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1.
J Hazard Mater ; 475: 134886, 2024 Aug 15.
Artigo em Inglês | MEDLINE | ID: mdl-38878435

RESUMO

Minimization of antibiotic resistance genes (ARGs) and potential pathogenic antibiotic-resistant bacteria (PARB) during anaerobic digestion (AD) is significantly impacted by temperature. However, knowledge on how ARGs and PARB respond to temperature transition from thermophilic to mesophilic is limited. Here, we combined metagenomic-based with culture-based approaches and revealed the risks of antimicrobial resistance and pathogenicity during transition from 55 °C to 35 °C for AD, with strategies of sharp (ST, one-step by 20 °C/d) and mild (MT, step-wise by 1 °C/d). Results indicated a lower decrease in methane production with MT (by 38.9%) than ST (by 88.8%). Phenotypic assays characterized a significant propagation of multi-resistant lactose-fermenting Enterobacteriaceae and indicator pathogens after both transitions, especially via ST. Further genomic evidence indicated a significant increase of ARGs (29.4-fold), virulence factor genes (1.8-fold) and PARB (65.3-fold) after ST, while slight enrichment via MT. Bacterial succession and enhanced horizontal transfer mediated by mobile genetic elements promoted ARG propagation in AD during transition, which was synchronously exacerbated through horizontal transfer mechanisms mediated by cellular physiological responses (oxidative stress, membrane permeability, bacterial conjugation and transformation) and co-selection mechanisms of biomethanation metabolic functions (acidogenesis and acetogenesis). This study reveals temperature-dependent resistome and pathogenicity development in AD, facilitating microbial risk control.


Assuntos
Farmacorresistência Bacteriana , Anaerobiose , Farmacorresistência Bacteriana/genética , Temperatura , Metano/metabolismo , Bactérias/genética , Bactérias/patogenicidade , Bactérias/metabolismo , Bactérias/efeitos dos fármacos , Antibacterianos/farmacologia , Resistência Microbiana a Medicamentos/genética , Fatores de Virulência/genética , Transferência Genética Horizontal , Enterobacteriaceae/genética , Enterobacteriaceae/patogenicidade , Enterobacteriaceae/efeitos dos fármacos , Enterobacteriaceae/metabolismo , Genes Bacterianos
2.
Int J Mol Sci ; 25(10)2024 May 09.
Artigo em Inglês | MEDLINE | ID: mdl-38791176

RESUMO

Extensive microbial interactions occur within insect hosts. However, the interactions between the Huanglongbing (HLB) pathogen and endosymbiotic bacteria within the Asian citrus psyllid (ACP, Diaphorina citri Kuwayama) in wild populations remain elusive. Thus, this study aimed to detect the infection rates of HLB in the ACP across five localities in China, with a widespread prevalence in Ruijin (RJ, 58%), Huidong (HD, 28%), and Lingui (LG, 15%) populations. Next, microbial communities of RJ and LG populations collected from citrus were analyzed via 16S rRNA amplicon sequencing. The results revealed a markedly higher microbial diversity in the RJ population compared to the LG population. Moreover, the PCoA analysis identified significant differences in microbial communities between the two populations. Considering that the inter-population differences of Bray-Curtis dissimilarity in the RJ population exceeded those between populations, separate analyses were performed. Our findings indicated an increased abundance of Enterobacteriaceae in individuals infected with HLB in both populations. Random forest analysis also identified Enterobacteriaceae as a crucial indicator of HLB infection. Furthermore, the phylogenetic analysis suggested a potential regulatory role of ASV4017 in Enterobacteriaceae for ACP, suggesting its possible attractant activity. This research contributes to expanding the understanding of microbial communities associated with HLB infection, holding significant implications for HLB prevention and treatment.


Assuntos
Enterobacteriaceae , Hemípteros , Filogenia , Doenças das Plantas , RNA Ribossômico 16S , Animais , Hemípteros/microbiologia , Enterobacteriaceae/genética , Enterobacteriaceae/classificação , Enterobacteriaceae/patogenicidade , RNA Ribossômico 16S/genética , Doenças das Plantas/microbiologia , China/epidemiologia , Citrus/microbiologia , Microbiota
3.
Microbiology (Reading) ; 170(4)2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38661713

RESUMO

Introduction. Leclercia adecarboxylata is a member of Enterobacterales, often considered an opportunistic pathogen. Recent reports have highlighted L. adecarboxylata as an emerging pathogen harbouring virulence and resistance determinants.Gap statement. Little information exists on virulence and resistance determinants in L. adecarboxylata strains isolated from environmental, food, and clinical samples.Aim. To determine the presence of resistance and virulence determinants and plasmid features in L. adecarboxylata strains isolated from environmental, food, and clinical samples, as well as their phylogenetic relationship.Results. All strains tested showed resistance to ß-lactams and quinolones but were sensitive to aminoglycosides and nitrofurans. However, even though fosfomycin resistance is considered a characteristic trait of L. adecarboxylata, the resistance phenotype was only observed in 50 % of the strains; bla TEM was the most prevalent BLEE gene (70 %), while the quinolone qnrB gene was observed in 60 % of the strains. Virulence genes were differentially observed in the strains, with adhesion-related genes being the most abundant, followed by toxin genes. Finally, all strains carried one to seven plasmid bands ranging from 7 to 125 kbps and harboured several plasmid addiction systems, such as ParDE, VagCD, and CcdAB in 80 % of the strains.Conclusions. L. adecarboxylata is an important emerging pathogen that may harbour resistance and virulence genes. Additionally, it has mobilizable genetic elements that may contribute to the dissemination of genetic determinants to other bacterial genera.


Assuntos
Antibacterianos , Enterobacteriaceae , Testes de Sensibilidade Microbiana , Filogenia , Plasmídeos , Fatores de Virulência , Antibacterianos/farmacologia , Plasmídeos/genética , Virulência/genética , Enterobacteriaceae/genética , Enterobacteriaceae/efeitos dos fármacos , Enterobacteriaceae/patogenicidade , Enterobacteriaceae/isolamento & purificação , Enterobacteriaceae/classificação , Fatores de Virulência/genética , Humanos , Infecções por Enterobacteriaceae/microbiologia , Fenótipo , Farmacorresistência Bacteriana/genética , Quinolonas/farmacologia , beta-Lactamas/farmacologia , Farmacorresistência Bacteriana Múltipla/genética , Microbiologia de Alimentos
4.
Antimicrob Agents Chemother ; 66(11): e0078722, 2022 11 15.
Artigo em Inglês | MEDLINE | ID: mdl-36200773

RESUMO

OXA-48 is the most common carbapenemase in Enterobacterales in Germany and many other European countries. Depending on the genomic location of blaOXA-48, OXA-48-producing isolates vary in phenotype and intra- and interspecies transferability of blaOXA-48. In most bacterial isolates, blaOXA-48 is located on one of seven variants of Tn1999 (Tn1999.1 to Tn1999.6 and invTn1999.2). Here, a novel Tn1999 variant, Tn1999.7, is described, which was identified in 11 clinical isolates from 2016 to 2020. Tn1999.7 differs from Tn1999.1 by the insertion of the 8,349-bp Tn3 family transposon Tn7442 between the lysR gene and blaOXA-48 open reading frame. Tn7442 carries genes coding for a restriction endonuclease and a DNA methyltransferase as cargo, forming a type III restriction modification system. Tn1999.7 was carried on an ~71-kb IncL plasmid in 9/11 isolates. In one isolate, Tn1999.7 was situated on an ~76-kb plasmid, harboring an additional insertion sequence in the plasmid backbone. In one isolate, the plasmid size is only ~63 kb due to a deletion adjacent to Tn7442 that extends into the plasmid backbone. Mean conjugation rates of the Tn1999.7-harboring plasmids in J53 ranged from 4.47 × 10-5 to 2.03 × 10-2, similar to conjugation rates of other pOXA-48-type IncL plasmids. The stability of plasmids with Tn1999.7 was significantly higher than that of a Tn1999.2-harboring plasmid in vitro. This increase in stability could be related to the insertion of a restriction-modification system, which can promote postsegregational killing. The increased plasmid stability associated with Tn1999.7 could contribute to the further spread of OXA-48.


Assuntos
Proteínas de Bactérias , Elementos de DNA Transponíveis , Plasmídeos , beta-Lactamases , Proteínas de Bactérias/genética , beta-Lactamases/genética , beta-Lactamases/metabolismo , Elementos de DNA Transponíveis/genética , Europa (Continente) , Alemanha , Plasmídeos/genética , Enterobacteriaceae/genética , Enterobacteriaceae/patogenicidade , Variação Genética
5.
Braz. j. biol ; 82: 1-9, 2022. map, ilus, tab
Artigo em Inglês | LILACS, VETINDEX | ID: biblio-1468416

RESUMO

Use of antibiotics inevitably leads to antimicrobial resistance. Selection for resistance occurs primarily within the gut of humans and animals as well as in the environment through natural resistance and residual antibiotics in streams and soil. We evaluated antimicrobial resistance in Gram negative bacteria from a river system in a rural community in Bahia, Brazil. Water was collected from the Jiquiriçá and Brejões rivers and the piped water supply. Additionally, stools were collected from a random sample of residents, cows, pigs and horses near the river. The samples were screened for bacteria resistant to ciprofloxacin, cefotaxime, and meropenem and identified biochemically at the genus and species levels. Microbial source tracking demonstrated that ruminant and human fecal contamination increased as the rivers neared the village center and decreased after the last residence. Antibiotic bacteria were identified from all samples (n = 32). No bacteria were resistant to carbapenems, but the majority of the enterobacteria were resistant to ciprofloxacin, even though this class of antibiotics is not commonly used in food animals in this region. Considering these facts, together with the pattern of human fecal contamination, a human source was considered most likely for these resistant isolates.


O uso de antibióticos inevitavelmente leva à resistência antimicrobiana. A seleção para resistência antimicrobiana ocorre principalmente no intestino de seres humanos e animais, bem como no meio ambiente, através da resistência natural e resíduos de antibióticos nos esgotos e no solo. Avaliamos a resistência antimicrobiana em bactérias Gram-negativas de um sistema fluvial em uma comunidade rural da Bahia, Brasil. A água foi coletada nos rios Jiquiriçá e Brejões e no abastecimento de água encanada. Além disso, foram coletadas amostras randomizadas de fezes de moradores, vacas, porcos e cavalos próximos ao rio. As amostras foram triadas para bactérias resistentes à ciprofloxacina, cefotaxima e meropenem e identificadas bioquimicamente nos níveis de gênero e espécie. O rastreamento de fontes microbianas demonstrou que a contaminação fecal de ruminantes e humanos aumentou à medida que os rios se aproximavam do centro da vila e diminuía após a última residência. Bactérias resistentes a antibióticos foram identificadas em todas as amostras (n = 32). Nenhuma bactéria demonstrou ser resistente aos carbapenêmicos testados, contudo, foi encontrado enterobactérias resistentes à ciprofloxacina, ainda que essa classe de antibióticos não seja comumente usada na medicina veterinária dos animais dessa região. Considerando esses fatos, juntamente com o padrão de contaminação fecal avaliado, a fonte de contaminação humana foi considerada a mais provável na interação desses isolados resistentes.


Assuntos
Bactérias Gram-Negativas/patogenicidade , Enterobacteriaceae/patogenicidade , Farmacorresistência Bacteriana , Fezes/microbiologia , Poluentes da Água/análise
6.
Braz. j. biol ; 82: 1-7, 2022. tab
Artigo em Inglês | LILACS, VETINDEX | ID: biblio-1468437

RESUMO

Microbiological studies of the sanitary and health status of psittacine birds that will be reintroduced is important in evaluating whether these animals act as carriers of pathogenic agents to other animals and humans. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a faster and more accurate method to identify bacteria than conventional microbiology methods. The aim of this study was to evaluate the health status of psittacines housed in captivity, by assessment of Gram-negative bacteria from fecal microbiota through MALDI- TOF MS identification. The results indicate high frequency of Gram-negative bacteria in feces (96.5%), especially from the Enterobacteriaceae family (88.7%). The most prevalent bacteria were Escherichia coli (39.0%), Proteus vulgaris (12.2%), Klebsiella spp. (12.1%) and Raoultella ornithinolytica (8.7%). Proteus hauseri, Citrobacter spp., Morganella morgannii, Providencia rettgeri, Enterobacter spp. and Escherichia hermannii were isolated with lower frequency. . All these agents are potentially pathogenic for parrots and can cause systemic infections in other animals and humans. These findings reinforce that MALDI- TOF MS proved to be a rapid and accurate method of identification of the microorganism and evaluation of the health status of psittacines, providing relevant data to assist decision-making regarding the sanitary protocols in wildlife centers, and possible future reintroduction of wild birds.


Estudos microbiológicos da sanidade de psitacídeos que serão reintroduzidos são importantes para avaliar se esses animais atuam como portadores de agentes patogênicos para outros animais e humanos. A espectrometria de massa por ionização/dessorção de matriz assistida por laser/tempo de vôo (MALDI-TOF MS) é um método mais rápido e preciso para identificar bactérias na comparação com métodos convencionais de microbiologia. O objetivo deste estudo foi avaliar o estado de saúde de psitacídeos cativos, identificando bactérias Gram-negativas da microbiota fecal por MALDI -TOF MS. Os resultados indicaram alta frequência de bactérias Gram-negativas nas fezes (96,5%), principalmente da família Enterobacteriaceae (88,7%). As mais prevalentes foram Escherichia coli (39,0%), Proteus vulgaris (12,2%), Klebsiella spp. (12,1%) e Raoultella ornithinolytica (8,7%). Proteus hauseri, Citrobacter spp., Morganella morgannii, Providencia rettgeri, Enterobacter spp. e Escherichia hermannii foram isolados com menor frequência. Todos esses agentes são potencialmente patogênicos para os papagaios e podem causar infecções sistêmicas em outros animais e seres humanos. Esses achados reforçam que o MALDI- TOF MS é um método rápido e preciso de identificação do microrganismo e avaliação do estado de saúde dos psitacídeos, fornecendo dados relevantes para auxiliar na tomada de decisões sobre os protocolos sanitários em centros de triagem de animais selvagens e sobre a possibilidade de reintrodução futura.


Assuntos
Animais , Bactérias Gram-Negativas/patogenicidade , Enterobacteriaceae/patogenicidade , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz , Papagaios/microbiologia
7.
Antimicrob Resist Infect Control ; 10(1): 171, 2021 12 23.
Artigo em Inglês | MEDLINE | ID: mdl-34949217

RESUMO

Duodenoscopy-associated infections occur worldwide despite strict adherence to reprocessing standards. The exact scope of the problem remains unknown because a standardized sampling protocol and uniform sampling techniques are lacking. The currently available multi-society protocol for microbial culturing by the Centers for Disease Control and Prevention, the United States Food and Drug Administration (FDA) and the American Society for Microbiology, published in 2018 is too laborious for broad clinical implementation. A more practical sampling protocol would result in increased accessibility and widespread implementation. This will aid to reduce the prevalence of duodenoscope contamination. To reduce the risk of duodenoscopy-associated pathogen transmission the FDA advised four supplemental reprocessing measures. These measures include double high-level disinfection, microbiological culturing and quarantine, ethylene oxide gas sterilization and liquid chemical sterilization. When the supplemental measures were advised in 2015 data evaluating their efficacy were sparse. Over the past five years data regarding the supplemental measures have become available that place the efficacy of the supplemental measures into context. As expected the advised supplemental measures have resulted in increased costs and reprocessing time. Unfortunately, it has also become clear that the efficacy of the supplemental measures falls short and that duodenoscope contamination remains a problem. There is a lot of research into new reprocessing methods and technical applications trying to solve the problem of duodenoscope contamination. Several promising developments such as single-use duodenoscopes, electrolyzed acidic water, and vaporized hydrogen peroxide plasma are already applied in a clinical setting.


Assuntos
Duodenoscópios/normas , Contaminação de Equipamentos/prevenção & controle , Reutilização de Equipamento/estatística & dados numéricos , Controle de Infecções/métodos , Controle de Infecções/normas , Antibacterianos/farmacologia , Infecção Hospitalar/prevenção & controle , Desinfecção/economia , Desinfecção/legislação & jurisprudência , Desinfecção/métodos , Farmacorresistência Bacteriana Múltipla , Enterobacteriaceae/efeitos dos fármacos , Enterobacteriaceae/patogenicidade , Infecções por Enterobacteriaceae/prevenção & controle , Infecções por Enterobacteriaceae/transmissão , Reutilização de Equipamento/normas , Humanos , Controle de Infecções/economia , Controle de Infecções/legislação & jurisprudência , Estados Unidos , United States Food and Drug Administration/legislação & jurisprudência
8.
EBioMedicine ; 73: 103644, 2021 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-34695658

RESUMO

BACKGROUND: The specific roles that gut microbiota, known pathogens, and host energy-regulating hormones play in the pathogenesis of non-edematous severe acute malnutrition (marasmus SAM) and moderate acute malnutrition (MAM) during outpatient nutritional rehabilitation are yet to be explored. METHODS: We applied an ensemble of sample-specific (intra- and inter-modality) association networks to gain deeper insights into the pathogenesis of acute malnutrition and its severity among children under 5 years of age in rural Gambia, where marasmus SAM is most prevalent. FINDINGS: Children with marasmus SAM have distinct microbiome characteristics and biologically-relevant multimodal biomarkers not observed among children with moderate acute malnutrition. Marasmus SAM was characterized by lower microbial richness and biomass, significant enrichments in Enterobacteriaceae, altered interactions between specific Enterobacteriaceae and key energy regulating hormones and their receptors. INTERPRETATION: Our findings suggest that marasmus SAM is characterized by the collapse of a complex system with nested interactions and key associations between the gut microbiome, enteric pathogens, and energy regulating hormones.  Further exploration of these systems will help inform innovative preventive and therapeutic interventions. FUNDING: The work was supported by the UK Medical Research Council (MRC; MC-A760-5QX00) and the UK Department for International Development (DFID) under the MRC/DFID Concordat agreement; Bill and Melinda Gates Foundation (OPP 1066932) and the National Institute of Medical Research (NIMR), UK. This network analysis was supported by NIH U54GH009824 [CLD] and NSF OCE-1558453 [CLD].


Assuntos
Metabolismo Energético , Microbioma Gastrointestinal , Hormônios/metabolismo , Interações Hospedeiro-Patógeno , Desnutrição Aguda Grave/etiologia , Desnutrição Aguda Grave/metabolismo , Biodiversidade , Estudos Transversais , Suscetibilidade a Doenças , Enterobacteriaceae/patogenicidade , Fezes/microbiologia , Gâmbia/epidemiologia , Humanos , Metagenoma , Metagenômica/métodos , Fenótipo , População Rural , Desnutrição Aguda Grave/diagnóstico , Desnutrição Aguda Grave/epidemiologia , Fatores de Virulência
9.
Lancet Infect Dis ; 21(12): 1677-1688, 2021 12.
Artigo em Inglês | MEDLINE | ID: mdl-34384533

RESUMO

BACKGROUND: Sepsis is a major contributor to neonatal mortality, particularly in low-income and middle-income countries (LMICs). WHO advocates ampicillin-gentamicin as first-line therapy for the management of neonatal sepsis. In the BARNARDS observational cohort study of neonatal sepsis and antimicrobial resistance in LMICs, common sepsis pathogens were characterised via whole genome sequencing (WGS) and antimicrobial resistance profiles. In this substudy of BARNARDS, we aimed to assess the use and efficacy of empirical antibiotic therapies commonly used in LMICs for neonatal sepsis. METHODS: In BARNARDS, consenting mother-neonates aged 0-60 days dyads were enrolled on delivery or neonatal presentation with suspected sepsis at 12 BARNARDS clinical sites in Bangladesh, Ethiopia, India, Pakistan, Nigeria, Rwanda, and South Africa. Stillborn babies were excluded from the study. Blood samples were collected from neonates presenting with clinical signs of sepsis, and WGS and minimum inhibitory concentrations for antibiotic treatment were determined for bacterial isolates from culture-confirmed sepsis. Neonatal outcome data were collected following enrolment until 60 days of life. Antibiotic usage and neonatal outcome data were assessed. Survival analyses were adjusted to take into account potential clinical confounding variables related to the birth and pathogen. Additionally, resistance profiles, pharmacokinetic-pharmacodynamic probability of target attainment, and frequency of resistance (ie, resistance defined by in-vitro growth of isolates when challenged by antibiotics) were assessed. Questionnaires on health structures and antibiotic costs evaluated accessibility and affordability. FINDINGS: Between Nov 12, 2015, and Feb 1, 2018, 36 285 neonates were enrolled into the main BARNARDS study, of whom 9874 had clinically diagnosed sepsis and 5749 had available antibiotic data. The four most commonly prescribed antibiotic combinations given to 4451 neonates (77·42%) of 5749 were ampicillin-gentamicin, ceftazidime-amikacin, piperacillin-tazobactam-amikacin, and amoxicillin clavulanate-amikacin. This dataset assessed 476 prescriptions for 442 neonates treated with one of these antibiotic combinations with WGS data (all BARNARDS countries were represented in this subset except India). Multiple pathogens were isolated, totalling 457 isolates. Reported mortality was lower for neonates treated with ceftazidime-amikacin than for neonates treated with ampicillin-gentamicin (hazard ratio [adjusted for clinical variables considered potential confounders to outcomes] 0·32, 95% CI 0·14-0·72; p=0·0060). Of 390 Gram-negative isolates, 379 (97·2%) were resistant to ampicillin and 274 (70·3%) were resistant to gentamicin. Susceptibility of Gram-negative isolates to at least one antibiotic in a treatment combination was noted in 111 (28·5%) to ampicillin-gentamicin; 286 (73·3%) to amoxicillin clavulanate-amikacin; 301 (77·2%) to ceftazidime-amikacin; and 312 (80·0%) to piperacillin-tazobactam-amikacin. A probability of target attainment of 80% or more was noted in 26 neonates (33·7% [SD 0·59]) of 78 with ampicillin-gentamicin; 15 (68·0% [3·84]) of 27 with amoxicillin clavulanate-amikacin; 93 (92·7% [0·24]) of 109 with ceftazidime-amikacin; and 70 (85·3% [0·47]) of 76 with piperacillin-tazobactam-amikacin. However, antibiotic and country effects could not be distinguished. Frequency of resistance was recorded most frequently with fosfomycin (in 78 isolates [68·4%] of 114), followed by colistin (55 isolates [57·3%] of 96), and gentamicin (62 isolates [53·0%] of 117). Sites in six of the seven countries (excluding South Africa) stated that the cost of antibiotics would influence treatment of neonatal sepsis. INTERPRETATION: Our data raise questions about the empirical use of combined ampicillin-gentamicin for neonatal sepsis in LMICs because of its high resistance and high rates of frequency of resistance and low probability of target attainment. Accessibility and affordability need to be considered when advocating antibiotic treatments with variance in economic health structures across LMICs. FUNDING: The Bill & Melinda Gates Foundation.


Assuntos
Antibacterianos/uso terapêutico , Resistência Microbiana a Medicamentos , Infecções por Enterobacteriaceae/tratamento farmacológico , Sepse Neonatal/tratamento farmacológico , Sepse Neonatal/microbiologia , Infecções Estafilocócicas/tratamento farmacológico , Antibacterianos/economia , Estudos de Coortes , Quimioterapia Combinada , Enterobacteriaceae/patogenicidade , Humanos , Recém-Nascido , Staphylococcus aureus/patogenicidade , Virulência
10.
Pediatr Infect Dis J ; 40(10): e370-e373, 2021 10 01.
Artigo em Inglês | MEDLINE | ID: mdl-34260488

RESUMO

Raoultella ornithinolytica is an opportunistic, aquaphilic and Gram-negative bacterium. Immune deficiency states and indwelling catheters provide a basis for most of the infections arising. R. ornithinolytica septicemia (ROS) is extremely rare in neonates but can be life threatening. Community-acquired ROS has not been described in neonates before. The diagnosis of neonatal septicemia is occasionally complicated by unusual clinical presentations. Pyloric stenosis is manifested by projectile, nonbilious vomiting and late findings, including weight loss, dehydration and electrolyte abnormalities beyond 4-6 weeks old. Community-acquired neonatal septicemia symptoms can sometimes be confused with symptoms of gastrointestinal obstructions in patients without risk factors for sepsis. Early diagnosis and appropriate antibiotics are essentials for a good prognosis in neonatal septicemia. Herein, we present a novel case of community-acquired ROS with an unusual presentation in a term infant and a review of the literature about ROS in the neonatal period.


Assuntos
Infecções por Enterobacteriaceae/diagnóstico , Enterobacteriaceae/patogenicidade , Sepse Neonatal/diagnóstico , Sepse Neonatal/microbiologia , Antibacterianos/uso terapêutico , Infecções Comunitárias Adquiridas/diagnóstico , Infecções Comunitárias Adquiridas/tratamento farmacológico , Infecções Comunitárias Adquiridas/microbiologia , Infecções por Enterobacteriaceae/sangue , Infecções por Enterobacteriaceae/tratamento farmacológico , Humanos , Recém-Nascido , Masculino , Sepse Neonatal/tratamento farmacológico
11.
Diagn Microbiol Infect Dis ; 101(3): 115472, 2021 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-34303084

RESUMO

There is minimal data on the optimal treatment of lower inoculum infections such as urinary tract infections (UTIs) caused by SPICE organisms which encode the betalactamase enzyme, AmpC. This single-center, retrospective review of adult hospitalized patients with UTIs caused by a SPICE organism compared outcomes amongst patients treated with drugs susceptible to AmpC hydrolysis versus drugs stable against AmpC. Of 156 patients, similar rates of clinical response, 30-day infection related readmission, 30-day infection recurrence, 30-day mortality rates, and median length of hospital stay were found between the two groups. Notably, 44% of patients with ceftriaxone resistance reported had recent ß-lactam exposure versus only 11% of patients without ceftriaxone resistance (P = 0.002). Based on our data, there does not appear to be a difference in clinical response or any of the secondary outcomes in patients with UTIs treated with AmpC stable and AmpC susceptible agents.


Assuntos
Enterobacteriaceae/enzimologia , Enterobacteriaceae/patogenicidade , Infecções Urinárias/microbiologia , beta-Lactamases/genética , Idoso , Idoso de 80 Anos ou mais , Antibacterianos , Ceftriaxona/farmacologia , Ceftriaxona/uso terapêutico , Enterobacteriaceae/efeitos dos fármacos , Enterobacteriaceae/genética , Infecções por Enterobacteriaceae/microbiologia , Infecções por Enterobacteriaceae/mortalidade , Feminino , Hospitalização/estatística & dados numéricos , Humanos , Masculino , Testes de Sensibilidade Microbiana , Pessoa de Meia-Idade , beta-Lactamases/biossíntese , beta-Lactamas/farmacologia , beta-Lactamas/uso terapêutico
12.
Int J Antimicrob Agents ; 58(2): 106371, 2021 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-34082028

RESUMO

OBJECTIVES: Colistin resistance mediated by plasmids for their rapid dissemination in Enterobacteriaceae is alarming. We aimed to characterize the genetic features of mcr-1 gene as well as the role of promoters in gene expression and levels of colistin resistance among clinical isolates of Enterobacteriaceae. METHODS: Clinical isolates of Enterobacteriaceae were collected in thirteen cities in China and screened for mcr-1 gene using polymerase chain reaction (PCR) amplification and sequencing. Antimicrobial susceptibility testing, transformation assay and plasmid sequencing, quantitative real-time PCR were performed for mcr-1-positive isolates. Promoter-probe vector pKK232-8 was utilized to assess the activity of the mcr-1 promoters. RESULTS: This study identified the mcr-1 gene in 15 clinical isolates of Enterobacteriaceae, among which 14 were resistant to colistin, with MICs of 4-8 mg/L, while one mcr-1-bearing isolate EC09 was susceptible to colistin, with an MIC of 0.5 mg/L. Moreover, mcr-1-harbouring plasmids from 10 clinical isolates were transferrable via transformation and belonged to different incompatibility groups (IncI2 and IncX4). Plasmid pEC09 failed to transform and belonged to IncP1. A genetic structure containing the mcr-1-pap2 element was detected in these plasmids. EC09 demonstrated the lowest transcription level of mcr-1 gene, as determined by quantitative real-time PCR, which was in accordance with its susceptibility to colistin. Furthermore, the promoter activity of mcr-1 in pEC09 was the lowest, as determined by promoter-probe vector pKK232-8. CONCLUSION: Promoter variations were associated with expression of the mcr-1 gene and ultimately the levels of colistin resistance.


Assuntos
Antibacterianos/farmacocinética , Antibacterianos/uso terapêutico , Colistina/farmacocinética , Colistina/uso terapêutico , Farmacorresistência Bacteriana/genética , Farmacorresistência Bacteriana Múltipla/efeitos dos fármacos , Enterobacteriaceae/genética , Infecções por Escherichia coli/tratamento farmacológico , Proteínas de Escherichia coli/genética , China , Enterobacteriaceae/patogenicidade , Humanos
13.
Microbiol Spectr ; 9(1): e0000321, 2021 09 03.
Artigo em Inglês | MEDLINE | ID: mdl-34106568

RESUMO

Gastrointestinal infections cause significant morbidity and mortality worldwide. The complexity of human biology and limited insights into host-specific infection mechanisms are key barriers to current therapeutic development. Here, we demonstrate that two-dimensional epithelial monolayers derived from human intestinal organoids, combined with in vivo-like bacterial culturing conditions, provide significant advancements for the study of enteropathogens. Monolayers from the terminal ileum, cecum, and ascending colon recapitulated the composition of the gastrointestinal epithelium, in which several techniques were used to detect the presence of enterocytes, mucus-producing goblet cells, and other cell types following differentiation. Importantly, the addition of receptor activator of nuclear factor kappa-B ligand (RANKL) increased the presence of M cells, critical antigen-sampling cells often exploited by enteric pathogens. For infections, bacteria were grown under in vivo-like conditions known to induce virulence. Overall, interesting patterns of tissue tropism and clinical manifestations were observed. Shigella flexneri adhered efficiently to the cecum and colon; however, invasion in the colon was best following RANKL treatment. Both Salmonella enterica serovars Typhi and Typhimurium displayed different infection patterns, with S. Typhimurium causing more destruction of the terminal ileum and S. Typhi infecting the cecum more efficiently than the ileum, particularly with regard to adherence. Finally, various pathovars of Escherichia coli validated the model by confirming only adherence was observed with these strains. This work demonstrates that the combination of human-derived tissue with targeted bacterial growth conditions enables powerful analyses of human-specific infections that could lead to important insights into pathogenesis and accelerate future vaccine development. IMPORTANCE While traditional laboratory techniques and animal models have provided valuable knowledge in discerning virulence mechanisms of enteric pathogens, the complexity of the human gastrointestinal tract has hindered our understanding of physiologically relevant, human-specific interactions; and thus, has significantly delayed successful vaccine development. The human intestinal organoid-derived epithelial monolayer (HIODEM) model closely recapitulates the diverse cell populations of the intestine, allowing for the study of human-specific infections. Differentiation conditions permit the expansion of various cell populations, including M cells that are vital to immune recognition and the establishment of infection by some bacteria. We provide details of reproducible culture methods and infection conditions for the analyses of Shigella, Salmonella, and pathogenic Escherichia coli in which tissue tropism and pathogen-specific infection patterns were detected. This system will be vital for future studies that explore infection conditions, health status, or epigenetic differences and will serve as a novel screening platform for therapeutic development.


Assuntos
Técnicas de Cultura de Células/métodos , Infecções por Enterobacteriaceae/microbiologia , Enterobacteriaceae/fisiologia , Trato Gastrointestinal/microbiologia , Organoides/microbiologia , Enterobacteriaceae/genética , Enterobacteriaceae/patogenicidade , Enterócitos/microbiologia , Células Epiteliais/citologia , Células Epiteliais/microbiologia , Epitélio/microbiologia , Trato Gastrointestinal/citologia , Humanos , Organoides/citologia , Virulência
14.
J Basic Microbiol ; 61(6): 524-546, 2021 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-33991346

RESUMO

Mark Achtman introduced the term "genetically monomorphic bacteria" (GM bacteria) for some human and plant pathogens. They displayed a great uniformity in terms of their "genetic" properties. This "uniformity" poses a challenge to microbiologists. To address these problems, we used CodonW and IslandViewer 3 as analytical tools and took Escherichia coli, Salmonella, and Shigella strains as a model organisms. We hypothesized that GM bacterium contains a common molecular signature among them. We have found a significant correlation regarding the number of protein-coding genes, predicted highly expressed genes, and the highest length of gene in this regard. On the other hand, the correspondence analysis of pathogenicity-related genes identified by IslandViewer 3 displayed a somewhat unique pattern in GM bacteria. The probable pathogenic genes are clustered into two separate groups, which is a hallmark of some pattern. Similar genes of non-monomorphic pathogenic strain clustered almost similarly, but the clusters are joined together, they are not completely separated. These features, in our considered view, may be considered as codon usages signatures of these bacteria, and E. coli in particular.


Assuntos
Uso do Códon/genética , Enterobacteriaceae/genética , Genoma Bacteriano/genética , Proteínas de Bactérias/genética , Enterobacteriaceae/patogenicidade , Genes Bacterianos , Marcadores Genéticos , Genômica , Proteínas Ribossômicas/genética , Virulência/genética
15.
Pathology ; 53(6): 763-767, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-33958177

RESUMO

There is limited literature examining the accuracy of the VITEK 2 Advanced Expert System (AES) in characterisation of ß-lactamase resistance patterns. We present a prospective single centre study to better ascertain the performance characteristics of this program. The VITEK 2 AES interpretation was compared to established laboratory phenotypic methods. The overall sensitivity for detection of broad-spectrum ß-lactamase by the AES was 95%, with a specificity of 78%. One or more discrepancies were noted in 36% of samples, with the majority of these (87/100) due to incorrect 'overcall' of a resistance mechanism. AES characterisation of AmpC resistance mechanisms was excellent. In contrast, the AES had poor specificity in classifying extended spectrum ß-lactamases (ESBLs). As a screening aid, the AES can be a valuable tool. However, optimal use requires an adequate working knowledge of resistance mechanisms in order to correctly interpret and accept the result output.


Assuntos
Antibacterianos/farmacologia , Enterobacteriaceae/patogenicidade , Sistemas Inteligentes , beta-Lactamases/metabolismo , Proteínas de Bactérias/metabolismo , Escherichia coli/efeitos dos fármacos , Hospitais , Humanos , Resistência beta-Lactâmica/efeitos dos fármacos
16.
PLoS Pathog ; 17(5): e1009510, 2021 05.
Artigo em Inglês | MEDLINE | ID: mdl-33956916

RESUMO

Protein conformational diseases are characterized by misfolding and toxic aggregation of metastable proteins, often culminating in neurodegeneration. Enteric bacteria influence the pathogenesis of neurodegenerative diseases; however, the complexity of the human microbiome hinders our understanding of how individual microbes influence these diseases. Disruption of host protein homeostasis, or proteostasis, affects the onset and progression of these diseases. To investigate the effect of bacteria on host proteostasis, we used Caenorhabditis elegans expressing tissue-specific polyglutamine reporters that detect changes in the protein folding environment. We found that colonization of the C. elegans gut with enteric bacterial pathogens disrupted proteostasis in the intestine, muscle, neurons, and the gonad, while the presence of bacteria that conditionally synthesize butyrate, a molecule previously shown to be beneficial in neurodegenerative disease models, suppressed aggregation and the associated proteotoxicity. Co-colonization with this butyrogenic strain suppressed bacteria-induced protein aggregation, emphasizing the importance of microbial interaction and its impact on host proteostasis. Further experiments demonstrated that the beneficial effect of butyrate depended on the bacteria that colonized the gut and that this protective effect required SKN-1/Nrf2 and DAF-16/FOXO transcription factors. We also found that bacteria-derived protein aggregates contribute to the observed disruption of host proteostasis. Together, these results reveal the significance of enteric infection and gut dysbiosis on the pathogenesis of protein conformational diseases and demonstrate the potential of using butyrate-producing microbes as a preventative and treatment strategy for neurodegenerative disease.


Assuntos
Butiratos/farmacologia , Proteínas de Caenorhabditis elegans/metabolismo , Caenorhabditis elegans/efeitos dos fármacos , Infecções por Enterobacteriaceae/complicações , Microbioma Gastrointestinal , Peptídeos/química , Proteostase , Animais , Caenorhabditis elegans/microbiologia , Proteínas de Caenorhabditis elegans/genética , Enterobacteriaceae/patogenicidade , Infecções por Enterobacteriaceae/microbiologia , Humanos , Peptídeos/efeitos dos fármacos , Peptídeos/metabolismo , Dobramento de Proteína
17.
J Am Soc Mass Spectrom ; 32(6): 1295-1299, 2021 Jun 02.
Artigo em Inglês | MEDLINE | ID: mdl-33856212

RESUMO

Pathogen identification is crucial to confirm bacterial infections and guide antimicrobial therapy. Although MALDI-TOF mass spectrometry (MS) serves as foundation for tools that enable rapid microbial identification, some bacteria remain challenging to identify. We recently showed that top-down proteomics (TDP) could be used to discriminate closely related enterobacterial pathogens (Escherichia coli, Shigella, and Salmonella) that are indistinguishable with tools rooted in the MALDI-TOF MS approach. Current TDP diagnostic relies on the identification of specific proteoforms for each species through a database search. However, microbial proteomes are often poorly annotated, which complicates the large-scale identification of proteoforms and leads to many unidentified high-quality mass spectra. Here, we describe a new computational pipeline called DiagnoTop that lists discriminative spectral clusters found in TDP data sets that can be used for microbial diagnostics without database search. Applied to our enterobacterial TDP data sets, DiagnoTop could easily shortlist high-quality discriminative spectral clusters, leading to increased diagnostic power. This pipeline opens new perspectives in clinical microbiology and biomarker discovery using TDP.


Assuntos
Bactérias/química , Bactérias/patogenicidade , Biologia Computacional/métodos , Software , Espectrometria de Massas em Tandem/métodos , Bases de Dados Factuais , Enterobacteriaceae/química , Enterobacteriaceae/patogenicidade , Bases de Conhecimento , Proteômica/métodos , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz , Fluxo de Trabalho
18.
PLoS One ; 16(4): e0250455, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33886664

RESUMO

Stethoscopes have been suggested to be a possible vector of contact transmission. However, only a few studies have focused on the prevalence of contamination by multidrug-resistant (MDR) bacteria and effectiveness of disinfection training to reduce. This study is to investigate the burden of stethoscope contamination with nosocomial pathogens and multidrug-resistant (MDR) bacteria and to analyze habit changes in disinfection of stethoscopes among healthcare workers (HCWs) before and after education and training. We performed a prospective pre and post quasi-experimental study. A total of 100 HCWs (55 doctors and 45 nurses) were recruited. HCWs were surveyed on their disinfection behavior and stethoscopes were cultured by pressing the diaphragm directly onto a blood agar plate before and after education on disinfection. Pulsed-field gel electrophoresis was performed to determine the relatedness of carbapenem-resistant Enterobacteriaceae. Most of the stethoscopes were contaminated with microorganisms before and after the intervention (97.9% and 91.5%, respectively). The contamination rate of stethoscopes with nosocomial pathogens before and after education was 20.8% and 19.2%, respectively. Stethoscope disinfection habits improved (55.1% vs 31.0%; p<0.001), and the overall bacterial loads of contamination were reduced (median colony-forming units, 15 vs 10; p = 0.019) after the intervention. However, the contamination rate by nosocomial pathogens and MDR bacteria did not decrease significantly. A carbapenemase-producing Klebsiella pneumoniae isolates from a stethoscope was closely related to isolates from the patients admitted at the same ward where the stethoscope was used. Stethoscopes were contaminated with various nosocomial pathogens including MDR bacteria and might act as a vehicle of MDR bacteria. Continuous, consistent education and training should be provided to HCWs using multifaceted approach to reduce the nosocomial transmission via stethoscopes.


Assuntos
Infecção Hospitalar/microbiologia , Enterobacteriaceae/efeitos dos fármacos , Klebsiella pneumoniae/efeitos dos fármacos , Estetoscópios/microbiologia , Adulto , Carbapenêmicos/farmacologia , Infecção Hospitalar/epidemiologia , Infecção Hospitalar/prevenção & controle , Desinfecção/normas , Contaminação de Medicamentos , Farmacorresistência Bacteriana Múltipla/genética , Enterobacteriaceae/patogenicidade , Contaminação de Equipamentos/prevenção & controle , Feminino , Pessoal de Saúde , Humanos , Klebsiella pneumoniae/patogenicidade , Masculino , Pessoa de Meia-Idade , Médicos , Estudos Prospectivos
19.
Sci Rep ; 11(1): 5116, 2021 03 04.
Artigo em Inglês | MEDLINE | ID: mdl-33664307

RESUMO

The World Health Organization (WHO) has articulated a priority pathogens list (PPL) to provide strategic direction to research and develop new antimicrobials. Antimicrobial resistance (AMR) patterns of WHO PPL in a tertiary health care facility in Southern India were explored to understand the local priority pathogens. Culture reports of laboratory specimens collected between 1st January 2014 and 31st October 2019 from paediatric patients were extracted. The antimicrobial susceptibility patterns for selected antimicrobials on the WHO PPL were analysed and reported. Of 12,256 culture specimens screened, 2335 (19%) showed culture positivity, of which 1556 (66.6%) were organisms from the WHO-PPL. E. coli was the most common organism isolated (37%), followed by Staphylococcus aureus (16%). Total of 72% of E. coli were extended-spectrum beta-lactamases (ESBL) producers, 55% of Enterobacteriaceae were resistant to 3rd generation cephalosporins due to ESBL, and 53% of Staph. aureus were Methicillin-resistant. The analysis showed AMR trends and prevalence patterns in the study setting and the WHO-PPL document are not fully comparable. This kind of local priority difference needs to be recognised in local policies and practices.


Assuntos
Infecções Bacterianas/tratamento farmacológico , Enterobacteriaceae/efeitos dos fármacos , Escherichia coli/efeitos dos fármacos , Staphylococcus aureus/efeitos dos fármacos , Antibacterianos/uso terapêutico , Infecções Bacterianas/epidemiologia , Infecções Bacterianas/microbiologia , Farmacorresistência Bacteriana/genética , Farmacorresistência Bacteriana Múltipla/genética , Enterobacteriaceae/patogenicidade , Escherichia coli/patogenicidade , Humanos , Índia/epidemiologia , Resistência a Meticilina/genética , Testes de Sensibilidade Microbiana , Staphylococcus aureus/patogenicidade , Centros de Atenção Terciária , Organização Mundial da Saúde , beta-Lactamases/genética
20.
Sci Rep ; 11(1): 6364, 2021 03 18.
Artigo em Inglês | MEDLINE | ID: mdl-33737534

RESUMO

To understand the inflammatory microenvironment and microbiome factors for prognosis of chronic rhinosinusitis with polyps (CRSwNP), we explored the difference in characteristics of the microbiome of the nasal sinuses and inflammatory cytokines between recurrent and non-recurrent groups. We collected nasal secretions and polyp tissue from 77 CRSwNP patients. Then, we extracted microbial DNA from cotton swabs, performed high-throughput sequencing based on 16S rRNA to detect bacterial community composition, and analyzed cytokines such as IL-5, IL-8, IL-17a, IL-17e, IL-18, IL-27 and INF-gamma from polyp tissue using Luminex. The eosinophil and neutrophil cells in the peripheral blood and polyp tissue were counted. Postoperative follow-up of patients with CRSwNP for 1 year was conducted to record the recurrence of nasal polyps and analyze the correlation between the recurrence of nasal polyps and the characteristics of inflammatory cytokines, inflammatory cell count and nasal microbial diversity. After 1 year of follow-up, there were 12 recurrent patients, including 5 males and 7 females. Postoperative recurrence of nasal polyps was not significantly correlated with age, sex, asthma, allergic rhinitis or other allergic diseases in CRSwNP patients. In terms of the total nasal symptom score, the recurrent group was significantly higher than the non-recurrent group. In nasal polyp tissues, eosinophils (40.83/HP) and neutrophils (30.83/HP) in patients with CRSwNP in the recurrent group were significantly higher than those in the non-recurrent group (13.72/HP), and neutrophils (18.5/HP) were also significantly higher in the recurrent group than the non-recurrent group. The expression levels of IFN-, IL-17A, IL-17E and IL-18 were significantly higher in the recurrent group than in the non-recurrent group, and the positive rates were not different. In Southwest China, Enterobacteria and anaerobic bacteria may be correlated with the inflammatory pattern expression of nasal polyps. The neutrophil-mediated inflammatory response plays an important role in patients with CRSwNP in Southwest China and is correlated with nasal polyp recurrence. Recurrence of nasal polyps after endoscopic sinus surgery may be potentially associated with a reduced abundance of protective microorganisms and an increased number of pathogenic microorganisms.


Assuntos
Enterobacteriaceae/genética , Inflamação/genética , Microbiota/genética , Pólipos Nasais/microbiologia , Adulto , Bactérias/citologia , Bactérias/genética , China/epidemiologia , Enterobacteriaceae/patogenicidade , Eosinófilos/microbiologia , Eosinófilos/patologia , Feminino , Humanos , Inflamação/epidemiologia , Inflamação/microbiologia , Inflamação/patologia , Masculino , Pessoa de Meia-Idade , Mucosa Nasal/microbiologia , Mucosa Nasal/patologia , Pólipos Nasais/epidemiologia , Pólipos Nasais/genética , Pólipos Nasais/patologia , Seios Paranasais/microbiologia , Seios Paranasais/patologia , Prognóstico , RNA Ribossômico 16S/genética , Rinite/epidemiologia , Rinite/genética , Rinite/microbiologia , Sinusite/epidemiologia , Sinusite/genética , Sinusite/microbiologia
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