Spatiotemporal Clustering of Mycobacterium tuberculosis Complex Genotypes in Florida: Genetic Diversity Segregated by Country of Birth

Abstract

BackgroundTuberculosis (TB) is caused by members of the Mycobacterium tuberculosis complex (MTBC). Although the MTBC is highly clonal, between-strain genetic diversity has been observed. In low TB incidence settings, immigration may facilitate the importation of MTBC strains with a potential to complicate TB control efforts.MethodsWe investigated the genetic diversity and spatiotemporal clustering of 2,510 MTBC strains isolated in Florida, United States, between 2009 and 2013 and genotyped using spoligotyping and 24-locus MIRU-VNTR. We mapped the genetic diversity to the centroid of patient residential zip codes using a geographic information system (GIS). We assessed transmission dynamics and the influence of immigration on genotype clustering using space-time permutation models adjusted for foreign-born population density and county-level HIV risk and multinomial models stratified by country of birth and timing of immigration in SaTScan.Principal FindingsAmong the 2,510 strains, 1,245 were reported among foreign-born persons; including 408 recent immigrants (<5 years). Strain allelic diversity (h) ranged from low to medium in most locations and was most diverse in urban centers where foreign-born population density was also high. Overall, 21.5% of cases among U.S.-born persons and 4.6% among foreign-born persons clustered genotypically and spatiotemporally and involved strains of the Haarlem family. One Haarlem space-time cluster identified in the mostly rural northern region of Florida included US/Canada-born individuals incarcerated at the time of diagnosis; two clusters in the mostly urban southern region of Florida were composed predominantly of foreign-born persons. Both groups had HIV prevalence above twenty percent.Conclusions/SignificanceAlmost five percent of TB cases reported in Florida during 2009–2013 were potentially due to recent transmission. Improvements to TB screening practices among the prison population and recent immigrants are likely to impact TB control. Due to the monomorphic nature of available markers, whole genome sequencing is needed to conclusively delineate recent transmission events between U.S. and foreign-born persons.

Spatial and temporal clustering analysis of tuberculosis in the mainland of China at the prefecture level, 2005–2015

“…A study from Canada used this method to reveal a complex coexistence of spatial and cohort clustering with the time of 1990 to 2013, and provided the basis for public health response [ 30 ]. Studies from Ghana [ 31 ] and American [ 32 ] about Mycobacterium tuberculosis strains or genotypes also found the spatio-temporal characteristics based on this method, which could guide the formulation of TB control and prevention policies. Though there were several studies in China have explored the distribution of TB, they were only restricted to a certain province or certain area, or the nationwide research just at the provincial level not the prefecture level.…”

Whole-Genome Sequencing and Bioinformatic Analysis of Isolates from Foodborne Illness Outbreaks of Campylobacter jejuni and Salmonella enterica

“…Research has shown that genetic diversity and genomic plasticity in bacteria increase with geographic distance ( 32 – 34 ), which can make it difficult to perform SNP-based analyses ( 35 ). As expected, the reference-free analysis and pipeline applied here were not affected by high levels of nucleotide diversity and identified over 4,000 shared, homologous, protein-coding genes, which enabled the construction of a high-resolution phylogenetic tree with high levels of statistical support for several clades.…”

Genetic diversity of drug and multidrug-resistant Mycobacterium tuberculosis circulating in Veracruz, Mexico

“…The use of tools that allow characterization and genotypic analysis of TB, such as 24-locus mycobacterial interspersed repetitive unit-variable-number tandem-repeat (MIRU-VNTR) and spacer oligonucleotide typing (spoligotyping), allow an understanding of the dynamics and complexity of the population structure of Mycobacterium tuberculosis within a population [ 3 , 4 ]. These procedures allow identification of the different lineages in circulation within specific regions and their relationship with potential pathogenicity and virulence [ 5 , 6 ] Also, several reports from different geographic regions have described the levels of association with demographic, epidemiological and drug resistance characteristics [ 7 – 12 ].…”