Integration of individualized and population-level molecular epidemiology data to model COVID-19 outcomes

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with enhanced transmissibility and immune escape have emerged periodically throughout the coronavirus disease 2019 (COVID-19) pandemic, but the impact of these variants on disease severity has remained unclear. In this single-center, retrospective cohort study, we examined the association between SARS-CoV-2 clade and patient outcome over a two-year period in Chicago, Illinois. Between March 2020 and March 2022, 14,252 residual diagnostic specimens were collected from SARS-CoV-2-positive inpatients and outpatients alongside linked clinical and demographic metadata, of which 2,114 were processed for viral whole-genome sequencing. When controlling for patient demographics and vaccination status, several viral clades were associated with risk for hospitalization, but this association was negated by the inclusion of population-level confounders, including case count, sampling bias, and shifting standards of care. These data highlight the importance of integrating non-virological factors into disease severity and outcome models for the accurate assessment of patient risk.

Machine Learning To Stratify Methicillin-Resistant Staphylococcus aureus Risk among Hospitalized Patients with Community-Acquired Pneumonia

Methicillin-resistant Staphylococcus aureus (MRSA) is an uncommon but serious cause of community-acquired pneumonia (CAP). A lack of validated MRSA CAP risk factors can result in overuse of empirical broad-spectrum antibiotics. We sought to develop robust models predicting the risk of MRSA CAP using machine learning using a population-based sample of hospitalized patients with CAP admitted to either a tertiary academic center or a community teaching hospital. Data were evaluated using a machine learning approach. Cases were CAP patients with MRSA isolated from blood or respiratory cultures within 72 h of admission; controls did not have MRSA CAP. The Classification Tree Analysis algorithm was used for model development. Model predictions were evaluated in sensitivity analyses. A total of 21 of 1,823 patients (1.2%) developed MRSA within 72 h of admission. MRSA risk was higher among patients admitted to the intensive care unit (ICU) in the first 24 h who required mechanical ventilation than among ICU patients who did not require ventilatory support (odds ratio [OR], 8.3; 95% confidence interval [CI], 2.4 to 32). MRSA risk was lower among patients admitted to ward units than among those admitted to the ICU (OR, 0.21; 95% CI, 0.07 to 0.56) and lower among ICU patients without a history of antibiotic use in the last 90 days than among ICU patients with antibiotic use in the last 90 days (OR, 0.03; 95% CI, 0.002 to 0.59). The final machine learning model was highly accurate (receiver operating characteristic [ROC] area = 0.775) in training and jackknife validity analyses. We identified a relatively simple machine learning model that predicted MRSA risk in hospitalized patients with CAP within 72 h postadmission.

Development of a workflow for the detection of vancomycin-resistant Enterococcus faecium and Enterococcus faecalis from rectal swabs using the spectra VRE medium

BACKGROUND

Spectra™ VRE agar (Remel, Lenexa, KS) is a chromogenic agar that is FDA approved for screening patients for VRE colonization. The package insert recommends confirming isolates with identification and susceptibility testing, but confirming every culture delays time to result. Given the agar's historic high specificity for E. faecium isolates, we theorized the agar could be utilized as a stand-alone screening to minimize reagents and time.

AIM

Our laboratory sought to develop a workflow to optimize the use of the medium.

METHODS

We plated 3,815 rectal swabs to the Spectra VRE agar and compared results to traditional identification and susceptibility testing.

RESULTS

Dark blue or purple colonies on the agar demonstrated a sensitivity of 98% and specificity of 85% for detection of VRE faecium, but light blue colonies were significantly less specific for E. faecalis.

CONCLUSIONS

We streamlined our workflow to accept dark blue or purple colonies as VRE faecium and plan to perform additional testing only on light blue colonies. Interestingly, higher quantity of growth increased the accuracy of the agar. In the future, growth quantity may be used to further streamline the workflow once more data is obtained.

1216. An Outbreak Investigation of Pulmonary Infections Caused by Mycobacterium abscessus in a Cardiothoracic Transplant Population

Background

Nontuberculous mycobacteria (NTM) are environmental organisms that can form biofilms in municipal water systems and as such are difficult to eliminate. Mycobacterium abscessus is a rapid-growing NTM that can cause skin and soft tissue, disseminated, and pulmonary infections. M. abscessus is difficult to treat, often requiring prolonged therapy with several antibiotics due to its intrinsic drug resistance. In 2021, our institution identified a significant increase in pulmonary infections caused by M. abscessus in the cardiothoracic transplant population.

Methods

All M. abscessus cases among inpatients at our institution were extracted from the electronic medical record (EMR) between January 2019 and September 2021. Clinical characteristics were determined through EMR review and included demographics, transplant status, specimen type, COVID-19 history, and patient care practices involving water. A multidisciplinary team conducted an investigation to identify possible variations in practice related to the source of water used for clinical care activities in this identified population.

Results

Between January 2021 and September 2021, there were 12 cases of M. abscessus among inpatients at our institution compared to 6 cases in 2019 and 5 in 2020 (Figure 1).

Between 2019 and 2020, post-heart and pre-/post-lung transplant patients comprised 9% of cases, 55% of cases were pulmonary infections, and none had a history of COVID-19 infection. In 2021, post-heart and pre-/post-lung transplant patients comprised 58% of cases, 83% of cases were pulmonary infections, and 33% of cases had a history of COVID-19 infection.

There were varying sources of water utilized for the clinical care activities in this identified population (Table 1). Figure 1Mycobacterium abscessus epidemic curveTable 1Patient Care Practices Involving Water

Conclusion

To investigate the potential outbreak, we are actively collecting water samples and swabs from water fixtures in both patient and nourishment rooms for water culturing. To mitigate a potential water-borne source, we will use sterile water for all clinical care practices involving water and for all patient water drinking needs in the post-heart and pre-/post-lung transplant population impacted by the outbreak. The only use of tap water is hand hygiene and patient bathing.

Disclosures

Asra Salim, MPH, CPH, FAPIC, IRhythym Technologies Inc: Stocks/Bonds Valentina Stosor, MD, DiaSorin: Advisor/Consultant|Eli Lilly and Company: Grant/Research Support|Med Learning Group: Honoraria Michael P. Angarone, DO, Abbvie: Advisor/Consultant Michael G. Ison, MD MS, GlaxoSmithKlein: Grant/Research Support|Pulmocide: Grant/Research Support|Viracor Eurfins: Advisor/Consultant Janna L. Williams, MD, Abbvie: COVID19 Infection Prevention Consultant.

180. Impact of a two-step diagnostic bundle on hospital-onset Clostridioides difficile infection rates and treatment across a large health system

Background

Distinguishing true Clostridioides difficile Infection (CDI) from colonization is a challenge, with nearly 20% of hospitalized adults being carriers of C. difficile. Polymerase chain reaction (PCR) testing alone is not able to distinguish colonization from infection, leading to over-diagnosis and unnecessary treatment. Despite interventions including pre-approval by antimicrobial stewardship programs (ASP), reportable hospital-onset CDI (HO-CDI) rates across our health system remained high. In 2021, we implemented a C. difficile PCR with reflex toxin enzyme immunoassay (EIA) testing strategy to improve diagnostic accuracy and treatment outcomes. The purpose of this study was to evaluate the impact of this two-step testing algorithm bundled with education, ASP support and order set changes on HO-CDI rates and C. difficile treatment across our health system.

Methods

PCR with EIA testing algorithm was implemented between May and August 2021 across seven hospitals within the Northwestern Medicine Health System. Multifaceted education was delivered to leadership and clinicians in person and electronically to. ASP performed daily diagnostic prospective audit and management support. Clinical decision support (CDS) was incorporated into order sets to promote diagnostic stewardship (Table 1, Figure 1). Standardization of analyst-developed tracking reports allowed for longitudinal monitoring across the system and at each facility, including unit- and patient-level data. Figure 1

Vancomycin-resistant Enterococcus outbreak in a pre- and post-cardiothoracic transplant population: Impact of discontinuing multidrug-resistant organism surveillance during the coronavirus disease 2019 pandemic

INTRODUCTION

Many institutions suspended surveillance and contact precautions for multidrug-resistant organisms (MDROs) at the outset of the coronavirus disease 2019 (COVID-19) pandemic due to a lack of resources. Once our institution reinstated surveillance in September 2020, a vancomycin-resistant Enterococcus (VRE) faecium outbreak was detected in the cardiothoracic transplant units, a population in which we had not previously detected outbreaks.

METHODS

An outbreak investigation was conducted using pulsed-field gel electrophoresis for strain typing and electronic medical record review to determine the clinical characteristics of involved patients. The infection prevention (IP) team convened a multidisciplinary process improvement team comprised of IP, cardiothoracic transplant nursing and medical leadership, environmental services, and the microbiology laboratory.

RESULTS

Between December 2020 and March 2021, the outbreak involved thirteen patients in the cardiothoracic transplant units, four index cases, and nine transmissions. Of the 13, seven (54%) were on the transplant service, including heart and lung transplant recipients, patients with ventricular assist devices, and a patient on extracorporeal membrane oxygenation as a bridge to lung transplantation. Four of 13 (31%) developed a clinical infection.

DISCUSSION

Cardiothoracic surgery/transplant patients may have a similar risk for VRE-associated morbidity as abdominal solid organ transplant and stem cell transplant patients, highlighting the need for aggressive outbreak management when VRE transmission is detected. Our experience demonstrates an unintended consequence of discontinuing MDRO surveillance in this population and highlights a need for education, monitoring, and reinforcement of foundational infection prevention measures to ensure optimal outcomes.

Impact of early antimicrobial stewardship intervention in patients with positive blood cultures: results from a randomized comparative study: Impact of stewardship on BSI outcomes

BACKGROUND

Antimicrobial stewardship intervention (ASI) appears necessary to realize the full benefits of rapid diagnostic technologies in clinical practice. This study aimed to compare clinical outcomes between early ASI paired with MALDI-TOF compared to MALDI-TOF with standard of care (SOC) reporting in patients with positive blood cultures.

METHODS

Adult patients with positive blood cultures and organism speciation via MALDI-TOF admitted between 2/2015 and 9/2015 were randomized to ASI or SOC in a 1:1 fashion. Patients admitted for at least 48 hours following positive culture were included in analyses. ASI was defined as a clinical assessment by a stewardship team member with non-binding treatment recommendations offered to the primary team. The primary outcome was time to definitive therapy. Secondary outcomes included post-culture length of stay (LOS), time to first change in antibiotics, and in-hospital mortality.

RESULTS

A total of 149 patients were included in analyses (76 in the ASI group and 73 in the SOC group). ASI and SOC arms did not differ according to age, sex, comorbidities, or severity of illness. Gram-positive organisms were common in both SOC and ASI arms (74.0 vs 61.8%, p=0.11). Time-to-definitive therapy was reduced, on average, by 30.3 hours in the ASI group (71.6 vs. 41.3 hours, p=0.01). Hospital LOS following the first positive blood culture was significantly shorter in the ASI group (8.7 vs. 11.2 days, p=0.049).

CONCLUSIONS

ASI combined with MALDI-TOF reduced the time to definitive therapy, time to first change in antibiotics, and was associated with a shorter post-culture LOS.

Diagnostic performance of Ion 16S metagenomics kit and Ion reporter metagenomics workflow for bacterial pathogen detection in culture-negative clinical specimens from sterile sources

PCR-based deep sequencing of 16S rRNA gene allows for detection of a wide array of bacterial pathogens in culture-negative specimens. Ion 16S metagenomics kit and Ion Reporter metagenomics workflow (Ion 16S mNGS) provides an end-to-end solution with integrated workflow. Ninety-eight clinical samples with the diagnosis generated with 16S rRNA gene PCR/chain termination (Sanger) sequencing (16S CS) was used to assess the performance of Ion 16S mNGS. Compared to species level detection of 16S CS, the Ion 16S mNGS had 88% sensitivity and 76% specificity. When accounting for genus level of detection, the Ion 16S mNGS had 100% sensitivity. Notably, Ion 16S mNGS generated diagnosis in 13% of 16S CS and culture-negative samples. In addition, Ion 16S mNGS had the advantage of detecting more than 1 pathogen in 16S CS positive samples. We showed that the workflow had high reproducibility.

584. Ventricular assist device infections with Pseudomonas aeruginosa

Background

Infection is a leading cause of morbidity and mortality in ventricular assist device (VAD) recipients. Pseudomonas aeruginosa (PA) is the second most common organism implicated in VAD infections, occurring in 10–50% of infections. The epidemiology of VAD recipients with PA infection are poorly described.

Methods

We identified patients (pts) at Northwestern Memorial Hospital with a VAD-specific PA infection from January 1, 2012 to Dec 31, 2019. VADs included the Heartmate II, Heartmate 3, and Heartware HVAD devices. VAD-specific infections were defined according to the 2013 ISHLT Guidelines.

Results

Seventeen out of 91 (18.7%) VAD infections were due to PA. Infections of the driveline exit site (DLES) occurred most commonly (n=15, 88.2%), followed by pocket (n=2, 11.8%) and pump (n=2, 11.8%) infections. Median time to infection after VAD implantation was 295 days (IQR 154 – 440 days). Eight (47.1%) pt isolates were not fluoroquinolone (FQ) susceptible. Resistance to multiple antibiotic classes was observed in pts in whom serial cultures were obtained. Median antibiotic treatment was 107 days (IQR 55 – 183 days, maximum 775 days). Five (29.4%) pts received FQ monotherapy on initial diagnosis, 3 (60%) of whom required change to a different class for resistance. Surgical debridement and VAD exchange were performed in 5 (29.4%) and 3 (17.6%) pts respectively. Co-pathogens were identified in 9 (52.9%) pts, the most common being Staphylococcus aureus (n=2) and Enterococcus spp (n=2). A total of 5 (29.4%) pts went on to successful heart transplantation; one had recurrent PA infection at the prior DLES requiring prolonged antibiotics and removal of retained DL material. All cause 1-year mortality rate was 11.7% (n = 2), both of whom died from cerebrovascular accidents.

Conclusion

VAD-specific infections with PA occurred late after device implantation and required prolonged antibiotic courses. Antimicrobial resistance was high at diagnosis and worsened in pts on prolonged therapy. Morbidity and mortality in pts with PA VAD infections were high. The preponderance of DLES infections warrants further study and highlights the need for improvements in DLES care and infection prevention strategies.

Disclosures

All Authors: No reported disclosures

Development of a protocol for detection of SARS-CoV-2 in sputum and endotracheal aspirates using Cepheid Xpert Xpress SARS-CoV-2

Sputum and endotracheal aspirates (ETs) are not among the vendor-approved specimens for the Cepheid Xpert SARS-CoV-2 assay. However, they are the common lower respiratory tract specimens submitted for laboratory diagnosis. Testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in lower respiratory tract samples is required for the discharge of patients from coronavirus disease (COVID) units at some institutions. We developed a protocol used for testing unliquified viscous sputum or tracheal aspirate with the Cepheid Xpert SARS-CoV-2 assay.

Optimizing a real-time PCR assay for rapid detection of Candida auris in nasal and axillary/groin samples

Introduction. Candida auris is an emerging fungal pathogen. The organism can cause invasive infections associated with high mortality, has been implicated in outbreaks in healthcare settings and is frequently resistant to multiple antifungal agents, making it a significant challenge to infection prevention and patient treatment.Aim. To implement a real-time PCR assay for detection of C. auris in patient surveillance samples collected with the Copan Liquid Amies elution swab (ESwab) collection and transport system.Methodology. We optimized a real-time PCR testing procedure based on the sample collection device used in our institution.Results . ESwab transport medium was strongly inhibitory to the real-time PCR. Removing the medium with centrifugation, followed by suspending the pellet in PBS-BSA buffer (concentration 1 %), sufficiently eliminated the inhibition. The manual sample preparation method, freeze-thaw followed by mechanical disruption, allowed the detection of C. auris at the lowest cell concentration.Conclusion . The optimized procedure was used to test 1414 patient surveillance samples. The real-time PCR detected all culture-positive samples with 100 % sensitivity and 100 % specificity.

2181. Yield and Impact of Molecular Diagnostics for Pathogen Detection in Pediatric Patients: 16/18S rRNA PCR and Noninvasive Assays

Background

Molecular diagnostic tests can identify bacterial and fungal pathogens from clinical samples. Nucleic acid detection tests include 16S and 18S rRNA gene PCR (16/18S PCR) and plasma next-generation sequencing (NGS). Other assays (fungal galactomannan and 1,3-β-d-glucan) detect structural factors. Our objective was to assess the utilization, yield, and impact of molecular diagnostics in pediatric patients who had samples sent for 16/18S PCR.

Methods

Sterile site fluid or tissue specimens were collected as part of standard care at Lurie Children’s Hospital, cultured, and sent to Northwestern Memorial Hospital for 16/18S PCR as clinically indicated. Medical records were reviewed for diagnostics, antibiotics, and clinical course.

Results

From 1/2016–8/2018, 236 samples were sent for 16 and/or 18S PCR from 183 patients. 83% had a concurrent ID consult. 16S PCR was done on 215 samples, 42 (20%) were positive, and 36 yielded species identification (Table 1). Antibacterial agents were administered prior to specimen collection in 73% and did not affect likelihood of positive 16S PCR. 18S PCR was sent on 163 samples; 12 (7.4%) were positive (Table 2) of which 10 were from immunocompromised hosts. 40% of patients were on antifungals prior to sample acquisition. 16/18S PCR impacted antimicrobial decision-making in 70 cases (30%). A pathogenic fungus was detected by PCR but not culture in 2 cases. Time to positivity of fungal culture was 1–15 days. Fungal culture was positive in 5 cases with-negative 18S PCR. Seventeen patients had positive serum 1,3-ß-D-glucan and/or galactomannan: 3 of which had positive 18S PCR, 5 with fungal growth, 5 presumed infection based on imaging, 1 Nocardia, and 3 noninfectious etiology. Plasma NGS was sent on 45 cases, was positive in 34, and affected clinical management in 10.

Conclusion

16S PCR can identify bacterial pathogens in the setting of negative culture and impact clinical care. Abscess, bronchial/pleural fluid, and brain/organ tissue were high yield specimens. 18S PCR can provide expeditious fungal identification in cases of suspected invasive disease, but fungal culture and serum molecular testing increase diagnostic yield. No single fungal test is comprehensive. Plasma NGS had relatively high yield and clinical impact in selected patients.

Disclosures

All authors: No reported disclosures.

Rapid Detection of Methicillin-Resistant Staphylococcus aureus in BAL: A Pilot Randomized Controlled Trial

BACKGROUND

Guidelines recommend empirical vancomycin or linezolid for patients with suspected pneumonia at risk for methicillin-resistant Staphylococcus aureus (MRSA). Unneeded vancomycin or linezolid use may unnecessarily alter host flora and expose patients to toxicity. We therefore sought to determine if rapid testing for MRSA in BAL can safely decrease use of vancomycin or linezolid for suspected MRSA pneumonia.

METHODS

Operating characteristics of the assay were initially validated against culture on residual BAL. A prospective, unblinded, randomized clinical trial to assess the effect of antibiotic management made on the basis of rapid diagnostic testing (RDT) compared with usual care was subsequently conducted, with primary outcome of duration of vancomycin or linezolid administration. Secondary end points focused on safety.

RESULTS

Sensitivity of RPCR was 95.7%, with a negative likelihood ratio of 0.04 for MRSA. The clinical trial randomized 45 patients: 22 to antibiotic management made on the basis of RDT and 23 to usual care. Duration of vancomycin or linezolid administration was significantly reduced in the intervention group (32 h [interquartile range, 22-48] vs 72 h [interquartile range, 50-113], P < .001). Proportions with complications and length of stay trended lower in the intervention group. Hospital mortality was 13.6% in the intervention group and 39.1% for usual care (95% CI of difference, -3.3 to 50.3, P = .06). Standardized mortality ratio was 0.48 for the intervention group and 1.18 for usual care.

CONCLUSIONS

A highly sensitive BAL RDT for MRSA significantly reduced use of vancomycin and linezolid in ventilated patients with suspected pneumonia. Management made on the basis of RDT had no adverse effects, with a trend to lower hospital mortality.

TRIAL REGISTRY

ClinicalTrials.gov; No. NCT02660554; URL: www.clinicaltrials.gov.

2297. The Diagnostic Yield of 16/18S rRNA PCR of Sterile Site Samples in Pediatric Patients

Background

16S ribosomal RNA (rRNA) and 18S rRNA gene polymerase chain reaction (16/18S PCR) with sequencing can provide expeditious bacterial or fungal pathogen identification from sterile site samples (cost $474/PCR). Our objective was to assess the utilization and diagnostic yield of 16/18S PCR of sterile site samples in pediatric patients.

Methods

Patients’ sterile site fluid or direct tissue specimens were collected and cultured at Lurie Children’s Hospital of Chicago and sent to Northwestern Memorial Hospital for 16/18S PCR as clinically indicated. Clinical data were reviewed including PCRs, cultures, and medical conditions.

Results

16/18S PCR testing increased over the study period. In total, 177 samples were sent for 16S and/or 18S PCR from 146 patients (January 2016–April 2018). Osteoarticular, CSF, pleural fluid and organ tissue (n = 28; lung=19, chest mass=2, liver=2, spleen=2, etc.) sites were most frequent. The yield of 16/18S PCR by source is listed in Table 1. Twenty-eight of 156 samples for 16S PCR were positive (17.9%); 21 with a single organism ID, one with two organisms, and 6 indeterminate. (Table 2). Of negative 16S PCR samples, one grew Mycobacterium avium complex in culture. 18S PCR was performed on 108 unique samples; 7 were positive (6.5%, Table 3). For 4 positive 18S PCRs, a fungus also grew in culture with 3 concordant results and one discordant. Two negative 18S PCR samples grew molds (Phellinus spp.; Blastomyces dermatitidis). All patients (100%) with positive 18S PCR were immunocompromised compared with 21% (6/28) with positive 16S PCR. Both 16S and 18S PCRs were sent on 87 samples of which 16S PCR was positive in 5, 18S PCR was positive in 3, and none had both 16/18S PCRs positive.

Conclusion

16/18S PCR can provide important infectious pathogen diagnostics. 16S PCR should be sent only if bacterial culture is negative with higher yield sites being brain, abscess, pleural effusion, bone/joint and CSF. 16S PCR appears useful if an anaerobic pathogen is likely but conditions are not optimal for recovery. 18S PCR is highest yield in patients at risk of fungal disease. 16 and 18S PCRs were often sent together, likely reflexively. Selective or sequential testing may be advisable for most cases, guided by the clinical index of suspicion. Best practices to optimize resource utilization and clinical impact are evolving.

Disclosures

All authors: No reported disclosures.

Contamination of Examination Gloves in patient Rooms and Implications for Transmission of Antimicrobial-Resistant Microorganisms

An assessment of bacterial contamination on examination gloves indicated that contaminated gloves may be a mechanism of indirect bacterial transmission from the hands of healthcare workers to patients. This mechanism is indicated by the recovery of identical Acinetobacter baumannii isolates from gloves and from the clinical cultures of a patient with invasive infection.

Outcomes of an enhanced surveillance program for carbapenem-resistant Enterobacteriaceae

Optimal surveillance strategies for identifying patients colonized with and at risk for transmitting carbapenem-resistant Enterobacteriaceae (CRE) are urgently needed. We instituted an enhanced surveillance program for CRE that identified unrecognized CRE-colonized patients but failed to identify possible CRE transmissions. We also identified risk factors associated with transmitting CRE.

Quantifying the clinical virulence of Klebsiella pneumoniae producing carbapenemase Klebsiella pneumoniae with a Galleria mellonella model and a pilot study to translate to patient outcomes

BACKGROUND

Previous studies may have overestimated morbidity and mortality due to Klebsiella pneumoniae producing carbapenemase (KPC) Klebsiella pneumoniae infections because of difficulties in modeling patient comorbidities. This pilot study sought to evaluate KPC virulence by combining clinical and Galleria mellonella models in patients with K. pneumoniae blood stream infections (BSIs).

METHODS

G. mellonella were inoculated using KPC(+) and KPC(-) isolates from these patients. Extent and rapidity of insect mortality was analyzed. Patients were stratified by KPC BSI status. Clinical outcomes of mortality and length of stay post-infection for survivors (LOS) were analyzed. Median virulence scores calculated from the insect studies were imputed in the clinical model.

RESULTS

The in-vivo model revealed greater mortality in KPC(-) isolates (p < 0.001). Fifteen patients with KPC(+) BSI were matched with 60 patients with KPC(-) BSI. Hospital mortality was greater in the KPC(+) group versus the KPC(-) group (OR 3.79, 95% CI 1.00 - 14.34). LOS was longer in the KPC(+) group (p < 0.01). Conversely the virulence score attenuated the association between KPC(+) status and mortality and LOS in the final translational models.

CONCLUSIONS

KPC(+) status was associated with decreased virulence in GM. Opposite findings were observed in patients. This pilot study demonstrates that measured virulence from GM may differ from human estimates of virulence.

Characterization of ciprofloxacin resistant Escherichia coli isolates among men undergoing evaluation for transrectal ultrasound guided prostate biopsy

PURPOSE

We determine the prevalence of ciprofloxacin resistant gram-negative bacilli in patients scheduled for transrectal ultrasound guided prostate biopsy, characterize the Escherichia coli strains recovered from this patient population, and characterize the mechanisms responsible for β-lactam and ciprofloxacin resistance.

MATERIALS AND METHODS

Rectal swabs from 991 patients were cultured for ciprofloxacin resistant gram-negative bacilli with a selective medium. Recovered E. coli isolates were further analyzed with susceptibility testing, pulsed field gel electrophoresis, plasmid isolation and sequencing.

RESULTS

A total of 193 ciprofloxacin resistant gram-negative bacilli were recovered and of these isolates 167 (87%) were E. coli. The prevalence of ciprofloxacin resistant E. coli in the study population was 17%. Only 38 (26%) of the 149 E. coli isolates that received susceptibility testing were susceptible to ampicillin and ampicillin-sulbactam. In select isolates transferrable plasmids carrying β-lactamase were responsible for the resistance to the β-lactam agents and other nonβ-lactam antimicrobials. Diverse combinations of gyrA and parC mutations associated with fluoroquinolone resistance were identified. Strain typing and plasmid typing indicated that the E. coli isolates did not share a common origin.

CONCLUSIONS

Of the patients in our study 17% carried ciprofloxacin resistant E. coli. Analysis of resistance mechanisms and plasmid analysis along with strain typing demonstrated that this patient population harbored organisms with heterogeneous phenotypic susceptibility, indicating that universal prophylaxis would not provide optimal coverage for patients undergoing transrectal ultrasound guided prostate biopsy.

Differences in clinical outcomes in patients with vancomycin-resistant enterococci according to linezolid susceptibility

STUDY OBJECTIVE

To evaluate the differences in clinical outcomes in patients with linezolid-intermediate or -resistant vancomycin-resistant enterococci (LIRVRE) isolates, as defined by the presence of the G2576T mutation, compared with patients who had linezolid-susceptible VRE (LSVRE) isolates in order to further discern the clinical relevance of linezolid resistance associated with this mutation.

DESIGN

Retrospective cohort study.

SETTING

Large tertiary care academic medical center.

PATIENTS

Eighteen adults (mean age 55.4 yrs) with LIRVRE (case patients) who were frequency matched to 54 adults (mean age 58.1 yrs) with LSVRE (control patients) in a 1:3 ratio based on site of culture and VRE species.

MEASUREMENTS AND MAIN RESULTS

Linezolid resistance was determined by phenotype and genotype (G2576T mutation by polymerase chain reaction). Patients with LIRVRE received more linezolid before isolation of the organism than did those with LSVRE (mean 8.6 vs 0.2 days, p<0.001). No difference in mortality was found; however, compared with controls, patients with LIRVRE were more likely to be transferred to the intensive care unit (56% vs 28%, p=0.032), had more surgical procedures for VRE (39% vs 15%, p=0.029), and had more echocardiograms performed (44% vs 19%, p=0.028) as a result of their VRE. Multivariate analysis revealed that surviving case patients had an increased duration of culture positivity of approximately 1.5 days (p=0.049) and a near statistically significant increase of postculture length of stay of approximately 2 days (p=0.053).

CONCLUSION

The clinical relevance of the G2576T mutation among enterococci remains unclear; however, the increased morbidity and resource utilization among patients with LIRVRE is a finding of concern. Careful monitoring of genotypically confirmed LIRVRE emergence and ongoing epidemiologic studies will be critical to better characterize the clinical relevance of linezolid resistance.

Screening for extended-spectrum beta-lactamase-producing Enterobacteriaceae among high-risk patients and rates of subsequent bacteremia

BACKGROUND

Bloodstream infections due to extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae have been associated with increased hospital costs, length of stay, and patient mortality. However, the role of routine inpatient surveillance for ESBL colonization in predicting related infection is unclear.

METHODS

From 2000 through 2005, we screened 17,872 patients hospitalized in designated high-risk units for rectal colonization with vancomycin-resistant enterococci and ESBL-producing Enterobacteriaceae using a selective culture medium. In patients with a bloodstream infection due to ESBL-producing Enterobacteriaceae (ESBL-BI) during the study period, surveillance results were evaluated for evidence of antecedent ESBL-producing Enterobacteriaceae colonization.

RESULTS

The rate of ESBL-producing Enterobacteriaceae colonization doubled during the 6-year study period, increasing from 1.33% of high-risk patients in 2000 to 3.21% in 2005. Among patients with ESBL-producing Enterobacteriaceae colonization, 49.6% also carried vancomycin-resistant enterococci. The number of ESBL-BIs increased >4-fold in 5 years, from 9 cases in 2001 to 40 cases in 2005. Of 413 patients colonized with ESBL-producing Enterobacteriaceae, 35 (8.5%) developed a subsequent ESBL-BI. Of concern, more than one-half of all ESBL-BIs occurred in patients who were not screened. These 56 patients received a diagnosis of ESBL-BI in the emergency department, when hospitalized in low-risk medical units, or at transfer from an acute or long-term health care facility.

CONCLUSIONS

Colonization with ESBL-producing Enterobacteriaceae is increasing at a rapid rate, and routine rectal surveillance for ESBL-producing Enterobacteriaceae may have clinical implications. However, in our experience, over one-half of patients with an ESBL-BI did not undergo screening through our current surveillance measures. As a result, targeted screening for ESBL-producing Enterobacteriaceae among additional patient populations may be integral to future ESBL-BI prevention and management efforts.

The clinical impact of linezolid susceptibility reporting in patients with vancomycin-resistant enterococci

Linezolid remains a mainstay of therapy for vancomycin-resistant enterococci (VREs), but resistance has emerged. We describe a cohort of 20 patients with linezolid-intermediate or resistant VRE (LIRVRE) reported by Etest and disk diffusion testing, 18 of whom demonstrated linezolid susceptibility by agar dilution on further investigation. Patients with reported LIRVRE were matched based on culture site and enterococcal species to patients with linezolid-susceptible VRE (LSVRE) in a 1:3 ratio. Patients with reported LIRVRE developed more nosocomial infections (P = .04), had more central lines placed (P = .04), and underwent more computed tomography scans related to VRE infection (P = .02). Multivariate analysis revealed increased surgical procedures related to VRE infections (P = .008), increased linezolid use during hospital stay (P = .03), and delayed culture and susceptibility results compared with those with LSVRE (P = .006). Therefore, inaccurate detection and reporting of LIRVRE by disk diffusion and Etest is associated with increased patient morbidity and resource use.

Comparison of testing methods for detection of decreased linezolid susceptibility due to G2576T mutation of the 23S rRNA gene in Enterococcus faecium and Enterococcus faecalis

E-test, Vitek 2, MicroScan, agar dilution, and disk diffusion were compared for detection of decreased linezolid susceptibility due to 23S rRNA gene G2576T mutation among 32 clinical Enterococcus strains initially reported as intermediate or resistant by E-test alone or Vitek 2 confirmed by E-test. Agar and broth dilution methods were in concordance with PCR detection of the mutation, and disk diffusion was somewhat less sensitive but equally specific.

Multidrug-resistant Pseudomonas aeruginosa cholangitis after endoscopic retrograde cholangiopancreatography: failure of routine endoscope cultures to prevent an outbreak

BACKGROUND

Nosocomial infections due to medical devices are of increasing concern to infection control practitioners. Attempts to prevent such infections have included surveillance cultures of endoscopes and bronchoscopes. In July 2002, the infectious disease consultation service was asked to see three patients with sepsis due to multidrug-resistant Pseudomonas aeruginosa after endoscopic retrograde cholangiopancreatography (ERCP).

OBJECTIVE

To describe an outbreak of multidrug-resistant P. aeruginosa sepsis after ERCP at an institution that performs routine surveillance cultures of endoscopes.

DESIGN

A traditional outbreak investigation supplemented by pulsed-field gel electrophoresis (PFGE) was undertaken, including a case-control analysis based on the hypothesis that all infected individuals had their ERCP performed with the same endoscope.

SETTING

A tertiary-care academic medical center.

RESULTS

The case-control analysis confirmed the hypothesis that undergoing ERCP with the implicated endoscope was associated with a culture positive for Pseudomonas (P = .01). The available strains were identical by PFGE. This outbreak occurred despite a negative surveillance culture of the implicated endoscope 1 month earlier.

CONCLUSIONS

Infectious morbidity can occur after endoscopy despite negative surveillance cultures. The practice of routine endoscope cultures does not prevent device-related infectious morbidity.

Pheromone-regulated genes required for yeast mating differentiation

Yeast cells mate by an inducible pathway that involves agglutination, mating projection formation, cell fusion, and nuclear fusion. To obtain insight into the mating differentiation of Saccharomyces cerevisiae, we carried out a large-scale transposon tagging screen to identify genes whose expression is regulated by mating pheromone. 91,200 transformants containing random lacZ insertions were screened for beta-galactosidase (beta-gal) expression in the presence and absence of alpha factor, and 189 strains containing pheromone-regulated lacZ insertions were identified. Transposon insertion alleles corresponding to 20 genes that are novel or had not previously been known to be pheromone regulated were examined for effects on the mating process. Mutations in four novel genes, FIG1, FIG2, KAR5/ FIG3, and FIG4 were found to cause mating defects. Three of the proteins encoded by these genes, Fig1p, Fig2p, and Fig4p, are dispensible for cell polarization in uniform concentrations of mating pheromone, but are required for normal cell polarization in mating mixtures, conditions that involve cell-cell communication. Fig1p and Fig2p are also important for cell fusion and conjugation bridge shape, respectively. The fourth protein, Kar5p/Fig3p, is required for nuclear fusion. Fig1p and Fig2p are likely to act at the cell surface as Fig1:: beta-gal and Fig2::beta-gal fusion proteins localize to the periphery of mating cells. Fig4p is a member of a family of eukaryotic proteins that contain a domain homologous to the yeast Sac1p. Our results indicate that a variety of novel genes are expressed specifically during mating differentiation to mediate proper cell morphogenesis, cell fusion, and other steps of the mating process.