Pairwise Genome Comparisons Research Articles

Comparative genome analyses of clinical and non-clinical Clostridioides difficile strains.

The pathogenic bacterium Clostridioides difficile is a worldwide health burden with increasing morbidity, mortality and antibiotic resistances. Therefore, extensive research efforts are made to unravel its virulence and dissemination. One crucial aspect for C. difficile is its mobilome, which for instance allows the spread of antibiotic resistance genes (ARG) or influence strain virulence. As a nosocomial pathogen, the majority of strains analyzed originated from clinical environments and infected individuals. Nevertheless, C. difficile can also be present in human intestines without disease development or occur in diverse environmental habitats such as puddle water and soil, from which several strains could already be isolated. We therefore performed comprehensive genome comparisons of closely related clinical and non-clinical strains to identify the effects of the clinical background. Analyses included the prediction of virulence factors, ARGs, mobile genetic elements (MGEs), and detailed examinations of the pan genome. Clinical-related trends were thereby observed. While no significant differences were identified in fundamental C. difficile virulence factors, the clinical strains carried more ARGs and MGEs, and possessed a larger accessory genome. Detailed inspection of accessory genes revealed higher abundance of genes with unknown function, transcription-associated, or recombination-related activity. Accessory genes of these functions were already highlighted in other studies in association with higher strain virulence. This specific trend might allow the strains to react more efficiently on changing environmental conditions in the human host such as emerging stress factors, and potentially increase strain survival, colonization, and strain virulence. These findings indicated an adaptation of the strains to the clinical environment. Further, implementation of the analysis results in pairwise genome comparisons revealed that the majority of these accessory genes were encoded on predicted MGEs, shedding further light on the mobile genome of C. difficile. We therefore encourage the inclusion of non-clinical strains in comparative analyses.

2285. Using Genomic Sequencing to Describe SARS-CoV-2 Transmission Dynamics in U.S. Major League Soccer Clubs

Abstract Background In 2020–2022, U.S. Major League Soccer (MLS) used SARS-CoV-2 mitigation protocols that included masking, social distancing, avoiding contact with others outside of training and games, testing, quarantine, and isolation. In addition to isolation for those who tested positive, a SARS-CoV-2 genomic sequencing strategy was developed to identify whether infections were associated with intra-league transmission. Methods Nasopharyngeal swabs were collected by MLS club medical staff from players and staff from February 2021 through September 2022. During this time, surveillance testing changed from daily to weekly to testing only symptomatic players and staff. SARS-CoV-2 positive samples were analyzed using amplicon-based whole genome sequencing. A phylogenetic tree was constructed using Nextstrain to visualize genomes from infected players and staff in the context of genomes available on GISAID circulating in the United States during corresponding time periods. To identify transmission links, all genomes were compared in a pairwise fashion. Genomes that were 0–2 nucleotides different were considered part of direct transmission clusters. Results Of 250 samples that were rtPCR positive for SARS-CoV-2, 215 (86%) were sequenced. Phylogenetic analysis showed a broad diversity of lineages, including some predominant overseas (e.g., AY.98.1). Pairwise comparison revealed SARS-CoV-2 sequences from 7 individuals appeared to be linked. These individuals were on 2 different MLS teams; there was an off-field exposure (dinner). Five (71%) had identical SARS-CoV-2 sequences; 2 had sequences that were 1 nucleotide different at the consensus level. Subconsensus genome analysis revealed that differences of 1 nucleotide were due to subconsensus mutations fluctuating below and above 50%, suggesting all 7 individuals were part of a transmission cluster. Phylogenetic analysis revealed that the sequences from the cluster were distinct from reference sequences and were likely a unique transmission chain. Conclusion SARS-CoV-2 transmission may occur within, and even between, professional sports teams. Pairwise comparison of individual genomes can provide improved granularity to identify clusters and understand SARS-CoV-2 transmission. Disclosures Davidson H. Hamer, MD, Kephera Diagnostics: Grant/Research Support|Takeda: Advisor/Consultant|Takeda: Grant/Research Support|Trinity Biotech, LLC: Advisor/Consultant|Valneva: Advisor/Consultant|Valneva: Grant/Research Support Daniel Bourque, MD, Kephera Diagnostics: Grant/Research Support

Ralstonia chuxiongensis sp. nov., Ralstonia mojiangensis sp. nov., and Ralstonia soli sp. nov., isolated from tobacco fields, are three novel species in the family Burkholderiaceae.

Eight Gram-negative, aerobic, motile with paired polar flagella and rod-shaped bacteria were isolated from six tobacco fields in Yunnan, PR China. 16S rRNA gene sequence analysis revealed that all the strains belonged to the genus Ralstonia. Among them, strain 22TCCZM03-6 had an identical 16S rRNA sequence to that of R. wenshanensis 56D2T, and the other strains were closely related to R. pickettii DSM 6297T (98.34–99.86%), R. wenshanensis 56D2T (98.70–99.64%), and R. insidiosa CCUG 46789T (97.34–98.56%). Genome sequencing yielded sizes ranging from 5.17 to 5.72 Mb, with overall G + C contents of 63.3–64.1%. Pairwise genome comparisons showed that strain 22TCCZM03-6 shared average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values above the species cut-off with R. wenshanensis 56D2T, suggesting that strain 22TCCZM03-6 is a special strain of the R. wenshanensis. Five strains, including 21MJYT02-10T, 21LDWP02-16, 22TCJT01-1, 22TCCZM01-4, and 22TCJT01-2, had ANI values >95% and dDDH values >70% when compared with each other. These five strains had ANI values of 73.32–94.17% and dDDH of 22.0–55.20% with the type strains of the genus Ralstonia individually, supporting these five strains as a novel species in the genus Ralstonia. In addition, strains 21YRMH01-3T and 21MJYT02-11T represent two independent species. They both had ANI and dDDH values below the thresholds for species delineation when compared with the type species of the genus Ralstonia. In strains 21YRMH01-3T and 21MJYT02-10T, the main fatty acids were summed features 3, 8, and C16:0; however, strain 21MJYT02-11T contained C16:0, cyclo-C17:0, and summed features 3 as major fatty acids. The main polar lipids, including diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine, were identified from strains 21YRMH01-3T, 21MJYT02-10T, and 21MJYT02-11T. The ubiquinones Q-7 and Q-8 were also detected in these strains, with Q-8 being the predominant quinone. Based on the above data, we propose that the eight strains represent one known species and three novel species in the genus Ralstonia, for which the names Ralstonia chuxiongensis sp. nov., Ralstonia mojiangensis sp. nov., and Ralstonia soli sp. nov. are proposed. The type strains are 21YRMH01-3T (=GDMCC 1.3534T = JCM 35818T), 21MJYT02-10T (=GDMCC 1.3531T = JCM 35816T), and 21MJYT02-11T (=GDMCC 1.3532T = JCM 35817T), respectively.

CuGenDBv2: an updated database for cucurbit genomics.

The Cucurbitaceae (cucurbit) family consists of about 1,000 species in 95 genera, including many economically important and popular fruit and vegetable crops. During the past several years, reference genomes have been generated for >20 cucurbit species, and variome and transcriptome profiling data have been rapidly accumulated for cucurbits. To efficiently mine, analyze and disseminate these large-scale datasets, we have developed an updated version of Cucurbit Genomics Database. The updated database, CuGenDBv2 (http://cucurbitgenomics.org/v2), currently hosts 34 reference genomes from 27 cucurbit species/subspecies belonging to 10 different genera. Protein-coding genes from these genomes have been comprehensively annotated by comparing their protein sequences to various public protein and domain databases. A novel 'Genotype' module has been implemented to facilitate mining and analysis of the functionally annotated variome data including SNPs and small indels from large-scale genome sequencing projects. An updated 'Expression' module has been developed to provide a comprehensive gene expression atlas for cucurbits. Furthermore, synteny blocks between any two and within each of the 34 genomes, representing a total of 595 pair-wise genome comparisons, have been identified and can be explored and visualized in the database.

A core genome multilocus sequence typing (cgMLST) analysis of Mycoplasma bovis isolates

Mycoplasma bovis (M. bovis) is an emerging major bovine pathogen, causing economic losses worldwide in the dairy and beef industry. Whole-genome sequencing (WGS) now allows high resolution for tracing clonal populations. Based on WGS, we developed the core genome multilocus sequence typing (cgMLST) scheme and applied it onto 151 genomes of clonal and non-clonal strains of M. bovis isolated from China, Australia, Israel, Denmark, Canada, and the USA. We used the complete genome of M. bovis PG45 as the reference genome. The pairwise genome comparison of these 151 genome sequences resulted in 478 cgMLST gene targets present in > 99.0 % clonal and non-clonal isolates with 100 % overlap and > 90 % sequence similarity. A total of 478 core genes were retained as cgMLST target genes of which an average of 90.4–99 % were present in 151 M. bovis genomes, while M. agalactiae (PG2) had 17.0 % and M. mycoides subsp. capri (PG3), M. ovipneumoniae (Y98), and M. arginine resulted in 0.0 % of good targets. When tested against the clonal and non-clonal strains, we found cgMLST clusters were congruent with the MLST-defined clonal groups, which had various degrees of diversity at the whole-genome level. Notably, cgMLST could distinguish between clonal and epidemiologically unrelated strains of the same clonal group, which could not be achieved using traditional MLST schemes. Our results showed that ninety-two M. bovis genomes from clonal group isolates had > 10 allele differences and unambiguously differentiated from unrelated outgroup strains. Additionally, cgMLST revealed that there might be several sub-clones of the emerging ST-52 clone. The cgMLST phylogenetic analysis results showed substantial agreement with geographical and temporal information. cgMLST enables the use of next-generation sequencing technology to bovine mycoplasma epidemiology at both the local and global levels. In conclusion, the novel cgMLST scheme not only showed discrimination resolution highly as compared with MLST and SNP cgMLST in sub-typing but also indicated the capability to reveal more population structure characteristics than MLST.

Optimising genomic approaches for identifying vancomycin-resistant Enterococcus faecium transmission in healthcare settings

Vancomycin-resistant Enterococcus faecium (VREfm) is a major nosocomial pathogen. Identifying VREfm transmission dynamics permits targeted interventions, and while genomics is increasingly being utilised, methods are not yet standardised or optimised for accuracy. We aimed to develop a standardized genomic method for identifying putative VREfm transmission links. Using comprehensive genomic and epidemiological data from a cohort of 308 VREfm infection or colonization cases, we compared multiple approaches for quantifying genetic relatedness. We showed that clustering by core genome multilocus sequence type (cgMLST) was more informative of population structure than traditional MLST. Pairwise genome comparisons using split k-mer analysis (SKA) provided the high-level resolution needed to infer patient-to-patient transmission. The more common mapping to a reference genome was not sufficiently discriminatory, defining more than three times more genomic transmission events than SKA (3729 compared to 1079 events). Here, we show a standardized genomic framework for inferring VREfm transmission that can be the basis for global deployment of VREfm genomics into routine outbreak detection and investigation.

Applying Synteny Networks (SynNet) to Study Genomic Arrangements of Protein-Coding Genes in Plants.

In comparative genomics, the study of synteny can be a powerful method for exploring genome rearrangements, inferring genomic ancestry, defining orthology relationships, determining gene and genome duplications, and inferring gene positional conservation patterns across taxa. In this chapter, we present a step-by-step protocol for microsynteny network (SynNet) analysis, as an alternative to traditional methods of synteny comparison, where nodes in the network represent protein-coding genes and edges represent the pairwise syntenic relationships. The SynNet pipeline consists of six main steps: (1) pairwise genome comparisons between all the genomes being analyzed, (2) detection of inter- and intrasynteny blocks, (3) generation of an entire synteny database (i.e., edgelist), (4) network clustering, (5) phylogenomic profiling of the gene family of interest, and (6) evolutionary inference. The SynNet approach facilitates the rapid analysis and visualization of synteny relationships (from specific genes, specific gene families up to all genes) across a large number of genomes.

Incorporating intergenic regions into reversal and transposition distances with indels.

Problems in the genome rearrangement field are often formulated in terms of pairwise genome comparison: given two genomes [Formula: see text] and [Formula: see text], find the minimum number of genome rearrangements that may have occurred during the evolutionary process. This broad definition lacks at least two important considerations: the first being which features are extracted from genomes to create a useful mathematical model, and the second being which types of genome rearrangement events should be represented. Regarding the first consideration, seminal works in the genome rearrangement field solely used gene order to represent genomes as permutations of integer numbers, neglecting many important aspects like gene duplication, intergenic regions, and complex interactions between genes. Regarding the second consideration, some rearrangement events are widely studied such as reversals and transpositions. In this paper, we shed light on the first consideration and created a model that takes into account gene order and the number of nucleotides in intergenic regions. In addition, we consider events of reversals, transpositions, and indels (insertions and deletions) of genomic material. We present a 4-approximation algorithm for reversals and indels, a [Formula: see text]-approximation algorithm for transpositions and indels, and a 6-approximation for reversals, transpositions, and indels.

Permethrin resistance in Aedes aegypti: Genomic variants that confer knockdown resistance, recovery, and death.

Pyrethroids are one of the few classes of insecticides available to control Aedes aegypti, the major vector of dengue, chikungunya, and Zika viruses. Unfortunately, evolving mechanisms of pyrethroid resistance in mosquito populations threaten our ability to control disease outbreaks. Two common pyrethroid resistance mechanisms occur in Ae. aegypti: 1) knockdown resistance, which involves amino acid substitutions at the pyrethroid target site—the voltage-gated sodium channel (VGSC)—and 2) enhanced metabolism by detoxification enzymes. When a heterogeneous population of mosquitoes is exposed to pyrethroids, different responses occur. During exposure, a proportion of mosquitoes exhibit immediate knockdown, whereas others are not knocked-down and are designated knockdown resistant (kdr). When these individuals are removed from the source of insecticide, the knocked-down mosquitoes can either remain in this status and lead to dead or recover within a few hours. The proportion of these phenotypic responses is dependent on the pyrethroid concentration and the genetic background of the population tested. In this study, we sequenced and performed pairwise genome comparisons between kdr, recovered, and dead phenotypes in a pyrethroid-resistant colony from Tapachula, Mexico. We identified single-nucleotide polymorphisms (SNPs) associated with each phenotype and identified genes that are likely associated with the mechanisms of pyrethroid resistance, including detoxification, the cuticle, and insecticide target sites. We identified high association between kdr and mutations at VGSC and moderate association with additional insecticide target site, detoxification, and cuticle protein coding genes. Recovery was associated with cuticle proteins, the voltage-dependent calcium channel, and a different group of detoxification genes. We provide a list of detoxification genes under directional selection in this field-resistant population. Their functional roles in pyrethroid metabolism and their potential uses as genomic markers of resistance require validation.

Flavobacterium turcicum sp. nov. and Flavobacterium kayseriense sp. nov. isolated from farmed rainbow trout in Turkey

During a study on culturable microorganisms from fish farms, four yellow-pigmented gram negative, rod shaped isolates, F-47T, F-339T, F-380 and F-400, were recovered from rainbow trout samples exhibiting clinical signs. Based on 16S rRNA gene sequence analysis, the strains were identified as members of the genus Flavobacterium. Strains F-47T and F-380 shared the highest 16S rRNA gene sequence identity level of 97.6% with the type strain of Flavobacterium frigoris DSM 15719T while strains F-339T and F-400 shared the highest identity level of 97.6% with the type strain of F. caseinilyticum AT-3-2T. A polyphasic taxonomic approach including phenotypic and genomic characterization as well as whole-cell MALDI-TOF mass spectrometry analyses was employed to ascertain the taxonomic position of the strains within the genus Flavobacterium. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) analyses between strains F-47T, F-339T and their close neighbours F. frigoris DSM 15719T and F. caseinilyticum AT-3-2T, respectively, confirmed that both strains represent novel species in the genus Flavobacterium. The DNA G+C contents of the strains F-47T and F-339T are 34.3% and 35.3%, respectively. It can be concluded on the basis of polyphasic characterization as well as pairwise genome comparisons that the strains F-47T and F-339T represent two novel species within the genus Flavobacterium, for which Flavobacterium kayseriense sp. nov. F-47T (=JCM 34195T=KCTC 82255T) and Flavobacterium turcicum sp. nov. F-339T (=JCM 34202T=KCTC 82262T) are proposed, respectively.

Detection of deformed wing virus (DWV) in the Vietnamese walking stick Medauroidea extradentata (Phasmatodea)

Deformed wing virus (DWV) is a single-stranded positive sense RNA virus that mainly infects honey bees (Apis mellifera) and can have devastating impacts on the colony. Recent studies have shown the presence of this virus in several species of Apis spp. and some other Hymenoptera, but our knowledge of their host range is very limited. We screened previously sequenced RNAseq libraries from different tissues of Vietnamese Walking Stick, Medauroidea extradentata (Phasmatodea) for DWV. We only found this virus in six libraries from anterior and posterior midgut tissue. From the midgut libraries we were able to construct a complete DWV genome sequence, which consisted of 10,140 nucleotides and included one open reading frame. Pairwise genome comparison confirmed strong similarity (98.89 %) of these assembled sequences with only 113 SNPs to the original DWV genome. We hypothesize the M. extradentata acquired this virus via a foodborne transmission by consuming DWV-infected material such as pollen or leaves contaminated with virus infected bee faeces.

CoreCruncher: Fast and Robust Construction of Core Genomes in Large Prokaryotic Data Sets

The core genome represents the set of genes shared by all, or nearly all, strains of a given population or species of prokaryotes. Inferring the core genome is integral to many genomic analyses, however, most methods rely on the comparison of all the pairs of genomes; a step that is becoming increasingly difficult given the massive accumulation of genomic data. Here, we present CoreCruncher; a program that robustly and rapidly constructs core genomes across hundreds or thousands of genomes. CoreCruncher does not compute all pairwise genome comparisons and uses a heuristic based on the distributions of identity scores to classify sequences as orthologs or paralogs/xenologs. Although it is much faster than current methods, our results indicate that our approach is more conservative than other tools and less sensitive to the presence of paralogs and xenologs. CoreCruncher is freely available from: https://github.com/lbobay/CoreCruncher. CoreCruncher is written in Python 3.7 and can also run on Python 2.7 without modification. It requires the python library Numpy and either Usearch or Blast. Certain options require the programs muscle or mafft.

The complete chloroplast genome of Isochrysis galbana and comparison with related haptophyte species

The haptophyte Isochrysis galbana is an algal species of commercial interest due to its ability to accumulate high levels of fucoxanthin. In this study, the complete chloroplast (cp) genome of I. galbana was sequenced using a combination of Illumina and third-generation sequencing platforms. This circular cp genome was 105,872 bp in length, consisting of a large single-copy (LSC) region of 54,838 bp and a small single-copy (SSC) region of 41,308 bp separated by two direct rDNA repeats of 4862 bp and 4864 bp. The cp genome contained 141 unique genes, including 112 protein-coding genes with no introns, 26 transfer-RNA (tRNA) genes and three ribosomal-RNA (rRNA) genes. Like canonical ribosomal operon repeat structure, two 16S-trnI-trnA-23S-5S ribosomal RNA operons were identified. A total of 32 pairs of small repeats and 45 perfect microsatellites were detected. All haptophyte chloroplasts sequenced to date apart from E. huxleyi have either a complete pair of canonical repeats with direct orientation or noncanonical inverted repeats that lost part of tRNAs, or they have lost the inverted repeat arrangement altogether. Additionally, imperfect ribosomal operon repeats were observed in most haptophytes. The non-identical 4.9 kb ribosomal direct-repeats in I. galbana cp genome were distinguished by three 1–2 bp-sized inserts/deletions (InDels) and 32 single nucleotide polymorphisms (SNPs). Pairwise chloroplast genome comparisons showed a high degree of conservation in genome structure, gene order and gene content between I. galbana and T. lutea, with an overall SNP mutation rate of 4.3 × 10−3 per site. Only 458 SNPs, 18 small InDels and one large insertion were detected between these two cp genomes. The transition-to-transversion (Ts/Tv) ratio was 1.79 and the predominant mutations were A/T to G/C transitions. Phylogenetic analysis of currently available haptophyte chloroplasts also reflected that I. galbana was most closely related to T. lutea. The Ka/Ks ratios of shared genes in Isochrysidales chloroplast genomes were less than 1, suggesting that those genes are under purifying selection. The phylogenetic tree yielded by plastome single-copy orthologous genes gives new evidence on the relationships among CASH lineages. This first I. galbana chloroplast genome will provide insight into the chloroplast architecture, function and evolution of this species and other haptophytes.

Campylobacter bacteriophage DA10: an excised temperate bacteriophage targeted by CRISPR-cas

BackgroundLytic bacteriophages that infect Campylobacter spp. have been utilized to develop therapeutic/decontamination techniques. However, the association of Campylobacter spp. and bacteriophages has been the focus of several strands of research aimed at understanding the complex relationships that have developed between predators and prey over evolutionary time. The activities of endogenous temperate bacteriophages have been used to evaluate genomic rearrangements and differential protein expression in host cells, and mechanisms of resistance to bacteriophage infection in campylobacters such as phase variation and CRISPR-mediated immunity.ResultsTemperate bacteriophage DA10 represents a novel excised and infective virus capable of replication in a restricted set of C. jejuni and C. coli hosts. Whole genome sequencing reveals that DA10 (35,379 bp) forms part of a novel group of temperate bacteriophages that have limited distribution among database host genome sequences. Analysis of potential host genomes reveals a robust response against DA10 and DA10-like bacteriophages is driven by CRISPR-mediated immunity with 75% of DA10 ORFs represented as ~ 30 bp spacer sequences in numerous Campylobacter Type II-C CRISPR arrays. Several DA10-like homologues have been identified in a small sub-set of C. jejuni and C. coli genome sequences (ranging from near complete integrated prophage sequences to fragments recognisable in the sequence read archive).ConclusionsA complete intact DA10-like prophage in C. jejuni CJ677CC520 provides evidence that the associations between host and DA10-like bacteriophages are long-standing in evolutionary timescales. Extensive nucleotide substitution and loss can be observed in the integrated DA10-like prophage of CJ677CC520 compared to other relatives as observed through pairwise genome comparisons. Examining factors that have limited the population expansion of the prophage, while others appear to have thrived and prospered (Mu-like, CJIE-like, and lytic Campylobacter bacteriophages) will assist in identifying the underlying evolutionary processes in the natural environment.

Phylogenetic Reconstruction Based on Synteny Block and Gene Adjacencies

Gene order can be used as an informative character to reconstruct phylogenetic relationships between species independently from the local information present in gene/protein sequences. PhyChro is a reconstruction method based on chromosomal rearrangements, applicable to a wide range of eukaryotic genomes with different gene contents and levels of synteny conservation. For each synteny breakpoint issued from pairwise genome comparisons, the algorithm defines two disjoint sets of genomes, named partial splits, respectively, supporting the two block adjacencies defining the breakpoint. Considering all partial splits issued from all pairwise comparisons, a distance between two genomes is computed from the number of partial splits separating them. Tree reconstruction is achieved through a bottom-up approach by iteratively grouping sister genomes minimizing genome distances. PhyChro estimates branch lengths based on the number of synteny breakpoints and provides confidence scores for the branches. PhyChro performance is evaluated on two data sets of 13 vertebrates and 21 yeast genomes by using up to 130,000 and 179,000 breakpoints, respectively, a scale of genomic markers that has been out of reach until now. PhyChro reconstructs very accurate tree topologies even at known problematic branching positions. Its robustness has been benchmarked for different synteny block reconstruction methods. On simulated data PhyChro reconstructs phylogenies perfectly in almost all cases, and shows the highest accuracy compared with other existing tools. PhyChro is very fast, reconstructing the vertebrate and yeast phylogenies in <15 min.

Phylogenomic revision of the family Streptosporangiaceae, reclassification of Desertactinospora gelatinilytica as Spongiactinospora gelatinilytica comb. nov. and a taxonomic home for the genus Sinosporangium in the family Streptosporangiaceae.

In recent years, the results of genome-based phylogenetic analyses have contributed to microbial systematics by increasing the availability of sequenced microbial genomes. Therefore, phylogenomic analysis within large taxa in the phylum Actinobacteria has appeared as a useful tool to clarify the taxonomic positions of ambiguous groups. In this study, we provide a revision of the actinobacterial family Streptosporangiaceae using a large collection of genome data and phylogenomics approaches. The phylogenomic analyses included the publicly available genome data of the members of the family Streptosporangiaceae and the state-of-the-art tools are used to infer the taxonomic affiliation of these species within the family. By comparing genome-based and 16S rRNA gene-based trees, as well as pairwise genome comparisons, the recently described genera Spongiactinospora and Desertactinospora are combined in the genus Spongiactinospora. In conclusion, a comprehensive phylogenomic revision of the family Streptosporangiaceae is proposed.

Isolation and comparative genomics of Mycobacterium tuberculosis isolates from cattle and their attendants in South India

The major human pathogen Mycobacterium tuberculosis is rarely reported to cause disease in other animals. Cases in livestock are thought to occur through contact with infected handlers, but previous studies evaluating putative livestock-human transmission used typing techniques with limited resolution. Here, we undertook cross-sectional surveillance for tuberculosis in 271 livestock handlers and 167 cattle on three farms in Chennai, India and defined the relatedness of cultured isolates using whole genome sequencing. Humans and livestock were screened for active mycobacterial infection, and opportunistic post-mortem examination was performed on comparative intradermal test-positive cattle that died. Four cattle and 6 handlers on two farms were culture-positive for M. tuberculosis; M. bovis was not isolated. All 10 isolates (one from each case) belonged to Lineage 1. Pairwise genome comparisons of single nucleotide polymorphism (SNP) differences ranged from 1 to 600 SNPs, but 3 isolate pairs were less than 5 SNPs different. Two pairs were from handlers and the third pair were from two cattle on the same farm. The minimum pairwise SNP difference between a cattle and human isolate was >250 SNPs. Our study confirms the presence of M. tuberculosis infection in cattle in India, sequencing of which characterised relatedness between human and cattle-derived isolates.

EvolClust: automated inference of evolutionary conserved gene clusters in eukaryotes.

MotivationThe evolution and role of gene clusters in eukaryotes is poorly understood. Currently, most studies and computational prediction programs limit their focus to specific types of clusters, such as those involved in secondary metabolism.ResultsWe present EvolClust, a python-based tool for the inference of evolutionary conserved gene clusters from genome comparisons, independently of the function or gene composition of the cluster. EvolClust predicts conserved gene clusters from pairwise genome comparisons and infers families of related clusters from multiple (all versus all) genome comparisons.Availability and implementation https://github.com/Gabaldonlab/EvolClust/.Supplementary information Supplementary data are available at Bioinformatics online.

Whole genome sequencing provides additional insights into recurrent tuberculosis classified as endogenous reactivation by IS6110 DNA fingerprinting

Recurrent tuberculosis (TB) after successful TB treatment occurs due to endogenous reactivation (relapse) or exogenous reinfection. We revisited the conclusions of relapse in a high TB incidence setting that were drawn on the basis of IS6110 restriction fragment length polymorphism (RFLP) analysis in a large retrospective cohort study in suburban Cape Town, South Africa. Using whole genome sequencing (WGS), we undertook pair-wise genome comparison of Mycobacterium tuberculosis strains cultured from diagnostic sputum samples collected at the index and recurrent TB episode for 25 recurrent TB cases who had been classified as relapse based on identical DNA fingerprint patterns in the earlier study. We found that paired strain genome sequences were identical or showed minimal variant differences in 22 of 25 recurrent TB cases, consistent with relapse. One showed 20 variant differences, suggestive of exogenous reinfection. Two of the 25 had mixed infections, each with the index episode strain detected as the dominant strain at recurrence in one of these patients, the minority strain harboured drug-resistance conferring mutations (rpoB, katG). In conclusion, our study highlights the additional value of WGS for investigating recurrent TB in settings with high infection pressure and closely related circulating strains, where the extent of re- and mixed infection may be underestimated.

Fast detection of maximal exact matches via fixed sampling of query K-mers and Bloom filtering of index K-mers.

Detection of maximal exact matches (MEMs) between two long sequences is a fundamental problem in pairwise reference-query genome comparisons. To efficiently compare larger and larger genomes, reducing the number of indexed k-mers as well as the number of query k-mers has been adopted as a mainstream approach which saves the computational resources by avoiding a significant number of unnecessary matches. Under this framework, we proposed a new method to detect all MEMs from a pair of genomes. The method first performs a fixed sampling of k-mers on the query sequence, and adds these selected k-mers to a Bloom filter. Then all the k-mers of the reference sequence are tested by the Bloom filter. If a k-mer passes the test, it is inserted into a hash table for indexing. Compared with the existing methods, much less number of query k-mers are generated and much less k-mers are inserted into the index to avoid unnecessary matches, leading to an efficient matching process and memory usage savings. Experiments on large genomes demonstrate that our method is at least 1.8 times faster than the best of the existing algorithms. This performance is mainly attributed to the key novelty of our method that the fixed k-mer sampling must be conducted on the query sequence and the index k-mers are filtered from the reference sequence via a Bloom filter. https://github.com/yuansliu/bfMEM. Supplementary data are available at Bioinformatics online.