Genetic diversity, mobilisation and spread of the yersiniabactin-encoding mobile element ICEKp inKlebsiella pneumoniaepopulations

ABSTRACTMobile genetic elements (MGEs) that frequently transfer within and between bacterial species play a critical role in bacterial evolution, and often carry key accessory genes that associate with a bacteria’s ability to cause disease. MGEs carrying antimicrobial resistance (AMR) and/or virulence determinants are common in opportunistic pathogenKlebsiella pneumoniae, which are a leading cause of highly drug-resistant infections in hospitals. Well-characterised virulence determinants inK. pneumoniaeinclude the polyketide synthesis lociybtandclb(also known aspks), encoding the iron-scavenging siderophore yersiniabactin and genotoxin colibactin respectively. These loci are located within an MGE called ICEKp, which is the most common virulence-associated MGE ofK. pneumoniae,providing a mechanism for these virulence factors to spread within the population.Here we apply population genomics to investigate the prevalence, evolution and mobility ofybtandclbinK. pneumoniaepopulations through comparative analysis of 2,498 whole genome sequences. Theybtlocus was detected in 40% ofK. pneumoniaegenomes, particularly amongst those associated with invasive infections. We identified 17 distinctybtlineages and 3clblineages, each associated with one of 14 different structural variants of ICEKp. Comparison with the wider Enterobacteriaceae population showed occasional ICEKpacquisition by other members. Theclblocus was present in 14% of allK. pneumoniaeand 38.4% ofybt+ genomes. Hundreds of independent ICEKpintegration events were detected affecting hundreds of phylogenetically distinctK. pneumoniaelineages, including ≥19 in the globally-disseminated carbapenem-resistant clone CG258. A novel plasmid-encoded form ofybtwas also identified, representing a new mechanism forybtdispersal inK. pneumoniaepopulations. These data show that MGEs carryingybtandclbcirculate freely in theK. pneumoniaepopulation, including among multidrug-resistant strains, and should be considered a target for genomic surveillance along with AMR determinants.AUTHOR SUMMARYKlebsiella pneumoniaeinfections are becoming increasingly difficult to treat with antibiotics. SomeK. pneumoniaestrains also carry extra genes that allow them to synthesise yersiniabactin, an iron-scavenging molecule, which enhances their ability to cause disease. These genes are located on a genetic element that can easily transfer between strains. Here, we screened 2498K. pneumoniaegenome sequences and found substantial diversity in the yersiniabactin genes and the associated genetic elements, including a novel mechanism of transfer, and detected hundreds of distinct yersiniabactin acquisition events betweenK. pneumoniaestrains. We show that these yersiniabactin mobile genetic elements are specifically adapted to theK. pneumoniaepopulation but also occasionally acquired by other bacterial members belonging to the Enterobacteriaceae family such asE. coli.These insights into the movement and genetics of yersiniabactin genes allow tracking of the evolution and spread of yersiniabactin in globalK. pneumoniaepopulations and monitoring for acquisition of yersiniabactin in antibiotic-resistant strains.

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Mobile genetic element insertions drive antibiotic resistance across pathogens

10.1101/527788 ◽

2019 ◽

Cited By ~ 1

Author(s):

Matthew G. Durrant ◽

Michelle M. Li ◽

Ben Siranosian ◽

Ami S. Bhatt

Keyword(s):

Antibiotic Resistance ◽

De Novo ◽

Bacterial Species ◽

Mobile Element ◽

Mobile Genetic Elements ◽

Mobile Elements ◽

Genetic Elements ◽

Element Insertion ◽

A Genome ◽

Mobile Element Insertion

AbstractMobile genetic elements contribute to bacterial adaptation and evolution; however, detecting these elements in a high-throughput and unbiased manner remains challenging. Here, we demonstrate ade novoapproach to identify mobile elements from short-read sequencing data. The method identifies the precise site of mobile element insertion and infers the identity of the inserted sequence. This is an improvement over previous methods that either rely on curated databases of known mobile elements or rely on ‘split-read’ alignments that assume the inserted element exists within the reference genome. We apply our approach to 12,419 sequenced isolates of nine prevalent bacterial pathogens, and we identify hundreds of known and novel mobile genetic elements, including many candidate insertion sequences. We find that the mobile element repertoire and insertion rate vary considerably across species, and that many of the identified mobile elements are biased toward certain target sequences, several of them being highly specific. Mobile element insertion hotspots often cluster near genes involved in mechanisms of antibiotic resistance, and such insertions are associated with antibiotic resistance in laboratory experiments and clinical isolates. Finally, we demonstrate that mutagenesis caused by these mobile elements contributes to antibiotic resistance in a genome-wide association study of mobile element insertions in pathogenicEscherichia coli. In summary, by applying ade novoapproach to precisely identify mobile genetic elements and their insertion sites, we thoroughly characterize the mobile element repertoire and insertion spectrum of nine pathogenic bacterial species and find that mobile element insertions play a significant role in the evolution of clinically relevant phenotypes, such as antibiotic resistance.

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Transmission of ESBL-producing Enterobacteriaceae and their mobile genetic elements—identification of sources by whole genome sequencing: study protocol for an observational study in Switzerland

BMJ Open ◽

10.1136/bmjopen-2018-021823 ◽

2018 ◽

Vol 8 (2) ◽

pp. e021823 ◽

Cited By ~ 12

Author(s):

Tanja Stadler ◽

Dominik Meinel ◽

Lisandra Aguilar-Bultet ◽

Jana S Huisman ◽

Ruth Schindler ◽

...

Keyword(s):

Observational Study ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Bacterial Species ◽

Mobile Genetic Elements ◽

University Hospital ◽

Whole Genome ◽

Hospital Acquired Infections ◽

Genetic Elements ◽

Hospital Acquired

IntroductionExtended-spectrum beta-lactamases (ESBL)-producing Enterobacteriaceae were first described in relation with hospital-acquired infections. In the 2000s, the epidemiology of ESBL-producing organisms changed as especially ESBL-producingEscherichia coliwas increasingly described as an important cause of community-acquired infections, supporting the hypothesis that in more recent years ESBL-producing Enterobacteriaceae have probably been imported into hospitals rather than vice versa. Transmission of ESBL-producing Enterobacteriaceae is complicated by ESBL genes being encoded on self-transmissible plasmids, which can be exchanged among the same and different bacterial species. The aim of this research project is to quantify hospital-wide transmission of ESBL-producing Enterobacteriaceae on both the level of bacterial species and the mobile genetic elements and to determine if hospital-acquired infections caused by ESBL producers are related to strains and mobile genetic elements predominantly circulating in the community or in the healthcare setting. This distinction is critical in prevention since the former emphasises the urgent need to establish or reinforce antibiotic stewardship programmes, and the latter would call for more rigorous infection control.Methods and analysisThis protocol presents an observational study that will be performed at the University Hospital Basel and in the city of Basel, Switzerland. ESBL-producing Enterobacteriaceae will be collected from any specimens obtained by routine clinical practice or by active screening in both inpatient and outpatient settings, as well as from wastewater samples and foodstuffs, both collected monthly over a 12-month period for analyses by whole genome sequencing. Bacterial chromosomal, plasmid and ESBL-gene sequences will be compared within the cohort to determine genetic relatedness and migration between humans and their environment.Ethics and disseminationThis study has been approved by the local ethics committee (Ethikkommission Nordwest-und Zentralschweiz) as a quality control project (Project-ID 2017–00100). The results of this study will be published in peer-reviewed medical journals, communicated to participants, the general public and all relevant stakeholders.

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A Novel and Direct Metamobilome Approach improves the Detection of Larger-sized Circular Elements across Kingdoms

10.1101/761098 ◽

2019 ◽

Cited By ~ 1

Author(s):

Katrine Skov Alanin ◽

Tue Sparholt Jørgensen ◽

Patrick Browne ◽

Bent Petersen ◽

Leise Riber ◽

...

Keyword(s):

Multiple Displacement Amplification ◽

Bacterial Species ◽

Human Health Risk ◽

Prokaryotic Genome ◽

Mobile Genetic Elements ◽

Wastewater Sample ◽

Mobile Dna ◽

Complex Samples ◽

Genetic Elements ◽

Dna Elements

AbstractMobile genetic elements (MGEs) are instrumental in natural prokaryotic genome editing, permitting genome plasticity and allowing microbes to accumulate immense genetic diversity. MGEs include DNA elements such as plasmids, transposons and Insertion Sequences (IS-elements), as well as bacteriophages (phages), and they serve as a vast communal gene pool. These mobile DNA elements represent a human health risk as they can add new traits, such as antibiotic resistance or virulence, to a bacterial strain. Sequencing libraries targeting circular MGEs, referred to as mobilomes, allows the expansion of our current understanding of the mechanisms behind the mobility, prevalence and content of these elements. However, metamobilomes from bacterial communities are not studied to the same extent as metagenomics, partly because of methodological biases arising from multiple displacement amplification (MDA), often used in previous metamobilome publications. In this study, we show that MDA is detrimental to the detection of larger-sized plasmids if small plasmids are present by comparing the abundances of reads mapping to plasmids in a wastewater sample spiked with a mock community of selected plasmids with and without MDA. Furthermore, we show that it is possible to produce samples consisting almost exclusively of circular MGEs and obtain a catalog of larger, complete, circular MGEs from complex samples without the use of MDA.ImportanceMobile genetic elements (MGEs) can transport genetic information between genomes in different bacterial species, adding new traits, potentially generating dangerous multidrug-resistant pathogens. In fact, plasmids and circular MGEs can encode bacterial genetic specializations such as virulence, resistance to metals, antimicrobial compounds, and bacteriophages, as well as the degradation of xenobiotics. For this reason, circular MGEs are crucial to investigate, but they are often missed in metagenomics and ecological studies. In this study, we present, for the first time, an improved method, which reduces the bias towards small MGEs and we demonstrate that this method can unveil larger, complete circular MGEs from complex samples without the use of multiple displacement amplification. This method may result in the detection of larger-sized plasmids that have hitherto remained unnoticed and therefore has the potential to reveal novel accessory genes, acting as possible targets in the development of preventive strategies directed at pathogens.

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Rapidly disseminating blaOXA-232 carrying Klebsiella pneumoniae belonging to ST231 in India: multiple and varied mobile genetic elements

BMC Microbiology ◽

10.1186/s12866-019-1513-8 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 5

Author(s):

Chaitra Shankar ◽

Purva Mathur ◽

Manigandan Venkatesan ◽

Agila Kumari Pragasam ◽

Shalini Anandan ◽

...

Keyword(s):

Klebsiella Pneumoniae ◽

Mobile Genetic Elements ◽

Genetic Elements

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CRISPR-Cas Loci of Yersinia pseudotuberculosis Strains with Different Genetic Determinants

Epidemiology and Vaccinal Prevention ◽

10.31631/2073-3046-2020-20-2-31-39 ◽

2020 ◽

Vol 19 (2) ◽

pp. 31-39

Author(s):

N. P. Peretolchina ◽

V. T. Klimov ◽

E. A. Voskresenskaya ◽

G. I. Kokorina ◽

E. A. Bogumilchik ◽

...

Keyword(s):

Clinical Manifestation ◽

Horizontal Transfer ◽

Yersinia Pseudotuberculosis ◽

Mobile Genetic Elements ◽

Severe Form ◽

Virulence Determinants ◽

Genetic Determinants ◽

Genetic Elements ◽

Serotype O ◽

Specific Virulence

Relevance. Yersinia pseudotuberculosis is a causative agent of pseudotuberculosis, a disease with polymorphism of clinical manifestation that is determined by the presence of specific virulence determinants: plasmid pVM82, pathogenicity islands HPI and YAPI, and superantigen YPM. Occurrence of new determinants depends on horizontal transfer of mobile genetic elements, hence, systems regulating horizontal transfer participate in evolution of pathogenic species. CRISPR-Cas is and adaptive protection system of prokaryotes against mobile genetic elements. Aim. The study analyzed an interaction between CRISPR-loci of Y. pseudotuberculosis and virulence determinants. Results. 86% of strains includes three CRISPR-loci: YP1, YP2, and YP3. Length of locus YP3 mostly depends on presence of virulence determinants in strains of Y. pseudotuberculosis serotype O:1b. Strains with virulence genes are able to cause a severe form of pseudotuberculosis and have longer locus than strains without determinants. Conclusion. Therefore, CRIPSRCas system of Y. pseudotuberculosis may participate in formation of a certain strain genotype that defines clinical manifestation of pseudotuberculosis.

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The extent of carbapenemase-encoding genes in public genome sequences

PeerJ ◽

10.7717/peerj.11000 ◽

2021 ◽

Vol 9 ◽

pp. e11000

Author(s):

Ingmar Janse ◽

Rick Beeloo ◽

Arno Swart ◽

Michael Visser ◽

Leo Schouls ◽

...

Keyword(s):

Resistance Genes ◽

Host Species ◽

Bacterial Species ◽

Antibiotic Resistance Gene ◽

Bacterial Genome ◽

Companion Animals ◽

Health Concern ◽

Genome Sequences ◽

Genetic Elements ◽

Encoding Genes

Genome sequences provide information on the genetic elements present in an organism, and currently there are databases containing hundreds of thousands of bacterial genome sequences. These repositories allow for mining patterns concerning antibiotic resistance gene occurrence in both pathogenic and non-pathogenic bacteria in e.g. natural or animal environments, and link these to relevant metadata such as bacterial host species, country and year of isolation, and co-occurrence with other resistance genes. In addition, the advances in the prediction of mobile genetic elements, and discerning chromosomal from plasmid DNA, broadens our view on the mechanism mediating dissemination. In this study we utilize the vast amount of data in the public database PATRIC to investigate the dissemination of carbapenemase-encoding genes (CEGs), the emergence and spread of which is considered a grave public health concern. Based on publicly available genome sequences from PATRIC and manually curated CEG sequences from the beta lactam database, we found 7,964 bacterial genomes, belonging to at least 70 distinct species, that carry in total 9,892 CEGs, amongst which blaNDM, blaOXA, blaVIM, blaIMP and blaKPC. We were able to distinguish between chromosomally located resistance genes (4,137; 42%) and plasmid-located resistance genes (5,753; 58%). We found that a large proportion of the identified CEGs were identical, i.e. displayed 100% nucleotide similarity in multiple bacterial species (8,361 out of 9,892 genes; 85%). For example, the New Delhi metallo-beta-lactamase NDM-1 was found in 42 distinct bacterial species, and present in seven different environments. Our data show the extent of carbapenem-resistance far beyond the canonical species Acetinobacter baumannii, Klebsiella pneumoniae or Pseudomonas aeruginosa. These types of data complement previous systematic reviews, in which carbapenem-resistant Enterobacteriaceae were found in wildlife, livestock and companion animals. Considering the widespread distribution of CEGs, we see a need for comprehensive surveillance and transmission studies covering more host species and environments, akin to previous extensive surveys that focused on extended spectrum beta-lactamases. This may help to fully appreciate the spread of CEGs and improve the understanding of mechanisms underlying transmission, which could lead to interventions minimizing transmission to humans.

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Properties of genes encoding transfer RNAs as integration sites for genomic islands and prophages in Klebsiella pneumoniae

10.1101/2020.11.02.365908 ◽

2020 ◽

Author(s):

Camilo Berríos-Pastén ◽

Rodolfo Acevedo ◽

Patricio Arros ◽

Macarena A. Varas ◽

Kelly L. Wyres ◽

...

Keyword(s):

Klebsiella Pneumoniae ◽

Integration Site ◽

Phylogenetic Analyses ◽

Bacterial Genome ◽

Mobile Genetic Elements ◽

Genomic Islands ◽

Genomic Context ◽

Genetic Elements ◽

Genes Encoding ◽

Integration Sites

ABSTRACTThe evolution of traits including antibiotic resistance, virulence, and increased fitness in Klebsiella pneumoniae and related species has been linked to the acquisition of mobile genetic elements through horizontal transfer. Among them, genomic islands (GIs) preferentially integrating at genes encoding tRNAs and the tmRNA (t(m)DNAs) would be significant in promoting chromosomal diversity. Here, we studied the whole set of t(m)DNAs present in 66 Klebsiella chromosomes, investigating their usage as integration sites and the properties of the integrated GIs. A total of 5,624 t(m)DNAs were classified based on their sequence conservation, genomic context, and prevalence. 161 different GIs and prophages were found at these sites, hosting 3,540 gene families including various related to virulence and drug resistance. Phylogenetic analyses supported the acquisition of several of these elements through horizontal gene transfer, likely mediated by a highly diverse set of encoded integrases targeting specific t(m)DNAs and sublocations inside them. Only a subset of the t(m)DNAs had integrated GIs and even identical tDNA copies showed dissimilar usage frequencies, suggesting that the genomic context would influence the integration site selection. This usage bias, likely towards avoiding disruption of polycistronic transcriptional units, would be conserved across Gammaproteobacteria. The systematic comparison of the t(m)DNAs across different strains allowed us to discover an unprecedented number of K. pneumoniae GIs and prophages and to raise important questions and clues regarding the fundamental properties of t(m)DNAs as targets for the integration of mobile genetic elements and drivers of bacterial genome evolution and pathogen emergence.

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Chromosomal Conjugative and Mobilizable Elements in Streptococcus suis: Major Actors in the Spreading of Antimicrobial Resistance and Bacteriocin Synthesis Genes

Pathogens ◽

10.3390/pathogens9010022 ◽

2019 ◽

Vol 9 (1) ◽

pp. 22 ◽

Cited By ~ 8

Author(s):

Virginie Libante ◽

Yves Nombre ◽

Charles Coluzzi ◽

Johan Staub ◽

Gérard Guédon ◽

...

Keyword(s):

Antimicrobial Resistance ◽

In Silico ◽

Bacterial Species ◽

Streptococcus Thermophilus ◽

Streptococcus Suis ◽

Mobile Genetic Elements ◽

Zoonotic Pathogen ◽

Genetic Elements ◽

Integrative Conjugative Elements

Streptococcus suis is a zoonotic pathogen suspected to be a reservoir of antimicrobial resistance (AMR) genes. The genomes of 214 strains of 27 serotypes were screened for AMR genes and chromosomal Mobile Genetic Elements (MGEs), in particular Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs). The functionality of two ICEs that host IMEs carrying AMR genes was investigated by excision tests and conjugation experiments. In silico search revealed 416 ICE-related and 457 IME-related elements. These MGEs exhibit an impressive diversity and plasticity with tandem accretions, integration of ICEs or IMEs inside ICEs and recombination between the elements. All of the detected 393 AMR genes are carried by MGEs. As previously described, ICEs are major vehicles of AMR genes in S. suis. Tn5252-related ICEs also appear to carry bacteriocin clusters. Furthermore, whereas the association of IME-AMR genes has never been described in S. suis, we found that most AMR genes are actually carried by IMEs. The autonomous transfer of an ICE to another bacterial species (Streptococcus thermophilus)—leading to the cis-mobilization of an IME carrying tet(O)—was obtained. These results show that besides ICEs, IMEs likely play a major role in the dissemination of AMR genes in S. suis.

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Diversification of plasmids in a genus of pathogenic and nitrogen-fixing bacteria

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2020.0466 ◽

2021 ◽

Vol 377 (1842) ◽

Cited By ~ 1

Author(s):

Alexandra J. Weisberg ◽

Marilyn Miller ◽

Walt Ream ◽

Niklaus J. Grünwald ◽

Jeff H. Chang

Keyword(s):

Mobile Genetic Elements ◽

Nitrogen Fixing ◽

Genome Sequences ◽

Theme Issue ◽

Nitrogen Fixing Bacteria ◽

Disease Symptoms ◽

Genetic Elements ◽

Virulence Plasmids ◽

Evolution Of Genomes

Members of the agrobacteria–rhizobia complex (ARC) have multiple and diverse plasmids. The extent to which these plasmids are shared and the consequences of their interactions are not well understood. We extracted over 4000 plasmid sequences from 1251 genome sequences and constructed a network to reveal interactions that have shaped the evolutionary histories of oncogenic virulence plasmids. One newly discovered type of oncogenic plasmid is a mosaic with three incomplete, but complementary and partially redundant virulence loci. Some types of oncogenic plasmids recombined with accessory plasmids or acquired large regions not known to be associated with pathogenicity. We also identified two classes of partial virulence plasmids. One class is potentially capable of transforming plants, but not inciting disease symptoms. Another class is inferred to be incomplete and non-functional but can be found as coresidents of the same strain and together are predicted to confer pathogenicity. The modularity and capacity for some plasmids to be transmitted broadly allow them to diversify, convergently evolve adaptive plasmids and shape the evolution of genomes across much of the ARC. This article is part of the theme issue ‘The secret lives of microbial mobile genetic elements’.

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Draft Genome Sequences of 14 Staphylococcus aureus Sequence Type 5 Isolates from California, USA

Genome Announcements ◽

10.1128/genomea.00098-17 ◽

2017 ◽

Vol 5 (13) ◽

Cited By ~ 4

Author(s):

Samantha J. Hau ◽

Darrell O. Bayles ◽

David P. Alt ◽

Tracy L. Nicholson

Keyword(s):

Staphylococcus Aureus ◽

Draft Genome ◽

Mobile Genetic Elements ◽

Sequence Type ◽

Genome Sequences ◽

Content Type ◽

Genetic Elements

ABSTRACT Staphylococcus aureus is part of the human epithelial microbiota; however, it is also a pathogen. The acquisition of mobile genetic elements plays a role in the virulence of S. aureus isolates and contributes to treatment failures. This report details the draft genome sequences of 14 clinical S. aureus isolates.

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