Multi-Omics Study of Keystone Species in a Cystic Fibrosis Microbiome.

Ecological networking and in vitro studies predict that anaerobic, mucus-degrading bacteria are keystone species in cystic fibrosis (CF) microbiomes. The metabolic byproducts from these bacteria facilitate the colonization and growth of CF pathogens like Pseudomonas aeruginosa. Here, a multi-omics study informed the control of putative anaerobic keystone species during a transition in antibiotic therapy of a CF patient. A quantitative metagenomics approach combining sequence data with epifluorescence microscopy showed that during periods of rapid lung function loss, the patient's lung microbiome was dominated by the anaerobic, mucus-degrading bacteria belonging to Streptococcus, Veillonella, and Prevotella genera. Untargeted metabolomics and community cultures identified high rates of fermentation in these sputa, with the accumulation of lactic acid, citric acid, and acetic acid. P. aeruginosa utilized these fermentation products for growth, as indicated by quantitative transcriptomics data. Transcription levels of P. aeruginosa genes for the utilization of fermentation products were proportional to the abundance of anaerobic bacteria. Clindamycin therapy targeting Gram-positive anaerobes rapidly suppressed anaerobic bacteria and the accumulation of fermentation products. Clindamycin also lowered the abundance and transcription of P. aeruginosa, even though this patient's strain was resistant to this antibiotic. The treatment stabilized the patient's lung function and improved respiratory health for two months, lengthening by a factor of four the between-hospitalization time for this patient. Killing anaerobes indirectly limited the growth of P. aeruginosa by disrupting the cross-feeding of fermentation products. This case study supports the hypothesis that facultative anaerobes operated as keystone species in this CF microbiome. Personalized multi-omics may become a viable approach for routine clinical diagnostics in the future, providing critical information to inform treatment decisions.

Proven COVID-19-associated pulmonary aspergillosis in patients with severe respiratory failure.

BACKGROUND: An increasing number of reports have described the COVID-19-associated pulmonary aspergillosis (CAPA) as being a further contributing factor to mortality. Based on a recent consensus statement supported by international medical mycology societies, it has been proposed to define CAPA as possible, probable, or proven on the basis of sample validity and thus diagnostic certainty. Considering current challenges associated with proven diagnoses, there is pressing need to study the epidemiology of proven CAPA. METHODS: We report the incidence of histologically diagnosed CAPA in a series of 45 consecutive COVID-19 laboratory-confirmed autopsies, performed at Padova University Hospital during the first and second wave of the pandemic. Clinical data, laboratory data and radiological features were also collected for each case. RESULTS: Proven CAPA was detected in 9 (20%) cases, mainly in the second wave of the pandemic (7/17 vs. 2/28 of the first wave). The population of CAPA patients consisted of seven males and two females, with a median age of 74 years. Seven patients were admitted to the intensive care unit. All patients had at least two comorbidities, and concomitant lung diseases were detected in three cases. CONCLUSION: We found a high frequency of proven CAPA among patients with severe COVID-19 thus confirming at least in part the alarming epidemiological data of this important complication recently reported as probable CAPA.

Bronchoalveolar lavage fluid analysis and mortality risk in systemic lupus erythematosus patients with pneumonia and respiratory failure.

BACKGROUND: Our aim was to characterize etiologic diagnoses obtained from bronchoalveolar lavage fluid (BALF) and blood specimens, and to identify risk factors for mortality in systemic lupus erythematosus (SLE) patients with pneumonia and respiratory failure. METHODS: We conducted a retrospective analysis of SLE patients with pneumonia and respiratory failure. Clinical characteristics, laboratory profiles, and microbiology in BALF and blood samples were evaluated. We performed univariable analyses to identify mortality risk factors. RESULTS: All 24 patients (F:M = 21:3, median age 46.5 years; disease duration 11 years) received mechanical ventilation (median duration: 11 days). Pathogens identified in BALF included Pneumocystis jiroveci (12 patients [50%]), cytomegalovirus (CMV, 7 patients [29.2%]), and bacteria (11 patients [45.8%]). Thirteen patients (54.2%) yielded pathogens in blood (CMV in 8 patients [33.3%] and Escherichia coli in 5 patients [20.8%]). Eight developed septic shock, and 9 died within 30 days. Univariable analysis identified thrombocytopenia (odds ratio [OR]: 8.0, 95% confidence interval [CI]: 1.23-52.25), bacteremia within 30 days before or after endotracheal intubation (OR: 8.0, 95% CI: 1.23-52.5), and P. jiroveci pneumonia (PJP, OR: 7.0, 95% CI: 1.04-46.95) as risk factors for 30-day mortality. Kaplan-Meier analysis confirmed an increased risk of 30-day mortality with thrombocytopenia and bacteremia. CONCLUSION: There are high prevalence rates of PJP and CMV infections as evidenced by BALF analyses in SLE patients with pneumonia and respiratory failure. BALF analysis can facilitate rescue therapy per pathogen. Thrombocytopenia, bacteremia, and PJP in SLE patients can increase their 30-day mortality, so warrant early and aggressive treatments.

Autopsy imaging for aspergillosis in King Penguin, an economically valuable zoo animal.

Autopsy imaging (Ai) was performed for a King Penguin. Ai-computed tomography (CT) revealed air sac membrane thickening, multiple nodules in the cranial air sac, suspected abscess, lung infiltration, and air sac contraction. Based on these findings, respiratory disorder was concerned. Aspergillosis, which is the highly observed in penguins, was considered as the primary differential diagnosis. The cultured sample showed characteristic conidial head of Aspergillus spp., the DNA of which was 100% identical to that of A. fumigatus. The cause of death was determined to respiratory failure due to aspergillosis. Ai-CT findings facilitated the dissection workflow and alerted the pathologist to potential hazards during the autopsy. Ai is useful to determine the cause of death and for readiness and safe pathological dissection.

Transient parkinsonism associated with acute Legionnaires' disease.

A 44-year-old right-handed man with a 5-day history of non-productive cough associated with subjective fevers/chills and night sweats presented to the emergency department with slurred speech. Radiography and urine antigen testing confirmed the diagnosis of Legionella pneumonia The hospital course was complicated by acute hypoxic respiratory failure that required 7 days of invasive mechanical ventilation. Following extubation, the patient had dysarthria and developed new parkinsonism features. Brain imaging revealed a non-specific focal lesion in the left frontal lobe of unclear significance. Ciprofloxacin was decided as the final antibiotic of choice for its favourable central nervous system profile. Levodopa-carbidopa was initiated to help activate the basal ganglia. The patient had complete resolution of pneumonia and transient parkinsonism. He was able to regain most of his baseline functional status with intensive rehabilitation.

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.

Meningeal rheumatoid nodules in a 55-year-old man presenting with chronic headaches and oculomotor nerve palsy: an uncommon extra-articular manifestation of rheumatoid arthritis.

Rheumatoid arthritis (RA) is a multisystem inflammatory disease which can involve many organ systems including the central nervous system (CNS). Though not very common, the results can be severely debilitating. The spectrum of the CNS involvement includes meningitis, encephalitis and occasionally rheumatoid nodules. Its presentation is variable, though very rarely it can present as focal neurological deficits. Imaging can be suggestive, but diagnosis usually requires tissue biopsy. Treatment consists of high-dose steroids and immunosuppressants. We describe the case of a 55-year-old male patient with a history of RA presenting with a third nerve palsy and headache who was found to have rheumatoid nodules on biopsy. CNS involvement in RA should be considered in anyone with rheumatoid arthritis who presents with focal neurological deficits, though infections and space-occupying lesions should also be ruled out.

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.

Outcome and Management of Refractory Respiratory Failure With Timely Extracorporeal Membrane Oxygenation: Single-Center Experience With Legionella Pneumonia.

OBJECTIVE:: To analyze the management and outcome of patients with refractory respiratory failure complicating severe Legionella pneumonia rescued with extracorporeal membrane oxygenation (ECMO) in our Center. DESIGN AND SETTING:: Observational study of patients with refractory respiratory failure treated with ECMO in Hospital S.João (Porto, Portugal), between November 2009 and September 2016. PARTICIPANTS:: A total of 112 patients rescued with ECMO, of which 14 had Legionella pneumonia. RESULTS:: Patients with Legionella pneumonia were slightly older than patients with acute respiratory failure of other etiologies (51 [48-56] vs 45 [35-54]), but with no significant differences in acute respiratory failure severity between groups: Pao2/Fio2 ratio 67 (60-75) versus 69 (55-85) and Respiratory Extracorporeal Membrane Oxygenation Survival Prediction score 4 (1-5) versus 2 (-1-4), respectively. Legionella pneumonia was associated with earlier ECMO initiation (days of invasive mechanical ventilation [IMV] before ECMO: 2.0 [1.0-4.0] vs 5.0 [2.0-9.5]). After IMV adjustment to "lung rest" settings, this group presented higher respiratory system (RS) static compliance (28.7 [18.8-37.4] vs 16.0 [10.0-20.8] mL/cmH2O) but required higher ECMO support (blood flow 5.0 [4.3-5.4] vs 4.2 [3.6-4.8]). Patients with Legionella pneumonia had shorter IMV (16 [14-23] vs 27 [20-42] days) and lower incidence of intensive care unit nosocomial infections (35.7% vs 64.3%), with a trend to higher hospital survival (85.7% vs 62.2%; P = .13). CONCLUSION:: In Legionella pneumonia complicated by refractory respiratory failure, ECMO support allowed patient stabilization under lung protective ventilation and high survival rates. Timely ECMO referral should be considered for Legionella pneumonia failing conventional treatment.

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.

Herpes zoster complicated by phrenic nerve palsy and respiratory compromise.

BACKGROUND: Herpes zoster can be associated with severe neurological complications. CASE PRESENTATION: In this article, we describe the case of a 54-year-old man with herpes zoster affecting his right upper chest and neck region complicated by phrenic nerve palsy and respiratory compromise. The diagnosis of herpes zoster was made based on the classic appearance of the rash and associated neuropathic-type pain. The diagnosis of phrenic nerve palsy was made by chest x-ray and ultrasound. CONCLUSION: Clinicians should be aware of the possibility of phrenic nerve palsy occurring in patients who have herpes zoster affecting the region of C3,4,5 dermatomes. Although symptoms of unilateral diaphragmatic paresis are usually mild, in patients with obesity or comorbid lung disease, new onset phrenic nerve palsy can lead to significant respiratory compromise.

Severe Acute Respiratory Infection (SARI) sentinel surveillance in the country of Georgia, 2015-2017.

BACKGROUND: Severe Acute Respiratory Infection (SARI) causes substantial mortality and morbidity worldwide. The country of Georgia conducts sentinel surveillance to monitor SARI activity and changes in its infectious etiology. This study characterizes the epidemiology of SARI in Georgia over the 2015/16 and 2016/17 influenza seasons, compares clinical presentations by etiology, and estimates influenza vaccine effectiveness using a test-negative design. METHODS: SARI cases were selected through alternate day systematic sampling between September 2015 and March 2017 at five sentinel surveillance inpatient sites. Nasopharyngeal swabs were tested for respiratory viruses and Mycoplasma pneumoniae using a multiplex diagnostic system. We present SARI case frequencies by demographic characteristics, co-morbidities, and clinical presentation, and used logistic regression to estimate influenza A vaccine effectiveness. RESULTS: 1,624 patients with SARI were identified. More cases occurred in February (28.7%; 466/1624) than other months. Influenza was the dominant pathogen in December-February, respiratory syncytial virus in March-May, and rhinovirus in June-November. Serious clinical symptoms including breathing difficulties, ICU hospitalization, and artificial ventilation were common among influenza A and human metapneumovirus cases. For influenza A/H3, a protective association between vaccination and disease status was observed when cases with unknown vaccination status were combined with those who were unvaccinated (OR: 0.53, 95% CI: 0.30, 0.97). CONCLUSIONS: Multi-pathogen diagnostic testing through Georgia's sentinel surveillance provides useful information on etiology, seasonality, and demographic associations. Influenza A and B were associated with more severe outcomes, although the majority of the population studied was unvaccinated. Findings from sentinel surveillance can assist in prevention planning.

Neisseria meningitidis sepsis in a patient with acute epiglottitis and respiratory failure.

A 78-year-old female patient presented to our emergency department with a 5-day history of throat pain, hoarseness and a progressive and dolorous submandibular swelling. Due to non-conclusive clinical examination and the stable but visibly affected patient, we performed a neck CT scan with intravenous contrast, which showed the thumbprint sign typical for acute epiglottitis. Within minutes, the patient's condition deteriorated and the patient was close to respiratory exhaustion. As intubation was severely complicated by massive swelling of the supraglottic soft tissue, the patient went into hypoxaemia and eventually cardiac arrest. After initiating reanimation protocol, eventually the airway was secured and Return of spontaneous circulation (ROSC) achieved after around 5 min. The initially sampled blood cultures revealed Neisseria meningitidis bactera emia and the patient was successfully treated accordingly. In patients with swelling of the upper airway, rapid clinical deterioration is possible. Diagnostics should not delay therapy, including administration of empiric antibiotics, steroids and intubation.

Microbiologic Diagnostic Workup of Acute Respiratory Failure with Pulmonary Infiltrates after Allogeneic Hematopoietic Stem Cell Transplantation: Findings in the Era of Molecular- and Biomarker-Based Assays.

Allogeneic hematopoietic stem cell transplantation (HSCT) recipients frequently develop acute respiratory failure (ARF) with pulmonary infiltrates. Molecular- and biomarker-based assays enhance pathogen detection, but data on their yield in this population are scarce. This was a retrospective single-center study of 156 consecutive HSCT recipients admitted to the intensive care unit (ICU) between May 2013 and July 2017. Findings from a microbiologic diagnostic workup using currently available methods on bronchoalveolar lavage (BAL) and blood samples from 66 patients (age, 58 years [range, 45 to 64]; HSCT to ICU, 176 days [range, 85 to 407]) with ARF and pulmonary infiltrates were analyzed. In 47 patients (71%) a causative pathogen was identified (fungal, n = 28; viral, n = 26; bacterial, n = 18). Polymicrobial findings involving several pathogen groups occurred in 20 patients (30%). Culture (12/16, 75%), galactomannan (13/15, 87%), and Aspergillus-PCR (8/9, 89%) from BAL but not serum galactomannan (6/14, 43%) helped to diagnose invasive aspergillosis (n = 16, 24%). Aspergillus-PCR detected azole resistance in 2 cases. Mucorales was found in 7 patients (11%; BAL culture, n = 6; Mucorales-PCR, n = 1). Patients with identified pathogens had higher Simplified Acute Physiology Score II scores (P = .049) and inferior ICU survival (6% versus 37%, P < .01), which largely related to the presence of an invasive fungal infection. Eight patients (12%) had 1 or more viruses with uncertain lung pathogenicity as the sole microbiologic finding. A diagnostic microbiologic workup incorporating molecular- and biomarker-based assays identified pathogens in most HSCT recipients with ARF and pulmonary infiltrates admitted to the ICU. Implications of polymicrobial infection and pathogen patterns in these patients warrant further investigation.