A stable home for an equine pathogen: valid publication of the binomial Prescottella equi gen. nov., comb. nov., and reclassification of four rhodococcal species into the genus Prescottella.

Opinion 106 of the Judicial Commission has clarified the nomenclature of the taxon variously named Rhodococcus equi, 'Prescottella equi' and Rhodococcus hoagii. As a consequence, we present here the genus name Prescottella and that of its nomenclatural type species, Prescottella equi comb. nov., for valid publication and propose the reclassification of four rhodococcal species as novel combinations in the genus, namely Prescottella agglutinans Guo et al. 2015 comb. nov., Prescottella defluvii Kämpfer et al. 2014 comb. nov., Prescottella soli Li et al. 2015 comb. nov. and Prescottella subtropica Lee et al. 2019 comb. nov. In addition, we note that a clinical isolate, strain 86-07 (=W8901), likely represents an additional species within the genus Prescottella. Nearly a century after the original description of the type strain of the type species as Corynebacterium equi, we provide a stable home for Prescottella equi and its relatives.

Decontamination Strategies Used for AFB Culture Significantly Reduce the Viability of Mycobacterium abscessus Complex in Sputum Samples from Patients with Cystic Fibrosis.

Nontuberculous mycobacteria are important respiratory pathogens in patients with cystic fibrosis (CF). For diagnosis, international guidelines recommend culture of sputum that has been decontaminated via chemical treatment. Fifty-six sputum samples from 32 patients known to be previously colonized or infected with NTM were subdivided, and the aliquots were subjected to six different decontamination strategies, followed by quantitative culture for NTM. Thirty sputum samples contained Mycobacterium abscessus complex (MABSC) and 11 contained Mycobacterium avium complex (MAC). Decontamination strategies included treatment with N-acetyl L-cysteine with 2% sodium hydroxide (NALC-NaOH), 4% NaOH, 1% chlorhexidine, 0.5 N sulfuric acid, 5% oxalic acid, double decontamination with NALC-NaOH, followed by 5% oxalic acid, and saline (0.85%) as a control. The samples were also cultured directly with no treatment. Treatment with NALC-NaOH resulted in an average reduction in colony count of 87% for MABSC when compared with direct culture. NaOH at 4% caused a 98.3% average reduction in colony count. All treatments that included NaOH resulted in colony counts that were statistically lower than those obtained from direct culture or the saline-treated control (p < 0.05). Standard treatments using sulfuric or oxalic acids were less deleterious, but still resulted in an average reduction in colony count of at least 30%. The viability of MAC was much less affected by most decontamination treatments. In conclusion, the viability of MABSC was severely compromised by standard decontamination regimens. This supports recent evidence showing that optimal recovery of MABSC is achieved by culture on an appropriate selective agar without decontamination of sputum samples.

Phosphonopeptides Revisited, in an Era of Increasing Antimicrobial Resistance.

Given the increase in resistance to antibacterial agents, there is an urgent need for the development of new agents with novel modes of action. As an interim solution, it is also prudent to reinvestigate old or abandoned antibacterial compounds to assess their efficacy in the context of widespread resistance to conventional agents. In the 1970s, much work was performed on the development of peptide mimetics, exemplified by the phosphonopeptide, alafosfalin. We investigated the activity of alafosfalin, di-alanyl fosfalin and ß-chloro-L-alanyl-ß-chloro-L-alanine against 297 bacterial isolates, including carbapenemase-producing Enterobacterales (CPE) (n = 128), methicillin-resistant Staphylococcus aureus (MRSA) (n = 37) and glycopeptide-resistant enterococci (GRE) (n = 43). The interaction of alafosfalin with meropenem was also examined against 20 isolates of CPE. The MIC50 and MIC90 of alafosfalin for CPE were 1 mg/L and 4 mg/L, respectively and alafosfalin acted synergistically when combined with meropenem against 16 of 20 isolates of CPE. Di-alanyl fosfalin showed potent activity against glycopeptide-resistant isolates of Enterococcus faecalis (MIC90; 0.5 mg/L) and Enterococcus faecium (MIC90; 2 mg/L). Alafosfalin was only moderately active against MRSA (MIC90; 8 mg/L), whereas ß-chloro-L-alanyl-ß-chloro-L-alanine was slightly more active (MIC90; 4 mg/L). This study shows that phosphonopeptides, including alafosfalin, may have a therapeutic role to play in an era of increasing antibacterial resistance.

Correction: 1.2 million kids and counting-Mobile science laboratories drive student interest in STEM.

[This corrects the article DOI: 10.1371/journal.pbio.2001692.].

1.2 million kids and counting-Mobile science laboratories drive student interest in STEM.

In today's increasingly technological society, a workforce proficient in science, technology, engineering, and mathematics (STEM) skills is essential. Research has shown that active engagement by K-12 students in hands-on science activities that use authentic science tools promotes student learning and retention. Mobile laboratory programs provide this type of learning in schools and communities across the United States and internationally. Many programs are members of the Mobile Lab Coalition (MLC), a nonprofit organization of mobile and other laboratory-based education programs built on scientist and educator collaborations. A recent survey of the member programs revealed that they provide an impressive variety of programming and have collectively served over 1.2 million students across the US.

Accumulation of coal combustion residues and their immunological effects in the yellow-bellied slider (Trachemys scripta scripta).

Anthropogenic activities such as industrial processes often produce copious amounts of contaminants that have the potential to negatively impact growth, survival, and reproduction of exposed wildlife. Coal combustion residues (CCRs) represent a major source of pollutants globally, resulting in the release of potentially harmful trace elements such as arsenic (As), cadmium (Cd), and selenium (Se) into the environment. In the United States, CCRs are typically stored in aquatic settling basins that may become attractive nuisances to wildlife. Trace element contaminants, such as CCRs, may pose a threat to biota yet little is known about their sublethal effects on reptiles. To assess the effects of CCR exposure in turtles, we sampled 81 yellow-bellied sliders (Trachemys scripta scripta) in 2014-2015 from CCR-contaminated and uncontaminated reference wetlands located on the Savannah River Site (Aiken, SC, USA). Specific aims were to (1) compare the accumulation of trace elements in T. s. scripta claw and blood samples between reference and CCR-contaminated site types, (2) evaluate potential immunological effects of CCRs via bacterial killing assays and phytohaemagglutinin (PHA) assays, and (3) quantify differences in hemogregarine parasite loads between site types. Claw As, Cd, copper (Cu), and Se (all p ≤ 0.001) and blood As, Cu, Se, and strontium (Sr; p ≤ 0.015) were significantly elevated in turtles from CCR-contaminated wetlands compared to turtles from reference wetlands. Turtles from reference wetlands exhibited lower bacterial killing (p = 0.015) abilities than individuals from contaminated sites but neither PHA responses (p = 0.566) nor parasite loads (p = 0.980) differed by site type. Despite relatively high CCR body burdens, sliders did not exhibit apparent impairment of immunological response or parasite load. In addition, the high correlation between claw and blood concentrations within individuals suggests that nonlethal tissue sampling may be useful for monitoring CCR exposure in turtles.

A Conceptual Model to Assess Stress-Associated Health Effects of Multiple Ecosystem Services Degraded by Disaster Events in the Gulf of Mexico and Elsewhere.

Few conceptual frameworks attempt to connect disaster-associated environmental injuries to impacts on ecosystem services (the benefits humans derive from nature) and thence to both psychological and physiological human health effects. To our knowledge, this study is one of the first, if not the first, to develop a detailed conceptual model of how degraded ecosystem services affect cumulative stress impacts on the health of individual humans and communities. Our comprehensive Disaster-Pressure State-Ecosystem Services-Response-Health (DPSERH) model demonstrates that oil spills, hurricanes, and other disasters can change key ecosystem components resulting in reductions in individual and multiple ecosystem services that support people's livelihoods, health, and way of life. Further, the model elucidates how damage to ecosystem services produces acute, chronic, and cumulative stress in humans which increases risk of adverse psychological and physiological health outcomes. While developed and initially applied within the context of the Gulf of Mexico, it should work equally well in other geographies and for many disasters that cause impairment of ecosystem services. Use of this new tool will improve planning for responses to future disasters and help society more fully account for the costs and benefits of potential management responses. The model also can be used to help direct investments in improving response capabilities of the public health community, biomedical researchers, and environmental scientists. Finally, the model illustrates why the broad range of potential human health effects of disasters should receive equal attention to that accorded environmental damages in assessing restoration and recovery costs and time frames.

Next-generation systematics: An innovative approach to resolve the structure of complex prokaryotic taxa.

Prokaryotic systematics provides the fundamental framework for microbiological research but remains a discipline that relies on a labour- and time-intensive polyphasic taxonomic approach, including DNA-DNA hybridization, variation in 16S rRNA gene sequence and phenotypic characteristics. These techniques suffer from poor resolution in distinguishing between closely related species and often result in misclassification and misidentification of strains. Moreover, guidelines are unclear for the delineation of bacterial genera. Here, we have applied an innovative phylogenetic and taxogenomic approach to a heterogeneous actinobacterial taxon, Rhodococcus, to identify boundaries for intrageneric and supraspecific classification. Seven species-groups were identified within the genus Rhodococcus that are as distantly related to one another as they are to representatives of other mycolic acid containing actinobacteria and can thus be equated with the rank of genus. It was also evident that strains assigned to rhodococcal species-groups are underspeciated with many misclassified using conventional taxonomic criteria. The phylogenetic and taxogenomic methods used in this study provide data of theoretical value for the circumscription of generic and species boundaries and are also of practical significance as they provide a robust basis for the classification and identification of rhodococci of agricultural, industrial and medical/veterinary significance.

Evaluation of Various Culture Media for Detection of Rapidly Growing Mycobacteria from Patients with Cystic Fibrosis.

Isolation of nontuberculous mycobacteria (NTM) from the sputum of patients with cystic fibrosis (CF) is challenging due to overgrowth by rapidly growing species that colonize the lungs of patients with CF. Extended incubation on Burkholderia cepacia selective agar (BCSA) has been recommended as an expedient culture method for the isolation of rapidly growing NTM in this setting. The aim of this study was to assess five selective media designed for the isolation of Burkholderia cepacia complex, along with two media designed for the isolation of mycobacteria (rapidly growing mycobacteria [RGM] medium and Middlebrook 7H11 agar), for their abilities to isolate NTM. All seven media were challenged with 147 isolates of rapidly growing mycobacteria and 185 isolates belonging to other species. RGM medium was then compared with the most selective brand of BCSA for the isolation of NTM from 224 sputum samples from patients with CF. Different agars designed for the isolation of B. cepacia complex varied considerably in their inhibition of other bacteria and fungi. RGM medium supported the growth of all isolates of mycobacteria and was more selective than any other medium. NTM were recovered from 17 of 224 sputum samples using RGM medium, compared with only 7 samples using the most selective brand of BCSA (P = 0.023). RGM medium offers a superior option, compared to other selective agars, for the isolation of rapidly growing mycobacteria from the sputum of patients with CF. Furthermore, the convenience of using RGM medium enables routine screening for rapidly growing NTM in all submitted sputum samples from patients with CF.

A novel culture medium for isolation of rapidly-growing mycobacteria from the sputum of patients with cystic fibrosis.

BACKGROUND: Isolation of mycobacteria from the sputum of patients with cystic fibrosis (CF) is challenging due to the overgrowth of cultures by other bacteria and fungi. In this setting, Burkholderia cepacia selective agar (BCSA) has been recommended as a convenient and effective culture medium for the isolation of rapidly-growing, non-tuberculous mycobacteria (NTM). A novel selective culture medium (RGM medium) was evaluated for the isolation of rapidly-growing NTM from the sputum of children and adults with CF. METHODS: A total of 118 isolates of rapidly-growing mycobacteria and 98 other bacteria and fungi were inoculated onto RGM medium. These were assessed for growth at 30°C over a seven day period. A total of 502 consecutive sputum samples were collected from 210 patients with CF. Each sample was homogenized and cultured onto RGM medium and also onto BCSA. Cultures were incubated for 10days at 30°C. RESULTS: Of 118 isolates of mycobacteria all but one grew well on RGM medium, whereas 94% of other bacteria and fungi were inhibited. A total of 55 sputum samples (from 33 distinct patients) yielded NTM using a combination of both RGM and BCSA (prevalence: 15.7%). NTM were recovered from 54 sputum samples using RGM medium compared with only 17 samples using BCSA (sensitivity 98% vs. 31%; P≤0.0001). A total of 419 isolates of non-mycobacteria were recovered from sputum samples on BCSA compared with 46 on RGM medium. CONCLUSIONS: RGM medium offers a simple and effective culture method for the isolation of rapidly-growing mycobacteria from sputum samples from patients with CF without decontamination of samples. RGM medium allows for the systematic screening of all sputum samples routinely referred for culture from patients with CF.

Genomic analyses confirm close relatedness between Rhodococcus defluvii and Rhodococcus equi (Rhodococcus hoagii).

Rhodococcus defluvii strain Ca11(T) was isolated from a bioreactor involved in extensive phosphorus removal. We have sequenced the whole genome of this strain, and our comparative genomic and phylogenetic analyses confirm its close relatedness with Rhodococcus equi (Rhodococcus hoagii) strains, which share >80 % of the gene content. The R. equi virulence plasmid is absent though most of the chromosomal R. equi virulence-associated genes are present in R. defluvii Ca11(T). These data suggest that although R. defluvii is an environmental organism, it has the potential to colonize animal hosts.

The evaluation of a food allergy and epinephrine autoinjector training program for personnel who care for children in schools and community settings.

With the dramatic increase in the incidence of food allergies, nurses and other school personnel are likely to encounter a child with food allergies. The objectives of this study were to assess the effectiveness of in-person training on enhancing knowledge about food allergies and improving self-confidence in preventing, recognizing, and treating food allergy reactions and to collect information about prior training and participation in response to food allergy incidents. A total of 4,818 individuals at 247 schools and community sites participated in the training program, which was delivered by a licensed registered nurse. Written evaluations, online surveys, and phone interviews were used to measure the impact including content retention, confidence, and behavior changes. The results of this study show that in-person training can increase participant's knowledge about food allergies and improve self-confidence in preventing, recognizing, and treating allergic reactions and that these gains were sustained over time.

Discovery of a cell wall porin in the mycolic-acid-containing actinomycete Dietzia maris DSM 43672.

The cell wall of the Gram-positive mycolic-acid-containing actinomycete Dietzia maris DSM 43672 was found to contain a pore-forming protein, as observed from reconstitution experiments with artificial lipid bilayer experiments in the presence of cell wall extracts. The cell wall porin was purified to homogeneity using different biochemical methods and had an apparent molecular mass of about 120 kDa on tricine-containing SDS/PAGE. The 120 kDa protein dissociated into subunits with a molecular mass of about 35 kDa when it was heated to 100 °C in 8 m urea. The 120 kDa protein, here named PorADm , formed ion-permeable channels in lipid bilayer membranes with a high single-channel conductance of about 5.8 nS in 1 m KCl. Asymmetric addition of PorADm to lipid bilayer membranes resulted in an asymmetric voltage dependence. Zero-current membrane potential measurements with different salt solutions suggested that the porin of D. maris is cation-selective because of negative charges localized at the channel mouth. Analysis of the single-channel conductance using non-electrolytes with known hydrodynamic radii indicated that the diameter of the cell wall channel is about 2 nm. The channel characteristics of the cell wall porin of D. maris are compared with those of other members of the mycolata. They share some common features because they are composed of small molecular mass subunits and form large and water-filled channels. The porin was subjected to protein analysis by mass spectrometry but its sequence had no significant homology to any known porin sequences.

Elevated levels of autoantibodies targeting the M1 muscarinic acetylcholine receptor and neurofilament medium in sera from subgroups of patients with schizophrenia.

Schizophrenia is a severe debilitating brain disorder with a poorly understood aetiology. Among the diverse aetiological clues lies evidence for immune abnormalities in some individuals. The aim of this study was to investigate the frequency and specificity of autoantibodies directed against the brain in people with schizophrenia. Sera were screened for reactivity against human brain tissue (hippocampus and prefrontal cortex). Neuronal cell body and filamentous patterns of brain tissue staining were observed significantly more frequently in sera from schizophrenia patients (n=30) compared to controls (n=24). Sera that showed a neuronal cell body pattern of staining on hippocampus reacted strongly to an extracellular epitope of the M1 muscarinic acetylcholine receptor (m1AChR) in ELISA. Both cell body staining and elevated m1AChR reactivity correlated with higher symptom scores for poverty of speech. Sera showing a filamentous staining pattern predominantly targeted microfilaments, intermediate filaments or neurofilaments, particularly neurofilament medium (NFM), which is a dopamine receptor interacting protein. By ELISA, there was strongly elevated reactivity against NFM in a subset (15%) of schizophrenia patients (n=101) compared to healthy controls (n=55) or patients with multiple sclerosis (n=32). These results support the hypothesis that neurotransmitter receptors or molecules involved in regulation of neurotransmission are targets of autoantibodies in some people with schizophrenia.

Nocardia kroppenstedtii sp. nov., an actinomycete isolated from a lung transplant patient with a pulmonary infection.

A novel actinomycete, strain N1286(T), isolated from a lung transplant patient with a pulmonary infection, was provisionally assigned to the genus Nocardia. The strain had chemotaxonomic and morphological properties typical of members of the genus Nocardia and formed a distinct phyletic line in the Nocardia 16S rRNA gene tree. Isolate N1286(T) was most closely related to Nocardia farcinica DSM 43665(T) (99.8% gene sequence similarity) but could be distinguished from the latter by the low level of DNA-DNA relatedness. These strains were also distinguishable on the basis of a broad range of phenotypic properties. It is concluded that strain N1286(T) represents a novel species of the genus Nocardia for which the name Nocardia kroppenstedtii sp. nov. is proposed. The type strain is N1286(T) ( = DSM 45810(T) = NCTC 13617(T)).

Comparative genomic analyses reveal a lack of a substantial signature of host adaptation in Rhodococcus equi ('Prescottella equi').

Rhodococcus equi ('Prescottella equi') is a pathogenic actinomycete primarily infecting horses but has emerged as an opportunistic human pathogen. We have sequenced the genome of the type strain of this species, R. equi strain C7(T) , and compared the genome with that of another foal isolate 103S and of a human isolate ATCC 33707. The R. equi strains are closely related to each other and yet distantly related to other rhodococci and Nocardia brasiliensis. The comparison of gene contents among R. equi strains revealed minor differences that could be associated with host adaptation from foals to humans, including the presence of a paa operon in the human isolate, which is potentially involved in pathogenesis.

Rhodococcus jostii: a home for Rhodococcus strain RHA1.

The taxonomic position of Rhodococcus strain RHA1, an effective degrader of polychlorinated biphenyls with a large linear chromosome, was established using a polyphasic approach. The morphological and chemotaxonomic properties of the strain were typical of members of the genus Rhodococcus. The strain shared a high level of 16S rRNA sequence similarity (99.9 %) with the type strain of Rhodococcus jostii, a member of the Rhodococcus erythropolis subclade. The two strains shared a DNA:DNA relatedness value well above the cut-off point recommended for the circumscription of genomic species and had a broad range of phenotypic properties in common. The combination of genomic and phenotypic data show strain RHA1 to be a bona fide member of the species Rhodococcus jostii.

Proposal to replace the illegitimate genus name Prescottia Jones et al. 2013 with the genus name Prescottella gen. nov. and to replace the illegitimate combination Prescottia equi Jones et al. 2013 with Prescottella equi comb. nov.

Recently we proposed that Rhodococcus equi (Magnusson 1923) Goodfellow and Alderson 1977 be transferred to a novel genus, Prescottia, as Prescottia equi comb. nov. However, in accordance with Principle 2 and Rule 51b(4) of the Bacteriological Code (1990 Revision), the bacterial genus name Prescottia Jones et al. 2013 is deemed illegitimate as this name has been used previously for a plant genus within the family Orchidaceae. Consequently, a new genus name, Prescottella gen. nov. is proposed for the bacterial taxon and a new combination Prescottella equi comb. nov. is proposed for the type species.

Glutathione reductase is essential for host defense against bacterial infection.

Glutathione reductase (Gsr) catalyzes the reduction of glutathione disulfide to glutathione, a major cellular antioxidant. We have recently shown that Gsr is essential for host defense against the gram-negative bacteria Escherichia coli in a mouse model of sepsis. Although we have demonstrated that Gsr is required for sustaining the oxidative burst and the development of neutrophil extracellular traps, the role of Gsr in other phagocytic functions remains unclear. It is also unclear whether Gsr-deficient mice exhibit host defense defects against gram-positive bacteria. In this study, we characterized the effects of Gsr deficiency on the innate immune responses to a gram-positive bacterium, group B Streptococcus, and to the gram-negative bacterial cell wall component lipopolysaccharide (LPS). We found that, like E. coli, group B Streptococcus resulted in a substantially more robust cytokine response and a markedly higher morbidity and mortality in Gsr-deficient mice than in wild-type mice. The increased morbidity and mortality were associated with greater bacterial burden in the Gsr-deficient mice. Interestingly, Gsr-deficient mice did not exhibit a greater sensitivity to LPS than did wild-type mice. Analysis of the neutrophils of Gsr-deficient mice revealed impaired phagocytosis. In response to thioglycollate stimulation, Gsr-deficient mice mobilized far fewer phagocytes, including neutrophils, macrophages, and eosinophils, into their peritoneal cavities than did wild-type mice. The defective phagocyte mobilization is associated with profound oxidation and aggregation of ascitic proteins, particularly albumin. Our results indicate that the oxidative defense mechanism mediated by Gsr is required for an effective innate immune response against bacteria, probably by preventing phagocyte dysfunction due to oxidative damage.

Salinispora pacifica sp. nov., an actinomycete from marine sediments.

A polyphasic analysis was carried out to clarify the taxonomic status of four marine actinomycete strains that share a phylogenetic relationship and phenotypic characteristics with the genus Salinispora. These strains formed a distinct lineage within the Salinispora 16S rRNA and gyrB trees and were found to possess a range of phenotypic properties and DNA:DNA hybridization values that distinguished them from the type strains of the two validly named species in this genus, Salinispora tropica (CNB-440(T), ATCC BAA-916(T)) and Salinispora arenicola (CNH-643(T), ATCC BAA-917(T)). The combined genotypic and phenotypic data support this conclusion. It is proposed that the strains be designated as Salinispora pacifica sp. nov., the type strain of which is CNR-114(T) (DSMZ YYYYT = KACC 17160(T)).