Clinical significance of a positive serology for mimivirus in patients presenting a suspicion of ventilator-associated pneumonia:

Detection of Mimivirus from respiratory samples in tuberculosis-suspected patients

Acanthamoeba polyphaga mimivirus (APMV), a species of amoeba-infecting giant viruses, has recently emerged as human respiratory pathogens. This study aimed to evaluate the presence of Mimivirus in respiratory samples, collected from tuberculosis (TB)-suspected patients. The study was performed on 10,166 clinical respiratory samples from April 2013 to December 2017. Mimivirus was detected using a suicide nested-polymerase chain reaction (PCR) and real-time PCR methods. Of 10,166 TB-suspected patients, 4 (0.04%) were positive for Mimivirus, including Mimivirus-53, Mimivirus-186, Mimivirus-1291, and Mimivirus-1922. Three out of four patients, hospitalized in the intensive care unit (ICU), were mechanically ventilated. All patients had an underlying disease, and the virus was detected in both sputum and bronchoalveolar lavage samples. In conclusion, Mimivirus was isolated from TB-suspected patients in a comprehensive study. The present results, similar to previous reports, showed that Mimiviruses could be related to pneumonia. Further studies in different parts of the world are needed to additional investigate the clinical importance of Mimivirus infection.

Pulmonary Infection Related to Mimivirus in Patient with Primary Ciliary Dyskinesia

Primary ciliary dyskinesia is a rare autosomal recessive disorder that causes oto-sino-pulmonary disease. We report a case of pulmonary infection related to mimivirus in a 10-year-old boy with primary ciliary dyskinesia that was identified using molecular techniques. Our findings indicate that the lineage C of mimivirus may cause pneumonia in humans.

Fecal Viral Community Responses to High-Fat Diet in Mice

Alterations in diet can have significant impact on the host, with high-fat diet (HFD) leading to obesity, diabetes, and inflammation of the gut. Although membership and abundances in gut bacterial communities are strongly influenced by diet, substantially less is known about how viral communities respond to dietary changes. Examining fecal contents of mice as the mice were transitioned from normal chow to HFD, we found significant changes in the relative abundances and the diversity in the gut of bacteria and their viruses. Alpha diversity of the bacterial community was significantly diminished in response to the diet change but did not change significantly in the viral community. However, the diet shift significantly impacted the beta diversity in both the bacterial and viral communities. There was a significant shift away from the relatively abundant Siphoviridae accompanied by increases in bacteriophages from the Microviridae family. The proportion of identified bacteriophage structural genes significantly decreased after the transition to HFD, with a conserved loss of integrase genes in all four experimental groups. In total, this study provides evidence for substantial changes in the intestinal virome disproportionate to bacterial changes, and with alterations in putative viral lifestyles related to chromosomal integration as a result of shift to HFD.IMPORTANCE Prior studies have shown that high-fat diet (HFD) can have profound effects on the gastrointestinal (GI) tract microbiome and also demonstrate that bacteria in the GI tract can affect metabolism and lean/obese phenotypes. We investigated whether the composition of viral communities that also inhabit the GI tract are affected by shifts from normal to HFD. We found significant and reproducible shifts in the content of GI tract viromes after the transition to HFD. The differences observed in virome community membership and their associated gene content suggest that these altered viral communities are populated by viruses that are more virulent toward their host bacteria. Because HFD also are associated with significant shifts in GI tract bacterial communities, we believe that the shifts in the viral community may serve to drive the changes that occur in associated bacterial communities.

Lack of evidence of mimivirus replication in human PBMCs

The Acanthamoeba polyphaga mimivirus (APMV) was first isolated during a pneumonia outbreak in Bradford, England, and since its discovery many research groups devoted efforts to understand whether this virus could be associated to human diseases, in particular clinical signs and symptoms of pneumonia. In 2013, we observed cytopathic effect in amoebas (rounding and lysis) inoculated with APMV inoculated PBMCs (peripheral blood mononuclear cell) extracts, and at that point we interpreted those results as mimivirus replication in human PBMCs. Based on these results we decided to further investigate APMV replication in human PBMCs, by transmission electron microscopy (TEM) and qPCR. No viral factory was observed in APMV inoculated PBMCs, at any analyzed time and M.O.I.s (multiplicity of infection), by checking 550 cells per condition tested. We also measured the variation of viral DNA by qPCR targeting helicase gene during the course of the TEM experiment in PBMCs, but the DNA levels stayed the same as the first time-point post infection. In summary, our newest qPCR and TEM results do not support previous statements (including ours) that mimivirus is able to replicate in humans PBMCs.

Giant Viruses of Amoebae: A Journey Through Innovative Research and Paradigm Changes

Giant viruses of amoebae were discovered serendipitously in 2003; they are visible via optical microscopy, making them bona fide microbes. Their lifestyle, structure, and genomes break the mold of classical viruses. Giant viruses of amoebae are complex microorganisms. Their genomes harbor between 444 and 2,544 genes, including many that are unique to viruses, and encode translation components; their virions contain >100 proteins as well as mRNAs. Mimiviruses have a specific mobilome, including virophages, provirophages, and transpovirons, and can resist virophages through a system known as MIMIVIRE (mimivirus virophage resistance element). Giant viruses of amoebae bring upheaval to the definition of viruses and tend to separate the current virosphere into two categories: very simple viruses and viruses with complexity similar to that of other microbes. This new paradigm is propitious for enhanced detection and characterization of giant viruses of amoebae, and a particular focus on their role in humans is warranted.

Giant Viruses of Amoebas: An Update

During the 12 past years, five new or putative virus families encompassing several members, namely Mimiviridae, Marseilleviridae, pandoraviruses, faustoviruses, and virophages were described. In addition, Pithovirus sibericum and Mollivirus sibericum represent type strains of putative new giant virus families. All these viruses were isolated using amoebal coculture methods. These giant viruses were linked by phylogenomic analyses to other large DNA viruses. They were then proposed to be classified in a new viral order, the Megavirales, on the basis of their common origin, as shown by a set of ancestral genes encoding key viral functions, a common virion architecture, and shared major biological features including replication inside cytoplasmic factories. Megavirales is increasingly demonstrated to stand in the tree of life aside Bacteria, Archaea, and Eukarya, and the megavirus ancestor is suspected to be as ancient as cellular ancestors. In addition, giant amoebal viruses are visible under a light microscope and display many phenotypic and genomic features not found in other viruses, while they share other characteristics with parasitic microbes. Moreover, these organisms appear to be common inhabitants of our biosphere, and mimiviruses and marseilleviruses were isolated from human samples and associated to diseases. In the present review, we describe the main features and recent findings on these giant amoebal viruses and virophages.

Aetiology of hospital-acquired pneumonia and trends in antimicrobial resistance

PURPOSE OF REVIEW

Hospital-acquired pneumonia (HAP) and ventilator-associated pneumonia (VAP) continue to present very significant diagnostic and management challenges. The development, introduction and use of a wider range of immunosuppressive therapies are leading to a broader spectrum of microorganisms causing HAP and VAP. The persistent clinical dilemma regarding their cause is that detection of a microorganism from a respiratory tract sample does not necessarily signify it is the causative agent of the pneumonia. The ever-increasing antibiotic resistance problem means that HAP and VAP are becoming progressively more difficult to treat. In this article, we review the cause, antimicrobial resistance, diagnosis and treatment of HAP and VAP and encapsulate recent developments and concepts in this rapidly moving field.

RECENT FINDINGS

Although the microbial causes of HAP and VAP remain at present similar to those identified in previous studies, there are marked geographical differences. Resistance rates among Gram-negative bacteria are continually increasing, and for any species, multiresistance is the norm rather than the exception. The development and introduction of rapid point-of-care diagnostics may improve understanding of the cause of HAP and VAP and has immense potential to influence the treatment and clinical outcomes in HAP/VAP, with patients likely to receive much faster, microorganism-specific treatment with obvious downstream improvements to clinical outcome and antimicrobial stewardship.

SUMMARY

We describe recent trends in aetiology of HAP and VAP and recent trends in antimicrobial resistance, including resistance mechanisms causing particular concern. The potential for novel molecular diagnostics to revolutionize the diagnosis and treatment of HAP/VAP is discussed.

Viral Sepsis

Viruses are the smallest infective agents currently known to affect humans and animals. The virus has a centrally situated nucleic acid, which is encased within a capsid consisting of a protein core. Viruses are obligatory intracellular microorganisms that live inside cells, using components of the nucleic acid and protein generating system of the host to replicate and trigger cell destruction leading to diseases. Alternatively, the host’s defense mechanisms lead to cell destruction in an attempt to clear cells infected by the viruses. The nucleic acid is RNA or DNA, which may be single-stranded or double-stranded [1]. The pathophysiology of viral infections may be attributed to the degeneration and cellular necrosis of the infected cells, leading to local and systemic inflammatory responses. The body’s defense mechanisms include phagocytosis, humoral and cell-mediated responses and the production of interferons [2]. Interferons prevent the local spread of viruses, whereas antibodies prevent viremia, ensure long-term immunity and sensitize infected cells to be destroyed by T-cells and macrophages [3, 4]. Cell-mediated immunity leads to an increase in cytotoxic cells that then release lymphokines, including interferon.

Looking at protists as a source of pathogenic viruses

In the environment, protozoa are predators of bacteria and feed on them. The possibility that some protozoa could be a source of human pathogens is consistent with the discovery that free-living amoebae were the reservoir of Legionella pneumophila, the agent of Legionnaires' disease. Later, while searching for Legionella in the environment using amoeba co-culture, the first giant virus, Acanthamoeba polyphaga mimivirus, was discovered. Since then, many other giant viruses have been isolated, including Marseilleviridae, Pithovirus sibericum, Cafeteria roenbergensis virus and Pandoravirus spp. The methods used to isolate all of these viruses are herein reviewed. By analogy to Legionella, it was originally suspected that these viruses could be human pathogens. After showing by indirect evidence, such as sero-epidemiologic studies, that it was possible for these viruses to be human pathogens, the recent isolation of some of these viruses (belonging to the Mimiviridae and Marseilleviridae families) in humans in the context of pathologic conditions shows that they are opportunistic human pathogens in some instances.

Mimiviridae, Marseilleviridae, and virophages as emerging human pathogens causing healthcare-associated infections

AIM

During the last decade it became obvious that viruses belonging to Mimiviridae and Marseilleviridae families (order Megavirales), may be potential causative agents of pneumonia. Thus, we have performed a review of the association of Mimiviridae, Marseilleviridae, and virophages with pneumonia, particularly healthcare-associated pneumonia, and other infections of the respiratory tract.

RESULTS AND DISCUSSION

According to the analysis of the published articles, viruses belonging to Mimiviridae family can be potential agents of both community-acquired and healthcare-associated pneumonia. In particular, these viruses may be associated with poor outcome in patients of intensive care units. The exact mechanism of their pathogenicity, however, still remains unclear. The discrepancies between the results obtained by serological and genomic methods could be explained by the high polymorphism of nucleotide sequences of Mimiviridae family representatives. Further investigations on the Mimiviridae pathogenicity and on the determination of Mimiviridae-caused pneumonia risk groups are required. However, the pathogenicity of the viruses belonging to Marseilleviridae family and virophages is unclear up to now.

Acanthamoeba polyphaga mimivirus and other giant viruses: an open field to outstanding discoveries

In 2003, Acanthamoeba polyphaga mimivirus (APMV) was first described and began to impact researchers around the world, due to its structural and genetic complexity. This virus founded the family Mimiviridae. In recent years, several new giant viruses have been isolated from different environments and specimens. Giant virus research is in its initial phase and information that may arise in the coming years may change current conceptions of life, diversity and evolution. Thus, this review aims to condense the studies conducted so far about the features and peculiarities of APMV, from its discovery to its clinical relevance.

Amoebas as mimivirus bunkers: increased resistance to UV light, heat and chemical biocides when viruses are carried by amoeba hosts

Amoebas of the genus Acanthamoeba are protists that are associated with human disease and represent a public health concern. They can harbor pathogenic microorganisms, acting as a platform for pathogen replication. Acanthamoeba polyphaga mimivirus (APMV), the type species of the genus Mimivirus, family Mimiviridae, represents the largest group of amoeba-associated viruses that has been described to date. Recent studies have demonstrated that APMV and other giant viruses may cause pneumonia. Amoebas can survive in most environments and tolerate various adverse conditions, including UV light irradiation, high concentrations of disinfectants, and a broad range of temperatures. However, it is unknown how the amoebal intracellular environment influences APMV stability and resistance to adverse conditions. Therefore, in this work, we evaluated the stability of APMV, either purified or carried by the amoeba host, under extreme conditions, including UV irradiation, heat and exposure to six different chemical biocides. After each treatment, the virus was titrated in amoebas using the TCID50 method. APMV was more stable in all resistance tests performed when located inside its host. Our results demonstrate that Acanthamoeba acts as a natural bunker for APMV, increasing viral resistance to extreme physical and chemical conditions. The data raise new questions regarding the survival of APMV in nature and in hospital environments.

Describing the silent human virome with an emphasis on giant viruses

Viruses are the most abundant obligate intracellular entities in our body. Until recently, they were only considered to be pathogens that caused a broad array of pathologies, ranging from mild disease to deaths in the most severe cases. However, recent advances in unbiased mass sequencing techniques as well as increasing epidemiological evidence have indicated that the human body is home to diverse viral species under non-pathological conditions. Despite these studies, the description of the presumably healthy viral flora, i.e. the normal human virome, is still in its infancy regarding viral composition and dynamics. This review summarizes our current knowledge of the human virome under non-pathological conditions.

Real-time PCR systems targeting giant viruses of amoebae and their virophages

Giant viruses that infect amoebae, including mimiviruses and marseilleviruses, were first described in 2003. Virophages were subsequently described that infect mimiviruses. Culture isolation with Acanthamoeba spp. and metagenomic studies have shown that these giant viruses are common inhabitants of our biosphere and have enabled the recent detection of these viruses in human samples. However, the genomes of these viruses display substantial genetic diversity, making it a challenge to examine their presence in environmental and clinical samples using conventional and real-time PCR. We designed and evaluated the performance of PCR systems capable of detecting all currently isolated mimiviruses, marseilleviruses and virophages to assess their prevalence in various samples. Our real-time PCR assays accurately detected all or most of the members of the currently delineated lineages of giant viruses infecting acanthamoebae as well as the mimivirus virophages, and enabled accurate classification of the mimiviruses of amoebae in lineages A, B or C. We were able to detect four new mimiviruses directly from environmental samples and correctly classified these viruses within mimivirus lineage C. This was subsequently confirmed by culture on amoebae followed by partial Sanger sequencing. PCR systems such as those implemented here may contribute to an improved understanding of the prevalence of mimiviruses, their virophages and marseilleviruses in humans.

Giant viruses of amoebae as potential human pathogens

Giant viruses infecting phagocytic protists are composed of mimiviruses, the record holders of particle and genome size amongst viruses, and marseilleviruses. Since the discovery in 2003 at our laboratory of the first of these giant viruses, the Mimivirus, a growing body of data has revealed that they are common inhabitants of our biosphere. Moreover, from the outset, the story of Mimivirus has been linked to that of patients exhibiting pneumonia and it was shown that patients developed antibodies to this amoebal pathogen. Since then, there have been several proven cases of human infection or colonization with giant viruses of amoebae, which are known to host several bacteria that are human pathogens. Mimiviruses and marseilleviruses represent a major challenge in human pathology, as virological procedures implemented to date have not used appropriate media to allow their culture, and molecular techniques have used filtration steps that likely prevented their detection. Nevertheless, there is an increasing body of evidence that mimiviruses might cause pneumonia and that humans carry marseilleviruses, and re-analyses of metagenomic databases have provided evidence that these giant viruses can be common in human samples. The proportion of human infections related to these giant mimiviruses and marseilleviruses and the precise short- and long-term consequences of these infections have been scarcely investigated so far and should be the subject of future works.

Mimivirus is not a frequent cause of ventilator-associated pneumonia in critically ill patients

Acanthamoeba polyphaga mimivirus (APMV) belongs to the amoebae‐associated microorganisms. Antibodies to APMV have been found in patients with pneumonia suggesting a potential role as a respiratory pathogen. In addition, positive serology for APMV was associated with an increased duration of mechanical ventilation and intensive care unit stay in patients with ventilator‐associated pneumonia. The aim of the present study was to assess the presence of APMV in bronchoalveolar lavage fluid samples of critically ill patients suspected of ventilator‐associated pneumonia. The study was conducted in the intensive care unit of the Maastricht University Medical Centre. All consecutive bronchoalveolar lavage fluid samples obtained between January 2005 and October 2009 from patients suspected of ventilator‐associated pneumonia were eligible for inclusion. All samples were analyzed by real‐time PCR targeting the APMV. A total of 260 bronchoalveolar lavage fluid samples from 214 patients (139 male, 75 female) were included. Bacterial ventilator‐associated pneumonia was confirmed microbiologically in 105 out of 260 (40%) suspected episodes of ventilator‐associated pneumonia (86 patients). The presence of APMV DNA could not be demonstrated in the bacterial ventilator‐associated pneumonia positive or in the bacterial ventilator‐associated pneumonia negative bronchoalveolar lavage fluid samples. Although suspected, APMV appeared not to be present in critically ill patients suspected of ventilator‐associated pneumonia, and APMV does not seem to be a frequent cause of ventilator‐associated pneumonia. J Med. Virol. 85:1836–1841, 2013. © 2013 Wiley Periodicals, Inc.

First isolation of Mimivirus in a patient with pneumonia

BACKGROUND

Mimiviridae Mimivirus, including the largest known viruses, multiply in amoebae. Mimiviruses have been linked to pneumonia, but they have never been isolated from patients. To further understand the pathogenic role of these viruses, we aimed to isolate them from a patient presenting with pneumonia.

METHODS

We cultured, on Acanthamoeba polyphaga amoebae, pulmonary samples from 196 Tunisian patients with community-acquired pneumonia during the period 2009-2010. An improved technique was used for Mimivirus isolation, which used agar plates where the growth of giant viruses is revealed by the formation of lysis plaques. Mimivirus serology was tested by microimmunofluorescence and by bidimensional immunoproteomic analysis using Mimivirus strains, to identify specific immunoreactive proteins. The new Mimivirus strain genome sequencing was performed on Roche 454 GS FLX Titanium, then AB SOLiD instruments.

RESULTS

We successfully isolated a Mimivirus (LBA111), the largest virus ever isolated in a human sample, from a 72-year-old woman presenting with pneumonia. Electron microscopy revealed a Mimivirus-like virion with a size of 554 ± 10 nm. The LBA111 genome is 1.23 megabases, and it is closely related to that of Megavirus chilensis. Furthermore, the serum from the patient reacted specifically to the virus compared to controls.

CONCLUSIONS

This is the first Mimivirus isolated from a human specimen. The findings presented above together with previous works establish that mimiviruses can be associated with pneumonia. The common occurrence of these viruses in water and soil makes them probable global agents that are worthy of investigation.

Evidence of the megavirome in humans

BACKGROUND

Megavirales is a proposed new virus order composed of Mimivirus, Marseillevirus and closely related viruses, as well as members of the families Poxviridae, Iridoviridae, Ascoviridae, Phycodnaviridae and Asfarviridae. The Megavirales virome, which we refer to as the megavirome, has been largely neglected until now because of the use of technical procedures that have jeopardized the discovery of giant viruses, particularly the use of filters with pore sizes in the 0.2-0.45-μm range. Concurrently, there has been accumulating evidence supporting the role of Mimivirus, discovered while investigating a pneumonia outbreak using amoebal coculture, as a causative agent in pneumonia.

OBJECTIVES

In this paper, we describe the detection of sequences related to Mimivirus and Marseillevirus in the gut microbiota from a young Senegalese man. We also searched for sequences related to Megavirales in human metagenomes publicly available in sequence databases.

RESULTS

We serendipitously detected Mimivirus- and Marseillevirus-like sequences while using a new metagenomic approach targeting bacterial DNA that subsequently led to the isolation of a new member of the family Marseilleviridae, named Senegalvirus, from human stools. This discovery demonstrates the possibility of the presence of giant viruses of amoebae in humans. In addition, we detected sequences related to Megavirales members in several human metagenomes, which adds to previous findings by several groups.

CONCLUSIONS

Overall, we present convergent evidence of the presence of mimiviruses and marseilleviruses in humans. Our findings suggest that we should re-evaluate the human megavirome and investigate the prevalence, diversity and potential pathogenicity of giant viruses in humans.

Serologic prevalence of amoeba-associated microorganisms in intensive care unit pneumonia patients

BACKGROUND

Patients admitted to intensive care units are frequently exposed to pathogenic microorganisms present in their environment. Exposure to these microbes may lead to the development of hospital-acquired infections that complicate the illness and may be fatal. Amoeba-associated microorganisms (AAMs) are frequently isolated from hospital water networks and are reported to be associated to cases of community and hospital-acquired pneumonia.

METHODOLOGY/PRINCIPAL FINDINGS

We used a multiplexed immunofluorescence assay to test for the presence of antibodies against AAMs in sera of intensive care unit (ICU) pneumonia patients and compared to patients at the admission to the ICU (controls). Our results show that some AAMs may be more frequently detected in patients who had hospital-acquired pneumonia than in controls, whereas other AAMs are ubiquitously detected. However, ICU patients seem to exhibit increasing immune response to AAMs when the ICU stay is prolonged. Moreover, concomitant antibodies responses against seven different microorganisms (5 Rhizobiales, Balneatrix alpica, and Mimivirus) were observed in the serum of patients that had a prolonged ICU stay.

CONCLUSIONS/SIGNIFICANCE

Our work partially confirms the results of previous studies, which show that ICU patients would be exposed to water amoeba-associated microorganisms, and provides information about the magnitude of AAM infection in ICU patients, especially patients that have a prolonged ICU stay. However, the incidence of this exposure on the development of pneumonia remains to assess.

Viral-associated Ventilator-associated Pneumonia

Nosocomial pneumonia is the most commonly acquired infection in intensive care units (ICUs). Its frequency is approximately 10 cases/1000 admissions; however, the incidence may increase to 20 times that number in patients undergoing invasive mechanical ventilation [1–3]. The overall incidence of ventilator-associated pneumonia (VAP) may range between 15 % to 20 % [2–6]. This complication prolongs the length of hospital stay, increases healthcare costs and may increase mortality [4, 5, 7, 8].

Repertoire of intensive care unit pneumonia microbiota

Despite the considerable number of studies reported to date, the causative agents of pneumonia are not completely identified. We comprehensively applied modern and traditional laboratory diagnostic techniques to identify microbiota in patients who were admitted to or developed pneumonia in intensive care units (ICUs). During a three-year period, we tested the bronchoalveolar lavage (BAL) of patients with ventilator-associated pneumonia, community-acquired pneumonia, non-ventilator ICU pneumonia and aspiration pneumonia, and compared the results with those from patients without pneumonia (controls). Samples were tested by amplification of 16S rDNA, 18S rDNA genes followed by cloning and sequencing and by PCR to target specific pathogens. We also included culture, amoeba co-culture, detection of antibodies to selected agents and urinary antigen tests. Based on molecular testing, we identified a wide repertoire of 160 bacterial species of which 73 have not been previously reported in pneumonia. Moreover, we found 37 putative new bacterial phylotypes with a 16S rDNA gene divergence ≥ 98% from known phylotypes. We also identified 24 fungal species of which 6 have not been previously reported in pneumonia and 7 viruses. Patients can present up to 16 different microorganisms in a single BAL (mean ± SD; 3.77 ± 2.93). Some pathogens considered to be typical for ICU pneumonia such as Pseudomonas aeruginosa and Streptococcus species can be detected as commonly in controls as in pneumonia patients which strikingly highlights the existence of a core pulmonary microbiota. Differences in the microbiota of different forms of pneumonia were documented.

Viral-Reactivated Pneumonia during Mechanical Ventilation: Is There Need for Antiviral Treatment?

Respiratory viruses are not a common cause of ventilator-associated pneumonia (VAP). Herpesviridae [Herpes simplex virus (HSV) and cytomegalovirus (CMV)] are detected frequently in the lower respiratory tract of ventilated patients. HSV is detected between days 7 and 14 of invasive mechanical ventilation (IMV); presence of the virus does not necessarily imply pathogenicity, but the association with adverse clinical outcomes supports the hypothesis of a pathogenic role in a variable percentage of patients. Bronchopneumonitis associated with HSV should be considered in patients with prolonged IMV, reactivation with herpetic mucocutaneous lesions and those belonging to a risk population with burn injuries or acute lung injury. Reactivation of CMV is common in critically ill patients and usually occurs between days 14 and 21 in patients with defined risk factors. The potential pathogenic role of CMV seems clear in patients with acute lung injury and persistent respiratory failure in whom there is no isolation of bacterial agent as a cause of VAP. The best diagnostic test is not defined although lung biopsies should be considered in addition to the usual methods before starting specific treatment. The role of mimivirus is uncertain and is yet to be defined, but the serologic evidence of this new virus in the context of VAP appears to be associated with adverse clinical outcomes.

The role of viruses in nosocomial pneumonia

PURPOSE OF REVIEW

The frequency and impact of viruses among intensive care unit (ICU) nonimmunocompromised patients remains controversial. This review analyzes their place as causal pathogens in ventilator-associated pneumonia, as well as their effects on ICU patients' outcomes.

RECENT FINDINGS

Herpesviruses, namely herpes simplex virus (HSV) and cytomegalovirus (CMV), are the most frequent viruses detected among nonimmunosuppressed ICU patients, as confirmed by recent prospective studies. Patients infected with these viruses show increased morbidity and, especially for CMV, mortality. An increase of bacterial or fungal superinfections was observed in ICU patients with CMV reactivation. A therapeutic trial of acyclovir (HSV antiviral) in ICU patients was negative. Concerning CMV, pathogenicity was suggested by histologic assessment in ICU patients, and recent murine models with a positive effect of prophylaxis with ganciclovir that prevented postseptic CMV reactivation and secondary lung damage.

SUMMARY

Using efficient and rapid virologic diagnostic tests (antigenemia or PCR), the identification of viruses in ICU patients is frequent. Their role in the occurrence of ventilator-acquired pneumonia and their impact on patient outcome depend on the virus. There is sufficient evidence suggesting CMV pathogenicity to conduct an interventional randomized trial using anti-CMV drugs.

[Ventilator-associated viral pneumonia]

Viral infections (especially respiratory infections) are not rare in critically ill non-immunocompromised patients. Efficient and rapid virologic diagnosis tests such as polymerase chain reaction (PCR) are now widely available. Herpesviridae (herpes simplex virus and cytomegalovirus) are the most frequent viruses detected among non-immunocompromised patients admitted to the intensive care unit (ICU). However, causal relationships between detected viruses and outcomes are still debated, with a variable level of demonstration among the different viruses. The aim of this review was to assess the role of viruses in causing mechanical ventilation-acquired pneumonias in non-immunocompromised ICU adult patients. We also discuss the possible physiopathology of these viral infections, as well as the opportunity for therapeutic interventions.

[Acute viral infections in immunocompetent patients]

Los virus tienen un papel importante dentro de las infecciones graves en los pacientes adultos, que en algunas ocasiones llegan a necesitar hospitalización e ingreso en unidades de cuidados intensivos, especialmente en casos de síndrome de distrés respiratorio del adulto y encefalitis. Las infecciones por virus influenza y parainfluenza, virus sincitial respiratorio, herpes virus y adenovirus son las que más frecuentemente causan estos cuadros. Se ha realizado una revisión de la literatura pormenorizada y actualizada de epidemiología, patogénesis, manifestaciones clínicas y aproximación terapéutica de las infecciones virales en pacientes inmunocompetentes. Por otro lado, si bien la neumonía asociada a ventilación mecánica tiene como etiología más frecuente las infecciones bacterianas, recientemente el papel de los virus como patógenos en estas infecciones está en debate, por lo que se hace una breve revisión de su papel etiopatogénico en la neumonía asociada a ventilación mecánica.

Horizontal gene transfers with or without cell fusions in all categories of the living matter

This article reviews the history of widespread exchanges of genetic segments initiated over 3 billion years ago, to be part of their life style, by sphero-protoplastic cells, the ancestors of archaea, prokaryota, and eukaryota. These primordial cells shared a hostile anaerobic and overheated environment and competed for survival. "Coexist with, or subdue and conquer, expropriate its most useful possessions, or symbiose with it, your competitor" remain cellular life's basic rules. This author emphasizes the role of viruses, both in mediating cell fusions, such as the formation of the first eukaryotic cell(s) from a united crenarchaeon and prokaryota, and the transfer of host cell genes integrated into viral (phages) genomes. After rising above the Darwinian threshold, rigid rules of speciation and vertical inheritance in the three domains of life were established, but horizontal gene transfers with or without cell fusions were never abolished. The author proves with extensive, yet highly selective documentation, that not only unicellular microorganisms, but the most complex multicellular entities of the highest ranks resort to, and practice, cell fusions, and donate and accept horizontally (laterally) transferred genes. Cell fusions and horizontally exchanged genetic materials remain the fundamental attributes and inherent characteristics of the living matter, whether occurring accidentally or sought after intentionally. These events occur to cells stagnating for some 3 milliard years at a lower yet amazingly sophisticated level of evolution, and to cells achieving the highest degree of differentiation, and thus functioning in dependence on the support of a most advanced multicellular host, like those of the human brain. No living cell is completely exempt from gene drains or gene insertions.

Acute viral infections in immunocompetent patients

Viruses play a significant role in serious infections in adults and sometimes lead to the need for hospitalization and admission to intensive care units, especially in cases of severe respiratory distress or encephalopathy. Influenza and parainfluenza viruses, syncytial respiratory virus, herpes viruses and adenovirures are the most frequent causes of these severe infections. A review of the literature has been performed in order to update the epidemiology, pathogenesis and therapeutic approach of viral infections affecting immunocompetent patients. Furthermore, ventilator-associated pneumonia (VAP) is the most frequent nosocomial infection in intensive care units and has a high morbidity and mortality rate. It is mainly a bacterial disease, although the potential role of viruses as pathogens or copathogens in VAP is under discussion. Therefore, a brief review of the potential pathogenic role of viruses in VAP has also been performed.

Detection of plant DNA in the bronchoalveolar lavage of patients with ventilator-associated pneumonia

Background

Hospital-acquired infections such as nosocomial pneumonia are a serious cause of mortality for hospitalized patients, especially for those admitted to intensive care units (ICUs). Despite the number of the studies reported to date, the causative agents of pneumonia are not completely known. Herein, we found by molecular technique that vegetable and tobacco DNA may be detected in the bronchoalveolar lavage from patients with ventilator-associated pneumonia (VAP).

Methodology/Principal Findings

In the present study, we studied bronchoalveolar lavage (BAL) from patients admitted to ICUs with ventilator-associated pneumonia. BAL fluids were assessed with molecular tests, culture and blood culture. We successfully identified plant DNA in six patients out of 106 (6%) with ventilator-associated pneumonia. Inhalation was confirmed in four cases and suspected in the other two cases. Inhalation was significantly frequent in patients with plant DNA (four out of six patients) than those without plant DNA (three out of 100 patients) (P<0.001). Nicotiana tabacum chloroplast DNA was identified in three patients who were smokers (cases 2, 3 and 6). Cucurbita pepo, Morus bombycis and Triticum aestivum DNA were identified in cases 1, 4 and 5 respectively. Twenty-three different bacterial species, two viruses and five fungal species were identified from among these six patients by using molecular and culture techniques. Several of the pathogenic microorganisms identified are reported to be food-borne or tobacco plant-associated pathogens.

Conclusions/Significance

Our study shows that plants DNA may be identified in the BAL fluid of pneumonia patients, especially when exploring aspiration pneumonia, but the significance of the presence of plant DNA and its role in the pathogenesis of pneumonia is unknown and remains to be investigated. However, the identification of these plants may be a potential marker of aspiration in patients with pneumonia.

Severe hospital-acquired pneumonia: a review for clinicians

Hospital-acquired pneumonia (HAP) is one of the most commonly encountered nosocomial infections. Patients who develop severe HAP experience considerable morbidity and mortality, and the condition results in a substantial expenditure of health care resources. A large body of scientific literature about HAP now exists. This article summarizes the current state of knowledge concerning severe HAP with an emphasis on recent advances in its diagnosis, treatment, and prevention.

Amoebal pathogens as emerging causal agents of pneumonia

Despite using modern microbiological diagnostic approaches, the aetiological agents of pneumonia remain unidentified in about 50% of cases. Some bacteria that grow poorly or not at all in axenic media used in routine clinical bacteriology laboratory but which can develop inside amoebae may be the agents of these lower respiratory tract infections (RTIs) of unexplained aetiology. Such amoebae-resisting bacteria, which coevolved with amoebae to resist their microbicidal machinery, may have developed virulence traits that help them survive within human macrophages, i.e. the first line of innate immune defence in the lung. We review here the current evidence for the emerging pathogenic role of various amoebae-resisting microorganisms as agents of RTIs in humans. Specifically, we discuss the emerging pathogenic roles of Legionella-like amoebal pathogens, novel Chlamydiae (Parachlamydia acanthamoebae, Simkania negevensis), waterborne mycobacteria and Bradyrhizobiaceae (Bosea and Afipia spp.).

Structural studies of the Sputnik virophage

The virophage Sputnik is a satellite virus of the giant mimivirus and is the only satellite virus reported to date whose propagation adversely affects its host virus' production. Genome sequence analysis showed that Sputnik has genes related to viruses infecting all three domains of life. Here, we report structural studies of Sputnik, which show that it is about 740 A in diameter, has a T=27 icosahedral capsid, and has a lipid membrane inside the protein shell. Structural analyses suggest that the major capsid protein of Sputnik is likely to have a double jelly-roll fold, although sequence alignments do not show any detectable similarity with other viral double jelly-roll capsid proteins. Hence, the origin of Sputnik's capsid might have been derived from other viruses prior to its association with mimivirus.