Distinct Expansion of Group II Introns Depends on the Type of Intron-encoded Protein and Genomic Signatures in Prokaryotes

Group II introns (G2Is) are self-splicing ribozymes that have retroelement characteristics in prokaryotes. Although G2Is are considered an important factor in the evolution of prokaryotes, comprehensive analyses of these introns among the tens of thousands of prokaryotic genomes currently available are still limited. Here, we developed a bioinformatic pipeline that systematically collects G2Is and applied it to prokaryotic genomes. We found that in bacteria, 25% (447 of 1,790) of the total representative species had an average of 5.3 G2Is, and in archaea, 9% (28 of 296) of the total representative species had an average of 3.0 G2Is. The greatest number of G2Is per species was 101 in Arthrospira platensis (phylum Cyanobacteriota). A comprehensive sequence analysis of the intron-encoded protein (IEP) in each G2I sequence was conducted and resulted in the addition of three new IEP classes (U1–U3) to the previous classification. This analysis suggested that about 30% of all IEPs are noncanonical IEPs. The number of G2Is per species was defined almost at the phylum level, and the type of IEP was associated as a factor in the G2I increase, i.e. there was an explosive increase in G2Is with bacterial C-type IEPs in the phylum Firmicutes and in G2Is with CL-type IEPs in the phylum Cyanobacteriota. We also systematically analyzed the relationship between genomic signatures and the mechanism of these increases in G2Is. This is the first study to systematically characterize G2Is in the prokaryotic phylogenies.

Feed Quality and Feeding Level Effects on Faecal Composition in East African Cattle Farming Systems

Effects of feeding levels below maintenance requirements of metabolizable energy (MER) and of feed supplementation on fecal nutrient and microbial C concentrations were evaluated. In experiment 1, Rhodes grass hay only was offered to Boran steers at 80%, 60%, and 40% of individual MER, while steers at 100% MER additionally received a concentrated mixture. This reduction in MER decreased N, increased fungal C but did not affect bacterial C concentrations in feces. In experiment 2, Holstein × Boran heifers were offered a poor-quality roughage diet without supplement, with sweet potato vine silage or with a urea-molasses block. These two supplements did not affect the fecal chemical composition or fungal C but increased bacterial C concentrations in feces. Across all data, the fungal C/bacterial C ratio was positively related to N and negatively to neutral detergent fiber concentrations in feces, indicating diet-induced shifts in the fecal microbial community.

Effectiveness of Antibacterial Prophylaxis during Induction Chemotherapy in Children with Acute Lymphoblastic Leukemia

Background. Pediatric patients with newly diagnosed acute lymphoblastic leukemia (ALL) are at high risk for developing bacterial infections, particularly during the induction treatment phase. Infections are the primary cause of treatment-related mortality during the induction phase, and also lead to prolonged hospitalization, as well as delays and dose modifications in planned chemotherapy. On DFCI ALL Consortium Protocol 05-001 (2005-2011), 26.6% of 794 enrolled patients (pts) experienced at least one infectious complication during induction. In the subsequent study, DFCI Protocol11-001, we studied whether the use of prophylactic fluoroquinolones during induction would decrease the incidence of bacterial infections. Patients and methods.Between 2012-2015, 229 pts with ALL (aged 1-21 years) were enrolled on Protocol 11-001 at 9 participating sites. Induction therapy, regardless of risk group, included vincristine, methylprednisolone, doxorubicin, low-dose methotrexate and pegylated L-asparaginase. Afebrile pts were started on fluoroquinolone prophylaxis at the time of initiation of therapy and continued until count recovery at the end of induction. Pts were switched to broad-spectrum antibiotics (eg, cefepime) for fever or documented infection. Pts with fever at presentation were started on broad spectrum antibiotics rather than fluoroquinolone, and either remained on broad-spectrum antibiotics or were switched to fluoroquinolone prophylaxis until count recovery per treating clinician. Antifungal prophylaxis was not required. All episodes of microbiologically documented bacterial infection, microbiologically and/or radiographically documented fungal infection, and Clostridium difficile (C. diff) enterocolitis were prospectively collected. Using a 1-sample binomial test, rates of infections on Protocol 11-001 were compared to those from the predecessor study, DFCI Protocol 05-001, which included nearly identical induction chemotherapy but did not include guidelines regarding antibiotic prophylaxis or duration during induction. Results. Of the 229 pts, 89% had B-ALL and 11% T-ALL. Median age was 5.1 yrs (range 1.0-20.9). Eighty-six afebrile pts (37.5%) were administered upfront antibiotic prophylaxis and 141 (61.6%) had fever at diagnosis and received broad-spectrum antibiotics; two afebrile patients did not receive antibiotic prophylaxis for unknown reasons. Of the 86 pts who began prophylaxis, 37 (43%) subsequently developed fever. Toxicity data was available for 222 pts. Thirty-eight episodes of infection occurred in 29 patients. Age, presenting white blood cell count and immunophenotype were not associated with the development of infection. The proportion of pts experiencing an infection on Protocol 11-001 (13.1%) was significantly lower than on Protocol 05-001 (26.6%, p<0.0001) [Figure 1]. The observed reduction was due to a decrease in the incidence of bacterial infection (9.9% vs 24.7%, p<0.0001). Of note, there were significantly fewer episodes of bacteremias due to Gram negative rods, S. aureus and S. viridans on Protocol 11-001 compared to 05-001. There was no significant difference in incidence of fungal infection between the two protocols (4.5% vs 3.9%, p=0.32). Twenty (9%) pts on 11-001 developed C. diff colitis during induction (16 Grade 2, 3 Grade 3, 1 Grade 4). The induction death rate on Protocol l 11-001 was 0.9% compared with 2% on Protocol 05-001 (p=0.24). Conclusion.The results of our prospective, multi-institutional non-randomized study indicate that treating newly diagnosed pediatric ALL pts with antibiotics throughout the induction phase (including the use of antibiotic prophylaxis for afebrile pts) is effective at reducing the incidence of bacterial infections, and does not result in an increase in fungal infections or a high incidence of C. diff colitis. Additional larger, randomized studies are necessary to confirm the safety and efficacy of this approach during the induction phase. Figure 1. Rate of induction (A) overall (bacterial/fungal), (B) bacterial, (C) fungal infections on Protocols 05-001 and 11-001 Figure 1. Rate of induction (A) overall (bacterial/fungal), (B) bacterial, (C) fungal infections on Protocols 05-001 and 11-001 Disclosures No relevant conflicts of interest to declare.