fastlin: an ultra-fast program for Mycobacterium tuberculosis complex lineage typing

Abstract

Summary

Fastlin is a bioinformatics tool designed for rapid Mycobacterium tuberculosis complex (MTBC) lineage typing. It utilizes an ultra-fast alignment-free approach to detect previously identified barcode single nucleotide polymorphisms associated with specific MTBC lineages. In a comprehensive benchmarking against existing tools, fastlin demonstrated high accuracy and significantly faster running times.

Availability and implementation

fastlin is freely available at https://github.com/rderelle/fastlin and can easily be installed using Conda.

1 Introduction

Lineage typing of Mycobacterium tuberculosis complex (MTBC), which notably includes the aetiological agent of tuberculosis disease, has evolved from traditional phenotypic methods to more advanced molecular techniques. Early methods relied on observable characteristics in the laboratory and broad classifications, while DNA-based methods like RFLP and spoligotyping provided increased resolution but had technical limitations (Jagielski et al. 2014).

The advent of whole-genome sequencing (WGS) has revolutionized the comparative analysis of MTBC samples, allowing for high-resolution classification (Wyllie et al. 2018, Diel et al. 2019). While large genomic deletions were initially proposed as lineage markers, the use of single nucleotide polymorphisms (SNPs) as barcode markers has gained prominence due to their higher abundance, enabling more precise identification and classification of MTBC lineages (Coll et al. 2014, Cancino-Muñoz et al. 2019, Napier et al. 2020).

The identification of barcode SNPs traditionally involves the alignment of WGS reads to a reference genome, the basis of popular tools such as TB-profiler (Phelan et al. 2019) and TbLG (Shitikov and Bespiatykh 2023). As it is primarily designed for general variant calling, read alignment is a complex and computationally intensive approach that scales poorly to large datasets. To overcome this challenge, we propose a new bioinformatics tool, fastlin, which uses an alignment-free approach and performs MTBC lineage typing in seconds rather than minutes.

2 Materials and methods

Fastlin is written in rust and takes as input a SNP barcode file and the directory containing the fastq files to be typed. The program essentially exploits the split-k-mer approach developed in SKA (Harris 2018), which uses k-mers split over a variable middle base, but with a significant speedup for lineage typing relying on the facts that: (i) fastlin does not need to compare and store all k-mers, only those relevant to barcode SNPs, and (ii) it typically does not need to scan all sequencing reads to identify barcode SNPs, assuming that the relevant reads are randomly distributed within the input fastq files.

The input barcode file contains all barcode SNPs with corresponding lineage names, and the 50 nucleotides upstream and downstream of each SNP, extracted from the genome of M.tuberculosis H37Rv; NC_000962.3. Fastlin then builds the barcode k-mers at the start of each run by combining (k−1)/2 downstream nucleotides, the barcode SNP and (k−1)/2 upstream nucleotides, with the k-mer size k being an odd number between 11 and 99 defined by the user (25 by default; see the Results section). The barcode k-mers are saved in memory together with their reverse complements. The input barcode file also contains the expected genome size, allowing fastlin to estimate the number of extracted k-mers needed to reach the user-defined k-mer coverage threshold (turned off by default).

K-mers are then extracted from the input fastq files and compared to the barcode k-mers until the entire fastq file is scanned, or until the number of extracted k-mers reaches the k-mer coverage threshold if one has been specified by the user. Once this process is finished, only those k-mers with a minimum number of occurrences are retained, and a lineage is validated if the number of retained k-mer barcodes reaches a user-defined threshold (3 by default). Finally, the coarser lineage names are removed (e.g. ‘4.1’ is removed if ‘4.1.2’ is detected), leading to the final lineage determination. If more than one lineage is detected, their abundances are calculated using the median of their barcode SNP occurrences. The relative frequency of each lineage can then be calculated as the ratio of their abundance divided by the sum of all final lineage abundances.

The barcode file used in this study and the Python scripts used to build and test it are available at https://github.com/rderelle/barcodes-fastlin. Sample analyses were performed using TB-profiler v5.0.0, QuantTB v1.01 and fastlin v0.1.0. Runtime benchmarks were performed with SKA v1.0 and TB-profiler v4.4.2 (with 6G RAM memory) and fastlin v0.1.0 on a Macbook Air laptop (M2, 8G RAM, 2022) using a single CPU. The 3139 MTBC samples were selected to represent all MTBC lineages as predicted by the TB-profiler database. The two most important contributors to this dataset were the Wellcome Trust and the UKHSA (formerly PHE), as part of the CRyPTiC consortium. All results mentioned in this manuscript, including runtimes, are available in Supplementary Data S1.

3 Results

For this case study, we used the barcodes identified in TB-profiler (Phelan et al. 2019). At the time of writing, this set included 1101 SNPs defining 125 MTBC major and minor lineages, with a minimum of 4 and a maximum of 10 SNPs per lineage. Since these barcode SNPs were identified using read mapping, we first determined the minimal k-mer size at which fastlin did not generate false positive SNP calls. Using k-mer sizes ranging from 11 to 99 nucleotides and three high-quality genome assemblies with known lineages, we found that only one barcode SNP was incorrectly detected with k-mer sizes above 19 (Supplementary Data S2). We discarded this problematic SNP barcode and set the default k-mer size to 25.

We then typed 3139 MTBC samples downloaded from the NCBI’s SRA database. To assess the quality of fastlin’s lineage predictions we compared them to the ones made by TB-profiler. Fastlin and TB-profiler predicted identical lineages for most samples, with disagreements found in only 68 samples (Supplementary Data S3). Most of these disagreements were in putative mixed samples (n = 51; 16 and 44 mixed samples identified by TB-profiler and fastlin, respectively) or in samples for which either TB-profiler or fastlin failed to identify any lineage (eight and one samples, respectively). Phylogenetic analyses of the eight nonmixed samples for which fastlin and TB-profiler predicted different lineages showed that fastlin accurately identified the correct lineage in all but one case (Supplementary Data S3).

We then re-analyzed the 3139 MTBC samples with a maximum k-mer coverage threshold of 80× (the median k-mer coverage of all samples was 91×). Theoretically, with a minimum number of occurrences for each barcode SNP set to four by default, fastlin should be able to type all samples at this coverage threshold. Using lineage predictions obtained by fastlin with default parameters as a reference, we only found five samples with coarser (truncated) lineage predictions (e.g. predicted lineage ‘2.2.1’ instead of ‘2.2.1.2’; ERR3276004, ERR3276023, and SRR7453034) and two samples without a lineage prediction (ERR3276012 and ERR3275788), all corresponding to BAM-derived fastq files as suggested by the presence of a BAM file in the SRA database alongside the fastq files for these samples. Since BAM files are usually sorted by genomic position for further analyses, the assumption of a random read distribution in fastq files made by fastlin when a k-mer coverage threshold is set did not hold for these samples, and they consequently required more reads than expected to be correctly typed.

Next, we assessed fastlin’s ability to detect mixtures of strains by analyzing a set of 47 pairs of M.tuberculosis samples initially produced to study cases of MTBC relapse and re-infection (Bryant et al. 2013) and subsequently re-analyzed to test the MTBC mixed strain detection tool QuantTB (Anyansi et al. 2020). We ran QuantTB, TB-profiler and fastlin on this dataset. Eleven samples were identified as mixed by at least one of these three tools, with 9, 6, and 10 mixed samples detected by QuantTB, TB-profiler, and fastlin, respectively (Fig. 1A and Supplementary Data S4). The sample identified as a mixture of strains solely by QuantTB consists of a mixture of closely related strains (Bryant et al. 2013), possibly belonging to the same lineage (sample 8a; Supplementary Data S4). Fastlin was the only tool to identify sample 45b as a mixed sample. We believe this sample indeed contains a strain mixture since (i) the lineage of its minor strain was also present in pure samples of this dataset, (ii) the minor strain was supported by six barcode SNPs, and (iii) this sample was also identified as mixed by Bryant et al. We repeated the fastlin analyses using maximum coverage thresholds ranging from 100× to 10×, in 10× increments. Fastlin successfully detected the 10 mixed samples down to a 60× maximum k-mer coverage (Supplementary Data S4). Using simulated mixtures of pairs of strains from distinct lineages, we also found that fastlin provides reliable estimates of strain frequencies down to 0.05 (RMSE = 2.47%; Supplementary Data S4).

Figure 1.

Fastlin benchmarking. (A) Detected mixed samples in Bryant et al. dataset. Samples with detected mixture are indicated with a colored box. (B) Runtimes obtained by TB-profiler, SKA (using k = 27), and fastlin (with default parameters in green, and with a maximum k-mer coverage of 80× in red). Note the logarithmic scale on the y-axis.

Finally, we compared the running times of fastlin with those of SKA and TB-profiler, chosen as representatives of k-mer-based and read-mapping tools, respectively. It is important to note that these two bioinformatics tools are not fully dedicated to lineage typing and generate more information than fastlin does (e.g. all SNPs, drug resistance predictions). For this benchmark we used 16 SRA samples representing a large range of sequencing depths, all composed of paired-end 150 bp reads. We observed that fastlin was at least an order of magnitude faster than SKA and TB-profiler, with running times ranging from 2 to 14 s per sample under default settings (Fig. 1B). Using a maximum k-mer coverage threshold of 80×, fastlin’s running times were consistently under 5 s. Fastlin also exhibited minimal memory footprint, reaching a maximum use of only 4 MB in this benchmark, whereas both SKA and TB-profiler require several GB.

4 Discussion

While primarily developed to achieve ultra-fast lineage typing, fastlin also shows accurate MTBC lineage prediction, comparable and in some cases superior to that of standard tools. Its lineage predictions are nearly identical to those made by TB-profiler, with the few discrepancies observed in nonmixed samples being mostly attributed to TB-profiler errors. Fastlin also shows an accurate identification of mixed-lineage samples and estimation of the associated lineage proportions. We believe that the identification of low-frequency strains is facilitated in fastlin by the absence of background noise related to read-alignments, which mapping-based methods need to mitigate with stringent parameters. Fastlin’s simplicity and efficiency make it a powerful tool for rapidly typing large MTBC datasets, with the potential for broader applications in lineage typing of other pathogens determined by a set of known barcodes.

Our analyses also uncover two limitations of fastlin. First, the presence of sorted reads in BAM-derived fastq files restricts the use of the maximum coverage threshold implemented in fastlin. Although this issue only affects the lineage prediction of seven files out of 3139 at a maximum coverage of 80×, this option is disabled by default, enabling fastlin to process all types of fastq files. However, in the case of in-house fastq files or fastq files of known provenance, we recommend specifying a maximum coverage threshold to further reduce fastlin’s runtime. Second, the detection of strain mixtures is intrinsically limited to the lineages defined by the SNP barcodes, and fastlin will fail to identify any mixture of strains belonging to the same lineage. If the identification of mixed samples is essential, we recommend the use of alternative tools with either larger reference datasets such as QuantTB (Anyansi et al. 2020) or database-free tools such as SplitStrains (Gabbassov et al. 2021).

While we tested fastlin with one specific set of MTBC barcode SNPs, new lineage classifications and their associated barcode SNPs have recently been proposed (Coscolla et al. 2021, Netikul et al. 2022, Shuaib et al. 2022, Shitikov and Bespiatykh 2023). To accommodate the evolving landscape of MTBC lineage typing, we made the scripts required to build and test custom barcode files available on GitHub. This will enable end-users to leverage fastlin with their barcode SNPs of choice. We recommend including a minimum of 4–5 SNPs per lineage, and considering all mutations rather than only synonymous SNPs, to ensure robust lineage classification.

Supplementary data

Supplementary data are available at Bioinformatics online.

Conflict of interest

None declared.

Funding

This work was supported by the NIHR Health Protection Research Unit in Respiratory Infections, in partnership with the UK Health Security Agency [NIHR200927]. The views expressed are those of the author(s) and not necessarily those of the NIHR or the Department of Health and Social Care. L.C. and N.A. acknowledge funding from the MRC Centre for Global Infectious Disease Analysis [MR/R015600/1], jointly funded by the UK Medical Research Council (MRC) and the UK Foreign, Commonwealth & Development Office (FCDO), under the MRC/FCDO Concordat agreement. For the purpose of open access, the authors have applied a Creative Commons Attribution (CC BY) licence to any Author Accepted Manuscript version arising.