bluuebunny/crossref_metadata_2025_split huggingface dataset:
A-245 Evaluation of an Automated MALDI-TOF Target and Antimicrobial Susceptibility Suspension Preparation Instrument
Authors: Rice F M , Larsen J , Graf E 
Published: October 2024

Abstract

Background
Several studies have shown that the implementation of automation in microbiology laboratories may allow for increased volume growth without the need for additional staffing. One of the more recently available pieces of microbiology automation, the COPAN Colibri, automates the manual steps of colony spotting and preparation of targets for use on MALDI-TOF instruments for bacterial identification. This same instrument can also prepare a diluted bacterial inoculum for immediate use on automated susceptibility testing platforms. We wanted to evaluate the performance of both of these functions in real-time with clinical cultures, to determine if implementation would be beneficial over current workflows.

Methods
The COPAN Colibri was operated following the manufacturer’s recommendations with the exception of the identification of gram-positive organisms. The Colibri is FDA cleared for MALDI-TOF target spotting, however not with the use of formic acid, nor is it FDA cleared for susceptibility suspension preparation. Preliminary data suggested that addition of formic acid was necessary for accurate identification. A subset of cultures were digitally read in real-time as part of clinical workflows, selected for Colibri MALDI-TOF target spotting and Vitek2 suspension preparation using the COPAN WebApp software. Targets were run on the MALDI Bioptyper Sirius (Bruker) and suspensions were run on Vitek2 (BioMerieux) using the pre-dilution mode using GN-99 and GN-801 cards for appropriate organisms. All results were compared to standard manual workflows.

Results
A total of 145 gram-negative and 60 gram-positive organisms were picked for MALDI-target spotting on Colibri. Compared to standard testing, 144 (99%) gram-negative and 57 (95%) gram-positive Colibri spotted isolates matched expected species-level identifications. 97 Gram negative bacilli were run on Vitek 2 generating 95.52% categorical agreement across all drugs but with 13 major errors (MEs) and 2 very major errors (VMEs), which exceeded the acceptable percentage for certain drugs. The total number of failed runs was 13 (13.34% of total GNB isolates run), and all required complete resetting of MALDI-spotting and suspension preparation.

Conclusions
The Colibri performed well for MALDI-TOF target spotting with the addition of formic acid for gram-positive organisms. It did not perform within the acceptable range for susceptibility suspension preparation as it exceeded the recommended cutoffs for MEs and VMEs for certain drugs. The proportion of failed runs due to instrument errors may offset any advantages in labor savings due to the need for repeat set up.
A-246 Can CRP be used to rule in or rule out elevated procalcitonin concentrations in the emergency department?
Authors: Hawkins R 
Published: October 2024

Abstract

Background
C-reactive Protein (CRP) and procalcitonin (PCT) are commonly used sepsis biomarkers but have very different properties. PCT rises earlier, has a shorter half-life and is more specific for sepsis than CRP. It is however significantly more expensive. This study examined whether CRP measurement can be used to screen for the need for PCT measurement in emergency department patients.

Methods
This was a retrospective study of anonymized records of paired CRP and PCT requests from the emergency department during 2023. All testing was performed using Beckman Coulter AU 5800 (CRP) and Roche e601 (PCT). PCT results were interpreted using the 2023 AACC guidelines on PCT use (PCT&lt;0.1 ug/L: strongly discourage antibiotic use; PCT 0.1-0.25: discourage antibiotic use; PCT 0.26-0.5: encourage antibiotic use; PCT&gt;0.5: strongly encourage antibiotic use) and the ability of CRP to predict PCT exceeding the various cutoffs was calculated using Microsoft Excel and Analyse-It statistical add-on.

Results
There were 1645 paired results available. The CRP concentrations at 95% and 99% sensitivity and specificity levels for the various PCT cutoffs are shown in the table, together with the projected reductions in PCT testing volumes if PCT testing is restricted to samples with CRP within the ranges defined by the 95% or 99% sensitivity/specificity values. For example, from the table, for PCT&gt;0.1 ug/L cutoff at 95% confidence, subsequent PCT measurement on the sample is only performed if CRP is between 3.4 and 90.5 mg/L.

Conclusions
Limiting PCT measurements to samples with CRP concentrations inside ranges based on the PCT cutoff of interest and the appropriate confidence level (95% or 99%) can potentially reduce PCT testing by 20-40% in emergency department patients. For laboratories which perform CRP and PCT analysis sequentially on different platforms, this approach allows significant reductions in PCT test volumes while ensuring testing is performed in equivocal cases.
A-253 Antimicrobial Susceptibility Pattern in Escherichia coli Isolated From Community-Acquired Urinary Tract Infections in the era Post-Covid-19
Authors: Ramadan-Boscolo D R , Nurmberger J M , Inoue F M , Lobo A P , de Andrade S S , Tufik S 
Published: October 2024

Abstract

Background
Urinary tract infections (UTI) are one of the most common infectious diseases diagnosed in the community as well as in hospitals. Community-acquired urinary tract infections caused by Escherichia coli represent the largest proportion of infectious diseases affecting women and a significant amount of oral antibiotics are prescribed daily to treat UTI in community outpatient clinics. Having knowledge of regional susceptibility data regarding E. coli is very important for selecting an appropriate empirical antibiotic. This study aimed to report the frequency and antimicrobial susceptibility of E. coli isolated from community-acquired urinary tract infections post-Covid-19 pandemic.

Methods
This study was a retrospective analysis from January to December 2023 based on the analysis of 24,019 uropathogens isolated from 182 outpatient health centers located in several regions of São Paulo city, Brazil. The urine samples were cultivated onto ChromID™CPS® agar plates by semi-quantitative technique using 1µL disposable loop, incubated at 35-37°C and the colony counting were read after 24h and 48h of incubation. The bacteria identification was performed by MALDI-TOF mass spectrometry (Vitek-MS), and the minimal inhibitory concentrations of antibiotics were determined using the Vitek®2 system, according to the manufacture’s recommendations. Only positive results with one bacterial species and a colony count ≥105 CFU/mL was considered for descriptive analysis.

Results
Of the 24,019 urine samples tested, 71.44% (17,159/24,019) were identified as Escherichia coli. The major frequency of E. coli infection occurred among women (90.48%) and the main age range was over 60 years (38.57%), while 21-30 comprised 16.5% of cases. The antimicrobial resistance profile for E. coli isolates showed 39.9% (6852/17158) of resistance to ciprofloxacin (MIC, &gt;0.5 mg/L), 34.7% (5,921/17,075) to trimethoprim/sulfamethoxazole (MIC, &gt;0.5 mg/L), 37.5% (6,371/17,002) to Amoxicillin/clavulanate (MIC, &gt;8 mg/L), 8.75% (1,501/17,592) to ceftriaxone (MIC, &gt;1 mg/L), 4.88% (837/17,138) to cefepime (MIC, &gt;4 mg/L), 3.64% (616/16,901) to piperacillin/tazobactam (MIC, &gt;8 mg/L), 11.07% (1,900/17,156) of gentamicin (MIC, &gt;2 mg/L), 0.43% (74/17,158) of amikacin (MIC, &gt;8 mg/L) and 2.23% (377/16,909) of fosfomycin (MIC, &gt;16 mg/L). High-level of susceptibility was detected to carbapenems with 99.94% (10/17159) to ertapenem (MIC, ≤0.5 mg/L) and 99.8% (4/17,159) to meropenem (MIC, ≤2 mg/L). The rate of Extended-spectrum beta-lactamase production was 8.1% (1391/17159).

Conclusions
This data could be used locally with other related samples, to properly interpret significant resistance patterns and choose the most appropriate antimicrobial for empirical treatment of patients with community-acquired urinary tract infections.
A-254 Increase of Stenotrophomonas maltophilia Isolates Non-Susceptible to Trimethoprim-Sulfamethoxazole and/or Levofloxacin at Brazilian Hospitals
Authors: Ramadan-Boscolo D R , Nurmberger J M , Inoue F M , Lobo A P , de Andrade S S , Tufik S 
Published: October 2024

Abstract

Background
Stenotrophomonas maltophilia is an emerging multidrug-resistant pathogen that exhibits intrinsic and acquired resistance to a wide variety of antimicrobial agents such as β-lactams, aminoglycosides, quinolone, tetracyclines and disinfectants. In addition to that, the increased resistance to sulfamethoxazole/trimethoprim (SMX/TMP) and Levofloxacin has been reported in the past few years, leading to few therapeutic options. This study aimed to describe the increase of Stenotrophomonas maltophilia clinical isolates recovered from Brazilian hospitals over a 6-year analysis (January 2018 to December 2023).

Methods
This study design was a retrospective, observational analysis based on microbiological data of emergent BGN-NF isolates detected in several Brazilian tertiary hospitals. The bacterial identification was performed by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF/MS) and the antimicrobial susceptibility profile to trimethoprim-sulfamethoxazole and levofloxacin was determined using disk-diffusion method and epsilometer method, respectively. Only one sample per patient was considered in this analysis.

Results
During the 6 year period, a total of 1,706 (2018; 221), (2019; 203), (2020; 294), (2021; 276), (2022; 294) and (2023; 418) Stenotrophomonas maltophilia strains were isolated from blood (n=626), respiratory tract (n=365), fluid and secretion (n=235), skin and soft tissue (n=162), urine (n=132), catheter tip (n=112), swab (n=36), bone fragment (n=29) and cerebrospinal fluid (n=9). The major frequency of S. maltophilia isolation occurred among man (52.6%) and the main age range was over 60 years (42.7%), while 0-10 comprised 16.6% of cases. Compared the 6-years period, the resistance rate to trimethoprim-sulfamethoxazole was 2.7%; 5.4%; 5.8%; 2.2%; 5.8%; 7.9% and levofloxacin was 3.6%; 3.4%; 3.1%; 3.3%; 1.7%; 2.9%, respectively. The resistance rate to trimethoprim-sulfamethoxazole and levofloxacin, simultaneously, was 0.23%.

Conclusions
The incidence rate of S. maltophilia infections has increased significantly, especially in the last year, followed by an increase in the pattern of resistance to trimethoprim-sulfamethoxazole. Regarding trimethoprim-sulfamethoxazole and levofloxacin co-resistance, very low rates were detected in our analysis. Our data point to a scenario wherein the presence of S. maltophilia may have been intensified by the covid-19 pandemic. Regional surveillance reports are extremely important and should be out to understand some aspects of the dynamics of bacterial resistance in both hospital and community settings.
A-262 Novel Hepatitis C Virus External Quality Control that is Stable at Ambient Temperature and Suitable For Use in Low-Resource Settings
Authors: Rivers S , Zhelev P , Alagic A , Gerbaba T , Patel R , Luscher M , Hughes K 
Published: October 2024

Abstract

Background
Notwithstanding the WHO’s initiative to eliminate viral hepatitis by 2030, there are currently 58 million individuals infected with Hepatitis C Virus (HCV). 73% of infected individuals live in low- and middle-income countries (LMIC) where conventional diagnostics are inaccessible due to high costs and lack of trained personnel. The emergence of low-complexity Point of Care tests is critical for improving accessibility and reducing the spread of infection. Additionally, there is a need for external quality controls (EQC) that monitor the accuracy of test results. Given that LMIC have limited access to laboratory equipment, EQC must have simplified handling procedures and storage conditions. Unfortunately, these materials are not available at scale. Microbix strived to develop HCV EQC swab formulations that are stable at ambient temperature. Since this format deviates from standard HCV diagnostic workflows, we sought to establish a simple yet reproducible workflow that can be followed by laboratories worldwide.

Methods
Microbix developed HCV swab-based EQC that are stable when stored at 2-30°C. The contrived specimens are formulated with protected synthetic HCV whole-genome nucleic acid and human cells. The formulation was quantified via ddPCR and benchmarked against the WHO HCV standard using Xpert® HCV Viral Load Fingerstick Assay. Sample performance was evaluated with various elution buffers (PrimeStore® MTM, eNAT®, TE buffer, Microbix’s proprietary buffer) and handling procedures that require minimal use of laboratory equipment. Each EQC workflow was assessed based on its ability to consistently demonstrate a viral load of 100-200 IU/mL when tested on Cepheid’s platform.

Results
The EQC tested positive for HCV when eluted in each buffer and processed using a hand-mixing procedure. Only the workflows that used PrimeStore® MTM or eNAT® consistently reported a viral load between 100-200 IU/mL.

Conclusions
Microbix developed an HCV swab-based EQC that is stable at ambient temperature; however, we observed that consistent elution conditions are imperative for achieving reproducible results. Our findings demonstrate that a universal workflow should be followed to standardize results across testing sites as deviations in elution buffers, volumes, and handling procedures can influence test outcomes.
A-278 Prevalence of Clostridium Difficile in Long-Term Care Facilities Using BD Max Cdiff Molecular Assay
Authors: Khoury R , Gudaitis P , Patel P , Gandhi A , Gudaitis D 
Published: October 2024

Abstract

Background
Clostridium difficile (C.Diff) is a gram positive anaerobe producing Enterotoxin and Cytotoxin (toxin A and B respectively); more than half of million infection is diagnosed yearly with more than 10% of the cases are in patients over 65 years old. Residents in Long-Term Care Facilities (LTCF) are more prone to have C. Diff infection (CDI) because of their age, the frequent use of antibiotics, fragilities, co-morbidity, and living environment. Diagnosing CDI is based on clinical signs and symptoms as well as laboratory tests; however, the enzyme immunoassays are reliable, the tissue culture cytotoxicity is labor intensive. The nucleic acid amplification tests are becoming more the standard as first step in the diagnosis. The BD MAX™ System is a PCR walkaway instrument that provides the sensitivity, specificity and faster turnaround for the C. diff.

Methods
The BD MAX™ System is an automated in-vitro diagnostic test for the direct qualitative detection of the C. difficile toxin B gene (tcdB) in human liquid or soft stool specimens from patients suspected of having Clostridium difficile Infection (CDI). Premier Toxins A & B is an enzyme immunoassay for the direct detection of Clostridium difficile toxin A and toxin B in stool samples. We collected data from 5,267 samples were collected from resident in LTCF and were run using the EIA assay, 275 samples were ran using the BD Max molecular assay. We had 31 samples that were run using both assays. Statistical analyses were done using Analyse-it.

Results
Female accounted for 60% of the patients tested; the positivity rate was 13.2% for female and 17.2 for male using the EIA. The positivity rate was 19.2% for female and 30.6% for male when using the molecular assay. The agreement between the EIA and the PCR was 87% based on 31 samples that were run for both assays.

Conclusions
The BD Max gave the benefit of a fully automated with high sensitivity and specificity for the presence of toxin B producing C. Diff. The difference between the methods could be due to the lack of the sensitivity in the EIA and the fact that the molecular assay might be picking up colonized specimen or the beginning or end of infection. However, the ability to diagnose CDI early and prevent spreading of the disease to other patients is a huge benefit to the facilities. We have to keep in mind also that C.diff infection can be prevented with appropriate use of antibiotics and implementing antibiotic stewardship and infection control plan to prevent and stop spreading of the infection.
A-279 Performance Evaluation of the Respiratory Viral for BD MAX™ System in Geriatric Population
Authors: Khoury R , Patel P , Gandhi A , Gudaitis D , Gudaitis P 
Published: October 2024

Abstract

Background
Respiratory Viral Infection is one of the most common infection in the geriatric population and cause major concern in the Long-Term Care Facilities. Influenza A and B, SARS-CoV-2, and respiratory syncytial virus (RSV) are responsible for most of the hospitalization and deaths among elderly patients. Rapid identification, treatment, and isolation are among the most important steps to fight the spreading of the infection.

Methods
The BD Respiratory Viral Panel for BD MAX™ System is an automated multiplexed real-time reverse transcriptase polymerase chain reaction (RT- PCR) test intended for the simultaneous, qualitative detection and differentiation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza A, influenza B, and/or respiratory syncytial virus (RSV) nucleic acid in nasopharyngeal swab (NPS) and anterior nasal swab (ANS) specimens from individuals with signs and symptoms of respiratory tract infection. The assay is targeting RNA from the nucleocapsid phosphoprotein gene (N1 and N2 regions) of the SARS-CoV-2, a conserved region of the matrix protein M1 gene for influenza A, conserved regions of the matrix protein M1 gene and HA gene for influenza B, conserved regions of the N and M genes for RSV, and the human RNase P gene. The assay was evaluated for: precision, reproducibility, accuracy, and correlation with BioGx for SARS-CoV-2, Solana (Quidel) for influenza A, influenza B and RSV; the percentage agreement for the evaluation steps was calculated. We ran 86 samples collected from patients residing in Long-Term Care Facilities. Statistical analyses were done using Analyse-it.

Results
The percentage agreement for precision, reproducibility, and accuracy were 100%. The patients’ correlation was 100% when compared to the existing molecular testing in the laboratory. Female patients accounted for 62.8% (54 female and 32 male); 2 patients were positive for both influenza A and RSV, and one patient was positive for both influenza A and SAR-CoV-2.

Conclusions
The Respiratory Viral panel for BD MAX™ System gave the benefit of a fully automated, high precision, accuracy and acceptable sensitivity assay; in addition, it offers easier collection (one swabs versus multiple swabs), faster turnaround time for four targets in less than three hours which allow for earlier isolation to prevent the spreading of the infection and initiating treatment when needed. As with every molecular assay avoiding contamination is very important to eliminated false positive results.
A-283 Serologic and molecular testing for the diagnosis of Rickettsia, Ehrlicha, and Anaplasma infections in patients in Maryland
Authors: Mullins K , Hoti N 
Published: October 2024

Abstract

Background
Rickettsia, Anaplasma, and Ehrlichia are underrecognized tick-borne pathogens of increasing human importance. As tick habitats are expanding and populations are increasing, human exposure to these pathogens is also increased in recent years. Unfortunately, while treatment is usually simple, diagnosis can be difficult as it requires specialized testing for clinical diagnosis - generally performed only at reference laboratories.

Methods
To better understand the prevalence, diagnosis, and testing patterns for Rickettisal infections, Anaplasmosis, and Ehrlichiosis in Maryland, a retrospective analysis of all serologic and molecular testing for Rickettsia, Anaplasma, and Ehrlichia species performed for the University of Maryland Medical System from 2018-2022 was conducted. Eight hospitals within the University of Maryland Medical System (Central Maryland and Maryland’s Eastern Shore) diagnose Rickettsia, Anaplasma, and Ehrlichia infections using serologic and molecular testing.

Results
Between 2018-2022, an average of 413 individuals were tested for Rickettsia, Anaplasma, and Ehrlichia each year. On average 315 serologic tests for Rocky Mountain Spotted Fever (RMSF) group Rickettsia, 195 serologic tests for Ehrlichia chaffeensis (Anaplasma serology is not available), and 165 molecular tests for the detection of Anaplasma and Ehrlichia species were ordered each year. Clinical indications for testing included tick bite, fever, chills, severe headaches, muscle aches, and rash. Overall, 17% of individuals tested were positive for IgG antibodies to RMSF group Rickettsia, however only 1% were positive for IgM antibodies. Further, 20% of individuals tested were positive for IgG antibodies to Ehrlichia chaffeensis, while &lt;1% were positive for IgM. Acute and convalescent samples were not tested for any individuals. Molecular evidence of infection was found in 8% of individuals tested. Nineteen precent were positive for Anaplasma phagocytophilum and the remaining 81% were positive for Ehrlichia chaffeensis. Interestingly, only two individuals had positive results from both molecular and serologic testing.

Conclusions
Results from serologic and molecular testing show that Rickettsia, Anaplasma, and Ehrlichia are important human pathogens with the potential to cause significant morbidity. However, lack of follow-up serology, and laboratory tests that confirm acute infection make definitive diagnosis difficult. Increased awareness of Rickettsial diseases and appropriate diagnostics is needed.
A-289 Multiple Gastric Polyps as an Unusual Presentation of Syphilitic Gastritis
Authors: de Andrade S S , Cilotti H P , Grecco L G , Agnol M D , Iriya K , Rigueiro M P , Yamassaki H O , Barata M C , Ramadan-Boscolo D R , Tufik S 
Published: October 2024

Abstract

Background
Syphilis is a sexually transmitted infection caused by Treponema pallidum and can clinically progress through four different stages. Syphilitic gastritis is one of the rare manifestations of the disease, harboring the potential to mimic several types of unrelated disorders such as malignant lymphomas, Langerhans cell histiocytosis, auto-immune gastritis and refractory Helicobacter pylori infection. The classics symptoms are weight loss, abdominal pain, and gastroparesis, nausea, vomiting and hematemesis. The most common endoscopic finding is gastric ulcers. The rising trends of syphilis in the last decade, detected in both developing and developed countries, calls for continued efforts for case detection on rare syphilis manifestations.

Methods
A 35-year-old male patient was submitted to gastric biopsy due to endoscopic findings of multiple polyps in the corpus and antrum of stomach. The material was processed and analyzed in a pathology laboratory in São Paulo, Brazil. Histological sections were stained with hematoxylin and eosin and immunohistochemical staining.

Results
The specimens exhibited intense inflammatory lympho-histiocytic infiltrate, rich in plasma cells, neutrophils and eosinophils affecting the gastric mucosa. Immunohistochemical staining revealed spiral-shaped bacteria consistent with T. pallidum affecting the gastric mucosa surface, adjacent to vessels, and permeating glands.

Conclusions
This case report has the goal of showing the occurrence of syphilitic gastritis, an uncommon extracutaneous manifestation of T. pallidum infection with the potential to mimic other etiologies. Due to the rarity of syphilitic gastritis and its non-specific symptoms, a combination of clinical, endoscopic, and histopathological findings is necessary to secure diagnosis of syphilitic gastritis. The advent of immunohistochemistry for T. pallidum has facilitated microscopic diagnosis, as special stains such as Warthin-Starry can still pose interpretation challenges.