The Coliform Kind: E. coli and Its “Cousins” The Good, the Bad, and the Deadly

Even though some intestinal bacteria strains are pathogenic and even deadly, most coliforms strains still show evidence of being one of God’s “very good” creations. In fact, bacteria serve an intrinsic role in the colon of the human body. These bacteria aid in the early development of the immune system and stimulate up to 80% of immune cells in adults. In addition, digestive enzymes, Vitamins K and B12, are produced byEscherichia coli and other coliforms. E. coli is the best-known bacteria that is classified as coliforms. The term “coliform” name was historically attributed due to the “Bacillus coli-like” forms. The bacteria are characteristically Gram-negative bacillus (rod-shaped) organisms found in the colons of man and animal. Typical genera include Escherichia, Citrobacter, Klebsiella, and Enterobacter. All these bacteria genera ferment lactose and are phenotypically similar. These genera are often used as indicators in testing the quality of water. Their presence indicates contamination that can cause transmission of infection. This leads to a bad reputation for the coliform kind. How could God consider this creation good if they cause disease

Serratia marcescens, the “Flame” Strain: The Genesis of a New Variant A Newly Described Strain with Prolific Pigment Produced at High Temperature

Serratia marcescens, a Gram-negative, rod-shaped, facultative anaerobe (Fig. 1), is ubiquitous in water, soil, and natural settings. It is easily grown in the lab and may serve as an ideal model for adaptation studies because of the natural color variation of S. marcescens (Gillen 2008). In this paper, we describe a new variant with prolific pigment (prodigiosin) production at high temperatures. In the wild and in buildings, S. marcescens is noted for the production of a bright red pigment called prodigiosin (Williams 1973). We have found a new strain that appears to have adapted to a relatively new pond system called Liberty Library Lake. It produces pigment up to 40°C without any enrichment to media. Most wild-type strains, like NIMA, produce pigment normally up to 30°C, but with extensive enrichment, wild-type strains can produce pigment up to 40°C. This new strain, called the “Flame” strain, not only produces prodigiosin to 39–40°C but also in higher abundance at 35°C and at a brighter hue. NIMA strains can produce pigment at 39–40°C with Serratia Synergy Agar (glycerol, peptone, agar) but not on TSA nor any common agar. It takes significant enhancement for any other Serratia marcescens strains to produce pigment even at 35°C. The Flame strain’s brief appearance in a local, small lake appears to be a phenotypic diversification and adaptation to an environmental perturbation this past school year. The environmental stress prior to its appearance was an autumn drought. Eventually, heavy rainfall occurred and the new strain was discovered. Its appearance coincided with an unusually high abundance of coliforms, avian Giardia, and Cryptosporidium, along with chemical treatment of the lake. The unusual conditions seem to favor a rapid phenotypic diversification and adaptation. The new strain still retains the pigment production at nearly 10°C higher for “normal” prodigiosin production by wild-type Serratia marcescens. This genesis of this new strain seems to have occurred as special conditions favored this new variant. It may be closer to a “proto-type” (ancestral) strain than to more common wild-type strains, like NIMA and BS303. It appears that most wild-type strains, like NIMA and BS303, may have lost this information over time since added enrichment is necessary to produce pigment at 39–40°C. The unusual conditions may have selected for this newly adapted strain to be common for a short time. Also as conditions returned to “normal,” a common wild-type strain reappeared at the local lake, and the Flame strain was no longer found. The objective of this article is to explain the mysterious origin of a new strain of Serratia marcescens that produces prodigiosin up to 40°C without any enrichment to media. This strain can naturally produce prolific pigment that is a bright, flame-red. Since Serratia marcescens offers protection from other microbes, UV light, and drought, it is a wonderful example of intelligent design commonly seen in the microbial world

First-Pass Meconium Samples from Healthy Term Vaginally-Delivered Neonates : An Analysis of the Microbiota

Acknowledgments The authors would like to thank the parents who consented to provide samples with limited notice at an emotional and stressful time. This work was supported entirely from personal donations to the neonatal endowments fund at Aberdeen Maternity Hospital and we thank families for their continued generosity, year-on-year. The Rowett Institute of Nutrition and Health receives funding from the Scottish Government (SG-RESAS). Funding: This work was funded from NHS Grampian Neonatal Endowments. The Rowett Institute receives funding from the Rural and Environmental Science and Analytical Services programme of the Scottish Government. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Peer reviewedPublisher PD

Examination of Genome-Wide Ortholog variation in clinical and environmental isolates of the fungal pathogen Aspergillus fumigatus

Aspergillus fumigatus is a cosmopolitan species of fungus responsible for thousands of cases of invasive disease annually. Clinical and environmental isolates of A. fumigatus exhibit extensive phenotypic differences, including differences related to virulence and antifungal drug resistance. Aspergillus fumigatus is both an environmental saprobe and an opportunistic human fungal pathogen. Knowledge of genomic variation across A. fumigatus isolates is essential for understanding the evolution of pathogenicity, virulence, and resistance to antifungal drugs. Here, we investigated 206 A. fumigatus isolates (133 clinical and 73 environmental isolates), aiming to identify genes with variable presence across isolates and test whether this variation was related to the clinical or environmental origin of isolates. The PanOrtho genome of A. fumigatus consists of 13,085 ortholog groups, of which 7,773 (59.4\%) are shared by all isolates (core groups) and 5,312 (40.6\%) vary in their gene presence across isolates (accessory groups plus singletons). Despite differences in the distribution of orthologs across all isolates, no significant differences were observed among clinical versus environmental isolates when phylogeny was accounted for. Orthologs that differ in their distribution across isolates tend to occur at low frequency and/or be restricted to specific isolates; thus, the degree of genomic conservation between orthologs of A. fumigatus is high. These results suggest that differences in the distribution of orthologs within A. fumigatus cannot be associated with the clinical or environmental origin of isolates. IMPORTANCE Aspergillus fumigatus is a cosmopolitan species of fungus responsible for thousands of cases of invasive disease annually. Clinical and environmental isolates of A. fumigatus exhibit extensive phenotypic differences, including differences related to virulence and antifungal drug resistance. A comprehensive survey of the genomic diversity present in A. fumigatus and its relationship to the clinical or environmental origin of isolates can contribute to the prediction of the mechanisms of evolution and infection of the species. Our results suggest that there is no significant variation in ortholog distribution between clinical and environmental isolates when accounting for evolutionary history. The work supports the hypothesis that environmental and clinical isolates of A. fumigatus do not differ in their gene contents.We thank Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) 2020/10536-9 (M.A.C.H.) and 2016/07870-9 (G.H.G.) and Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) 301058/2019-9 and 404735/2018-5 (G.H.G.), both in Brazil, and National Institutes of Health/National Institute of Allergy and Infectious Diseases (R01AI153356) (A.R. and G.H.G.), in the United States.Peer ReviewedPostprint (published version

Representational predicaments at three Hong Kong sites

Representational predicaments arise when a job incumbent believes that attributions and images assumed by dominant authorities unfavourably ignore, or disproportionately and unfavourably emphasize, aspects of the incumbent\u27s own work and social identity. This is likely to happen when the incumbent does not have a close relationship with a dominant authority, and when power asymmetries give the former relatively little control over which aspects of their work and social identity are made visible or invisible to the latter. We draw on critical incident interviews from three organizations to illustrate a typology of six types of representational predicament: invasive spotlighting, idiosyncratic spotlighting, embedded background work, paradoxical social visibility, standardization of work processes, and standardization of work outputs. We analyse responses to representational predicaments according to whether they entailed exit, voice, loyalty, or neglect. Incumbents tended to respond with loyalty if they felt able and willing to accommodate their work behaviour and/or social identity to the dominant representations, and if there were sufficient compensatory factors, such as intrinsic rewards from the work or solidarity with colleagues. Exit or neglect appeared to reflect the belief that it was impossible to accommodate. Power asymmetries appeared to deter voice. Individual employees with a close and cordial working relationship with a member of a dominant authority group, or who were relationally networked to one, appeared not to experience representational predicaments

Effects of antibiotic resistance, drug target attainment, bacterial pathogenicity and virulence, and antibiotic access and affordability on outcomes in neonatal sepsis: an international microbiology and drug evaluation prospective substudy (BARNARDS)

Background Sepsis is a major contributor to neonatal mortality, particularly in low-income and middle-income countries (LMICs). WHO advocates ampicillin–gentamicin as first-line therapy for the management of neonatal sepsis. In the BARNARDS observational cohort study of neonatal sepsis and antimicrobial resistance in LMICs, common sepsis pathogens were characterised via whole genome sequencing (WGS) and antimicrobial resistance profiles. In this substudy of BARNARDS, we aimed to assess the use and efficacy of empirical antibiotic therapies commonly used in LMICs for neonatal sepsis. Methods In BARNARDS, consenting mother–neonates aged 0–60 days dyads were enrolled on delivery or neonatal presentation with suspected sepsis at 12 BARNARDS clinical sites in Bangladesh, Ethiopia, India, Pakistan, Nigeria, Rwanda, and South Africa. Stillborn babies were excluded from the study. Blood samples were collected from neonates presenting with clinical signs of sepsis, and WGS and minimum inhibitory concentrations for antibiotic treatment were determined for bacterial isolates from culture-confirmed sepsis. Neonatal outcome data were collected following enrolment until 60 days of life. Antibiotic usage and neonatal outcome data were assessed. Survival analyses were adjusted to take into account potential clinical confounding variables related to the birth and pathogen. Additionally, resistance profiles, pharmacokinetic–pharmacodynamic probability of target attainment, and frequency of resistance (ie, resistance defined by in-vitro growth of isolates when challenged by antibiotics) were assessed. Questionnaires on health structures and antibiotic costs evaluated accessibility and affordability. Findings Between Nov 12, 2015, and Feb 1, 2018, 36 285 neonates were enrolled into the main BARNARDS study, of whom 9874 had clinically diagnosed sepsis and 5749 had available antibiotic data. The four most commonly prescribed antibiotic combinations given to 4451 neonates (77·42%) of 5749 were ampicillin–gentamicin, ceftazidime–amikacin, piperacillin–tazobactam–amikacin, and amoxicillin clavulanate–amikacin. This dataset assessed 476 prescriptions for 442 neonates treated with one of these antibiotic combinations with WGS data (all BARNARDS countries were represented in this subset except India). Multiple pathogens were isolated, totalling 457 isolates. Reported mortality was lower for neonates treated with ceftazidime–amikacin than for neonates treated with ampicillin–gentamicin (hazard ratio [adjusted for clinical variables considered potential confounders to outcomes] 0·32, 95% CI 0·14–0·72; p=0·0060). Of 390 Gram-negative isolates, 379 (97·2%) were resistant to ampicillin and 274 (70·3%) were resistant to gentamicin. Susceptibility of Gram-negative isolates to at least one antibiotic in a treatment combination was noted in 111 (28·5%) to ampicillin–gentamicin; 286 (73·3%) to amoxicillin clavulanate–amikacin; 301 (77·2%) to ceftazidime–amikacin; and 312 (80·0%) to piperacillin–tazobactam–amikacin. A probability of target attainment of 80% or more was noted in 26 neonates (33·7% [SD 0·59]) of 78 with ampicillin–gentamicin; 15 (68·0% [3·84]) of 27 with amoxicillin clavulanate–amikacin; 93 (92·7% [0·24]) of 109 with ceftazidime–amikacin; and 70 (85·3% [0·47]) of 76 with piperacillin–tazobactam–amikacin. However, antibiotic and country effects could not be distinguished. Frequency of resistance was recorded most frequently with fosfomycin (in 78 isolates [68·4%] of 114), followed by colistin (55 isolates [57·3%] of 96), and gentamicin (62 isolates [53·0%] of 117). Sites in six of the seven countries (excluding South Africa) stated that the cost of antibiotics would influence treatment of neonatal sepsis

Cell- and Virus-Mediated Regulation of the Barrier-to-Autointegration Factor’s Phosphorylation State Controls Its DNA Binding, Dimerization, Subcellular Localization, and Antipoxviral Activity

Barrier-to-autointegration factor (BAF) is a DNA binding protein with multiple cellular functions, including the ability to act as a potent defense against vaccinia virus infection. This antiviral function involves BAF’s ability to condense double-stranded DNA and subsequently prevent viral DNA replication. In recent years, it has become increasingly evident that dynamic phosphorylation involving the vaccinia virus B1 kinase and cellular enzymes is likely a key regulator of multiple BAF functions; however, the precise mechanisms are poorly understood. Here we analyzed how phosphorylation impacts BAF’s DNA binding, subcellular localization, dimerization, and antipoxviral activity through the characterization of BAF phosphomimetic and unphosphorylatable mutants. Our studies demonstrate that increased phosphorylation enhances BAF’s mobilization from the nucleus to the cytosol, while dephosphorylation restricts BAF to the nucleus. Phosphorylation also impairs both BAF’s dimerization and its DNA binding activity. Furthermore, our studies of BAF’s antiviral activity revealed that hyperphosphorylated BAF is unable to suppress viral DNA replication or virus production. Interestingly, the unphosphorylatable BAF mutant, which is capable of binding DNA but localizes predominantly to the nucleus, was also incapable of suppressing viral replication. Thus, both DNA binding and localization are important determinants of BAF’s antiviral function. Finally, our examination of how phosphatases are involved in regulating BAF revealed that PP2A dephosphorylates BAF during vaccinia infection, thus counterbalancing the activity of the B1 kinase. Altogether, these data demonstrate that phosphoregulation of BAF by viral and cellular enzymes modulates this protein at multiple molecular levels, thus determining its effectiveness as an antiviral factor and likely other functions as well

Barrier to autointegration factor (BAF) inhibits vaccinia virus intermediate transcription in the absence of the viral B1 kinase

Barrier to autointegration factor (BAF/BANF1) is a cellular DNA-binding protein found in the nucleus and cytoplasm. Cytoplasmic BAF binds to foreign DNA and can act as a defense against vaccinia DNA replication. To evade BAF, vaccinia expresses the B1 kinase, which phosphorylates BAF and blocks its ability to bind DNA. Interestingly, B1 is also needed for viral intermediate gene expression via an unknown mechanism. Therefore, we evaluated the impact of B1-BAF signaling on vaccinia transcription. Strikingly, the decrease in vaccinia transcription caused by loss of B1 can be rescued by depletion of BAF. The repressive action of BAF is greatest on a viral promoter, and is more modest when non-vaccinia promoters are employed, which suggests BAF acts in a gene specific manner. These studies expand our understanding of the role of the B1 kinase during infection and provide the first evidence that BAF is a defense against viral gene expression

Barrier to Autointegration Factor Becomes Dephosphorylated during HSV-1 Infection and Can Act as a Host Defense by Impairing Viral DNA Replication and Gene Expression

BAF (Barrier to Autointegration Factor) is a highly conserved DNA binding protein that senses poxviral DNA in the cytoplasm and tightly binds to the viral genome to interfere with DNA replication and transcription. To counteract BAF, a poxviralencoded protein kinase phosphorylates BAF, which renders BAF unable to bind DNA and allows efficient viral replication to occur. Herein, we examined how BAF phosphorylation is affected by herpes simplex virus type 1 (HSV-1) infection and tested the ability of BAF to interfere with HSV-1 productive infection. Interestingly, we found that BAF phosphorylation decreases markedly following HSV-1 infection. To determine whether dephosphorylated BAF impacts HSV-1 productive infection, we employed cell lines stably expressing a constitutively unphosphorylated form of BAF (BAF-MAAAQ) and cells overexpressing wild type (wt) BAF for comparison. Although HSV-1 production in cells overexpressing wtBAF was similar to that in cells expressing no additional BAF, viral growth was reduced approximately 80% in the presence of BAF-MAAAQ. Experiments were also performed to determine the mechanism of the antiviral activity of BAF with the following results. BAF-MAAAQ was localized to the nucleus, whereas wtBAF was dispersed throughout cells prior to infection. Following infection, wtBAF becomes dephosphorylated and relocalized to the nucleus. Additionally, BAF was associated with the HSV- 1 genome during infection, with BAF-MAAAQ associated to a greater extent than wtBAF. Importantly, unphosphorylated BAF inhibited both viral DNA replication and gene expression. For example, expression of two regulatory proteins, ICP0 and VP16, were substantially reduced in cells expressing BAF-MAAAQ. However, other viral genes were not dramatically affected suggesting that expression of certain viral genes can be differentially regulated by unphosphorylated BAF. Collectively, these results suggest that BAF can act in a phosphorylation-regulated manner to impair HSV-1 transcription and/or DNA replication, which is similar to the antiviral activity of BAF during vaccinia infection

DESARROLLO DE UN SISTEMA DE MONITOREO DE RADIACIÓN SOLAR BASADO EN UN ESPECTRÓMETRO DE AMPLIO ESPECTRO

La eficiencia cuántica de materiales fotovoltaicos depende de la longitud de onda de la radiación incidente, el espectro solar influye en la producción de energía producida por estos sistemas. En el presente trabajo, se diseñó y construyó un prototipo funcional de un sistema de medición de radiación solar (global y difusa) basado en un espectrómetro de amplio espectro para el monitoreo solar en Cochabamba, Bolivia, conjuntamente con un sistema similar instalado en Kingston, Ontario. Los datos obtenidos en dos regiones con características geográficas muy distintas ayudarán en el estudio y optimización de materiales fotovoltaicos, para su implementación en diferentes partes del mundo, con características particulares de radiación incidente. Los resultados obtenidos serán publicados para que otras regiones también se beneficien de sistemas fotovoltaicos con materiales optimizados según las características geográficas. Para la construcción mecánica del sistema, se utilizaron perfiles de aluminio de 60x30 mm. Esta estructura metálica sujeta a una fibra óptica de cuarzo lleva la radiación solar al espectrómetro Ocean Optics USB4000 (200-900 nm). La electrónica del sistema de control, está gobernada por un microcontrolador Arduino UNO, el cual se encarga de sincronizar el movimiento de dos motores PAP bipolares y la toma de datos en el espectrómetro que se activa con un trigger externo. La característica principal del sistema es permitir la medición del espectro de los componentes global y difuso de la radiación solar en diferentes ángulos de incidencia. El sistema mecánico ajusta un extremo de una fibra óptica de 0 a 90 grados en dirección norte, cada nueve grados, midiendo la radiación global y mediante una banda mecánica que produce sombra sobre la fibra óptica, mide la radiación difusa. Las medidas son tomadas cada hora y el rango espectral abarcado es del UVA, VIS y parte del IR cercano. Se realizaron pruebas preliminares en dos ciudades de Bolivia y se demostró que la cantidad de radiación UVA es mayor en el El Alto (4062 msnm), la ciudad con mayor elevación, en comparación con Cochabamba que se encuentra a 2570 msnm