Dataset Information

Genomic epidemiology of Lineage 4 Mycobacterium tuberculosis subpopulations in New York City and New Jersey, 1999-2009.

ABSTRACT: Whole genome sequencing (WGS) has rapidly become an important research tool in tuberculosis epidemiology and is likely to replace many existing methods in public health microbiology in the near future. WGS-based methods may be particularly useful in areas with less diverse Mycobacterium tuberculosis populations, such as New York City, where conventional genotyping is often uninformative and field epidemiology often difficult. This study applies four candidate strategies for WGS-based identification of emerging M. tuberculosis subpopulations, employing both phylogenomic and population genetics methods.M. tuberculosis subpopulations in New York City and New Jersey can be distinguished via phylogenomic reconstruction, evidence of demographic expansion and subpopulation-specific signatures of selection, and by determination of subgroup-defining nucleotide substitutions. These methods identified known historical outbreak clusters and previously unidentified subpopulations within relatively monomorphic M. tuberculosis endemic clone groups. Neutrality statistics based on the site frequency spectrum were less useful for identifying M. tuberculosis subpopulations, likely due to the low levels of informative genetic variation in recently diverged isolate groups. In addition, we observed that isolates from New York City endemic clone groups have acquired multiple non-synonymous SNPs in virulence- and growth-associated pathways, and relatively few mutations in drug resistance-associated genes, suggesting that overall pathoadaptive fitness, rather than the acquisition of drug resistance mutations, has played a central role in the evolutionary history and epidemiology of M. tuberculosis subpopulations in New York City.Our results demonstrate that some but not all WGS-based methods are useful for detection of emerging M. tuberculosis clone groups, and support the use of phylogenomic reconstruction in routine tuberculosis laboratory surveillance, particularly in areas with relatively less diverse M. tuberculosis populations. Our study also supports the use of wider-reaching phylogenomic and population genomic methods in tuberculosis public health practice, which can support tuberculosis control activities by identifying genetic polymorphisms contributing to epidemiological success in local M. tuberculosis populations and possibly explain why certain isolate groups are apparently more successful in specific host populations.

SUBMITTER: Brown TS

PROVIDER: S-EPMC5117616 | biostudies-literature | 2016 Nov

REPOSITORIES: biostudies-literature

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Genomic epidemiology of Lineage 4 Mycobacterium tuberculosis subpopulations in New York City and New Jersey, 1999-2009.

Brown Tyler S TS Narechania Apurva A Walker John R JR Planet Paul J PJ Bifani Pablo J PJ Kolokotronis Sergios-Orestis SO Kreiswirth Barry N BN Mathema Barun B

BMC genomics 20161121 1

<h4>Background</h4>Whole genome sequencing (WGS) has rapidly become an important research tool in tuberculosis epidemiology and is likely to replace many existing methods in public health microbiology in the near future. WGS-based methods may be particularly useful in areas with less diverse Mycobacterium tuberculosis populations, such as New York City, where conventional genotyping is often uninformative and field epidemiology often difficult. This study applies four candidate strategies for WG ...[more]

PMID: 27871225

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Project description:The five boroughs of New York City (NYC) were early epicenters of the Covid-19 pandemic in the United States, with over 380,000 cases by May 31. High caseloads were also seen in nearby counties in New Jersey (NJ), Connecticut (CT) and New York (NY). The pandemic started in the area in March with an exponential rise in the number of daily cases, peaked in early April, briefly declined, and then, showed clear signs of a second peak in several counties. We will show that despite control measures such as lockdown and restriction of movement during the exponential rise in daily cases, there was a significant net migration of households from NYC boroughs to the neighboring counties in NJ, CT and NY State. We propose that the second peak in daily cases in these counties around NYC was due, in part, to the movement of people from NYC boroughs to these counties. We estimate the movement of people using "Change of Address" (CoA) data from the US Postal Service, provided under the "Freedom of Information Act" of 1967. To identify the timing of the second peak and the number of cases in it, we use a previously proposed SIR model, which accurately describes the early stages of the coronavirus pandemic in European countries. Subtracting the model fits from the data identified, we establish the timing and the number of cases, N CS , in the second peak. We then related the number of cases in the second peak to the county population density, P, and the excess Change of Address, E CoA, into each county using the simple model which fits the data very well with α = 0.68, β = 0.31 (R 2 = 0.74, p = 1.3e-8). We also find that the time between the first and second peaks was proportional to the distance of the county seat from NY Penn Station, suggesting that this migration of households and disease was a directed flow and not a diffusion process. Our analysis provides a simple method to use change of address data to track the spread of an infectious agent, such as SARS-Cov-2, due to migrations away from epicenters during the initial stages of a pandemic.

Dataset Information

Genomic epidemiology of Lineage 4 Mycobacterium tuberculosis subpopulations in New York City and New Jersey, 1999-2009.

Publications

Genomic epidemiology of Lineage 4 Mycobacterium tuberculosis subpopulations in New York City and New Jersey, 1999-2009.

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