bluuebunny/crossref_metadata_2025_split huggingface dataset:
656. Development and Application of a Pragmatic Algorithm for the Detection of Carbapenemase-Producing Pseudomonas aeruginosa (CP-PA)
Authors: Gill Christian M , Asempa Tomefa E , Nicolau David P 
Published: January 2021

Abstract

Background
Historically, carbapenem-resistance in P. aeruginosa (PA) has been mediated by inducible AmpC, drug efflux, and porin loss; however, carbapenemase production is an increasingly recognized entity. Of these mechanisms, carbapenemases can drastically reduce treatment options and rapidly disseminate. Since broad applications of phenotypic (mCIM/eCIM) and PCR-based detection can be labor intensive and costly, we developed an MIC derived algorithm to streamline use of these definitive carbapenemase detection methodologies.

Methods
To develop the testing criteria, a challenge set of PA (n=92), NDM, IMP, VIM, KPC, SPM, GES, cephalosporinase or efflux/porin mutation and wild-type isolates were utilized. Broth microdilution MICs were determined for: ceftazidime (CAZ), cefepime (FEP), piperacillin/tazobactam (TZP), meropenem (MEM), imipenem (IPM), ceftolozane/tazobactam (C/T), and ceftazidime/avibactam (CZA). To assess the utility of CAZ, FEP, TZP, and C/T screening criteria from the challenge set, 1,209 clinical PA isolates from a US surveillance program were tested. Confirmatory genotypic and phenotypic testing for evidence of carbapenemases was conducted on all criteria-derived isolates using the Xpert Carba-R assay and the modified carbapenem inactivation method (mCIM)/EDTA-modified carbapenem inactivation method (eCIM), respectively.

Results
Test performance and characteristics of the challenge set are displayed in Table 1. Of the 1,209 clinical isolates, 230 (19%) were IPM and MEM resistant. 116 isolates met the defined criteria (using most common anti-pseudomonal β-lactams) of: IPM and MEM resistance; non-susceptibility to CAZ, FEP, and TZP. Carba-R identified 5 carbapenemase-producing isolates (all blaVIM-positive), while the mCIM/eCIM detected 7 carbapenemase-producing isolates (including the 5 blaVIM-positive isolates).
Table 1. Characteristics of the Challenge Set of 92 P. aeruginosa isolates utilized in algorithm development.

Conclusion
In the presence of carbapenem resistance, non-susceptibility to FEP, CAZ, and TZP (or C/T when available) is a useful starting point to delineate CP-PA versus non-CP-PA. This MIC criterion combined with either mCIM/eCIM or PCR-based testing is a pragmatic and streamlined approach to identify CP-PA, while providing vital information to guide therapeutic and infection control measures.

Disclosures
David P. Nicolau, PharmD, Cepheid (Other Financial or Material Support, Consultant, speaker bureau member or has received research support.)Merck & Co., Inc. (Consultant, Grant/Research Support, Speaker’s Bureau)Wockhardt (Grant/Research Support)
658. Effect of HIV Status on Tuberculosis Load as Detected by Xpert MTB/RIF in Sputum vs. Saliva Samples
Authors: Burger Zoe C , Aung Si Thu , Aung Hlaing Thazin , Rodwell Timothy , Seifert Marva 
Published: January 2021

Abstract

Background
Tuberculosis (TB) is the most common co-infection among people living with HIV, but HIV positivity is associated with a lower Mycobacterium tuberculosis (MTB) bacillary load in sputum, making TB often difficult to diagnose with current diagnostic solutions. GeneXpert MTB/RIF (Cepheid, USA), a rapid, molecular diagnostic assay, has transformed the TB diagnostic landscape and can be used to diagnose TB and limited drug resistance in HIV patients from direct clinical samples in &lt; 2 hours, but results can be significantly affected by sample bacterial load, which is quantified by the GeneXpert MTB/RIF (Xpert) instrument using Ct values. Our primary objective was to assess how a patient’s HIV status affected their MTB bacterial load in sputum vs. saliva samples submitted for Xpert diagnosis of TB.

Methods
We completed a retrospective analysis of &gt;4,000 patient records from the Myanmar National TB Program captured as part of a nation-wide electronic reporting system developed with the assistance of FIND (Geneva). De-identified records included HIV status, Xpert testing results, and for a subset of patients, specimen type. With this diagnostic information, we compared the distribution of MTB load (quantified by Xpert Ct values) in sputum and saliva in HIV positive vs. HIV negative patients using STATA.

Results
Based on mean Ct value comparison independent of HIV status, saliva samples (mean Ct = 22.7) contained a significantly lower bacterial load of MTB as compared to sputum samples (mean Ct=19.2, p &lt; .001).Within saliva samples, a lower bacterial load was also detected in HIV positive patients (mean Ct = 26.9) compared to HIV negative patients (mean Ct = 22.3, p&lt; .05). Similarly, in sputum samples, a lower bacterial load was detected in HIV positive patients (mean Ct = 21.6) compared to HIV negative patients (mean Ct = 19.0, p &lt; .001) (Figure 1).
Figure 1. Ct Values by HIV Status and Specimen Type

Conclusion
Sputum samples have a significantly higher bacterial load on average compared to saliva samples independent of HIV status. Additionally, when looking at both saliva and sputum as sample types, HIV positive patients have significantly lower bacterial load than individuals who are HIV negative. Based on these results, sputum is the optimal sample type for Xpert TB detection, especially in people living with HIV.

Disclosures
All Authors: No reported disclosures
659. Evaluation of Four Chromogenic Agars for Urine Culture Including Time and Cost Savings Analysis
Authors: Capistran Eve , Lévesque Simon , Martin Philippe , Girard Diane , Papirakis Marie-Eve , Cloutier Claudia , Cameron Mélissa , Brown Nathalie , LeBlanc Louiselle 
Published: January 2021

Abstract

Background
With a volume of approximately 5000 urine culture specimens per month in our tertiary-care university center hospital’s microbiology laboratory, we wanted to evaluate methods aiming to improve workflow and performance while reducing turnaround time and potentially overall cost.

Methods
310 urine culture specimens as well as selected less frequent pathogens (A. urinae - 26 strains, C. urealyticum - 4 strains) were plated on four chromogenic agars in parallel with standard protocol MacConkey (MAC) and blood agar (BA). Chromogenic agars evaluated were: UriSelectTM 4 (Bio-Rad), CHROMID® CPS® Elite (bioMérieux), BrillanceTM UTI ClarityTM agar Biplate (Oxoid) and BDTM CHROMagarTM Orientation (BD). Primary outcome was overall growth performance for frequent pathogens and for gram positives, where chromogenic agars were previously reported to underperform.The number of additional tests needed and the appreciation of different media by laboratory personnel were also assessed. A sub-analysis measured the total time required to plate and to read 50 consecutive specimens comparatively for the 4 chromogenic agars and for MAC/BA.

Results
Global performance was 90% for Uriselect, 88% for ChromID, 89% for Chromagar and 81% for Brillance compared to 84% for standard method. ChromID and Brillance supported the growth of more A. urinae and C. urealyticum than the other 2 chromogenic agars. All monoplate chromogenic agars were appreciated equally by technologists. In addition, for all chromogenic agars, working time was reduced by half as compared to MAC/BA. We estimated a time economy of approximately 80 hours per month in our laboratory, translating in a net annual economy.

Conclusion
All 4 chromogenic medias evaluated in our study had an acceptable performance, with specific strengths and weaknesses for each one. The choice of ChromID CPS Elite (bioMérieux) for our center was based on pre-established criteria including performance for more fastidious gram positives, best time and cost economy, and compatibility with current identification method and susceptibility testing platform. However, since the 4 chromogenic agars have been adequately verified in our laboratory, we consider that they could be interchangeable if needed.

Disclosures
All Authors: No reported disclosures
662. Identification of Clinically Relevant Microbes with the MasSpec Pen
Authors: Povilaitis Sydney C , Chakraborty Ashish D , Downey Rachel D , Hauger Sarmistha Bhaduri , Eberlin Livia 
Published: January 2021

Abstract

Background
In the age of antimicrobial resistance, rapid identification of infectious agents is critical for antimicrobial stewardship and effective therapy. To this end, ambient ionization mass spectrometry techniques have been applied for rapid identification of microbes directly from culture isolates. We have developed a handheld, mass spectrometry-based device, the MasSpec Pen, that permits direct molecular analysis of a biological sample in seconds (Scheme 1). Here, we employ the MasSpec Pen to identify clinically relevant microbes directly from culture isolates.

Methods
Staphylococcus aureus, Staphylococcus epidermidis, Group A and B Streptococcus, Kingella kingae (K.k), and Pseudomonas aeruginosa (P.a) were cultured on 5% sheep’s blood nutrient agar at 37 °C overnight. Colonies were transferred to a glass slide where they were analyzed directly with the MasSpec Pen coupled to a Q Exactive mass spectrometer (Thermo Scientific) in negative ion mode. For MasSpec Pen analysis, a 10 µL droplet of water was held in contact with the sample surface for 3 seconds and then aspirated to the mass spectrometer for analysis.
Data was normalized and the molecular features resulting from the analysis solvent and nutrient medium were removed. The least absolute shrinkage and selection operator (lasso) statistical method was used to build classification models for prediction of bacterial identity. Model performance was evaluated by leave-one-out cross-validation and a validation set of samples.
Scheme 1: MasSpec Pen workflow

Results
Various small molecules were detected including metabolites and glycerophospholipid species. The mass spectral profiles for each species exhibited qualitative differences among them (Figure 1). Additionally, several quorum-sensing molecules were observed in P.a. including hydroxy-heptyl-quinoline (m/z 242.155).
Lasso statistical classifiers were created to differentiate organisms at the level of Gram type, genus, and species with each model comprised of a sparse set of molecular features. Accuracies of 90% or greater were achieved for all lasso models and as high as 98% for the differentiation of Staphylococcus (Staph.) and Streptococcus (Strep.).
Figure 1: Molecular profiles of species analyzed

Figure 2: Statistical classification results

Conclusion
These results demonstrate the potential of the MasSpec Pen as a tool for clinical analysis of infected biospecimens.

Disclosures
Sydney C. Povilaitis, BA, MS Pen Technologies, Inc. (Other Financial or Material Support, Patent) Livia Eberlin, PhD, MS Pen Technolpogies, Inc. (Board Member, Shareholder)
663. Improved Detection of ESBL and AmpC Beta-Lactamase Producing Isolates of Enterobacteriaceae in Pediatric Patients with Bloodstream Infections Using Combined Genotypic and Phenotypic Antimicrobial Susceptibility Testing
Authors: Khalil Nadim , Powell Eleanor , Mortensen Joel 
Published: January 2021

Abstract

Background
Infections secondary to pathogens resistant to third-generation cephalosporins (3GC), such as extended-spectrum (ESBL) and AmpC β-lactamase (AmpC) producing Enterobacteriaceae, are increasing. Currently, there are no recommendations regarding identification of AmpC in Citrobacter, Enterobacter, Morganella and Serratia spp. (CEMS organisms). This study’s aim was to increase the detection of AmpC and ESBL producing Enterobacteriaceae in blood cultures from pediatric population by combining genotypic with phenotypic antimicrobial susceptibility testing (AST).

Methods
All first time Enterobacteriaceae isolates recovered from blood cultures of pediatric patients at CCHMC between January 2017 and December 2018 were evaluated. The Check-MDR CT103XL assay was used to determine the presence of AmpC and ESBL. AST was performed using the Vitek 2 platform. Phenotypic ESBL resistance was defined by resistant to either ceftriaxone of ceftazidime using CLSI breakpoints. Combined cefoxitin resistance with ceftriaxone or ceftazidime resistance was used to define phenotypic AmpC (EUCAST standards).

Results
There were 170 isolates, from 147 patients, with 21 (12.4%) AmpC and 18 (10.6%) ESBL genes detected. Using AST, 11 (6.5%) and 26 (15.3%) isolates met AmpC and ESBL phenotypic criteria respectively. However, 14 of the isolates with AmpC genes detected and 2 of isolates with ESBL genes detected failed to meet phenotypic criteria. In addition, 4 (19%) of 21 AmpC isolates were susceptible to cefoxitin and 3GC while both E. coli and S. marcescens genotypic ESBL isolates were susceptible to 3GC.
Number of AmpC- and ESBL- Producing Isolates Detected Using Phenotypic Method a,b, Genotypic Method and Combined Testing

Conclusion
We identified 16 (9.4%) isolates with resistance genes detected but that failed to meet phenotypic criteria.
Without molecular testing, patients with these isolates may have been treated with 3GC which could have resulted in treatment failure.
The addition of genotypic testing to AST improved the identification of AmpC and ESBL organisms and provided clinically relevant data to guide treatment of resistant organisms. Combined testing is also beneficial for infection control and epidemiological purposes.

Disclosures
All Authors: No reported disclosures
665. Lower Indeterminate Rates and Resolution by Retesting Using a Single Lithium-Heparin Tube Blood Collection Method for the QuantiFERON®-TB Gold Plus (QFT®-Plus)
Authors: Clark Richard B , Master Ronald N , Kapoor Hema , Bi Caixia , Kroll Martin H , Salm Ann , Meyer William B 
Published: January 2021

Abstract

Background
The QuantiFERON-TB Gold Plus (QFT-Plus) test is an assay for detecting a cell-mediated immune response to M. tuberculosis (MTB). The assay measures the in vitro quantitative IFN-γ responses to MTB or control antigens in an incubated blood sample. There are 2 options for QFT-Plus blood collection. One option is a lithium-heparin transport tube with sample aliquots subsequently transferred to 4 QFT-Plus Blood Collection Tubes (1-tube QFT-Plus); the 2nd option is to directly collect the blood sample in 4 QFT-Plus collection tubes (4-tube QFT-Plus). In this study, we compared the indeterminate (IND) rates by the 2 blood collection methods to assess which method was superior.

Methods
For both blood collection methods, QFT-Plus ELISA testing was performed at various Quest Diagnostics sites as specified in the assay’s package insert. A retrospective data analysis of results for the above 2 blood processing methods was conducted. Also, we evaluated the rates of IND results in follow up blood collections. Statistical analyses were performed by the proportion test.

Results
In 2019, the IND result rate for greater than an 1.8 million 1-tube QFT-Plus draws was less than 1% whereas, the IND result rate for 0.3 million 4-tube draws was 4% This difference was significant. The overall MTB positive rate was 7% for the 1-tube method and 6% for the 4-tube method. Within a one-month interval following an initial blood collection event, 464 patients with an original IND result had a 2nd blood sample collected and tested. Only 35% of the 2nd blood collection events produced an IND result, with 52% of the 2nd sample results reporting as negative and 13% were positive.

Conclusion
This study found that the 1-tube QFT-Plus collection method reduces the IND rates by 4-fold compared to the observed rate in the 4-tube process. Additionally, two thirds of patients with an initial IND result resolved to either a positive or a negative result when retested within 1 month.

Disclosures
All Authors: No reported disclosures
669. Rapid Molecular Testing of Sputum for Identification of Pulmonary Tuberculosis: Impact on Duration of Respiratory Isolation
Authors: Acosta Tommy J Parraga , Vahia Amit T , Hanna Zachary W , Nair Sashi N , Tibbetts Robert , Alangaden George J , Samuel Linoj 
Published: January 2021

Abstract

Background
Current guidelines recommend molecular testing directly on sputum of patients with suspected pulmonary tuberculosis (TB) to facilitate discontinuation of airborne infection isolation (AII). Henry Ford Hospital (HFH), a tertiary care center in Detroit, MI serves a population at high-risk for TB. Molecular testing of sputum using GeneXpert/MTB RIF (Xpert; Cepheid) (GXTB) was implemented at HFH on March 2019. Providers were permitted to remove patients from AII using 3 negative acid-fast bacillus smears (AFB) or 2 negative GXTB results. We evaluated the impact of GXTB on duration of AII over a 2-year period: Pre-implementation (January 2018 to February 2019) and post-implementation (March 2019 to February 2020).

Methods
Retrospective data was abstracted for all patients placed in AII during the study period. Demographic data, TB risk factors, duration of AII, length of hospital stay (LOS), accuracy and turn-around-times (TAT) of AFB and GXTB were compared in the pre- and post-implementation periods. Categorical variables were studied using chi-square testing, and continuous variables were studied using T-test or Mann Whitney U test as appropriate.

Results
During the study period, 269 patients with suspected TB were placed in AII: 137 pre-implementation and 132 post-implementation. Clinical characteristics and TB risk factors were generally comparable in both groups (Table 1). Abnormal chest X-ray was more frequent in patients in the post-implementation phase. All cases of culture positive TB were detected by AFB and GXTB. TAT of AFB results before and after implementation were similar and ranged from 20-24 hours (Table 2). In the post-implementation period, TAT of GXTB compared to AFB was 6.35 vs 21.28 hours (p &lt; 0.0001). Duration of AII was shortened by almost 24 hours (70.2 vs 93.7 hours, p=0.031) (Table 3). Time from first sample collection to final results of all samples was 19.2 vs 52.6 hours, p&lt; 0.0001. There was no difference in total LOS pre and post-implementation.
Table 1. Clinical Characteristics of Patients with Suspected Pulmonary Tuberculosis

Table 2. Turnaround times (TAT) of AFB and GeneXpert/MTB (Xpert) RIF before and after implementation

Table 3. Duration of Airborne Isolation, Total Turn-Around Times, and Hospital Length of Stay in the Pre- and Post-implementation Period

Conclusion
Implementation of rapid direct molecular testing reduced the duration of respiratory isolation for patients with suspected pulmonary TB. Further provider education regarding the reliability of GXTB in excluding TB may be necessary to reduce overall hospital LOS.

Disclosures
All Authors: No reported disclosures
670. Rapid, Non-invasive Detection of Invasive Mycoplasma hominis Infection using the Karius Test, A Next-Generation Sequencing Test for Microbial Cell-free DNA in Plasma
Authors: Edward Priya , Via William V La , Arshad Mehreen , Gajurel Kiran 
Published: January 2021

Abstract

Background
Mycoplasma hominis is typically associated with genital infections in women and is a rare cause of musculoskeletal infections often in immunocompromised hosts. Diagnosis of invasive Mycoplasma hominis infections are difficult due to challenges in culturing these organisms. Molecular diagnostics require an index of suspicion which may not be present at the time of tissue sampling. Accurate, rapid diagnosis of Mycoplasma hominis infections are important for antibiotic management.

Methods
Two cases of invasive Mycoplasma hominis infections are presented in which the Karius test (KT) was used to make the diagnosis. The KT is a CLIA certified/CAP-accredited next-generation sequencing (NGS) plasma test that detects microbial cell-free DNA (mcfDNA). After mcfDNA is extracted and NGS performed, human reads are removed and remaining sequences are aligned to a curated database of &gt; 1400 organisms. Organisms present above a statistical threshold are reported. Case review was performed for clinical correlation.

Results
A young woman with lupus nephritis status post renal transplant developed persistent fever with progressive multifocal culture-negative osteoarticular infection despite empiric ceftriaxone. An adolescent female presented with an ascending pelvic infection progressing to purulent polymicrobial peritonitis (see table) requiring surgical debridement and cefipime, metronidazole and micafungin therapy; her course was complicated by progressive peritonitis/abscesses. Karius testing detected high-levels of Mycoplasma hominis mcfDNA in both cases – at 3251 molecules/microliter (MPM) in the first case and 3914 MPM in the second case. The normal range of Mycoplasma hominis mcfDNA in a cohort of 684 normal adults is 0 MPM. The patients rapidly improved with atypical coverage with doxycycline and levofloxaxin.
Clinical findings in 2 patients with M. hominis infection detected by the Karius Test

Conclusion
Open-ended, plasma-based NGS for mcfDNA provides a rapid, non-invasive method to diagnose invasive Mycoplasma hominis infection. This case series highlights the potential to diagnose infections caused by fastidious pathogens to better inform antimicrobial therapy and achieve favorable outcomes.

Disclosures
William V. La Via, MD, Karius (Employee)
672. The Pediatric Endotracheal Aspirate Culture Survey (Petacs): Examining Practice Variation Across Pediatric Microbiology Laboratories in the United States
Authors: Prinzi Andrea , Curtis Donna , Parker Sarah , Ziniel Sonja 
Published: January 2021

Abstract

Background
In the absence of evidence-based laboratory guidelines, the workup and interpretation of tracheal aspirate (TA) cultures remains controversial and confusing within the fields of clinical microbiology, infectious diseases, and critical care.

Methods
Between January 22 and February 24, 2020, we conducted a national, web-based survey of microbiology laboratory personnel in free-standing pediatric hospitals and adult hospitals containing pediatric facilities regarding the laboratory practices used for TA specimens. We hypothesized that there would be substantial center-level variability in laboratory processes of TA cultures.

Results
The response rate for the survey was 48%. There was a high level of variability in the criteria used for all processes including specimen receipt, Gram staining and culture reporting. Nearly a quarter of respondents (23%) reject TA specimens based on Gram stain criteria, and 56% of labs require that a minimum number of Gram stain fields be reviewed prior to reporting results. Overall, non-academic hospital laboratories and pediatric-only laboratories are more likely to identify, report and perform susceptibility testing on organisms from tracheal aspirate cultures, regardless of organism quantity or predominance.

Conclusion
There is a substantial amount of process variability among pediatric microbiology laboratories that affects TA culture reporting, which is used to make treatment decisions. This variation within and among labs makes clinical outcome studies related to TA cultures very difficult. Research is needed to determine best laboratory practices for TA culture workup and to provide evidence for the development of clinical guidelines.

Disclosures
All Authors: No reported disclosures