Bloodstream Infections

Risk factors of bloodstream infection in erythroderma from atopic dermatitis, psoriasis, and drug reactions: a retrospective observational cohort study

Background

Atopic dermatitis (AD), psoriasis, and drug reactions associated with erythroderma are frequently complicated by infections. However, bloodstream infection (BSI) have received less research attention.

Objectives

This study aimed to investigate the clinical characteristics and risk factors associated with BSI in patients with erythroderma.

Methods

A retrospective analysis was conducted on 141 erythroderma cases. Eleven cases were identified as having BSI. Clinical records of both BSI and non-BSI groups were reviewed and compared.

Results

BSI was diagnosed in 7.80% (11/141) of erythroderma cases, with a breakdown of 7.14% in AD, 2.00% in psoriasis, and 17.14% in drug reactions. Notably, all positive skin cultures (7/7) showed bacterial isolates concordant with blood cultures. Univariate logistic regression analysis revealed several significant associations with BSI, including temperature (≤36.0 or ≥38.5 °C; odds ratio (OR) = 28.06; p < 0.001), chilling (OR = 22.10; p < 0.001), kidney disease (OR = 14.64; p < 0.001), etiology of drug reactions (OR = 4.18; p = 0.03), albumin (ALB) (OR = 0.86; p < 0.01), C-reaction protein (CRP) (OR = 1.01; p = 0.02), interleukin 6 (IL-6) (OR = 1.02; p = 0.02), and procalcitonin (PCT) (OR = 1.07; p = 0.03). Receiver operating characteristic (ROC) curves demonstrated significant associations with ALB (p < 0.001; the area under curve (AUC) = 0.80), PCT (p = 0.009; AUC = 0.74), and CRP (p = 0.02; AUC = 0.71).

Conclusions

Increased awareness of BSI risk is essential in erythroderma management. Patients with specific risk factors, such as abnormal body temperature (≤36.0 or ≥38.5 °C), chilling sensations, kidney disease, a history of drug reactions, elevated CRP (≥32 mg/L), elevated PCT (≥1.00 ng/ml), and low albumin (≤31.0 g/L), require close monitoring for BSI development.

Antibiogram of Bacteria Isolated from Bloodstream Infection-Suspected Patients at the University of Gondar Comprehensive Specialized Hospital in Northwest Ethiopia: A Retrospective Study

Background

Bacterial bloodstream infections (BSIs) are the leading cause of sepsis-related morbidity and mortality worldwide. The emergence and spread of antimicrobial resistance (AMR) in bacteria is also a growing global concern. As a result, data on bacterial profile and their antibiogram are essential for strategies to contain drug resistance, improve the quality of patient care, and strengthen health systems.

Methods

Retrospective data from bacteriological results of blood samples of BSI-suspected patients from 2018 to 2021 were collected using a data collection sheet. Standard bacteriological techniques were followed during sample collection, culture preparation, bacterial identification, and antibiotic susceptibility testing (AST). We used Epi Info version 7 to enter and clean the data and then exported it to SPSS version 26 for analysis. Logistic regression models were used to measure the association between variables. A p value <0.05 with a 95% confidence interval was considered as statistically significant.

Result

Of the total 2,795 blood culture records, 455 (16.3%) were culture positive for bacteria, with Klebsiella pneumoniae (26%) and Staphylococcus aureus (24.6%) being the leading isolates. The isolates were highly resistant to common antibiotics, with more than 80% of them being resistant to ceftriaxone and penicillin. Moreover, about 43% of isolates were multidrug resistant (MDR), with Klebsiella pneumoniae (65.5%), Acinetobacter species (56.7%), and Citrobacter species (53.8%) being the most common MDR isolates. Age and diagnosis year were significantly associated with the presence of bacterial BSIs (p value <0.05).

Conclusion

Bacterial BSI and AMR were growing concerns in the study area. Bacteremia was more common in children under the age of five, and it decreased as the patient's age increased. The alarming rate of AMR, such as MDR blood isolates, calls for periodic and continuous monitoring of antibiotic usage in the study area.

Assessing the quality of antimicrobial prescribing in solid organ transplant recipients: a new frontier in antimicrobial stewardship

Background

Post-transplant infections remain a leading cause of morbidity and mortality in solid organ transplant recipients (SOTRs) and local standardized antimicrobial treatment guidelines may contribute to improved clinical outcomes. Our study assessed the rate of therapeutic compliance with local standard guidelines in the treatment of common infections in SOTR, and their associated outcomes.

Methods

Consecutive adult SOTRs admitted to the transplant floor from January-September 2020 and were treated for an infectious syndrome were followed until discharge or for 30 days following the date of diagnosis, whichever was shorter. Data was extracted from electronic medical records. Guideline compliance was characterized as either appropriate, effective but unnecessary, undertreatment, or inappropriate.

Results

Nine hundred and thirty-six SOTR were admitted to the transplant ward, of which 328 patients (35%) received treatment for infectious syndromes. Guidelines were applicable to 252 patients, constituting 275 syndromes: 86 pneumonias; 82 urinary tract infections; 40 intra-abdominal infections; 38 bloodstream infections; and 29 C. difficile infections. 200/246 (81%) of infectious syndromes received appropriate or effective but unnecessary empiric treatment. In addition, appropriate tailoring of antimicrobials resulted in a significant difference in 30-day all-cause mortality (adjusted OR of 0.07, 95% CI 0.01-0.38; P = .002). Lastly, we found that guideline-compliant empiric therapy was found to prevent the development of multi-drug resistance in a time-dependent analysis (adjusted HR of 0.21, 95% CI 0.08-0.52; P = .001).

Conclusion

Our data show that adherence to locally developed guidelines was associated with reduced mortality and resistant-organism development in our cohort of SOTR.

Impact of a hospital sepsis management protocol on the selection of empirical antibiotics in infectious disease consultations

It is well-established that Infectious Diseases consultation (IDC) enhances the prognosis of bloodstream infections. However, it is unclear if adoption of an institutional sepsis protocol would lead to any further improvement in a setting where IDC and infectious diseases approval (IDA) - available throughout 7 days/24 hours -are mandatory for administering broad spectrum antibiotics. We aimed to evaluate the influence of the institutional sepsis protocol developed by Department of Infectious Diseases and Clinical Microbiology on the selection of appropriate empirical antibiotics by IDC through focusing on patients who had bloodstream infections caused by Extended-spectrum β-lactamase (ESBL) producing Escherichia coli and Klebsiella pneumoniae, which poses a therapeutic challenge. One hundred and fifty-three adult patients (58 patients in the pre-protocol period and 95 patients in the post-protocol period), who received empirical antibiotic treatment for ESBL-producing E. coli and K. pneumoniae, in whom at least one systemic antibiotic was started either on the day blood cultures were drawn or not later than 24 hours were included in the study, retrospectively. The primary outcome was whether the empirical treatment regimen included a carbapenem that was accepted as the appropriate treatment based on the results of the MERINO trial. Secondary outcomes included empirical treatment based on pre-defined risk factors suggesting multidrug resistance (MDR), 30-day inpatient mortality, and appropriate antibacterial treatment according to antimicrobial susceptibility test (AST) results. The median age (Interquartile range) was 61 (48-70.5) years and 76 (49.7%) out of 153 patients were male. The patients in the post-protocol period were older compared to the pre-protocol period (54 years vs 64 years, p = 0.045). The Charlson Comorbidity Index was higher during the post-protocol period compared to the pre-protocol period (4 vs 5, p=0.038). At least one risk factor for MDR bacteria infection was present in 147 (96.1%) of the 153 patients. While the rate of risk factors for MDR bacteria infections did not differ significantly between the pre-protocol and post-protocol periods, the post-protocol period showed a significantly higher level of appropriate antibiotic treatment according to the presence of MDR risk factors compared to the pre-protocol period (44.8% vs 64.2%, p=0.019). There was a significant increase in the use of carbapenems in the post-protocol period compared to the pre-protocol period (34.5% vs. 56.8%, p=0.007). When the subgroup of patients who were likely to have infection caused by ESBL-producing bacteria is taken into consideration, the carbapenem use was more frequent in the post-protocol period (37.8% vs 68.9%, p=0.002). The rate of appropriate empirical treatment according to AST was not statistically different between pre-protocol and post-protocol period. The 30-day mortality rates were similar in both periods (24.1% vs 31.5, p=0.33). However, the rate of susceptibility to piperacillin-tazobactam was statistically higher in the pre-protocol period (82.6% vs 46.2%, p=0.016) when 39.7% of the patients received piperacillin-tazobactam as the empirical treatment. This study highlights the significance of using a structured protocol to attain appropriate empirical treatment for patients suspected of sepsis, even in a setting where IDC is readily available.

Reliability of Droplet Digital PCR Alone and in Combination with Interleukin-6 and Procalcitonin for Prognosis of Bloodstream Infection

Purpose

Bloodstream infection(BSI) is linked with high mortality, underscoring the significance of prompt etiological diagnosis for timely and precise treatment. This study aims to investigate the diagnostic value of droplet digital polymerase chain reaction(ddPCR) in combination with conventional inflammatory markers [interleukin-6(IL-6) and procalcitonin(PCT)] concerning disease progression and treatment prognosis in BSI patients. Furthermore, the study aims to explore a more efficient clinical application strategy.

Patients and Methods

This prospective case seried study centers on 176 patients suspected of or confirmed with BSI. Blood samples were collected to extract nucleic acids for identifying pathogens (bacteria, fungi, and viruses) and determining copy loads via ddPCR.

Results

The sensitivity of ddPCR was markedly higher compared to the culture method (74.71% vs 31.03%). A positive correlation existed between bacterial load and levels of inflammatory markers [IL-6 (P=0.0182), PCT (P=0.0029), and CRP (P=0.0005)]. In suspected BSI cases, the combination of ddPCR and inflammatory markers could predict sepsis risk [ROC: Area under the curve(AUC)=0.6071, P=0.0383]. Within confirmed BSI patients, the ddPCR bacterial load of those with SOFA<7 was lower than that of the SOFA≥7 (P=0.0334). ddPCR (OR: 1.789, P=0.035) monitoring combined with PCT (OR: 1.787, P=0.035) holded predictive value for SOFA progression (AUC=0.7913, P=0.0003). Similarly, BSI survivors displayed a lower burden than non-survivors (P=0.0170). Additionally, ddPCR combinated with IL-6 provided a more accurate and expedited insight into clinical outcomes prediction for BSI confirmed patients (AUC=0.7352, P=0.0030). Serial monitoring of bacterial load by ddPCR effectively mirrored the clinical course of BSI in patients. Notably, patients with positive ddPCR virus infection exhibited significantly reduced lymphocyte counts (P=0.0003).

Conclusion

In a clinical context, qualitative ddPCR results and quantitative continuous monitoring can more precisely assess sepsis progression and treatment prognosis in BSI patients. Furthermore, ddPCR results offer quicker and more accurate reference points for clinical antibacterial and antiviral interventions.

A high-speed microscopy system based on deep learning to detect yeast-like fungi cells in blood

Background: Blood-invasive fungal infections can cause the death of patients, while diagnosis of fungal infections is challenging. Methods: A high-speed microscopy detection system was constructed that included a microfluidic system, a microscope connected to a high-speed camera and a deep learning analysis section. Results: For training data, the sensitivity and specificity of the convolutional neural network model were 93.5% (92.7-94.2%) and 99.5% (99.1-99.5%), respectively. For validating data, the sensitivity and specificity were 81.3% (80.0-82.5%) and 99.4% (99.2-99.6%), respectively. Cryptococcal cells were found in 22.07% of blood samples. Conclusion: This high-speed microscopy system can analyze fungal pathogens in blood samples rapidly with high sensitivity and specificity and can help dramatically accelerate the diagnosis of fungal infectious diseases.

Metagenomic next-generation sequencing in detecting pathogens in pediatric oncology patients with suspected bloodstream infections

BACKGROUND

Studies on mNGS application in pediatric oncology patients, who are at high risk of infection, are quite limited.

METHODS

From March 2020 to June 2022, a total of 224 blood samples from 195 pediatric oncology patients who were suspected as bloodstream infections were enrolled in this study. Their clinical and laboratory data were retrospectively reviewed, and the diagnostic performance of mNGS was assessed.

RESULTS

Compared to the reference tests, mNGS showed significantly higher sensitivity (89.8% vs 32.5%, P < 0.001) and clinical agreement (76.3% vs 51.3%, P < 0.001) in detecting potential pathogens and distinguishing BSI from non-BSI. Especially, mNGS had an outstanding performance for virus detection, contributing to 100% clinical diagnosed virus. Samples from patients with neutropenia showed higher incidence of bacterial infections (P = 0.035). The most identified bacteria were Escherichia coli, and the overall infections by gram-negative bacteria were significantly more prevalent than those by gram-positive ones (90% vs 10%, P < 0.001). Overall, mNGS had an impact on the antimicrobial regimens' usage in 54.3% of the samples in this study.

CONCLUSIONS

mNGS has the advantage of rapid and effective pathogen diagnosis in pediatric oncology patients with suspected BSI, especially for virus.

IMPACT

Compared with reference tests, mNGS showed significantly higher sensitivity and clinical agreement in detecting potential pathogens and distinguishing bloodstream infections (BSI) from non-BSI. mNGS is particularly prominent in clinical diagnosed virus detection. The incidence of bacterial infection was higher in patients with neutropenia, and the overall infection rate of Gram-negative bacteria was significantly higher than that of Gram-positive bacteria. mNGS affects the antimicrobial regimens' usage in more than half of patients.

Comparison of metagenomic next-generation sequencing and blood culture for diagnosis of bloodstream infections

Objectives

This study aimed to evaluate the clinical performance of plasma cell-free DNA (cfDNA) next-generation sequencing (NGS) for pathogen detection in patients with sepsis.

Methods

A total of 43 pairs of blood and plasma samples form 33 blood culture-positive patients were used as testing samples in metagenomic NGS (mNGS) and NGS of 16S ribosomal RNA gene amplicons (16S rRNA NGS). The results of routine tests, including microbial culture, complete blood count, and biochemical tests, were collected from electronic medical records.

Results

Using blood as an mNGS testing sample, the proportion of host DNA was 99.9%, with only three bacteria and no fungi detected. When using plasma in mNGS, the proportion of host DNA was approximately 97%, with 84 bacteria and two fungi detected. Notably, 16S rRNA NGS detected 15 and 16 bacteria in 43 pairs of blood and plasma samples, respectively. Blood culture detected 49 bacteria (23 gram-negative bacilli and 26 gram-positive cocci) and four fungi, with 14 bacteria considered contaminants by clinical microbiologists. For all blood cultures, plasma cfDNA mNGS detected 78.26% (19/23) gram-negative rods, 17% (2/12) gram-positive cocci, and no fungi. Compared to blood cultures, the sensitivity and specificity of plasma cfDNA mNGS for detecting bacteria and fungi were 62.07% and 57.14%, respectively.

Conclusion

Compared to blood, plasma is more suitable for the detection of bloodstream infections using mNGS and is less affected by host DNA. The positive detection rate of plasma cfDNA mNGS for bloodstream infections caused by gram-negative bacteria was higher than that caused by gram-positive cocci.

Isolation of total DNA from Placenta Samples, both Fresh and following Formalin and Paraffin Treatment

The isolation of DNA from placental tissue suspected of infection is an important tool for identifying microorganisms such as bacteria, fungi, and viruses associated with complications during and after pregnancy. While experts primarily process placental tissue, the preservation methods employed pose challenges to extracting complete DNA. Therefore, selecting the appropriate protocol is paramount to achieving greater efficiency in obtaining genetic material.

Quantification of bacterial DNA in blood using droplet digital PCR: a pilot study

We used droplet digital PCR (ddPCR) assays to detect/quantify DNA from Escherichia coli, Klebsiella pneumoniae, Staphylococcus aureus, and Enterococcus spp. in blood samples. Bacterial DNA from clinical strains (4 < n < 12) was extracted, quantified and diluted (10-0.0001 ng/µL) and ddPCR assays were performed in triplicate. These ddPCR assays showed low replication variability, low detection limit (1-0.1 pg/µL), and genus/species specificity. ddPCR assays were also used to quantify bacterial DNA obtained from spiked blood (1 × 104-1 CFU/mL) of each bacterial genus/species. Comparison between ddPCR assays and bacterial culture was performed by Pearson correlation. There was an almost perfect correlation (r ≥ 0.997, P ≤ 0.001) between the number of CFU/mL from bacterial culture and the number of gene copies/mL detected by ddPCR. The time from sample preparation to results was determined to be 3.5 to 4 hours. The results demonstrated the quantification capacity and specificity of the ddPCR assays to detect/quantify 4 of the most important bloodstream infection (BSI) bacterial pathogens directly from blood. SIGNIFICANCE AND IMPACT: This pilot study results support the potential of ddPCR for the diagnosis and/or severity stratification of BSI. Applied to patients' blood samples it can improve diagnosis and diminish sample-to-results time, improving patient care.

Aerobic Bacterial Profile of Sepsis and Its Antibiotic Susceptibility Pattern Among Patients in a Rural Tertiary Care Center

Background Bloodstream infections (BSI) are one of the most life-threatening infections associated with high morbidity and mortality. Early diagnosis with appropriate and timely treatment improves the patient outcome. The recent surge in multidrug-resistant (MDR) strains is a matter of concern. This study aims to determine the bacterial etiology and antibiotic sensitivity pattern in BSI among different age groups. Materials and methods The microbiological data of blood culture and sensitivity between April 2019 and April 2021 were extracted from the laboratory records and analyzed for the bacterial profile and antibiotic sensitivity pattern. Results Out of the total 3893 blood cultures received during the study period from April 2019 to April 2021, 194 pathogens were isolated, accounting for a prevalence of 4.98%. Among 194 patients with culture-proven BSI, 54.12% (105/194) were adults, and 45.87% (89/194) were children. Of these 194 bacterial isolates, 58.76% (114/194) were gram-negative bacteria, and 41.24% (80/194) were gram-positive bacteria. With regard to the bacteria isolated, Enterococcus species with 23.71% (46/194) and Acinetobacter species with 22.16% (43/194) were the most common bacteria. The prevalence of MDR was 59.27% (115/194). Notable MDR types were methicillin-resistant Staphylococcus aureus (MRSA) in 15/22 (68.2%) and extended-spectrum beta-lactamase (ESBL) producers in 15/48 (31.25%) cases. Conclusion There is a significant geographical diversity of bacteria causing sepsis and their antibiotic susceptibility pattern. Recent trends show that multidrug-resistant gram-negative bacilli are the predominant isolates causing BSI. Increased antibiotic resistance is leading to treatment failure and poor clinical outcomes. Hence, there is a need to monitor antibiotic resistance among patients with BSI.

Performance of next-generation sequencing for diagnosis of blood infections by Klebsiella pneumoniae

Objective

Klebsiella pneumoniae (Kp) bloodstream infections (BSI) can be a life-threatening opportunistic infection. We aimed to evaluate the diagnostic accuracy of metagenomic next-generation sequencing (mNGS) for Kp BSI.

Methods

We retrospectively analyzed 72 patients suspected with bloodstream infection and mNGS Kp positive in peripheral blood, who were hospitalized in our hospital from January 2022 to January 2023. Clinical data and laboratory parameters were collected. All patients had blood drawn and other samples for blood mNGS, blood cultures (BC) and other cultures (OC). The accuracy of mNGS results was analyzed according to infection site, clinical indicators, therapeutic effect and routine culture results. The detection of pathogenic microorganisms by blood mNGS and routine culture was compared.

Results

Among 72 infection patients, 29 cases (40.28%) were BC positive, 43 cases (59.72%) were other culture (OC) positive, 16 cases (22.22%) were both BC and OC positive, 56 cases were positive for both mNGS and routine culture. Among the 56 double-positive cases, mNGS and conventional cultures were completely consistent in 27 cases, partially consistent in 15 cases, and completely inconsistent in 14 cases. Using the clinical diagnosis as the reference standard, There were 51 cases consistent with the results of mNGS with Kp BSI, the clinical consistency was 70.83% (51/72). The coincidence rate of mNGS and clinical diagnosis was higher than that of BC (54.17%, 39/72), indicating a statistically significant difference between the two methods (P<0.01).

Conclusions

Current evidence indicates that mNGS exhibits excellent accuracy for the diagnosis of Kp BSI. Although it cannot replace blood culture detection technology, it can be used as a supplement to provide stronger diagnostic capabilities for BSI and optimize treatment.

Development of a novel integrated isothermal amplification system for detection of bacteria-spiked blood samples

Bloodstream infection (BSI) caused by bacteria is highly pathogenic and lethal, and easily develops whole-body inflammatory state. Immediate identification of disease-causing bacteria can improve patient prognosis. Traditional testing methods are not only time-consuming, but such tests are limited to laboratories. Recombinase polymerase amplification combined with lateral flow dipstick (RPA-LFD) holds great promise for rapid nucleic acid detection, but the uncapping operation after amplification easily contaminates laboratories. Therefore, the establishment of a more effective integrated isothermal amplification system has become an urgent problem to be solved. In this study, we designed and fabricated a hermetically sealed integrated isothermal amplification system. Combining with this system, a set of RPA-LFD assays for detecting S. aureus, K. peneumoniae, P. aeruginosa, and H. influenza in BSI were established and evaluated. The whole process could be completed in less than 15 min and the results can be visualized by the naked eye. The developed RPA-LFD assays displayed a good sensitivity, and no cross-reactivity was observed in seven similar bacterial genera. The results obtained with 60 clinical samples indicated that the developed RPA-LFD assays had high specifcity and sensitivity for identifying S. aureus, K. peneumoniae, P. aeruginosa, and H. influenza in BSI. In conclusion, our results showed that the developed RPA-LFD assay is an alternative to existing PCR-based methods for detection of S. aureus, K. peneumoniae, P. aeruginosa, and H. influenza in BSI in primary hospitals.

Comparison of 3 diagnostic platforms for identification of bacteria and yeast from positive blood culture bottles

Managing bloodstream infections requires fast and accurate diagnostics. Culture-based diagnostic methods for identification from positive blood culture require 24-hour subculture, potentially delaying time to appropriate therapy. Positive blood cultures were collected (n = 301) from September 2021 to August 2022 at the University of Maryland Medical Center. Platforms compared were BioFire® BCID2, Sepsityper®, and short-term culture. For monomicrobial cultures, FilmArray® BCID2 identified 88.3% (241/273) of pathogens. Rapid Sepsityper® identified 76.9% (210/273) of pathogens. Sepsityper® extraction identified 82.4% (225/273) of pathogens. Short-term culture identified 83.5% (228/273) of pathogens. For polymicrobial cultures, Sepsityper®, short-term culture, and BioFire® BCID2 had complete identifications at 10.7% (3/28), 0%, and 92.9% (26/28), respectively. Time-to-results for Rapid Sepsityper®, Sepsityper® extraction, BioFire® BCID2, and Short-term culture were 35, 52, 65, and 306 minutes, respectively. Performance of these platforms can reduce time-to-results and may help effectively treat bloodstream infections faster. Accuracy, time-to-result, and hands-on time are important factors when evaluation diagnostic platforms.

Predictive models for short-term mortality and length of hospital stay among adults with community-onset bacteraemia before and during the COVID-19 pandemic: application of early data dynamics

BACKGROUND

The development of scoring systems to predict the short-term mortality and the length of hospital stay (LOS) in patients with bacteraemia is essential to improve the quality of care and reduce the occupancy variance in the hospital bed.

METHODS

Adults hospitalised with community-onset bacteraemia in the coronavirus disease 2019 (COVID-19) and pre-COVID-19 eras were captured as the validation and derivation cohorts in the multicentre study, respectively. Model I incorporated all variables available on day 0, Model II incorporated all variables available on day 3, and Models III, IV, and V incorporated the variables that changed from day 0 to day 3. This study adopted the statistical and machine learning (ML) methods to jointly determine the prediction performance of these models in two study cohorts.

RESULTS

A total of 3,639 (81.4%) and 834 (18.6%) patients were included in the derivation and validation cohorts, respectively. Model IV achieved the best performance in predicting 30-day mortality in both cohorts. The most frequently identified variables incorporated into Model IV were deteriorated consciousness from day 0 to day 3 and deteriorated respiration from day 0 to day 3. Model V achieved the best performance in predicting LOS in both cohorts. The most frequently identified variables in Model V were deteriorated consciousness from day 0 to day 3, a body temperature ≤ 36.0 °C or ≥ 39.0 °C on day 3, and a diagnosis of complicated bacteraemia.

CONCLUSIONS

For hospitalised adults with community-onset bacteraemia, clinical variables that dynamically changed from day 0 to day 3 were crucial in predicting the short-term mortality and LOS.

Distribution and Antibiotic Resistance Analysis of Blood Culture Pathogens in a Tertiary Care Hospital in China in the Past Four Years

Purpose

This study aimed to investigate the antibiotic resistance patterns and clinical distribution of blood culture-positive isolates at Suining Central Hospital between 2018 and 2021. The findings of this study can provide a basis for ensuring rational and effective use of antibiotic therapy in clinical settings.

Methods

This retrospective study analyzed the data of 3660 non-repeating strains that tested positive for clinical blood culture, collected from the microbiology laboratory of Suining Central Hospital between January 2018 and December 2021. The identification of bacterial species and their antibiotic resistance patterns were analyzed.

Results

The study found that 76.7% of the bacterial strains identified were Gram-negative bacteria, while 23.3% were Gram-positive bacteria. Escherichia coli (44.8%), Klebsiella spp. (19.2%), Staphylococcus aureus (9.2%), Enterococcus spp. (5.3%), and Enterobacter spp. were the top five bacterial ratios observed. These bacteria were detected most frequently in the Digestion Center, intensive care unit (ICU), Neurology Center, Urology Department, and Hematology Department. Among the Staphylococcus spp., methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-resistant coagulase-negative staphylococci (MRCNS) were detected at rates of 39.3% and 71.8%, respectively. However, no vancomycin- or linezolid-resistant staphylococci were identified. Enterococcus faecalis showed higher susceptibility to most antibiotic than Enterococcus faecium, except for tetracycline. The resistance rates of E. coli and Klebsiella spp. to meropenem and imipenem were low, but the resistance rates for other antibiotic were above 40%.

Conclusion

The results of this study show a rising incidence of bacterial antibiotic resistance in positive blood culture specimens at Suining Central Hospital. Clinicians should carefully consider the importance of blood culture antibiotic susceptibility testing to ensure effective treatment. The Department of Microbiology at Suining Central Hospital should regularly analyze the distribution of pathogenic bacteria and antibiotic resistance in blood cultures to ensure the most effective treatment possible.

Clinical Impact of the BIOFIRE Blood Culture Identification 2 Panel in Adult Patients with Bloodstream Infection: A Multicentre Observational Study in the United Arab Emirates

Rapid pathogen identification is key to the proper management of patients with bloodstream infections (BSIs), especially in the intensive care setting. This multicentre study compared the time to pathogen identification results in 185 patients admitted to intensive care with a confirmed BSI, using conventional methods (n = 99 patients) and upon implementation of the BIOFIRE^® Blood Culture Identification 2 (BCID2) Panel, a rapid molecular test allowing for the simultaneous identification of 43 BSI-related nucleic acids targets (n = 86 patients). The median time to result informing optimal antibiotic therapy was significantly shorter following the implementation of the BCID2 Panel (92 vs. 28 h pre vs. post BCID2 implementation; p < 0.0001). BCID2 usage in addition to conventional methods led to the identification of at least one pathogen in 98.8% patients vs. 87.9% using conventional methods alone (p = 0.003) and was associated with a lower 30-day mortality (17.3% vs. 31.6%, respectively; p = 0.019). This study at three intensive care units in the United Arab Emirates therefore demonstrates that, in addition to conventional microbiological methods and an effective antimicrobial stewardship program, the BCID2 Panel could improve the clinical outcome of patients admitted to the intensive care unit with a confirmed BSI.

Diagnostic performance and clinical impact of blood metagenomic next-generation sequencing in ICU patients suspected monomicrobial and polymicrobial bloodstream infections

Introduction

Early and effective application of antimicrobial medication has been evidenced to improve outcomes of patients with bloodstream infection (BSI). However, conventional microbiological tests (CMTs) have a number of limitations that hamper a rapid diagnosis.

Methods

We retrospectively collected 162 cases suspected BSI from intensive care unit with blood metagenomics next-generation sequencing (mNGS) results, to comparatively evaluate the diagnostic performance and the clinical impact on antibiotics usage of mNGS.

Results and discussion

Results showed that compared with blood culture, mNGS detected a greater number of pathogens, especially for Aspergillus spp, and yielded a significantly higher positive rate. With the final clinical diagnosis as the standard, the sensitivity of mNGS (excluding viruses) was 58.06%, significantly higher than that of blood culture (34.68%, P<0.001). Combing blood mNGS and culture results, the sensitivity improved to 72.58%. Forty-six patients had infected by mixed pathogens, among which Klebsiella pneumoniae and Acinetobacter baumannii contributed most. Compared to monomicrobial, cases with polymicrobial BSI exhibited dramatically higher level of SOFA, AST, hospitalized mortality and 90-day mortality (P<0.05). A total of 101 patients underwent antibiotics adjustment, among which 85 were adjusted according to microbiological results, including 45 cases based on the mNGS results (40 cases escalation and 5 cases de-escalation) and 32 cases on blood culture. Collectively, for patients suspected BSI in critical condition, mNGS results can provide valuable diagnostic information and contribute to the optimizing of antibiotic treatment. Combining conventional tests with mNGS may significantly improve the detection rate for pathogens and optimize antibiotic treatment in critically ill patients with BSI.

Epidemiology of Bloodstream Infections and Antimicrobial Susceptibility Pattern in ICU and Non-ICU Wards: A Four-Year Retrospective Study in Isfahan, Iran

Background

Bloodstream infections (BSIs) are one of the causes of morbidity and mortality in hospitalised patients. This study evaluated BSI's incidence, trend, antimicrobial susceptibility patterns and mortality in AL Zahra Hospital in Isfahan, Iran.

Materials and Methods

This retrospective study was conducted in AL Zahra Hospital from March 2017 to March 2021. The Iranian nosocomial infection surveillance system was used for data gathering. The data included demographic and hospital data, type of bacteria, and antibiotic susceptibility findings and were analysed in SPSS-18 software.

Results

The incidence of BSIs was 1.67% and 0.47%, and the mortality was 30% and 15.2% in the intensive care unit (ICU) and non-ICU wards, respectively. In the ICU, the mortality was correlated with the use of the catheter, type of organism and year of study, but in non-ICU, correlated with age, gender, use of the catheter, ward, year of study and duration between the incidence of BSIs and discharging/death. Staphylococcus epidermidis, Acinetobacter spp. and Klebsiella spp. were the most frequent germs isolated in all wards. Vancomycin (63.6%) and Gentamycin (37.7%) for ICU and Vancomycin (55.6%) and Meropenem (53.3) for other wards were the most sensitive antibiotics.

Conclusion

Despite the few rate of BSI in the last four years in AL Zahra Hospital, our data showed that its incidence and mortality in the ICU ward are significantly more than in other hospital wards. We recommend prospective multicentre studies to know the total incidence of BSI, local risk factors and patterns of pathogens causing BSI.

Antimicrobial resistance prevalence of Escherichia coli and Staphylococcus aureus amongst bacteremic patients in Africa: a systematic review

OBJECTIVES

Antimicrobial resistance (AMR) is a global concern among infectious diseases. Bloodstream infections can potentially become life-threatening if they become untreatable with conventional antimicrobials. This review aims to provide an understanding of the AMR prevalence and trends of common bacteremic pathogens, namely Escherichia coli and Staphylococcus aureus in the World Health Organization (WHO) Africa region.

METHODS

PubMed and Google Scholar were searched using relevant keywords for published human studies (excluding case reports and reviews) reporting bacteremic AMR data on the pathogens of interest between 2008 and 2019. Two reviewers independently screened the articles against a pre-defined eligibility criterion. Data extraction and analysis were achieved with different platforms: Covidence, Excel, R version 3.6.3, and QGIS v3.4.5. The pooled prevalence, 95% confidence intervals, and I² index (a measure of heterogeneity) were calculated for the various pathogen-antibiotic combinations.

RESULTS

Five hundred sixty-two papers were retrieved, with 27 papers included in the final analysis. Only 23.4% (11/47) of member states of the WHO African region had reports on AMR in bacteremia. The Clinical and Laboratory Standards Institute (CLSI) (78.5%) was the most common standard used in the region. For E. coli, the pooled resistance was: cefotaxime (42%), imipenem (4%), meropenem (0%), and colistin (0%). For S. aureus, the calculated pooled resistance was cloxacillin (34%), oxacillin (12%), and vancomycin (0%). There was a high degree of variation across studies (I² > 90%).

CONCLUSION

The pooled resistance rates indicate a concerning degree of methicillin-resistant and Extended Spectrum-ß-lactamase-producing pathogens. The paucity of AMR data also presents challenges for a comprehensive understanding of the situation in the region. Continent-wide and standardized surveillance efforts therefore need strengthening.

Circulating Microbial Cell-Free DNA in Health and Disease

Human blood contains low biomass of circulating microbial cell-free DNA (cfmDNA) that predominantly originates from bacteria. Numerous studies have detected circulating cfmDNA in patients with infectious and non-infectious diseases, and in healthy individuals. Remarkable differences were found in the microbial composition of healthy subjects and patients compared to cohorts with various diseases or even patients with diversified prognoses, implying that these alterations may be associated with disease development. Although the function of circulating cfmDNA needs to be elucidated (whether it acts as a bystander of dysbiosis or a key player in disease development), several studies have demonstrated its potential as a non-invasive biomarker that may improve diagnosis and treatment efficacy. The origin of circulating cfmDNA is still the subject of much deliberation, but studies have identified members of various microbiome niches, including the gut, oral cavity, airways, and skin. Further studies investigating the origin and function of circulating cfmDNA are needed. Moreover, low-biomass microbiome studies are prone to contamination, therefore stringent negative experimental control reactions and decontamination frameworks are advised in order to detect genuine circulating cfmDNA.

Photo-responsive polymeric micelles for the light-triggered release of curcumin targeting antimicrobial activity

Nanocarriers have been successfully used to solubilize, deliver, and increase the bioavailability of curcumin (CUR), but slow CUR release rates hinder its use as a topical photosensitizer in antimicrobial photodynamic therapy. A photo-responsive polymer (PRP) was designed for the light-triggered release of CUR with an effective light activation-dependent antimicrobial response. The characterization of the PRP was compared with non-responsive micelles comprising Pluronics™ P123 and F127. According to the findings, the PRP formed photo-responsive micelles in the nanometric scale (< 100 nm) with a lower critical micelle concentration (3.74 × 10^-4 M^-1, 5.8 × 10^-4 M^-1, and 7.2 × 10^-6 M^-1 for PRP, F127, P123, respectively, at 25°C) and higher entrapment efficiency of CUR (88.7, 77.2, and 72.3% for PRP, F127, and P123 micelles, respectively) than the pluronics evaluated. The PRP provided enhanced protection of CUR compared to P123 micelles, as demonstrated in fluorescence quenching studies. The light-triggered release of CUR from PRP occurred with UV light irradiation (at 355 nm and 25 mW cm^-2) and a cumulative release of 88.34% of CUR within 1 h compared to 80% from pluronics after 36 h. In vitro studies showed that CUR-loaded PRP was non-toxic to mammal cell, showed inactivation of the pathogenic microorganisms Candida albicans, Pseudomonas aeruginosa, and methicillin-resistant Staphylococcus aureus, and decreased biofilm biomass when associated with blue light (455  nm, 33.84 J/cm²). The findings show that the CUR-loaded PRP micelle is a viable option for antimicrobial activity.

Machine learning algorithm as a prognostic tool for venous thromboembolism in allogeneic transplant patients

As a serious complication after allogenic hematopoietic stem cell transplantation (allo-HSCT), venous thromboembolism (VTE) is significantly related to increased nonrelapse mortality. Therefore distinguishing patients at high risk of death who should receive specific therapeutic management is key to improving survival. This study aimed to establish a machine learning-based prognostic model for the identification of post-transplantation VTE patients who have a high risk of death. We retrospectively evaluated 256 consecutive VTE patients who underwent allo-HSCT at our center between 2008 and 2019. These patients were further randomly divided into (1) a derivation (80%) cohort of 205 patients and (2) a test (20%) cohort of 51 patients. The least absolute shrinkage and selection operator (LASSO) approach was used to choose the potential predictors from the primary dataset. Eight machine learning classifiers were used to produce 8 candidate models. A 10-fold cross-validation procedure was used to internally evaluate the models and to select the best-performing model for external assessment using the test cohort. In total, 256 of 7238 patients were diagnosed with VTE after transplantation. Among them, 118 patients (46.1%) had catheter-related venous thrombosis, 107 (41.8%) had isolated deep-vein thrombosis (DVT), 20 (7.8%) had isolated pulmonary embolism (PE), and 11 (4.3%) had concomitant DVT and PE. The 2-year overall survival (OS) rate of patients with VTE was 68.8%. Using LASSO regression, 8 potential features were selected from the 54 candidate variables. The best-performing algorithm based on the 10-fold cross-validation runs was a logistic regression classifier. Therefore a prognostic model named BRIDGE was then established to predict the 2-year OS rate. The areas under the curves of the BRIDGE model were 0.883, 0.871, and 0.858 for the training, validation, and test cohorts, respectively. The Hosmer-Lemeshow goodness-of-fit test showed a high agreement between the predicted and observed outcomes. Decision curve analysis indicated that VTE patients could benefit from the clinical application of the prognostic model. A BRIDGE risk score calculator for predicting the study result is available online (47.94.162.105:8080/bridge/). We established the BRIDGE model to precisely predict the risk for all-cause death in VTE patients after allo-HSCT. Identifying VTE patients who have a high risk of death can help physicians treat these patients in advance, which will improve patient survival.

Changes in Antimicrobial Resistance and Etiology of Blood Culture Isolates: Results of a Decade (2010-2019) of Surveillance in a Northern Region of Colombia

Background

Bloodstream infections (BSI) are important causes of morbidity and mortality worldwide. Antimicrobial surveillance is essential for identifying emerging resistance and generating empirical treatment guides, the purpose of this study is to analyze trends in antimicrobial susceptibility of BSI from 2010 to 2019 in healthcare institutions from Medellin and nearby towns in Colombia.

Methods

A Whonet database was analyzed from the GERMEN antimicrobial surveillance network; frequency and antibiotic susceptibility trends were calculated on more frequent microorganisms using Mann Kendall and Sen’s Slope Estimator Test.

Results

61,299 isolates were included; the three microorganisms more frequent showed a significant increasing trend through time E. coli (Sen’s Slope estimator = 0.7 p = <0.01) S. aureus (Sen’s Slope estimator = 0.60 p = <0.01) and K. pneumonia (Sen’s Slope estimator = 0.30 p = <0.01). E. coli showed a significant increase trend in cefepime and ceftazidime resistance, while K. pneumoniae showed a significant increase in resistance to cefepime, ciprofloxacin, and gentamicin. P. aeruginosa increases its susceptibility to all analyzed antibiotics and S. aureus to oxacillin. No increasing trend was observed for carbapenem resistance.

Conclusion

An upward trends was observed in more frequent microorganisms and resistance to third and fourth-generation cephalosporins for E. coli and K pneumoniae; in contrast, not increasing trends in antibiotic resistance was observed for P. aeruginosa and S. aureus. The essential role of AMR-surveillance programs is to point out and identify these trends, which should improve antibiotic resistance control.

Antimicrobial Resistance and Associated Risk Factors of Gram-Negative Bacterial Bloodstream Infections in Tikur Anbessa Specialized Hospital, Addis Ababa

Background

Bloodstream infections (BSIs) are significant causes of morbidity and mortality in Ethiopia and worldwide. Alarming is the rapid global spread of antimicrobial resistance (AMR) in bacteria.

Objective

To determine the microbial profile, antimicrobial susceptibility pattern, and associated risk factors for bloodstream infections in Tikur Anbessa Specialized Hospital (TASH) Addis Ababa Ethiopia.

Methods

A cross-sectional study was conducted between September 2018 and March 2019. Blood collected twice from each septicemia suspected patient were processed following standard bacteriological procedures. AST was performed by using the disk diffusion test according to CLSI 2017 and 2018 guidelines. Data captured in Epidata were cleaned and analyzed by SPSS version 21 software.

Results

The prevalence of BSI was 28.06% and a higher proportion of pathogene detected were gram-negative bacteria (GNB) (54.5%) and gram-positive bacteria (GPB) (45.43%). The most abundant bacterial species were Klebsiella pneumoniae 17.6%, CoNS 15.2%, and Acinetobacter spp 11.0%. Culture positivity was associated with age below 6 years, neonates AOR p=<0.001, infants AOR p=<0.001, Pre-school P=0.002, ICU admission COR p=<0.001, length of admission >5 days COR P=0.016, temperature greater than 38°C, AOR p=0.013, instrument usage during medical care AOR, p=<0.001, chronic illness AOR p=0.027, and neonatal incubation AOR p=0.013. GNB average drug resistance rate was 57.9% of the commonly used antibiotics and the most efficient and inefficient drugs were amikacin (10.8%) and ampicillin (94.6%). The gram-negative isolates showed a 95.3% rate of multi-drug resistance; and MDR, XDR, and PDR were observed at 55.8%, 32.2%, and 7.3%, of isolates respectively. This finding shows children especially neonates were highly affected by drug resistant BSI.

Conclusion

Pediatric patients and ICU patients are more affected by BSI, and drug-resistant bacteria are a major problem. Therefore, appropriate intervention approaches need to be implemented.

Burden of bacterial bloodstream infections and recent advances for diagnosis

Bloodstream infections (BSIs) and subsequent organ dysfunction (sepsis and septic shock) are conditions that rank among the top reasons for human mortality and have a great impact on healthcare systems. Their treatment mainly relies on the administration of broad-spectrum antimicrobials since the standard blood culture-based diagnostic methods remain time-consuming for the pathogen's identification. Consequently, the routine use of these antibiotics may lead to downstream antimicrobial resistance and failure in treatment outcomes. Recently, significant advances have been made in improving several methodologies for the identification of pathogens directly in whole blood especially regarding specificity and time to detection. Nevertheless, for the widespread implementation of these novel methods in healthcare facilities, further improvements are still needed concerning the sensitivity and cost-effectiveness to allow a faster and more appropriate antimicrobial therapy. This review is focused on the problem of BSIs and sepsis addressing several aspects like their origin, challenges, and causative agents. Also, it highlights current and emerging diagnostics technologies, discussing their strengths and weaknesses.

Machine-learning based prediction and analysis of prognostic risk factors in patients with candidemia and bacteraemia: a 5-year analysis

Bacteraemia has attracted great attention owing to its serious outcomes, including deterioration of the primary disease, infection, severe sepsis, overwhelming septic shock or even death. Candidemia, secondary to bacteraemia, is frequently seen in hospitalised patients, especially in those with weak immune systems, and may lead to lethal outcomes and a poor prognosis. Moreover, higher morbidity and mortality associated with candidemia. Owing to the complexity of patient conditions, the occurrence of candidemia is increasing. Candidemia-related studies are relatively challenging. Because candidemia is associated with increasing mortality related to invasive infection of organs, its pathogenesis warrants further investigation. We collected the relevant clinical data of 367 patients with concomitant candidemia and bacteraemia in the first hospital of China Medical University from January 2013 to January 2018. We analysed the available information and attempted to obtain the undisclosed information. Subsequently, we used machine learning to screen for regulators such as prognostic factors related to death. Of the 367 patients, 231 (62.9%) were men, and the median age of all patients was 61 years old (range, 52-71 years), with 133 (36.2%) patients aged >65 years. In addition, 249 patients had hypoproteinaemia, and 169 patients were admitted to the intensive care unit (ICU) during hospitalisation. The most common fungi and bacteria associated with tumour development and Candida infection were Candida parapsilosis and Acinetobacter baumannii, respectively. We used machine learning to screen for death-related prognostic factors in patients with candidemia and bacteraemia mainly based on integrated information. The results showed that serum creatinine level, endotoxic shock, length of stay in ICU, age, leukocyte count, total parenteral nutrition, total bilirubin level, length of stay in the hospital, PCT level and lymphocyte count were identified as the main prognostic factors. These findings will greatly help clinicians treat patients with candidemia and bacteraemia.

Blood Culture Contamination: A Single General Hospital Experience of 2-Year Retrospective Study

In the event of blood culture contamination (BCC), blood culture (BC) needs to be repeated. This may delay appropriate treatment, prolong hospitalization and, consequently, increase its costs. The aim of the study was to assess the frequency of BCC and associated factors in a general hospital in Poland based on reports of BC in samples submitted for laboratory testing in 2019−2020. BCC is recognized when bacteria (especially those belonging to natural human microbiota) are isolated from a single sample and no clinical signs indicated infection. True positive BC is confirmed by the growth of bacteria in more than one set of blood samples with the corresponding clinical signs present. The structure of BC sets, microorganisms, and laboratory costs of BCC were analyzed. Out of 2274 total BC cases, 11.5% were true positive BC and 9.5% were BCC. Of all the BCC identified in the entire hospital, 72% was from Internal Medicine (IM) and Intensive Care Unit (ICU) combined. When single sets for BC were used in IM in 2020, the use increased to 85% compared with 2019 (p < 0.05). The predominant isolates were coagulase-negative staphylococci (84%). The estimated extra laboratory costs of BCC exceeded EUR 268,000. The BCC was a more serious problem than expected, including non-recommended using of single BC sets. Compliance with the BC collection procedure should be increased in order to reduce BCC and thus extra hospital costs.

Development and validation of a risk score for predicting positivity of blood cultures and mortality in patients with bacteremia and fungemia

INTRODUCTION

Bacteremia is a major cause of morbidity and mortality in hospitalized patients. Predictors of mortality are critical for the management and survival of hospitalized patients. The objective of this study was to determine the factors related to blood culture positivity and the risk factors for mortality in patients whose blood cultures were collected.

METHODS

A prospective 2-cohort study (derivation with 784 patients and validation with 380 patients) based on the Pitt bacteremia score for all patients undergoing blood culture collection. The score was obtained from multivariate analysis. The Kaplan-Meier survival curve of the cohort derivation and the cohort validation groups was calculated, and the difference was assessed using a log-rank test. Mortality-related factors were older age, extended hospitalization, > 10% of immature cells in the leukogram, lower mean blood pressure, elevated heart rate, elevated WBC count, and elevated respiratory rate. These continuous variables were dichotomized according to their significance level, and a cut-off limit was created.

RESULTS

The area under the ROC curve (AUC) was 0.789. The score was validated in a group of 380 patients who were prospectively evaluated.

CONCLUSION

Prolonged hospitalization, body temperature, and elevated heart rate were related to positive blood cultures. The Pitt score can be used to assess the risk of death; however it can be individualized according to the epidemiology of each hospital.

Clonality, virulence genes, and antibiotic resistance of Staphylococcus aureus isolated from blood in Shandong, China

BACKGROUND

Bloodstream infection (BSI) caused by Staphylococcus aureus (S. aureus) can be life-threatening and pose a great challenge to infection control and clinical treatment. However, little information exists regarding the characterization of S. aureus in BSI patients in Shandong, China. To identify the clonality, virulence genes, and antibiotic resistance of S. aureus in blood, a total of 101 nonrepetitive blood isolates were collected. The antibiotic resistance phenotypes were determined, and virulence genes were analyzed with polymerase chain reaction (PCR). Finally, the genetic relatedness was investigated with Staphylococcus chromosomal cassette mec (SCCmec) typing for methicillin-resistant S. aureus (MRSA) isolates, Staphylococcal protein A (spa), and multilocus sequence typing (MLST) for all of 101 isolates.

RESULTS

Of the 101 S. aureus isolates, 24 MRSA isolates and 77 methicillin-susceptible S. aureus (MSSA) isolates were identified. Overall, MRSA isolates had higher resistance rates than MSSA isolates when exposed to any of the 15 antibiotics tested in this study except for trimethoprim/sulfamethoxazole. Among the 17 virulence genes tested in this study, hla, hld, and hlg could be detected in all isolates. MRSA isolates were more likely to carry seb and hlb genes, while MSSA isolates were more likely to carry seg and sei genes. Thirty-five sequence types (STs) and 49 spa types were identified, of which ST59-t437 and ST398-t571 were the most abundant. These two genotypes were also the most abundant ST-spa types in MRSA and MSSA isolates, but their abundances shifted over time, with ST398-t571 being the predominant genotype from 2016 to 2017, and ST59-t437 from 2018 to 2020. Besides, all the ST59-t437 isolates harbored hlgb gene, whereas most (88.9%) ST398-t571 did not. In addition, twenty-four MRSA isolates were subject to SCCmec typing. SCCmec IVa was the most prevalent SCCmec type, and all the ST59-t437 MRSA isolates were SCCmec IVa. We also observed 15 new STs, and some of them were MRSA.

CONCLUSION

These findings provide additional observations and epidemiological data for blood S. aureus isolates, which can improve future infection-control measures and aid in potential clinical treatments in hospitals and other clinical settings.

Impact of Nutritional Assessment on the Clinical Outcomes of Patients with Non-albicans Candidemia: A Multicenter Study

Several studies have demonstrated that malnutrition is a negative prognostic factor for clinical outcomes. However, there is limited evidence for the effect of malnutrition on clinical outcomes in patients with candidemia. We investigated the relationship between malnutrition and all-cause 28-day mortality among patients with non-albicans candidemia. Between July 2011 and June 2014, all adult patients with non-albicans candidemia, including C. tropicalis, C. glabrata, C. parapsilosis and so on, were enrolled. The Malnutrition Universal Screening Tool (MUST) scores were used to determine the patients' nutritional status before the onset of candidemia. A total of 378 patients were enrolled; 43.4% developed septic shock and 57.1% had a high risk of malnutrition (MUST ≥ 2). The all-cause 28-day mortality rate was 40.7%. The Cox proportional hazards model revealed that C. tropicalis (HR, 2.01; 95% CI, 1.24-3.26; p = 0.005), Charlson comorbidity index (HR, 1.10; 95% CI, 1.03-1.18; p = 0.007), Foley catheter use (HR, 1.68; 95% CI, 1.21-1.35; p = 0.002), concomitant bacterial infections (HR, 1.55; 95% CI, 1.11-2.17; p = 0.010), low platelet count (HR, 3.81; 95% CI, 2.45-5.91; p < 0.001), not receiving antifungals initially (HR, 4.73; 95% CI, 3.07-7.29; p < 0.001), and MUST ≥ 2 (HR, 1.54; 95% CI, 1.09-2.17; p = 0.014) were independently associated with all-cause 28-day mortality. A simple screening tool for nutritional assessment should be used for patients with non-albicans candidemia to detect early clinical deterioration, and a tailored nutritional care plan should be established for malnourished individuals, to improve their clinical outcomes.

Mass Spectrometry Proteotyping-Based Detection and Identification of Staphylococcus aureus, Escherichia coli, and Candida albicans in Blood

Bloodstream infections (BSIs), the presence of microorganisms in blood, are potentially serious conditions that can quickly develop into sepsis and life-threatening situations. When assessing proper treatment, rapid diagnosis is the key; besides clinical judgement performed by attending physicians, supporting microbiological tests typically are performed, often requiring microbial isolation and culturing steps, which increases the time required for confirming positive cases of BSI. The additional waiting time forces physicians to prescribe broad-spectrum antibiotics and empirically based treatments, before determining the precise cause of the disease. Thus, alternative and more rapid cultivation-independent methods are needed to improve clinical diagnostics, supporting prompt and accurate treatment and reducing the development of antibiotic resistance. In this study, a culture-independent workflow for pathogen detection and identification in blood samples was developed, using peptide biomarkers and applying bottom-up proteomics analyses, i.e., so-called "proteotyping". To demonstrate the feasibility of detection of blood infectious pathogens, using proteotyping, Escherichia coli and Staphylococcus aureus were included in the study, as the most prominent bacterial causes of bacteremia and sepsis, as well as Candida albicans, one of the most prominent causes of fungemia. Model systems including spiked negative blood samples, as well as positive blood cultures, without further culturing steps, were investigated. Furthermore, an experiment designed to determine the incubation time needed for correct identification of the infectious pathogens in blood cultures was performed. The results for the spiked negative blood samples showed that proteotyping was 100- to 1,000-fold more sensitive, in comparison with the MALDI-TOF MS-based approach. Furthermore, in the analyses of ten positive blood cultures each of E. coli and S. aureus, both the MALDI-TOF MS-based and proteotyping approaches were successful in the identification of E. coli, although only proteotyping could identify S. aureus correctly in all samples. Compared with the MALDI-TOF MS-based approaches, shotgun proteotyping demonstrated higher sensitivity and accuracy, and required significantly shorter incubation time before detection and identification of the correct pathogen could be accomplished.

Serum N-Glycomics Stratifies Bacteremic Patients Infected with Different Pathogens

Bacteremia—i.e., the presence of pathogens in the blood stream—is associated with long-term morbidity and is a potential precursor condition to life-threatening sepsis. Timely detection of bacteremia is therefore critical to reduce patient mortality, but existing methods lack precision, speed, and sensitivity to effectively stratify bacteremic patients. Herein, we tested the potential of quantitative serum N-glycomics performed using porous graphitized carbon liquid chromatography tandem mass spectrometry to stratify bacteremic patients infected with Escherichia coli (n = 11), Staphylococcus aureus (n = 11), Pseudomonas aeruginosa (n = 5), and Streptococcus viridans (n = 5) from healthy donors (n = 39). In total, 62 N-glycan isomers spanning 41 glycan compositions primarily comprising complex-type core fucosylated, bisecting N-acetylglucosamine (GlcNAc), and α2,3-/α2,6-sialylated structures were profiled across all samples using label-free quantitation. Excitingly, unsupervised hierarchical clustering and principal component analysis of the serum N-glycome data accurately separated the patient groups. P. aeruginosa-infected patients displayed prominent N-glycome aberrations involving elevated levels of fucosylation and bisecting GlcNAcylation and reduced sialylation relative to other bacteremic patients. Notably, receiver operating characteristic analyses demonstrated that a single N-glycan isomer could effectively stratify each of the four bacteremic patient groups from the healthy donors (area under the curve 0.93–1.00). Thus, the serum N-glycome represents a new hitherto unexplored class of potential diagnostic markers for bloodstream infections.

Significant Differences in Host-Pathogen Interactions Between Murine and Human Whole Blood

Murine infection models are widely used to study systemic candidiasis caused by C. albicans. Whole-blood models can help to elucidate host-pathogens interactions and have been used for several Candida species in human blood. We adapted the human whole-blood model to murine blood. Unlike human blood, murine blood was unable to reduce fungal burden and more substantial filamentation of C. albicans was observed. This coincided with less fungal association with leukocytes, especially neutrophils. The lower neutrophil number in murine blood only partially explains insufficient infection and filamentation control, as spiking with murine neutrophils had only limited effects on fungal killing. Furthermore, increased fungal survival is not mediated by enhanced filamentation, as a filament-deficient mutant was likewise not eliminated. We also observed host-dependent differences for interaction of platelets with C. albicans, showing enhanced platelet aggregation, adhesion and activation in murine blood. For human blood, opsonization was shown to decrease platelet interaction suggesting that complement factors interfere with fungus-to-platelet binding. Our results reveal substantial differences between murine and human whole-blood models infected with C. albicans and thereby demonstrate limitations in the translatability of this ex vivo model between hosts.

Developing Diagnostic and Therapeutic Approaches to Bacterial Infections for a New Era: Implications of Globalization

In just a few months, the current coronavirus pandemic has exposed the need for a more global approach to human health. Indeed, the quick spread of infectious diseases and their unpredictable consequences, in terms of human lives and economic losses, will require a change in our strategy, both at the clinical and the research level. Ultimately, we should be ready to fight against infectious diseases affecting a huge number of people in different parts of the world. This new scenario will require rapid, inexpensive diagnostic systems, applicable anywhere in the world and, preferably, without the need for specialized personnel. Also, treatments for these diseases must be versatile, easily scalable, cheap, and easy to apply. All this will only be possible with joint support of the governments, which will have to make the requirements for the approval of new therapies more flexible. Meanwhile, the pharmaceutical sector must commit to prioritizing products of global interest over the most profitable ones. Extreme circumstances demand a vehement response, and any profit losses may well pay dividends going forward. Here, we summarize the developing technologies destined to face the current and future health challenges derived from infectious diseases and discuss which ones have more possibilities of being implemented.

Clinical Utilization of Blood and Urine Cultures and Incidences of Bacteremia and Bacteriuria in a Hospital in Thailand

Background

To effectively treat sepsis and urinary tract infection (UTI), blood and urine cultures should be used appropriately and relative to incidences of bacteremia and bacteriuria. This study aimed to investigate the use of blood and urine cultures and incidences of bacteremia and bacteriuria in a hospital in Thailand.

Material/Methods

Medical records of patients admitted from 2016 to 2018 were randomly selected and data in the records were anonymously extracted for investigation.

Results

From 12 000 records, data on blood and urine cultures were extracted from 9% and 4% of them, respectively. The negative rate of blood culture was 87.48%. Bacteremia was detected in 10.22%. The positive rate of urine culture was 27.38% and the contamination rate was 31.26%. Escherichia coli was the most common cause of community-onset bacteremia and bacteriuria. Methicillin-resistant coagulase-negative staphylococci and Acinetobacter baumannii were the most common cause of hospital-acquired bacteremia while yeasts were the most common cause of hospital-acquired UTI.

Conclusions

A high negative rate of blood culture may result not only from its low sensitivity but also from liberal test use to identify sepsis in some conditions. Improper urine collection is the main problem with use of urine culture.

A rapid high-throughput sequencing-based approach for the identification of unknown bacterial pathogens in whole blood

High-throughput DNA sequencing (HTS) of pathogens in whole blood samples is hampered by the high host/pathogen nucleic acids ratio. We describe a novel and rapid bacterial enrichment procedure whose implementation is exemplified in simulated bacteremic human blood samples. The procedure involves depletion of the host DNA, rapid HTS and bioinformatic analyses. Following this procedure, Y. pestis, F. tularensis and B. anthracis spiked-in samples displayed an improved host/pathogen DNA ratio of 2.5-5.9 orders of magnitude, in samples with bacteria spiked-in at 103-105 CFU/ml. The procedure described in this study enables rapid and detailed metagenomic profiling of pathogens within 8-9 h, circumventing the challenges imposed by the high background present in the bacteremic blood and by the unknown nature of the sample.

Occurrence of Albifimbria verrucaria in the Blood of a Female Child With Neuroblastoma

We report for the first time the occurrence of a filamentous fungus, Albifimbria verrucaria, in the blood of a pediatric neuroblastoma patient. The Albifimbria genus comprises common soil-inhabiting and saprophytic fungi and has been isolated as a plant pathogen in Northern and Southern Italy. As a human pathogen, A. verrucaria has been implicated in keratitis and can produce trichothecene toxins, which are weakly cytotoxic for mammalian cell lines. A. verrucaria was isolated from blood during the follow-up of a previous coagulase-negative Staphylococcus catheter-related infection. Lung nodules, compatible with fungal infection, had been observed on a CT scan 6 months earlier; they still persist. Possible routes of transmission were considered to be airborne, catheter related, or transfusion dependent, as the patient had undergone platelet and red blood cell transfusions during rescue chemotherapy. No filamentous fungi were isolated from sputum or CVCs. In conclusion, we describe an unprecedented fungemia caused by A. verrucaria and show how an unexpected pathogen may be acquired from the environment by patients at high risk due to immunosuppression. The route of transmission remains unknown.

Rapid multiplex detection of the resistance genes mecA, vanA and vanB from Gram-positive cocci-positive blood cultures using a PCR-dipstick technique

Introduction. Among the causative agents of bloodstream infections (BSIs), methicillin-resistant Staphylococcus aureus (MRSA) or vancomycin-resistant Enterococcus (VRE) are the key causative pathogens. Their rapid detection directly from Gram-positive cocci-positive blood culture specimens will promote timely treatment and help to implement effective infection control measures.Aim. We aim to develop a PCR-dipstick technique for the rapid detection of MRSA and VRE directly from positive blood culture specimens.Methodology. PCR-dipstick is a PCR-based multiplex detection technique where DNA-DNA hybridization is employed, and the results are interpreted with the naked eye. It was designed to target three drug resistance genes: mecA in MRSA and vanA/vanB in VRE from positive blood culture specimens. A total of 120 clinical isolates were used to evaluate the sensitivity and specificity of PCR-dipstick. Then, PCR-dipstick was examined for MRSA and VRE detection directly from positive blood cultures.Results. PCR-dipstick showed 100 % sensitivity and specificity in detecting mecA, vanA and vanB genes directly from bacterial colonies in comparison with multiplex PCR for genomic DNA followed by agarose gel electrophoresis. Further, it could differentially detect multiple resistant genes in pooled bacterial colonies (n=10). Ultimately, PCR-dipstick could detect MRSA and VRE in positive blood cultures in ~3 h.Conclusion. The results of the current study substantiate that PCR-dipstick can be used as an efficient detection system for MRSA and VRE directly from Gram-positive cocci-positive blood cultures. Its affordability and rapidity indicate that PCR-dipstick can be an effective tool for controlling nosocomial pathogens.

Early mortality attributable to PICC-lines in 4 public hospitals of Marseille from 2010 to 2016 (Revised V3)

INTRODUCTION

Peripherally inserted central catheters (PICC-line) are devices inserted through peripheral venous access. In our institution, this technology has been rapidly adopted by physicians in their routine practice. Bacteremia on catheters remains an important public health issue in France. However, the mortality attributable to bacteremia on PICC-line remains poorly evaluated in France and in the literature in general. We report in our study an exhaustive inventory of bacteremia on PICC-line and their 30 days mortality, over a 7 years period.

MATERIAL AND METHODS

From January 2010 to December 2016, we retrospectively matched PICC-line registers of the radiology department, blood culture records of the microbiology laboratory and medical records from the Hospital Information Systems.

RESULTS

The 11,334 hospital stays during which a PICC-line was inserted were included over a period of 7 years. Among them, 258 episodes of PICC-line-associated bacteremia were recorded, resulting in a prevalence of 2.27%. Hematology units: 20/324 (6.17%), oncology units: 55/1375 (4%) and hepato-gastro-enterology units: 42/1142 (3.66%) had the highest prevalence of PICC-line related bacteremia. The correlation analysis, when adjusted by exposure and year, shows that the unit profile explains 72% of the variability in the rate of bacteremia with a P = .023. Early bacteremia, occurring within 21 days of insertion, represented 75% of cases. The crude death ratio at 30 days, among patients PICC-line associated bacteremia was 57/11 334 (0.50%). The overall 30-day mortality of patients with PICC-line with and without bacteremia was 1369/11334 (12.07%). On day 30, mortality of patients with bacteremia associated PICC-line was 57/258 or 22.09% of cases, compared to a mortality rate of 1311/11076, or 11.83% in the control group (P < .05, RR 2.066 [1.54-2.75]). Kaplan-Meier survival analysis revealed a statistically significant excess mortality between patients with PICC-line associated bacteremia and PICC-line carriers without bacteremia (P < .0007, hazard ratio 1.89 [1307-2709]).

CONCLUSION

Patients with PICC-line associated bacteremia have a significant excess mortality. The implementation of a PICC-line should remain the last resort after a careful assessment of the benefit/risk ratio by a senior doctor.

The Epidemiology of Bloodstream Infections and Antimicrobial Susceptibility Patterns: A Nine-Year Retrospective Study at St. Dominic Hospital, Akwatia, Ghana

Background

Bloodstream infections are among the top causes of morbidity and mortality in people of all ages, especially in immunocompromised patients in sub-Saharan Africa. This study aimed at describing the epidemiology of bloodstream infections and antimicrobial susceptibility pattern over a nine-year period at St. Dominic Hospital, Akwatia, in the Eastern Region of Ghana.

Method

This study retrospectively analysed data from 4,489 patients who were referred to the Laboratory Department for blood culture and sensitivity testing from January 2009 to December 2017. Sociodemographic data included age, gender, and patients' department. Blood culture results were retrieved from archival records in the laboratory. The authorities of St. Dominic Hospital granted approval for the study.

Results

The incidence of bloodstream infection over the 9 years was 51.4 positive cultures per 100,000 hospital attendance. Staphylococcus aureus was the leading causative agent of bacteraemia for the first two scalar years (2009–2011 (38.9%) and 2012–2014 (42.2%)) while coagulase-negative staphylococcus (CoNS) (50.5%) was predominant for the last scalar year (2015–2017), followed by Staphylococcus aureus (169/587 (28.8%)). The highest incidence of bloodstream infections was recorded in the wet seasons (months of May (8.9 per 10,000 persons) and October (10.1 per 10,000 persons)). The bacterial isolates demonstrated high resistance to tetracyclines (390/531 (73.4%)), penicillins (1282/1669 (76.8%)), and sulphonamides (450/499 (90.2%)).

Conclusion

Bloodstream infection and antimicrobial resistance are high in patients seeking healthcare in Akwatia. This therefore calls for concerted efforts aimed at reducing the incidence in the study area.

Prevalence of Bloodstream Infections in Children With Short-Bowel Syndrome With a Central Line Presenting to Emergency Department With Fever

BACKGROUND

Children with short-bowel syndrome (SBS) have significant morbidity and mortality from bloodstream infections (BSIs). We studied the prevalence of BSI in children with SBS and identified possible predictors of BSI.

METHODS

This retrospective cohort study included patients with SBS who presented to Holtz Children's Hospital from April 1, 2009, to June 30, 2014, with fever or reported fever. Data including vital signs, white blood cell (WBC) count, C-reactive protein (CRP) levels, and blood and urine cultures were reviewed. We calculated the prevalence of BSI and its confidence level. We also assessed the odds of BSI with increases in WBC and CRP values.

RESULTS

A total of 246 encounters were evaluated. The adjusted calculated prevalence rate for BSI in children with SBS and fever was 55% (95% CI, 42.3%-65.4%). There were 114 gram-negative infections (72.6%), 46 gram-positive infections (29.3%), and 17 fungal infections (10.8%). Using the regression model, each additional 10 units above 20 mg/L CRP increased the odds of BSI by 26%. There was no association between WBC count and the presence of BSI.

CONCLUSION

Children with fever and SBS are at high risk for BSI with gram-positive and gram-negative organisms as well as fungus. WBC count at presentation is a poor predictor of BSI. Though elevated CRP increased the odds of BSI, its low negative predictive value made it a poor predictor of BSI in these patients. Children with SBS and fever should be treated urgently with broad-spectrum antibiotics.

Direct Identification of 80 Percent of Bacteria from Blood Culture Bottles by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry Using a 10-Minute Extraction Protocol

Matrix-assisted laser desorption ionization-time of flight mass spectrometry is not widely used to identify bacteria directly from positive blood culture bottles (BCBs) because of overlong protocols. The objective of this work was to develop and evaluate a simple extraction protocol for reliable identification from BCBs. The 10-min protocol was applied over a 5-month period. Direct identifications on day 0 were compared with those obtained from colonies on day 1 [log(score) of ≥2]. We evaluated a range of seven log(score) thresholds on day 0 from 1.4 to 2.0 to find the lower confidence score that provides the higher percentage of direct identifications without loss of accuracy. With a log(score) threshold of ≥1.5 at day 0, our protocol allowed us to identify 80% of bacteria in 632 BCBs (96% of Enterobacteriaceae, 95% of Staphylococcus aureus, 92% of enterococci, and 62% of streptococci). At least one bacterial species of the mixture was identified in 77% of the polymicrobial samples. The rapidity and reliability of the protocol were factors in its adoption for routine use, allowing us to save up to 24 h in identifying 80% of the bacteria in the BCBs and, thus, to supply useful information to adapt antibiotic therapy when necessary. We currently provide reliable daily direct identifications of staphylococci, enterococci, Enterobacteriaceae, Pseudomonas aeruginosa, and beta-hemolytic streptococci.

Trichosporon dohaense, a rare pathogen of human invasive infections, and literature review

Background

Trichosporon dohaense is a rare fungal species that has not been described in human invasive infections.

Patients and methods

In this study, we investigated two T. dohaense isolates from patients with invasive infections in two hospitals in China, as part of the China Hospital Invasive Fungal Surveillance Net (CHIF-NET) program. Both patients were under immunocompromised conditions.

Results

On chromogenic agar, T. dohaense isolates were dark blue, similar to the color of Candida. tropicalis, but the characteristic moist colony appearance was quite different from that of T. asahii. The two isolates were misidentified as T. asahii and T. inkin by the VITEK 2 YST system. The rDNA internal transcribed spacer (ITS) region and the D1/D2 domain sequences of the two T. dohaense isolates were 100% identical to T. dohaense type strain CBS10761^T. The sequence of the intergenic spacer region-1 also clearly distinguished the species. Of the three matrix-assisted laser desorption/ionization time-of-flight mass spectrometry systems, Bruker Biotyper and Autobio MS correctly identified the two isolates to species level, whereas Vitek MS systems misidentified them as T. ovoides or T. asteroides. Echinocandins exhibited no in vitro activities against the two T. dohaense isolates. In addition, the isolates exhibited intermediate susceptibility to fluconazole (with minimal inhibitory concentrations [MICs] of 8 and 16 µg/mL) and itraconazole, voriconazole, and posaconazole (MICs of 0.25-1 µg/mL). T. dohaense demonstrated susceptibility to amphotericin B with MIC of 1 µg/mL. The MICs of fluconazole and voriconazole in our study were higher than the MIC₅₀ of 62 for T. asahii isolates (4 and 0.064 µg/mL) in the CHIF-NET program.

Conclusion

This case study points to a possible emergence of T. dohaense as an opportunistic human invasive fungal pathogen, and the reduced susceptibility should be noted.

Rapid diagnostics for bloodstream infections: A primer for infection preventionists

Accurate and rapid antimicrobial susceptibility testing with pathogen identification in bloodstream infections is critical to life results for early sepsis intervention. Advancements in rapid diagnostics have shortened the time to results from days to hours and have had positive effects on clinical outcomes and on efforts to combat antimicrobial resistance when paired with robust antimicrobial stewardship programs. This article provides infection preventionists with a working knowledge of available rapid diagnostics for bloodstream infections.