Endobronchial Metastases in Colorectal Adenocarcinoma

Between 1982 and 1990, 2388 brochoscopic examinations were carried out in patients with cancer in our hospital. A diagnosis of endobronchial metastasis was established in 30 patients (2.09 %), with the following primary tumors in descending order of frequency: breast, large bowel, melanoma, neuroblastoma, leiomyosarcoma and endometrial. Despite the rarity of endobronchial metastases secondary to colon adenocarcinoma, we were able to study 3 cases from our Center. In one case the diagnosis of endobronchial metastasis was simultaneous with that of the primary tumor, and in the other 2 this metastatic complication occurred 16 and 42 months, after the original diagnosis. When this complication occurred, the stage of the disease was advanced in all 3 cases: 2 were Dukes’ stage C and one stage D. Although this metastatic location usually implies a very negative prognosis as regards life expectancy, it did not seem to significantly reduce the latter in our patients.

Enhancing biodegradation of C16-alkyl quaternary ammonium compounds using an oxygen-based membrane biofilm reactor

Quaternary ammonium compounds (QACs) (e.g., hexadecyltrimethyl-ammonium bromide, CTAB) are emerging contaminants with widespread use as surfactants and disinfectants. Because the initial step of QAC biodegradation is mono-oxygenation, QAC degraders require O₂, but normal aeration leads to serious foaming. Here, we developed and tested an oxygen-based membrane biofilm reactor (O₂-MBfR) that delivers O₂ by diffusion through the walls of hollow-membranes to a biofilm accumulating on the outer surface of membranes. The O₂-MBfR sustained QAC biodegradation even with high and toxic QAC input concentrations, up to 400 mg/L CTAB. Bubbleless O₂ transfer completely eliminated foaming, and biofilm accumulation helped the QAC biodegraders resist toxicity. Pseudomonas, Achromobacter, Stenotrophomonas, and members of the Xanthomonadaceae family were dominant in the biofilm communities degrading CTAB, and their proportions depended on the O₂-delivery capacity of the membranes. Bacteria capable of biodegrading QACs often harbor antibiotic resistance genes (ARGs) that help them avoid QAC toxicity. Gene copies of ARGs were detected in biofilms and liquid, but the levels of ARGs were 5- to 35-fold lower in the liquid than in the biofilm. In summary, the O₂-MBfR achieved aerobic biodegradation of CTAB with neither foaming nor toxicity, and it also minimized the spread of ARGs.

Functionality of tRNAs encoded in a mobile genetic element from an acidophilic bacterium

The genome of the acidophilic, bioleaching bacterium Acidithiobacillus ferrooxidans, strain ATCC 23270, contains 95 predicted tRNA genes. Thirty-six of these genes (all 20 species) are clustered within an actively excising integrative-conjugative element (ICEAfe1). We speculated that these tRNA genes might have a role in adapting the bacterial tRNA pool to the codon usage of ICEAfe1 genes. To answer this question, we performed theoretical calculations of the global tRNA adaptation index to the entire A. ferrooxidans genome with and without the ICEAfe1 encoded tRNA genes. Based on these calculations, we observed that tRNAs encoded in ICEAfe1 negatively contribute to adapt the tRNA pool to the codon use in A. ferrooxidans. Although some of the tRNAs encoded in ICEAfe1 are functional in aminoacylation or protein synthesis, we found that they are expressed at low levels. These findings, along with the identification of a tRNA-like RNA encoded in the same cluster, led us to speculate that tRNA genes encoded in the mobile genetic element ICEAfe1 might have acquired mutations that would result in either inactivation or the acquisition of new functions.

Microbiota Transfer Therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study

BACKGROUND

Autism spectrum disorders (ASD) are complex neurobiological disorders that impair social interactions and communication and lead to restricted, repetitive, and stereotyped patterns of behavior, interests, and activities. The causes of these disorders remain poorly understood, but gut microbiota, the 1013 bacteria in the human intestines, have been implicated because children with ASD often suffer gastrointestinal (GI) problems that correlate with ASD severity. Several previous studies have reported abnormal gut bacteria in children with ASD. The gut microbiome-ASD connection has been tested in a mouse model of ASD, where the microbiome was mechanistically linked to abnormal metabolites and behavior. Similarly, a study of children with ASD found that oral non-absorbable antibiotic treatment improved GI and ASD symptoms, albeit temporarily. Here, a small open-label clinical trial evaluated the impact of Microbiota Transfer Therapy (MTT) on gut microbiota composition and GI and ASD symptoms of 18 ASD-diagnosed children.

RESULTS

MTT involved a 2-week antibiotic treatment, a bowel cleanse, and then an extended fecal microbiota transplant (FMT) using a high initial dose followed by daily and lower maintenance doses for 7-8 weeks. The Gastrointestinal Symptom Rating Scale revealed an approximately 80% reduction of GI symptoms at the end of treatment, including significant improvements in symptoms of constipation, diarrhea, indigestion, and abdominal pain. Improvements persisted 8 weeks after treatment. Similarly, clinical assessments showed that behavioral ASD symptoms improved significantly and remained improved 8 weeks after treatment ended. Bacterial and phagedeep sequencing analyses revealed successful partial engraftment of donor microbiota and beneficial changes in the gut environment. Specifically, overall bacterial diversity and the abundance of Bifidobacterium, Prevotella, and Desulfovibrio among other taxa increased following MTT, and these changes persisted after treatment stopped (followed for 8 weeks).

CONCLUSIONS

This exploratory, extended-duration treatment protocol thus appears to be a promising approach to alter the gut microbiome and virome and improve GI and behavioral symptoms of ASD. Improvements in GI symptoms, ASD symptoms, and the microbiome all persisted for at least 8 weeks after treatment ended, suggesting a long-term impact.

TRIAL REGISTRATION

This trial was registered on the ClinicalTrials.gov, with the registration number  NCT02504554.

Interpreting Interactions between Ozone and Residual Petroleum Hydrocarbons in Soil

We evaluated how gas-phase O₃ interacts with residual petroleum hydrocarbons in soil. Total petroleum hydrocarbons (TPH) were 18 ± 0.6 g/kg soil, and TPH carbon constituted ∼40% of the dichloromethane-extractable carbon (DeOC) in the soil. At the benchmark dose of 3.4 kg O₃/kg initial TPH, TPH carbon was reduced by nearly 6 gC/kg soil (40%), which was accompanied by an increase of about 4 gC/kg soil in dissolved organic carbon (DOC) and a 4-fold increase in 5-day biochemical oxygen demand (BOD₅). Disrupting gas channeling in the soil improved mass transport of O₃ to TPH bound to soil and increased TPH removal. Ozonation resulted in two measurable alterations of the composition of the organic carbon. First, part of DeOC was converted to DOC (∼4.1 gC/kg soil), 75% of which was not extractable by dichloromethane. Second, the DeOC containing saturates, aromatics, resins, and asphaltenes (SARA), was partially oxidized, resulting in a decline in saturates and aromatics, but increases in resins and asphaltenes. Ozone attack on resins, asphaltenes, and soil organic matter led to the production of NO₃^-, SO₄^2-, and PO₄^3-. The results illuminate the mechanisms by which ozone gas interacted with the weathered petroleum residuals in soil to generate soluble and biodegradable products.

Prevalence of bovine milk pathogens in Azorean pastures: mobile versus fixed milking machines

The aims of the present study were (1) to evaluate the influence of using mobile (n=47) or fixed (n=45) milking machines in Azorean herds on the apparent prevalence of several milk pathogens in bulk tank milk (BTM) and (2) to determine whether separated subclinical mastitic cows can serve, in real time, as predictors of milk pathogen prevalence for the remaining animals at the herd level. The use of a mobile or fixed milking machine influenced (P≤0.05) the prevalence of Staphylococcus aureus (72.3 per cent; n=34 v 51.1 per cent; n=23, respectively) and Klebsiella species (46.8 per cent; n=22 v 26.7 per cent; n=12, respectively). S aureus (95 per cent CI OR 1.1 to 6.0) and Klebsiella species (95 per cent CI OR 1.0 to 5.8) were 2.5 times more likely to increase in the BTM of herds using mobile milking machines. The prevalence of coagulase-negative staphylococci (100 per cent; n=92), Escherichia coli (75.0 per cent), Corynebacterium bovis (57.6 per cent), Enterococcus species (55.4 per cent), Streptococcus dysgalactiae (51.1 per cent), Streptococcus uberis (41.3 per cent), Actinomyces pyogenes or Peptostreptococcus indolicus (41.3 per cent) and Streptococcus agalactiae (32.6 per cent) in BTM remained similar among the herds. κ coefficients were always <0.70, indicating intra-herd disagreement of the prevalence of milk pathogens between BTM and separated milking cows. Milking hygiene should be improved in pastures, focusing specifically on herds that use a mobile milking machine. The segregated cows at milking time are not good predictors of milk pathogens in BTM.

Palladium Recovery in a H2-Based Membrane Biofilm Reactor: Formation of Pd(0) Nanoparticles through Enzymatic and Autocatalytic Reductions

Recovering palladium (Pd) from waste streams opens up the possibility of augmenting the supply of this important catalyst. We evaluated Pd reduction and recovery as a novel application of a H2-based membrane biofilm reactor (MBfR). At steady states, over 99% of the input soluble Pd(II) was reduced through concomitant enzymatic and autocatalytic processes at acidic or near neutral pHs. Nanoparticulate Pd(0), at an average crystallite size of 10 nm, was recovered with minimal leaching and heterogeneously associated with microbial cells and extracellular polymeric substances in the biofilm. The dominant phylotypes potentially responsible for Pd(II) reduction at circumneutral pH were denitrifying β-proteobacteria mainly consisting of the family Rhodocyclaceae. Though greatly shifted by acidic pH, the biofilm microbial community largely bounced back when the pH was returned to 7 within 2 weeks. These discoveries infer that the biofilm was capable of rapid adaptive evolution to stressed environmental change, and facilitated Pd recovery in versatile ways. This study demonstrates the promise of effective microbially driven Pd recovery in a single MBfR system that could be applied for the treatment of the waste streams, and it documents the role of biofilms in this reduction and recovery process.

Screening for active tuberculosis in high-risk groups

OBJECTIVE

To evaluate an active case-finding strategy among drug users (DUs), economically disadvantaged individuals and recent immigrants from hyperendemic countries, a population at high risk of developing tuberculosis (TB).

METHODS

Retrospective, observational study carried out by the Tuberculosis Unit of the City of Barcelona from September 2009 to December 2012. All participants underwent chest X-ray and were screened for symptoms.

RESULTS

Of 5982 participants screened, 30 TB cases were detected (total prevalence 0.5%): 26 were pulmonary, 8 were smear-positive and 2 were resistant to multiple drugs. Directly observed treatment was advised for 19 patients (63%). TB prevalence in the recent immigrants group was significantly greater (1.77%) than in all other groups studied: economically disadvantaged individuals 0.30% (RR 5.9, 95%CI 2.30-15.14); DUs 0.62% (RR 2.05, 95%CI 0.91-4.64), non-recent immigrants 0.41% (RR 4.31, 95%CI 1.68-11.4); and all native-born individuals 0.41% (RR 4.33, 95%CI 1.71-10.92). The rate was much greater than the estimated prevalence for the general population of the city (∼20 cases/100,000 population).

CONCLUSIONS

In high-risk groups, active case finding can be used as a public health intervention to detect a large number of TB cases.

Diagnostic accuracy study of multiplex PCR for detecting tuberculosis drug resistance

OBJECTIVE

To study the diagnostic accuracy of a multiplex real-time PCR (Anyplex II MTB/MDR/XDR, Seegene, Corea) that detects Mycobacterium tuberculosis resistant to isoniazid (INH), rifampicin (RIF), fluoroquinolones (FLQ) and injectable drugs (kanamycin [KAN], amikacin [AMK] and capreomycin [CAP]) in isolates and specimens.

METHODS

One hundred fourteen cultured isolates and 73 sputum specimens were retrospectively selected. Results obtained with multiplex PCR were compared with those obtained with BACTEC. Discordant results between multiplex PCR and BACTEC were tested by alternative molecular methods.

RESULTS

Sensitivity and specificity of multiplex PCR for detecting drug resistance in isolates were 76.5% and 100%, respectively, for INH; 97.2% and 96.0%, respectively, for RIF; 70.4% and 87.9%, respectively, for FLQ; 81.5% and 84.8%, respectively, for KAN; 100% and 60%, respectively, for AMK, and 100% and 72.3%, respectively, for CAP. Sensitivity and specificity of Anyplex for detecting drug resistance in specimens were 93.3% and 100%, respectively, for INH; 100% and 100%, respectively, for RIF; 50.0% and 100%, respectively, for FLQ; and 100% and 94.4%, respectively, for both KAN and CAP. Among the discordant results, 87.7% (71/81) of results obtained with the multiplex PCR were concordant with at least one of the alternative molecular methods.

CONCLUSIONS

This multiplex PCR may be a useful tool for the rapid identification of drug resistant tuberculosis in isolates and specimens, thus allowing an initial therapeutic approach. Nevertheless, for a correct management of patients, results should be confirmed by a phenotypic method.

Long-term safety of early consumption of Lactobacillus fermentum CECT5716: A 3-year follow-up of a randomized controlled trial

Lactobacillus fermentum CECT5716 is a probiotic strain originally isolated from human breast milk. Previous clinical studies in infants showed that the early administration of a milk formula containing this probiotic strain was safe and may be useful for the prevention of community-acquired infections. This is a 3-year follow-up study aimed at evaluating the long-term effects produced by the early consumption of an infant formula supplemented with L. fermentum CECT5716 (experimental group, EG) compared with a control formula without the probiotic (control group, CG). The infants included in this follow-up study had previously completed a 5-month randomized double-blind controlled trial (from 1 to 6 months of age), where the safety and tolerance of the probiotic formula was evaluated. The main outcome of the follow-up study was the growth of the children. The secondary outcomes included the incidence of infectious and non-infectious diseases, parameters related with intestinal function and faecal microbiota. At 3 years, the mean values of weight, length and head circumference were similar in children of the EG compared with those of the CG. No differences were observed in the incidence of infectious and non-infectious diseases or disorders related with intestinal function. The pattern of faecal microbiota was also similar between both groups. In conclusion, this 3-year study shows that the early administration of the probiotic of L. fermentum CECT5716 in an infant formula is safe and it does not produce measurable differences in children compared with a control formula.

AID TB resistance line probe assay for rapid detection of resistant Mycobacterium tuberculosis in clinical samples

OBJECTIVES

To determine the sensitivity and specificity of AID TB Resistance line probe assay (AID Diagnostika, Germany) to detect Mycobacterium tuberculosis and its resistance to first- and second-line drugs in clinical samples using BACTEC 460TB as the reference standard.

METHODS

The test consists on three strips to detect resistance to isoniazid/rifampicin, fluoroquinolones/ethambutol, and kanamycin/amikacin/capreomycin/streptomycin, respectively. This test was performed on 65 retrospectively selected clinical samples corresponding to 32 patients.

RESULTS

A valid result was obtained for 92.3% (60/65), 90.8% (59/65) and 78.5% (51/65) of the samples tested, considering the three strips, respectively. Global concordance rates between AID and BACTEC for detecting resistance to isoniazid, rifampicin, fluoroquinolones, ethambutol, kanamycin/capreomycin and streptomycin were 98.3% (59/60), 100% (60/60), 91.5% (54/59), 72.9% (43/59), 100% (51/51) and 98.0% (50/51), respectively. Regarding the discordant results obtained between AID and BACTEC, the alternative molecular methods performed (GenoType MTBDRplus, GenoType MTBDRsl [Hain Lifescience, Germany] and/or pyrosequencing) confirmed the genotypic result in 90.9% (20/22) of the cases.

CONCLUSIONS

AID line probe assay is a useful tool for the rapid detection of drug resistance in clinical samples enabling an initial therapeutic approach. Nevertheless, for a correct management of drug resistant tuberculosis patients, molecular results should be confirmed by a phenotypic method.

Sequencing and de novo assembly of the red cusk-eel (Genypterus chilensis) transcriptome

The red cusk-eel (Genypterus chilensis) is an endemic fish species distributed along the coasts of the Eastern South Pacific. Biological studies on this fish are scarce, and genomic information for G. chilensis is practically non-existent. Thus, transcriptome information for this species is an essential resource that will greatly enrich molecular information and benefit future studies of red cusk-eel biology. In this work, we obtained transcriptome information of G. chilensis using the Illumina platform. The RNA sequencing generated 66,307,362 and 59,925,554 paired-end reads from skeletal muscle and liver tissues, respectively. De novo assembly using the CLC Genomic Workbench version 7.0.3 produced 48,480 contigs and created a reference transcriptome with a N50 of 846bp and average read coverage of 28.3×. By sequence similarity search for known proteins, a total of 21,272 (43.9%) contigs were annotated for their function. Out of these annotated contigs, 33.5% GO annotation results for biological processes, 32.6% GO annotation results for cellular components and 34.5% GO annotation results for molecular functions. This dataset represents the first transcriptomic resource for the red cusk-eel and for a member of the Ophidiimorpharia taxon.

Monitoring changes in anti-tuberculosis treatment: associated factors determined at the time of diagnosis

OBJECTIVES

To determine predictive factors for changes in standard anti-tuberculosis chemotherapy at the time of diagnosis.

METHODS

A prospective study was performed among tuberculosis (TB) patients treated at specialised centres during 2008-2009. Treatment outcome was monitored per standard guidelines. Treatment was considered successful if the patient was cured or completed treatment. Factors associated with treatment modification were analysed at the bivariate and multivariate levels using logistic regression.

RESULTS

A total of 427 patients were included in the study. The initial standard treatment regimen was retained for 249 patients (58.3%), extended to 9 months for 36 (8.4%) and changed for 142 (33.3%). Factors associated with a change of regimen at the multivariate level were female sex, age ≥ 50 years, human immunodeficiency virus infection, comorbidities, alcoholism, hospitalisation and culture-positive sputum. Drug resistance and toxicity were analysed independently. Treatment outcome was successful in 97.2% of cases without a regimen change and in 87.3% of those with a changed regimen (P < 0.001).

CONCLUSION

Factors associated with changes in the initial anti-tuberculosis regimen should be considered for rigorous follow-up. Results obtained through individualised treatment provided by specialists were good despite the complexity of the cases treated.

Central arterial hemodynamic effects of dark chocolate ingestion in young healthy people: a randomized and controlled trial

Introduction. The aim of this study was to assess the vascular benefits of dark chocolate in healthy and young individuals. Methods. A randomized and controlled trial was carried out involving 60 healthy volunteers, randomized into two groups: control group (CG; n = 30) and intervention group (IG; n = 30). The IG ingested a daily dosage of 10 g of dark chocolate (>75% cocoa) for a month. Blood pressure (BP), flow-mediated dilation (FMD), arterial stiffness index (ASI), aortic pulse wave velocity (PWV), and pulse wave analysis (PWA) were assessed at baseline and one week after the one-month intervention period. Results. Arterial function improved after intervention in the IG, with PWV decreasing from 6.13 ± 0.41 m/s to 5.83 ± 0.53 m/s (P = 0.02), with no significant differences observed in the CG. A significant decrease in ASI (0.16 ± 0.01 to 0.13 ± 0.01; P < 0.001) and AiX (-15.88 ± 10.75 to -22.57 ± 11.16; P = 0.07) was also depicted for the IG. Endothelial function improved in the IG, with the FMD increasing 9.31% after the 1-month intervention (P < 0.001), with no significant variation in the CG. Conclusion. The daily ingestion of 10 g dark chocolate (>75% cocoa) during a month significantly improves vascular function in young and healthy individuals.