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1.
PLoS One ; 19(5): e0302000, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38709720

RESUMO

Wastewater surveillance represents an alternative approach to regulating contamination and the early detection of infectious agents and outbreaks of diseases of public health importance. This study evaluated domestic wastewater effects on recreational waters in estuarine and seawater bodies in Guayas and Santa Elena provinces in Ecuador, South America. Fecal indicator bacteria (thermotolerant coliforms) served as key indicators for evaluation. Physical, chemical, and microbiological quality markers following the Ecuadorian environmental quality standard and the discharge of effluents to the water resource were analyzed. Samples were collected from 44 coastal sites and 2 oxidation lagoons during the dry and rainy seasons of 2020 and 2021, respectively. SARS-CoV-2 RNA was detected in samples with higher E. coli concentrations using reverse transcription quantitative PCR to detect the genes N and ORF1ab. All samples analyzed for SARS-CoV-2 showed Ct ˂ 40 for at least one gene. Four samples showed at least 20 genome copies of gene N per reaction. These were at an artisanal fishing port, an estuarine area (Palmar), a recreational bay, and an oxidation lagoon. A moderate correlation was found between SARS-CoV-2 RNA, thermotolerant coliform and E. coli (p-value ≤ 0.0037), and a strong and positive correlation between thermotolerant coliform and E. coli. (p-value ≤ 0.00001), highlighting the utility of these established parameters as a proxy of the virus. Significant differences were found in the concentrations of thermotolerant coliforms between seasons (p-value = 0.016) and sites (p-value = 0.005). The highest levels of coliforms were found in the dry season (63000 MPN/100 mL) in Anconcito and during the rainy season (14000 MPN/100 mL) at Esterillo in Playas County. It is recommended that the decentralized autonomous governments of the surveyed provinces in Ecuador implement urgent corrective actions and establish medium-term mechanisms to minimize a potential contamination route. Additional parameters must be included in the monitoring, such as Enterococcus and intestinal parasites, due to their public health implications. In the oxidation lagoons, maintenance actions must be carried out, including the dissolution of sediments, an increase in water retention times, and in situ treatment of the sludge, to improve the system's performance.


Assuntos
COVID-19 , RNA Viral , SARS-CoV-2 , Esgotos , Qualidade da Água , Equador , Esgotos/virologia , Esgotos/microbiologia , SARS-CoV-2/isolamento & purificação , SARS-CoV-2/genética , RNA Viral/genética , RNA Viral/isolamento & purificação , RNA Viral/análise , COVID-19/epidemiologia , COVID-19/virologia , Humanos , Enterobacteriaceae/isolamento & purificação , Enterobacteriaceae/genética , Microbiologia da Água , Monitoramento Ambiental/métodos , Água do Mar/virologia , Água do Mar/microbiologia , Escherichia coli/genética , Escherichia coli/isolamento & purificação , Águas Residuárias/virologia , Águas Residuárias/microbiologia
2.
BMC Vet Res ; 20(1): 174, 2024 May 03.
Artigo em Inglês | MEDLINE | ID: mdl-38702700

RESUMO

Antimicrobial resistance is considered one of the most critical threat for both human and animal health. Recently, reports of infection or colonization by carbapenemase-producing Enterobacterales in companion animals had been described. This study report the first molecular characterization of NDM-producing Enterobacterales causing infections in companion animals from Argentina. Nineteen out of 3662 Enterobacterales isolates analyzed between October 2021 and July 2022 were resistant to carbapenemes by VITEK2C and disk diffusion method, and suspected to be carbapenemase-producers. Ten isolates were recovered from canine and nine from feline animals. Isolates were identified as K. pneumoniae (n = 9), E. coli (n = 6) and E. cloacae complex (n = 4), and all of them presented positive synergy among EDTA and carbapenems disks, mCIM/eCIM indicative of metallo-carbapenemase production and were also positive by PCR for blaNDM gene. NDM variants were determined by Sanger sequencing method. All 19 isolates were resistant to ß-lactams and aminoglycosides but remained susceptible to colistin (100%), tigecycline (95%), fosfomycin (84%), nitrofurantoin (63%), minocycline (58%), chloramphenicol (42%), doxycycline (21%), enrofloxacin (5%), ciprofloxacin (5%) and trimethoprim/sulfamethoxazole (5%). Almost all isolates (17/19) co-harbored blaCTX-M plus blaCMY, one harbored blaCTX-M alone and the remaining blaCMY. E. coli and E. cloacae complex isolates harbored blaCTX-M-1/15 or blaCTX-M-2 groups, while all K. pneumoniae harbored only blaCTX-M-1/15 genes. All E. coli and E. cloacae complex isolates harbored blaNDM-1, while in K. pneumoniae blaNDM-1 (n = 6), blaNDM-5 (n = 2), and blaNDM-1 plus blaNDM-5 (n = 1) were confirmed. MLST analysis revealed the following sequence types by species, K. pneumoniae: ST15 (n = 5), ST273 (n = 2), ST11, and ST29; E. coli: ST162 (n = 3), ST457, ST224, and ST1196; E. cloacae complex: ST171, ST286, ST544 and ST61. To the best of our knowledge, this is the first description of NDM-producing E. cloacae complex isolates recovered from cats. Even though different species and clones were observed, it is remarkable the finding of some major clones among K. pneumoniae and E. coli, as well as the circulation of NDM as the main carbapenemase. Surveillance in companion pets is needed to detect the spread of carbapenem-resistant Enterobacterales and to alert about the dissemination of these pathogens among pets and humans.


Assuntos
Antibacterianos , Doenças do Gato , Doenças do Cão , Infecções por Enterobacteriaceae , beta-Lactamases , Animais , Gatos , Cães , Doenças do Gato/microbiologia , Doenças do Gato/epidemiologia , beta-Lactamases/genética , Argentina/epidemiologia , Infecções por Enterobacteriaceae/veterinária , Infecções por Enterobacteriaceae/microbiologia , Infecções por Enterobacteriaceae/epidemiologia , Antibacterianos/farmacologia , Doenças do Cão/microbiologia , Doenças do Cão/epidemiologia , Testes de Sensibilidade Microbiana , Animais de Estimação , Enterobacteriaceae/efeitos dos fármacos , Enterobacteriaceae/isolamento & purificação , Enterobacteriaceae/genética , Enterobacteriaceae/enzimologia , Escherichia coli/efeitos dos fármacos , Escherichia coli/genética , Klebsiella pneumoniae/efeitos dos fármacos , Klebsiella pneumoniae/genética , Klebsiella pneumoniae/isolamento & purificação , Klebsiella pneumoniae/enzimologia
3.
Rev Med Suisse ; 20(872): 866-871, 2024 May 01.
Artigo em Francês | MEDLINE | ID: mdl-38693798

RESUMO

Multi-resistant Enterobacterales (MRE) are on the increase worldwide, with the main mechanism of resistance acquisition being horizontal transfer of plasmids coding for extended-spectrum betalactamase and/or carbapenemase. Low- and middle-income countries are the most affected, but surveillance in low-endemicity countries, such as Switzerland, is essential. International travel is one of the sources of MRE dissemination in the community, with the main risk factors for acquiring MRE being a stay in South or Southeast Asia and the use of antibiotics during travel. Other factors, notably animal and environmental, also explain this increase. Measures encompassing a One Health approach are therefore needed to address this issue.


Les entérobactéries multirésistantes (EMR) sont en augmentation dans le monde, avec comme mécanisme principal d'acquisition de résistance le transfert horizontal de plasmides codant pour une bêtalactamase à spectre étendu et/ou une carbapénèmase. Les pays à bas et moyens revenus sont les plus touchés, mais une surveillance dans les pays à faible endémicité, comme la Suisse, est essentielle. Les voyages internationaux sont l'une des sources de dissémination d'EMR dans la communauté, avec comme facteurs de risque principaux d'acquisition d'EMR un séjour en Asie du Sud ou du Sud-Est et l'utilisation d'antibiotiques durant le voyage. D'autres facteurs, notamment animaliers et environnementaux, expliquent aussi cette augmentation. Ainsi, il est nécessaire que des mesures englobant une approche « One Health ¼ répondent à cette problématique.


Assuntos
Antibacterianos , Farmacorresistência Bacteriana Múltipla , Infecções por Enterobacteriaceae , Enterobacteriaceae , Viagem , Humanos , Infecções por Enterobacteriaceae/epidemiologia , Infecções por Enterobacteriaceae/microbiologia , Infecções por Enterobacteriaceae/tratamento farmacológico , Enterobacteriaceae/efeitos dos fármacos , Antibacterianos/farmacologia , Fatores de Risco , Animais , Saúde Única , Plasmídeos , beta-Lactamases/genética
4.
J Med Life ; 17(1): 41-49, 2024 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-38737657

RESUMO

Multi-drug resistant (MDR) Enterobacterales remain a major clinical problem. Infections caused by carbapenem-resistant strains are particularly difficult to treat. This study aimed to assess the clinical and epidemiological characteristics of MDR Enterobacterales isolates. A total of 154 non-repetitive clinical isolates, including Escherichia coli (n = 66), Klebsiella pneumoniae (n = 70), and other Enterobacterales (n = 18), were collected from the Diagnostic Microbiology Laboratory at King Fahad Hospital of the University. Most E. coli isolates were collected from urine specimens (n = 50, 75.8%) and resistance against the third and fourth-generation cephalosporins (ceftriaxone, ceftazidime, cefixime, and cefepime) and fluoroquinolones (ciprofloxacin and levofloxacin) was assessed. Clonal relatedness analysis using enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC-PCR) revealed two clones (E. coli A and B), each comprising two strains. Most K. pneumoniae samples were collected from respiratory specimens (27.1%, 20 samples), and the strains showed overall resistance to most of the antimicrobials tested (54%‒100%). Moreover, clonal-relatedness analysis using ERIC-PCR revealed seven major clones of K. pneumoniae. These findings suggest nosocomial transmission among some identical strains and emphasize the importance of strict compliance with infection prevention and control policies and regulations. Environmental reservoirs could facilitate this indirect transmission, which needs to be investigated.


Assuntos
Antibacterianos , Farmacorresistência Bacteriana Múltipla , Humanos , Farmacorresistência Bacteriana Múltipla/genética , Arábia Saudita/epidemiologia , Antibacterianos/farmacologia , Antibacterianos/uso terapêutico , Testes de Sensibilidade Microbiana , Masculino , Feminino , Enterobacteriaceae/efeitos dos fármacos , Enterobacteriaceae/isolamento & purificação , Enterobacteriaceae/genética , Infecções por Enterobacteriaceae/epidemiologia , Infecções por Enterobacteriaceae/microbiologia , Infecções por Enterobacteriaceae/tratamento farmacológico , Klebsiella pneumoniae/efeitos dos fármacos , Klebsiella pneumoniae/isolamento & purificação , Klebsiella pneumoniae/genética , Infecção Hospitalar/microbiologia , Infecção Hospitalar/epidemiologia , Infecção Hospitalar/tratamento farmacológico , Adulto , Escherichia coli/efeitos dos fármacos , Escherichia coli/isolamento & purificação , Escherichia coli/genética , Pessoa de Meia-Idade , Hospitais Universitários
5.
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
6.
Emerg Microbes Infect ; 13(1): 2337678, 2024 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-38629492

RESUMO

Despite carbapenems not being used in animals, carbapenem-resistant Enterobacterales (CRE), particularly New Delhi metallo-ß-lactamase-producing CRE (NDM-CRE), are prevalent in livestock. Concurrently, the incidence of human infections caused by NDM-CRE is rising, particularly in children. Although a positive association between livestock production and human NDM-CRE infections at the national level was identified, the evidence of direct transmission of NDM originating from livestock to humans remains largely unknown. Here, we conducted a cross-sectional study in Chengdu, Sichuan Province, to examine the prevalence of NDM-CRE in chickens and pigs along the breeding-slaughtering-retail chains, in pork in cafeterias of schools, and in colonizations and infections from children's hospital and examined the correlation of NDM-CRE among animals, foods and humans. Overall, the blaNDM increases gradually along the chicken and pig breeding (4.70%/2.0%) -slaughtering (7.60%/22.40%) -retail (65.56%/34.26%) chains. The slaughterhouse has become a hotspot for cross-contamination and amplifier of blaNDM. Notably, 63.11% of pork from the school cafeteria was positive for blaNDM. The prevalence of blaNDM in intestinal and infection samples from children's hospitals was 21.68% and 19.80%, respectively. whole genome sequencing (WGS) analysis revealed the sporadic, not large-scale, clonal spread of NDM-CRE along the chicken and pig breeding-slaughtering-retail chain, with further spreading via IncX3-blaNDM plasmid within each stage of whole chains. Clonal transmission of NDM-CRE is predominant in children's hospitals. The IncX3-blaNDM plasmid was highly prevalent among animals and humans and accounted for 57.7% of Escherichia coli and 91.3% of Klebsiella pneumoniae. Attention should be directed towards the IncX3 plasmid to control the transmission of blaNDM between animals and humans.


Assuntos
Infecções por Enterobacteriaceae , Enterobacteriaceae , Criança , Humanos , Animais , Suínos , Enterobacteriaceae/genética , Estudos Transversais , Antibacterianos/farmacologia , Testes de Sensibilidade Microbiana , Galinhas , Escherichia coli/genética , beta-Lactamases/genética , Infecções por Enterobacteriaceae/epidemiologia , Infecções por Enterobacteriaceae/veterinária , Klebsiella pneumoniae/genética , Plasmídeos
7.
Biosensors (Basel) ; 14(4)2024 Apr 16.
Artigo em Inglês | MEDLINE | ID: mdl-38667187

RESUMO

Antimicrobial-resistant (AMR) bacteria pose a significant global health threat, and bacteria that produce New Delhi metallo-ß-lactamase (NDM) are particularly concerning due to their resistance to most ß-lactam antibiotics, including carbapenems. The emergence and spread of NDM-producing genes in food-producing animals highlight the need for a fast and accurate method for detecting AMR bacteria. We therefore propose a PCR-coupled CRISPR/Cas12a-based fluorescence assay that can detect NDM-producing genes (blaNDM) in bacteria. Thanks to its designed gRNA, this CRISPR/Cas12a system was able to simultaneously cleave PCR amplicons and ssDNA-FQ reporters, generating fluorescence signals. Our method was found to be highly specific when tested against other foodborne pathogens that do not carry blaNDM and also demonstrated an excellent capability to distinguish single-nucleotide polymorphism. In the case of blaNDM-1 carrying E. coli, the assay performed exceptionally well, with a detection limit of 2.7 × 100 CFU/mL: 100 times better than conventional PCR with gel electrophoresis. Moreover, the developed assay detected AMR bacteria in food samples and exhibited enhanced performance compared to previously published real-time PCR assays. Thus, this novel PCR-coupled CRISPR/Cas12a-based fluorescence assay has considerable potential to improve current approaches to AMR gene detection and thereby contribute to mitigating the global threat of AMR.


Assuntos
Proteínas de Bactérias , Proteínas Associadas a CRISPR , Sistemas CRISPR-Cas , Carbapenêmicos , Endodesoxirribonucleases , beta-Lactamases , Carbapenêmicos/farmacologia , beta-Lactamases/genética , Enterobacteriáceas Resistentes a Carbapenêmicos/genética , Enterobacteriaceae/genética , Enterobacteriaceae/efeitos dos fármacos , Antibacterianos/farmacologia , Escherichia coli/genética , Escherichia coli/efeitos dos fármacos , Técnicas Biossensoriais , Farmacorresistência Bacteriana/genética
8.
J Water Health ; 22(4): 673-688, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38678421

RESUMO

This study assessed the bacteriological quality of raw, treated, and distributed water from Ede-Erinle and Opa reservoirs in Osun State, Nigeria. This was to determine the potability of water from these waterwork stations. Eighteen sampling points were established across the two reservoir networks for this study. Samples were collected bi-monthly for two annual cycles. Serial dilution and pour plate methods were employed for the enumeration of bacterial load. Total heterotrophic bacteria count (THBC) and total coliform bacteria count (TCBC) were enumerated on nutrient and MacConkey agar at 37 °C, respectively. Bacterial isolates were characterized using biochemical identification methods with reference to Bergey's Manual of Determinative Bacteriology. Bacterial isolates and biofilm formation were further identified molecularly through the PCR method using specific universal primers. Mean values of THBC and TCBC in distributed water from Ede-Erinle (9.61 × 104 ± 1.50 × 104 CFU/mL; 69.56 ± 26.81 CFU/mL) and Opa waterworks (9.58 × 104 ± 2.55 × 104 CFU/mL; 142.94 ± 44.41 CFU/mL) exceeded permissible limits for drinking water. Paenibacillus lautus, Bacillus pseudomycoides, Pseudomonas aeruginosa, and Pseudomonas stutzeri showed biofilm-forming capacity. The study concluded that the presence of coliforms and biofilm-forming bacteria in distributed water implies that the water is unfit for consumption without further treatment.


Assuntos
Biofilmes , Água Potável , Enterobacteriaceae , Microbiologia da Água , Abastecimento de Água , Nigéria , Enterobacteriaceae/isolamento & purificação , Água Potável/microbiologia , Bactérias/isolamento & purificação , Bactérias/classificação , Bactérias/genética , Purificação da Água/métodos
9.
Artigo em Inglês | MEDLINE | ID: mdl-38652096

RESUMO

A Gram-negative, motile, rod-shaped bacterial strain, CA-0114T, was isolated from the midgut of a western honey bee, Apis mellifera. The isolate exhibited ≤96.43 % 16S rRNA gene sequence identity (1540 bp) to members of the families Enterobacteriaceae and Erwiniaceae. Phylogenetic trees based on genome blast distance phylogeny and concatenated protein sequences encoded by conserved genes atpD, fusA, gyrB, infB, leuS, pyrG and rpoB separated the isolate from other genera forming a distinct lineage in the Enterobacteriaceae. In both trees, the closest relatives were Tenebrionicola larvae YMB-R21T and Tenebrionibacter intestinalis BIT-L3T, which were isolated previously from Tenebrio molitor L., a plastic-eating mealworm. Digital DNA-DNA hybridization, orthologous average nucleotide identity and average amino acid identity values between strain CA-0114T and the closest related members within the Enterobacteriaceae were ≤23.1, 75.45 and 76.04 %, respectively. The complete genome of strain CA-0114T was 4 451669 bp with a G+C content of 52.12 mol%. Notably, the apparent inability of strain CA-0114T to ferment d-glucose, inositol and l-rhamnose in the API 20E system is unique among closely related members of the Enterobacteriaceae. Based on the results obtained through genotypic and phenotypic analysis, we propose that strain CA-0114T represents a novel species and genus within the family Enterobacteriaceae, for which we propose the name Apirhabdus apintestini gen. nov., sp. nov. (type strain CA-0114T=ATCC TSD-396T=DSM 116385T).


Assuntos
Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano , Enterobacteriaceae , Ácidos Graxos , Hibridização de Ácido Nucleico , Filogenia , RNA Ribossômico 16S , Análise de Sequência de DNA , Animais , Abelhas/microbiologia , RNA Ribossômico 16S/genética , Enterobacteriaceae/classificação , Enterobacteriaceae/isolamento & purificação , Enterobacteriaceae/genética , DNA Bacteriano/genética , Ácidos Graxos/análise , Genoma Bacteriano
10.
Enferm. infecc. microbiol. clín. (Ed. impr.) ; 42(4): 205-207, Abr. 2024. tab
Artigo em Inglês | IBECS | ID: ibc-232176

RESUMO

Introduction: Early and adequate treatment of bloodstream infections decreases patient morbidity and mortality. The objective is to develop a preliminary method for rapid antibiotic susceptibility testing (RAST) in enterobacteria with inducible chromosomal AmpC. Methods: RAST was performed directly on spiked blood cultures of 49 enterobacteria with inducible chromosomal AmpC. Results were read at 4, 6 and 8h of incubation. Commercial broth microdilution was considered the reference method. Disks of 10 antibiotics were evaluated. Results: The proportion of readable tests at 4h was 85%. All RAST could be read at 6 and 8h. For most antibiotics, the S or R result at 4, 6 and 8h was greater than 80% after tentative breakpoints were established and Area of Technical Uncertainty was defined. Conclusions: This preliminary method seems to be of practical use, although it should be extended to adjust the breakpoints and differentiate them by species.(AU)


Introducción: El tratamiento precoz y adecuado de las bacteriemias disminuye la morbilidad y mortalidad de los pacientes. El objetivo es desarrollar un método preliminar de pruebas rápidas de sensibilidad antibiótica (PRSA) en enterobacterias con AmpC cromosómica inducible. Métodos: Las PRSA se realizaron directamente de hemocultivos simulados positivos para 49 enterobacterias con AmpC cromosómica inducible. Los resultados se leyeron a las 4, 6 y 8 horas de incubación. La microdilución en caldo comercial se consideró el método de referencia. Se evaluaron discos de 10 antibióticos. Resultados: La proporción de pruebas legibles a las 4 horas fue del 85%. Todas las PRSA pudieron leerse a las 6 y 8 horas. Para la mayoría de los antibióticos, el resultado S o R a las 4, 6 y 8 horas fue superior al 80%, después de que se establecieran puntos de corte provisionales y se definiera el área de incertidumbre técnica. Conclusiones: Este método preliminar parece ser de utilidad práctica, aunque debería ampliarse para ajustar los puntos de corte y diferenciar por especies.(AU)


Assuntos
Humanos , Masculino , Feminino , Antibacterianos , Testes de Sensibilidade Microbiana , Enterobacteriaceae , Antibacterianos/farmacologia , beta-Lactamases
11.
PLoS One ; 19(4): e0293861, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38603714

RESUMO

The goal of this study was to characterize the bacterial diversity on different melon varieties grown in different regions of the US, and determine the influence that region, rind netting, and variety of melon has on the composition of the melon microbiome. Assessing the bacterial diversity of the microbiome on the melon rind can identify antagonistic and protagonistic bacteria for foodborne pathogens and spoilage organisms to improve melon safety, prolong shelf-life, and/or improve overall plant health. Bacterial community composition of melons (n = 603) grown in seven locations over a four-year period were used for 16S rRNA gene amplicon sequencing and analysis to identify bacterial diversity and constituents. Statistically significant differences in alpha diversity based on the rind netting and growing region (p < 0.01) were found among the melon samples. Principal Coordinate Analysis based on the Bray-Curtis dissimilarity distance matrix found that the melon bacterial communities clustered more by region rather than melon variety (R2 value: 0.09 & R2 value: 0.02 respectively). Taxonomic profiling among the growing regions found Enterobacteriaceae, Bacillaceae, Microbacteriaceae, and Pseudomonadaceae present on the different melon rinds at an abundance of ≥ 0.1%, but no specific core microbiome was found for netted melons. However, a core of Pseudomonadaceae, Bacillaceae, and Exiguobacteraceae were found for non-netted melons. The results of this study indicate that bacterial diversity is driven more by the region that the melons were grown in compared to rind netting or melon type. Establishing the foundation for regional differences could improve melon safety, shelf-life, and quality as well as the consumers' health.


Assuntos
Bacillaceae , Cucumis melo , Cucurbitaceae , Estados Unidos , Cucurbitaceae/microbiologia , Cucumis melo/microbiologia , RNA Ribossômico 16S/genética , Bactérias/genética , Enterobacteriaceae
12.
PLoS One ; 19(4): e0289190, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38603727

RESUMO

The emergence and spread of ß-lactamase-producing Enterobacteriaceae poses a significant threat to public health, necessitating the rapid detection and investigation of the molecular epidemiology of these pathogens. We modified a multiplex real-time (RT)-PCR to concurrently detect ß-lactamase genes (blaCTX-M, blaTEM, and blaSHV) and Enterobacteriaceae 16S ribosomal RNA. qPCR probes and primers were validated using control isolates, and the sensitivity and specificity assessed. The optimised multiplex qPCR was used to screen 220 non-clinical Enterobacteriaceae from food animals and in-contact humans in Southeast Nigeria selected on cefotaxime-supplemented agar plates. Binary logistic regression was used to explore factors associated with the presence of the blaTEM and blaSHV genes in these isolates, and a subset of isolates from matched sampling sites and host species were whole genome sequenced, and their antimicrobial resistance (AMR) and plasmid profiles determined. The sensitivity and specificity of the qPCR assay was 100%. All isolates (220/220) were positive for Enterobacteriaceae ribosomal 16S rRNA and blaCTX-M, while 66.4% (146/220) and 9% (20/220) were positive for blaTEM and blaSHV, respectively. The prevalence of blaTEM and blaSHV varied across different sampling sites (farm, animal market and abattoirs). Isolates from Abia state were more likely to harbour blaTEM (OR = 2.3, p = 0.04) and blaSHV (OR = 5.12,p = 0.01) than isolates from Ebonyi state; blaTEM was more likely to be detected in isolates from food animals than humans (OR = 2.34, p = 0.03), whereas the reverse was seen for blaSHV (OR = 7.23, p = 0.02). Furthermore, Klebsiella and Enterobacter isolates harboured more AMR genes than Escherichia coli, even though they were isolated from the same sample. We also identified pan resistant Klebsiella harbouring resistance to ten classes of antimicrobials and disinfectant. Therefore, we recommend ESKAPE pathogens are included in AMR surveillance in future and suggest qPCRs be utilised for rapid screening of Enterobacteriaceae from human and animal sources.


Assuntos
Enterobacteriaceae , beta-Lactamases , Animais , Humanos , beta-Lactamases/genética , Nigéria/epidemiologia , Epidemiologia Molecular , RNA Ribossômico 16S/genética , Escherichia coli/genética , Antibacterianos/farmacologia , Testes de Sensibilidade Microbiana
13.
Food Microbiol ; 121: 104520, 2024 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-38637082

RESUMO

Sequence-based analysis of fermented foods and beverages' microbiomes offers insights into their impact on taste and consumer health. High-throughput metagenomics provide detailed taxonomic and functional community profiling, but bacterial and yeast genome reconstruction and mobile genetic elements tracking are to be improved. We established a pipeline for exploring fermented foods microbiomes using metagenomics coupled with chromosome conformation capture (Hi-C metagenomics). The approach was applied to analyze a collection of spontaneously fermented beers and ciders (n = 12). The Hi-C reads were used to reconstruct the metagenome-assembled genomes (MAGs) of bacteria and yeasts facilitating subsequent comparative genomic analysis, assembly scaffolding and exploration of "plasmid-bacteria" links. For a subset of beverages, yeasts were isolated and characterized phenotypically. The reconstructed Hi-C MAGs primarily belonged to the Lactobacillaceae family in beers, along with Acetobacteraceae and Enterobacteriaceae in ciders, exhibiting improved quality compared to conventional metagenomic MAGs. Comparative genomic analysis of Lactobacillaceae Hi-C MAGs revealed clustering by niche and suggested genetic determinants of survival and probiotic potential. For Pediococcus damnosus, Hi-C-based networks of contigs enabled linking bacteria with plasmids. Analyzing phylogeny and accessory genes in the context of known reference genomes offered insights into the niche specialization of beer lactobacilli. The subspecies-level diversity of cider Tatumella spp. was disentangled using a Hi-C-based graph. We obtained highly complete yeast Hi-C MAGs primarily represented by Brettanomyces and Saccharomyces, with Hi-C-facilitated chromosome-level genome assembly for the former. Utilizing Hi-C metagenomics to unravel the genomic content of individual species can provide a deeper understanding of the ecological interactions within the food microbiome, aid in bioprospecting beneficial microorganisms, improving quality control and improving innovative fermented products.


Assuntos
Saccharomyces cerevisiae , Saccharomyces , Saccharomyces cerevisiae/genética , Cerveja/microbiologia , Bactérias/genética , Plasmídeos , Saccharomyces/genética , Metagenoma , Metagenômica , Enterobacteriaceae/genética
14.
Wei Sheng Yan Jiu ; 53(2): 250-256, 2024 Mar.
Artigo em Chinês | MEDLINE | ID: mdl-38604961

RESUMO

OBJECTIVE: To compare the differences in gut microbiome composition between children with good neurodevelopment and those with delayed neurodevelopment, and to analyze the relationship between gut microbiome and the neurodevelopment status of infants in early life. METHODS: The mothers were included at the Second West China Hospital from November 2020 to April 2021. Their infant stools were collected on day 0 and day 90 after birth, and the follow-up questionnaires at the corresponding time points were completed. Additionally, the Ages and Stages Questionnaires-Third Edition(ASQ-3) were completed by mothers at 12 months of age. The structure and diversity of gut microbiota were examined by 16S rRNA sequencing, and the relationship between gut microbiome and ASQ-3 questionnaire scores in early life was analyzed. RESULTS: According to the ASQ-3 scores, mothers and infants into neurodevelopment good group(G group, n=18) and neurodevelopmental delay group(D group, n=10). Compared with the D group, the relative abundance of the Firmicutes was significantly higher in the G group at day 0(P<0.05), while the level of the Proteobacteria was lower(P<0.05). At day 90 after birth, the relative abundance of the Actinobacteria, Bifidobacteriaceae and Enterococcaceae was significantly higher in the G group(P<0.05). In addition, alpha diversity was not statistically different between the two groups. Spearman's correlation analysis showed that Clostridiaceae of the postnatal day 0 infants was positively correlated with the communication domain score, but negatively associated with gross motor domain score in children at 12 months of age, whereas the relative abundance of Proteobacteria and Enterobacteriaceae of children at postnatal day 90 was negatively associated with communication development, while the relative abundance of Erysipelatoclostridiaceae showed a negative correlation with gross motor domain scores. CONCLUSION: The structure of the gut microbiome in early life between neurodevelopment good and delayed infants, and were associated with the development of communication and gross motor domain in infants at 12 months of age, suggesting that gut microbiome in early life may be related to the level of neurodevelopment in infants.


Assuntos
Microbioma Gastrointestinal , Lactente , Criança , Feminino , Humanos , RNA Ribossômico 16S/genética , Mães , Bactérias/genética , Enterobacteriaceae
15.
BMC Infect Dis ; 24(1): 367, 2024 Apr 02.
Artigo em Inglês | MEDLINE | ID: mdl-38566010

RESUMO

BACKGROUND: Street foods are any foods or drinks prepared or sold by street vendors in an open space. The purpose of this study was to determine the Bacteriological safety and antibiotic resistance patterns of Staphylococcus aureus and Enterobacteriaceae isolated from street foods. METHOD: A laboratory-based cross-sectional study was used from December 2022 to February 2023 on street foods of Addis Ababa, Hawassa, Dire Dawa, and Jimma towns of Ethiopia. 525 street foods and 175 water samples were taken from 175 street food vending stalls. Proportional allocation to the total town population and stratified sampling techniques were used to select vending stalls. Samples were analyzed for the presence of bacteria following the standard microbiological methods used for the isolation, enumeration, and identification of bacteria. Pour plate technique was used to transfer the suspension to MacConkey agar, Mannitol Salt Agar, and Salmonella Shigella Agar. The antibiotic susceptibility test was performed using the Kirby-Bauer disk diffusion method. SPSS software was used to analyze the data. RESULT: Out of 525 food samples, 279 (53%) were contaminated by bacteria. From 175 water samples, 95 (54.3%) were contaminated with Escherichia coli. From both samples in total, eleven bacterial species were isolated. Staphylococcus aureus was the most frequently isolated species. Shigella, Klebsiella, and Salmonella group A have statistically significant with the type of food. Erythromycin (54%), Streptomycin (17%), and Amoxicillin (14%) were the most resistant antibiotics. Least resistance was observed to Ciprofloxacin (5%). CONCLUSION: Street foods of the selected towns were highly contaminated with various antibiotic-resistant organisms. Hence, the relevant authorities ought to ensure the proper handling of street food by enforcing safety measures. Additionally, they should initiate a widespread awareness campaign promoting the prudent use of antibiotics among both street food vendors and the broader population.


Assuntos
Shigella , Infecções Estafilocócicas , Humanos , Enterobacteriaceae , Staphylococcus aureus , Etiópia , Estudos Transversais , Ágar , Cidades , Microbiologia de Alimentos , Bactérias , Antibacterianos/farmacologia , Escherichia coli , Resistência Microbiana a Medicamentos , Água
16.
Front Cell Infect Microbiol ; 14: 1345935, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38572315

RESUMO

Introduction: Bacterial resistance is a major threat to public health worldwide. To gain an understanding of the clinical infection distribution, drug resistance information, and genotype of CRE in Dongguan, China, as well as the resistance of relevant genotypes to CAZ-AVI, this research aims to improve drug resistance monitoring information in Dongguan and provide a reliable basis for the clinical control and treatment of CRE infection. Methods: VITEK-2 Compact automatic analyzer was utilized to identify 516 strains of CRE collected from January 2017 to June 2023. To determine drug sensitivity, the K-B method, E-test, and MIC methods were used. From June 2022 to June 2023, 80 CRE strains were selected, and GeneXpert Carba-R was used to detect and identify the genotype of the carbapenemase present in the collected CRE strains. An in-depth analysis was conducted on the CAZ-AVI in vitro drug sensitivity activity of various genotypes of CRE, and the results were statistically evaluated using SPSS 23.0 and WHONET 5.6 software. Results: This study identified 516 CRE strains, with the majority (70.16%) being K.pneumoniae, followed by E.coli (18.99%). Respiratory specimens had highest detection rate with 53.77% identified, whereas urine specimens had the second highest detection rate with 17.99%. From June 2022 to June 2023, 95% of the strains tested using the CRE GeneXpert Carba-R assay possessed carbapenemase genes, of which 32.5% were blaNDM strains and 61.25% blaKPC strains. The results showed that CRE strains containing blaKPC had a significantly higher rate of resistance to amikacin, cefepime, and aztreonam than those harboring blaNDM. Conclusions: The CRE strains isolated from Dongguan region demonstrated a high resistance rate to various antibiotics used in clinical practice but a low resistance rate to tigecycline. These strains produce Class A serine carbapenemases and Class B metals ß-lactamases, with the majority of them carrying blaNDM and blaKPC. Notably, CRE strains with blaKPC and blaNDM had significantly lower resistance rates to tigecycline. CAZ-AVI showed a good sensitivity rate with no resistance to CRE strains carrying blaKPC. Therefore, CAZ-AVI and tigecycline should be used as a guide for rational use of antibiotics in clinical practice to effectively treat CRE.


Assuntos
Compostos Azabicíclicos , Carbapenêmicos , Ceftazidima , Enterobacteriaceae , Enterobacteriaceae/genética , Carbapenêmicos/farmacologia , Tigeciclina/farmacologia , Sistemas de Distribuição no Hospital , Antibacterianos/farmacologia , Antibacterianos/uso terapêutico , Combinação de Medicamentos , beta-Lactamases/genética , Proteínas de Bactérias/genética , Proteínas de Bactérias/farmacologia , Cefalosporinas/farmacologia , Klebsiella pneumoniae/genética , Genótipo , Testes de Sensibilidade Microbiana
17.
Gut Microbes ; 16(1): 2333413, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38561312

RESUMO

Urinary tract infections (UTIs) are among the most common late-onset infections in preterm infants, characterized by nonspecific symptoms and a pathogenic spectrum that diverges from that of term infants and older children, which present unique diagnostic and therapeutic challenges. Existing data on the role of gut microbiota in UTI pathogenesis in this demographic are limited. This study aims to investigate alterations in gut microbiota and fecal calprotectin levels and their association with the development of UTIs in hospitalized preterm infants. A longitudinal case-control study was conducted involving preterm infants admitted between January 2018 and October 2020. Fecal samples were collected weekly and analyzed for microbial profiles and calprotectin levels. Propensity score matching, accounting for key perinatal factors including age and antibiotic use, was utilized to match samples from UTI-diagnosed infants to those from non-UTI counterparts. Among the 151 preterm infants studied, 53 were diagnosed with a UTI, predominantly caused by Enterobacteriaceae (79.3%) and Enterococcaceae (19.0%). Infants with UTIs showed a significantly higher abundance of these families compared to non-UTI infants, for both Gram-negative and positive pathogens, respectively. Notably, there was a significant pre-UTI increase in the abundance of pathogen-specific taxa in infants later diagnosed with UTIs, offering high predictive value for early detection. Shotgun metagenomic sequencing further confirmed the dominance of specific pathogenic species pre-UTI and revealed altered virulence factor profiles associated with Klebsiella aerogenes and Escherichia coli infections. Additionally, a decline in fecal calprotectin levels was observed preceding UTI onset, particularly in cases involving Enterobacteriaceae. The observed pathogen-specific alterations in the gut microbiota preceding UTI onset offer novel insight into the UTI pathogenesis and promising early biomarkers for UTIs in preterm infants, potentially enhancing the timely management of this common infection. However, further validation in larger cohorts is essential to confirm these findings.


Assuntos
Microbioma Gastrointestinal , Infecções Urinárias , Lactente , Criança , Humanos , Recém-Nascido , Adolescente , Estudos de Casos e Controles , Escherichia coli , Recém-Nascido Prematuro , Antibacterianos/uso terapêutico , Enterobacteriaceae , Complexo Antígeno L1 Leucocitário
18.
BMC Infect Dis ; 24(1): 444, 2024 Apr 26.
Artigo em Inglês | MEDLINE | ID: mdl-38671365

RESUMO

INTRODUCTION: Carbapenemase-producing Enterobacterales (CPE) are an important public health threat, with costly operational and economic consequences for NHS Integrated Care Systems and NHS Trusts. UK Health Security Agency guidelines recommend that Trusts use locally developed risk assessments to accurately identify high-risk individuals for screening, and implement the most appropriate method of testing, but this presents many challenges. METHODS: A convenience sample of cross-specialty experts from across England met to discuss the barriers and practical solutions to implementing UK Health Security Agency framework into operational and clinical workflows. The group derived responses to six key questions that are frequently asked about screening for CPE. KEY FINDINGS: Four patient groups were identified for CPE screening: high-risk unplanned admissions, high-risk elective admissions, patients in high-risk units, and known positive contacts. Rapid molecular testing is a preferred screening method for some of these settings, offering faster turnaround times and more accurate results than culture-based testing. It is important to stimulate action now, as several lessons can be learnt from screening during the COVID-19 pandemic, as well as from CPE outbreaks. CONCLUSION: Further decisive and instructive information is needed to establish CPE screening protocols based on local epidemiology and risk factors. Local management should continually evaluate local epidemiology, analysing data and undertaking frequent prevalence studies to understand risks, and prepare resources- such as upscaled screening- to prevent increasing prevalence, clusters or outbreaks. Rapid molecular-based methods will be a crucial part of these considerations, as they can reduce unnecessary isolation and opportunity costs.


Assuntos
Proteínas de Bactérias , Infecções por Enterobacteriaceae , Programas de Rastreamento , beta-Lactamases , Humanos , Infecções por Enterobacteriaceae/diagnóstico , Infecções por Enterobacteriaceae/microbiologia , Inglaterra , beta-Lactamases/metabolismo , beta-Lactamases/genética , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Programas de Rastreamento/métodos , Enterobacteriáceas Resistentes a Carbapenêmicos/isolamento & purificação , Hospitais , COVID-19/diagnóstico , SARS-CoV-2 , Enterobacteriaceae/enzimologia , Enterobacteriaceae/isolamento & purificação , Enterobacteriaceae/genética
19.
BMC Microbiol ; 24(1): 136, 2024 Apr 24.
Artigo em Inglês | MEDLINE | ID: mdl-38658819

RESUMO

OBJECTIVES: In the recent years, multidrug resistant (MDR) neonatal septicemia-causing Enterobacterales has been dramatically increased due to the extended-spectrum beta-lactamases (ESBLs) and AmpC enzymes. This study aimed to assess the antibiotic resistance pattern, prevalence of ESBLs/AmpC beta-lactamase genes, and Enterobacterial Repetitive Intergenic Consensus Polymerase Chain Reaction (ERIC-PCR) fingerprints in Enterobacterales isolated from neonatal sepsis. RESULTS: In total, 59 Enterobacterales isolates including 41 (69.5%) Enterobacter species, 15 (25.4%) Klebsiella pneumoniae and 3 (5.1%) Escherichia coli were isolated respectively. Resistance to ceftazidime and cefotaxime was seen in all of isolates. Furthermore, all of them were multidrug-resistant (resistant to three different antibiotic categories). The phenotypic tests showed that 100% of isolates were ESBL-positive. Moreover, AmpC production was observed in 84.7% (n = 50/59) of isolates. Among 59 ESBL-positive isolates, the highest percentage belonged to blaCTX-M-15 gene (66.1%) followed by blaCTX-M (45.8%), blaCTX-M-14 (30.5%), blaSHV (28.8%), and blaTEM (13.6%). The frequency of blaDHA, blaEBC, blaMOX and blaCIT genes were 24%, 24%, 4%, and 2% respectively. ERIC-PCR analysis revealed that Enterobacterales isolates were genetically diverse. The remarkable prevalence of MDR Enterobacterales isolates carrying ESBL and AmpC beta-lactamase genes emphasizes that efficient surveillance measures are essential to avoid the more expansion of drug resistance amongst isolates.


Assuntos
Antibacterianos , Proteínas de Bactérias , Farmacorresistência Bacteriana Múltipla , Infecções por Enterobacteriaceae , Testes de Sensibilidade Microbiana , Sepse Neonatal , beta-Lactamases , beta-Lactamases/genética , Humanos , Irã (Geográfico)/epidemiologia , Recém-Nascido , Farmacorresistência Bacteriana Múltipla/genética , Infecções por Enterobacteriaceae/microbiologia , Infecções por Enterobacteriaceae/epidemiologia , Antibacterianos/farmacologia , Prevalência , Proteínas de Bactérias/genética , Sepse Neonatal/microbiologia , Sepse Neonatal/epidemiologia , Enterobacteriaceae/genética , Enterobacteriaceae/efeitos dos fármacos , Enterobacteriaceae/enzimologia , Enterobacteriaceae/isolamento & purificação , Klebsiella pneumoniae/genética , Klebsiella pneumoniae/efeitos dos fármacos , Klebsiella pneumoniae/isolamento & purificação , Klebsiella pneumoniae/enzimologia , Enterobacter/genética , Enterobacter/efeitos dos fármacos , Enterobacter/isolamento & purificação , Enterobacter/enzimologia , Escherichia coli/genética , Escherichia coli/efeitos dos fármacos , Escherichia coli/isolamento & purificação
20.
Enferm Infecc Microbiol Clin (Engl Ed) ; 42(4): 205-207, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38575276

RESUMO

INTRODUCTION: Early and adequate treatment of bloodstream infections decreases patient morbidity and mortality. The objective is to develop a preliminary method for rapid antibiotic susceptibility testing (RAST) in enterobacteria with inducible chromosomal AmpC. METHODS: RAST was performed directly on spiked blood cultures of 49 enterobacteria with inducible chromosomal AmpC. Results were read at 4, 6 and 8h of incubation. Commercial broth microdilution was considered the reference method. Disks of 10 antibiotics were evaluated. RESULTS: The proportion of readable tests at 4h was 85%. All RAST could be read at 6 and 8h. For most antibiotics, the S or R result at 4, 6 and 8h was greater than 80% after tentative breakpoints were established and Area of Technical Uncertainty was defined. CONCLUSIONS: This preliminary method seems to be of practical use, although it should be extended to adjust the breakpoints and differentiate them by species.


Assuntos
Hemocultura , Enterobacteriaceae , Humanos , Testes de Sensibilidade Microbiana , beta-Lactamases/genética , Antibacterianos/farmacologia
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