Pneumonia Pathogen Detection and Microbial Interactions in Polymicrobial Episodes

Sabri Bousbia; Didier Raoult; Bernard La Scola


Future Microbiol. 2013;8(5):633-660. 

In This Article

Abstract and Introduction


Recent reports show that microbial communities associated with respiratory infections, such as pneumonia and cystic fibrosis, are more complex than expected. Most of these communities are polymicrobial and might comprise microorganisms originating from several diverse biological and ecological sources. Moreover, unexpected bacteria in the etiology of these respiratory infections have been increasingly identified. These findings were established with the use of efficient microbiological diagnostic tools, particularly molecular tools based on common gene amplification, followed by cloning and sequencing approaches, which facilitated the identification of the polymicrobial flora. Similarly, recent investigations reported that microbial interactions might exist between species in polymicrobial communities, including typical pneumonia pathogens, such as Pseudomonas aeruginosa and Candida albicans. Here, we review recent tools for microbial diagnosis, in particular, of intensive care unit pneumonia and the reported interactions between microbial species that have primarily been identified in the etiology of these infections.


According to the WHO, respiratory infections are the third leading cause of death worldwide (the first cause in low-income countries), resulting in nearly 4.18 million deaths per year. They are the second cause of infection, among hospitalized patients, after urinary infections. In intensive care units (ICUs), hospital-acquired pneumonia, particularly ventilator-associated pneumonia (VAP), is the first cause of infection.[1–3] It has been recognized as a major and serious health risk complicating illnesses and causing morbidity and mortality, and is mostly associated with elevated economic impact on public health services.[1,4] VAP might occur in 7–70% of ventilated patients.[5] The identification of the etiologic pathogen is routinely required after the clinical diagnosis. Defining the role of a pathogen in pneumonia depends on many criteria such as its loads, the type of sample, the tools used for its detection, and the type of the pathogen. Moreover, clinical data are mostly combined with those criteria to interpret the real role of the microorganism. The current microbial diagnosis of pathogens primarily relies on the culture of respiratory samples collected using several approaches, such as tracheal aspiration and bronchoalveolar lavage (BAL). The quantification of CFU and antibiotic susceptibility testing are subsequently performed to determine the pathogenic profiles of the isolates.[6] Other microbial laboratory strategies to detect microbial agents, particularly for atypical pathogens, are based on PCR, serology and urinary antigen testing (Figure 1). Members of the microbial community identified in respiratory samples from ICU pneumonia patients include Pseudomonas aeruginosa, staphylococci, enterobacteria, Candida albicans, influenza virus (IFV), HSV-1 and -2, and CMV.[3] Other atypical pathogens (pathogens rarely identified in pneumonia or that cannot be cultured by axenic media) have been increasingly reported.[7,8] However, the etiologic agent remains unknown in nearly 30% of cases, suggesting that unknown pathogens cause many pneumonia cases or that the existing methods lack accuracy or sensitivity for the identification of these pathogens. The accurate identification of etiologic pathogens might improve therapy regimens and the control of infected patients to avoid illness complications. It may also allow de-escalation of the wide-spread empirical antimicrobial regimen that prevents overuse of antibiotics and, thus, emergence of antimicrobial resistance. In recent years, several studies have aimed to determine the microbial community of infectious lung diseases, including pneumonia, using different molecular assays. Most of these studies have been performed using broad-range primers to amplify bacterial 16S rDNA genes, followed by cloning and different sequencing approaches. The use of such methods facilitates the identification of a wide spectrum of microorganisms, particularly fastidious or uncultured bacteria that have not previously been identified.[9–13] Moreover, evidence of infection with ameba-associated microorganisms was identified in 19.0% of pneumonia incidences.[14] Furthermore, recent reports showed that more than one pathogen causes respiratory infections, demonstrating a polymicrobial aspect.[15–17] In parallel, recent studies have reported that interactions between parasitic species might occur and that infection with a given microorganism might increase or decrease the susceptibility to infection with another microorganism or generate a cross-immunity response.[17] These interactions might be observed among the typical pathogens that cause respiratory infection, such as P. aeruginosa and C. albicans.

Figure 1.

Common strategies for the microbial diagnosis of intensive care unit pneumonia.
Most routine culture methods implemented in microbial laboratories primarily rely on the diagnosis of pathogens in respiratory samples. Otherwise, as the lung is an important site in direct contact with the blood, pathogens must be also searched for in blood. Bloodstream infection can occur at the same time as pneumonia or be a secondary infection after a pneumonia episode. Investigation of microbial antigens in urine samples also allows rapid and early detection of pathogens and, thus, allows rapid management of patients by starting curative therapy (recommended within the 6 h following the infection).
BAL: Bronchoalveolar lavage; ICU: Intensive care unit; MALDI-TOF MS: Matrix-assisted laser desorption ionization TOF mass spectrometry; qPCR: Real-time PCR.

Here, we review novel advances in the laboratory diagnostic tools used to explore the polymicrobial community of pulmonary infections, particularly ICU pneumonia, and relevant research on microbial interactions between different species, with a focus on typical and atypical pneumonia pathogens, which might provide knowledge concerning the real role of identified pathogens in pneumonia.