Single Nucleotide Polymorphism Analysis Indicates Genetic Distinction and Reduced Diversity of Swine-Associated Methicillin Resistant Staphylococcus aureus (MRSA) ST5 Isolates Compared to Clinical MRSA ST5 Isolates

Livestock associated methicillin resistant S. aureus (LA-MRSA) are lineages adapted to livestock species. LA-MRSA can be transmitted to humans and public health concerns exist because livestock may be the largest MRSA reservoir outside of hospital settings. Although the predominant European (ST398) and Asian (ST9) lineages of LA-MRSA are considered livestock adapted, North American swine also harbor ST5, a globally disseminated and highly pathogenic lineage. This study applied whole genome sequencing and single nucleotide polymorphism (SNP) typing to compare the population structure and genetic relatedness between swine associated and human clinical MRSA ST5 isolates. The established high-resolution phylogenomic framework revealed that LA-MRSA and human clinical MRSA ST5 are genetically distinct. LA-MRSA isolates were found to be clonal within farms, while greater genome diversity was observed among sampled clinical MRSA ST5. Analysis of the accessory genome demonstrated that LA-MRSA ST5 isolates and clinical MRSA ST5 isolates harbor different AMR genes and virulence factors, consistent with the SNP analysis. Collectively, our data indicate LA-MRSA and clinical MRSA ST5 isolates are distinct and the swine reservoir is likely of minimal significance as a source of clinical MRSA ST5 infections

Closed genome and comparative phylogenetic analysis of the clinical multidrug resistant Shigella sonnei strain 866

Shigella sonneiis responsible for the majority of shigellosis infections in the US with over 500,000 cases reported annually. Here, wepresent the complete genome of the clinical multidrug resistant (MDR) strain 866, which is highly susceptible to bacteriophageinfections. The strain has a circular chromosome of 4.85 Mb and carries a 113 kb MDR plasmid. This IncB/O/K/Z-type plasmid, termedp866, confers resistance to five different classes of antibiotics including ß-lactamase, sulfonamide, tetracycline, aminoglycoside, andtrimethoprim. Comparative analysis of the plasmid architecture and gene inventory revealed that p866 shares its plasmid backbonewith previously described IncB/O/K/Z-typeShigellaspp. andEscherichiacoliplasmids, but is differentiated by the insertion of antibioticresistance cassettes, which we found associated with mobile genetic elements such as Tn3, Tn7, and Tn10. A whole genome-derivedphylogenetic reconstruction showed the evolutionary relationships ofS. sonneistrain 866 and the four establishedShigellaspecies,highlighting the clonal nature ofS. sonnei

Tuberculosis and COVID-19 in the elderly: factors driving a higher burden of disease

Mycobacterium tuberculosis (M.tb) and SARS-CoV-2 are both infections that can lead to severe disease in the lower lung. However, these two infections are caused by very different pathogens (Mycobacterium vs. virus), they have different mechanisms of pathogenesis and immune response, and differ in how long the infection lasts. Despite the differences, SARS-CoV-2 and M.tb share a common feature, which is also frequently observed in other respiratory infections: the burden of disease in the elderly is greater. Here, we discuss possible reasons for the higher burden in older adults, including the effect of co-morbidities, deterioration of the lung environment, auto-immunity, and a reduced antibody response. While the answer is likely to be multifactorial, understanding the main drivers across different infections may allow us to design broader interventions that increase the health-span of older people

Estudio del fago portador de la “Cytolethal Distending Toxin” de tipo V en el medio ambiente

La toxina Cdt (“Cytolethal Distending Toxin”) fue descrita por primera vez en 1987 por Johnson y Lior como una nueva toxina producida por Escherichia coli. Es una toxina de tipo AB2 que bloquea el ciclo celular eucariota en las fases G2/M de la mitosis, cosa que provoca una distensión celular de hasta 5 veces el tamaño normal, y finalmente se produce la apoptosis. En la actualidad, la Cdt ha sido descrita en un gran número de bacterias Gram negativas como Vibrio, Helicobacter, o Campylobacter, entre otros. Está codificada por tres genes adyacentes (cdtA, cdtB y cdtC) que muestran diferentes grados de similitud entre géneros, siendo CdtB la subunidad catalítica que actúa como una ADNasa de tipo I, y CdtA y CdtC las subunidades que transportan a CdtB al núcleo. En E. coli han sido descritas 5 variantes, localizadas en el cromosoma (Cdt-II), en el plásmido pVir (Cdt-III) o rodeadas de secuencias homólogas a genes de fagos de tipo lambda o P2 (Cdt-I, Cdt-IV y Cdt-V). El hecho de que cdt se encuentre en diferentes géneros bacterianos con secuencias adyacentes homólogas a genes de fagos, así como que no aparezca asociado significativamente a otros factores de virulencia, sugiere que estos genes cdt son adquiridos por transferencia horizontal a través de fagos. Estos fagos Cdt pueden ser inducidos a partir de la cepa huésped y transmitir el gen de la toxina a otras cepas, causando la aparición de nuevas cepas virulentas. Además de en ambientes clínicos, se han encontrado fagos Cdt en agua residual y, tal como veremos en este estudio, también en agua de río, hecho que refuerza su potencial papel como transmisores de la toxina en el medio ambiente. Por tanto, un aspecto importante a tener en cuenta es la persistencia y la estabilidad de estos fagos en las diferentes condiciones ambientales. Por ello, en este trabajo, se ha estudiado la estabilidad de los fagos Cdt bajo diferentes condiciones de temperatura (4ºC, 22ºC y 37ºC) y pH (3, 7 y 9), y bajo diferentes tratamientos de inactivación: calor (60ºC y 70ºC, 30 y 60 min), luz UV (1, 5, 10 y 30 min), cloración (1, 3, 5, 10, 20 y 30 min) e inactivación natural. Para ello se han aislado dos fagos Cdt-V de muestras ambientales, y se han monitorizado mediante ensayos de infectividad (ufp/ml) y mediante cuantificación de copias genómicas por qPCR en cada una de las condiciones ensayadas. Además, se han comparado los resultados obtenidos con la estabilidad de fagos Stx, también de elevada persistencia ambiental, bajo las mismas condiciones. Por su propia naturaleza, y tal y como se ha visto en este trabajo y en estudios anteriores, los fagos son mucho más resistentes a ciertos tratamientos de desinfección e inactivación natural que las bacterias huésped, reafirmando su papel como reservorios de genes de virulencia en el medio ambiente. Además, se han descrito ciertas morfologías de fagos que permitirían una mayor persistencia a dichos tratamientos. Si los fagos consiguen sobrevivir a los tratamientos comúnmente utilizados en la eliminación de las bacterias, podrían transducir el gen de la toxina a otras cepas. Por tanto, no se puede descartar su potencial en la generación de nuevas cepas patógenas emergentes. Además de la persistencia de los fagos Cdt-V, también se ha estudiado su capacidad de inducción y de generación de lisógenos, así como su morfología y su estructura genética. Gracias a ello, se ha podido determinar a qué familia pertenecen y observar su capacidad de evolución y adaptación al lisogenizar a un nuevo huésped.Cdt toxin (“Cytolethal Distending Toxin”) was first described by Johnson and Lior in 1987. It is an AB5 toxin that blocks the eukariotic cell cycle between G2 and M phases, which distends the cells, since cell division ceases but growth continues. Cdt is produced by different Gram negative pathogenic microorganisms, including Escherichia coli, Vibrio, Campylobacter and Helicobacter, among others. It consists of three subunits (CdtA, CdtB, and CdtC) that are encoded by three adjacent genes. The catalytic subunit CdtB is homologous to DNase I and it is the most conserved gene, and the other subunits act as binding proteins that deliver CdtB into target cells. Five variants of the toxin have been reported in E. coli, located in the chromosome (Cdt-II), in the conjugative plasmid pVir (Cdt-III) or flanked by lambda-like or P2 bacteriophage genes (Cdt-I, Cdt-IV and Cdt-V). The fact that Cdt is present in different microorganisms and, in some cases flanked by bacteriophage genes, and not significantly associated to other virulence factors, suggest that cdt genes are acquired by horizontal transfer by means of bacteriophages. These Cdt phages could be induced from the host and transduce the toxin to other strains, causing the emergence of new virulent strains. Cdt phages have not only been isolated from clinical samples, but also from environmental samples. For the potential role of these phages in cdt transduction, it is important to consider and study the persistence of Cdt phages in different environmental conditions. In this work, it has been studied the stability of two Cdt phages isolated from the environment under different conditions and inactivation treatments (temperature, pH, heat treatment, UV treatment, chlorination and natural inactivation). Moreover, the results were compared with Stx phages stability (that also have a significantly environmental prevalence) under the same conditions. The fact that Cdt and Stx phages and, in general, all phages, are more resistent to all the treatments and conditions than their natural hosts, reinforces their potential role as a reservoir of virulence genes in the environment. We have also characterized Cdt phages: its capacity of induction and lisogenization, morphology and genetic structure, to understand better the performance of these phages

Mycobacteriophages as Potential Therapeutic Agents against Drug-Resistant Tuberculosis

The current emergence of multi-, extensively-, extremely-, and total-drug resistant strains of Mycobacterium tuberculosis poses a major health, social, and economic threat, and stresses the need to develop new therapeutic strategies. The notion of phage therapy against bacteria has been around for more than a century and, although its implementation was abandoned after the introduction of drugs, it is now making a comeback and gaining renewed interest in Western medicine as an alternative to treat drug-resistant pathogens. Mycobacteriophages are genetically diverse viruses that specifically infect mycobacterial hosts, including members of the M. tuberculosis complex. This review describes general features of mycobacteriophages and their mechanisms of killing M. tuberculosis, as well as their advantages and limitations as therapeutic and prophylactic agents against drug-resistant M. tuberculosis strains. This review also discusses the role of human lung micro-environments in shaping the availability of mycobacteriophage receptors on the M. tuberculosis cell envelope surface, the risk of potential development of bacterial resistance to mycobacteriophages, and the interactions with the mammalian host immune system. Finally, it summarizes the knowledge gaps and defines key questions to be addressed regarding the clinical application of phage therapy for the treatment of drug-resistant tuberculosis

Mycobacteriophages as Potential Therapeutic Agents against Drug-Resistant Tuberculosis

The current emergence of multi-, extensively-, extremely-, and total-drug resistant strains of Mycobacterium tuberculosis poses a major health, social, and economic threat, and stresses the need to develop new therapeutic strategies. The notion of phage therapy against bacteria has been around for more than a century and, although its implementation was abandoned after the introduction of drugs, it is now making a comeback and gaining renewed interest in Western medicine as an alternative to treat drug-resistant pathogens. Mycobacteriophages are genetically diverse viruses that specifically infect mycobacterial hosts, including members of the M. tuberculosis complex. This review describes general features of mycobacteriophages and their mechanisms of killing M. tuberculosis, as well as their advantages and limitations as therapeutic and prophylactic agents against drug-resistant M. tuberculosis strains. This review also discusses the role of human lung micro-environments in shaping the availability of mycobacteriophage receptors on the M. tuberculosis cell envelope surface, the risk of potential development of bacterial resistance to mycobacteriophages, and the interactions with the mammalian host immune system. Finally, it summarizes the knowledge gaps and defines key questions to be addressed regarding the clinical application of phage therapy for the treatment of drug-resistant tuberculosis

New Developments and Insights in the Improvement of Mycobacterium tuberculosis Vaccines and Diagnostics Within the End TB Strategy

Purpose of review The alignment of sustainable development goals (SDGs) with the End Tuberculosis (TB) strategy provides an integrated roadmap to implement key approaches towards TB elimination. This review summarizes current social challenges for TB control, and yet, recent developments in TB diagnosis and vaccines in the context of the End TB strategy and SDGs to transform global health. Recent findings Advances in non-sputum based TB biomarkers and whole genome sequencing technologies could revolutionize TB diagnostics. Moreover, synergistic novel technologies such as mRNA vaccination, nanovaccines and promising TB vaccine models are key promising developments for TB prevention and control. Summary The End TB strategy depends on novel developments in point-of-care TB diagnostics and effective vaccines. However, despite outstanding technological developments in these fields, TB elimination will be unlikely achieved if TB social determinants are not fully addressed. Indeed, the End TB strategy and SDGs emphasize the importance of implementing sustainable universal health coverage and social protection

Closed genome and comparative phylogenetic analysis of the clinical multidrug resistant Shigella sonnei strain 866

Shigella sonneiis responsible for the majority of shigellosis infections in the US with over 500,000 cases reported annually. Here, wepresent the complete genome of the clinical multidrug resistant (MDR) strain 866, which is highly susceptible to bacteriophageinfections. The strain has a circular chromosome of 4.85 Mb and carries a 113 kb MDR plasmid. This IncB/O/K/Z-type plasmid, termedp866, confers resistance to five different classes of antibiotics including ß-lactamase, sulfonamide, tetracycline, aminoglycoside, andtrimethoprim. Comparative analysis of the plasmid architecture and gene inventory revealed that p866 shares its plasmid backbonewith previously described IncB/O/K/Z-typeShigellaspp. andEscherichiacoliplasmids, but is differentiated by the insertion of antibioticresistance cassettes, which we found associated with mobile genetic elements such as Tn3, Tn7, and Tn10. A whole genome-derivedphylogenetic reconstruction showed the evolutionary relationships ofS. sonneistrain 866 and the four establishedShigellaspecies,highlighting the clonal nature ofS. sonnei