Carriage of distinct blaKPC-2 and blaOXA-48 plasmids in a single ST11 hypervirulent Klebsiella pneumoniae isolate in Egypt

Background Carbapenem-resistant hypervirulent K. pneumoniae (CR-hvKP) causes serious infections with significant morbidity and mortality. However, the epidemiology and transmission mechanisms of CR-hvKP and the corresponding carbapenem-resistant plasmids require further investigation. Herein, we have characterized an ST11 K. pneumoniae strain EBSI041 from the blood sample encoding both hypervirulence and carbapenem resistance phenotypes from a patient in Egypt. Results K. pneumoniae strain EBSI041 showed multidrug-resistance phenotypes, where it was highly resistant to almost all tested antibiotics including carbapenems. And hypervirulence phenotypes of EBSI041 was confirmed by the model of Galleria mellonella infection. Whole-genome sequencing analysis showed that the hybrid plasmid pEBSI041-1 carried a set of virulence factors rmpA, rmpA2, iucABCD and iutA, and six resistance genes aph(3′)-VI, armA, msr(E), mph(E), qnrS, and sul2. Besides, blaOXA-48 and blaSHV-12 were harboured in a novel conjugative IncL-type plasmid pEBSI041-2. The blaKPC-2-carrying plasmid pEBSI041-3, a non-conjugative plasmid lacking the conjugative transfer genes, could be transferred with the help of pEBSI041-2, and the two plasmids could fuse into a new plasmid during co-transfer. Moreover, the emergence of the p16HN-263_KPC-like plasmids is likely due to the integration of pEBSI041-3 and pEBSI041-4 via IS26-mediated rearrangement. Conclusion To the best of our knowledge, this is the first report on the complete genome sequence of KPC-2- and OXA-48-coproducing hypervirulent K. pneumoniae from Egypt. These results give new insights into the adaptation and evolution of K. pneumoniae during nosocomial infections.

DO PROBIOTICS HAVE A FUTURE IN NEONATOLOGY? (ANALYSIS OF THE LATEST DATA. PART 3)

The issue of feasibility and effectiveness of probiotics use in newborns is still discussable. A position letter of the Committee on nutrition of the European Society for Pediatric NutritionGastroenterology, Hepatology, and(ESPGHAN) and the Working group of the ESPGHAN on probiotics and prebiotics issues was published in May 2020 in “Pediatric Gastroenterology and Nutrition” magazine as for the use of probiotics in premature newborns. The third part of the literature continues with the position paper and the results of many randomized controlled clinical trials of probiotics. The article considers the answers to 6 clinical questions posed by the working group of the Committee to assess the feasibility of use, routes of administration, dosage and duration of use, as well as the effectiveness and quality of probiotic drugs. It was proved that probiotics, in general, could decrease the level of necrotising enterocolitis, sepsis, and mortality. On the other hand, an increasing number of commercial products containing probiotics of non optimal quality are available. In addition, a large number of departments in the world regularly suggest probiotic supplements as a treatment standard despite the absence of any solid evidence. Moreover, the emphasis was placed on issues of safety of probiotic supplements for premature newborns. Guarantee of quality of probiotic product is deliverance of probiotic strains by transfer genes of resistance to antibiotics, the ability to regularly detect sepsis while using probiotics.

Next-Generation Vaccines Based on Self-Amplifying RNA

Recently, nucleic acid-based RNA and DNA vaccines have represented a better solution to avoid infectious diseases than “traditional” live and non-live vaccines. Synthetic RNA and DNA molecules allow scalable, rapid, and cell-free production of vaccines in response to an emerging disease such as the current COVID-19 pandemic. The development process begins with laboratory transcription of sequences encoding antigens, which are then formulated for delivery. The various potent of RNA over live and inactivated viruses are proven by advances in delivery approaches. These vaccines contain no infectious elements nor the risk of stable integration with the host cell genome compared to conventional vaccines. Conventional mRNA-based vaccines transfer genes of interest (GOI) of attenuated mRNA viruses to individual host cells. Synthetic mRNA in liposomes forms a modern, refined sample, resulting in a safer version of live attenuated RNA viruses. Self-amplifying RNA (saRNA) is a replicating version of mRNA-based vaccines that encode both (GOI) and viral replication machinery. saRNA is required at lower doses than conventional mRNA, which may improve immunization. Here we provide an overview of current mRNA vaccine approaches, summarize highlight challenges and recent successes, and offer perspectives on the future of mRNA vaccines.

DO PROBIOTICS HAVE A FUTURE IN NEONATOLOGY?

The issue of feasibility and effectiveness of probiotics use in newborns is still discussable. A position letter of the Committee on nutrition of the European Society for Pediatric Gastroenterology, Hepatology, and Nutrition (ESPGHAN) and the Working group of the ESPGHAN on probiotics and prebiotics issues was published in May 2020 in “Pediatric Gastroenterology and Nutrition” magazine as for the use of probiotics in premature newborns. It stated that over 10,000 premature newborns from all over the world had taken part in random controlled probiotics tests. It was proved that probiotics, in general, could decrease the level of necrotizing enterocolitis, sepsis, and mortality. But the question of choice of microorganism strains, dosing, and duration of medication course remains open. On the other hand, an increasing number of commercial products containing probiotics of non optimal quality are available. In addition, a large number of departments in the world regularly suggest probiotic supplements as a treatment standard despite the absence of any solid evidence. According to the data of the latest meta-analysis, effectiveness in decreasing mortality and incidence was found in the minority of investigated strains or combinations. In the position letter authors wanted to give advice which specific strains can be potentially used and which cannot. Moreover, the emphasis was placed on issues of safety of probiotic supplements for premature newborns. Guarantee of quality of probiotic product is deliverance of probiotic strains by transfer genes of resistance to antibiotics and the possibility of regular identification of probiotic sepsis. There is a conditional recommendation (with a low credibility of evidence) to provide eitherLactobacillus rhamnosus GG ATCC53103, or combination of Bifidobacterium infantis Bb-02, Bifidobacterium lactis Bb-12, and Streptococcus thermophilus TH-4 for decreasing a risk of the necrotizing enterocolitis development subject to all issues of safety.

Strange Genetics

This chapter relates how, in the 1950s, Esther and Joshua Lederberg and their colleagues uncovered a whole new kind of genetic transfer involving plasmids and viruses. In plants and animals, genetic recombination is integrated within the processes of sexual reproduction. Imagine if you could trade genes with strangers at will! That’s what bacteria can do. Esther Lederberg’s discoveries of the F-plasmid and the λ‎ bacteriophage were happy accidents that occurred while she working to complete her dissertation research. Serendipity happens to those who are very attentive, broadly experienced, and open to surprises. Esther Lederberg discovered a transferable factor, the F-factor, that could transform recipients into donors. Then she discovered a lysogenic virus, hiding harmlessly inside the chromosome of its bacterial host. These two surprising discoveries showed that bacteria could transfer genes and pieces of chromosomes horizontally, as opposed to the classical inheritance of plants and animals which pass on genetic traits vertically, down through generations.

PixR, a novel activator of conjugative transfer of IncX4 resistance plasmids, mitigates the fitness cost of mcr-1 carriage in Escherichia coli

The emergence of the plasmid-borne colistin resistance gene mcr-1 threats public health. IncX4-type plasmids are one of the most epidemiologically successful vehicles for spreading mcr-1 worldwide. Since MCR-1 is known for imposing a fitness cost to its host bacterium, the successful spread of mcr-1-bearing plasmids might be linked to high conjugation frequency, which would enhance the maintenance of the plasmid in the host without antibiotic selection. However, the mechanism of IncX4 plasmids conjugation remains unclear. In this study, we used high-density transposon mutagenesis to identify factors required for IncX4 plasmid transfer and 18 genes were identified, including five with annotations unrelated to conjugation. The Cappable-seq and RNA-seq analysis confirmed that a novel transcriptional regulator gene, pixR, directly regulates the transfer of IncX4 plasmids by binding the promoter of 13 essential transfer genes to increase their transcription. Plasmid invasion and co-culture competition assays revealed that pixR is essential for the spread and persistence of mcr-1>-bearing IncX4 plasmids in bacterial populations, and effective conjugation is crucial for alleviating the fitness cost exerted by mcr-1 carriage. The existence of the IncX4-specific pixR gene increases plasmid transmissibility while promoting the invasion and persistence of mcr-1-bearing plasmids in bacterial populations, which helps explain their global prevalence.

Plasmid- and strain-specific factors drive variation in ESBL-plasmid spread in vitro and in vivo

Horizontal gene transfer, mediated by conjugative plasmids, is a major driver of the global rise of antibiotic resistance. However, the relative contributions of factors that underlie the spread of plasmids and their roles in conjugation in vivo are unclear. To address this, we investigated the spread of clinical Extended Spectrum Beta-Lactamase (ESBL)-producing plasmids in the absence of antibiotics in vitro and in the mouse intestine. We hypothesised that plasmid properties would be the primary determinants of plasmid spread and that bacterial strain identity would also contribute. We found clinical Escherichia coli strains natively associated with ESBL-plasmids conjugated to three distinct E. coli strains and one Salmonella enterica serovar Typhimurium strain. Final transconjugant frequencies varied across plasmid, donor, and recipient combinations, with qualitative consistency when comparing transfer in vitro and in vivo in mice. In both environments, transconjugant frequencies for these natural strains and plasmids covaried with the presence/absence of transfer genes on ESBL-plasmids and were affected by plasmid incompatibility. By moving ESBL-plasmids out of their native hosts, we showed that donor and recipient strains also modulated transconjugant frequencies. This suggests that plasmid spread in the complex gut environment of animals and humans can be predicted based on in vitro testing and genetic data.

The History of Methicillin-Resistant Staphylococcus aureus in Brazil

Since the emergence of MRSA in the 1960s, a gradual increase in infections by resistant bacteria has been observed. Clinical manifestations may vary from brand to critical condition due to host risk factors, as well as pathogen virulence and resistance. The high adaptability and pathogenic profile of MRSA clones contributed to its spread in hospital and community settings. In Brazil, the first MRSA isolates were reported in the late 1980s, and since then different genetic profiles, such as the Brazilian epidemic clone (BEC) and other clones considered a pandemic, became endemic in the Brazilian population. Additionally, Brazil’s MRSA clones were shown to be able to transfer genes involved in multidrug resistance and enhanced pathogenic properties. These events contributed to the rise of highly resistant and pathogenic MRSA. In this review, we present the main events which compose the history of MRSA in Brazil, including numbers and locations of isolation, as well as types of staphylococcal cassette chromosome mec (SCCmec) found in the Brazilian territory.

Unexpected conservation and global transmission of agrobacterial virulence plasmids

The accelerated evolution and spread of pathogens are threats to host species. Agrobacteria require an oncogenic Ti or Ri plasmid to transfer genes into plants and cause disease. We developed a strategy to characterize virulence plasmids and applied it to analyze hundreds of strains collected between 1927 and 2017, on six continents and from more than 50 host species. In consideration of prior evidence for prolific recombination, it was surprising that oncogenic plasmids are descended from a few conserved lineages. Characterization of a hierarchy of features that promote or constrain plasticity allowed inference of the evolutionary history across the plasmid lineages. We uncovered epidemiological patterns that highlight the importance of plasmid transmission in pathogen diversification as well as in long-term persistence and the global spread of disease.