Microbial Biosynthesis and Applications of Gentamicin: A Critical Appraisal

Structural insights into thesubstrate binding sites of O-carbamoyltransferase VtdB from Streptomyces sp. NO1W98

The O-carbamoyltransferase VtdB catalyzes the carbamoylation of venturicidin B, which is essential for the biosynthesis of the antibiotic venturicidin A. Here, the crystal structures of VtdB and VtdB in complex with the intermediate carbamoyladenylate (VtdB^CAO) were determined at resolutions of 2.99 Å and 2.90 Å, respectively. The structures resemble the conserved YrdC-like and specific Kae1-like domains. A magnesium ion and the intermediate carbamoyladenylate were also observed in the Kae1-like domain of VtdB. The structure of VtdB^CAO in complex with the substrate venturicidin B was modeled by a molecular docking method to better understand the substrate binding mode, revealing a novel venturicidin B binding pocket.

An Efficient High-Throughput Screening of High Gentamicin-Producing Mutants Based on Titer Determination Using an Integrated Computer-Aided Vision Technology and Machine Learning

The "design-build-test-learn" (DBTL) cycle has been adopted in rational high-throughput screening to obtain high-yield industrial strains. However, the mismatch between build and test slows the DBTL cycle due to the lack of high-throughput analytical technologies. In this study, a highly efficient, accurate, and noninvasive detection method of gentamicin (GM) was developed, which can provide timely feedback for the high-throughput screening of high-yield strains. First, a self-made tool was established to obtain data sets in 24-well plates based on the color of the cells. Subsequently, the random forest (RF) algorithm was found to have the highest prediction accuracy with an R² value of 0.98430 for the same batch. Finally, a stable genetically high-yield strain (998 U/mL) was successfully screened out from 3005 mutants, which was verified to improve the titer by 72.7% in a 5 L bioreactor. Moreover, the verified new data sets were updated on the model database in order to improve the learning ability of the DBTL cycle.

Transrectal ultrasound-guided seminal vesicle catheterization with continuous antibiotic infusion for the treatment of refractory hematospermia

The aim of the present study was to describe transrectal ultrasound (TRUS)-guided seminal vesicle catheterizations with continuous antibiotic infusion in patients with persistent hematospermia. A retrospective record review of 45 patients with refractory hematospermia treated with TRUS-guided seminal vesicle catheterization between 2010 and 2017 was performed. Seminal vesicle puncture and catheterization was performed under TRUS guidance for all patients. Antibiotic irrigation was used to rinse the seminal vesicle until the outflow fluid was clear. The trocar sleeve was left in situ and fixed on the skin of the perineum at the end of the procedure. All patients underwent a 24-h continuous infusion of antibiotic solution through the catheter. The patients were followed up to 3 years for the presence of hematospermia. The duration of refractory hematospermia was between 6 months and 9 years. A total of 14 patients exhibited consecutive hematospermia, while the remaining patients exhibited intermittent episodes. On TRUS, 15 cases of ejaculatory duct cyst, 7 cases of ejaculatory duct expansion, 3 cases of ejaculatory duct stones, 6 cases of seminal vesicle expansion, 8 cases of seminal vesicle stones and 5 cases of seminal vesicle wall or ejaculation wall calcification were diagnosed. A total of 41 patients completed the scheduled treatment plan; however, the catheter was dissociated on the 3rd or 4th day of catheterization in 4 patients. After a 1-3 year follow-up, hematospermia was not observed in 42 patients (93.33%) with recurrence in the remaining 3 patients. In conclusion, TRUS-guided seminal vesicle catheterization with continuous antibiotic infusion appeared to be a safe and effective method for the treatment of hematospermia.

Antibiotic Resistance of Escherichia coli from Humans and Black Rhinoceroses in Kenya

Upsurge of antibiotic resistance in wildlife poses unprecedented threat to wildlife conservation. Surveillance of antibiotic resistance at the human-wildlife interface is therefore needed. We evaluated differences in antibiotic resistance of Escherichia coli isolates from human and the endangered black rhinoceros in Lambwe Valley, Kenya. We used standard microbiological techniques to carry out susceptibility assays using eight antibiotics of clinical and veterinary importance. Standard PCR method was used to characterize antibiotic resistance genes. There was no difference in resistance between E. coli isolates from human and those from rhinoceros (U = 25, p = 0.462). However, higher resistance in isolates from humans was noted for cotrimoxazole (p = 0.000, OR = 0.101), ceftriaxone (p = 0.005, OR = 0.113) and amoxicillin/clavulanic acid (p = 0.017, OR = 0.258), whereas isolates from rhinoceros showed higher gentamicin resistance (p = 0.001, OR = 10.154). Multi-drug resistance phenotype was 69.0% in humans and 43.3% in rhinoceros. Isolates from both species contained bla_TEM, tetA, tetB, dfrA1 and sul1 genes. Resistance profiles in the two species suggest potential for cross-transfer of resistance genes or exposure to comparable selective pressure and call for a multi-sectorial action plan on surveillance of antibiotic resistance at the human-wildlife interface. Genome-wide studies are needed to explicate the direction of transfer of genes that confer antibiotic resistance at the human-wildlife interface.

Dioclea violacea lectin modulates the gentamicin activity against multi-resistant strains and induces nefroprotection during antibiotic exposure

Gentamicin is an aminoglycoside antibiotic used to treat infections of various origins. In the last few decades, the constant use of gentamicin has resulted in increased bacterial resistance and nephrotoxicity in some cases. In this study, we examined the ability of Dioclea violacea lectin (DVL) in modulate the antimicrobial activity of gentamicin and reduce the nephrotoxicity induced by this drug. The minimum inhibitory concentration (MIC) obtained for DVL against all strains studied was not clinically relevant (MIC ≥ 1024 μg/mL). However, when DVL was combined with gentamicin, a significant increase in antibiotic action was observed against Staphylococcus aureus and Escherichia coli. DVL also reduced antibiotic tolerance in S. aureus during 10 days of continuous treatment. In addition, DVL presented a nephroprotective effect, reducing sodium excretion, N-Gal expression and urinary protein, that are important markers of glomerular and tubular injuries. Taken together, studies of inhibition of hemagglutinating activity, fluorescence spectroscopy and molecular docking revealed that gentamicin can interact with DVL via the carbohydrate recognition domain (CRD), suggesting that the results obtained in this study may be directly related to the interaction of DVL-gentamicin and with the ability of the lectin to interact with glycans present in the cells of the peritoneum.

Synergistic Activity of Fosfomycin, Ciprofloxacin, and Gentamicin Against Escherichia coli and Pseudomonas aeruginosa Biofilms

Gram-negative (GN) rods cause about 10% periprosthetic joint infection (PJI) and represent an increasing challenge due to emergence of antimicrobial resistance. Escherichia coli and Pseudomonas aeruginosa are among the most common cause of GN-PJI and ciprofloxacin is the first-line antibiotic. Due to emergence of fluoroquinolone resistance, we evaluated in vitro the activity of fosfomycin, ciprofloxacin, and gentamicin, alone and in combinations, against E. coli and P. aeruginosa biofilms. Conventional microbiological tests and isothermal microcalorimetry were applied to investigate the anti-biofilm activity of the selected antibiotics against standard laboratory strains as well as clinical strains isolated from patients with prosthetic joint associated infections. The biofilm susceptibility to each antibiotic varied widely among strains, while fosfomycin presented a poor anti-biofilm activity against P. aeruginosa. Synergism of two-pair antibiotic combinations was observed against different clinical strains from both species. Highest synergism was found for the fosfomycin/gentamicin combination against the biofilm of E. coli strains (75%), including a gentamicin-resistant but fosfomycin-susceptible strain, whereas the gentamicin/ciprofloxacin combination presented synergism with higher frequency against the biofilm of P. aeruginosa strains (71.4%). A hypothetical bacteriolysis effect of gentamicin could explain why combinations with this antibiotic seem to be particularly effective. Still, the underlying mechanism of the synergistic effect on biofilms is unknown. In conclusion, combinatorial antibiotic application has shown to be more effective against biofilms compared to monotherapy. Further in vivo and clinical studies are essential to define the potential treatment regimen based on our results.

Evaluation of the clinical use of the ETN PROtect® in non-union therapy

INTRODUCTION

Non-union of a long bone fracture remains a challenge in orthopaedic and trauma surgery. In the current study, we sought to determine the clinical effectiveness of tibial non-union treatment utilizing an antibiotic-coated intramedullary nail (Expert Tibia Nail (ETN) PROtect®) regarding prevention and treatment of infection and the clinical outcome.

PATIENTS AND METHODS

36 patients suffering from tibial non-unions that were treated with the ETN PROtect® in the course of non-union treatment between February 2010 and March 2015 were included in this clinical observational study. Clinical and radiological examinations were performed preoperatively as well as 4, 6 and 12 weeks and 6 and 12 months postoperatively as part of a standardized follow-up program. Data regarding perioperative complications, weight-bearing capacity, radiological signs of consolidation and subjective health status were assessed at each time point. Laboratory parameters such as C-reactive protein (CRP) and leukocyte count were collected preoperatively in order to assess the patients' risk profile for infection.

RESULTS

Patients had an average of 6.2 previous surgeries and 22 patients (61.1%) had a positive bacterial culture from intraoperatively removed tissue during the first operative treatment. 29 patients (80.6%) achieved full weight-bearing after an average of 7.7 months, furthermore 80.6% of patients achieved osseous consolidation. 3 deep infections occurred, including one amputation. Subjective health status increase based on the SF-12 questionnaire during our follow-up program.

CONCLUSION

The results from the current study indicate that the use of the ETN PROtect® in the applied non-union therapy has a high clinical effectiveness regarding osseous consolidation and time to weight bearing. In addition, the use of gentamicin-coated nails in the treatment of tibial non-unions might contribute to both successful treatment of the underlying infection and prevention of perioperative infection. The gentamicin-coated nail may serve as a beneficial adjunct treatment in the applied non-union therapy in addition to all established techniques in the treatment of infected non-unions.

Overproduction of gentamicin B in industrial strain Micromonospora echinospora CCTCC M 2018898 by cloning of the missing genes genR and genS

In pharmaceutical industry, isepamicin is mainly manufactured from gentamicin B, which is produced by Micromonospora echinospora as a minor component of the gentamicin complex. Improvement of gentamicin B production through metabolic engineering is therefore important to satisfy the increasing demand for isepamicin. We hypothesized that gentamicin B was generated from gentamicin JI-20A via deamination of the C2’ amino group. Using kanJ and kanK as the gene probes, we identified the putative deamination-related genes, genR and genS, through genome mining of the gentamicin B producing strain M. echinospora CCTCC M 2018898. Interestingly, genR and genS constitute a gene cassette located approximately 28.7 kb away from the gentamicin gene cluster. Gene knockout of genR and genS almost abolished the production of gentamicin B in the mutant strain, suggesting that these two genes, which are responsible for the last steps in gentamicin B biosynthesis, constitute the missing part of the known gentamicin biosynthetic pathway. Based on these finding, we successfully constructed a gentamicin B high-yielding strain (798 mg/L), in which an overexpression cassette of genR and genS was introduced. Our work fills the missing piece to solve the puzzle of gentamicin B biosynthesis and may inspire future metabolic engineering efforts to generate gentamycin B high-yielding strains that could eventually satisfy the need for industrial manufacturing of isepamicin.

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Two missing genes in the biosynthetic pathway of gentamicin B were found.

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CRISPR/Cas9 was applied successfully to delete genes in Micromonospora echinospora.

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Overexpression of genR/S cassette improved gentamicin B titer by 64% in current industrial strain.

Antimicrobial discovery from natural and unusual sources

OBJECTIVES

Whether vertebrates/invertebrates living in polluted environments are an additional source of antimicrobials.

KEY FINDINGS

Majority of antimicrobials have been discovered from prokaryotes and those which are of eukaryotic origin are derived mainly from fungal and plant sources. With this in mind, it is important to note that pests, such as cockroaches come across pathogenic bacteria routinely, yet thrive in polluted environments. Other animals, such as snakes thrive from feeding on germ-infested rodents. Logically, such species must have developed an approach to protect themselves from these pathogens, yet they have largely been ignored as a potential source of antimicrobials despite their remarkable capability to fight disease-causing organisms.

SUMMARY

Animals living in polluted environments are an underutilized source for potential antimicrobials, hence it is believed that several novel bioactive molecule(s) will be identified from these sources to counter increasingly resistant bacterial infections. Further research will be necessary in the development of novel antimicrobial(s) from these unusual sources which will have huge clinical impact worldwide.

Draft Genome Sequence of Micromonospora sp. Strain WMMA1996, a Marine Sponge-Associated Bacterium

Micromonospora sp. strain WMMA1996 was isolated in 2013 off the coast of the Florida Keys, United States, from a marine sponge as part of bacterial coculture-based drug discovery initiatives. Analysis of the ∼6.44-Mb genome reveals this microbe’s potential role in the discovery of new drugs.

Biosynthetic pathways of aminoglycosides and their engineering

Despite decades long clinical usage, aminoglycosides still remain a valuable pharmaceutical source for fighting Gram-negative bacterial pathogens, and their newly identified bioactivities are also renewing interest in this old class of antibiotics. As Nature's gift, some aminoglycosides possess natural defensive structural elements that can circumvent drug resistance mechanisms. Thus, a detailed understanding of aminoglycoside biosynthesis will enable us to apply Nature's biosynthetic strategy towards expanding structural diversity in order to produce novel and more robust aminoglycoside analogs. The engineered biosynthesis of novel aminoglycosides is required not only to develop effective therapeutics against the emerging 'superbugs' but also to reinvigorate antibiotic lead discovery in readiness for the emerging post-antibiotic era.

The impact of storage conditions upon gentamicin coated antimicrobial implants

A systematic approach was developed to investigate the stability of gentamicin sulfate (GS) and GS/poly (lactic-co-glycolic acid) (PLGA) coatings on hydroxyapatite surfaces. The influence of environmental factors (light, humidity, oxidation and heat) upon degradation of the drug in the coatings was investigated using liquid chromatography with evaporative light scattering detection and mass spectrometry. GS coated rods were found to be stable across the range of environments assessed, with only an oxidizing atmosphere resulting in significant changes to the gentamicin composition. In contrast, rods coated with GS/PLGA were more sensitive to storage conditions with compositional changes being detected after storage at 60 °C, 75% relative humidity or exposure to light. The effect of γ-irradiation on the coated rods was also investigated and found to have no significant effect. Finally, liquid chromatography-mass spectrometry analysis revealed that known gentamines C1, C1a and C2 were the major degradants formed. Forced degradation of gentamicin coatings did not produce any unexpected degradants or impurities.

Patients' safety: is there a systemic release of gentamicin by gentamicin-coated tibia nails in clinical use?

INTRODUCTION

Osteitis is one of the most serious complications in orthopedic surgery. Expert Tibia Nail (ETN) PROtect™ coated with a biodegradable layer of gentamicin-laden polymer was developed for prophylaxis of osteomyelitis. In systemic administration, gentamicin has only a small therapeutic index and serious side effects; it is potentially nephrotoxic as well as ototoxic. It is not yet known if relevant gentamicin concentrations are released into the systemic circulation after implantation of gentamicin-coated nails. In order to evaluate the patients' risks profiles and increase patient safety, we measured gentamicin levels in pre- and postoperative serum samples of patients undergoing implantation of ETN PROtect.

METHODS

Twenty-five patients who received ETN PROtect between March 2012 and August 2014 were included in this study. Collection of blood samples occurred before the operation, at weeks 1-4, 3 and 6 months, and up to 1 year after the implantation. Measurement of gentamicin levels in serum samples was performed at the central laboratory of Heidelberg University Hospital. Additionally, laboratory parameters, C-reactive protein, leukocyte number, urea and creatinine concentrations were analyzed in routine controls before and after operating and assessed for systemic side effects.

RESULTS

Over the course of this prospective observational study, we were able to determine that gentamicin-coated nails do not release gentamicin into the systemic circulation above the lowest detectable level of 0.2 mg/dL. There were slight increases in the mean inflammation and renal retention markers, but no gentamicin-associated side effects could be linked to implantation. Furthermore, no allergic reactions could be detected during our study.

CONCLUSION

Our findings suggest that there is no relevant release of gentamicin into the systemic circulation causing a systemic effect, and serious side effects due to gentamicin-coated tibia nails should not be feared. Postoperative monitoring of renal function does not seem necessary because of the implantation of ETN PROtect.

Antibacterial Discovery and Development: From Gene to Product and Back

Concern over the reports of antibiotic-resistant bacterial infections in hospitals and in the community has been publicized in the media, accompanied by comments on the risk that we may soon run out of antibiotics as a way to control infectious disease. Infections caused by Enterococcus faecium, Staphylococcus aureus, Klebsiella species, Clostridium difficile, Acinetobacter baumannii, Pseudomonas aeruginosa, Escherichia coli, and other Enterobacteriaceae species represent a major public health burden. Despite the pharmaceutical sector's lack of interest in the topic in the last decade, microbial natural products continue to represent one of the most interesting sources for discovering and developing novel antibacterials. Research in microbial natural product screening and development is currently benefiting from progress that has been made in other related fields (microbial ecology, analytical chemistry, genomics, molecular biology, and synthetic biology). In this paper, we review how novel and classical approaches can be integrated in the current processes for microbial product screening, fermentation, and strain improvement.

Gentamicin-impregnated collagen sponge for preventing sternal wound infection after cardiac surgery

The frequency of sternal wound infection (SWI) after cardiac surgery ranges from 0.5% to 8% and is associated with significant morbidity, mortality, and treatment cost. Perioperative antibiotic prophylaxis is not sufficient to fully prevent the contamination of the surgical access site. One of the most effective methods for the prevention of wound infection seems to be the use of gentamicin-impregnated collagen sponge, which is successfully used in abdominal and orthopedic surgery. Surgically implantable topical antibiotics can reduce wound infection in cardiac patients as well, but the efficacy of SWI prevention in cardiac surgery still raises many questions.

Histone deacetylase inhibitor, sodium butyrate, attenuates gentamicin-induced nephrotoxicity by increasing prohibitin protein expression in rats

The major purpose in our study was to investigate the effects of sodium butyrate (NaBu) on nephrotoxicity induced by gentamicin in rats and determine further whether the protective effect is mediated by modulation of prohibitin protein expression. Gentamicin was injected intraperitoneally (100 mg/kg body weight) once daily for 8 days to induce nephrotoxicity. The effect of acute and chronic treatment of sodium butyrate on nephrotoxicity induced by gentamicin was assessed. Various doses of sodium butyrate (50, 100, 200 mg/kg, i.p.) was administered 30 min prior to the daily gentamicin injection. Histological analysis was used to evaluate the lesions in kidney after gentamicin administration. Expression of prohibitin was evaluated with immunohistochemical and western blot analysis. The present study demonstrated that gentamicin treatment for 8 consecutive days significantly increased in the levels of blood urea nitrogen, creatinine, kidney injury molecule (KIM-1) and neutrophil gelatinase-associated lipocalin (NGAL) which indicated nephrotoxicity induced by gentamicin. In addition, chronic treatment with NaBu significantly attenuated gentamicin-induced nephrotoxicity by increasing activities of superoxide dismutase, catalase and reduced glutathione. Immunohistochemical studies in gentamicin-induced rats also demonstrated an increase in the levels of inducible prohibitin after treatment with sodium butyrate. Our results indicated that sodium butyrate, a histone deacetylase inhibitor, decreased gentamicin-induced nephrotoxicity by enhancing renal antioxidant enzymes activity and the expression of prohibitin protein.