Prediction of rifampicin resistance beyond the RRDR using structure-based machine learning approaches.

Rifampicin resistance is a major therapeutic challenge, particularly in tuberculosis, leprosy, P. aeruginosa and S. aureus infections, where it develops via missense mutations in gene rpoB. Previously we have highlighted that these mutations reduce protein affinities within the RNA polymerase complex, subsequently reducing nucleic acid affinity. Here, we have used these insights to develop a computational rifampicin resistance predictor capable of identifying resistant mutations even outside the well-defined rifampicin resistance determining region (RRDR), using clinical M. tuberculosis sequencing information. Our tool successfully identified up to 90.9% of M. tuberculosis rpoB variants correctly, with sensitivity of 92.2%, specificity of 83.6% and MCC of 0.69, outperforming the current gold-standard GeneXpert-MTB/RIF. We show our model can be translated to other clinically relevant organisms: M. leprae, P. aeruginosa and S. aureus, despite weak sequence identity. Our method was implemented as an interactive tool, SUSPECT-RIF (StrUctural Susceptibility PrEdiCTion for RIFampicin), freely available at https://biosig.unimelb.edu.au/suspect_rif/ .

Antimicrobial activity of the lupane triterpene 3ß,6ß,16ß-trihydroxylup-20(29)-ene isolated from Combretum leprosum Mart.

Introduction. Combretum leprosum (Combretaceae) is commonly found in the Northeast Region of Brazil and is known for several bioactivities, including antimicrobial ones. Because of increasing bacterial antibiotic resistance, natural products from several plants have been studied as putative adjuvants to antibiotic activity, including products from C. leprosum. Aims. This study was carried out to investigate the structural properties, bactericidal activity and antibiotic modifying action of the lupane triterpene 3ß,6ß,16ß-trihydroxylup-20(29)-ene (CLF1) isolated from C. leprosum Mart. leaves.Methods. The CLF1 was evaluated by the Fourier transform infrared spectroscopy method and the antibacterial activity of this compound was assayed alone and in association with antibiotics by microdilution assay.Results. Spectroscopic studies confirmed the molecular structure of the CLF1 and permitted assignment of the main infrared bands of this natural product. Microbiological assays showed that this lupane triterpene possesses antibacterial action with clinical relevance against Staphylococcus aureus. The CLF1 triterpene increased antimicrobial activity against the multidrug-resistant Escherichia coli 06 strain when associated with the antibiotics gentamicin and amikacin. Synergistic effects were observed against the S. aureus 10 strain in the presence of the CLF1 triterpene with the antibiotic gentamicin.Conclusion. In conclusion, the CLF1 compound may be useful in the development of antibacterial drugs against the aforementioned bacteria.

Effectiveness of topical green tea against multidrug-resistant Staphylococcus aureus in cases of primary pyoderma: An open controlled trial.

BACKGROUND: Antimicrobial activity of green tea against Staphylococcus aureus both in vitro and in vivo has been reported recently. Studies on clinical efficacy and safety of green tea as antibacterial agent against S. aureus in human cases are rare. OBJECTIVES: To evaluate the clinical effectiveness and safety of topical green tea on primary pyoderma caused by S. aureus. We also attempted to determine the minimum inhibitory concentration of green tea against S. aureus and methicillin-resistant S. aureus. METHODS: Open label, prospective, placebo-controlled study included community-acquired primary pyoderma cases caused by S. aureus. Severity grading was done on a scale of 1-5. Green tea ointment 3% and placebo ointment were used. Cure was defined on the basis of negative culture and assessment of clinical improvement. Minimum inhibitory concentration was determined by agar dilution method. Data were analyzed using Statistical Package for Social Sciences (SPSS) software version 16. RESULTS: Of the 372 patients, 250 received green tea and 122 received placebo. Multidrug-resistant S. aureus was isolated in 89.1% in green tea group and 81.1% in placebo group, respectively. Methicillin-resistant S. aureus was isolated in 24 patients. Cure was seen in 86% in green tea group and 6.6% in placebo group which was statistically very significant. The number of days for comprehensive cure in green tea group was 9.2 ± 6.4 days. All patients with methicillin-resistant S. aureus infection in the green tea group were cured. Minimum inhibitory concentration of green tea against S. aureus was 0.0265 ± 0.008 µg/ml and against methicillin-resistant S. aureus was 0.0205 ± 0.003 µg/ml. LIMITATIONS OF THE STUDY: Comparative trial was not conducted in the same patient with different lesions; children less than seven years were not considered as the school authorities did not permit for younger children to be included in the study and true randomization and blinding of investigators were not done. CONCLUSIONS: Green tea has a significant antibacterial effect against multidrug-resistant S. aureus. Minimum inhibitory concentration of green tea is established and is promising in methicillin-resistant S. aureus infections.

Bactericidal and Fungicidal Activity in the Gas Phase of Sodium Dichloroisocyanurate (NaDCC).

Sodium dichloroisocyanurate (NaDCC) is usually employed as a disinfectant for the treatment of water, environmental surfaces and medical equipment principally for its effectiveness as a microbicide agent. In this study, we explore the possibility of a new use for NaDCC by investigating the microbicidal activity of chlorine, which derives from the hydrolysis of NaDCC mediated by air humidity, and by testing its effect on the neutralization of microbes present in domestic waste. NaDCC was inserted in a plastic garbage can where LB agar plates, with different dilutions of a known title of four different microorganisms (Escherichia coli, Staphylococcus aureus, Debaryomyces hansenii and Aspergillus brasiliensis), were weakly inserted. The molecular chlorine (Cl2) levels present in the garbage can were quantified using an iodometric titration. The gas emitted in the garbage can presented a strong microbicide effect, inhibiting the proliferation of all four microorganisms and for four consecutive weeks, thus showing that NaDCC hydrolysis, mediated by air humidity, is able to ensure the decontamination of restricted environments, avoiding the proliferation of both Gram-positive and Gram-negative bacteria as well as fungi.

Study of the antibacterial activity in the gas phase of a chemical formulation for household waste management.

UNLABELLED: The aim of this study was to formulate a product (microbicide mixture) that could slow down the bacterial proliferation during the storage of household waste. We used harmless and natural components, known for their antimicrobial properties, in the liquid phase at direct contact with the microbes. The antimicrobial activity of the microbicide mixture formulated was evaluated over a range of concentration in two types of tests, in the liquid and in the gas phase. Once the efficacy of antimicrobial agent in the liquid phase in direct contact with the microbe (Escherichia coli) was confirmed, we adopted a new approach to evaluate the effect of the vapour phase both on the microbes' growth and on its duration. Here, we show that the perfect combination that gives rise to an antimicrobial mixture useful to control microbial growth (Staphylococcus aureus, Escherichia coli, Debaryomyces hansenii or Penicillium citrinum) up to 4 weeks is the one between more volatile agents (2-propanol and limonene) and a less volatile agent (cinnamaldehyde). The pleasant smell as well as the synergic antibacterial and antifungal function of the natural components of this mixture makes it attractive in domestic waste management. SIGNIFICANCE AND IMPACT OF THE STUDY: The novelty of this work is two-fold: on the one hand, to test various antimicrobial components of different volatility in a single microbicide mixture, and on the other, to study antimicrobial activity in the gas phase, other than the liquid phase. While previous authors tested the components individually as antimicrobial agents in the liquid phase at direct contact with the microbes, we tested them altogether as a mixture both in the liquid and in gas phase. The aim of this study was to disinfect small environments, such as garbage containers, by favouring the diffusion of the vapour phase to avoid the growth of microbes. This study proposes a new approach in the management and storage of household waste by inhibiting bacterial proliferation in the garbage can.

Leprosy ulcers in a rural hospital of Ethiopia: pattern of aerobic bacterial isolates and drug sensitivities.

BACKGROUND: Plantar ulcers, which commonly occur in leprosy patients, tend to recur increasing physical disability. The aim of this study is to identify both the bacteriological profile of these ulcers and the antibiotic susceptibility of the isolated bacteria. MATERIALS AND METHODS: 68 leprosy patients with chronic ulcers attending the in-patient department of Gambo General Hospital, West Arsi, were included in this study. Proper sample collection, inoculation on culture media, and final identification using biochemical methods were undertaken. RESULTS: 66 patients (97.1%) had a positive culture. A total of 81 microorganisms were isolated. Multiple organisms (two or more) were isolated in 15 (22.7% out of positive culture) patients. The main isolation was Proteus spp (30.9%), followed by Escherichia coli (21.0%), Staphylococcus aureus (18.5%) and Pseudomonas aeruginosa (9.9%). In the total number of the isolated bacteria, the antibiotics with less resistance were gentamicin (18.5%), fosfomycin (22.2%) cefoxitin (24.7%), ceftriaxone (25.9%) ciprofloxacin (25.9%), and amoxicillin-clavulanic acid (28.49%). CONCLUSION: The bacteriological study of plantar ulcers of leprosy patients revealed Enterobacteriaceae and S. aureus as the main pathogens involved in such infections. The results of this study may guide empirical therapy in a rural area hospital where culture and susceptibility testing facilities are scarce.

[Evaluation of the effect of Lactobacillus rhamnosus probiotic culture added to yogurt over Staphylococcus aureus, Escherichia coli O157:H7, Listeria monocytogenes and Salmonella enteritidis populations]. / Evaluación del efecto del cultivo probiótico Lactobacillus rhamnosus adicionado a yogurt natural y con probi6ticos comerciales sobre poblaciones de Staphylococcus aureus, Escherichia coli O157:H7, Listeria monocytogenes y Salmonella enteritidis.

The effect of different types of probiotics present in yogurt over known populations of Staphylococcus aureus, Escherichia coli O157:H7, Listeria monocytogenes and Salmonella enteritidis was evaluated. The three types of yogurt used were: without added probiotics, with added probiotics (Lactobacillus casei CRL_431 and L. acidophilus CRL_730 CHR HANSEN) and another one with the same probiotics mentioned above and Lactobacillus rhamnosus (LR-35) culture. About 10(9) CFU/ mL of each potentially pathogenic bacteria was added to each type of yogurt tested, and kept in refrigeration at 4 degrees C during its shelf life, about 30 days. Bacterial count was done the initial day and every four days. Results obtained show that there is a difference in the inhibition between yogurts without added probiotics and the commercial yogurt with added probiotics; there is a clear inhibitory effect of the last one over S. aureus, E. coli O157:H7 and Listeria monocytogenes. The yogurt with added probiotics and L. rhamnosus did not show any additional inhibitory effect over the bacteria tested when compared with the yogurt with added probiotics. S. enteritidis could not be evaluated because it was not detectable in any yogurt samples evaluated four days after its inoculation. This study confirms the antagonic effect of probiotic cultures over potentially pathogenic bacteria for human beings and animals that may be present in food. Nevertheless, the use of L. rhamnosus did not produce any additional inhibitory effect.

Evaluación del efecto del cultivo probiótico Lactobacillus rhamnosus adicionado a yogurt natural y con probi6ticos comerciales sobre poblaciones de Staphylococcus aureus, Escherichia coli O157: H7, Listeria monocytogenes y Salmonella enteritidis / Evaluation of the effect of Lactobacillus rhamnosus probiotic culture added to yogurt over Staphylococcus aureus, Escherichia coli O157: H7, Listeria monocytogenes and Salmonella enteritidis populations

Se evaluó el efecto de diferentes tipos de cultivos probióticos en yogurt sobre poblaciones conocidas de Staphylococcus aureus, Escherichia coli O157:H7, Listeria monocytogenes y Salmonella enteritidis. Los tres tipos diferentes de yogurt comercial utilizados fueron: sin probióticos adicionados, con probióticos CHR HANSEN® (Lactobacillus casei CRL_431 y L. acidophilus CRL_730) y otro con los mismos probióticos mencionados anteriormente, adicionado con cultivo de Lactobacillus rhamnosus (LR-35). Se inoculó aproximadamente 109 UFC/mL de cada bacteria potencialmente patógena en los diferentes tipos de yogurt, se mantuvo en refrigeración a 4ºC durante la vida útil de cada uno de estos alimentos (aproximadamente 30 días) y se realizó un recuento bacteriano cada cuatro días incluyendo el mismo día de la inoculación. Los resultados obtenidos demuestran que, existe diferencia en cuanto a inhibición entre los yogures sin probióticos y el yogurt comercial con probióticos, observándose un efecto inhibitorio evidente, por parte del segundo sobre las poblaciones de S. aureus, E. coli O157:H7 y L. monocytogenes. Con respecto a los yogures comerciales con probióticos más L. rhamnosus, no se observó alguna diferencia con respecto al efecto inhibitorio que poseen los yogures con probióticos L. casei y L. acidophilus . En los yogures en que se evaluó S. enteritidis se obtuvo la muerte de ésta al cabo de cuatro días. El presente estudio confirma el efecto antagónico que poseen los cultivos probióticos sobre bacterias potencialmente patógenas para el ser humano y animales que pueden estar contenidas en los alimentos.No obstante, el uso del probiótico Lactobacillus rhamnosus no ejerce un efecto inhibitorio adicional.

The effect of different types of probiotics present in yogurt over known populations of Staphylococcus aureus, Escherichia coli O157:H7, Listeria monocytogenes and Salmonella enteritidis was evaluated. The three types of yogurt used were: without added probiotics, with added probiotics (Lactobacillus casei CRL_431 and L. acidophilus CRL_730 CHR HANSEN®) and another one with the same probiotics mentioned above and Lactobacillus rhamnosus (LR-35) culture. About 109 CFU/ mL of each potentially pathogenic bacteria was added to each type of yogurt tested, and kept in refrigeration at 4ºC during its shelf life, about 30 days. Bacterial count was done the initial day and every four days. Results obtained show that there is a difference in the inhibition between yogurts without added probiotics and the commercial yogurt with added probiotics; there is a clear inhibitory effect of the last one over S. aureus, E coli O157:H7 and Listeria monocytogenes. The yogurt with added probiotics and L. rhamnosus did not show any additional inhibitory effect over the bacteria tested when compared with the yogurt with added probiotics. S. enteritidis could not be evaluated because it was not detectable in any yogurt samples evaluated four days after its inoculation. This study confirms the antagonic effect of probiotic cultures over potentially pathogenic bacteria for human beings and animals that may be present in food. Nevertheless, the use of L. rhamnosus did not produce any additional inhibitory effect.

Microbiological transformation of two labdane diterpenes, the main constituents of Madia species, by two fungi.

Microbial transformation of 13R,14R,15-trihydroxylabd-7-ene (5) and 13R,14R,15-trihydroxylabd-8(17)-ene (6) by the fungus Debaryomyces hansenii gave 1 (13R,14R,15-trihydroxy-6-oxolabd-8-ene) and 3 (7alpha,13R,14R,15-tetrahydroxy-labd-8(17)-ene), respectively. While, microbial transformation of 5 by Aspergillus niger afforded 2 (3beta,13R,14R,15-tetrahydroxy-labd-7-ene), and 13R,14R,15-trihydroxylabd-8,17-ene (6) gave 3 and 4 (3R,14R,15-3-oxotetrahydroxy-labd-7-ene). The structures of the new compounds, 1 and 2, were assigned by 1D and 2D high-field NMR spectroscopic methods. Antimicrobial activity of these compounds were tested and their MIC were determined.

Prevalence of methicillin-resistant Staphylococcus aureus (MRSA) in community-acquired primary pyoderma.

BACKGROUND: Although prevalence of MRSA strains is reported to be increasing, there are no studies of their prevalence in community-acquired primary pyodermas in western India. AIMS: This study aimed at determining the prevalence of MRSA infection in community-acquired primary pyodermas. METHODS: Open, prospective survey carried out in a tertiary care hospital in Mumbai. MATERIALS AND METHODS: Eighty-six patients with primary pyoderma, visiting the dermatology outpatient, were studied clinically and microbiologically. Sensitivity testing was done for vancomycin, sisomycin, gentamicin, framycetin, erythromycin, methicillin, cefazolin, cefuroxime, penicillin G and ciprofloxacin. Phage typing was done for MRSA positive strains. RESULTS: The culture positivity rate was 83.7%. Staphylococcus aureus was isolated in all cases except two. Barring one, all strains of Staphylococcus were sensitive to methicillin. CONCLUSIONS: Methicillin resistance is uncommon in community-acquired primary pyodermas in Mumbai. Treatment with antibacterials active against MRSA is probably unwarranted for community-acquired primary pyodermas.

Antimicrobial activities of seven novel tetramethylpiperidine-substituted phenazines against multiple-drug-resistant Gram-positive bacteria.

BACKGROUND: A dramatic increase in multiple-drug-resistant (MDR) Gram-positive pathogens has occurred in recent times, leading to increased rates or morbidity and mortality and also associated with high costs for the treatment of these infections. It is clear that there is an urgent need for the development of effective antimicrobial agents. The anti-bacterial activity of seven 2,2,6,6-tetramethylpiperidine (TMP)-substituted phenazines, compared to clofazimine (B663), were tested against 70 clinical isolates of methicillin-resistant Staphylococcus aureus, MDR Streptococcus pneumoniae and resistant Enterococcus sp. METHODS: Standard minimum inhibitory concentration agar dilution susceptibility tests were done on all isolates, including ATCC control strains. RESULTS: All the TMP-substituted phenazines were more active than clofazimine against all isolates tested. Compound B4125 was the most active by inhibiting all growth of the organisms tested, including vancomycin-resistant Enterococcus faecium. CONCLUSION: Clofazimine has been shown to have anti-staphylococcal activity. We demonstrate enhanced anti-bacterial activity of TMP-substituted phenazines against drug-resistant Gram-positive organisms compared to clofazimine.

Anti-staphylococcal activity and mode of action of clofazimine.

OBJECTIVES: Infections caused by Staphylococcus aureus might be treated with agents whose primary indications are for other infections. Clofazimine, an established anti-mycobacterial drug, could be such a candidate. However, the anti-staphylococcal properties of clofazimine have not been fully described and its mode of action, possibly involving inhibition of both RNA polymerase and a membrane-located target, has not been explored in detail. We have now conducted experiments to address these issues. METHODS: Using established procedures, we examined the activity of clofazimine against a range of clinical isolates of S. aureus and determined whether it was bactericidal, exhibited a post-antibiotic effect (PAE), or interacted synergically with other agents. The potential for emergence of clofazimine-resistant mutants was also examined. Mode of action studies involved macromolecular synthesis assays, cross-screening against rifampicin-resistant mutants, susceptibility of RNA polymerase to clofazimine in vitro and several methods to detect drug-induced membrane damage. RESULTS: Clofazimine demonstrated good anti-staphylococcal activity encompassing MSSA, MRSA and GISA. It was bactericidal and resistant mutants could not be isolated. Clofazimine did not exhibit a PAE and failed to act synergically with other drugs. No evidence for specific inhibition of RNA polymerase was obtained. Clofazimine caused non-specific inhibition of DNA, RNA and protein synthesis, consistent with membrane-damaging activity that was detected in three independent assays for membrane disrupting agents. CONCLUSIONS: Clofazimine is a potent anti-staphylococcal agent. It appears to be a membrane-disrupting agent and does not inhibit RNA polymerase.

Synergy in a medicinal plant: antimicrobial action of berberine potentiated by 5'-methoxyhydnocarpin, a multidrug pump inhibitor.

Multidrug resistance pumps (MDRs) protect microbial cells from both synthetic and natural antimicrobials. Amphipathic cations are preferred substrates of MDRs. Berberine alkaloids, which are cationic antimicrobials produced by a variety of plants, are readily extruded by MDRs. Several Berberis medicinal plants producing berberine were found also to synthesize an inhibitor of the NorA MDR pump of a human pathogen Staphylococcus aureus. The inhibitor was identified as 5'-methoxyhydnocarpin (5'-MHC), previously reported as a minor component of chaulmoogra oil, a traditional therapy for leprosy. 5'-MHC is an amphipathic weak acid and is distinctly different from the cationic substrates of NorA. 5'-MHC had no antimicrobial activity alone but strongly potentiated the action of berberine and other NorA substrates against S. aureus. MDR-dependent efflux of ethidium bromide and berberine from S. aureus cells was completely inhibited by 5'-MHC. The level of accumulation of berberine in the cells was increased strongly in the presence of 5'-MHC, indicating that this plant compound effectively disabled the bacterial resistance mechanism against the berberine antimicrobial.

[Nature and sensitivity of bacteria superinfecting plantar ulcers caused by leprosy at the Marchoux Institute, Bamako, Mali]. / Nature et sensibilité des bactéries surinfectant les maux perforants plantaires d'origine lépreuse à l'Institut Marchoux, Bamako, Mali.

To determine potential usefulness of antimicrobial agents and to guide their prescription in the treatment of leprosy plantar ulcers, we conducted an in vitro study about germs' nature and sensitivity to antibiotics. We took samples of plantar ulcers secretion from 107 patients at Marchoux Institute. 92.5% of those ulcers were infected. These samples revealed 145 strains of micro-organisms among those, Staphylococcus aureus (70 strains) and genus Pseudomonas (41 strains) were the most frequent. These bacteria were resistant to several antibiotics currently used at Marchoux Institute (tetracycline, penicillin, cotrimoxazol and erythromicin). Antibiotics, efficient at 80% on tested strains, were expensive for patients. They cannot be recommended for the treatment of local infections. These results outline that the main treatment in plantar ulcers is based upon antiseptic solutions and keeping feet at rest. Antibiotherapy in case of extension of local infection would be based on the results of a previous study of sensitivity.

Effect of anti-leprosy drugs on superoxide anion production by rat peritoneal macrophage with special reference to light exposed clofazimine.

The present study describes the in vitro effect of anti-leprosy drugs on superoxide anion (O2-) production by rat resident peritoneal macrophages. Of the three drugs tested i.e. clofazimine, rifampicin and dapsone, the first was most effective in increasing O2- production in a dose dependent manner, while rifampicin had some stimulatory effect and dapsone exhibited minimal action. Furthermore, when clofazimine and dapsone were added together it was observed that the increase of O2- production by macrophages due to clofazimine was not significantly altered by the addition of dapsone. Moreover, it was found that killed Mycobacterium leprae could induce a lesser amount of O2- production in comparison to that of Staphylococcus aureus and the enhancement of O2- release due to clofazimine was stimulus dependent. This increase of O2- release after addition of clofazimine was inhibited by the addition of p-bromophenacyl bromide. Another interesting finding was that the enhancement of O2- production by clofazimine gradually decreased as clofazimine was exposed to light for days. On further investigation it was found that ultraviolet, NMR, infrared and mass spectra of the light unexposed and exposed drug were similar, but the diffusion current of the polarogram of light exposed drug was remarkably more than that observed in light unexposed drug, indicating, thereby, a possible increase in the electron accepting capacity of the light reacted molecule. As far as we know this is the first report describing the effect of light exposed clofazimine on the respiratory burst activity of macrophages.