The I<i>n</i>S<i>ilico</i>Genotyper (ISG): an open-source pipeline to rapidly identify and annotate nucleotide variants for comparative genomics applications

Jw, Sahl; Sm, Beckstrom-Sternberg; J, Babic-Sternberg; Jd, Gillece; Cm, Hepp; Auerbach, Rk; Tembe, Waibhav; Dm, Wagner; Ps, Keim; Pearson, Talima

doi:10.1101/015578

Cited by 37 publications

(51 citation statements)

References 14 publications

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“…2B) demonstrated for lineages such as O157 EHEC1 that the repA genes exhibit lineage specificity. Analysis of the FIB repA gene (34). There were 75,504 SNP sites that were identified in all of the genomes analyzed, and these were concatenated into a representative sequence for each genome and used to generate a phylogeny.…”

Section: Resultsmentioning

confidence: 99%

“…Phylogenomic analysis of 210 AEEC genomes and a diverse collection of 25 E. coli and Shigella genomes was performed as previously described (33,34) (see Table S1 in the supplemental material). These isolates are identified as attaching and effacing E. coli (AEEC) based on the molecular presence of the locus of enterocyte effacement (LEE) region and have not been functionally examined for the attaching and effacing phenotype.…”

Section: Methodsmentioning

confidence: 99%

“…Additional classification that was not based on these canonical virulence genes was accomplished by comparing the core genomes using phylogenomic analysis. Single nucleotide polymorphisms (SNPs) were detected relative to the completed genome sequence of the phylogroup F laboratory isolate E. coli IAI39 using the In Silico Genotyper (ISG) (34), which uses MUMMER v.3.22 (35) for SNP detection. The SNP sites that were identified in all genomes analyzed were concatenated and used for phylogenetic analysis as previously described (33).…”

Section: Methodsmentioning

confidence: 99%

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Comparative Genomics Provides Insight into the Diversity of the Attaching and Effacing Escherichia coli Virulence Plasmids

et al. 2015

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cAttaching and effacing Escherichia coli (AEEC) strains are a genomically diverse group of diarrheagenic E. coli strains that are characterized by the presence of the locus of enterocyte effacement (LEE) genomic island, which encodes a type III secretion system that is essential to virulence. AEEC strains can be further classified as either enterohemorrhagic E. coli (EHEC), typical enteropathogenic E. coli (EPEC), or atypical EPEC, depending on the presence or absence of the Shiga toxin genes or bundle-forming pilus (BFP) genes. Recent AEEC genomic studies have focused on the diversity of the core genome, and less is known regarding the genetic diversity and relatedness of AEEC plasmids. Comparative genomic analyses in this study demonstrated genetic similarity among AEEC plasmid genes involved in plasmid replication conjugative transfer and maintenance, while the remainder of the plasmids had sequence variability. Investigation of the EPEC adherence factor (EAF) plasmids, which carry the BFP genes, demonstrated significant plasmid diversity even among isolates within the same phylogenomic lineage, suggesting that these EAF-like plasmids have undergone genetic modifications or have been lost and acquired multiple times. Global transcriptional analyses of the EPEC prototype isolate E2348/69 and two EAF plasmid mutants of this isolate demonstrated that the plasmid genes influence the expression of a number of chromosomal genes in addition to the LEE. This suggests that the genetic diversity of the EAF plasmids could contribute to differences in the global virulence regulons of EPEC isolates. Enterohemorrhagic Escherichia coli (EHEC) and enteropathogenic E. coli (EPEC) are diarrheagenic types of E. coli that can be collectively termed attaching and effacing E. coli (AEEC) due to similarities in their virulence mechanisms (1). EHEC can cause more severe illness, including mild to severe bloody diarrhea and hemolytic-uremic syndrome (HUS), resulting in kidney failure and death, with the majority of cases occurring in the developed world (1, 2). Meanwhile, EPEC is a leading cause of lethality associated with diarrhea in young children in developing countries (3, 4).A major component of the virulence of AEEC is the locus of enterocyte effacement (LEE) genomic island, which encodes a type III secretion system (T3SS) (1,5,6). Similar to other diarrheagenic types of E. coli, such as enteroaggregative E. coli (EAEC), uropathogenic E. coli (UPEC), and enterotoxigenic E. coli (ETEC), the virulence mechanisms of AEEC involve genes carried by phage and plasmids (1, 7-9). The ability of EHEC to cause severe illness has been attributed to the presence of Shiga toxin genes (1, 2). In addition, nearly all of the O157:H7 EHEC isolates associated with food-borne illness in the United States carry the virulence-associated plasmid pO157 (92 kb), which encodes an ␣-hemolysin (hlyA) (10-12) and additional putative virulence factors (13,14). Similarly, the severity of illness attributed to typical EPEC has been associated with a virulenc...

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Comparative Genomics Provides Insight into the Diversity of the Attaching and Effacing Escherichia coli Virulence Plasmids

et al. 2015

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“…In this study, we sequenced the genomes of 254 Acinetobacter species isolates and characterized these genomes using whole-genome phylogenetic analysis (41), MLST (31,32), and large-scale BLAST score ratio analysis (LS-BSR) (42). The genomic content within these isolates, in addition to 61 sequenced reference genomes, demonstrates tremendous diversity in the Acinetobacter species.…”

mentioning

confidence: 99%

Use of Comparative Genomics To Characterize the Diversity of Acinetobacter baumannii Surveillance Isolates in a Health Care Institution

Wallace

Daugherty

Nagaraj

et al. 2016

Antimicrob Agents Chemother

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Despite the increasing prevalence of the nosocomial pathogen Acinetobacter baumannii, little is known about which genomic components contribute to clinical presentation of this important pathogen. Most whole-genome comparisons of A. baumannii have focused on specific genomic regions associated with phenotypes in a limited number of genomes. In this work, we describe the results of a whole-genome comparative analysis of 254 surveillance isolates of Acinetobacter species, 203 of which were A. baumannii, isolated from perianal swabs and sputum samples collected as part of an infection control active surveillance program at the University of Maryland Medical Center. The collection of surveillance isolates includes both carbapenem-susceptible and -resistant isolates. Based on the whole-genome phylogeny, the A. baumannii isolates collected belong to two major phylogenomic lineages. Results from multilocus sequence typing indicated that one of the major phylogenetic groups of A. baumannii was comprised solely of strains from the international clonal lineage 2. The genomic content of the A. baumannii isolates was examined using large-scale BLAST score ratio analysis to identify genes that are associated with carbapenem-susceptible and -resistant isolates, as well as genes potentially associated with the source of isolation. This analysis revealed a number of genes that were exclusive or at greater frequency in each of these classifications. This study is the most comprehensive genomic comparison of Acinetobacter isolates from a surveillance study to date and provides important information that will contribute to our understanding of the success of A. baumannii as a human pathogen. The Acinetobacter genus is comprised of 34 named species, many of which are found ubiquitously in the environment (1). The most clinically relevant species are members of what is known as the Acinetobacter calcoaceticus-baumannii (Acb) complex, which include A. baumannii, A. nosocomialis, A. pittii, and A. calcoaceticus (2). The organisms of the Acb complex are difficult to distinguish from each other using traditional culturing and molecular diagnostic methods employed in the current clinical microbiology laboratories (3). A. baumannii is the most frequently isolated Acinetobacter species in the health care setting (4), partly due to its ability to survive on abiotic surfaces for long periods of time (5), as well as its ability to rapidly develop antibiotic resistance (6). It is an important emerging nosocomial pathogen associated with common infections, multidrug resistance, and a high transmission rate within hospitals all over the world (7).Prior genomic studies of A. baumannii have mainly focused on multidrug-resistant strains and have identified key determinants associated with resistance (8-14). A genomic comparison of six clinical isolates of A. baumannii concluded that despite extensive genome-wide similarity, the resistance gene repertoire was highly variable, even in the genomically closely related isolates (10). In addition, anothe...

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“…The resistance genes were present mostly in genomes of three different clusters in the heatmap, of which two of the clusters also contained the csi and hha coli genomes that carry genes with similarity to those of pB171_90. A SNP-based phylogeny was generated using ISG as previously described (35,70). There were 149,150 conserved SNP sites identified among all of the E. coli genomes analyzed relative to the reference E. coli strain IAI39 (GenBank accession number NC_011750.1) that were used to construct a maximum-likelihood phylogeny with 100 bootstrap values using RAxML v.7.2.8 (71).…”

Section: Resultsmentioning

confidence: 99%

Characterization of a Large Antibiotic Resistance Plasmid Found in Enteropathogenic Escherichia coli Strain B171 and Its Relatedness to Plasmids of Diverse E. coli and Shigella Strains

Hazen

Michalski

Nagaraj

et al. 2017

Antimicrob Agents Chemother

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Enteropathogenic Escherichia coli (EPEC) is a leading cause of severe infantile diarrhea in developing countries. Previous research has focused on the diversity of the EPEC virulence plasmid, whereas less is known regarding the genetic content and distribution of antibiotic resistance plasmids carried by EPEC. A previous study demonstrated that in addition to the virulence plasmid, reference EPEC strain B171 harbors a second, larger plasmid that confers antibiotic resistance. To further understand the genetic diversity and dissemination of antibiotic resistance plasmids among EPEC strains, we describe the complete sequence of an antibiotic resistance plasmid from EPEC strain B171. The resistance plasmid, pB171_90, has a completed sequence length of 90,229 bp, a GC content of 54.55%, and carries protein-encoding genes involved in conjugative transfer, resistance to tetracycline (tetA), sulfonamides (sulI), and mercury, as well as several virulence-associated genes, including the transcriptional regulator hha and the putative calcium sequestration inhibitor (csi). In silico detection of the pB171_90 genes among 4,798 publicly available E. coli genome assemblies indicates that the unique genes of pB171_90 (csi and traI) are primarily restricted to genomes identified as EPEC or enterotoxigenic E. coli. However, conserved regions of the pB171_90 plasmid containing genes involved in replication, stability, and antibiotic resistance were identified among diverse E. coli pathotypes. Interestingly, pB171_90 also exhibited significant similarity with a sequenced plasmid from Shigella dysenteriae type I. Our findings demonstrate the mosaic nature of EPEC antibiotic resistance plasmids and highlight the need for additional sequence-based characterization of antibiotic resistance plasmids harbored by pathogenic E. coli. KEYWORDS EPEC, Escherichia coli, mosaic, plasmidT here has been an alarming increase in the frequency of antibiotic resistance in bacterial pathogens. Multidrug-resistant Enterobacteriaceae are of particular concern and include some groups of disease-causing Escherichia coli (1-3). E. coli strains have been identified that are resistant to all routinely prescribed antibiotics, including colistin, which is a last resort treatment option for carbapenem-resistant Enterobacteriaceae (4-7). The most widely reported antibiotic-resistant E. coli strains are those belonging to multilocus sequence type (MLST) 131 (ST131), which are usually identified as extraintestinal pathogenic E. coli (ExPEC) and often exhibit resistance to fluoroquinolones, as well as extended-spectrum cephalosporins (1,8). E. coli can also serve as a reservoir of antibiotic resistance genes, including mph(A), which confers resistance to macrolides such as azithromycin (9). E. coli strains from healthy volunteers in different

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The InSilicoGenotyper (ISG): an open-source pipeline to rapidly identify and annotate nucleotide variants for comparative genomics applications

Cited by 37 publications

References 14 publications

Comparative Genomics Provides Insight into the Diversity of the Attaching and Effacing Escherichia coli Virulence Plasmids

Comparative Genomics Provides Insight into the Diversity of the Attaching and Effacing Escherichia coli Virulence Plasmids

Use of Comparative Genomics To Characterize the Diversity of Acinetobacter baumannii Surveillance Isolates in a Health Care Institution

Characterization of a Large Antibiotic Resistance Plasmid Found in Enteropathogenic Escherichia coli Strain B171 and Its Relatedness to Plasmids of Diverse E. coli and Shigella Strains

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