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 Comprehensive genome data analysis establishes a triple whammy of carbapenemases, ICEs and multiple clinically-relevant bacteria

2019 ◽  
Author(s):  
João Botelho ◽  
Joana Mourão ◽  
Adam P. Roberts ◽  
Luísa Peixe
Keyword(s):  
Escherichia Coli ◽  
Pseudomonas Aeruginosa ◽  
Klebsiella Pneumoniae ◽  
Bacterial Species ◽  
Beta Lactamase ◽  
Bacterial Genomes ◽  
Genome Database ◽  
Integrative And Conjugative Elements ◽  
Encoding Genes ◽  
Clinically Relevant Bacteria

AbstractCarbapenemases inactivate most β-lactam antibiotics, including carbapenems and have been frequently reported among Enterobacteriaceae, Acinetobacter spp. and Pseudomonas spp. Traditionally, the horizontal gene transfer of carbapenemase encoding genes (CEGs) has been linked to plasmids. However, given that integrative and conjugative elements (ICEs) are possibly the most abundant conjugative elements among prokaryotes, we conducted an in-silico analysis to ascertain the likely role of ICEs in the spread of CEGs among all bacterial genomes (n=182,663). We detected 17,520 CEGs, of which 66 were located within putative ICEs among several bacterial species (including clinically-relevant bacteria as Pseudomonas aeruginosa, Klebsiella pneumoniae and Escherichia coli). Most CEGs detected within ICEs belong to the IMP, NDM and SPM metallo-beta-lactamase families, and the serine beta-lactamase KPC and GES families. Different mechanisms were likely responsible for acquisition of these genes. The majority of CEG-bearing ICEs belong to the MPFG, MPFT and MPFF classes and often encode resistance to other antibiotics (e.g., aminoglycosides and fluoroquinolones). This study provides a snapshot of the different CEGs associated with ICEs among available bacterial genomes and sheds light on the underappreciated contribution of ICEs to the spread of carbapenem resistance globally.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 StatementCarbapenems are commonly used to treat severe infections in humans. Resistance is often mediated by carbapenemases. These enzymes degrade carbapenems and are frequently present in plasmids. Here, we demonstrate that common carbapenemase-encoding genes (CEGs) found in clinical isolates (e.g. blaKPC, blaGES, blaIMP, blaNDM, blaVIM) can also be located within integrative and conjugative elements (ICEs). CEG-bearing ICEs belong to three mating-pair formation families. These mobile elements may be particularly important in bacteria where plasmids do not seem to play a significant role in the spread of antibiotic resistance genes, as Pseudomonas spp. This study considerably expands the knowledge of the repertoire of CEGs-bearing ICEs among clinically-relevant bacterial pathogens, such as Pseudomonas aeruginosa, Klebsiella pneumoniae and Escherichia coli.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 extracted 66 ICEs in fasta format and the outputs for the profile HMMs scanned on the 386 putative MGEs identified in this study are deposited on figshare at https://figshare.com/projects/_Comprehensive_genome_data_analysis_establishes_a_triple_whammy_of_carbapenemases_ICEs_and_multiple_clinically-relevant_bacteria/78369.

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 Presence of Chromosomal crpP-like Genes Is Not Always Associated with Ciprofloxacin Resistance in Pseudomonas aeruginosa Clinical Isolates Recovered in ICU Patients from Portugal and Spain

2021 ◽  
Vol 9 (2) ◽  
pp. 388
Author(s):  
Marta Hernández-García ◽  
María García-Castillo ◽  
Sergio García-Fernández ◽  
Diego López-Mendoza ◽  
Jazmín Díaz-Regañón ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Protein Function ◽  
Resistance Mechanism ◽  
Amino Acid Position ◽  
Genomic Islands ◽  
Missense Mutations ◽  
The Novel ◽  
Surveillance Studies ◽  
Ciprofloxacin Resistance ◽  
Chromosomal Mutations

CrpP enzymes have been recently described as a novel ciprofloxacin-resistance mechanism. We investigated by whole genome sequencing the presence of crpP-genes and other mechanisms involved in quinolone resistance in MDR/XDR-Pseudomonas aeruginosa isolates (n = 55) with both ceftolozane-tazobactam susceptible or resistant profiles recovered from intensive care unit patients during the STEP (Portugal) and SUPERIOR (Spain) surveillance studies. Ciprofloxacin resistance was associated with mutations in the gyrA and parC genes. Additionally, plasmid-mediated genes (qnrS2 and aac(6′)-Ib-cr) were eventually detected. Ten chromosomal crpP-like genes contained in related pathogenicity genomic islands and 6 different CrpP (CrpP1-CrpP6) proteins were found in 65% (36/55) of the isolates. Dissemination of CrpP variants was observed among non-related clones of both countries, including the CC175 (Spain) high-risk clone and CC348 (Portugal) clone. Interestingly, 5 of 6 variants (CrpP1-CrpP5) carried missense mutations in an amino acid position (Gly7) previously defined as essential conferring ciprofloxacin resistance, and decreased ciprofloxacin susceptibility was only associated with the novel CrpP6 protein. In our collection, ciprofloxacin resistance was mainly due to chromosomal mutations in the gyrA and parC genes. However, crpP genes carrying mutations essential for protein function (G7, I26) and associated with a restored ciprofloxacin susceptibility were predominant. Despite the presence of crpP genes is not always associated with ciprofloxacin resistance, the risk of emergence of novel CrpP variants with a higher ability to affect quinolones is increasing. Furthermore, the spread of crpP genes in highly mobilizable genomic islands among related and non-related P. aeruginosa clones alert the dispersion of MDR pathogens in hospital settings.

scholarly journals Whole-Genome Sequencing Reveals Diversity of Carbapenem-Resistant Pseudomonas aeruginosa Collected Through the Emerging Infections Program

2020 ◽  
Vol 41 (S1) ◽  
pp. s513-s514
Author(s):  
Richard Stanton ◽  
Jonathan Daniels ◽  
Erin Breaker ◽  
Davina Campbell ◽  
Joseph Lutgring ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
High Risk ◽  
Efflux Pump ◽  
Resistance Mutation ◽  
Carbapenem Resistance ◽  
Emerging Infections ◽  
Carbapenem Resistant ◽  
Antimicrobial Resistance Genes ◽  
Chromosomal Mutations ◽  
Sequence Types

Background: Carbapenem-resistant Pseudomonas aeruginosa (CRPA) is a frequent cause of healthcare-associated infections (HAIs). The CDC Emerging Infections Program (EIP) conducted population and laboratory-based surveillance of CRPA in selected areas in 8 states from August 1, 2016, through July 31, 2018. We aimed to describe the molecular epidemiology and mechanisms of resistance of CRPA isolates collected through this surveillance. Methods: We defined a case as the first isolate of P. aeruginosa resistant to imipenem, meropenem, or doripenem from the lower respiratory tract, urine, wounds, or normally sterile sites identified from a resident of the EIP catchment area in a 30-day period; EIP sites submitted a systematic random sample of isolates to CDC for further characterization. Of 1,021 CRPA clinical isolates submitted, 707 have been sequenced to date using an Illumina MiSeq. Sequenced genomes were classified using the 7-gene multilocus sequence typing (MLST) scheme, and a core genome MLST (cgMLST) scheme was used to determine phylogeny. Antimicrobial resistance genes were identified using publicly available databases, and chromosomal mechanisms of carbapenem resistance were determined using previously validated genetic markers. Results: There were 189 sequence types (STs) among the 707 sequenced genomes (Fig. 1). The most frequently occurring were high-risk clones ST235 (8.5%) and ST298 (4.7%), which were found across all EIP sites. Carbapenemase genes were identified in 5 (<1%) isolates. Overall, 95.6% of the isolates had chromosomal mutations associated with carbapenem resistance: 93.2% had porinD-associated mutations that decrease membrane permeability to the drugs; 24.8% had mutations associated with overexpression of the multidrug efflux pump MexAB-OprM; and 22.9% had mutations associated with overexpression of the endogenous β-lactamase ampC. More than 1 such chromosomal resistance mutation type was present in 37.8% of the isolates. Conclusions: The diversity of the sequence types demonstrates that HAIs caused by CRPA can arise from a variety of strains and that high-risk clones are broadly disseminated across the EIP sites but are a minority of CRPA strains overall. Carbapenem resistance in P. aeruginosa was predominantly driven by chromosomal mutations rather than acquired mechanisms (ie, carbapenemases). The diversity of the CRPA isolates and the lack of carbapenemase genes suggest that this ubiquitous pathogen can readily evolve chromosomal resistance mechanisms, but unlike carbapenemases, these cannot be easily spread through horizontal transfer.Funding: NoneDisclosures: None

scholarly journals Ciprofloxacin Resistance in Clinical Isolates of Pseudomonas aeruginosa from Italian Patients

Drugs ◽  
1995 ◽  
Vol 49 (Supplement 2) ◽  
pp. 175-176 ◽  
Author(s):  
G. Corti ◽  
F. Paradisi ◽  
E. Giganti ◽  
G. Buffini ◽  
E. Tortoli ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Clinical Isolates ◽  
Ciprofloxacin Resistance

scholarly journals Investigation of Ciprofloxacin Resistance and Its Mechanisms in Clinical Pseudomonas aeruginosa Isolates

ANKEM Dergisi ◽  
2021 ◽  
Author(s):  
Nilüfer Uzunbayır Akel ◽  
Yamaç Tekintaş ◽  
Fethiye Ferda Yılmaz ◽  
İsmail Öztürk ◽  
Mustafa Ökeer ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Efflux Pump ◽  
Resistance Mechanisms ◽  
Regulatory Genes ◽  
Quinolone Resistance ◽  
University Hospital ◽  
Clinical Samples ◽  
Genetic Groups ◽  
Ciprofloxacin Resistance ◽  
Polymerase Chain

Pseudomonas aeruginosa is one of the most important causes of hospital infections. Although different antibiotic groups are used for the treatment of P.aeruginosa infections, quinolone groups are distinguished by the advantages of oral administration. However, in recent years, resistance against members of this group has made treatment more difficult. The aim of this study was to investigate the epidemiological relationship and possible mechanisms of resistance in ciprofloxacin resistant P. aeruginosa isolates from Ege University Hospital. The identification of P.aeruginosa bacteria isolated from clinical samples in Ege University Medical Faculty Medical Microbiology Laboratory was determined by VITEK MS automated systems by VITEK compact, antimicrobial susceptibility. The epidemiological relationships of the ciprofloxacin resistant isolates were determined by Enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR). The presence of qnrA, qnrB, qnrS, qepA genes, the quinolone resistance genes and nfxB, mexR, the regulatory genes of the efflux pump, was determined by PCR. The phenylalanine-arginine β-naphthylamide (PAβN) assay was used to determine the activation of the efflux pump. Twenty-two isolates (26.5 %) were found resistant to ciprofloxacin. According to the ERIC-PCR results, 11 unrelated clones were detected. Ciprofloxacin minimum inhibitory concentration (MIC) values were decreased 2-64 times in 10 isolates in the presence of PAIN. No ciprofloxacin MIC change was detected in one isolate. The presence of pump regulatory genes was determined in 10 of the 11 representative isolates, while only qnrB of the genes associated with quinolone resistance was detected in seven representative isolates. qnrA, qnrS, qepA genes were not detected in any isolate. Ciprofloxacin resistant P.aeruginosa isolates are isolated from our hospital. It is noteworthy that the isolates belonging to different genetic groups are in circulation in clinics. Basic resistance mechanisms are thought to be efflux pumps and qnrB genes.

scholarly journals Integrative and Conjugative Elements (ICE) and Associated Cargo Genes within and across Hundreds of Bacterial Genera

2020 ◽  
Author(s):  
James H Kaufman ◽  
Ignacio Terrizzano ◽  
Gowri Nayar ◽  
Ed Seabolt ◽  
Akshay Agarwal ◽  
...  
Keyword(s):  
Big Data ◽  
Data Analysis ◽  
Big Data Analysis ◽  
Gene Exchange ◽  
Bacterial Genomes ◽  
Phenotypic Properties ◽  
Evolutionary Mechanism ◽  
Data Resource ◽  
Integrative And Conjugative Elements ◽  
Susceptibility Assay

AbstractHorizontal gene transfer mediated by integrative and conjugative elements (ICE) is considered an important evolutionary mechanism of bacteria. It allows organisms to quickly evolve new phenotypic properties including antimicrobial resistance (AMR) and virulence. The rate of ICE-mediated cargo gene exchange has not yet been comprehensively studied within and between bacterial taxa. In this paper we report a big data analysis of ICE and associated cargo genes across over 200,000 bacterial genomes representing 1,345 genera. Our results reveal that half of bacterial genomes contain one or more known ICE features (“ICE genomes”), and that the associated genetic cargo may play an important role in the spread of AMR genes within and between bacterial genera. We identify 43 AMR genes that appear only in ICE genomes and never in non-ICE genomes. A further set of 95 AMR genes are found >5x more often in ICE versus non-ICE genomes. In contrast, only 29 AMR genes are observed more frequently (at least 5:1) in non-ICE genomes compared to ICE genomes. Analysis of NCBI antibiotic susceptibility assay data reveals that ICE genomes are also over-represented amongst phenotypically resistant isolates, suggesting that ICE processes are critical for both genotypic and phenotypic AMR. These results, as well as the underlying big data resource, are important foundational tools for understanding bacterial evolution, particularly in relation to important bacterial phenotypes such as AMR.

scholarly journals Epidemiology, molecular characterisation and antimicrobial susceptibility of Neisseria gonorrhoeae isolates in Madrid, Spain, in 2016

2019 ◽  
Vol 147 ◽  
Author(s):  
M. D. Guerrero-Torres ◽  
M. B. Menéndez ◽  
C. S. Guerras ◽  
E. Tello ◽  
J. Ballesteros ◽  
...  
Keyword(s):  
Neisseria Gonorrhoeae ◽  
Antimicrobial Susceptibility ◽  
Strong Association ◽  
Clinical Samples ◽  
Transmitted Infection ◽  
Sexually Transmitted ◽  
High Incidence ◽  
Ciprofloxacin Resistance ◽  
Sequence Types ◽  
Infection Clinic

Abstract With the aim to elucidate gonococcal antimicrobial resistance (AMR)–risk factors, we undertook a retrospective analysis of the molecular epidemiology and AMR of 104 Neisseria gonorrhoeae isolates from clinical samples (urethra, rectum, pharynx and cervix) of 94 individuals attending a sexually transmitted infection clinic in Madrid (Spain) from July to October 2016, and explored potential links with socio-demographic, behavioural and clinical factors of patients. Antimicrobial susceptibility was determined by E-tests, and isolates were characterised by N. gonorrhoeae multi-antigen sequence typing. Penicillin resistance was recorded for 15.4% of isolates, and most were susceptible to tetracycline, cefixime and azithromycin; a high incidence of ciprofloxacin resistance (~40%) was found. Isolates were grouped into 51 different sequence types (STs) and 10 genogroups (G), with G2400, ST5441, ST2318, ST12547 and G2992 being the most prevalent. A significant association (P = 0.015) was evident between HIV-positive MSM individuals and having a ciprofloxacin-resistant strain. Likewise, a strong association (P = 0.047) was found between patient age of MSM and carriage of isolates expressing decreased susceptibility to azithromycin. A decrease in the incidence of AMR gonococcal strains and a change in the strain populations previously reported from other parts of Spain were observed. Of note, the prevalent multi-drug resistant genogroup G1407 was represented by only three strains in our study, while the pan-susceptible clones such as ST5441, and ST2318, associated with extragenital body sites were the most prevalent.

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.

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