Abbott Molecular Research Articles

Update on Mpox Management: Epidemiology, Vaccines and Therapeutics, and Regulatory Changes.

Mpox, caused by the monkeypox virus (MPXV), is categorized into two primary clades: Clade I and Clade II, with notable outbreaks linked to Clade IIb. Historically endemic in Africa, recent years have seen significant global spread. The World Health Organization (WHO) declared mpox a Public Health Emergency of International Concern in August 2024, highlighting the emergence of Clade Ib outside Africa and the broadening demographic impact of the outbreak. This review updates the current status of mpox vaccines and treatments, including their safety and effectiveness. There are two US Food and Drug Administration (FDA)-approved vaccines for the prevention of mpox disease, JynneosTM and ACAM2000®. The JynneosTM vaccine, recommended for high-risk individuals, has seen limited uptake despite its efficacy in preventing disease. Tecovirimat, while FDA-approved for smallpox and available in the European Union for mpox, has shown mixed results in recent trials, with new data suggesting limited effectiveness in Clade I infections and emergence of new mutations with resistance to this drug. Brincidofovir and Vaccinia Immune Globulin Intravenous offer additional treatment options, particularly for severe cases, although their use is constrained by regulatory and logistical challenges. Furthermore, the WHO recently approved the first commercial molecular assay, the Alinity m MPXV assay by Abbott Molecular Inc., for emergency use-an essential step in expanding testing capacity in regions experiencing mpox outbreaks. These updates underscore the critical need for continued research to enhance therapeutic outcomes and adapt public health strategies. Ensuring equitable access to vaccines, treatments, and diagnostics remains a significant challenge as the global community responds to the evolving mpox situation.

Mycoplasma genitalium Infections Among Participants in an HIV Pre-exposure Prophylaxis Program in Hanoi, Vietnam.

Mycoplasma genitalium causes a sexually transmitted infection and is also emerging as an important antimicrobial resistant pathogen. Data on M. genitalium infections among men who have sex with men (MSM) in low-resource settings are sparse. From January to December 2022, participants in an HIV pre-exposure prophylaxis (PrEP) program in Hanoi, Vietnam were enrolled into the study. Demographic, behavioral, and clinical characteristics were collected. Self-collected urine, rectal, and pharyngeal specimens were tested for M. genitalium using the Alinity m STI Assay (Abbott Molecular, USA). Univariate and multivariate logistic regression were performed to assess for factors associated with infections. Among 477 participants, the median age was 25.3 years (21.7-29.6) and 92.2% (n = 440) identified as MSM; 48.6% had ≥2 sex partners and 38.1% reported condomless anal sex in the prior month. The overall prevalence of M. genitalium infection was 10.9% (52/477); 7.3% (34/464) rectal, 3.2% (15/476) urethral, and 1.9% (9/476) pharyngeal. Infections were asymptomatic in 71.2% (37/52). Among those with M. genitalium , 30.7% (16/52) were co-infected with either Neisseria gonorrhoeae or Chlamydia trachomatis. Among those reporting rectal (n = 51) or urethral (n = 35) symptoms, but without C. trachomatis or N. gonorrhoeae co-infections, five (9.8%) had rectal infections and one (2.9%) had urethral infection. Participants with M. genitalium were more likely to be asymptomatic than participants without M. genitalium (adjusted odds ratio, 1.93; 95% confidence interval, 1.01-3.71). Mycoplasma genitalium infections were common among primarily MSM engaged in an HIV PrEP program in Vietnam. The prevalence was highest in rectal specimens and nearly three quarters of M. genitalium infections were asymptomatic. Testing for M. genitalium infections among those with symptoms is important to enable pathogen-directed therapy. Additional research on antimicrobial resistance and treatment strategies for M. genitalium in low-resource settings is needed.

Evaluation of the analytical and clinical performance of the Abbott Alinity m instrument for the quantification of HIV-1 RNA plasma viral load in a reference laboratory in Rio de Janeiro, Brazil.

We sought to evaluate the analytical performance of the Alinity m system (Abbott Molecular) and to compare the clinical performance of HIV-1 assays on the Alinity m and m2000 RealTime platforms (Abbott Molecular). The sensitivity, precision, and accuracy of the Alinity m instrument were determined using a panel of standard samples (n = 46). The carryover effect was assessed by analyzing HIV-negative clinical samples (n = 20). Clinical performance of the Alinity m and m2000 RealTime platforms was compared using surplus HIV-positive patient plasma samples (n = 39). The Alinity m HIV-1 assay demonstrated 100% sensitivity, a high precision (coefficient of variation (s/x̄) × 100 ≤1.5% [SD ≤ 0.05] logarithm to base 10 [log10] copies/mL), and partial accuracy over the quantification range. Analysis of clinical samples suggested that the Alinity m HIV-1 assay does not cause carryover effect and produced a mean bias of 0.209 log10 copies/mL (95% CI, 0.153-0.265) compared with the m2000 RealTime System. The Alinity m instrument's performance correlated to that of the m2000 RealTime platform and showed excellent sensitivity, precision, and accuracy, despite producing overquantification not clinically relevant for disease management. Furthermore, use of the Alinity m platform can reduce turnaround time.

Impact of molecular ciprofloxacin resistance testing in management of gonorrhoea in a large urban clinic

ObjectivesAntibiotic resistance in gonorrhoea is of significant public health concern with the emergence of resistance to last-line therapies such as ceftriaxone. Despite around half of Neisseria gonorrhoeae isolates tested in...

Letermovir use may impact on the Cytomegalovirus DNA fragmentation profile in plasma from allogeneic hematopoietic stem cell transplant recipients.

Cytomegalovirus (CMV) DNA in plasma is mainly unprotected and highly fragmented. The size of the amplicon largely explains the variation in CMV DNA loads quantified across PCR platforms. In this proof-of-concept study, we assessed whether the CMV DNA fragmentation profile may vary across allogeneic hematopoietic stem cell transplant recipients (allo-SCT), within the same patient over time, or is affected by letermovir (LMV) use. A total of 52 plasma specimens from 14 nonconsecutive allo-SCT recipients were included. The RealTime CMV PCR (Abbott Molecular), was used to monitor CMV DNA load in plasma, and fragmentation was assessed with a laboratory-designed PCR generating overlapping amplicons (around 90-110 bp) within the CMV UL34, UL80.5, and UL54 genes. Intrapatient, inter-patient, and LMV-associated qualitative and quantitative variations in seven amplicons were observed. These variations were seemingly unrelated to the CMV DNA loads measured by the Abbott PCR assay. CMV DNA loads quantified by UL34_4, UL54.5, and UL80.5_1 PCR assays discriminate between LMV and non-LMV patients. Our observations may have relevant implications in the management of active CMV infection in allo-SCT recipients, either treated or not with LMV, although the data need further validation.

Comparison of the Alinity M STI with the GeneXpert CT/NG for the detection of sexually transmitted microorganisms

We assess the performances of the Alinity M STI assay (Abbott Molecular) in comparison to the Xpert CT/NG assay (Cepheid). We first retrospectively used a collection of 70 frozen samples of which 33, 31, and 6 were positives for Chlamydia trachomatis (CT), Neisseria gonorrhoea (NG), and both micro-organisms respectively. The Alinity M STI and the Xpert CT/NG results were in accordance for all. The mean difference in cycle threshold values between the Xpert CT/NG and the Alinity M STI were -1.6 and 0.0 for CT and NG respectively.Then 214 fresh samples collected from 121 patients were prospectively tested with both instruments. Anal swabs, throat swabs, vaginal swabs, and urines accounted each for about 25%. Seven (3.2%) samples of which 5 anal swabs, provided inconclusive results with the Alinity M STI. In conclusion, the Alinity M STI is an accurate device for the microbiological diagnosis of NG and CT infections.

1703. Pseudo-Outbreak of Methicillin-Resistant Staphylococcus aureus in a Neonatal Intensive Care Unit: Implications for Surveillance

Abstract Background We conduct weekly surveillance screening for methicillin-resistant Staphylococcus aureus (MRSA) in our neonatal intensive care unit (NICU). In September 2021, we noted an increase in positive MRSA screening results and identified 2 patients with MRSA wound infection. We conducted an investigation to explore the possibility of in-unit transmission. Methods We launched a multi-pronged investigation that included additional patient screening. Surveillance isolates were assessed for the presence of MRSA using chromogenic agar. Additional antimicrobial sensitivity testing was performed on an automated bacterial identification system if chromogenic agar results were inconclusive, fig 1 & 2. We also conducted audits of staff hand hygiene, enhanced cleaning and disinfection of shared patient-care equipment, implemented standardized chlorhexidine gluconate (CHG) scrub use for NICU staff upon unit entry, and added new CHG bathing for certain patients. Positive control chromogenic agar plate Ambiguous chromogenic agar results Results Over the course of a 6-week long investigation, 18 neonates were found to be MRSA-positive on surveillance swabs using chromogenic agar. In the first 2 weeks of the investigation, PFGE showed that 9 MRSA isolates were genetically distinct. Over the next weeks, additional MRSA-positive surveillance swabs were collected and ultimately 15 isolates underwent whole genome sequencing at the Mass. State Public Health Laboratory. Only 2 pairs of isolates appeared related. Antimicrobial resistance genes were identified and revealed only 6 of the 15 isolates contained the mecA gene consistent with MRSA. As a result, all 18 positive surveillance swabs obtained during the investigation underwent full identification and sensitivity testing confirming only 6 samples contained MRSA and 12 contained methicillin-sensitive Staphylococcus aureus (MSSA). Testing discordance with breakthrough MSSA growth was reported to the chromogenic agar manufacturer. Conclusion Our investigation identified that an increase in MRSA-positive surveillance swabs was a pseudo-outbreak due to false-positive MSSA growth on MRSA selective media. At the conclusion of this investigation, the need for ongoing surveillance swabs was re-evaluated and ultimately discontinued. Clinical NICU specimens are now monitored in real-time by Infection Control. Disclosures James Kirby, MD, D(ABMM), Abbott Molecular: Educational Grant

A-302 Agreement Assessment Between Molecular and Rapid Tests in Respiratory Viruses Detection

Abstract Background Diseases caused by respiratory viruses are the most frequent diseases in humans and have a significant impact on morbidity and mortality worldwide. Due to their transmission nature, these viruses are able to widespread dissemination. The pandemic caused by COVID-19 highlights this potential, however, other respiratory viruses also continue to circulate such as Respiratory Syncytial Virus (RSV) and Influenza (FLU). Efficient diagnostic tools are necessary, especially in endemic regions. Although molecular tests are gold standards, rapid tests (RTs) represent a great alternative once they are more accessible, faster, easier to manage, and can be performed at the point of care. Therefore, this work aimed to evaluate the analytical performance of RTs compared to molecular tests in the detection of viral antigens of RSV or FLU in swab samples. Methods Swab samples in saline solution (n = 60) were tested by qPCR molecular assay Multiplex Alinity m Resp-4-Plex Assay (Abbott Molecular) and RTs immunofluorescence-based (ECO-F RSV ag and ECO-F Influenza A/B—ECO Diagnostica). For the molecular assay, samples were prepared according to the manufacturer's instructions. For RTs, samples were submitted to the extraction buffer, incubated for 10 or 15 minutes respectively, and analyzed by ECO Reader F200 equipment, according to the manufacturer's instructions. It uses a cut-off value ≥1.00 for positive samples and <1.00 for negative samples. Results All negative samples (RSV = 20; FLU = 20) in molecular test were concordant with RTs results. The number of positive samples detected by molecular test was 4 and 16 for FLU and RSV respectively, while RTs detected a lower number of positive samples (FLU = 2; RSV = 10). Both RTs achieved a specificity of 100%; sensibility was 62, 50% for RSV and 50% for FLU. Using Cohen's Kappa index to assess the agreement between the compared tests, it was obtained the expected and observed values of 0.83 and 0.53 for RSV and 0.92 and 0.78 for FLU, which represents an index of 0.649 and 0.625 respectively. These results indicate substantial agreement between the tests, although the sensitivity of the molecular assay was superior. Conclusion Molecular tests can be used to confirm the results of RTs, once they are the gold standard for diagnosis. However, they have a high operational cost, which makes RTs a good alternative to help in the screening of these respiratory diseases, especially in resource-limited settings, allowing effective treatment and management for the patient.

Evolution of genomic profiles in primary and recurrent brain gliomas.

e14042 Background: Diffuse gliomas are highly heterogenous tumors with variable biological behaviors, including high intratumor and extratumor heterogeneity, and with occurrence of recurrent lesions in majority of patients. During disease progression, gliomas undergo cellular and genomic evolution with newly acquired genetic properties. However, the mechanism of this complicated process associated with treatment failure is poorly understood. In this retrospective study, we performed cytogenomic analyses of primary and recurrent tumors in five patients with diffuse glioma who underwent surgical resections or biopsies of multiple recurrences. Methods: One primary and at least two recurrent freshly resected tumor tissues from each patient were analyzed using combination of cytogenomic methods. To assess specific and random copy number alterations (CNAs), I-FISH (Abbott Molecular, MetaSystems), array CGH/SNP (Agilent) and MLPA (MRC Holland) were performed. Methylation of MGMT promoter was investigated by methylation-specific MLPA (MRC Holland) and mutations of 67 genes associated with solid tumors were assessed by target NGS (Archer VariantPlex Solid Tumor, Invitae). Results: All five patients (three men and two women) experienced recurrence with newly acquired genetic or epigenetic changes. We observed a higher frequency of CNAs in recurrent gliomas than in primary tumors. Moreover, several aberrations were not detected in recurrence despite being found in earlier samples. As a primary event we proved mutation R132H of IDH1 gene. In addition, we detected methylation of the MGMT promoter, CDKN2A/B homozygous deletion, and RB1 deletion as later events that were probably associated with higher tumor grades. Besides the typical genomic changes, we detected many aberrations with unknown or unclear prognostic relevance (e.g. inframe deletion in TP53, p.Met243_Asn247del, etc.). The progression to a higher grade of glioma occurred in four patients. Conclusions: The evolutional patterns in glioma depend on clonal selection caused by CNAs, mutations, genetic drift, intratumor heterogeneity and/or the patient’s treatment. Recurrence may arise from one major tumor clone or from one or more subclones within the primary tumor through. Integrated cytogenomic analyses of genetic/epigenetic profiles of primary and all recurrent tissues can contribute to a better understanding of mechanisms responsible for these processes and to identification of new alterations related to gliomas progression and/or resistance to treatment. These biomarkers could subsequently serve as new therapeutic targets for personalized treatment.

Screening for monkeypox virus infections in men who have sex with men in a sexual health clinic in Hanoi, Viet Nam.

Screening for monkeypox virus infections in men who have sex with men in a sexual health clinic in Hanoi, Viet Nam.

Secular decrease in chromosomal mosaicism in cultured and uncultured peripheral blood cells of six patients with mosaic Down syndrome.

As noted in a review paper,1 a large-scale study revealed that approximately 1.1%–3.8% of all children with Down syndrome (DS) are born with mosaic DS.2, 3 DS is diagnosed postnatally by chromosome G-banding analysis of peripheral blood cultures, and most patients do not undergo subsequent repeat analysis. We present secular changes in the mosaic ratio of six patients with mosaic DS. The G-banding, chromosome 21 fluorescence in situ hybridization (chr21 FISH) from peripheral blood cultures and the chr21 FISH analysis of uncultured blood cells showed a drastic reduction in the mosaic ratio in five patients aged between 7 and 23 years. The mosaic ratio of a child aged 3 years and 3 months gradually, but not drastically, decreased over time. However, no decrease in the mosaic ratio was seen in the buccal mucosa or fibroblasts by chr21 FISH in any mosaic patient. Low-invasive chromosomal analyses of 100 cells per patient from different tissues were performed by SRL, Inc. The analyses were as follows (Table 1). (1) T lymphocyte chromosome analyses of cultured peripheral blood samples by PHA (phytohemagglutinin) stimulation, including (1-a) G-banding and (1-b) chr21 FISH analysis using chromosome 21q22.13-q22.2 probes (Vysis, Abbott Molecular); (2) chr21 FISH analysis of uncultured blood cells, including various leukocytes, instead of bone marrow puncture; (3) chr21 FISH analysis of epithelial cells from the buccal mucosa; and (4) chr21 FISH analysis of fibroblasts cultured from a tooth extraction. The six patients (A–F) with mosaic DS (five females and one male) were aged from 3 years and 3 months to 23 years (Table 1). Five patients (B–F) aged between 7 and 23 years showed drastically decreased mosaic ratios (1%–8%) by G-banding, and FISH analysis of the peripheral blood culture and of uncultured blood cells compared with the postnatal result (Table 1, the red font). Patient A showed a gradual decrease in mosaicism on G-banding and FISH of the peripheral blood culture and by FISH analysis of uncultured blood cells at 11 months, 2 years and 9 months, and 3 years and 3 months of age compared with the postnatal result (Table 1, the red font). However, none of the six patients showed a decreased mosaic ratio in the buccal mucosa analysis or tooth-extraction-derived-fibroblast FISH analysis. Previously, two reports documented a decreased mosaic ratio in mosaic DS patients during early childhood, mainly in peripheral blood cultures.4, 5 We studied longitudinal changes in the mosaic ratio of six mosaic DS patients, including young adults. No decrease was observed in the epithelial cells of the buccal mucosa or cultured fibroblasts. The observed secular decrease in the mosaic ratio in cultured and uncultured peripheral blood cells did not appear to be a mechanism of trisomy rescue because six adult patients with standard trisomy 21 and one patient with translocated trisomy 21 showed no decrease in trisomy cell number in cultured and uncultured peripheral blood cells over time (Table S1, the green font). Within the bone marrow, hematopoietic stem cells exist in a hypoxic microenvironment (niche) and are in a quiescent (G0), undifferentiated state.6 In this microenvironment, trisomy cells are considered more detrimental to viability than normal cells, which may explain the secular decrease in chromosomal mosaicism with mosaic DS in this study. Permission has been obtained from the patients' mothers for the participation in this study. Financial support was provided by JSPS KAKENHI (Grant number: JP18K02497). The authors declare no conflict of interest. This study has received ethical approval from Tokyo Kasei University Ethics Committee (Ita h-29-5) and the Tokyo Metropolitan Tobu Medical Center for Children with Developmental Disabilities Ethics Committee (29MoriTobuCe256-1). TABLE S1. Chromosomal analyses of the trisomy ratio of eight patients, seven with standard trisomy 21 and one translocated trisomy 21 (patient H). Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.

High-risk human papillomavirus genotype distribution among women with gynecology complaints in northwest Ethiopia

BackgroundHuman papillomavirus (HPV) genotypes differ by geographic location. With the advent of HPV vaccination and HPV-based cervical screening tests in Ethiopia, a nationwide dataset on the genotype distribution of HPV among women has paramount importance in the fight against cervical cancer. However, there is limited data in this regard in the northwest part of the country. Therefore, this study aimed to identify the genotype distribution of high-risk HPVs among women presenting with cervical abnormalities.MethodsA health facility-based cross-sectional study was conducted at Felege Hiwot Comprehensive Specialized Hospital (FHCSH), Bahir Dar–Ethiopia. Women aged ≥ 30 years who visited the hospital gynecology unit from 01 March 2019 to 30 October 2021 were included. Following general and pelvic examinations, a senior gynecologist collected cervical punch biopsies for histopathological examinations and cervical swabs for HR-HPV detection using the Abbott Alinity m system (Abbott Molecular, Des Plaines, IL, USA). Extended genotyping was carried out with the INNO-LiPA HPV Genotyping Extra II assay (INNO-LiPA; Fujirebio Europe, Ghent, Belgium) as per the manufacturer protocols at the Institute of Virology, Leipzig University Hospital, Germany.ResultsWe included 355 women with a mean age of 46.4 ± 11.4 years. The majority of the participants, 277 (79.4%) were sexually active before the age of 18 years and 180 (51.6%) had multiple sexual partners. Forty-eight (13.5%) of the participants were HIV positive. The proportion of HR-HPV was 53.0% (n = 188; 95%CI: 47.8–58.1%). From these samples, 13 different HR-HPV types with a total of 258 sequences were identified. The detection of HR-HPV increased significantly with an increase in the age of the participants. The predominant identified HR-HPV was HPV16, 50.4% followed by HPV31 (9.7%), HPV33 (8.5%), HPV39, and HPV68 each (5.8%) and HPV18 (4.7%). Of the total HR-HPV-positive women, 23.9% (45/188) were infected with multiple HR-HPV types. All HPV16, HPV18, HPV35, and HPV45 genotypes (as a single or in coinfections) were found to be associated with either high-grade lesions or cervical cancer.ConclusionsHR-HPV infection was reportedly higher among women in the present study area. Based on our findings, we strongly recommend the nonavalent HPV vaccine for immunization and any HPV-based screening method to take into consideration the predominant genotypes circulating in the country. The role of multiple HPV infections in high-grade cervical lesions entails further study in Ethiopia.

1248. Relationship Between ALT and New HBV Biomarkers in HBV/HIV Coinfected Persons Started on Antiviral Therapy

Abstract Background While HBV DNA has served as a primary biomarker of HBV infection, newer biomarkers including pre-genomic HBV RNA (pgRNA) and quantitative HBV surface antigen (qHBsAg) may prognosticate treatment responses better. We analyzed the changes in these biomarkers over time following initiation of antiviral therapy in persons living with HIV (PLWH) to determine the relationship to ALT, a key marker of liver injury. FigureBiomarker changes Methods NIH AIDS Clinical Trials Group Study 5127 enrolled HBV/HIV PLWH into a Phase 2 treatment trial that randomized them to receive 48 weeks of either tenofovir (TDF) or adefovir (ADV). ALT and HBV DNA were evaluated as measures of treatment response. Stored samples were tested for HBV pgRNA and qHBsAg at baseline, 4, 12, 24, 36, and 48 weeks. HBV pgRNA was isolated using RNA-selective extraction chemistry followed by a multiplex RT-qPCR that targets the HBV X and core targets on the m2000 system (Abbott Molecular, Des Plaines, Illinois). A sensitive second-generation assay with a lower limit of quantification (LLOQ) of 10 copies/mL was utilized. Quantitative HBsAg was determined by Abbott ARCHITECT (List# 6C36) with a LLOQ of 0.05 IU/mL. Data were analyzed using SAS® version 9.4. Results Overall, 47 study participants had sufficient samples for biomarker testing. Participants were predominantly male (93.6%) and identified as white, non-Hispanic (55.3%) or black (34%). Groups were evenly randomized to receive either TDF (n=23) or ADV (n=24). Baseline ALT mean was 64.9 U/L, and HBV DNA was 9.1 (+1.6) copies/mL. Pre-treatment pgRNA serum concentration was 7.0 (+1.3) log U/mL, and qHBsAg was 195,574 (+272,190) IU/mL. Over the course of treatment, pgRNA was significantly correlated with the change in serum ALT levels (r=0.48; p=0.0035) but not HBV DNA (r=0.21; p=0.226). ALT was negatively correlated with qHBsAg (r=-0.52; p=0.02). pgRNA was also highly negatively correlated with qHBsAg (r=-0.49l; p=0.03) but not HBV DNA (r=0.13; p=0.59). (Figure). Conclusion HBV pgRNA is a better predictor of ALT change – a key measure of hepatocyte injury – than HBV DNA in PLWH who are initiated on nucleotide/nucleoside therapy. Quantitative HBsAg is inversely associated with ALT levels, supporting the hypothesis that HBsAg inhibits immune mediated injury to hepatocytes. Disclosures Michael E. Stec, MSc, Abbott Laboratories: Employee of Abbott|Abbott Laboratories: Stocks/Bonds mark C. Anderson, PhD, Abbott Laboratories: Employment|Abbott Laboratories: Stocks/Bonds Marion G. Peters, MD, Aligos: Advisor/Consultant|antios: Advisor/Consultant|Excision Biotherapeutics: DSMB Gavin Cloherty, PhD, Abbott: Employee|Abbott: Stocks/Bonds|Abbott Labs: Employee.

183. Impact of Revised Piperacillin/Tazobactam Clinical Breakpoints on Enterobacterales Isolates Identified in Blood Cultures

Abstract Background Enterobacterales are a significant cause of bloodstream infections (BSI) in hospitalized patients. Prior evidence suggests that treatment with piperacillin/tazobactam may not be ideal for BSI. Piperacillin/tazobactam clinical breakpoints were recently updated by the Clinical and Laboratory Standards Institute (CLSI). Methods We retrospectively evaluated Enterobacterales blood isolates identified by MALDI-TOF (Vitek MS, bioMérieux) between January 1, 2017 through December 31, 2021 at Rush University Medical Center in Chicago, Illinois. Antimicrobial susceptibility testing was performed using NM43 or NM56 panels on the MicroScan WalkAway 96 (Beckman Coulter). The range of dilutions of piperacillin/tazobactam included on both panels was 8/4 to 64/4 μg/mL. Minimal inhibitory concentrations (MIC) were interpreted using current CLSI breakpoints. Results We evaluated 1597 Enterobacterales isolates. Most isolates identified were Escherichia coli [n=806 (50%)] and Klebsiella pneumoniae [n=358 (22%)]. The majority of isolates (90.4%) were susceptible; 28 (1.8%) isolates were susceptible-dose dependent and 125 (7.8%) were resistant to piperacillin/tazobactam using the new CLSI breakpoints (Table). 236 isolates had a multidrug-resistant phenotype, of which 216 (92%) were confirmed as an ESBL. Among ESBL-producing isolates, the majority (81%) were susceptible [MIC ≤ 8 µg/mL) to piperacillin/tazobactam. Isolates with confirmed carbapenemase production had off-scale MICs ( > 64 µg/mL) (Figure). Piperacillin/Tazobactam Breakpoint Revision Table Overall changes in piperacillin/tazobactam interpretations using revised breakpoints. MDR-Enterobacterales piperacillin/tazobactam MIC distributions Piperacillin/tazobactam minimal inhibitory concentration distributions among multidrug-resistant Enterobacterales isolates. Conclusion While there was an increase in resistance, our results indicate that most Enterobacterales isolates tested susceptible to piperacillin/tazobactam using the revised CLSI breakpoints. Disclosures Nicholas M. Moore, PhD, D(ABMM), Abbott Molecular: Grant/Research Support|Cepheid: Grant/Research Support.

403. Strain Epidemiology of Clostridioides difficile across Three Geographically Distinct Medical Centers in Chicago

Abstract Background Clostridioides difficile infections (CDI) are caused by a large and diverse group of strains with differences in prevalence and associated morbidity. Over the past 20 years the C. difficile (CD) molecular epidemiology has changed as the prevalence of the epidemic strain recognized as restriction endonuclease analysis (REA) group BI or PCR-Ribotype group (RT) 027 has decreased. The objective of this study was to determine the current epidemiology of CD in the city of Chicago. Methods Baseline characteristics and symptoms were compared for 81 patients who tested positive for CD by PCR (tcdB) between 9/1/2021 and 10/7/2021 at 3 hospitals in the city of Chicago. Patients were classified as having healthcare-associated CDI (HA-CDI) if symptoms began >72 hours after hospital admission, community-associated CDI (CA-CDI) if symptoms began ≤72 hours prior to admission, and community-onset healthcare-associated CDI (COHA-CDI) if they had been hospitalized ≤4 weeks prior to CDI diagnosis. Available stools were cultured and recovered CD isolates underwent REA typing. Determination of CD colonization was made by review of symptoms including chronicity of symptoms, stool frequency, and response to treatment. Results Among all patients, 33% (27/81) were CA-CDI, 28% (23/81) COHA-CDI, 11% (9/81) HA-CDI, and 27% (22/81) were classified as colonized. Primary CDI accounted for 66% (39/59) of the infections. Among patients with a primary CDI, 46% (18/39) of patients were classified as CA-CDI whereas COHA-CDI and HA-CDI accounted for 54% (21/39) of infections. REA group Y was the most common group strain accounting for 29% (22/75) of isolates. (Figure 1) REA group Y accounted for 26% (7/27) of CA-CDI compared to 0 REA group BI [p=0.06], and REA group Y accounted for 35% (7/20) of all colonized patients. (Figure 2) Figure 1Figure 2 Conclusion There has been a marked change in the CD epidemiology within the city of Chicago since 2009 when REA group BI accounted for 61% of CDI (Black et al ICHE 2011; 32:897-902). REA group Y (typically identified as RT 014/020) is now the most common group strain in Chicago supplanting REA group BI (RT027). REA group Y appears to be associated primarily with CA-CDI and CD colonization. A detailed genomic analysis of REA group Y is required to determine potential reservoirs of REA group Y. Disclosures Mary K. Hayden, MD, Sanofi: Member, clinical adjudication panel Nicholas M. Moore, PhD, D(ABMM), Abbott Molecular: Grant/Research Support|Cepheid: Grant/Research Support Amanda Harrington, PhD, Beckman Coulter, Inc.: Clinical trial data collection funded by Beckman Coulter, Inc.|bioMeriuex/BioFire: Grant/Research Support Dale N. Gerding, MD, Destiny Pharma plc.: Advisor/Consultant Stuart Johnson, M.D., Ferring Pharmaceuticals: Membership on Ferring Publication Steering Committee|Ferring Pharmaceuticals: Employee|Summit Plc: Advisor/Consultant.

2001. Clinical management changes after positive multiplex gastrointestinal pathogen panel testing for evaluation of diarrhea

Abstract Background IDSA guidelines for diarrhea include pathogen-specific management. Compared to non-molecular tests, multiplex gastrointestinal pathogen panels (GIPPs) may allow for more timely and cost-effective diagnoses and care. However, this has yet to be definitively demonstrated. Our objective was to determine the impact of positive GIPP results on clinical management, including antimicrobial use. Methods We performed a retrospective study of patients with diarrhea and a positive GIPP result (xTAG Gastrointestinal Pathogen Panel, Luminex) at an academic, tertiary-care medical center from January-December 2018. We excluded immunocompromised patients (solid organ or stem cell transplant, HIV with absolute CD4 count < 200 cells/µL, primary immunodeficiency, and immunosuppressive medications including biologics). We collected patient and clinical data via electronic medical record review. Our primary outcome of interest was change in antimicrobial usage. Results A total of 2,333 GIPP tests were performed of which 266 (11.4%) were positive. Of 193 patients who met inclusion criteria, 34% were tested in an emergency room, 38% in outpatient clinics, and 29% on inpatient wards. Of these, 55% were men, 65% were white, and the median age was 31 years (interquartile range, IQR 5-56). The median turnaround time from GIPP collection to result was 31 hours (IQR 24-53). The most frequently identified pathogens were norovirus, Salmonella, and Campylobacter (Figure 1). In 43% of patients, results led to one or more management changes including antibiotic discontinuation (8%) and antibiotic initiation (25%). Antibiotics were most often discontinued for norovirus (Figure 1A) and started for Campylobacter (Figure 1B). Other management changes occurred in 13% of patients, including avoidance of further diagnostic testing and isolation precaution change. The median turnaround time did not differ for GIPPs that were (30 hours; IQR 22-50) or were not (32 hours; IQR 25-56) associated with management change. Conclusion Positive GIPP results can prompt changes in antimicrobial treatment in non-immunocompromised patients with diarrhea. Future efforts will evaluate the appropriateness of these management changes. Disclosures Melissa B. Miller, PhD, Abbott Molecular: Grant/Research Support|Agena Biosciences: Board Member|ArcBio: Grant/Research Support|Cepheid: Board Member|Luminex Molecular Diagnostics: Board Member|QIAGEN: Board Member|QIAGEN: Grant/Research Support|Sherlock Biosciences: Advisor/Consultant|Talis Biomedical: Board Member|Thermo Fisher: Honoraria|Werfen: Board Member.

1916. Evaluation of nasal swab collection methods on a university campus during the SARS-CoV-2 pandemic

Abstract Background Characterizing SARS-CoV-2 outbreaks on university campuses is critical for informed public health measures and understanding transmission dynamics. Figure 1.Dropbox and Kiosk Samples Collected September 10, 2021 to April 23, 2022. Methods Faculty, staff, and students at a major public university in Seattle, WA, USA were enrolled in a COVID-19 testing study. Individuals could test using observed self-swabs at on-campus kiosks or unobserved self-swabs using a kit and returning it to a dropbox on campus. Sample collection volume for observed self-swabs was limited by staffing and space. All samples were returned to the laboratory and tested for SARS-CoV-2 by qRT-PCR. Results From September 10, 2021 to April 23, 2022, 38,400 individuals were enrolled in the study. Of these individuals, 5,089 used dropboxes only, 14,421 used kiosks only, and 5,820 used both. A total of 21,653 dropbox swabs and 75,493 observed self-swabs were collected. Median age was similar between individuals using dropboxes and observed self-swabs (20 vs. 22 years). A greater proportion of dropbox users were students compared to faculty and staff (students made up 83% of dropbox only population, 75% of kiosk only, and 86% of both, χ² p-value< 0.0001). Symptom data was reported for 65,349 swabs. Dropbox users were less likely to have symptoms compared to observed self-swab users (24% of swabs vs. 54%, χ² p-value< 0.0001). SARS-CoV-2 positivity was slightly lower for dropboxes compared to kiosks (4% vs. 5%; p=0.001). Dropboxes were highly utilized during periods of increased testing demand, including after academic breaks and variant emergence (Figure 1). Of the total tests distributed for use, a greater proportion of dropbox kits were unable to be resulted (6%) compared to observed self-swab kits (0.02%). Conclusion Dropboxes provided a flexible, high-volume collection method at times of increased testing demand. Individuals who used dropboxes were less likely to report symptoms and slightly less likely to test positive, suggesting a role for dropbox utilization in high-risk asymptomatic individuals during periods of high community transmission on a university campus. Disclosures Geoffrey S. Gottlieb, MD, PhD, Abbott Molecular Diagnostics: Grant/Research Support|Alere Technologies: Grant/Research Support|BMGF: Grant/Research Support|BMS: Grant/Research Support|Cerus Corp.: Grant/Research Support|Gilead Sciences: Grant/Research Support|Janssen Pharmaceutica: Grant/Research Support|Merck & Co: Grant/Research Support|Roche Molecular Systems: Grant/Research Support|THERA Technologies/TaiMed Biologics: Grant/Research Support|ViiV Healthcare: Grant/Research Support Helen Y. Chu, MD, MPH, Cepheid: Reagents|Ellume: Advisor/Consultant|Gates Ventures: Grant/Research Support|Merck: Advisor/Consultant|Pfizer: Advisor/Consultant.

Comparison of ROS1-rearrangement detection methods in a cohort of surgically resected non-small cell lung carcinomas

Patients with non-small cell lung cancer (NSCLC) harboring a ROS proto-oncogene 1 (ROS1)-rearrangement respond to treatment with ROS1 inhibitors. To distinguish these rare cases, screening with immunohistochemistry (IHC) for ROS1 protein expression has been suggested. However, the reliability of such an assay and the comparability of the antibody clones has been debated. Therefore we evaluated the diagnostic performance of current detection strategies for ROS1-rearrangement in two NSCLC-patient cohorts. Resected tissue samples, retrospectively collected from consecutive NSCLC-patients surgically treated at Uppsala University Hospital were incorporated into tissue microarrays [all n=676, adenocarcinomas (AC) n=401, squamous cell carcinomas (SCC) n=213, other NSCLC n=62]. ROS1-rearrangements were detected using fluorescence in situ hybridization (FISH) (Abbott Molecular; ZytoVision). In parallel, ROS1 protein expression was detected using IHC with three antibody clones (D4D6, SP384, EPMGHR2) and accuracy, sensitivity, and specificity were determined. Gene expression microarray data (Affymetrix) and RNA-sequencing data were available for a subset of patients. NanoString analyses were performed for samples with positive or ambiguous results (n=21). Using FISH, 2/630 (0.3% all NSCLC; 0.5% non-squamous NSCLC) cases were positive for ROS1 fusion. Additionally, nine cases demonstrated ambiguous FISH results. Using IHC, ROS1 protein expression was detected in 24/665 (3.6% all NSCLC; 5.1% non-squamous NSCLC) cases with clone D4D6, in 18/639 (2.8% all NSCLC; 3.9% non-squamous NSCLC) cases with clone SP384, and in 1/593 (0.2% all NSCLC; 0.3% non-squamous NSCLC) case with clone EPMGHR2. Elevated RNA-levels were seen in 19/369 (5.1%) cases (Affymetrix and RNA-sequencing combined). The overlap of positive results between the assays was poor. Only one of the FISH-positive cases was positive with all antibodies and demonstrated high RNA-expression. This rearrangement was confirmed in the NanoString-assay and also in the RNA-sequencing data. Other cases with high protein/RNA-expression or ambiguous FISH were negative in the NanoString-assay. The occurrence of ROS1 fusions is low in our cohorts. The IHC assays detected the fusions, but the accuracy varied depending on the clone. The presumably false-positive and uncertain FISH results questions this method for detection of ROS1-rearrangements. Thus, when IHC is used for screening, transcript-based assays are preferable for validation in clinical diagnostics.

Unexpectedly High Prevalence of iAMP21 in Children with Acute Lymphoblastic Leukemia in Mexico: A Report from the "Mexico in Alliance with St. Jude” (MAS) Collaborative Group

Keywords: acute lymphoblastic leukemia, intra-amplification of chromosome 21, genetic characterization. Mexico in Alliance with St. Jude (MAS) has carried out a multi-center collaboration for children with acute lymphoblastic leukemia (ALL) in Mexico since 2019. The "Bridge Project” has granted access to diagnostic tests that allow genetic characterization of children with ALL in participating centers. The Molecular Genetics Laboratory of Hospital Infantil Teleton de Oncologia (HITO) serves as the referral laboratory. 253 newly diagnosed ALL patients from 5 hospitals in Mexico have utilized a comprehensive diagnostic panel that includes cytogenetic and molecular tests to identify relevant abnormalities. iAMP21 is recognized by the 2017 World Health Organization (WHO) Classification of Tumors of Hematopoietic and Lymphoid Tissues as a characteristic genetic alteration of B-lineage Leukemia/Lymphoma, with a reported incidence of up to 2-5%. It involves amplification of the RUNX1 gene and/or duplication of chromosome 21 dup(21q), and defines a relatively new cytogenetic subgroup in B-lineage ALL with poor prognosis, derived from the genetic instability of chromosome 21.The heterogeneity of iAMP21 contributes to the difficulty in its detection with the sole use of conventional cytogenetic techniques, rendering Fluorescent In Situ Hybridization (FISH) as a better strategy for the distinction between iAMP21 (amplification in tandem) and the sporadic gain of copies of the RUNX1 gene. METHODS: We performed a comprehensive diagnostic panel for 253 patients with ALL; the FISH B-cell lymphoid panel included (KMT2A, ETV6 (TEL)/RUNX1 (AML1), BCR/ ABL, E2A/(TCF3)/(PBX1) and the T-cell lymphoid panel included (MLL, BCR / ABL, E2A / (TCF3) / (PBX1), TLX1, TLX3, CDKN2A and TRA / D). Diagnosis of iAMP21 was made using the interphase FISH technique with the LSI ETV6/RUNX1 (Vysis®) double color double fusion probe (Abbott Molecular®, Ill), and Cytocell probe (OGT Company®, NY). A finding of ≥ 5 RUNX1 gene signals in interphase FISH and/or more than 3 signals within chromosome 21 was considered positive for the identification of iAMP21. Samples were processed according to the specifications to the AGT Cytogenetics Laboratory Manual. FISH analysis was performed by analyzing 200 interphase cells. When ETV6/ RUNX1 probes are used, samples of patients carrying iAMP21 usually show two normal copies of the ETV6 signal and multiple RUNX1 signals (three or more additional signals) and are negative for the ETV6-RUNX1 fusion gene. RESULTS: Among 253 patients with ALL, 233 cases were of lineage B (92%) and 20 (8%) were of lineage T. FISH was reported negative in 57 (23%) and positive in 185 (73%) cases, 11 results were not available (4.3%). We detected iAMP21 in 28 (11%); these cases were classified as high risk. We also report t(12;21) in 41 (16%), MLL gene disruption t(4;11) in 10 (4%), t(1;19) in 14 (6%), and t(9;22) in 7 (3%); 75 (30%) patients had nonspecific genetic gains. The T lineage showed CDKN2A del(9)(p21) in 6 (2.5%) and TRA/D(14)(q11.2) rearrangement in 4 (1.7%) cases. CONCLUSION: Our experience shows that FISH analysis with the ETV6/RUNX1 probe is useful for identifying iAMP21, a chromosomal abnormality with prognostic significance. Genetic risk factors in the Hispanic population that adversely impact survival in Latin America are not yet fully identified. The Molecular genetic analysis and the fluorescence in situ hybridization (FISH) technique are the basic methods used to detect the presence of the most common genetic abnormalities, the presence or absence of which has an impact on the patient's classification into the appropriate risk group. Our findings from this cohort point to an increased prevalence of iAMP21 in ALL patients in Mexico. We will soon incorporate gene sequencing to the diagnostic panel and improve the characterization of these patients. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Prevalence of t(11;14) Multiple Myeloma in Real-World Setting: Interim Analysis from the Medici Study

Introduction: Multiple myeloma (MM) is the second most common hematologic malignancy characterized by bone marrow infiltration by monoclonal plasma cells (PC). Several well-defined genetic abnormalities have been identified as relevant with the disease. Although novel therapies have improved overall survival most patients with MM will eventually relapse or become refractory (RR). Therefore, there is an emerging need for better therapeutic regimens including personalized medicine based on specific biomarkers. Venetoclax (Ven) is a selective and potent oral B-cell lymphoma-2 (BCL-2) inhibitor that has shown significant antimyeloma activity in patients with t(11;14) RRMM (Kumar et al. Blood 2017; 130 (22): 2401-2409). In the phase 3 BELLINI (NCT02755597) study, patients with t(11;14) RRMM showed improved response rates and progression-free survival when treated with Ven in combination with bortezomib and dexamethasone compared to placebo-bortezomib-dexamethasone (Kumar et al. Lancet Oncol. 2020; 21:1630-1642). These results suggest that t(11;14)-based selection of patients with MM may represent a potential biomarker for venetoclax-based treatment regimens. An ongoing phase 3 study, CANOVA (NCT03539744), is evaluating the combination of Ven and dexamethasone in patients with t(11;14) RRMM compared to standard of care pomalidomide-dexamethasone (Mateos et al. J Clin Oncol 2020; 38: no. 15_suppl) . Understanding the prevalence of t(11;14) MM in a real-world setting will provide important insights for targeted therapy in this patient subpopulation. Therefore, the MEDICI study was designed to evaluate the real-world prevalence of t(11;14) as detected by interphase fluorescence in situ hybridization (FISH) technology in patients with MM. Methods: MEDICI (NCT04721002) is an ongoing, prospective, multicenter minimally interventional study. The primary objective is to determine the prevalence of t(11;14) in both newly diagnosed (ND) and RRMM as determined by interphase FISH analysis of monoclonal bone marrow (BM) PCs. All patients (≥18 years) included in the study signed informed consent. BM aspirates (BMA) were collected as part of standard of care procedures performed at diagnosis and disease relapse. Patients with no BMA sample at the time of diagnosis or confirmation of relapse were excluded from the trial. The primary endpoint was the t(11;14) status of the earliest bone marrow sample collected at initial diagnosis or across subsequent lines of therapies. CD138-enriched BMA samples were evaluated for t(11;14) by FISH (Abbott Molecular). Results: Sixty-two patients were included at the time of the interim analysis (data cut-off 09 March 2022). Median age was 67.5 years, 51.6% were male and 95.2% were Caucasian. Patients with ECOG performance status ≤2/>2/unknown was 83.9%/8.1%/8.1%. ISS stage across patients were stage I (30.6%), stage II (22.6%), stage III (33.9%) and unknown (12.9%) respectively. Del 17p was observed in 6.5% of patients and gain of chromosome 1q in 25.8% of patients. There were 36 and 26 patients with NDMM and RRMM respectively. One patient had longitudinal samples. The overall prevalence of patients with t(11;14) MM was 30.0%, which was similar between NDMM (25.0%) and RRMM (37.5%) patients (Table). The distribution of patients across the observed t(11;14) FISH fusion (F) categories (1F/2F/≥3F) for NDMM was 33.3%/22.2%/22.2% and 44.4%/55.6%/0.0% in RRMM pts (Table). Across lines (L) of therapy, the distribution of t(11;14)+ patients were similar between 1L (25.0%) , 2L (35.7%), and 3L+ (36.4%) (Table). The distribution of t(11;14)+ patients across disease stage was also similar between stage I (31.6%), stage II (28.6%), and stage III (25.0%) respectively. There were 8 patients with unknown stage of disease, 3 among them were t(11;14)+. Conclusion: Interim analysis of MEDICI demonstrated that prevalence of t(11;14) was consistent across ND and RRMM setting and independent of line of therapy and disease stage. This study is currently ongoing, and further updates will be provided upon presentation. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal