Predictive factors of true bacteremia and the clinical utility of blood cultures as a prognostic tool in patients with community-onset pneumonia

Characterizing the blood microbiota in healthy and febrile domestic cats via 16s rRNA sequencing

This study aimed to evaluate the blood bacterial microbiota in healthy and febrile cats. High-quality sequencing reads from the 16S rRNA gene variable region V3-V4 were obtained from genomic blood DNA belonging to 145 healthy cats, and 140 febrile cats. Comparisons between the blood microbiota of healthy and febrile cats revealed dominant presence of Actinobacteria, followed by Firmicutes and Proteobacteria, and a lower relative abundance of Bacteroidetes. Upon lower taxonomic levels, the bacterial composition was significantly different between healthy and febrile cats. The families Faecalibacterium and Kineothrix (Firmicutes), and Phyllobacterium (Proteobacteria) experienced increased abundance in febrile samples. Whereas Thioprofundum (Proteobacteria) demonstrated a significant decrease in abundance in febrile. The bacterial composition and beta diversity within febrile cats was different according to the affected body system (Oral/GI, systemic, skin, and respiratory) at both family and genus levels. Sex and age were not significant factors affecting the blood microbiota of febrile cats nor healthy ones. Age was different between young adult and mature adult healthy cats. Alpha diversity was unaffected by any factors. Overall, the findings suggest that age, health status and nature of disease are significant factors affecting blood microbiota diversity and composition in cats, but sex is not.

Positive Rate and Utility of Blood Culture among Nursing and Healthcare-associated Pneumonia Inpatients: A Cross-sectional Study

Objective Although blood cultures to identify the presence of bacteremia are recommended for nursing- and healthcare-associated pneumonia (NHCAP), the incidence of true bacteremia and the relationship between true bacteremia and the outcome remain unclear. Physicians can therefore sometimes be confused regarding whether or not blood cultures should be obtained for NHCAP patients. This study assessed the incidence of true bacteremia and the relationship between true bacteremia and the outcome of NHCAP in a Japanese hospital setting. Methods We retrospectively analyzed NHCAP patients hospitalized between April 2016 and March 2021. The primary outcome was the incidence of true bacteremia in blood cultures. The incidence of true bacteremia was also examined according to quick Sequential Organ Failure Assessment (qSOFA) and A-DROP scores. In addition, we compared the incidence of true bacteremia between survivors and non-survivors. Results In total, 205 patients were included in this study. Blood cultures were obtained from 150 of the 205 patients (73.2%). Positive blood cultures were detected in 26 patients (17.3%), of which only 8 cases (5.3%; 95% confidence interval, 2.3-10.2%) were considered true bacteremia. Trend analyses for the incidence of true bacteremia according to qSOFA and A-DROP scores did not show any statistically significant results (p=0.49 for qSOFA; p=0.14 for A-DROP). The proportion of true bacteremia cases did not differ significantly between survivors and non-survivors. Conclusions The incidence of true bacteremia among NHCAP patients was very low. A strategy for determining indications for obtaining blood cultures from NHCAP patients needs to be established.

Adherence to use of blood cultures according to current national guidelines and their impact in patients with community acquired pneumonia: A retrospective cohort

BACKGROUND

Community acquired pneumonia (CAP) is the most frequent cause of mortality secondary to infectious etiologies. Recommendations about the use of blood cultures in the diagnosis and treatment of CAP has been a contentious topic of debate and ever-changing recommendations.

METHODS

A cohort study was conducted in a community teaching hospital. All the patients that were admitted with a diagnosis of CAP, between January and December of 2019 were included. Sociodemographic and clinical characteristics were obtained. Blood cultures results were obtained, and it was evaluated if they were done in compliance with current recommendations by the Infectious Disease Society of America (IDSA).

RESULTS

721 patients were included in the study. Median age was 68 years and 50% of the patients were male (n = 293). Patients presented from home (84%) and the most common comorbidities were hypertension and diabetes (68% and 31%). 96 patients had positive blood culture and 34% (n = 247) of all the blood cultures were adequately ordered. 80 patients died or went to hospice and the median length of hospital stay in our cohort was 7 days. The multivariate model showed that mortality was associated with positive blood cultures (OR = 3.1 95%CI 1.63-5.87) and appropriateness of blood cultures (OR = 2.96 95% CI 1.2-5.7).

CONCLUSION

Adequate use of blood cultures in patients with CAP might have some association with the outcomes of this disease. However, a prospective study evaluating the utility of this test following current IDSA recommendations is needed to understand their impact in mortality and morbidity.

Clinical Value of Metagenomic Next-Generation Sequencing in Immunocompromised Patients with Sepsis

BACKGROUND Sepsis is a serious threat to human life, particularly in immunocompromised patients; hence, early diagnosis and targeted treatment are important. Metagenomic next-generation sequencing (NGS) has significant advantages over traditional diagnostic methods. This study investigated the clinical value of NGS for pathogen identification in immunocompromised patients with sepsis. MATERIAL AND METHODS From July 2020 to September 2021, 90 consecutive patients with sepsis were enrolled in this prospective study. The patients were divided into 2 groups: an immunocompromised group (n=30) and an immunocompetent group (n=60). The pathogens causing sepsis were concurrently identified using NGS and traditional diagnostic methods. The pathogen detection rates and the spectrum of pathogens identified were compared according to the method of detection and between the immunocompromised and immunocompetent groups. RESULTS Of the 90 patients, 77 (86%) were positive for 1 or more pathogens using NGS, and 50 (56%) were positive using traditional detection methods. The positivity rate of sputum and bronchoalveolar lavage fluid was higher than that of blood samples. Pneumocystis jirovecii and cytomegalovirus infections were more common in the immunocompromised group than in the immunocompetent group. CONCLUSIONS The performance of NGS in identifying pathogens for patients with sepsis is better than that of traditional detection methods, especially in immunocompromised patients. Pneumocystis jirovecii and cytomegalovirus infections are more common in immunocompromised patients.

Blood cultures and blood microbiota analysis as surrogates for bronchoalveolar lavage fluid analysis in dogs with bacterial pneumonia

Background

Diagnosis of canine bacterial pneumonia relies on airway lavage to confirm septic, suppurative inflammation, and a positive bacterial culture. Considering risks of bronchoalveolar lavage fluid (BALF) collection, minimally invasive methods like culture or next generation sequencing of blood would be appealing. In dogs with bacterial pneumonia, our study aims included (1): determining proportion of agreement between cultivable bacteria in BALF and blood (2); characterizing BALF, blood, and oropharyngeal (OP) microbiota and determining if bacteria cultured from BALF were present in these communities; and (3) comparing relatedness of microbial community composition at all three sites. Bacterial cultures were performed on BALF and blood. After DNA extraction of BALF, blood and OP, 16S rRNA amplicon libraries were generated, sequenced, and compared to a bacterial gene sequence database.

Results

Disregarding one false positive, blood cultures were positive in 2/9 dogs (5 total isolates), all 5 isolates were present in BALF cultures (16 total isolates). Based on sequencing data, all sites had rich and diverse microbial communities. Comparing cultured BALF bacterial genera with sequenced taxa, all dogs had ≥1 cultured isolate present in their microbiota: cultured BALF isolates were found in microbiota of BALF (12/16), blood (7/16), and OP (6/11; only 7 dogs had OP swabs). Of 394 distinct taxa detected in BALF, these were present in 75% OP and 45% blood samples. BALF community composition was significantly different than OP (p = 0.0059) and blood (p = 0.0009).

Conclusions

Blood cultures are insensitive but specific for cultured BALF bacteria in canine bacterial pneumonia. Cultivable BALF bacteria were present in BALF, blood and OP microbiota to differing degrees.

The clinical significance of simultaneous detection of pathogens from bronchoalveolar lavage fluid and blood samples by metagenomic next-generation sequencing in patients with severe pneumonia

Introduction. Bloodstream infection is a common complication in patients with severe pneumonia and is regarded as an independent risk factor for prediction of poor outcome. Metagenomic next-generation sequencing (mNGS) has been widely applied for pathogen determination of various clinical specimens from patients with infectious diseases. However, the clinical significance of and necessity for simultaneous pathogen detection of both blood samples and bronchoalveolar lavage fluid (BALF) by mNGS in patients with severe pneumonia remains unclear.Hypothesis/Gap Statement. Simultaneous detection of pathogens from both BALF and blood samples in patients with severe pneumonia helps to determine the complication of the bloodstream infection.Aims. This study aimed to elucidate the clinical significance and necessity of pathogen detection simultaneously in both blood samples and BALF samples with the application of mNGS in patients with severe pneumonia.Methods. In this study, 20 patients with severe pneumonia were enrolled and the potential pathogens in both BALF and blood samples were detected simultaneously by conventional microbial examination and mNGS tests. Moreover, multiple consecutive microbial detections were undertaken to investigate the dynamic variation of pathogens during the course of disease progression in two of the 20 patients.Results. In 85 % (17/20) of the patients with severe pneumonia, various pathogens were determined positively in the BALF by mNGS, including 10 cases with bacterial infection, five cases with viral infection and two cases with fungal infection. By contrast, pathogens in 50 % (10/20) of cases could be detected positively in the BALF by conventional microbial tests. Among 17 severe pneumonia patients with mNGS-positive BALF, pathogens were also identified in 10 cases with mNGS-positive blood samples. By contrast, only one patient complicated with a bloodstream infection could be found by conventional bacterial culture. Moreover, the pathogens from BALF were highly consistent with that from blood samples detected by mNGS in the early stage of the disease. With disease progression and after recurrent antibiotic treatment, significant dynamic changes of the microbial species from the BALF and blood samples could be clearly found by mNGS.Conclusions. This study emphasizes the utility of mNGS in the rapid simultaneous detection of pathogens from both BALF and blood samples in patients with severe pneumonia, and could allow determination of bloodstream infection and guide clinicians regarding antimicrobial treatments.

Prediction of blood culture outcome using hybrid neural network model based on electronic health records

Background

Blood cultures are often performed to detect patients who has a serious illness without infections and patients with bloodstream infections. Early positive blood culture prediction is important, as bloodstream infections may cause inflammation of the body, even organ failure or death. However, existing work mainly adopts statistical models with laboratory indicators, and fails to make full use of textual description information from EHRs.

Methods

We study the problem of positive blood culture prediction by using neural network model. Specifically, we first construct dataset from raw EHRs. Then we propose a hybrid neural network which incorporates attention based Bi-directional Long Short-Term Memory and Autoencoder networks to fully capture the information in EHRs.

Results

In order to evaluate the proposed method, we constructe a dataset which consists of totally 5963 patients who had one or more blood cultures tests during hospitalization. Experimental results show that the proposed neural model gets 91.23% F-measure for this task.

Conclusions

The comparison results of different models demonstrated the effectiveness of our model. The proposed model outperformed traditional statistical models.

Impact of urinary tract infection on nursing and healthcare-associated pneumonia

Nursing and healthcare-associated pneumonia (NHCAP), a concept of pneumonia proposed by the Japanese Respiratory Society, mostly occurs among elderly people in long-term care facilities. Similarly, the risk of urinary tract infection (UTI) also increases with age, with UTIs common among those in long-term care. Therefore, NHCAP is sometimes complicated by the presence of a UTI. However, pneumonia complicated by a UTI has not been clinically well characterized. We retrospectively analyzed 376 patients with NHCAP admitted to our hospital over a three-year period. Sixty-seven patients (17.8%) showed complications by a UTI. Patients with a UTI had lower renal function (higher blood urea nitrogen [P = 0.001], higher creatinine [P = 0.001]), lower systolic blood pressure (P = 0.04), higher A-DROP scores (P = 0.005) and higher positive blood culture rates (P = 0.03) than those without a UTI. Furthermore, based on urine, sputum and blood culture results, nearly half of the microorganisms (4/7) in blood cultures were identical with those of urine, suggesting that a concurrent UTI increases positive blood culture rates. Multivariate analysis showed that UTI was not an independent factor associated with 30-day mortality (P = 0.17), although patients with a UTI showed higher 30-day mortality (P = 0.04) than those without a UTI in univariate analysis. In summary, patients with NHCAP and a UTI were more prone to complications than those without a UTI, although UTI itself did not affect the prognosis of patients with NHCAP. A concurrent UTI had a negative impact on the severity of NHCAP.

Antimicrobial resistance in bacterial pathogens among hospitalised patients with severe invasive infections

The most severe infections are invasive infections, due to the fact that the germs can accumulate in multiple sites and produce a body-wide infection known as sepsis. Septic shock has the highest mortality rate among non-traumatic medical conditions. In this study, we aimed to evaluate the incidence and prevalence of invasive infections in a hospital environment. Another second objective was to establish the aetiology of invasive infections in our hospital and the antibiotic resistance profile of the germs involved, which are both important for determining the therapeutic approach for the treatment of these infections. The study included 505 hospitalized patients from which we collected a total of 974 blood cultures. For the analysis of the blood cultures, we used an automated incubator. The bottles flagged as positive were subcultured on blood agar, and the grown colonies were identified using an identification system. Invasive infections had a prevalence rate of 27.72% in our hospital. From the 974 blood cultures, we isolated 170 bacterial strains: Staphylococcus aureus (SA; 63 strains, 37.06%), Klebsiella spp. (27 strains, 15.88%), coagulase-negative staphylococci (CoNS; 18 strains, 10.59%), Enterococcus spp. (17 strains, 10.00%), Escherichia coli (12 strains, 7.06%), Streptococcus spp. (11 strains, 6.47%) and other bacterial species. The prevalence of methicillin-resistant SA (MRSA) in our study was 36.51% from the SA strains. The MRSA prevalence differed significantly according to age (37.50% in adults vs. 28.57% in children, P=0.047) and ICU admission (42.42% in ICU patients vs. 30.00% in non-ICU patients, P=0.018). We performed a multivariate analysis of the invasive infection risk which detected as significant predictors the admission into the cardiology ward and plastic surgery ward. On the whole, the findings of this study indicate that the high prevalence of Gram-positive cocci in blood cultures, mostly SA, with multidrug resistance has important consequences for the management of invasive infections.

Machine learning for fast identification of bacteraemia in SIRS patients treated on standard care wards: a cohort study

Bacteraemia is a life-threating condition requiring immediate diagnostic and therapeutic actions. Blood culture (BC) analyses often result in a low true positive result rate, indicating its improper usage. A predictive model might assist clinicians in deciding for whom to conduct or to avoid BC analysis in patients having a relevant bacteraemia risk. Predictive models were established by using linear and non-linear machine learning methods. To obtain proper data, a unique data set was collected prior to model estimation in a prospective cohort study, screening 3,370 standard care patients with suspected bacteraemia. Data from 466 patients fulfilling two or more systemic inflammatory response syndrome criteria (bacteraemia rate: 28.8%) were finally used. A 29 parameter panel of clinical data, cytokine expression levels and standard laboratory markers was used for model training. Model tuning was performed in a ten-fold cross validation and tuned models were validated in a test set (80:20 random split). The random forest strategy presented the best result in the test set validation (ROC-AUC: 0.729, 95%CI: 0.679–0.779). However, procalcitonin (PCT), as the best individual variable, yielded a similar ROC-AUC (0.729, 95%CI: 0.679–0.779). Thus, machine learning methods failed to improve the moderate diagnostic accuracy of PCT.

Bacteremia Prediction Model for Community-acquired Pneumonia: External Validation in a Multicenter Retrospective Cohort

OBJECTIVE

Many studies have described constructing a prediction model for bacteremia in community-acquired pneumonia (CAP), but these studies were not validated in external heterogeneous groups. The objective of this study was to test the generalizability of a previous bacteremia prediction model for CAP by external validation.

METHODS

This multicenter retrospective cohort analysis was performed in eight tertiary urban hospital emergency departments (EDs). We reviewed adult patients who were hospitalized after presentation to the ED with CAP. We categorized the enrolled patients into three groups according to the bacteremia prediction model score and calculated the number of patients with or without a blood culture-positive result. We performed a multivariable analysis to identify significant predictors for bacteremia.

RESULTS

Among the enrolled 2,001 patients, 1,592 (79.6%), 371 (18.5%), and 38 (1.9%) were stratified to a low-, moderate-, and high-risk group, respectively, and this proportion was similar with previous study. Each group had a bacteremia-positive rate as follows: 1.2% for the low-risk group, 7.2% for the moderate-risk group, and 31.5% for the high-risk group. The area under the receiver operating characteristic curve for the bacteremia model in the external validation cohort was 0.81, and there was no significant difference with that of the previous internal validation cohort (p = 0.246). Assuming that blood cultures were not performed in the low-risk patients, the sensitivity and specificity of this model were 0.68 and 0.81, respectively. Additionally, the positive predictive value and negative predictive value were 9.54 and 98.87%, respectively. A platelet count less than 130 × 10⁹ cells/L, albumin less than 3.3 mg/dL, and C-reactive protein greater than 17 mg/dL were identified as significant predictors with a sensitivity and specificity of 0.70 and 0.83, respectively.

CONCLUSION

The bacteremia prediction model was well validated in the general population and could help physicians make the decision to reduce the number of blood cultures in patients with CAP.