PanGP: A tool for quickly analyzing bacterial pan-genome profile

Zhao, Yongbing; Jia, Xiaoyun; Yang, Junhui; Ling, Yunchao; Zhang, Zhang; Yu, Jun; Wu, Jiayan; Xiao, Jingfa

doi:10.1093/bioinformatics/btu017

Cited by 171 publications

(141 citation statements)

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“…Analysis of the C. difficile RT014 pan, core, and accessory genome was performed using Roary v3.6.0 (Page et al, 2015) and PanGP v1.0.1 (Zhao et al, 2014). Roary was run with default parameters.…”

Section: Methodsmentioning

confidence: 99%

Genome Analysis of Clostridium difficile PCR Ribotype 014 Lineage in Australian Pigs and Humans Reveals a Diverse Genetic Repertoire and Signatures of Long-Range Interspecies Transmission

et al. 2017

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Clostridium difficile PCR ribotype (RT) 014 is well-established in both human and porcine populations in Australia, raising the possibility that C. difficile infection (CDI) may have a zoonotic or foodborne etiology. Here, whole genome sequencing and high-resolution core genome phylogenetics were performed on a contemporaneous collection of 40 Australian RT014 isolates of human and porcine origin. Phylogenies based on MLST (7 loci, STs 2, 13, and 49) and core orthologous genes (1260 loci) showed clustering of human and porcine strains indicative of very recent shared ancestry. Core genome single nucleotide variant (SNV) analysis found 42% of human strains showed a clonal relationship (separated by ≤2 SNVs in their core genome) with one or more porcine strains, consistent with recent inter-host transmission. Clones were spread over a vast geographic area with 50% of the human cases occurring without recent healthcare exposure. These findings suggest a persistent community reservoir with long-range dissemination, potentially due to agricultural recycling of piggery effluent. We also provide the first pan-genome analysis for this lineage, characterizing its resistome, prophage content, and in silico virulence potential. The RT014 is defined by a large “open” pan-genome (7587 genes) comprising a core genome of 2296 genes (30.3% of the total gene repertoire) and an accessory genome of 5291 genes. Antimicrobial resistance genotypes and phenotypes varied across host populations and ST lineages and were characterized by resistance to tetracycline [tetM, tetA(P), tetB(P) and tetW], clindamycin/erythromycin (ermB), and aminoglycosides (aph3-III-Sat4A-ant6-Ia). Resistance was mediated by clinically important mobile genetic elements, most notably Tn6194 (harboring ermB) and a novel variant of Tn5397 (harboring tetM). Numerous clinically important prophages (Siphoviridae and Myoviridae) were identified as well as an uncommon accessory gene regulator locus (agr3). Conservation in the pathogenicity locus and S-layer correlated with ST affiliation, further extending the concept of clonal C. difficile lineages. This study provides novel insights on the genetic variability and strain relatedness of C. difficile RT014, a lineage of emerging One Health importance. Ongoing molecular and genomic surveillance of strains in humans, animals, food, and the environment is imperative to identify opportunities to reduce the overall CDI burden.

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Section: Methodsmentioning

confidence: 99%

Genome Analysis of Clostridium difficile PCR Ribotype 014 Lineage in Australian Pigs and Humans Reveals a Diverse Genetic Repertoire and Signatures of Long-Range Interspecies Transmission

et al. 2017

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“…The genome core gene sequences were identified and selected by the PanGP [19] software package, and a BLAST Matrix was constructed using a cutoff of 1e-5, 40% identity and 50% coverage. Aligned core genes were connected together with the same direction (MLST-like).…”

Section: Methodsmentioning

confidence: 99%

Phylogenetic analysis of family Neisseriaceae based on genome sequences and description of Populibacter corticis gen. nov., sp. nov., a member of the family Neisseriaceae, isolated from symptomatic bark of Populus × euramericana canker

Han

Sang

et al. 2017

PLoS ONE

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Two Gram-stain negative aerobic bacterial strains were isolated from the bark tissue of Populus × euramericana. The novel isolates were investigated using a polyphasic approach including 16S rRNA gene sequencing, genome sequencing, average nucleotide identity (ANI) and both phenotypic and chemotaxonomic assays. The genome core gene sequence and 16S rRNA gene phylogenies suggest that the novel isolates are different from the genera Snodgrassella and Stenoxybacter. Additionally, the ANI, G+C content, main fatty acids and phospholipid profile data supported the distinctiveness of the novel strain from genus Snodgrassella. Therefore, based on the data presented, the strains constitute a novel species of a novel genus within the family Neisseriaceae, for which the name Populibacter corticis gen. nov., sp. nov. is proposed. The type strain is 15-3-5T (= CFCC 13594T = KCTC 42251T).

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“…The open reading frames (ORFs) were at least 300 bp long. Core gene sets were determined by pan-genome analysis pipeline (PGAP) with default parameters using all of the 46 C. difficile strains and reference strain 630 (21). The contigs from the draft genomes were aligned to the C. difficile MLST database (http://pubmlst.org/cdifficile/) to determining the sequence type (ST) using Mummer (22).…”

Section: Methodsmentioning

confidence: 99%

Phenotypic and Genotypic Analysis of Clostridium difficile Isolates: a Single-Center Study

et al. 2014

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f Clostridium difficile infections (CDI) are a growing concern in North America, because of their increasing incidence and severity. Using integrated approaches, we correlated pathogen genotypes and host clinical characteristics for 46 C. difficile infections in a tertiary care medical center during a 6-month interval from January to June 2010. Multilocus sequence typing (MLST) demonstrated 21 known and 2 novel sequence types (STs), suggesting that the institution's C. difficile strains are genetically diverse. ST-1 (which corresponds to pulsed-field gel electrophoresis strain type NAP1/ribotype 027) was the most prevalent (32.6%); 43.5% of the isolates were binary toxin gene positive, of which 75% were ST-1. All strains were ciprofloxacin resistant and metronidazole susceptible, and 8.3% and 13.0% of the isolates were resistant to clindamycin and tetracycline, respectively. The corresponding resistance loci, including potential novel mutations, were identified from the whole-genome sequencing (WGS) of the resistant strains. Core genome single nucleotide polymorphisms (SNPs) determining the phylogenetic relatedness of the 46 strains recapitulated MLST types and provided greater interstrain differentiation. The disease severity was greatest in patients infected with ST-1 and/or binary gene-positive strains, but genome-wide SNP analysis failed to provide additional associations with CDI severity within the same STs. We conclude that MLST and core genome SNP typing result in the same phylogenetic grouping of the 46 C. difficile strains collected in a single hospital. WGS also has the capacity to differentiate those strains within STs and allows the comparison of strains at the individual gene level and at the whole-genome level. The most common C. difficile strain that has emerged in the past decade in North America and some areas in Europe has been classified as 027 by ribotyping, NAP1 by pulsed-field gel electrophoresis (PFGE), BI by restriction endonuclease analysis, and ST-1 by multilocus sequence typing (MLST). ST-1 strains account for half of the sporadic hospital-associated CDI in some settings (5). Some studies have reported that ST-1 strains elaborate C. difficile toxins (TCDs) at high concentrations; its purported hypervirulence is plausibly related to this trait. This strain has single and 18-bp deletions of tcdC, a negative regulator of tcdA and tcdB. These mutations cause premature stops, and this truncation is believed to cause toxin overproduction (6, 7). However, this assumption was challenged by recent studies showing no significant difference in toxin production between hypervirulent and nonhypervirulent C. difficile strains, and no association of the tcdC genotype and toxin production (8, 9).C. difficile strains containing cdtA and cdtB binary toxin genes are associated with greater mortality in their hosts than strains in which these genes are absent (10). However, it is not clear if the binary toxin genes increase the virulence of ST-1 or if they are simply epidemiologic markers of C. difficile...

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PanGP: A tool for quickly analyzing bacterial pan-genome profile

Cited by 171 publications

References 9 publications

Genome Analysis of Clostridium difficile PCR Ribotype 014 Lineage in Australian Pigs and Humans Reveals a Diverse Genetic Repertoire and Signatures of Long-Range Interspecies Transmission

Genome Analysis of Clostridium difficile PCR Ribotype 014 Lineage in Australian Pigs and Humans Reveals a Diverse Genetic Repertoire and Signatures of Long-Range Interspecies Transmission

Phylogenetic analysis of family Neisseriaceae based on genome sequences and description of Populibacter corticis gen. nov., sp. nov., a member of the family Neisseriaceae, isolated from symptomatic bark of Populus × euramericana canker

Phenotypic and Genotypic Analysis of Clostridium difficile Isolates: a Single-Center Study

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