Diagnostic Microbiology of the Immunocompromised Host

This chapter briefly reviews the components of host defense and the types of infections that are most likely to occur with specific defects in the defense mechanisms. It describes the infections that occur in patients with a variety of primary and secondary immunodeficiency disorders so as to provide illustrative examples. Patients on potent immunosuppressive regimens are at risk for fungal infections. The majority of these infections are caused by Candida and Aspergillus species. A variety of fungal infections that are kept in check by granuloma formation have also been reported for these patients, the most common of which are disseminated histoplasmosis, cryptococcosis, coccidioidomycosis, and aspergillosis. The period from 1 to 6 months after transplantation is the critical time after transplantation during which infections unique to the immunocompromised hosts most often arise. Based upon information provided in the chapter, the types of infections, the drugs being used, and other symptoms should help to focus the laboratory workup on specific parts of the immune system. Immunocompromised hosts have an increased susceptibility to infections for a wide variety of reasons. The chapter lays the groundwork for understanding why an individual patient may have an increased susceptibility to specific types of pathogens.

Since AIDS was first reported 26 years ago, more scientific effort at both the national and international levels has been focused on human immunodeficiency virus (HIV) than on any other virus in modern history. There is still no vaccine available for prevention of HIV infection, but multiple antiretroviral (ARV) drugs are available for combination therapy to control the infection. Many laboratory technologies, including conventional or rapid immunological and molecular methods, have been developed and used for diagnosis of HIV infection, surveillance, epidemiology, and monitoring of therapy. Tests for initial diagnosis of infection include enzyme immunoassay (EIA) or enzyme-linked immunosorbent assay (ELISA), Western blotting (WB) and other confirmatory assays, rapid immunoassay, quantitative viral RNA detection assays (commonly known as viral load [VL] assays), and qualitative proviral DNA assays. Tests for determining prognosis and for monitoring of ARV therapy include VL assays, genotyping, and phenotyping assays. The current HIV-1 VL assays offer reliable testing with excellent sensitivity and specificity. While genotypic testing is an indirect measure of drug susceptibility, it is the primary methodology for the analysis of HIV drug resistance. Currently, the report and interpretation are based on HIV-1 mutations that are known to be associated with drug resistance. In summary, there have been many achievements in diagnostic microbiology for patients who are immunocompromised because of HIV infection. Newer immunological and molecular technologies will continue to lead the way in laboratory diagnosis of infection caused by HIV.

Cytomegalovirus (CMV) has four fundamental structural elements: an outer lipid envelope, tegument, a nucleocapsid, and an internal nucleoprotein core that contains its genome. These components are essential for the biology of the virus and, as discussed in this chapter, are also major targets for diagnostic and therapeutic modalities. The clinical manifestations of CMV are also similar to those of solid organ transplants (SOT) patients and can be classified as CMV syndrome or tissue-invasive disease. Overall, there are important limitations to the clinical application of serology for the diagnosis of acute CMV infection in immunocompromised individuals. The major limitation of pp65 antigenemia assays is the lack of standardization across laboratories and the subjective and operator-dependent nature of the assay. Some experts argue that the presence of virus in a cell-free environment such as plasma is more indicative of active viral replication. One of the most common clinical applications of the antigenemia and molecular diagnostic tests is in the strategy of preemptive therapy, an approach of CMV prevention whereby an antiviral drug is administered upon the detection of CMV. The major toxicity of ganciclovir is myelosuppression, and this usually resolves upon the discontinuation of the drug. The major limiting toxicity of foscarnet and cidofovir is nephrotoxicity, and this has relegated them to use as alternative agents. CMV is an important pathogen that causes severe disease in immunocompromised hosts, including transplant patients, patients with AIDS, and immunologically immature newborns.

Epstein-Barr virus (EBV) or human herpesvirus 4 (HHV-4) and Kaposi's sarcoma-associated virus (KSHV or HHV-8) are distantly related gammaherpesviruses, both of which have associations with cancer in humans. Developments in nucleic acid detection techniques have brought new diagnostic capabilities to bear, revealing new associations and activities of these viruses in the setting of immunosuppression. In this chapter, the authors review these disease associations and the techniques that are currently being used to diagnose EBV and KSHV infections. Therefore, diagnostic approaches to EBV infection rely mainly on detecting serologic responses to classical EBV antigens and more recently, on nucleic acid amplification and quantitation techniques. EBV serology is based on detecting humoral responses to the following three classes of antigen: viral capsid antigen (VCA), early antigen (EA), and Epstein-Barr nuclear antigen (EBNA). The major concern with using detection of viral DNA as a marker of viral infection is an apparent lack of sensitivity and indecision on which tissue type is best suited for detection of viral DNA. In summary, serological assays are the best method for determining HHV-8 infection, and assays designed to detect lytic cycle proteins, especially lytic immunofluorescence assays (IFAs), are the most sensitive assays currently available.

The four viruses herpes simplex virus (HSV), varicella-zoster virus (VZV), human herpesvirus 6 (HHV-6), and human herpesvirus 7 (HHV-7), discussed in this chapter, are all members of the family Herpesviridae. Each organism is discussed separately in order to better describe the specific details of the pathogenesis, epidemiology, and diagnostic testing. The majority of cases of HSV reactivation occur in the initial few weeks after transplantation, at the time of maximum pharmacologic immunosuppression. As the majority of immunocompromised patients have recurrent infections with HSV, the role of serology in these patients is of limited diagnostic value. Detection of HSV DNA does not require live virus; therefore, specimen quality is not jeopardized by delays in transport time or fluctuations in transport temperature like it would be for viral culture. Tyrosine kinase-negative VZV strains have been identified, and infections caused by the strains should be treated with foscarnet. The immunocompromised states covered in the chapter include patients who have undergone bone marrow and solid organ transplantation. The majority of the literature surrounding the role of HHV-6 in the transplant population regards patients with bone marrow transplantation. A study compared staining for HHV-6 by using immunohistochemistry and in situ hybridization to polymerase chain reaction (PCR) analysis of tonsillar epithelia of nonimmunosuppressed individuals undergoing tonsillectomy in an attempt to determine if lymphoid tissue was a site of latency in the immunocompetent population. Molecular methods of detection for each of these viruses are sensitive, specific, and available with a relatively short turnaround time.

Adenovirus infections are most common among children, people living in close quarters or closed populations, such as college students and military recruits, and immunocompromised patients. Among immunocompromised patients, infection is most commonly described for transplant recipients; adenovirus infection in such patients is the primary focus of this chapter. In hematopoietic stem cell transplantation (HSCT) recipients, adenovirus is commonly associated with upper and/or lower respiratory tract infection, gastrointestinal (GI) disease, hepatitis, and cystitis. Adenovirus infection has been reported for a wide variety of solid organ transplant (SOT) recipient populations, including those receiving heart, lung, liver, intestinal, and renal transplants. The diagnostic approach to patients with adenovirus disease is complex. Sensitivities for immunofluorescence assays performed on primary specimens have ranged from 28 to 75%, while other antigen detection methods have had sensitivities that ranged from 43 to 89%. Electron microscopy may be used to identify adenovirus, particularly in stool. In summary, definitive diagnosis typically combines pathologic evidence of invasive adenoviral disease with positive culture or polymerase chain reaction (PCR) from the site of infection. Few labs are able to perform antiviral susceptibility testing.

RNA respiratory viruses, including influenza virus, respiratory syncytial virus (RSV), parainfluenza virus (PIV), human metapneumovirus (hMPV), human rhinovirus (HRV), and coronavirus (CoV), are increasingly being recognized as causing significant morbidity, graft failure, and death among immunocompromised patient populations. Respiratory viral infections are associated with increased risk of death, development of viral pneumonia, and coinfections, particularly bacterial pneumonia and invasive aspergillosis. Respiratory viral infections are associated with both acute and chronic rejection. Antiviral resistance is an emerging issue among immunocompromised patients infected with influenza virus, although resistance testing is not yet widely available outside the research setting. Unlike the case for RSV and influenza virus, no rapid antigen test kits are available for detection of PIV. There are several monoclonal antibody (MAb) systems that allow for identification and differentiation of the different PIV serotypes in primary patient samples and in cell cultures. There are currently five clinically significant human coronaviruses recognized, namely, OC43, 229E, NL63, HKU1, and severe acute respiratory syndrome CoV (SARS-CoV).

The genus Enterovirus is currently comprised of 68 distinct serotypes within the family Picornaviridae. Enterovirus (EV) infections occur worldwide, although rates of infections may vary noticeably by location and are seasonal in nature. Clinical syndromes associated with EV infection in immunocompromised hosts such as primary B-cell-associated immunodeficiencies, transplant recipients and malignancy have been provided in this chapter. Among hereditary B-cell-associated immunodeficiency syndromes, X-linked agammaglobulinemia (XLA), common variable and severe combined immunodeficiency syndromes, and X-linked hyper-immunoglobulin M (XHIM) syndrome have been associated with persistent progressive EV infection. Of one cardiac transplant and seven stem cell transplant recipients with radiographic evidence of lower respiratory tract disease due to EV, five developed acute respiratory distress syndrome (ARDS), three required mechanical ventilation, and three died. Viral pneumonia is a frequent complication in patients undergoing intensive chemotherapy for treatment of hematologic malignancies. Available laboratory diagnostic techniques to identify EV infection include nucleic acid detection, culture, serology, and antigen detection. Nucleic acid amplification methods, such as reverse transcription-polymerase chain reaction (RT-PCR) and nucleic acid sequence-based amplification, have replaced culture-based techniques as the gold standard for detection of EV, given the significant increase in sensitivity and the rapid turnaround time. The recent availability of real-time PCR methods has further facilitated the rapid and sensitive detection of EV in the cerebrospinal fluid (CSF) and other types of specimens.

Until the discovery of Human bocavirus, Parvovirus B19 was the only member of the large Parvoviridae family to be associated unequivocally with human disease. During acute infection, parvovirus B19 has been detected in the nasopharynx, blood, bone marrow, liver, skin, cerebrospinal fluid, and synovium. It is not clear whether parvovirus B19 is eliminated from the host or remains in an inactive state capable of reactivation. It is possible that parvovirus B19 may integrate into the human genome, as occurs with other parvoviruses, such as minute virus of mice and dependoviruses. Acquisition of parvovirus B19 infection begins in childhood and continues throughout life. Infection with parvovirus occurs year-round but may peak in late winter to early summer. Parvovirus B19 has also been linked to myocarditis, a variety of neurologic syndromes, uveitis, hepatitis, renal syndromes, vasculitis, and chronic fatigue syndrome. No vaccine or antiviral is available for parvovirus B19 infection. Detection of immunoglobulin M (IgM) and IgG antibodies is the mainstay of parvovirus B19 diagnosis in the immunocompetent host. Parvovirus B19 is an infrequent but serious and treatable cause of chronic anemia in immunocompromised hosts.

This chapter discusses the most common causes of invasive mold infections, and provides a brief mention of particular molds that are less frequent causes of infection. The hyaline septate molds are covered first, with emphasis on Aspergillus species, Fusarium species, and Pseudallescheria boydii. A section talks about two dimorphic fungal pathogens, Histoplasma capsulatum and Penicillium marneffei, and also about less commonly encountered hyaline septate molds. Next, it discusses the zygomycetes, and Rhizopus and Mucor species are included because they are the genera most frequently encountered. Clinical Laboratory Standards Institute (CLSI) document 38-A addresses the standard broth dilution methods for determining antifungal resistance in the filamentous fungi . Alternatively, some authors have shown the utility of other methods, such as the Etest, for determining antifungal resistance in the filamentous fungi. The presence of a single colony of a mold in a respiratory specimen may simply represent the presence of transient fungal flora or a plate contaminant; however, it could also be evidence of an invasive fungal infection in an immunocompromised host. Every mycology laboratory should be able to definitively identify certain filamentous fungi. Microscopic examination reveals the spore morphology, the conidiophore, and the method of conidiogenesis. These features, when studied with identification keys and atlases, should afford the identification of the most commonly encountered filamentous fungi.

The number of yeast species documented to cause invasive infections in humans has increased. Several uncommon Candida species have now been described to cause invasive infection in humans. A case of cryptococcosis due to the Vancouver Island strain of Cryptococcus gattii acquired in Washington State was also recently reported. Other Cryptococcus species are also increasingly being recognized as causes of invasive disease among immunocompromised hosts. A list of ascomycetous yeasts such as Clavispora, Debaryomyces and Dipodascus reported to cause human disease have been discussed in the chapter. Compared to ascomycetes, yeasts of the phylum Basidiomycota are generally less frequently implicated in human disease. Malassezia and Trichosporon are some of the basidiomycetous yeasts that have been discussed in the chapter. Culture methods remain the most frequently utilized laboratory tools for the diagnosis of invasive yeast infections. Various diagnostic approaches including chromogenic media, rapid biochemical assays, commercial biochemical panels, in vitro susceptibility testing, and molecular identification techniques are analyzed in the chapter.

In general terms, the mycobacteria are divided into the Mycobacterium tuberculosis complex (MTBC) and the nontuberculous mycobacteria (NTM). NTM immune reconstitution syndrome (IRS), in contrast, may be seen in HIV-infected patients with no previous history of mycobacterial disease, apparently representing an unmasking of subclinical disease in these cases. The most frequently isolated pathogens were rapidly growing mycobacteria, followed by M. kansasii and M. haemophilum, for kidney transplant recipients; M. kansasii, M. avium complex (MAC), and M. haemophilum for heart recipients; MAC, M. abscessus, and M. haemophilum for lung recipients; and MAC for liver transplant recipients. Historically, mycobacteria have been detected and identified by using the conventional methods of acid-fast bacilli (AFB) smear and culture. Specimens are digested and decontaminated using a sodium hydroxide and N-acetyl-L-cysteine method to prepare a concentrated sediment. This sediment can then be used to prepare smears for microscopy and to inoculate media for recovery of mycobacterial growth. The niacin test is one that provides information to separate M. tuberculosis from other mycobacteria: M. tuberculosis produces detectable amounts of niacin, while most NTM and M. bovis do not. Fluorochrome stains are more sensitive than carbol-fuchsin stains, and broth-based culture systems are more sensitive than solid media for isolation of mycobacteria. Clinical equipment (e.g., bronchoscopes) may become contaminated by mycobacteria and then inadequately high-level disinfected or sterilized, causing contamination of specimens from subsequent patients examined with the same instrument or transmission of tuberculosis.

The group of gram-positive bacillary organisms broadly known as “aerobic actinomycetes” consists of a vast array of taxonomically heterogeneous and divergent genera. This chapter deals only with those genera having the most impact on human health care, i.e., those that usually affect primarily patients with immunocompromising conditions. The combination of increasing conditions impairing host resistance to invasion by environmental pathogens and the rapidly progressing technological capability to identify isolates recovered from such patients has allowed a wide expansion of the species known to be capable of causing disease in humans (albeit under special circumstances). A better understanding of the epidemiology, clinical course, and antimicrobial susceptibilities of aerobic actinomycetes is essential. Molecular identification and typing techniques will also bring a better understanding of the interrelatedness of the various genera and species. Evidence-based evaluation is paramount to rapid diagnosis and early choice in therapeutic modalities, aimed to achieve better outcomes in patients. Clinical laboratories must become aware of the role now played by the aerobic actinomycetes in disease and must work with clinical care providers to determine when identification, susceptibility testing, and therapeutic or surgical interventions are necessary.

This chapter includes some of the opportunistic parasites that can cause disease in immunocompromised patients. Although most parasitic infections are known to cause more severe symptoms when a host's immune system is impaired, the representative organisms presented in this chapter have been identified as causing the most severe disease in this population group. Malaria, Trypanosoma spp., Toxoplasma gondii, and Leishmania spp. are the principal parasites that may be transmitted with bone marrow, kidney, or liver homografts, and microsporidia are the principle parasites transmitted with xeno-transplants. The organisms discussed in the chapter are Entamoeba histolytica, free-living amebae, Giardia lamblia, T. gondii, Cryptosporidium spp., Cyclospora cayetanensis, Isospora belli, Sarcocystis spp., microsporidia, Leishmania spp., Strongyloides stercoralis, and Sarcoptes scabiei (crusted scabies). It is important for the laboratorian and clinician to be aware of problems that these organisms can cause in immunocompromised patients and of the proper diagnostic techniques and their clinical relevance. Organism eradication is effective using cotrimoxazole, trimethoprimsulfamethoxazole (TMP-SMX), pyrimethaminesulfadiazine, primaquine phosphate-nitrofurantoin, and primaquine phosphate-chloroquine phosphate. The drug of choice is TMP-SMX, which is classified as an investigational drug for treatment of Isospora belli infection. The diagnosis can be confirmed by demonstration of the mites, eggs, or scybala (fecal pellets).

This chapter focuses on the infectious etiologies and more common noninfectious causes of lower respiratory tract syndromes among major immunosuppressed populations. The changing epidemiology of infections in the era of highly active antiretroviral therapy (HAART) in the case of human immunodeficiency virus (HIV)-positive patients and the impacts of both newer immunosuppressant therapies and anti-infective prophylaxis for other immunocompromised hosts are discussed. The chapter emphasizes diagnostic approaches and practice algorithms. Both solid organ transplant (SOT) and hematopoietic stem cell transplant (HSCT) patients are particularly at risk for Legionella pneumonia, whereas the risk in HIV patients is not substantially higher than that seen in nonimmunocompromised patients. Plain chest radiographs are often inadequate for the immunocompromised host but may be helpful in the setting of new infiltrates. A recent retrospective study was performed in a medical/surgical intensive care unit on patients admitted with severe community-acquired pneumonia. A recent retrospective study was performed in a medical/surgical intensive care unit on patients admitted with severe community-acquired pneumonia. The performance of the immunochromatographic assay in this study was comparable to that in other published series. Tests for measurement of antibody are more useful for prescreening patients likely to be at risk for reactivation of infection or in the case of SOT and HSCT recipients, who are at risk for new infection from a seropositive donor. Studies reporting upon the diagnostic utility of bronchoalveolar lavage (BAL) and transbronchial biopsy (TBB) provide conflicting and often controversial findings.

Infections of the reproductive system and external genitalia in immunocompromised hosts most commonly result from reactivation of latent viruses, leading to genital lesions and other significant sequelae, as seen with reactivation of herpes simplex virus (HSV) infection in transplant patients. Infections with human papillomavirus (HPV) occur frequently and are often severe in patients with primary and secondary immunodeficiencies or with human immunodeficiency virus (HIV) infection. This chapter covers major genitourinary tract infections seen in different immunocompromised patient populations but does not address all possible infections of the reproductive system and external genitalia in these patients. Urinary tract infections (UTIs) in immunocompromised patients have been most well studied among transplant patients and HIV-infected patients. In chronic granulomatous disease, severe infections of the skin, central nervous system, mouth, and gastrointestinal system are seen, and genitourinary tract infections caused by gram-negative organisms, Staphylococcus spp., and Candida spp. can develop. The major effects of cancer chemotherapy include myelosuppression and disruption of normal anatomic barriers. Diagnostic approaches such as radiographic methods, surgical pathology methods and microbiological methods are discussed in the chapter. The most important microbiological method for diagnosing UTI in immunocompromised patients is quantitative culture of bacteria from urine or biopsy specimens, with susceptibility testing to detect resistant organisms. The major microbiological method for diagnosis of UTI, including cystitis and pyelonephritis, is the quantitative urine culture.

Gastrointestinal infections in the immunocompromised host are caused by the common bacterial, viral, fungal, and parasitic agents that also cause infections in the immunocompetent host. Lower gastrointestinal infections may be associated with fever, abdominal pain, nausea, vomiting, and diarrhea. Noncompliance with medications is a major risk factor for development of opportunistic infections. Other risk factors for developing gastrointestinal infections in the compromised host include the use of cytokine antagonists and newer immunotherapies that deplete lymphocyte subpopulations. Watery and persistent diarrhea is the most common manifestation in children; fever and vomiting are also relatively common. Disseminated visceral disease syndrome is the most common clinical presentation in AIDS patients (~70%). Due to the numerous microbial agents causing gastrointestinal infections in the immunocompromised patient, the diagnostic workup can be both prolonged and costly. There are several approaches to differential diagnosis of immunocompromised patients with gastrointestinal infections. Patients with uncomplicated acute gastroenteritis may be classified as having either community-acquired, nosocomially acquired, or persistent infections, as suggested by the Infectious Diseases Society of America. The approach to the diagnosis of gastrointestinal infections, particularly diarrheal illnesses, in the immunocompromised host is rather complex, and there is no simple diagnostic algorithm to follow.

This chapter provides a framework for the assessment and laboratory evaluation of immunocompromised patients presenting with central nervous system (CNS) infections. Infections of the meninges, brain, and spinal cord result in meningitis, encephalitis, and myelitis, respectively. While the chapter is limited to CNS infections, noninfectious conditions may be presented in a similar fashion. Mycobacterial and fungal meningitides tend to cause subacute or chronic meningitis. Granulomatous amoebic encephalitis in immunocompromised hosts is caused by Acanthamoeba species, free-living parasites that cause CNS infection characterized by multiple mass lesions throughout the brain. Myelitis is often seen in combination with encephalitis or meningitis and can be presented as either an acute or chronic condition. CNS manifestations of tuberculosis are diverse, but tuberculous meningitis is the most frequent form, with neuroimaging findings including basilar meningeal enhancement, hydrocephalus, and infarctions in the supratentorial brain parenchyma and/or brain stem. PCR amplification of viral nucleic acid in the cerebrospinal fluid (CSF) is sensitive and specific, and test turnaround time has been shortened significantly, to just a few hours, by incorporating either colorimetric enzyme immunoassay or real-time detection methods. While this chapter outlines many of the most common etiologic agents, with the emergence of new infections, the migration of infectious agents into new geographic niches, and the advent of an increasing array of medications with suppressive effects on the immune system, the field continues to evolve.

The spectrum of microorganisms causing bacteremia and fungemia in immunocompromised hosts has changed over the last decade, owing in large part to widespread use of chemoprophylaxis, differences in immunosuppressive regimens, and significant increases in the use of long-term indwelling devices. This chapter discusses the approach to immunocompromised patients with suspected bacteremia and fungemia, with particular emphasis on culture-independent diagnostic methods. The authors briefly address the predilection of specific microorganisms to cause invasive bloodstream infections among certain immunocompromised populations and discuss individual risk factors associated with the development of bacteremia and fungemia. The culturing of blood from patients with suspected bloodstream infections has remained one of the most important diagnostic tests performed by the microbiology laboratory. Over the last several decades, improvements in blood culture media and continuously monitoring blood culture systems have greatly enhanced the diagnostic value of blood cultures for the detection of bacteremia and candidemia. The sensitivity of blood cultures is excellent for the detection of nonfastidious bacterial pathogens and increases with the volume of blood collected. Laboratorians can continue to optimize the use of blood cultures for the diagnosis of bloodstream infections and to encourage their clinicians to obtain at least two sets of blood cultures by separate venipuncture before starting antimicrobial therapy.

Soft tissue infections can occur in any host when a microorganism is introduced accidentally into these tissues. Prostheses and medical devices predispose the patient to infections due to their foreign body effects that disrupt anatomic integrity and favor microbial entry, colonization, or attachment to the device in all hosts, whether they are immunocompromised or not. The interaction between the host and the microorganism determines whether infection takes place, its course, and its outcome. At the opposite ends of this delicate balance, rare but highly virulent microorganisms, such as Yersinia pestis, Bacillus anthracis, and Francisella tularensis, can strike any host, while common, minimally virulent microbes may infect only the most vulnerable hosts, such as those with immature or defective immune functions or those with prostheses or medical devices. Intravascular catheters provide a window to the bloodstream or to a target organ (such as the heart), where hemodynamics or organ functions may be measured and therapeutic drugs, nutrients, and radiological contrast materials are delivered. Patients with prosthetic devices, cancer, or other immune defects or weakness are prone to various skin and soft tissue infections.

The immunocompromised host is at increased risk of acquiring hospital-associated infections (HAIs), resulting in excessive morbidity and mortality, prolonged length of stay (LOS), and considerable cost to medical facilities. Traditionally, infections are classified as either hospital acquired (nosocomial), when symptoms manifest after 72 hours of hospital admission, or community acquired, when infections occur before this time frame. The chapter presents an overview of the prominent emerging pathogens that cause sepsis and respiratory disease-related HAIs in immunocompromised patients. The clinical impact of evolving antimicrobialresistant strains and their financial burden are discussed, along with the critical role of the diagnostic microbiology laboratory in providing tests that detect and identify these pathogens in a clinically relevant time frame. One report that examined early transplant-related mortality after cord blood transplantation from unrelated donors cited a rate close to 50%, mainly due to infectious complications. In this study, infections due to multidrug resistance (MDR) Acinetobacter spp. demonstrated a higher mortality rate than those due to cytomegalovirus disease. The majority of patients with ventilator-associated pneumonia (VAP) can be divided into two subgroups according to the time of onset of the disease. Targeted strategies that have been employed with the aim of reduction of selection of MDR gram-negative pathogens include intense monitoring of trends in high-risk units, modifications of formularies, massive education of prescribers, and strict enforcement of infection control practices. The majority of clinical microbiology laboratories still rely on culture-dependent methodologies for the isolation, identification, and antimicrobial susceptibility testing of respiratory tract pathogens.

The focused and unique health care management of the immunocompromised patient has grown significantly over the last several decades. Biomarkers of the immune response, such as procalcitonin (PCT), are evolving in clinical utility for the diagnosis of severe bacterial infections such as sepsis, for prediction of sepsis complications, and for therapeutic follow-up. Microbial and fungal infections are among the most common causes of high morbidity and mortality in critically ill patients in the United States; mortality rates can exceed 80%. Several molecular platforms are slated to play a role in advancing the diagnostic capabilities of clinical laboratories. Only time, cost-benefit studies, and practical evidence-based reviews can reveal the ultimate utility of these methods for diagnosis of infections in the immunocompromised population. Rapid testing for genetic resistance markers is an emerging clinical practice that can not only identify the potential for drug resistance but also help distinguish ambiguous breakpoints associated with susceptibility testing. Biomarkers of the immune response, such as PCT, are useful for the diagnosis of severe bacterial infections such as sepsis, for prediction of sepsis complications, and for therapeutic follow-up. Immunocompromised patients are a unique population, for which extreme measures may be required to make relevant diagnoses, prevent infection, or prevent overuse of health care resources.