Human Pulmonary Infections Research Articles

Draft genome sequences of 12 Mycolicibacterium fortuitum isolates from human pulmonary infections in Veracruz, Mexico.

Mycolicibacterium fortuitum, a fast-growing nontuberculous mycobacterium, is a significant pathogen in healthcare-associated infections, encompassing skin, soft tissue, and pulmonary diseases. In this study, we present draft genome sequences from 12 M. fortuitum strains isolated from sputum samples from patients diagnosed with pulmonary infections in Mexico.

Mice with lung airway ciliopathy develop persistent Mycobacterium abscessus lung infection and have a proinflammatory lung phenotype associated with decreased T regulatory cells.

Human pulmonary infection with non-tuberculous mycobacteria (NTM) such as Mycobacterium abscessus (Mabs) occurs in seemingly immunocompetent patients with underlying structural lung disease such as bronchiectasis in which normal ciliary function is perturbed. In addition to alterations in mucociliary clearance, the local immunologic milieu may be altered in patients with structural lung disease, but the nature of these changes and how they relate to NTM persistence remain unclear. We used a mouse strain containing a conditional floxed allele of the gene IFT88, which encodes for the protein Polaris. Deletion of this gene in adult mice reportedly leads to loss of cilia on lung airway epithelium and to the development of bronchiectasis. In a series of experiments, IFT88 control mice and IFT88 KO mice received different preparations of Mabs lung inocula with lung CFU assessed out to approximately 8 weeks post-infection. In addition, cytokine levels in bronchoalveolar lavage (BAL) fluid, lung T cell subset analysis, and lung histopathology and morphometry were performed at various time points. Mabs embedded in agarose beads persisted in the lungs of IFT88 KO mice out to approximately 8 weeks (54 days), while Mabs agarose beads in the lungs of IFT88 control mice was cleared from the lungs of all mice at this time point. T cells subset analysis showed a decrease in the percentage of CD4+FoxP3+ T cells in the total lymphocyte population in the lungs of IFT88 KO mice relative to IFT88 control mice. Proinflammatory cytokines were elevated in the BAL fluid from infected IFT88 KO mice compared to infected IFT88 control mice, and histopathology showed an increased inflammatory response and greater numbers of granulomas in the lungs of infected IFT88 KO mice compared to the lungs of infected IFT88 control mice. Scanning lung morphometry did not show a significant difference comparing lung airway area and lung airway perimeter between IFT88 KO mice and IFT88 control mice. Persistent lung infection in our model was established using Mabs embedded in agarose beads. The utility of using IFT88 mice is that a significant difference in Mabs lung CFU is observed comparing IFT88 KO mice to IFT88 control mice thus allowing for studies assessing the mechanism(s) of Mabs lung persistence. Our finding of minimal differences in lung airway area and lung airway diameter comparing IFT88 KO mice to IFT88 control mice suggests that the development of a proinflammatory lung phenotype in IFT88 KO mice contributes to Mabs lung persistence independent of bronchiectasis. The contribution of cilia to immune regulation is increasingly recognized, and our results suggest that ciliopathy associated with structural lung disease may play a role in NTM pulmonary infection via alteration of the local immunologic lung milieu.

Evaluating Bacterial Pathogenesis Using a Model of Human Airway Organoids Infected with Pseudomonas aeruginosa Biofilms.

Pseudomonas aeruginosa is one of the leading invasive agents of human pulmonary infection, especially in patients with compromised immunity. Prior studies have used various in vitro models to establish P. aeruginosa infection and to analyze transcriptomic profiles of either the host or pathogen, and yet how much those works are relevant to the genuine human airway still raises doubts. In this study, we cultured and differentiated human airway organoids (HAOs) that recapitulate, to a large extent, the histological and physiological features of the native human mucociliary epithelium. HAOs were then employed as a host model to monitor P. aeruginosa biofilm development. Through dual-species transcriptome sequencing (RNA-seq) analyses, we found that quorum sensing (QS) and several associated protein secretion systems were significantly upregulated in HAO-associated bacteria. Cocultures of HAOs and QS-defective mutants further validated the role of QS in the maintenance of a robust biofilm and disruption of host tissue. Simultaneously, the expression magnitude of multiple inflammation-associated signaling pathways was higher in the QS mutant-infected HAOs, suggesting that QS promotes immune evasion at the transcriptional level. Altogether, modeling infection of HAOs by P. aeruginosa captured several crucial facets in host responses and bacterial pathogenesis, with QS being the most dominant virulence pathway showing profound effects on both bacterial biofilm and host immune responses. Our results revealed that HAOs are an optimal model for studying the interaction between the airway epithelium and bacterial pathogens. IMPORTANCE Human airway organoids (HAOs) are an organotypic model of human airway mucociliary epithelium. The HAOs can closely resemble their origin organ in terms of epithelium architecture and physiological function. Accumulating studies have revealed the great values of the HAO cultures in host-pathogen interaction research. In this study, HAOs were used as a host model to grow Pseudomonas aeruginosa biofilm, which is one of the most common pathogens found in pulmonary infection cases. Dual transcriptome sequencing (RNA-seq) analyses showed that the cocultures have changed the gene expression pattern of both sides significantly and simultaneously. Bacterial quorum sensing (QS), the most upregulated pathway, contributed greatly to biofilm formation, disruption of barrier function, and subversion of host immune responses. Our study therefore provides a global insight into the transcriptomic responses of both P. aeruginosa and human airway epithelium.

ATYPICAL PRESENTATION OF MYCOBACTERIUM CHIMAERA PNEUMONIA FOLLOWING TRANSESOPHAGEAL ECHOCARDIOGRAPHY

ATYPICAL PRESENTATION OF MYCOBACTERIUM CHIMAERA PNEUMONIA FOLLOWING TRANSESOPHAGEAL ECHOCARDIOGRAPHY

Comparative Genomics of Mycobacterium avium Complex Reveals Signatures of Environment-Specific Adaptation and Community Acquisition.

ABSTRACTNontuberculous mycobacteria, including those in the Mycobacterium avium complex (MAC), constitute an increasingly urgent threat to global public health. Ubiquitous in soil and water worldwide, MAC members cause a diverse array of infections in humans and animals that are often multidrug resistant, intractable, and deadly. MAC lung disease is of particular concern and is now more prevalent than tuberculosis in many countries, including the United States. Although the clinical importance of these microorganisms continues to expand, our understanding of their genomic diversity is limited, hampering basic and translational studies alike. Here, we leveraged a unique collection of genomes to characterize MAC population structure, gene content, and within-host strain dynamics in unprecedented detail. We found that different MAC species encode distinct suites of biomedically relevant genes, including antibiotic resistance genes and virulence factors, which may influence their distinct clinical manifestations. We observed that M. avium isolates from different sources—human pulmonary infections, human disseminated infections, animals, and natural environments—are readily distinguished by their core and accessory genomes, by their patterns of horizontal gene transfer, and by numerous specific genes, including virulence factors. We identified highly similar MAC strains from distinct patients within and across two geographically distinct clinical cohorts, providing important insights into the reservoirs which seed community acquisition. We also discovered a novel MAC genomospecies in one of these cohorts. Collectively, our results provide key genomic context for these emerging pathogens and will facilitate future exploration of MAC ecology, evolution, and pathogenesis.IMPORTANCE Members of the Mycobacterium avium complex (MAC), a group of mycobacteria encompassing M. avium and its closest relatives, are omnipresent in natural environments and emerging pathogens of humans and animals. MAC infections are difficult to treat, sometimes fatal, and increasingly common. Here, we used comparative genomics to illuminate key aspects of MAC biology. We found that different MAC species and M. avium isolates from different sources encode distinct suites of clinically relevant genes, including those for virulence and antibiotic resistance. We identified highly similar MAC strains in patients from different states and decades, suggesting community acquisition from dispersed and stable reservoirs, and we discovered a novel MAC species. Our work provides valuable insight into the genomic features underlying these versatile pathogens.

Draft Genome Sequence of the Environmental Fungus Scedosporium dehoogii.

Today, the genus Scedosporium comprises at least ten species with four of them, Scedosporium apiospermum, Scedosporium boydii, Scedosporium aurantiacum and Scedosporium minutisporum capable of colonizing the lungs of patients with cystic fibrosis. Scedosporium dehoogii, which is also common in the soil, has never been reported as causing human pulmonary infections. Here we report the first genome sequence for S. dehoogii, an invaluable resource to understand the genetic bases of pathogenesis in the genus Scedosporium.

Evodiamine alleviates lipopolysaccharide-induced pulmonary inflammation and fibrosis by activating apelin pathway.

Inflammation can cause a series of inflammatory lung disease, which seriously endangers human health. Pulmonary fibrosis is a kind of inflammatory disease with end-stage lung pathological changes. It has complicated and unknown pathogenesis and is still lack of effective therapeutic drugs. LPS-induced inflammation is a common feature of many infectious inflammations such as pneumonia, bacteremia, glomerulonephritis, etc. Evodiamine, one of the main components of Evodia rutaecarpa, is an alkaloid with excellent antiinflammatory effects. In this study, we evaluated the protective capacities of evodiamine on LPS-induced inflammatory damages in vitro and in vivo. MTT method, flow cytometry, immunofluorescence, and other methods were used for in vitro study to determine the protective capacities of evodiamine. The results suggest that evodiamine can protect murine macrophages from the LPS-nigericin-induced damages by (a) inhibiting cellular apoptosis, (b) inhibiting inflammatory cytokines releasing, and (c) activating the apelin pathway. We also used the exogenous apelin-13 peptide co-cultured with LPS-nigericin in RAW264.7 cells and found that apelin-13 contributes to protecting the effects of evodiamine. In vivo, the ELISA method and immunohistochemistry were used to examine inflammatory cytokines, apelin, and histological changes. BALB/c mice were exposed to LPS and subsequent administration of evodiamine （p.o.）for some time, the results of the alveolar lavage fluid and the tissue slices showed that evodiamine treatment alleviated the pulmonary inflammation and fibrosis, stimulated apelin expression and inhibited the inflammatory cytokines. These results provide a basis for the protective effect and mechanism of evodiamine in LPS-induced inflammation and suggest that it might be potential therapeutics in human pulmonary infections.

Development of reverse transcription loop-mediated isothermal amplification assays for point-of-care testing of avian influenza virus subtype H5 and H9.

Avian influenza (AIV) outbreaks can induce fatal human pulmonary infections in addition to economic losses to the poultry industry. In this study, we aimed to develop a rapid and sensitive point-of-care AIV test using loop-mediated isothermal amplification (LAMP) technology. We designed three sets of reverse transcription LAMP (RT-LAMP) primers targeting the matrix (M) and hemagglutinin (HA) genes of the H5 and H9 subtypes. RT-LAMP targeting the universal M gene was designed to screen for the presence of AIV and RT-LAMP assays targeting H5-HA and H9-HA were designed to discriminate between the H5 and H9 subtypes. All three RT-LAMP assays showed specific amplification results without nonspecific reactions. In terms of sensitivity, the detection limits of our RT-LAMP assays were 100 to 1,000 RNA copies per reaction, which were 10 times more sensitive than the detection limits of the reference reverse‒transcription polymerase chain reaction (RT-PCR) (1,000 to 10,000 RNA copies per reaction). The reaction time of our RT-LAMP assays was less than 30 min, which was approximately four times quicker than that of conventional RT-PCR. Altogether, these assays successfully detected the existence of AIV and discriminated between the H5 or H9 subtypes with higher sensitivity and less time than the conventional RT-PCR assay.

Drug resistance pattern of Mycobacterium abscessus: Change of pattern in 20-year period after the first report of human pulmonary infection in Thailand

Background: Mycobacterium abscessus is a new emerging problematic mycobacterial infection seen in several countries including Thailand, a tropical country in Indochina, at present. This infection usually has the problem of antibiotic resistance. Methods: The authors hereby review and reappraise the pattern of drug resistance pattern of M. abscessus to study the change of pattern in 20-year period after the first report of human pulmonary infection in Thailand. Results: The drug resistance pattern is observable, and there are some remained nonresistant drugs. Conclusion: In our setting, drug resistance of M. abscessus has been an important problem for a long time. Nevertheless, there is still no much change of the pattern of drug resistance.

Disseminated nontuberculous mycobacterial disease in a cat caused by Mycobacterium sp. strain MFM001

Mycobacterium sp. strain MFM001 (MFM001), a new strain of slow-growing nontuberculous mycobacteria not associated with the Mycobacterium avium complex, led to disseminated mycobacterial disease characterized by transmural granulomatous gastroenterocolitis of lepromatous type in a cat treated with immunosuppressive medication. MFM001 was found to be closely related to M. kyorinense or M. celatum by partial sequence of 16S rDNA, and identical with an unspecified M. sp. strain B10-07.09.0206 isolated from a human pulmonary infection in Germany. MFM001 should be considered as a pathogenic organism in cats, especially in immunocompromised animals.

Burkholderia gladioli infection isolated from the blood cultures of newborns in the neonatal intensive care unit.

Burkholderia gladioli was described as a plant pathogen, and it is a rare cause of infection in humans that is primarily associated with human pulmonary infections, such as chronic granulomatous disease and cystic fibrosis. The neonatal respiratory system is not fully developed and cannot expel bacterial aerosol properly. A total of 2,676 newborns in the neonatal intensive care unit were retrospectively analysed in Putian City, Fujian Province, China, from 2011 to 2014. All of the blood samples were tested for C-reactive protein (CRP), procalcitonin (PCT) and white blood cell (WBC). B. gladioli infections were determined and analysed using a blood culture system. Antibiotic susceptibility testing was performed using the K-B method. Of the 2,676 participants, 87 (3.25%) had a positive B. gladioli blood culture that occurred >72h after birth, including a premature group (54.0%, asphyxia [vs. 9.20%], fever [vs. 13.80%], pneumonia [vs. 6.90%] and hyperbilirubinaemia [vs. 8.05%]) and newborns with necrotising enterocolitis (NEC) (vs. 5.75%). The mean ± standard deviation (SD) of the CRP level was 12.31 ± 0.26mg/L and that of the PCT level was 1.53 ± 0.21ng/ml in the 87 B. gladioli-infected newborns. Most of the B. gladioli isolates were sensitive to many antimicrobial agents and did not lead to serious consequences. All of the B. gladioli-infected newborns were unhealthy, especially the premature infants. B. gladioli might be a causative bacteraemia agent in neonates, it appears to have pathogenic potential in newborns and its sensitivity to antibiotics may be a beneficial factor.

Receptor-mediated signaling in Aspergillus fumigatus.

Aspergillus fumigatus is the most pathogenic species among the Aspergilli, and the major fungal agent of human pulmonary infection. To prosper in diverse ecological niches, Aspergilli have evolved numerous mechanisms for adaptive gene regulation, some of which are also crucial for mammalian infection. Among the molecules which govern such responses, integral membrane receptors are thought to be the most amenable to therapeutic modulation. This is due to the localization of these molecular sensors at the periphery of the fungal cell, and to the prevalence of small molecules and licensed drugs which target receptor-mediated signaling in higher eukaryotic cells. In this review we highlight the progress made in characterizing receptor-mediated environmental adaptation in A. fumigatus and its relevance for pathogenicity in mammals. By presenting a first genomic survey of integral membrane proteins in this organism, we highlight an abundance of putative seven transmembrane domain (7TMD) receptors, the majority of which remain uncharacterized. Given the dependency of A. fumigatus upon stress adaptation for colonization and infection of mammalian hosts, and the merits of targeting receptor-mediated signaling as an antifungal strategy, a closer scrutiny of sensory perception and signal transduction in this organism is warranted.

Targeting iron uptake to controlPseudomonas aeruginosainfections in cystic fibrosis

The aerobic Gram-negative bacterium Pseudomonas aeruginosa is an opportunistic pathogen responsible for life-threatening acute and chronic infections in humans. As part of chronic infection P. aeruginosa forms biofilms, which shield the encased bacteria from host immune clearance and provide an impermeable and protective barrier against currently available antimicrobial agents. P. aeruginosa has an absolute requirement for iron for infection success. By influencing cell-cell communication (quorum sensing) and virulence factor expression, iron is a powerful regulator of P. aeruginosa behaviour. Consequently, the imposed perturbation of iron acquisition systems has been proposed as a novel therapeutic approach to the treatment of P. aeruginosa biofilm infection. In this review, we explore the influence of iron availability on P. aeruginosa infection in the lungs of the people with the autosomal recessive condition cystic fibrosis as an archetypal model of chronic P. aeruginosa biofilm infection. Novel therapeutics aimed at disrupting P. aeruginosa are discussed, with an emphasis placed on identifying the barriers that need to be overcome in order to translate these promising in vitro agents into effective therapies in human pulmonary infections.

Human pulmonary infections with bovine and environment (atypical) mycobacteria in jos, Nigeria.

To examine sputum specimens from patients with persistent bronchopulmonary disorders for mycobacterium species and to characterize the recovered isolates with a view to determining the extent of involvement of environmental mycobacteria in pulmonary infections. Analytical study using standard microscopy, culture and biochemical test for the identification of mycobacterium species. Jos University Teaching Hospital (JUTH) and 2 referral hospitals: Plateau Specialist Hospital and Evangelical Churches of West Africa (ECWA) Evangel Hospital in Jos, Nigeria. Three hundred and twenty nine (329) volunteer new patients seen at the chest clinic and general out patient departments with broncho-pulmonary disorders. Patients already on anti-tuberculosis were excluded from the study. Subjects were administered antituberculosis drugs and or other treatment regimes after proper diagnosis Sixty-five (65) mycobacterial isolates were obtained and differentiated into human tubercle bacilli, bovine and or environmental (atypical) mycobacteria on the basis of nine identification tests. Of the 65 mycobacterial isolates subjected to the tests, 40 (61.54%) were identified as mycobacterium tuberculosis, 10 (15.38%) as M. bovis and 15 (23.08%) as environmental mycobacteria. Among the environmental group, 9 (20.69%) were classified as M. avium 3 (3.45%) each as M. kansasi and M. fortuitum. The study confirms the involvement of bovine and environmental mycobacteria in pulmonary infections. This may be related to the rising prevalence of HIV/AIDS globally. The need for adequate bacteriological analysis in current-day diagnosis of pulmonary tuberculosis in indicated.

Nocardia mikamii sp. nov., isolated from human pulmonary infections in the USA

Four nocardioform bacterial strains isolated from clinical respiratory sources were characterized using a polyphasic taxonomic approach. On the basis of 16S rRNA gene sequence analyses, these strains were found to be 100 % similar to each other and were shown to belong to the genus Nocardia. Chemotaxonomic data [major menaquinone: ω-cyclic isoprene side chain MK-8(H₄(cycl)); major polar lipids: diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannosides; major fatty acids: monounsaturated fatty acids with a considerable amount of tuberculostearic acid; and mycolic acids (52-62 carbon atoms)] were consistent with the assignment of the novel strains to the genus Nocardia. Comparative phylogenetic analysis of the 16S rRNA gene sequences showed that the novel strains were related to Nocardia cerradoensis DSM 44546(T) (99.8 %) and Nocardia aobensis JCM 12352(T) (99.6 %). Analysis of gyrB gene sequences showed these strains were related to N. aobensis (96.6 %) and to N. cerradoensis (96.3 %). The results suggest that gyrB gene sequencing is a more powerful tool than 16S rRNA gene sequencing for taxonomic identification within the genus Nocardia. DNA-DNA hybridization and physiological and biochemical tests supported the genotypic and phenotypic differentiation of the novel strains from related species. These data indicated that the new strains represent a novel species within the genus Nocardia, for which the name Nocardia mikamii sp. nov. is proposed, with strain W8061(T) (=DSM 45174(T)=JCM 15508(T)) as the type strain.

The pathology of human and murine pulmonary infection with Cryptococcus neoformans var. gattii

Human infection by Cryptococcus neoformans var. neoformans is well characterised and usually occurs in immunocompromised patients. Less is known about infection by Cryptococcus neoformans var. gattii, which usually produces disease in previously normal individuals. In two cases of human pulmonary infection by Cryptococcus neoformans var. gattii, we observed a mixed inflammatory pattern, including granulomas associated with numerous T lymphocytes and a lymphocytic interstitial pneumonitis with B lymphocytes and formation of follicles. We also established a murine model of pulmonary infection by Cryptococcus neoformans var. gattii, which reproduced most of these features. This model is likely to prove useful in studies of the pathogenesis of this infection.

Human Extrapulmonary Dirofilariasis in Texas

Human pulmonary infection due to the dog heartworm, Dirofilaria immitis, has been reported in the medical literature for many decades. Extrapulmonary infection due to this pathogen is less widely reported, including only nine cases in North America. We report a case of extrapulmonary dirofilariasis manifested as asymptomatic nodular lesions in the anterior abdominal wall of a patient having exploratory laparotomy for carcinoma. We review previously reported cases and discuss the pathophysiology of both pulmonary and extrapulmonary dirofilariasis.

Necrotizing Pneumonia Caused by Mixed Infection with Actinobacillus actinomycetemcomitans and Actinomyces israelii: Case Report and Review

Actinobacillus actinomycetemcomitans is an important cause of human pulmonary infections, either alone or with Actinomyces species. It may be critical to isolate Actinobacillus in patients with pulmonary infection for selection of an effective antimicrobial regimen. Clindamycin has superseded penicillin as the sole antimicrobial drug for anaerobic bacterial necrotizing pneumonia and abscess. In the case presented herein, therapy with clindamycin failed to halt worsening necrotizing pneumonia or to prevent hematogenous dissemination. After clindamycin-resistant A. actinomycetemcomitans in addition to Actinomyces israelii were isolated, the patient was treated with penicillin, ciprofloxacin, and cefazolin and was ultimately cured.

Rhodococcus equi Causing Human Pulmonary Infection: Review of 29 Cases

Rhodococcus equi is a gram-positive pleomorphic bacillus that has been identified as a life-threatening pulmonary pathogen in the immunocompromised host. Infection with R equi may go unrecognized by physicians unacquainted with its presentation and unaware of the organism's ability to mimic diphtheroids and to stain weakly positive with an acid-fast stain.

Human pulmonary infection with Corynebacterium equi

A 28 year old man with no underlying disease developed a cavity and multiple nodules in the lung from which Corynebacterium equi was isolated. He experimented with organic solvents and microorganisms including Corynebacterium species for several years. Computed tomography of his pulmonary lesions revealed that these nodules were related to the bronchial tree. Histologically, the lesions were compatible with nonspecific inflammatory changes. The clinician must suspect the pulmonary infections with Corynebacterium species even if the patient has no underlying disease.