Population Structure among <i>Mycobacterium tuberculosis</i> Isolates from Pulmonary Tuberculosis Patients in Colombia

<div><p>Background</p><p>Phylogeographic composition of <i>M. tuberculosis</i> populations reveals associations between lineages and human populations that might have implications for the development of strategies to control the disease. In Latin America, lineage 4 or the Euro-American, is predominant with considerable variations among and within countries. In Colombia, although few studies from specific localities have revealed differences in <i>M. tuberculosis</i> populations, there are still areas of the country where this information is lacking, as is a comparison of Colombian isolates with those from the rest of the world.</p><p>Principal Findings</p><p>A total of 414 <i>M. tuberculosis</i> isolates from adult pulmonary tuberculosis cases from three Colombian states were studied. Isolates were genotyped using <i>IS6110</i>-restriction fragment length polymorphism (RFLP), spoligotyping, and 24-locus Mycobacterial interspersed repetitive units variable number tandem repeats (MIRU-VNTRs). SIT42 (LAM9) and SIT62 (H1) represented 53.3% of isolates, followed by 8.21% SIT50 (H3), 5.07% SIT53 (T1), and 3.14% SIT727 (H1). Composite spoligotyping and 24-locus MIRU- VNTR minimum spanning tree analysis suggest a recent expansion of SIT42 and SIT62 evolved originally from SIT53 (T1). The proportion of Haarlem sublineage (44.3%) was significantly higher than that in neighboring countries. Associations were found between <i>M. tuberculosis</i> MDR and SIT45 (H1), as well as HIV-positive serology with SIT727 (H1) and SIT53 (T1).</p><p>Conclusions</p><p>This study showed the population structure of <i>M. tuberculosis</i> in several regions from Colombia with a dominance of the LAM and Haarlem sublineages, particularly in two major urban settings (Medellín and Cali). Dominant spoligotypes were LAM9 (SIT 42) and Haarlem (SIT62). The proportion of the Haarlem sublineage was higher in Colombia compared to that in neighboring countries, suggesting particular conditions of co-evolution with the corresponding human population that favor the success of this sublineage.</p></div

Orphan strains (n = 20) and corresponding spoligotyping defined lineages/sublineages recorded among a total of 414 <i>M. tuberculosis</i> strains from Colombian patients.

<p>* Lineage designations for orphan patterns were done manually as Expert-based interpretations using revised SpolDB4 rules.</p><p>** Drug resistance (Drug R) information is shown as: 0, unknown; 1, pansusceptible; 2, MDRTB, i.e., combined resistance to INH-RIF (with or without resistance to other drugs); 3, any other resistance(s); 4, proven XDRTB.</p

Description of clusters containing 5 or more isolates in this study, and their worldwide distribution in the SITVIT2 database.

<p>* Worldwide distribution is reported for regions with more than 3% of a given SITs as compared to their total number in the SITVIT2 database. The definition of macro-geographical regions and sub-regions (<a href="http://unstats.un.org/unsd/methods/m49/m49regin.htm" target="_blank">http://unstats.un.org/unsd/methods/m49/m49regin.htm</a>) is according to the United Nations; Regions: AFRI (Africa), AMER (Americas), ASIA (Asia), EURO (Europe), and OCE (Oceania), subdivided in: E (Eastern), M (Middle), C (Central), N (Northern), S (Southern), SE (South-Eastern), and W (Western). Furthermore, CARIB (Caribbean) belongs to Americas, while Oceania is subdivided in 4 sub-regions, AUST (Australasia), MEL (Melanesia), MIC (Micronesia), and POLY (Polynesia). Note that in our classification scheme, Russia has been attributed a new sub-region by itself (Northern Asia) instead of including it among rest of the Eastern Europe. It reflects its geographical localization as well as due to the similarity of specific TB genotypes circulating in Russia (a majority of Beijing genotypes) with those prevalent in Central, Eastern and South-Eastern Asia.</p><p>** The 3 letter country codes are according to <a href="http://en.wikipedia.org/wiki/ISO_3166-1_alpha-3" target="_blank">http://en.wikipedia.org/wiki/ISO_3166-1_alpha-3</a>; countrywide distribution is only shown for SITs with ≥3% of a given SITs as compared to their total number in the SITVIT2 database.</p

Minimum spanning tree (MST) illustrating evolutionary relationships between <i>M. tuberculosis</i> spoligotypes identified in our study

<p>(<b>A</b>). MST constructed with spoligotyping. (B) MST constructed with 24-locus MIRU-VNTR (<b>C</b>) Composite MST with spoligotyping and MIRU-VNTRs markers. MST were constructed on all isolates (n = 414, including 20 orphan patterns). The phylogenetic tree connects each genotype based on degree of changes required to go from one allele to another. The structure of the tree is represented by branches (continuous vs. dashed and dotted lines) and circles representing each individual pattern. Note that the length of the branches represents the distance between patterns while the complexity of the lines (continuous, gray dashed and gray dotted) denotes the number of allele/spacer changes between two patterns: solid lines, 1 or 2 or 3 changes (thicker ones indicate a single change, while the thinner ones indicate 2 or 3 changes); gray dashed lines represent 4 changes; and gray dotted lines represent 5 or more changes. The size of the circle is proportional to the total number of isolates in our study, illustrating unique isolates (smaller nodes) versus clustered isolates (bigger nodes). The color of the circles indicates the phylogenetic lineage to which the specific pattern belongs. Note that orphan patterns are circled in orange. Patterns colored in yellow indicate a strain with an unknown signature (unclassified).</p