Metagenomic analysis of fecal samples in colorectal cancer Egyptians patients post colectomy: A pilot study.

One of the most prevalent malignancies that significantly affects world health is colorectal cancer (CRC). While genetics are involved in a portion of CRC patients, most cases are sporadic. The microbiome composition could be a new source of tumor initiation and progression. This research was conducted to investigate the microbiota composition of CRC patients post colectomy at taxonomic and functional levels. Using a next-generation sequencing approach, using an Illumina Novaseq 6000, the fecal samples of 13 patients were analyzed and the obtained data was subjected to a bioinformatics analysis. The bacterial abundance and uniqueness varied in CRC patients alongside differences in bacterial counts between patients. Bacteroides fragilis, Bacteroides vulgatus, Escherichia coli, and Fusobacterium nucleatum were among the pro-cancerous microorganisms found. Concurrently, bacteria linked to CRC progression were detected that have been previously linked to metastasis and recurrence. At the same time, probiotic bacteria such as Bifidobacterium dentium, Bifidobacterium bifidum, and Akkermansia muciniphila increased in abundance after colectomies. Additionally, numerous pathways were deferentially enriched in CRC, which emerged from functional pathways based on bacterial shotgun data. CRC-specific microbiome signatures include an altered bacterial composition. Our research showed that microbial biomarkers could be more usefully employed to explore the link between gut microbiota and CRC using metagenomic techniques in the diagnosis, prognosis, and remission of CRC, thereby opening new avenues for CRC treatment.

Multi-omics analysis of fecal samples in colorectal cancer Egyptians patients: a pilot study.

BACKGROUND: Colorectal cancer (CRC) is a public health concern and the second most common disease worldwide. This is due to genetic coding and is influenced by environmental aspects, in which the gut microbiota plays a significant role. The purpose of this study was to compare the microbiota makeup of CRC patients with that of healthy control and to identify upregulated and downregulated proteins and metabolites in CRC patients. Using a next-generation sequencing approach, fecal samples of five females (4 CRC patients and one healthy control) were analyzed by BGI DNBSEQ-T7, Hong Kong, China. Furthermore, proteomics and metabolomics analysis were performed using LC-MS/MS technique. RESULTS: Dysbiosis of gut microbiota has been observed in patients with CRC, with an increase in microbiota diversity at all taxonomic levels relative to healthy control. Where, at the functional level the bacterial species participate in many different pathways among them de novo nucleotide synthesis and amino acids pathways were aberrantly upregulated in CRC patients. Proteomics and metabolomics profiles of CRC patients showed different proteins and metabolites, a total of 360 and 158 proteins and metabolites, respectively were highly expressed compared to healthy control with fold change ≥ 1.2. Among the highly expressed proteins were transketolase, sushi domain-containing protein, sulfide quinone oxidoreductase protein, AAA family ATPase protein, carbonic anhydrase, IgG Fc-binding protein, nucleoside diphosphate kinase protein, arylsulfatase, alkaline phosphatase protein, phosphoglycerate kinase, protein kinase domain-containing protein, non-specific serine/threonine protein kinase, Acyl-CoA synthetase and EF-hand domain-containing protein. Some of the differential metabolites, Taurine, Taurocholic acid, 7-ketodeoxycholic acid, Glycochenodeoxycholic acid, Glycocholic acid, and Taurochenodeoxycholic acid that belong to bile acids metabolites. CONCLUSIONS: Some bacterial species, proteins, and metabolites could be used as diagnostic biomarkers for CRC. Our study paves an insight into using multi-omics technology to address the relationship between gut microbiota and CRC.

Molecular Characterization of ß-Lactam Resistant Streptococcus pneumoniae.

BACKGROUND: Streptococcus pneumoniae (S. pneumoniae) is a commensal bacterium that normally colonizes the human nasopharyngeal cavity. Once disseminated, it can cause several diseases, ranging from non-invasive infections such as acute otitis media and sinusitis through to invasive infections with higher mortality. Antibiotic resistance among S. pneumoniae has increased dramatically and penicillin-resistant strains have spread worldwide with pneumococcus also being resistant to other types of antibiotics like erythromycin, tetracycline, and chloram-phenicol. The aim of the present study was to study the susceptibility of the isolated strains to ß-lactam and other antibiotics from different classes and to determine the prevalence of ß-lactam resistance genes among S. pneumoniae clinical isolates. METHODS: From a total of 178 sputum samples, isolates identified by standard microbiological method as S. pneu-moniae were subjected to antibiotic susceptibility tests to ß-lactam and non ß-lactam antimicrobial agents by disk diffusion method. Biofilm formation was detected by microtitration plate and the resistance genotype was also determined using multiplex PCR technique with primers designed for PBP genes. RESULTS: Out of 178 sputum samples, sixty isolates were recovered as Streptococcus pneumoniae. Most of isolates were multidrug-resistant (MDR) possessing a high (> 0.2) multiple antibiotic resistance index (MAR) value. Biofilm formation ability of isolates were strong, moderate, weak, and none, accounting for 21.67%, 45%, 25%, and 8.33% biofilm formers, respectively, and it was found that pbp1a, pbp2b, and pbp2x were present in 33 (55%), 25 (41.7%), and 45 (75%) of isolates, respectively. CONCLUSIONS: Streptococcus pneumoniae clinical isolates have an alteration in PBP resistance genes in response to ß-lactam therapy which subsequently lead to increased MDR phenomena among these clinically important pathogens. These findings necessitate continuous monitoring of antimicrobial resistance to guide the empirical treatment of pneumococcal disease, as well as to encourage reflections to support public immunizations strategies.