bluuebunny/crossref_metadata_2025_split huggingface dataset:
A-251 Comparison of Antimicrobial Susceptibility Profiles of Enterobacteriaceae spp. Isolates from Retail Meat Products Imported from USA and Brazil or Domestically Produced on Caribbean Islands of St. Kitts and Grenada
Authors: Luthra T , Varghese K , Martens A , Fakayode O , Harrington J 
Published: September 2023

Abstract

Background
Enterobacteriaceae species, including Escherichia coli, Klebsiella and Salmonella, are endogenous colonizers of gastrointestinal tract of livestock animals, which pose potential health threats to humans, particularly for individuals with compromised immune systems (Guentzel 1996). The emergence of drug-resistant strains due to the overuse of antibiotics in agricultural practices have increased the urgency to evaluate zoonotic bacteria and to assess potential impact on human and animal health (Llor 2014).

Project Aim and Methods
The aim of this study is to compare the microbial prevalence and antimicrobial resistance profiles of Enterobacteriaceae isolates present on pork and poultry products domestically produced in the Caribbean Islands, St. Kitts and Grenada as compared to poultry imported from USA and Brazil. This study was conducted over a 4-year time period at University of Medicine and Health Sciences (UMHS) in St Kitts and at St. George’s University (SGU), Grenada. Microbial colonies were isolated on MacConkey agar after 24-hour incubation at 36°C in Buffered Peptone Water and identified using standard biochemical assays and API-20E test kit. Antimicrobial susceptibility was evaluated using the Kirby-Bauer disc diffusion on Mueller-Hinton plates.

Results
A total of 44 meat products from Caribbean Islands and 49 meat samples from Brazil and USA were processed to yield 64 and 60 bacterial isolates, respectively. Bacterial colonies isolated from imported meat products displayed higher incidence of antibiotic susceptibility to multiple classes of drugs (MDR = Multiple Drug Resistant) as compared to domestically produced meats. The prevalence of MDR bacteria was 45% MDR isolates from USA-imported chicken as compared to 13% MDR bacteria isolated from chicken domestically raised.

Conclusions
Imported meats exhibit a higher prevalence of antimicrobial resistance, particularly in the beta-lactam class of antibiotics, including amoxicillin and cephalosporins and fluroquinolones. The overuse of subtherapeutic antibiotics in mass scale livestock production is likely creating selective pressure for the overabundance of MDR strains in the gastrointestinal tract of animals. The findings of this study will be communicated to relevant community leaders and organizations in order to inform the development of strategies aimed at reducing the prevalence of antimicrobial resistance and identifying appropriate treatment options for associated infections.
A-262 Analytical and Clinical Validation of a Multiplex RT-PCR based Mpox Assay
Authors: Upadhyay P , Reddy J , Singh V 
Published: September 2023

Abstract

Background
The 2022 non-endemic spread of Mpox in the western hemisphere was a unique public health challenge in the backdrop of the COID19 pandemic. To address the public health emergency where Mpox transmission was unlike previous instances, HealthtrackRX was one of the first independent diagnostics labs to develop a multiplexed RT-PCR based test for Mpox. In the present study analytical and clinical validation results for the Mpox RT-PCR test are presented.

Methods
The multiplexed pan-orthopox/pan-Mpox RT-PCR test was validated using inactivated Mpox (Clade I and II) viral samples establishing the limit of detection (LoD). Clinical validation of the test was performed against the FDA approved test at CDC and a commercially available pan-Orthpox assay. Sensitivity and specificity performance against interfering substance, pathogens and other poxviruses was also established. All statistical analysis were performed using R version 3.6.0.

Results
The multiplexed pan-Orthopox/pan-Mpox RT-PCR test successfully detected both Clade I and II Mpox and the LoD was established at 102 RNA copies/µl.The in-house developed Mpox test displayed 100% concordance against the FDA approved CDC pan-orthopox test and the pan-orthopox RT-PCR test from Thermo Fisher. The test showed no interference from a number of sexually transmitted pathogens and could successfully discern Mpox from several other poxviruses. With the exception of ethanol, no substances (from the FDA recommended list) interfered with the test performance. A total of 1712 patient samples were collected (July 25th, 2022, to February 1st, 2023) and tested for the presence of Mpox.

Conclusion
We have demonstrated the development, validation, and commercialization of a multiplexed RT-PCR based pan-orthopox/pan-Mpox diagnostic test for Mpox. Our data shows the feasibility of rapidly developing and deploying a PCR based test against an emerging infectious disease.
A-267 Evaluation of the Quidel Sofia 2 Rapid Lyme Test in a Modified Two-tier Testing Protocol
Authors: Lewandrowski K , Branda J , Turbett S , Lee-lewandrowski E 
Published: September 2023

Abstract

Background
Several Modified two-tier testing algorithms (MTTT) for Lyme disease involving sequential enzyme immunoassays (EIA) have been approved by the FDA as an alternative to conventional two-tiered testing using EIA followed by immunoblot. The MTTT algorithms are reported to be more sensitive than conventional two-tiered algorithm’s especially in early Lyme disease. The Quidel Sofia 2 Lyme assay utilizes lateral flow with fluorescence detection (FIA) providing a rapid on-demand instrument-read alternative to central laboratory batch mode testing We compared the Quidel assay as a first-tier test in an MTTT algorithm to the Zeus Scientific VlsE1/pepC10 IgG/IgM enzyme immunoassay (EIA) followed by the Zeus monovalent IgM and IgG EIA as the confirmatory test.

Methods
Serum specimens (n = 179) were obtained from consecutive samples sent to our clinical laboratory for Lyme serology testing. For the first-tier the samples were tested using the Zeus EIA VlsE1/pepC10 lgG/IgM test and the Quidel Sofia 2 Lyme FIA assay. Positive or equivocal first-tier tests were then tested using the Zeus monovalent IgM and IgG EIA as the confirmatory test.

Results
The positive percent agreement was 100%, the negative percent agreement 97.9 % with an overall agreement of 98.3%. The Kappa statistic was 0.945 (95% confidence interval 0.883–1.000 indicating “almost perfect” agreement).

Conclusion
The Quidel Sofia Lyme test performs well when compared to the Zeus test in a two-tiered testing MTTT algorithm. Obtaining samples to evaluate Lyme serologic tests can be challenging. Our data should prove useful for facilities considering the use of the Quidel assay.
A-274 Validation of Cefepime-Taniborbactam MIC Antimicrobial Susceptibility Test for MicroScan Dried Gram-Negative MIC Panels from a Multicenter Assessment of Enterobacterales and Pseudomonas aeruginosa
Authors: Garner O , Harrington A , Emery C , DesJarlais S , Diaz J , Chipman A , Hastey C 
Published: September 2023

Abstract

Background
Cefepime-taniborbactam is an investigational agent with activity against carbapenem and multidrug-resistant Enterobacterales and Pseudomonas aeruginosa.1 Given the need for accurate antimicrobial susceptibility testing results to support patient care decisions, a multicenter study was conducted with Enterobacterales and Pseudomonas aeruginosa clinical isolates on investigational MicroScan Dried Gram-negative MIC (MSDGN) panels with cefepime-taniborbactam.2

Materials/Methods
MSDGN panels were evaluated at three clinical sites by comparing MIC values obtained using MSDGN panels to MICs utilizing CLSI broth microdilution reference panels. The study included 490/491 Enterobacterales and 65 Pseudomonas aeruginosa clinical isolates tested using Prompt® and turbidity methods of inoculation during the combined efficacy and challenge phases. MSDGN panels were incubated at 35 ± 1°C and read on the WalkAway System, the autoSCAN-4 instrument, and visually at 16–20 h. Frozen reference panels were prepared according to CLSI/ISO methodology, incubated for 16–20 h and read visually.

Results
Essential agreement was calculated compared to MIC results from frozen reference panels for isolates tested in efficacy and challenge and found in the following table.

Conclusion
Cefepime-taniborbactam MIC results for Enterobacterales and Pseudomonas aeruginosa obtained with the MSDGN panel correlate well with MICs obtained using frozen reference panels in this multicenter study.Pending approval by the US Food and Drug Administration; not available for in vitro diagnostic use in the US. Not for Distribution in the US.Pending submission and clearance by the US Food and Drug Administration; not yet available for in vitro diagnostic use in the US.For Investigational Use Only. Performance characteristics of this product have not been established.Read methodEnterobacterales Essential agreement (EA) % (n/N)Pseudomonas aeruginosaEssential agreement (EA) % (n/N)PromptTurbidityPromptTurbidityWalkAway90.0 (441/490)99.2 (487/491)100.0 (65/65)100.0 (65/65)autoSCAN-494.3 (462/490)99.0 (486/491)98.5 (64/65)98.5 (64/65)Visually92.7 (454/490)99.2 (487/491)100.0 (65/65)100.0 (65/65)Abbreviations: Prompt, Prompt inoculation method, Turbidity, Turbidity inoculation method.
A-277 Health Economic Impact of use of GCAL Calprotectin Immunoassay for Early Detection of Infection in Intensive Care Patients
Authors: Jaquemar M , Larsson A , Havelka A 
Published: September 2023

Abstract

Background
Early diagnosis of bacterial infections in critically ill patients is challenging, as the clinical manifestation is non-specific. Neutrophil activation is a major response to bacterial infection and calprotectin an important marker for neutrophil mediated inflammation. Earlier studies have shown the ability of calprotectin to predict bacterial infections before onset of clinical symptoms. With early diagnosis of bacterial infections delayed treatment will be avoided as well as deterioration due to severe infections/sepsis.

Methods
A decision tree model is employed to estimate the impact of calprotectin analysis for early detection of bacterial infection and thus, the earlier start of antibiotic treatment compared to other diagnostic comparators such are white blood cell count, procalcitonin, C-reactive protein, and no testing. The analysis is based on patients admitted to an ICU in a Swedish hospital. The model allows for different diagnostic outcomes based on correctly and incorrectly diagnosis of bacterial infection and timing of antibiotic treatment: patient survival, length of stay in ICU and in general ward and total costs.

Results
The base-case results show that predictively measuring of calprotectin in an ICU, using GCAL® assay reduces total costs by approximately 13 000–18 000 EUR per patient, overall mortality rate by 0.11, and mean length of stay in an ICU and general ward by 1.3–2 days and 6–8 days, respectively.

Conclusion
The base-case scenario identified GCAL® Calprotectin Immunoassay as cost-effective for a patient cohort presenting in a Swedish ICU. Compared to the comparators, GCAL® saves total costs, reduces the mean duration of in-patient care, and reduces in-hospital mortality in those patients. In the sensitivity analysis, when key model inputs are varied, GCAL® Calprotectin Immunoassay remains the dominant option.
A-278 Development and Validation of Platform Independent, Turbidimetric Sars-CoV-2 Total Antibody Assay
Authors: Jaquemar M , Nilsen T , Safdari A , Haukebø A , Trosten E , Havelka A , Olsvik Ø 
Published: September 2023

Abstract

Background
The outbreak of the SARS-CoV-2 pandemic and continuous presence of the virus in the community require efficient tests for monitoring the anti-SARS-CoV-2 levels and management of the vaccination response in the population. Gentian AS, in collaboration with the University of Tromsø, has developed a quantitative SARS-CoV-2 antibody assay that captures the full immune response detecting antibodies targeting the S1-subunit with high sensitivity and specificity and is calibrated against the WHO international standard.

Methods
The immunoassay was developed and validated on turbidimetric instruments Cobas c501 from Roche and BS240 BS/240Pro from Mindray. Pre-pandemic samples from healthy donors or patients, were used for evaluation of clinical specificity. Samples from patients infected with Sars-CoV-2 virus or vaccinated against the virus were used for evaluation of clinical sensitivity.

Results
The assay has a calibration range from 0 to 1000 BAU/mL. No antigen excess was observed up to 2500 BAU/mL. Precision achieved a CV &lt;20 % for samples with a concentration ≤ 165 BAU/mL, and &lt;10 % for samples &gt;165 BAU/mL. No clinically relevant cross reactivity towards 13 antibodies, including antibodies against other Corona viruses was observed. The assay was able to detect antibodies generated in response to different vaccines and Alpha, Beta, Gamma, Delta and Omicron virus variants. Sensitivity and specificity of the assay met the acceptance criteria set out from the MDCG 2021–21 guideline, ≥90% and &gt;99% respectively.

Conclusion
The Gentian SARS-CoV-2 total antibody assay is a platform independent high-throughput assay with high sensitivity and specificity for assessment of antibody response after a natural infection and/or vaccination. The assay can ensure effective and reliable monitoring of the immunity and can be used for planning and management of the vaccination response in the community.
A-288 Molecular Detection of Mycobacterium tuberculosis in Pulmonary and Extra-Pulmonary Samples. Data from a Brazilian Clinical Laboratory
Authors: Nurmberger J M , de Carvalho G C , Perez B B , Santos M N , Ramadan D R , Tufik S 
Published: September 2023

Abstract

Background
Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), is among the leading infectious causes of death in developing countries. In humans, TB presents as a progressive granulomatous infectious disease that affects lungs causing pulmonary tuberculosis, but can also affect intestines, meninges, bones, joints, lymph nodes, skin and other body tissues causing extra-pulmonary tuberculosis. The aim of this study was to evaluate the frequency of tuberculosis cases detected during the COVID-19 period and the emergence of cases with extrapulmonary diagnosis.

Methods
This study was a retrospective analysis from January 2017 to December 2022 based on the analysis of 3105 clinical samples processed by the molecular biology section of AFIP Laboratory. All clinical samples were isolated from pulmonary and extra-pulmonary sites recovered from inpatients admitted in several Brazilian tertiary hospitals. In Brief, the DNA extraction was performed according to the type of patient’s samples and, then submitted to Real-Time PCR (qPCR) method using a commercial kit, which contains specific primers and probes to the M. tuberculosis genome.

Results
Of the 3105 samples tested, 222 (14%) samples were positive for the presence of M. tuberculosis. Out of which, 120/1405 (8,5%) were detected in the pre-Covid-19 period (2017–2019) and 102/1700 (6%) were detected in Covid-19 period (2020–2022). The prevalence of M. tuberculosis infection was 64.5% and 35.5% among men and females, respectively. The main age range was 41 to 50 years (44.7%), while over 60 years comprised 13.5% of cases (Fig. 1). Between the isolate sites, 67.1% of the M. tuberculosis cases were detected in pulmonary and 32.8% in extra-pulmonary body sites, of which, cerebrospinal fluid and blood are among the most frequent, followed by cervical lymph node, ascitic fluid, gastric lavage, urine and others. A total of 95% of M. tuberculosis was detected in patients assisted by public health service. We did not have access to patient’s symptoms, clinical history or further diagnostic procedures.

Conclusion
Comparing the two periods of the study, a reduction in the positivity rate of new cases was observed in the pandemic period, perhaps this fact can be associated with restrictions on access to the diagnosis of other pathologies in the pandemic period. Despite no information about the severity of the infection, male gender prevalence and age range from 41 to 50 years group need further attention.
A-295 Validation of Two New Real Time PCR Assays for the Detection and Differentiation of Plasmodium
Authors: Cisteró P , Franco-Marín E , Dehesa-García B , García-Manrique B , Alonso H , Matambisso G , Mbeve H , Ndimande N , Mayor A 
Published: September 2023

Abstract

Background
Malaria (or paludism), the mosquito-borne parasitic disease caused by Plasmodium, is a major global public health threat among communicable diseases. The objective of this study was to determine the clinical performance of VIASURE Malaria Real Time PCR Detection Kit and VIASURE Malaria differentiation Real Time PCR Detection Kit using dried blood spot on filter paper samples.The aim of this retrospective study was to validate and compare the clinical sensitivity and specificity of the VIASURE assays with the reference method used in the laboratory.

Methods
The Malaria assay, which detects the genus Plasmodium spp. and the differentiation assay, which distinguishes the main human pathogenic Plasmodium species: P. falciparum, P. ovale, P. vivax, P. malariae and P. knowlesi, were used in comparison with an 18S rRNA in-house malaria screening and differentiation assays. A total of 300 blood on filter paper collected from 2016 to 2019, from patients with clinical suspicion of malaria in the Manhiça-Magude district of southern Mozambique were analysed. The DNA extraction was carried out using the Chelex® 100 sodium method and the thermocycler employed was Applied Biosystems 7500 Real-Time PCR System.

Results
A total of 77 samples were considered as Plasmodium spp.-positive by both assays, 1 false positive result and 15 false negative results for VIASURE were obtained and 207 samples showed to be negative for this target by both assays. Regarding species differentiation: VIASURE assay showed 58 true positive and 3 false negative results for P. falciparum, 2 true positive results for P. malariae and 1 true positive and 1 false negative result for P. ovale. After data analysis, the sensitivity and specificity values obtained were:

Conclusion
This retrospective study demonstrated the good sensibility and specificity of both VIASURE molecular assays using this extraction method on dried blood spots.
A-298 Performance Analysis of Three Mpox Real Time PCR Kits With Lesion Swab Clinical Samples
Authors: Peris M , Franco-Marín E , Dehesa-García B , García-Manrique B , Alonso H 
Published: September 2023

Abstract

Background
The appearance of skin lesions can be a symptom of infection or reactivation of the HSV-1, HSV-2, VZV or T. pallidum or even monkeypox virus infection. Due to the contact-bound ease of spread of these pathogens, an accurate and fast diagnosis, such as PCR-based testing, is key to a good epidemiological management. The aim of this study was to determine the clinical performance of three qPCR assays.

Methods
A total of 334 cutaneous swabs collected from patients attended at the Hospital Universitario Miguel Servet were analysed using the three assays under study: VIASURE Herpes virus 1, Herpes virus 2 & Varicella Zoster Virus Real Time PCR Detection Kit, VIASURE Treponema pallidum Real Time PCR Detection Kit and VIASURE Mpox Real Time PCR Detection Kit. Samples were collected between December 2021 and November 2022. These samples were requested through the Biobanco del Sistema de Salud de Aragón (BSSA) and have the approval of the Aragón Ethics Committee (PI22/409). DNA/RNA extraction was performed using the automated extraction method magLEAD® 12gC instrument with the MagDEA Dx SV kit and amplification was performed using the thermocycler CFX96™ Real-Time PCR Detection System (BioRad). The obtained results were compared with the reference assays RealStar® Orthopoxvirus PCR Kit 1.0 (Altona) and Allplex™ Genital ulcer assay (Seegene®).

Results
After data analysis a very good overall agreement was obtained for all the studied targets.

Conclusion
The assays under study demonstrated to be a good tool for differential analysis in skin lesions compatible with HSV-1, HSV-2, VZV, T. pallidum or mpox virus infection. In addition, the shared thermal protocol of the assays allowed for the simultaneous detection in the sample, creating a personalized panel option for the user, as opposed to the reference assays employed, which required two separate analyses, taking longer to reach the full assessment of the sample.
A-299 Clinical Performance Validation of 7 qPCR Kits for the Specific Diagnosis of 5 Enteric Viruses in Clinical Stool Samples
Authors: Costafreda M , Bosch A , Pintó R M , Dehesa-García B , García-Manrique B , Alonso H , Guix S 
Published: September 2023

Abstract

Background
Among the most prevalent enteric viruses associated with gastroenteritis are norovirus (NoV), rotavirus (RV), astrovirus (AstV), sapovirus (SaV) and adenovirus (AdV). The diagnosis of infections associated with gastroenteritis viruses is mainly based on the detection of the genome of these viruses by molecular methods, mainly qPCR and RTqPCR reactions. The aim of this study was to validate the diagnostic performance of 7 qPCR diagnostic kits of the “VIASURE Real Time PCR Detection Kits” series with respect to commercial reference kits used for the diagnosis of these pathogens.

Methods
A total of 318 clinical stool samples were used, including: 213 stool samples from children from sporadic cases of gastroenteritis collected between 2016–2018; 94 samples from outbreaks of gastroenteritis caused by NoV between 2017–2019; and 11 samples from healthy children with asymptomatic enteric virus infections collected between 2017–2018. Seven VIASURE kits were used for the specific detection of enteric viruses. At the same time, samples were also tested with the following commercial kits used as reference methods: RIDA®GENE Viral Stool Panel II (rotavirus, adenovirus 40/41 and astrovirus) and RIDA®GENE Sapovirus, RIDA®GENE Norovirus I & II. In the case of AdV, the positivity of the samples was confirmed using the qPCR protocol published by Heim et al. (2003).

Results
The results obtained are summarized in Table 1.

Conclusion
The results obtained show a high sensitivity and specificity of the VIASURE kits for the detection of rotavirus, adenovirus, sapovirus, astrovirus and norovirus GI and GII (in the latter case using both the monoplex and multiplex product). In addition, it should be noted that all these kits share the same thermal protocol, thus allowing their joint use for the simultaneous diagnosis of these 5 enteric viruses.