Performance of CHROMagar ESBL media for the surveillance of extended-spectrum cephalosporin-resistant Enterobacterales (ESCrE) from rectal swabs in Botswana

Introduction. Lack of laboratory capacity hampers consistent national antimicrobial resistance (AMR) surveillance. Chromogenic media may provide a practical screening tool for detection of individuals colonized by extended-spectrum beta-lactamase (ESBL)-producing organisms.Hypothesis. CHROMagar ESBL media represent an adequate screening method for the detection of extended-spectrum cephalosporin-resistant Enterobacterales (ESCrE), isolated from rectal swabs.Aim. To evaluate the performance of CHROMagar ESBL media to accurately identify ESCrE isolates from rectal swab samples attained from hospitalized and community participants.Methodology. All participants provided informed consent prior to enrolment. Rectal swabs from 2469 hospital and community participants were inoculated onto CHROMagar ESBL. The performance of CHROMagar ESBL to differentiate Escherichia coli and Klebsiella spp., Enterobacter spp. and Citrobacter spp. (KEC spp.) as well as select for extended-spectrum cephalosporin resistance were compared to matrix-assisted laser desorption/ionization-time-of-flight MS (MALDI-TOF-MS) and VITEK-2 automated susceptibility testing.Results. CHROMagar ESBL had a positive and negative agreement of 91.2 % (95 % CI, 88.4-93.3) and 86.8 % (95 % CI, 82.0-90.7) for E. coli and 88.1 % (95 % CI 83.2-92.1) and 87.6 % (95 % CI 84.7-90.2) for KEC spp. differentiation, respectively, when compared to species ID by MALDI-TOF-MS. When evaluated for phenotypic susceptibilities (VITEK-2), 88.1 % (714/810) of the isolates recovered on the selective agar exhibited resistance to third-generation cephalosporins.Conclusion. The performance characteristics of CHROMagar ESBL media suggest that they may be a viable screening tool for the identification of ESCrE from hospitalized and community participants and could be used to inform infection prevention and control practices in Botswana and potentially other low-and middle-income countries (LMICs). Further studies are required to analyse the costs and the impact on time-to-result of the media in comparison with available laboratory methods for ESCrE surveillance in the country.

Clostridioides difficile dynamic electronic order panel, an effective automated intervention to reduce inappropriate inpatient ordering

BACKGROUND

Ordering Clostridioides difficile diagnostics without appropriate clinical indications can result in inappropriate antibiotic prescribing and misdiagnosis of hospital onset C. difficile infection. Manual processes such as provider review of order appropriateness may detract from other infection control or antibiotic stewardship activities.

METHODS

We developed an evidence-based clinical algorithm that defined appropriateness criteria for testing for C. difficile infection. We then implemented an electronic medical record-based order-entry tool that utilized discrete branches within the clinical algorithm including history of prior C. difficile test results, laxative or stool-softener administration, and documentation of unformed bowel movements. Testing guidance was then dynamically displayed with supporting patient data. We compared the rate of completed C. difficile tests after implementation of this intervention at 5 hospitals to a historic baseline in which a best-practice advisory was used.

RESULTS

Using mixed-effects Poisson regression, we found that the intervention was associated with a reduction in the incidence rate of both C. difficile ordering (incidence rate ratio [IRR], 0.74; 95% confidence interval [CI], 0.63-0.88; P = .001) and C. difficile-positive tests (IRR, 0.83; 95% CI, 0.76-0.91; P < .001). On segmented regression analysis, we identified a sustained reduction in orders over time among academic hospitals and a new reduction in orders over time among community hospitals.

CONCLUSIONS

An evidence-based dynamic order panel, integrated within the electronic medical record, was associated with a reduction in both C. difficile ordering and positive tests in comparison to a best practice advisory, although the impact varied between academic and community facilities.

Risk Factors for Community Colonization With Extended-Spectrum Cephalosporin-Resistant Enterobacterales (ESCrE) in Botswana: An Antibiotic Resistance in Communities and Hospitals (ARCH) Study

BACKGROUND

The epidemiology of extended-spectrum cephalosporin-resistant Enterobacterales (ESCrE) in low- and middle-income countries (LMICs) is poorly described. Identifying risk factors for ESCrE colonization is critical to inform antibiotic resistance reduction strategies because colonization is typically a precursor to infection.

METHODS

From 15 January 2020 to 4 September 2020, we surveyed a random sample of clinic patients at 6 sites in Botswana. We also invited each enrolled participant to refer up to 3 adults and children. All participants had rectal swabs collected that were inoculated onto chromogenic media followed by confirmatory testing. Data were collected on demographics, comorbidities, antibiotic use, healthcare exposures, travel, and farm and animal contact. Participants with ESCrE colonization (cases) were compared with noncolonized participants (controls) to identify risk factors for ESCrE colonization using bivariable, stratified, and multivariable analyses.

RESULTS

A total of 2000 participants were enrolled. There were 959 (48.0%) clinic participants, 477 (23.9%) adult community participants, and 564 (28.2%) child community participants. The median (interquartile range) age was 30 (12-41) and 1463 (73%) were women. There were 555 cases and 1445 controls (ie, 27.8% of participants were ESCrE colonized). Independent risk factors (adjusted odds ratio [95% confidence interval]) for ESCrE included healthcare exposure (1.37 [1.08-1.73]), foreign travel [1.98 (1.04-3.77]), tending livestock (1.34 [1.03-1.73]), and presence of an ESCrE-colonized household member (1.57 [1.08-2.27]).

CONCLUSIONS

Our results suggest healthcare exposure may be important in driving ESCrE. The strong links to livestock exposure and household member ESCrE colonization highlight the potential role of common exposure or household transmission. These findings are critical to inform strategies to curb further emergence of ESCrE in LMICs.

Distinct community structures of the fungal microbiome and respiratory health in adults with cystic fibrosis

BACKGROUND

The respiratory tract fungal microbiome in cystic fibrosis (CF) has been understudied despite increasing recognition of fungal pathogens in CF lung disease. We sought to better understand the fungal communities in adults with CF, and to define relationships between fungal profiles and clinical characteristics.

METHODS

We enrolled 66 adults with CF and collected expectorated sputum, spirometry, Cystic Fibrosis Questionnaire-revised, and clinical data. Fungi were molecularly profiled by sequencing of the internal transcribed spacer (ITS) region. Total fungal abundance was measured by quantitative PCR. Relative abundance and qPCR-corrected abundances were determined. Selective fungus culture identified cultivable fungi. Alpha diversity and beta diversity were measured and relationships with clinical parameters were interrogated.

RESULTS

Median age was 29 years and median FEV1 percent predicted 58%. Members of the Candida genus were the most frequent dominant taxa in CF sputum. Apiotrichum, Trichosporon, Saccharomyces cerevisiae, and Scedosporium were present in high relative abundance in few samples; whereas, Aspergillus species were detected at low levels. Higher FEV1% predicted and CFTR modulator use were associated with greater alpha-diversity. Chronic azithromycin use was associated with lower alpha-diversity. Patients with acute pulmonary had distinct fungal community composition compared to clinically stable subjects. Differing yeast species were mainly responsible for the community differences.

CONCLUSION

The respiratory tract fungal microbiome in adults with CF is associated with lung function, pulmonary exacerbation status, macrolide use, and CFTR modulator use. Future work to better understand fungal diversity in the CF airway and its impact on lung health is necessary.

90. Risk Factors for Community Colonization with Extended-Spectrum Cephalosporin-Resistant Enterobacterales (ESCrE) in Botswana An Antibiotic Resistance in Communities and Hospitals (ARCH) Study

Background

The epidemiology of ESCrE in low- and middle-income countries (LMICs) is poorly described. While risk factors for ESCrE clinical infection have been studied, little is known of the epidemiology of ESCrE colonization. Identifying risk factors for ESCrE colonization specifically is nonetheless critical to inform antibiotic resistance reduction strategies.

Methods

This study was conducted in 6 clinics located in 3 districts in Botswana. In each clinic, we surveyed a random sample of outpatients. We also invited each enrolled clinic subject to refer up to 3 adults. Each adult clinic or community subject was also invited to refer their children. All subjects had rectal swabs collected which were inoculated onto chromogenic media for preliminary identification of ESCrE. Final identification and susceptibility testing were performed using MALDI-TOF MS and VITEK-2, respectively. Data were collected on demographics, comorbidities, antibiotic use, healthcare exposures, travel, and farm and animal contact. Subjects with ESCrE colonization (cases) were compared to non-colonized subjects (controls). Bivariable and multivariable analyses were conducted to identify risk factors for ESCrE colonization.

Results

Enrollment occurred from 1/15/20–9/4/20 and 2,000 subjects were enrolled. There were 959 (48.0%) clinic subjects, 477 (23.9%) adult community subjects, and 564 (28.2%) child community subjects. 725 (36.3%) subjects lived in the same household as another subject. The median (IQR) age was 30 (12–41) and 1,463 (73%) were female. There were 555 cases and 1,445 controls (i.e., 27.8% of subjects were ESCrE colonized). Unadjusted comparisons are noted in Table 1. Independent risk factors for ESCrE were younger age, hospital exposure, travel, and presence of an ESCrE colonized household member (Table 2).

Conclusion

ESCrE colonization was common and associated with several exposures. Our results suggest even modest healthcare exposure may be important in driving ESCrE. The strong link to household member ESCrE colonization highlights the potential role of household transmission or common exposure. These findings warrant further prospective studies and provide vital information to inform strategies to curb further emergence of ESCrE in LMICs.

Disclosures

All Authors: No reported disclosures.

Colonization with extended-spectrum cephalosporin-resistant Enterobacterales (ESCrE) and carbapenem-resistant Enterobacterales (CRE) in healthcare and community settings in Botswana: an antibiotic resistance in communities and hospitals (ARCH) study

OBJECTIVES

Although extended-spectrum cephalosporin-resistant Enterobacterales (ESCrE) and carbapenem-resistant Enterobacterales (CRE) are a global challenge, data on these organisms in low- and middle-income countries are limited. In this study, we sought to characterize colonization data critical for greater antibiotic resistance surveillance efforts.

METHODS

This study was conducted in three hospitals and six clinics in Botswana. We conducted ongoing surveillance of adult patients in hospitals and clinics and adults and children in the community. All participants underwent rectal swab sampling to identify ESCrE and CRE.

RESULTS

Enrollment occurred from January 15, 2020, to September 4, 2020, but paused from April 2, 2020, to May 21, 2020, because of a countrywide COVID-19 lockdown. Of 5088 individuals approached, 2469 (49%) participated. ESCrE colonization prevalence was 30.7% overall (43% for hospital participants, 31% for clinic participants, 24% for adult community participants, and 26% for child community participants) (P <0.001). A total of 42 (1.7%) participants were colonized with CRE. CRE colonization prevalence was 1.7% overall (6.8% for hospital participants, 0.7% for clinic participants, 0.2% for adult community participants, and 0.5% for child community participants) (P <0.001). ESCrE and CRE prevalence varied substantially across regions and was significantly higher prelockdown versus postlockdown.

CONCLUSIONS

ESCrE colonization was high in all settings in Botswana. CRE prevalence in hospitals was also considerable. Colonization prevalence varied by region and clinical setting and decreased after a countrywide lockdown.

Development and Evaluation of a Molecular Hepatitis A Virus Assay for Serum and Stool Specimens

Hepatitis A virus (HAV) is an emerging public health concern and there is an urgent need for ways to rapidly identify cases so that outbreaks can be managed effectively. Conventional testing for HAV relies on anti-HAV IgM seropositivity. However, studies estimate that 10–30% of patients may not be diagnosed by serology. Molecular assays that can directly detect viral nucleic acids have the potential to improve diagnosis, which is key to prevent the spread of infections. In this study, we developed a real-time PCR (RT-PCR) assay to detect HAV RNA for the identification of acute HAV infection. Primers were designed to target the conserved 5′-untranslated region (5′-UTR) of HAV, and the assay was optimized on both the Qiagen Rotor-Gene and the BD MAX. We successfully detected HAV from patient serum and stool samples with moderate differences in sensitivity and specificity depending on the platform used. Our results highlight the clinical utility of using a molecular assay to detect HAV from various specimen types that can be implemented in hospitals to assist with diagnostics, treatment and prevention.

743. Colonization with Extended-Spectrum Cephalosporin-Resistant Enterobacterales (ESCrE) in Healthcare and Community Settings in Botswana: An Antibiotic Resistance in Communities and Hospitals (ARCH) Study

Background

Although ESCrE are a global challenge, data on ESCrE in low- and middle-income countries are limited. In particular, colonization data are critical for larger antibiotic resistance efforts. We characterized the colonization prevalence of ESCrE in various settings in Botswana.

Methods

This study was conducted in 3 hospitals and 6 clinics located in 3 districts in Botswana. In each hospital, we conducted surveillance of adult patients. Adult clinic patients were also randomly selected for participation. Finally, we enrolled community subjects by inviting each enrolled clinic subject to refer up to 3 adults. Each adult clinic or community subject was also allowed to refer their children. All subjects had rectal swabs obtained which were inoculated onto chromogenic media for preliminary identification of ESCrE. Final identification and susceptibility testing were performed using MALDI-TOF MS and VITEK-2, respectively. Genotyping was done for identification of extended-spectrum beta-lactamase (ESBL) genes.

Results

Enrollment occurred from 1/15/20-9/4/20 but paused from 4/2/20-5/21/20 due to a countrywide COVID lockdown. Of 5,088 subjects approached, 2,469 (49%) participated. Enrollment by subject type was: hospital – 469 (19%); clinic – 959 (39%); community adult – 477 (19%); and community child – 564 (23%). Of 2,469 subjects, the median (interquartile range) age was 32 years (19-44) and 1,783 (72%) were female. 759 (31%) subjects were colonized with at least one ESCrE; 130 subjects were colonized with multiple strains. E. coli (n=663) and K. pneumoniae (n=121) were most common. ESCrE colonization prevalence was 43% for hospital subjects, 31% for clinic subjects, 24% for adult community subjects, and 26% for child community subjects (p&lt; 0.001)). ESCrE prevalence varied significantly across regions (Figure 1) and was significantly higher pre-lockdown vs post-lockdown (Figure 2). CTX-M was the most common ESBL gene (Figure 3).

Figure 1. ESCrE Colonization - Study Sites

Conclusion

ESCrE colonization was common in both healthcare and community settings in Botswana. Colonization prevalence varies by region and clinical setting and decreased following a countrywide lockdown. These findings provide important clues regarding potential drivers of ESCrE that might serve as targets for intervention.

Disclosures

Robert Gross, MD, MSCE, Pfizer (Other Financial or Material Support, Serve on DSMB for drug unrelated to HIV) Ebbing Lautenbach, MD, MPH, MSCE, Merck (Other Financial or Material Support, Member of Data and Safety Monitoring Board (DSMB))

733. Carbapenem-Resistant Enterobacterales (CRE) Colonization Prevalence in Botswana: an Antibiotic Resistance in Communities and Hospitals (ARCH) Study

Background

Although CRE are a global threat, data in low- and middle-income countries are scarce. Colonization data are vital for informing antibiotic resistance strategies. We characterized the colonization prevalence of CRE in various settings in Botswana.

Methods

This study was conducted in 3 districts in Botswana (1 hospital and 2 clinics per district). Adult inpatients and clinic patients were randomly selected for enrollment. Community subjects were enrolled by inviting each enrolled clinic subject to refer up to 3 adults. Each adult clinic or community subject was also asked to refer their children. All subjects had rectal swabs obtained and inoculated on selective chromogenic media for preliminary identification of CRE. Final identification and susceptibility testing were performed using MALDI-TOF MS and VITEK-2, respectively. CRE underwent genotyping for carbapenemase genes.

Results

Subjects were enrolled from 1/15/20-9/4/20 with a pause from 4/2/20-5/21/20 due to a countrywide COVID lockdown. Of 5,088 subjects approached, 2,469 (49%) participated. Enrollment by subject type was: hospital – 469 (19%); clinic – 959 (39%); community adult – 477 (19%); and community child – 564 (23%). Of 2,469 subjects, the median (interquartile range) age was 32 years (19-44) and 1,783 (72%) were female. 42 (1.7%) subjects were colonized with at least one CRE; 10 subjects were colonized with multiple strains. E. coli (n=17), K. pneumoniae (n=20), and E. cloacae complex (n=11) were most common. CRE colonization prevalence was 6.8% for hospital subjects, 0.7% for clinic subjects, 0.2% for adult community subjects, and 0.5% for child community subjects (p&lt; 0.001)). CRE prevalence varied across regions (Figure 1) and was significantly higher pre- vs post-lockdown (Figure 2). VIM and NDM were the most common carbapenemase genes (Figure 3).

Figure 1. CRE Colonization - Study Sites

Conclusion

CRE colonization was significantly higher in hospital vs community settings in Botswana. CRE prevalence varied by region and decreased significantly following a countrywide lockdown. With CRE prevalence still modest, elucidating risk factors for CRE colonization holds promise in developing strategies to curb further emergence of CRE. Additional investigation of the CRE isolates without identified resistance genes is warranted.

Disclosures

Robert Gross, MD, MSCE, Pfizer (Other Financial or Material Support, Serve on DSMB for drug unrelated to HIV) Ebbing Lautenbach, MD, MPH, MSCE, Merck (Other Financial or Material Support, Member of Data and Safety Monitoring Board (DSMB))

82. Assessment of Clinical Outcomes and Antibiotic Prescribing Patterns Following Implementation of the GenMark ePlex® Blood Culture Identification Panel for Gram-positive Bloodstream Infections

Background

Rapid diagnostic testing (RDT) of bloodstream pathogens provides key information sooner than conventional identification and susceptibility testing. The GenMark ePlex® blood culture identification gram-positive (BCID-GP) panel is a molecular-based multiplex platform, with 20 Gram-positive target pathogens and 4 bacterial resistance genes that can be detected within 1.5 hours of blood culture positivity. Published studies have evaluated the accuracy of the ePlex® BCID-GP panel compared to traditional identification methods; however, studies evaluating the impact of this panel on clinical outcomes and prescribing patterns are lacking.

Methods

This multi-center, quasi-experimental study evaluated clinical outcomes and prescribing patterns before (December 2018 – June 2019) and after (August 2019 – January 2020) implementation of the ePlex® BCID-GP panel in June 2019. Hospitalized, adult patients with growth of Enterococcus faecalis, Enterococcus faecium, or Staphylococcus aureus from blood cultures were included. The primary endpoint was time to targeted antibiotic therapy, defined as time from positive Gram-stain to antibiotic adjustment for the infecting pathogen.

Results

A total of 200 patients, 100 in each group, were included. Time to targeted therapy was 47.9 hours in the pre-group versus 24.8 hours in the post-group (p&lt; 0.0001). Time from Gram-stain to organism identification was 23.03 hours (pre) versus 2.56 hours (post), p&lt; 0.0001. There was no statistically significant difference in time from Gram-stain to susceptibility results, hospital length of stay (LOS), or all-cause 30-day mortality.

Conclusion

Implementation of the GenMark ePlex® BCID-GP panel reduced time to targeted antibiotic therapy by nearly 24 hours. Clinical outcomes including hospital LOS and all-cause 30-day mortality did not show a statistical difference, although analysis of a larger sample size is necessary to appropriately assess these outcomes. This study represents the effect of RDT implementation alone, in the absence of stewardship intervention, on antibiotic prescribing patterns. These findings will inform the design of a dedicated RDT antimicrobial stewardship intervention at our institution, while also being generalizable to other institutions with RDT capabilities.

Disclosures

All Authors: No reported disclosures

751. Impact of Changing from a Three-step to Two-step Testing Algorithm for the Diagnosis of Clostridioides difficile

Background

The optimal method for laboratory diagnosis of Clostridioides difficile infection (CDI) remains undefined and national guidelines do not make a recommendation for a preferred diagnostic algorithm. Aiming to improve infection control measures, the Hospital of the University of Pennsylvania changed its testing process for the diagnosis of CDI from a 3-step to a 2-step algorithm (Figure 1) in September 2018. Starting an algorithm with nucleic acid amplification testing (NAAT) has been hypothesized to lead to potential diagnostic uncertainty if the result is positive by NAAT alone, as this test cannot distinguish between active infection and colonization.

Three-Step and Two-Step Diagnostic Testing Algorithms

Methods

This retrospective, single-center, quasi-experimental study included patients ≥ 18 years of age that tested positive for C. difficile between May 1^st, 2018 and January 31^st, 2019. The study period encompassed 4 months prior to the algorithm change, a 1-month washout immediately following the change, and the subsequent 4 months. The primary outcome was proportion of patients who tested positive for C. difficile and received targeted treatment for CDI. Secondary outcomes included total number of patients who tested positive for C. difficile and received targeted treatment for CDI, duration of treatment for CDI, and hospital length of stay.

Results

Sixty-nine patients in the pre-group (3-step) and 75 patients in the post-group (2-step) tested positive for C. difficile. A higher proportion of patients in the post-group tested positive by NAAT alone (59.4% vs. 73.3%). CDI severity and prior history of CDI were similar between groups. The primary outcome occurred in 89.9% of patients in the pre-group and 83.8% in the post-group (p=0.213). Sixty-two patients in each group received targeted treatment for CDI (p=0.213), median treatment duration was 15 (IQR 11.25-25.75) and 14 (IQR 11-25) days (p=0.505), and median hospital length of stay was 9 (IQR 3-15) and 6 (IQR 3-20) days (p=0.690) in the pre-group and post-group, respectively.

Conclusion

Although there was a higher percentage of patients in the post-group that tested positive for C. difficile by NAAT alone, there was no difference in the proportion or total number of patients who received targeted CDI treatment between time periods.

Disclosures

All Authors: No reported disclosures

Comparison of Saliva and Nasopharyngeal Swabs for SARS-CoV-2 Detection in an Emergency Department and Ambulatory Testing Locations

Introduction/Objective

Nasopharyngeal (NP) swabs have been the traditional specimen source used for testing for respiratory viruses. However, at the start of the COVID-19 pandemic, several studies suggested that saliva could also be used as a specimen source for testing for SARS-CoV-2. Despite potential benefits, there was limited data on the characteristics of this specimen type and few commercial assays with FDA emergency use authorization allowed saliva as a specimen source. In order to explore the feasibility and validate using saliva as a specimen source for ambulatory and emergency department patients we designed a study to compare saliva to NP swabs for SARS-CoV-2 testing.

Methods/Case Report

Specimens were collected in the emergency department and ambulatory testing sites between May 6, 2020-July 7, 2020. Nasopharyngeal swabs were collected as part of routine clinical practice and patients were given written instructions to self-collect 1mL of saliva into a sterile specimen cup with or without a straw. SARS-CoV-2 testing was performed in parallel with both specimen types using the TaqPath COVID-19 Combo Kit (Thermo Fisher Waltham, MA). Saliva was diluted 1:1 in saline prior to testing. Specimens were transported to the lab at 4C and frozen at -80C prior to testing.

Results (if a Case Study enter NA)

Seventy-four patients had both an NP swab and saliva tested in this study. Thirty of the 74 patients (41%) were unable to produce the full 1mL of saliva requested, but all samples had sufficient volume for testing after dilution. There were 34 positive samples obtained with an 82% positive agreement between the NP swabs and saliva. In 6 cases, the NP swab was positive, and the paired saliva was negative. In 1 case, only the saliva was positive. The average Ct of the positive NP swabs with a paired negative saliva sample was 39.6. There was only a single invalid test for one of the saliva samples.

Conclusion

Saliva was a straightforward sample to collect and test for SARS-CoV-2. Challenges included obtaining sufficient sample and a less predictable matrix that required dilution to ensure proper pipeting. In this study, NP swabs were more sensitive for detection of SARS-CoV-2. Paired saliva was more often negative in patients shedding small amounts of SARS-CoV-2 based on a high Ct of the positive NP sample.

Quantifying the Impact of Nasopharyngeal Specimen Quality on Severe Acute Respiratory Syndrome Coronavirus 2 Test Performance

BACKGROUND

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reverse-transcription polymerase chain reaction (RT-PCR) cycle threshold (Ct) has been used to estimate quantitative viral load, with the goal of targeting isolation precautions for individuals with coronavirus disease 2019 (COVID-19) and guiding public health interventions. However, variability in specimen quality can alter the Ct values obtained from SARS-CoV-2 clinical assays. We sought to define how variable nasopharyngeal (NP) swab quality impacts clinical SARS-CoV-2 test sensitivity.

METHODS

We performed amplification of a human gene target (β-actin) in parallel with a clinical RT-PCR targeting the SARS-CoV-2 ORF1ab gene for 1282 NP specimens collected from patients with clinical concern for COVID-19. We evaluated the relationship between NP specimen quality, characterized by late Ct values for the human gene target β-actin Ct, and the probability of SARS-CoV-2 detection via logistic regression, as well as the linear relationship between SARS-CoV-2 and β-actin Ct.

RESULTS

Low-quality NP swabs are less likely to detect SARS-CoV-2 (odds ratio, 0.607 [95% credible interval {CrI}, .487-.753]). We observed a positive linear relationship between SARS-CoV-2 and β-actin Ct values (slope, 0.181 [95% CrI, .097-.264]), consistent with a reduction in detection of 0.181 cycles for each additional cycle of the β-actin target. COVID-19 disease severity was not associated with β-actin Ct values.

CONCLUSIONS

Variability in NP specimen quality significantly impacts the performance of clinical SARS-CoV-2 assays, and caution should be taken when interpreting quantitative SARS-CoV-2 Ct results. If unrecognized, low-quality NP specimens, which are characterized by a low level of amplifiable human DNA target, may limit the successful application of SARS-CoV-2 Ct values to direct infection control and public health interventions.

157. patient to Environment Transmission of Multidrug-resistant Bacteria Within Intensive Care Units

Background

Identifying risk factors for environmental contamination with multidrug-resistant organisms (MDROs) is essential to prioritize methods for prevention of hospital transmission.

Methods

Patients admitted to an ICU with an MDRO detected on clinical culture in the prior 30 days were enrolled. Patients (4 body sites) and high-touch objects (HTO) (3 composite sites) in ICU rooms were sampled. Environmental transmission was defined by shared MDRO species cultured on patient and HTO cultures obtained on multiple time points during the patient’s stay. Risk factors for environmental transmission were identified with logistic regression.

Results

Forty-five patients were included (median 2 days of longitudinal sampling [IQR 1–4 days]). Enrollment anatomic cultures included extended-spectrum beta-lactamase-producing Enterobacterales (ESBLE) (n=12, 27%), carbapenem-resistant organisms (CRO) (n=4, 9%), methicillin-resistant S.aureus (MRSA) (n=11, 24%), vancomycin-resistant Enterococci (VRE) (n=4, 9%), and C.difficile (CDIFF) (n=14, 31%). Patient colonization during serial sampling was common with CRO (n=21, 47%), ESBLE (n=16, 36%), and VRE (n=16, 36%) and less so with MRSA (n=7, 16%) and CDIFF (n=5, 11%). Detection of MDROs on environmental surfaces was also common with identification of CRO in 47% of patient rooms (n=21) and ESBLE in 29% (n=13); MRSA (n=2, 4%), VRE (n=9, 20%), and CDIFF (n=3, 7%) were rarer. Patient to environment transmission was observed in 40% of rooms (n=18). Thirteen (29%) rooms had foreign MDRO contamination (i.e., one not detected on a body culture), most (n=10) with CRO. Environmental MDROs were most common in bathroom/sinks (n=22), followed by surfaces near the patient (n=10), and least common surfaces often touched by staff within the room (n=6).

On multivariable logistic regression, naïve to clustering by patient, recent receipt of a proton pump inhibitor (OR 2.35, 95% CI 1.00 – 5.52, P=0.049) and presence of one or more wounds (OR 2.56, 95% CI 1.05 – 6.26, P=0.038) were significantly associated with environmental transmission (OR 1.56, 95% CI 1.01 – 2.43, P=0.046) (Table 1).

Conclusion

MDRO contamination of patient rooms is common with detection of organisms attributed to, and foreign to, the occupant.

Disclosures

Michael Z. David, MD PhD, GSK (Consultant)

Impact of Nasopharyngeal Specimen Quality on SARS-CoV-2 Test Sensitivity

BACKGROUND

The SARS-CoV-2 reverse-transcription polymerase chain reaction (RT-PCR) cycle of threshold (Ct) has been used to estimate quantitative viral load, with the goal of targeting isolation precautions for individuals with COVID-19 and guiding public health interventions. However, variability in specimen quality can alter the Ct values obtained from SARS-CoV-2 clinical assays. We sought to define how variable nasopharyngeal (NP) swab quality impacts clinical SARS-CoV-2 test sensitivity.

METHODS

We performed amplification of a human gene target (β-actin) in parallel with a clinical RT-PCR targeting the SARS-CoV-2 ORF1ab gene for 1311 NP specimens collected from patients with clinical concern for COVID-19. We evaluated the relationship between NP specimen quality, characterized by high Ct values for the human gene target β-actin Ct, and the probability of SARS-CoV-2 detection via logistic regression, as well as the linear relationship between SARS-CoV-2 and β-actin Ct.

RESULTS

Low quality NP swabs are less likely to detect SARS-CoV-2 (odds ratio 0.654, 95%CI 0.523 to 0.802). We observed a positive linear relationship between SARS-CoV-2 and β-actin Ct values (slope 0.169, 95%CI 0.092 to 0.247). COVID-19 disease severity was not associated with β-actin Ct values.

CONCLUSIONS

Variability in NP specimen quality accounts for significant differences in the sensitivity of clinical SARS-CoV-2 assays. If unrecognized, low quality NP specimens, which are characterized by a low level of amplifiable human DNA target, may limit the application of SARS-CoV-2 Ct values to direct infection control and public health interventions.

Investigating hospital Mycobacterium chelonae infection using whole genome sequencing and hybrid assembly

Mycobacterium chelonae is a rapidly growing nontuberculous mycobacterium that is a common cause of nosocomial infections. Here we describe investigation of a possible nosocomial transmission of M. chelonae at the Hospital of the University of Pennsylvania (HUP). M. chelonae strains with similar high-level antibiotic resistance patterns were isolated from two patients who developed post-operative infections at HUP in 2017, suggesting a possible point source infection. The isolates, along with other clinical isolates from other patients, were sequenced using the Illumina and Oxford Nanopore technologies. The resulting short and long reads were hybrid assembled into draft genomes. The genomes were compared by quantifying single nucleotide variants in the core genome and assessed using a control dataset to quantify error rates in comparisons of identical genomes. We show that all M. chelonae isolates tested were highly dissimilar, as indicated by high pairwise SNV values, consistent with environmental acquisition and not a nosocomial point source. Our control dataset determined a threshold for evaluating identity between strains while controlling for sequencing error. Finally, antibiotic resistance genes were predicted for our isolates, and several single nucleotide variants were identified that have the potential to modulated drug resistance.

Clinical Outcomes of Clofazimine Use for Rapidly Growing Mycobacterial Infections

Background

Rapidly growing mycobacteria (RGM) have high rates of intrinsic antibiotic resistance and require prolonged antibiotic therapies associated with considerable toxicity. Less toxic and more effective therapies are needed. One promising agent is clofazimine (CFZ), an antibiotic with favorable in vitro data but limited clinical data in RGM.

Methods

We performed a retrospective cohort study of all patients treated for RGM infection with a CFZ-containing regimen in the University of Pennsylvania Health System between 1/1/2010 and 12/31/2016. Primary outcome was clinical cure, defined as no evidence of clinical or microbiologic infection recurrence after 1 year following the completion of treatment. Secondary outcomes included clinical, radiologic, and microbiologic response; all-cause mortality; infection-specific mortality; and treatment-related adverse events. Descriptive and unadjusted analyses were performed to elucidate associations between pertinent demographic and comorbidity data, clinical presentation, treatment history, and treatment outcomes.

Results

We treated 55 patients with CFZ for RGM infection during the study period in combination with a median of 5 other antibiotic agents during each treatment course. Clinical cure with initial treatment regimen was achieved in 43% of patients with pulmonary infection and 71% of patients with non-pulmonary infection. CFZ was well tolerated in our cohort and was discontinued prematurely in 20% of patients, but only in the context of discontinuing all antibiotic agents.

Conclusions

As part of multidrug therapy, CFZ is well tolerated and may be effective in patients with RGM infection, especially non-pulmonary and non-Mycobacterium abscessus complex infections.

Dual β-Lactam Combinations Highly Active against Mycobacterium abscessus Complex In Vitro

As a consequence of a growing population of immunocompromised individuals, including transplant recipients and cystic fibrosis patients, there has been a dramatic increase in chronic infections caused by Mycobacterium abscessus complex (MABC) strains that are usually recalcitrant to effective antibiotic therapy. The recent rise of macrolide resistance in MABC has further complicated this clinical dilemma, dramatizing the need for novel agents. The repurposing of current antibiotics is one rapid path from discovery to patient care. In this study, we have discovered that dual β-lactams, and specifically the combination of ceftazidime with either ceftaroline or imipenem, are synergistic and have clinically relevant activities, with MIC50s of 0.25 (ceftaroline with 100 µg/ml ceftazidime) and 0.5 µg/ml (imipenem with 100 µg/ml ceftazidime) against clinical MABC isolates. Similar synergy was observed in time-kill studies against the M. abscessus ATCC 19977 strain using clinically achievable concentrations of either imipenem (4 µg/ml) or ceftaroline (2 µg/ml), as the addition of ceftazidime at concentrations of ≥50 µg/ml showed a persistent bactericidal effect over 5 days. Treatment of THP-1 human macrophages infected with three different M. abscessus clinical isolates supported the in vitro findings, as the combination of 100 µg/ml ceftazidime and 0.125 µg/ml ceftaroline or 100 µg/ml ceftazidime and 0.25 µg/ml imipenem dramatically reduced the CFU counts to near baseline levels of infection. This study's finding that there is synergy between certain β-lactam combinations against M. abscessus infection provides optimism toward identifying an optimum dual β-lactam treatment regimen.IMPORTANCE The emergence of chronic MABC infections among immunocompromised populations and their inherent and acquired resistance to effective antibiotic therapy have created clinical challenges in advancing patients for transplant surgery and treating those with disease. There is an urgent need for new treatment regimens, and the repurposing of existing antibiotics provides a rapid strategy to advance a laboratory finding to patient care. Our recent discoveries that dual β-lactams, specifically the combination of ceftazidime with ceftaroline or ceftazidime with imipenem, have significant in vitro MIC values and kill curve activities and are effective against infected THP-1 human macrophages provide optimism for a dual β-lactam treatment strategy against MABC infections. The unexpected synergistic activities reported in this study create a new path of discovery to repurpose the large family of β-lactam drugs.

Identification of Clinically Relevant Mycobacterial Species After Extended Incubation Times in the BACTEC MGIT System

Objectives

Traditionally, for mycobacterial culture both solid and broth media are used and routinely held for 6 weeks minimum to optimize yield. We retrospectively reviewed all positive mycobacterial cultures over a 12-month period to assess growth kinetics of clinically relevant isolates.

Methods

From January to December 2015, 658 positive mycobacteria cultures by solid (7H11 and 7H10 plates) and/or broth (BACTEC MGIT) media were identified and reviewed.

Results

In broth-only cultures, 21 of 153 (13.7%) from 21 patients were positive after 28 days' incubation. Subsequent chart review revealed the following species: 11 Mycobacterium avium intracellulare complex (MAI), five Mycobacterium tuberculosis (MTB), and five other non-MTB/MAI mycobacteria. Two of the cases of MTB were first-time isolates, and 11.4% of MTB-positive cultures became positive after 4 weeks' incubation.

Conclusions

These data provide strong evidence reaffirming that clinically meaningful results are frequently detected after extended incubation times by broth-only methods, including several MTB isolates.

1525. Evaluation of Clinical Outcomes With Fosfomycin for E. coli and Non-E. coli Enterobacteriaceae Urinary Tract Infections

Background

Fosfomycin is a broad-spectrum oral antibiotic increasingly used for the treatment of uncomplicated and complicated urinary tract infections (UTIs). The Clinical and Laboratory Standards Institute (CLSI) does not support fosfomycin susceptibility testing on urinary isolates outside of Enterococcus faecalis and Escherichia coli. This is in light of building evidence and concern for the presence of chromosomal fosA gene in non-E. coli Enterobacteriaceae. Regardless, clinicians have continued to test and use fosfomycin for these pathogens due to multidrug resistance or intolerance to other agents without ample data on clinical implications.

Methods

This retrospective study included patients who received fosfomycin for the treatment of a UTI caused by any Enterobacteriaceae for which fosfomycin testing was performed from March 2016 through April 2018. We separated patients who received fosfomycin for the treatment of UTIs caused by E. coli from those caused by other Enterobacteriaceae for comparison. The primary outcome is the rate of clinical success at 48 hours, defined as the absence of UTI symptoms and normalization of vital signs. The secondary outcome is the rate of recurrent UTIs caused by the same pathogen within 30 days of the index infection.

Results

There were 28 separate episodes of E. coli UTIs in 24 patients and 25 separate episodes of non-E. coli UTIs in 26 patients included into this study. Patients were mostly balanced between the two groups and were on average about 64 years old, mostly females (61%), and had an average Charlson Comorbidity Index of 5. All E. coli isolates were susceptible to fosfomycin, while only 82.8% non-E. coli isolates were fosfomycin-susceptible. The rates of clinical success were similar between the E. coli and non-E. coli groups (89.3% vs. 88.5%). There was a higher rate of recurrence of the same UTI with E. coli (15.4%) than with non-E. coli (4.8%).

Conclusion

Findings from this small study suggest favorable outcomes with use of fosfomycin for non-E. coli Enterobacteriaceae. Despite recommendations against testing and use of fosfomycin in these pathogens, it appears that in vitro resistance does not always correlate with clinical response.

Disclosures

All authors: No reported disclosures.

Symmetry breakdown of electron emission in extreme ultraviolet photoionization of argon

Short wavelength free-electron lasers (FELs), providing pulses of ultrahigh photon intensity, have revolutionized spectroscopy on ionic targets. Their exceptional photon flux enables multiple photon absorptions within a single femtosecond pulse, which in turn allows for deep insights into the photoionization process itself as well as into evolving ionic states of a target. Here we employ ultraintense pulses from the FEL FERMI to spectroscopically investigate the sequential emission of electrons from gaseous, atomic argon in the neutral as well as the ionic ground state. A pronounced forward-backward symmetry breaking of the angularly resolved emission patterns with respect to the light propagation direction is experimentally observed and theoretically explained for the region of the Cooper minimum, where the asymmetry of electron emission is strongly enhanced. These findings aim to originate a better understanding of the fundamentals of photon momentum transfer in ionic matter.

Note: Soft X-ray transmission polarizer based on ferromagnetic thin films

A transmission polarizer for producing elliptically polarized soft X-ray radiation from linearly polarized light is presented. The setup is intended for use at synchrotron and free-electron laser beamlines that do not directly offer circularly polarized light for, e.g., X-ray magnetic circular dichroism (XMCD) measurements or holographic imaging. Here, we investigate the degree of ellipticity upon transmission of linearly polarized radiation through a cobalt thin film. The experiment was performed at a photon energy resonant to the Co L₃-edge, i.e., 778 eV, and the polarization of the transmitted radiation was determined using a polarization analyzer that measures the directional dependence of photo electrons emitted from a gas target. Elliptically polarized radiation can be created at any absorption edge showing the XMCD effect by using the respective magnetic element.

Data from the analytical performance of the Abaxis Piccolo Xpress point of care analyzer in whole blood, serum, and plasma

The objective of this study was to examine the analytical performance of 14 comprehensive metabolic panel analytes on the Abaxis Piccolo Xpress® Point of Care analyzer in serum, plasma, and whole blood. A method comparison was performed on all three specimen types intended for use on the Piccolo Xpress®: serum, heparinized plasma, and whole blood. This data is also presented in Murata et al. (2015) [1]. This article includes the actual Bland-Altman bias plots of the difference in results obtained for analytes in the comprehensive metabolic panel from the Abaxis Piccolo Xpress and the comparison instrument, the Ortho Vitros.

Single Shot Polarization Characterization of XUV FEL Pulses from Crossed Polarized Undulators

Polarization control is a key feature of light generated by short-wavelength free-electron lasers. In this work, we report the first experimental characterization of the polarization properties of an extreme ultraviolet high gain free-electron laser operated with crossed polarized undulators. We investigate the average degree of polarization and the shot-to-shot stability and we analyze aspects such as existing possibilities for controlling and switching the polarization state of the emitted light. The results are in agreement with predictions based on Gaussian beams propagation.

Characterization of spatial coherence of synchrotron radiation with non-redundant arrays of apertures

A method to characterize the spatial coherence of soft X-ray radiation from a single diffraction pattern is presented. The technique is based on scattering from non-redundant arrays (NRAs) of slits and records the degree of spatial coherence at several relative separations from 1 to 15 µm, simultaneously. Using NRAs the spatial coherence of the X-ray beam at the XUV X-ray beamline P04 of the PETRA III synchrotron storage ring was measured as a function of different beam parameters. To verify the results obtained with the NRAs, additional Young's double-pinhole experiments were conducted and showed good agreement.

Protein signature for non-small cell lung cancer prognosis

BACKGROUND

Current histopathological classification and TNM staging have limited accuracy in predicting survival and stratifying patients for appropriate treatment. The goal of the study is to determine whether the expression pattern of functionally important regulatory proteins can add additional values for more accurate classification and prognostication of non-small lung cancer (NSCLC).

METHODS

The expression of 108 proteins and phosphoproteins in 30 paired NSCLC samples were assessed using Protein Pathway Array (PPA). The differentially expressed proteins were further confirmed using a tissue microarray (TMA) containing 94 NSCLC samples and were correlated with clinical data and survival.

RESULTS

Twelve of 108 proteins (p-CREB(Ser133), p-ERK1/2(Thr202/Tyr204), Cyclin B1, p-PDK1(Ser241), CDK4, CDK2, HSP90, CDC2p34, β-catenin, EGFR, XIAP and PCNA) were selected to build the predictor to classify normal and tumor samples with 97% accuracy. Five proteins (CDC2p34, HSP90, XIAP, CDK4 and CREB) were confirmed to be differentially expressed between NSCLC (n=94) and benign lung tumor (n=19). Over-expression of CDK4 and HSP90 in tumors correlated with a favorable overall survival in all NSCLC patients and the over-expression of p-CREB(Ser133) and CREB in NSCLC correlated with a favorable survival in smokers and those with squamous cell carcinoma, respectively. Finally, the four proteins (CDK4, HSP90, p-CREB and CREB) were used to calculate the risk score of each individual patient with NSCLC to predict survival.

CONCLUSION

In summary, our data demonstrated a broad disturbance of functionally important regulatory proteins in NSCLC and some of these can be selected as clinically useful biomarkers for diagnosis, classification and prognosis.

Angular momentum sensitive two-center interference

In quantum mechanics the Young-type double-slit experiment can be performed with electrons either traveling through a double slit or being coherently emitted from two inversion symmetric molecular sites. In the latter one the valence photoionization cross sections of homonuclear diatomic molecules were predicted to oscillate over kinetic energy almost 50 years ago. Beyond the direct proof of the oscillatory behavior of these photoionization cross sections σ, we show that the angular distribution of the emitted electrons reveals hitherto unexplored information on the relative phase shift between the corresponding partial waves through two-center interference patterns.

Effective replication of human influenza viruses in mice lacking a major alpha2,6 sialyltransferase

The hemagglutinins of influenza viruses isolated from humans typically prefer binding to sialic acid in an alpha2,6 linkage. Presumably, the virus uses the presence of these receptors on the respiratory tract to gain entrance into the host cell. The ST6Gal I sialyltransferase knock-out mouse lacks the main enzyme necessary for the attachment of alpha2,6 sialic acid to N-linked glycoproteins on the cell surface. Yet even in the absence of detectable alpha2,6 sialic acid in the mouse respiratory tract, human influenza viruses can still infect these mice and grow to similar titers in the lung and trachea as compared to wild-type animals. This work demonstrates that the presence of a major alpha2,6 sialic acid on N-linked glycoproteins is not essential for human influenza virus infection in mice.

A two-amino acid change in the hemagglutinin of the 1918 influenza virus abolishes transmission

The 1918 influenza pandemic was a catastrophic series of virus outbreaks that spread across the globe. Here, we show that only a modest change in the 1918 influenza hemagglutinin receptor binding site alters the transmissibility of this pandemic virus. Two amino acid mutations that cause a switch in receptor binding preference from the human alpha-2,6 to the avian alpha-2,3 sialic acid resulted in a virus incapable of respiratory droplet transmission between ferrets but that maintained its lethality and replication efficiency in the upper respiratory tract. Furthermore, poor transmission of a 1918 virus with dual alpha-2,6 and alpha-2,3 specificity suggests that a predominant human alpha-2,6 sialic acid binding preference is essential for optimal transmission of this pandemic virus. These findings confirm an essential role of hemagglutinin receptor specificity for the transmission of influenza viruses among mammals.

Sequence analysis and receptor specificity of the hemagglutinin of a recent influenza H2N2 virus isolated from chicken in North America

Influenza viruses bind host cells following an interaction between the viral hemagglutinin (HA) protein and host cell sialylated glycoproteins and glycolipids. Differences in binding affinities of the HAs for different types of sialic acid linkages (alpha2-3 vs. alpha2-6) contribute to determining the host range of an influenza virus. The ability of an avian influenza virus HA to bind the human form of the receptor may be one requirement for an avian virus to propagate in the human population. In this paper, we describe the characterization of the HA from an H2N2 virus isolated from a Pennsylvania chicken farm in 2004. Sequence analysis revealed that this HA is a member of the Eurasian clade, and receptor binding studies show that it maintains its specificity for the avian influenza virus alpha2-3 linked sialic acid receptor.

Glycan microarray analysis of the hemagglutinins from modern and pandemic influenza viruses reveals different receptor specificities

Influenza A virus specificity for the host is mediated by the viral surface glycoprotein hemagglutinin (HA), which binds to receptors containing glycans with terminal sialic acids. Avian viruses preferentially bind to alpha2-3-linked sialic acids on receptors of intestinal epithelial cells, whereas human viruses are specific for the alpha2-6 linkage on epithelial cells of the lungs and upper respiratory tract. To define the receptor preferences of a number of human and avian H1 and H3 viruses, including the 1918 H1N1 pandemic strains, their hemagglutinins were analyzed using a recently described glycan array. The array, which contains 200 carbohydrates and glycoproteins, not only revealed clear differentiation of receptor preferences for alpha2-3 and/or alpha2-6 sialic acid linkage, but could also detect fine differences in HA specificity, such as preferences for fucosylation, sulfation and sialylation at positions 2 (Gal) and 3 (GlcNAc, GalNAc) of the terminal trisaccharide. For the two 1918 HA variants, the South Carolina (SC) HA (with Asp190, Asp225) bound exclusively alpha2-6 receptors, while the New York (NY) variant, which differed only by one residue (Gly225), had mixed alpha2-6/alpha2-3 specificity, especially for sulfated oligosaccharides. Only one mutation of the NY variant (Asp190Glu) was sufficient to revert the HA receptor preference to that of classical avian strains. Thus, the species barrier, as defined by the receptor specificity preferences of 1918 human viruses compared to likely avian virus progenitors, can be circumvented by changes at only two positions in the HA receptor binding site. The glycan array thus provides highly detailed profiles of influenza receptor specificity that can be used to map the evolution of new human pathogenic strains, such as the H5N1 avian influenza.

A single amino acid substitution in 1918 influenza virus hemagglutinin changes receptor binding specificity

The receptor binding specificity of influenza viruses may be important for host restriction of human and avian viruses. Here, we show that the hemagglutinin (HA) of the virus that caused the 1918 influenza pandemic has strain-specific differences in its receptor binding specificity. The A/South Carolina/1/18 HA preferentially binds the alpha2,6 sialic acid (human) cellular receptor, whereas the A/New York/1/18 HA, which differs by only one amino acid, binds both the alpha2,6 and the alpha2,3 sialic acid (avian) cellular receptors. Compared to the conserved consensus sequence in the receptor binding site of avian HAs, only a single amino acid at position 190 was changed in the A/New York/1/18 HA. Mutation of this single amino acid back to the avian consensus resulted in a preference for the avian receptor.

Overruled: objections to optical disk archiving

In summary, while the Federal Rules of Evidence neglect to specifically address the admission of optical disk evidence, the Rules do recognize the reliability and admissibility of records maintained with modern computer storage techniques. In certain cases, information stored on optical disk will constitute original information; in others, the information will constitute an admissible duplicate. Regardless of the classification, the optical disk evidence should be admissible if the party offering the evidence can establish that the optical disk storage and retrieval process accurately reproduces the original document. The admission of medical records stored on optical disk will be challenged. The technology involved in optical disk storage, however, makes optical disk information more reliable than magnetic disk information. As a result, optical disk evidence currently should survive challenges more readily than magnetic disk evidence.