Helicobacter pylori is a human gastric pathogen implicated as the major cause of peptic ulcer and second leading cause of gastric cancer (~70%) around the world. Conversely, an increased resistance to antibiotics and hindrances in the development of vaccines against H. pylori are observed. Pan-genome analyses of the global representative H. pylori isolates consisting of 39 complete genomes are presented in this paper. Phylogenetic analyses have revealed close relationships among geographically diverse strains of H. pylori. The conservation among these genomes was further analyzed by pan-genome approach; the predicted conserved gene families (1,193) constitute ~77% of the average H. pylori genome and 45% of the global gene repertoire of the species. Reverse vaccinology strategies have been adopted to identify and narrow down the potential core-immunogenic candidates. Total of 28 nonhost homolog proteins were characterized as universal therapeutic targets against H. pylori based on their functional annotation and protein-protein interaction. Finally, pathogenomics and genome plasticity analysis revealed 3 highly conserved and 2 highly variable putative pathogenicity islands in all of the H. pylori genomes been analyzed.

Methicillin-resistant Staphylococcus aureus (MRSA) is a multi-drug resistant and opportunistic pathogen. The emergence of new clones of MRSA in both healthcare settings and the community warrants serious attention and epidemiological surveillance. However, epidemiological data of MRSA isolates from Pakistan are limited. We performed a whole-genome-based comparative analysis of two (P10 and R46) MRSA strains isolated from two provinces of Pakistan to understand the genetic diversity, sequence type (ST), and distribution of virulence and antibiotic-resistance genes. The strains belong to ST113 and harbor the SCCmec type IV encoding mecA gene. Both the strains contain two plasmids, and three and two complete prophage sequences are present in P10 and R46, respectively. The specific antibiotic resistance determinants in P10 include two aminoglycoside-resistance genes, aph(3’)-IIIa and aad(6), a streptothrin-resistance gene sat-4, a tetracycline-resistance gene tet(K), a mupirocin-resistance gene mupA, a point mutation in fusA conferring resistance to fusidic acid, and in strain R46 a specific plasmid associated gene ant(4’)-Ib. The strains harbor many virulence factors common to MRSA. However, no Panton-Valentine leucocidin (lukF-PV/lukS-PV) or toxic shock syndrome toxin (tsst) genes were detected in any of the genomes. The phylogenetic relationship of P10 and R46 with other prevailing MRSA strains suggests that ST113 strains are closely related to ST8 strains and ST113 strains are a single-locus variant of ST8. These findings provide important information concerning the emerging MRSA clone ST113 in Pakistan and the sequenced strains can be used as reference strains for the comparative genomic analysis of other MRSA strains in Pakistan and ST113 strains globally.

An unknown pathogen that caused an unknown respiratory disease in humans was discovered in China city of Wuhan, where it was given the name "new coronavirus. “or COVID-19. COVID-19 epidemiology and clinical features in Pakistan is the focus of this study. Objective: This study aimed to evaluate the burden of COVID-19 in Swat, which might be helpful in preventing viral transmission in Pakistan. Methods: The current Retrospective study was carried out in a tertiary care hospital in district Swat Pakistan from April 2020 to June 2021. For the study, data were collected from local population who were suspicious or merely for screening reasons they visit to hospital at Swat Teaching Hospital, Swat, Pakistan. To find out the association between age group and COVID -19, a Chi-square test was used with a p-value less than 0.05. Results: A total of 11610 samples were analyzed in this study. The average patient's age was 40 years. Among total, there were 2230 (19%) cases were positive. The gender distributions of Covid-19, females were more affected 1128 (50.60%) than males 1102 (49.40%), but no significant difference in incidence rate. Adults accounted for COVID-19 active cases, 886 (40%) patients in the age range of 21-40 years, 686 (31%) in the age range of 41-60 years, 391 (17.5%), and 155 (7%), 45 (2%), and 40 (1.7%) patients in the age range of 61-80, 11-20, and 80-100 and 1-10 years, respectively. The research comprised a total of 27 older patients who met the locally recognized threshold of being elderly. A total of 40 (1.7%) of the juvenile patients were also infected. Conclusion: In this study patients in the age range of 21-40 years and compared to men females were more likely to be affected.