2011; Wilson, Allard & Brown, 2013).

Whole-genome sequencing (WGS) has become an affordable approach for such studies (Bertelli & Greub, 2013; Chen et al., 2013; Cornejo et al., 2013; Croucher et al., 2013; Pérez-Lago et al., 2013; Sheppard et al., 2013; Wielgoss et al., 2013). New technologies make it possible to compile datasets that were not even dreamed of twenty years ago (Chewapreecha et al., 2014; Marttinen et al., 2012; Nasser et al., 2014; Sheppard et al., 2013) which, in turn, is prompting scientists to ask new questions regarding pathogen distribution, diversity, identification, origin, and phenotype (Butler et al., 2013; Castillo-Ramirez et al., 2012; Grad & Waldor, 2013; Holt et al., 2012; Hong et al., 2014; Spoor et al., 2013).

Because there are now a variety of molecular survey approaches (whole genome sequencing (WGS), multi-locus sequence typing (MLST), and single nucleotide polymorphism (SNP) data) with different costs and resolution abilities, we explored the impact of these different approaches on inferences of population dynamics, transmission patterns, and parameter estimation. For instance, tracking the origin of bioterrorism agents depends on identifying diagnostic mutations, as in the anthrax attacks of 2001 (Read et al., 2002), or accurately identifying the subspecies of origin (Hong et al., 2014), and understanding the extent to which sampling strategy and choice of molecular survey approach affects temporal and spatial inferences.

Here, we set out to investigate how molecular survey approaches compare, using three select agents as models, namely Yersinia pestis (causative agent of plague), Burkholderia pseudomallei (causative agent of melioidosis), and Brucella spp. (febrile disease). These bacterial species are relevant from health and biosecurity perspectives, and there exists a sizable amount of genomic and supporting information (date of collection, geographic location, and host) for them. Also, they allow for interesting contrasts including comparing intraspecific datasets (Y. pestis v. B. pseudomallei), one from monomorphic bacteria (clonal), and the other from polymorphic bacteria, as well as interspecific comparisons (Y. pestis and B. pseudomallei vs. Brucella spp.)

Thus, we present and analyze new draft genomic sequences for 20 Brucella spp., 20 Y. pestis, and 20 B. pseudomallei isolates, which we combine with publicly available genomes (totaling 115 genomes) to compare inferences on evolutionary relationships, dates and rates, and geographic and host structure. Do molecular survey approaches, as currently practiced, produce incongruent inferences? We performed a comparison with real-world examples using species that represent genetic diversities of relevance to clinical molecular epidemiology. We applied different molecular survey approaches (WGS, SNPs, MLST) to evaluate whether these can recover equivalent evolutionary relationships, evolutionary rates and divergence dates, and whether phylogenies inferred with these approaches represent equivalent geographic and host structures.

Methods

Strain selection and sequencing

DNA was isolated from 20 strains of Burkholderia pseudomallei, Yersinia pestis, and Brucella spp. from the Brigham Young University Select Agent Archive. Samples were selected for sequencing to provide a range of (1) time of isolation, (2) geographic spread, and (3) host association (Table 1). DNA isolation followed standard protocols for select agents and was conducted at the Brigham Young University BSL-3 facility. All DNA preparations received a Certification of Sterility (10% of the final DNA preparation from each isolate was plated for sterility on appropriate agar, and after a minimum of five days of incubation at 37 °C, the samples showed no growth, indicating they contained no viable organisms) before being prepared for sequencing.

Table 1:
Summary of genomes sequenced and collected in this study.
Metadata on strain source, host, location and date of collection also provided when available.
NCBI Accession
number
Species Strain Source Host Location Date of
collection
SRX286342 Burkholderia pseudomallei 5 Public Health LaboratoryService, London Sheep Australia 1949
SRX286347 Burkholderia pseudomallei 6 Public Health LaboratoryService, London Human Bangladesh 1960
SRX286346 Burkholderia pseudomallei 9 Public Health LaboratoryService, London Human Pakistan 1988
SRX286345 Burkholderia pseudomallei 18 Public Health LaboratoryService, London Monkey Indonesia 1990
SRX286357 Burkholderia pseudomallei 24 Public Health LaboratoryService, London Horse France 1976
SRX286354 Burkholderia pseudomallei 25 Public Health LaboratoryService, London Soil Madagascar 1977
SRX286353 Burkholderia pseudomallei 31 Public Health LaboratoryService, London Water drain Kenya 1992
SRX286352 Burkholderia pseudomallei 33 Public Health LaboratoryService, London Manure France 1976
SRX286350 Burkholderia pseudomallei 35 Public Health LaboratoryService, London Human Vietnam 1963
SRX286348 Burkholderia pseudomallei 68 Public Health LaboratoryService, London Human Fiji 1992
SRX286359 Burkholderia pseudomallei 91 Public Health LaboratoryService, London Sheep Australia 1984
SRX286361 Burkholderia pseudomallei 104 Public Health LaboratoryService, London Goat Australia 1990
SRX286363 Burkholderia pseudomallei 208 Public Health LaboratoryService, London Human Ecuador 1990
SRX286364 Burkholderia pseudomallei 4075 Public Health LaboratoryService, London Human Holland 1999
SRX286418 Burkholderia pseudomallei Darwin-035 Royal Darwin Hospital Human Australia 2003
SRX286420 Burkholderia pseudomallei Darwin-051 Royal Darwin Hospital Dog Australia 1992
SRX286421 Burkholderia pseudomallei Darwin-060 Royal Darwin Hospital Pig Australia 1992
SRX286422 Burkholderia pseudomallei Darwin-077 Royal Darwin Hospital Bird Australia 1994
SRX286423 Burkholderia pseudomallei Darwin-150 Royal Darwin Hospital Soil Australia 2006
SRX286344 Burkholderia pseudomallei 80800117 Utah Department of Health Human USA 2008
NC_017832.1 NC_017831.1 Burkholderia pseudomallei 1026b hhayden@u.washington.edu Human Thailand 1993
NC_009078.1 NC_009076.1 Burkholderia pseudomallei 1106a J. Craig Venter Institute (JCVI) Human Thailand 1993
NC_012695.1 Burkholderia pseudomallei MSHR346 Joint Genome Institute/LANL Center Human Australia 1996
NC_006351.1 NC_006350.1 Burkholderia pseudomallei k96243 Sanger Institute Human Thailand 1996
NC_018529.1 NC_018527.1 Burkholderia pseudomallei BPC006 Third Military MedicalUniversity Human China 2008
NZ_CM000774.1 NZ_CM000775.1 Burkholderia pseudomallei 1106b J. Craig Venter Institute (JCVI) Human Thailand 1996
NZ_CM000833.1 NZ_CM000832.1 Burkholderia pseudomallei 1710a J. Craig Venter Institute (JCVI) Human Thailand 1996
NC_007435.1 NC_007434.1 Burkholderia pseudomallei 1710b J. Craig Venter Institute (JCVI) Human Thailand 1999
NC_009074.1 NC_009075.1 Burkholderia pseudomallei 668 J. Craig Venter Institute (JCVI) Human Australia 1995
NZ_CM001156.1 NZ_CM001157.1 Burkholderia pseudomallei Bp22 Genome Institute of Singapore Human Singapore 1989
NC_007651 NC_007650 Burkholderia thailandensis E264 J. Craig Venter Institute (JCVI) Soil Thailand 1994
SRX278648 Brucella abortus 1004, Strain 2032 National Animal Disease Center Bovine Missouri, USA 1990
SRX278790 Brucella abortus 1007, Strain 2045 National Animal Disease Center Bovine Florida, USA 1990
SRX278791 Brucella abortus 1019, Strain 2038 National Animal Disease Center Bovine Tennessee, USA 1990
SRX278792 Brucella abortus 1022, Strain 2073 National Animal Disease Center Bovine Georgia, USA 1990
SRX278793 Brucella abortus 1146, Strain 8-953 National Animal Disease Center Elk Montana, USA 1992
SRX278794 Brucella abortus 1668, Strain 00-666 National Animal Disease Center Elk Wyoming, USA 2000
SRX278891 Brucella abortus YELL-99-067 Idaho National Engineering and Environmental Laboratory Bison (amniotic fluid) Wyoming, USA 1999
SRX282032 Brucella abortus 1614, Strain
Weinheimer 4
National Animal Disease Center Bovine Texas, USA 2000
SRX282039 Brucella canis 1107, Strain 1-107 National Animal Disease Center Canine Missouri, USA 1990
SRX282040 Brucella melitensis 1253, Strain
Ether, L657
National Animal Disease Center Caprine Unknown 1994
SRX282041 Brucella melitensis BA 4837 New Mexico Departmentof Health Human New Mexico, USA 2003
SRX282042 Brucella melitensis 70000565 Utah Department of Health Blood, Human Utah, USA 2000
SRX282044 Brucella melitensis 80600020 Utah Department of Health Blood, Human Utah, USA 2006
SRX282045 Brucella melitensis 80800076 Utah Department of Health Human California, USA 2008
SRX282046 Brucella neotomae 1156, Strain 5K33, ATCC#23459 National Animal Disease Center Desert wood rat Unknown, USA 1992
SRX282047 Brucella ovis 1117, Strain 1-507 National Animal Disease Center Ovine Georgia, USA 1991
SRX282048 Brucella ovis 1698, Strain
13551-2114; 1985:Dhyatt
National Animal Disease Center Ovine (semen) Ft. Collins, Colorado, USA 2001
SRX282050 Brucella species 70100304 Utah Department of Health Blood, Human USA- Utah 2001
SRX282053 Brucella suis 1103, Strain 2483 National Animal Disease Center Porcine South Carolina, USA 1990
SRX282057 Brucella suis 1108, Strain 1-138 National Animal Disease Center Porcine New Jersey, USA 1990
NC_016777.1 NC_016795.1 Brucella abortus A13334 Macrogen Bovine Korea Unknown
NC_006932.1 NC_006933.1 Brucella abortus bv 1, 9-941 USDA Bovine Wyoming, USA Unknown
NC_010740.1 NC_010742.1 Brucella abortus S19 Crasta OR Bovine Unknown, USA 1923
NC_010103.1 NC_010104.1 Brucella canis ATCC 23365 DOE Joint Genome Institute Dog Unknown Unknown
NC_016796.1 NC_016778.1 Brucella canis HSK A52141 National VeterinaryResearch and Quarantine Dog South Korea Unknown
NC_012442.1 NC_012441.1 Brucella melitensis ATCC 23457 Los Alamos National Lab Human India 1963
NC_017244.1 NC_017245.1 Brucella melitensis M28 Chinese National Human GenomeCenter at Shanghai Sheep China 1955
NC_003317.1 NC_003318.1 Brucella melitensis bv 1, 16M Integrated Genomics Inc Goat Unknown, USA Unknown
NC_007618.1 NC_007624.1 Brucella melitensis bv. 1 Abortus 2308 Lawrence Livermore National Lab Standard laboratory strain Unknown Unknown
NC_017246.1 NC_017247.1 Brucella melitensis M5-90 Chinese National Human GenomeCenter at Shanghai Standard laboratory strain Unknown Unknown
NC_017248.1 NC_017283.1 Brucella melitensis bv. 3 NI China Agricultural University Bovine Inner Mongolia, China 2007
CP001578.1 CP001579.1 Brucella microti CCM 4915 Sudic S Vole Czech Republic 2000
NC_009505.1 NC_009504.1 Brucella ovis ATCC 25840 J. Craig Venter Institute Sheep Australia 1960
NC_015858.1 NC_015857.1 Brucella pinnipedialis B2/94 Zygmunt, M.S. Seal UK 1994
NC_016775.1 NC_016797.1 Brucella suis VBI22 Harold R. Garner Bovine, milk Texas, USA Unknown
NC_004311.2 NC_004310.3 Brucella suis bv 1, 1330 J. Craig Venter Institute Pig Unknown, USA 1950
NC_010167.1 NC_010169.1 Brucella suis ATCC 23445 Joint Genome Institute/LANL Center Hare UK 1951
NC_009667.1 NC_009668.1 Ochrobactrum anthropi ATCC 49188 DOE Joint Genome Institute Arsenical cattle-dipping fluid Australia 1988
SRX282065 Yersinia pestis 4954 New Mexico Departmentof Health Human NM, USA 1987
SRX282089 Yersinia pestis 1901b New Mexico Departmentof Health Human NM, USA 1983
SRX282090 Yersinia pestis Java (D88) Michigan State University Unknown Far East Unknown
SRX282091 Yersinia pestis Kimberley (D17) Michigan State University Unknown Near East Unknown
SRX282092 Yersinia pestis KUMA (D11) Michigan State University Unknown Manchuria, China Unknown
SRX282093 Yersinia pestis TS (D5) Michigan State University Unknown Far East Unknown
SRX282094 Yersinia pestis 8607116 New Mexico Departmentof Health Dog NM, USA Unknown
SRX282095 Yersinia pestis 1866 New Mexico Departmentof Health Squirrel NM, USA Unknown
SRX282096 Yersina pestis 4139 New Mexico Departmentof Health Cat NM, USA 1995
SRX286281 Yersinia pestis 4412 New Mexico Departmentof Health Human NM, USA 1991
SRX286283 Yersinia pestis 2965 New Mexico Departmentof Health Human NM, USA 1995
SRX286290 Yersinia pestis 2055 New Mexico Departmentof Health Human NM, USA 1998
SRX286302 Yersinia pestis 2106 New Mexico Departmentof Health Human NM, USA 2001
SRX286303 Yersinia pestis 2772 New Mexico Departmentof Health Cat NM, USA 1984
SRX286304 Yersinia pestis 3357 New Mexico Departmentof Health Mountain lion NM, USA 1999
SRX286305 Yersinia pestis AS 2509 New Mexico Departmentof Health Rodent NM, USA 2004
SRX286306 Yersinia pestis AS 200900596 New Mexico Departmentof Health Rabbit, liver/spleen United States, Santa Fe, NM 2009
SRX286307 Yersinia pestis V-6486 New Mexico Departmentof Health Llama Las Vegas, NM, USA Unknown
SRX286340 Yersinia pestis KIM (D27) Michigan State University Human Iran/Kurdistan 1968
SRX286341 Yersinia pestis AS200901509 New Mexico Departmentof Health Liver/spleen, prairie dog Santa Fe, NM, USA 2009
NC_017168.1 Yersinia pestis A1122 Los Alamos National Lab Ground squirrel California 1939
NC_010159.1 Yersinia pestis Angola J. Craig Venter Institute (JCVI) Human Angola Unknown
NC_008150.1 Yersinia pestis Antiqua DOE Joint Genome Institute Human Congo 1965
PRJNA54473 Yersinia pestis B42003004 J. Craig Venter Institute (JCVI) Marmota baibacina China 2003
PRJNA54563 Yersinia pestis CA88-4125 DOE Joint Genome Institute Human California 1988
NC_003143.1 Yersinia pestis CO92 Sanger Institute Human/cat Colorado 1992
NC_017154.1 Yersinia pestis D106004 Chinese Center for DiseaseControl and Prevention Apodemus chevrieri Yulong County, China 2006
NC_017160.1 Yersinia pestis D182038 Chinese Center for DiseaseControl and Prevention Apodemus chevrieri Yunnan, China 1982
PRJNA54471 Yersinia pestis E1979001 J. Craig Venter Institute (JCVI) Eothenomys miletus China 1979
PRJNA54469 Yersinia pestis F1991016 J. Craig Venter Institute (JCVI) Flavus rattivecus China 1991
PRJNA54399 Yersinia pestis FV-1 The Translational GenomicsResearch Institute Prairy dog Arizona 2001
PRJNA55339 Yersinia pestis India 195 DOE Joint Genome Institute Human India Unknown
PRJNA54383 Yersinia pestis IP275 The Institute for Genomic Research Human Madagascar 1995
NC_009708.1 Yersinia pseudotuberculosis IP31758 J. Craig Venter Institute (JCVI) Human Russia 1966
PRJNA54475 Yersinia pestis K1973002 J. Craig Venter Institute (JCVI) Marmota himalaya China 1973
PRJNA42495 Yersinia pestis KIM D27 J. Craig Venter Institute (JCVI) Human Iran/Kurdistan 1968
NC_004088.1 Yersinia pestis KIM10+ Genome Center of Wisconsin Human Iran/Kurdistan 1968
NC_017265.1 Yersinia pestis Medievalis str. Harbin 35 Virginia Bioinformatics Institute Human China 1940
PRJNA54477 Yersinia pestis MG05-1020 J. Craig Venter Institute (JCVI) Human Madagascar 2005
NC_005810.1 Yersinia pestis Microtus 91001 Academy of Military Medical Sciences, The Institute of Microbiology andEpidemiology, China Microtus brandti China 1970
NC_008149.1 Yersinia pestis Nepal516 Genome Center of Wisconsin Human/soil Nepal 1967
PRJNA55343 Yersinia pestis Pestoides A DOE Joint Genome Institute Human FSU 1960
PRJNA58619 Yersinia pestis Pestoides F DOE Joint Genome Institute Human FSU Unknown
PRJNA55341 Yersinia pestis PEXU2 Enteropathogen Resource Integration Center (ERIC) BRC Rodent Brazil 1966
PRJNA54479 Yersinia pestis UG05-045 J. Craig Venter Institute (JCVI) Human Uganda 2005
PRJNA47317 Yersinia pestis Z176003 CCDC Marmota himalayana Tibet 1976
DOI: 10.7717/peerj.761/table-1

The DNA samples were prepared for multiplexed (single-end, 82 cycles) sequencing using a Illumina GAIIx genome analyzer (Illumina Inc., San Diego, CA). For each isolate, genomic library preparations were generated using a Nextera DNA Sample Prep Kit. Post-library quality control and quantification was done using BioAnalyzer 2100 high-sensitivity chips and KAPA SYBR FAST Universal 2X qPCR Master Mix. Post processing of reads was performed by the RTA/SCS v1.9.35.0 and CASAVA 1.8.0. Reads were trimmed to the Q30 level using CLCBio’s quality_trim program, and CutAdapt v0.95 was used to excise adapter and transposon contamination.

All sequencing run data and metadata were deposited in the Sequence Read Archive (SRA) under three projects, SRP022877, SRP022862, and SRP023117 for Y. pestis, Brucella spp., and B. pseudomallei, respectively.

Dataset collection

Short reads were quality filtered (average read quality >30 Phred) and mapped against reference genomes employing the Burrows–Wheeler Transform algorithm, as implemented in SOAP (Li et al., 2008). The resulting SAM/BAM files were filtered for duplicate reads that might have arisen by PCR, and consensus sequences were called in Geneious 6.1.6 (Kearse et al., 2012; Li et al., 2009). Additionally, we retrieved full genomes along with host, collection date, and country of origin metadata for B. pseudomallei (11), Brucella spp. (18) and Y. pestis (26) from GenBank, GOLD, IMG, Patric, Broad Institute, and Pathema databases and resources totaling 115 genomes (Table 1; geographic distribution in Map S1) (Benson et al., 2010; Brinkac et al., 2010; Gillespie et al., 2011; Liolios et al., 2008; Markowitz et al., 2012). From the assembled genomes we derived all datasets as described below.

Multi-locus sequence type markers for B. pseudomallei, namely ace, gltB, gmhD, lepA, lipA, narK, and ndh were retrieved from the PubMLST database (http://bpseudomallei.mlst.net). For Brucella spp., we resorted to markers used by Whatmore, Perrett & MacMillan (2007) i.e., gap, aroA, glk, dnaK, gyrB, trpE, cobQ, omp25, and int-hyp. Likewise, for Y. pestis we obtained markers from PubMLST (Yersinia spp.; http://pubmlst.org/yersinia/) aarF, dfp, galR, glnS, hemA, rfaE, and speA. In addition, we obtained markers from Achtman et al. (1999) (dmsA, glnA, manB, thrA, tmk, and trpE) and from Revazishvili et al. (2008) (16S rDNA, gyrB, yhsp, psaA and recA). We created a custom BLAST (Altschul et al., 1990) database with our new genome sequences combined with the publicly available genomes for all three species groups.

We created datasets based on SNPs by searching for k-mer = 25 (SNP on position 13) among unaligned genomes, as implemented in kSNP 2.0 (Gardner & Hall, 2013; Gardner & Slezak, 2010). We chose this implementation because it does not depend on arbitrarily selecting a reference genome, it can take draft and unassembled sequence data (including low-coverage genomes), and it is fast and widely used in epidemiological studies (Epson et al., 2014; Pettengill et al., 2014; Raphael et al., 2014; Timme et al., 2013). Briefly, the optimal k-mer size was estimated using Kchooser, which identifies threshold value of k for which non-unique k-mers are the result of real genome redundancy, not chance. We kept all SNPs that were shared among all taxa in a given dataset (core SNP subset), which were used to build matrices for downstream analyses. The matrices used contained only variable bi-allelic sites from non-overlapping k-mers and their size is described in Table 2.

Table 2:
Genetic diversity and dataset length for different species and molecular survey approaches.
MLST SNP Genome
Chromosome I Chromosome II Chromosome I Chromosome II
Mean Variance Mean Variance Mean Variance Mean Variance Mean Variance
Bp theta 36.05 127.39 7807.03 5593613.54 4333.68 1724029.33 4666.60 1999005.02 2187.99 439709.21
pi 4.45E–03 5.15E–06 9.58E–02 2.18E–03 9.69E–02 2.24E–03 5.67E–03 7.66E–06 7.14E–03 1.21E–05
length 3518.00 31189.00 17313.00 289172.00 108654.00
Br theta 112.58 1205.64 914.77 78109.73 234.25 5161.72 635.85 37782.92 2046.37 390305.58
pi 1.00E–02 2.46E–05 8.01E–02 1.54E–03 7.66E–02 1.43E–03 7.96E–03 1.52E–05 1.62E–02 6.25E–05
length 4409.00 3628.00 929.00 24110.00 36223.00
Yp theta 36.17 120.42 3204.65 883301.99 527.40 24020.48
pi 4.97E–04 6.68E–08 5.60E–02 7.40E–04 4.55E–04 4.94E–08
length 20498.00 14116.00 281149.00
DOI: 10.7717/peerj.761/table-2

Notes:

Bp

Burkholderia pseudomallei

Br

Brucella spp.

Yp

Yersinia pestis

We created full genome datasets by aligning complete genome sequences in Mauve 2.3.1 (Darling, Mau & Perna, 2010) and then used the resulting multiple sequence alignment directly and/or reduced for phylogenetic inference. The reduced full genome dataset consisted of all Locally Collinear Blocks (LCBs) detected by Mauve that were greater than 10 Kb and randomly subsampled up to a total of 300 Kb present across all taxa in a given dataset.

Diversity and phylogenetic analyses

We measured genetic diversity as the substitution rate-scaled effective population size Θ for all molecular survey approaches (MLST, SNP, WGS), as implemented in the ‘pegas’ package in R (Paradis, 2010). We inferred phylogenies, both with and without assuming a molecular clock. Clock phylogenies were inferred using Bayesian Inference (BI) and Markov Chain Monte Carlo (MCMC) simulations as implemented in Beast 1.7.5 (restricting the analysis to those sequences with recorded dates) and using the Beagle library to speed up analysis (Ayres et al., 2012; Drummond et al., 2012). We assumed a General Time Reversible (GTR) substitution model for all three data approaches with a discrete gamma distribution (4 categories) to model rate heterogeneity (MLST datasets were partitioned by gene with a model fit per gene; rate heterogeneity was not modeled for SNP datasets). We unsuccessfully tried to partition the genome dataset by gene, but phylogenetic inference did not reach convergence. Briefly, MCMC simulations were run until a single chain reached convergence, as diagnosed by its trace and ESS values (>400; ranging from 2E8 to 2E9 steps; 10% burnin) in Tracer 1.5 (http://tree.bio.ed.ac.uk/software/tracer/) and tree distributions were summarized in TreeAnnotator 1.7.5 (10–20% of trees were discarded as burnin). The molecular clock (strict clock model) was calibrated using isolate collection dates and a uniform distribution (from 0 to 1) as clock prior. We also used BI for non-clock phylogenies as implemented in MrBayes 3.2 (Ronquist et al., 2012) where we ran 8 chains (6 heated), 2E7 generations each. As in the clock phylogenies, we used visual inspection of the traces as well as the average standard deviation of split frequencies to assess convergence. All trees were rooted by using outgroups (Yersinia pseudotuberculosis IP31758, Ochrobactrum anthropic, and Burkholderia thailandensis E264).

In order to compare tree topologies, we applied two topology metrics, Robinson–Foulds (RF, Robinson & Foulds, 1981) and Matching Splits Clusters (MC, Bogdanowicz & Giaro, 2012) to compare topologies across different molecular survey approaches and among chromosomes as implemented in TreeCmp (Bogdanowicz & Giaro, 2012). We also assessed the extent to which phylogenies and traits (host range, sample collection site, and sampling date) were correlated through Bayesian Tip-Significance testing by estimating the Association Index (AI, Wang et al., 2001) and Parsimony Score (PS, Slatkin & Maddison, 1989) as implemented in BaTs (Parker, Rambaut & Pybus, 2008). Figures were plotted using ggplot2 (Wickham, 2009) and APE (Paradis, Claude & Strimmer, 2004) packages, and high posterior density (HPD) intervals were estimated using TeachingDemos package (Snow & Snow, 2013).

Results and Discussion

Sequencing technologies and statistical phylogenetic methods are arming researchers with powerful tools to track infectious agents over space and time with unprecedented resolution (Holt et al., 2012; Lewis et al., 2010). However, with multiple molecular survey approaches and a battery of analytical methods, it is not clear how these interact.

Using 115 genomic sequences (60 this study + 55 GenBank), we compared inferences regarding genetic diversity, substitution rates and node ages, tree topologies, structure and phylogenies inferred from different molecular survey approaches. We use the term “molecular survey approaches” to refer to either MLST, SNP, or WGS approaches, and the term “species datasets” or simply “dataset” to refer either to B. pseudomallei, Brucella spp. or Y. pestis sequence data belonging to any of these species/genera. Given the difficulty of current algorithm implementations in reading and analyzing whole bacterial genomes, we decided to randomly sub-sample core homologous regions to compile genomic data that we termed “genome” (see Methods for details).

Diversity and datasets

Datasets sizes varied in length by data approach, species, and genomic partition (chromosome I/II). Notably, we intended to include as many genes as possible for the MLST schemes, which resulted in partitioned datasets ranging from 7 to 18 genes. In the case of Y. pestis, the MLST dataset constituted a larger dataset than the SNP dataset due to the low variability in this species. The interspecific dataset, i.e., Brucella spp., rendered the smallest dataset for all data approaches (least number of sites) as opposed to intraspecific datasets (Y. pestis; B. pseudomallei) that ended up being one or two orders of magnitude longer (Table 2; square brackets).

In order to characterize the present genetic diversity of our datasets, we estimated effective population size using a segregating sites model (Θ; Watterson’s theta) and nucleotide diversity (π) (Nei, 1987; Paradis, 2010; Watterson, 1975). Nucleotide diversity ranked higher for SNPs compared to other approaches for the same species, as these data only contain binary variable sites (Table 2). Nucleotide diversity was higher for B. pseudomallei than for Brucella spp. and Y. pestis when SNP data were analyzed. However, this was not observed for either MLST or genome data, where nucleotide diversity ranked higher for Brucella spp. compared to B. pseudomallei. Y. pestis nucleotide diversity was consistently lower compared to other datasets across molecular approaches. Θ estimates were higher for B. pseudomallei than others for SNP and genome data, but not MLST data where Brucella spp. yielded the larger Θ (Table 2).

Rates and ages

We tested whether different data approaches resulted in different inferences regarding substitution rates and node ages while maintaining other parameters constant, i.e., clock calibrations, substitution models, tip dates, coalescent tree priors, and taxa (different partition scheme; see Methods for details). Substitution rate estimates were always higher for SNP data compared to genome data, irrespective of species datasets used (Fig. 1). Rates estimated from MLST data were largely overlapping with estimates from genome data for Y. pestis and Brucella spp. including median values (highlighted in Figs. 1B1C). However, this was not the case for the B. pseudomallei dataset where, although the distributions overlapped, median values for the substitution rate estimate from MLST data were higher by at least an order of magnitude compared to estimates from other approaches (MLST rate median = 6.30E−7; genome chr I = 6.17E−8; genome chr II = 2.48E−7; SNP chr I = 1.06E−6; SNP chr II = 9.94E−7 [rates in substitutions per site per year]).

Substitution rates for all datasets as estimated from different molecular survey approaches.

Figure 1: Substitution rates for all datasets as estimated from different molecular survey approaches.

Genome/SNP chr I/II refers to estimates from different chromosomes. Burkholderia pseudomallei (A), Brucella spp. (B), and Yersinia pestis (C). Note different scale for species rates.

Remarkably, when collecting node ages and comparing them across data approaches, we found that highest posterior density intervals (95% HPD) overlapped substantially in the case of Y. pestis and Brucella spp. datasets (Figs. 2B2C). We observed the same trend with SNP and genome approaches when analyzing B. pseudomallei datasets, but not with MLST data (Fig. 2A). Interestingly, in Y. pestis node age estimates we observed that 95% HPD intervals were narrower in SNP and genome data than in MLST data. This suggests that, though different molecular survey approaches result in markedly different substitution rate estimates, node ages 95% HPD are largely overlapping and thus not significantly different.

Median node ages in years.

Figure 2: Median node ages in years.

Burkholderia pseudomallei (A), Brucella spp. (B), and Yersinia pestis (C) median estimates and their 95% highest posterior density (HPD) interval according to molecular survey approach (only chromosome I showed; see Fig. S1). Nodes are numbered from youngest to oldest.

Substitution rate estimates differ substantially (up to 2 orders of magnitude), though their posterior distributions overlap to various degrees. Generally, substitution rate estimates drawn from SNP data were higher than those from MLST and genome data. However, node ages are largely consistent across molecular survey approaches, especially for Brucella spp. data (interspecific and intermediate diversity dataset). This supports the practice of using SNP data coupled to Bayesian inference coalescent methods to infer divergence times, even though traditional reversible substitution models are not specifically designed for this molecular approach. Substitution models based on models for discrete morphological character changes have been suggested, but are not widely popular (Lewis, 2001).

Phylogenies and topology comparisons

We wanted to determine whether different data approaches produce different phylogenies and to quantify the extent of any observed differences in topology (dataset sizes in Table 2). We inferred phylogenies for every species under all three molecular survey approaches, partitioned by chromosome when appropriate, without assuming a molecular clock and outgroup rooted (see ‘Methods’). We used two topology metrics, Matching Clusters (MC), rooted version of Matching splits (Bogdanowicz & Giaro, 2012), and R–F Clusters (RC), rooted version of Robinson–Foulds metric (Bogdanowicz, Giaro & Wróbel, 2012; Robinson & Foulds, 1981). MC distances reflect the minimal number of cluster (or clade) movements needed so that the two phylogenies are topologically equivalent. RC distances measure the average number of cluster differences between two phylogenies. Likewise, MC distances can be interpreted as reflecting changes deep in a phylogeny, and RC distances, in turn, as reflecting changes at the tip of the phylogenies or for more recent relationships. In general, we found that the phylogenies inferred using MLST data are less resolved and more poorly supported (posterior probabilities) than those inferred by either SNP or genome data for all species datasets (Fig. 3 and Fig. S3). This is also reflected in MC distances, where topologies inferred by MLST data are as distant, or more so, to SNP/genome based topologies than between SNP and genome topologies, with some exceptions (Table 3).

Burkholderia pseudomallei phylogenies by survey approach.

Figure 3: Burkholderia pseudomallei phylogenies by survey approach.

MLST phylogeny (A) is less resolved and poorly supported compared to SNP (B) and genome (C) phylogenies (only chromosome I showed).
Table 3:
Topology distances among phylogenies inferred using different molecular survey approaches.
Bolded rows show tree comparisons between different chromosomes under the same molecular survey approach.
Species Tree comparisons Matching cluster R–F cluster
B. pseudomallei mlst snp-I 181 16
B. pseudomallei mlst snp-II 162 17
B. pseudomallei mlst genome-I 149 18
B. pseudomallei mlst genome-II 116 18
B. pseudomallei snp-I snp-II 33 7
B. pseudomallei snp-I genome-I 56 17
B. pseudomallei snp-I genome-II 91 17
B. pseudomallei snp-II genome-I 47 19
B. pseudomallei snp-II genome-II 72 16
B. pseudomallei genome-I genome-II 63 14
Brucella spp. mlst snp-I 34 5
Brucella spp. mlst snp-II 10 1.5
Brucella spp. mlst genome-I 73 4.5
Brucella spp. mlst genome-II 56 5
Brucella spp. snp-I snp-II 24 5.5
Brucella spp. snp-I genome-I 61 5.5
Brucella spp. snp-I genome-II 40 5
Brucella spp. snp-II genome-I 63 5
Brucella spp. snp-II genome-II 50 4.5
Brucella spp. genome-I genome-II 67 7.5
Y. pestis mlst snp 223 13.5
Y. pestis mlst genome 103 8
Y. pestis snp genome 124 8.5
DOI: 10.7717/peerj.761/table-3

Notes:

Genome/SNP-I/II, chromosome I or II; R–F Cluster, Robinson–Foulds for rooted trees metric.

For Brucella spp. and Y. pestis, MC distances are clearly higher between SNP/genome and MLST; however, RC distances do not follow this trend. Since MC metric concentrates more on differences corresponding to branches deep in the topologies as opposed to RC, these results suggest that SNP and genome topologies have more similar backbones when compared to each other than MLST topologies. Likewise, MLST topologies are more similar at the tips rather than deep in the topologies (Fig. 3 and Table 3). Of course, to determine which approach is more accurate would require a dataset of known evolutionary history, but SNP and genome approaches appear to be more consistent with one another, especially for the deeper nodes.

Slowly evolving pathogens can be difficult to track as their populations accrue fewer substitutions, and/or genomic changes may or may not reflect ecological processes, such as host switches or geographic spread (see below for association testing). For instance, phylogenies inferred using MLST data were less resolved and poorly supported compared to their SNP and genome counterparts, even though in some cases (e.g., Brucella spp./Y. pestis) the MLST dataset size was larger than the SNP size dataset. This argues for the need to acquire genome data, as those data constitute the ultimate source of genealogical information, especially when analyzing monomorphic or clonal species, i.e., Y. pestis (Achtman, 2008; Achtman et al., 1999). We also found that strongly supported phylogenies, e.g., those based on SNP and genome data, can support conflicting hypotheses and thus will be misleading. For instance, B. pseudomallei clades, including isolates 1106a, 1106b, Bp22, and BPC006, all show posterior probabilities = 1, yet their relationships differ, hence a caveat when analyzing SNP/genome data and drawing conclusions about relationships amongst isolates.

Phylogenetic associations with geography, time, and host

Phylogenetic inference often is performed to infer ecological processes that leave a genomic imprint. Phylogeny-trait associations are essential to elucidate these processes. Accordingly, we estimated the Association Index (AI), and Parsimony Score (PS) on three traits (sampling location, sampling time, and host), and tested whether different answers were obtained by molecular survey. Results for B. pseudomallei showed significant association with sampling location and sampling time, but not with host for most of the datasets (AI and PS; Table 4). Likewise, Y. pestis datasets were significantly associated with sampling location and, to some extent, with sampling time and host. Interestingly, Brucella spp. showed significant genetic structure to be associated with both sampling location and host, but not sampling time (Table 4).

Table 4:
Trait-phylogeny association statistics.
Significant associations (p value <0.05) were found between traits (sampling location/host/time) and phylogenies inferred by using different data approaches. Association index (AI); Parsimony Score (PS); genome/SNP-I/II, chromosome I or II.
Statistic Trait
Sampling location
B. pseudomallei Brucella spp. Y. pestis
AI MLST, genome-I, genome-II, SNP-I, SNP-II MLST, genome-I, genome-II, SNP-I, SNP-II MLST, genome, SNP
PS MLST, genome-I, genome-II, SNP-II MLST, SNP-II MLST, genome, SNP
Host
B. pseudomallei Brucella spp. Y. pestis
AI None MLST, genome-I, genome-II, SNP-I, SNP-II Genome, SNP
PS None MLST, genome-I, genome-II, SNP-I, SNP-II None
Time
AI Genome-I, genome-II None Genome
PS None None Genome
DOI: 10.7717/peerj.761/table-4

Irrespective of the molecular survey approach used, phylogenies derived from B. pseudomallei showed a significant association with sampling location but not with host, suggesting similar evolutionary forces acting on B. pseudomallei in different hosts, or that B. pseudomallei isolates are highly endemic to the sites from which they were isolated. Similarly, Brucella spp. phylogenies were associated with both sampling location and host, irrespective of the data approach used, which most likely reflects metabolic and geographic constraints on gene flow. Interestingly, for Y. pestis, no significant association of host and MLST data was observed, which most likely reflects lack of signal, given the absence of resolution of phylogenies in its posterior distribution.

Molecular survey approaches have different sets of assumptions and properties that must be considered before an analysis is done. Similarly, statistical models that are employed may be suited for certain data approaches and not others. Here, we used popular phylogenetic methods for all molecular approaches to test whether congruent inferences could be obtained, even though some might violate particular model assumptions. The MLST method targets housekeeping genes that are likely to be maintained across taxonomic levels, hence amenable for evolutionary inferences. Yet, similar to other molecular survey approaches, they are likely to be subjected to selective pressures, which may or may not impact evolutionary inferences because of molecular convergence (Castoe et al., 2009; Edwards, 2009) and estimation of branch lengths (Ho et al., 2011; Roje, 2014). Other trade-offs of MLST have been discussed elsewhere, mainly with respect to utility and how they can be refashioned in the post-genomic era (Maiden et al., 2013; Pérez-Losada et al., 2013). On the other hand, sampling bias can influence phylogenetic analysis (Lachance & Tishkoff, 2013). Here, we obtained SNP data without using reference data and included globally sampled genomes and stringent quality controls (high Phred scores, long k-mers) to diminish ascertainment and discovery bias (Gonçalves da Silva et al., 2014). However, standard nucleotide substitution models, such as GTR, are not designed to account for binary sites-only datasets nor Bayesian Inference methods, which typically factor in invariable sites, influencing branch length estimation and impacting parameter estimates such as substitution rate and divergence time. Nonetheless, they have been used to date the spread of bacteria and other pathogens (Comas et al., 2013; Holt et al., 2010; Holt et al., 2012; Okoro et al., 2012; Pepperell et al., 2013). We speculate, based on these results, that analysis of SNP data to survey genomic variation is robust and can produce inferences that are not substantially different from WGS data. However, a recent study using simulated data has shown that using SNPs and a single reference introduce systematic biases and errors in phylogenetic inference (Bertels et al., 2014).

Conclusions

The field of bacterial population genomics is advancing rapidly with larger datasets (more taxa, more sites) increasingly available, including whole-genomes, making greater resolution possible and more powerful exploration of complex issues (Chewapreecha et al., 2014; Nasser et al., 2014). The results of analyses reported here show that the molecular survey that is used can have a critical impact on substitution rate and phylogenetic inference. However, node dates and trait associations are relatively consistent irrespective of the survey tool used. We found substitution rates vary widely depending on the approach taken, and SNP and genomic datasets yield different, but strongly supported phylogenies. Overall, inferences were more sensitive to molecular survey in the low diversity Y. pestis dataset, compared to the B. pseudomallei and Brucella spp. datasets.

Substitution rate estimates are important because, coupled to sampling dates, they allow tracking infections in space and time, and thus provide an essential epidemiological tool for monitoring and control of infectious diseases. The results presented strongly suggest that future studies should consider discordances between inferences derived from different molecular survey methods, especially with respect to substitution rate estimates.

In practice, other variables also influence what type of survey approach to use, and there are foreseeable cases where it might be practical to choose for MLST over WGS/SNPs, e.g., cost, equipment, ease of use, and necessary expertise. More importantly, coupling multiple molecular survey approaches could be useful in gaining biological insights (e.g., genome evolution, gene synteny, and content using WGS) and genotyping large numbers of samples using MLSTs.

Importantly, for whole genome analysis, a subset of data is selected to run existing software to estimate population genetic parameters. Clearly, there is a need to expand the range of methods to include whole genome data analysis. However, as bacterial genomics matures, current methods will need to be modified and extended to handle the stream of data now being generated.

Supplemental Information

Median node ages for *Burkholderia pseudomallei *(A), *Brucella spp. *(B)

DOI: 10.7717/peerj.761/supp-1

Phylogenies by molecular survey approach. *Brucella *spp. phylogenies (A) and Y. pestis phylogenies (B)

DOI: 10.7717/peerj.761/supp-2

SRA Accession numbers for all 60 genomes contributed in this study

DOI: 10.7717/peerj.761/supp-3

Supplemental Map

Geographic distribution of isolates used in this study

DOI: 10.7717/peerj.761/supp-4

Datasets, Clock and non-clock phylogenies for all molecular survey approaches and species

DOI: 10.7717/peerj.761/supp-5