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J Clin Microbiol. Sep 2010; 48(9): 3403–3406.
Published online Jun 30, 2010. doi:  10.1128/JCM.00370-10
PMCID: PMC2937716

High-Resolution Typing by Integration of Genome Sequencing Data in a Large Tuberculosis Cluster[down-pointing small open triangle]

Abstract

To investigate whether genome sequencing yields more useful markers than those currently used to study the epidemiology of tuberculosis, it was applied to three Mycobacterium tuberculosis isolates of the Harlingen outbreak. Our findings suggest that single nucleotide polymorphisms can be used to identify transmission chains in restriction fragment length polymorphism clusters.

Molecular typing contributes significantly to our understanding of the epidemiology of tuberculosis. A variety of genetic markers, such as IS6110 restriction fragment length polymorphism (RFLP) and variable-number tandem repeat (VNTR) typing, are currently used for DNA fingerprinting of Mycobacterium tuberculosis isolates (2, 7, 12-14, 23). Unfortunately, these markers do not distinguish primary and subsequent sources of infection in long-term DNA fingerprinting surveillance, as the turnover of these markers is not in range with the pace of transmission (4-6). Therefore, molecular typing is inaccurate when applied for extended time periods in a given area.

In the Netherlands, IS6110 RFLP typing has been routinely used for molecular epidemiology since the early 1990s. A remarkably large outbreak began in the city of Harlingen in 1992, and this cluster grew to over 100 cases in 2008 and is still expanding (10, 11). Although a small subset of isolates of this cluster exhibited a single transposition or deletion of IS6110, it soon became impossible to distinguish sources of infection and secondary and subsequent cases in the cluster. Some contact chains in the Harlingen cluster were suggested by contact tracing, performed according to the stone-in-the-pond principle (15, 25), but the exact transmission chains could not be validated by fingerprinting of the M. tuberculosis isolates, as most of the isolates revealed the same DNA fingerprints.

For this study, three isolates from two chains of transmission in the Harlingen cluster that could be accurately determined by contact tracing were selected for genome sequencing (Fig. (Fig.1).1). The bacterial isolates exhibited no change in antituberculosis drug resistance or any other observable change in phenotype. Sequencing and analysis of strains SH1 and SH5, as well as the tempo and mode of evolutionary changes between these two isolates, were described in one of our earlier studies (19). The DNA of strain SH9, purified according to the method of van Soolingen et al. (24), was de novo sequenced on a GS FLX Titanium system, and assembly of raw sequencing reads with an average read length of 400 bases was performed by using the Genome Sequencer software, version 2.0.0.22. Sequence reads, contigs, and quality scores were provided by Microsynth AG, Switzerland. The SH9 sequence consisted of 214,283,462 high-quality bases assembled in 401 contigs with 4,207,440 bases (50.9-fold coverage). In total, 95.4% of the theoretical genome size of 4.41 Mb was available for analysis. From the in silico comparison of the three genomes, eight polymorphic single nucleotide polymorphisms (SNPs) were verified by subsequent resequencing on an ABI 3730xl sequencer (Table (Table11).

FIG. 1.
Schematic depiction of two contact chains from the Harlingen (H) cluster suggested by contact tracing. Time is depicted by the horizontal bar; patients are numbered H1 to H9. Bacterial isolates of patients marked with an asterisk were subjected to genome ...
TABLE 1.
Single nucleotide polymorphisms identified by genome sequencing of three Mycobacterium tuberculosis Harlingen isolates and used as markers in this study

All 104 isolates of the IS6110 Harlingen cluster were tested for the presence of these eight SNPs. The bacterial isolates were designated with an “S” (for strain) followed by their patient number (for example, H44 for Harlingen patient 44). Identified polymorphic sites were concatenated, and these aligned sequences were clustered using a neighbor-joining algorithm with ClustalW version 2.0.1 (22), which divided the Harlingen cluster into five SNP clusters (Fig. (Fig.22 A).

FIG. 2.
(A) Clustering of the single nucleotide polymorphism (SNP) types of the isolates of the Harlingen IS6110 restriction fragment length polymorphism (RFLP) cluster. Application of the SNP markers to the isolates of the Harlingen cluster divided the IS6110 ...

To assign index cases within an SNP cluster, the dates of isolation of the strains were included for isolates of patients in one of the contact chains (Fig. (Fig.1)1) and for isolates in one of the new SNP clusters. The patient with the earliest isolate in each SNP cluster was defined as the index case. The earliest identified case is, however, not necessarily the first source of transmission. Delays in the timely diagnosis of tuberculosis may occur because of differences in health care-seeking behavior and lack of symptoms or expertise of care providers. In our study, the contact tracing information supported the index cases assigned by this model. For all other isolates, the time that had passed since the diagnosis of the index case was calculated and added as separate branches in Fig. Fig.2B2B.

By applying genome sequencing data, the number of possible infection routes was minimized for all patients. For patients whose isolates were part of the newly identified SNP clusters, a most likely scheme of transmission events was created (Fig. (Fig.33).

FIG. 3.
Most likely transmission scheme suggested by single nucleotide polymorphism (SNP) typing, temporal, and contact tracing data. Black arrows indicate the most likely transmission events based on the SNP type clustering and integration of temporal data and ...

For one patient who had had two episodes of tuberculosis, in 1996 (isolate SH88.a) and 1999 (isolate SH88.b), SNP typing confirmed a suspected reinfection by the Harlingen strain from a secondary source in the Harlingen outbreak and excluded a possible endogenous reactivation of the disease. The isolate of the first disease episode of this patient was part of the largest cluster (SNP type GTGGCTGT), and the isolate of the second disease episode exhibited SNP type GTGCCTGT (underlining represents a mutation event), which supported a reinfection by patient H3. Patient H88 was married to patient H3; a reinfection by his partner is in agreement with the contact tracing information.

Genome sequencing of three isolates of the Harlingen cluster allowed us to determine SNPs and distinguish between isolates with higher discriminatory power than IS6110 RFLP and identified separate transmission chains within the cluster. These SNPs (and their discriminatory power) are specific for the Harlingen cluster and, for example, are not present in strain H37Rv, and determination of SNPs in other clusters requires genome sequencing of patient isolates of those clusters. Although the sequencing of only a few isolates of the Harlingen outbreak led to a phylogenetic discovery bias (17, 20), i.e., other samples of this IS6110 RFLP cluster most likely have other SNPs in addition to the ones reported here, it did not prohibit the disclosure of secondary and tertiary sources (patients H3 and H4) in the first transmission chain. Moreover, the first and second isolates of patient H4 exhibited the same SNP types as isolates of three other patients (patients H81, H86, and H89) that were infected by this case. In a later year, patient H4 had a reactivation of tuberculosis, and the isolated bacteria had another SNP type, also found in the isolates of another three patients (including patient H5) who were supposedly infected during the reactivation stage of patient H4 (Fig. (Fig.33).

The isolates of patients H7 and H8 exhibited no polymorphisms compared to SH1. The suggested contact chain leading to patient H9 was therefore not confirmed by this study. Moreover, no other isolates with the SNPs 5 to 8 were found in the Harlingen cluster. As all diagnosed active tuberculosis cases in the Netherlands are part of the Dutch database, it can be assumed that either patient H9 did not infect other persons in the Netherlands or infected cases did not (yet) progress to active disease.

After careful considerations of the costs and the technological limitations, genome sequencing will probably become the new standard method for typing of M. tuberculosis in the future and will replace existing typing methods because of its higher discriminatory power (16) and the decreasing prices for sequencing (8, 18, 26). Genome sequencing will elucidate transmission chains among patients that are clustered by currently used DNA fingerprinting methods. Future sequencing techniques will probably identify more polymorphisms between isolates because of technical progress, such as longer sequencing reads (1, 9, 21) and improved read accuracies. When genome sequencing of M. tuberculosis isolates becomes routinely available, identification, prediction of drug resistance, and epidemiological typing can be included in a single rapid analysis (3, 26, 27). In summary, we expect that genome sequencing will become a useful diagnostic tool with unprecedented possibilities.

Acknowledgments

We thank the staff at the Tuberculosis Reference Laboratory, RIVM, for technical assistance.

This work was supported by the RIVM SOR project S/230136/01/GA and by the EU-supported TBadapt project 37919.

Footnotes

[down-pointing small open triangle]Published ahead of print on 30 June 2010.

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