scholarly journals Acquisition of Beta-Lactamase by Neisseria meningitidis through Possible Horizontal Gene Transfer

2018 ◽  
Vol 62 (9) ◽  
Author(s):  
Eva Hong ◽  
Ala-Eddine Deghmane ◽  
Muhamed-Kheir Taha
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Genome Sequencing ◽  
Meningococcal Disease ◽  
Bacterial Species ◽  
Whole Genome ◽  
Beta Lactamase ◽  
Content Type ◽  
Beta Lactamases ◽  
Lactamase Gene

ABSTRACT We report the detection in France of a beta-lactamase-producing invasive meningococcal isolate. Whole-genome sequencing of the isolate revealed a ROB-1-type beta-lactamase gene that is frequently encountered in Haemophilus influenzae, suggesting horizontal transfer between isolates of these bacterial species. Beta-lactamases are exceptional in meningococci, with no reports for more than 2 decades. This report is worrying, as the expansion of such isolates may jeopardize the effective treatment against invasive meningococcal disease.

scholarly journals Haemophilus to meningococci transfer of beta-lactamase

2018 ◽  
Author(s):  
Eva Hong ◽  
Ala-Eddine Deghmane ◽  
Muhamed-Kheir Taha
Keyword(s):  
Haemophilus Influenzae ◽  
Whole Genome Sequencing ◽  
Effective Treatment ◽  
Genome Sequencing ◽  
Meningococcal Disease ◽  
Horizontal Transfer ◽  
Bacterial Species ◽  
Whole Genome ◽  
Beta Lactamase ◽  
Beta Lactamases

AbstractWe report the detection in France of a beta-lactamase producing invasive meningococcal isolate. Whole genome sequencing of the isolate revealed ROB-1 type beta-lactamase that is frequently encountered in Haemophilus influenzae suggesting horizontal transfer between isolates of these bacterial species. Beta-lactamases are exceptional in meningococci with no reports from more than two decades. This report is worrying as the expansion of such isolates may jeopardize the effective treatment against invasive meningococcal disease.

scholarly journals Spread of Plasmids Carrying Multiple GES Variants

2016 ◽  
Vol 60 (8) ◽  
pp. 5040-5043 ◽  
Author(s):  
Gaelle Cuzon ◽  
Pierre Bogaerts ◽  
Caroline Bauraing ◽  
Te-Din Huang ◽  
Rémy A. Bonnin ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Enterobacter Cloacae ◽  
Conjugative Plasmid ◽  
Whole Genome ◽  
Content Type ◽  
Extended Spectrum

ABSTRACTFive GES-producingEnterobacteriaceaeisolates that displayed an extended-spectrum β-lactamase (ESBL) phenotype harbored two GES variants: GES-7 ESBL and GES-6 carbapenemase. In all isolates, the two GES alleles were located on the same integron that was inserted into an 80-kb IncM1 self-conjugative plasmid. Whole-genome sequencing suggestedin vivohorizontal gene transfer of the plasmid along with clonal diffusion ofEnterobacter cloacae. To our knowledge, this is the first description in Europe of clusteredEnterobacteriaceaeisolates carrying two GES β-lactamases, of which one has extended activity toward carbapenems.

scholarly journals An Evolutionary Link between Natural Transformation and CRISPR Adaptive Immunity

mBio ◽  
2012 ◽  
Vol 3 (5) ◽  
Author(s):  
Peter Jorth ◽  
Marvin Whiteley
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Bacterial Diversity ◽  
Natural Transformation ◽  
Bacterial Species ◽  
Comparative Genomic ◽  
Content Type ◽  
Immune Systems ◽  
Adaptive Immune ◽  
Adaptive Immune Systems

ABSTRACTNatural transformation by competent bacteria is a primary means of horizontal gene transfer; however, evidence that competence drives bacterial diversity and evolution has remained elusive. To test this theory, we used a retrospective comparative genomic approach to analyze the evolutionary history ofAggregatibacter actinomycetemcomitans, a bacterial species with both competent and noncompetent sister strains. Through comparative genomic analyses, we reveal that competence is evolutionarily linked to genomic diversity and speciation. Competence loss occurs frequently during evolution and is followed by the loss of clustered regularly interspaced short palindromic repeats (CRISPRs), bacterial adaptive immune systems that protect against parasitic DNA. Relative to noncompetent strains, competent bacteria have larger genomes containing multiple rearrangements. In contrast, noncompetent bacterial genomes are extremely stable but paradoxically susceptible to infective DNA elements, which contribute to noncompetent strain genetic diversity. Moreover, incomplete noncompetent strain CRISPR immune systems are enriched for self-targeting elements, which suggests that the CRISPRs have been co-opted for bacterial gene regulation, similar to eukaryotic microRNAs derived from the antiviral RNA interference pathway.IMPORTANCEThe human microbiome is rich with thousands of diverse bacterial species. One mechanism driving this diversity is horizontal gene transfer by natural transformation, whereby naturally competent bacteria take up environmental DNA and incorporate new genes into their genomes. Competence is theorized to accelerate evolution; however, attempts to test this theory have proved difficult. Through genetic analyses of the human periodontal pathogenAggregatibacter actinomycetemcomitans, we have discovered an evolutionary connection between competence systems promoting gene acquisition and CRISPRs (clustered regularly interspaced short palindromic repeats), adaptive immune systems that protect bacteria against genetic parasites. We show that competentA. actinomycetemcomitansstrains have numerous redundant CRISPR immune systems, while noncompetent bacteria have lost their CRISPR immune systems because of inactivating mutations. Together, the evolutionary data linking the evolution of competence and CRISPRs reveals unique mechanisms promoting genetic heterogeneity and the rise of new bacterial species, providing insight into complex mechanisms underlying bacterial diversity in the human body.

scholarly journals Draft Genome Sequence of a blaNDM-1- and blaPME-1-Harboring Pseudomonas aeruginosa Clinical Isolate from Pakistan

2019 ◽  
Vol 8 (17) ◽  
Author(s):  
Sidra Irum ◽  
Robert F. Potter ◽  
Rubina Kamran ◽  
Zeeshan Mustafa ◽  
Meghan A. Wallace ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Pseudomonas Aeruginosa ◽  
Genome Sequencing ◽  
Draft Genome ◽  
Whole Genome ◽  
Beta Lactamase ◽  
Content Type ◽  
Extended Spectrum Beta Lactamase ◽  
Carbapenem Resistant ◽  
Airway Colonization

We performed Illumina whole-genome sequencing on a carbapenem-resistant Pseudomonas aeruginosa strain isolated from a cystic fibrosis patient with chronic airway colonization. The draft genome comprises 6,770,411 bp, including the carbapenemase bla NDM-1 and the extended-spectrum beta-lactamase bla PME-1.

scholarly journals Food Workers as a Reservoir of Extended-Spectrum-Cephalosporin-Resistant Salmonella Strains in Japan

2020 ◽  
Vol 86 (13) ◽  
Author(s):  
Hiroaki Shigemura ◽  
Eri Sakatsume ◽  
Tsuyoshi Sekizuka ◽  
Hiroshi Yokoyama ◽  
Kunihiko Hamada ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Bacterial Species ◽  
Diffusion Method ◽  
Whole Genome ◽  
Disk Diffusion Method ◽  
Content Type ◽  
Extended Spectrum ◽  
Food Workers ◽  
M 14

ABSTRACT Dissemination of extended-spectrum-cephalosporin (ESC)-resistant Salmonella, especially extended-spectrum-β-lactamase (ESBL)-producing Salmonella, is a concern worldwide. Here, we assessed Salmonella carriage by food workers in Japan to clarify the prevalence of ESC-resistant Salmonella harboring blaCTX-M. We then characterized the genetic features, such as transposable elements, of blaCTX-M-harboring plasmids using whole-genome sequencing. A total of 145,220 stool samples were collected from food workers, including cooks and servers from several restaurants, as well as food factory workers, from January to October 2017. Isolated salmonellae were subjected to antimicrobial susceptibility testing (disk diffusion method), and whole-genome sequencing was performed for Salmonella strains harboring blaCTX-M. Overall, 164 Salmonella isolates (0.113%) were recovered from 164 samples, from which we estimated that at least 0.113% (95% confidence interval [CI]: 0.096 to 0.132%) of food workers may carry Salmonella. Based on this estimation, 3,473 (95% CI = 2,962 to 4,047) individuals among the 3,075,330 Japanese food workers are likely to carry Salmonella. Of the 158 culturable isolates, seven showed resistance to ESCs: three isolates harbored blaCMY-2 and produced AmpC β-lactamase, while four ESBL-producing isolates harbored blaCTX-M-14 (n = 1, Salmonella enterica serovar Senftenberg) or blaCTX-M-15 (n = 3, S. enterica serovar Haardt). blaCTX-M-15 was chromosomally located in the S. Haardt isolates, which also contained ISEcp1, while the S. Senftenberg isolate contained an IncFIA(HI1)/IncHI1A/IncHI1B(R27) hybrid plasmid carrying blaCTX-M-14 along with ISEcp1. This study indicates that food workers may be a reservoir of ESBL-producing Salmonella and associated genes. Thus, these workers may contribute to the spread of blaCTX-M via plasmids or mobile genetic elements such as ISEcp1. IMPORTANCE Antimicrobial-resistant Salmonella bacteria arise in farm environments through imprudent use of antimicrobials. Subsequently, these antimicrobial-resistant strains, such as extended-spectrum-β-lactamase (ESBL)-producing Salmonella, may be transmitted to humans via food animal-derived products. Here, we examined Salmonella carriage among food handlers in Japan. Overall, 164 of 145,220 fecal samples (0.113%) were positive for Salmonella. Among the 158 tested isolates, four were identified as ESBL-producing isolates carrying ESBL determinants blaCTX-M-15 or blaCTX-M-14. In all cases, the genes coexisted with ISEcp1, regardless of whether they were located on the chromosome or on a plasmid. Our findings suggest that food workers may be a reservoir of ESBL-producing strains and could contribute to the spread of resistance genes from farm-derived Salmonella to other bacterial species present in the human gut.

scholarly journals Whole-Genome Sequencing of Human ClinicalKlebsiella pneumoniaeIsolates Reveals Misidentification and Misunderstandings ofKlebsiella pneumoniae,Klebsiella variicola, andKlebsiella quasipneumoniae

mSphere ◽  
2017 ◽  
Vol 2 (4) ◽  
Author(s):  
S. Wesley Long ◽  
Sarah E. Linson ◽  
Matthew Ojeda Saavedra ◽  
Concepcion Cantu ◽  
James J. Davis ◽  
...  
Keyword(s):  
Homologous Recombination ◽  
Klebsiella Pneumoniae ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Clinical Microbiology ◽  
Whole Genome ◽  
Beta Lactamase ◽  
Opportunistic Pathogens ◽  
Content Type ◽  
Strain Collection

ABSTRACTKlebsiella pneumoniaeis a major threat to public health, causing significant morbidity and mortality worldwide. The emergence of highly drug-resistant strains is particularly concerning. There has been a recognition and division ofKlebsiella pneumoniaeinto three distinct phylogenetic groups:Klebsiella pneumoniae,Klebsiella variicola, andKlebsiella quasipneumoniae.K. variicolaandK. quasipneumoniaehave often been described as opportunistic pathogens that have less virulence in humans thanK. pneumoniaedoes. We recently sequenced the genomes of 1,777 extended-spectrum-beta-lactamase (ESBL)-producingK. pneumoniaeisolates recovered from human infections and discovered that 28 strains were phylogenetically related toK.variicolaandK. quasipneumoniae. Whole-genome sequencing of 95 additional non-ESBL-producingK. pneumoniaeisolates recovered from patients found 12K. quasipneumoniaestrains. Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) analysis initially identified all patient isolates asK. pneumoniae, suggesting a potential pitfall in conventional clinical microbiology laboratory identification methods. Whole-genome sequence analysis revealed extensive sharing of core gene content and plasmid replicons among theKlebsiellaspecies. For the first time, strains of bothK. variicolaandK. quasipneumoniaewere found to carry theKlebsiella pneumoniaecarbapenemase (KPC) gene, while anotherK. variicolastrain was found to carry the New Delhi metallo-beta-lactamase 1 (NDM-1) gene.K. variicolaandK. quasipneumoniaeinfections were not less virulent thanK. pneumoniaeinfections, as assessed by in-hospital mortality and infection type. We also discovered evidence of homologous recombination in oneK. variicolastrain, as well as one strain from a novelKlebsiellaspecies, which challenge the current understanding of interrelationships between clades ofKlebsiella.IMPORTANCEKlebsiella pneumoniaeis a serious human pathogen associated with resistance to multiple antibiotics and high mortality.K. variicolaandK. quasipneumoniaeare closely related organisms that are generally considered to be less-virulent opportunistic pathogens. We used a large, comprehensive, population-based strain collection and whole-genome sequencing to investigate infections caused by these organisms in our hospital system. We discovered thatK. variicolaandK. quasipneumoniaeisolates are often misidentified asK. pneumoniaeby routine clinical microbiology diagnostics and frequently cause severe life-threatening infections similar toK. pneumoniae. The presence of KPC inK. variicolaandK. quasipneumoniaestrains as well as NDM-1 metallo-beta-lactamase in oneK. variicolastrain is particularly concerning because these genes confer resistance to many different beta-lactam antibiotics. The sharing of plasmids, as well as evidence of homologous recombination, between these three species ofKlebsiellais cause for additional concern.

A blaVIM-1 positive Aeromonas hydrophila strain in a near-drowning patient: evidence for interspecies plasmid transfer within the patient

2019 ◽  
Vol 14 (14) ◽  
pp. 1191-1197 ◽  
Author(s):  
Thijs Bosch ◽  
Rogier Schade ◽  
Fabian Landman ◽  
Leo Schouls ◽  
Karin van Dijk
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Resistance Genes ◽  
Aeromonas Hydrophila ◽  
Whole Genome ◽  
Illumina Hiseq ◽  
Near Drowning ◽  
Long Read

Aim: To show that a strain of Aeromonas hydrophila became resistant to carbapenems by interspecies transfer of a plasmid using long-read sequencing. Material & methods: Whole genome sequencing of the four isolates was done using Illumina Hiseq, while the plasmid was reconstructed using the MinION sequencer. The resistome was identified with ResFinder. Results: Whole genome sequencing and long-read sequencing showed that all isolates carried a blaVIM-1 gene located on a 165 kb incA/C plasmid. ResFinder confirmed that the resistome of the plasmid, comprising 13 resistance genes, was identical within all isolates. Discussion: Long-read sequencing using the MinION successfully reconstructed a plasmid that was identical in all isolates, providing evidence for horizontal gene transfer of this blaVIM-1 gene carrying plasmid within the patient.

scholarly journals Unveiling New Aspects of Meningococcal Carriage and Disease Prevention

2015 ◽  
Vol 54 (1) ◽  
pp. 2-4
Author(s):  
Magnus Gottfredsson
Keyword(s):  
Disease Prevention ◽  
Neisseria Meningitidis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Meningococcal Disease ◽  
Invasive Meningococcal Disease ◽  
Whole Genome ◽  
Traditional Methods ◽  
Content Type ◽  
Phenotypic Methods

Recently, two protein-based vaccines have been approved for the prevention of invasive meningococcal disease caused byNeisseria meningitidisserogroup B (MenB). It is therefore important to study carefully if and how these pathogens respond to widespread vaccination. Traditionally, meningococci have been classified on the basis of capsular phenotypes, but variable levels of capsule expression can influence the results, mainly among MenB strains. In this issue, Jones and colleagues (J Clin Microbiol 54:25–34, 2016,http://dx.doi.org/10.1128/JCM.01447-15) compare whole-genome sequencing to traditional phenotypic methods of classifying meningococci. They demonstrate that for MenB in particular, sequencing-based methods are far superior to traditional methods, especially when it comes to characterizing carriage isolates. This has important implications for future surveillance.

scholarly journals Taking the Gonococcus-Human Relationship to a Whole New Level: Implications for the Coevolution of Microbes and Humans

mBio ◽  
2011 ◽  
Vol 2 (3) ◽  
Author(s):  
William M. Shafer ◽  
Elizabeth A. Ohneck
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Neisseria Gonorrhoeae ◽  
Bacterial Species ◽  
Human Relationship ◽  
Content Type ◽  
Long Interspersed Nuclear Element

ABSTRACTWhile horizontal gene transfer occurs frequently among bacterial species, evidence for the transfer of DNA from host to microbe is exceptionally rare. However, the recent report by Anderson and Seifert [mBio 2(1):e00005-11, 2011] provides evidence for such an event with the finding that 11% ofNeisseria gonorrhoeaestrains harbor a 685-bp sequence that is 98 to 100% identical to the human long interspersed nuclear element L1. While the function of this element in gonococci remains unclear, this finding significantly impacts our consideration of the coevolution of hosts and microbes, particularly that of humans and pathogens.

scholarly journals Whole-Genome Sequencing and Annotation of Clostridium tyrobutyricum Strain Cirm BIA 2237, Isolated from Silage

2019 ◽  
Vol 8 (30) ◽  
Author(s):  
Edouard Munier ◽  
Hélène Licandro-Séraut ◽  
Christine Achilleos ◽  
Rémy Cachon ◽  
Eric Beuvier
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Complete Genome ◽  
Bacterial Species ◽  
Whole Genome ◽  
Clostridium Tyrobutyricum ◽  
Content Type ◽  
Complete Genome Sequencing

Clostridium tyrobutyricum is the main bacterial species leading to the late blowing defect, a major cause of spoilage in semihard and hard cheeses. This study reports the complete genome sequencing, assembly, and annotation of C. tyrobutyricum strain Cirm BIA 2237, formerly called CNRZ 608, isolated from silage.

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