Hospital-Associated Infections

Clinical and epidemiological aspects of Candida yeast infections and rational use of antifungals

Aim: The objective of this study was to evaluate the clinical and epidemiological aspects of Candida infections. Methods: The study relied on the analysis of electronic medical records. Results: Among 183 patients with positive fungal infections, 57 were from the community and 126 from hospitals. Females predominated in both groups (82.4% in the community, 54.7% in hospitals). Non-albicans Candida spp. accounted for 62.8% of cases. Antifungal therapy was prescribed for 67 patients, with a 55.6% mortality rate. Conclusion: The increasing prevalence of non-albicans Candida species highlights the need for better candidiasis monitoring and control, especially concerning antifungal use amidst rising antimicrobial resistance, particularly in empirical therapy scenarios.

Epidemiology, Clinical, and Microbiological Characteristics of Multidrug-Resistant Gram-Negative Bacteremia in Qatar

Antimicrobial resistance is a global healthcare threat with significant clinical and economic consequences peaking at secondary and tertiary care hospitals where multidrug-resistant Gram-negative bacteria (MDR GNB) lead to poor outcomes. A prospective study was conducted between January and December 2019 for all invasive bloodstream infections (BSIs) secondary to MDR GNB in Qatar identified during routine microbiological service to examine their clinical, microbiological, and genomic characteristics. Out of 3238 episodes of GNB BSIs, the prevalence of MDR GNB was 13% (429/3238). The predominant MDR pathogens were Escherichia coli (62.7%), Klebsiella pneumoniae (20.4%), Salmonella species (6.6%), and Pseudomonas aeruginosa (5.3%), while out of 245 clinically evaluated patients, the majority were adult males, with the elderly constituting almost one-third of the cohort and with highest observed risk for prolonged hospital stays. The risk factors identified included multiple comorbidities, recent healthcare contact, previous antimicrobial therapy, and admission to critical care. The in-hospital mortality rate was recorded at 25.7%, associated with multiple comorbidities, admission to critical care, and the acquisition of MDR Pseudomonas aeruginosa. Resistant pathogens demonstrated high levels of antimicrobial resistance but noticeable susceptibility to amikacin and carbapenems. Genomic analysis revealed that Escherichia coli ST131 and Salmonella enterica ST1 were the predominant clones not observed with other pathogens.

Association Between First Post-operative Day Urine Output Following Kidney Transplantation and Short-Term and Long-Term Outcomes: A Retrospective Cohort Study

Background

The relationship between post-operative urine output (UO) following kidney transplantation and long-term graft function has not been well described.

Objective

In this study, we examined the association between decreased UO on post-operative day 1 (POD1) and post-transplant outcomes.

Design

This is a retrospective cohort study.

Setting

Atlantic Canada.

Patients

Patients from the 4 Atlantic Canadian provinces (Nova Scotia, New Brunswick, Newfoundland, and Prince Edward Island) who received a live or deceased donor kidney transplant from 2006 through 2019 through the multiorgan transplant program at the Queen Elizabeth II Health Sciences Centre (QEII) hospital in Halifax, Nova Scotia.

Measurements

Using multivariable Cox proportional hazards models, we assessed the association of low POD1 UO (defined as ≤1000 mL) with death-censored graft loss (DCGL). In secondary analyses, we used adjusted logistic regression or Cox models as appropriate to assess the impact of UO on delayed graft function (DGF), prolonged length of stay (greater than the median for the entire cohort), and death.

Results

Of the 991 patients included, 151 (15.2%) had a UO ≤1000 mL on POD1. Low UO was independently associated with DCGL (hazard ratio [HR] = 4.00, 95% confidence interval [CI] = 95% CI = 1.55-10.32), DGF (odds ratio [OR] = 45.25, 95% CI = 23.00-89.02), and prolonged length of stay (OR = 5.06, 95% CI = 2.95-8.69), but not death (HR = 0.81, 95% CI = 0.31-2.09).

Limitations

This was a single-center, retrospective, observational study and therefore has inherent limitations of generalizability, data collection, and residual confounding.

Conclusions

Overall, reduced post-operative UO following kidney transplantation is associated with an increased risk of DCGL, DGF, and prolonged hospital length of stay.

Clinical and Laboratory Diagnosis of Legionella Pneumonia

Legionella pneumonia is a relatively rare but extremely progressive pulmonary infection with high mortality. Traditional cultural isolation remains the gold standard for the diagnosis of Legionella pneumonia. However, its harsh culture conditions, long turnaround time, and suboptimal sensitivity do not meet the clinical need for rapid and accurate diagnosis, especially for critically ill patients. So far, pathogenic detection techniques including serological assays, urinary antigen tests, and mass spectrometry, as well as nucleic acid amplification technique, have been developed, and each has its own advantages and limitations. This review summarizes the clinical characteristics and imaging findings of Legionella pneumonia, then discusses the advances, advantages, and limitations of the various pathogenetic detection techniques used for Legionella pneumonia diagnosis. The aim is to provide rapid and accurate guiding options for early identification and diagnosis of Legionella pneumonia in clinical practice, further easing healthcare burden.

Bacterial Community and Genomic Analysis of Carbapenem-Resistant Acinetobacter baumannii Isolates from the Environment of a Health Care Facility in the Western Region of Saudi Arabia

The escalating transmission of hospital-acquired infections, especially those due to antimicrobial-resistant bacteria, is a major health challenge worldwide. In this study, a culturomic analysis of bacterial community in a tertiary care hospital in the western region of Saudi Arabia is performed using environmental samples. The genome sequencing of four Acinetobacter baumannii was performed on isolates recovered from an intensive care unit (ICU) environment and clinical samples. A total of 361 bacterial isolates from surface and air samples were identified by MALDI-TOF technique or 16S rRNA gene sequencing. The isolates were classified into 70 distinct species, including ESKAPE pathogens. Resistance in Gram-positive isolates was mainly found to be against benzylpenicillin, azithromycin, ampicillin, and trimethoprim/sulfamethoxazole. Carbapenem- and multidrug-resistant isolates of A. baumannii and Klebsiella pneumonia were found on the ICU surfaces. Genome sequencing revealed that the carbapenem-resistant A. baumannii isolate from ICU environment was linked with those of clinical origin. The isolate Ab133-HEnv was classified as a novel sequence type (ST2528) based on a new allele of Oxf_gdhB-286. Three beta-lactam-antibiotic-resistance genes, bla_ADC-25, bla_OXA-23, and bla_OXA-66, were found in most of the analyzed genomes. Collectively, the results of this study highlight the spread of antimicrobial-resistant nosocomial pathogens in a health care facility in Saudi Arabia.

Microbiota restoration reduces antibiotic-resistant bacteria gut colonization in patients with recurrent Clostridioides difficile infection from the open-label PUNCH CD study

BACKGROUND

Once antibiotic-resistant bacteria become established within the gut microbiota, they can cause infections in the host and be transmitted to other people and the environment. Currently, there are no effective modalities for decreasing or preventing colonization by antibiotic-resistant bacteria. Intestinal microbiota restoration can prevent Clostridioides difficile infection (CDI) recurrences. Another potential application of microbiota restoration is suppression of non-C. difficile multidrug-resistant bacteria and overall decrease in the abundance of antibiotic resistance genes (the resistome) within the gut microbiota. This study characterizes the effects of RBX2660, a microbiota-based investigational therapeutic, on the composition and abundance of the gut microbiota and resistome, as well as multidrug-resistant organism carriage, after delivery to patients suffering from recurrent CDI.

METHODS

An open-label, multi-center clinical trial in 11 centers in the USA for the safety and efficacy of RBX2660 on recurrent CDI was conducted. Fecal specimens from 29 of these subjects with recurrent CDI who received either one (N = 16) or two doses of RBX2660 (N = 13) were analyzed secondarily. Stool samples were collected prior to and at intervals up to 6 months post-therapy and analyzed in three ways: (1) 16S rRNA gene sequencing for microbiota taxonomic composition, (2) whole metagenome shotgun sequencing for functional pathways and antibiotic resistome content, and (3) selective and differential bacterial culturing followed by isolate genome sequencing to longitudinally track multidrug-resistant organisms.

RESULTS

Successful prevention of CDI recurrence with RBX2660 correlated with taxonomic convergence of patient microbiota to the donor microbiota as measured by weighted UniFrac distance. RBX2660 dramatically reduced the abundance of antibiotic-resistant Enterobacteriaceae in the 2 months after administration. Fecal antibiotic resistance gene carriage decreased in direct relationship to the degree to which donor microbiota engrafted.

CONCLUSIONS

Microbiota-based therapeutics reduce resistance gene abundance and resistant organisms in the recipient gut microbiome. This approach could potentially reduce the risk of infections caused by resistant organisms within the patient and the transfer of resistance genes or pathogens to others.

TRIAL REGISTRATION

ClinicalTrials.gov, NCT01925417 ; registered on August 19, 2013.

Evaluation of a portable Ultraviolet C (UV-C) device for hospital surface decontamination

Background

Surface decontamination of hospital environments is essential to ensure the safety of health professionals and patients. This process is usually performed through active chemicals substances with high toxicity, and new decontamination technologies that do not leave residues have been currently used, such as UV-C light. Thus, the objective of the present study is to evaluate the effectiveness of a portable UV-C light device on the viability of standard pathogenic strains and other microorganisms isolated from different surfaces of a public health hospital.

Methods

In vitro decontamination was performed by applying Biosept Home© UV-C to Staphylococcus aureus, Staphylococcus epidermidis, Escherichia coli, Pseudomonas aeruginosa, Salmonella enterica and Candida albicans. In real conditions, the application was made on different surfaces of a hospital. The device used in the experiment haa a 254 nm UV-C light and a radiation intensity of 45.6 mW/cm² over a distance of 1 cm from the surfaces. The light dose was 0.912 J/cm² for 20 s of application in both conditions (in vitro and hospital).

Results

After in vitro decontamination with UV-C light no bacterial growth was observed, demonstrating 100 % of bacterial inactivation under the conditions tested. Additionally, there was a reduction of approximately 4 logs for the yeast C. albicans. In all hospital surfaces, the number of colonies of microorganisms was significantly reduced after the procedure.

Conclusion

The results suggest that Biosept Home© UV-C is efficient and constitutes a promosing intervention for disinfection protocols in hospitals and clinics.

Study of key RNA metabolism proteins in Enterococcus faecalis

The control of mRNA turnover is essential in bacteria to allow rapid adaptation, especially in opportunistic pathogen like Enterococcus faecalis. This mechanism involves RNase and DEAD-box helicases that are key elements in RNA processing and their associations form the degradosome with accessory proteins. In this study, we investigated the function of four RNases (J1, J2, Y and III) and three DEAD-box helicases (CshA, CshB, CshC) present in most Enterococci. The interactions of all these RNA metabolism actors were investigated in vitro, and the results are in accordance with a degradosome structure close to the one of Bacillus subtilis. At the physiological level, we showed that RNase J1 is essential, whereas RNases J2 and III have a role in cold, oxidative and bile salts stress response, and RNase Y in general fitness. Furthermore, RNases J2, Y and III mutants are affected in virulence in the Galleria mellonella infection model. Concerning DEAD-box helicases, all of them are involved in cold shock response. Since the ΔcshA mutant was the most stress impacted strain, we studied this DEAD-box helicase CshA in more detail. This showed that CshA autoregulates its own expression by binding to its mRNA 5'Unstranslated Region. Interestingly, CshC is also involved in the expression control of CshA by a hitherto unprecedented mechanism.

Complete Genome Sequences of Two Avilamycin-Resistant Enterococcus faecium Strains Isolated from Chicken in the United States

Avilamycin-resistant Enterococcus spp. have never been reported in the United States. Here, we report the complete genome sequences of two avilamycin-resistant (Avi^r) Enterococcus faecium strains isolated from a retail chicken and a cecal sample from a young chicken. Both isolates are multidrug resistant (MDR) and carry emtA on MDR plasmids.

Indoor hospital air and the impact of ventilation on bioaerosols: a systematic review

Healthcare-acquired infections (HAIs) continue to persist in hospitals, despite the use of increasingly strict infection-control precautions. Opportunistic airborne transmission of potentially pathogenic bioaerosols may be one possible reason for this persistence. Therefore, this study aimed to systematically review the concentrations and compositions of indoor bioaerosols in different areas within hospitals and the effects of different ventilation systems. Electronic databases (Medline and Web of Science) were searched to identify articles of interest. The search was restricted to articles published from 2000 to 2017 in English. Aggregate data was used to examine the differences in mean colony forming units per cubic metre (cfu/m³) between different hospital areas and ventilation types. A total of 36 journal articles met the eligibility criteria. The mean total bioaerosol concentrations in the different areas of the hospitals were highest in the inpatient facilities (77 cfu/m³, 95% confidence interval (CI): 55-108) compared with the restricted (13cfu/m³, 95% CI: 10-15) and public areas (14 cfu/m³, 95% CI: 10-19). Hospital areas with natural ventilation had the highest total bioaerosol concentrations (201 cfu/m³, 95% CI: 135-300) compared with areas using conventional mechanical ventilation systems (20 cfu/m³, 95% CI: 16-24). Hospital areas using sophisticated mechanical ventilation systems (such as increased air changes per hour, directional flow and filtration systems) had the lowest total bioaerosol concentrations (9 cfu/m³, 95% CI: 7-13). Operating sophisticated mechanical ventilation systems in hospitals contributes to improved indoor air quality within hospitals, which assists in reducing the risk of airborne transmission of HAIs.

CLIA-waived molecular influenza testing in the emergency department and outpatient settings

Respiratory tract infections are a common cause of visits to emergency departments and outpatient settings. Infections with influenza viruses A and B in particular, are responsible for significant morbidity and mortality in both pediatric and adult populations worldwide. A significant number of influenza diagnoses occur in the emergency departments with many being performed using rapid influenza diagnostic tests (RIDT) which have sensitivities as low as 30% depending on the specific RIDT and patient population. More recently, rapid molecular tests for the detection of influenza viruses A and B have become commercially available as point-of-care platforms. In the United States, several of these new tests are approved by the Food and Drug Administration as CLIA-waived tests. In this report, we review the data on the analytical and clinical performance of RIDTs and CLIA-waived molecular tests, present and discuss potential key challenges and opportunities for implementation of CLIA-waived molecular tests at or near point of care in the emergency departments and outpatient settings.

Whole-genome sequencing based characterization of antimicrobial resistance in Enterococcus

Whole-genome sequencing (WGS) has transformed our understanding of antimicrobial resistance, yielding new insights into the genetics underlying resistance. To date, most studies using WGS to study antimicrobial resistance have focused on gram-negative bacteria in the family Enterobacteriaceae, such as Salmonella spp. and Escherichia coli, which have well-defined resistance mechanisms. In contrast, relatively few studies have been performed on gram-positive organisms. We sequenced 197 strains of Enterococcus from various animal and food sources, including 100 Enterococcus faecium and 97 E. faecalis. From analyzing acquired resistance genes and known resistance-associated mutations, we found that resistance genotypes correlated with resistance phenotypes in 96.5% of cases for the 11 drugs investigated. Some resistances, such as those to tigecycline and daptomycin, could not be investigated due to a lack of knowledge of mechanisms underlying these phenotypes. This study showed the utility of WGS for predicting antimicrobial resistance based on genotype alone.

Multicenter Evaluation of the ePlex Respiratory Pathogen Panel for the Detection of Viral and Bacterial Respiratory Tract Pathogens in Nasopharyngeal Swabs

The performance of the new ePlex Respiratory Pathogen (RP) panel (GenMark Diagnostics) for the simultaneous detection of 19 viruses (influenza A virus; influenza A H1 virus; influenza A 2009 H1 virus; influenza A H3 virus; influenza B virus; adenovirus; coronaviruses [HKU1, OC43, NL63, and 229E]; human rhinovirus/enterovirus; human metapneumovirus; parainfluenza viruses 1, 2, 3, and 4; and respiratory syncytial virus [RSV] [RSV subtype A and RSV subtype B]) and 2 bacteria (Mycoplasma pneumoniae and Chlamydia pneumoniae) was evaluated. Prospectively and retrospectively collected nasopharyngeal swab (NPS) specimens (n = 2,908) were evaluated by using the ePlex RP panel, with the bioMérieux/BioFire FilmArray Respiratory Panel (BioFire RP) as the comparator method. Discordance analysis was performed by using target-specific PCRs and bidirectional sequencing. The reproducibility of the assay was evaluated by using reproducibility panels comprised of 6 pathogens. The overall agreement between the ePlex RP and BioFire RP results was >95% for all targets. Positive percent agreement with the BioFire RP result for viruses ranged from 85.1% (95% confidence interval [CI], 80.2% to 88.9%) to 95.1% (95% CI, 89.0% to 97.9%), while negative percent agreement values ranged from 99.5% (95% CI, 99.1% to 99.7%) to 99.8% (95% CI, 99.5% to 99.9%). Additional testing of discordant targets (12%; 349/2,908) confirmed the results of ePlex RP for 38% (131/349) of samples tested. Reproducibility was 100% for all targets tested, with the exception of adenovirus, for which reproducibilities were 91.6% at low virus concentrations and 100% at moderate virus concentrations. The ePlex RP panel offers a new, rapid, and sensitive “sample-to-answer” multiplex panel for the detection of the most common viral and bacterial respiratory pathogens.

Risk factors for health care-associated infection in hospitalized adults: Systematic review and meta-analysis

BACKGROUND

Health care-associated infections (HAIs) are a public health problem that increase health care costs. This article aimed to systematically review the literature and meta-analyze studies investigating risk factors (RFs) independently associated with HAIs in hospitalized adults.

METHODS

Electronic databases (MEDLINE, Embase, and LILACS) were searched to identify studies from 2009-2016. Pooled risk ratios (RRs) or odds ratios (ORs) or mean differences (MDs) and 95% confidence intervals (CIs) were calculated and compared across the groups. This review followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses statement.

RESULTS

Of 867 studies, 65 met the criteria for review, and the data of 18 were summarized in the meta-analysis. The major RFs independently associated with HAIs were diabetes mellitus (RR, 1.76; 95% CI, 1.27-2.44), immunosuppression (RR, 1.24; 95% CI, 1.04-1.47), body temperature (MD, 0.62; 95% CI, 0.41-0.83), surgery time in minutes (MD, 34.53; 95% CI, 22.17-46.89), reoperation (RR, 7.94; 95% CI, 5.49-11.48), cephalosporin exposure (RR, 1.77; 95% CI, 1.30-2.42), days of exposure to central venous catheter (MD, 5.20; 95% CI, 4.91-5.48), intensive care unit (ICU) admission (RR, 3.76; 95% CI, 1.79-7.92), ICU stay in days (MD, 21.30; 95% CI, 19.81-22.79), and mechanical ventilation (OR, 12.95; 95% CI, 6.28-26.73).

CONCLUSIONS

Identifying RFs that contribute to develop HAIs may support the implementation of strategies for their prevention, therefore maximizing patient safety.