Population Structure of Clinical Pseudomonas aeruginosa from West and Central African Countries

Cholley, Pascal; Ka, R.; Guyeux, Christophe; Thouverez, Michelle; Guessennd, Nathalie; Ghebremedhin, Beniam; Frank, Thierry; Bertrand, Xavier; Hocquet, Didier

doi:10.1371/journal.pone.0107008

Cited by 26 publications

(22 citation statements)

References 46 publications

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“…So, the spread of these different STs among the community is independent from the antimicrobial resistance, but other features could be involved such as host adaptation (virulence, biofilm activity…). Among the diversities of STs found in this work, intercontinental clones were encountered: ST27, ST244, ST274, ST277, ST395, ST446, and ST560 [ 27 ]. ST244 that was detected in three strains from both regions is a global P. aeruginosa clone identified in several countries, among different origins (clinical, animal, and environmental), and associated with different antimicrobial resistance phenotypes (MDR or susceptible strains) and genotypes (carbapenemase-positive or negative) [ 27 – 30 ].…”

Section: Discussionmentioning

confidence: 99%

“…Among the diversities of STs found in this work, intercontinental clones were encountered: ST27, ST244, ST274, ST277, ST395, ST446, and ST560 [ 27 ]. ST244 that was detected in three strains from both regions is a global P. aeruginosa clone identified in several countries, among different origins (clinical, animal, and environmental), and associated with different antimicrobial resistance phenotypes (MDR or susceptible strains) and genotypes (carbapenemase-positive or negative) [ 27 – 30 ]. P. aeruginosa belonging to ST313 and ST274 have been already described as intestinal colonisers in healthy humans [ 8 ], although ST274 has been also previously described in carbapenem-susceptible P. aeruginosa isolates [ 3 , 8 ], associated with cystic fibrosis patients, and is considered as an epidemic clone circulating in Spain [ 29 , 31 , 32 ].…”

Section: Discussionmentioning

confidence: 99%

“…P. aeruginosa belonging to ST313 and ST274 have been already described as intestinal colonisers in healthy humans [ 8 ], although ST274 has been also previously described in carbapenem-susceptible P. aeruginosa isolates [ 3 , 8 ], associated with cystic fibrosis patients, and is considered as an epidemic clone circulating in Spain [ 29 , 31 , 32 ]. P. aeruginosa strains ascribed to ST27, ST252, ST253 (clonal complex PA14), ST395, and ST560 have been previously observed in clinical animal and environmental samples [ 14 , 27 , 31 , 33 , 34 ].…”

Section: Discussionmentioning

confidence: 99%

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Pseudomonas aeruginosa Isolates from Spanish Children: Occurrence in Faecal Samples, Antimicrobial Resistance, Virulence, and Molecular Typing

Ruiz-Roldán

Bellés

Bueno

et al. 2018

BioMed Research International

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Pseudomonas aeruginosa is a major opportunistic human pathogen, responsible for nosocomial infections and infections in patients with impaired immune systems. Little data exist about the faecal colonisation by P. aeruginosa isolates in healthy humans. The occurrence, antimicrobial resistance phenotype, virulence genotype, and genetic lineages of P. aeruginosa from faecal samples of children from two different Spanish regions were characterised. Seventy-two P. aeruginosa were isolated from 1,443 faecal samples. Low antimicrobial resistance levels were detected: ceftazidime (8%), cefepime (7%), aztreonam (7%), gentamicin (3%), ciprofloxacin (1%), and imipenem (1%); susceptibility to meropenem, amikacin, tobramycin, levofloxacin, and colistin. Four multidrug-resistant strains were found. Important differences were detected between both geographical regions. Forty-one sequence types were detected among the 48 tested strains. Virulence and quorum sensing genes were analysed and 13 virulotypes were detected, being 26 exoU-positive strains. Alteration in protein OprD showed eight different patterns. The unique imipenem-resistant strain showed a premature stop codon in OprD. Intestinal colonisation by P. aeruginosa, mainly by international clones (as ST244, ST253, and ST274), is an important factor for the systemic infections development and the environmental dissemination. Periodic active surveillance is useful to identify these community human reservoirs and to control the evolution of antibiotic resistance and virulence activity.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Pseudomonas aeruginosa Isolates from Spanish Children: Occurrence in Faecal Samples, Antimicrobial Resistance, Virulence, and Molecular Typing

Ruiz-Roldán

Bellés

Bueno

et al. 2018

BioMed Research International

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“…Despite the low genomic diversity between strains and the conservation of virulence genes, some strains called ‘high-risk clones’ are more prone to disseminate. This feature is certainly related, but could not be totally attributed, to their resistance to antibiotics [ 47 ]. The study of more ‘high-risk clones’ could identify particular genes responsible for their spread in clinical settings.…”

Section: Discussionmentioning

confidence: 99%

What It Takes to Be a Pseudomonas aeruginosa? The Core Genome of the Opportunistic Pathogen Updated

et al. 2015

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Pseudomonas aeruginosa is an opportunistic bacterial pathogen able to thrive in highly diverse ecological niches and to infect compromised patients. Its genome exhibits a mosaic structure composed of a core genome into which accessory genes are inserted en bloc at specific sites. The size and the content of the core genome are open for debate as their estimation depends on the set of genomes considered and the pipeline of gene detection and clustering. Here, we redefined the size and the content of the core genome of P. aeruginosa from fully re-analyzed genomes of 17 reference strains. After the optimization of gene detection and clustering parameters, the core genome was defined at 5,233 orthologs, which represented ~ 88% of the average genome. Extrapolation indicated that our panel was suitable to estimate the core genome that will remain constant even if new genomes are added. The core genome contained resistance determinants to the major antibiotic families as well as most metabolic, respiratory, and virulence genes. Although some virulence genes were accessory, they often related to conserved biological functions. Long-standing prophage elements were subjected to a genetic drift to eventually display a G+C content as higher as that of the core genome. This contrasts with the low G+C content of highly conserved ribosomal genes. The conservation of metabolic and respiratory genes could guarantee the ability of the species to thrive on a variety of carbon sources for energy in aerobiosis and anaerobiosis. Virtually all the strains, of environmental or clinical origin, have the complete toolkit to become resistant to the major antipseudomonal compounds and possess basic pathogenic mechanisms to infect humans. The knowledge of the genes shared by the majority of the P. aeruginosa isolates is a prerequisite for designing effective therapeutics to combat the wide variety of human infections.

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“…seudomonas aeruginosa has a nonclonal population structure with a few multidrug-resistant clusters, called "high-risk clones," that frequently produce acquired ␤-lactamases with an extended spectrum and are responsible for outbreaks in hospitals worldwide (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13). The quick implementation of infection control measures for relevant patients may tackle the spread of these epidemic clones, but current identification is long and complex since it is based on the analysis of nucleotidic sequences.…”

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Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry Identifies Pseudomonas aeruginosa High-Risk Clones

et al. 2015

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We show here that matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) accurately and quickly identified the five high-risk clones of Pseudomonas aeruginosa sequence type 111 (ST111), ST175, ST235, ST253, and ST395. The use of this screening technique by clinical microbiology laboratories may tackle the spread of high-risk clones by the quick implementation of hygiene control procedures for relevant patients. Pseudomonas aeruginosa has a nonclonal population structure with a few multidrug-resistant clusters, called "high-risk clones," that frequently produce acquired ␤-lactamases with an extended spectrum and are responsible for outbreaks in hospitals worldwide (1-13). The quick implementation of infection control measures for relevant patients may tackle the spread of these epidemic clones, but current identification is long and complex since it is based on the analysis of nucleotidic sequences. A quick and easy method for identifying high-risk clones of P. aeruginosa is then needed. Matrixassisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) was recently integrated into the routine workflow of medical microbiology laboratories for microbial identification and has been further used for subspecies characterization (14). Here, we evaluated the ability of MALDI-TOF MS to identify high-risk clones of P. aeruginosa.Identification of peak biomarkers for five major high-risk clones of P. aeruginosa. In order to identify five major high-risk clones of P. aeruginosa (sequence type 111 [ST111], ST175, ST235, ST253, and ST395), we first defined recognition models with a training set of 46 isolates with known STs distributed homogeneously in the phylogenetic tree (Table 1 and Fig. 1). Frozen bacteria were streaked onto Mueller-Hinton agar (Bio-Rad) and incubated for 18 h at 37°C. As previously reported (15), each isolate was extracted with the ethanol-formic acid method recommended by Bruker Daltonik and analyzed with a Microflex LT mass spectrometer (Bruker Daltonik), which generated 24 raw spectra. We analyzed the spectra with the software ClinProTools 3.0 (Bruker Daltonik), which defined six models based on peak biomarkers (Table 1). The reliability and accuracy of each model were assessed through the recognition capabilities and the crossvalidation values. The models identified all the tested high-risk clones of P. aeruginosa with high recognition capabilities (Ͼ96%) and cross-validation values ranging from 72.5% to 100% (Table 1). Four models directly identified ST111, ST175, ST253, and ST395, while the identification of ST235 required a preliminary stage to identify cluster 1, which encompasses ST235 (Fig. 1).We then manually examined the spectra with ClinProTools 3.0 to assess the relevance of the peak biomarkers of each model (Table 1). Peaks were defined as biomarkers in a model because of their presence or absence or relative abundance between two tested classes. Figure 2 details only the peak biomarkers in which presence or absence was specif...

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Population Structure of Clinical Pseudomonas aeruginosa from West and Central African Countries

Cited by 26 publications

References 46 publications

Pseudomonas aeruginosa Isolates from Spanish Children: Occurrence in Faecal Samples, Antimicrobial Resistance, Virulence, and Molecular Typing

Pseudomonas aeruginosa Isolates from Spanish Children: Occurrence in Faecal Samples, Antimicrobial Resistance, Virulence, and Molecular Typing

What It Takes to Be a Pseudomonas aeruginosa? The Core Genome of the Opportunistic Pathogen Updated

Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry Identifies Pseudomonas aeruginosa High-Risk Clones

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