scholarly journals ICEs Are the Main Reservoirs of the Ciprofloxacin-Modifying crpP Gene in Pseudomonas aeruginosa

Genes ◽  
2020 ◽  
Vol 11 (8) ◽  
pp. 889
Author(s):  
João Botelho ◽  
Filipa Grosso ◽  
Luísa Peixe
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Intracellular Trafficking ◽  
Mobile Elements ◽  
Pair Formation ◽  
Mating Pair ◽  
Direct Repeats ◽  
Integrative And Conjugative Elements ◽  
Complete Genomes ◽  
Sequence Types ◽  
Core Genes

The ciprofloxacin-modifying crpP gene was recently identified in a plasmid isolated from a Pseudomonas aeruginosa clinical isolate. Homologues of this gene were also identified in Escherichia coli, Klebsiella pneumoniae and Acinetobacter baumannii. We set out to explore the mobile elements involved in the acquisition and spread of this gene in publicly available and complete genomes of Pseudomonas spp. All Pseudomonas complete genomes were downloaded from NCBI’s Refseq library and were inspected for the presence of the crpP gene. The mobile elements carrying this gene were further characterized. The crpP gene was identified only in P. aeruginosa, in more than half of the complete chromosomes (61.9%, n = 133/215) belonging to 52 sequence types, of which the high-risk clone ST111 was the most frequent. We identified 136 crpP-harboring integrative and conjugative elements (ICEs), with 93.4% belonging to the mating-pair formation G (MPFG) family. The ICEs were integrated at the end of a tRNALys gene and were all flanked by highly conserved 45-bp direct repeats. The crpP-carrying ICEs contain 26 core genes (2.2% of all 1193 genes found in all the ICEs together), which are present in 99% or more of the crpP-harboring ICEs. The most frequently encoded traits on these ICEs include replication, transcription, intracellular trafficking and cell motility. Our work suggests that ICEs are the main vectors promoting the dissemination of the ciprofloxacin-modifying crpP gene in P. aeruginosa.

scholarly journals ICEs are the main reservoirs of the ciprofloxacin-modifying crpP gene in Pseudomonas aeruginosa

2020 ◽  
Author(s):  
João Botelho ◽  
Filipa Grosso ◽  
Luísa Peixe
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Direct Repeats ◽  
Bacterial Genomes ◽  
Genome Database ◽  
Integrative And Conjugative Elements ◽  
Data Files ◽  
Supplementary Material ◽  
Ciprofloxacin Resistance ◽  
Chromosomal Mutations ◽  
Sequence Types

AbstractThe ciprofloxacin-modifying crpP gene was recently identified in a plasmid isolated from a clinical Pseudomonas aeruginosa clinical isolate. Homologues of this gene were also identified in Escherichia coli, Klebsiella pneumoniae and Acinetobacter baumannii. We set out to explore the mobile genetic elements involved in the acquisition and spread of this gene in publicly available and complete genomes of Pseudomonas. The crpP gene was identified only in P. aeruginosa, in more than half of the complete chromosomes (61.9%, n=133/215) belonging to 52 sequence types, of which the high-risk clone ST111 was the most frequent. We identified 136 crpP-harboring ICEs, with 93.4% belonging to the mating-pair formation G (MPFG) family. The ICEs were integrated at the end of a tRNALys gene and were all flanked by highly conserved 45-bp direct repeats. The core ICEome contains 26 genes (2.2% of all genes), which are present in 99% or more of the crpP-harboring ICEs. The most frequently encoded traits on these ICEs include replication, transcription, intracellular trafficking and cell motility. Our work reveals that ICEs are the main vectors promoting the dissemination of the ciprofloxacin-modifying crpP gene in P. aeruginosa.Author NotesAll supporting data has been provided within the article or through supplementary data files. Supplementary material is available with the online version of this article.Impact StatementA high proportion of Pseudomonas aeruginosa clinical isolates are resistant to ciprofloxacin. Resistance to this antibiotic is often mediated by chromosomal mutations, but recently horizontally transferred genes have been identified. We assessed the repartition of the ciprofloxacin-modifying crpP gene among Pseudomonas genomes and we characterized the mobile elements associated with its acquisition. We found that this gene is prevalent in P. aeruginosa and frequently associated with integrative and conjugative elements (ICEs). Importantly, we also identified highly conserved direct repeats that can be used to accurately delimit crpP-carrying ICEs in P. aeruginosa genomes.Data SummaryAll the bacterial genomes scanned in this study have been deposited previously in the National Center for Biotechnology Information genome database and are listed on the supplementary tables. The newick files used to create the trees in Figures 1 and 4 are deposited on figshare at https://figshare.com/projects/ICEs_are_the_main_reservoirs_of_the_ciprofloxacin-modifying_crpP_gene_in_Pseudomonas_aeruginosa/79308.

scholarly journals Carbapenemases on the move: it’s good to be on ICE

2018 ◽  
Author(s):  
João Botelho ◽  
Adam P. Roberts ◽  
Ricardo León-Sampedro ◽  
Filipa Grosso ◽  
Luísa Peixe
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Antibiotic Resistance ◽  
Attachment Site ◽  
Pair Formation ◽  
Class I ◽  
Integrative And Conjugative Elements ◽  
Class I Integrons

AbstractThe evolution and spread of antibiotic resistance is often mediated by mobile geneticelements. Integrative and conjugative elements (ICEs) are the most abundant conjugativeelements among prokaryotes. However, the contribution of ICEs to horizontal gene transferof antibiotic resistance has been largely unexplored. Here we report that ICEs belonging tomating-pair formation (MPF) classes G and T are highly prevalent among the opportunisticpathogen Pseudomonas aeruginosa, contributing to the spread of carbapenemase-encodinggenes (CEGs). Most CEGs of the MPFG class were encoded within class I integrons, which co-harbour genes conferring resistance to other antibiotics. The majority of the integrons werelocated within Tn3-like and composite transposons. A conserved attachment site could bepredicted for the MPFGclass ICEs. MPFTclass ICEs carried the CEGs within compositetransposons which were not associated with integrons. The data presented here provides aglobal snapshot of the different CEG-harbouring ICEs and sheds light on the underappreciatedcontribution of these elements for the evolution and dissemination of antibiotic resistanceon P. aeruginosa.

scholarly journals Antibiotic Resistance Characteristics of Pseudomonas aeruginosa Isolated from Keratitis in Australia and India

Antibiotics ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 600
Author(s):  
Mahjabeen Khan ◽  
Fiona Stapleton ◽  
Stephen Summers ◽  
Scott A. Rice ◽  
Mark D. P. Willcox
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Genetic Variation ◽  
Acquired Resistance ◽  
Drug Resistant ◽  
Beta Lactams ◽  
Mmr Genes ◽  
Large Numbers ◽  
Indian Isolates ◽  
Sequence Types ◽  
Core Genes

This study investigated genomic differences in Australian and Indian Pseudomonas aeruginosa isolates from keratitis (infection of the cornea). Overall, the Indian isolates were resistant to more antibiotics, with some of those isolates being multi-drug resistant. Acquired genes were related to resistance to fluoroquinolones, aminoglycosides, beta-lactams, macrolides, sulphonamides, and tetracycline and were more frequent in Indian (96%) than in Australian (35%) isolates (p = 0.02). Indian isolates had large numbers of gene variations (median 50,006, IQR = 26,967–50,600) compared to Australian isolates (median 26,317, IQR = 25,681–33,780). There were a larger number of mutations in the mutL and uvrD genes associated with the mismatch repair (MMR) system in Indian isolates, which may result in strains losing their efficacy for DNA repair. The number of gene variations were greater in isolates carrying MMR system genes or exoU. In the phylogenetic division, the number of core genes were similar in both groups, but Indian isolates had larger numbers of pan genes (median 6518, IQR = 6040–6935). Clones related to three different sequence types—ST308, ST316, and ST491—were found among Indian isolates. Only one clone, ST233, containing two strains was present in Australian isolates. The most striking differences between Australian and Indian isolates were carriage of exoU (that encodes a cytolytic phospholipase) in Indian isolates and exoS (that encodes for GTPase activator activity) in Australian isolates, large number of acquired resistance genes, greater changes to MMR genes, and a larger pan genome as well as increased overall genetic variation in the Indian isolates.

Assessment of the microbiological quality of natural mineral waters according to the manufacturing time of 20 L returnable packs in Brazil

2020 ◽  
Vol 367 (15) ◽  
Author(s):  
Isabelle da Silva Luz ◽  
Luiza Vasconcellos ◽  
Valéria de Mello Medeiros ◽  
Catia Aparecida Chaia Miranda ◽  
Carla de Oliveira Rosas ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Microbiological Quality ◽  
Human Adenovirus ◽  
Mineral Waters ◽  
Microbiological Contamination ◽  
Natural Mineral ◽  
Norovirus Gii ◽  
Manufacturing Time ◽  
Sequence Types

ABSTRACT This study aimed to assess the microbiological quality of natural mineral waters commercialized in 20 L returnable packs in Brazil by investigating the presence of bacteria and viruses in packs with different manufacturing times (Tm). With this purpose, 99 water samples from 33 lots (n = 3/batch) of 15 brands, obtained from packs with three intervals of Tm, were analyzed. Total coliforms (16.2%), Pseudomonas aeruginosa (9.9%), sulphite-reducing Clostridium (5.0%) and Escherichia coli (2.0%) were detected but enterococci and norovirus GII not. Regarding brands, 11 (73.3%) presented unsatisfactory results for at least one of the lots analyzed. Pseudomonas aeruginosa analysis revealed six sequence types and strains were susceptible to all antibiotics tested and were able to produce biofilms. Human adenovirus (4) and norovirus GI (9) were also identified in nine samples randomly selected. Natural mineral waters commercialized in 20 L packs with Tm ≥ 2 years presented more microbiological contamination (P ≤ 0.012) than ones with a Tm of 0–1 year or a Tm of 1–2 years. These results suggest that the validity period of reusable 20 L packs should be reduced or that they can no longer be reused.

scholarly journals The Resistome of Pseudomonas aeruginosa in Relationship to Phenotypic Susceptibility

2014 ◽  
Vol 59 (1) ◽  
pp. 427-436 ◽  
Author(s):  
Veronica N. Kos ◽  
Maxime Déraspe ◽  
Robert E. McLaughlin ◽  
James D. Whiteaker ◽  
Paul H. Roy ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Multidrug Resistant ◽  
Clinical Isolates ◽  
Genetic Determinants ◽  
Content Type ◽  
Susceptibility Data ◽  
Next Generation Sequencing Ngs ◽  
Sequence Types ◽  
Generation Sequencing ◽  
Phenotypic Susceptibility

ABSTRACTMany clinical isolates ofPseudomonas aeruginosacause infections that are difficult to eradicate due to their resistance to a wide variety of antibiotics. Key genetic determinants of resistance were identified through genome sequences of 390 clinical isolates ofP. aeruginosa, obtained from diverse geographic locations collected between 2003 and 2012 and were related to microbiological susceptibility data for meropenem, levofloxacin, and amikacin. β-Lactamases and integron cassette arrangements were enriched in the established multidrug-resistant lineages of sequence types ST111 (predominantly O12) and ST235 (O11). This study demonstrates the utility of next-generation sequencing (NGS) in defining relevant resistance elements and highlights the diversity of resistance determinants withinP. aeruginosa. This information is valuable in furthering the design of diagnostics and therapeutics for the treatment ofP. aeruginosainfections.

scholarly journals Pseudomonas aeruginosa Genotype Prevalence in Dutch Cystic Fibrosis Patients and Age Dependency of Colonization by Various P. aeruginosa Sequence Types

2009 ◽  
Vol 47 (12) ◽  
pp. 4096-4101 ◽  
Author(s):  
R. van Mansfeld ◽  
R. Willems ◽  
R. Brimicombe ◽  
H. Heijerman ◽  
F. T. van Berkhout ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Pseudomonas Aeruginosa ◽  
Age Dependency ◽  
Sequence Types

scholarly journals Draft Genome Sequences of Nine Pseudomonas aeruginosa Strains, Including Eight Clinical Isolates: TABLE 1 

2015 ◽  
Vol 3 (5) ◽  
Author(s):  
Patricio Jeraldo ◽  
Scott A. Cunningham ◽  
Daniel Quest ◽  
Robert A. Sikkink ◽  
Daniel O’Brien ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Draft Genome ◽  
Clinical Isolates ◽  
Genome Sequences ◽  
Mate Pair ◽  
Sequence Types ◽  
Mate Pair Library

We report on nine draft genomes of Pseudomonas aeruginosa isolates, assembled using a hybrid paired-end and Nextera mate-pair library approach. Eight are of clinical origin, and one is the ATCC 27853 strain. We also report their multilocus sequence types.

scholarly journals Complete Nucleotide Sequence of the Conjugative Tetracycline Resistance Plasmid pFBAOT6, a Member of a Group of IncU Plasmids with Global Ubiquity

2004 ◽  
Vol 70 (12) ◽  
pp. 7497-7510 ◽  
Author(s):  
Glenn Rhodes ◽  
Julian Parkhill ◽  
Christine Bird ◽  
Kerrie Ambrose ◽  
Matthew C. Jones ◽  
...  
Keyword(s):  
Secretory Pathway ◽  
Transfer Functions ◽  
Genetic Load ◽  
Tetracycline Resistance ◽  
Complete Sequence ◽  
Pair Formation ◽  
Broad Host Range ◽  
Mating Pair ◽  
Associated Bacteria ◽  
Type Iv

ABSTRACT This study presents the first complete sequence of an IncU plasmid, pFBAOT6. This plasmid was originally isolated from a strain of Aeromonas caviae from hospital effluent (Westmorland General Hospital, Kendal, United Kingdom) in September 1997 (G. Rhodes, G. Huys, J. Swings, P. McGann, M. Hiney, P. Smith, and R. W. Pickup, Appl. Environ. Microbiol. 66:3883-3890, 2000) and belongs to a group of related plasmids with global ubiquity. pFBAOT6 is 84,748 bp long and has 94 predicted coding sequences, only 12 of which do not have a possible function that has been attributed. Putative replication, maintenance, and transfer functions have been identified and are located in a region in the first 31 kb of the plasmid. The replication region is poorly understood but exhibits some identity at the protein level with replication proteins from the gram-positive bacteria Bacillus and Clostridium. The mating pair formation system is a virB homologue, type IV secretory pathway that is similar in its structural organization to the mating pair formation systems of the related broad-host-range (BHR) environmental plasmids pIPO2, pXF51, and pSB102 from plant-associated bacteria. Partitioning and maintenance genes are homologues of genes in IncP plasmids. The DNA transfer genes and the putative oriT site also exhibit high levels of similarity with those of plasmids pIPO2, pXF51, and pSB102. The genetic load region encompasses 54 kb, comprises the resistance genes, and includes a class I integron, an IS630 relative, and other transposable elements in a 43-kb region that may be a novel Tn1721-flanked composite transposon. This region also contains 24 genes that exhibit the highest levels of identity to chromosomal genes of several plant-associated bacteria. The features of the backbone of pFBAOT6 that are shared with this newly defined group of environmental BHR plasmids suggest that pFBAOT6 may be a relative of this group, but a relative that was isolated from a clinical bacterial environment rather than a plant-associated bacterial environment.

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