Antimicrobial Susceptibility of Microorganisms Isolated from Patients with Intraabdominal Infection in Korea: a Multicenter Study

Prediction of microbe-drug associations based on a modified graph attention variational autoencoder and random forest

Introduction

The identification of microbe-drug associations can greatly facilitate drug research and development. Traditional methods for screening microbe-drug associations are time-consuming, manpower-intensive, and costly to conduct, so computational methods are a good alternative. However, most of them ignore the combination of abundant sequence, structural information, and microbe-drug network topology.

Methods

In this study, we developed a computational framework based on a modified graph attention variational autoencoder (MGAVAEMDA) to infer potential microbedrug associations by combining biological information with the variational autoencoder. In MGAVAEMDA, we first used multiple databases, which include microbial sequences, drug structures, and microbe-drug association databases, to establish two comprehensive feature matrices of microbes and drugs after multiple similarity computations, fusion, smoothing, and thresholding. Then, we employed a combination of variational autoencoder and graph attention to extract low-dimensional feature representations of microbes and drugs. Finally, the lowdimensional feature representation and graphical adjacency matrix were input into the random forest classifier to obtain the microbe-drug association score to identify the potential microbe-drug association. Moreover, in order to correct the model complexity and redundant calculation to improve efficiency, we introduced a modified graph convolutional neural network embedded into the variational autoencoder for computing low dimensional features.

Results

The experiment results demonstrate that the prediction performance of MGAVAEMDA is better than the five state-of-the-art methods. For the major measurements (AUC =0.9357, AUPR =0.9378), the relative improvements of MGAVAEMDA compared to the suboptimal methods are 1.76 and 1.47%, respectively.

Discussion

We conducted case studies on two drugs and found that more than 85% of the predicted associations have been reported in PubMed. The comprehensive experimental results validated the reliability of our models in accurately inferring potential microbe-drug associations.

Paediatric ventriculoperitoneal shunt failures: 12-year experience from a Singapore children's hospital

PURPOSE

Cerebrospinal fluid (CSF) shunt failures in children are devastating. The primary aims of this study are to, firstly, review our institutional series of ventriculoperitoneal shunt (VPS) insertions and identify factors associated with shunt failure.

METHODS

This is a single-institution, retrospective study conducted over a 12-year period. All patients under 18 years old with VPS inserted were included. Variables of interest such as patient characteristics, hydrocephalus aetiology, shunt implant details, and outcomes were subjected to statistical analyses.

RESULTS

A total of 214 VPS patients were selected for this study. The mean age at VPS insertion was 6 months with a mean follow-up duration of 44 months. The most common type of hydrocephalus was obstructive (n = 142, 66.4%), and the most frequent aetiology was tumour-related (n = 66, 30.8%). The 30-day shunt failure rate was 9.3%: 9 infections (4.2%), 7 occlusions (3.3%), and 4 others (1.9%). After multivariable analysis, only recent central nervous system (CNS) infection prior to VPS insertion remained significant (OR 15.4 (1.3-175), p = 0.028).

CONCLUSION

This is the first, large-scale local study focused on the shunt failure in Singaporean children. Significant findings in our study demonstrate that recently treated CNS infection is a factor associated with 30-day shunt failure while the values of CSF constituents were not contributory.

A Six-Year Retrospective Study of Microbiological Characteristics and Antimicrobial Resistance in Specimens from a Tertiary Hospital’s Surgical Ward

Surgery has revolutionized the practice of medicine by allowing the treatment of conditions amenable to conservative medical management with some of them pathophysiologically involving the prevalence of pathogenic microorganisms. On the other hand, infections such as surgical site infections or urinary tract infections may complicate patients hospitalized in surgical wards leading to considerable morbidity, mortality, and increased healthcare-associated costs. The aim of this study was to present the microbiological characteristics and antimicrobial resistance of all isolates identified in microbiological specimens from a surgical ward of a tertiary hospital in Greece during a six-year period. Only specimens that yielded at least one microorganism were included in the analysis. In total, 1459 strains in 789 positive cultures were isolated. The most common sample sent to the microbiology department was pus from surgical wounds. The most common pathogens among all 1459 strains isolated were Enterobacterales at 33% (n = 482), however, the most common genus was Enterococcus at 22.3% (n = 326). Antimicrobial resistance against third-generation cephalosporins was 23% (n = 111/482) among Enterobacterales, while, the rate of vancomycin-resistant enterococci (VRE) was 18.5% (n = 60/324) among Enterococcus species and was increasing in the last years of the study. Antimicrobial resistance of Acinetobacter baumannii to carbapenems was 68.8% (n = 11/16), which was lower than the corresponding rate in other wards in Greece. The antimicrobial resistance rates noted herein raise questions regarding the appropriateness of currently suggested antimicrobials in guidelines and imply that a revision could be required. Practicing clinicians should always be aware of local microbiological data that allow the selection of appropriate antimicrobials for the management of infections. Finally, the increasing rates of VRE noted herein mandate further actions from the point of infection control and antimicrobial stewardship.

Effect of restricting piperacillin/tazobactam prescription on rates of antimicrobial resistance in gram-negative bacteria and antibiotic consumption

The increasing resistance of gram-negative bacteria is a serious global public health concern. One way to prevent increasing antibiotic resistance is by implementing the antibiotic stewardship program. This study aimed to assess the changes in the consumption of antimicrobials and antimicrobial resistance rates after implementing piperacillin/tazobactam restriction. This study was conducted at Kandong Sacred Heart Hospital. We retrospectively collected and analysed data between October 2018 and May 2021 to evaluate antibiotic consumption and resistance patterns after restricting piperacillin/tazobactam. This study included two periods, a 16-month pre-restriction period and a 16-month post-restriction period. During the study period, there was a significant decrease in the consumption of piperacillin/tazobactam after implementing the restriction policy (127.82 ± 9.39 to 104.82 ± 15.66 defined daily doses/1000 patient days, p < 0.001). A significant decrease in the resistance rate of Acinetobacter spp. was observed for cefepime (p = 0.001), ceftazidime (p = 0.004), levofloxacin (p = 0.021), meropenem (p = 0.002) and piperacillin (p = 0.028). The introduction of piperacillin/tazobactam restriction reduced their use and positively impacted the resistance rates of Acinetobacter spp., carbapenem-resistant Pseudomonas spp. and carbapenem-resistant Enterobacteriaceae which are major threats to nosocomial infections.

Korean Guidelines for Use of Antibiotics for Intra-abdominal Infections in Adults

The guidelines are intended to provide practical information for the correct use of antibiotics for intra-abdominal infections in Korea. With the aim of realizing evidence-based treatment, these guidelines for the use of antibiotics were written to help clinicians find answers to key clinical questions that arise in the course of patient care, using the latest research results based on systematic literature review. The guidelines were prepared in consideration of the data on the causative pathogens of intra-abdominal infections in Korea, the antibiotic susceptibility of the causative pathogens, and the antibiotics available in Korea.

Genomics and pathotypes of the many faces of Escherichia coli

Escherichia coli is the most researched microbial organism in the world. Its varied impact on human health, consisting of commensalism, gastrointestinal disease, or extraintestinal pathologies, has generated a separation of the species into at least eleven pathotypes (also known as pathovars). These are broadly split into two groups, intestinal pathogenic E. coli (InPEC) and extraintestinal pathogenic E. coli (ExPEC). However, components of E. coli's infinite open accessory genome are horizontally transferred with substantial frequency, creating pathogenic hybrid strains that defy a clear pathotype designation. Here, we take a birds-eye view of the E. coli species, characterizing it from historical, clinical, and genetic perspectives. We examine the wide spectrum of human disease caused by E. coli, the genome content of the bacterium, and its propensity to acquire, exchange, and maintain antibiotic resistance genes and virulence traits. Our portrayal of the species also discusses elements that have shaped its overall population structure and summarizes the current state of vaccine development targeted at the most frequent E. coli pathovars. In our conclusions, we advocate streamlining efforts for clinical reporting of ExPEC, and emphasize the pathogenic potential that exists throughout the entire species.

Abdominal fascia dehiscence: is there a connection to a special microbial spectrum?

INTRODUCTION

Acute fascia dehiscence (FD) is a threatening complication occurring in 0.4-3.5% of cases after abdominal surgery. Prolonged hospital stay, increased mortality and increased rate of incisional hernias could be following consequences. Several risk factors are controversially discussed. Even though surgical infection is a known, indisputable risk factor, it is still not proven if a special spectrum of pathogens is responsible. In this study, we investigated if a specific spectrum of microbial pathogens is associated with FD.

METHODS

We performed a retrospective matched pair analysis of 53 consecutive patients with an FD after abdominal surgery in 2010-2016. Matching criteria were gender, age, primary procedure and surgeon. The primary endpoint was the frequency of pathogens detected intraoperatively, the secondary endpoint was the occurrence of risk factors in patients with (FD) and without (nFD) FD.

RESULTS

Intraabdominal pathogens were detected more often in the FD group (p = 0.039), with a higher number of Gram-positive pathogens. Enterococci were the most common pathogen (p = 0.002), not covered in 73% (FD group) compared to 22% (nFD group) by the given antibiotic therapy. Multivariable analysis showed detection of Gram-positive pathogens, detection of enterococci in primary laparotomy beside chronic lung disease, surgical site infections and continuous steroid therapy as independent risk factors.

CONCLUSION

Risk factors are factors that reduce wound healing or increase intra-abdominal pressure. Furthermore detection of Gram-positive pathogens especially enterococci was detected as an independent risk factor and its empirical coverage could be advantageous for high-risk patients.

Predictive value of immune cell counts and neutrophil-to-lymphocyte ratio for 28-day mortality in patients with sepsis caused by intra-abdominal infection

Background

The current study aimed to evaluate the value of immune cell counts and neutrophil-to-lymphocyte ratio (NLR) when attempting to predict 28-day mortality.

Methods

We conducted an observational retrospective study that included consecutive septic patients. Severity scores on the first day and peripheral circulating immune cell counts (at day 1, day 3, day 5 and day 7 of admission) were collected during each patient’s emergency intensive care unit stay. We assessed the associations of peripheral circulating immune cell counts and NLR with the severity of illness. The relationships between 28-day mortality and peripheral circulating immune cell counts and NLR with were evaluated using Cox proportional cause-specific hazards models.

Results

A total of 216 patients diagnosed with sepsis caused by IAI were enrolled. The lymphocyte counts (days 1, 3, 5 and 7) and monocyte counts (days 3, 5 and 7) were significantly lower in non-survivors (n = 72) than survivors (n = 144). The NLR values at each time point were significantly higher in non-survivors. The day 1 lymphocyte counts, as well as the monocyte counts, were significantly lower in the highest-scoring group, when stratified by the Acute Physiology and Chronic Health Evaluation II and Sequential Organ Failure Assessment scores, than in the other groups (p < 0.05). The day 1 NLR was significantly higher in the highest-scoring group than in the other groups (p < 0.05). The day 5 and day 7 lymphocyte counts, day 3 and day 7 monocyte counts and day 7 NLR were significant predictors of 28-day mortality in the Cox proportional hazards models (day 5 lymphocyte count: hazard ratio, 0.123 (95% CI, 0.055–0.279), p < 0.001; day 7 lymphocyte count: hazard ratio, 0.115 (95% CI, 0.052–0.254), p < 0.001; day 3 monocyte count: hazard ratio, 0.067 (95% CI, 0.005–0.861), p = 0.038; day 7 monocyte count: hazard ratio, 0.015 (95% CI, 0.001–0.158), p < 0.001; day 7 NLR: hazard ratio, 0.773 (95% CI, 0.659–0.905), p = 0.001).

Conclusions

The results showed that circulating lymphocytes and monocytes were dramatically decreased within 7 days in non-survivors following sepsis from an IAI. Lymphocyte counts, monocyte counts and NLR appeared to be associated with the severity of illness, and they may serve as independent predictors of 28-day mortality in septic patients with IAIs.

Early Procalcitonin Assessment in the Emergency Department in Patients with Intra-Abdominal Infection: An Excess or a Need?

Background: Intra-abdominal infection (IAI) is a wide range of intra-abdominal disease. Management involves empirical therapy and source control. Procalcitonin (PCT) has been suggested to assist in defining individual infection status and delivering individualized therapy. The aim of this study was to investigate the effects on patient outcomes of an early procalcitonin (PCT) assessment (in the emergency department [ED]) in patients with IAI. Methods: This was a retrospective, mono-centric study evaluating consecutive patients admitted to the ED from 2015 to 2019 with diagnosis of IAI. According to whether there had been PCT determination in the ED, patients were divided into no ePCT determination (no-ePCT) and early PCT determination in the ED (ePCT). The primary endpoint was the intra-hospital mortality rate. Secondary endpoints were occurrence of major complications and length of hospital stay (LOS). The propensity score match (PSM) was generated using a logistic regression model on the baseline covariates considered to be potentially influencing the decision to determine PCT in the ED and confounding factors identified as significant at a preliminary statistical analysis with respect to in-hospital death. Results: A series of 3,429 patients were included. The ePCT group consisted to 768 (22.4%), whereas the no-ePCT group contained 2,661 patients (77.6%). When the PSM was matched to the two groups, no significant difference was observed. Considering patients with uncomplicated infections, the PCT determination was associated with a higher mortality rate. We found no significant differences regarding outcomes with the exception of LOS, which was slightly longer in the ePCT group. However, we observed a tendency toward a minor difference in the number of complications in the ePCT group, in particular a reduced rate of progression to sepsis. Conclusion: Early PCT determination could be irrelevant in IAIs. The PCT value may be cost-effective and possibly improve the prognosis in cIAIs. Further research is needed to understand the optimal use of PCT, including in combination with other emerging diagnostic tests.

Association Mining to Identify Microbe Drug Interactions Based on Heterogeneous Network Embedding Representation

Accurately identifying microbe-drug associations plays a critical role in drug development and precision medicine. Considering that the conventional wet-lab method is time-consuming, labor-intensive and expensive, computational approach is an alternative choice. The increasing availability of numerous biological data provides a great opportunity to systematically understand complex interaction mechanisms between microbes and drugs. However, few computational methods have been developed for microbe drug prediction. In this work, we leverage multiple sources of biomedical data to construct a heterogeneous network for microbes and drugs, including drug-drug interactions, microbe-microbe interactions and microbe-drug associations. And then we propose a novel Heterogeneous Network Embedding Representation framework for Microbe-Drug Association prediction, named (HNERMDA), by combining metapath2vec with bipartite network recommendation. In this framework, we introduce metapath2vec, a heterogeneous network representation learning method, to learn low-dimensional embedding representations for microbes and drugs. Following that, we further design a bias bipartite network projection recommendation algorithm to improve prediction accuracy. Comprehensive experiments on two datasets, named MDAD and aBiofilm, demonstrated that our model consistently outperformed five baseline methods in three types of cross-validations. Case study on two popular drugs (i.e., Ciprofloxacin and Pefloxacin) further validated the effectiveness of our HNERMDA model in inferring potential target microbes for drugs.

Is the Isolation of Pseudomonas aeruginosa Associated with Outcomes from Intra-Abdominal Infection? No, But the Receipt of an Empiric Anti-Pseudomonal Agent Is

Background: Pseudomonas aeruginosa is isolated at variable rates from intra-abdominal infections (IAI). Not all recommended empiric regimens for IAI include anti-Pseudomonas aeruginosa activity, for example, ceftriaxone and metronidazole. We hypothesized that within an adult population, Pseudomonas aeruginosa is a relatively rare isolate and has no association with mortality, and thus, empiric therapy with anti-Pseudomonas aeruginosa activity is not warranted. Patients and Methods: All IAI with positive cultures treated between 1997 and 2017 at a single institution were analyzed. This data set was divided into two cohorts, namely, those with cultures positive for Pseudomonas aeruginosa and those without. Demographics and in-hospital mortality were compared by Student t-test and χ² analysis. Predictors of isolation of Pseudomonas aeruginosa and in-hospital mortality were done by logistic regression (LR) analysis. Results: In total, 2,420 IAIs were identified, 104 (4.3%) with Pseudomonas aeruginosa and 2,316 (95.7%) without. Major demographic differences between patients with Pseudomonas aeruginosa and those without included a higher rate of health-care-associated infections (87/104, 83.7% vs. 621/2316, 26.8%; p = 0.02), a higher rate of intensive care unit (ICU)-acquired infections (23/104, 22.1% vs. 329/2316, 14.2%; p = 0.04) and a higher Acute Physiology and Chronic Health Evaluation (APACHE) II score (17.7 ± 0.8 vs. 14.5 ± 0.2; p < 0.0001). There was an increased rate of Pseudomonas aeruginosa isolation with increasing APACHE II score. Independent predictors of isolation of Pseudomonas aeruginosa by LR included APACHE II score and days of hospitalization prior to diagnosis. Crude in-hospital mortality was similar between groups: Pseudomonas aeruginosa 14/104 (13.5%) and 276/2316 (11.9%), p = 0.79. After controlling for age, gender, APACHE II, prior transfusion, immunosuppression status, solid organ transplant status, healthcare-association, and days of hospitalization prior to diagnosis, the isolation of Pseudomonas aeruginosa was not associated with mortality. Conclusion: Pseudomonas aeruginosa is infrequently isolated and overall not associated with mortality. Nonetheless, there may be a population that merits empiric anti-Pseudomonas aeruginosa therapy: those with APACHE II ≥20 or a significant length of hospitalization prior to diagnosis.