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1.
BMC Infect Dis ; 20(1): 816, 2020 Nov 10.
Artigo em Inglês | MEDLINE | ID: mdl-33167886

RESUMO

BACKGROUND: The prevalence of Staphylococcus aureus varies depending on the healthcare facility, region and country. To understand its genetic diversity, transmission, dissemination, epidemiology and evolution in a particular geographical location, it is important to understand the similarities and variations in the population being studied. This can be achieved by using various molecular characterisation techniques. This study aimed to provide detailed molecular characterisation of South African mecA-positive S. aureus blood culture isolates by describing the SCCmec types, spa types and to lesser extent, the sequence types obtained from two consecutive national surveillance studies. METHODS: S. aureus blood culture isolates from a national laboratory-based and enhanced surveillance programme were identified and antimicrobial susceptibility testing was performed using automated systems. A real-time PCR assay confirmed the presence of the methicillin-resistance determinant, mecA. Conventional PCR assays were used to identify the SCCmec type and spa type, which was subsequently analysed using the Ridom StaphType™ software. Multilocus sequence typing was performed on selected isolates using conventional methods. MRSA clones were defined by their sequence type (ST), SCCmec type and spa type. RESULTS: A detailed description of findings is reported in this manuscript. SCCmec type III predominated overall followed by type IV. A total of 71 different spa types and 24 novel spa types were observed. Spa type t037 was the most common and predominated throughout followed by t1257. Isolates were multidrug resistant; isolates belonging to all SCCmec types were resistant to most of the antibiotics with the exception of type I; isolates with spa type t045 showed resistance to all antibiotics except vancomycin. The most diverse SCCmec-spa type complex was composed of the SCCmec type IV element and 53 different spa types. CONCLUSION: Although ST data was limited, thereby limiting the number of clones that could be identified, the circulating clones were relatively diverse.


Assuntos
Proteínas de Bactérias/genética , Variação Genética , Sequências Repetitivas Dispersas/genética , Staphylococcus aureus Resistente à Meticilina/genética , Proteínas de Ligação às Penicilinas/genética , Infecções Estafilocócicas/epidemiologia , Proteína Estafilocócica A/genética , Antibacterianos/farmacologia , Antibacterianos/uso terapêutico , Proteínas de Bactérias/sangue , Hemocultura , Farmacorresistência Bacteriana Múltipla/efeitos dos fármacos , Farmacorresistência Bacteriana Múltipla/genética , Humanos , Meticilina/farmacologia , Meticilina/uso terapêutico , Resistência a Meticilina/efeitos dos fármacos , Staphylococcus aureus Resistente à Meticilina/efeitos dos fármacos , Staphylococcus aureus Resistente à Meticilina/isolamento & purificação , Testes de Sensibilidade Microbiana , Tipagem de Sequências Multilocus , Proteínas de Ligação às Penicilinas/sangue , Reação em Cadeia da Polimerase em Tempo Real , África do Sul/epidemiologia , Infecções Estafilocócicas/tratamento farmacológico , Infecções Estafilocócicas/microbiologia , Vancomicina/farmacologia , Vancomicina/uso terapêutico
2.
Mem Inst Oswaldo Cruz ; 115: e200371, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33174904

RESUMO

BACKGROUND: Acinetobacter baumannii outbreaks have been associated with pandemic International Clones (ICs), but the virulence factors involved with their pathogenicity are sparsely understood. Pigment production has been linked with bacterial pathogenicity, however, this phenotype is rarely observed in A. baumannii. OBJECTIVES: This study aimed to characterise the reddish-brown pigment produced by A. baumannii strains, and to determine its biosynthetic pathway by genomic approaches. METHODS: Pigment characterisation and antimicrobial susceptibility were conducted by phenotypic tests. The clonal relationship was obtained by pulsed field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST). The genome of an A. baumannii was obtained for characterisation of genes involved with pigment production. FINDINGS: The pyomelanin was the pigment produced by A. baumannii. Strains were extensively drug resistant and belonged to the IC-5/ST79. The pyomelanin biosynthetic pathway was determined and presented a particular architecture concerning the peripheral (tyrB, phhB and hpd) and central (hmgB, hmgC and hmgR) metabolic pathway genes. The identification of a distant HmgA homologue, probably without dioxygenase activity, could explain pyomelanin production. Virulence determinants involved with adherence (csuA/BABCDE and a T5bSS-carrying genomic island), and iron uptake (basABCDEFGHIJ, bauABCDEF and barAB) were characterised. MAIN CONCLUSION: There is a biosynthetic pathway compatible with the pyomelanin production observed in persistent A. baumannii IC-5 strains.


Assuntos
Infecções por Acinetobacter/microbiologia , Acinetobacter baumannii/efeitos dos fármacos , Acinetobacter baumannii/genética , Vias Biossintéticas/genética , Melaninas , Acinetobacter baumannii/isolamento & purificação , Antibacterianos/farmacologia , Eletroforese em Gel de Campo Pulsado , Humanos , Testes de Sensibilidade Microbiana , Tipagem de Sequências Multilocus , Pandemias , beta-Lactamases
3.
Zhonghua Yu Fang Yi Xue Za Zhi ; 54(10): 1121-1126, 2020 Oct 06.
Artigo em Chinês | MEDLINE | ID: mdl-33115199

RESUMO

Objective: To investigate the prevalence of Escherchia albertii in Shanxi province. Methods: The chicken intestines were enriched in EC broth. The eae gene was detected by PCR, and the eae-positive EC enrichments were inoculated in MacConkey agar plate. The eae-positive lactose non-fermenting isolates were presumed as Escherchia albertii, and then analyzed by triplex-PCR, 16S rDNA sequencing and MLST. Results: Two suspected Escherchia albertii were isolated from 250 samples of chicken intestines. It was identified as Escherchia albertii by phenotypic, specific genes,16S rDNA sequencing, and MLST analyses. The cytolethal distending toxin B (cdtB) showed positive by PCR,and they were clusted to Ⅱ/Ⅲ/Ⅴ group by sequencing. Conclusion: This study showed that the Escherchia albertii was existed in Shanxi province, China.


Assuntos
Escherichia , Animais , China , Escherichia/genética , Tipagem de Sequências Multilocus , Reação em Cadeia da Polimerase
4.
Shokuhin Eiseigaku Zasshi ; 61(4): 126-131, 2020.
Artigo em Japonês | MEDLINE | ID: mdl-33012766

RESUMO

Campylobacter is one of the most important causes of food-borne infectious diseases. Antibiotics are rarely needed to treat campylobacteriosis, but occasionally used in severe or prolonged cases. Consumption of contaminated bovine liver is a source of campylobacteriosis. Bovine liver can be contaminated with Campylobacter on the surface and inside by the bile at slaughterhouses. Therefore, we investigated the current prevalence and characteristics of Campylobacter in bovine bile at a slaughterhouse. Campylobacter was isolated from 35.7% (55/154) of bile samples. C. jejuni and C. fetus were the two most frequent species. High antimicrobial resistant rates in C. jejuni were observed against tetracycline (63.0%) and ciprofloxacin (44.4%). Multi-locus sequence typing divided C. jejuni isolates (27 isolates) into 12 sequence types (STs) in which ST806 was the most frequent ST and accounted for 37.0%. All C. fetus were identified as C. fetus subsp. fetus which can cause systemic infections. High antimicrobial resistant rates in C. fetus were observed against ciprofloxacin (66.6%), streptomycin (58.3%) and tetracycline (33.3%). All the C. fetus isolates were divided into two STs, ST3 (16 isolates) and ST6 (8 isolates). Of the 16 ST3 isolates, 15 (93.8%) were resistant to both streptomycin and ciprofloxacin. Our data shows high prevalence of Campylobacter in bovine bile and their high rates of antimicrobial resistance. Preventing bile contamination of bovine liver at slaughterhouses is thus considered to be one of control measures to reduce the risk of Campylobacter infections.


Assuntos
Bile , Campylobacter , Vesícula Biliar , Animais , Anti-Infecciosos/farmacologia , Bile/microbiologia , Campylobacter/classificação , Campylobacter/efeitos dos fármacos , Campylobacter/genética , Campylobacter/isolamento & purificação , Bovinos , Farmacorresistência Bacteriana , Microbiologia de Alimentos , Vesícula Biliar/microbiologia , Tipagem de Sequências Multilocus , Prevalência
5.
Epidemiol Mikrobiol Imunol ; 69(3): 134-141, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33086855

RESUMO

AIM: In order to improve the surveillance of invasive pneumococcal disease (IPD), the National Reference Laboratory (NRL) for Streptococcal Infections implemented whole genome sequencing (WGS) of Streptococcus pneumoniae. This article reports the first WGS data on S. pneumoniae isolates in the Czech Republic. MATERIAL AND METHODS: Thirty-five isolates of S. pneumoniae from IPD recovered in 2017-2019 were selected for WGS. These were serotypes 4, 8, 9V, 19A, and 22F, which were determined by the Quellung reaction in combination with endpoint multiplex PCR (mPCR). Multilocus sequence typing (MLST) is routinely used for more detailed analysis termed sequence typing. The selected isolates were analysed by WGS on the Illumina MiSeq platform. The sequences obtained were processed using the Velvet de novo Assembler software. The assembled genomes were uploaded into the PubMLST database, using the BIGSdb platform, and then scanned automatically and molecularly characterized. The isolates were compared at three resolution levels: seven MLST genes, 53 ribosomal genes (rMLST), and 1420 genes (all loci). The all loci scheme covers MLST genes, ribosomal genes, and core genome MLST genes (cgMLST). These are all currently defined genes of S. pneumoniae available in the PubMLST database. Distance matrices based on the number and variability of all loci analysed were generated automatically using the Genome Comparator tool. Phylogenetic networks were created and edited with the SplitsTree4 package, using the NeighborNet algorithm. The final graphics were edited with the Inkscape software. RESULTS: Based on an overall view of the phylogenetic networks, it can be concluded that the genetic lines within each of S. pneumoniae serotypes 4, 8, 9V, 19A, and 22F are highly unrelated, to the same extent as if the isolates were of different serotypes. S. pneumoniae isolates of the same serotype, whether or not of the same sequence type, can be described, based on the results, as a non-homogeneous group with a number of unrelated genetic clusters that share genes assigning them to a specific serotype. WGS has also shown its discriminatory power, allowing the assignment of isolates of the same serotype and sequence type to different genetic clusters. CONCLUSION: Of the methods used so far in the Czech Republic, WGS allows the most detailed characterization of S. pneumoniae isolates. It is highly desirable to integrate it in the molecular surveillance of IPD in the Czech Republic, similarly to other countries in Europe and in the world.


Assuntos
Infecções Pneumocócicas , Sequenciamento Completo do Genoma , República Tcheca , Europa (Continente) , Humanos , Tipagem de Sequências Multilocus , Filogenia
6.
BMC Bioinformatics ; 21(1): 441, 2020 Oct 07.
Artigo em Inglês | MEDLINE | ID: mdl-33028201

RESUMO

BACKGROUND: Inferring phylogenetic relationships of polyploid species and their diploid ancestors (leading to reticulate phylogenies in the case of an allopolyploid origin) based on multi-locus sequence data is complicated by the unknown assignment of alleles found in polyploids to diploid subgenomes. A parsimony-based approach to this problem has been proposed by Oberprieler et al. (Methods Ecol Evol 8:835-849, 2017), however, its implementation is of limited practical value. In addition to previously identified shortcomings, it has been found that in some cases, the obtained results barely satisfy the applied criterion. To be of better use to other researchers, a reimplementation with methodological refinement appears to be indispensable. RESULTS: We present the AllCoPol package, which provides a heuristic method for assigning alleles from polyploids to diploid subgenomes based on the Minimizing Deep Coalescences (MDC) criterion in multi-locus sequence datasets. An additional consensus approach further allows to assess the confidence of phylogenetic reconstructions. Simulations of tetra- and hexaploids show that under simplifying assumptions such as completely disomic inheritance, the topological errors of reconstructed phylogenies are similar to those of MDC species trees based on the true allele partition. CONCLUSIONS: AllCoPol is a Python package for phylogenetic reconstructions of polyploids offering enhanced functionality as well as improved usability. The included methods are supplied as command line tools without the need for prior programming knowledge.


Assuntos
Interface Usuário-Computador , Alelos , Bases de Dados Genéticas , Leucanthemum/classificação , Leucanthemum/genética , Tipagem de Sequências Multilocus , Filogenia , Poliploidia
7.
Int J Food Microbiol ; 335: 108857, 2020 Dec 16.
Artigo em Inglês | MEDLINE | ID: mdl-32947144

RESUMO

Cronobacter species (Cronobacter spp.) are important foodborne pathogens that can infect and cause serious life-threatening diseases in infants and immunocompromised elderly. This study aimed to acquire data on Cronobacter spp. contamination of aquatic products in China from 2011 to 2016. In total, 800 aquatic products were tested, and the overall contamination rate for Cronobacter spp. was 3.9% (31/800). The average contamination level of the positive samples was 2.05 MPN/g. Four species and nine serotypes were identified among 33 isolates, of which the C. sakazakii serogroup O1 (n = 9) was the primary serotype. The majority of Cronobacter spp. strains harbored highest resistance against cephalothin (84.8%), followed by tetracycline (6.1%), trimethoprim/sulfameth-oxazole (3.0%) and chloramphenicol (3.0%). Two isolates were resistant to three antibiotics. In total, 26 sequence types and 33 CRISPR types (including 6 new STs and 26 new CTs) were identified, which indicates the extremely high diversity of Cronobacter spp. in aquatic products. Pathogenic C. sakazakii ST4, ST1, and C. malonaticus ST7 were also observed. Overall, this large-scale study revealed the relatively low prevalence and high genetic diversity of Cronobacter spp. in aquatic products in China, and the findings provide valuable information that can guide the establishment of effective measures for the control and precaution of Cronobacter spp. in aquatic products during production processes.


Assuntos
Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas , Cronobacter/classificação , Cronobacter/isolamento & purificação , Farmacorresistência Bacteriana , Alimentos Marinhos/microbiologia , Antibacterianos/farmacologia , Cefalotina/farmacologia , China , Cloranfenicol/farmacologia , Cronobacter sakazakii/classificação , Cronobacter sakazakii/isolamento & purificação , Contaminação de Alimentos , Microbiologia de Alimentos , Variação Genética , Tipagem de Sequências Multilocus , Prevalência , Sorotipagem , Tetraciclina/farmacologia , Trimetoprima/farmacologia
8.
Antimicrob Resist Infect Control ; 9(1): 154, 2020 09 22.
Artigo em Inglês | MEDLINE | ID: mdl-32962759

RESUMO

BACKGROUND: Currently, hospitals have been forced to divert substantial resources to cope with the ongoing coronavirus disease 2019 (COVID-19) pandemic. It is unclear if this situation will affect long-standing infection prevention practices and impact on healthcare associated infections. Here, we report a nosocomial cluster of vancomycin-resistant enterococci (VRE) that occurred on a COVID-19 dedicated intensive care unit (ICU) despite intensified contact precautions during the current pandemic. Whole genome sequence-based typing (WGS) was used to investigate genetic relatedness of VRE isolates collected from COVID-19 and non-COVID-19 patients during the outbreak and to compare them to environmental VRE samples. METHODS: Five VRE isolated from patients (three clinical and two screening samples) as well as 11 VRE and six vancomycin susceptible Enterococcus faecium (E. faecium) samples from environmental sites underwent WGS during the outbreak investigation. Isolate relatedness was determined using core genome multilocus sequence typing (cgMLST). RESULTS: WGS revealed two genotypic distinct VRE clusters with genetically closely related patient and environmental isolates. The cluster was terminated by enhanced infection control bundle strategies. CONCLUSIONS: Our results illustrate the importance of continued adherence to infection prevention and control measures during the COVID-19 pandemic to prevent VRE transmission and healthcare associated infections.


Assuntos
Coinfecção/tratamento farmacológico , Infecção Hospitalar/epidemiologia , Infecções por Bactérias Gram-Positivas/tratamento farmacológico , Infecções por Bactérias Gram-Positivas/epidemiologia , Enterococos Resistentes à Vancomicina/efeitos dos fármacos , Betacoronavirus , Coinfecção/microbiologia , Infecções por Coronavirus/patologia , Infecção Hospitalar/tratamento farmacológico , Infecção Hospitalar/microbiologia , Surtos de Doenças , Genoma Bacteriano/genética , Infecções por Bactérias Gram-Positivas/microbiologia , Humanos , Controle de Infecções , Unidades de Terapia Intensiva , Tipagem de Sequências Multilocus , Pandemias , Pneumonia Viral/patologia , Prevenção Primária , Enterococos Resistentes à Vancomicina/genética , Enterococos Resistentes à Vancomicina/isolamento & purificação , Sequenciamento Completo do Genoma
9.
Rev Soc Bras Med Trop ; 53: e20190422, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32935773

RESUMO

INTRODUCTION: The average annual incidence of cryptococcosis in Colombia is 0.23 cases per 100,000 inhabitants in the general population, and 1.1 cases per 1000 in inhabitants with Acquired Immune Deficiency Syndrome (AIDS). In addition, the causal fungus has been isolated from the environment, with serotypes A-B and C in different regions. This study aims to determine the genetic association between clinical and environmental isolates of C. neoformans/C. gattii in Colombia. METHODS: Multilocus sequence typing (MLST) was used to identify possible clones, providing information about the epidemiology, ecology, and etiology of this pathogen in Colombia. RESULTS: A total of 110 strains, both clinical (n=61) and environmental (n=49), with 21 MLST sequence types (ST) of C. neoformans (n=14STs) and C. gattii (n=7STs) were identified. The STs which shared clinical and environmental isolate sources were grouped in different geographical categories; for C. neoformans, ST93 was identified in six departments, ST77 in five departments; and for C. gattii, ST25 was identified in three departments and ST79 in two. CONCLUSIONS: High genetic diversity was found in isolates of C. neoformans/gattii by MLST, suggesting the presence of environmental sources harboring strains which may be sources of infection for humans, especially in immunocompromised patients; these data contribute to the information available in the country on the distribution and molecular variability of C. neoformans and C. gattii isolates recovered in Colombia.


Assuntos
Criptococose , Cryptococcus gattii , Cryptococcus neoformans , Colômbia , Variação Genética , Genótipo , Humanos , Tipagem de Sequências Multilocus , Técnicas de Tipagem Micológica
10.
Dis Aquat Organ ; 141: 53-69, 2020 Sep 17.
Artigo em Inglês | MEDLINE | ID: mdl-32940251

RESUMO

Streptococcus iniae is a Gram-positive, opportunistically zoonotic bacterium infective to a wide variety of farmed and wild fish species worldwide. Outbreaks in wild fish can have detrimental environmental and cultural impacts, and mortality events in aquaculture can result in significant economic losses. As an emerging or re-emerging pathogen of global significance, understanding the coalescing factors contributing to piscine streptococcosis is crucial for developing strategies to control infections. Intraspecific antigenic and genetic variability of S. iniae has made development of autogenous vaccines a challenge, particularly where the diversity of locally endemic S. iniae strains is unknown. This study genetically and phenotypically characterized 11 S. iniae isolates from diseased wild and farmed fish from North America, Central America, and the Caribbean. A multilocus sequence analysis (MLSA) scheme was developed to phylogenetically compare these isolates to 84 other strains of Streptococcus spp. relevant to aquaculture. MLSA generated phylogenies comparable to established genotyping methods, and isolates formed distinct clades related to phenotype and host species. The endothelial Oreochromis mossambicus bulbus arteriosus cell line and whole blood from rainbow trout Oncorhynchus mykiss, Nile tilapia Oreochromis niloticus, and white sturgeon Acipenser transmontanus were used to investigate the persistence and virulence of the 11 isolates using in vitro assays. In vivo challenges using an O. niloticus model were used to evaluate virulence by the intragastric route of infection. Isolates showed significant differences (p < 0.05) in virulence and persistence, with some correlation to genogroup, establishing a basis for further work uncovering genetic factors leading to increased pathogenicity.


Assuntos
Doenças dos Peixes , Infecções Estreptocócicas/veterinária , Streptococcus iniae , Animais , Região do Caribe , América Central , Tipagem de Sequências Multilocus/veterinária , Índias Ocidentais
11.
PLoS One ; 15(9): e0239146, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32976521

RESUMO

The first objective of this study was to determine the GenoType NTM-DR assay performance for subspecies identification in Mycobacterium abscessus complex isolates. The second objective was to evaluate the GenoType NTM-DR assay ability to detect clarithromycin and amikacin resistance in M. abscessus complex isolates compared with drug susceptibility testing (DST) and PCR sequencing of the erm(41), rrl and rrs genes. The concordance between the GenoType NTM-DR and MLST results concerning subspecies identification was 100%. The wild type and mutated alleles of the rrl and rrs genes were detected by the GenoType NTM-DR assay and PCR sequencing with 100% (115/115) agreement. Similarly, 100% concordance between GenoType NTM-DR and DST was observed for clarithromycin and amikacin testing. Sensitivity for the detection of clarithromycin and amikacin resistance was 100%. The GenoType NTM-DR assay provides a robust and complementary tool to the gold standard methods (MLST and broth microdilution) for subspecies identification and drug resistance detection.


Assuntos
Antibacterianos/farmacologia , Farmacorresistência Bacteriana/genética , Técnicas de Genotipagem/instrumentação , Testes de Sensibilidade Microbiana/instrumentação , Mycobacterium abscessus/genética , Kit de Reagentes para Diagnóstico , Amicacina/farmacologia , Amicacina/uso terapêutico , Antibacterianos/uso terapêutico , Claritromicina/farmacologia , Claritromicina/uso terapêutico , Análise Mutacional de DNA/instrumentação , DNA Bacteriano/genética , DNA Bacteriano/isolamento & purificação , Genes Bacterianos/genética , Humanos , Tipagem de Sequências Multilocus , Mutação , Infecções por Mycobacterium não Tuberculosas/tratamento farmacológico , Infecções por Mycobacterium não Tuberculosas/microbiologia , Mycobacterium abscessus/isolamento & purificação , Reação em Cadeia da Polimerase
12.
PLoS One ; 15(9): e0238991, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32946486

RESUMO

BACKGROUND: Invasive Staphylococcus aureus infections are a common cause of morbidity and mortality in children. In the early 2000's the proportion of infections due the methicillin-resistant S. aureus (MRSA) increased rapidly. We described the clinical and molecular epidemiology of invasive S. aureus disease in a pediatric population. METHODS: We prospectively identified children in Utah with invasive S. aureus infections. Medical records were reviewed to determine diagnosis and clinical characteristics. Isolates were genotyped using multi-locus sequence typing. The presence of genes encoding the Panton-Valentine leukocidin (PVL) was determined using polymerase chain reaction. RESULTS: Over a 4-year period between January 2009 and December 2012, we identified 357 children, hospitalized at Primary Children's Hospital, with invasive S. aureus infections and isolates available for the study. Methicillin-susceptible S. aureus (MSSA) caused 79% of disease, while MRSA caused only 21% of disease. Mortality associated with invasive S. aureus infection was 3.6%. The most common diagnoses were osteoarticular infections (38%) followed by central line associated blood stream infections (19%) and pneumonia (12%). We identified 41 multi-locus sequence types. The majority of isolates belonged to 6 predominant clonal complexes (CC5, CC8, CC15, CC30, CC45, CC59). PVL was present in a minority (16%) of isolates, of which most were ST8 MRSA. CONCLUSIONS: MSSA was the primary cause of invasive S. aureus infections at our institution throughout the study period. A limited number of predominant strains accounted for the majority of invasive disease. The classic virulence factor PVL was uncommon in MSSA isolates. Further study is needed to improve our understanding of S. aureus virulence and disease pathogenesis.


Assuntos
Staphylococcus aureus Resistente à Meticilina/isolamento & purificação , Infecções Estafilocócicas/epidemiologia , Staphylococcus aureus/genética , Antibacterianos/uso terapêutico , Técnicas de Tipagem Bacteriana/métodos , Criança , Pré-Escolar , Feminino , Genótipo , Humanos , Masculino , Staphylococcus aureus Resistente à Meticilina/genética , Staphylococcus aureus Resistente à Meticilina/patogenicidade , Testes de Sensibilidade Microbiana , Epidemiologia Molecular/métodos , Tipagem de Sequências Multilocus/métodos , Infecções Estafilocócicas/genética , Staphylococcus aureus/patogenicidade , Utah/epidemiologia , Fatores de Virulência/genética
13.
Int J Syst Evol Microbiol ; 70(10): 5197-5204, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32821032

RESUMO

A novel endogenous actinobacteria strain, designated TRM 66187T, was isolated from Lycium ruthenicum sampled at Alar, Xinjiang, Northwest PR China, and characterized using a polyphasic taxonomic approach. Phylogenetic analysis based on 16S rRNA gene sequences affiliated strain TRM 66187T with the genus Streptomyces. The whole-cell sugar pattern of TRM 66187T consisted of galactose, glucose and ribose. The predominant menaquinones were MK-9(H4) and MK-9(H6). Major cellular fatty acids were iso-C14:0, iso-C15:0, anteiso-C15:0 and anteiso-C16:0. The detected polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside and two unidentified polar lipids. The G+C content of strain TRM 66187T was 71.8 mol%. Results of phylogenetic analysis showed that strain TRM 66187T had 98.48% 16S rRNA gene sequence similarity to the closest described species Streptomyces qinglanensis DSM 42035T. The average nucleotide identity value between strain TRM 66187T and the closest related strain Streptomyces qinglanensis DSM 42035T was calculated to be 77.2%. The digital DNA-DNA hybridization value between them was 22.4%. Multilocus sequence analyses based on five housekeeping genes (atpD, gyrB, recA, rpoB and trpB) also indicated that strain TRM 66187T should be assigned to the genus Streptomyces. On the basis of evidence from this polyphasic study, strain TRM 66187T should be designated as representing a novel species of the genus Streptomyces, for which the name Streptomyces lycii sp. nov. is proposed. The type strain is TRM 66187T (=LMG 31493T=CCTCC AA 2018094T).


Assuntos
Lycium/microbiologia , Filogenia , Streptomyces/classificação , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos/química , Genes Bacterianos , 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
14.
Int J Syst Evol Microbiol ; 70(10): 5363-5372, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32853134

RESUMO

Thirty-three Yersinia strains previously characterized by the French Yersinia National Reference Laboratory (YNRL) and isolated from humans and animals were suspected to belong to six novel species by a recently described core genome multilocus sequence typing scheme. These strains and five additional strains from the YNRL were characterized using a polyphasic taxonomic approach including a phylogenetic analysis based on 500 core genes, determination of average nucleotide identity (ANI), determination of DNA G+C content and identification of phenotypic features. Phylogenetic analysis confirmed that the 38 studied strains formed six well-demarcated clades. ANI values between these clades and their closest relatives were <94.7 % and ANI values within each putative novel species were >97.5 %. Distinctive biochemical characteristics were identified in five out of the six novel species. All of these data demonstrated that the 38 strains belong to six novel species of the genus Yersinia: Yersinia artesiana sp. nov., type strain IP42281T (=CIP 111845T=DSM 110725T); Yersinia proxima sp. nov., type strain IP37424T (=CIP 111847T=DSM 110727T); Yersinia alsatica sp. nov., type strain IP38850T (=CIP 111848T=DSM 110726T); Yersinia vastinensis sp. nov., type strain IP38594T (=CIP 111844T=DSM 110738T); Yersinia thracica sp. nov., type strain IP34646T (=CIP 111842T=DSM 110736T); and Yersinia occitanica sp. nov., type strain IP35638T (=CIP 111843T=DSM 110739T).


Assuntos
Filogenia , Yersinia/classificação , Animais , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Fezes/microbiologia , Humanos , Tipagem de Sequências Multilocus , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Yersinia/isolamento & purificação
15.
PLoS One ; 15(8): e0232305, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32785271

RESUMO

Shiga toxin-producing Escherichia coli (STEC) that cause severe disease predominantly carry the toxin gene variant stx2a. However, the role of Shiga toxin in the ruminant reservoirs of this zoonotic pathogen is poorly understood and strains that cause severe disease in humans (HUSEC) likely constitute a small and atypical subset of the overall STEC flora. The aim of this study was to investigate the presence of stx2a in samples from cattle and to isolate and characterize stx2a-positive E. coli. In nationwide surveys in Sweden and Norway samples were collected from individual cattle or from cattle herds, respectively. Samples were tested for Shiga toxin genes by real-time PCR and amplicon sequencing and stx2a-positive isolates were whole genome sequenced. Among faecal samples from Sweden, stx1 was detected in 37%, stx2 in 53% and stx2a in 5% and in skin (ear) samples in 64%, 79% and 2% respectively. In Norway, 79% of the herds were positive for stx1, 93% for stx2 and 17% for stx2a. Based on amplicon sequencing the most common stx2 types in samples from Swedish cattle were stx2a and stx2d. Multilocus sequence typing (MLST) of 39 stx2a-positive isolates collected from both countries revealed substantial diversity with 19 different sequence types. Only a few classical LEE-positive strains similar to HUSEC were found among the stx2a-positive isolates, notably a single O121:H19 and an O26:H11. Lineages known to include LEE-negative HUSEC were also recovered including, such as O113:H21 (sequence type ST-223), O130:H11 (ST-297), and O101:H33 (ST-330). We conclude that E. coli encoding stx2a in cattle are ranging from strains similar to HUSEC to unknown STEC variants. Comparison of isolates from human HUS cases to related STEC from the ruminant reservoirs can help identify combinations of virulence attributes necessary to cause HUS, as well as provide a better understanding of the routes of infection for rare and emerging pathogenic STEC.


Assuntos
Bovinos/microbiologia , Toxina Shiga II/genética , Escherichia coli Shiga Toxigênica/genética , Animais , Reservatórios de Doenças/microbiologia , Infecções por Escherichia coli/epidemiologia , Infecções por Escherichia coli/microbiologia , Variação Genética , Genoma Bacteriano , Síndrome Hemolítico-Urêmica/epidemiologia , Síndrome Hemolítico-Urêmica/microbiologia , Humanos , Tipagem de Sequências Multilocus , Noruega/epidemiologia , Prevalência , Reação em Cadeia da Polimerase em Tempo Real , Escherichia coli Shiga Toxigênica/citologia , Escherichia coli Shiga Toxigênica/isolamento & purificação , Suécia/epidemiologia , Virulência/genética , Zoonoses/epidemiologia , Zoonoses/microbiologia
16.
PLoS Negl Trop Dis ; 14(8): e0008573, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32841248

RESUMO

BACKGROUND: Leptospirosis has gained much attention in Sri Lanka since its large outbreak in 2008. However, most of the cases were clinically diagnosed and information on Leptospira genotypes and serotypes currently prevailing in the country is lacking. METHODOLOGY/PRINCIPAL FINDINGS: We retrospectively analyzed 24 Leptospira strains from human patients as well as isolated and characterized three Leptospira strains from black rats using the microscopic agglutination test with antisera for 19 serovars and multilocus sequence typing. The isolates were identified as Leptospira borgpetersenii sequence types (STs) 143 and 144; L. interrogans STs 30, 34, 43, 44, 74, 75, 80, 308, 313, 314, 316, and 317; and L. kirschneri ST318. Six of the 15 STs were identified for the first time in this study. Five serogroups such as Autumnalis, Grippotyphosa, Hebdomadis, Javanica, and Pyrogenes were detected among the isolates. Contrary to previous studies, various genotypes including novel STs were isolated during an outbreak in Southern Province. L. borgpetersenii serogroup Javanica ST143 was isolated both from a human and black rat. CONCLUSIONS/SIGNIFICANCE: This study revealed that genetically diverse Leptospira strains currently circulate in Sri Lanka: some genotypes have been circulating and others have emerged recently, which may explain the recent surge of leptospirosis patients with varying clinical manifestations and frequent outbreaks of leptospirosis. Black rats were identified as the source of infection for humans, but reservoir animals for other genotypes remain unknown.


Assuntos
Genótipo , Leptospira/classificação , Leptospira/genética , Leptospira/isolamento & purificação , Leptospirose/microbiologia , Tipagem de Sequências Multilocus/métodos , Adolescente , Adulto , Idoso , Testes de Aglutinação , Animais , Criança , DNA Bacteriano/análise , Reservatórios de Doenças , Feminino , Humanos , Leptospirose/epidemiologia , Masculino , Pessoa de Meia-Idade , Estudos Retrospectivos , Análise de Sequência de DNA , Sorogrupo , Sorotipagem , Sri Lanka/epidemiologia , Adulto Jovem
17.
Zhonghua Yu Fang Yi Xue Za Zhi ; 54(8): 849-853, 2020 Aug 06.
Artigo em Chinês | MEDLINE | ID: mdl-32842314

RESUMO

Objective: To identify the epidemic clones of MRSA isolates at a hospital in shanghai. Methods: A total of 72 MRSA isolates have been isolated from a second grade hospital between 2017 and 2018, including 32 CA-MRSA isolates, 13 HA-MRSA isolates and 26 MRSA isolates from environment. In this study, MLST and PFGE typing methods were used to analyze the molecular epidemiology of the MRSA isolates. Results: A total of 72 MRSA isolates have been obtained including 46 isolates from clinical specimens, 26 isolates from environments. The 46 MRSA isolates from clinical specimens consisted of 33 CA-MRSA (community-acquired MRSA) and 13 HA-MRSA (hospital-acquired MRSA). Furthermore, these patients infected with MRSA isolates were mostly distributed in the department of geriatrics (34.8%, 16/46), internal medicine (26.1%, 12/46) and surgery (26.1%, 12/46). MLST typing results showed that ST764 was predominant in isolates from both clinical specimens and hospital environments. Furthermore, PFGE typing results showed that most ST764 MRSA had high homolog (>90%). Conclusion: ST764 MRSA isolates might spread in community, hospital and environments. Therefore, continuous monitoring of MRSA and its variation may be useful in understanding the involvement of epidemic clone, and in searching new strategies to control MRSA infection.


Assuntos
Infecções Comunitárias Adquiridas , Infecção Hospitalar/epidemiologia , Staphylococcus aureus Resistente à Meticilina , Infecções Estafilocócicas/epidemiologia , Antibacterianos , China/epidemiologia , Eletroforese em Gel de Campo Pulsado , Humanos , Meticilina , Testes de Sensibilidade Microbiana , Epidemiologia Molecular , Tipagem de Sequências Multilocus
18.
PLoS Negl Trop Dis ; 14(8): e0008533, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32776937

RESUMO

Campylobacter is the leading bacterial cause of gastroenteritis worldwide and its incidence is especially high in low- and middle-income countries (LMIC). Disease epidemiology in LMICs is different compared to high income countries like the USA or in Europe. Children in LMICs commonly have repeated and chronic infections even in the absence of symptoms, which can lead to deficits in early childhood development. In this study, we sequenced and characterized C. jejuni (n = 62) from a longitudinal cohort study of children under the age of 5 with and without diarrheal symptoms, and contextualized them within a global C. jejuni genome collection. Epidemiological differences in disease presentation were reflected in the genomes, specifically by the absence of some of the most common global disease-causing lineages. As in many other countries, poultry-associated strains were likely a major source of human infection but almost half of local disease cases (15 of 31) were attributable to genotypes that are rare outside of Peru. Asymptomatic infection was not limited to a single (or few) human adapted lineages but resulted from phylogenetically divergent strains suggesting an important role for host factors in the cryptic epidemiology of campylobacteriosis in LMICs.


Assuntos
Infecções Assintomáticas , Infecções por Campylobacter/epidemiologia , Infecções por Campylobacter/microbiologia , Campylobacter jejuni/genética , Animais , Infecções por Campylobacter/diagnóstico , Infecções por Campylobacter/fisiopatologia , Campylobacter jejuni/classificação , Pré-Escolar , Estudos de Coortes , Diarreia/epidemiologia , Genômica , Genótipo , Interações Hospedeiro-Parasita , Humanos , Lactente , Recém-Nascido , Estudos Longitudinais , Tipagem Molecular , Tipagem de Sequências Multilocus , Peru/epidemiologia , Filogenia , Aves Domésticas/microbiologia
19.
J Vet Sci ; 21(4): e57, 2020 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-32735095

RESUMO

BACKGROUND: Streptococcus dysgalactiae subspecies equisimilis (SDSE) acts as an etiological agent for lameness, neurological signs, and high mortality in pigs. Despite its importance in pig industries and zoonotic potential, little is known about the effects of this pathogen. OBJECTIVES: This study aimed to determine the molecular characteristics and antimicrobial resistance of SDSE strains isolated from diseased pigs. METHODS: A total 11 SDSE isolates were obtained from diseased pigs. Bacterial identification, PCR for virulence genes, emm typing, and antimicrobial resistance genes, multilocus sequence typing, and antimicrobial susceptibility test were performed. RESULTS: Nine isolates were from piglets, and 8 showed lameness, sudden death, or neurological signs. The isolates were PCR-positive for sla (100%), sagA (100%), and scpA (45.5%), and only 1 isolate amplified the emm gene (stL2764). Eight different sequence types were detected, categorized into 2 clonal complexes and 4 singletons. All the isolates in this study were included in a small cluster, which also contained other strains derived from humans and horses. The minimum inhibitory concentrations for the tested beta-lactams were low, while those for macrolides, tetracyclines, and fluoroquinolones were relatively high. PCR analysis of the macrolide and tetracycline resistance genes demonstrated that the isolates carried erm(B) (18.2%, n = 2), mef(A/E) (9.1%, n = 1), tet(M) (18.2%, n = 2), and tet(O) (90.2%, n = 10). Two isolates presented a mutation in parC, which is associated with fluoroquinolone resistance. CONCLUSION: This study provided insight into swine-derived SDSE, as it is related to veterinary medicine, and elucidated its zoonotic potential, in the context of molecular epidemiology and antimicrobial resistance in public health.


Assuntos
Farmacorresistência Bacteriana/genética , Infecções Estreptocócicas/veterinária , Streptococcus/efeitos dos fármacos , Doenças dos Suínos/diagnóstico , Animais , Antibacterianos/farmacologia , Testes de Sensibilidade Microbiana/veterinária , Tipagem de Sequências Multilocus/veterinária , República da Coreia , Infecções Estreptocócicas/diagnóstico , Infecções Estreptocócicas/microbiologia , Streptococcus/genética , Suínos , Doenças dos Suínos/microbiologia
20.
Epidemiol Infect ; 148: e172, 2020 08 03.
Artigo em Inglês | MEDLINE | ID: mdl-32741426

RESUMO

Outbreaks of cyclosporiasis, a food-borne illness caused by the coccidian parasite Cyclospora cayetanensis have increased in the USA in recent years, with approximately 2300 laboratory-confirmed cases reported in 2018. Genotyping tools are needed to inform epidemiological investigations, yet genotyping Cyclospora has proven challenging due to its sexual reproductive cycle which produces complex infections characterized by high genetic heterogeneity. We used targeted amplicon deep sequencing and a recently described ensemble-based distance statistic that accommodates heterogeneous (mixed) genotypes and specimens with partial genotyping data, to genotype and cluster 648 C. cayetanensis samples submitted to CDC in 2018. The performance of the ensemble was assessed by comparing ensemble-identified genetic clusters to analogous clusters identified independently based on common food exposures. Using these epidemiologic clusters as a gold standard, the ensemble facilitated genetic clustering with 93.8% sensitivity and 99.7% specificity. Hence, we anticipate that this procedure will greatly complement epidemiologic investigations of cyclosporiasis.


Assuntos
Cyclospora/genética , Ciclosporíase/epidemiologia , Ciclosporíase/parasitologia , Interpretação Estatística de Dados , Tipagem de Sequências Multilocus/métodos , Análise por Conglomerados , Bases de Dados Factuais , Fezes/parasitologia , Marcadores Genéticos , Haplótipos , Humanos
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