Comparative genomics analysis and characterization of Shiga toxin-producing Escherichia coli O157:H7 strains reveal virulence genes, resistance genes, prophages and plasmids.

Escherichia coli O157:H7 is a foodborne pathogen that has been linked to global disease outbreaks. These diseases include hemorrhagic colitis and hemolytic uremic syndrome. It is vital to know the features that make this strain pathogenic to understand the development of disease outbreaks. In the current study, a comparative genomic analysis was carried out to determine the presence of structural and functional features of O157:H7 strains obtained from 115 National Center for Biotechnology Information database. These strains of interest were analysed in the following programs: BLAST Ring Image Generator, PlasmidFinder, ResFinder, VirulenceFinder, IslandViewer 4 and PHASTER. Five strains (ECP19-198, ECP19-798, F7508, F8952, H2495) demonstrated a great homology with Sakai because of a few regions missing. Five resistant genes were identified, however, Macrolide-associated resistance gene mdf(A) was commonly found in all genomes. Majority of the strains (97%) were positive for 15 of the virulent genes (espA, espB, espF, espJ, gad, chuA, eae, iss, nleA, nleB, nleC, ompT, tccP, terC and tir). The plasmid analysis demonstrated that the IncF group was the most prevalent in the strains analysed. The prophage and genomic island analysis showed a distribution of bacteriophages and genomic islands respectively. The results indicated that structural and functional features of the many O157:H7 strains differ and may be a result of obtaining mobile genetic elements via horizontal gene transfer. Understanding the evolution of O157:H7 strains pathogenicity in terms of their structural and functional features will enable the development of detection and control of transmission strategies.

The Impact of SARS-CoV-2 Lineages (Variants) and COVID-19 Vaccination on the COVID-19 Epidemic in South Africa: Regression Study.

Background: Emerging SARS-CoV-2 variants have been attributed to the occurrence of secondary, tertiary, quaternary, and quinary COVID-19 epidemic waves threatening vaccine efforts owing to their immune invasiveness. Since the importation of SARS-CoV-2 in South Africa, with the first reported COVID-19 case on March 5, 2020, South Africa has observed 5 consecutive COVID-19 epidemic waves. The evolution of SARS-CoV-2 has played a major role in the resurgence of COVID-19 epidemic waves in South Africa and across the globe. Objective: We aimed to conduct descriptive and inferential statistical analysis on South African COVID-19 epidemiological data to investigate the impact of SARS-CoV-2 lineages and COVID-19 vaccinations in South African COVID-19 epidemiology. Methods: The general methodology involved the collation and stratification, covariance, regression analysis, normalization, and comparative inferential statistical analysis through null hypothesis testing (paired 2-tailed t tests) of South African COVID-19 epidemiological data. Results: The mean daily positive COVID-19 tests in South Africa's first, second, third, fourth, and fifth COVID-19 epidemic wave periods were 11.5% (SD 8.58%), 11.5% (SD 8.45%), 13.3% (SD 9.72%), 13.1% (SD 9.91%), and 14.3% (SD 8.49%), respectively. The COVID-19 transmission rate in the first and second COVID-19 epidemic waves in South Africa was similar, while the COVID-19 transmission rate was higher in the third, fourth, and fifth COVID-19 epidemic waves than in the aforementioned waves. Most COVID-19 hospitalized cases in South Africa were in the general ward (60%-79.1%). Patients with COVID-19 on oxygen were the second-largest admission status (11.2%-16.8%), followed by patients with COVID-19 in the intensive care unit (8.07%-16.7%). Most patients hospitalized owing to COVID-19 in South Africa's first, second, third, and fourth COVID-19 epidemic waves were aged between 40 and 49 years (16.8%-20.4%) and 50 and 59 years (19.8%-25.3%). Patients admitted to the hospital owing to COVID-19 in the age groups of 0 to 19 years were relatively low (1.98%-4.59%). In general, COVID-19 hospital admissions in South Africa for the age groups between 0 and 29 years increased after each consecutive COVID-19 epidemic wave, while for age groups between 30 and 79 years, hospital admissions decreased. Most COVID-19 hospitalization deaths in South Africa in the first, second, third, fourth, and fifth COVID-19 epidemic waves were in the ages of 50 to 59 years (15.8%-24.8%), 60 to 69 years (15.9%-29.5%), and 70 to 79 years (16.6%-20.7%). Conclusions: The relaxation of COVID-19 nonpharmaceutical intervention health policies in South Africa and the evolution of SARS-CoV-2 were associated with increased COVID-19 transmission and severity in the South African population. COVID-19 vaccination in South Africa was strongly associated with a decrease in COVID-19 hospitalization and severity in South Africa.

Atividade física e comportamento sedentário: comparação entre alunos de ensino médio e universitários / Comparison of physical activity and sedentary behavior levels in secondary and university students

Objetivo: comparar níveis de atividade física e comporta-mento sedentário entre estudantes de ensino médio e uni-versitários. Métodos: estudo transversal com 202 estudan-tes do ensino médio e 171 universitários. O Questionário Global de Atividade Física foi aplicado aos participantes. Porcentagens, os testes Qui-quadrado e Mann-Whitney, e regressão linear foram utilizados para a análise dos dados. Resultados: cerca de 63% e 32% dos estudantes de ensino médio e universitários, respectivamente, relataram níveis altos de atividade física, enquanto 84,7% e 71,9% deles, res-pectivamente, atenderam às diretrizes para comportamento sedentário. A pontuação dos estudantes de ensino médio foi significativamente maior que a dos alunos universitários em atividade física vigorosa (p=0,004), moderada (p<0,001), e total (p<0,001). As diferenças encontradas foram maio-res entre mulheres. Conclusão: os alunos do ensino médio apresentaram maiores escores de atividade física e despen-deram menos tempo em comportamentos sedentários. (AU)

Identification of novel semen and saliva specific methylation markers and its potential application in forensic analysis.

Differential DNA methylation in human tissues has been widely used to develop markers for body fluid identification in forensics. In the present study, identification of potential tissue specific differentially methylated regions (tDMRs) was based on mining differentially expressed genes in surrogate tissues for blood, saliva, semen and vaginal fluid. Genes specifically over expressed in one of the surrogate tissues viz: blood, salivary glands, testis, prostrate, cervix, uterus and ovary were identified from genome wide expression datasets. We hypothesized that over expression in surrogate tissues for body fluids could be correlated with differential methylation. Methylation information from two methylation datasets, NGSmethDB and ENCODE were integrated and heavily methylated gene body CpG islands (CGI) representing the body fluids were extracted. From a total of 53 potential genes the present study reports, two genes, ZNF282 and HPCAL1 which were preferentially expressed in cervix with comparatively reduced expression in other surrogate tissues. Methylated CGIs were targeted to design primers for methylation specific PCR (MSP) and bisulphite sequencing (BS). The ZNF282 CpG sites displayed semen-specific hypomethylation while HPCAL1 CpGs showed saliva-specific hypomethylation. Clone-based bisulphite sequencing also revealed significant hypomethylation in the target body fluids. To evaluate the stability of methylation profiles, the ZNF282 tDMR was tested and each body fluid was subjected to five different forensic simulated conditions (dry at room temperature, wet in an exicator, outside on the ground, sprayed with alcohol and sprayed with bleach) for 50 days. Under the condition "outside on the ground", saliva showed a significant decrease in methylation level by bisulphite sequencing analysis over time. Complete methylation profiles were obtained only for vaginal fluid under all conditions and no differences in methylation levels were observed for this fluid after 50 days. Thus, ZNF282 and HPCAL1 tDMRs can be used as reliable semen and saliva identification markers respectively.