Identification, Genome Sequencing, and Characterizations of Sourced from Pakistan

Overview

Journal Microorganisms

Specialty Microbiology

Date 2023 Nov 25

PMID 38004670

Authors

Anees Fatima

Muhammad Ibrahim

Adil Naseer

Arshid Pervez

Muhammad Asad

Aamer Ali Shah

Fariha Hasan

Wadi B Alonazi

Ifra Ferheen

Samiullah Khan

Affiliations

Soon will be listed here.

Abstract

The stomach's colonization by () results in gastritis, ulcers, and stomach cancer. Frequently, pain is treated with medication, but resistant infections are not. Therefore, it is important to find pharmacological targets and improved treatments for resistant strains. The aim of the current study was sampling, identification, drug susceptibility testing following genome sequencing and comparative genome-wide analysis of selected strains from Pakistan with three representative strains for virulence and drug-resistant characteristics. Based on culture, biochemistry, and molecular biology, 84 strains of were identified, which made up 47% of the enrolled cases. Among all strains, the highest resistance was reported for metronidazole with 82 strains (98%), followed by clarithromycin with 62 resistant strains (74%). Among metronidazole-resistant strains, 38 strains (46%) were also resistant to clarithromycin, contributing 61% of clarithromycin resistant cases. Two strains, HPA1 and HPA2, isolated from 'gastritis' and 'gastric ulcer' patients, respectively, were further processed for WGS. The draft genome sequences of strains HPA1 and HPA2 encode 1.66 Mbp and 1.67 Mbp genome size, 24 and 4 contiguous DNA sequences, and 1650 and 1625 coding sequences, respectively. Both the genomes showed greater than 90% similarity with the reference strain ATCC 43504/PMSS1. The antibiotic-resistant genes were identified among all the strains with overall similarity above 95%, with minor differences in the sequence similarity. Using the virulent gene data obtained from the Virulence Factor Database, 75 to 85 virulent genes were identified in the five genome assemblies with various key genes such as cytolethal distending toxin (), type IV secretion system, PAI, plasticity region, cell-motility- and flagellar-associated genes, neutrophil-activating protein (HP-NAP), T4SS effector cytotoxin-associated gene A (), and urease-associated genes and etc. Sequence similarity between the virulence factors found in this study and reference genes was at least 90%. In summary, the results of our study showed the relationship between clinical results and specific strains' (HPA1 and HPA2) genetics such as antibiotic resistance and specific virulence factors. These findings provide valued understanding of the epidemiology of -associated diseases. Moreover, identification and genomics analysis have provided insights into the epidemiology, genetic diversity, pathogenicity, and potential drug resistance genes of strains, offering a foundation for developing more targeted and effective medical interventions, including anti-virulent medications.

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