GrapeTree: Visualization of core genomic relationships among 100,000 bacterial pathogens

Zhou, Zhemin; Alikhan, Nabil-Fareed; Sergeant, Martin J.; Luhmann, Nina; Vaz, Cátia; Francisco, Alexandre P.; Carriço, João André; Achtman, Mark

doi:10.1101/216788

Cited by 127 publications

(179 citation statements)

References 37 publications

Supporting

Mentioning

178

Contrasting

Unclassified

Order By: Relevance

“…Sources of the strains include humans (48%), poultry (32%), pigs (6%), cattle (5%), dogs (4%), horses (0.6%) and others (5%). The main countries that have contributed to the dataset are The Netherlands, USA, UK, and Germany.The phylogenetic GrapeTree(Zhou et al, 2017) of IncI1 and IncIγ plasmids was obtained at the pMLST website using ST and country of isolation datasets. The most represented STs are labelled, and slices are coloured by country of isolation(Figure 3).…”

mentioning

confidence: 99%

Contemporary IncI1 plasmids involved in the transmission and spread of antimicrobial resistance in Enterobacteriaceae

Carattoli

Villa

Fortini

et al. 2021

Plasmid

View full text Add to dashboard Cite

IncI1 has become one of the most common plasmid families in contemporary Enterobacteriaceae from both human and animal sources. In clinical epidemiology, this plasmid type ranks first as the confirmed vehicle of transmission of extended spectrum beta-lactamase and plasmid AmpC genes in isolates from food-producing animals. In this review, we describe the epidemiology and evolution of IncI1 plasmids and closely related IncIγ plasmids. We highlight the emergence of epidemic plasmids circulating among different bacterial hosts in geographically distant countries, and we address the phylogeny of the IncI1 and IncIγ family based on plasmid Multilocus Sequence Typing. Highlights  Contemporary and historical IncI1 plasmids share a conserved backbone, and evolution is attributed to acquisition of clinically relevant antimicrobial resistance determinants.  Phylogenetic analysis performed on pMLST alleles identified two major plasmid lineages that differ in their pil cluster sequences.  IncI1 and IncIγ plasmids that carry ESBL and AmpC genes spread among different Enterobacteriaceae isolated from human, animal and environmental sources.

show abstract

mentioning

confidence: 99%

Contemporary IncI1 plasmids involved in the transmission and spread of antimicrobial resistance in Enterobacteriaceae

Carattoli

Villa

Fortini

et al. 2021

Plasmid

View full text Add to dashboard Cite

show abstract

“…GrapeTree was used to produce and visualize a minimum spanning tree (MST) based on the comparison of cgMLST allelic profiles of ST11 K. pneumoniae isolates. 35…”

Section: Phylogenetic Analysismentioning

confidence: 99%

<p>Hybrid Genome Assembly and Annotation of a Pandrug-Resistant <em>Klebsiella pneumoniae</em> Strain Using Nanopore and Illumina Sequencing</p>

Ruan

Chen

et al. 2020

IDR

View full text Add to dashboard Cite

Background: The prevalence of multidrug-resistant Klebsiella pneumoniae is increasingly being implicated worldwide in a variety of infections with high mortalities. Here, we report the complete genome sequence of K. pneumoniae strain KP58, a pandrug-resistant K. pneumoniae strain that exhibits high levels of resistance to colistin and tigecycline in China. Methods: The K. pneumoniae strain KP58 was recovered from a urine sample of a female patient hospitalized in a tertiary hospital in Hangzhou, China. Antimicrobial susceptibility testing was performed and the minimum inhibitory concentrations (MICs) were determined. Whole-genome sequencing was performed using Illumina and Oxford nanopore sequencing technologies. Genomic features, antimicrobial resistance genes and virulence genes were comprehensively analysed by various bioinformatics approaches. In addition, genomic epidemiological and phylogenetic analyses of K. pneumoniae KP58 and closely related isolates were performed using the core genome multilocus sequence typing (cgMLST) analysis in BacWGSTdb, an online bacterial whole-genome sequence typing and source tracking database. Results: K. pneumoniae KP58 was resistant to all antimicrobial agents tested, including tigecycline and colistin. Combining the two sequencing technologies allowed a high-quality complete genome sequence of K. pneumoniae KP58 comprising one circular chromosome and five circular plasmids to be obtained. This strain harbours a variety of acquired antimicrobial resistance and virulence determinants. It also carried an ISKpn26-like insertion in the disrupted mgrB gene, which confers colistin resistance. The tigecycline resistance was associated with overexpression of the AcrAB efflux system. The closest relative of K. pneumoniae KP58 was another clinical isolate recovered from Hangzhou that differed by only 10 cgMLST loci. Conclusion: The dataset presented in this study provides essential insights into the evolution of antimicrobial-resistant K. pneumoniae in hospital settings and assists in the development of effective control strategies. Appropriate surveillance and control measures are essential to prevent its further dissemination.

show abstract

“…The relationship among 20 isolates based on clonal complexes is re ected in minimum spanning tree diagram (Fig. 4) [19].…”

Section: Comparison Of Dnak Gene Expression In Clinical C Jejuni Strmentioning

confidence: 99%

High prevalence of Campylobacter jejuni CC21 and CC257 clonal complexes in children with gastroenteritis in Iran: A global analysis

Sarhangi

Bakhshi

2020

Preprint

View full text Add to dashboard Cite

Aims: The aim of this study was to assess the distribution of GBS-related lipo-oligosaccharide (LOS) classes and capsular genotypes among Iranian clinical C. jejuni strains and to assess its relation with dnaK gene expression. Moreover, a comprehensive study of C. jejuni MLST-genotypes and global comparison with peer sequences worldwide was intended.Methods: Distribution of sialylated-LOS classes and specific capsular genotypes were investigated in C.jejuni of clinical origin. The expression of dnaK in C. jejuni strains was measured by Real-Time-PCR. MLST-genotyping was performed to investigate the clonal relationship of clinical C. jejuni strains and comparison with global sequences worldwide.Results: C. jejuni HS23/36c was the predominant genotype (45%), followed by HS2 (20%), and HS19 and HS4 (each 10%). A total of 80% of isolates were assigned to LOS class B and C. Higher expression level of dnaK gene was detected in strains with HS23/36c, HS2 and HS4 capsular genotypes and sialylated LOS classes B or C in this study. MLST analysis showed that isolates were highly diverse and represented 6 different sequence types and 3 clonal complexes. ST-21 and ST-257 complexes were dominants (75%) in our C.jejuni strains. The CC21 was the largest CC in our collection which is consistent with global C.jejuni strains worldwide. No new ST and no common ST with our neighbor countries was detected in this study.Conclusion: Global analysis of MLST results demonstrated that ST-50 (CC21) was widely distributed in different countries, while ST-19 (CC21) and ST-257 (CC257) was less ubiquitously spread. Overall, CC21 and CC353 complexes were most frequent and most widely distributed clonal complexes around the world; although, CC353 was not detected in this study. This shows a picture of movement of dominant Campylobacter strains worldwide. The occurrence of identical clonal complexes with different capsular types and LOS classes in this study is consistent with genetic variation in circulating identical genotypes and their evolution toward different pathotypes probably through acquisition of different genetic elements including LOS and CPS gene clusters.

show abstract

GrapeTree: Visualization of core genomic relationships among 100,000 bacterial pathogens

Abstract: 21

Cited by 127 publications

References 37 publications

Contemporary IncI1 plasmids involved in the transmission and spread of antimicrobial resistance in Enterobacteriaceae

Contemporary IncI1 plasmids involved in the transmission and spread of antimicrobial resistance in Enterobacteriaceae

<p>Hybrid Genome Assembly and Annotation of a Pandrug-Resistant <em>Klebsiella pneumoniae</em> Strain Using Nanopore and Illumina Sequencing</p>

High prevalence of Campylobacter jejuni CC21 and CC257 clonal complexes in children with gastroenteritis in Iran: A global analysis

Contact Info

Product

Resources

About