Evaluation of Ordering Practices, Microbial Yield, and Clinical Utility of Urinary Stone Cultures

Urinary stones are a global problem. While it has been established that microorganisms can be associated with urinary stone formation, data on best practices for microbial culture and clinical interpretation of microbial culture of urinary stone specimens are limited. Our objective was to investigate the microorganisms present in urinary stone cultures (usc) and companion urine cultures. We conducted a retrospective study at a tertiry hospital examining cultures submitted between October 2018 and October 2021. We collected data from electronic medical records of patients who had at least at least one usc performed. As part of routine clinical workup, all urinary stone specimens submitted for culture were ground using a disposable tissue grinder and inoculated on a tryptic soy agar with 5% sheep blood agar plate (BAP), a chocolate agar plate (CHOC), and a MacConkey agar plate (MAC), streaked for isolation and incubated in 5% CO2 at 35°C for up to three days. Urine cultures were performed using the Kiestra TLA system with 10 µL of inoculum onto each of a BAP and MAC, and plates were examined at 16 and 24 hours of incubation. For urine specimens submitted from a straight or “in and out” catheter, 10,000 CFU/mL was the threshold for workup. From clean-voided, midstream, ileostomy, nephrostomy, or indwelling/Foley catheter specimens, 100,000 CFU/mL was the threshold for workup. The final clinical significance of cultures is determined by evaluating the culture result in light of the patient’s clinical presentation. For usc and urine cultures, clinically insignificant growth was considered no growth or when no pathogens were recovered in culture. Urine cultures with more than 3 species over threshold were considered contaminated. A total of 1,049 usc were performed from 854 patients (55.3% female). The median patient age was 61 years (IQR 49-70). The most frequent microorganisms reported in usc cultures were Proteus mirabilis (N=98), Enterococcus faecalis (N=75), and Escherichia coli (N=73). No pathogen was identified from 57% of usc. 441 usc were performed in a context of urine culture (+/-2 days) in 336 (39.3%) patients. In addition, 138 patients (16.1%) had more than 1 usc, being the maximum as 11 usc performed in one patient. The most common urine/USC concordant result was no growth in 165 of 441 cultures (37.4%), followed by coagulase negative Staphylococcus. Cohen’s kappa obtained from usc and urine culture results was 0.45, which is not the minimum acceptable agreement. A pathogen was identified from usc in 43% of cases. Usc and urine cultures rarely resulted in concordant results, but the most common concordant result was no growth in culture. Additional studies are warranted to evaluate the impact of usc results on patient care, including antimicrobial use and correlation of microbes isolated with stone chemical composition.

Deep Convolutional Neural Networks Implementation for the Analysis of Urine Culture

BACKGROUND

Urine culture images collected using bacteriology automation are currently interpreted by technologists during routine standard-of-care workflows. Machine learning may be able to improve the harmonization of and assist with these interpretations.

METHODS

A deep learning model, BacterioSight, was developed, trained, and tested on standard BD-Kiestra images of routine blood agar urine cultures from 2 different medical centers.

RESULTS

BacterioSight displayed performance on par with standard-of-care-trained technologist interpretations. BacterioSight accuracy ranged from 97% when compared to standard-of-care (single technologist) and reached 100% when compared to a consensus reached by a group of technologists (gold standard in this study). Variability in image interpretation by trained technologists was identified and annotation "fuzziness" was quantified and found to correlate with reduced confidence in BacterioSight interpretation. Intra-testing (training and testing performed within the same institution) performed well giving Area Under the Curve (AUC) ≥0.98 for negative and positive plates, whereas, cross-testing on images (trained on one institution's images and tested on images from another institution) showed decreased performance with AUC ≥0.90 for negative and positive plates.

CONCLUSIONS

Our study provides a roadmap on how BacterioSight or similar deep learning prototypes may be implemented to screen for microbial growth, flag difficult cases for multi-personnel review, or auto-verify a subset of cultures with high confidence. In addition, our results highlight image interpretation variability by trained technologist within an institution and globally across institutions. We propose a model in which deep learning can enhance patient care by identifying inherent sample annotation variability and improving personnel training.

354. SARS-CoV-2 Viral Viability Culture and Sequencing from Immunocompromised Patients with Persistently Positive SARS-CoV-2 PCR Results

Background

Immunocompromised (IC) patients (pts) can have prolonged SARS-CoV-2 PCR positivity, even after resolution of COVID-19 symptoms. This study aimed to determine if viable virus could be detected in samples collected > 21 days after an initial positive (pos) SARS-CoV-2 PCR in IC pts.

Methods

We obtained 20 remnant SARS-CoV-2 PCR pos nasopharyngeal swabs from IC pts (bone marrow or solid organ transplant, high dose steroids, immunosuppressive medications) with a pos repeat PCR within the previous 30 days. The repeat specimens were cultured on Vero-hACE2-TMPRSS2 cells and incubated for 96 hours to assess viral viability. Viable RNA and infectious virus in the cultured cells were measured by qPCR and infectious plaque assays. RNA sequencing was performed on a HiSeq platform (Illumina). Samples also underwent SARS-CoV-2 antigen (Ag) testing (BD Veritor). Clinical data were extracted from the electronic health record by chart review.

Results

Pt characteristics are in Table 1. Viral cultures from the repeat specimen were negative (neg) for 18 pts and pos for 2 (Table 2). Pt 1 is a 60M treated with obinatuzumab 19 days prior to his first pos PCR test, with repeat specimen collected 21 days later (cycle threshold (Ct) not available). Pt 1 had a low viral titer (27 PFU/mL) & a D614G mutation on sequencing. Pt 2 is a 75M treated with rituximab 10 days prior to his first pos PCR test, with repeat specimen collected 23 days later (Ct 27.56/27.74). Pt 2 had a high viral titer (2e6 PFU/mL) and D614G, S98F, and S813I mutations.

Demographics of Study Population (N=20)

Conclusion

90% of specimens collected > 21 days after an initial pos SARS-CoV-2 PCR did not have viable virus detected on their repeat specimen. The 2 pts with pos viral cultures had active hematologic malignancies treated with an anti-CD20 mAb at the time of COVID-19 diagnosis. One pt had a high concentration of active, viable virus. No known variants of concern were noted in this cohort, collected in Q2 2020, though prolonged replication is a risk for variant development. Further data are needed about risk factors for persistent viable viral shedding & methods to prevent transmission of viable virus from IC hosts.

Disclosures

Victoria J. Fraser, MD, CDC Epicenters (Grant/Research Support)Cigna/Express Scripts (Other Financial or Material Support, Spouse is Chief Clinical Officer)Doris Duke Fund to Retain Clinical Scientists (Grant/Research Support, Research Grant or Support)Foundation for Barnes-Jewish Hospital (Grant/Research Support, Research Grant or Support)NIH (Grant/Research Support, Research Grant or Support) Victoria J. Fraser, MD, Centers for Disease Control and Prevention (Individual(s) Involved: Self): Grant/Research Support, Research Grant or Support; Cigna/Express Scripts (Individual(s) Involved: Spouse/Partner): Employee; Doris Duke Charitable Foundation (Individual(s) Involved: Self): Grant/Research Support, Research Grant or Support; National Institutes of Health (Individual(s) Involved: Self): Grant/Research Support, Research Grant or Support; The Foundation for Barnes-Jewish Hospital (Individual(s) Involved: Self): Grant/Research Support, Research Grant or Support Michael S. Diamond, MD, PhD, Carnival Corporation (Consultant)Emergent BioSolutions (Grant/Research Support)Fortress Biotech (Consultant)Immunome (Advisor or Review Panel member)Inbios (Consultant)Moderna (Grant/Research Support, Advisor or Review Panel member)Vir Biotechnology (Consultant, Grant/Research Support) Carey-Ann Burnham, PhD, BioFire (Grant/Research Support, Other Financial or Material Support)bioMerieux (Grant/Research Support)Cepheid (Consultant, Grant/Research Support)Luminex (Grant/Research Support)Roche (Other Financial or Material Support) Carey-Ann Burnham, PhD, BioFire (Individual(s) Involved: Self): Grant/Research Support; bioMerieux (Individual(s) Involved: Self): Grant/Research Support, Scientific Research Study Investigator, Speakers’ bureau; Cepheid (Individual(s) Involved: Self): Consultant, Grant/Research Support, Scientific Research Study Investigator; Luminex (Individual(s) Involved: Self): Scientific Research Study Investigator Hilary Babcock, MD, MPH, FIDSA, FSHEA, Nothing to disclose

Evaluation of cefiderocol activity for Gram-negative bacteria and performance of cefiderocol disk diffusion testing using multiple brands of Mueller Hinton Agar

Cefidericol is a cephalosporin-siderophore antibiotic for the treatment of multidrug resistant Gram-negative bacteria. Similar to other cephalosporin antibiotics, the lethal mechanism of action is due to inhibition of penicillin binding proteins leading to lysis of the bacteria. However, unlike previously developed antibiotics, the siderophore portion of cefidericol is able to bind iron and then be actively transported into the periplasmic space. To ascertain the feasibility of cefidericol antibiotic susceptibility testing in the Barnes-Jewish Clinical Microbiology Laboratory, we collected a cohort of multidrug Enterobacteriacae (5 Enterobacter cloace, 8 Escherichia coli, 12 Klebsiella pneumoniae), Pseudomonas aeruginosa (n=23), Stenotrophomonas maltophila (n=24), and Acinetobacter baumannii (n=25). We evaluated activity of cefidericol on these strains, and the performance of disk diffusion using three different brands of Mueller-Hinton Agar (BD, Hardy, and Remel). The reference method for comparison was an FDA-cleared broth microdilution panel containing cefidericol (ThermoFisher Scientific). Using CLSI breakpoints, we found that disk diffusion with BD agar had 96% categorical agreement for Enterobacterales, 100% for P. aeruginosa, 92% for A. baumannii, 96% for S. maltophila. We found that Hardy had 96% categorical agreement for Enterobacterales, 92% for P. aeruginosa, 92% for A. baumannii, 96% for S. maltophila. Finally, we found that Hardy had 96% categorical agreement for Enterobacterales, 92% for P. aeruginosa, 92% for A. baumannii, 96% for S. maltophila. Minor errors on any media never exceed 4% and there were no very major errors. Resistance to cefidericol within our cohort of selected antibiotic resistant bacteria was rare, one E. coli isolate and two P. aeruginosa isolates had minimal inhibitory concentrations (MICs) > 32 μg/mL. The highest MICs for one isolate of A. baumannii and one isolate S. maltophila was 8 μg/mL and 4 μg/mL, respectively, both of which were intermediate. There was no difference in the distribution of zone disk diffusion diameter for A. baumannii or Enterobacterales. However, there was a significant difference in the distribution of zone disk diffusion diameters for P. aeruginosa and S. maltophila on BD vs Hardy agar. The median for P. aeruginosa on BD is 25 mm while it is 29 mm on Hardy. The trend for S. maltophila is the opposite as the median for BD was 31.5 mm and 28.5 mm for Hardy. Use of FDA vs CLSI vs EUCAST breakpoints significantly changes outcome of susceptibility testing for broth microdilution and disk diffusion. As one example for broth microdilution of A. baumannii, we had one isolate intermediate using CLSI breakpoints, 4 resistant using EUCAST breakpoints, and 4 resistant and 3 intermediate isolates using FDA breakpoints. Our work demonstrates that cefedericol testing can be performed in a routine format, with certain organismal differences on Mueller-Hinton agar, and that different interpretative criteria significantly change outcomes.

The azithromycin to prevent wheezing following severe RSV bronchiolitis-II clinical trial: Rationale, study design, methods, and characteristics of study population

Severe respiratory syncytial virus (RSV) bronchiolitis in early life is a significant risk factor for future recurrent wheeze (RW) and asthma. The goal of the Azithromycin to Prevent Wheezing following severe RSV bronchiolitis II (APW-RSV II) clinical trial is to evaluate if azithromycin treatment in infants hospitalized with RSV bronchiolitis reduces the occurrence of RW during the preschool years. The APW-RSV II clinical trial is a double-blind, placebo-controlled, parallel-group, randomized trial, including otherwise healthy participants, ages 30 days-18 months, who are hospitalized due to RSV bronchiolitis. The study includes an active randomized treatment phase with azithromycin or placebo for 2 weeks, and an observational phase of 18-48 months. Two hundred participants were enrolled during three consecutive RSV seasons beginning in the fall of 2016 and were randomized to receive oral azithromycin 10 mg/kg/day for 7 days followed by 5 mg/kg/day for an additional 7 days, or matched placebo. The study hypothesis is that in infants hospitalized with RSV bronchiolitis, the addition of azithromycin therapy to routine bronchiolitis care would reduce the likelihood of developing post-RSV recurrent wheeze (≥3 episodes). The primary clinical outcome is the occurrence of a third episode of wheezing, which is evaluated every other month by phone questionnaires and during yearly in-person visits. A secondary objective of the APW-RSV II clinical trial is to examine how azithromycin therapy changes the upper airway microbiome composition, and to determine if these changes are related to the occurrence of post-RSV RW. Microbiome composition is characterized in nasal wash samples obtained before and after the study treatments. This clinical trial may identify the first effective intervention applied during severe RSV bronchiolitis to reduce the risk of post-RSV RW and ultimately asthma.

650. Clinical Performance Evaluation of Virtuo Blood Culture System in a Tertiary Care Hospital

Background

Bloodstream infections are a major cause of morbidity and mortality. BACT/ALERT VIRTUO (VIRTUO) blood culture system is an automated, closed system used with resin-containing media which may enhance the growth of microorganisms. Our objective was to assess the real-world performance of the VIRTUO system.

Methods

We retrospectively reviewed all blood cultures performed between January-December 2018 (VersaTREK) and January-December 2019 (VIRTUO) at a 1250-bed academic medical center. Blood culture positivity rates, contamination rates, and time from collection to arrival in the laboratory were compared pre- versus post-VIRTUO implementation. Contamination was defined as a single blood culture with common skin microbiota.

Results

A total of 101803 blood cultures were performed during the study period: 48969 (48.1%) were processed with VersaTREK system and 52834 (51.9%) with VIRTUO system. A decreased median time from collection until arrival to the laboratory was seen post-implementation (2.0 pre- vs. 0.8 hours post-implementation, p< 0.001). The positivity rate increased from 3987 (8.1%) pre-implementation to 6141 (11.6%) post-implementation (p < 0.001) (Table and Figure). Staphylococcus aureus was the most frequently isolated species for both periods and had higher recovery rate with the VIRTUO system (717 (1.5%) pre- vs. 1764 (3.3%) post-implementation, p< 0.001). Higher recovery rate was also noted for other Staphylococcus spp. in the post-implementation period (985 (2.0%) pre- vs. 1644 (3.1%) post-implementation, p< 0.001). No difference in the organism recovery rate was noted for Streptococcus spp., Enterococcus faecium, E. faecalis, Pseudomonas aeruginosa, Enterobacterales, and Candida spp. The inpatient contamination rate was higher post-implementation (1.5% pre- vs. 1.9% post-implementation, p < 0.001).

Comparison of blood culture positivity rate pre- vs. post-implementation, by culture location

Conclusion

The VIRTUO system showed a higher rate of positive blood cultures compared to the VersaTREK system primarily from a higher detection of Staphylococcus spp. Further studies are needed to assess whether an increased rate of positive blood cultures is associated with changes in management and clinical outcomes.

Disclosures

All Authors: No reported disclosures

154. comparative Genomics Reveals Extra-hospital Transmission Networks of Carbapenem-resistant acinetobacter Baumannii sustained over Multiple Years in a US Midwest City

Background

The transmission dynamics of Acinetobacter baumannii (Ab) outside the setting of hospital outbreaks is underinvestigated. The BJC Healthcare System in St. Louis, MO has not experienced an Ab hospital outbreak since 2012. Despite this, nearly 60% of all BJC Ab isolates are carbapenem-resistant Ab (CrAb).

Methods

We acquired whole genome sequences (WGSs) of 110 Ab isolates identified in five BJC hospitals from July 2017 to May 2019. We performed multilocus sequence typing, core genome alignment and pairwise average nucleotide identity analysis to compare WGSs from BJC isolates and GenBank-available WGSs of Ab isolates from other US hospitals. Further epidemiologic characterization was performed using BJC electronic medical records and detailed chart review.

Results

Though the majority of CrAb isolates in other US studies belonged to globally-prevalent sequence type 2 (ST2 [Pasteur scheme]), 62% and 26% of BJC CrAb index isolates belonged to the unrelated ST499 and ST406, respectively. BJC ST499 and ST406 isolates were phylogenetically distinct compared to corresponding isolates from other US hospitals. Under the assumption that Ab transmission occurs primarily through nosocomial spread, we expected BJC isolates from the same hospital and timespan to share the highest degree of homogeneity. However, geotemporal proximity between ST499 or ST406 BJC isolates was a poor predictor of their genetic relatedness, according to multiple comparative methods. Review of patient metadata did not identify epidemiological links between BJC isolates within phylogenetic subgroups.

Conclusion

We combined comparative genomics and detailed clinical chart review to characterize the transmission dynamics of two emerging US CrAb sequence types, ST499 and ST406. Though these highly homogeneous Ab isolates were identified over two years in multiple BJC hospitals, we found no evidence of robust intra-hospital transmission networks. Instead, it appears that these CrAb isolates independently emerged from yet-to-be-identified regional, extra-hospital Ab populations. To neutralize the threat of drug-resistant infections in the US, it is essential to identify, characterize and disrupt emergent CrAb transmission networks that exist outside of hospital environments.

Disclosures

All Authors: No reported disclosures

292. Impact of the BACT/ALERT VIRTUO blood culture system in the management of Staphylococcus aureus bacteremia

Background

Staphylococcus aureus bacteremia (SAB) is a major cause of mortality. Recovery of SA may be enhanced with new blood culture systems resulting in a longer observed duration of bacteremia.

Methods

We performed a 24-month retrospective study of adults hospitalized with SAB at a 1250-bed academic hospital. Between 1/2018-12/2018 the VersaTREK system was used and 1/2019-12/2019 the BACT/ALERT VIRTUO (VIRTUO) system was used. We excluded patients without an Infectious Diseases (ID) consult. We defined SAB duration as short (1–2 days), intermediate (3–6 days), or prolonged (>7 days). We compared SAB detection and management pre- and post-implementation of VIRTUO.

Results

456 patients had SAB during study period; 420 (92%) had ID consultation: 178 (42%) pre- and 242 (58%) post-implementation. Similar proportion of methicillin-resistant SAB was seen (44.9% pre- vs. 36.8% post-implementation, p=0.09). Post-implementation, patients were more likely to have intermediate (22.4% pre- vs. 40.1% post-implementation; p< 0.001) and prolonged SAB duration (3.9% pre- vs. 13.6% post-implementation; p< 0.001). Median time to positivity for the index blood culture was shorter (19.9 pre- vs. 15.0 hours post-implementation, p< 0.001). Dual anti-staphylococcal therapy was used more frequently in the post-implementation period (6.2% pre- vs. 15.7% post-implementation, p=0.003). No difference was noted in frequency of diagnostic studies (transesophageal echocardiography, magnetic resonance imaging, and computed tomography). Source control was similar (46.1% pre- vs. 45.0% post-implementation; p=0.84) but the median time to source-control was shorter post-implementation (4 pre- vs. 2 days post-implementation; p=0.02). Median planned duration of intravenous antibiotics did not vary between pre- and post-implementation periods (6 vs. 6 weeks, p=0.31). There was no difference in 90-day readmissions (38.2% pre- vs. 34.3% post-implementation; p=0.41).

Conclusion

VIRTUO blood culture system decreased time to positivity and increased frequency of prolonged SAB compared to the VersaTREK system. This resulted in increased use of dual anti-staphylococcal therapy and shorter time to source-control, but no difference in interventions, planned duration of antibiotics, or readmissions.

Disclosures

All Authors: No reported disclosures

Diagnostic Accuracy of Synovial Lactate, Polymerase Chain Reaction, or Clinical Examination for Suspected Adult Septic Arthritis

BACKGROUND

Adult septic arthritis can be challenging to differentiate from other causes of acute joint pain. The diagnostic accuracy of synovial lactate and polymerase chain reaction (PCR) remains uncertain.

OBJECTIVE

Our aim was to quantify the diagnostic accuracy of synovial lactate, PCR, and clinical evaluation for adults with possible septic arthritis in the emergency department (ED).

METHODS

We report a prospective sampling of ED patients aged ≥ 18 years with knee symptoms concerning for septic arthritis. Clinicians and research assistants independently performed history and physical examination. Serum and synovial laboratory testing was ordered at the discretion of the clinician. We analyzed frozen synovial fluid specimens for l- and d-lactate and PCR. The criterion standard for septic arthritis was bacterial growth on synovial culture and treated by consultants with operative drainage, prolonged antibiotics, or both. Diagnostic accuracy measures included sensitivity, specificity, likelihood ratios, interval likelihood ratios, and receiver operating characteristic area under the curve.

RESULTS

Seventy-one patients were included with septic arthritis prevalence of 7%. No finding on history or physical examination accurately ruled in or ruled out septic arthritis. Synovial l- and d-lactate and PCR were inaccurate for the diagnosis of septic arthritis. Synovial white blood cell count and synovial Gram stain most accurately rule in and rule out septic arthritis.

CONCLUSIONS

Septic arthritis prevalence in ED adults is lower than reported previously. History and physical examination, synovial lactate, and PCR are inadequate for the diagnosis of septic arthritis. Synovial white blood cell count and Gram stain are the most accurate tests available for septic arthritis.

Evaluation of NG-Test Carba 5 for Rapid Phenotypic Detection and Differentiation of Five Common Carbapenemase Families: Results of a Multicenter Clinical Evaluation

NG-Test Carba 5 is a rapid in vitro multiplex immunoassay for the phenotypic detection and differentiation of five common carbapenemase families (KPC, OXA-48-like, VIM, IMP, and NDM) directly from bacterial colonies. The assay is simple to perform and has recently received U.S. Food and Drug Administration clearance. A method comparison study was performed at geographically diverse medical centers (n = 3) in the United States, where 309 Enterobacterales and Pseudomonas aeruginosa isolates were evaluated by NG-Test Carba 5 (NG Biotech, Guipry, France), the Xpert Carba-R assay (Cepheid, Inc., Sunnyvale, CA), the modified carbapenem inactivation method (mCIM), the EDTA-modified carbapenem inactivation method, and disk diffusion with carbapenems. Colonies from tryptic soy agar with 5% sheep blood (blood agar) and MacConkey agar were tested, and the results were compared to those obtained by a composite reference method. Additionally, a fourth medical center performed a medium comparison study by evaluating the performance characteristics of NG-Test Carba 5 from blood, MacConkey, and Mueller-Hinton agars with 110 isolates of Enterobacterales and P. aeruginosa These results were compared to the expected genotypic and mCIM results. For the multicenter method comparison study, the overall positive percent agreement (PPA) and the overall negative percent agreement (NPA) of NG-Test Carba 5 with the composite reference method were 100% for both blood and MacConkey agars. The medium comparison study at the fourth site showed that the PPA ranged from 98.9% to 100% and that the NPA ranged from 95.2% to 100% for blood, MacConkey, and Mueller-Hinton agars. NG-Test Carba 5 accurately detected and differentiated five common carbapenemase families from Enterobacterales and P. aeruginosa colonies on commonly used agar media. The results of this test will support a streamlined laboratory work flow and will expedite therapeutic and infection control decisions.

Improving Characterization of Understudied Human Microbiomes Using Targeted Phylogenetics

Whole-genome bacterial sequences are required to better understand microbial functions, niche-specific bacterial metabolism, and disease states. Although genomic sequences are available for many of the human-associated bacteria from commonly tested body habitats (e.g., feces), as few as 13% of bacterium-derived reads from other sites such as the skin map to known bacterial genomes. To facilitate a better characterization of metagenomic shotgun reads from underrepresented body sites, we collected over 10,000 bacterial isolates originating from 14 human body habitats, identified novel taxonomic groups based on full-length 16S rRNA gene sequences, clustered the sequences to ensure that no individual taxonomic group was overselected for sequencing, prioritized bacteria from underrepresented body sites (such as skin and respiratory and urinary tracts), and sequenced and assembled genomes for 665 new bacterial strains. Here, we show that addition of these genomes improved read mapping rates of Human Microbiome Project (HMP) metagenomic samples by nearly 30% for the previously underrepresented phylum Fusobacteria, and 27.5% of the novel genomes generated here had high representation in at least one of the tested HMP samples, compared to 12.5% of the sequences in the public databases, indicating an enrichment of useful novel genomic sequences resulting from the prioritization procedure. As our understanding of the human microbiome continues to improve and to enter the realm of therapy developments, targeted approaches such as this to improve genomic databases will increase in importance from both an academic and a clinical perspective.IMPORTANCE The human microbiome plays a critically important role in health and disease, but current understanding of the mechanisms underlying the interactions between the varying microbiome and the different host environments is lacking. Having access to a database of fully sequenced bacterial genomes provides invaluable insights into microbial functions, but currently sequenced genomes for the human microbiome have largely come from a limited number of body sites (primarily feces), while other sites such as the skin, respiratory tract, and urinary tract are underrepresented, resulting in as little as 13% of bacterium-derived reads mapping to known bacterial genomes. Here, we sequenced and assembled 665 new bacterial genomes, prioritized from a larger database to select underrepresented body sites and bacterial taxa in the existing databases. As a result, we substantially improve mapping rates for samples from the Human Microbiome Project and provide an important contribution to human bacterial genomic databases for future studies.

2847. Comparative Genomics and Clonal Tracking of Multi-drug-Resistant Uropathogens Implicates the Fecal Microbiome as a Potential Reservoir for Recurrent Urinary Tract Infections

Background

Multi-drug-resistant organisms (MDRO) have complicated the treatment of urinary tract infections (UTIs), especially in patients with recurrent UTIs (rUTI). The objective of this pilot prospective cohort study is to determine the role of the fecal microbiome in rUTIs.

Methods

Stool and urine specimens were prospectively collected from patients with MDRO UTIs at 6 time points during and after the UTI, and with any rUTI. Specimens underwent semi-quantitative culture on differential and selective media for MDROs, and isolates underwent phenotypic susceptibility testing and whole-genome sequencing. Comparative genomics and clonal tracking were used to detect clonal uropathogen strains in the urinary and gastrointestinal tracts. Resistance genes, resistance-plasmids, and virulence genes of MDROs were characterized in silico.

Results

A total of 110 isolates (95 Escherichia coli, 2 Klebsiella pneumoniae, 13 Proteus mirabilis) were cultured from the urine and stool of 15 patients (7 non-rUTI, 8 rUTI). Clonal uropathogens were isolated between the urinary tract and their intestinal reservoir (Figure 1). Integration of clonality information with semiquantitative culturing implicated three potential routes for recurrence of UTIs: (i) bladder colonization following an intestinal bloom of uropathogens, (ii) reinfection from an external source, and (III) bacterial persistence within the urinary tract (Figures 2 and 3). Antibiotic susceptibility testing and genomic profiling indicated that antibiotic-resistant uropathogen populations colonizing the urinary tract and intestinal reservoir at symptomatic and asymptomatic timepoints have similar resistance profiles that are largely determined via a pool of shared resistance plasmids (Figure 3).

Conclusion

This study provides the first time-resolved analysis of uropathogen persistence following UTIs, showing that clonal antibiotic-resistant uropathogens can be detected in both the urine and stool at varying time points post-initial infection. The study implicates 3 potential routes of rUTI, including uropathogen persistence within the gut microbiota, reinfection from an external source, and persistent bacteriuria. Study findings could be utilized to inform future diagnostics and therapies for treatment of rUTIs.

Disclosures

Carey-Ann Burnham, PhD, BioFire: Research Grant; bioMerieux: Research Grant; Cepheid: Research Grant; Luminex: Research Grant.

Processing of Positive Blood Cultures Using a Total Laboratory Automation System: Workflow and Clinical Validation

Automated systems for culture-based microbiology are in the early phase of implementation in clinical laboratories. Here, our objective was to evaluate the performance of the BD Kiestra Total Laboratory Automation (TLA) System for inoculation, incubation, and imaging of positive blood culture broth specimens. To optimize parameters for clinical testing, 56 clinical specimens were processed using both TLA and manual standard-of-care (SOC) methods. For TLA processing, 3 mL positive blood culture broth (35 VersaTREK: 19 aerobic, 16 anaerobic; 21 BD BACTEC: 15 aerobic, 6 anaerobic) was transferred to a no-additive vacutainer using a safety adapter and syringe. This aliquot was then placed on TLA for fully automated processing: 10 µL was inoculated to blood, chocolate, and MacConkey agar (Remel) and, for anaerobic bottles only, Brucella blood agar (Hardy Diagnostics). Kiestra cross-streak pattern 5 was optimal for obtaining isolated colonies and was superior to quadrant-streaking methods. Additional media types were added based on Gram stain results of the positive blood specimen: CandiSelect (Bio-Rad) and Sabouraud Dextrose (Remel) were added if yeast were identified, and Colistin Nalidixic Acid agar (Remel) for Gram stains with mixed Gram-positive and Gram-negative morphology. Plates were imaged at 6, 8, 10, 12, 18, 38, and 62 hours. Anaerobic media were placed by the system in a media stacker, incubated off-line, and then imaged on the TLA at 24, 48, and 72 hours. SOC cultures were evaluated after overnight incubation and on days 2 and 3. Organism identification was performed using MALDI-TOF MS (Bruker). Based on our evaluation, optimal parameters for clinical implementation of TLA were identified. Microbial growth was scant at 6 hours of incubation, but by 8 hours, small discrete colonies were observed for most aerobes. Thus, imaging parameters selected for routine clinical testing were 8, 18, and 38 hours for aerobic media and one image taken at 38 hours for anaerobic media. TLA and SOC culture results had 96% agreement (29 Gram positive, 12 Gram negative, 5 mixed, 6 yeast, 1 no growth). Two specimens with a second low-abundance bacterial population were observed on TLA that were not observed with SOC. Reproducibility of TLA was tested by processing 6 positive samples in triplicate and found to be 100%. There was no carryover or contamination noted between specimens processed simultaneously on TLA. To evaluate if implementation of TLA impacted epidemiology of positive blood cultures, we compared the 10 most common organisms recovered pre- and post-TLA implementation (August-November 2017 compared to August-November 2018). We found these organisms were not significantly impacted by TLA processing. In conclusion, automated processing of positive blood cultures improves laboratory workflows and facilitates faster workup at 8 hours of incubation. These results demonstrate that automation is a viable avenue for the processing of positive blood cultures.

Rapid Emergence of Daptomycin Resistance in Nonstriatum Corynebacterium Species: A Multicenter Study

Members of the genus Corynebacterium are increasingly recognized as causes of opportunistic infection; some species can be multidrug resistant, posing a treatment challenge. Daptomycin is frequently used as therapy of last resort in this setting, but previous work from our group demonstrated the ability of C striatum clinical isolates to rapidly develop high-level resistance to daptomycin, both in vivo and in vitro. Here, our objective was to expand this investigation into a multicenter study evaluating multiple Corynebacterium species. Corynebacterium strains from three tertiary-care academic medical centers (total, n = 76; site 1, n = 44; site 2, n = 15; site 3, n = 17) were evaluated, representing 16 species. Isolates were identified during routine clinical testing and reported to species level in accordance with each laboratory’s standard operating procedures. Identification of each species was confirmed using both VITEK MS and Bruker BioTyper MALDI-TOF MS. MICs to daptomycin (Etest), vancomycin (Etest), and telavancin (Liofilchem) at baseline were determined using gradient diffusion methods on Mueller-Hinton agar with blood (Hardy Diagnostics). Each isolate was then inoculated in duplicate to 5 mL Tryptic Soy Broth. A daptomycin Etest was submerged in one tube from each pair, and growth was observed after 24-hour incubation. If turbidity was observed in the tube with daptomycin, MICs for each of the 3 antimicrobials were reassessed. High-level daptomycin resistance emerged in 24 strains: C aurimucosum (1/1 isolate tested), C bovis (1/2), C jeikeium (2/11), C macginleyi (3/3), C resistens (1/1), C simulans (1/1), C striatum (14/14 isolates), and C ulcerans (1/1). The majority of these isolates had MIC values >256 µg/mL following exposure to daptomycin. Forty-eight other isolates remained susceptible to daptomycin: C afermentans (1/1), C amycolatum (19/20), C diphtheriae (1/1), C jeikeium (7/11), C kroppenstedtii (2/2), C propinquum (3/3), C pseudodiphtheriticum (6/6), C tuberculostearicum (0/6), and C urealyticum (0/3). Many of these isolates did not undergo MIC testing postdaptomycin exposure in broth due to complete lack of growth. Among those that did (n = 19), the median daptomycin MIC was 0.38 µg/mL (mean 0.42 µg/mL; range 0.023-1.0 µg/mL). One isolate of C bovis and two isolates of C jeikeium yielded variable susceptibility to daptomycin; a subset of resistant colonies grew adjacent to the gradient diffusion strip. Upon isolation and further MIC testing, these colonies maintained high-level resistance. In addition, one isolate of C amycolatum exhibited high-level daptomycin resistance (MIC >256 µg/mL) prior to in vitro exposure. All isolates in the cohort were susceptible to vancomycin and telavancin, both before and after daptomycin exposure. Our findings suggest that multiple Corynebacterium species can rapidly develop high-level daptomycin resistance after a short period of exposure to this antimicrobial. This finding has important clinical implications, especially in the treatment of invasive infections or infections of indwelling medical devices.

Stop Waiting for Tomorrow: Early Disk Diffusion—An Accurate Method for Antimicrobial Susceptibility Testing With Reduced Turnaround Time

Background

Disk diffusion is a slow but reliable reference method for measuring antimicrobial susceptibility. Our objective was to improve the turnaround time for this method by reducing the culture incubation period prior to disk diffusion testing (referred to as early disk diffusion [eDD] testing).

Methods

Clinical isolates (n = 13) and quality control (QC) strains (n = 8) of bacteria, including 6 Staphylococcus aureus, 3 Enterococcus faecium, 3 Enterococcus faecalis, 3 Escherichia coli, 3 Pseudomonas aeruginosa, 2 Klebsiella pneumoniae, and 1 Enterobacter cloacae, were inoculated on blood agar by quadrant streaking and were incubated at 35○C for 6 hours (eDD6), 10 hours (eDD10), or 24 hours (standard [sDD]) before disk diffusion testing was set up in accordance with CLSI guidelines using Mueller Hinton Agar (Hardy Diagnostics) and clinically appropriate antimicrobial agents (total: 24). Experiments were performed sequentially in triplicate with zones measured by two independent readers.

Results

Examination of 6-hour blood agar plates showed limited growth in the first 1 to 2 quadrants while 10-hour growth plates had 4-quadrant growth and individual colonies in most cases. Despite limited growth on 6-hour plates, there were adequate bacteria to produce a 0.5 McFarland standard for disk diffusion testing for all 126 eDD replicates. Results were evaluable for 1,206 of 1,206 (100%) of eDD and 603 of 603 (100%) of standard disk diffusion (sDD). A comparison of early vs standard disk diffusion showed that eDD6 had 3 of 154 (1.9%) very major errors and 6 of 449 (1.3%) major errors, whereas eDD10 had no very major errors and 3 of 449 (0.7%) minor errors. Very major errors in eDD6 included a 1-mm difference between eDD6 and sDD for cefoxitin inhibition of S aureus as well as 4- and 6-mm differences between eDD6 replicates and sDD for nitrofurantoin inhibition of E cloacae. There was similar categorical agreement of eDD6 (96.7%) and eDD10 (96.7%) with sDD. Overall, there was a very good correlation of eDD6 (r2 = 0.98) and eDD10 (r2 = 0.99) with sDD. When grouping results by bacterial species, there was no more than 1-mm difference in median antimicrobial inhibition between eDD6, eDD10, and sDD. Of note, 5 of 7 bacterial species had the same median zone size when comparing eDD6 or eDD10 with sDD. There was also very little difference between early and standard methods when examining bacteria-drug combinations, with a similar zone size (difference in mode <2 mm) in 67 of 69 (97%) eDD6 and 66 of 69 (96%) eDD10 compared to sDD. Test results for QC isolates agreed with the CLSI recommended ranges in 97 of 99 (98%) eDD6, 97 of 99 (98%) eDD10, and 96 of 99 (97%) sDD.

Conclusion

Early disk diffusion testing is a simple and accurate method of antimicrobial susceptibility testing that can reduce time to results by as much as 18 hours with no additional cost.

Comparative Genomics of Antibiotic-Resistant Uropathogens Implicates Three Routes for Recurrence of Urinary Tract Infections

The rise of antimicrobial resistance in uropathogens has complicated the management of urinary tract infections (UTIs), particularly in patients who are afflicted by recurrent episodes of UTIs. Antimicrobial-resistant (AR) uropathogens persistently colonizing individuals at asymptomatic time points have been implicated in the pathophysiology of UTIs. The dynamics of uropathogen persistence following the resolution of symptomatic disease are, however, mostly unclear. To further our understanding, we determined longitudinal AR uropathogen carriage and clonal persistence of uropathogenic Escherichia coli, Proteus mirabilis, and Klebsiella pneumoniae isolates in the intestinal and urinary tracts of patients affected by recurrent and nonrecurrent UTIs. Clonal tracking of isolates in consecutively collected urine and fecal specimens indicated repeated transmission of uropathogens between the urinary tract and their intestinal reservoir. Our results further implicate three independent routes of recurrence of UTIs: (i) following an intestinal bloom of uropathogenic bacteria and subsequent bladder colonization, (ii) reinfection of the urinary tract from an external source, and (iii) bacterial persistence within the urinary tract. Taken together, our observation of clonal persistence following UTIs and uropathogen transmission between the intestinal and urinary tracts warrants further investigations into the connection between the intestinal microbiome and recurrent UTIs.IMPORTANCE The increasing antimicrobial resistance of uropathogens is challenging the continued efficacy of empiric antibiotic therapy for UTIs, which are among the most frequent bacterial infections worldwide. It has been suggested that drug-resistant uropathogens could persist in the intestine after the resolution of UTI and cause recurrences following periurethral contamination. A better understanding of the transmission dynamics between the intestinal and urinary tracts, combined with phenotypic characterization of the uropathogen populations in both habitats, could inform prudent therapies designed to overcome the rising resistance of uropathogens. Here, we integrate genomic surveillance with clinical microbiology to show that drug-resistant clones persist within and are readily transmitted between the intestinal and urinary tracts of patients affected by recurrent and nonrecurrent UTIs. Thus, our results advocate for understanding persistent intestinal uropathogen colonization as part of the pathophysiology of UTIs, particularly in patients affected by recurrent episodes of symptomatic disease.

Genotypic and Phenotypic Characterization of Antimicrobial Resistance in Neisseria gonorrhoeae: a Cross-Sectional Study of Isolates Recovered from Routine Urine Cultures in a High-Incidence Setting

The objectives of this study were to perform genomic and phenotypic characterization of antimicrobial resistance in Neisseria gonorrhoeae isolates recovered from urine samples from patients in St. Louis, MO, USA. Sixty-four clinical isolates were banked over a 2-year period and subjected to antimicrobial susceptibility testing (AST) by Kirby-Bauer disk diffusion (penicillin, tetracycline, cefuroxime, and ciprofloxacin) and gradient diffusion (tetracycline, doxycycline, azithromycin, ceftriaxone, cefixime, ciprofloxacin, gemifloxacin, and delafloxacin). The medical records for the patients were evaluated to determine the demographics, location, and prescribed treatment regimen. Isolate draft genomes were assembled from Illumina shotgun sequencing data, and resistance determinants were identified by ResFinder and PointFinder. Of the 64 isolates, 97% were nonsusceptible to penicillin, with resistant isolates all containing the blaTEM-1b gene; 78 and 81% of isolates were nonsusceptible to tetracycline and doxycycline, respectively, with resistant isolates all containing the tet(M) gene. One isolate was classified as non-wild-type to azithromycin, and all isolates were susceptible to ceftriaxone; 89% of patients received this combination of drugs as first-line therapy. Six percent of isolates were resistant to ciprofloxacin, with most resistant isolates containing multiple gyrA and parC mutations. Correlation between disk and gradient diffusion AST devices was high for tetracycline and ciprofloxacin (R2 > 99% for both). The rates of N. gonorrhoeae antibiotic resistance in St. Louis are comparable to current rates reported nationally, except ciprofloxacin resistance was less common in our cohort. Strong associations between specific genetic markers and phenotypic susceptibility testing hold promise for the utility of genotype-based diagnostic assays to guide directed antibiotic therapy.IMPORTANCENeisseria gonorrhoeae causes the sexually transmitted infection gonorrhea, which is most commonly diagnosed using a DNA-based detection method that does not require growth and isolation of N. gonorrhoeae in the laboratory. This is problematic because the rates of antibiotic resistance in N. gonorrhoeae are increasing, but without isolating the organism in the clinical laboratory, antibiotic susceptibility testing cannot be performed on strains recovered from clinical specimens. We observed an increase in the frequency of urine cultures growing N. gonorrhoeae after we implemented a total laboratory automation system for culture in our clinical laboratory. Here, we report on the rates of resistance to multiple historically used, first-line, and potential future-use antibiotics for 64 N. gonorrhoeae isolates. We found that the rates of antibiotic resistance in our isolates were comparable to national rates. Additionally, resistance to specific antibiotics correlated closely with the presence of genetic resistance genes, suggesting that DNA-based tests could also be designed to guide antibiotic therapy for treating gonorrhea.

Draft Genome Sequence of a bla NDM-1- and bla PME-1-Harboring Pseudomonas aeruginosa Clinical Isolate from Pakistan

We performed Illumina whole-genome sequencing on a carbapenem-resistant Pseudomonas aeruginosa strain isolated from a cystic fibrosis patient with chronic airway colonization. The draft genome comprises 6,770,411 bp, including the carbapenemase bla NDM-1 and the extended-spectrum beta-lactamase bla PME-1 This isolate harbors 3 prophages, 14 antibiotic resistance genes, and 257 virulence genes.

Pitfalls Associated With the Use of Molecular Diagnostic Panels in the Diagnosis of Cryptococcal Meningitis

We report the case of a kidney transplantation patient on chronic immunosuppressive therapy presenting with subacute meningitis. The final diagnosis of cryptococcal meningitis was delayed due to 2 false-negative cryptococcal results on a molecular diagnostic panel. Caution with such platforms in suspected cryptococcal meningitis is needed.

Blockade of the negative co-stimulatory molecules PD-1 and CTLA-4 improves survival in primary and secondary fungal sepsis

Introduction

Fungal sepsis is an increasingly common problem in intensive care unit patients.Mortality from fungal sepsis remains high despite antimicrobial therapy that is highly active against most fungal pathogens, a finding consistent with defective host immunity that is present in many patients with disseminated fungemia.One recently recognized immunologic defect that occurs in patients with sepsis is T cell "exhaustion" due to increased expression of programmed cell death -1 (PD-1).This study tested the ability of anti-PD-1 and anti-programmed cell death ligand -1 (anti-PD-L1) antagonistic antibodies to improve survival and reverse sepsis-induced immunosuppression in two mouse models of fungal sepsis.

Methods

Fungal sepsis was induced in mice using two different models of infection, that is, primary fungal sepsis and secondary fungal sepsis occurring after sub-lethal cecal ligation and puncture (CLP).Anti-PD-1 and anti-PD-L1 were administered 24 to 48 h after fungal infection and effects on survival, interferon gamma production, and MHC II expression were examined.

Results

Anti-PD-1 and anti-PD-L1 antibodies were highly effective at improving survival in primary and secondary fungal sepsis.Both antibodies reversed sepsis-induced suppression of interferon gamma and increased expression of MHC II on antigen presenting cells.Blockade of cytotoxic T-lymphocyte antigen-4 (CTLA-4), a second negative co-stimulatory molecule that is up-regulated in sepsis and acts like PD-1 to suppress T cell function, also improved survival in fungal sepsis.

Conclusions

Immuno-adjuvant therapy with anti-PD-1, anti-PD-L1 and anti-CTLA-4 antibodies reverse sepsis-induced immunosuppression and improve survival in fungal sepsis.The present results are consistent with previous studies showing that blockade of PD-1 and CTLA-4 improves survival in bacterial sepsis.Thus, immuno-adjuvant therapy represents a novel approach to sepsis and may have broad applicability in the disorder.Given the relative safety of anti-PD-1 antibody in cancer clinical trials to date, therapy with anti-PD-1 in patients with life-threatening sepsis who have demonstrable immunosuppression should be strongly considered.

Effectiveness of measures to eradicate Staphylococcus aureus carriage in patients with community-associated skin and soft-tissue infections: a randomized trial

BACKGROUND

Despite a paucity of evidence, decolonization measures are prescribed for outpatients with recurrent Staphylococcus aureus skin and soft-tissue infection (SSTI).

OBJECTIVE

Compare the effectiveness of 4 regimens for eradicating S. aureus carriage.

DESIGN

Open-label, randomized controlled trial. Colonization status and recurrent SSTI were ascertained at 1 and 4 months.

SETTING

Barnes-Jewish and St. Louis Children's Hospitals, St. Louis, Missouri, 2007-2009.

PARTICIPANTS

Three hundred patients with community-onset SSTI and S. aureus colonization in the nares, axilla, or inguinal folds.

INTERVENTIONS

Participants were randomized to receive no therapeutic intervention (control subjects) or one of three 5-day regimens: 2% mupirocin ointment applied to the nares twice daily, intranasal mupirocin plus daily 4% chlorhexidine body washes, or intranasal mupirocin plus daily dilute bleach water baths.

RESULTS

Among 244 participants with 1-month colonization data, modified intention-to-treat analysis revealed S. aureus eradication in 38% of participants in the education only (control) group, 56% of those in the mupirocin group (P = .03 vs controls), 55% of those in the mupirocin and chlorhexidine group (P = .05), and 63% off those in the mupirocin and bleach group (P = .006). Of 229 participants with 4-month colonization data, eradication rates were 48% in the control group, 56% in the mupirocin only group (P = .40 vs controls), 54% in the mupirocin and chlorhexidine group (P = .51), and 71% in the mupirocin and bleach group (P = .02). At 1 and 4 months, recurrent SSTIs were reported by 20% and 36% of participants, respectively.

CONCLUSIONS

An inexpensive regimen of dilute bleach baths, intranasal mupirocin, and hygiene education effectively eradicated S. aureus over a 4-month period. High rates of recurrent SSTI suggest that factors other than endogenous colonization are important determinants of infection. Trial registration. ClinicalTrials.gov identifier: NCT00513799.

The natural history of contemporary Staphylococcus aureus nasal colonization in community children

The natural history of contemporary Staphylococcus aureus nasal colonization was evaluated in community children during a 1-year period. Methicillin-susceptible S. aureus nasal carriage was more persistent than methicillin-resistant S. aureus nasal carriage, which was usually self-limited. Children with persistent staphylococcal colonization often carried identical strains. Identification of persistent methicillin-resistant S. aureus carriers might inform strategies for decolonization and reduction of staphylococcal transmission.

PCR-I High Resolution Positron Tomograph Using Analog Coding

PCR-I has been designed and built to demonstrate the concept of analog coding to provide high resolution positron tomographic images without interpolative motion. The instrument uses 360 bismuth germanate (BGO) detectors coupled through a lucite light pipe to 90 phototubes. The measured resolution at the center is 4.8 mm. A straightforward extension of the concept will lead to a tomograph capable of obtaining resolution below 3 mm for low energy positron emitters. The sensitivity of PCR-I is 46 000/s for a 20 cm diameter phantom uniformly filled with 1 muCi/cc of a positron emitter. Parameters related to dead time and random and prompt scatter coincidences have been studied. Phantom measurements demonstrate the resolution and uniformity of PCR-I. Animal studies carried out to date include 18F in rat skeleton, 11C-palmitate and 11C-labeled red cells in dog heart and blood flow, and blood volume in monkey brain using C15O2 and C15O.

NUMEDICS: a system for on-line data processing in nuclear medicine

A multiterminal system --NUMEDICS--has been developed to study the problems of on-line acquisition, processing, and display of scintigraphic data. The hardware-software configuration of NUMEDICS permits simultaneous and independent operation of terminals in the Division of Nuclear Medicine, the Physics Research Laboratory, and the Cyclotron Laboratory of the Massachusetts General Hospital. This paper describes the hardware and software developments in NUMEDICS which have been proven to be of value in clinical and research applications. These features are illustrated by applications to the evaluation of left ventricular performance, three-dimensional imaging, and functional imaging of rCBF.