Genomic Characterization of Carbapenem-Resistant Bacteria from Beef Cattle Feedlots.

Carbapenems are considered a last resort for the treatment of multi-drug-resistant bacterial infections in humans. In this study, we investigated the occurrence of carbapenem-resistant bacteria in feedlots in Alberta, Canada. The presumptive carbapenem-resistant isolates (n = 116) recovered after ertapenem enrichment were subjected to antimicrobial susceptibility testing against 12 different antibiotics, including four carbapenems. Of these, 72% of the isolates (n = 84) showed resistance to ertapenem, while 27% of the isolates (n = 31) were resistant to at least one other carbapenem, with all except one isolate being resistant to at least two other drug classes. Of these 31 isolates, 90% were carbapenemase positive, while a subset of 36 ertapenem-only resistant isolates were carbapenemase negative. The positive isolates belonged to three genera; Pseudomonas, Acinetobacter, and Stenotrophomonas, with the majority being Pseudomonas aeruginosa (n = 20) as identified by 16S rRNA gene sequencing. Whole genome sequencing identified intrinsic carbapenem resistance genes, including blaOXA-50 and its variants (P. aeruginosa), blaOXA-265 (A. haemolyticus), blaOXA-648 (A. lwoffii), blaOXA-278 (A. junii), and blaL1 and blaL2 (S. maltophilia). The acquired carbapenem resistance gene (blaPST-2) was identified in P. saudiphocaensis and P. stutzeri. In a comparative genomic analysis, clinical P. aeruginosa clustered separately from those recovered from bovine feces. In conclusion, despite the use of selective enrichment methods, finding carbapenem-resistant bacteria within a feedlot environment was a rarity.

Comparative Genomic Analysis of Enterococci across Sectors of the One Health Continuum.

Enterococci are Gram-positive bacteria that can be isolated from a variety of environments including soil, water, plants, and the intestinal tract of humans and animals. Although they are considered commensals in humans, Enterococcus spp. are important opportunistic pathogens. Due to their presence and persistence in diverse environments, Enterococcus spp. are ideal for studying antimicrobial resistance (AMR) from the One Health perspective. We undertook a comparative genomic analysis of the virulome, resistome, mobilome, and the association between the resistome and mobilome of 246 E. faecium and 376 E. faecalis recovered from livestock (swine, beef cattle, poultry, dairy cattle), human clinical samples, municipal wastewater, and environmental sources. Comparative genomics of E. faecium and E. faecalis identified 31 and 34 different antimicrobial resistance genes (ARGs), with 62% and 68% of the isolates having plasmid-associated ARGs, respectively. Across the One Health continuum, tetracycline (tetL and tetM) and macrolide resistance (ermB) were commonly identified in E. faecium and E. faecalis. These ARGs were frequently associated with mobile genetic elements along with other ARGs conferring resistance against aminoglycosides [ant(6)-la, aph(3')-IIIa], lincosamides [lnuG, lsaE], and streptogramins (sat4). Study of the core E. faecium genome identified two main clades, clade 'A' and 'B', with clade A isolates primarily originating from humans and municipal wastewater and carrying more virulence genes and ARGs related to category I antimicrobials. Overall, despite differences in antimicrobial usage across the continuum, tetracycline and macrolide resistance genes persisted in all sectors.

Genomic Characterization of Enterococcus hirae From Beef Cattle Feedlots and Associated Environmental Continuum.

Enterococci are commensal bacteria of the gastrointestinal tract of humans, animals, and insects. They are also found in soil, water, and plant ecosystems. The presence of enterococci in human, animal, and environmental settings makes these bacteria ideal candidates to study antimicrobial resistance in the One-Health continuum. This study focused on Enterococcus hirae isolates (n = 4,601) predominantly isolated from beef production systems including bovine feces (n = 4,117, 89.5%), catch-basin water (n = 306, 66.5%), stockpiled bovine manure (n = 24, 0.5%), and natural water sources near feedlots (n = 145, 32%), and a few isolates from urban wastewater (n = 9, 0.2%) denoted as human-associated environmental samples. Antimicrobial susceptibility profiling of a subset (n = 1,319) of E. hirae isolates originating from beef production systems (n = 1,308) showed high resistance to tetracycline (65%) and erythromycin (57%) with 50.4% isolates harboring multi-drug resistance, whereas urban wastewater isolates (n = 9) were resistant to nitrofurantoin (44.5%) and tigecycline (44.5%) followed by linezolid (33.3%). Genes for tetracycline (tetL, M, S/M, and O/32/O) and macrolide resistance erm(B) were frequently found in beef production isolates. Antimicrobial resistance profiles of E. hirae isolates recovered from different environmental settings appeared to reflect the kind of antimicrobial usage in beef and human sectors. Comparative genomic analysis of E. hirae isolates showed an open pan-genome that consisted of 1,427 core genes, 358 soft core genes, 1701 shell genes, and 7,969 cloud genes. Across species comparative genomic analysis conducted on E. hirae, Enterococcus faecalis and Enterococcus faecium genomes revealed that E. hirae had unique genes associated with vitamin production, cellulose, and pectin degradation, traits which may support its adaptation to the bovine digestive tract. E. faecium and E. faecalis more frequently harbored virulence genes associated with biofilm formation, iron transport, and cell adhesion, suggesting niche specificity within these species.

Germline Mutation Analysis in Sporadic Breast Cancer Cases With Clinical Correlations.

Demographics for breast cancers vary widely among nations. The frequency of germline mutations in breast cancers, which reflects the hereditary cases, has not been investigated adequately and accurately in highly-consanguineous Pakistani population. In the present discovery case series, germ-line mutations in twenty-seven breast cancer candidate genes were investigated in eighty-four sporadic breast cancer patients along with the clinical correlations. The germ-line variants were also assessed in two healthy gender-matched controls. The clinico-pathological features were evaluated by descriptive analysis and Pearson χ2 test (with significant p-value <0.05). The most frequent parameters associated with hereditary cancer cases are age and ethnicity. Therefore, the analyses were stratified on the basis of age (≤40 years vs. >40 years) and ethnicity. The breast cancer gene panel assay was carried out by BROCA, which is a genomic capture, massively parallel next generation sequencing assay on Illumina Hiseq2000 with 100bp read lengths. Copy number variations were determined by partially-mapped read algorithm. Once the mutation was identified, it was validated by Sanger sequencing. The ethnic analysis stratified on the basis of age showed that the frequency of breast cancer at young age (≤40 years) was higher in Sindhis (n = 12/19; 64%) in contrast to patients in other ethnic groups. Majority of the patients had stage III (38.1%), grade III (50%), tumor size 2-5 cm (54.8%), and invasive ductal carcinoma (81%). Overall, the analysis revealed germ-line mutations in 11.9% of the patients, which was not significantly associated with younger age or any particular ethnicity. The mutational spectrum was restricted to three genes: BRCA1, BRCA2, and TP53. The identified mutations consist of seven novel germ-line mutations, while three mutations have been reported previously. All the mutations are predicted to result in protein truncation. No mutations were identified in the remaining twenty-four candidate breast cancer genes. The present study provides the framework for the development of hereditary-based preventive and treatment strategies against breast cancers in Pakistani population.

Absence of Glutathione S-Transferase Theta 1 Gene Is Significantly Associated With Breast Cancer Susceptibility in Pakistani Population and Poor Overall Survival in Breast Cancer Patients: A Case-Control and Case Series Analysis.

PURPOSE: Deletion of Glutathione S-Transferase Theta 1 (GSTT1) encoding gene is implicated in breast cancer susceptibility, clinical outcomes, and survival. Contradictory results have been reported in different studies. The present investigation based on a representative Pakistani population evaluated the GSTT1-absent genotype in breast cancer risk and prognosis. METHODS: A prospective study comprising case-control analysis and case series analysis components was designed. Peripheral blood samples were collected from enrolled participants. After DNA extraction, GSTT1 genotyping was carried out by a multiplex PCR with ß-globin as an amplification control. Association evaluation of GSTT1 genotypes with breast cancer risk, specific tumor characteristics, and survival were the primary endpoints. RESULTS: A total of 264 participants were enrolled in the molecular investigation (3 institutions). The study included 121 primary breast cancer patients as cases and 143 age-matched female subjects, with no history of any cancer, as controls. A significant genetic association between GSTT1-absent genotype and breast cancer susceptibility (p-value: 0.03; OR: 2.13; 95% CI: 1.08-4.29) was reported. The case-series analysis showed lack of association of GSTT1 genotypes with menopause (p-value: 0.86), tumor stage (p-value: 0.12), grade (p-value: 0.32), and size (p-value: 0.07). The survival analysis revealed that GSTT1-absent genotype cases had a statistically significant shorter overall survival (OS) than those with the GSTT1-present genotype cases (mean OS: 23 months vs 33 months). The HR (95% CI) for OS in patients carrying GSTT1-absent genotype was 8.13 (2.91-22.96) when compared with the GSTT1-present genotype. CONCLUSIONS: The present study is the first report of an independent significant genetic association between GSTT1-absent genotype and breast cancer susceptibility in a Pakistani population. It is also the foremost report of the association of this genotype with OS in breast cancer cases. Upon further validation, GSTT1 variation may serve as a marker for devising better population-specific strategies. The information may have translational implications in the screening and treatment of breast cancers.

Threats of COVID-19 to Achieving United Nations Sustainable Development Goals in Africa.

The negative impacts of the COVID-19 pandemic have been exacerbated in Africa by hunger, poor health care, poor educational systems, poverty, and lack of potable water and sanitation. With the pandemic and a worrying global recession as a result of COVID-19, our ability to achieve the 17 United Nations sustainable development goals (SDGs) in the post-pandemic era has been questioned. There is concern that the economic stagnation caused by COVID-19 will not only push more populations below the poverty line but also limit international support to ensure progress toward achieving the SDGs in Africa. This article highlights how the COVID-19 pandemic could threaten the actualization of the SDGs in Africa. We assessed relevant published literature, observations, and current global trends. Our results suggest that although the improvement of healthcare systems has become a priority in Africa, there is a need to ensure that some SDGs are not sacrificed to achieve control of the pandemic. Despite the pandemic, African countries need to identify policies that will not compromise the implementation of the SDGs and/or jeopardize previously achieved SDG targets.

Association between PNPLA3rs738409 polymorphism decreased kidney function in postmenopausal type 2 diabetic women with or without non-alcoholic fatty liver disease.

AIM: Evidence is emerging that PNPLA3 rs738409 polymorphism (the major genetic variant associated with susceptibility to non-alcoholic fatty liver disease [NAFLD]) is associated with chronic kidney disease (CKD) in non-diabetic individuals. Currently, little is known about this association in type 2 diabetic (T2DM) patients with and without NAFLD. METHODS: We studied 101 Caucasian post-menopausal women with T2DM, consecutively attending our diabetes outpatient service during a 3-month period. Glomerular filtration rate (eGFRCKD-EPI) was estimated using the CKD-Epidemiology Collaboration (CKD-EPI) equation, whilst albuminuria was measured with an immunonephelometric assay on morning spot urine samples. NAFLD was detected either by fatty liver index (FLI ≥ 60, n = 101) or by ultrasonography (n = 77). Genotyping was performed by TaqMan-Based RT-PCR system. RESULTS: Eight patients had G/G, 41 G/C and 52 C/C PNPLA3 rs738409 genotypes, and 21 (20.8%) patients had CKD (eGFRCKD-EPI < 60 mL/min/1.73 m2 or abnormal albuminuria). Compared to those with G/C or C/C genotypes, patients with G/G genotype had significantly lower eGFRCKD-EPI (63.7 ± 11 vs. 77.4 ± 17 vs. 81.9 ± 15 mL/min/1.73 m2, P = 0.014) and higher prevalence of CKD (50% vs. 24.4% vs. 13.5%, P = 0.04). After adjustment for age, duration of diabetes, haemoglobin A1c, HOMA-estimated insulin resistance, systolic blood pressure, hypertension treatment and FLI ≥ 60, rs738409 G/G genotype was independently associated with both lower eGFRCKD-EPI (ß coefficient: -15.5, 95% CI -26.0 to -5.0, P = 0.004) and higher risk of CKD (adjusted-odds ratio 8.05, 95% CI 1.26-41.4, P = 0.03). Similar results were found when we adjusted for hepatic steatosis on ultrasography (instead of FLI ≥ 60). CONCLUSION: Regardless of the presence of NAFLD and common cardio-renal risk factors, in post-menopausal women with T2DM, the G/G genotype of rs738409 in the PNPLA3 gene was strongly associated with lower eGFRCKD-EPI and higher prevalence of CKD.

Association between non-alcoholic fatty liver disease and bone turnover biomarkers in post-menopausal women with type 2 diabetes.

AIM: Information is lacking on the association between non-alcoholic fatty liver disease (NAFLD) and bone mineral density (BMD) or circulating bone turnover biomarkers in post-menopausal women with type 2 diabetes (T2DM). METHODS: We recruited 77 white post-menopausal women with T2DM, who consecutively attended our diabetes outpatient service during a 3-month period. Liver ultrasonography and transient elastography (Fibroscan®) were used for diagnosing and staging NAFLD. A dual energy X-ray absorptiometry, and serum levels of 25-hydroxyvitamin D3 [25(OH)D], parathyroid hormone and multiple bone turnover biomarkers (periostin, sclerostin, dickkopf-related protein-1 [DKK-1], C-terminal telopeptide of type 1 collagen [sCTX], procollagen type 1 N-terminal propeptide [P1NP], receptor activator of nuclear factor-kB ligand [RANKL]) were also measured. RESULTS: Overall, 10 patients had NAFLD with clinically significant fibrosis (i.e., liver stiffness measurement > 7 kPa), 52 had NAFLD without fibrosis and 15 patients were free from steatosis. Although the three patient groups had comparable values of BMD, after adjustment for age, waist circumference, HOMA-insulin resistance and serum 25(OH)D levels, patients with NAFLD and significant fibrosis had significantly higher sclerostin levels (54.1 ± 16.4 vs. 36.1 ± 11.9 vs. 42.3 ± 14.7 pmol/L) and lower levels of serum DKK-1 (26.6 ± 17.8 vs. 49.0 ± 22.4 vs. 42.9 ± 19.4 pmol/L), RANKL (0.04 ± 0.03 vs. 0.08 ± 0.06 vs. 0.11 ± 0.06 pmol/L) and sCTX (0.16 ± 0.09 vs. 0.29 ± 0.17 vs. 0.40 ± 0.28 ng/mL) compared to other groups. Serum periostin and P1NP levels did not significantly differ between the groups. CONCLUSION: In post-menopausal women with T2DM, the presence of NAFLD and clinically significant fibrosis was strongly associated with a low bone turnover, which may reflect the presence of qualitative bone abnormalities.

Carbon-Nanohorn Based Nanofluids for a Direct Absorption Solar Collector for Civil Application.

Direct solar absorption has been often considered in the past as a possible solution for solar thermal collectors for residential and small commercial applications. A direct absorption could indeed improve the performance of solar collectors by skipping one step of the heat transfer mechanism in standard devices and having a more convenient temperature distribution inside the collector. Classical solar thermal collectors have a metal sheet as absorber, designed such that water has the minimum temperature in each transversal section, in order to collect as much solar thermal energy as possible. On the other hand, in a direct configuration, the hottest part of the system is the operating fluid and this allows to have a more efficient conversion. Nanofluids, i.e., fluids with a suspension of nanoparticles, such as carbon nanohorns, could be a good and innovative family of absorbing fluids owing to their higher absorption coefficient compared to the base fluid and stability under moderate temperature gradients. Moreover, carbon nanohorns offer the remarkable advantage of a reduced toxicity over other carbon nanoparticles. In this work, a three-dimensional model of the absorption phenomena in nanofluids within a cylindrical tube is coupled with a computational fluid dynamics (CFD) analysis of the flow and temperature field. Measured optical properties of nanofluids at different concentrations have been implemented in the model. Heat losses due to conduction, convection and radiation at the boundaries are considered as well.

Optical Properties of Mixed Nanofluids Containing Carbon Nanohorns and Silver Nanoparticles for Solar Energy Applications.

Different kinds of nanofluids show peculiar characteristics. In this work, a mixed nanofluid consisting of single-wall carbon nanohorns and silver nanoparticles aqueous suspensions is prepared and optically characterized, in the perspective to merge the favorable optical characteristics of carbon nanohorn-based nanofluids to the good thermal properties of silver-nanofluids. For the samples, both the spectral extinction and the scattering albedo at discrete wavelengths have been investigated. The silver nanoparticle plasmonic peak in the visible range further improves the overall nanofluid sunlight absorption properties, opening interesting perspectives for using such mixed nanofluids as solar absorber and heat transfer media in solar thermal collectors.

Optical design of a light-emitting diode lamp for a maritime lighthouse.

Traffic signaling is an emerging field for light-emitting diode (LED) applications. This sustainable power-saving illumination technology can be used in maritime signaling thanks to the recently updated norms, where the possibility to utilize LED sources is explicitly cited, and to the availability of high-power white LEDs that, combined with suitable lenses, permit us to obtain well-collimated beams. This paper describes the optical design of a LED-based lamp that can replace a traditional lamp in an authentic marine lighthouse. This source recombines multiple separated LEDs realizing a quasi-punctual localized source. Advantages can be lower energy consumption, higher efficiency, longer life, fewer faults, slower aging, and minor maintenance costs. The proposed LED source allows us to keep and to utilize the old Fresnel lenses of the lighthouse, which very often have historical value.

Carbon nanohorns-based nanofluids as direct sunlight absorbers.

The optimization of the poor heat transfer characteristics of fluids conventionally employed in solar devices are at present one of the main topics for system efficiency and compactness. In the present work we investigated the optical and thermal properties of nanofluids consisting in aqueous suspensions of single wall carbon nanohorns. The characteristics of these nanofluids were evaluated in view of their use as sunlight absorber fluids in a solar device. The observed nanoparticle-induced differences in optical properties appeared promising, leading to a considerably higher sunlight absorption. We found that the thermal conductivity of the nanofluids was higher than pure water. Both these effects, together with the possible chemical functionalization of carbon nanohorns, make this new kind of nanofluids very interesting for increasing the overall efficiency of the sunlight exploiting device.

Sinus membrane elevation in combination with placement of blasted implants: a 3-year case report of sinus augmentation without grafting material.

Owing to the increasing use of dental implants to restore edentulous conditions, clinicians often face situations where available bone volumes are reduced and need to be augmented before implant placement. This is common in the posterior maxilla, where the presence of the maxillary sinus combined with severe atrophy of the bone crest, owing to long-standing edentulism or pathological conditions, might preclude implant placement. Techniques to augment the sinus floor in combination with several grafting materials are commonly used to restore adequate volumes for implantation. Recent studies have described bone reformation and integration of oxidized implants by simple elevation of the sinus membrane without any grafting material. The aim of this case report is to document the application of the sinus membrane elevation technique in combination with the placement of 3 blasted microthreaded implants in a patient who was clinically and radiographically followed up for 3 years. During the follow-up period, the blasted implants were all stable and intraoral radiographs showed that the bone reformed in contact with the implants and remained stable.

Alpha-tryptophan synthase of Isatis tinctoria: gene cloning and expression.

Indole producing reaction is a crux in the regulation of metabolite flow through the pathways and the coordination of primary and secondary product biosynthesis in plants. Indole is yielded transiently from indole-3-glycerol phosphate and immediately condensed with serine to give tryptophan, by the enzyme tryptophan synthase (TS). There is evidence that plant TS, like the bacterial complex, functions as an alpha beta heteromer. In few species, e.g. maize, are known enzymes, related with the TS alpha-subunit (TSA), able to catalyse reaction producing indole, which is free to enter the secondary metabolite pathways. In this contest, we searched for TSA and TSA related genes in Isatis tinctoria, a species producing the natural blue dye indigo. The It-TSA cDNA and the full-length exons/introns genomic region were isolated. The phylogenetic analysis indicates that It-TSA is more closely related to Arabidopsis thaliana At-T14E10.210 TSA (95.7% identity at the amino acid level) with respect to A. thaliana At-T10P11.11 TSA1-like (63%), Zea mays indole-3-glycerol phosphate lyase (54%), Z. mays TSA (53%), and Z. mays indole synthase (50%). The It-TSA cDNA was also able to complement an Escherichia coli trpA mutant. To examine the involvement of It-TSA in the biosynthesis of secondary metabolism compounds, It-TSA expression was tested in seedling grown under different light conditions. Semi-quantitative RT-PCR showed an increase in the steady-state level of It-TSA mRNA, paralleled by an increase of indigo and its precursor isatan B. Our results appear to indicate an involvement for It-TSA in indigo precursor synthesis and/or tryptophan biosynthesis.

Cryptogenic stroke in children: possible role of patent foramen ovale.

Stroke is a rare disorder in childhood. The majority of these cases is of an ischemic nature. In spite of the long list of known causes, many strokes remain undetermined, so-called cryptogenic strokes. Increasing evidence indicates that, in the young adults, many cases of cryptogenic stroke are presumably due to paradoxical embolism. In childhood, this is usually not considered, unless in the context of a complex cyanotic heart disease. We present two cases, a 6-year-old boy and an 11-year-old girl who had an episode of cerebral ischemia documented by MRI, and in whom the only anomaly found was a patent foramen ovale (PFO) with intermittent left to right shunt at rest, but with a large right to left shunt during the Valsalva maneuvre. We assumed that, in our cases, in the absence of identifiable causes, the cerebral ischemia was most likely due to paradoxical embolism through the PFO. Of course, as in the adult, the paradoxical embolism could not be proved, but in our opinion it remains the most concrete possibility. Therefore, in presence of a cryptogenic stroke, a PFO should be investigated also in children.

Sub-100-ps amplitude-modulation mode-locked Tm-Ho:BaY2F8 laser at 2.06 microm.

We report the generation of sub-100-ps pulse trains near the 2.06-microm wavelength in an actively mode-locked diode-pumped Tm-Ho:BaYF laser operating at room temperature. Transform-limited, 97-ps Gaussian pulses at a 100-MHz repetition rate with an average power in excess of 20 mW and with a carrier wavelength tunable by approximately 50 nm near 2.066 microm are demonstrated.