(A) Phylogeny of 775 tuberculosis (TB) isolates collected during the years 2014 and 2016. Each ring represents genomic clusters detected by different single nucleotide polymorphism (SNP) thresholds …
Genomic cluster types; Spanish: clusters including only Spanish-born cases; foreign: clusters including only foreign-born cases; mix: clusters including Spanish and foreign-born cases.
Cluster ID; number of Spanish. Foreign and unknown origin cases and total cluster size are indicated.
(A) Clustered samples using different pairwise distance thresholds, bars denote the number of cases within clusters for each single nucleotide polymorphism (SNP) threshold. Gray dashed line …
(A) Distribution of local-born cases clustered by different pairwise distance SNP thresholds. Cases are expressed as the percentage of the plotted samples. Pie charts represent the proportion of …
Bayesian dating results for all clusters (CL) from Oxfordshire.
Data include information of cluster date (in years AD); cluster distances (min, max, mean, and median); most recent common ancestor (MRCA) time in years (AD) with corresponding 95% highest probability density (HPD) intervals and cluster time span or duration.
Number of transmission links (TLs) traced back to 150 years before 2016 for Oxfordshire dataset.
Median time of all the local TLs pointed in Figure 3—figure supplement 1 were classified in different time windows. The total number of links within each time window is indicated even if they were links within a genomic cluster (total_CL) or not (total_noCL). Sampling period for Oxfordshire is 2007–2012.
Bayesian dating results for all clusters (CL) from Valencia region.
Data include information of cluster date (in years AD); cluster distances (min, max, mean, and median); most recent common ancestor (MRCA) time in years (AD) with corresponding 95% highest probability density (HPD) intervals and cluster time span or duration.
Number of transmission links (TLs) traced back to 150 years before 2016 for Oxfordshire dataset.
Median time of all the local TLs pointed in Figure 3—figure supplement 1 were classified in different time windows. The total number of links within each time window is indicated even if they were links within a genomic cluster (total_CL) or not (total_noCL). Sampling period for Oxfordshire is 2007–2012.
Number of transmission links (TLs) traced back to 150 years before 2016 for Malawi dataset.
Analysis performed for Malawi. Median time of all the TLs pointed in Figure 3—figure supplement 2 were classified in different time windows. The total number of links within each time window is indicated even if they were links within a genomic cluster (total_CL) or not (total_noCL). Color code for links outside clusters (no_CL) are the same as in Figure 3—figure supplement 2. Sampling period for Malawi is 2008–2010.
Number of transmission links (TLs) traced up to 150 years before 2016 for Valencia dataset.
Median time of all the TLs pointed in Figure 3—figure supplements 3–6 were classified in different time windows. The total number of links within each time window is indicated even if they were links within a genomic cluster (total_CL) or not (total_noCL). Color code for links outside clusters (no_CL) are the same as in Figure 3—figure supplements 3–6. Sampling period for Valencia is 20014–2016. The percentage of Spanish cases within each TL was evaluated in a global phylogeny as a proxi of the origin of the node.
Sample names in bold represent local born cases. Local clusters (CLs) are highlighted in orange and mixed CLs in green (those including foreign cases). The CL numbers are crossreferenced in Figure …
Sample names in bold represent local born cases. Local clusters (CLs) are highlighted in orange and mixed CLs in green (those including foreign cases). The CL numbers are crossreferenced in Figure …
Sample names in bold represent local born cases. Local clusters (CL) are highlighted in orange and mixed CL in green (those including foreign cases). The CL numbers are crossreferenced in Figure …
Sample names in bold represent local born cases. Local clusters are highlighted in orange and mixed clusters in green (those including foreign cases). CL numbers are crossreferencied in Figure …
Sample names in bold represent local born cases. Local clusters are highlighted in orange and mixed clusters in green (those including foreign cases). CL numbers are crossreferencied in Figure …
Sample names in bold represent local born cases. Local clusters are highlighted in orange and mixed clusters in green (those including foreign cases). CL numbers are crossreferencied in Figure …
(A) (Left) The complete phylogeny, including all bacterial isolates and displaying multiple transmission events over time (located at nodes for simplification). This scenario allows the …
MTBC, Mycobacterium tuberculosis complex; WGS, whole genome sequencing.
(A) Complete phylogeny, including all bacterial isolates. Dashed lines represent missing samples that could not be retrieved during the sampling period (gray dashed lines). Transmission events are …
Bars represent the percentage of cases in gClusters (by 12 SNPs) for each time period. Boxplots represent the age distribution of patients within the clusters. Differences between the age cases for …
Correlation was calculated for each dataset.
Times of the oldest and youngest local gClusters obtained by a Bayesian analysis are presented, with values in years (AD) and 95% highest posterior density given in brackets. The number of gClusters …
Dataset | Sampling period | Local samples | N local gCluster | Local clustering | Median distance range | Oldest gCluster | Youngest gCluster |
---|---|---|---|---|---|---|---|
Oxfordshire | 2006–2012 | 74 | 6 | 27% | 0–7 | 1993 (1982–2003) | 2009 (2003–2012) |
Malawi | 2008–2010 | 106 | 40 | 49.80% | 0–14 | 1979 (1968–1988) | 2009 (2004–2010) |
Valencia region | 2014–2016 | 456 | 65 | 47.40% | 0–11 | 1985 (1972–1996) | 2015 (2012–2016) |
Origen | #total_patients | %_reported* | cases_expected |
---|---|---|---|
MAURITANIA | 1 | no data | |
SENEGAL | 7 | 20 | 1.4 |
GUINEA EQ | 6 | no data | |
CAMEROON | 1 | 12 | 0.12 |
MALI | 4 | 20 | 0.8 |
NIGERIA | 2 | 11 | 0.2 |
MOROCCO | 47 | no Africanum reported | |
IVORY | 1 | 22 | 0.2 |
ALGERIA | 5 | no data |
Samples included in this study and all clinical.
Laboratory and epidemiological data associated. WGS data includes all the information obtained by WGS; run accession number are included in the ENA projects PRJEB29604 and PRJEB38719; depth coverage. MTBC lineage. genomic and epidemiological clusters ID. Patient information including: age, gender, country of birth, year of arrival to Spain, and province of residence in the Valencia region. NA indicates not available epidemiological information.
Beast input file (.xml) indicating ascertainment bias correction implemented.
Demographic.
clinical and epidemiological data for all culture positive cases and sequenced samples reported between 2014 and 2016 in Valencia region.
Statistical analysis of clustered vs. unique TB cases.
Age, sex, place of birth, sputum smear, and disease type were considered in the analysis for all TB cases and for Spanish-born only.
Epidemiological cluster evaluation.
Clusters identified by epidemiological links were compared against genomic clustering. Similarities and discrepancies between both methods are described for all samples. Cluster size and pairwise distance among the samples included in the cluster are mentioned. Median time and 95% HPD (highest posterior density) of the most common ancestor (tMRCA) for the cluster obtained by both approaches are provided. For mean and median values. Only the clusters with tMRCA were considered.
Performance of the WGS method for transmission.
Values were extracted from 724 clinical TB isolates and assumed epidemiological links from contact tracing as the gold standard. NPV, negative predictive value; PPV, positive predictive value.
Patients mean age for those cases within genomic clusters which ancestors’ age are included in different time windows in Valencia region.