Comparative Genomics of cpn60-Defined Enterococcus hirae Ecotypes and Relationship of Gene Content Differences to Competitive Fitness.

Natural microbial communities undergo selection-driven succession with changes in environmental conditions and available nutrients. In a previous study of the pig faecal Enterococcus community, we demonstrated that cpn60 universal target (UT) sequences could resolve phenotypically and genotypically distinct ecotypes of Enterococcus spp. that emerged over time in the faecal microbiome of growing pigs. In this study, we characterized genomic diversity in the identified Enterococcus hirae ecotypes in order to define further the nature and degree of genome content differences between taxa resolved by cpn60 UT sequences. Genome sequences for six representative isolates (two from each of three ecotypes) were compared. Differences in phosphotransferase systems and amino acid metabolism pathways for glutamine, proline and selenocysteine were observed. Differences in the lac family phosphotransferase system corresponded to lactose utilization phenotypes of the isolates. Competitive fitness of the E. hirae ecotypes was evaluated by in vitro growth competition assays in pig faecal extract medium. Isolates from E. hirae-1 and E. hirae-2 ecotypes were able to out-compete isolates from the E. hirae-3 ecotype, consistent with the relatively low abundance of E. hirae-3 relative to E. hirae-1 and E. hirae-2 previously observed in the pig faecal microbiome, and with observed differences between the ecotypes in gene content related to biosynthetic capacity. Results of this study provide a genomic basis for the definition of ecotypes within E. hirae and confirm the utility of the cpn60 UT sequence for high-resolution profiling of complex microbial communities.

CRISPRs of Enterococcus faecalis and E. hirae isolates from pig feces have species-specific repeats but share some common spacer sequences.

Clustered regularly interspaced short palindromic repeats (CRISPR) are currently a topic of interest in microbiology due to their role as a prokaryotic immune system. Investigations of CRISPR distribution and characterization to date have focused on pathogenic bacteria, while less is known about CRISPR in commensal bacteria, where they may have a significant role in the ecology of the microbiota of humans and other animals, and act as a recorder of interactions between bacteria and viruses. A combination of PCR and sequencing was used to determine prevalence and distribution of CRISPR arrays in Enterococcus faecalis and Enterococcus hirae isolates from the feces of healthy pigs. Both type II CRISPR-Cas and Orphan CRISPR (without Cas genes) were detected in the 195 isolates examined. CRISPR-Cas was detected in 52 (46/88) and 42 % (45/107) E. faecalis and E. hirae isolates, respectively. The prevalence of Orphan CRISPR arrays was higher in E. faecalis isolates (95 %, 84/88) compared with E. hirae isolates (49 %, 53/107). Species-specific repeat sequences were identified in Orphan CRISPR arrays, and 42 unique spacer sequences were identified. Only two spacers matched previously characterized pig virome sequences, and many were apparently derived from chromosomal sequences of enterococci. Surprisingly, 17 (40 %) of the spacers were detected in both species. Shared spacer sequences are evidence of a lack of species specificity in the agents and mechanisms responsible for integration of spacers, and the abundance of spacer sequences corresponding to bacterial chromosomal sequences reflects interspecific interactions within the intestinal microbiota.

COVID 19 Associated Mucormycosis: Preventable Risk Factors Leading to a Better Prognosis: A Case Series.

India was severely affected by the second wave of coronavirus disease (COVID­19), leading to sudden expansive spread of Mucormycosis, presenting with sinusitis, blackish mucus secretions, discolouration of palate, facial pain, swelling and blurring of vision. Hyperglycemia, hypercoagulable state and elevated levels of serum ferritin were the major contributing factors in progression of the deadly disease. To highlight the correlation between Diabetes Mellitus, hyperferritenimia and elevated levels of D-Dimer with increased rate of incidence and poor prognosis of the disease. This study was undertaken in KLES Dr Prabhakar Kore Hospital & MRC, Belagavi, including 30 patients, between April to July 2021. Serum ferritin, HbA1C and D-Dimer were evaluated for patients on admission, along with the other routine blood investigations. The mean age was 50 years (49.99 ± 1.8), with a male predominance of 83.33% (25 Male patients). 93.33% patients had uncontrolled Diabetes Mellitus with a mean value of 10.12% (± 0.37) indicating Diabetes Mellitus to be the prime risk factor. The raised levels of serum ferritin with a mean of 662.01 ng/ml (± 129.18) and high levels of D-Dimer (Mean- 761.33 ± 151.8 ng/ml) also demonstrated their role as interlinked factors. Mucor epidemic was caused by convergence of interlinked risk factors. Awareness of red flag clinical features, prompt diagnosis, early initiation of treatment with amphotericin-B with aggressive surgical debridement are essential for successful outcome, to avoid high rate of mortality and morbidity rates in the mucormycosis patients.