Dataset for Genome Sequencing and De Novo Assembly of the Candidate Phyla Radiation in Supragingival PlaqueRead the full article
Canadian Journal of Infectious Diseases and Medical Microbiology publishes original research articles and review articles related to infectious diseases of bacterial, viral and parasitic origin.
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Association of Antibiotic Resistance Traits in Uropathogenic Escherichia coli (UPEC) Isolates
Background. Antimicrobial resistance (AMR) is a global health problem which is constantly evolving and varies spatially and temporally. Resistance to a particular antibiotic may serve as a selection and coselection marker for the same or different antibiotic classes. Therefore, this cross-sectional study was conducted to predict the association of phenotypic and genotypic resistance traits in uropathogenic Escherichia coli (UPEC). Method. A total of 42 UPEC from 83 urine samples were investigated for the prevalence and association of phenotypic and genotypic AMR traits. Antibiogram profiling was carried out by Kirby–Bauer’s disc diffusion method and AMR genes (ARGs) were detected by PCR. Result. UPECs were isolated from 50.60% (42/83) of the samples examined. Of these, 80.95% of cases were derived from females, and 38.10% of cases were found in the age group of 21–30 years. The isolates were shown to have a high frequency of resistance to tetracycline (92.86%), followed by sulfonamide (71.43%), ampicillin (52.38%), trimethoprim-sulfamethoxazole (47.62%), and 28.57% each to streptomycin, chloramphenicol, and erythromycin. The most prevalent antimicrobial resistance genes (ARGs) in these isolates were tet(A) (78.57%), tet(B) (76.19%), sul1 (61.91%), dfrA1 (35.71%), blaSHV (26.19%), cmlA (19.05%), and CITM, qnrA, and catA1 each at 11.91%. According to statistical analysis, ampicillin, sulfonamide, trimethoprim-sulfamethoxazole, and ciprofloxacin resistance were strongly correlated with the presence of blaSHV, sul1, dfrA1, and qnrA, respectively. Nonsignificant associations were observed between ciprofloxacin-tetracycline, sulfonamide-erythromycin pairs as well as between tet(A) and tet(B) genes. Besides, coselection was also assumed in the case of chloramphenicol resistance genes, namely, catA1 and cmlA. Conclusion. Both the phenotypic and genetic resistance traits were found in the UPEC isolates. Statistical association and coselection phenomena among AMR phenotypes and genotypes were also observed but required to be validated in a broad-scale study. However, these findings might have important implications for the development of an AMR prediction model to tackle future AMR outbreaks.
In-Hospital Macro-, Meso-, and Micro-Drivers and Interventions for Antibiotic Use and Resistance: A Rapid Evidence Synthesis of Data from Canada and Other OECD Countries
Hospitals continue to face challenges in reducing incorrect antibiotic use due to social and cultural factors at the level of the health system, the care facility, the provider, and the patient. The objective of this paper is to highlight the social and cultural drivers of antimicrobial use and resistance and targeted interventions for secondary and tertiary care settings in Canada and other OECD countries. This paper is an extension of the synthesis conducted for the Public Health Agency of Canada’s 2019 Spotlight Report: Preserving Antibiotics Now and Into the Future. We conducted a systematic review with a few modifications to meet rapid timelines. We conducted a search in Ovid MEDLINE and McMaster University’s evidence databases for systematic reviews and then for individual Canadian studies. To cast a wider net, we searched OECD organization websites and screened reference lists from systematic reviews. We synthesized the evidence narratively and categorized the evidence into macro-, meso-, and microlevel. A total of 70 studies were (a) from OCED countries and summarized evidence of potential sociocultural antimicrobial resistance and use barriers or facilitators and/or interventions addressing these challenges; (b) systematic reviews with 50% of included studies that are situated in secondary and tertiary settings; and (c) published in Canada’s two official languages, English and French. We found that hospital structures and policies may influence antibiotic utilization and variations in antimicrobial management. Microlevel factors may sway inappropriate prescribing among clinicians. The amount and type of antibiotics used may affect resistance rates. Interventions were mainly comprised of antibiotic stewardship and training that modify clinician behavior and that educate patients and carers. This evidence synthesis illustrates the various drivers of, and interventions for, antimicrobial use and resistance at the macro-, meso-, and microlevel in secondary and tertiary settings. We demonstrate that upstream drivers may lead to downstream events that influence antimicrobial resistance.
Physicochemical Properties and Biological Activities of Garden Cress (Lepidium sativum L.) Seed and Leaf Oil Extracts
Garden cress (Lepidium sativum L.) seed is a rich source of proteins, dietary fiber, omega-3 fatty acids, iron, and other essential nutrients and phytochemicals. The aim of the present study was to investigate the physicochemical properties and biological activities of garden cress (L. sativum) seed and leaf oil extracts using solvent extraction methods. The result indicated that oil yield (25.75 ± 2.48%) and specific gravity (0.84 ± 0.08) were significantly ( based on least significance difference t-test) higher for seed oil extract. Seed oil also presented significantly () higher antioxidant activities with respect to ascorbic acid content (24.21 ± 3.04%) and DPPH (2, 2-diphenyl-1-picrylhydrazyl) (26.55 ± 0.21%) values. The leaf oil extract has exhibited stronger antibacterial activity with a maximum zone of inhibition (18.50 mm), a minimum inhibitory concentration (MIC) of 0.05 µg/ml, and a minimum bactericidal concentration (MBC) of 0.05 µg/ml against Staphylococcus aureus. Leaf oil extract has also demonstrated stronger antifungal activity with a maximum zone of inhibition (18.50 mm), MIC (0.25 µg/ml), and a minimum fungicidal concentration (MFC) of 0.50 µg/ml against Aspergillus Niger. The result suggesting that leaf oil presented superior antimicrobial but inferior antioxidant potential than seed oil in garden cress.
COVID-19 Mortality in Children: A Referral Center Experience from Iran (Mofid Children’s Hospital, Tehran, Iran)
Background. The novel coronavirus disease 2019 (COVID-19) started in Wuhan, China, in December 2019. It spread widely around the world and was described as a pandemic by the World Health Organization (WHO). The knowledge regarding the mortality rate and risk factors of COVID-19 among the pediatric population is lacking. In this regard, we aimed to report the clinical and laboratory characteristics of deceased pediatric patients with SARS-CoV-2 infection. Method. This cross-sectional study was conducted in Mofid Children’s Hospital, Tehran, Iran, from February 2020 to April 2021. Recorded documents of 59 pediatric patients (under 18 years old) assumed to have COVID-19 who had died in the COVID-19 ward and COVID-19 intensive care unit (ICU) were retrospectively evaluated. All statistical analyses were performed using SPSS software (v. 26.0, Chicago, IL). A value of less than 0.05 was considered statistically significant. Results. From 711 COVID-19 definite and suspected patients, 59 children died. Of these deceased pediatric patients, 34 were boys (57.62%) and 25 were girls (42.37%), with a total mean age of 5.6 years. The median length of stay in the hospital was 10 days (range 1–215). 91.52% had underlying comorbidities of which neurological diseases accounted for the largest share. 54 patients were admitted to the ICU and 83.05% of them had intubation during their hospitalization. In addition, the most common reasons for death in our study were related to respiratory and multiorgan failure. Conclusion. According to our knowledge, we are the first team to report such a thorough study in the field of COVID-19 pediatric mortality in Iran. Mortality was observed in all age groups of children, especially in those with previous comorbidities, specifically neurological disease. Abnormally elevated tests of ESR, CRP, LDH, AST, and ALT as well as the presence of proteinuria and hematuria were found in more than 50% of patients in our investigations, and ICU admission between both definite and suspected groups had significant differences, so monitoring and considering these factors may help to control and reduce the progression of the disease to death.
Clinical Analysis of Bloodstream Infection of Escherichia coli in Patients with Pancreatic Cancer from 2011 to 2019
Background. Pancreatic cancer patients were particularly predisposed to develop Escherichia coli (E. coli) bloodstream infection (BSI); however, little information is currently available. We set out to find E. coli BSI’s risk factors in pancreatic cancer to provide valuable experience. Methods. We retrospectively analyzed the clinical data of pancreatic cancer patients (31 cases with E. coli BSI and 93 cases without BSI) by a case-control study. SPSS 17.0 was adopted to perform univariate and multivariate analyses. Bacterial resistance analysis was performed by Whonet 5.6. Results. Hospitalization days ≥7 days, number of admissions ≥2 times, surgery, chemotherapy, the type of antibiotics used ≥2 species, albumin<40.0 g/L, and prealbumin < 0.2 g/L were the potential risk factors for pancreatic cancer patients with E. coli BSI (). Multivariate logistic regression showed hospitalization days ≥7 days (OR = 11.196, 95% CI = 0.024–0.333, ), surgery (OR = 32.053, 95% CI = 0.007–0.137, ), and chemotherapy (OR = 6.174, 95% CI = 0.038–0.688, ) were the independent risk factors for E. coli BSI of pancreatic cancer patients. E. coli resistant to carbapenems was rare; they were susceptible to cephamycin and piperacillin/tazobactam. The 90-day mortality rate of the infected group was significantly higher than the control group (41.9% versus 8.6%, ). Conclusions. Hospitalization days ≥7 days, surgery, and chemotherapy are the independent risk factors for E. coli BSI of pancreatic cancer patients, which allows us to identify patients at potential risk and perform preventive treatment in time.
Tocilizumab, an Exploratory Treatment for Severe COVID-19 Patients
The coronavirus disease 2019 (COVID-19) may cause cytokine storm and respiratory illness such as pneumonia and progressive respiratory failure. Tocilizumab (TCZ), a monoclonal antibody that targets the interleukin-6 (IL-6) receptor, was approved as an alternative treatment for severe COVID-19 patients despite limited real-world clinical data in China. In the present study, we will discuss and evaluate the treatment response of TCZ therapy in patients with COVID-19. The clinical characteristics, treatment, laboratory parameters of IL-6, C-reactive protein (CRP), lymphocyte counts before and after TCZ therapy, and clinical outcomes in the 13 patients with COVID-19 were retrospectively evaluated according to the related medical records. The results showed that 13 patients with COVID-19 were totally included in this study. One of them was moderately ill, 8 were seriously ill, and 4 were critically ill. Eleven patients received TCZ administration once, while the other 2 patients received it twice. The median level of IL-6 before TCZ administration was 27.91 (7.42–210.90) pg/mL. Serum IL-6 level tended to further spike firstly and then gradually decreased after TCZ therapy in 10 patients. A persistent and dramatic increase of IL-6 was observed in 2 patients who were finally dead. The CRP levels of 76.92% (10/13) of the patients were above the normal range before the start of TCZ therapy and gradually declined after the TCZ treatment. No. 1 and No. 10 patients finally died accompanied by the corresponding lymphocyte counts persistently dropping. No. 13 patient became exacerbated possibly due to inducing severe bacterial infection after TCZ treatment, while the other 10 patients showed clinical improvement. In summary, the study revealed that TCZ may have a certain therapeutic effect on severe COVID-19 patients with a risk of the cytokine storm. It is necessary to further evaluate the efficacy and safety of TCZ by rigorous randomized controlled trial in the next step.