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1.
Int J Syst Evol Microbiol ; 70(2): 1315-1320, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31860429

RESUMO

The taxonomic status of all Pseudocitrobacter species was re-evaluated by comparative genomics based on whole genome sequencing. As a result, it is obvious that Pseudocitrobacter anthropi is a later heterotypic synonym of Pseudocitrobacter faecalis. In addition, genome-based analysis of strain CPO20170097T, isolated from a patient in northern Denmark was allocated to the genus Pseudocitrobacter. This strain showed significant genotypic and phenotypic differences from P. faecalis and it is proposed that this strain represents a novel species of the genus, for which the name Pseudocitrobacter vendiensis sp. nov. is proposed with the type strain CPO20170097T (=CCUG 73096T=LMG 31042T).


Assuntos
Enterobacteriaceae/classificação , Filogenia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Dinamarca , Ácidos Graxos/química , Genômica , Humanos , Hibridização de Ácido Nucleico , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Sequenciamento Completo do Genoma
2.
Lett Appl Microbiol ; 70(1): 42-47, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31642085

RESUMO

The increasing frequency of class A KPC enzymes, class B metallo-ß-lactamases (MBLs) and class D OXA-48 enzymes in Enterobacteriaceae makes their early identification urgent. A simple commercial MASTDISCS combi Carba plus disc system (MAST-Carba plus) was designed for the identification of MBLs, KPC and OXA-48 carbapenemase genes in Enterobacteriaceae. To validate the MAST-Carba plus, a total of 77 isolates of carbapenemase-producing Enterobacteriaceae (CPE) and 84 isolates of noncarbapenemase-producing Enterobacteriaceae (non-CPE) were selected for differentiation of the genes of Enterobacteriaceae by MAST-Carba plus. Meanwhile, the carbapenemase genes such as blaKPC , blaIMP , blaVIM , blaNDM-1 and blaOXA-48 were detected by PCR (polymerase chain reaction). Thus, when considered on the basis of PCR results, the sensitivity of MAST-Carba plus detection of KPC strains is 82·3%, the specificity is 100·0%, the positive predictive value is 100·0% and the negative predictive value is 92·4%. For MBLs strains, the sensitivity is 100·0%, the specificity is 97·1%, the positive predictive value is 84·6% and the negative predictive value is 100·0%. For OXA-48 strains, the sensitivity is 100·0%, the specificity is 99·4%, the positive predictive value is 80·0% and the negative predictive value is 100·0%. Our findings suggest that MAST-Carba plus is a rapid and promising method for identifying the MBLs, KPC and OXA-48 carbapenemase genes in Enterobacteriaceae, which could be exploited in basic microbiology laboratory to prevent the transmission of CPE. SIGNIFICANCE AND IMPACT OF THE STUDY: Not only detection of carbapenemases but also identification of their genes accurately and rapidly in Enterobacteriaceae is still a major challenge for clinical laboratories in order to prevent the transmission of carbapenemase-producing Enterobacteriaceae (CPE). Therefore, this study aimed to evaluate the performance of a new rapid method (MASTDISCS combi Carba plus) for the identification of metallo-ß-lactamases (MBLs), KPC and OXA-48 carbapenemase genes in Enterobacteriaceae clinical isolates.


Assuntos
Proteínas de Bactérias/análise , Infecções por Enterobacteriaceae/microbiologia , Enterobacteriaceae/enzimologia , Enterobacteriaceae/isolamento & purificação , Ensaios Enzimáticos/métodos , beta-Lactamases/análise , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Enterobacteriaceae/classificação , Enterobacteriaceae/genética , Humanos , Testes de Sensibilidade Microbiana , Reação em Cadeia da Polimerase , Sensibilidade e Especificidade , beta-Lactamases/genética , beta-Lactamases/metabolismo
3.
Bratisl Lek Listy ; 120(12): 935-940, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31855054

RESUMO

OBJECTIVES: We focused on detecting the most frequent resistance mechanisms in selected multidrug-resistant (MDR) strains and determining their antimicrobial resistance. BACKGROUND: MDR pathogens pose urgent public health threat due to limited treatment options, rigorous control measures and significant mortality. METHODS: We confirmed extended-spectrum ß-lactamase (ESBL) and carbapenemase producing Enterobacteriaceae through guidelines, as well following ß-lactamases: AmpC by cloxacillin, class A carbapenemase with phenylboronic acid, class B metallo-ß-lactamase with ethylenediaminetetraacetic acid. Multilocus sequence typing was used to investigate 20 Escherichia coli strains. RESULTS: Overall 205 mostly ESBL Escherichia coli demonstrated resistance against amikacin (4.7 %), tigecycline (1.2 %), and no resistance to ceftazidime/avibactam, meropenem, nitrofurantoin and fosfomycin. Out of 41 Klebsiella species (spp.), 37 (90.2 %) showed carbapenemase activity, 13 (35.1 %) of class A and 24 (64.9 %) of class B. Resistance was following: meropenem 66.7 %, tigecyclin 10.2 % and colistin 0 %. From Enterobacter spp. 21 strains, 14 (66.7 %) were ESBL, 5 produced ESBL and/or AmpC and 2 were MDR. We ascertained 14 (70 %) E. coli sequence type - ST131. CONCLUSIONS: The study revealed various resistance mechanisms in concert with different agents and association of specific ST131 within E. coli. These characteristics considerably contribute to emergence of antimicrobial resistance (Tab. 4, Ref. 30).


Assuntos
Antibacterianos/farmacologia , Proteínas de Bactérias/metabolismo , Enterobacteriáceas Resistentes a Carbapenêmicos/efeitos dos fármacos , Enterobacteriaceae/enzimologia , Escherichia coli/efeitos dos fármacos , Escherichia coli/enzimologia , Klebsiella pneumoniae/efeitos dos fármacos , beta-Lactamases/metabolismo , Adulto , Idoso , Proteínas de Bactérias/genética , Enterobacteriáceas Resistentes a Carbapenêmicos/enzimologia , Enterobacteriáceas Resistentes a Carbapenêmicos/genética , Enterobacteriáceas Resistentes a Carbapenêmicos/isolamento & purificação , Farmacorresistência Bacteriana , Enterobacteriaceae/classificação , Infecções por Enterobacteriaceae/microbiologia , Escherichia coli/genética , Escherichia coli/isolamento & purificação , Humanos , Klebsiella pneumoniae/genética , Klebsiella pneumoniae/isolamento & purificação , Testes de Sensibilidade Microbiana , Pessoa de Meia-Idade , beta-Lactamases/genética
4.
Rev Chilena Infectol ; 36(4): 433-441, 2019 Aug.
Artigo em Espanhol | MEDLINE | ID: mdl-31859766

RESUMO

BACKGROUND: Infections caused by extended-spectrum beta-lactamases enterobacteria (ESBL-EP) have implications for neonatal morbidity and mortality. AIM: To describe the prevalence of ESBL-EP in neonatal sepsis and associated factors. METHODS: A prospective cohort study was conducted from August 2016 to August 2017; newborn babies (NB) hospitalized in the Hospital Civil de Guadalajara "Dr. Juan I. Menchaca" were included. The ESBL-EP were investigated by double-disk synergy test and its association with clinical and demographic characteristics of the NB. RESULTS: A total of 1,501 hospitalized NB were studied, with an average gestational age of 36.3 weeks. They were diagnosed 196 neonatal sepsis events, the most frequent etiologies were enterobacteria (45.5%). Resistance to ampicilin was found in 88.8% and to broad spectrum cephalosporins in more than 42% of the strains; 22.9% of them were ESBL phenotype. Apgar ≤ 7 at five minutes of life (OR 4.6; 95% CI 1.47-14.6) and gestational age < 37 weeks (OR 5.4; 95% CI 1.04-27.) increase the risk. CONCLUSION: In enterobacteria that cause neonatal sepsis, 22.9% were EP-ESBL; infection was more likely in patients with Apgar ≤ 7 at five minutes of age and in preterm infants.


Assuntos
Antibacterianos/farmacologia , Infecção Hospitalar/microbiologia , Infecções por Enterobacteriaceae/microbiologia , Enterobacteriaceae/efeitos dos fármacos , Sepse Neonatal/microbiologia , beta-Lactamases/biossíntese , Adolescente , Adulto , Criança , Enterobacteriaceae/classificação , Feminino , Humanos , Recém-Nascido , Unidades de Terapia Intensiva Neonatal , Masculino , Testes de Sensibilidade Microbiana , Pessoa de Meia-Idade , Prevalência , Estudos Prospectivos , Fatores de Risco , Adulto Jovem
5.
World J Microbiol Biotechnol ; 35(11): 172, 2019 Oct 31.
Artigo em Inglês | MEDLINE | ID: mdl-31673798

RESUMO

The present study was designed with the objective of improving growth and nodulation of soybean [Glycine max (L.) Merill] with co-inoculation of native Bradyrhizobium sp. (LSBR-3) (KF906140) and non-rhizobial nodule endophytic diazotroph Leclercia adecarboxylata (LSE-1) (KX925974) with multifunctional plant growth promoting (PGP) traits in cereal based cropping system (Rice-Wheat). A total of 40 endophytic bacteria from cultivated and wild sp. of soybean were screened for multifarious PGP traits and pathogenicity test. Based on PGP traits, antagonistic activities and bio-safety test; L. adecarboxylata (LSE-1) was identified with 16 S rRNA gene sequencing along with the presence of nifH (nitrogen fixation) and ipdc (IAA production) genes. Dual inoculant LSE-1 and LSBR-3 increased indole acetic acid (IAA), P & Zn-solubilization, 1-aminocyclopropane-1-carboxylate deaminase (ACCD) activity, siderophore, biofilm formation and exo-polysaccharides in contrast to single inoculation treatment. Further, assessment of dual inoculant LSBR-3 + LSE-1 improved growth parameters, nodulation, soil enzymes activities, nutrient accumulation and yield as compared to single as well as un-inoculated control treatment under field conditions. Single inoculant LSBR-3 improved yield by 8.84% over control. Further, enhancement of 4.15% grain yield was noticed with LSBR-3 + LSE-1 over LSBR-3 alone treatment. Application of LSBR-3 + LSE-1 gave superior B:C ratio (1.29) and additional income approximately 116 USD ha-1 in contrast to control treatment. The present results thus, is the first report of novel endophytic diazotroph L. adecarboxylata (LSE-1) as PGPR from Indian conditions particularly in Punjab region for exploiting as potential PGPR along with Bradyrhizobium sp. (LSBR-3) in soybean.


Assuntos
Bradyrhizobium/isolamento & purificação , Bradyrhizobium/fisiologia , Enterobacteriaceae/isolamento & purificação , Enterobacteriaceae/fisiologia , Desenvolvimento Vegetal , Raízes de Plantas/microbiologia , Soja/crescimento & desenvolvimento , Soja/microbiologia , Proteínas de Bactérias/genética , Biofilmes/crescimento & desenvolvimento , Bradyrhizobium/classificação , Bradyrhizobium/genética , Endófitos , Enterobacteriaceae/classificação , Enterobacteriaceae/genética , Fertilizantes , Ácidos Indolacéticos/metabolismo , Fixação de Nitrogênio/genética , Nutrientes , Oryza/microbiologia , Oxirredutases/genética , Filogenia , RNA Ribossômico 16S/genética , Nódulos Radiculares de Plantas/microbiologia , Sideróforos , Soja/química , Triticum/microbiologia
6.
BMC Infect Dis ; 19(1): 979, 2019 Nov 21.
Artigo em Inglês | MEDLINE | ID: mdl-31752702

RESUMO

BACKGROUND: Fluoroquinolones are commonly recommended as treatment for urinary tract infections (UTIs). The development of resistance to these agents, particularly in gram-negative microorganisms complicates treatment of infections caused by these organisms. This study aimed to investigate antimicrobial resistance of different Enterobacteriaceae species isolated from hospital- acquired and community-acquired UTIs against fluoroquinolones and correlate its levels with the existing genetic mechanisms of resistance. METHODS: A total of 440 Enterobacteriaceae isolates recovered from UTIs were tested for antimicrobial susceptibility. Plasmid-mediated quinolone resistance (PMQR) genes and mutations in the quinolone resistance-determining regions (QRDRs) of gyrA and parC genes were examined in quinolone-resistant strains. RESULTS: About (32.5%) of isolates were resistant to quinolones and (20.5%) were resistant to fluoroquinolones. All isolates with high and intermediate resistance phenotypes harbored one or more PMQR genes. QnrB was the most frequent gene (62.9%) of resistant isolates. Co-carriage of 2 PMQR genes was detected in isolates (46.9%) with high resistance to ciprofloxacin (CIP) (MICs > 128 µg/mL), while co-carriage of 3 PMQR genes was detected in (6.3%) of resistant isolates (MICs > 512 µg/mL). Carriage of one gene only was detected in intermediate resistance isolates (MICs of CIP = 1.5-2 µg/mL). Neither qnrA nor qnrC genes were detected. The mutation at code 83 of gyrA was the most frequent followed by Ser80-Ile in parC gene, while Asp-87 Asn mutation of gyrA gene was the least, where it was detected only in high resistant E. coli isolates (MIC ≥128 µg/mL). A double mutation in gyrA (Lys154Arg and Ser171Ala) was observed in high FQs resistant isolates (MIC of CIP < 128 µg/mL). CONCLUSION: FQs resistance is caused by interact between PMQR genes and mutations in both gyrA and parC genes while a mutation in one gene only can explain quinolone resistance. Accumulation of PMQR genes and QRDR mutations confers high resistance to FQs.


Assuntos
Antibacterianos/farmacologia , Proteínas de Bactérias/genética , Infecção Hospitalar/microbiologia , Farmacorresistência Bacteriana , Infecções por Enterobacteriaceae/microbiologia , Enterobacteriaceae/genética , Quinolonas/farmacologia , Infecções Urinárias/microbiologia , Adulto , Proteínas de Bactérias/metabolismo , Ciprofloxacino/farmacologia , Enterobacteriaceae/classificação , Enterobacteriaceae/efeitos dos fármacos , Enterobacteriaceae/isolamento & purificação , Feminino , Fluoroquinolonas/farmacologia , Humanos , Masculino , Testes de Sensibilidade Microbiana , Pessoa de Meia-Idade , Mutação , Plasmídeos/genética , Plasmídeos/metabolismo , Adulto Jovem
7.
Lett Appl Microbiol ; 69(6): 399-402, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31618795

RESUMO

The sugar glider (Petaurus breviceps) is a small, arboreal, nocturnal, gliding mammalian possum belonging to the marsupial infraclass. Exotic marsupials, including sugar gliders, are becoming popular companion pets and, consequently, the risk of potential infections that can be transmitted to humans should be investigated. Data on the role of the sugar glider as a possible carrier of pathogenic and zoonotic bacteria are scarce and fragmentary. Therefore, this study is aimed at evaluating the prevalence of potentially zoonotic bacteria (Salmonella spp., Escherichia coli, Campylobacter spp., Pseudomonas spp., Klebsiella spp., Listeria monocytogenes and Yersinia enterocolitica) in 64 sugar gliders kept as pets in Italy. The highest prevalence of infection pertained to members of the family Enterobacteriaceae, in particular Citrobacter spp. (50%), Enterobacter spp. (28·1%) and Klebsiella pneumoniae (15·6%); Pseudomonas aeruginosa was isolated from 10 out of 64 samples (15·6%). All strains of Klebsiella pneumoniae exhibited some level of resistance to multiple antimicrobials (ampicillin, amoxicillin-clavulanic acid and doxycycline). SIGNIFICANCE AND IMPACT OF THE STUDY: The results of this study show that sugar gliders may act as carriers of potentially pathogenic agents for humans and other animal species, therefore caution should be exercised in the handling and contact with these animals.


Assuntos
Farmacorresistência Bacteriana Múltipla/fisiologia , Enterobacteriaceae/efeitos dos fármacos , Enterobacteriaceae/isolamento & purificação , Marsupiais/microbiologia , Animais de Estimação/microbiologia , Animais , Enterobacteriaceae/classificação , Itália
8.
BMJ Case Rep ; 12(7)2019 Jul 11.
Artigo em Inglês | MEDLINE | ID: mdl-31300600

RESUMO

A late preterm male infant of 36 weeks gestation and a birth weight of 2100 g was admitted on day 35 of life with complaints of respiratory distress and lethargy. He was diagnosed as a case of sepsis screen positive culture negative sepsis and was managed with respiratory support and intravenous antibiotics for 10 days. The infant improved clinically and was on spoon feeds by day 14 of admission. On day 14 of admission, he developed new-onset respiratory distress and was diagnosed as a case of nosocomial pneumonia based on chest radiography findings. The blood culture grew a rare organism Cedecea lapagei and a diagnosis of sepsis was also made. The antibiotics were tailored as per the blood culture sensitivity pattern and the infant had clinical improvement in the next 72 hours.


Assuntos
Antibacterianos/uso terapêutico , Infecções por Enterobacteriaceae/diagnóstico , Enterobacteriaceae/isolamento & purificação , Combinação Piperacilina e Tazobactam/uso terapêutico , Respiração Artificial , Síndrome do Desconforto Respiratório do Recém-Nascido/microbiologia , Sepse/diagnóstico , Enterobacteriaceae/classificação , Infecções por Enterobacteriaceae/tratamento farmacológico , Infecções por Enterobacteriaceae/fisiopatologia , Humanos , Lactente , Letargia , Masculino , Respiração Artificial/efeitos adversos , Síndrome do Desconforto Respiratório do Recém-Nascido/tratamento farmacológico , Síndrome do Desconforto Respiratório do Recém-Nascido/fisiopatologia , Sepse/tratamento farmacológico , Punção Espinal , Resultado do Tratamento
9.
Int J Food Microbiol ; 306: 108260, 2019 Oct 02.
Artigo em Inglês | MEDLINE | ID: mdl-31302488

RESUMO

The aim of this study was to determine the bacteriological quality of bottled water samples obtained from small purification plants located in Mexico City and to identify potentially pathogenic nontuberculous mycobacteria (NTM) species found in these samples. All 111 samples analyzed were positive for aerobic mesophilic bacteria (AMB) and 46 (41.4%) did not comply with Mexico's Official Guidelines. Sixty-nine (62.1%) and 23 (20.7%) water samples were positive for total coliforms (TC) and fecal coliforms (FC), respectively. A total of 81 (72.9%) of the water samples exceeded the maximum allowed limit stipulated in the guideline. Thirty-three (29.7%) of the purified water samples were positive for NTM, being recovered a total of 40 isolates. These NTM isolates were identified using three molecular markers (hsp65, rrs and rpoB genes) which corresponded to the fast-growing mycobacteria M. chelonae (n = 12), M. porcinum (n = 8), M. senegalense (n = 5), M. abscessus (n = 4), M. septicum (n = 4), M. wolinskyi (n = 3), M. mucogenicum (n = 2), M. fortuitum (n = 1) and M. sp. (n = 1). In seven purified water samples, two different NTM species were isolated simultaneously. Overall, these results showed that most of the purified bottled water samples analyzed in this study had unsatisfactory microbiological quality and some harbored NTM associated with illness. Our data could hasten health authorities to intensify efforts in the routine monitoring of activities in the purified bottled water industry in order to supply safe and healthy water to the public.


Assuntos
Água Potável/microbiologia , Enterobacteriaceae/isolamento & purificação , Micobactérias não Tuberculosas/isolamento & purificação , Purificação da Água , Qualidade da Água , Enterobacteriaceae/classificação , Enterobacteriaceae/genética , Humanos , Incidência , México , Micobactérias não Tuberculosas/classificação , Micobactérias não Tuberculosas/genética
10.
Int J Syst Evol Microbiol ; 69(10): 3155-3160, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31355737

RESUMO

A novel Kosakonia strain WCHEs120001T was recovered from the wound secretion of a patient at West China Hospital, Chengdu, PR China, in 2017. The strain was Gram-stain-negative, facultatively anaerobic, motile, and non-spore-forming. A preliminary analysis based on the 16S rRNA gene sequence revealed that this strain was closely related to members of the genus Kosakonia. The strain was subjected to whole genome sequencing. Phylogenetic analysis based on core gene sequences of type strains of all Enterobacteriaceae species revealed that this strain belonged to the genus Kosakonia but were distinct from any previously known Kosakonia species. Both average nucleotide identity (ANI) and in silico DNA-DNA hybridisation (isDDH) values between strain WCHEs120001T and type strains of all known Kosakonia species were 82.02 to 92.37% and 25.6 to 50.9 %, respectively, which are lower than the 95 % (ANI) and 70 % (isDDH) cutoff for species delineation. The major fatty acids of the strain WCHEs120001T are C16 : 0, sum of C16:1ω7c/C16:1ω6c and C18:1ω7c, which are similar to other Kosakonia species. Genomic DNA G+C content of strain WCHEs120001T was 53.33 mol%. Strain WCHEs120001T is positive for methyl-d-glucopyranoside but does not ferment adonitol, d-arabitol, dulcitol and melibiose, which distinguishes it from all other Kosakonia species. Genotypic and phenotypic characteristics indicate that strain WCHEs120001T represents a novel species of the genus Kosakonia, for which the name Kosakonia quasisacchari sp. nov. is proposed. The type strain of K. quasisacchari sp. nov. is WCHEs120001T (=GDMCC1.1570T=NCTC 14272T).


Assuntos
Enterobacteriaceae/classificação , Filogenia , Infecção dos Ferimentos/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Enterobacteriaceae/isolamento & purificação , Ácidos Graxos/química , Humanos , Hibridização de Ácido Nucleico , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
11.
Int J Syst Evol Microbiol ; 69(8): 2440-2444, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31166160

RESUMO

Strains 2B12T, FVG1-MFV-O17 and FVG10-MFV-A16 were isolated from fresh water samples collected in Asia and Europe. The nucleotide sequences of the gapA barcodes revealed that all three strains belonged to the same cluster within the genus Dickeya. Using 13 housekeeping genes (fusA, rpoD, rpoS, glyA, purA, groEL, gapA, rplB, leuS, recA, gyrB, infB and secY), multilocus sequence analysis confirmed the existence of a new clade. When the genome sequences of these three isolates and other Dickeya species were compared, the in silico DNA-DNA hybridization and average nucleotide identity values were found to be no more than 45.50 and 91.22 %, respectively. The closest relative species was Dickeya fangzhongdai. Genome comparisons also highlighted genetic traits differentiating the new strains from D. fangzhongdai strains DSM 101947T (=CFBP 8607T) and B16. Phenotypical tests were performed to distinguish the three strains from D. fangzhongdai and other Dickeya species. The name Dickeya undicola sp. nov. is proposed with strain 2B12T (=CFBP 8650T=LMG 30903T) as the type strain.


Assuntos
Enterobacteriaceae/classificação , Água Doce/microbiologia , Filogenia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Enterobacteriaceae/isolamento & purificação , França , Genes Bacterianos , Genômica , Malásia , Tipagem de Sequências Multilocus , Hibridização de Ácido Nucleico , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
12.
EBioMedicine ; 43: 333-337, 2019 May.
Artigo em Inglês | MEDLINE | ID: mdl-31072770

RESUMO

BACKGROUND: Urinary tract infections are known to be caused by bacteria, but the potential implications of archaea have never been studied in this context. METHODS: In two different university hospital centres we used specific laboratory methods for the detection and culture of archaeal methanogens in 383 urine specimens prospectively collected for diagnosing urinary tract infection (UTI). FINDINGS: Methanobrevibacter smithii was detected by quantitative PCR and sequencing in 34 (9%) of the specimens collected from 34 patients. Escherichia coli, Klebsiella pneumoniae, Enterobacter sp., Enterococcus faecium and mixed cultures were detected along with M. smithii in eighteen, six, three, one and six urine samples, respectively. Interestingly, using our specific culture method for methanogens, we also isolated M. smithii in 31 (91%) of the 34 PCR positive urine samples. Genotyping the 31 isolates using multispacer sequence typing revealed three different genotypes which have been previously reported in intestinal microbiota. Antibiotic susceptibility testing found the 31 isolates to be in vitro susceptible to metronidazole (MIC: 1 mg/L) but resistant to fosfomycin, sulfamethoxazole-trimethoprim, amoxicillin-clavulanate and ofloxacin, commonly used to treat bacterial UTI. Finally, 19 (54%) of the 34 patients in whose urine samples M. smithii was detected were diagnosed with UTIs, including cystitis, pyelonephritis and prostatitis. INTERPRETATION: Our results show that M. smithii is part of the urinary microbiota of some individuals and could play a role in community-acquired UTI in association with enteric bacteria. FUND: This study was supported by IHU Méditerranée Infection, Marseille, France.


Assuntos
Técnicas Bacteriológicas , Técnicas de Cocultura , Enterobacteriaceae/crescimento & desenvolvimento , Methanobrevibacter/crescimento & desenvolvimento , Infecções Urinárias/diagnóstico , Infecções Urinárias/microbiologia , Adulto , Idoso , Enterobacteriaceae/classificação , Enterobacteriaceae/genética , Feminino , Humanos , Masculino , Methanobrevibacter/classificação , Methanobrevibacter/genética , Pessoa de Meia-Idade , Estudos Retrospectivos , Urinálise
13.
ISME J ; 13(9): 2306-2318, 2019 09.
Artigo em Inglês | MEDLINE | ID: mdl-31089259

RESUMO

Longitudinal human gut microbiome datasets generated using community-level, sequence-based approaches often report a sub-set of long-lived "resident" taxa that rarely, if ever, are lost. This result contrasts with population-level turnover of resident clones on the order of months to years. We hypothesized that the disconnect between these results is due to a relative lack of simultaneous discrimination of the human gut microbiome at both the community and population-levels. Here, we present results of a small, longitudinal cohort study (n = 8 participants) of healthy human adults that identifies static and dynamic members of the gut microbiome at the clone level based on cultivation/genetic discrimination and at the operational taxonomic unit/amplified sequence variant levels based on 16S rRNA sequencing. We provide evidence that there is little "stability" within resident clonal populations of the common gut microbiome bacterial family, Enterobacteriaceae. Given that clones can vary substantially in genome content and that evolutionary processes operate on the population level, these results question the biological relevance of apparent stability at higher taxonomic levels.


Assuntos
Enterobacteriaceae/isolamento & purificação , Microbioma Gastrointestinal , Adulto , Evolução Biológica , Estudos de Coortes , Enterobacteriaceae/classificação , Enterobacteriaceae/genética , Feminino , Trato Gastrointestinal/microbiologia , Voluntários Saudáveis , Humanos , Estudos Longitudinais , Masculino , Microbiota , Filogenia , RNA Ribossômico 16S/genética
14.
mBio ; 10(3)2019 05 28.
Artigo em Inglês | MEDLINE | ID: mdl-31138751

RESUMO

Oral infection of C57BL/6J mice with Toxoplasma gondii results in a marked bacterial dysbiosis and the development of severe pathology in the distal small intestine that is dependent on CD4+ T cells and interferon gamma (IFN-γ). This dysbiosis and bacterial translocation contribute to the development of ileal pathology, but the factors that support the bloom of bacterial pathobionts are unclear. The use of microbial community profiling and shotgun metagenomics revealed that Toxoplasma infection induces a dysbiosis dominated by Enterobacteriaceae and an increased potential for nitrate respiration. In vivo experiments using bacterial metabolic mutants revealed that during this infection, host-derived nitrate supports the expansion of Enterobacteriaceae in the ileum via nitrate respiration. Additional experiments with infected mice indicate that the IFN-γ/STAT1/iNOS axis, while essential for parasite control, also supplies a pool of nitrate that serves as a source for anaerobic respiration and supports overgrowth of Enterobacteriaceae Together, these data reveal a trade-off in intestinal immunity after oral infection of C57BL/6J mice with T. gondii, in which inducible nitric oxide synthase (iNOS) is required for parasite control, while this host enzyme is responsible for specific modification of the composition of the microbiome that contributes to pathology.IMPORTANCE Toxoplasma gondii is a protozoan parasite and a leading cause of foodborne illness. Infection is initiated when the parasite invades the intestinal epithelium, and in many host species, this leads to intense inflammation and a dramatic disruption of the normal microbial ecosystem that resides in the healthy gut (the so-called microbiome). One characteristic change in the microbiome during infection with Toxoplasma-as well as numerous other pathogens-is the overgrowth of Escherichia coli or similar bacteria and a breakdown of commensal containment leading to seeding of peripheral organs with gut bacteria and subsequent sepsis. Our findings provide one clear explanation for how this process is regulated, thereby improving our understanding of the relationship between parasite infection, inflammation, and disease. Furthermore, our results could serve as the basis for the development of novel therapeutics to reduce the potential for harmful bacteria to bloom in the gut during infection.


Assuntos
Disbiose/imunologia , Microbioma Gastrointestinal , Intestino Delgado/imunologia , Intestino Delgado/patologia , Ativação de Macrófagos , Nitratos/metabolismo , Toxoplasmose Animal/imunologia , Animais , Citocinas/análise , Enterobacteriaceae/classificação , Feminino , Inflamação , Interferon gama/imunologia , Intestino Delgado/microbiologia , Intestino Delgado/parasitologia , Camundongos , Camundongos Endogâmicos BALB C , Camundongos Endogâmicos C57BL , Óxido Nítrico Sintase Tipo II/imunologia , Toxoplasma/patogenicidade , Toxoplasmose Animal/microbiologia
15.
New Microbiol ; 42(2): 114-117, 2019 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-31034082

RESUMO

Matrix Assisted Laser Desorption/Ionization-Time of Flight (MALDI-TOF) Vitek MS system is a useful technique to identify bacteria strains isolated in clinical samples. In this paper, we applied this method to KPC-producing Enterobacteriaceae detection through the determination of a specific 11,109 (±8) Da peak. We assayed the presence, specificity and reliability of this peak on routine workflow through the analysis of 183 Enterobacteriaceae strains isolated from clinical samples and characterized by classical approaches. The peak was detected in 95.5% (129/135) of carbapenemase-producing strains spectra compared with the 48 extended spectrum beta-lactamase producing controls strains, which all lacked this peak. Hence, this 11,109 Da peak determination showed a Positive Predictive Value (PPV) of 100% and a Negative Predictive Value (NPV) of 94.4%. The characterization of this specific peak in a MALDI-TOF Vitek MS system might be considered a valuable tool to reveal KPC-producing Enterobacteriaceae especially in KPC endemic region.


Assuntos
Técnicas de Tipagem Bacteriana/métodos , Enterobacteriaceae , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz , Técnicas de Tipagem Bacteriana/normas , Enterobacteriaceae/química , Enterobacteriaceae/classificação , Infecções por Enterobacteriaceae/microbiologia , Humanos , Reprodutibilidade dos Testes , beta-Lactamases/metabolismo
16.
Int J Syst Evol Microbiol ; 69(6): 1826-1830, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-30994436

RESUMO

A Gram-stain-negative, rod-shaped, facultatively anaerobic bacterium, designated as strain HYN0051T, was isolated from lake water. 16S rRNA gene sequence analyses indicated that the isolate shares the highest sequence similarity with the genus Pragia (97.1 %) of the family Enterobacteriaceae. Strain HYN0051T did not form a rigid clade with the genus Pragia in any of the phylogenetic trees, demonstrating the novel generic status of the isolate. The genome of strain HYN0051T (CP029185) is a single circular chromosome of 3.84 Mb. The major fatty acids detected were C14 : 0, C16 : 0, summed feature 2 (C12 : 0 aldehyde and/or unknown 10.928), summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c). The isoprenoid quinones were Q-8, MK-8 and DMK-8. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine and one unidentified phospholipid. The genome size, G+C content and fatty acid profile were very similar to that of the genus Pragia, but the composition of isoprenoid quinones and polar lipids, and numerous phenotypic properties also supported the distinctiveness of the new isolate from the genus Pragia. Thus, based on phylogenetic and phenotypic data, a novel species of a new genus, Limnobaculum parvum gen. nov., sp. nov., is proposed. The type strain of Limnobaculum parvum is HYN0051T (=KACC 19186T=NBRC 112742T).


Assuntos
Enterobacteriaceae/classificação , Lagos/microbiologia , Filogenia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Enterobacteriaceae/isolamento & purificação , Ácidos Graxos/química , Fosfolipídeos/química , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
17.
PLoS One ; 14(4): e0215428, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30986251

RESUMO

OBJECTIVES: Large-scale clinical studies investigating associations between intestinal microbiota signatures and human diseases usually rely on stool samples. However, the timing of repeated stool sample collection cannot be predefined in longitudinal settings. Rectal swabs, being straightforward to obtain, have the potential to overcome this drawback. Therefore, we assessed the usability of rectal swabs for microbiome sampling in a cohort of hematological and oncological patients. STUDY DESIGN: We used a pipeline for intestinal microbiota analysis from deep rectal swabs which was established and validated with test samples and negative controls. Consecutively, a cohort of patients from hematology and oncology wards was established and weekly deep rectal swabs taken during their admissions and re-admissions. RESULTS: Validation of our newly developed pipeline for intestinal microbiota analysis from rectal swabs revealed consistent and reproducible results. Over a period of nine months, 418 rectal swabs were collected longitudinally from 41 patients. Adherence to the intended sampling protocol was 97%. After DNA extraction, sequencing, read pre-processing and filtering of chimeric sequences, 405 of 418 samples (96.9%) were eligible for further analyses. Follow-up samples and those taken under current antibiotic exposure showed a significant decrease in alpha diversity as compared to baseline samples. Microbial domination occurred most frequently by Enterococcaceae (99 samples, 24.4%) on family level and Enterococcus (90 samples, 22.2%) on genus level. Furthermore, we noticed a high abundance of potential skin commensals in 99 samples (24.4%). SUMMARY: Deep rectal swabs were shown to be reliable for microbiome sampling and analysis, with practical advantages related to high sampling adherence, easy timing, transport and storage. The relatively high abundance of putative skin commensals in this patient cohort may be of potential interest and should be further investigated. Generally, previous findings on alpha diversity dynamics obtained from stool samples were confirmed.


Assuntos
Enterobacteriaceae , Enterococcus , Fezes/microbiologia , Microbioma Gastrointestinal , Neoplasias Hematológicas/microbiologia , Manejo de Espécimes , Estudos de Coortes , Enterobacteriaceae/classificação , Enterobacteriaceae/crescimento & desenvolvimento , Enterococcus/classificação , Enterococcus/genética , Feminino , Humanos , Masculino
19.
Clin Microbiol Infect ; 25(10): 1173-1179, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-30825674

RESUMO

BACKGROUND: There is an ongoing controversy on the role of the healthcare-associated pneumonia (HCAP) label in the treatment of patients with pneumonia. OBJECTIVE: To provide an update of the literature on patients meeting criteria for HCAP between 2014 and 2018. SOURCES: The review is based on a systematic literature search using PubMed-Central full-text archive of biomedical and life sciences literature at the U.S. National Institutes of Health's National Library of Medicine (NIH/NLM). CONTENT: Studies compared clinical characteristics of patients with HCAP and community-acquired pneumonia (CAP). HCAP patients were older and had a higher comorbidity. Mortality rates in HCAP varied from 5% to 33%, but seemed lower than those cited in the initial reports. Criteria behind the HCAP classification differed considerably within populations. Microbial patterns differed in that there was a higher incidence of methicillin-resistant Staphylococcus aureus (MRSA) and Pseudomonas aeruginosa, and, to a lesser extent, enterobacteriaceae. Definitions and rates of multidrug-resistant (MDR) pneumonia also varied considerably. Broad-spectrum guideline-concordant treatment did not reduce mortality in four observational studies. The HCAP criteria performed poorly as a predictive tool to identify MDR pneumonia or pathogens not covered by treatment for CAP. A new score (Drug Resistance in Pneumonia, DRIP) outperformed HCAP in the prediction of MDR pathogens. Comorbidity and functional status, but not different microbial patterns, seem to account for increased mortality. IMPLICATIONS: HCAP should no longer be used to identify patients at risk of MDR pathogens. The use of validated predictive scores along with implementation of de-escalation strategies and careful individual assessment of comorbidity and functional status seem superior strategies for clinical management.


Assuntos
Infecções Bacterianas/epidemiologia , Infecções Bacterianas/patologia , Enterobacteriaceae/isolamento & purificação , Pneumonia Associada a Assistência à Saúde/diagnóstico , Pneumonia Associada a Assistência à Saúde/patologia , Pseudomonas aeruginosa/isolamento & purificação , Staphylococcus aureus/isolamento & purificação , Idoso , Idoso de 80 Anos ou mais , Infecções Bacterianas/microbiologia , Gerenciamento Clínico , Farmacorresistência Bacteriana Múltipla , Enterobacteriaceae/classificação , Enterobacteriaceae/efeitos dos fármacos , Feminino , Pneumonia Associada a Assistência à Saúde/microbiologia , Pneumonia Associada a Assistência à Saúde/mortalidade , Humanos , Incidência , Masculino , Pseudomonas aeruginosa/efeitos dos fármacos , Staphylococcus aureus/efeitos dos fármacos , Estados Unidos
20.
Appl Microbiol Biotechnol ; 103(9): 3887-3897, 2019 May.
Artigo em Inglês | MEDLINE | ID: mdl-30820635

RESUMO

Heavy metal pollution in agricultural soils has become a widespread serious problem with the rapid industrialization and urbanization in the past two decades. Cadmium (Cd2+) is of the most concern in soils due to its high toxicity. It is necessary to develop remediation strategies to remove or neutralize its toxic effects in Cd-contaminated soil. Microbial bioremediation is a promising technology to treat heavy metal-contaminated soils. In this study, Cd-resistant bacterium, isolated from heavy metal-polluted soil in Southern China, was characterized as Raoultella sp. strain X13 on the basis of its biochemical profile and 16S rRNA. We investigated the characterization of Cd2+ distribution in different cellular compartments after Cd2+ uptake. Cd2+ uptake by strain X13 was mainly by ion exchange and chelation binding tightly to the cell wall. In addition, X13 plant growth-promoting characteristics suggested that X13 could solubilize phosphate and produce indole acetic acid. Pot experiments for the remediation of Cd-contaminated soil in situ by X13 inoculation demonstrated that X13 application to Cd-contaminated soils significantly promoted pak choi growth and improved production. We also found that X13 substantially reduced the Cd2+ bioavailability for pak choi. Therefore, strain X13 is an effective treatment for potential application in Cd2+ remediation as well as for sustainable agronomic production programs in Cd-contaminated soils.


Assuntos
Inoculantes Agrícolas/metabolismo , Brassica/crescimento & desenvolvimento , Cádmio/metabolismo , Enterobacteriaceae/metabolismo , Poluentes do Solo/metabolismo , Inoculantes Agrícolas/classificação , Inoculantes Agrícolas/genética , Inoculantes Agrícolas/isolamento & purificação , Brassica/metabolismo , Brassica/microbiologia , Enterobacteriaceae/classificação , Enterobacteriaceae/genética , Enterobacteriaceae/isolamento & purificação , Ácidos Indolacéticos/metabolismo , Fosfatos/metabolismo , Solo/química , Microbiologia do Solo
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