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1.
Zhonghua Jie He He Hu Xi Za Zhi ; 45(6): 552-559, 2022 Jun 12.
Artigo em Chinês | MEDLINE | ID: mdl-35658379

RESUMO

Objective: To compare the diagnostic performance of next-generation sequencing (NGS) detection methods in sputum samples and Mycobacterium tuberculosis strains, in order to explore the feasibility of the NGS method to detect drug resistance in sputum specimens. Methods: In this retrospective study, the sputum specimens and corresponding clinical isolates of 50 pulmonary tuberculosis patients admitted to Beijing Chest Hospital from January 2017 to December 2017 were collected. The gene mutations of katG, inhA, rpoB, embA, embB, rpsL, rrs, gyrA, gyrB and tlyA in sputum specimens and corresponding clinical isolates were detected by NGS method. The phenotypic drug susceptibility test (DST) of the strains was carried out by the proportion method. Using DST results as a reference, the sensitivity, specificity, positive predictive value and negative predictive value of the NGS method for clinical strains and sputum specimens, as well as the consistency statistic (Kappa) with phenotype DST were calculated respectively. The Chi-square test was used to compare the accuracy of the NGS testing in sputum samples and strain samples. Results: The results showed that rpoB(63.83%, 30/47) and rrs(57.45%, 27/47) were the most common mutated genes, followed by katG(46.81%, 22/47), rpsL(29.79%, 14/47), gyrA(27.66%, 13/47), embB(21.28%, 10/47), tlyA(12.77%, 6/47), gyrB(8.51%, 4/47), and inhA promoter(19.15%, 9/47), embA promoter region (12.77%, 6/47) mutation. when the NGS method was compared with the resistance phenotype of isoniazid, rifampicin, ethambutol, second-line injectable drugs (streptomycin, capreomycin, kanamycin, amikacin), levofloxacin, the sensitivity were 85.71%, 91.67%, 77.78%, 81.82%, 100.00%, 87.50%, 100.00%, 69.23%, and the specificity were 100.00%, 94.12, 87.50%, 89.47%, 97.06%, 96.97%, 94.29%, 89.29% in sputum samples, while in strain samples, the sensitivity were 92.86%, 100.00%, 81.82%, 86.96%, 88.89%, 80.00%, 100.00%, 85.71%. The specificity were 100.00%, 92.86%, 87.10%, 94.74%, 100.00%, 100.00%, 97.14%, 92.86%. Compared with the phenotypic drug susceptibility results, the NGS method has better detection performance for isoniazid, rifampicin, capreomycin, kanamycin, and amikacin in sputum specimens (Kappa≥0.75); while among the strains, the NGS method had a good detection performance for isoniazid, rifampicin, streptomycin, capreomycin, kanamycin, amikacin and levofloxacin (Kappa≥0.75). With the accuracy of the NGS method for detecting strains as a reference, there was no statistically significant difference in the accuracy of all drug resistance detected between strains and sputum specimens. Conclusions: This study showed that the NGS technology was effective in predicting the resistance of isoniazid, rifampicin, and second-line injectable drugs (capreomycin, kanamycin and amikacin) by detecting sputum samples and strain genotypes, suggesting the feasibility and potential of direct detection of sputum samples by the NGS method as an early detection method for drug resistance.


Assuntos
Mycobacterium tuberculosis , Tuberculose dos Linfonodos , Tuberculose Resistente a Múltiplos Medicamentos , Amicacina/farmacologia , Antituberculosos/farmacologia , Antituberculosos/uso terapêutico , Capreomicina/farmacologia , Farmacorresistência Bacteriana Múltipla/genética , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Humanos , Isoniazida/farmacologia , Canamicina/farmacologia , Levofloxacino/farmacologia , Testes de Sensibilidade Microbiana , Estudos Retrospectivos , Rifampina/farmacologia , Escarro/microbiologia , Estreptomicina/farmacologia , Tuberculose Resistente a Múltiplos Medicamentos/diagnóstico
2.
World J Microbiol Biotechnol ; 38(8): 132, 2022 Jun 11.
Artigo em Inglês | MEDLINE | ID: mdl-35689134

RESUMO

This study was aimed at the isolation and identification of Arcobacter spp. and Campylobacter spp. from fresh vegetables sold at district markets in the Kayseri province, and at the determination of the antibacterial susceptibility of the recovered isolates. For this purpose, a total of 175 vegetable samples, including 35 spinach, 35 lettuce, 35 parsley, 35 arugula, and 35 radish samples, were collected. While the pre-enrichment and membrane filtration techniques were used for the isolation of Arcobacter spp., the pre-enrichment and direct inoculation methods were used for the isolation of Campylobacter spp. The isolates were identified by means of phenotypic tests and the polymerase chain reaction (PCR), using genus- and species-specific primers. In addition, the susceptibilities of the isolates to amoxicillin-clavulanic acid, enrofloxacin, erythromycin, gentamicin, neomycin, streptomycin, and tetracycline were determined by the disk diffusion method. Out of the 175 vegetable samples tested, 93 (53.14%) were found to be positive for Arcobacter spp., and 119 Arcobacter spp. isolates were recovered from these 93 positive samples. All of the samples examined were found to be negative for Campylobacter spp. One hundred one (86%) and 14 (10%) of the 119 Arcobacter isolates obtained were identified as A. butzleri and A. cryaerophilus, respectively, but four isolates could not be identified at the species level by mPCR. Mixed contamination with more than one species and/or genotypes of Arcobacter was detected in 24 of the positive samples. While all of the Arcobacter isolates were susceptible to erythromycin, gentamicin, streptomycin, and tetracycline, 2 (1.68%), 2 (1.68%), and 5 (4.20%) isolates were resistant to amoxicillin/clavulanic acid, enrofloxacin, and neomycin, respectively. Consequently, the determination of a high prevalence of arcobacters and mixed contamination with more than one species and/or genotypes of arcobacters in vegetables often consumed raw by humans demonstrated that the consumption of raw vegetables may be a risk to the public health.


Assuntos
Arcobacter , Campylobacter , Antibacterianos/farmacologia , Arcobacter/genética , Campylobacter/genética , Enrofloxacina , Eritromicina/farmacologia , Microbiologia de Alimentos , Gentamicinas , Humanos , Neomicina , Prevalência , Estreptomicina , Tetraciclinas , Verduras
3.
Food Chem ; 393: 133413, 2022 Nov 01.
Artigo em Inglês | MEDLINE | ID: mdl-35751206

RESUMO

Detrimental health effects caused by the intake of food contaminated with streptomycin have drawn concerns on effective monitoring using sensitive and selective methods. In this work, a DNA hydrogel surface enhanced Raman spectroscopy (SERS) sensor was successfully developed for the ultrasensitive determination of streptomycin residues in foods. The sensor used a DNA hydrogel containing DNAzyme (Pb-DNAzyme), triggering release of the Raman reporter 4-mercaptobenzonitrile, which was detected using a gold nanorods (AuNRs) array. The linear range of the sensor was 0.01-150 nM and the limit of detection was 4.85 × 10-3 nM. Tests conducted with four streptomycin structural analogues confirmed the sensor was specific. Milk and honey samples spiked with streptomycin were analysed, resulting in standard recoveries in the range 98.2-117.3%. These findings demonstrated that such a sensor can be used for ultrasensitive detection of streptomycin in foods.


Assuntos
Técnicas Biossensoriais , DNA Catalítico , Nanopartículas Metálicas , Técnicas Biossensoriais/métodos , DNA/química , DNA Catalítico/química , Ouro/química , Hidrogéis , Limite de Detecção , Nanopartículas Metálicas/química , Análise Espectral Raman/métodos , Estreptomicina
4.
Microbiol Spectr ; 10(3): e0271421, 2022 Jun 29.
Artigo em Inglês | MEDLINE | ID: mdl-35658579

RESUMO

Defining the precise relationship between resistance mutations and quantitative phenotypic drug susceptibility testing will increase the value of whole-genome sequencing (WGS) for predicting tuberculosis drug resistance. However, a large number of WGS data sets currently lack corresponding quantitative phenotypic data-the MICs. Using MYCOTBI plates, we determined the MICs to nine antituberculosis drugs for 154 clinical multidrug-resistant tuberculosis isolates from the Shenzhen Center for Chronic Disease Control in Shenzhen, China. Comparing MICs with predicted drug-resistance profiles inferred by WGS showed that WGS could predict the levels of resistance to isoniazid, rifampicin, streptomycin, fluoroquinolones, and aminoglycosides. We also found some mutations that may not be associated with drug resistance, such as EmbB D328G, mutations in the gid gene, and C-12T in the eis promoter. However, some strains carrying the same mutations showed different levels of resistance to the corresponding drugs. The MICs of different strains with the RpsL K88R, fabG1 C-15T mutations and some with mutations in embB and rpoB, had MICs to the corresponding drugs that varied by 8-fold or more. This variation is unexplained but could be influenced by the bacterial genetic background. Additionally, we found that 32.3% of rifampicin-resistant isolates were rifabutin-susceptible, particularly those with rpoB mutations H445D, H445L, H445S, D435V, D435F, L452P, S441Q, and S441V. Studying the influence of bacterial genetic background on the MIC and the relationship between rifampicin-resistant mutations and rifabutin resistance levels should improve the ability of WGS to guide the selection of medical treatment regimens. IMPORTANCE Whole-genome sequencing (WGS) has excellent potential in drug-resistance prediction. The MICs are essential indications of adding a particular antituberculosis drug dosage or changing the entire treatment regimen. However, the relationship between many known drug-resistant mutations and MICs is unclear, especially for rarer ones. The results showed that WGS could predict resistance levels to isoniazid, rifampicin, streptomycin, fluoroquinolones, and aminoglycosides. However, some mutations may not be associated with drug resistance, and some others may confer various MICs to strains carrying them. Also, 32.3% of rifampicin (RIF)-resistant strains were classified as sensitive to rifabutin (RFB), and some mutations in the rpoB gene may be associated with this phenotype. Our data on the MIC distribution of strains with some rarer mutations add to the accumulated data on the resistance level associated with such mutations to help guide further research and draw meaningful conclusions.


Assuntos
Mycobacterium tuberculosis , Tuberculose Resistente a Múltiplos Medicamentos , Aminoglicosídeos/uso terapêutico , Antituberculosos/farmacologia , Antituberculosos/uso terapêutico , Proteínas de Bactérias/genética , Farmacorresistência Bacteriana Múltipla/genética , Fluoroquinolonas/farmacologia , Humanos , Isoniazida , Testes de Sensibilidade Microbiana , Mutação , Rifabutina/uso terapêutico , Rifampina/farmacologia , Rifampina/uso terapêutico , Estreptomicina , Tuberculose Resistente a Múltiplos Medicamentos/tratamento farmacológico , Tuberculose Resistente a Múltiplos Medicamentos/microbiologia
5.
Food Chem ; 393: 133351, 2022 Nov 01.
Artigo em Inglês | MEDLINE | ID: mdl-35689929

RESUMO

Antibiotic abuse has caused serious health risks for human beings for long. To address the problem, novel and facile detection techniques are highly desired. Here, an effective multiplex immunochromatographic platform (MICP) with synthesis-free and cost-effective merits is established for simultaneous detection of antibiotics on a single immunochromatographic assay (ICA) strip. Adopting crystal violet (CV) as a signal tag for multiplex ICA allows for direct coupling with multiple antibodies in several minutes. By combining CV and ICA perfectly, this convenient strategy offers improvements in convenience, speed, flexibility, and portability, eventually ensuring the optimized effectiveness of this approach. As a result, the established platform is successfully used to detect streptomycin (STR) and chloramphenicol (CAP) with visual detection mode, and the obtained total recoveries of milk and honey real samples changed from 83.82 to 113.38% with total RSD values of 0.48 to 4.15%.


Assuntos
Cloranfenicol , Estreptomicina , Antibacterianos/análise , Cloranfenicol/análise , Cromatografia de Afinidade/métodos , Contaminação de Alimentos/análise , Violeta Genciana , Humanos , Limite de Detecção
6.
Pol J Microbiol ; 71(2): 205-215, 2022 May 31.
Artigo em Inglês | MEDLINE | ID: mdl-35675816

RESUMO

Drug-resistant Mycobacterium tuberculosis (DR-MTB) is a major health threat to human beings. This study aimed to evaluate the prevalence and drug resistance profile of MTB. Data were collected from 2,296 newly diagnosed, and 246 retreated tuberculosis (TB) patients who attended the Advisory Clinic for Chest Diseases and Respiratory in Basra province from January 2016 to December 2020. Both new diagnostic and retreated TB cases showed that DR-MTB cases were significantly higher at age 15-34 years, pulmonary TB, and urban residents but with no significant difference regarding gender. The drugs resistance was significantly higher among the retreated cases compared with the new diagnostic patients (20.3% vs. 2.4%, p < 0.0001), with the percentage of the resistance to first-line drugs in primary and secondary cases including isoniazid (1% and 17.1%), rifampicin (0.78% and 15.8%), ethambutol (0.56% and 8.5%), streptomycin (1.3% and 9.75%). Notice that the most common drug resistance was against streptomycin with 1.3% in new patients and against isoniazid (17.1%) in retreated patients. The rate of total drug-resistant TB, multi-drug resistant TB, mono-drug resistant TB, and rifampicin-resistant TB among new tuberculosis cases increased in this period from 2.2 to 6.7%, 0.17 to 1.6%, 0.85 to 4%, and 0.17 to 4%, with a percentage change of 204.54, 841.17, 370.58, 22.5%, respectively. The rates of poly drug-resistant TB and ethambutol-resistant-TB dropped in this period by 15.96%, and 0.7%, with a decrease from 1.19 to 1% and from 1 to 0.3%, respectively. Similarly, the increase of drug-resistant TB among secondary cases has also occurred. In conclusion, the temporal trend showed an increase in the rate of drug resistance of M. tuberculosis since 2016, with a predominant multi-drug-resistant TB and isoniazid-resistant TB.


Assuntos
Mycobacterium tuberculosis , Tuberculose Resistente a Múltiplos Medicamentos , Tuberculose , Adolescente , Adulto , Antituberculosos/farmacologia , Farmacorresistência Bacteriana Múltipla , Etambutol/uso terapêutico , Humanos , Iraque/epidemiologia , Isoniazida/farmacologia , Prevalência , Rifampina , Estreptomicina/uso terapêutico , Tuberculose/epidemiologia , Tuberculose Resistente a Múltiplos Medicamentos/tratamento farmacológico , Tuberculose Resistente a Múltiplos Medicamentos/epidemiologia , Adulto Jovem
7.
PLoS One ; 17(6): e0265068, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35709194

RESUMO

A series of newer previously synthesized fluorinated chalcones and their 2-amino-pyridine-3-carbonitrile and 2-amino-4H-pyran-3-carbonitrile derivatives were screened for their in vitro antitubercular activity and in silico methods. Compound 40 (MIC~ 8 µM) was the most potent among all 60 compounds, whose potency is comparable with broad spectrum antibiotics like ciprofloxacin and streptomycin and three times more potent than pyrazinamide. Additionally, compound 40 was also less selective and hence non-toxic towards the human live cell lines-LO2 in its MTT assay. Compounds 30, 27, 50, 41, 51, and 60 have exhibited streptomycin like activity (MIC~16-18 µM). Fluorinated chalcones, pyridine and pyran derivatives were found to occupy prime position in thymidylate kinase enzymatic pockets in molecular docking studies. The molecule 40 being most potent had shown a binding energy of -9.67 Kcal/mol, while docking against thymidylate kinase, which was compared with its in vitro MIC value (~8 µM). These findings suggest that 2-aminopyridine-3-carbonitrile and 2-amino-4H-pyran-3-carbonitrile derivatives are prospective lead molecules for the development of novel antitubercular drugs.


Assuntos
Chalcona , Chalconas , Aminopiridinas , Antituberculosos/química , Antituberculosos/farmacologia , Humanos , Simulação de Acoplamento Molecular , Estrutura Molecular , Estudos Prospectivos , Piranos , Estreptomicina , Relação Estrutura-Atividade
8.
Comput Intell Neurosci ; 2022: 3141807, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35634067

RESUMO

The drug resistance and influencing factors of patients with pulmonary tuberculosis were investigated, and a dual attention dilated residual network (DADRN) algorithm was proposed. The algorithm was applied to process and analyze lung computed tomography (CT) images of 400 included patients with pulmonary tuberculosis. Besides, sparse code book algorithm and bag of visual word (BOVW) algorithms were introduced and compared, and the influencing factors of pulmonary tuberculosis drug resistance were analyzed. The results demonstrated that the localization precision of lung consolidation, nodules, and cavities by the DADRN algorithm reached 91.2%, 92.5%, and 93.8%, respectively. The recall rate of the three algorithms amounted to 83.55%, 84.5%, and 86.4%, respectively. Both localization precision and recall rate of the DADRN algorithm were higher than those of other two algorithms (P < 0.05). The drug resistance rate of streptomycin, isoniazid, and rifampin of the patients aged between 40 and 59 was all higher than those of the patients in other age groups. The drug resistance rate of streptomycin, isoniazid, and rifampin of retreated patients was all higher than those of patients initially treated. The drug resistance rate of streptomycin, isoniazid, and rifampin of the patients with tuberculosis contact was all higher than those of the patients without tuberculosis contact (P < 0.05). Based on the above results, the accuracy of CT images processed by dual attention-based dilated residual classification network algorithm was higher than that processed by other two algorithms. Age, medical history, and history of exposure to tuberculosis were the influencing factors of the drug resistance of patients with pulmonary tuberculosis.


Assuntos
Tuberculose Resistente a Múltiplos Medicamentos , Tuberculose Pulmonar , Tuberculose , Adulto , Algoritmos , Antituberculosos/uso terapêutico , Humanos , Inteligência , Isoniazida/uso terapêutico , Pulmão , Pessoa de Meia-Idade , Rifampina/uso terapêutico , Estreptomicina/uso terapêutico , Tomografia Computadorizada por Raios X , Tuberculose/tratamento farmacológico , Tuberculose Resistente a Múltiplos Medicamentos/diagnóstico por imagem , Tuberculose Resistente a Múltiplos Medicamentos/tratamento farmacológico , Tuberculose Pulmonar/diagnóstico por imagem , Tuberculose Pulmonar/tratamento farmacológico
9.
Int J Infect Dis ; 121: 47-54, 2022 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-35523300

RESUMO

OBJECTIVES: To evaluate the performance of nucleotide matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) in predicting the drug resistance of Mycobacterium tuberculosis. METHODS: A total of 115 rifampin-resistant and 53 rifampin-susceptible tuberculosis (TB) clinical isolates were randomly selected from TB strains stored at -80℃ in the clinical laboratory of Shanghai Pulmonary Hospital. Nucleotide MALDI-TOF-MS was performed to predict the drug resistance using phenotypic susceptibility as the gold standard. RESULTS: The overall assay sensitivities and specificities of nucleotide MALDI-TOF-MS were 92.2% and 100.0% for rifampin, 90.9% and 98.6% for isoniazid, 71.4% and 81.2% for ethambutol, 85.1% and 93.1% for streptomycin, 94.0% and 100.0% for amikacin, 77.8% and 99.3% for kanamycin, 75.0% and 93.3% for ofloxacin, and 75.0% and 93.3% for moxifloxacin. The concordances between nucleotide MALDI-TOF-MS antimicrobial susceptibility testing (AST) and phenotypic AST were 94.6% (rifampin), 90.1% (isoniazid), 79.2% (ethambutol), 89.9% (streptomycin), 99.4% (amikacin), 97.0% (kanamycin), 88.1% (ofloxacin), and 88.0% (moxifloxacin). CONCLUSION: Nucleotide MALDI-TOF-MS could be a promising tool for rapid detection of Mycobacterium tuberculosis drug sensitivity to rifampin, isoniazid, ethambutol, streptomycin, amikacin, kanamycin, ofloxacin, and moxifloxacin.


Assuntos
Mycobacterium tuberculosis , Tuberculose dos Linfonodos , Amicacina , Antituberculosos/farmacologia , China , Resistência a Medicamentos , Etambutol , Humanos , Isoniazida , Canamicina , Testes de Sensibilidade Microbiana , Moxifloxacina , Nucleotídeos , Ofloxacino , Rifampina , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz/métodos , Estreptomicina
10.
Sci Rep ; 12(1): 7693, 2022 05 11.
Artigo em Inglês | MEDLINE | ID: mdl-35562174

RESUMO

Cambodia has one of the highest tuberculosis (TB) incidence rates in the WHO Western Pacific region. Remarkably though, the prevalence of multidrug-resistant TB (MDR-TB) remains low. We explored the genetic diversity of Mycobacterium tuberculosis (MTB) circulating in this unique setting using whole-genome sequencing (WGS). From October 2017 until January 2018, we collected one hundred sputum specimens from consenting adults older than 21 years of age, newly diagnosed with bacteriologically confirmed TB in 3 districts of Phnom Penh and Takeo provinces of Cambodia before they commence on their TB treatment, where eighty MTB isolates were successfully cultured and sequenced. Majority of the isolates belonged to Lineage 1 (Indo-Oceanic) (69/80, 86.25%), followed by Lineage 2 (East Asian) (10/80, 12.5%) and Lineage 4 (Euro-American) (1/80, 1.25%). Phenotypic resistance to both streptomycin and isoniazid was found in 3 isolates (3/80, 3.75%), while mono-resistance to streptomycin and isoniazid was identical at 2.5% (N = 2 each). None of the isolates tested was resistant to either rifampicin or ethambutol. The specificities of genotypic prediction for resistance to all drugs tested were 100%, while the sensitivities of genotypic resistance predictions to isoniazid and streptomycin were lower at 40% (2/5) and 80% (4/5) respectively. We identified 8 clusters each comprising of two to five individuals all residing in the Takeo province, making up half (28/56, 50%) of all individuals sampled in the province, indicating the presence of multiple ongoing transmission events. All clustered isolates were of Lineage 1 and none are resistant to any of the drugs tested. This study while demonstrating the relevance and utility of WGS in predicting drug resistance and inference of disease transmission, highlights the need to increase the representation of genotype-phenotype TB data from low and middle income countries in Asia and Africa to improve the accuracies for prediction of drug resistance.


Assuntos
Mycobacterium tuberculosis , Tuberculose dos Linfonodos , Tuberculose Resistente a Múltiplos Medicamentos , Antituberculosos/farmacologia , Antituberculosos/uso terapêutico , Camboja/epidemiologia , Farmacorresistência Bacteriana Múltipla/genética , Humanos , Isoniazida/uso terapêutico , Testes de Sensibilidade Microbiana , Estreptomicina , Tuberculose Resistente a Múltiplos Medicamentos/tratamento farmacológico , Tuberculose Resistente a Múltiplos Medicamentos/epidemiologia , Tuberculose Resistente a Múltiplos Medicamentos/microbiologia
11.
Microbiologyopen ; 11(2): e1269, 2022 04.
Artigo em Inglês | MEDLINE | ID: mdl-35478290

RESUMO

This study compared the antimicrobial resistance (AMR) among commensal Escherichia coli in the fecal microbiota of young calves raised on organic and on conventional dairy farms in Switzerland. Further, fecal carriage of extended-spectrum beta-lactamase (ESBL) producing Enterobacteriaceae was assessed for calves from both farming systems. Where possible, data on antimicrobial usage (AMU) were obtained. Antimicrobial susceptibility testing was performed on a total of 71 isolates using the disk diffusion method. ESBL producers were characterized by polymerase chain reaction-based multilocus sequence typing and sequencing of the blaESBL genes. Organically raised calves were significantly more likely to harbor E. coli that showed AMR to ampicillin (odds ratio [OR]: 2.78, 95% confidence interval [CI]: 1.02-7.61, p = 0.046), streptomycin (OR: 3.22, 95% CI: 1.17-8.92, p = 0.046), kanamycin (OR: 11.3, 95% CI: 2.94-43.50, p < 0.001), and tetracycline (OR: 3.25, 95% CI: 1.13-9.31, p = 0.028). Calves with reported AMU were significantly more likely to harbor E. coli with resistance to ampicillin (OR: 3.91, 95% CI: 1.03-14.85, p = 0.045), streptomycin (OR: 4.35, 95% CI: 1.13-16.7, p = 0.045), and kanamycin (OR: 8.69, 95% CI: 2.01-37.7, p = 0.004). ESBL-producing Enterobacteriaceae (18 E. coli and 3 Citrobacter braakii) were detected exclusively among samples from conventionally farmed calves (OR: infinity [∞], 95% CI: 2.3-∞, p < 0.0013). The observations from this study suggest that AMR is highly prevalent among commensal E. coli in young dairy calves, irrespective of the farm management system, with proportions of certain resistance phenotypes higher among organic calves. By contrast, the occurrence of ESBL producers among young dairy calves may be linked to factors associated with conventional farming.


Assuntos
Anti-Infecciosos , Infecções por Escherichia coli , Ampicilina , Animais , Antibacterianos/farmacologia , Anti-Infecciosos/farmacologia , Bovinos , Farmacorresistência Bacteriana , Enterobacteriaceae , Escherichia coli , Infecções por Escherichia coli/epidemiologia , Infecções por Escherichia coli/veterinária , Fazendas , Canamicina , Prevalência , Estreptomicina , Suíça/epidemiologia , beta-Lactamases/genética
12.
Microbiol Res ; 260: 127020, 2022 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-35462115

RESUMO

Many studies have shown the efficacy of phage therapy in reducing intestinal pathogens. However, phage-based probiotic treatment is poorly studied in view of effects on the gut microbiota and intestinal inflammation. In this study, a lytic or a temperate phage (each at 4 ×108 PFU per day) or a streptomycin solution (40 mg per day) were administered to mice via drinking water for 31 days. Subsequently, mice were challenged with Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium). S. Typhimurium does not serve as the host bacterium and is not lysed by both phages. For intestinal inflammation evaluation, mice were given one dose of streptomycin for 24 h before the S. Typhimurium challenge. High-throughput sequencing analysis revealed that the phylum Firmicutes became the most abundant in mice pretreated with phages. The alpha diversity of gut bacteria was higher in phage treated than in streptomycin treated mice. Moreover, pretreatment with the lytic and the temperate phage before the S. Typhimurium challenge increased two beneficial genera, Lactobacillus and Bifidobacterium. According to the pathological analysis of ileum, cecum, and serum, temperate or lytic gut phage pretreatment of mice markedly reduced intestinal inflammation, concomitant with lower serum concentration of lipopolysaccharides (LPS) and diamine oxidase (DAO). The oral pretreatments of mice (ST, Lyt, Lys, SM) generally caused an increased expression of IL-1ß, TNF-α, IFN-γ, IL-4, and IL-10 compared to the matching control. However, in mice pretreated with the lytic phage, the mRNA expression for the pro-inflammatory cytokine TNF-α was not significantly higher than that of the control group. No significant differences were detected for peripheral blood B lymphocytes, CD3 +T cells, and the CD4 + /CD8 + ratio in mice pretreated with the lytic and lysogenic phage. This study demonstrated that even lytic phages not targeting the pathogenic serovar Salmonella Typhimurium alleviated intestinal dysbiosis and inflammation in challenged mice.


Assuntos
Bacteriófagos , Salmonelose Animal , Animais , Disbiose/terapia , Inflamação/terapia , Camundongos , Salmonelose Animal/microbiologia , Salmonella typhimurium , Estreptomicina
13.
Microbiol Spectr ; 10(2): e0198721, 2022 04 27.
Artigo em Inglês | MEDLINE | ID: mdl-35234510

RESUMO

Helicobacter pylori is a human pathogen competent for natural transformation. Intrinsic and acquired antibiotic resistance contribute to the survival and multiplication of H. pylori under antibiotics. While drug-resistance dissemination by natural transformation (NT)-mediated horizontal gene transfer remains poorly understood in H. pylori. The purpose of the study was to investigate the role of H. pylori porins (HopA, HopB, HopC, HopD, and HopE) in the intrinsic antibiotic resistance and to preliminarily reveal the potential effect of HopE and HopD porins in streptomycin resistance acquisition after NT in the presence of antibiotics. Using traditional antibiotic susceptibility tests and growth curve analysis, we found the MIC values of metronidazole, clarithromycin, levofloxacin, tetracycline, rifampin, and streptomycin in mutants lacking HopE and/or HopD were significantly elevated compare to those in wild-type strain. The quantitative analysis of the tetramethyl rhodamine isothiocyanate (TRITC)-labeled streptomycin accumulation at the single-cell level showed reduced streptomycin intracellular fluorescence in ΔhopE and ΔhopD mutant cells. Furthermore, in the presence of translation-inhibiting antibiotic streptomycin, the resistance acquisition frequency was decreased in the wild-type strain, which could be reversed by mutants lacking HopE and HopD that restored relatively high resistance acquisition frequencies. By transforming a pUC19-rpsLmut-sfgfp linear plasmid carrying a streptomycin conferring mutation, we observed that the impaired ability of rpsLmut synthesis in the wild-type strain was restored in the ΔhopE and ΔhopD mutant transformants. Our study revealed that in the presence of streptomycin, resistance acquisition at least partially relied on the deletion of the hopE and hopD genes, because their loss reduced streptomycin concentration in the cell and thus restored the expression of the resistance-conferring gene, which was inhibited by streptomycin in wild-type strain. The loss of HopE and HopD influx activity may also preserve resistance acquisition by transformation in the presence of antibiotics with other modes of action. IMPORTANCE Helicobacter pylori is constitutively competent for natural transformation (NT) and possesses an efficient system for homologous recombination, which could be utilized to study the NT-mediated horizontal gene transfer induced antibiotic resistance acquisition. Bacterial porins have drawn renewed attention because of their crucial role in antibiotic susceptibility. From the perspective of porin-mediated influx in H. pylori, our study preliminarily revealed the important role of HopE and HopD porins not only in preserving the intrinsic susceptibility to specific antibiotic but also in evading acquired antibiotic resistance by NT in the presence of translation-inhibiting antimicrobial. Therefore, the loss of HopE or HopD porin in H. pylori genomes, combined with the large number of secreted or cell-free genetic elements carrying mutations conferring antibiotic resistance, may raise the possibility that this mechanism plays a potential role in the propagation of antibiotic resistance within H. pylori communities.


Assuntos
Anti-Infecciosos , Infecções por Helicobacter , Helicobacter pylori , Antibacterianos/farmacologia , Antibacterianos/uso terapêutico , Anti-Infecciosos/farmacologia , Farmacorresistência Bacteriana/genética , Helicobacter pylori/genética , Humanos , Testes de Sensibilidade Microbiana , Porinas/genética , Porinas/farmacologia , Estreptomicina/farmacologia
14.
Microbiol Spectr ; 10(2): e0251621, 2022 04 27.
Artigo em Inglês | MEDLINE | ID: mdl-35311541

RESUMO

Our objective was to evaluate the performance of whole-genome sequencing (WGS) from early positive liquid cultures for predicting Mycobacterium tuberculosis complex (MTBC) drug resistance. Clinical isolates were obtained from tuberculosis patients at Shanghai Pulmonary Hospital (SPH). Antimicrobial susceptibility testing (AST) was performed, and WGS from early Bactec mycobacterial growth indicator tube (MGIT) 960-positive liquid cultures was performed to predict the drug resistance using the TB-Profiler informatics platform. A total of 182 clinical isolates were enrolled in this study. Using phenotypic AST as the gold standard, the overall sensitivity and specificity for WGS were, respectively, 97.1% (89.8 to 99.6%) and 90.4% (83.4 to 95.1%) for rifampin, 91.0% (82.4 to 96.3%) and 95.2% (89.1 to 98.4%) for isoniazid, 100.0% (89.4 to 100.0%) and 87.3% (80.8 to 92.1%) for ethambutol, 96.6% (88.3 to 99.6%) and 61.8% (52.6 to 70.4%) for streptomycin, 86.8% (71.9 to 95.6%) and 95.8% (91.2 to 98.5%) for moxifloxacin, 86.5% (71.2 to 91.5%) and 95.2% (90.3 to 98.0%) for ofloxacin, 100.0% (54.1 to 100.0%) and 67.6% (60.2 to 74.5%) for amikacin, 100.0% (63.1 to 100.0%) and 67.2% (59.7 to 74.2%) for kanamycin, 62.5% (24.5 to 91.5%) and 88.5% (82.8 to 92.8%) for ethionamide, 33.3% (4.3 to 77.7%) and 98.3% (95.1 to 99.7%) for para-aminosalicylic acid, and 0.0% (0.0 to 12.3%) and 100.0% (97.6 to 100.0%) for cycloserine. The concordances of WGS-based AST and phenotypic AST were as follows: rifampin (92.9%), isoniazid (93.4%), ethambutol (89.6%), streptomycin (73.1%), moxifloxacin (94.0%), ofloxacin (93.4%), amikacin (68.7%), kanamycin (68.7%), ethionamide (87.4%), para-aminosalicylic acid (96.2%) and cycloserine (84.6%). We conclude that WGS could be a promising approach to predict MTBC resistance from early positive liquid cultures. IMPORTANCE In this study, we used whole-genome sequencing (WGS) from early positive liquid (MGIT) cultures instead of solid cultures to predict drug resistance of 182 Mycobacterium tuberculosis complex (MTBC) clinical isolates to predict drug resistance using the TB-Profiler informatics platform. Our study indicates that WGS may be a promising method for predicting MTBC resistance using early positive liquid cultures.


Assuntos
Ácido Aminossalicílico , Mycobacterium tuberculosis , Tuberculose Resistente a Múltiplos Medicamentos , Amicacina , Antituberculosos/farmacologia , Antituberculosos/uso terapêutico , China , Ciclosserina , Resistência a Medicamentos , Etambutol , Etionamida , Humanos , Isoniazida , Canamicina , Testes de Sensibilidade Microbiana , Moxifloxacina , Ofloxacino , Rifampina , Estreptomicina , Tuberculose Resistente a Múltiplos Medicamentos/diagnóstico , Tuberculose Resistente a Múltiplos Medicamentos/tratamento farmacológico , Tuberculose Resistente a Múltiplos Medicamentos/microbiologia
15.
Genes (Basel) ; 13(3)2022 02 24.
Artigo em Inglês | MEDLINE | ID: mdl-35327964

RESUMO

Whole-genome sequencing of a soil isolate Bacillus pumilus, strain 7P, and its streptomycin-resistant derivative, B. pumilus 3-19, showed genome sizes of 3,609,117 bp and 3,609,444 bp, respectively. Annotation of the genome showed 3794 CDS (3204 with predicted function) and 3746 CDS (3173 with predicted function) in the genome of strains 7P and 3-19, respectively. In the genomes of both strains, the prophage regions Bp1 and Bp2 were identified. These include 52 ORF of prophage proteins in the Bp1 region and 38 prophages ORF in the Bp2 region. Interestingly, more than 50% of Bp1 prophage proteins are similar to the proteins of the phi105 in B. subtilis. The DNA region of Bp2 has 15% similarity to the DNA of the Brevibacillus Jimmer phage. Degradome analysis of the genome of both strains revealed 148 proteases of various classes. These include 60 serine proteases, 48 metalloproteases, 26 cysteine proteases, 4 aspartate proteases, 2 asparagine proteases, 3 threonine proteases, and 2 unclassified proteases. Likewise, three inhibitors of proteolytic enzymes were found. Comparative analysis of variants in the genomes of strains 7P and 3-19 showed the presence of 81 nucleotide variants in the genome 3-19. Among them, the missense mutations in the rpsL, comA, spo0F genes and in the upstream region of the srlR gene were revealed. These nucleotide polymorphisms may have affected the streptomycin resistance and overproduction of extracellular hydrolases of the 3-19 strain. Finally, a plasmid DNA was found in strain 7P, which is lost in its derivative, strain 3-19. This plasmid contains five coding DNA sequencing (CDS), two regulatory proteins and three hypothetical proteins.


Assuntos
Bacillus pumilus , Bacillus pumilus/genética , Nucleotídeos , Peptídeo Hidrolases , Prófagos/genética , Estreptomicina
16.
PLoS One ; 17(3): e0264588, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35324924

RESUMO

The ability of microorganisms to generate resistance outcompetes with the generation of new and efficient antibiotics. Therefore, it is critically required to develop novel antibiotic agents and treatments to control bacterial infections. Green synthesized metallic and metal oxide nanoparticles are considered as the potential means to target bacteria as an alternative to antibiotics. Nanoconjugates have also attracted attention because of their increased biological activity as compared to free antibiotics. In the present investigation, silver nanoparticles (AgNPs), zinc oxide nanoparticles (ZnO NPs), copper oxide nanoparticles (CuO NPs), and iron oxide nanoparticles (FeO NPs) have been synthesized by using leaf extract of Ricinus communis. Characterization of nanoparticles was done by using UV-Vis Spectroscopy, Fourier Transform Infrared Spectroscopy, Scanning Electron Microscopy, Energy Dispersive X-Ray Analyzer, X-ray Diffraction Analysis, and Dynamic Light Scattering Particle Size Analyzer. Interestingly, Streptomycin when combined with AgNPs, ZnO NPs, CuO NPs, and FeO NPs showed enhanced antibacterial activity against clinical isolates of S. aureus which suggested synergism between the nanoparticles and antibiotics. The highest enhanced antibacterial potential of Streptomycin was observed in conjugation with ZnO NPs (11 ± 0.5 mm) against S. aureus. Minimum inhibitory concentration of conjugates of AgNPs, ZnO NPs, CuO NPs, and FeO NPs with streptomycin against S. aureus was found to be 3.12, 2.5,10, and 12.5 µg/mL respectively. The considerable point of the present investigation is that S. aureus, which was resistant to streptomycin becomes highly susceptible to the same antibiotic when combined with nanoparticles. This particular observation opens up windows to mitigate the current crisis due to antibiotic resistance to combat antimicrobial infections efficiently.


Assuntos
Nanopartículas Metálicas , Óxido de Zinco , Antibacterianos/química , Antibacterianos/farmacologia , Nanopartículas Metálicas/química , Testes de Sensibilidade Microbiana , Extratos Vegetais/química , Prata/farmacologia , Espectroscopia de Infravermelho com Transformada de Fourier , Staphylococcus aureus , Estreptomicina/farmacologia , Difração de Raios X , Óxido de Zinco/química , Óxido de Zinco/farmacologia
17.
Appl Environ Microbiol ; 88(7): e0251321, 2022 04 12.
Artigo em Inglês | MEDLINE | ID: mdl-35285707

RESUMO

Phage-based biocontrol is an emerging method for managing the plant pathogen Erwinia amylovora. Control of E. amylovora in North America is achieved chiefly through the application of streptomycin and has led to the development of streptomycin resistance. Resistant E. amylovora can be tracked through the analysis of CRISPR spacer sequences. An alternative to antibiotics are bacterial viruses, known as phages, which lyse their hosts during replication to control the bacterial population. Endogenous CRISPR-Cas systems act as phage resistance mechanisms however, preliminary genomic analysis suggests this activity is limited in E. amylovora. This leaves the functionality of the CRISPR-Cas system, any clade-based differences, and the impact which this system may have on phage-based biocontrol in question. In this study, the CRISPR arrays from 127 newly available genomic sequences of E. amylovora were analyzed through a novel bioinformatic pipeline. Through this, the Eastern and Western North American clades were shown to be incompatible with the current PCR-based approaches for tracking E. amylovora given the size and composition of their CRISPR arrays. Two artificial CRISPR arrays were designed to investigate the functionality of the CRISPR-Cas system in E. amylovora. This system was capable of curing a targeted plasmid and providing phage resistance but was not the source of phage resistance observed within the controls. This suggests that while the CRISPR-Cas system is an important defense mechanism for invasive plasmids, an as yet unidentified mechanism is the primary source of phage resistance in E. amylovora. IMPORTANCE Erwinia amylovora is an economically significant agricultural pathogen found throughout the world. In North America, E. amylovora has developed streptomycin resistance and therefore alternative treatments using phages have received increased attention. In this study, we analyzed recently published genomes to determine that two significant groups of E. amylovora are poorly identified using the current, CRISPR-based tracking methods. We also showed that the CRISPR-Cas system and an unidentified mechanism work together to provide a significant degree of resistance against one of the phages proposed for phage-based biocontrol.


Assuntos
Bacteriófagos , Erwinia amylovora , Bacteriófagos/genética , Sistemas CRISPR-Cas , Erwinia amylovora/genética , Plasmídeos/genética , Estreptomicina
18.
Mar Drugs ; 20(3)2022 Feb 24.
Artigo em Inglês | MEDLINE | ID: mdl-35323461

RESUMO

In this study, a detailed chemical investigation of a streptomycin-resistant strain of the deep-sea marine, actinomycete Amycolatopsis sp. WP1, yielded six novel amycolachromones A-F (1-6), together with five known analogues (7-11). Amycolachromones A-B (1-2) possessed unique dimer skeletons. The structures and relative configurations of compounds 1-11 were elucidated by extensive spectroscopic data analyses combined with X-ray crystal diffraction analysis. Plausible biogenetic pathways of amycolachromones A-F were also proposed.


Assuntos
Amycolatopsis/química , Cromonas/isolamento & purificação , Amycolatopsis/metabolismo , Antibacterianos , Organismos Aquáticos/química , Cromonas/química , Cromonas/metabolismo , Farmacorresistência Bacteriana , Estrutura Molecular , Estreptomicina
19.
Sci Total Environ ; 821: 153537, 2022 May 15.
Artigo em Inglês | MEDLINE | ID: mdl-35101502

RESUMO

The emergence of antibiotic resistance in retort to environmental pollutants during wastewater treatment still remains elusive. Here, we first to investigate the emergence of antibiotic resistance in an environmental non-pathogenic bacterium, Pseudoxanthomonas mexicana isolated from a lab-scale bioreactor treating wastewater containing streptomycin. The molecular mechanism of antibiotic resistance development was evaluated in its genomic, transcriptional, and proteomic levels. The streptomycin resistant (SR) strain showed strong resistance to streptomycin (MIC > 600 µg/mL) as well to sulfamethoxazole, ampicillin, and kanamycin (≥250 µg/mL). A 13.4 kb class-1-integron array consisting of a new arrangement of gene cassette (IS6100-sul1-aadA2-catB3-aacA1-2-aadB-int1-IS256-int) linked with Tn5393c transposon was identified in the SR strain, which has only been reported in clinical pathogens so far. iTRAQ-LC-MS/MS proteomics revealed 22 up-regulated proteins in the SR strain growing under 100 mg L-1 streptomycin, involving antibiotic resistance, toxin production, stress response, and ribosomal protein synthesis. At the mRNA level, elevated expressions of ARGs (strA, strB, and aadB) and 30S-ribosomal protein genes (rpsA and rpsU) were observed in the SR strain. The results highlighted the genomic plasticity and multifaceted regulatory mechanism employed by P. mexicana in adaptation to high-level streptomycin during biological wastewater treatment.


Assuntos
Estreptomicina , Águas Residuárias , Antibacterianos/farmacologia , Reatores Biológicos , Cromatografia Líquida , Farmacorresistência Bacteriana Múltipla/genética , Testes de Sensibilidade Microbiana , Proteômica , Estreptomicina/farmacologia , Espectrometria de Massas em Tandem , Xanthomonadaceae
20.
Proc Biol Sci ; 289(1968): 20212514, 2022 02 09.
Artigo em Inglês | MEDLINE | ID: mdl-35135346

RESUMO

In the past decade, the broadcast-spray application of antibiotics in US crops has increased exponentially in response to bacterial crop pathogens, but little is known about the sublethal impacts on beneficial organisms in agroecosystems. This is concerning given the key roles that microbes play in modulating insect fitness. A growing body of evidence suggests that insect gut microbiomes may play a role in learning and behaviour, which are key for the survival of pollinators and for their pollination efficacy, and which in turn could be disrupted by dietary antibiotic exposure. In the laboratory, we tested the effects of an upper-limit dietary exposure to streptomycin (200 ppm)-an antibiotic widely used to treat bacterial pathogens in crops-on bumblebee (Bombus impatiens) associative learning, foraging and stimulus avoidance behaviour. We used two operant conditioning assays: a free movement proboscis extension reflex protocol focused on short-term memory formation, and an automated radio-frequency identification tracking system focused on foraging. We show that upper-limit dietary streptomycin exposure slowed training, decreased foraging choice accuracy, increased avoidance behaviour and was associated with reduced foraging on sucrose-rewarding artificial flowers flowers. This work underscores the need to further study the impacts of antibiotic use on beneficial insects in agricultural systems.


Assuntos
Agricultura , Exposição Dietética , Estreptomicina , Animais , Antibacterianos/farmacologia , Aprendizagem da Esquiva , Abelhas , Produtos Agrícolas , Flores , Polinização/fisiologia , Estreptomicina/farmacologia
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