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1.
Artigo em Inglês | MEDLINE | ID: mdl-35192451

RESUMO

A novel coagulase-negative Staphylococcus strain (NTUH-S172T) was isolated from human blood culture in Taiwan with preliminary identification of Staphylococcus saprophyticus. 16S rRNA gene analysis and multilocus sequence analysis (MLSA) showed that NTUH-S172T was most closely related to Staphylococcus haemolyticus. The average nucleotide identity and digital DNA-DNA hybridization values with the whole genome sequence were <95 % and<70 % when compared to the related species. Strain NTUH-S172T could be distinguished from S. haemolyticus by urease production and from Staphylococcus borealis by nitrate reduction. In addition, the matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) spectrum of NTHU-S172T was significantly different from that of S. haemolyticus, which could be used in clinical identification. In conclusion, it is proposed that this isolate represents a novel species, named Staphylococcus taiwanensis sp. nov., with type strain NTUH-S172T (=BCRC 81315T=JCM 34726T).


Assuntos
Sangue/microbiologia , Ácidos Graxos , Filogenia , Staphylococcus , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Humanos , Hibridização de Ácido Nucleico , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Staphylococcus/classificação , Staphylococcus/isolamento & purificação , Taiwan
2.
Gut Microbes ; 14(1): 2029674, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35130114

RESUMO

Portal hypertension (PH) in liver cirrhosis leads to increased gut permeability and the translocation of bacteria across the gut-liver axis. Microbial DNA has recently been detected in different blood compartments; however, this phenomenon has not been thoroughly analyzed in PH. This study aimed to explore circulating bacterial DNA signatures, inflammatory cytokines, and gut permeability markers in different blood compartments (peripheral and hepatic veins) of patients with cirrhosis and PH. The 16S rRNA blood microbiome profiles were determined in 58 patients with liver cirrhosis and 46 control patients. Taxonomic differences were analyzed in relation to PH, liver function, inflammatory cytokines, and gut permeability markers. Circulating plasma microbiome profiles in patients with cirrhosis were distinct from those of the controls and were characterized by enrichment of Comamonas, Cnuella, Dialister, Escherichia/Shigella, and Prevotella and the depletion of Bradyrhizobium, Curvibacter, Diaphorobacter, Pseudarcicella, and Pseudomonas. Comparison of peripheral and hepatic vein blood compartments of patients with cirrhosis did not reveal differentially abundant taxa. Enrichment of the genera Bacteroides, Escherichia/Shigella, and Prevotella was associated with severe PH (SPH) in both blood compartments; however, circulating microbiome profiles could not predict PH severity. Escherichia/Shigella and Prevotella abundance was correlated with IL-8 levels in the hepatic vein. In conclusion, we demonstrated a distinct circulating blood microbiome profile in patients with cirrhosis, showing that specific bacterial genera in blood are marginally associated with SPH, Model for End-Stage Liver Disease score, and inflammation biomarkers; however, circulating microbial composition failed to predict PH severity.


Assuntos
Bactérias/genética , Sangue/microbiologia , DNA Bacteriano/sangue , Microbioma Gastrointestinal , Hipertensão Portal/microbiologia , Cirrose Hepática/microbiologia , Adulto , Bactérias/classificação , Bactérias/isolamento & purificação , Fenômenos Fisiológicos Bacterianos , Translocação Bacteriana , Biomarcadores/sangue , Feminino , Humanos , Hipertensão Portal/sangue , Hipertensão Portal/complicações , Interleucina-8/sangue , Cirrose Hepática/sangue , Cirrose Hepática/complicações , Masculino , Pessoa de Meia-Idade
3.
Gene ; 822: 146355, 2022 May 15.
Artigo em Inglês | MEDLINE | ID: mdl-35189248

RESUMO

BACKGROUND: Carbapenem-resistant Enterobacteriaceae (CRE) have been thoroughly studied as the pathogens associated with hospital acquired infections. However, data on Serratia marcescens are not enough. S. marcescens is now becoming a propensity for its highly antimicrobial-resistant clinical infections. METHODS: Four carbapenem-resistant S. marcescens (CR-SM) isolates were obtained from hospitalized patients through routine microbiological experiments. We assembled the isolates genomes using whole genome sequencing (WGS) and compared their resistome and virulome patterns. RESULTS: The average length and CG content of chromosomes was 5.33 Mbp and 59.8%, respectively. The number of coding sequences (CDSs) ranged from 4,959 to 4,989. All strains had one single putative conjugative plasmid with IncL incompatibility (Inc) group. The strains harbored blaCTX-M-15, blaTEM-1 and blaSHV-134. All plamsids were positive for blaOXA-48. No blaNDM-1, blaKPC, blaVIM and blaIMP were identified. The blaSRT-2 and aac(6')-Ic genes were chromosomally-encoded. Class 1 integron was detected in strains P8, P11 and P14. The Escher_RCS47 and Salmon_SJ46 prophages played major role in plasmid-mediated carraige of extended spectrum ß-lactamases (ESBLs). The CR-SM strains were equipt with typical virulence factors of oppotunistic pathogens including biofilm formation, adhesins, secretory systems and siderophores. The strains did not have ability to produce prodigiosin but were positive for chitinase and EstA. CONCLUSION: The presence of conjugative plasmids harboring major ß-lactamases within prophage and class 1 integron structures highlights the role of different mobile genetic elements (MGEs) in distribution of AMR factors and more specifically carbapenemases. More molecular studies are required to determine the status of carbapenem resistance in clinical starins. However, appropriate strategies to control the global dissemination of CR-SM are urgent.


Assuntos
Carbapenêmicos/farmacologia , Farmacorresistência Bacteriana Múltipla , Prófagos/genética , Serratia marcescens/classificação , Sequenciamento Completo do Genoma/métodos , Adulto , Composição de Bases , Sangue/microbiologia , Líquido da Lavagem Broncoalveolar/microbiologia , Tamanho do Genoma , Genoma Bacteriano , Sequenciamento de Nucleotídeos em Larga Escala , Hospitalização , Humanos , Masculino , Filogenia , Plasmídeos/genética , Serratia marcescens/genética , Serratia marcescens/isolamento & purificação , Serratia marcescens/virologia , Fatores de Virulência/genética , Adulto Jovem , beta-Lactamases/genética
4.
Sci Rep ; 12(1): 1241, 2022 01 24.
Artigo em Inglês | MEDLINE | ID: mdl-35075206

RESUMO

It has been hypothesised that oral bacteria can migrate, through the blood, from the mouth to the arterial plaques, thus exacerbating atherosclerosis. This study compared bacteria present in the peripheral blood of individuals with and without coronary artery disease (CAD). RNA sequences obtained from blood were downloaded from GEO (GSE58150). Eight patients with coronary artery calcification (CAC) scoring > 500 and eight healthy individuals were analysed. After conducting quality control, the sequences were aligned to the hg38 reference genome using Hisat2. Bacterial taxa were analysed by inputting the unmapped sequences into Kraken. Ecological indices were calculated using Vegan. The package DESeq2 was used to compare the counts of bacteria per standard rank between groups. A total of 51 species were found only in patients with CAD and 41 were exclusively present in healthy individuals. The counts of one phylum, one class, three orders, two families and one genus were significantly different between the analysed groups (p < 0.00032, FDR < 10%), including the orders Cardiobacteriales, Corynebacteriales and Fusobacteriales. Twenty-three bacterial species belonging to the subgingival plaque bacterial complexes were also identified in the blood of individuals from both the groups; Fusobacterium nucleatum was significantly less frequent in patients with CAD (p = 0.0012, FDR = 4.8%). Furthermore, the frequency of another 11 bacteria differed significantly among patients with CAD than that among healthy individuals (p < 0.0030, FDR < 10%). These bacteria have not been previously reported in patients with atherosclerosis and periodontitis. The presence of members of the subgingival plaque bacterial complexes in the blood of patients with CAC supports the hypothesis that the periodontopathogens can be disseminated through the blood flow to other body parts where they may enhance inflammatory processes that can lead to the development or exacerbation of atherosclerosis.


Assuntos
Sangue/microbiologia , Doença da Artéria Coronariana/microbiologia , Placa Dentária/microbiologia , Doenças Periodontais/complicações , Estudos de Casos e Controles , Feminino , Humanos , Pessoa de Meia-Idade , Doenças Periodontais/microbiologia
5.
PLoS One ; 17(1): e0263188, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35085360

RESUMO

BACKGROUND: Schistosomiasis is a neglected tropical parasitic and chronic disease affecting hundreds of millions of people. Adult schistosomes reside in the blood stream of the definitive mammalian host. These helminth parasites possess two epithelial surfaces, the tegument and the gastrodermis, both of which interact with the host during immune evasion and in nutrient uptake. METHODS: Female ARC Swiss mice (4-6 weeks old) were infected percutaneously with Schistosoma japonicum cercariae freshly shed from Oncomelania hupensis quadrasi snails (Philippines strain). Fluorescent in situ hybridisation (FISH) was performed by using fresh adult S. japonicum perfused from those infected mice. Adult S. japonicum worms were processed to isolate the tegument from the carcass containing the gastrodermis; blood and bile were collected individually from infected and uninfected mice. Total DNA extracted from all those samples were used for microbiome profiling. RESULTS: FISH and microbiome profiling showed the presence of bacterial populations on two epithelial surfaces of adult worms, suggesting they were distinct not only from the host blood but also from each other. Whereas microbial diversity was reduced overall in the parasite epithelial tissues when compared with that of host blood, specific bacterial taxa, including Anoxybacillus and Escherichia, were elevated on the tegument. Minimal differences were evident in the microbiome of host blood during an active infection, compared with that of control uninfected blood. However, sampling of bile from infected animals identified some differences compared with controls, including elevated levels of Limnohabitans, Clostridium and Curvibacter. CONCLUSIONS: Using FISH and microbial profiling, we were able to demonstrate, for the first time, that bacteria are presented on the epithelial surfaces of adult schistosomes. These schistosome surface-associated bacteria, which are distinct from the host blood microenvironment, should be considered as a new and important component of the host-schistosome interaction. The importance of individual bacterial species in relation to schistosome parasitism needs further elucidation.


Assuntos
Sangue/microbiologia , Epitélio/microbiologia , Microbiota/genética , Schistosoma japonicum/microbiologia , Esquistossomose Japônica/sangue , Animais , Anoxybacillus/genética , Bile/microbiologia , Cercárias , Clostridium/genética , Comamonadaceae/genética , DNA Bacteriano/genética , DNA Bacteriano/isolamento & purificação , Modelos Animais de Doenças , Escherichia coli/genética , Feminino , Hibridização in Situ Fluorescente/métodos , Masculino , Camundongos , RNA Ribossômico 16S/genética , Schistosoma japonicum/isolamento & purificação , Esquistossomose Japônica/parasitologia , Caramujos/parasitologia
6.
Eur J Clin Microbiol Infect Dis ; 41(1): 163-167, 2022 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-34529167

RESUMO

We describe a case of recurrent catheter-related blood stream infections (BSI) with Staphylococcus aureus, in which the first isolate tested susceptible to penicillin, while subsequent isolates were resistant. Phenotypic susceptibility correlated with the absence/presence of the blaZ gene. The in vitro stability of penicillin resistance was investigated by subculturing single colonies. In two out of five colonies, phenotypical resistance was lost after a single subculture, which correlated with loss of the blaZ gene. This in vitro phenomenon probably resulted in a very major error in the microbiology report of the first BSI, where penicillin had been recommended as treatment.


Assuntos
Antibacterianos/farmacologia , Bacteriemia/microbiologia , Proteínas de Bactérias/genética , Infecções Relacionadas a Cateter/microbiologia , Penicilinas/farmacologia , Infecções Estafilocócicas/microbiologia , Staphylococcus aureus/efeitos dos fármacos , beta-Lactamases/genética , Bacteriemia/tratamento farmacológico , Proteínas de Bactérias/metabolismo , Sangue/microbiologia , Infecções Relacionadas a Cateter/tratamento farmacológico , Humanos , Testes de Sensibilidade Microbiana , Resistência às Penicilinas , Infecções Estafilocócicas/tratamento farmacológico , Staphylococcus aureus/enzimologia , Staphylococcus aureus/genética , Staphylococcus aureus/metabolismo , beta-Lactamases/metabolismo
7.
Microbiologyopen ; 10(6): e1247, 2021 11.
Artigo em Inglês | MEDLINE | ID: mdl-34964298

RESUMO

The relatively long turnaround time and low sensitivity of traditional blood culture-based diagnosis may delay effective antibiotic therapy for patients with bloodstream infections (BSIs). A rapid and sensitive pathogen detection method is urgently required to reduce the morbidity and mortality associated with BSIs. Acinetobacter baumannii and Klebsiella pneumoniae are two major microorganisms that cause BSIs. Here we report a novel droplet digital polymerase chain reaction (ddPCR) assay that can detect A. baumannii and K. pneumoniae in blood samples within 4 h, with a specificity of 100% for each strain and a limit of detection at 0.93 copies/µl for A. baumannii and 0.27 copies/µl for K. pneumoniae. Clinical validation of 170 patients with suspected BSIs showed that compared to blood cultures that detected four (2.4%) A. baumannii cases and seven (4.1%) K. pneumoniae cases, ddPCR detected 23 (13.5%) A. baumannii cases, 26 (15.3%) K. pneumoniae cases, and four (2.4%) co-infection cases, including the 11 cases detected via blood culture. In addition, patients who tested positive via ddPCR alone (n = 42) had significantly lower serum concentrations of procalcitonin and lactate, SOFA and APACHE II scores, and 28-day mortality than those reported positive via both blood culture and ddPCR (n = 11), suggesting that patients with less severe symptoms can potentially benefit from ddPCR-based diagnosis. In conclusion, our study suggests that ddPCR represents a sensitive and rapid method for identifying causal pathogens in blood samples and guiding treatment decisions in the early stages of BSIs.


Assuntos
Infecções por Acinetobacter/diagnóstico , Acinetobacter baumannii/isolamento & purificação , Bacteriemia/diagnóstico , Infecções por Klebsiella/diagnóstico , Klebsiella pneumoniae/isolamento & purificação , Infecções por Acinetobacter/microbiologia , Acinetobacter baumannii/genética , Idoso , Bacteriemia/microbiologia , Sangue/microbiologia , Feminino , Humanos , Infecções por Klebsiella/microbiologia , Klebsiella pneumoniae/genética , Masculino , Reação em Cadeia da Polimerase/métodos , Reprodutibilidade dos Testes , Sensibilidade e Especificidade
8.
Gut Microbes ; 13(1): 1993583, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34747333

RESUMO

Gut microbiota have myriad roles in host physiology, development, and immunity. Though confined to the intestinal lumen by the epithelia, microbes influence distal systems via poorly characterized mechanisms. Recent work has considered the role of extracellular vesicles in interspecies communication, but whether they are involved in systemic microbe-host interaction is unclear. Here, we show that distinctive nanoparticles can be isolated from mouse blood within 2.5 h of consuming Lacticaseibacillus rhamnosus JB-1. In contrast to blood nanoparticles from saline-fed mice, they reproduced lipoteichoic acid-mediated immune functions of the original bacteria, including activation of TLR2 and increased IL-10 expression by dendritic cells. Like the fed bacteria, they also reduced IL-8 induced by TNF in an intestinal epithelial cell line. Though enriched for host neuronal proteins, these isolated nanoparticles also contained proteins and viral (phage) DNA of fed bacterial origin. Our data strongly suggest that oral consumption of live bacteria rapidly leads to circulation of their membrane vesicles and phages and demonstrate a nanoparticulate pathway whereby beneficial bacteria and probiotics may systemically affect their hosts.


Assuntos
Bacteriófagos/isolamento & purificação , Sangue/microbiologia , Sangue/virologia , Células Dendríticas/efeitos dos fármacos , Vesículas Extracelulares/metabolismo , Lactobacillus rhamnosus/metabolismo , Probióticos/farmacologia , Animais , Bacteriófagos/genética , Células Dendríticas/imunologia , Vesículas Extracelulares/química , Interleucina-8/genética , Interleucina-8/imunologia , Mucosa Intestinal/imunologia , Mucosa Intestinal/microbiologia , Lactobacillus rhamnosus/genética , Masculino , Camundongos , Camundongos Endogâmicos BALB C/genética
9.
Int J Syst Evol Microbiol ; 71(11)2021 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-34788212

RESUMO

A Gram-stain-negative, aerobic, non-endospore-forming organism isolated from horse blood was studied for its taxonomic allocation. On the basis of 16S rRNA gene sequence similarity comparisons, strain M6-77T grouped within the genus Devosia and was most closely related to Devosia elaeis (97.6 %) and Devosia indica (97.55 %). The 16S rRNA gene sequence similarity to type strains of other Devosia species was below 97.5 %. The average nucleotide identity and digital DNA-DNA hybridization values between the M6-77T genome assembly and those of the closest relative Devosia type strains were <85 and <25 %, respectively. Strain M6-77T grew optimally at 25-37 °C (range: 10-36 °C), at a pH range of pH 6.5-10.5 and in the presence of up to 3 % (w/v) NaCl. The fatty acid profile from whole-cell hydrolysates supported the allocation of the strain to the genus Devosia. Major fatty acids were C18 : 1 ω7c, 11-methyl C18 : 1 ω7c and C16 : 0. The quinone system consisted exclusively of ubiquinone Q-10. The polar lipid profile was composed of the major lipids diphosphatidylglycerol, phosphatidylglycerol and three unidentified glycolipids. In the polyamine pattern, putrescine was predominant and spermidine was detected in moderate amounts. The diamino acid of the peptidoglycan was meso-diaminopimelic acid. In addition, the results of physiological and biochemical tests also allowed phenotypic differentiation of strain M6-77T from the closely related species. Hence, M6-77T represents a new species of the genus Devosia, for which we propose the name Devosia equisanguinis sp. nov., with M6-77T (=CIP 111628T=LMG 30659T=CCM 8868T) as the type strain.


Assuntos
Sangue/microbiologia , Cavalos/microbiologia , Hyphomicrobiaceae/classificação , Filogenia , Animais , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Glicolipídeos/química , Hyphomicrobiaceae/isolamento & purificação , Hibridização de Ácido Nucleico , Fosfolipídeos/química , Poliaminas/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Ubiquinona/análogos & derivados , Ubiquinona/química
11.
PLoS Negl Trop Dis ; 15(9): e0009704, 2021 09.
Artigo em Inglês | MEDLINE | ID: mdl-34478439

RESUMO

BACKGROUND: Community acquired bacteremia (CAB) is a common cause of sepsis in low and middle-income countries (LMICs). However, knowledge about factors associated with outcomes of CAB in LMICs is limited. METHODOLOGY/PRINCIPAL FINDINGS: A prospective observational study (Ubon-sepsis) of adults admitted to a referral hospital with community-acquired infection in Northeastern Thailand was conducted between March 1, 2013 and February 1, 2017. In the present analysis, patients with a blood culture collected within 24 hours of admission that was positive for one of the three most common pathogens were studied. Clinical features, management, and outcomes of patients with each cause of CAB were compared. Of 3,806 patients presenting with community-acquired sepsis, 155, 131 and 37 patients had a blood culture positive for Escherichia coli, Burkholderia pseudomallei and Staphylococcus aureus, respectively. Of these 323 CAB patients, 284 (89%) were transferred from other hospitals. 28-day mortality was highest in patients with B. pseudomallei bactaeremia (66%), followed by those with S. aureus bacteraemia (43%) and E. coli (19%) bacteraemia. In the multivariable Cox proportional hazards model adjusted for age, sex, transfer from another hospital, empirical antibiotics prior to or during the transfer, and presence of organ dysfunction on admission, B. pseudomallei (aHR 3.78; 95%CI 2.31-6.21) and S. aureus (aHR 2.72; 95%CI 1.40-5.28) bacteraemias were associated with higher mortality compared to E. coli bacteraemia. Receiving empirical antibiotics recommended for CAB caused by the etiologic organism prior to or during transfer was associated with survival (aHR 0.58; 95%CI 0.38-0.88). CONCLUSIONS/SIGNIFICANCE: Mortality of patients with CAB caused by B. pseudomallei was higher than those caused by S. aureus and E. coli, even after adjusting for presence of organ dysfunction on admission and effectiveness of empirical antibiotics received. Improving algorithms or rapid diagnostic tests to guide early empirical antibiotic may be key to improving CAB outcomes in LMICs.


Assuntos
Bacteriemia/microbiologia , Burkholderia pseudomallei/fisiologia , Infecções Comunitárias Adquiridas/microbiologia , Escherichia coli/fisiologia , Staphylococcus aureus/fisiologia , Adulto , Idoso , Idoso de 80 Anos ou mais , Antibacterianos/uso terapêutico , Bacteriemia/tratamento farmacológico , Bacteriemia/epidemiologia , Bacteriemia/mortalidade , Sangue/microbiologia , Burkholderia pseudomallei/efeitos dos fármacos , Burkholderia pseudomallei/genética , Burkholderia pseudomallei/isolamento & purificação , Infecções Comunitárias Adquiridas/tratamento farmacológico , Infecções Comunitárias Adquiridas/epidemiologia , Infecções Comunitárias Adquiridas/mortalidade , Escherichia coli/efeitos dos fármacos , Escherichia coli/genética , Escherichia coli/isolamento & purificação , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Estudos Prospectivos , Staphylococcus aureus/efeitos dos fármacos , Staphylococcus aureus/genética , Staphylococcus aureus/isolamento & purificação , Tailândia/epidemiologia , Adulto Jovem
12.
Artigo em Inglês | MEDLINE | ID: mdl-34494947

RESUMO

Three Gram-positive bacterial strains, BML-BC004, BML-BC017 and BML-BC059, isolated from blood samples from three inpatients in Japan, were identified as members of Bacillus cereus using matrix-assisted laser desorption ionization time-of-flight MS. The 16S rRNA gene sequences of these three strains were more than 97.1 % similar to 18 type strains belonging to the B. cereus group. Whole-genome comparisons, using average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH), confirmed that the three strains represented three individual distinct species belonging to the B. cereus group. A phylogenetic tree showed that BML-BC004, BML-BC017 and BML-BC059 were located close to B. luti, B. mobilis and B. paramycoides, respectively. Based on these phylogenetic and phenotypic data, including values below the threshold for ANI and dDDH, the three strains should be classified as representing three different novel species of the B. cereus group: Bacillus sanguinis sp. nov., with type strain BML-BC004T (=DSM 111102T=JCM 34122T), Bacillus paramobilis sp. nov., with type strain BML-BC017T (=DSM 111100T=JCM 34124T) and Bacillus hominis sp. nov., with type strain BML-BC059T (=DSM 111101T=JCM 34125T).


Assuntos
Bacillus cereus/classificação , Sangue/microbiologia , Filogenia , Bacillus cereus/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Humanos , Japão , Hibridização de Ácido Nucleico , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
13.
Eur J Med Res ; 26(1): 85, 2021 Aug 03.
Artigo em Inglês | MEDLINE | ID: mdl-34344456

RESUMO

BACKGROUND: Streptococcus suis (Ss) is a Gram-positive and anaerobic zoonotic pathogen that is susceptible to all populations and can cause meningitis, septicemia, endocarditis and arthritis in humans. METHODS: In this study, patients with meningitis who were admitted to our hospital with negative blood and cerebrospinal fluid culture were divided into a next-generation sequencing group and a control group. In the next-generation sequencing group, we used the next-generation sequencing method to detect pathogenic bacteria in the patients' cerebrospinal fluid. In the control group, we used blood and cerebrospinal fluid bacterial culture method to detect pathogenic bacteria in the patients' cerebrospinal fluid. The detection rates of pathogenic bacteria in the cerebrospinal fluid of the two groups were compared and analyzed. RESULTS: A total of 18 patients were included in this study, including 8 patients in the next-generation sequencing group and 10 patients in the control group. The mean age (P = 0.613) and mean disease duration (P = 0.294) were similar in both groups. Patients in the next-generation sequencing group had a leukocyte count of 13.13 ± 4.79 × 109, a neutrophil percentage of 83.39 ± 10.36%, and a C-reactive protein level of 134.95 ± 107.69 mg/L. Patients in the control group had a temperature of 38.32 ± 1.07, a leukocyte count of 8.00 ± 2.99 × 109, and a neutrophil percentage of 74.61 ± 8.89%, and C-reactive protein level was 4.75 ± 6.8 mg/L. The statistical results showed that the leukocytes (P = 0.013) and C-reactive protein levels (P = 0.001) were significantly higher in the patients of the next-generation sequencing group than in the control group. No statistically significant differences were seen in body temperature and neutrophil percentage between the two groups (P > 0.05). The incidence of intracranial pressure and meningeal irritation signs were similar in the two groups (P > 0.05). The detection rate of Streptococcus suis in the cerebrospinal fluid of patients in the next-generation sequencing group was 100%, and the detection rate of Streptococcus suis in the cerebrospinal fluid of the control group was 0%. CONCLUSION: The detection rate of Streptococcus suis infection in cerebrospinal fluid by next-generation sequencing was significantly higher than that by blood and cerebrospinal fluid bacterial culture. Therefore, the diagnosis of porcine streptococcal meningitis by next-generation sequencing method is worthy of clinical promotion and application.


Assuntos
Sangue/microbiologia , Líquido Cefalorraquidiano/microbiologia , Técnicas de Cultura/métodos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Meningites Bacterianas/diagnóstico , Infecções Estreptocócicas/diagnóstico , Streptococcus suis/isolamento & purificação , Animais , Estudos de Casos e Controles , Líquido Cefalorraquidiano/metabolismo , Feminino , Seguimentos , Humanos , Masculino , Meningites Bacterianas/sangue , Meningites Bacterianas/líquido cefalorraquidiano , Meningites Bacterianas/microbiologia , Pessoa de Meia-Idade , Prognóstico , Infecções Estreptocócicas/sangue , Infecções Estreptocócicas/líquido cefalorraquidiano , Infecções Estreptocócicas/microbiologia , Streptococcus suis/genética , Suínos
14.
Int J Legal Med ; 135(6): 2555-2565, 2021 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-34373945

RESUMO

A quite intriguing subject being intensively researched in the forensic toxicology field is the source of postmortem determined blood ethanol concentration: antemortem ingestion or postmortem microbial production. Our previous research on microbial ethanol production has reported a quantitative relationship between the ethanol and the higher alcohols and 1-butanol produced by Escherichia coli, Clostridium perfrigens, and Clostridium sporogenes. In this contribution, we continue our research reporting on the following: (i) the patterns of ethanol, higher alcohols, and 1-butanol production by the microbes Klebsiella pneumoniae, Staphylococcus aureus, and Enterococcus faecalis (all being aerobic/facultative anaerobic species, common corpse's colonizers, and ethanol producers), under controlled laboratory conditions, (ii) the mathematical modeling, with simple mathematical equations, of the correlation between ethanol concentration and the other studied alcohols' concentrations, by performing multiple linear regression analysis of the results, and (iii) the applicability of the constructed models in microbial cultures developed under different temperature than that used to build the models, in denatured blood cultures and in real postmortem cases. The aforementioned alcohols were proved to be all indicators of ethanol production, both in qualitative and quantitative terms. 1-Propanol was the most significant alcohol in modeling microbial ethanol production, followed by methyl-butanol. The K. pneumoniae's models achieved the best scoring in applicability (E < 40%) compared to the S. aureus and E. faecalis models, both at laboratory microbial cultures at 37 °C and real postmortem cases. Overall, a noteworthy accuracy in estimating the microbial ethanol in cultures and autopsy blood is achieved by the employed simple linear models.


Assuntos
Sangue/microbiologia , Enterococcus faecalis/química , Etanol/análise , Klebsiella pneumoniae/química , Staphylococcus aureus/química , 1-Butanol/análise , 1-Propanol/análise , Aerobiose , Anaerobiose , Autopsia , Concentração Alcoólica no Sangue , Butanóis/análise , Humanos , Modelos Teóricos , Pentanóis/análise
16.
Methods Mol Biol ; 2341: 127-131, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34264468

RESUMO

Staphylococcus aureus is an important human pathogen that causes a plethora of diverse infections within the human host that range in severity from the relatively minor to the severe. Of note, bloodstream infections caused by this organism result in high mortality rates, often following failed rounds of surgical and antibiotic intervention. The capacity for S. aureus to exist in blood is driven by myriad virulence factors that engage in a manipulation of various host responses to evade destruction and ensure survival. These include both secreted elements, such as coagulase and von Willebrand factor protein, as well as surface displayed factors, including clumping factor A and fibronectin binding protein A. In addition to this, there are a number of other loci within the S. aureus genome whose products have been shown to contribute to blood survival by more indirect means. Accordingly, ex vivo whole human blood survival assays are often used as a preliminary study to investigate host-bacterial interactions in an effort to delineate the pathogenicity of S. aureus strains. Herein we provide a detailed assessment of the protocol required to perform such studies.


Assuntos
Sangue/microbiologia , Staphylococcus aureus/crescimento & desenvolvimento , Fatores de Virulência/metabolismo , Proteínas de Bactérias/metabolismo , Sangue/metabolismo , Interações Hospedeiro-Patógeno , Humanos , Viabilidade Microbiana , Infecções Estafilocócicas/microbiologia , Staphylococcus aureus/metabolismo , Staphylococcus aureus/patogenicidade
17.
Microbiol Spectr ; 9(1): e0022121, 2021 09 03.
Artigo em Inglês | MEDLINE | ID: mdl-34232100

RESUMO

Bloodstream infections are a major cause of morbidity and mortality and result in significant costs to health care systems. Rapid identification of the causative agent of bloodstream infections is critical for patient treatment and improved outcomes. Multiplex PCR systems that provide bacterial identification directly from the blood culture bottle allow for earlier detection of pathogens. The GenMark Dx ePlex blood culture identification (BCID) panels have an expanded number of targets for both identification and genotypic markers of antimicrobial resistance. The performance of the ePlex BCID Gram-negative (GN) and Gram-positive (GP) panels were evaluated in a predominantly pediatric oncology population. A total of 112 blood cultures were tested by the ePlex BCID GN and GP panels and results were compared to those from standard-of-care testing. Accuracy for on-panel organisms was 89% (CI, 76% to 95%) for the Gram-positive panel, with four misidentifications and one not detected, and 93% (CI, 82% to 98%) for the Gram-negative panel, with two misidentifications and one not detected. The results showed good overall performance of these panels for rapid, accurate detection of bloodstream pathogens in this high-risk population. IMPORTANCE Bloodstream infections are a major cause of morbidity and mortality and result in significant costs to health care systems. Rapid identification of the causative agent of bloodstream infections is critical for patient treatment and improved outcomes. Multiplex PCR systems that provide bacterial identification directly from the blood culture bottle allow for earlier characterization of pathogens. The GenMark Dx ePlex blood culture identification (BCID) panels, recently cleared by the FDA, have an expanded number of targets for both identification and resistance, much larger than other, automated, broad-panel PCR assays. The performance of the ePlex BCID Gram-negative and Gram-positive panels was evaluated in a predominantly pediatric oncology population, providing a unique look at its performance in a high-risk group, where rapid diagnostic information for bloodstream infections could be of particular value for clinical care providers.


Assuntos
Bacteriemia/microbiologia , Bactérias/isolamento & purificação , Técnicas de Tipagem Bacteriana/métodos , Técnicas de Diagnóstico Molecular/métodos , Reação em Cadeia da Polimerase/métodos , Bacteriemia/diagnóstico , Bactérias/classificação , Bactérias/genética , Sangue/microbiologia , Hemocultura , Humanos , Pediatria/estatística & dados numéricos , Estudos Prospectivos
18.
Forensic Sci Int Genet ; 53: 102537, 2021 07.
Artigo em Inglês | MEDLINE | ID: mdl-34090061

RESUMO

Current body fluid identification methods do not reveal any information about the time since deposition (TsD) of biological traces, even though determining the age of traces could be crucial for the investigative process. To determine the utility of microbial RNA markers for TsD estimation, we examined RNA sequencing data from five forensically relevant body fluids (blood, menstrual blood, saliva, semen, and vaginal secretion) over seven time points, ranging from fresh to 1.5 years. One set of samples was stored indoors while another was exposed to outdoor conditions. In outdoor samples, we observed a consistent compositional shift, occurring after 4 weeks: this shift was characterized by an overall increase in non-human eukaryotic RNA and an overall decrease in prokaryotic RNA. In depth analyses showed a high fraction of tree, grass and fungal signatures, which are characteristic for the environment the samples were exposed to. When examining the prokaryotic fraction in more detail, three bacterial phyla were found to exhibit the largest changes in abundance, namely Actinobacteria, Proteobacteria and Firmicutes. More detailed analyses at the order level were done using a Lasso regression analysis to find a predictive subset of bacterial taxa. We found 26 bacterial orders to be indicative of sample age. Indoor samples did not reveal such a clear compositional change at the domain level: eukaryotic and prokaryotic abundance remained relatively stable across the assessed time period. Nonetheless, a Lasso regression analysis identified 32 bacterial orders exhibiting clear changes over time, enabling the prediction of TsD. For both indoor and outdoor samples, a larger number (around 60%) of the bacterial orders identified as indicative of TsD are part of the Actinobacteria, Proteobacteria and Firmicutes. In summary, we found that the observed changes across time are not primarily due to changes associated with body fluid specific bacteria but mostly due to accumulation of bacteria from the environment. Orders of these environmental bacteria could be evaluated for TsD prediction, considering the location and environment of the crime scene. However, further studies are needed to verify these findings, determine the applicability across samples, replicates, donors, and other variables, and also to further assess the effect of different seasons and locations on the samples.


Assuntos
Sangue/microbiologia , Muco do Colo Uterino/microbiologia , RNA Bacteriano/análise , Saliva/microbiologia , Sêmen/microbiologia , Análise de Sequência de RNA , Crime , Impressões Digitais de DNA , Exposição Ambiental , Feminino , Marcadores Genéticos , Humanos , Masculino , Menstruação , Repetições de Microssatélites , Fatores de Tempo
19.
Microbiologyopen ; 10(3): e1210, 2021 06.
Artigo em Inglês | MEDLINE | ID: mdl-34180598

RESUMO

In the microbiological diagnosis of bloodstream infections (BSI), blood culture (BC) is considered the gold standard test despite its limitations such as low sensitivity and slow turnaround time. A new FDA-cleared and CE-marked platform utilizing magnetic resonance to detect amplified DNA of the six most common and/or problematic BSI pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Escherichia coli; referred to as ESKAPEc) is available and may shorten the time to diagnosis and potentially improve antimicrobial utilization. Whole blood samples from hospitalized patients with clinical signs of sepsis were analyzed using the T2Bacteria Panel (T2Biosystems) and compared to simultaneously collected BC. Discrepant results were evaluated based on clinical infection criteria, combining supporting culture results and the opinion of treating physicians. A total of 55 samples from 53 patients were evaluated. The sensitivity and specificity of the T2Bacteria panel was 94% (16 out of 17 detections of T2Bacteria-targeted organisms) and 100%, respectively, with 36.4% (8 of 22) causes of BSI detected only by this method. The T2Bacteria Panel detected pathogens on average 55 hours faster than standard BC. In our study, 9 of 15 patients with positive T2Bacteria Panel results received early-targeted antibiotic therapy and/or modification of antimicrobial treatment based on T2Bacteria Panel findings. Given the high reliability, faster time to detection, and easy workflow, the technique qualifies as a point-of-care testing approach.


Assuntos
Antibacterianos/farmacologia , Gestão de Antimicrobianos/métodos , Bacteriemia/microbiologia , Sangue/microbiologia , Acinetobacter baumannii/efeitos dos fármacos , Acinetobacter baumannii/genética , Acinetobacter baumannii/isolamento & purificação , Bacteriemia/sangue , Bacteriemia/tratamento farmacológico , Hemocultura , Enterococcus faecium/efeitos dos fármacos , Enterococcus faecium/genética , Enterococcus faecium/isolamento & purificação , Escherichia coli/efeitos dos fármacos , Escherichia coli/genética , Escherichia coli/isolamento & purificação , Humanos , Klebsiella pneumoniae/efeitos dos fármacos , Klebsiella pneumoniae/genética , Klebsiella pneumoniae/isolamento & purificação , Estudos Prospectivos , Pseudomonas aeruginosa/efeitos dos fármacos , Pseudomonas aeruginosa/genética , Pseudomonas aeruginosa/isolamento & purificação , Staphylococcus aureus/efeitos dos fármacos , Staphylococcus aureus/genética , Staphylococcus aureus/isolamento & purificação
20.
Microbiol Spectr ; 9(1): e0017521, 2021 09 03.
Artigo em Inglês | MEDLINE | ID: mdl-34190590

RESUMO

The use of molecular-based diagnostic testing, such as the Luminex Verigene system, to rapidly identify the most common bacterial isolates from blood cultures is an important tool that reduces the duration of inappropriate antibiotics and decreases mortality. However, 5 to 15% of microorganisms recovered from blood culture are unable to be identified by the Verigene Gram-negative (BC-GN) or Gram-positive (BC-GP) assays. In this retrospective, observational study, we evaluate the identities and antimicrobial susceptibility patterns of 229 isolates that were not identified by either the Verigene BC-GN or BC-GP assay. The results presented here suggest that important, clinically relevant information about antimicrobial susceptibility patterns can still be inferred even when isolates are not identified by Verigene. We also examined changes in antibiotic use for patients with "unidentified" Verigene results at our institution and found that this subgroup represents an opportunity to optimize empirical antibiotic therapy. IMPORTANCE Rapid diagnostic testing to identify bloodstream pathogens has arisen as an important tool both to ensure adequate antimicrobial therapy is given early and to aid in antimicrobial stewardship by allowing for more rapid deescalation of inappropriate antimicrobial therapy. However, there is a paucity of data regarding the significance of isolates that are not able to be identified by rapid diagnostic testing. In this study, we report the identification to the species level and antimicrobial susceptibilities among isolates that were not identified by one such rapid diagnostic platform, the Verigene system. This study provides important insight into how a strong understanding of the strengths and limitations of a given rapid diagnostic platform, coupled with insight into local antibiotic susceptibility patterns, can allow for more nuanced and thoughtful empirical antibiotic selection.


Assuntos
Antibacterianos/farmacologia , Bactérias/efeitos dos fármacos , Bactérias/isolamento & purificação , Infecções Bacterianas/diagnóstico , Infecções Bacterianas/microbiologia , Sangue/microbiologia , Adulto , Idoso , Gestão de Antimicrobianos , Bactérias/classificação , Bactérias/genética , Infecções Bacterianas/sangue , Infecções Bacterianas/tratamento farmacológico , Hemocultura , Feminino , Humanos , Masculino , Análise em Microsséries , Pessoa de Meia-Idade , Técnicas de Diagnóstico Molecular , Estudos Retrospectivos
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