Multimodal surveillance of healthcare associated infections in an intensive care unit of a large teaching hospital

Investigation of bacterial and fungal population structure on environmental surfaces of three medical institutions during the COVID-19 pandemic

Objectives

To evaluate the population structure of environmental bacteria and fungi in three different types of medical institutions and the potential risks due to antibiotic resistance during the coronavirus disease 2019 (COVID-19) pandemic.

Methods

One hundred twenty-six environmental surface samples were collected from three medical institutions during the COVID-19 pandemic. A total of 6,093 and 13,514 representative sequences of 16S and ITS ribosomal RNA (rRNA) were obtained by amplicon sequencing analysis. The functional prediction was performed using the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States tool based on the Greengenes database and the FAPROTAX database.

Results

On environmental surfaces in three medical institutions during the COVID-19 pandemic, Firmicutes (51.6%) and Bacteroidetes (25%) were the dominant bacteria, while Ascomycota (39.4%) and Basidiomycota (14.2%) were the dominant fungi. A number of potential bacterial and fungal pathogens were successfully identified by the metagenomic approach. Furthermore, compared with the bacterial results, the fungi showed a generally closer Bray Curtis distance between samples. The overall ratio of Gram-negative bacteria to Gram-positive bacteria was about 3:7. The proportion of stress-tolerant bacteria in medical institutions A, B and C reached 88.9, 93.0 and 93.8%, respectively. Anaerobic bacteria accounted for 39.6% in outdoor environments, 77.7% in public areas, 87.9% in inpatient areas and 79.6% in restricted areas. Finally, the β-Lactam resistance pathway and polymyxin resistance pathway were revealed through functional prediction.

Conclusion

We described the microbial population structure changes in three different types of medical institutions using the metagenomic approach during the COVID-19 pandemic. We found that the disinfection measures performed by three healthcare facilities may be effective on the “ESKAPE” pathogens, but less effective on fungal pathogens. Moreover, emphasis should be given to the prevention and control of β-lactam and polymyxin antibiotics resistance bacteria during the COVID-19 pandemic.

Effectiveness of an Active and Continuous Surveillance Program for Intensive Care Units Infections Based on the EPIC III (Extended Prevalence of Infection in Intensive Care) Approach

We evaluated the effectiveness of the Extended Prevalence of Infection in Intensive Care (EPIC) III data collection protocol as an active surveillance tool in the eight Intensive Care Units (ICUs) of the Intensive and Critical Care Department of the University Hospital of Turin. A total of 435 patients were included in a six-day study over 72 ICU beds. 42% had at least one infection: 69% at one site, 26% at two sites and 5% at three or more sites. ICU-acquired infections were the most common (64%), followed by hospital-associated infections (22%) and community-acquired (20%), considering that each patient may have developed more than one infection type. 72% of patients were receiving at least one antibiotic: 48% for prophylaxis and 52% for treatment. Mortality, the length of ICU and hospital stays were 13%, 14 and 29 days, respectively, being all estimated to be significantly different in patients without and with infection (8% vs. 20%; 4 vs. 20 and 11 vs. 50 (p < 0.001). Our data confirm a high prevalence of infections, sepsis and the use of antimicrobials. The repeated punctual prevalence survey seems an effective method to carry out the surveillance of infections and the use of antimicrobials in the ICU. The use of the European Centre for Disease Prevention and Control (ECDC) definitions and the EPIC III protocol seems strategic to allow comparisons with national and international contexts.

Acinetobacter baumannii Isolates from COVID-19 Patients in a Hospital Intensive Care Unit: Molecular Typing and Risk Factors

Infections caused by Acinetobacter baumannii represent a major concern for intensive care unit (ICU) patients. However, the epidemiology of these infections among COVID-19 patients has not been fully explored. The aims of this study were (i) to characterize the clonal spread of A. baumannii among COVID-19 patients admitted to the ICU of the Umberto I hospital of Rome during the first year of the pandemic and (ii) to identify risk factors for its acquisition. Isolates were analysed by pulsed-field gel electrophoresis, and a multivariable regression model was constructed. Adjusted odds ratios (aORs) and 95% confidence intervals (CIs) were calculated. Overall, 193 patients were included, and 102 strains were analysed. All isolates had highly antibiotic-resistant profiles and derived from two genotypes. The cumulative incidence of A. baumannii acquisition (colonization or infection) was 36.8%. Patients with A. baumannii had higher mortality and length of stay. Multivariable analysis showed that previous carbapenem use was the only risk factor associated with A. baumannii acquisition (aOR: 4.15, 95% CI: 1.78–9.64). We documented substantial A. baumannii infections and colonization and high levels of clonal transmission. Given the limited treatment options, effective prevention and containment strategies to limit the spread of A. baumannii should be implemented.

Comparing the Occurrence of Healthcare-Associated Infections in Patients with and without COVID-19 Hospitalized during the Pandemic: A 16-Month Retrospective Cohort Study in a Hospital Intensive Care Unit

The COVID-19 pandemic has increased the healthcare-associated infection (HAI) risk in intensive care unit (ICU) patients. However, a comparison between patients with and without COVID-19 in terms of HAI incidence has been rarely explored. In this study, we characterized the occurrence of HAI among patients with and without COVID-19 admitted to the ICU of the Umberto I hospital of Rome during the first 16 months of the pandemic and also identified risk factors for HAI acquisition. Patients were divided into four groups according to their ICU admission date. A multivariable conditional risk set regression model for multiple events was constructed for each admission period. Adjusted hazard ratios and 95% confidence intervals were calculated. Overall, 352 COVID-19 and 130 non-COVID-19 patients were included, and a total of 361 HAIs were recorded. We found small differences between patients with and without COVID-19 in the occurrence and type of HAI, but the infections in the two cohorts mostly involved different microorganisms. The results indicate that patient management was likely an important factor influencing the HAI occurrence during the pandemic. Effective prevention and control strategies to reduce HAI rates should be implemented.

Antimicrobial Stewardship in College and University Health Settings: A Public Health Opportunity

Antimicrobial resistance poses a significant threat to public health and safety across the globe. Many factors contribute to antibiotic resistance, most especially are the concerns of excessive prescribing and misuse of antibiotics. Because patient expectations for antibiotics may contribute to prescriber pressures, experts recommend targeting antimicrobial stewardship (AMS) education efforts towards prescribers as well as patients in outpatient settings. Undergraduate university students are a unique and promising target population for AMS efforts because they are in a transformative life stage of social, cognitive, and physical development in which they are learning to independently care for themselves without the presence or influence of parents. By introducing AMS education during this transition, university students may adopt positive antibiotic use behaviors that they will carry throughout their lives. Not only will their personal health be improved, but widespread adoption of AMS in university settings may have a broader effect on public health of present and future generations. Despite public health opportunities, minimal research has examined AMS in university health settings. This article explores current evidence on knowledge, attitudes, and use of antibiotics among university students and discusses opportunities for AMS initiatives in college and university health settings.

Place in Therapy of the Newly Available Armamentarium for Multi-Drug-Resistant Gram-Negative Pathogens: Proposal of a Prescription Algorithm

The worldwide propagation of antimicrobial resistance represents one of the biggest threats to global health and development. Multi-drug-resistant organisms (MDROs), including carbapenem-resistant non-fermenting Gram-negatives and Enterobacterales, present a heterogeneous and mutating spread. Infections by MDRO are often associated with an unfavorable outcome, especially among critically ill populations. The polymyxins represented the backbone of antibiotic regimens for Gram-negative MDROs in recent decades, but their use presents multiple pitfalls. Luckily, new agents with potent activity against MDROs have become available in recent times and more are yet to come. Now, we have the duty to make the best use of these new therapeutic tools in order not to prematurely compromise their effectiveness and at the same time improve patients’ outcomes. We reviewed the current literature on ceftazidime/avibactam, meropenem/vaborbactam and cefiderocol, focusing on antimicrobial spectrum, on the prevalence and mechanisms of resistance development and on the main in vitro and clinical experiences available so far. Subsequently, we performed a step-by-step construction of a speculative algorithm for a reasoned prescription of these new antibiotics, contemplating both empirical and targeted use. Attention was specifically posed on patients with life-risk conditions and in settings with elevated prevalence of MDRO.

Epidemiological Characterization and the Impact of Healthcare-Associated Pneumonia in Patients Admitted in a Northern Portuguese Hospital

Pneumonia is one of the main causes of hospitalization and mortality. It’s the fourth leading cause of death worldwide. Healthcare-associated infections are the most frequent complication of healthcare and affect hundreds of millions of patients around the world, although the actual number of patients affected is unknown due to the difficulty of reliable data. The main goal of this manuscript is to describe the epidemiological characteristics of patients admitted with pneumonia and the impact of healthcare-associated pneumonia (HCAP) in those patients. It is a quantitative descriptive study with retrospective analysis of the clinical processes of 2436 individuals for 1 year (2018) with the diagnosis of pneumonia. The individuals with ≤5 years old represented 10.4% (n = 253) and ≥65 were 72.6% (n = 1769). 369 cases resulted in death, which gives a sample lethality rate of 15.2%. The severity and mortality index were not sensitive to the death event. We found 30.2% (n = 735) individuals with HCAP and 0.41% (n = 59) with ventilator-associated pneumonia (VAP). In only 59 individuals (2.4%) the agent causing pneumonia was isolated. The high fatality rate obtained shows that pneumonia is a major cause of death in vulnerable populations. Moreover, HCAP is one of the main causes of hospital admissions from pneumonia and death and the most pneumonias are treated empirically. Knowledge of the epidemiology characterization of pneumonia, especially associated with healthcare, is essential to increase the skills of health professionals for the prevention and efficient treatment of pneumonia.

The "Torment" of Surgical Antibiotic Prophylaxis among Surgeons

Surgical antibiotic prophylaxis (SAP) is one of the peri-operative measures for preventing surgical site infections (SSIs). Its goal is to counteract the proliferation of bacteria in the surgical site during intervention in order to reduce the risk of SSIs. SAP should be administered for surgical interventions where the benefit expected (prevention of SSIs) is higher compared to the risk (serious side effects, such as acute kidney injury, Clostridioides difficile infection, and the spread of antimicrobial resistance). In prescribing SAP, surgeons should have both the awareness necessary “to handle antibiotics with care”, and the knowledge required to use them appropriately.

The impact of the COVID-19 pandemic on healthcare-associated infections in intensive care unit patients: a retrospective cohort study

Background

During the intensive care units’ (ICUs) reorganization that was forced by the COVID-19 emergency, attention to traditional infection control measures may have been reduced. Nevertheless, evidence on the effect of the COVID-19 pandemic on healthcare-associated infections (HAIs) is still limited and mixed. In this study, we estimated the pandemic impact on HAI incidence and investigated the HAI type occurring in COVID-19 patients.

Methods

Patients admitted to the main ICU of the Umberto I teaching hospital of Rome from March 1st and April 4th 2020 were compared with patients hospitalized in 2019. We assessed the association of risk factors and time-to-first event through multivariable Fine and Grey’s regression models, that consider the competitive risk of death on the development of HAI (Model 1) or device related-HAI (dr-HAI, Model 2) and provide estimates of the sub-distribution hazard ratio (SHR) and its associated confidence interval (CI). A subgroup analysis was performed on the 2020 cohort.

Results

Data from 104 patients were retrieved. Overall, 59 HAIs were recorded, 32 of which occurred in the COVID-19 group. Patients admitted in 2020 were found to be positively associated with both HAI and dr-HAI onset (SHR: 2.66, 95% CI 1.31–5.38, and SHR: 10.0, 95% CI 1.84–54.41, respectively). Despite being not confirmed at the multivariable analysis, a greater proportion of dr-HAIs seemed to occur in COVID-19 patients, especially ventilator-associated pneumonia, and catheter-related urinary tract infections.

Conclusions

We observed an increase in the incidence of patients with HAIs, especially dr-HAIs, mainly sustained by COVID-19 patients. A greater susceptibility of these patients to device-related infections was hypothesized, but further studies are needed.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13756-021-00959-y.

Prior Antibiotic Therapy and the Onset of Healthcare-Associated Infections Sustained by Multidrug-Resistant Klebsiella pneumoniae in Intensive Care Unit Patients: A Nested Case-Control Study

Epidemiological research has demonstrated direct relationships between antibiotic consumption and the emergence of multidrug-resistant (MDR) bacteria. In this nested case-control study, we assessed whether prior exposure to antibiotic therapy and its duration affect the onset of healthcare-associated infections (HAIs) sustained by MDR Klebsiella pneumoniae (MDR-Kp) in intensive care unit patients. Cases were defined as patients who developed an MDR-Kp HAI. Controls matched on sex and the length of intensive care unit (ICU) stay were randomly selected from the at-risk population. Any antibiotic agent received in systemic administration before the onset of infection was considered as antibiotic exposure. Multivariable conditional logistic regression analyses were performed to estimate the effect of prior exposure to each antibiotic class (Model 1) or its duration (Model 2) on the onset of HAIs sustained by MDR-Kp. Overall, 87 cases and 261 gender-matched controls were compared. In Model 1, aminoglycosides and linezolid independently increased the likelihood of developing an MDR-Kp HAI, whereas exposure to both linezolid and penicillins reduced the effect of linezolid alone. In Model 2, cumulative exposure to aminoglycosides increased the likelihood of the outcome, as well as cumulative exposures to penicillins and colistin, while a previous exposure to both penicillins and colistin reduced the influence of the two antibiotic classes alone. Our study confirms that aminoglycosides, penicillins, linezolid, and colistin may play a role in favoring the infections sustained by MDR-Kp. However, several double exposures in the time window before HAI onset seemed to hinder the selective pressure exerted by individual agents.

The Incidence of Healthcare-Associated Infections, Their Clinical Forms, and Microbiological Agents in Intensive Care Units in Southern Poland in a Multicentre Study from 2016 to 2019

INTRODUCTION

Healthcare-associated infections (HAIs) are a serious problem of modern medicine. Patients hospitalized in intensive care units (ICUs) develop HAI significantly more often than patients in other hospital units.

MATERIALS AND METHODS

Analysis involved HAIs from three ICUs in southern Poland. The study was conducted in 2016-2019 on the basis of methodology recommended by the Healthcare-Associated Infections Surveillance Network (HAI-Net) and European Centre for Disease Prevention and Control (ECDC). The objective was to analyse HAIs, their clinical forms, and microbiological agents.

RESULTS

The study included 3028 patients hospitalized for 26,558 person-days (pds) in ICU. A total of 540 HAIs were detected; incidence per 100 hospitalizations was 17.8%, incidence density per 1000 pds was 20.3. The mortality of patients with HAI was 16%, and in Clostridioidesdifficile infection (CDI), the mortality was 28%. The most common clinical form of HAI was bloodstream infection (BSI): 209 cases (incidence rate 6.9%), followed by pneumonia (PN): 131 (incidence rate 4.3%), and urinary tract infection (UTI): 110 cases (incidence rate 3.6%). The most frequently isolated bacteria were Klebsiella pneumoniae 16.4%, Acinetobacter baumannii 14.4%, Staphylococcus aureus 11.8%, and Escherichia coli 11.4%.

CONCLUSIONS

A two-fold higher incidence rate of BSI was detected compared to the average incidence in European countries. BSI of unknown source (BSI-UNK) was predominant. K. pneumoniae and A. baumannii bacteria were the most often isolated microorganisms causing HAI. Infection control based on incidence rate for each type of infection is necessary in ICU to assess the epidemiological situation.

Acinetobacter baumannii: Its Clinical Significance in Human and Veterinary Medicine

Acinetobacter baumannii is a Gram-negative, opportunistic pathogen, causing severe infections difficult to treat. The A. baumannii infection rate has increased year by year in human medicine and it is also considered as a major cause of nosocomial infections worldwide. This bacterium, also well known for its ability to form biofilms, has a strong environmental adaptability and the characteristics of multi-drug resistance. Indeed, strains showing fully resistant profiles represent a worrisome problem in clinical therapeutic treatment. Furthermore, A. baumannii-associated veterinary nosocomial infections has been reported in recent literature. Particularly, carbapenem-resistant A. baumannii can be considered an emerging opportunistic pathogen in human medicine as well as in veterinary medicine.