Piggy: a rapid, large-scale pan-genome analysis tool for intergenic regions in bacteria

Thorpe, Harry A.; Bayliss, Sion C.; Sheppard, Samuel K.; Feil, Edward J.

doi:10.1093/gigascience/giy015

Cited by 55 publications

(59 citation statements)

References 39 publications

(72 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…aureus (Thorpe et al, 2018). Here, we find evidence of three intrahost switching events, two of which occurred between genes associated with quorum sensing.…”

Section: Discussionmentioning

confidence: 55%

See 1 more Smart Citation

Long-term intrahost evolution of methicillin resistant Staphylococcus aureus among cystic fibrosis patients with respiratory carriage

Azarian

Ridgway

Zhen

et al. 2019

Preprint

View full text Add to dashboard Cite

Staphylococcus aureus is the most commonly identified airway colonizer of cystic fibrosis (CF) patients, and infections with methicillin-resistant S. aureus (MRSA) are associated with poor outcomes. Yet, little is known about the intrahost evolution of S. aureus among CF patients. We investigated convergent evolution and adaptation of MRSA among four CF patients with longterm respiratory carriage. For each patient, we performed whole-genome sequencing on an average of 21 isolates (range: 19-23) carried for a mean of 1,403 days (range: 903-1,679), including 25 pairs of isolates collected on the same day. We then assessed intrahost diversity, population structure, evolutionary history, and signatures of adaptation in the context of patient age, antibiotic treatment, and co-colonizing microbes. We conducted tests of gene-wide diversifying selection and identified instances of switched intergenic regions (IGRs), which may be associated with gene expression. Phylogenetic analysis delineated distinct multilocus sequence type ST5 (n=3) and ST72 (n=1) clonal populations in addition to sporadic, non-clonal isolates, and uncovered a putative transmission event. Variation in antibiotic resistance was observed within clonal populations, even among isolates collected on the same day. Coalescent analysis revealed rates of molecular evolution ranging from 2.21 to 8.64 nucleotide polymorphisms per genome per year. Estimated lineage ages were consistent with acquisition of colonization in early childhood and subsequent persistence of multiple sub-populations. Selection analysis focused on 1,622 core genes shared by all four clonal populations (n=79). Eleven genes were variable in three subjects -most notable, ATP-dependent protease clpX, 2-oxoglutarate dehydrogenase odhA, fmtC, and transcription-repair coupling factor mfd. Only one gene, staphylococcal protein A (spa), was found to have evidence of gene-wide diversifying selection. We identified three instances of intrahost IGR switching events, two of which flanked genes related to quorum sensing. The ecology of microbes in the airways of CF patients is undeniably complex, posing challenges for management. We illustrate appreciable intrahost diversity as well as persistence of a dominant lineage. We also show that intrahost adaptation is a continual process, despite purifying selective pressure, and provide targets that should be investigated further for their function in CF adaptation. Contribution to the FieldStaphylococcus aureus is the most commonly identified airway colonizer of cystic fibrosis (CF) patients, and infections with methicillin-resistant S. aureus (MRSA) are associated with poor outcomes. Yet, little is known about the intrahost evolution of S. aureus among CF patients. We investigated convergent evolution and adaptation of MRSA among four CF patients with longterm respiratory carriage. We found that each patient possessed a single predominant strain in addition to transient non-clonal isolates. Considerable genomic diversity was observed among intrahost popula...

show abstract

“…aureus (Thorpe et al, 2018). Here, we find evidence of three intrahost switching events, two of which occurred between genes associated with quorum sensing.…”

Section: Discussionmentioning

confidence: 55%

“…SNPs in the core genome were then used to assess intrahost population structure with RhierBAPS (Cheng et al, 2013;Tonkin-Hill et al, 2018). Last, Piggy v1.4 was used to assess intergenic regions (IGR) and identify "switched" IGRs upstream of genes, which could impact gene expression (Thorpe et al, 2018).…”

Section: Inter-and Intrahost Population Structurementioning

confidence: 99%

Long-term intrahost evolution of methicillin resistant Staphylococcus aureus among cystic fibrosis patients with respiratory carriage

Azarian

Ridgway

Zhen

et al. 2019

Preprint

View full text Add to dashboard Cite

show abstract

“…We created de novo a ssemblies using SPAdes (version 3.12.0) 66 and quality filtered contigs to ensure coverage greater than 10X, length greater than 500 base pairs, and total genome size approximately equal to the FA1090 genome size (2.0 to 2.3 Mbp). We annotated assemblies with Prokka (version 1.13) 67 , and clustered core genes using Roary (version 3.12) 68 and core intergenic regions using piggy (version 1.2) 69 . A recombination-corrected phylogeny of all isolates was constructed by running Gubbins (version 2.3.4) on the aligned pseudogenomes and visualized in iTOL (version 4.4.2) 70–72 .…”

Section: Methodsmentioning

confidence: 99%

Increased antibiotic susceptibility inNeisseria gonorrhoeaethrough adaptation to the cervical environment

Mortimer

Hicks

et al. 2020

Preprint

View full text Add to dashboard Cite

28Neisseria gonorrhoeae is an urgent public health threat due to rapidly increasing incidence and 29 antibiotic resistance. In contrast with the trend of increasing resistance, clinical isolates that 30 have reverted to susceptibility regularly appear, prompting questions about which pressures 31 compete with antibiotics to shape gonococcal evolution. Here, we used genome-wide 32 association on the largest collection of N. gonorrhoeae isolates to date (n=4882) to identify loss-33 of-function (LOF) mutations in the efflux pump mtrCDE operon as a mechanism of increased 34 antibiotic susceptibility and demonstrate that these mutations are overrepresented in cervical 35 isolates relative to urethral isolates (odds ratio (OR) = 3.74, 95% CI [1.98-6.70]). In support of a 36 model in which pump expression incurs a fitness cost in this niche, cervical isolates were also 37 enriched relative to urethral isolates in LOF mutations in the mtrCDE activator mtrA (OR = 8.60,) and in farA, a subunit of the FarAB efflux pump (OR = 6.25, 95% CI [3.90-39 9.83]). In total, approximately 1 in 3 cervical isolates (36.4%) contained a LOF mutation in either 40 the efflux pump components mtrC or farA or the activator mtrA. Our findings extend beyond N. 41 gonorrhoeae to other Neisseria: mtrC LOF mutations are rare (<1%) in the primarily 42 nasopharyngeal-colonizing N. meningitidis in a collection of 14,798 genomes but enriched in a 43 heterosexual urethritis-associated lineage (8.6%, p = 9.90×10 -5 ), indicating that efflux pump 44 downregulation contributes broadly to the adaptation of pathogenic Neisseria to the female 45 urogenital tract. Overall, our findings highlight the impact of integrating microbial population 46 genomics with host metadata and demonstrate how host environmental pressures can lead to 47 increased antibiotic susceptibility. 48 49 50 51Neisseria gonorrhoeae is the causative agent of the sexually transmitted disease gonorrhea. 52Antibiotics have played a key role in shaping gonococcal evolution 1-3 , with N. gonorrhoeae 53 gaining resistance to each of the first line antibiotics used to treat it 4-6 . As N. gonorrhoeae is an 54 obligate human pathogen, the mucosal niches it infects-most commonly including the urethra, 55 cervix, pharynx, and rectum-must also influence its evolution 7 . The gonococcal phylogeny 56 suggests the interaction of these factors, with an ancestral split between a relatively drug-57 susceptible lineage circulating primarily in heterosexuals and a relatively drug-resistant lineage 58 circulating primarily in men who have sex with men 3 . 59 60 Despite the deeply concerning increase in antibiotic resistance reported in gonococcal 61 populations globally 8 , some clinical isolates of N. gonorrhoeae have become more susceptible 62 to antibiotics 9,10 . This unexpected phenomenon prompts questions about which environmental 63 pressures could be drivers of increased susceptibility and the mechanisms by which 64 suppression or reversion of resistance may occur. To address these questions, we analy...

show abstract

“…Over the last decade, advances in whole genome sequencing technologies and bioinformatic analyses have allowed the cataloguing of genes and intergenic regions that make up the pangenomes of many species [2][3][4][5][6][7][8].…”

Section: Introductionmentioning

confidence: 99%

“…Current approaches define genes on the basis of strict sequence identity thresholds [2,3,7,8], e-value cutoffs [5,6] and bit score ratios [4]. However, genes accrue variation at different rates under the influence of positive and purifying selection [9].…”

Section: Introductionmentioning

confidence: 99%

PIRATE: A fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria

Bayliss

Thorpe

Coyle

et al. 2019

Preprint

View full text Add to dashboard Cite

Cataloguing the distribution of genes within natural bacterial populations is essential for understanding evolutionary processes and the genetic basis of adaptation. Here we present a pangenomics toolbox, PIRATE (Pangenome Iterative Refinement And Threshold Evaluation), which identifies and classifies orthologous gene families in bacterial pangenomes over a wide range of sequence similarity thresholds. PIRATE builds upon recent scalable software developments to allow for the rapid interrogation of thousands of isolates. PIRATE clusters genes (or other annotated features) over a wide range of amino-acid or nucleotide identity thresholds and uses the clustering information to rapidly classify paralogous gene families into either putative fission/fusion events or gene duplications. Furthermore, PIRATE orders the pangenome using a directed graph, provides a measure of allelic variation and estimates sequence divergence for each gene family. We demonstrate that PIRATE scales linearly with both number of samples and computation resources, allowing for analysis of large genomic datasets, and compares favorably to other popular tools. PIRATE provides a robust framework for analysing bacterial pangenomes, from largely clonal to panmictic species.Availability: PIRATE is implemented in Perl and is freely available under an GNU GPL 3 open source license from https://github.com/SionBayliss/PIRATE. Contact: s.bayliss@bath.ac.uk

show abstract

Piggy: a rapid, large-scale pan-genome analysis tool for intergenic regions in bacteria

Cited by 55 publications

References 39 publications

Long-term intrahost evolution of methicillin resistant Staphylococcus aureus among cystic fibrosis patients with respiratory carriage

Long-term intrahost evolution of methicillin resistant Staphylococcus aureus among cystic fibrosis patients with respiratory carriage

Increased antibiotic susceptibility inNeisseria gonorrhoeaethrough adaptation to the cervical environment

PIRATE: A fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria

Contact Info

Product

Resources

About