Comparative Genomics of Borderline Oxacillin-Resistant Staphylococcus aureus Detected during a Pseudo-outbreak of Methicillin-Resistant S. aureus in a Neonatal Intensive Care Unit

Active surveillance for methicillin-resistant Staphylococcus aureus (MRSA) is a component of our neonatal intensive care unit (NICU) infection prevention efforts. Recent atypical trends prompted review of 42 suspected MRSA isolates. Species identification was confirmed by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), and methicillin resistance was reevaluated by PBP2a lateral flow assay, cefoxitin/oxacillin susceptibility testing, mecA and mecC PCR, and six commercially available MRSA detection agars. All isolates were confirmed S. aureus, but only eight were MRSA (cefoxitin resistant, PBP2a positive, mecA positive, growth on all MRSA screening agars). One MRSA isolate was cefoxitin susceptible but PBP2a and mecA positive, and the remaining 33 were cefoxitin susceptible, PBP2a negative, and mecA negative; interestingly, these isolates grew inconsistently across MRSA screening agars and had susceptibility profiles consistent with that of borderline oxacillin-resistant S. aureus (BORSA). Comparative genomic analyses found these BORSA isolates to be phylogenetically diverse and not representative of clonal expansion or shared gene content, though clones of two NICU strains were infrequently observed over 8 months. We identified 6 features-substitutions and truncations in PBP2, PBP4, and GdpP and beta-lactamase hyperproduction-that were used to generate a random forest classifier to distinguish BORSA from methicillin-susceptible S. aureus (MSSA) in our cohort. Our model demonstrated a robust ability to predict the BORSA phenotype among isolates collected across two continents (validation area under the curve [AUC], 0.902). Taking these findings together, we observed an unexpected prevalence of BORSA in our NICU, BORSA misclassification by existing MRSA screening methods, and markers that are together discriminatory for BORSA and MSSA within our cohort. This work has implications for epidemiological reporting of MRSA rates for centers using different screening methods. IMPORTANCE In this study, we found a high prevalence of Staphylococcus aureus isolates exhibiting a borderline oxacillin resistance phenotype (BORSA) in our neonatal intensive care unit (NICU) serendipitously due to the type of MRSA screening agar used by our laboratory for active surveillance cultures. Subsequent phenotypic and molecular characterization highlighted an unexpected prevalence and variability of BORSA isolates. Through whole-genome sequencing, we interrogated core and accessory genome content and generated a random forest classification model to identify mutations and truncations in the PBP2, PBP4, and GdpP proteins and beta-lactamase hyperproduction, which correlated with BORSA and MSSA phenotypes among S. aureus clinical isolates collected across two continents. In consideration of these findings, this work will help clinical microbiology laboratories and clinicians identify MRSA screening shortfalls and draw attention to the non-mecA-mediated BORSA phenotype.

[Reducing Abnormal Culture Rates of Digestive Endoscopy in a Health Management Center]

BACKGROUND

Endoscopic evaluation plays an indispensable role in medical treatments designed to prevent, diagnose, and cure gastrointestinal disease. Surveillance culture monitoring may be useful in monitoring the outcome of reprocessing.

PURPOSE

In this project, microbiologic surveillance cultures were employed to improve the quality of flexible endoscope disinfection.

RESOLUTION

This project, implemented from February 1st, 2018 to February 28th, 2019, used several approaches to improve the positive culture rate. We redesigned and implemented the standard operating procedures for endoscope reprocessing, established an in-service training course, provided education materials on reprocessing, and installed a storage cabinet that custom-built to accommodate the endoscope.

RESULTS

The positive culture rate was reduced from 5.8% to 0%.

CONCLUSIONS

Endoscopy culturing is a useful method to assess the effectiveness of standard reprocessing procedures. The development of guidelines and skill practices should follow current, evidence-based practice and infection prevention principles, and related documents should be organized. We suggest regularly deploying quality-improvement techniques to improve performance and service delivery.

The Value of Adding Surveillance Cultures to Fluoroquinolone Prophylaxis in the Management of Multiresistant Gram Negative Bacterial Infections in Acute Myeloid Leukemia

Multidrug resistant Gram-Negative Bacterial Infections (MR-GNBI) are an increasing cause of mortality in acute myeloid leukemia (AML), compromising the success of antineoplastic therapy. We prospectively explored a novel strategy, including mandatory fluoroquinolone prophylaxis, weekly surveillance cultures (SC) and targeted antimicrobial therapy for febrile neutropenia, aimed to reduce infectious mortality due to MR-GNBI. Over 146 cycles of chemotherapy, cumulative incidence of colonization was 50%. Half of the colonizations occurred in the consolidation phase of treatment. Application of this strategy led to a significant reduction in the incidence of GNB and carbapenemase-producing Klebisella pneumoniae (cpKp) species, resulting in a reduction of infectious mortality (HR 0.35 [95%, CI 0.13–0.96], p = 0.042). In multivariate analysis, fluroquinolone prophylaxis in addition to SC was associated with improved survival (OR 0.55 [95% CI 0.38–0.79], p = 0.001). Targeted therapy for colonized patients did not overcome the risk of death once cpKp or XDR Pseudomonas aeruginosa infections were developed. Mortality rate after transplant was similar between colonized and not colonized patients. However only 9% of transplanted patients were colonized by cpkp. In conclusion, colonization is a common phenomenon, not limited to the induction phase. This strategy reduces infectious mortality by lowering the global incidence of GN infections and the spread of resistant species.

Surveillance cultures for detection of rectal and lower respiratory tract carriage of colistin-resistant Gram-negative bacilli in intensive care unit patients: comparison of direct plating and pre-enrichment step

Purpose. Increasing consumption of colistin as treatment for infections with multidrug-resistant (MDR) Gram-negative bacilli (GNB) has been accompanied by increasingly frequent reports of colistin-resistant (ColR) MDR GNB. Higher selective pressure creates a favourable environment that can facilitate the spread of ColR isolates. Monitoring of asymptomatic ColR GNB carriage can give us a better understanding of this emerging healthcare problem, particularly in wards with higher polymyxin selective pressure and prevalence of carbapenem-resistant GNB. Our aim was to assess the ColR GNB colonization rate in intensive care unit (ICU) patients and evaluate the performance of two surveillance protocols using a selective medium.Methodology. A prospective study included 739 surveillance samples (rectal swabs and tracheal aspirates) from 330 patients that were screened for ColR GNB carriage using SuperPolymyxin medium. Two approaches were used: direct sample plating and overnight pre-enrichment of samples followed by plating. Colistin resistance was confirmed with broth microdilution. ColR isolates were molecularly screened for plasmid-mediated mcr genes.Results. A total of 44/739 samples (45 ColR GNB isolates) were positive for ColR GNB, which included 31/330 (9.4 %) colonized patients; mcr genes were not detected. The direct plating method only identified 17/45 (37.8 %) isolates correctly, whereas the pre-enrichment protocol identified all 45 ColR GNB.Conclusion. The colonization rate among our ICU patients was 9.4  %. Based on our findings, the pre-enrichment step is necessary for the determination of ColR GNB carriage - even though the time to result takes an additional day, fewer than half of ColR GNB carriers were detected using the direct plating protocol.

Utility of CHROMagar mSuperCARBA for surveillance cultures of carbapenemase-producing Enterobacteriaceae

Culture of carbapenemase-producing Enterobacteriaceae (CPE) as part of active surveillance is one of the most useful strategies for successful infection control programmes. Our objective was to compare the recently introduced CHROMagar mSuperCARBA agar for CPE detection in surveillance cultures from perineal swabs with the US Centers for Disease Control and Prevention method. Our results showed that this agar is a useful and affordable alternative (sensitivity 93.05%, specificity 96.21%, diagnostic accuracy 95.2%) to detect CPE in hospital settings.

Surveillance cultures growing carbapenem-Resistant Acinetobacter baumannii predict the development of clinical infections: a retrospective cohort study

BACKGROUND

We aimed to determine the effect of the presence of carbapenem-resistant Acinetobacter baumannii in accordance with surveillance cultures on the subsequent development of clinical infections by this organism.

METHODS

This retrospective cohort study was conducted at a tertiary hospital from January 2010 to November 2011. We included all consecutive patients admitted to the trauma intensive care unit, who had weekly surveillance cultures performed (from rectum, and if intubated, respiratory secretions), and without evidence of A. baumannii infections prior to the collection of the first surveillance culture. Univariable and multivariable analyses were performed using log-binomial regression. Survival analyses were performed using Cox proportional hazards.

RESULTS

Three hundred sixty-four patients were included, of whom 49 (13.5%) had carbapenem-resistant A. baumannii on surveillance cultures. Patients with positive surveillance cultures had 8.4 (95% confidence interval [CI], 5.6-12.7; P < .0001) times the risk of developing a subsequent A. baumannii infection compared with patients who remained negative on surveillance cultures. Multivariable analysis showed significant associations between clinical infection and both positive surveillance cultures (relative risk [RR], 5.9 [95% CI, 3.8-9.3]; P < .0001) and mechanical ventilation (RR, 4.3 [95% CI, 1.03-18.2]; P = .05). On survival analyses, the only variable associated with the development of clinical infections was the presence of positive surveillance cultures (hazard ratio, 16.3 [95% CI, 9.1-29.1]; P < .001).

CONCLUSIONS

Presence of carbapenem-resistant A. baumannii on surveillance cultures is strongly associated with subsequent development of carbapenem-resistant A. baumannii infections. Prevention efforts should be focused at limiting the acquisition of this organism during hospitalization.

Methicillin-resistant Staphylococcus aureus in patients with congenital heart disease in the pediatric intensive care unit

BACKGROUND

Methicillin-resistant Staphylococcus aureus (MRSA) colonization has been recognized as a significant problem among hospitalized patients. Available data about prevalence of MRSA among children with congenital heart disease (CHD) are minimal. The aim of the study was to determine the prevalence of MRSA colonization and to identify risk factors for MRSA colonization among children <19 years old with CHD admitted to a pediatric intensive care unit (PICU).

METHODS

Admission and weekly MRSA nasal surveillance testing was performed, and patients were stratified into six risk groups based on the Risk Adjustment for Congenital Heart Surgery-1 Method. The MRSA-colonized children were compared to the MRSA noncolonized children.

RESULTS

During the 3-year study period, there were 372 admissions of children with CHD to the PICU. Of the 372, 72 (19.4%) had no surveillance cultures performed or had no prior history of MRSA and were excluded from further analysis. Of the remaining 300 admissions, 29 (9.7%) (263 individual children) were found to be colonized. The mean age of the 263 children when first admitted to the PICU was 3.29 years (range 0.03-18.30, median 0.66). Age distribution was not significantly different between the colonized and noncolonized groups (P = .236). Gender (P = .667), race (P = .837), and CHD complexity (P = .395) were not significantly associated with colonization. The odds of being colonized if previously hospitalized were 4.42 times greater than if not previously hospitalized (95% confidence interval 1.89, 10.34).

CONCLUSION

Routine MRSA surveillance should be performed in patients with CHD to identify colonized patients.

Surveillance cultures in pediatric allogeneic hematopoietic stem cell transplantation

The value of surveillance cultures in predicting systemic infections and in guiding antimicrobial treatment is controversial. We investigated 57 pediatric allo-SCTs between 2007 and 2009. ALL (34), AML (5), and severe aplastic anemia (4) were the largest patient groups. Conditioning was TBI-based in 87% and 54% developed GVHD (21% grade III-IV). Of the 2594 weekly colonization samples, 24% were positive (fecal bacteria 86%, fecal fungi 16%, Clostridium difficile 16%; throat bacteria 17% and throat fungi 4%). Enterobacteria and enterococci were the most common fecal findings, staphylococci and streptococci in the throat. Of the bacterial stool samples pretransplant, 74% (mostly enterococci) were resistant to our first-line antibiotics (ceftazidime and cloxacillin). Candida species accounted for the majority of the fungal findings: 62% of the fecal and 78% in the throat. A total of 170 clinical infection episodes were recorded, and in 12 of these, the bacterial blood culture was positive. In 4/12 cases, the pathogen was detected in surveillance culture previously, leading to sensitivity and specificity of 33.3 and 47.4%, respectively. Positive predictive value of bacterial surveillance cultures was 0.9%. The antimicrobial treatment was changed in only five cases based on the surveillance culture results. Weekly surveillance cultures seldom provided clinical benefit and were not cost-effective.

Yield of fungal surveillance cultures in pediatric hematopoietic stem cell transplant patients: a retrospective analysis and survey of current practice

BACKGROUND

Fungal surveillance cultures (FSCs) have been proposed as predictors for development of invasive fungal disease (IFD) and identifiers of the causative organism, although data supporting these are limited and predate universal initiation of antifungal prophylaxis. We aimed to define the epidemiology of fungal colonization and investigate the utility of FSCs for predicting IFD in recipients of pediatric hematopoietic stem cell transplantation (HSCT).

METHODS

FSCs performed from 2007 to 2011 on HSCT patients and laboratory and clinical data were reviewed, and incidence of IFD was determined. Descriptive analyses of culture results were performed to determine the yield of FSCs and their utility. A Web-based survey of national pediatric HSCT providers was undertaken to evaluate current practice and the relevance of our results.

RESULTS

Five thousand six hundred eighteen FSCs from nares, throat, and stool from 360 patients were processed. Of these, 14.8% were positive: 30.3% from stool, 13.2% from throat, and 0.9% from nares; 64.4% of patients had >1 positive FSCs. Thirty (8.3%) patients had IFD. IFD occurred in 7.9% and 10.1% of patients with positive and negative FSCs, respectively (P = .25). Antifungal coverage was changed in 69 patients (29.9%) after positive FSC; 8.6% developed IFD (n = 2 of 6 pathogen concordance with FSC) compared with 6.7% (P = .59) who had no treatment change (n = 3 of 11 concordance). The response rate to the survey was 70.8%; 40% of institutions reported performing routine FSC. Twenty-five percent of providers would not change management based on FSC results; overall rating of usefulness of FSCs was low.

CONCLUSIONS

Although FSCs are commonly performed for pediatric HSCT patients, they have limited utility for predicting IFD.

The presence of antibiotic-resistant nosocomial pathogens in endotracheal tube biofilms and corresponding surveillance cultures

Mechanically ventilated patients often develop ventilator-associated pneumonia (VAP). Soon after intubation, a mixed biofilm harboring microbial pathogens is formed on the endotracheal tube (ET). It is believed that this biofilm contributes to the development of VAP. Unfortunately, the causative agent is often not known at the time VAP is suspected, and early therapy often relies on the identification of surveillance cultures (SC). It is thus important to know whether these SC can predict the microbial flora in ET biofilms. In this study, we compare the presence of a number of antibiotic-resistant nosocomial bacteria (Enterobacter aerogenes, Escherichia coli, Micrococcus luteus, Pseudomonas aeruginosa, Staphylococcus aureus, and Staphylococcus epidermidis) and of Candida albicans in cultures from ET biofilms and SC (i.e. sputum samples, nose swabs, and throat swabs) of 20 mechanically ventilated patients. Our data indicate that there is a good correlation between the presence of (antibiotic-resistant) pathogens in ET biofilms and SC.