Improved EGFR mutation detection using combined exosomal RNA and circulating tumor DNA in NSCLC patient plasma

First-in-human study of LY3039478, an Oral Notch signaling inhibitor in advanced or metastatic cancer

Abstract

Background

Deregulated Notch signaling due to mutation or overexpression of ligands and/or receptors is implicated in various human malignancies. Gamma-secretase inhibitors inhibit Notch signaling by preventing cleavage of transmembrane domain of Notch protein. LY3039478 is a novel, potent Notch inhibitor decreases Notch signaling and its downstream biologic effects. In this first-in-human study, we report the safety, pharmacokinetic (PK) profile, pharmacodynamic effects, and antitumor activity of LY3039478 in patients with advanced or metastatic cancer.

Methods

This phase I, open-label, multicenter, nonrandomized, and dose-escalation phase study determined and confirmed the recommended phase II dose of LY3039478 (oral dose: 2.5–100 mg, TIW on a 28-day cycle). The primary objectives are to determine (part A) and confirm (part B) a recommended phase II dose that may be safely administered to patients with advanced or metastatic cancer, and secondary objectives include evaluation of safety, tolerability, PK parameters, and preliminary antitumor activity of LY3039478.

Results

A total of 110 patients were treated with LY3039478 monotherapy between 31 October 2012 and 15 July 2016. Dose-limiting toxicities were thrombocytopenia, colitis and nausea. Most adverse events were gastrointestinal. The recommended phase II dose was 50 mg TIW, because of its better tolerability compared to 75 mg. The pharmacokinetics of LY3039478 appeared dose proportional. Pharmacodynamic data indicate an approximately 80% inhibition of plasma Aβ, and >50% inhibition of Notch-regulated genes hairy and enhancer of split-1, cyclin D1 and Notch-regulated ankyrin repeat at 45-to 100-mg dose. Clinical activity (tumor necrosis, metabolic response or tumor shrinkage) was observed in patients with breast cancer, leiomyosarcoma, and adenoid cystic carcinoma.

Conclusion

Potent inhibition of Notch signaling by LY3039478 was well tolerated at doses associated with target engagement, and demonstrated evidence of clinical activity in heavily pretreated patients. Further investigation with LY3039478 as monotherapy and in combination with targeted agent or chemotherapy is ongoing.

Clinicaltrials.gov ID

NCT01695005

Venetoclax, bendamustine, and rituximab in patients with relapsed or refractory NHL: a phase 1b dose-finding study

Abstract

Background

Venetoclax is a selective, potent inhibitor of the anti-apoptotic BCL-2 protein approved for treatment of chronic lymphocytic leukemia. We conducted a dose-finding study of venetoclax in combination with bendamustine-rituximab (BR) in patients with relapsed/refractory non-Hodgkin's lymphoma (NHL).

Patients and methods

BR was given for 6 cycles at standard doses. Intermittent and continuous oral venetoclax administration was explored at 50mg–1200mg daily doses. Co-primary objectives included safety, pharmacokinetics, maximum tolerated dose (MTD), and recommended phase 2 dose (RP2D); secondary objective was preliminary efficacy.

Results

Sixty patients were enrolled: 32 with follicular lymphoma (FL), 22 with diffuse large B-cell lymphoma (DLBCL), and 6 with marginal zone lymphoma (MZL). Nausea (70%), neutropenia (68%), diarrhea (55%), and thrombocytopenia (52%) were the most frequent adverse events (AEs). Most common grade 3/4 AEs were neutropenia (60%) and lymphopenia (38%). Serious AEs were reported in 24 patients; the most frequent were febrile neutropenia and disease progression (8% each). Five patients died from either disease progression (n = 4) or respiratory failure (n = 1). MTD was not reached; RP2D for venetoclax-BR combination was established as 800 mg daily continuously. Venetoclax pharmacokinetic exposure with and without BR was comparable. For all patients, overall response rate (ORR) was 65%. Median duration of overall response (DOR), overall survival (OS), and progression-free survival (PFS) was 38.3 months (95% confidence interval (CI): 10.4–NR), not yet reached, and 10.7 months (95% CI: 4.3–21.0), respectively.

Conclusions

This study established the safety profile of venetoclax in combination with BR, and results demonstrated tolerability and preliminary efficacy of the combination. Additional follow-up is needed to better determine the future role of BR plus venetoclax in the treatment of relapsed/refractory B-cell NHL.

Toxicity of oxaliplatin rechallenge in metastatic colorectal cancer

Phase 3, randomised trial of avelumab versus physician’s choice of chemotherapy as third-line treatment for patients with advanced gastric or gastro-oesophageal junction cancer: primary analysis of JAVELIN Gastric 300

Abstract

Background

There currently are no internationally recognised treatment guidelines for patients with advanced gastric cancer/gastro-oesophageal junction cancer (GC/GEJC) in whom two prior lines of therapy have failed. The randomised, phase 3 JAVELIN Gastric 300 trial compared avelumab vs physician's choice of chemotherapy as third-line therapy in patients with advanced GC/GEJC.

Patients and methods

Patients with unresectable, recurrent, locally advanced, or metastatic GC/GEJC were recruited at 147 sites globally. All patients were randomised to receive either avelumab 10 mg/kg by intravenous infusion every 2 weeks or physician's choice of chemotherapy (paclitaxel 80 mg/m² on days 1, 8, and 15 or irinotecan 150 mg/m² on days 1 and 15, each of a 4-week treatment cycle); patients ineligible for chemotherapy received best supportive care. The primary endpoint was overall survival (OS). Secondary endpoints included progression-free survival (PFS), objective response rate (ORR), and safety.

Results

A total of 371 patients were randomised. The trial did not meet its primary endpoint of improving OS (median, 4.6 vs 5.0 months; hazard ratio [HR] = 1.1 [95% CI 0.9–1.4]; P = 0.81) or the secondary endpoints of PFS (median, 1.4 vs 2.7 months; HR = 1.73 [95% CI 1.4–2.2]; P > 0.99) or ORR (2.2% vs 4.3%) in the avelumab vs chemotherapy arms, respectively. Treatment-related adverse events (TRAEs) of any grade occurred in 90 patients (48.9%) and 131 patients (74.0%) in the avelumab and chemotherapy arms, respectively. Grade ≥3 TRAEs occurred in 17 patients (9.2%) in the avelumab arm and in 56 patients (31.6%) in the chemotherapy arm.

Conclusions

Treatment of patients with GC/GEJC with single-agent avelumab in the third-line setting did not result in an improvement in OS or PFS compared to chemotherapy. Avelumab showed a more manageable safety profile than chemotherapy.

Trial registration

ClinicalTrials.gov: NCT02625623

Taking responsibility for health in an epistemically polluted environment

Abstract

Proposals for regulating or nudging healthy choices are controversial. Opponents often argue that individuals should take responsibility for their own health, rather than be paternalistically manipulated for their own good. In this paper, I argue that people can take responsibility for their own health only if they satisfy certain epistemic conditions, but we live in an epistemic environment in which these conditions are not satisfied. Satisfying the epistemic conditions for taking responsibility, I argue, requires regulation of this environment. I describe some proposals for such regulation and show that we cannot reject all regulation in the name of individual responsibility. We must either regulate individuals' healthy choices or regulate the epistemic environment.

Combined OCT distance and FBG force sensing cannulation needle for retinal vein cannulation: in vivo animal validation

Abstract

Purpose

Retinal vein cannulation is an experimental procedure during which a clot-dissolving drug is injected into an obstructed retinal vein. However, due to the fragility and minute size of retinal veins, such procedure is considered too risky to perform manually. With the aid of surgical robots, key limiting factors such as: unwanted eye rotations, hand tremor and instrument immobilization can be tackled. However, local instrument anatomy distance and force estimation remain unresolved issues. A reliable, real-time local interaction estimation between instrument tip and the retina could be a solution. This paper reports on the development of a combined force and distance sensing cannulation needle, and its experimental validation during in vivo animal trials.

Methods

Two prototypes are reported, relying on force and distance measurements based on FBG and OCT A-scan fibres, respectively. Both instruments provide an 80  \(\upmu \hbox {m}\) needle tip and have outer shaft diameters of 0.6 and 2.3 mm, respectively.

Results

Both prototypes were characterized and experimentally validated ex vivo. Then, paired with a previously developed surgical robot, in vivo experimental validation was performed. The first prototype successfully demonstrated the feasibility of using a combined force and distance sensing instrument in an in vivo setting.

Conclusion

The results demonstrate the feasibility of deploying a combined sensing instrument in an in vivo setting. The performed study provides a foundation for further work on real-time local modelling of the surgical scene. This paper provides initial insights; however, additional processing remains necessary.

Inter-institutional variations regarding Barrett’s esophagus diagnosis

Abstract

Background

Barrett's esophagus (BE) is a known precursor for development of esophageal adenocarcinoma and surveillance of affected patients is necessary when cancer progression risk is considered to be high. However, the accuracy of BE diagnosis may not be homogenous among institutions with endoscopy units. We investigated inter-institutional variability by examining the accuracy of endoscopic diagnosis of BE at 4 different hospitals.

Methods

The accuracy of BE diagnosis at the 4 hospitals was retrospectively reviewed by 6 expert endoscopists, who independently reviewed endoscopic images of approximately 500 consecutive patients examined at each hospital without information regarding the diagnosis by the on-site endoscopists. When the expert reviewers made different diagnosis, a final diagnosis was made by consensus. That was then compared with the diagnosis of the attending endoscopists at each hospital and their concordance was calculated separately for each endoscopy unit. In addition, the relationship between diagnostic accuracy and endoscopic experience was assessed.

Results

The prevalence of BE diagnosis by the on-site endoscopists was not homogenous and varied widely (17.2–96.8%). In 1 hospital, over-diagnosis was the cause of dissimilarity, while under-diagnosis was the cause in two hospitals. Diagnostic accuracy by the attending endoscopists in all 4 hospitals ranged from 44.6 to 83.1% (P < 0.05). There was no significant association between diagnostic accuracy and endoscopic experience or board licensing status of the on-site endoscopists.

Conclusion

Diagnostic accuracy for BE was not homogenous among 4 hospitals, and problems related to over- and under-diagnosis should be considered.

Observations on the Term Bhavaṅga as Described in the Jié tuō dào lùn (* Vimuttimagga ): Its Proper English Translation and Understanding

Abstract

The term bhavaṅga is regarded as a unique technical term of Theravāda abhidhamma tradition, and the text Jié tuō dào lùn, i.e. the Chinese translation of *Vimuttimagga, mentions yŏufēnxīn the Chinese counterpart of bhavaṅga eleven times. These occurrences are found in the section of the text on the cognitive process. The text is, however, too abstruse to understand the term easily, and the existing translations of it are imperfect. Subsequently, the term in the Jié tuō dào lùn has been considered and interpreted by former translations in the same way as it is in other Pāli abhidhamma texts. Indeed, the Jié tuō dào lùn has more than similar definitions for bhavaṅga. It is described as the inactive state of mind from which the active states of mind arise. On the other hand, there are also a number of small but significant differences in its description of bhavaṅga. It has no sub-states, and there are no technical terms for conditional relations with other states of mind. The similarities and differences found in the discussion of bhavaṅga shed light on some salient features of the Jié tuō dào lùn.

Characterization of multiple antibiotic resistant clinical strains of Staphylococcus isolated from pregnant women vagina

Abstract

Vagina which is one of the important reservoirs for Staphylococcus and in pregnant women pathogenic strains may infect the child during the birth or by vertical transmission. A total of 68 presumptive Staphylococcus strains isolated from human vagina were found to be gram-positive cocci, and only 32 (47%) isolates were found beta-hemolytic. Matrix-assisted laser desorption/ionization time-of-flight mass-spectrometry (MALDI-TOF MS) results confirmed 33 isolates belonged to Staphylococcus which consisting of 6 species, i.e., S. aureus (14), S. vitulinus (7), S. epidermidis (4), S cohnii (3), S. equorum (3), and S. succinus (2). Further, the result of antibiotic susceptibility tests showed that large proportions (76%–100%) of the isolates were resistant to multiple antibiotics and more often resistant to penicillin (100%), ampicillin (100%), oxacillin (97%), oxytetracycline (97%), vancomycin (97%), rifampin (85%), erythromycin (82%), and streptomycin (76%). In the present study, only the sec enterotoxin gene was detected in four S. aureus strains. DNA fingerprints of the 33 isolates that were generated using random amplified polymorphic DNA (RAPD) and enterobacterial repetitive intergenic consensus (ERIC) PCR analysis revealed great genetic relatedness of isolates. High prevalence of vaginal colonization with multiple antibiotic-resistant staphylococci among pregnant women was observed which were emerged from the single respective species clones that underwent evolution. The vertical transmission of these multiple antibiotic-resistant Staphylococcus species to the infant is possible; therefore, the findings of this study emphasize the need for regular surveillance of antibiotic-resistant bacterial strains in pregnant women in this area.

Small mammals as sentinels of antimicrobial-resistant staphylococci

Abstract

A total of 39 coagulase-negative staphylococci and seven Staphylococcus aureus strains were isolated from small mammal feces, i.e., the striped field mouse (Apodemus agrarius) and the yellow-necked mouse (A. flavicollis) in two sampling areas, deciduous forest and karst plains. MALDI-TOF analysis revealed five species of coagulase-negative staphylococci: S. sciuri, S. hominis, S. warneri, S. haemolyticus, and S. xylosus. All strains were susceptible to tetracycline, linezolid, vancomycin, and teicoplanin. Three MRSA strains with the mecA gene were detected. The beta-lactamase gene blaZ was detected in ampicillin-resistant staphylococci and in the high-level resistant strains (oxacillin over 2 mg/L) mecA gene. The mecC gene was not detected by PCR. Erythromycin-resistant staphylococci harbored the ermC gene and/or the efflux gene msrA. There were no detectable dfr genes in trimethoprim-resistant staphylococci and the rifampicin-resistant strains were without mutation in the rpoB gene. In summary, wild small mammals may serve as sentinels of mecA-positive S. aureus with erythromycin resistance genes ermC and efflux msrA. Small mammals appear to be useful indicators of antibiotic resistance.

Genotyping of Mycobacterium tuberculosis using whole genome sequencing

Abstract

Tuberculosis (TB) is considered one of the most serious infectious diseases worldwide. Effective control of tuberculosis infection involves multiple steps, such as reliable detection, treatment, an epidemiological control as a part of case management, and further surveillance and monitoring of TB spread in the human population. Due to the accelerating advances in molecular biology, especially in DNA sequencing, in the past decade, the application of these methods has become crucial for TB evolution studies, differentiation of Mycobacterium tuberculosis genotypes, and their distribution. Currently, several molecular genetic methods are available. The oldest typing methods (e.g., IS6110-RFLP, spoligotyping, and MIRU-VNTR) can discover the chain of transmission to the patient. Currently, whole genome sequencing facilitates is furthermore able to identify the source of infection, the transmission trays among individuals sharing the same isolate, as well as determination of the TB evolution and its resistance to antituberculotic agents. It is obvious that this technique will become a new gold standard in genotyping methods in tuberculosis molecular epidemiological studies. In this article, molecular genetic typing methods with a special focus on whole genome sequencing and data management are reviewed.

Difficulties in identifying the bacterial species from the genus Clostridium in a case of injury-related osteitis

Abstract

Most Clostridium species are part of saprophytic microflora in humans and animals; however, some are well-known human pathogens. We presented the challenges in identifying the Clostridium species isolated from a patient with an infected open dislocation of the proximal interphalangeal joint of the fourth digit of the right hand. The clinical materials were intraoperative samples collected from a patient diagnosed with an injury-related infection, with soft tissue loss and tendon sheath involvement. The available biochemical, molecular, and genetic techniques were used in identifying the isolated bacteria. The isolated bacterium was shown to have low biochemical activity; hence, it was not definitively identified via biochemical tests Api 20A or Rapid 32A. Vitek 2 and mass spectrometry methods were equally inconclusive. Clostridium tetani infection was strongly suspected based on the bacterium's morphology and the appearance of its colonies on solid media. It was only via the 16S rRNA sequencing method, which is non-routine and unavailable in most clinical laboratories, that this pathogen was excluded. Despite appropriate pre-laboratory procedures, which are critical for obtaining reliable test results, the routine methods of anaerobic bacterium identification are not always useful in diagnostics. Diagnostic difficulties occur in the case of environment-derived bacteria of low or not fully understood biological activity, which are absent from databases of automatic bacterial identification systems.

Virulence-associated genes and antibiotic susceptibility among vaginal and rectal Escherichia coli isolates from healthy pregnant women in Poland

Abstract

Vaginal and/or rectal Escherichia coli colonization of pregnant women is sometimes associated with neonatal infections. Despite the relevance of these strains, they have been rarely described before. Thus, the aim of this study was to compare vaginal (VEC) and rectal E. coli (REC) isolates in respect of antimicrobial susceptibility and the frequency of virulence-associated genes (VAGs). The antimicrobial susceptibility of 50 VEC and 50 REC isolates was performed by using the disc diffusion method, and VAGs were detected by PCR. There were no significant differences in the antimicrobial resistance between VEC and REC. Both VEC and REC isolates were mostly resistant to ticarcillin (36 and 30%) and ampicillin (36 and 22%). None of the tested isolates was positive for ESBL. Gene's fimH, fimA, sfa/foc, iutA, ibeA, hlyF, and neuC were detected, respectively, in 98, 92, 32, 28, 12, 8, and 2% of VEC and in 94, 72, 12, 34, 8, 10, and 8% of REC isolates. The co-occurrence of fimA/H and sfa/foc genes was significantly more prevalent among VEC isolates, in comparison to REC isolates. The study indicated that VEC and REC isolates are quite similar in terms of antimicrobial non-susceptibility and VAGs.

Isolation and identification of siderophores produced by cyanobacteria

Abstract

Cyanobacteria are one of the most successful and oldest forms of life that are present on Earth. They are prokaryotic photoautotrophic microorganisms that colonize so diverse environments as soil, seawater, and freshwater, but also stones, plants, or extreme habitats such as snow and ice as well as hot springs. This diversity in the type of environment they live in requires a successful adaptation to completely different conditions. For this reason, cyanobacteria form a wide range of different secondary metabolites. In particular, the cyanobacteria living in both freshwater and sea produce many metabolites that have biological activity. In this review, we focus on metabolites called siderophores, which are low molecular weight chemical compounds specifically binding iron ions. They have a relatively low molecular weight and are produced by bacteria and also by fungi. The main role of siderophores is to obtain iron from the environment and to create a soluble complex available to microbial cells. Siderophores play an important role in microbial ecology; for example, in agriculture they support the growth of many plants and increase their production by increasing the availability of Fe in plants. The aim of this review is to demonstrate the modern use of physico-chemical methods for the detection of siderophores in cyanobacteria and the use of these methods for the detection and characterization of the siderophore-producing microorganisms. Using high-performance liquid chromatography-mass spectrometry (LC-MS), it is possible not only to discover new chemical structures but also to identify potential interactions between microorganisms. Based on tandem mass spectrometry (MS/MS) analyses, previous siderophore knowledge can be used to interpret MS/MS data to examine both known and new siderophores.

The absence or presence of a lytic coliphage affects the response of Escherichia coli to heat, chlorine, or UV exposure

Abstract

Disinfection aims at maximal inactivation of target organisms and the sustainable suppression of their regrowth. Whereas many disinfection efforts achieve efficient inactivation when the effect is measured directly after treatment, there are questions about the sustainability of this effect. One aspect is that the treated bacteria might recover and regain the ability to grow. In an environmental context, another question is how amenable surviving bacteria are to predation by omnipresent bacteriophages. Provisional data suggested that bacteria when subjected to sublethal heat stress might develop a phage-resistant phenotype. The result made us wonder about the susceptibility to phage-mediated lysis for bacteria exposed to a gradient of chlorine and UV-LED disinfection strengths. Whereas bacteria exposed to low sublethal chlorine doses still underwent phage-mediated lysis, the critical chlorine Ct of 0.5 mg min/L eliminated this susceptibility and induced phage resistance in the cells that survived treatment. In the case of UV, even the smallest tested dose of 2.8 mJ/cm² abolished phage lysis leading to direct regrowth. Results suggest that bacteria surviving disinfection might have higher environmental survival chances directly after treatment compared to non-treated cells. A reason could possibly lie in their compromised metabolism that is essential for phage replication.

Antibiotic resistance profiles of coagulase-positive and coagulase-negative staphylococci from pit latrine fecal sludge in a peri-urban South African community

Abstract

The aim of this study was to assess pit latrine samples from a peri-urban community in KwaZulu-Natal (South Africa) for the presence of multidrug-resistant (MDR) Staphylococcus spp. Standard procedures were used to isolate Staphylococcus spp. from pit latrine fecal sludge samples, with confirmation at genus level by polymerase chain reaction (PCR). Sixty-eight randomly selected pit latrine Staphylococcus spp. isolates were further characterized by using established disk diffusion procedures. An average Staphylococcus spp. count of 2.1 × 10⁵ CFU per g fecal material was established using two randomly selected pit latrine samples. Of the 68-selected Staphylococcus spp. pit latrine isolates, 49% were identified as coagulase positive, 51% as coagulase negative and 65% (12 coagulase positive, 32 coagulase negative isolates) were categorized as MDR. The majority (66/68) of Staphylococcus spp. isolates displayed resistance to fusidic acid while only 5/68 isolates displayed resistance to chloramphenicol. The pit latrine samples analyzed in this study are a source of MDR Staphylococcus spp., highlighting the need for proper hygiene and sanitation regimes in rural communities using these facilities.

Autolytic hydrolases affect sexual and asexual development of Aspergillus nidulans

Abstract

Radial growth, asexual sporulation, and cleistothecia formation as well as extracellular chitinase and proteinase formation of Aspergillus nidulans were monitored in surface cultures in order to study the physiological role of extracellular hydrolase production in carbon-stressed cultures. We set up carbon-stressed and carbon-overfed experimental conditions by varying the starting glucose concentration within the range of 2.5 and 40 g/L. Glucose starvation induced radial growth and hydrolase production and enhanced the maturation of cleistothecia; meanwhile, glucose-rich conditions enhanced mycelial biomass, conidia, and cleistothecia production. Double deletion of chiB and engA (encoding an extracellular endochitinase and a β-1,3-endoglucanase, respectively) decreased conidia production under carbon-stressed conditions, suggesting that these autolytic hydrolases can support conidia formation by releasing nutrients from the cell wall polysaccharides of dead hyphae. Double deletion of prtA and pepJ (both genes encode extracellular proteases) reduced the number of cleistothecia even under carbon-rich conditions except in the presence of casamino acids, which supports the view that sexual development and amino acid metabolism are tightly connected to each other in this fungus.

Detection of Streptococcus pyogenes virulence genes in Streptococcus dysgalactiae subsp. equisimilis from Vellore, India

Abstract

Streptococcus dysgalactiae subsp. equisimilis (SDSE), belonging to the group C and G streptococci, are human pathogens reported to cause clinical manifestations similar to infections caused by Streptococcus pyogenes. To scrutinize the distribution of gene coding for S. pyogenes virulence factors in SDSE, 255 isolates were collected from humans infected with SDSE in Vellore, a region in southern India, with high incidence of SDSE infections. Initial evaluation indicated SDSE isolates comprising of 82.35% group G and 17.64% group C. A multiplex PCR system was used to detect 21 gene encoding virulence-associated factors of S. pyogenes, like superantigens, DNases, proteinases, and other immune modulatory toxins. As validated by DNA sequencing of the PCR products, sequences homologous to speC, speG, speH, speI, speL, ssa and smeZ of the family of superantigen coding genes and for DNases like sdaD and sdc were detected in the SDSE collection. Furthermore, there was high abundance (48.12% in group G and 86.6% in group C SDSE) of scpA, the gene coding for C5a peptidase in these isolates. Higher abundance of S. pyogenes virulence factor genes was observed in SDSE of Lancefield group C as compared to group G, even though the incidence rates in former were lower. This study not only substantiates detection of S. pyogenes virulence factor genes in whole genome sequenced SDSE but also makes significant contribution towards the understanding of SDSE and its increasing virulence potential.

A Raman-spectroscopy-based approach for detection and discrimination of Streptococcus thermophilus and Lactobacillus bulgaricus phages at low titer in raw milk

Abstract

In this study, a method combining Raman spectroscopy with chemometric analysis was developed for detection of phage presence in raw milk and discrimination of Streptococcus thermophilus and Lactobacillus bulgaricus phages which are among the main phages causing problems in dairy industry. For this purpose, S. thermophilus and L. bulgaricus phages were added into raw milk separately, and then some pretreatments such as fat separation, removal of casein, and filtration were applied to the raw milk samples. Raman spectra of the samples were collected and then analyzed using principal component analysis in order to discriminate these phages in raw milk. In the next step, dilutions of S. thermophilus phages in pretreated raw milk were prepared, and Raman spectra were collected. These spectra were analyzed by using partial least squares method to quantify phages in low titer. Consequently, it has been demonstrated that S. thermophilus and L. bulgaricus phages, which have titers sufficient to fail the fermentation (~ 10⁷ pfu/mL) and have lower titers (10²–10³ pfu/mL), could be discriminated from antibiotic and each other. Additionally, low concentrations of S. thermophilus phages (10² pfu/mL) could be detected through Raman spectroscopy with a short analysis time (60 min) and high coefficient of determination (R²) values for both calibration (0.985) and validation (0.906) with a root mean square error of calibration of 70.54 and root mean square error of prediction of 165.47. However, a lower success was achieved with L. bulgaricus phages and the obtained coefficient of determination values were not sufficiently high (0.649).

Monitoring of resistance genes in Listeria monocytogenes isolates and their presence in the extracellular DNA of biofilms: a case study from the Czech Republic

Abstract

The alarming occurrence of antibiotic resistance genes in food production demands continuous monitoring worldwide. One reservoir of resistance genes is thought to be eDNA. There is currently little available information in Europe about either the extracellular DNA distribution of the bacterium or the spread of resistance genes in L. monocytogenes. Therefore, our aims were to give insight into the Listeria monocytogenes resistance situation in the Czech Republic and assess the presence of resistance genes in their extracellular DNA (eDNA). First, susceptibility tests were performed on 49 isolates of L. monocytogenes with selected antibiotics. Next, we tested DNA of suspected isolates for the presence of resistance genes in both planktonic cells and the eDNA of biofilms. Finally, fluorescent confocal microscopy was used to observe the eDNA pattern of selected isolates under conditions that mimicked the food processing environment and the human body. Susceptibility tests found isolates intermediate resistant to chloramphenicol, tetracycline, and ciprofloxacin as well as isolates resistant to ciprofloxacin. For all suspected isolates, PCR confirmed the presence of the gene lde encoding efflux pump in both types of DNA. When the biofilm was observed using confocal laser scanning microscope, the eDNA distribution patterns varied considerably according to the culture conditions. Furthermore, the food and clinical isolates varied in terms of the amount of eDNA detected. The presence of an efflux pump in both types of DNA suggests that the eDNA might serve as a reservoir of resistance genes. Surprising differences were observed in the eDNA pattern. Our results suggest that the current risk of the spread of L. monocytogenes resistance genes is low in the Czech Republic, but they also indicate the need for continuous long-term monitoring of the situation.

From agro-industrial wastes to single cell oils: a step towards prospective biorefinery

Abstract

The reserves of fossil-based fuels, which currently seem sufficient to meet the global demands, is inevitably on the verge of exhaustion. Contemporary raw material for alternate fuel like biodiesel is usually edible plant commodity oils, whose increasing public consumption rate raises the need of finding a non-edible and fungible alternate oil source. In this quest, single cell oils (SCO) from oleaginous yeasts and fungi can provide a sustainable alternate of not only functional but also valuable (polyunsaturated fatty acids (PUFA)-rich) lipids. Researches are been increasingly driven towards increasing the SCO yield in order to realize its commercial importance. However, bulk requirement of expensive synthetic carbon substrate, which inflates the overall SCO production cost, is the major limitation towards complete acceptance of this technology. Even though substrate cost minimization could make the SCO production profitable is uncertain, it is still essential to identify suitable cheap and abundant substrates in an attempt to potentially reduce the overall process economy. One of the most sought-after in-expensive carbon reservoirs, agro-industrial wastes, can be an attractive replacement to expensive synthetic carbon substrates in this regard. The present review assess these possibilities referring to the current experimental investigations on oleaginous yeasts, and fungi reported for conversion of agro-industrial feedstocks into triacylglycerols (TAGs) and PUFA-rich lipids. Multiple associated factors regulating lipid accumulation utilizing such substrates and impeding challenges has been analyzed. The review infers that production of bulk oil in combination to high-value fatty acids, co-production strategies for SCO and different microbial metabolites, and reutilization and value addition to spent wastes could possibly leverage the high operating costs and help in commencing a successful biorefinery. Rigorous research is nevertheless required whether it is PUFA-rich oil production (for competing with algal omega oils) or neutral bulk oil production (for overcoming yield limitations and managing process economy) to establish this potential source as future resource.

Unusual oral mucosal microbiota after hematopoietic cell transplantation with glycopeptide antibiotics: potential association with pathophysiology of oral mucositis

Abstract

Severe oral mucositis occurs frequently in patients receiving hematopoietic stem cell transplantation (HCT). Oral mucosal bacteria can be associated with progression of oral mucositis, and systemic infection may occur via ulcerative oral mucositis. However, little information is available regarding the oral microbiota after HCT. Here, PCR-denaturing gradient gel electrophoresis (DGGE) was performed to characterize the oral mucosal microbiota, which can be affected by antibiotics, before and after HCT. Sixty reduced-intensity HCT patients were enrolled. Three patients with the least antibiotic use (quinolone prophylaxis and/or β-lactam monotherapy group) and three patients with the most antibiotic use (β-lactam-glycopeptide combination therapy group) were selected. Bacterial DNA samples obtained from the oral mucosa before and after HCT were subjected to PCR-DGGE. The trajectory of oral mucositis was evaluated. The oral mucosal microbiota in the β-lactam-glycopeptide combination therapy group was different from that in the quinolone prophylaxis and/or β-lactam monotherapy group, and Staphylococcus spp. and Enterococcus spp. were identified. Lautropia mirabilis was dominant in one patient. Ulcerative oral mucositis was observed only in the β-lactam-glycopeptide combination therapy group. In conclusion, especially with the use of strong antibiotics, such as glycopeptides, the oral mucosal microbiota differed completely from that under normal conditions and consisted of Staphylococcus spp., Enterococcus spp., and unexpectedly L. mirabilis. The normal oral microbiota consists not only of bacteria, but these unexpected bacteria could be involved in the pathophysiology as well as systemic infection via oral mucositis. Our results can be used as the basis for future studies in larger patient populations.