Your browser doesn't support javascript.
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 5.826
Filtrar
1.
Artigo em Inglês | MEDLINE | ID: mdl-32178603

RESUMO

From 1 January to 31 December 2018, thirty-six institutions around Australia participated in the Australian Enterococcal Sepsis Outcome Programme (AESOP). The aim of AESOP 2018 was to determine the proportion of enterococcal bacteraemia isolates in Australia that were antimicrobial resistant, and to characterise the molecular epidemiology of the E. faecium isolates. Of the 1,248 unique episodes of bacteraemia investigated, 93.5% were caused by either E. faecalis (54.2%) or E. faecium (39.3%). Ampicillin resistance was not detected in E. faecalis but was detected in 89.4% of E. faecium. Vancomycin non-susceptibility was not detected in E. faecalis but was reported in 45.0% of E. faecium. Overall 49.3% of E. faecium isolates harboured vanA or vanB genes. Of the vanA/vanB positive E. faecium isolates, 52.9% harboured vanA genes and 46.2% vanB genes; 0.8% harboured both vanA and vanB genes. The percentage of E. faecium bacteraemia isolates resistant to vancomycin in Australia is substantially higher than that seen in most European countries. E. faecium consisted of 59 multilocus sequence types (STs) of which 74.4% of isolates were classified into six major STs containing ten or more isolates. All major STs belong to clonal cluster (CC) 17, a major hospital-adapted polyclonal E. faecium cluster. The predominant STs (ST17, ST1424, ST796, ST80, ST1421, and ST262) were found across most regions of Australia. The most predominant clone was ST17 which was identified in all regions except the Australian Capital Territory and the Northern Territory. Overall, 55.8% of isolates belonging to the six predominant STs harboured vanA or vanB genes. The AESOP 2018 study has shown that enterococcal bacteraemias in Australia are frequently caused by polyclonal ampicillin-resistant high-level gentamicin-resistant vanA- or vanB-harbouring E. faecium which have limited treatment options.


Assuntos
Antibacterianos , Bacteriemia , Enterococcus faecium , Enterococcus , Sepse , Antibacterianos/farmacologia , Território da Capital Australiana , Bacteriemia/epidemiologia , Farmacorresistência Bacteriana , Enterococcus/efeitos dos fármacos , Enterococcus faecium/efeitos dos fármacos , Enterococcus faecium/isolamento & purificação , Humanos , Epidemiologia Molecular , Tipagem de Sequências Multilocus , Northern Territory , Sepse/epidemiologia , Sepse/microbiologia
2.
Med Oral Patol Oral Cir Bucal ; 25(2): e240-e251, 2020 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-32040467

RESUMO

BACKGROUND: Dental caries is considered as one of the most significant global health problem over the world. Dental caries initiates from bacterial shifts within the supragingival biofilm, then a polymicrobial biofilm is formed on the surface of tooth, and finally various bacterial species aggregate in a complex-organized manner. The exploiting variability in 16S rRNA gene sequence has been considered as a cost-efficient high-throughput characterization approach in human oral microbiome investigations. The aim of this study is to characterize bacterial species associated with superficial dental biofilm, underlying carious dentine and root caries lesion by16S rRNA gene-based metagenomic analysis. MATERIAL AND METHODS: Herein, the bacterial communities in carious dentin lesion, biofilm and root canal samples of 30 subjects (aged 4-76 years) admitted to a clinic in Tehran during 2017 were investigated using a culture independent approach. Total genomic DNA of each tissue was subjected to metagenomic identification of bacteria using a nested PCR assay and 16S rRNA library construction method. RESULTS: 31 samples collected from 30 consenting patients (29 samples from 29 patients ant two biofilm samples from one patient). Bioinformatics analyses of a-800bp sequences of the second step of Nested-PCR revealed presence of 156 bacterial isolates in carious (n=45), biofilm (n=81) and root canal (n=30) specimens. Prevotella spp., Lactobacillus vaginalis, and streptococcus spp. showed higher prevalence in carious dentin, root and biofilm samples, respectively. CONCLUSIONS: Exploring the dental microbiota and comparing them in health or diseased conditions is critical step in the determination of human general health. The method applied in this study could identify bacteria related to the three dental lesions. However, due to lack of data for comparison in Genbank or because of the sequence similarity lower than 98% for most identified bacteria, the use of more powerful approaches like NGS platforms or typing of multiple loci (MLST) in future studies is recommended.


Assuntos
Cárie Dentária , Adolescente , Adulto , Idoso , Bactérias , Criança , Pré-Escolar , Estudos Transversais , Humanos , Irã (Geográfico) , Pessoa de Meia-Idade , Tipagem de Sequências Multilocus , RNA Ribossômico 16S , Adulto Jovem
3.
Emerg Microbes Infect ; 9(1): 320-331, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32037975

RESUMO

Background: Multidrug-resistant bacteria, especially those with high virulence, are an emerging problem in clinical settings.Methods: We conducted a multicentre epidemiological and comparative genomic analysis on the evolution, virulence and antimicrobial resistance of carbapenem-resistant Enterobacteriaceae in patients with bacterial liver abscesses from 2012 to 2016.Results: A total of 477 bacterial isolates were collected. Enterobacteriaceae were the main pathogen (89.3%) with K. pneumoniae (52.4%) predominating followed by Escherichia coli (26.8%). All CRKps (3.2%) were of sequence type (ST) 11 and serotypes K47 or K64, and simultaneously possessed acquired blaKPC-2/blaKPC-5 and blaCTX-M-65 together with the multidrug transporter EmrE. Seven Hv-CRKps (five ST11-K47, two ST11-K64) were confirmed by bacteriological test, neutrophil killing assay and Galleria mellonella infection model. Genomic analysis indicated that the emergence of one ST11-K64 Hv-CRKp strain was related to the acquisition of rmpA/rmpA2 genes and siderophore gene clusters, while ST11-K47 Hv-CRKp lacked these traditional virulence genes. Further complete genome analysis of one ST11-K47 Hv-CRKp strain, R16, showed that it acquired a rare plasmid (pR16-Hv-CRKp1) carrying blaKPC-2, blaSHV-12, blaTEM-1, blaCTX-M-65, rmtB and a predicted virulence gene R16_5486 simultaneously.Conclusion: The emergence of the ST11-K47/K64 Hv-CRKps, which are simultaneously multidrug-resistant and hypervirulent, requires urgent control measures to be implemented.


Assuntos
Enterobacteriáceas Resistentes a Carbapenêmicos/isolamento & purificação , Infecções por Klebsiella/microbiologia , Klebsiella pneumoniae/isolamento & purificação , Abscesso Hepático/microbiologia , Idoso , Técnicas de Tipagem Bacteriana , Enterobacteriáceas Resistentes a Carbapenêmicos/classificação , China , Farmacorresistência Bacteriana Múltipla , Feminino , Humanos , Klebsiella pneumoniae/classificação , Masculino , Testes de Sensibilidade Microbiana , Pessoa de Meia-Idade , Tipagem de Sequências Multilocus , Plasmídeos/genética , Sorogrupo , Virulência
4.
Int J Syst Evol Microbiol ; 70(2): 1099-1105, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31909704

RESUMO

We investigated the taxonomic relationship between Streptomyces antimycoticus, Streptomyces castelarensis, Streptomyces sporoclivatus, and Streptomyces violaceusniger. Digital DNA-DNA hybridisation using whole genome sequences and multilocus sequence analysis indicated that S. antimycoticus, S. castelarensis, and S. sporoclivatus belong to the same genomospecies. Previously reported phenotypic data also supported this synonymy. Therefore, S. castelarensis and S. sporoclivatus should be reclassified as later heterotypic synonyms of S. antimycoticus. The type strain of S. antimycoticus is NBRC 12839T (=ATCC 23880T=CBS 660.68T=RIA 1198T=CGMCC 4.1591T=DSM 40284T=JCM 4228T=JCM 4621T=KCTC 9694T=NRRL 2421T=NRRL ISP-5284T=VKM Ac-1824T). This study also revealed that genome sequence-published S. violaceusniger NRRL F-8817 should be reclassified into S. antimycoticus.


Assuntos
Filogenia , Streptomyces/classificação , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Tipagem de Sequências Multilocus , Hibridização de Ácido Nucleico , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
5.
Parasitol Res ; 119(2): 713-724, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31912276

RESUMO

Intra-leukocytic gamonts consistent with the description of Hepatozoon griseisciuri Clark, 1958 are reported for the first time in Canadian eastern gray squirrels (Sciurus carolinensis Gmelin, 1788). Polymerase chain reaction (PCR) amplification and direct Sanger sequencing identified a pair of distinct genotypes at both a nuclear and mitochondrial locus; two 18S ribosomal RNA gene sequences (rDNA; genotype A and genotype B: 1816 base pairs (bp); 98.8% pairwise identity) and 2 distinct complete mitochondrial genome sequences (genotype A: 6311 bp; genotype B: 6114 bp; 89.1% pairwise identity) were obtained from 3 H. griseisciuri-infected squirrels sampled in Guelph, Ontario. The genetic content of both circular-mapping mitochondrial genomes was conventional for apicomplexan protists; each encoded for 3 protein-coding genes (cytochrome c oxidase subunit I (COI); cytochrome c oxidase subunit III (COIII); and cytochrome B (CytB)), 14 fragmented large subunit rDNA, 10 fragmented small subunit rDNA, and 8 unassigned rDNA. These genotypes, based on sequences obtained from a pair of loci from two parasite genomes, confirm the presence of at least two Hepatozoon species infecting Ontario eastern gray squirrels, one of which is likely to be conspecific with H. griseisciuri.


Assuntos
Eucoccidiida/classificação , Eucoccidiida/genética , Sciuridae/parasitologia , Animais , Citocromos b/genética , DNA Ribossômico/genética , Complexo IV da Cadeia de Transporte de Elétrons/genética , Eucoccidiida/isolamento & purificação , Genoma Mitocondrial/genética , Genótipo , Tipagem de Sequências Multilocus , Ontário , Filogenia , RNA Ribossômico 18S/genética
6.
BMC Infect Dis ; 20(1): 53, 2020 Jan 16.
Artigo em Inglês | MEDLINE | ID: mdl-31948401

RESUMO

BACKGROUND: This study was conducted to understand the molecular epidemiology of circulating Chlamydia trachomatis (Ct) strains in Sapporo, Japan. METHODS: A total of 713 endocervical samples collected from April 2016 to March 2019 were screened for Ct. The obtained Ct positive samples were analyzed by ompA genotyping and multilocus sequence analysis (MLSA). RESULTS: Eighty-three (11.6%) samples were positive for Ct plasmid DNA. Sequence analysis of the ompA gene from the 61 positive cases revealed eight genotypes: F (40.9%), E (19.6%), D (14.7%), G (9.8%), H (6.5%), I (3.2%), K (3.2%), and J (1.6%). The globally dominant genotype E and F strains were highly conserved with 13 ompA genetic variants being detected, whereas genotype D strains were the most diverse. Genetic characterization of D strains revealed that D1 genetic variants may be potentially specific to Sapporo. MLSA revealed 13 unique sequence types (STs) including four novel STs from 53 positive samples, with the globally dominant STs 39 and 19 being predominant. STs 39, 34, and 21 were exclusively associated with genotypes E and F indicating their global dominance. Novel ST70 and ST30 were specifically associated with genotype D. CONCLUSION: Our study has revealed the circulation of genetically diverse Ct strains in the women population of Sapporo, Japan. We suggest identifying a transmission network of those successful strains and implementing public health prevention strategies to control the spread of Ct in Sapporo.


Assuntos
Infecções por Chlamydia/microbiologia , Chlamydia trachomatis/genética , Chlamydia trachomatis/isolamento & purificação , Adulto , Proteínas da Membrana Bacteriana Externa/genética , Técnicas de Tipagem Bacteriana , Infecções por Chlamydia/epidemiologia , Chlamydia trachomatis/classificação , Feminino , Variação Genética , Genótipo , Humanos , Japão/epidemiologia , Tipagem de Sequências Multilocus
7.
Microbes Environ ; 35(1)2020.
Artigo em Inglês | MEDLINE | ID: mdl-31996499

RESUMO

In central Europe, soybean cultivation is gaining increasing importance to reduce protein imports from overseas and make cropping systems more sustainable. In the field, despite the inoculation of soybean with commercial rhizobia, its nodulation is low. In many parts of Europe, limited information is currently available on the genetic diversity of rhizobia and, thus, biological resources for selecting high nitrogen-fixing rhizobia are inadequate. These resources are urgently needed to improve soybean production in central Europe. The objective of the present study was to identify strains that have the potential to increase nitrogen fixation by and the yield of soybean in German soils. We isolated and characterized 77 soybean rhizobia from 18 different sampling sites. Based on a multilocus sequence analysis (MLSA), 71% of isolates were identified as Bradyrhizobium and 29% as Rhizobium. A comparative analysis of the nodD and nifH genes showed no significant differences, which indicated that the soybean rhizobia symbiotic genes in the present study belong to only one type. One isolate, GMF14 which was tolerant of a low temperature (4°C), exhibited higher nitrogen fixation in root nodules and a greater plant biomass than USDA 110 under cold conditions. These results strongly suggest that some indigenous rhizobia enhance biological nitrogen fixation and soybean yield due to their adaption to local conditions.


Assuntos
Bradyrhizobium/fisiologia , Rhizobium/fisiologia , Microbiologia do Solo , Soja/crescimento & desenvolvimento , Soja/microbiologia , Agricultura , Proteínas de Bactérias/genética , Bradyrhizobium/classificação , Bradyrhizobium/genética , Bradyrhizobium/metabolismo , Temperatura Baixa , Alemanha , Tipagem de Sequências Multilocus , Fixação de Nitrogênio/genética , Oxirredutases/genética , Filogenia , Rhizobium/classificação , Rhizobium/genética , Rhizobium/metabolismo , Nódulos Radiculares de Plantas/microbiologia , Estresse Fisiológico , Simbiose/genética
8.
J Med Microbiol ; 69(1): 96-103, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31769400

RESUMO

Enteroaggregative Escherichia coli (EAEC), a highly heterogeneous pathotype of E. coli classified as typical and atypical, are an emerging cause of acute and persistent diarrhea. We aimed to investigate whether population living in rural geographic areas, impacts in the heterogeneity, dissemination and antimicrobial susceptibility of EAEC strains. EAEC isolates (n=73) were analysed for the presence of 23 putative virulence factors, plasmid and antimicrobial resistance profiles, biofilm formation, pulsedfield gel electrophoresis (PFGE) and by multilocus sequence typing (MLST). The agg3A, agg4A, agn43, aap, shf, astA, pet, pic/set1A and sat genes, biofilm forming and antimicrobial resistance were statistically associated with typical EAEC. A low frequency of all isolates was resistant or showed a multidrug-resistance profile. No isolate showed the same plasmid profile. In total, 58 different pulsotypes were observed. Sixteen isolates analysed by MLST belonged to 15 different sequence types (ST) and showed a different PFGE pattern and virulence-gene profile. The fact that the communities are semi-isolated did not impact on the peculiar heterogeneity of EAEC, being characterized as epidemiologically independent strains.


Assuntos
Diarreia/epidemiologia , Diarreia/microbiologia , Infecções por Escherichia coli/epidemiologia , Infecções por Escherichia coli/microbiologia , Escherichia coli/classificação , Escherichia coli/genética , Heterogeneidade Genética , Criança , Pré-Escolar , Feminino , Humanos , Lactente , Recém-Nascido , Masculino , Testes de Sensibilidade Microbiana , Tipagem de Sequências Multilocus , Plasmídeos/análise , População Rural
9.
Arch Microbiol ; 202(1): 115-125, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31501949

RESUMO

Staphylococcus aureus is part of the normal flora of animals, and represents one of the leading causes of contagious mastitis in dairy herds worldwide. Sixty-seven epidemiologically unrelated S. aureus isolates from nasal and mastitis milk samples of dairy-producing animals (32 cows, 25 sheep, and 10 goats) were characterized by antimicrobial susceptibility testing and spa typing followed by multilocus sequence typing (MLST) on representative isolates and SCCmec-typing on methicillin-resistant S. aureus (MRSA) isolates. The highest resistance was observed to penicillin (64.2%, 43/67), followed by tetracycline (23.9%, 16/67), erythromycin (22.4%, 15/67), and streptomycin (17.9%, 12/67). In general, 18 spa types (including newly identified t16958) and 13 sequence types (STs) belonging to 8 clonal complexes (CCs) were detected. The cow-associated isolates were mainly assigned to CC5 (n = 18, related to t267-ST97, t521-ST352, t527-ST97, t304-ST6, and t084-ST15), followed by CC398 (n = 6, t937-ST291), CC45 (n = 3, t230-ST45), CC88 (n = 2, t2526-ST88), CC22 (n = 2, t3680-ST22), and CC522 (n = 1, t3576-ST522). Small ruminant isolates were mostly clustered into CC522 (n = 29, related to t3576, t1534, t16958, t7308, t7311, t7305 [ST522], t1534-ST2057, and t5428-ST2079). Two isolates from cows with mastitis were found to be MRSA, exhibited a composite profile of t937-ST291-SCCmecIV. No isolates carried the PVL and mecC genes. A significant difference in clonal types of S. aureus isolates from cows in comparison with those from small ruminants was found. This study demonstrated the circulation of diverse clones of S. aureus among dairy animals in Iran, with a different clonal composition between cows and small ruminants. The current study also reports MRSA-related mastitis in dairy cows, emphasizing the need for comprehensive surveillance.


Assuntos
Antibacterianos/farmacologia , Genótipo , Testes de Sensibilidade Microbiana/veterinária , Ruminantes/microbiologia , Infecções Estafilocócicas/veterinária , Staphylococcus aureus/efeitos dos fármacos , Animais , Bovinos , Indústria de Laticínios , Farmacorresistência Bacteriana/efeitos dos fármacos , Feminino , Staphylococcus aureus Resistente à Meticilina/efeitos dos fármacos , Tipagem de Sequências Multilocus , Ovinos , Infecções Estafilocócicas/microbiologia
10.
Int J Syst Evol Microbiol ; 70(1): 530-536, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31613739

RESUMO

Strain LMG 30378T was isolated from a hydrogen-oxidizing bacteria enrichment reactor inoculated with forest soil. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that this strain belonged to the genus Achromobacter. Multilocus sequence analysis combined with sequence analysis of a 765 bp nrd A gene fragment both showed Achromobacter agilis LMG 3411T and Achromobacter denitrificans LMG 1231T to be the closest-related neighbours to strain LMG 30378T. Genome sequence analysis revealed a draft genome of 6.81 Mb with a G+C content of 67.2 mol%. In silico DNA-DNA hybridization with A. denitrificans LMG 1231T and A. agilis LMG 3411T showed 42.7 and 42.5% similarity, respectively, confirming that strain LMG 30378T represented a novel Achromobacter species. Phenotypic and metabolic characterization revealed acid phosphatase activity and the absence of phosphoamidase activity as distinctive features. The draft genome composes all necessary metabolic components to fix carbon dioxide and to oxidize molecular hydrogen, suggesting that strain LMG 30378T is a key organism in the enrichment reactor. Together, these data demonstrate that strain LMG 30378T represents a novel species of the genus Achromobacter, for which the name Achromobacter veterisilvae sp. nov. is proposed. The type strain is LMG 30378T (=CCUG 71558T).


Assuntos
Achromobacter/classificação , Reatores Biológicos/microbiologia , Filogenia , Microbiologia do Solo , Achromobacter/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases , Bélgica , DNA Bacteriano/genética , Ácidos Graxos/química , Florestas , Hidrogênio , Tipagem de Sequências Multilocus , Hibridização de Ácido Nucleico , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
11.
Arch Microbiol ; 202(1): 143-151, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31535159

RESUMO

A gram-stain-negative, aerobic, non-spore-forming, rod-shaped, non-motile bacterium strain R4HLG17T was isolated from Tamarix ramosissima roots growing in Kumtag desert. The strain grew at salinities of 0-16% (w/v) NaCl (optimum 5-6%), pH 5-9 (optimum 7) and at 16-45 °C. Based on 16S rRNA gene sequence similarity, strain R4HLG17T belonged to the family Halomonadaceae and was most closely related to Halomonas lutea DSM 23508T(95.1%), followed by Halotalea alkalilenta AW-7T(94.8%), Salinicola acroporae S4-41T(94.8%), Salinicola halophilus CG4.1T(94.6%), and Larsenimonas salina M1-18T(94.4%). Multilocus sequence analysis (MLSA) based on the partial sequences of 16S rRNA, atpA, gyrB, rpoD, and secA genes indicated that the strain R4HLG17T formed an independent and monophyletic branch related to other genera of Halomonadaceae, supporting its placement as a new genus in this family. The draft genome of strain R4HLG17T was 3.6 Mb with a total G + C content of 55.1%. The average nucleotide identity to Halomonas lutea DSM 23508T was 83.5%. Q-9 was detected as the major respiratory quinone and summed feature 8 (C18:1ω7c/C18:1ω6c), summed feature 3 (C16:1ω7c/C16:1ω6c), and C16:0 as predominant cellular fatty acids. On the basis of chemotaxonomic, phylogenetic, and phenotypic evidence, strain R4HLG17T is concluded to represent a novel species of a new genus within Halomonadaceae, for which the name Phytohalomonas tamaricis gen. nov., sp. nov., is proposed. The type strain is R4HLG17T (=ACCC 19929T=KCTC 52415T).


Assuntos
Halomonadaceae/classificação , Raízes de Plantas/microbiologia , Tamaricaceae/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Clima Desértico , Ácidos Graxos/análise , Halomonadaceae/química , Halomonadaceae/genética , Tipagem de Sequências Multilocus , Hibridização de Ácido Nucleico , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Especificidade da Espécie
12.
Int J Syst Evol Microbiol ; 70(1): 465-472, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31639072

RESUMO

A novel actinobacterium, designated strain NEAU-C40T, was isolated from the rhizosphere soil of rice (Oryza sativa L.) collected from Northeast Agricultural University in Harbin, Heilongjiang province, north-east PR China, and was characterized using a polyphasic approach. On the basis of results of 16S rRNA gene sequence analysis, strain NEAU-C40T belongs to the genus Streptomyces, and shares highest sequence similarities with Streptomyces polygonati CGMCC 4.7237T (97.9%) and Streptomyces abietis DSM 42080T (97.9%). Morphological and chemotaxonomic characteristics of the strain also supported its assignment to the genus Streptomyces. Cell walls contained ll-diaminopimelic acid and the whole-cell hydrolysates were glucose, rhamnose and ribose. The major menaquinones were identified as MK-9(H8) and MK-9(H6). The major fatty acids were iso-C16:0, anteiso-C15:0, C16:0 and anteiso-C17:0. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol mannoside and an unidentified lipid. The genomic DNA G+C content of strain NEAU-C40T was 71.8 mol%. Moreover, multilocus sequence analysis based on five other housekeeping genes (atp D, gyr B, rpo B, rec A and trp B) and the low level of DNA-DNA relatedness allowed the isolate to be differentiated from its most closely related strains. On the basis of phenotypic, genotypic and phylogenetic data, strain NEAU-C40T can be characterized to represent a novel species of the genus Streptomyces, for which the name Streptomyces oryziradicis sp. nov. is proposed. The type strain is NEAU-C40T (=DSM 107943T=CCTCC AA 2018038T).


Assuntos
Oryza , Filogenia , Rizosfera , Microbiologia do Solo , Streptomyces/classificação , Técnicas de Tipagem Bacteriana , Composição de Bases , Parede Celular/química , China , DNA Bacteriano/genética , Ácido Diaminopimélico/química , Ácidos Graxos/química , Tipagem de Sequências Multilocus , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Streptomyces/isolamento & purificação , Vitamina K 2/análogos & derivados , Vitamina K 2/química
13.
J Dairy Sci ; 103(1): 852-857, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31733863

RESUMO

We performed a survey aimed at analyzing milk samples collected from cows with mastitis for the presence of extended-spectrum ß-lactamase (ESBL)-producing Escherichia coli. Single-quarter mastitic milk samples obtained from 400 cows in 23 Greek dairy herds with a history of E. coli mastitis were processed for the selective isolation of ESBL-producing E. coli. The antimicrobial susceptibility of the ESBL-producing isolates was analyzed using agar disk diffusion, and minimum inhibitory concentrations of colistin were determined by broth microdilution. We used PCR followed by DNA sequencing to characterize the ß-lactamases and mcr-1 (colistin resistance) genes, and for phylotyping and multilocus sequence typing. We found a total of 89/400 (22.25%) E. coli isolates from 12/23 (52%) farms. Six isolates originating from 6 cows on a single farm were ESBL producers and were resistant to cefquinome, amoxicillin-clavulanic acid, aztreonam, ampicillin, and colistin. Five of these isolates were resistant to trimethoprim-sulfamethoxazole, and 5 to streptomycin. The 6 ESBL producers were mcr-1-positive and carried blaTEM-1 genes; 3 also carried blaCTX-M genes, and 3 carried blaSHV genes. All of the ESBL producers belonged to phylogroup A, multilocus sequence type ST666 (n = 5), or a single locus variant of ST666 (n = 1). To our knowledge, this is the first report of endemic bovine mastitis caused by mcr-1-positive, ESBL-producing E. coli. These results highlight the value of active surveillance of antimicrobial resistance not commonly tested by diagnostic laboratories for the early detection of novel resistant strains.


Assuntos
Colistina/farmacologia , Infecções por Escherichia coli/veterinária , Escherichia coli/isolamento & purificação , Mastite Bovina/microbiologia , Animais , Antibacterianos/farmacologia , Bovinos , Cefalosporinas/farmacologia , Indústria de Laticínios , Farmacorresistência Bacteriana , Escherichia coli/efeitos dos fármacos , Escherichia coli/enzimologia , Escherichia coli/genética , Infecções por Escherichia coli/microbiologia , Proteínas de Escherichia coli/biossíntese , Fazendas , Feminino , Grécia , Testes de Sensibilidade Microbiana , Leite , Tipagem de Sequências Multilocus , beta-Lactamases/biossíntese , beta-Lactamases/genética
15.
Emerg Microbes Infect ; 9(1): 1-4, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-31859589

RESUMO

CRISPR-based typing was performed to subtype isolates of S. Typhimurium and its monophasic variant Salmonella 4,[5],12:i:- from humans and animals between 2009 and 2017 in China. CRISPR typing classified all isolates into two lineages and four sub-lineages. All isolates from Lineage II and Lineage IB-1 were Salmonella Typhimurium. All of Salmonella 4,[5],12:i: - isolates were distributed in Lineage IA and Lineage IB-2, which all belonged to ST34 by MLST typing. Only Lineage IB-2 contained ST34 isolates from both Salmonella Typhimurium and Salmonella 4,[5],12:i:-. Among the isolates of ST34, TST4 was identified as the most common CRISPR type representing 86.5% of Salmonella 4,[5],12:i:- and 14.5 % of Salmonella Typhimurium mainly from pigs and humans. This study demonstrated that TST4-ST34 isolates were predominant in Salmonella 4,[5],12:i:-, and pig was the main reservoir for Salmonella 4,[5],12:i:- in China, which might have the potential to transmit to humans by pig production.


Assuntos
Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas , Reservatórios de Doenças , Técnicas de Genotipagem/métodos , Carne/microbiologia , Salmonella typhimurium/classificação , Salmonella typhimurium/isolamento & purificação , Sus scrofa , Animais , China , Diarreia/microbiologia , Eletroforese em Gel de Campo Pulsado , Humanos , Tipagem de Sequências Multilocus , Filogenia , Infecções por Salmonella/microbiologia , Salmonella typhimurium/genética
16.
Acta Trop ; 201: 105189, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31580847

RESUMO

Since the description of the Leishmania genus, its identification and organization have been a challenge. A high number of molecular markers have been developed to resolve phylogenetic differences at the species level and for addressing key epidemiological and population genetics questions. Based on Multilocus enzyme electrophoresis (MLEE), Multilocus sequence typing (MLST) schemes have been developed using different gene candidates. From 38 original gene targets proposed by other authors, 27 of them were chosen. In silico selection was made by analyzing free access genomic sequence data of 33 Leishmania species, one Paraleishmania representative, and one outgroup, in order to select the best 15 loci. De novo amplifications and primers redesign of these 15 genes were analyzed over a panel of 20 reference strains and isolates. Phylogenetic analysis was made at every step. Two MLST schemes were selected. The first one was based on the analysis of three-gene fragments, and it is suitable for species assignment as well as basic phylogenetic studies. By the addition of seven-genes, an approach based on the analysis of ten-gene fragments was also proposed. This is the first work that two optimized MLST schemes have been suggested, validated against a phylogenetically diverse panel of Leishmania isolates. MLST is potentially a powerful phylogenetic approach, and most probably the new gold standard for Leishmania spp. characterization.


Assuntos
Leishmania/genética , Tipagem de Sequências Multilocus/métodos , Leishmania/classificação , Filogenia
17.
APMIS ; 128(1): 25-34, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31628820

RESUMO

Eradication failure of Helicobacter pylori infection could play a causal role in progression of gastric disorders. In this study, infection with H. pylori was followed in gastric biopsies of symptomatic adult patients at two phases during 1-year period. Analyses were done to show association of therapeutic regimens with the refractory infection, changes in sequence types (STs) and minimum inhibitory concentration (MIC) values, and progression of histopathological changes. Infection with H. pylori was confirmed in 32.3% (57/170) of the patients. Persistent infection with H. pylori was confirmed in 14 out of the 25 patients (56%) who participated at the second phase of the study. A difference between primary and secondary resistance rates to clarithromycin (49% vs 64.3%), metronidazole (76.36% vs 100%), and ciprofloxacin (45% vs 57.1%) was detected. Although the re-emerged strains in patients with refractory infection did not show alteration in STs, their MIC50 values showed twofold increases for clarithromycin and ciprofloxacin. While ciprofloxacin containing regimens were more successful, failure of metronidazole containing regimens was detected in 77% of the patients. Consequently, inappropriate medication has an impact on refractory H. pylori infection, which could cause to a rise in resistance levels to antibiotics and progression of pathological disorders.


Assuntos
Antibacterianos/uso terapêutico , Farmacorresistência Bacteriana Múltipla , Infecções por Helicobacter/tratamento farmacológico , Infecções por Helicobacter/patologia , Helicobacter pylori/efeitos dos fármacos , Idoso , Idoso de 80 Anos ou mais , Antibacterianos/farmacologia , Técnicas de Tipagem Bacteriana , Biópsia , Ciprofloxacino/farmacologia , Claritromicina/farmacologia , Feminino , Seguimentos , Técnicas Histológicas , Humanos , Concentração Inibidora 50 , Masculino , Testes de Sensibilidade Microbiana , Pessoa de Meia-Idade , Tipagem de Sequências Multilocus , Estômago/microbiologia , Estômago/patologia
18.
Lett Appl Microbiol ; 70(1): 29-35, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31631350

RESUMO

The objective of this study was to undertake a microbiological survey of foods, animal faeces and wastewater samples for Clostridium difficile, and determine the genotypes and antimicrobial susceptibilities of isolates. A total of 211 samples were tested for C. difficile using culture methods. Thirteen toxigenic C. difficile isolates were obtained; ten from wastewater samples, one each from pig and duck faeces and another from a raw meat product. Eight PCR-ribotypes (RTs) were identified, including two novel RTs (878 and 879). Single-nucleotide polymorphism analysis using WGS data for all isolates provided greater discrimination between C. difficile isolates within the same RT and multilocus sequence typing (MLST) profiles. All C. difficile isolates were found to be susceptible to the first-line human antimicrobials used to treat C. difficile infection. SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first study to report the isolation of Clostridium difficile from animals, food and wastewater in New Zealand (NZ) and provides important data with respect to ribotypes and multilocus sequence typing profiles, whole genome sequence and antimicrobial susceptibilities. The results highlight the need for further investigations into the epidemiology of C. difficile in NZ and to elucidate the role of the environmental and food sources as transmission routes of human infection.


Assuntos
Clostridium difficile/isolamento & purificação , Fezes/microbiologia , Carne/microbiologia , Águas Residuárias/microbiologia , Animais , Antibacterianos/farmacologia , Clostridium difficile/classificação , Clostridium difficile/efeitos dos fármacos , Clostridium difficile/genética , Patos , Contaminação de Alimentos/análise , Genótipo , Humanos , Testes de Sensibilidade Microbiana , Tipagem de Sequências Multilocus , Nova Zelândia , Suínos
19.
Ann Lab Med ; 40(1): 15-20, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31432634

RESUMO

BACKGROUND: Carbapenem-resistant K. pneumoniae 2297, isolated from a patient treated with tigecycline for pneumonia, developed tigecycline resistance, in contrast to carbapenem-resistant isolate 1215, which was collected four months prior to the 2297 isolate. Mechanisms underlying tigecycline resistance were elucidated for the clinical isolates. METHODS: The tigecycline minimum inhibitory concentration (MIC) was determined using the broth microdilution method, with or without phenylalanine-arginine ß-naphthylamide (PABN), and whole-genome sequencing was carried out by single-molecule real-time sequencing. The expression levels of the genes acrA, oqxA, ramA, rarA, and rpoB were determined by reverse-transcription quantitative PCR. RESULTS: Both isolates presented identical antibiograms, except for tigecycline, which showed an MIC of 0.5 mg/L in 1215 and 2 mg/L in 2297. The addition of PABN to tigecycline-resistant 2297 caused a four-fold decrease in the tigecycline MIC to 0.5 mg/L, although acrA expression (encoding the AcrAB efflux pump) was upregulated by 2.5 fold and ramA expression (encoding the pump activator RamA) was upregulated by 1.4 fold. We identified a 6,096-bp fragment insertion flanking direct TATAT repeats that disrupted the romA gene located upstream of ramA in the chromosome of K. pneumoniae 2297; the insertion led the ramA gene promoter replacement resulting in stronger activation of the gene. CONCLUSIONS: The K. pneumoniae isolate developed tigecycline resistance during tigecycline treatment. It was related to the overexpression of the AcrAB resistance-nodulation-cell division efflux system due to promoter replacement.


Assuntos
Proteínas de Bactérias/metabolismo , Farmacorresistência Bacteriana/genética , Klebsiella pneumoniae/genética , Proteínas de Membrana Transportadoras/metabolismo , Antibacterianos/farmacologia , Antibacterianos/uso terapêutico , Proteínas de Bactérias/genética , Genoma Bacteriano , Humanos , Infecções por Klebsiella/diagnóstico , Infecções por Klebsiella/tratamento farmacológico , Infecções por Klebsiella/microbiologia , Klebsiella pneumoniae/efeitos dos fármacos , Klebsiella pneumoniae/isolamento & purificação , Proteínas de Membrana Transportadoras/genética , Testes de Sensibilidade Microbiana , Tipagem de Sequências Multilocus , Regiões Promotoras Genéticas , Tigeciclina/farmacologia , Tigeciclina/uso terapêutico , Sequenciamento Completo do Genoma , beta-Lactamases/genética , beta-Lactamases/metabolismo
20.
Rev Chilena Infectol ; 36(5): 585-590, 2019 Oct.
Artigo em Espanhol | MEDLINE | ID: mdl-31859799

RESUMO

BACKGROUND: Listeria monocytogenes is a foodborne pathogen that causes listeriosis, a disease that can present as febrile gastroenteritis or as an invasive form that has high mortality rates. So far, the genetic diversity of strains of L. monocytogenes isolated from patients, foods and environmental sources in Chile has been poorly studied. AIM: To characterize genetically L. monocytogenes strains received by the Institute of Public Health of Chile (ISP) between 2007 and 2014. METHODS: We selected 94 strains of L. monocytogenes corresponding to 94 different pulsotypes identified by pulsed field gel electrophoresis (PFGE), DNA was extracted and serotyping was performed by polymerase chain reaction (PCR) and multilocus sequence typing (MLST). RESULTS: The most common serotype was 4b (55.3%), followed by serotypes 1/2a (25.5%), 1/2b (17%) and 1/2c (2.2%). 32 sequence-type (ST) were identified, of which 4 were new, and the predominant ones were ST1 (28.7%) and ST2 (13.8%). All the strains of L. monocytogenes were grouped in Lineages I and II. CONCLUSIONS: A great genetic variability was observed in the strains of L. monocytogenes analyzed, being predominant the ST1 and ST2, both belonging to Lineage I. Our results contribute to know the population structure of this pathogen in Chile and its presence in clinical samples, food and the environment.


Assuntos
Listeria monocytogenes/genética , Listeria monocytogenes/isolamento & purificação , Chile , Eletroforese em Gel de Campo Pulsado , Microbiologia Ambiental , Microbiologia de Alimentos , Variação Genética , Humanos , Listeriose/microbiologia , Tipagem de Sequências Multilocus , Reação em Cadeia da Polimerase , Sorotipagem , Fatores de Tempo
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA