Longitudinal multicompartment characterization of host-microbiota interactions in patients with acute respiratory failure

Critical illness can significantly alter the composition and function of the human microbiome, but few studies have examined these changes over time. Here, we conduct a comprehensive analysis of the oral, lung, and gut microbiota in 479 mechanically ventilated patients (223 females, 256 males) with acute respiratory failure. We use advanced DNA sequencing technologies, including Illumina amplicon sequencing (utilizing 16S and ITS rRNA genes for bacteria and fungi, respectively, in all sample types) and Nanopore metagenomics for lung microbiota. Our results reveal a progressive dysbiosis in all three body compartments, characterized by a reduction in microbial diversity, a decrease in beneficial anaerobes, and an increase in pathogens. We find that clinical factors, such as chronic obstructive pulmonary disease, immunosuppression, and antibiotic exposure, are associated with specific patterns of dysbiosis. Interestingly, unsupervised clustering of lung microbiota diversity and composition by 16S independently predicted survival and performed better than traditional clinical and host-response predictors. These observations are validated in two separate cohorts of COVID-19 patients, highlighting the potential of lung microbiota as valuable prognostic biomarkers in critical care. Understanding these microbiome changes during critical illness points to new opportunities for microbiota-targeted precision medicine interventions.

Fecal microbiota transplantation significantly improved respiratory failure of amyotrophic lateral sclerosis

Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease that leads to respiratory failure, and eventually death. However, there is a lack of effective treatments for ALS. Here we report the results of fecal microbiota transplantation (FMT) in two patients with late-onset classic ALS with a Japan ALS severity classification of grade 5 who required tracheostomy and mechanical ventilation. In both patients, significant improvements in respiratory function were observed following two rounds of FMT, leading to weaning off mechanical ventilation. Their muscle strength improved, allowing for assisted standing and mobility. Other notable treatment responses included improved swallowing function and reduced muscle fasciculations. Metagenomic and metabolomic analysis revealed an increase in beneficial Bacteroides species (Bacteroides stercoris, Bacteroides uniformis, Bacteroides vulgatus), and Faecalibacterium prausnitzii after FMT, as well as elevated levels of metabolites involved in arginine biosynthesis and decreased levels of metabolites involved in branched-chain amino acid biosynthesis. These findings offer a potential rescue therapy for ALS with respiratory failure and provide new insights into ALS in general.

Candida palmioleophila isolation in Italy from two cases of systemic infection, after a CHROMagar and Vitek system mis-identification as C. albicans

A correct, fast, reliable identification method is pivotal in nosocomial environments to guide treatment strategies, whereas misidentification might lead to treatment failure. For routine identifications the Vitek system and CHROMagar are widely used but not always reliable, especially now with an increasing number of new emerging fungal pathogens that need careful identification. Here we describe two cases of candidemia, due to Candida palmioleophila previously misidentified as Candida albicans by using the Vitek2 system and CHROMagar. The first case is a 54-year-old man with an infected ulcer in the lower right limb, treated with a targeted therapy using a central venous catheter (CVC). After two months he developed a CVC-related candidemia MDR identified as C. albicans. The second case is a 2-month-old male baby that was admitted to the neonatal unit with acute respiratory failure due to a severe community-acquired bilateral pneumonia; blood cultures were all positive for C. albicans MDR. The isolated strains where re-identified with Maldi-Tof and DNA sequencing as C. palmioleophila. From the identification point of view, CHROMagar can be clearly misleading, especially because CHROMagar types currently available are not designed to discriminate new emerging species, suggesting that systems other than MALDI-TOF and marker sequencing may be inadequate even for routine identification and could contribute to producing misleading identifications and therapeutically wrong practices, leading to failures and patient death.

Lung abscess by Actinomyces odontolyticus and Parvimonas micra co-infection presenting as acute respiratory failure: A case report

RATIONALE

Actinomyces odontolyticus and Parvimonas micra are very rare causative organisms of lung abscess and acute respiratory failure.

PATIENT CONCERNS

A 49-year-old male patient visited the emergency room with a complaint of sudden onset of shortness of breath, and he developed acute respiratory failure rapidly.

DIAGNOSIS

An abscess in the left lower lung field was diagnosed on the computed tomography scan of chest.

INTERVENTIONS

Immediate treatment with intravenous antibiotics was initiated along with a pigtail catheter insertion for pus drainage.

OUTCOMES

A odontolyticus was cultured on the drained pus and P micra was identified by a blood culture. The patient was successfully weaned from the mechanical ventilator and the lung abscess was completely resolved.

LESSONS

To the best of our knowledge, this is the first case report of mixed infection with A odontolyticus and P micra, which caused acute respiratory failure in an immune-competent patient. Therefore, physicians should consider the possibility of these organisms as causative pathogens of a fulminant pulmonary infection even in an immune-competent patient.

Severe Community-acquired Pneumonia Caused by Acinetobacter baumannii Successfully Treated with the Initial Administration of Meropenem Based on the Sputum Gram Staining Findings

A 62-year-old man with diabetes mellitus and a two-day history of fever and dyspnea presented at our hospital. He was diagnosed with community-acquired pneumonia (CAP), septic shock, and respiratory failure. Sputum Gram staining revealed Gram-negative coccobacilli. Based on the Gram staining findings and history, Acinetobacter baumannii was considered as one of the causative organisms of his CAP. Consequently, he was successfully treated with the initial administration of meropenem. We suggest that A. baumannii should be considered as one of the possible causative organisms of CAP based on a fulminant clinical course, and the presence of Gram-negative coccobacilli.

Clinical features of fatal severe fever with thrombocytopenia syndrome that is complicated by invasive pulmonary aspergillosis

INTRODUCTION

Severe fever with thrombocytopenia syndrome (SFTS) has been prevalent in parts of Asia during recent years. However, SFTS with invasive pulmonary aspergillosis (IPA) is rare, and it is important to understand its clinical features.

MATERIALS AND METHODS

Total four cases of SFTS with IPA are reviewed and detailing the disease progression, treatment options, and prognosis were summarized and analyzed.

RESULTS

The patients with SFTS-associated IPA first presented with fever, gastrointestinal symptoms, thrombocytopenia, leukopenia, and multiple organ failure. After 1-2 weeks, the patients developed mild polypnea and wheezing rales, and quickly developed dyspnea and respiratory failure. Tracheal intubation was usually performed, but did not relieve the intractable airway spasm and pulmonary ventilation failure. Bronchoscopy confirmed that the antifungal treatment was ineffective and the aspergillosis had worsened. All patients died of type 2 respiratory failure caused by continued airway obstruction and spasticity.

CONCLUSIONS

Given the high mortality rate in this series, there is a need for increased awareness of SFTS-associated IPA. Additional examinations should be performed in these cases, and early-stage antifungal treatment with organ support may be helpful.

Leptospirosis-associated catastrophic respiratory failure supported by extracorporeal membrane oxygenation

A previously healthy, 39-year-old obese farmer, arrived hypotensive and tachycardic, with fever, myalgia, headache, abdominal pain, diarrhea, and progressive dyspnea. Ten days before symptoms onset, he was in direct contact with mice and working in a contaminated drain. Patient laboratory showed acute kidney injury and thrombocytopenia. Chest X-ray exhibited bilateral diffuse interstitial infiltrates. First-line empirical antibiotics were started and influenza discarded. Patient evolved with severe respiratory failure, associated with hemoptysis, and rapidly severe hemodynamic compromise. Despite neuromuscular blockade and prone positioning, respiratory failure increased. Accordingly, veno-venous ECMO was initiated, with bilateral femoral extraction and jugular return. After ECMO connection, there was no significant improvement in oxygenation, and low pre-membrane saturations and low arterial PaO2 of the membrane showed that we were out of the limits of the rated flow. Thus, a second membrane oxygenator was installed in parallel. Afterward, oxygenation improved, with subsequent perfusion enhancement. Regarding etiology, due to high suspicion index, Leptospira serology was performed, coming back positive and meropenem was maintained. The patient ultimately recovered and experience excellent outcome. The clinical relevance of the case is the scared evidence of leptospirosis-associated severe respiratory failure treated with ECMO. This experience emphasizes the importance of an optimal support, which requires enough membrane surface and flow for an obese, highly hyperdynamic patient, during this reversible disease. A high index of suspicion is needed for an adequate diagnosis of leptospirosis to implement the correct treatment, particularly in the association of respiratory failure, pulmonary hemorrhage, and an epidemiological-related context.

Pyomyositis Complicated by Deep Venous Thrombosis - A Unique Case of Reverse Lemierre's Syndrome

We report a case of a young individual who presented with fever and swelling of right upper and lower limbs for 3 weeks. Subsequently he developed shortness of breath and decreased urine output and had to be mechanically ventilated. Ultrasound screening of the lower limb had shown deep venous thrombosis (DVT) and thus the diagnosis of pulmonary thromboembolism (PTE) seemed probable. However the workup for PTE was negative and patient's fever continued and his condition deteriorated. Evaluation for an infective locus led to the diagnosis of pyomyositis and DVT appeared to have developed secondary to the muscle inflammation as a part of Reverse Lemierre's syndrome. Thus this case highlights the importance of considering this diagnosis in a similar setting and not to ascribe every case of respiratory failure in a background of DVT to be due to PTE.

Pulmonary and Vertebral Mycobacterium avium Disease in a HIV-negative 71-year-old Man - A Case Report

Nontuberculous mycobacteria (NTM) caused pulmonary disease is on increase worldwide, especially in countries with decreasing time trend of tuberculosis incidence. NTM skeletal affection is rare. Mycobacterium avium related disease, with still unclear clinical and radiologic features, is in current focus of both clinicians and researchers. An exhausted severely ill 71-year-old man was admitted on emergency due to cough, dyspnea and lumbar back pain to be diagnosed with terminal phase M. avium disease. Three sputum smears were positive for acid fast bacilli and M. avium was identified with hybridization reaction by means of GenoType ® MTBC (Hain). Apart from pulmonary disease, compressive fractures of the 12th thoracic and 1-4th lumbar vertebrae were detected. We found age, chronic alcoholism, previous professional exposure, tobacco smoking, chronic obstructive pulmonary disease and previous tuberculosis as risk factors for NTM disease in the HIV-negative patient. Despite combined antibiotic treatment, disease had lethal outcome. This case report might contribute to clinicians' awareness and improved knowledge on this sort of pathology, and lead to earlier diagnosis with possibly better disease outcome.

THE PATIENT-DOCTOR-PSYCHOLOGIST TRIANGLE IN A CASE Of SEVERE IMUNOSUPRESSION IN THE HIV INFECTION

In the last two years the Romanian adult population infected with the human immunodeficiency virus (HIV) has increased due to sexual transmission, both heterosexual and homosexual. The case presented is that of a 33 year-old man, admitted to the Infectious Diseases Hospital in Iasi with acute respiratory failure and a confirmation of Kaposi's sarcoma. Tests later proved positive for HIV, the patient being included in the stage AIDS C3 (acute immunodeficiency syndrome). The respiratory failure was suspected to be caused by Pneumocystis carinii and cotrimoxazol therapy, oxygen therapy and anti-retroviral therapy were established. He was also referred to the oncology hospital for treatment of Kaposi's sarcoma. The patient's adherence to therapy was influenced by a strong doctor-patient relationship, as well as by psychological counseling and support. Creating a functional doctor-patient-psychologist team is key throughout the HIV-positive patient's existence, for supporting long term adherence to therapy and acceptance of the diagnosis. This case highlights the need for a strong psychosocial compartment in every medical center that deals with HIV-infected individuals.

Botulism with Unusual Rapid Progression to Complete Paralysis in a Child

Botulism is a severe neuroparalytic illness which is difficult to diagnose accurately, especially in children. We report a child with type A botulism intoxication, with very rapid progression to coma-like consciousness and respiratory failure. Careful physical examinations led to the suspicion of botulism, and electrophysiologic examinations, including electroencephalogram and repetitive nerve stimulation tests, further supported the diagnosis. Hospitalization due to botulism had a great emotional impact on the patient and psychological support was crucial.

Severe Legionella pneumophila pneumonia and non-invasive ventilation: presentation of two cases and brief review of the literature

Legionella pneumophila is an agent also well known to be frequently responsible for severe community acquired pneumonia. Recent studies regarding severe community-acquired pneumonia have shown that Legionella pneumophila is the second most common cause of admission to ICU, not far behind pneumococcal pneumonia. The mortality of severe Legionella pneumonia is high (30%). We report two cases of severe respiratory failure due to Legionella pneumophila type 1 treated with non-invasive ventilation in the Respiratory Intermediate Care Unit of a Department of Respiratory Medicine with good outcomes. Severe community-acquired pneumonia is the most common cause of ARDS, and it is the primary reason for Intensive Care Unit admission with invasive mechanical ventilation. Delay in ICU admission is probably associated with a poorer outcome. The use of non-invasive ventilation in severe community acquired pneumonia is controversial. However, after recent pandemics, the number of studies reporting good rates of success for NIV has increased. Both our patients were managed in a respiratory intermediate care unit, avoiding invasive ventilation and invasive monitoring, which lowered costs yet was equally effective in providing a good outcome when compared to intubation in the Intensive Care Unit.

Tetanus--a case report with severe autonomic instability and: a review of the literature

BACKGROUND

Tetanus is an infection that can be associated with a high mortality especially in developing countries. Critical care which may include artificial control of respiration is crucial in survival, but cardiovascular complications from autonomic instability remains an important cause of death. The objective of this report is to highlight this important cause of mortality despite artificial control of ventilation to prevent respiratory arrest.

METHOD

The medical record of the patient and relevant literature were reviewed.

RESULT

A 29-year old male following a wound on the lower limb presented with clinical features suggestive of tetanus. Incubation period was short and immunization history was uncertain. Basic treatment directed at removing source of infection and neutralisation of unbound toxin was however commenced. Following signs of imminent respiratory failure due to severe uncontrollable spasms, controlled mechanical ventilation was instituted in the critical care unit (CCU). However, the patient succumbed to cardiac arrest as a result of severe autonomic instability, despite aggressive cardiopulmonary resuscitation.

CONCLUSION

Cardiovascular arrest from severe autonomic instability remains an important cause of mortality in tetanus despite artificial ventilation. Early management with appropriate therapy is advisable to prevent its occurrence.

Severe invasive listeriosis--case report

Listeriosis is a rare food borne infection which, in the invasive form, presents as bloodstream infection, central nervous system infection, materno-fetal infection, or focal infection. Certain immunosuppressive conditions have been identified as risk factors for severe invasive disease. The invasive forms of listeriosis are associated with a high case fatality rate. We present the case of a 62-year-old male with an unremarkable medical history admitted to the Iasi Infectious Diseases Hospital for fever. headache, ataxia, and diplopia. Physical examination revealed high temperature, confusion, relative bradycardia, and signs of meningeal irritation. Laboratory test showed leukocyt osis with neutrophilia. pathological CSF findings (high WBC count with predominance of neutrophils, low glucose and high protein levels), increased liver enzymes (ALAT, ASAT, AP, gammaGT), and important renal impairment (normal levels at presentation). No abnormalities at chest x-ray, cranial CT and abdominal ultrasound. CSF and blood cultures were positive for Listeria monocytogenes. Under antibiotics (ampicillin and ciprofloxacin), the course was marked by respiratory failure requiring mechanical ventilation, coma, hypotension, tachycardia. and death 12 days after admission. The particularity of this case consists in the association of the two classical forms of invasive listeriosis, meningitis and bacteriemia, with a focal infection. acute hepatitis, and a course marked by multiple organ dysfunction syndromes and exitus in a previously apparently healthy individual.

Adiaspiromycosis causing respiratory failure and a review of human infections due to Emmonsia and Chrysosporium spp

We report a case of a 27-year-old male who presented with respiratory distress that required mechanical ventilation. Transbronchial biopsy revealed adiaspores of the fungus Emmonsia crescens within granulomata, a condition known as adiaspiromycosis. The patient received amphotericin products and corticosteroids, followed by itraconazole, and made a full recovery. Emmonsia crescens is a saprobe with a wide distribution that is primarily a rodent pathogen. The clinical characteristics of the 20 cases of human pulmonary adiaspiromycosis reported since the last comprehensive case review in 1993 are described here, as well as other infections recently reported for the genus Emmonsia. Pulmonary adiaspiromycosis has been reported primarily in persons without underlying host factors and has a mild to severe course. It remains uncertain if the optimal management of severe pulmonary adiaspiromycosis is supportive or if should consist of antifungal treatment, corticosteroids, or a combination of the latter two. The classification of fungi currently in the genus Emmonsia has undergone considerable revision since their original description, including being grouped with the genus Chrysosporium at one time. Molecular genetics has clearly differentiated the genus Emmonsia from the Chrysosporium species. Nevertheless, there has been a persistent confusion in the literature regarding the clinical presentation of infection with fungi of these two genera; to clarify this matter, the reported cases of invasive Chrysosporium infections were reviewed. Invasive Chrysosporium infections typically occur in impaired hosts and can have a fatal course. Based on limited in vitro susceptibility data for Chrysosporium zonatum, amphotericin B is the most active drug, itraconazole susceptibility is strain-dependent, and fluconazole and 5-fluorocytosine are not active.

Disseminated Nocardiosis caused by Nocardia concava with acute respiratory failure and central nervous system involvement treated with linezolid

Nocardia concava was identified as a new species in 2005; however, the clinical manifestations of Nocardia concava infection have yet to be clarified. We herein present the case of an immunosuppressed patient who developed disseminated nocardiosis caused by N. concava with multiple abscesses in the lungs, cutis, subcutaneous tissue, skeletal muscles and kidneys accompanied by central nervous system involvement, including meningitis and ventriculitis. The patient was cured with appropriate treatment including linezolid after testing for susceptibility. Linezolid should be considered as an alternative agent for treating disseminated nocardiosis because of its effective distribution to multiple sites.

[Problems in the diagnosis of ornithosis]

The paper describes 3 cases of ornithosis that could be detected by clinical and laboratory studies using immunological assays. In one case, its diagnosis was made late when the infection occurred in a woman working in a travel agency in Cyprus. The two other cases having an occupational contact (pet shop workers) were observed to have its acute form. All the described cases showed lung involvement characterized by external respiratory failure, one of the most common manifestations of ornithosis (psittacosis). Among the practically used laboratory tests, the indirect hemagglutination reaction is an accessible and effective serological assay for the diagnosis of ornithosis.

[Clinical features and course of patients with tuberculosis requiring intensive care]

BACKGROUND

To describe the characteristics of patients with tuberculosis (TB) requiring intensive care and to identify the risk factors for mortality.

METHODS

We conducted a retrospective, cohort study, between January 2006 and December 2009. The patients with TB, admitted in Pneumology Clinic Hospital, Iasi, requiring advanced life support in intensive care unit (ICU), were included. We assessed different clinical parameters to identify the factors that predict in-hospital mortality. The primary outcome was the in-hospital mortality.

RESULTS

During the study period, 27 patients with TB required intensive care. Of them, 16 (59.3%) had acute respiratory failure and 6 (22.2%) required mechanical ventilation. Eighteen (66.7%) patients died. Acute respiratory failure, acute hepatic failure and mechanical ventilation significantly correlate with a high in-hospital mortality rate.

CONCLUSIONS

In this study we found a high mortality rate in TB patients requiring intensive care, identifying some risk factors.

Common association of haemolytic uraemic syndrome with invasive Streptococcus pneumoniae infection in five Chinese paediatric patients

Haemolytic uraemic syndrome is an important cause of acute renal impairment in childhood. We review the incidence, and clinical and laboratory features of haemolytic uraemic syndrome in a Chinese population. Five patients were identified from 2006 to 2008. All patients were young children with associated invasive Streptococcus pneumoniae pulmonary infection. Serotypes 3, 14, and 19A were confirmed in four patients. The classical post-diarrhoeal form associated with Escherichia coli (O157:H7) infection was not seen. One patient died of acute respiratory failure. Streptococcus pneumoniae infection, as an associated condition in haemolytic uraemic syndrome, is important and relatively common in Chinese patients, especially among children. The acute clinical picture is similar to that reported in the western literature, except for an uncommon association with meningitis. The medium-term renal outcome of the Chinese population appears to be more favourable than the Caucasians. Widespread vaccination against Streptococcus pneumoniae may have resulted in changes in bacterial epidemiology and clinicians should be continuously aware of this severe disease. The use of washed blood components for transfusion in the acute stage requires further study.

Large-area burns with pandrug-resistant Pseudomonas aeruginosa infection and respiratory failure

BACKGROUND

Infection due to pandrug-resistant Pseudomonas aeruginosa (PDRPA) has become a challenge in clinical practice. The aim of this research was to summarize the treatment of large-area burns (60% - 80%) with PDRPA infection and respiratory failure in our hospital over the last two years, and to explore a feasible treatment protocol for such patients.

METHODS

We retrospectively analyzed the treatment of five patients with large-area burns accompanied by PDRPA infection and respiratory failure transferred to our hospital from burn units in hospitals in other Chinese cities from January 2008 to February 2010. Before PDRPA infection occurred, all five patients had open wounds with large areas of granulation because of the failure of surgery and dissolving of scar tissue; they had also undergone long-term administration of carbapenems. This therapy included ventilatory support, rigorous repair of wounds, and combined antibiotic therapy targeted at drug-resistance mechanisms, including carbapenems, ciprofloxacin, macrolide antibiotics and β-lactamase inhibitors.

RESULTS

Four patients recovered from burns and one died after therapy.

CONCLUSIONS

First, compromised immunity caused by delayed healing of burn wounds in patients with large-area burns and long-term administration of carbapenems may be the important factors in the initiation and progression of PDRPA infection. Second, if targeted at drug-resistance mechanisms, combined antibiotic therapy using carbapenems, ciprofloxacin, macrolide antibiotics and β-lactamase inhibitors could effectively control PDRPA infection. Third, although patients with large-area burns suffered respiratory failure and had high risks from anesthesia and surgery, only aggressive skin grafting with ventilatory support could control the infection and save lives. Patients may not be able to tolerate a long surgical procedure, so the duration of surgery should be minimized, and the frequency of surgery increased.

Clinical outcomes and prognostic factors in patients with tuberculous destroyed lung

OBJECTIVE

To characterise the prognosis and identify factors contributing to mortality in patients with tuberculous destroyed lung (TDL).

DESIGN

Following a retrospective review of clinical data and radiographic findings, 169 patients with TDL were enrolled in this study. All patients were graded on a 4-point scale (field score 1-4) based on the extent of destroyed lung parenchyma on chest radiography.

RESULTS

The mean patient age was 64 years (range 33-90); 103 (61%) were male. The median number of hospitalisations was 1 (range 0-11) during follow-up, with a mean duration of 31 months (range 0-172). Pneumonia developed in 96 patients (57%), while 50 patients (30%) developed acute respiratory failure requiring mechanical ventilation, 37 (22%) haemoptysis, 24 (14%) spontaneous pneumothorax and 22 (13%) reactivation of tuberculosis. Overall mortality was 28% (47/169), with a median survival of 39 months (range 0-176) after diagnosis. TDL-related mortality was 19% (32/169), and a field score ≥ 3 was the only independent predictor of shorter survival based on a Cox proportional hazards model (HR 3.520, 95%CI 1.51-8.20, P = 0.004).

CONCLUSION

TDL has a poor prognosis, particularly in patients with more extensive lung destruction.

[Malignant pertussis: an underdiagnosed illness]

PURPOSE

Malignant pertussis is a rare life-threatening illness characterized by severe respiratory failure, severe leukocytosis, and pulmonary hypertension. The purpose of this study was to determine the prevalence of malignant pertussis in infants admitted to a pediatric intensive care unit (PICU) for severe acute respiratory failure associated with severe leukocytosis.

METHODS

This retrospective study was based on review of the medical charts of infants aged less than 3 months admitted to the PICU between 2006 and 2008 for severe acute respiratory failure requiring mechanical ventilation with leukocytosis greater than 50,000/mm3. Clinical and laboratory data were collected. Polymerase chain reaction (PCR) for detection of Bordetella pertussis was performed on nasopharyngeal washes (NPW) stored at -70 degrees C.

RESULTS

Ten patients meeting inclusion criteria were identified. Median age was 2.1 months (range, 0.6 - 3). None of the infants had been vaccinated against pertussis. Although PCR for pertussis was positive in all ten cases, presumptive diagnosis was made in only 3 patients during hospitalization. Nine patients died within a mean of 4.7 +/- 3.3 days after admission. The cause of death was refractory shock and hypoxemia in all cases. Only one patient survived.

CONCLUSION

Malignant pertussis is a severe disease that is almost always fatal. It was underdiagnosed in our PICU. Use of PCR for detection of B. pertussis, i.e., the reference method, should be promoted in developing countries.