Lymphopenia is associated with broad host response aberrations in community-acquired pneumonia.

OBJECTIVES: Lymphopenia at hospital admission occurs in over one-third of patients with community-acquired pneumonia (CAP), yet its clinical relevance and pathophysiological implications remain underexplored. We evaluated outcomes and immune features of patients with lymphopenic CAP (L-CAP), a previously described immunophenotype characterized by admission lymphocyte count <0.724 × 109 cells/L. METHODS: Observational study in 149 patients admitted to a general ward for CAP. We measured 34 plasma biomarkers reflective of inflammation, endothelial cell responses, coagulation, and immune checkpoints. We characterized lymphocyte phenotypes in 29 patients using spectral flow cytometry. RESULTS: L-CAP occurred in 45 patients (30.2%) and was associated with prolonged time-to-clinical-stability (median 5 versus 3 days), also when we accounted for competing events for reaching clinical stability and adjusted for baseline covariates (subdistribution hazard ratio 0.63; 95% confidence interval 0.45-0.88). L-CAP patients demonstrated a proportional depletion of CD4 T follicular helper cells, CD4 T effector memory cells, naïve CD8 T cells and IgG+ B cells. Plasma biomarker analyses indicated increased activation of the cytokine network and the vascular endothelium in L-CAP. CONCLUSIONS: L-CAP patients have a protracted clinical recovery course and a more broadly dysregulated host response. These findings highlight the prognostic and pathophysiological relevance of admission lymphopenia in patients with CAP.

Pneumonia pattern recognition on ultra-low-dose CT does not allow for a reliable differentiation between viral and bacterial pneumonia: A multicentre observer study.

PURPOSE: While a reliable differentiation between viral and bacterial pneumonia is not possible with chest X-ray, this study investigates whether ultra-low-dose chest-CT (ULDCT) could be used for this purpose. METHODS: In the OPTIMACT trial 281 patients had a final diagnosis of pneumonia, and 96/281 (34%) had one or more positive microbiology results: 60 patients viral pathogens, 48 patients bacterial pathogens. These 96 ULDCT's were blindly and independently evaluated by two chest radiologists, who reported CT findings, pneumonia pattern, and most likely type of pathogen. Differences between groups were analysed for each radiologist separately, diagnostic accuracy was evaluated by calculating sensitivity. RESULTS: The dominant CT finding significantly differed between the viral and bacterial pathogen groups (p = 0.04; p = 0.04). Consolidation was the most frequent dominant CT finding in both patients with viral and bacterial pathogens, but was observed significantly more often in those with a bacterial pathogen: 32/60 and 22/60 versus 38/48 and 31/48 (p = 0.005; p = 0.004). The lobar pneumonia pattern was more frequently observed in patients with a bacterial pathogen: 23/48 and 18/48, versus 10/60 and 8/60 for viral pathogens (p < 0.001; p = 0.004). For the bronchopneumonia and interstitial pneumonia patterns the proportions of viral and bacterial pathogens were not significantly different. Both radiologists suggested a viral pathogen correctly (sensitivity) in 6/60 (10%), for a bacterial pathogen this was 34/48 (71%). CONCLUSION: Reliable differentiation between viral and bacterial pneumonia could not be made by pattern recognition on ULDCT, although a lobar pneumonia pattern was significantly more often observed in bacterial infection.

Plasma protein biomarkers reflective of the host response in patients developing Intensive Care Unit-acquired pneumonia.

BACKGROUND: Immune suppression has been implicated in the occurrence of pneumonia in critically ill patients. We tested the hypothesis that Intensive Care Unit (ICU)-acquired pneumonia is associated with broad host immune aberrations in the trajectory to pneumonia, encompassing inflammatory, endothelial and coagulation responses. We compared plasma protein biomarkers reflecting the systemic host response in critically ill patients who acquire a new pneumonia (cases) with those who do not (controls). METHODS: We performed a nested case-control study in patients undergoing mechanical ventilation at ICU admission with an expected stay of at least 48 h enrolled in 30 hospitals in 11 European countries. Nineteen host response biomarkers reflective of key pathophysiological domains were measured in plasma obtained on study inclusion and day 7, and-in cases-on the day of pneumonia diagnosis. RESULTS: Of 1997 patients, 316 developed pneumonia (15.8%) and 1681 did not (84.2%). Plasma protein biomarker analyses, performed in cases and a randomly selected subgroup of controls (1:2 ratio to cases, n = 632), demonstrated considerable variation across time points and patient groups. Yet, cases showed biomarker concentrations suggestive of enhanced inflammation and a more disturbed endothelial barrier function, both at study enrollment (median 2 days after ICU admission) and in the path to pneumonia diagnosis (median 5 days after ICU admission). Baseline host response biomarker aberrations were most profound in patients who developed pneumonia either shortly (< 5 days, n = 105) or late (> 10 days, n = 68) after ICU admission. CONCLUSIONS: Critically ill patients who develop an ICU-acquired pneumonia, compared with those who do not, display alterations in plasma protein biomarker concentrations indicative of stronger proinflammatory, procoagulant and (injurious) endothelial cell responses. TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT02413242, posted April 9th, 2015.

Limited Clinical Impact of Ultralow-Dose Computed Tomography in Suspected Community-Acquired Pneumonia.

Patients clinically suspected of community-acquired pneumonia (CAP) were randomized between ultralow-dose chest computed tomography ([ULDCT] 261 patients) and chest radiograph ([CXR] 231 patients). We did not find evidence that performing ULDCT instead of CXR affects antibiotic treatment policy or patient outcomes. However, in a subgroup of afebrile patients, there were more patients diagnosed with CAP in the ULDCT group (ULDCT, 106 of 608 patients; CXR, 71 of 654 patients; P = .001).

The yield of chest X-ray or ultra-low-dose chest-CT in emergency department patients suspected of pulmonary infection without respiratory symptoms or signs.

OBJECTIVE: The yield of pulmonary imaging in patients with suspected infection but no respiratory symptoms or signs is probably limited, ultra-low-dose CT (ULDCT) is known to have a higher sensitivity than Chest X-ray (CXR). Our objective was to describe the yield of ULDCT and CXR in patients clinically suspected of infection, but without respiratory symptoms or signs, and to compare the diagnostic accuracy of ULDCT and CXR. METHODS: In the OPTIMACT trial, patients suspected of non-traumatic pulmonary disease at the emergency department (ED) were randomly allocated to undergo CXR (1210 patients) or ULDCT (1208 patients). We identified 227 patients in the study group with fever, hypothermia, and/or elevated C-reactive protein (CRP) but no respiratory symptoms or signs, and estimated ULDCT and CXR sensitivity and specificity in detecting pneumonia. The final day-28 diagnosis served as the clinical reference standard. RESULTS: In the ULDCT group, 14/116 (12%) received a final diagnosis of pneumonia, versus 8/111 (7%) in the CXR group. ULDCT sensitivity was significantly higher than that of CXR: 13/14 (93%) versus 4/8 (50%), a difference of 43% (95% CI: 6 to 80%). ULDCT specificity was 91/102 (89%) versus 97/103 (94%) for CXR, a difference of - 5% (95% CI: - 12 to 3%). PPV was 54% (13/24) for ULDCT versus 40% (4/10) for CXR, NPV 99% (91/92) versus 96% (97/101). CONCLUSION: Pneumonia can be present in ED patients without respiratory symptoms or signs who have a fever, hypothermia, and/or elevated CRP. ULDCT's sensitivity is a significant advantage over CXR when pneumonia has to be excluded. CLINICAL RELEVANCE STATEMENT: Pulmonary imaging in patients with suspected infection but no respiratory symptoms or signs can result in the detection of clinically significant pneumonia. The increased sensitivity of ultra-low-dose chest CT compared to CXR is of added value in vulnerable and immunocompromised patients. KEY POINTS: • Clinical significant pneumonia does occur in patients who have a fever, low core body temperature, or elevated CRP without respiratory symptoms or signs. • Pulmonary imaging should be considered in patients with unexplained symptoms or signs of infections. • To exclude pneumonia in this patient group, ULDCT's improved sensitivity is a significant advantage over CXR.

Ultra-low-dose CT versus chest X-ray for patients suspected of pulmonary disease at the emergency department: a multicentre randomised clinical trial.

BACKGROUND: Chest CT displays chest pathology better than chest X-ray (CXR). We evaluated the effects on health outcomes of replacing CXR by ultra-low-dose chest-CT (ULDCT) in the diagnostic work-up of patients suspected of non-traumatic pulmonary disease at the emergency department. METHODS: Pragmatic, multicentre, non-inferiority randomised clinical trial in patients suspected of non-traumatic pulmonary disease at the emergency department. Between 31 January 2017 and 31 May 2018, every month, participating centres were randomly allocated to using ULDCT or CXR. Primary outcome was functional health at 28 days, measured by the Short Form (SF)-12 physical component summary scale score (PCS score), non-inferiority margin was set at 1 point. Secondary outcomes included hospital admission, hospital length of stay (LOS) and patients in follow-up because of incidental findings. RESULTS: 2418 consecutive patients (ULDCT: 1208 and CXR: 1210) were included. Mean SF-12 PCS score at 28 days was 37.0 for ULDCT and 35.9 for CXR (difference 1.1; 95% lower CI: 0.003). After ULDCT, 638/1208 (52.7%) patients were admitted (median LOS of 4.8 days; IQR 2.1-8.8) compared with 659/1210 (54.5%) patients after CXR (median LOS 4.6 days; IQR 2.1-8.8). More ULDCT patients were in follow-up because of incidental findings: 26 (2.2%) versus 4 (0.3%). CONCLUSIONS: Short-term functional health was comparable between ULDCT and CXR, as were hospital admissions and LOS, but more incidental findings were found in the ULDCT group. Our trial does not support routine use of ULDCT in the work-up of patients suspected of non-traumatic pulmonary disease at the emergency department. TRIAL REGISTRATION NUMBER: NTR6163.

The host response in different aetiologies of community-acquired pneumonia.

BACKGROUND: Community-acquired pneumonia (CAP) can be caused by a variety of pathogens, of which Streptococcus pneumoniae, Influenza and currently SARS-CoV-2 are the most common. We sought to identify shared and pathogen-specific host response features by directly comparing different aetiologies of CAP. METHODS: We measured 72 plasma biomarkers in a cohort of 265 patients hospitalized for CAP, all sampled within 48 hours of admission, and 28 age-and sex matched non-infectious controls. We stratified the biomarkers into several pathophysiological domains- antiviral response, vascular response and function, coagulation, systemic inflammation, and immune checkpoint markers. We directly compared CAP caused by SARS-CoV-2 (COVID-19, n=39), Streptococcus pneumoniae (CAP-strep, n=27), Influenza (CAP-flu, n=22) and other or unknown pathogens (CAP-other, n=177). We adjusted the comparisons for age, sex and disease severity scores. FINDINGS: Biomarkers reflective of a stronger cell-mediated antiviral response clearly separated COVID-19 from other CAPs (most notably granzyme B). Biomarkers reflecting activation and function of the vasculature showed endothelial barrier integrity was least affected in COVID-19, while glycocalyx degradation and angiogenesis were enhanced relative to other CAPs. Notably, markers of coagulation activation, including D-dimer, were not different between the CAP groups. Ferritin was most increased in COVID-19, while other systemic inflammation biomarkers such as IL-6 and procalcitonin were highest in CAP-strep. Immune checkpoint markers showed distinctive patterns in viral and non-viral CAP, with highly elevated levels of Galectin-9 in COVID-19. INTERPRETATION: Our investigation provides insight into shared and distinct pathophysiological mechanisms in different aetiologies of CAP, which may help guide new pathogen-specific therapeutic strategies. FUNDING: This study was financially supported by the Dutch Research Council, the European Commission and the Netherlands Organization for Health Research and Development.

Association between dexamethasone treatment and the host response in COVID-19 patients admitted to the general ward.

Dexamethasone improves clinical outcomes in COVID-19 patients requiring supplementary oxygen. We investigated possible mechanisms of action by comparing sixteen plasma host response biomarkers in general ward patients before and after implementation of dexamethasone as standard of care. 48 patients without and 126 patients with dexamethasone treatment were sampled within 48 h of admission. Endothelial cell and coagulation activation biomarkers were comparable. Dexamethasone treatment was associated with lower plasma interleukin (IL)-6 and IL-1 receptor antagonist levels, whilst other inflammation parameters were not affected. These data argue against modification of vascular-procoagulant responses as an early mechanism of action of dexamethasone in COVID-19.

Association of Hyperferritinemia With Distinct Host Response Aberrations in Patients With Community-Acquired Pneumonia.

BACKGROUND: Strongly elevated ferritin levels have been proposed to reflect systemic hyperinflammation in patients admitted to the intensive care unit. Knowledge of the incidence and pathophysiological implications of hyperferritinemia in patients with acute infection admitted to a non-intensive care setting is limited. METHODS: We determined the association between hyperferritinemia, defined by 2 cutoff values (500 and 250 ng/mL), and aberrations in key host response mechanisms among patients with community-acquired pneumonia (CAP) on admission to a general hospital ward (clinicaltrials.gov NCT02928367; trialregister.nl NTR6163). RESULTS: Plasma ferritin levels were higher in patients with CAP (n = 174; median [interquartile ranges], 259.5 [123.1-518.3] ng/mL) than in age- and sex-matched controls without infection (n = 50; 102.8 [53.5-185.7] ng/mL); P < .001); they were ≥500 ng/mL in 46 patients (26%) and ≥250 ng/mL in 90 (52%). Measurements of 26 biomarkers reflective of distinct pathophysiological domains showed that hyperferritinemia was associated with enhanced systemic inflammation, neutrophil activation, cytokine release, endothelial cell activation and dysfunction, and activation of the coagulation system. Results were robust across different cutoff values. CONCLUSIONS: Hyperferritinemia identifies patients with CAP with a broad deregulation of various host response mechanisms implicated in the pathogenesis of sepsis. This could inform future therapeutic strategies targeting subgroups within the CAP population.

Gut Microbiome Modulation by Antibiotics in Adult Asthma: A Human Proof-of-Concept Intervention Trial.

Although the pathophysiology of asthma is complex, perturbation of the gut microbiota has been associated with an increased risk of asthma development in childhood.1 Disruption and subsequent dysregulation of gut microbiota-related immunologic processes have also been linked to disease severity and response to treatment.2.

Plasma Ferritin as Marker of Macrophage Activation-Like Syndrome in Critically Ill Patients With Community-Acquired Pneumonia.

OBJECTIVES: Plasma ferritin levels above 4,420 ng/mL have been proposed as a diagnostic marker for macrophage activation-like syndrome in sepsis and used for selection of sepsis patients for anti-inflammatory therapy. We here sought to determine the frequency, presentation, outcome, and host response aberrations of macrophage activation-like syndrome, as defined by admission ferritin levels above 4,420 ng/mL, in critically ill patients with community-acquired pneumonia. DESIGN: A prospective observational cohort study. SETTING: ICUs in two tertiary hospitals in the Netherlands. PATIENTS: One hundred fifty-three patients admitted with community-acquired pneumonia. MEASUREMENTS AND MAIN RESULTS: Patients were stratified in community-acquired pneumonia-macrophage activation-like syndrome (n = 15; 9.8%) and community-acquired pneumonia-control groups (n = 138; 90.2%) based on an admission plasma ferritin level above or below 4,420 ng/mL, respectively. Community-acquired pneumonia-macrophage activation-like syndrome patients presented with a higher disease severity and had a higher ICU mortality (46.7% vs 12.3% in community-acquired pneumonia-controls; p = 0.002). Twenty-three plasma biomarkers indicative of dysregulation of key host response pathways implicated in sepsis pathogenesis (systemic inflammation, cytokine responses, endothelial cell activation, and barrier function, coagulation activation) were more disturbed in community-acquired pneumonia-macrophage activation-like syndrome patients. Hematologic malignancies were overrepresented in community-acquired pneumonia-macrophage activation-like syndrome patients (33.3% vs 5.1% in community-acquired pneumonia-controls; p = 0.001). In a subgroup analysis excluding patients with hematologic malignancies (n = 141), differences in mortality were not present anymore, but the exaggerated host response abnormalities in community-acquired pneumonia-macrophage activation-like syndrome patients remained. CONCLUSIONS: Macrophage activation-like syndrome in critically ill patients with community-acquired pneumonia occurs more often in patients with hematologic malignancies and is associated with deregulation of multiple host response pathways.

Disruptions of Anaerobic Gut Bacteria Are Associated with Stroke and Post-stroke Infection: a Prospective Case-Control Study.

In recent years, preclinical studies have illustrated the potential role of intestinal bacterial composition in the risk of stroke and post-stroke infections. The results of these studies suggest that bacteria capable of producing volatile metabolites, including trimethylamine-N-oxide (TMAO) and butyrate, play opposing, yet important roles in the cascade of events leading to stroke. However, no large-scale studies have been undertaken to determine the abundance of these bacterial communities in stroke patients and to assess the impact of disrupted compositions of the intestinal microbiota on patient outcomes. In this prospective case-control study, rectal swabs from 349 ischemic and hemorrhagic stroke patients (median age, 71 years; IQR: 67-75) were collected within 24 h of hospital admission. Samples were subjected to 16S rRNA amplicon sequencing and subsequently compared with samples obtained from 51 outpatient age- and sex-matched controls (median age, 72 years; IQR, 62-80) with similar cardiovascular risk profiles but without active signs of stroke. Plasma protein biomarkers were analyzed using a combination of nuclear magnetic resonance (NMR) spectroscopy and liquid chromatography-mass spectrometry (LC-MS). Alpha and beta diversity analyses revealed higher disruption of intestinal communities during ischemic and hemorrhagic stroke compared with non-stroke matched control subjects. Additionally, we observed an enrichment of bacteria implicated in TMAO production and a loss of butyrate-producing bacteria. Stroke patients displayed two-fold lower plasma levels of TMAO than controls (median 1.97 vs 4.03 µM, Wilcoxon p < 0.0001). Finally, lower abundance of butyrate-producing bacteria within 24 h of hospital admission was an independent predictor of enhanced risk of post-stroke infection (odds ratio 0.77, p = 0.005), but not of mortality or functional patient outcome. In conclusion, aberrations in trimethylamine- and butyrate-producing gut bacteria are associated with stroke and stroke-associated infections.

The circular RNA landscape in specific peripheral blood mononuclear cells of critically ill patients with sepsis.

BACKGROUND: Dysregulation of the host immune response is a pathognomonic feature of sepsis. Abnormal physiological conditions are understood to shift efficient linear splicing of protein-coding RNA towards non-canonical splicing, characterized by the accumulation of non-coding circularized (circ)RNA. CircRNAs remain unexplored in specific peripheral blood mononuclear cells (PBMCs) during sepsis. We here sought to identify and characterize circRNA expression in specific PBMCs of patients with sepsis due to community-acquired pneumonia (CAP) relative to healthy subjects. METHODS: The study comprised a discovery cohort of six critically ill patients diagnosed with sepsis due to community-acquired pneumonia and four (age, gender matched) healthy subjects. PBMCs were isolated, and fluorescence-activated cell sorting was used to purify CD14+ monocytes, CD4+, CD8+ T cells, and CD19+ B cells for RNA sequencing. CD14+ monocytes from independent six healthy volunteers were purified, and total RNA was treated with or without RNase R. RESULTS: RNA sequencing of sorted CD14+ monocytes, CD4+, CD8+ T cells, and CD19+ B cells from CAP patients and healthy subjects identified various circRNAs with predominantly cell-specific expression patterns. CircRNAs were expressed to a larger extent in monocytes than in CD4+, CD8+ T cells, or B cells. Cells from CAP patients produced significantly higher levels of circRNA as compared to healthy subjects. Considering adjusted p values, circVCAN (chr5:83519349-83522309) and circCHD2 (chr15:93000512-93014909) levels in monocytes were significantly altered in sepsis. Functional inference per cell-type uncovered pathways mainly attuned to cell proliferation and cytokine production. In addition, our data does not support a role for these circRNAs in microRNA sequestration. Quantitative PCR analysis in purified monocytes from an independent group of healthy volunteers confirmed the existence of circVCAN and circCHD2. CONCLUSIONS: We provide a benchmark map of circRNA expression dynamics in specific immune cell subsets of sepsis patients secondary to CAP. CircRNAs were more abundant in immune cells of sepsis patients relative to healthy subjects. Further studies evaluating circRNA expression in larger cohorts of sepsis patients are warranted.

Classifying the diagnosis of study participants in clinical trials: a structured and efficient approach.

BACKGROUND: A challenge in imaging research is a diagnostic classification of study participants. We hypothesised that a structured approach would be efficient and that classification by medical students, residents, and an expert panel whenever necessary would be as valid as classification of all patients by experts. METHODS: OPTIMACT is a randomised trial designed to evaluate the effectiveness of replacing chest x-ray for ultra-low-dose chest computed tomography (CT) at the emergency department. We developed a handbook with diagnostic guidelines and randomly selected 240 cases from 2,418 participants enrolled in OPTIMACT. Each case was independently classified by two medical students and, if they disagreed, by the students and a resident in a consensus meeting. Cases without consensus and cases classified as complex were assessed by a panel of medical specialists. To evaluate the validity, 60 randomly selected cases not referred to the panel by the students and the residents were reassessed by the specialists. RESULTS: Overall, the students and, if necessary, residents were able to assign a diagnosis in 183 of the 240 cases (76% concordance; 95% confidence interval [CI] 71-82%). We observed agreement between students and residents versus medical specialists in 50/60 cases (83% concordance; 95% CI 74-93%). CONCLUSIONS: A structured approach in which study participants are assigned diagnostic labels by assessors with increasing levels of medical experience was an efficient and valid classification method, limiting the workload for medical specialists. We presented a viable option for classifying study participants in large-scale imaging trials (Netherlands National Trial Register number NTR6163).

OPTimal IMAging strategy in patients suspected of non-traumatic pulmonary disease at the emergency department: chest X-ray or ultra-low-dose chest CT (OPTIMACT) trial-statistical analysis plan.

BACKGROUND: A chest X-ray is a standard imaging procedure in the diagnostic work-up of patients suspected of having non-traumatic pulmonary disease. Compared to a chest X-ray, an ultra-low-dose (ULD) chest computed tomography (CT) scan provides substantially more detailed information on pulmonary conditions. To what extent this translates into an improvement in patient outcomes and health care efficiency is yet unknown. The OPTimal IMAging strategy in patients suspected of non-traumatic pulmonary disease at the emergency department: chest X-ray or ultra-low-dose chest CT (OPTIMACT) study is a multicenter, pragmatic, non-inferiority randomized controlled trial designed to evaluate replacement of chest X-ray by ULD chest CT in the diagnostic work-up of such patients, in terms of patient-related health outcomes and costs. During randomly assigned periods of 1 calendar month, either conventional chest X-ray or ULD chest CT scan was used as the imaging strategy. This paper presents in detail the statistical analysis plan of the OPTIMACT trial, developed prior to data analysis. METHODS/RESULTS: Functional health at 28 days is the primary clinical outcome. Functional health at 28 days is measured by the physical component summary scale of the Short Form (SF)-12 questionnaire version 1. Secondary outcomes are mental health (mental component summary scale of the SF-12), length of hospital stay, mortality within 28 days, quality-adjusted life year equivalent during the first 28 days (derived from the EuroQol five-dimension, five-level instrument), correct diagnoses at emergency department discharge as compared to the final post hoc diagnosis at day 28, number of patients in follow-up because of incidental findings on chest X-ray or ULD chest CT, and health care costs. CONCLUSIONS: After this pragmatic trial we will have precise estimates of the effectiveness of replacing chest X-ray with ULD chest CT in terms of patient-related health outcomes and costs. TRIAL REGISTRATION: Netherlands National Trial Register: NTR6163. Registered on 6 December 2016.

Impact of antimicrobial therapy on the gut microbiome.

The gut microbiome is now considered an organ unto itself and plays an important role in health maintenance and recovery from critical illness. The commensal organisms responsible for the framework of the gut microbiome are valuable in protection against disease and various physiological tasks. Critical illness and the associated interventions have a detrimental impact on the microbiome. While antimicrobials are one of the fundamental and often life-saving modalities in septic patients, they can also pave the way for subsequent harm because of the resulting damage to the gut microbiome. Contributing to many of the non-specific signs and symptoms of sepsis, the balance between the overuse of antimicrobials and the clinical need in these situations is often difficult to delineate. Given the potency of antimicrobials utilized to treat septic patients, the effects on the gut microbiome are often rapid and long-lasting, in which case full recovery may never be observed. The overgrowth of opportunistic pathogens is of significant concern as they can lead to infections that become increasingly difficult to treat. Continued research to understand the disturbances within the gut microbiome of critically ill patients and their outcomes is essential to help develop future therapies to circumvent damage to, or restore, the microbiome. In this review, we discuss the impact of the antimicrobials often used for the treatment of sepsis on the gut microbiota.