Analysis of COMPASS, a New Comprehensive Plasmid Database Revealed Prevalence of Multireplicon and Extensive Diversity of IncF Plasmids

Douarre, Pierre-Emmanuel; Mallet, Ludovic; Radomski, Nicolas; Felten, Arnaud; Mistou, Michel‐Yves

doi:10.3389/fmicb.2020.00483

Cited by 73 publications

(84 citation statements)

References 55 publications

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“…Following sporadic reports of occasional clinical isolates displaying a convergence of the phenotypes, Gu et al (2018) reported on a lethal outbreak at a Chinese hospital of a carbapenem-resistant and hypervirulent K. pneumoniae (CRhvKP) clone of ST11 that had acquired hypervirulence-associated factors encoded on a plasmid. ST11 is the most prevalent CRKP clone in China, and subsequent reports indicate that ST11 strains having acquired the hypervirulence phenotype has become the most prevalent CRhvKP population in China and an emerging high-risk clone (Lee et al, 2017;Zhou et al, 2020). Nonetheless, sporadic reports on CRhvKP of other STs are increasing in prevalence (Lee et al, 2017;Dong et al, 2018;Liu et al, 2019), indicating that the convergence of carbapenem resistance and hypervirulence in K. pneumoniae is not isolated to a single genetic event and that, worryingly, the number of CRhvKP strains is increasing.…”

Section: Introductionmentioning

confidence: 99%

Hypervirulence Markers Among Non-ST11 Strains of Carbapenem- and Multidrug-Resistant Klebsiella pneumoniae Isolated From Patients With Bloodstream Infections

et al. 2020

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Multidrug-resistant Klebsiella pneumoniae and hypervirulent K. pneumoniae (hvKP) have traditionally been considered two individual populations; however, strains displaying both phenotypes have emerged during the recent decade. Understanding the genotypic and phenotypic basis of the convergence could be of clinical importance. In this study, we aimed to evaluate the pathogenicity associated with different combinations of genotypes (i.e., sequence types, virulence factors, and capsular serotypes) and phenotypes (i.e., hypermucoviscosity and drug susceptibility) in K. pneumoniae. A total of 11 K. pneumoniae isolates causing bloodstream infections were included in the study, and they were assigned to seven STs (ST23, ST15, ST268, ST660, ST86, ST65, and ST1660) and carried various K-loci (KL1, KL2, KL16, KL20, and KL24). Hypermucoviscosity was observed for six isolates. bla KPC−2 was detected in six carbapenem-resistant isolates, and the remaining ones were either multidrugresistant or resistant to two types of antibiotics. Aerobactin-and yersiniabactin-encoding genes were detected in all isolates. Although rmpA2 was detected in all isolates, most contained frameshift mutations (82%). Genes encoding salmochelin, RmpA, and PEG344 were detected in seven isolates. Colibactin-encoding genes were carried by six isolates. Discrepancies among measured virulence in Galleria mellonella and the serum-killing assay, and genotypes and phenotypes were detected. The results illustrate the complexity and difficulty with the current knowledge of hypervirulence to predict the phenotype by using genetic and phenotypic markers. Additionally, the emergence of carbapenem resistance in two isolates of KPC-2-producing hvKP of different sequence types emphasizes the urgency with which reliable clinical diagnostics for hvKP is needed.

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Section: Introductionmentioning

confidence: 99%

Hypervirulence Markers Among Non-ST11 Strains of Carbapenem- and Multidrug-Resistant Klebsiella pneumoniae Isolated From Patients With Bloodstream Infections

et al. 2020

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“…The plasmid additionally carried IncR, which is frequently detected together with IncF on chimeric plasmids in Enterobacterales ( 10 ). Plasmids fusions between IncFII and IncR can be mediated during antibiotic pressure ( 11 ), and cointegration of different replicons is suggested as an adaptive mechanism for extending the host range and thereby plasmid survival and dissemination ( 10 ). bla CTX-M-15 has been associated with both IncR and IncFII K plasmids as well as an IncR/IncFII K multireplicon plasmid ( 11 – 15 ).…”

Section: Discussionmentioning

confidence: 99%

Horizontal Plasmid Transfer among Klebsiella pneumoniae Isolates Is the Key Factor for Dissemination of Extended-Spectrum β-Lactamases among Children in Tanzania

Pedersen

Tellevik

Kommedal

et al. 2020

mSphere

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Increased knowledge about the role of horizontal gene transfer is key to improve our understanding of the spread of antimicrobial resistance (AMR) in human populations. We therefore studied the dissemination of the blaCTX-M-15 extended-spectrum-β-lactamase (ESBL) gene in Klebsiella pneumoniae isolates obtained from stool samples from hospitalized children and healthy controls below 2 years of age in Dar es Salaam, Tanzania, from August 2010 to July 2011. We performed Illumina whole-genome sequencing (WGS) to characterize resistance genes, multilocus sequence type (MLST), plasmid incompatibility group (Inc), and plasmid MLST of 128 isolates of K. pneumoniae with blaCTX-M-15 recovered from both healthy and hospitalized children. We assessed the phylogenetic relationship using single nucleotide polymorphism (SNP)-based analysis and resolved the sequences of five reference plasmids by Oxford Nanopore technology to investigate plasmid dissemination. The WGS analyses revealed the presence of a blaCTX-M-15-positive IncFIIK5/IncR plasmid with a highly conserved backbone in 70% (90/128) of the isolates. This plasmid, harboring genes encoding resistance to most β-lactams, aminoglycosides, trimethoprim-sulfamethoxazole, and chloramphenicol, was present in phylogenetically very diverse K. pneumoniae strains (48 different MLSTs) carried by both hospitalized and healthy children. Our data strongly suggest widespread horizontal transfer of this ESBL-carrying plasmid both in hospitals and in the general population. IMPORTANCE Horizontal spread of plasmids carrying multiple resistance genes is considered an important mechanism behind the global health problem caused by multidrug-resistant bacteria. Nevertheless, knowledge about spread of plasmids in a community is limited. Our detailed molecular analyses of K. pneumoniae isolated from hospitalized and healthy children in Tanzania disclosed an epidemic spread of a resistance plasmid. In this study population, we revealed horizontal plasmid transfer among K. pneumoniae as the key factor for dissemination of ESBLs. Traditional outbreak investigation and surveillance focus on the spread of bacterial clones, and short-read sequencing can result in erroneous plasmid composition. Our approach using long-read sequencing reveals horizontal gene transfer of antimicrobial resistance, and therefore has a potential impact on outbreak investigations and approaches to limit spread of AMR.

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“…MOBcluster uses single linkage clustering with a cutoff of a mash distance of 0.05 (corresponding to 95% ANI). A recent large-scale study [12] showed MOB-typer to have a higher correct classification rate than the widely used PlasmidFinder [36]. The measures were calculated using the scikit-learn (version 0.22.2) Python module [38].…”

Section: Discussionmentioning

confidence: 99%

“…IncF plasmids are a diverse group of Enterobacteriaceae-associated replicons which mediate the transfer of AMR genes. They have also been observed in other Proteobacteria, such as Aeromonadaceae and Comamonadaceae [12]. In particular, their involvement in the dissemination of genes encoding extended-spectrum β-lactamases (ESBLs), such as bla-CTX-M-15 , is of major clinical concern [13,14], and almost 40% of plasmid-borne carbapenemases are carried on IncF plasmids [15].…”

Section: Introductionmentioning

confidence: 99%

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Genomic network analysis of an environmental and livestock IncF plasmid population

Matlock

Chau

AbuOun

et al. 2020

Preprint

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IncF plasmids are diverse and of great clinical significance, often carrying genes conferring antimicrobial resistance (AMR) such as extended-spectrum β-lactamases, particularly in Enterobacteriaceae. Organising this plasmid diversity is challenging, and current knowledge is largely based on plasmids from clinical settings. Here, we present a network community analysis of a large survey of IncF plasmids from environmental (influent, effluent, and upstream/downstream waterways surrounding wastewater treatment works) and livestock settings. We use a tractable and scalable methodology to examine the relationship between plasmid metadata and network communities. This reveals how niche (sampling compartment and host genera) partition and shape plasmid diversity. We also perform pangenome-style analyses on network communities. We show that such communities define unique combinations of core genes, with limited overlap. Building plasmid phylogenies based on alignments of these core genes, we demonstrate that plasmid accessory function is closely linked to core gene content. Taken together, our results suggest that stable IncF plasmid backbone structures can persist in environmental settings while allowing dramatic variation in accessory gene content that may be linked to niche adaptation. The recent association of IncF plasmids with AMR likely reflects their suitability for rapid niche adaptation.

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Analysis of COMPASS, a New Comprehensive Plasmid Database Revealed Prevalence of Multireplicon and Extensive Diversity of IncF Plasmids

Cited by 73 publications

References 55 publications

Hypervirulence Markers Among Non-ST11 Strains of Carbapenem- and Multidrug-Resistant Klebsiella pneumoniae Isolated From Patients With Bloodstream Infections

Hypervirulence Markers Among Non-ST11 Strains of Carbapenem- and Multidrug-Resistant Klebsiella pneumoniae Isolated From Patients With Bloodstream Infections

Horizontal Plasmid Transfer among Klebsiella pneumoniae Isolates Is the Key Factor for Dissemination of Extended-Spectrum β-Lactamases among Children in Tanzania

Genomic network analysis of an environmental and livestock IncF plasmid population

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