Time-to-positivity of Mycobacterium avium complex in broth culture associates with culture conversion

Background

Mycobacterial time to positivity (TTP) in liquid culture media has predictive value for longer term outcomes in pulmonary tuberculosis, but has not been thoroughly studied in nontuberculous mycobacterial pulmonary disease. This study sought to evaluate for association between TTP and sputum culture conversion to negative in pulmonary disease caused by Mycobacterium avium complex (MAC).

Methods

Data from the CONVERT trial (NCT02344004) that evaluated efficacy of guideline-based-therapy with or without amikacin liposome inhalation suspension in adults with refractory MAC-PD (Mycobacterium avium complex pulmonary disease) were analyzed. We evaluated TTP measures for sputum obtained prior to study treatment initiation and at monthly visits, assessing reproducibility of measures as well as association of TTP with culture conversion on treatment.

Results

Data from 71 participants with at least one screening visit TTP value were analyzed. For participants who provided more than one sputum sample at a given visit, there was moderate between-sample reliability, with median intraclass correlation coefficient 0.62 (IQR 0.50, 0.70). Median TTP at screening was longer in those participants who subsequently achieved vs. did not achieve culture conversion (10.5 [IQR 9.4] days vs. 4.2 [IQR 2.8] days, p = 0.0002). Individuals with culture conversion by study treatment month 6 were more likely to have a screening TTP > 5 days compared to those who did not achieve culture conversion (OR 15.4, 95% CI 1.9, 716.7, p = 0.0037) and had increasing TTPs over time.

Conclusions

TTP prior to and on treatment is associated with microbiological treatment response in patients with MAC-PD.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-022-07250-4.

Poly (acetyl, arginyl) glucosamine disrupts Pseudomonas aeruginosa biofilms and enhances bacterial clearance in a rat lung infection model

Pseudomonas aeruginosa is a common opportunistic pathogen that can cause chronic infections in multiple disease states, including respiratory infections in patients with cystic fibrosis (CF) and non-CF bronchiectasis. Like many opportunists, P. aeruginosa forms multicellular biofilm communities that are widely thought to be an important determinant of bacterial persistence and resistance to antimicrobials and host immune effectors during chronic/recurrent infections. Poly (acetyl, arginyl) glucosamine (PAAG) is a glycopolymer that has antimicrobial activity against a broad range of bacterial species, and also has mucolytic activity, which can normalize the rheological properties of cystic fibrosis mucus. In this study, we sought to evaluate the effect of PAAG on P. aeruginosa bacteria within biofilms in vitro, and in the context of experimental pulmonary infection in a rodent infection model. PAAG treatment caused significant bactericidal activity against P. aeruginosa biofilms, and a reduction in the total biomass of preformed P. aeruginosa biofilms on abiotic surfaces, as well as on the surface of immortalized cystic fibrosis human bronchial epithelial cells. Studies of membrane integrity indicated that PAAG causes changes to P. aeruginosa cell morphology and dysregulates membrane polarity. PAAG treatment reduced infection and consequent tissue inflammation in experimental P. aeruginosa rat infections. Based on these findings we conclude that PAAG represents a novel means to combat P. aeruginosa infection, and may warrant further evaluation as a therapeutic.

Association of Candida albicans and Cbp+ Streptococcus mutans with early childhood caries recurrence

Early childhood caries (ECC) recurrence occurs in approximately 40% of treated cases within one year. The association of Streptococcus mutans and Candida albicans with the onset of ECC is well known. Also, S. mutans strains harboring collagen-binding proteins (Cbps) avidly bind to collagen-rich dentin and are linked to increased caries risk. Here, we investigated the presence of Cbp⁺ S. mutans and C. albicans in saliva and dental plaque of children with varying caries statuses, and their salivary microbiome. In this cross-sectional study, 143 children who were caries-free (n = 73), treated for ECC with no signs of recurrence after 6 months (n = 45), or treated for ECC and experiencing recurrence within 6 months following treatment (n = 25) were enrolled. Co-infection with C. albicans and S. mutans, especially Cbp⁺ S. mutans, was strongly associated with caries recurrence. Subjects of the recurrence group infected with Cbp⁺ S. mutans showed a greater burden of Candida spp. and of Mutans streptococci in dentin than those infected with Cbp^- strains. Salivary microbiome analysis revealed that Streptococcus parasanguinis was overrepresented in the caries recurrence group. Our findings indicate that Cbp⁺ S. mutans and C. albicans are intimately associated with caries recurrence, contributing to the establishment of recalcitrant biofilms.

A glycopolymer improves vascoelasticity and mucociliary transport of abnormal cystic fibrosis mucus

Cystic fibrosis (CF) is characterized by increased mucus viscosity and delayed mucociliary clearance that contributes to progressive decline of lung function. Mucus in the respiratory and GI tract is excessively adhesive in the presence of airway dehydration and excess extracellular Ca2+ upon mucin release, promoting hyperviscous, densely packed mucins characteristic of CF. Therapies that target mucins directly through ionic interactions remain unexploited. Here we show that poly (acetyl, arginyl) glucosamine (PAAG), a polycationic biopolymer suitable for human use, interacts directly with mucins in a Ca2+-sensitive manner to reduce CF mucus viscoelasticity and improve its transport. Notably, PAAG induced a linear structure of purified MUC5B and altered its sedimentation profile and viscosity, indicative of proper mucin expansion. In vivo, PAAG nebulization improved mucociliary transport in CF rats with delayed mucus clearance, and cleared mucus plugging in CF ferrets. This study demonstrates the potential use of a synthetic glycopolymer PAAG as a molecular agent that could benefit patients with a broad array of mucus diseases.

Energia de Micro-ondas para Controle de Micro-Organismos em Próteses Dentárias de Resina Acrílica: Revisão de Literatura

A irradiação por microondas vem sendo estudada como método alternativo de desinfecção e esterilização de prótese dentária. A literatura tem demonstrado ser um método eficaz, mas ainda não foram publicados estudos associando ação antimicrobiana com total ausência de prejuízos nas propriedades da resina acrílica. O objetivo deste estudo foi revisar a literatura, verificando os protocolos de potência e tempo utilizados, com análises microbiológicas e de propriedades, como rugosidade superficial, microdureza, resistência flexural e estabilidade dimensional. Foi realizada uma pesquisa na base de dados Pubmed, utilizando os descritores “microwaves”, “disinfection” e “acrylic resins”, encontrando 47 títulos, destes foram incluídos artigos em inglês, sem limitação de tempo e que estivessem de acordo com o objetivo do trabalho e excluídos estudos de revisão de literatura, sendo, então, 25 artigos selecionados. Foi constatado que a potência 650W por 3 minutos inviabilizou totalmente o crescimento de diversos micro-organismos. Contudo, os estudos que avaliaram as propriedades físico-mecânicas apresentaram resultados bastante conflitantes, não revelando concordância com relação ao protocolo de potência e tempo. No entanto, a maioria demonstrou que as alterações encontradas eram clinicamente insignificantes. Diante desses achados, observa-se que ainda não existe um protocolo padrão estabelecido para utilização da energia de microondas na resina acrílica, garantindo a eficácia antimicrobiana, sem danos a peça protética.Palavras-chave: Micro-ondas. Desinfecção. Resinas Acrílicas.

Utilização de Micro-ondas para Esterilização de Resina Acrílica com Biofilme de Candida albicans Formado in vitro: Estudo Experimental

Este estudo teve como objetivo estabelecer um protocolo de esterilização por micro-ondas para resina acrílica contaminada por Candida albicans. Dezoito discos de resina acrílica termopolimerizável (10x2 mm) foram previamente esterilizados em plasma de peróxido de hidrogênio. Três espécimes foram utilizados para confirmação da esterilidade dos discos. Os outros 15 discos foram imersos individualmente em BHI caldo contendo células de C. albicans em concentração inicial 1x106 UFC/mL e incubados por 48 horas a 37°C. Em seguida, os espécimes contaminados foram divididos em 5 grupos (n3): controle negativo (CN), sem tratamento experimental 1 (E1) irradiado em micro-ondas por 3 min a 450W experimental 2 (E2) irradiado por 3 min a 650W experimental 3 (E3) irradiado por 5 min a 450 W experimental 4 (E4) irradiado por 5 min a 650W. Os espécimes foram irradiados em 50 mL de água destilada. Em seguida, os discos foram incubados individualmente em tubos de ensaio contendo o meio de cultura tioglicolato por 21 dias a 37°C. Diariamente, foi observado se houve turvação do meio de cultura, indicando o crescimento de leveduras. Os tubos que apresentaram turvação tiveram seu meio plaqueado em ágar Sabouraud Dextrose e as placas de petri incubadas a 37°C por 48 horas. O grupo CN apresentou turvação com contagem média de 1,09x107 UFC/mL. Os grupos experimentais não apresentaram turvação, indicando eliminação total do micro-organismo. Concluiu-se que o tratamento com micro-ondas se mostrou eficaz na esterilização dos espécimes de resina acrílica contaminados por C. albicans.Palavras-chave: Acrylic Resin. Microwaves. Sterilization.

Uso de Plasma Frio no Controle de Biofilme de Candida albicans em Próteses Dentárias de Resina Acrílica: Revisão de Literatura

O trabalho objetivou avaliar o uso do plasma frio no controle de biofilmes de Candida em próteses de resina acrílica. Realizou-se uma busca na base de dados Pubmed, utilizando as seguintes palavras-chave combinadas entre si: “cold plasma”, “Candida albicans” e “acrylic resins”, no período de 2010 a 2017. Foram encontrados 478 resultados na busca e selecionados 7 artigos científicos, utilizando como critério de inclusão: estudos in vitro e/ou clínico experimentais controlados, envolvendo a utilização de plasma frio em superfícies de resina acrílica e/ou que avaliaram crescimento de Candida albicans nestas. A literatura relata que o plasma frio, disponível em diferentes composições de gases, apresenta como mecanismo principal de ação aumentar a hidrofilia das superfícies em resina, fortificando ligações químicas e, assim, desfavorecendo a aderência inicial de Candida albicans, o que daria início ao processo de colonização – e futuro surgimento de infecção oral – por este fungo oportunista. Também aumenta a microdureza das próteses e, assim, a sua resistência à corrosão porém não exibe efeitos significantes sobre propriedades como rugosidade superficial, módulo de elasticidade e resistência flexural. Conclui-se que o uso do plasma pode ser promissora na prevenção da adesão fúngica às bases protéticas, sem alterar negativamente as propriedades físicas e mecânicas dos materiais envolvidos porém, há escassez na literatura de trabalhos que o compare com outros mecanismos anti-fúngicos e estudos clínicos a longo prazo.Palavras-chave: Cold Plasma. Candida albicans. Acrylic Resins.

Efeito Profilático da Aplicação de Plasma de Baixa Temperatura na Formação de Biofilme de Candida albicans em Superfície de Resina Acrílica: Estudo Piloto

Foi avaliado se a aplicação do plasma de argônio em superfície de resina acrílica evitaria ou dificultaria a formação de biofilme de Candida albicans in vitro. Dez discos de resina acrílica termopolimerizável (10x2mm) estéreis, com rugosidade de superfície média de 0,2 µm, foram distribuídos aleatoriamente em dois grupos (n5): grupo controle, sem tratamento prévio, e grupo plasma, no qual foi aplicado plasma de argônio 10W/1bar, durante 1minuto, em toda sua superfície, antes da inoculação. Os discos foram colocados individualmente em poços de uma placa de 24 poços, imersos em meio de cultura Sabouraud caldo, com inóculo de 1% (106 unidades formadoras de colônia – UFC/mL) de Candida albicans (ATCC 10231). A placa foi incubada em estufa bacteriológica, a 37°C por 48 horas, para a formação do biofilme. Em seguida, os discos foram removidos, colocados em tubos com 1mL de solução NaCl 0,9% e agitados, para realização de diluição seriada 1:10, 1:100, 1:1000, 1:10000, 1:100000. O plaqueamento foi realizado em ágar Sabouraud Dextrose, e as placas de petri foram incubadas a 37°C por 48 horas. O experimento foi realizado em triplicata. Procedeu-se a contagem de UFC/mL e os dados de ambos os grupos foram comparados pelo teste de Mann Whitney (a0,05). Não foi observada diferença estatística significante entre o grupo controle (19600 UFC/mL) e o grupo plasma (21400 UFC/mL) (p0,4543). Diante das limitações deste estudo piloto, foi concluído que o tratamento prévio com plasma de argônio não foi capaz de evitar e nem dificultar a formação de biofilme de C. albicans em superfície de resina acrílica.Palavras-chave: Gases em Plasma. Candida albican. Adesão.

Implementation of a successful eradication protocol for Burkholderia Cepacia complex in cystic fibrosis patients

Background

Infection with Burkholderia cepacia complex (Bcc) results in a heterogeneous clinical course ranging from asymptomatic colonization of the airways to fulminant respiratory failure in patients with cystic fibrosis (CF). Early eradication of Pseudomonas aeruginosa improves clinical outcomes. The efficacy and clinical outcomes following implementation of an eradication protocol for Bcc are less well understood.

Methods

We developed and implemented a single center Bcc eradication protocol that included an intensive combination of intravenous, inhaled, and oral antibiotic therapies based on in vitro sensitivities. We conducted a retrospective cohort analysis of clinical outcomes compared to patients with chronic Bcc infection.

Results

Six patients were identified as having a newly acquired Bcc colonization and were placed on the eradication protocol. Sequential sputum samples after completion of the protocol demonstrated sustained clearance of Bcc in all patients. Lung function and nutritional status remained stable in the year following eradication.

Conclusion

Clearance of Bcc from sputum cultures using a standardized protocol was successful at one year and was associated with clinical stability.

Paternal cocaine taking elicits epigenetic remodeling and memory deficits in male progeny

This corrects the article DOI: 10.1038/mp.2017.8.

Paternal cocaine taking elicits epigenetic remodeling and memory deficits in male progeny

Paternal environmental perturbations including exposure to drugs of abuse can produce profound effects on the physiology and behavior of offspring via epigenetic modifications. Here we show that adult drug-naive male offspring of cocaine-exposed sires have memory formation deficits and associated reductions in NMDA receptor-mediated hippocampal synaptic plasticity. Reduced levels of the endogenous NMDA receptor co-agonist d-serine were accompanied by increased expression of the d-serine degrading enzyme d-amino acid oxidase (Dao1) in the hippocampus of cocaine-sired male progeny. Increased Dao1 transcription was associated with enrichment of permissive epigenetic marks on histone proteins in the hippocampus of male cocaine-sired progeny, some of which were enhanced near the Dao1 locus. Finally, hippocampal administration of d-serine reversed both the memory formation and synaptic plasticity deficits. Collectively, these results demonstrate that paternal cocaine exposure produces epigenetic remodeling in the hippocampus leading to NMDA receptor-dependent memory formation and synaptic plasticity impairments only in male progeny, which has significant implications for the male descendants of chronic cocaine users.

Recent Achievements in Characterizing the Histone Code and Approaches to Integrating Epigenomics and Systems Biology

Functional epigenetic regulation occurs by dynamic modification of chromatin, including genetic material (i.e., DNA methylation), histone proteins, and other nuclear proteins. Due to the highly complex nature of the histone code, mass spectrometry (MS) has become the leading technique in identification of single and combinatorial histone modifications. MS has now overcome antibody-based strategies due to its automation, high resolution, and accurate quantitation. Moreover, multiple approaches to analysis have been developed for global quantitation of posttranslational modifications (PTMs), including large-scale characterization of modification coexistence (middle-down and top-down proteomics), which is not currently possible with any other biochemical strategy. Recently, our group and others have simplified and increased the effectiveness of analyzing histone PTMs by improving multiple MS methods and data analysis tools. This review provides an overview of the major achievements in the analysis of histone PTMs using MS with a focus on the most recent improvements. We speculate that the workflow for histone analysis at its state of the art is highly reliable in terms of identification and quantitation accuracy, and it has the potential to become a routine method for systems biology thanks to the possibility of integrating histone MS results with genomics and proteomics datasets.

Identification and Quantification of Histone PTMs Using High-Resolution Mass Spectrometry

DNA is organized into nucleosomes, composed of 147 base pairs of DNA wrapped around an octamer of histone proteins including H2A, H2B, H3, and H4. Histones are critical regulators of many nuclear processes, including transcription, DNA damage repair, and higher order chromatin structure. Much of their function is mediated through extensive and dynamic posttranslational modification (PTM) by nuclear enzymes. Histone PTMs are thought to form a code, where combinations of PTMs are responsible for specific biological functions. Here, we present protocols to identify and quantify histone PTMs using nanoflow liquid chromatography coupled to mass spectrometry (MS). We first describe how to purify histones and prepare them for MS. We then describe three MS platforms for histone PTM analysis, including bottom-up, middle-down, and top-down approaches, and explain the relative benefits and pitfalls of each approach. We also include tips to increase the throughput of large experiments.

Acute Fibrinous Organizing Pneumonia: A Case Report and Literature Review

Acute fibrinous organizing pneumonia (AFOP) is a distinct histopathologic pattern of lung injury with the hallmark feature of intra-alveolar fibrin deposits with associated organizing pneumonia, type II pneumocyte hyperplasia, and a patchy lymphohistiocytic proliferation. We describe the case of a previously healthy 47-year-old man who presented with a 4-day history of worsening dyspnea, cough, and nocturnal fevers and miliary nodules on chest imaging. Subsequently, there was an indication of AFOP when he underwent open lung biopsy. AFOP has been associated with a variety of underlying conditions including rheumatologic diseases, medications, and infections, and several cases were idiopathic. This case highlights the importance for radiologists to be aware of this uncommon pattern of lung injury and to consider it in the differential when encountering bilateral miliary infiltrates on chest imaging.

Recurrent inflammatory pseudotumor of the jaw with perineural intracranial invasion demonstrating sustained response to Rituximab

Corticosteroids are the mainstay of treatment of inflammatory pseudotumor (IPT) of the head and neck; however, involvement of the skull base and mandible can be unresponsive to steroids and require surgical resection. IPT is known to usually contain a CD20+ lymphocyte subgroup. Rituximab, a chimeric anti-CD20 antibody, has been successfully utilized in the treatment of other CD20+ diseases, including the similar idiopathic orbital inflammatory disease. This is the first report to describe successful treatment with Rituximab of a recurrent IPT of the mandible with trigeminal spread and leptomeningeal involvement with clinical and radiologic evidence demonstrating a sustained response to therapy.

Heterozygosity and gene flow in populations of Calomys laucha (Rodentia, Cricetidae)

Enzyme polymorphism was studied by means of starch gel electrophoresis on five population samples of Calomys laucha collected in different sites and seasons. C. laucha, a cricetid rodent inhabiting preferentially cultivated fields in the central-eastern plains of Argentina, is a reservoir-host of Junin virus, agent of Argentine hemorrhagic fever. Results show high levels of genic variability in all the samples (P from 62.50 to 77.27; H from 0.118 to 0.163) and low genetic distance among populations (D from 0.0024 to 0.0167). Estimations of gene flow (mean Nm = 10.78) indicate a high migration capability of the species and the possibility of further dispersal of Junin virus.

Sugar additives for MALDI matrices improve signal allowing the smallest nucleotide change (A:T) in a DNA sequence to be resolved

Sample preparation for matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) of DNA is critical for obtaining high quality mass spectra. Sample impurity, solvent content, substrate surface and environmental conditions (temperature and humidity) all affect the rate of matrix-analyte co-crystallization. As a result, laser fluence threshold for desorption/ionization varies from spot to spot. When using 3-hydroxypicolinic acid (3-HPA) as the matrix, laser fluence higher than the threshold value reduces mass resolution in time-of-flight (TOF) MS as the excess energy transferred to DNA causes metastable decay. This can be overcome by either searching for 'hot' spots or adjusting the laser fluence. However, both solutions may require a significant amount of operator manipulation and are not ideal for automatic measurements. We have added various sugars for crystallization with the matrix to minimize the transfer of excess laser energy to DNA molecules. Fructose and fucose were found to be the most effective matrix additives. Using these additives, mass resolution for DNA molecules does not show noticeable deterioration as laser energy increases. Improved sample preparation is important for the detection of single nucleotide polymorphisms (SNPs) using primer extension with a single nucleotide. During automatic data acquisition it is difficult to routinely detect heterozygous A/T mutations, which requires resolving a mass difference of 9 Da, unless a sugar is added during crystallization.

Synthesis of glycosyl-1-phosphates via dehydrative glycosylation

[reaction: see text] Direct synthetic access to glycosyl-1-phosphates is accomplished with the dehydrative coupling of carbohydrate hemiacetals and dialkyl phosphates, employing dibenzothiophene-5-oxide and triflic anhydride. The procedure offers a new and versatile method for efficient preparation of a host of glycosyl-1-phosphates of variable structure with good control over anomeric selectivity.

Evolution of the mitochondrial DNA control region in the Anopheles gambiae complex

We have sequenced the AT-rich control region of the mitochondrial DNA (mtDNA) of six species in the Afrotropical Anopheles gambiae complex and the closely related A. christyi. Contrary to expectations, the AT-rich region in this group is evolving rather slowly, more slowly than the third position of mtDNA protein-coding genes. Despite being relatively conserved between species, we detected intraspecific and intra-individual (heteroplasmy) variation in this region. Phylogenetically, we found we could place the rare endemic A. bwambae as a sister taxon to A. melas, the same evolutionary position as indicated by chromosomal inversions. The outgroup, A. christyi, gave evidence of the root of the tree. In comparing the molecular trees with that deduced by chromosomal inversions, they are completely congruent with the exception of the placement of A. arabiensis. The anomalous position of this species can be explained by introgression with A. gambiae. From the phylogenetic position, we could infer mtDNA gene flow from A. gambiae to A. arabiensis.

Microgeographic distribution of allele frequencies in populations of Calomys laucha (Rodentia, Cricetidae)

The microgeographic differentiation of allelic frequencies was analysed in two population samples of Calomys laucha, collected in a grid set in cultivated fields at Laguna Larga (Córdoba province, Argentina). One of the samples (n = 79) was obtained in May (Autumn), when the population density is at a maximum, and the other (n = 85) in November (spring), at the onset of reproductive activity. FST values for the November sample show significant differences between the six groups over which the sample was divided. FIT values show an excess of homozygotes for some loci in both samples. FIS reveals an excess of homozygotes within each of the groups. These results indicate the existence of subdivision in the population. Because C. laucha is a reservoir host of the Junin virus, an agent of endemic disease, this social organization may have epidemiological implications. Stratification of C. laucha populations into small breeding units could be one of the factors responsible for the high genic variability detected in this species.