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1.
Artigo em Inglês | MEDLINE | ID: mdl-33199384

RESUMO

Fosfomycin is a decades-old antibiotic, currently reused because of its activity against multidrug-resistant bacteria. Here, we used a combined in vitro/in silico approach to search for fosfomycin resistance determinants in 25 new bacterial species isolated from the human microbiota. Putative resistance genes were cloned into a susceptible Escherichia coli strain. MIC values increased from 1 µg/ml to 1,024 µg/ml. Here, we report a new family of potential chromosomal fosfomycin resistance genes, named fosM.


Assuntos
Fosfomicina , Microbiota , Antibacterianos/farmacologia , Bactérias , Farmacorresistência Bacteriana/genética , Fosfomicina/farmacologia , Humanos , Testes de Sensibilidade Microbiana
2.
Antimicrob Agents Chemother ; 65(9): e0255720, 2021 08 17.
Artigo em Inglês | MEDLINE | ID: mdl-34152818

RESUMO

Antibiotic resistance genes exist naturally in various environments far from human usage. Here, we investigated multidrug-resistant Klebsiella pneumoniae, a common pathogen of chimpanzees and humans. We screened antibiotic-resistant K. pneumoniae from 48 chimpanzee stools and 38 termite mounds (n = 415 samples) collected in protected areas in Senegal. The microsatellite method was used to identify chimpanzee individuals (n = 13). Whole-genome sequencing was performed on K. pneumoniae complex isolates to identify antibiotic-resistant genes and characterize clones. We found a high prevalence of carbapenem-resistant K. pneumoniae among chimpanzee isolates (18/48 samples from 7/13 individuals) and ceftriaxone resistance among both chimpanzee individuals (19/48) and termite mounds (7/415 termites and 3/38 termite mounds). The blaOXA-48 and the blaKPC-2 genes were carried by international pOXA-48 and pKPC-2 plasmids, respectively. The ESBL plasmid carried blaCTX-M-15, blaTEM-1B, and blaOXA-1 genes. Genome sequencing of 56 isolates identified two major clones associated with hospital-acquired infections of K. pneumoniae (ST307 and ST147) in chimpanzees and termites, suggesting circulation of strains between the two species, as chimpanzees feed on termites. The source and selection pressure of these clones in this environment need to be explored.


Assuntos
Isópteros , Infecções por Klebsiella , Animais , Antibacterianos/farmacologia , Antibacterianos/uso terapêutico , Proteínas de Bactérias/genética , Células Clonais , Humanos , Infecções por Klebsiella/tratamento farmacológico , Klebsiella pneumoniae/genética , Testes de Sensibilidade Microbiana , Pan troglodytes , Plasmídeos , Senegal , beta-Lactamases/genética
3.
J Antimicrob Chemother ; 76(7): 1655-1657, 2021 06 18.
Artigo em Inglês | MEDLINE | ID: mdl-33893490

RESUMO

There is a discrepancy between antibiotic use in medicine and agriculture in the intertropical zone and frequency of antibiotic resistance in clinical bacteria in these countries. We provide evidence that glyphosate (a herbicide but also an antibiotic drug) could be a possible driver of antibiotic resistance in countries where this herbicide is widely used because of modification of the microbial environment. Emergence of resistance in bacteria and fungi is correlated with glyphosate use in the world over the last 40 years.


Assuntos
Antibacterianos , Farmacorresistência Bacteriana , Antibacterianos/farmacologia , Bactérias , Glicina/análogos & derivados , Glicina/farmacologia , Glifosato
4.
Eur J Clin Microbiol Infect Dis ; 40(11): 2403-2406, 2021 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-33830365

RESUMO

A 26-year-old girl with a longstanding colonization by Pandoraea nosoerga underwent liver-lung transplantation for cystic fibrosis (CF) in 2018. Her brother also suffering from CF was also colonized by P. nosoerga. Despite appropriate perioperative antibiotic therapy, she had post-transplant bacteremic pneumonia caused by extensively drug-resistant P. nosoerga. Drug repurposing was used to optimize treatment options. The cause of post-transplant contamination was studied by comparative whole-genome sequencing including pre- and post-transplant strains and her brother's strains. Post-transplant contamination appeared to be due to her own pre-transplant strain, emphasizing the urgent need to study and implement effective decontamination protocols before transplantation.


Assuntos
Fibrose Cística/cirurgia , Infecções por Bactérias Gram-Negativas/microbiologia , Transplante de Fígado/efeitos adversos , Transplante de Pulmão/efeitos adversos , Complicações Pós-Operatórias/microbiologia , Adulto , Antibacterianos/uso terapêutico , Burkholderiaceae/genética , Burkholderiaceae/isolamento & purificação , Burkholderiaceae/fisiologia , Evolução Fatal , Feminino , Infecções por Bactérias Gram-Negativas/tratamento farmacológico , Infecções por Bactérias Gram-Negativas/mortalidade , Humanos , Fígado/cirurgia , Pulmão/microbiologia , Pulmão/cirurgia , Complicações Pós-Operatórias/tratamento farmacológico , Complicações Pós-Operatórias/mortalidade
5.
Eur J Clin Microbiol Infect Dis ; 40(7): 1547-1551, 2021 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-33515096

RESUMO

Candida auris is an emerging multiresistant pathogen causing nosocomial fungal infection. Specific detection and identification are necessary. Our goal is to develop a new qPCR system that enables rapid detection of C. auris, based on a GPI (glycosyl-phosphatidylinositol) protein-encoding gene. This system is reproducible and sensitive with a limit of detection of 13 C. auris CFU/qPCR reaction. The 100% specificity of this system is confirmed on 2073 clinical and environmental samples, 50 different bacterial species, and 9 Candida spp. (70 strains). This system is suitable to correctly identify C. auris infections and to trace its source.


Assuntos
Candida/isolamento & purificação , Reação em Cadeia da Polimerase em Tempo Real/métodos , Microbiologia Ambiental , Reprodutibilidade dos Testes , Sensibilidade e Especificidade , Especificidade da Espécie
6.
Eur J Clin Microbiol Infect Dis ; 40(5): 1073-1077, 2021 May.
Artigo em Inglês | MEDLINE | ID: mdl-33184752

RESUMO

We described three clinical cases of pyogenic liver abscess caused by hypervirulent Klebsiella pneumoniae (hvKp) successfully treated by prolonged antibiotherapy, in which one case was complicated by endophthalmitis. Whole genome sequencing helped to confirm the diagnosis of these hvKp strains, which belong to clonal complexes CC86 and CC23 and carried hvKp-associated genes (magA and/or rmpA). This syndrome is increasingly reported in France and Europe and raises questions about the source of infection.


Assuntos
Infecções por Klebsiella/microbiologia , Klebsiella pneumoniae/genética , Klebsiella pneumoniae/patogenicidade , Abscesso Hepático/microbiologia , Sequenciamento Completo do Genoma , Adulto , Idoso , França/epidemiologia , Genoma Bacteriano , Humanos , Infecções por Klebsiella/epidemiologia , Masculino , Pessoa de Meia-Idade , Virulência
7.
Eur J Clin Microbiol Infect Dis ; 40(6): 1199-1207, 2021 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-33411174

RESUMO

The objective of this study is to determine the acquisition of multidrug-resistant (MDR) bacteria and antibiotic resistance-encoding genes by French Hajj pilgrims and associated risk factors. Pilgrims traveling during the 2017 and 2018 Hajj were recruited. All pilgrims underwent two successive systematic nasopharyngeal and rectal swabs, pre- and post-Hajj. Specific culture media were used to screen for MDR bacteria, including methicillin-resistant Staphylococcus aureus (MRSA), carbapenem-resistant bacteria, and extended spectrum beta-lactamase producing Enterobacteriaceae (ESBL-E). qPCR was used to identify antibiotic resistance-encoding genes from cultured isolates. Direct screening of genes encoding for colistin resistance (mcr-1, 2, 3, 4, 5, and 8) from nasopharyngeal and rectal swabs was performed using qPCR, and positive qPCR results were simultaneously tested by sequencing. There were 268 pilgrims included. The percentage of pilgrims acquiring MDR bacteria during the Hajj was 19.4%. A total of 81 strains were isolated (1 carbapenem-resistant Acinetobacter baumannii, 12 MRSA, and 68 ESBL-E). ESBL-E strains were found in rectal samples of 6.0% pilgrims pre-Hajj and of 16.4% pilgrims post-Hajj. Only 0.4% pilgrims were positive for CARB post-Hajj and 1.9% carried nasal MRSA pre- and post-Hajj. In addition, 23 (8.6%) post-Hajj rectal swabs were positive for mcr genes (19 mcr-1 gene and 4 mcr-4 gene). No significant association was found between co-factors and acquisition of MDR bacteria or mcr genes. MDR bacteria and genes are acquired by pilgrims during the Hajj mass gathering. Rationalization of antibiotic consumption and implementation of measures to prevent transmission of bacteria among pilgrims during the event are of paramount importance.


Assuntos
Antibacterianos/farmacologia , Bactérias/efeitos dos fármacos , Bactérias/isolamento & purificação , Proteínas de Bactérias/genética , Farmacorresistência Bacteriana Múltipla , Nasofaringe/microbiologia , Reto/microbiologia , Adulto , Idoso , Idoso de 80 Anos ou mais , Bactérias/classificação , Bactérias/genética , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Religião , Arábia Saudita , Viagem/estatística & dados numéricos , Adulto Jovem
8.
Euro Surveill ; 26(21)2021 05.
Artigo em Inglês | MEDLINE | ID: mdl-34047270

RESUMO

BackgroundFrance is a low prevalence country for colistin resistance. Molecular and epidemiological events contributing to the emergence of resistance to colistin, one of the 'last-resort' antibiotics to treat multidrug-resistant Gram-negative infections, are important to investigate.AimThis retrospective (2014 to 2017) observational study aimed to identify risk factors associated with acquisition of colistin-resistant Klebsiella pneumoniae (CRKP) in hospitals in Marseille, France, and to molecularly characterise clinical isolates.MethodsTo identify risk factors for CRKP, a matched-case-control (1:2) study was performed in two groups of patients with CRKP or colistin-susceptible K. pneumoniae respectively. Whole-genome-sequences (WGS) of CRKP were compared with 6,412 K. pneumoniae genomes available at the National Center for Biotechnology Information (NCBI).ResultsMultivariate analysis identified male sex and contact with a patient carrying a CRKP as significant independent factors (p < 0.05) for CRKP acquisition, but not colistin administration. WGS of nine of 14 CRKP clinical isolates belonged to the same sequence type (ST)307. These isolates were from patients who had been hospitalised in the same wards, suggesting an outbreak. Comparison of the corresponding strains' WGS to K. pneumoniae genomes in NCBI revealed that in chromosomal genes likely playing a role in colistin resistance, a subset of five specific mutations were significantly associated with ST307 (p < 0.001).ConclusionA ST307 CRKP clone was identified in this study, with specific chromosomal mutations in genes potentially implicated in colistin resistance. ST307 might have a propensity to be or become resistant to colistin, however confirming this requires further investigations.


Assuntos
Colistina , Infecção Hospitalar/microbiologia , Farmacorresistência Bacteriana , Infecções por Klebsiella , Antibacterianos/farmacologia , Proteínas de Bactérias , Células Clonais , Colistina/farmacologia , Infecção Hospitalar/epidemiologia , Epidemias , França/epidemiologia , Hospitais , Humanos , Infecções por Klebsiella/tratamento farmacológico , Infecções por Klebsiella/epidemiologia , Klebsiella pneumoniae/genética , Masculino , Testes de Sensibilidade Microbiana , Estudos Retrospectivos , Fatores de Risco
9.
Emerg Infect Dis ; 26(7): 1605-1607, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32568042

RESUMO

A woman in France was diagnosed with pulmonary tuberculosis caused by Mycobacterium bovis after a ritual sheep sacrifice in her home country of Tunisia. This investigation sheds light on ritual sacrifice of sheep as a circumstance in which religious tradition and practices can expose millions of Muslims worldwide to this disease.


Assuntos
Mycobacterium bovis , Mycobacterium tuberculosis , Tuberculose Pulmonar , Animais , Comportamento Ritualístico , Feminino , França , Humanos , Mycobacterium bovis/genética , Ovinos , Tuberculose Pulmonar/diagnóstico , Tuberculose Pulmonar/epidemiologia , Tunísia/epidemiologia
10.
J Antimicrob Chemother ; 75(6): 1410-1414, 2020 06 01.
Artigo em Inglês | MEDLINE | ID: mdl-32101613

RESUMO

OBJECTIVES: The antiviral zidovudine has been recently identified as an active drug against resistant Enterobacteriaceae, but prevalence of resistance to this compound remains unknown. The aim was to estimate the prevalence of clinical Escherichia coli isolates resistant to zidovudine and to decipher the mechanism of zidovudine resistance. METHODS: We screened 537 isolates on zidovudine-containing agar plates and studied their thymidine kinase (tdk) gene sequences, the putative target involved in zidovudine resistance. Moreover, sequence analysis of 633 complete genomes of E. coli was performed to investigate mutation in the tdk gene. A comparative genomic analysis was done on an in vitro zidovudine-resistant mutant. RESULTS: After screening on our medium containing 2.7 mg/L (10 µM) zidovudine, nine strains had a zidovudine MIC >26.7 mg/L. The gene was absent in three isolates, inactivated by an IS (IS1X2 and ISApl1) in two isolates and mutated in four isolates. A genomic analysis of 633 E. coli genomes showed heterogeneity of the tdk gene sequence, with 27 different sequences. Among them, three genomes showed an inactivation of the gene (IS, stop codon and no tdk gene sequence). The in vitro mutant E. coli had 27 SNPs in eight genes of the core genome compared with the initial strain. CONCLUSIONS: Our study reports zidovudine-resistant clinical isolates of E. coli, presumably related to tdk inactivation. Diversity of Tdk in bacterial genomes can be large. Other mechanisms need to be considered in zidovudine resistance. The use of zidovudine in antibiotic-resistant infections needs to be in combination and should be tested before clinical administration.


Assuntos
Infecções por Escherichia coli , Proteínas de Escherichia coli , Antibacterianos/farmacologia , Farmacorresistência Bacteriana/genética , Escherichia coli/genética , Genômica , Humanos , Testes de Sensibilidade Microbiana , Timidina Quinase/genética , Zidovudina/farmacologia
11.
Eur J Clin Microbiol Infect Dis ; 39(8): 1573-1580, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32358740

RESUMO

Infectious meningitis is a medical urgency and rapid detection of the causative pathogen into the cerebrospinal fluid (CSF) is mandatory to guide the management of patients. We compared the performances of the multiplexed PCR FilmArray® ME panel with standard microbiological analyses, for rapid diagnosis of infectious meningitis. All the CSF samples received in our routine laboratory for the diagnosis of infectious meningitis were prospectively analyzed by the FilmArray® ME panel for the detection of fourteen targets in parallel to standard routine real-time PCR assays and bacterial culture. We reviewed clinical and biological records of patients for whom a discrepant result was obtained to achieve a definite diagnosis. Among 1124 CSF samples tested over a 43-week period, 113 (10.1%) and 87 (7.74%) were positive using the FilmArray® ME panel and the standard techniques, respectively. Among 40 CSF samples which yielded discrepant results, 34 were positive only using the FilmArray® ME panel and 6 were positive only using standard techniques. A total of 16/34 (47.1%) FilmArray® ME panel-positive CSF, and 6/6 (100%) of standard technique-positive CSF were interpreted as true positive. We were able to estimate the sensitivity, the specificity, the positive predictive value, and the negative predictive value of the FilmArray® ME panel at 94.2%, 98.2%, 84.3%, and 99.4%, respectively. The FilmArray® ME panel is an efficient tool for the rapid diagnosis of infectious meningitis at the point-of-care. Its higher sensitivity compared with that of standard molecular biology and culture techniques yields an increase of true positive diagnosis.


Assuntos
Meningite/diagnóstico , Reação em Cadeia da Polimerase Multiplex/instrumentação , Adulto , Criança , Estudos de Coortes , Enterovirus/genética , Enterovirus/isolamento & purificação , Feminino , Humanos , Masculino , Meningite/líquido cefalorraquidiano , Meningite/microbiologia , Meningite/virologia , Testes Imediatos , Estudos Prospectivos , Sensibilidade e Especificidade
12.
BMC Microbiol ; 19(1): 60, 2019 03 18.
Artigo em Inglês | MEDLINE | ID: mdl-30885126

RESUMO

BACKGROUND: The recent description of the first plasmid-mediated colistin-resistant gene mcr-1, conferring transferable and low-level resistance to colistin, raised concern about the need to implement a rapid and reliable screening method to detect colistin-resistant clinical isolates. The only valid method to assess the MIC of colistin is the broth microdilution according to the joint CLSI-EUCAST Polymyxin Breakpoints Working Group. UMIC Colistine is a ready-to-use broth microdilution kit developed to easily assess colistin MIC by proposing unitary polystyrene strips containing 11 concentrations of dehydrated colistin. Here, we evaluated the UMIC Colistine kit on 235 Gram-negative rods (176 Enterobacterales, including 70 harboring a mcr gene, and 59 non-fermentative), through comparison to the reference broth microdilution method prepared in accordance with EN ISO 20776-1:2006 standard. Reproducibility of the UMIC Colistine was assayed with the three recommended quality control strains E. coli ATCC 25922, E. coli NCTC 13846 (mcr-1 positive), and P. aeruginosa ATCC 27853, as for stability testing. RESULTS: Categorical agreement was 100% with 63.4% (n = 149) of colistin-resistant strains, and 36.6% (n = 86) of colistin-susceptible strains with both methods (S ≤ 2 µg/mL and R > 2 µg/mL). No major error or very major error was reported. Essential agreement was 94.0% (n = 221), and 100% for detection of colistin-resistant strains as compared to the reference method. Pearson's correlation between UMIC Colistine and the reference method was 0.98. Reproducibility of the UMIC Colistine system was 97.8% with MICs of the quality control strains within the target ranges. However, some isolates had lower MIC with UMIC Colistine, but that did not change their categorization as colistin-susceptible, and this phenomenon should be further explored. CONCLUSIONS: The UMIC Colistine kit is an easy to perform unitary device that showed excellent results when compared to the reference method. The UMIC Colistine system is a rapid and reliable broth microdilution method that is suitable to assess the colistin MIC of clinical isolates in clinical microbiology laboratories.


Assuntos
Antibacterianos/farmacologia , Colistina/farmacologia , Farmacorresistência Bacteriana , Bactérias Gram-Negativas/efeitos dos fármacos , Kit de Reagentes para Diagnóstico , Animais , Genes Bacterianos , Humanos , Testes de Sensibilidade Microbiana , Reprodutibilidade dos Testes
13.
Eur J Clin Microbiol Infect Dis ; 38(2): 395-407, 2019 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-30515637

RESUMO

Since effective empirical antibiotic therapy is a key factor for survival, local antibiotic resistance epidemiology is critical. We aimed to identify current trends in antibiotic resistance for key antibiotics obtained over 16 years (2001-2016) for invasive infections corresponding to empirical treatment in a large hospital centre in Marseille, France.From January 2014 to December 2016, we have collected all data on antibiotic susceptibility from public laboratory hospitals, and a retrospective analysis was performed on key antibiotics in blood cultures since 2001. A total of 99,932 antibiotic susceptibility testings (ASTs) were analysed, and proportion of pan-drug resistant (PDR = resistant to all antibiotics tested) and extensively drug-resistant (XDR = resistant to all except for two classes) strains were < 0.03 and 0.5%, respectively. Between 2001 and 2016, we found an increase of resistance to third-generation cephalosporins for E. coli invasive strains (0% vs 17.8%; p < 10-5) and K. pneumoniae (8% vs 35.4%; p = 0.001) along with a decrease of methicillin-resistant S. aureus strains (31% vs 19.8%; p = 0.006). Moreover, during the 3-year period, a significant increase of wild-type strains, susceptible to all antibiotics tested, was observed in invasive infections. Regarding bacteraemia involving Enterobacteriaceae and S. aureus, empirical therapy is effective in > 99% cases. Active epidemiological surveillance is necessary because antibiotic resistance remains unpredictable.


Assuntos
Antibacterianos/farmacologia , Doenças Transmissíveis/microbiologia , Farmacorresistência Bacteriana , Testes de Sensibilidade Microbiana/estatística & dados numéricos , Bacteriemia/microbiologia , Bactérias/efeitos dos fármacos , Bactérias/isolamento & purificação , Farmacorresistência Bacteriana/efeitos dos fármacos , França/epidemiologia , Hospitais , Estudos Retrospectivos
14.
Emerg Infect Dis ; 24(9): 1683-1690, 2018 09.
Artigo em Inglês | MEDLINE | ID: mdl-30124405

RESUMO

Culturomics has permitted discovery of hundreds of new bacterial species isolated from the human microbiome. Profiles generated by using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry have been added to the mass spectrometer database used in clinical microbiology laboratories. We retrospectively collected raw data from MALDI-TOF mass spectrometry used routinely in our laboratory in Marseille, France, during January 2012-March 2018 and analyzed 16S rDNA sequencing results from misidentified strains. During the study period, 744 species were identified from clinical specimens, of which 21 were species first isolated from culturomics. This collection involved 105 clinical specimens, accounting for 98 patients. In 64 cases, isolation of the bacteria was considered clinically relevant. MALDI-TOF mass spectrometry was able to identify the species in 95.2% of the 105 specimens. While contributing to the extension of the bacterial repertoire associated with humans, culturomics studies also enlarge the spectrum of prokaryotes involved in infectious diseases.


Assuntos
Bactérias/isolamento & purificação , Infecções por Bactérias Gram-Negativas/epidemiologia , Infecções por Bactérias Gram-Positivas/epidemiologia , Bactérias/classificação , Bactérias/genética , Técnicas de Tipagem Bacteriana , Controle de Doenças Transmissíveis , DNA Bacteriano , França/epidemiologia , Infecções por Bactérias Gram-Negativas/microbiologia , Infecções por Bactérias Gram-Negativas/prevenção & controle , Infecções por Bactérias Gram-Positivas/microbiologia , Infecções por Bactérias Gram-Positivas/prevenção & controle , Humanos , Sensibilidade e Especificidade , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz
15.
J Antimicrob Chemother ; 73(7): 1862-1871, 2018 07 01.
Artigo em Inglês | MEDLINE | ID: mdl-29718423

RESUMO

Objectives: Efflux in bacteria is a ubiquitous mechanism associated with resistance to antimicrobials agents. Efflux pump inhibitors (EPIs) have been developed to inhibit efflux mechanisms and could be a good alternative to reverse colistin resistance, but only CCCP has shown good activity. The aim of our study was to identify CCCP activity in a collection of 93 Gram-negative bacteria with known and unknown colistin resistance mechanisms including isolates with mcr-1 plasmid-mediated colistin resistance. Methods: Colistin MIC was evaluated with and without CCCP and the fold decrease of colistin MIC was calculated for each strain. In order to evaluate the effect of this combination, a time-kill study was performed on five strains carrying different colistin resistance mechanisms. Results: Overall, CCCP was able to reverse colistin resistance for all strains tested. The effect of CCCP was significantly greater on intrinsically colistin-resistant bacteria (i.e. Proteus spp., Serratia marcescens, Morganella morganii and Providencia spp.) than on other Enterobacteriaceae (P < 0.0001). The same was true for bacteria with a heteroresistance mechanism compared to bacteria with other colistin resistance mechanisms (P < 0.0001). A time-kill study showed the combination was bacteriostatic on strains tested. Conclusions: These results suggest an efflux mechanism, especially on intrinsically resistant bacteria and Enterobacter spp., but further analysis is needed to identify the molecular support of this mechanism. EPIs could be an alternative for restoring colistin activity in Gram-negative bacteria. Further work is necessary to identify new EPIs that could be used in humans.


Assuntos
Proteínas de Bactérias/genética , Carbonil Cianeto m-Clorofenil Hidrazona/farmacologia , Colistina/farmacologia , Farmacorresistência Bacteriana Múltipla , Bactérias Gram-Negativas/efeitos dos fármacos , Antibacterianos/farmacologia , Enterobacteriaceae/efeitos dos fármacos , Infecções por Enterobacteriaceae/microbiologia , Escherichia coli/efeitos dos fármacos , Proteínas de Escherichia coli/genética , Infecções por Bactérias Gram-Negativas/microbiologia , Humanos , Testes de Sensibilidade Microbiana , Plasmídeos/genética , Ionóforos de Próton/farmacologia
16.
BMC Microbiol ; 18(1): 88, 2018 08 20.
Artigo em Inglês | MEDLINE | ID: mdl-30126365

RESUMO

BACKGROUND: Chronic Lung Allograft Dysfunction (CLAD) is the main cause of morbidity and mortality after the first year following lung transplantation (LTx). Risk factors of CLAD have been extensively studied, but the association between gram-negative bacteria (GNB) bronchial colonization and the development of CLAD is controversial. The purpose of our study was to investigate the association between post-transplant recolonization with the same species or de-novo colonization with a new GNB species and CLAD. The same analysis was performed on a sub-group of patients at the strain level using Matrix Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry technique. RESULTS: Forty adult cystic fibrosis (CF) patients who underwent a first bilateral LTx in the University Hospital of Marseille, between January 2010 and December 2014, were included in the study. Patients with GNB de-novo colonization had a higher risk of developing CLAD (OR = 6.72, p = 0.04) and a lower rate of CLAD-free survival (p = 0.005) compared to patients with GNB recolonization. No conclusion could be drawn from the subgroup MALDI-TOF MS analysis at the strain level. CONCLUSION: Post-LTx GNB airway recolonization seems to be a protective factor against CLAD, whereas de-novo colonization with a new species of GNB seems to be a risk factor for CLAD.


Assuntos
Aloenxertos/microbiologia , Fibrose Cística/etiologia , Fibrose Cística/microbiologia , Bactérias Gram-Negativas/patogenicidade , Infecções por Bactérias Gram-Negativas/microbiologia , Transplante de Pulmão/efeitos adversos , Sistema Respiratório/microbiologia , Adolescente , Adulto , Anti-Infecciosos/uso terapêutico , Fibrose Cística/epidemiologia , Feminino , França , Bactérias Gram-Negativas/isolamento & purificação , Infecções por Bactérias Gram-Negativas/epidemiologia , Humanos , Imunossupressores/uso terapêutico , Masculino , Pessoa de Meia-Idade , Pneumonia , Disfunção Primária do Enxerto/etiologia , Disfunção Primária do Enxerto/microbiologia , Testes de Função Respiratória , Estudos Retrospectivos , Fatores de Risco , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz/métodos , Adulto Jovem
17.
Artigo em Inglês | MEDLINE | ID: mdl-28416544

RESUMO

Here, we report the description of a colistin-heteroresistant Klebsiella pneumoniae isolate fortuitously isolated from the stool sample of a patient with suspicion of tuberculosis in a public hospital of Marseille, France. In the colistin-resistant subpopulation, a mutation in the mgrB gene leading to a premature stop codon was found, and the hypermucoviscous phenotype was lost. Susceptibility to other antibiotics remained unchanged. To our knowledge, this is the first identification of such a colistin-heteroresistant Klebsiella pneumoniae isolate in France.


Assuntos
Antibacterianos/farmacologia , Colistina/farmacologia , Klebsiella pneumoniae/efeitos dos fármacos , Proteínas de Bactérias/genética , Farmacorresistência Bacteriana/genética , França , Testes de Sensibilidade Microbiana
18.
Antonie Van Leeuwenhoek ; 110(9): 1121-1132, 2017 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-28509971

RESUMO

Using a polyphasic taxonomic strategy, an aerobic, Gram-negative, non-motile, yellow pigmented rod isolated from a sputum sample of a patient with pneumonia was characterised. This bacterial strain, designated G972T, could not be identified by our systematic MALDI-TOF screening on a MicroFlex. This led to the sequencing of the 16S rRNA gene, which shows 98.57% sequence identity with that of Chryseobacterium indologenes 16777T, the phylogenetic closely related type strain of a species with standing in nomenclature, which putatively classifies it as a new species. The major cell fatty acids were identified as 13-methyl-tetradecanoic acid (61%), 3-hydroxy-heptadecanoic acid (16%) and 15-methyl-11-hexadecenoic acid (11%). D-glucose, D-mannose, aesculin, D-maltose, D-trehalose, and gentibiose are the main carbon source. Digital DNA-DNA hybridization (dDDH) estimation and average nucleotide identity values (ANI) of the strain G972T against genomes of the type strains of related species ranged between 18.9 and 32.8% and between 71.46 and 83.61%, respectively, thus confirming again the new species status of the strain. Here, we describe the characteristics of this organism, complete genome sequence and annotation. The 5,390,132 bp size genome contains 4867 protein-coding genes, 89 RNAs (three genes are 5S rRNA, one gene is 16S rRNA, one gene is 23S rRNA and 84 tRNAs) with 35.51% GC content. Finally, on the basis of these polyphasic data, consisting of phenotypic and genomic analyses, we conclude that strain strain G972T (= DSM 103388T = CSUR P2233T) represents a novel species for which we propose the name Chryseobacterium timonianum. The 16S rRNA and genome sequences are available in GenBank database under accession numbers LT161886 and FJVD00000000.


Assuntos
Chryseobacterium/classificação , Chryseobacterium/genética , Filogenia , Pneumonia/microbiologia , Aminoácidos/metabolismo , Composição de Bases , Chryseobacterium/química , Ácidos Graxos/química , Tamanho do Genoma , Genoma Bacteriano , Humanos , Fenótipo , RNA Ribossômico 16S/genética , Especificidade da Espécie , Escarro/microbiologia , Açúcares/metabolismo
19.
Genome Med ; 16(1): 86, 2024 Jul 09.
Artigo em Inglês | MEDLINE | ID: mdl-38982539

RESUMO

BACKGROUND: The Mycobacterium avium complex (MAC) comprises the most frequent non-tuberculous mycobacteria (NTM) in Central Europe and currently includes twelve species. M. avium (MAV), M. intracellulare subsp. intracellulare (MINT), and M. intracellulare subsp. chimaera (MCH) are clinically most relevant. However, the population structure and genomic landscape of MAC linked with potential pathobiological differences remain little investigated. METHODS: Whole genome sequencing (WGS) was performed on a multi-national set of MAC isolates from Germany, France, and Switzerland. Phylogenetic analysis was conducted, as well as plasmids, resistance, and virulence genes predicted from WGS data. Data was set into a global context with publicly available sequences. Finally, detailed clinical characteristics were associated with genomic data in a subset of the cohort. RESULTS: Overall, 610 isolates from 465 patients were included. The majority could be assigned to MAV (n = 386), MCH (n = 111), and MINT (n = 77). We demonstrate clustering with less than 12 SNPs distance of isolates obtained from different patients in all major MAC species and the identification of trans-European or even trans-continental clusters when set into relation with 1307 public sequences. However, none of our MCH isolates clustered closely with the heater-cooler unit outbreak strain Zuerich-1. Known plasmids were detected in MAV (325/1076, 30.2%), MINT (62/327, 19.0%), and almost all MCH-isolates (457/463, 98.7%). Predicted resistance to aminoglycosides or macrolides was rare. Overall, there was no direct link between phylogenomic grouping and clinical manifestations, but MCH and MINT were rarely found in patients with extra-pulmonary disease (OR 0.12 95% CI 0.04-0.28, p < 0.001 and OR 0.11 95% CI 0.02-0.4, p = 0.004, respectively) and MCH was negatively associated with fulfillment of the ATS criteria when isolated from respiratory samples (OR 0.28 95% CI 0.09-0.7, p = 0.011). With 14 out of 43 patients with available serial isolates, co-infections or co-colonizations with different strains or even species of the MAC were frequent (32.6%). CONCLUSIONS: This study demonstrates clustering and the presence of plasmids in a large proportion of MAC isolates in Europe and in a global context. Future studies need to urgently define potential ways of transmission of MAC isolates and the potential involvement of plasmids in virulence.


Assuntos
Genoma Bacteriano , Genômica , Complexo Mycobacterium avium , Infecção por Mycobacterium avium-intracellulare , Filogenia , Complexo Mycobacterium avium/genética , Complexo Mycobacterium avium/isolamento & purificação , Humanos , Infecção por Mycobacterium avium-intracellulare/microbiologia , Infecção por Mycobacterium avium-intracellulare/epidemiologia , Europa (Continente) , Masculino , Feminino , Genômica/métodos , Sequenciamento Completo do Genoma , Idoso , Pessoa de Meia-Idade , Plasmídeos/genética , Polimorfismo de Nucleotídeo Único , Farmacorresistência Bacteriana/genética , Adulto , Virulência/genética
20.
J Med Internet Res ; 15(4): e68, 2013 Apr 16.
Artigo em Inglês | MEDLINE | ID: mdl-23591700

RESUMO

BACKGROUND: There is no functional pharmacovigilance system in Cambodia to our knowledge. Mobile phone-based tools, such as short message service (SMS) text messages, are increasingly used for surveillance purposes. OBJECTIVE: To pilot-test the FrontlineSMS mobile phone-based tool for notification of adverse events, using Cambodia's only International Vaccination Center at the Institut Pasteur du Cambodge as a field site. METHODS: People receiving vaccinations, aged over 18 years, and who owned a cell phone were recruited in the study following informed consent. The names and mobile phone numbers of the participants interviewed were entered each day into the FrontlineSMS software. Two days after being vaccinated, participants received an automatically generated SMS text message asking whether any adverse events had occurred. Their SMS reply was number-coded and exported from the software daily to an Excel spreadsheet and examined before being saved. If the participant replied with a code for a severe adverse event (8 or 9), they were automatically advised to consult the nearest doctor. RESULTS: The active surveillance study was conducted over 72 days in the spring of 2012. Patients agreed to be asked by SMS text message whether unwanted events had occurred after vaccination. Of 1331 persons aged over 18 years referred to the vaccination unit, 184 (13.8%) were asked and agreed to participate. When texted for clinical status 48 hours after vaccination, 52 (28.3%) participants did not reply, 101 (54.9%) sent an immediate SMS reply, and 31 (16.8%) sent an SMS reply after additional prompting. Of the initial 184 participants, 132 (71.7%) replied. These 132 participants received 135 vaccine doses and 109 (82.6%) reported no adverse events, whereas 23 (17.4%) reported adverse events, all benign. CONCLUSIONS: Notification using an SMS-based text message system is already used in Cambodia for syndromic surveillance in health centers and reporting by health care workers. Our results show that such tools can also be useful for notification by patients or health users in Cambodia, especially in an urban setting.


Assuntos
Farmacovigilância , Envio de Mensagens de Texto , Adolescente , Adulto , Sistemas de Notificação de Reações Adversas a Medicamentos , Idoso , Idoso de 80 Anos ou mais , Camboja , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Projetos Piloto , Software , Telemedicina/métodos , Vacinação/efeitos adversos , Adulto Jovem
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