Techniques for noninvasive diagnosis of lower respiratory tract infections. Which tests to order, when to consider invasive procedures

Although sputum culture and Gram's staining have been the traditional methods for determining the cause of lower respiratory tract infections, oropharyngeal contamination and improper sputum collection can limit their usefulness. Nevertheless, these noninvasive techniques remain a rapid means of gathering diagnostic clues. Alternative approaches include acid-fast sputum stains, direct immunofluorescence examination, enzyme immunoassays, DNA probes, and serologic testing. However, for critically ill patients, invasive procedures (such as bronchoscopy and thoracentesis) can provide more definitive diagnoses to guide selection of antimicrobial therapy.     

Exophiala dermatitidis

Exophiala is a genus comprising several species of opportunistic black yeasts, which belongs to Ascomycotina. It is a rare cause of fungal infections. However, infections are often chronic and recalcitrant, and while the number of cases is steadily increasing in both immunocompromised and immunocompetent people, detailed knowledge remains scarce regarding infection mechanisms, virulence factors, specific predisposing factors, risk factors, and host response. The most common manifestations of Exophiala infection are skin infections, and the most frequent type of deep infection is pulmonary infection due to inhalation. The invasive disease ranges from cutaneous or subcutaneous infection to systemic dissemination to internal organs. The final identification of the causative organism should be achieved through a combination of several methods, including the newly introduced diagnostic analysis, matrix-assisted laser desorption/ ionization-time-of-flight mass spectrometry, together with sequencing of the ribosomal ribonucleic acid internal transcribed spacer region of the fungi, and histological and culture findings. Regarding treatment, because anti-infective agents and natural compounds exhibited poor antibiofilm activity, few treatments have ultimately been found to be effective for specific antifungal therapy, so the optimal antifungal therapy and duration of therapy for these infections remain unknown. Therefore, most forms of disease caused by Exophiala dermatitidis require aggressive combination therapies: Both surgical intervention and aggressive antifungal therapy with novel compounds and azoles are necessary for effective treatment.     

Management of respiratory infections in the elderly

Respiratory infections are common at all ages but are particularly sinister among the elderly because of the fragility and chronic comorbidity associated with this age group. The three types of respiratory infection in the elderly are community-acquired pneumonia, acute exacerbation of chronic obstructive pulmonary disease and nonpneumonic respiratory tract infection. The etiology of these three types of infection includes classic bacteria, atypical pathogens and respiratory viruses. The relative frequency of each of the etiological groups as the causative agent of the infection varies significantly among these types of infection, but in all three types a significant proportion of infections involves more than one pathogen. The causative agent of respiratory infection in the elderly cannot be determined on the basis of clinical manifestation or the results of routine imaging procedures or laboratory tests. Thus, initial antibiotic therapy in these patients should be empiric, based on accepted guidelines. In recent years, the antipneumococcal fluoroquinolones have gained in stature as one of the best options to treat these infections. Pneumococcal and influenza vaccinations can reduce morbidity and mortality from respiratory infections in the elderly, so it is important that all elderly individuals are vaccinated through a structured program in the framework of primary care. The economic impact of respiratory infections in the elderly is primarily associated with the requirement for hospitalization in many of the cases. Any action that can reduce hospitalization rates has important economic ramifications. In light of the difficulty in reaching an early etiologic diagnosis in respiratory infections, it is essential to invest in the development of a compact diagnostic kit for the early stages of the disease, which could change reality in this important area of medicine.     

Management of respiratory infections in the elderly

Respiratory infections are common at all ages but are particularly sinister among the elderly because of the fragility and chronic comorbidity associated with this age group. The three types of respiratory infection in the elderly are community-acquired pneumonia, acute exacerbation of chronic obstructive pulmonary disease and nonpneumonic respiratory tract infection. The etiology of these three types of infection includes classic bacteria, atypical pathogens and respiratory viruses. The relative frequency of each of the etiological groups as the causative agent of the infection varies significantly among these types of infection, but in all three types a significant proportion of infections involves more than one pathogen. The causative agent of respiratory infection in the elderly cannot be determined on the basis of clinical manifestation or the results of routine imaging procedures or laboratory tests. Thus, initial antibiotic therapy in these patients should be empiric, based on accepted guidelines. In recent years, the antipneumococcal fluoroquinolones have gained in stature as one of the best options to treat these infections. Pneumococcal and influenza vaccinations can reduce morbidity and mortality from respiratory infections in the elderly, so it is important that all elderly individuals are vaccinated through a structured program in the framework of primary care. The economic impact of respiratory infections in the elderly is primarily associated with the requirement for hospitalization in many of the cases. Any action that can reduce hospitalization rates has important economic ramifications. In light of the difficulty in reaching an early etiologic diagnosis in respiratory infections, it is essential to invest in the development of a compact diagnostic kit for the early stages of the disease, which could change reality in this important area of medicine.     

Identification of human picornaviruses by nucleic acid probes

Human picornaviruses include rhinoviruses and enteroviruses which are responsible for both common and severe clinical diseases. Rhinoviruses are a frequent cause of respiratory infections while members of enterovirus subgroups, polio, coxsackie and ECHO viruses are often responsible for infections of the central nervous system, myocarditis, myositis etc. Human picornaviruses consist of nearly two hundred serotypes and therefore their specific identification after virus isolation, or the diagnosis based on the detection of immune response in patients, is problematic and does not usually provide virological diagnosis at the acute phase of illness. New methods for detection of picornavirus genomic RNA together with increasing knowledge of the nucleotide sequences of this virus group offer interesting possibilities for diagnostic procedures. Spot hybridization, in situ hybridization and enzymatic amplification of specific sequences have successfully been used for this purpose. Probes covering the 5' non-coding part of the genome, and also sequences derived from the region coding for non-structural proteins, can be used as broadly reacting reagents in picornavirus detection. Specific sequences are mainly found in the capsid protein region of the genome. cDNA probes and synthetic oligonucleotides are useful in rapid identification of picornaviruses after amplification in cell cultures and in epidemiological analysis. The biochemical amplification methods may enable recognition of picornaviruses directly in clinical samples in the near future. In situ hybridization methods have been of special interest because they can be used to reveal the presence of enterovirus genomes in biopsy specimens from e.g. affected heart muscle in patients with myocarditis and cardiomyopathy.     

Metabolomics of urinary tract infection: a new uroscope in town

Urinary tract infection (UTI) is a potentially life-threatening infectious disease. For rapid directed therapy of UTIs, it is essential to determine the causative microorganism. To date, there is no single test that has been proven to reliably, rapidly and accurately identify the etiologic organism in UTI. The molecular methods for diagnosing the cause of UTI and prognostic development of clinically important metabolomic evaluations and their limitations for use in the diagnosis and monitoring of infections are discussed in this review article. The application of the emerging investigative device NMR spectroscopy as a surrogate method for the diagnosis of UTI is also addressed.     

Fungal central nervous system infections: prevalence and diagnosis

Fungal infections of the central nervous system (CNS) are rare but they pose a significant challenge. Their prevalence spans a wide array of hosts including immunosuppressed and immunocompetent individuals, patients undergoing neurosurgical procedures and those carrying implantable CNS devices. Cryptococcus neoformans and Aspergillus spp. remain the most common pathogens. Magnetic resonance imaging can help localize the lesions, but diagnosis is challenging since invasive procedures may be needed for the retrieval of tissue, especially in cases of fungal abscesses. Antigen and antibody tests are available and approved for use in the cerebrospinal fluid (CSF). PCR-based techniques are promising but they are not validated for use in the CSF. This review provides an overview on the differential diagnosis of the fungal CNS disease based on the host and the clinical syndrome and suggests the optimal use of diagnostic techniques. It also summarizes the emergence of Cryptococcus gatti and an unanticipated outbreak caused by Exserohilum rostratum.     

Genetics of neuromuscular disorders

Neuromuscular disorders affect the peripheral nervous system and muscle. The principle effect of neuromuscular disorders is therefore on the ability to perform voluntary movements. Neuromuscular disorders cause significant incapacity, including, at the most extreme, almost complete paralysis. Neuromuscular diseases include some of the most devastating disorders that afflict mankind, for example motor neuron disease. Neuromuscular diseases have onset any time from in utero until old age. They are most often genetic. The last 25 years has been the golden age of genetics, with the disease genes responsible for many genetic neuromuscular disorders now identified. Neuromuscular disorders may be inherited as autosomal dominant, autosomal recessive, or X-linked traits. They may also result from mutations in mitochondrial DNA or from de novo mutations not present in the peripheral blood DNA of either parent. The high incidence of de novo mutation has been one of the surprises of the recent increase in information about the genetics of neuromuscular disorders. The disease burden imposed on families is enormous including decision making in relation to presymptomatic diagnosis for late onset neurodegenerative disorders and reproductive choices. Diagnostic molecular neurogenetics laboratories have been faced with an ever-increasing range of disease genes that could be tested for and usually a finite budget with which to perform the possible testing. Neurogenetics has moved from one known disease gene, the Duchenne muscular dystrophy gene in July 1987, to hundreds of disease genes in 2011. It can be anticipated that with the advent of next generation sequencing (NGS), most, if not all, causative genes will be identified in the next few years. Any type of mutation possible in human DNA has been shown to cause genetic neuromuscular disorders, including point mutations, small insertions and deletions, large deletions and duplications, repeat expansions or contraction and somatic mosaicism. The diagnostic laboratory therefore has to be capable of a large number of techniques in order to identify the different mutation types and requires highly skilled staff. Mutations causing neuromuscular disorders affect the largest human proteins for example titin and nebulin. Successful molecular diagnosis can make invasive and expensive diagnostic procedures such as muscle biopsy unnecessary. Molecular diagnosis is currently largely based on Sanger sequencing, which at most can sequence a small number of exons in one gene at a time. NGS techniques will facilitate molecular diagnostics, but not for all types of mutations. For example, NGS is not good at identifying repeat expansions or copy number variations. Currently, diagnostic molecular neurogenetics is focused on identifying the causative mutation(s) in a patient. In the future, the focus might move to prevention, by identifying carriers of recessive diseases before they have affected children. The pathobiology of many of the diseases remains obscure, as do factors affecting disease severity. The aim of this review is to describe molecular diagnosis of genetic neuromuscular disorders in the past, the present and speculate on the future.     

MRSA respiratory tract infection]

Sputum isolates of MRSA have been on the increase, recently. Preventive measures against MRSA nosocomial infections have become important in Japanese hospitals. Clinical study was performed on 29 patients from whom MRSA was isolated more than 10(7) cfu/ml using the quantitative sputum culture method. All had a history of admission, therefore nosocomial infections caused by MRSA could very often occur. MRSA was determined as a causative organism in 3 on the basis of symptoms, laboratory data, chest X-rays, and effect of antimicrobial agents. These three patients improved by a single or combined administration of minocycline, arbekacin and/or fosfomycin. In 15 patients, MRSA was frequently isolated, but was thought to be colonized. In 3 patients, MRSA was not isolated without administration of antimicrobial agents thereafter. It was supposed that most of MRSA isolates from sputum were not the causative organism of the respiratory tract infection.     

Acute respiratory failure caused by secondary alveolar proteinosis in a patient with acute myeloid leukemia: a case report

Pulmonary alveolar proteinosis (PAP) is a rare cause of chronic respiratory failure due to progressive alveolar accumulation of a periodic acid-schiff (PAS) positive proteinaceous material. In some cases, the rapid accumulation of intra-alveolar material leads to acute respiratory failure (ARF). We report the causative role of secondary PAP in the case of a 26-year-old man with acute myeloid leukemia who developed fever, increased serum lactate deshydrogenase level and ARF, and required mechanical ventilation. The diagnosis of PAP was established by the examination of material obtained by bronchoalveolar lavage (BAL). Respiratory improvement occurred several days after the patient had recovered from neutropenia. This report underlines the importance of the early diagnosis of PAP as a potential cause of ARF in leukemic patients. Adequate stain on BAL fluid provides the diagnosis and avoids repeated invasive procedures and inappropriate treatments. Received: 21 July 1997 Accepted: 12 December 1997     

Epidemiology and diagnosis of Shiga toxin-producing Escherichia coli infections.

Shiga toxin-producing Escherichia coli (STEC) have been identified as a worldwide cause of serious human gastrointestinal disease and the life-threatening hemolytic uremic syndrome. The most common serotype implicated is E. coli O157: H7, but infections involving various non-O157 serotypes have been found with increasing frequency in many countries. Food-borne outbreaks caused by STEC can affect large numbers of people and cause serious morbidity, making the bacteria one of the most important emerging pathogens. Because there is no specific treatment of the disease currently available, there is an urgent need for effective preventive measures based on a detailed understanding of the epidemiology of STEC infections. Such measures will also be dependent on the availability of rapid, sensitive, and simple procedures for the detection of the pathogens both in human samples and in samples of nonhuman origin such as food. This review summarizes the current knowledge on the epidemiology of STEC infection and presents a survey of laboratory methods currently available for diagnosis of STEC. Special attention is given to new diagnostic procedures for the less readily detectable non-O157 STEC strains and to simple procedures, usually based on commercially available kits, that can be used in routine clinical microbiological laboratories.     

Adult respiratory distress syndrome associated with miliary tuberculosis

Three patients with respiratory failure resulting from miliary tuberculosis had a characteristic clinical presentation that included a long history of a prominent cough, dyspnea, weight loss, tachycardia, tachypnea, pulmonary adventitious sounds, and hepatomegaly. Hematologic investigation showed a normal white cell count with marked left shift in the morphology of white cells in all three patients, and evidence of disseminated intravascular coagulation in one patient. In only one patient was the initial sputum positive for acid-fast bacilli; in the others, invasive diagnostic procedures including lumbar puncture, bone marrow trephine, and open-lung biopsy were necessary for diagnosis. Miliary tuberculosis should be suspected in patients with adult respiratory distress syndrome of unknown etiology. Simple diagnostic procedures such as sputum, bronchial brushings, and urine examination should be followed by bone marrow trephine, liver biopsy, transbronchial lung biopsy, and lumbar puncture if physical signs of meningitis are present.     

Laboratory in the diagnosis and management of urinary tract infections

The laboratory is essential in the diagnosis and management of UTIs. The presence of pyuria and bacteriuria, the two most important indicators of UTIs, are most accurately determined by standard techniques. In quantitating pyuria, the finding of greater than or equal to 10 leukocytes/mm3 of urine by either hemocytometry or direct microscopy correlates highly with symptomatic, culture-proven UTIs. The determination of bacteriuria by direct microscopy is inaccurate, particularly at lower levels of bacteriuria; thus, quantitative urine cultures remain the most accurate measure of bacteriuria. Significant bacteriuria, previously defined as greater than or equal to 10(5) CFU/ml of urine, has been redefined with the observation that as few as 10(2) CFU/ml can be associated with significant pyuria and symptoms suggestive of cystitis. The need for routine and posttreatment urine cultures in nonpregnant women with acute dysuria remains controversial, but current data suggest that they are usually unnecessary. Rapid diagnostic tests for detection of pyuria and bacteriuria are designed to increase efficiency and decrease cost in the diagnosis of UTI. Unfortunately, none of these techniques can quantitate pyuria or bacteriuria as accurately as the standard methods, but the level of accuracy offered by the standard methods is not always necessary in the care of patients with uncomplicated UTIs. These tests are particularly well suited for screening asymptomatic high-risk populations. Noninvasive localization techniques continue to be explored as possible alternatives to invasive localization procedures, but they remain largely research tools that are not readily available to the practicing clinician. Understanding the applicability and appropriate use of newer technologies in the evaluation of patients with UTIs and how these technologies complement the standard diagnostic techniques will lead to better, more efficient, and less costly patient care.     

Viral pneumonias. Infection in the immunocompromised host

Three herpesviruses--herpes simplex, varicella-zoster, and cytomegalovirus--commonly cause respiratory tract infections in immunocompromised patients. Adenoviruses and measles virus are also significant causes of respiratory disease in this population. Diagnosis of herpesvirus infections is difficult because these viruses can establish latency and are often shed intermittently in the absence of invasive disease. A positive respiratory tract culture of herpesviruses alone is not diagnostic of active invasive disease. Preventive measures should focus on limiting the patient's exposure to active infection, broad use of available vaccines in children and susceptible adults, and use of hyperimmune globulin and chemoprophylaxis in high-risk patients. Adenovirus pneumonia is diagnosed by viral culture and rapid antigen detection assays, whereas measles pneumonia is often identifiable by the characteristic rash. Treatment of either adenovirus or measles pneumonia is primarily supportive.     

Diagnosis of pulmonary lesions in acute respiratory insufficiency in patients with depressed hemopoiesis

AIM: To analyse causes of acute respiratory failure (ARF) and methods of diagnosis of pulmonary lesions in patients with depressed hemopoiesis (DH). MATERIAL AND METHODS: 50 patients with DH and ARF were examined according to the protocol including x-ray, computed tomography, fibrobronchoscopy with bronchoalveolar lavage, cytological, bacteriological, virusological studies of the lavage fluid, biopsy of the lung. The algorithm of the protocol is provided. RESULTS: Sensitivity of the lavage fluid in diagnosis of fungal, bacterial, pneumocystic and cytomegaloviral infections was 84, 78, 93 and 93%, respectively. The cytologic examination of the lavage fluid may detect lung infiltration with blood tumors. In complicated diagnostic cases lung biopsy verified pulmonary lesion but its conduction aggravated the patients' condition. ARF patients with DH, bacterial flora, fungi, cytomegalovirus and pneumocystic infection, pulmonary tumor involvement, pulmonary lesions in ATRA-syndrome, non-infectious lesions of the lungs after bone marrow transplantation were found in 38, 18, 40, 18, 8 and 4% of cases, respectively. CONCLUSION: DH patients with ARF should be examined by the protocol including both non-invasive and invasive diagnostic methods. Accurate diagnosis of ARF causes is the basic reserve in the treatment of such patients.     

Case report of non-healing wounds presenting to a DGH, South East London

Mycobacterium marinum infections (fish tank granuloma) are infrequently encountered and when they do arise, they can pose a diagnostic challenge for clinicians. They can present as non-healing wounds along with several other presentations that may not be typical, as patients can have other comorbidities that cause immunosuppression and invasive symptoms of the disease. Treatment regimens vary in length, and are based on the patient's response to treatment couple with resolution of symptoms. Rifampicin and ethambutol are effective treatment options, together with use of macrolides. A thorough history from patients must be taken as to establish contact with aquatic animals.     

Obligate aerobic,gram-positive,weak acid-fast,nonmotile bacilli,Tsukamurella tyrosinosolvens: Minireview of a rare opportunistic pathogen

Tsukamurella species are obligate aerobic, gram-positive, weak acid-fast, nonmotile bacilli. They are found in various environments, such as soil, water, sludge, and petroleum reservoir wastewater, and belong to the order Actinomycetales. In 2016, there was a reclassification of species within the genus Tsukamurella, merging the species Tsukamurella tyrosinosolvens (T. tyrosinosolvens) and Tsukamurella carboxydivorans. Tsukamurella species are clinically considered to be a rare opportunistic pathogen, because most reported cases have been related to bacteremia and intravascular prosthetic devices and immunosuppression. To date, it has been isolated only from human specimens, and has always been associated with clinical disease; human infections are very rare. Reported infections have included pneumonia, brain abscesses, catheter-related bloodstream infections, ocular infections, bacteremia, and sepsis presenting with septic pulmonary emboli in patients who are immunocompromised. To date, there is no commercially available test for identification. On the other hand, sequence-based identification, including matrix-assisted laser desorption ionization time-of-flight mass spectrometry, is an alternative method for identifying clinical isolates that are either slow growers or difficult to identify through biochemical profiling. The golden standards for diagnosis and optimal management still remain to be determined. However, newer molecular biological techniques can provide accurate identification, and contribute to the appropriate selection of definitive therapy for infections caused by this organism. Combinations of several antimicrobial agents have been proposed for treatment, though the length of treatment for infections has yet to be determined, and should be individualized according to clinical response. Immunocompromised patients often experience severe cases due to infection, and life-threatening T. tyrosinosolvens events associated with dissemination and/or failure of source control have occurred. Favorable prognoses can be achieved through earlier identification of the cause of infection, as well as successful management, including appropriate antibiotic therapy together with source control. Further analyses of similar cases are required to establish the most adequate diagnostic methods and treatment regimens for infections.     

Candida infections in non-neutropenic children after the neonatal period

There are a variety of diseases, from local mucous membrane infections to invasive systemic infections, that are caused by Candida species. As a causative agent, Candida albicans is the most common; however, the other Candida species can also cause the same clinical syndromes. Most invasive fungal infections in children occur in the hospital setting. Candidemia is a serious condition associated with high morbidity and mortality and increased healthcare costs in pediatric patients. Children at the highest risk are those with prolonged intensive care unit stays, reduced immune function, recent surgery, prior bacterial infection, prior use of antibiotics and/or corticosteroids and other immunosuppressive agents, as well as use of a central venous catheter, total parenteral nutrition, mechanical ventilation and dialysis. Positive blood culture is the gold standard of candidemia; it should not be accepted as contamination or colonization in children with an intravascular catheter. However, in oropharyngeal or vulvovaginal candidiasis, culture of lesions is rarely indicated unless the disease is recalcitrant or recurrent. Recovery of Candida from the sputum should usually be considered as colonization and should not be treated with antifungal therapy. Antigen and antibody detecting tests are evaluated in invasive Candida infections; however, there are no published results in children, and their roles in diagnosis are also unclear. For the therapy of invasive Candida infections in non-neutropenic patients, fluconazole or an echinocandin is usually recommended. Alternatively, amphotericin B deoxycholate or lipid formulations of amphotericin B can also be used. The recommended therapy of Candida meningitis is amphotericin B combined with flucytosine. The combination therapy for Candida infections is usually not indicated. Prophylaxis in non-neonatal, immunocompetent children is not recommended.     

Diagnosis of ventilator-associated pneumonia: focus on nonbronchoscopic techniques (nonbronchoscopic bronchoalveolar lavage, including mini-BAL, blinded protected specimen brush, and blinded bronchial sampling) and endotracheal aspirates

The ideal diagnostic approach for ventilator-associated pneumonia currently is based on invasive procedures to obtain respiratory tract cultures. Given the lack of consensus and relatively poor acceptance of full bronchoscopic bronchoalveolar lavage (BAL) and protected specimen brush (PSB), less invasive procedures have been developed. We review the nonbronchoscopic procedures (nonbronchoscopic bronchoalveolar lavage, including mini-BAL, blinded protected specimen, and blinded bronchial sampling) and endotracheal aspiration. We provide a critique of the methods used, the types of catheters inserted, and the sample collection methods. Most studies were flawed in that antibiotic use before initiation of the procedure was not controlled. The variability of both the methods and the criteria for the gold standard in the numerous investigations show that these procedures are neither standardized nor proven to be accurate and often did not improve management. Pending future studies, use of endotracheal aspirates without the use of quantitation seems to be a reasonable approach for clinicians who are not committed to an invasive procedure.     

Alveolar-interstitial pneumopathy after gold-salts compounds administration, requiring mechanical ventilation

The pulmonary toxicity of gold salts is an uncommon cause of life-threatening respiratory failure. Currently, patients who suffer from this do not need mechanical ventilation, and the toxicity can be difficult to diagnose when it occurs in patient with an illness producing pulmonary manifestations. We report a case of severe respiratory failure due to gold salt toxicity in a patient suffering from rheumatoid arthritis requiring mechanical ventilation. At such a time, the poor respiratory function makes some diagnostic procedures harmful. The diagnosis can be made after the exclusion of other causes of rheumatoid lung when the patient's poor respiratory status precludes invasive exploration. The clinical findings, radiological features, and results of pulmonary function tests may be enough to diagnose gold-related pneumopathy. This avoids the need for bronchoscopic examination or transfer of the patient for computed tomography. Attention must be paid to this complication because the outcome and functional prognosis are better when pulmonary involvement is gold related: in our case steroid therapy was life-saving and induced complete recovery of the lung damage. Received: 16 March 1998 Accepted: 18 June 1998