Genotypic Testing Research Articles

Genotyping and susceptibility testing uncovers large azole-resistant Candida tropicalis clade in Alexandria, Egypt

Candida tropicalis is an emerging medically relevant Candida species. The yeast primarily causes opportunistic infections in intensive care units and is highly prevalent in tropical countries. The genetic diversity within this species is high, and nosocomial transmission has been reported. C. tropicalis genotyping of isolates from low- and middle-income countries is underrepresented when compared with that from high-income countries. Also, in Egypt, only limited genotyping has been conducted for C. tropicalis isolates, while antifungal resistance seems to increase, especially against azoles. Antifungal susceptibility testing was performed on 64 C. tropicalis isolates from ICU patients collected from multiple hospitals in Alexandria, Egypt. Genotyping by means of short tandem repeat (STR) and whole genome sequencing (WGS) single nucleotide polymorphism (SNP) analysis was performed. Using antifungal susceptibility testing, fluconazole resistance was observed in 24 isolates (38%), of which 23 harboured an ERG11 G464S substitution, previously shown to cause resistance in Candida albicans. STR genotyping showed that these 23 isolates were related, forming a distinct resistant clade. WGS SNP analysis subsequently confirmed this genetic relationship, although isolates within this clade differed in at least 429 SNPs, suggesting that these were independently introduced. Overall, STR and WGS SNP analysis of this collection indicates limited C. tropicalis nosocomial transmission in Alexandria, while the presence of this large azole-resistant C. tropicalis clade within this city hampers the treatment of intensive care unit patients.

Optimizing Antiretroviral Therapy in Heavily ART-Experienced Patients with Multi-Class Resistant HIV-1 Using Proviral DNA Genotypic Resistance Testing

Resistance to multiple antiretroviral drugs among people living with HIV (PLWH) can result in a high pill burden, causing toxicity and drug interactions. Thus, the goal is to simplify treatment regimens while maintaining effectiveness. However, former resistance analysis data may not be current or complete. The use of proviral DNA genotyping may assist in selecting appropriate treatment options. A retrospective study was carried out on individuals belonging to the Cologne HIV cohort with a resistance history to two or more antiretroviral (ARV) classes and on non-standard antiretroviral therapy (ART). Patients required former viral RNA and a recent proviral DNA resistance test to be available prior to the switch to ART. Potential discrepancies between resistance test results obtained through RNA and proviral DNA methods and the consequent virological and clinical outcomes following ART adjustments were analyzed. Out of 1250 patients, 35 were eligible for inclusion in this study. The median length of known HIV infection was 27 years, and the median duration of ART was 22 years. Of the 35 participants, 16 had received all five ARV classes. Based on proviral DNA genotyping results, ART was simplified in 17 patients. At the last follow-up examination after changing therapy, 15 patients had HIV RNA <50 copies/mL (median 202 days, range 21–636). The mean number of pills per day decreased from eight to three, and the median intake frequency decreased from two to one time/day (ranges 1–2). Our study supports the use of proviral DNA genotyping as a safe strategy for switching to simplified ART regimens. However, the lack of extensive research on the advantages of proviral DNA genotyping makes it challenging to fully assess its benefits in terms of treatment selection.

Transitioning to Dolutegravir in a Programmatic Setting: Virological Outcomes and Associated Factors Among Treatment-Naive Patients With HIV-1 in the Kilombero and Ulanga Antiretroviral Cohort in Rural Tanzania.

Virological outcome data after programmatic transition from non-nucleoside reverse transcriptase inhibitor (NNRTI)-based to dolutegravir (DTG)-based antiretroviral therapy (ART) regimens in sub-Saharan Africa (SSA) outside of clinical trials are scarce. We compared viral suppression and associated factors in treatment-naïve people living with HIV (PLHIV) starting DTG- based versus NNRTI-based ART. We compared virological suppression at 12 months, after treatment initiation in the two cohorts of participants aged ≥15 years, initiating DTG- and NNRTI-based ART. Drug resistance was assessed among participants with viremia ≥50 copies/mL on DTG. Viral suppression was achieved for 165/195 (85%) and 154/211 (73%) participants in the DTG- and NNRTI- cohorts, respectively (P = 0.003). DTG-based ART was associated with >2 times the odds of viral suppression versus NNRTI-based ART (adjusted odds ratio, 2.10 [95% confidence interval {CI}, 1.12-3.94]; adjusted risk ratio, 1.11 [95% CI, 1.00-1.24]). HIV-1 genotypic resistance testing (GRT) before ART initiation was done in 14 of 30 viremic participants on DTG, among whom nucleoside reverse transcriptase inhibitor (NRTI), NNRTI, and protease inhibitors resistance was detected in 0 (0%), 2 (14%) and 1 (7%), respectively. No resistance was found in the 2 of 30 participants with available GRT at the time of viremia ≥50 copies/mL. Virological suppression at 1 year was higher in participants initiating DTG- versus NNRTI-based ART. In those with viremia ≥50 copies/mL on DTG-based ART, there was no pretreatment or acquired resistance to the DTG co-administered NRTIs, although the number of samples tested was small.

A Novel Microfluidic Dielectrophoresis Technology to Enable Rapid Diagnosis of Mycobacteria tuberculosis in Clinical Samples

To achieve the global efforts to end tuberculosis, affordable diagnostics suitable for true point-of-care implementation are required to reach the missing millions. In addition, diagnostics with increased sensitivity and expanded drug susceptibility testing are needed to address drug resistance and to diagnose low-bacterial burden cases. The laboratory-on-a-chip technology described herein used dielectrophoresis to selectively isolate Mycobacterium tuberculosis from sputum samples, purifying the bacterial population ahead of molecular confirmation by multiplex real-time quantitative PCR. After optimization using a panel of 50 characterized sputum samples, the performance of the prototype was assessed against the current gold standards, screening 100 blinded sputum samples using characterized and biobanked sputum provided by Foundation for Innovative New Diagnostics. Concordance with culture diagnosis was 100% for smear-negative samples and 87% for smear-positive samples. Of the smear-positive samples, the high burden sample concordance was 100%. Samples were diagnosed on the basis of visual assessment of the dielectrophoresis array and by multiplex real-time quantitative PCR assay. The results described herein demonstrate the potential of the CAPTURE-XT technology to provide a powerful sample preparation tool that could function as a front-end platform for molecular detection. This versatile tool could equally be applied as a visual detection diagnostic, potentially associated withbacterial identification for low-cost screening or coupled with an expanded PCR assay for genotypic drug susceptibility testing.

Concordance between Genotypic and Phenotypic Drug-Resistant Profiles of Shigella Isolates from Taiyuan City, Shanxi Province, China, 2005 to 2016.

Antimicrobial resistance in Shigella spp. is a global public health concern. In this study, the AMR phenotypic profiles of 10 kinds of antibiotics were compared with the genotypic profiles using genomic analysis of 218 Shigella isolates from Taiyuan City, Shanxi Province, China, 2005 to 2016. Core genome Multilocus Sequence Typing (cgMLST) based on the EnteroBase Escherichia/Shigella scheme was used to obtain the genetic relatedness of Shigella isolates. Multiple-drug resistance was observed in 96.79% Shigella spp., and the resistance to antimicrobial agents varied between S. flexneri and S. sonnei. The genotypic results correlated well with the phenotypic profiles with concordance rates of 96.42% and 94.50% in S. flexneri and S. sonnei isolates, respectively, from Taiyuan City, Shanxi Province. The sensitivity and specificity of the genotypic antimicrobial susceptibility testing (AST) were 97.56% and 95.34% for S. flexneri, and 95.65% and 93.31% for S. sonnei isolates, respectively. A discrepancy of genotypic and phenotypic AST results existed in some cephalosporin- and azithromycin-resistant Shigella isolates; there were no clear resistance patterns to predict ciprofloxacin resistance. There were major discrepancies between genotypic and phenotypic AST in the genotypically resistant but phenotypically susceptible isolates. The drug-resistance patterns and essential drug-resistance genes to predict the phenotypic drug-resistant profiles were the discrepancies between S. flexneri and S. sonnei isolates. Phylogenetic analysis showed that isolates of the same cluster but with different antibiotic-resistance gene patterns occurred because of the loss or gain of antibiotic-resistance genes located in the plasmids and multidrug-resistance islands. IMPORTANCE Antimicrobial resistance in Shigella spp. has become a global public health concern. In this study, we identified the antimicrobial susceptibility testing (AST) characteristics based on genomic sequences of 218 Shigella isolates and analyzed the correlation between genotypic and phenotypic antibiotic resistance profiles of Shigella spp., especially for fluoroquinolone, macrolides, and third-generation cephalosporins. Our results show that the genotypic results correlated with the phenotypic profiles with concordance rates of 96.42% and 94.50% in S. flexneri and S. sonnei isolates, respectively. The drug-resistance patterns and essential drug-resistance genes to predict the phenotypic drug-resistant profiles of S. flexneri and S. sonnei isolates in Taiyuan city were distinct. The discrepancy between genotypic and phenotypic AST was considerable in the genotypically resistant but phenotypically susceptible isolates. The information on drug resistance and resistance genes in this study can offer more details on the prevalence of drug resistance of Shigella spp.

Treatment-emergent reverse transcriptase resistance during antiretroviral therapy with bictegravir, tenofovir alafenamide, and emtricitabine: A case series.

Bictegravir/tenofovir alafenamide/emtricitabine (BIC/TAF/FTC) is a complete regimen for the treatment of HIV with a high barrier to resistance and few reported cases of treatment failure. We present three cases of treatment-emergent resistance to nucleoside/nucleotide reverse transcriptase inhibitors (NRTIs) in patients with suboptimal treatment adherence and assess whether the resistance-associated mutations were present before BIC/TAF/FTC initiation or emerged during therapy. We used genotypic drug resistance testing by Sanger sequencing to identify emergent resistance mutations in plasma viral load specimens collected after combination antiretroviral therapy initiation in all participants. Additionally, we performed ultra-deep sequencing by Illumina MiSeq on the earliest available plasma HIV-1 viral load specimen and on any available specimens closest in time to the initiation of BIC/TAF/FTC therapy to identify low-abundance resistance mutations present in the viral quasispecies. All three participants developed NRTI resistance after prolonged exposure and incomplete adherence to BIC/TAF/FTC. The T69N, K70E, M184I, and/or T215I mutations identified in clinical samples at the time of virological failure were not present on deep sequencing of either baseline samples or samples collected before BIC/TAF/FTC initiation. Despite a generally high genetic barrier to resistance, NRTI resistance-associated mutations may emerge during therapy with BIC/TAF/FTC in the setting of suboptimal adherence.

Mortality and morbidity related to hepatitis C virus infection in hospitalized adults-A propensity score matched analysis.

The World Health Organization (WHO) aims to reduce HCV mortality, but estimates are difficult to obtain. We aimed to identify electronic health records of individuals with HCV infection, and assess mortality and morbidity. We applied electronic phenotyping strategies on routinely collected data from patients hospitalized at a tertiary referral hospital in Switzerland between 2009 and 2017. Individuals with HCV infection were identified using International Classification of Disease (ICD)-10 codes, prescribed medications and laboratory results (antibody, PCR, antigen or genotype test). Controls were selected using propensity score methods (matching by age, sex, intravenous drug use, alcohol abuse and HIV co-infection). Main outcomes were in-hospital mortality and attributable mortality (in HCV cases and study population). The non-matched dataset included records from 165,972 individuals (287,255 hospital stays). Electronic phenotyping identified 2285 stays with evidence of HCV infection (1677 individuals). Propensity score matching yielded 6855 stays (2285 with HCV, 4570 controls). In-hospital mortality was higher in HCV cases (RR 2.10, 95%CI 1.64 to 2.70). Among those infected, 52.5% of the deaths were attributable to HCV (95%CI 38.9 to 63.1). When cases were matched, the fraction of deaths attributable to HCV was 26.9% (HCV prevalence: 33%), whilst in the non-matched dataset, it was 0.92% (HCV prevalence: 0.8%). In this study, HCV infection was strongly associated with increased mortality. Our methodology may be used to monitor the efforts towards meeting the WHO elimination targets and underline the importance of electronic cohorts as a basis for national longitudinal surveillance.

Cost-effectiveness of Arg16Gly in ADRB2 pharmacogenomic-guided treatment for pediatric asthma

ABSTRACT Objectives To assess the cost-effectiveness of Arg16Gly ADRB2 pharmacogenomic testing compared with no Arg16Gly ADRB2 testing to guide the use of long-acting β2 receptor agonist (LABA) in asthma patients aged 1 to 5 years in China. Methods This economic evaluation developed a Markov model with four health states (no exacerbation, mild exacerbation, moderate-to-severe exacerbation, and death). Transition probabilities were estimated from the rate of exacerbations, the case-fatality rate of patients hospitalized for exacerbations, and natural mortality. Costs included drug costs and exacerbation management costs. Cost inputs and utilities for each health state were gained from public databases and the literatures. Costs and quality-adjusted life years (QALYs) were estimated for ten years. Deterministic and probabilistic sensitivity analyses were performed. Results In the base case analysis, in contrast to the group without the genotype test, the incremental total cost was -¥334.7, and the incremental QALY was 0.001 in the Arg16Gly ADRB2 genotyping group. Therefore, the Arg16Gly ADRB2 test group was the dominant strategy for children with asthma in China. The sensitivity analyses showed that the model was relatively stable. Conclusion Arg16Gly ADRB2 testing before using LABA is a cost-effective approach compared with no gene testing for pediatric asthma.

Distribution of alpha1 antitrypsin rare alleles in six countries: Results from the Progenika diagnostic network

BackgroundKnowledge of the frequency of rare SERPINA1 mutations could help in the management of alpha1 antitrypsin deficiency (AATD). The present study aims to assess the frequencies of rare and null alleles and their respiratory and hepatic pathogenicity.MethodsThis is a secondary analysis of a study that evaluated the viability of the Progenika diagnostic genotyping system in six different countries by analyzing 30,827 samples from cases of suspected AATD. Allele-specific genotyping was carried out with the Progenika A1AT Genotyping Test which analyses 14 mutations in buccal swabs or dried blood spots samples. SERPINA1 gene sequencing was performed for serum AAT-genotype discrepancies or by request of the clinician. Only cases with rare mutations were included in this analysis.ResultsThere were 818 cases (2.6%) carrying a rare allele, excluding newly identified mutations. All were heterozygous except for 20 that were homozygous. The most frequent alleles were the M-like alleles, PI*Mmalton and PI*Mheerlen. Of the 14 mutations included in the Progenika panel, there were no cases detected of PI*Siiyama, PI*Q0granite falls and PI*Q0west. Other alleles not included in the 14-mutation panel and identified by gene sequencing included PI*Mwürzburg, PI*Zbristol, and PI*Zwrexham, and the null alleles PI*Q0porto, PI*Q0madrid, PI*Q0brescia, and PI*Q0kayseri.ConclusionsThe Progenika diagnostic network has allowed the identification of several rare alleles, some unexpected and not included in the initial diagnostic panel. This establishes a new perspective on the distribution of these alleles in different countries. These findings may help prioritize allele selection for routine testing and highlights the need for further research into their pathogenetic role.

Clinical outcomes with frontline immunotherapy (IO) in BRAF-mutant NSCLC.

e21089 Background: Oncogenic BRAF mutations are present in approximately 4% of non-small cell lung cancers (NSCLC). They are categorized as class I, II, or III according to their effect on the MAPK pathway. Little is known about how oncogenic BRAF mutations influence tumor PD-L1 expression and response to IO. We evaluated the clinical outcomes of frontline IO among BRAF classes. Methods: We performed a retrospective analysis of patients with BR AF-mutant NSCLC from January 1, 2012 through March 30, 2020. BRAF mutations were detected using next-generation sequencing or genotyping methods. PD-L1 expression was assessed using 22C3 or SP263 assays. Patient demographics were collected through electronic medical records review. In those with advanced/metastatic disease, we captured response to anticancer therapies using standardized real-world (rw) criteria and calculated rwOS using Kaplan-Meier method with log-rank test. Results: Of all 9,004 lung cancer patients (all histologies) with genotyping testing, 79 had NSCLC and an oncogenic BRAF mutation. 52% were females, 95% had adenocarcinoma, 81% were active/former smokers, and 76% had PD-L1 ≥1%. 39 patients had class I, 24 had class II, and 16 had class III mutations. Of these, 43 patients had advanced/metastatic disease evaluable for response. Patients with class I mutations who received first-line IO trended towards improved rwOS (42.6 months) vs. frontline anti-BRAF therapy (22.7 months; p= 0.51) and chemotherapy (19.6 months; p= 0.63). Patients with non-class I mutations, also trended towards improved rwOS with frontline IO (18.8 months) compared to frontline chemotherapy (9.9 months; p= 0.25). Outcomes were better in all patients with PD-L1 levels ≥1% and ≥50% who received IO. Patients with non-class I variants tended to have shorter rwOS with IO or chemotherapy compared to those with class I mutations (Table 1). Despite an overall trend towards improved outcomes with first-line IO, results did not reach significance likely due to the limited number of evaluable patients. Conclusions: The use of frontline IO may be associated with better outcomes than frontline chemotherapy or targeted therapies in patients with BRAF-mutant NSCLC. Patients with class I mutations and/or higher tumor PD-L1 expression seem to derive the most benefit. [Table: see text]

Correlating symptoms to infectivity among vaccinated healthcare workers with COVID-19

Background: Directing COVID-19 diagnostic testing to healthcare workers (HCWs) who are likely to be infected has potential to reduce staffing shortages and decrease opportunity for in-hospital transmission; however, HCWs with COVID-19 may exhibit a range of symptoms. We assessed the burden of symptoms in relation to cycle threshold (Ct) values as a surrogate for viral shedding in vaccinated healthcare workers. Methods: We retrospectively reviewed employee health records of COVID-19–vaccinated employees who tested positive for SARS-CoV-2 between December 2020 and January 2022 at 2 academic hospital systems. We reviewed demographic data, reasons for testing including symptoms, exposure history, medical history, vaccination dates, Ct values, and genotypes when available. We compared mean Ct values between symptomatic and minimally symptomatic cases using independent sample t tests. Patients were defined as minimally symptomatic if they had no symptoms or a single symptom that is not cough, fever, or anosmia at the time of testing. Patients were defined as more symptomatic if they reported >1 symptom or cough, fever, or anosmia. Results: In total, 298 HCWs tested positive for COVID-19. Most positive cases were female (73%), white (78%), and had patient-facing roles (77%). Genotypic testing (n = 109) revealed that most genotypes belonged to the SARS-CoV-2 delta variant (AY lineages, B1.617.2). More cases were minimally symptomatic (62%) than were more symptomatic (38%). None required hospitalization during the study period. Mean Ct values (n = 141) showed no significant difference between more symptomatic and minimally symptomatic cases (19.8 vs 20.6; P = .40) (Fig. 1). Also, there was no significant difference in mean Ct value, comparing those with vaccination 90 days prior to positive (20.52 vs 19.88; P = .537). Conclusions: Our study shows no significant difference in cycle threshold values between minimally symptomatic and more symptomatic infections in vaccinated HCWs. In addition, HCWs exhibit high viral load even when infected within 90 days after vaccination. When considering whether to attend work, HCWs should be aware that mild symptoms and recent vaccination do not necessarily reflect low transmissibility and that they should follow CDC guidance regarding when to return to work.Disclosures: None

Prediction of amyloid‐beta accumulating normal cognitive elderly

AbstractBackgroundAmyloid‐β (Aβ) accumulation, a major biomarker in Alzheimer’s disease (AD), induces tau accumulation, eventually resulting in cognitive decline. However, Aβ trajectory in cognitively normal participants has not been extensively investigated, yet. Modeling of Aβ trajectory remains an important goal, as future treatments targeting Aβ are expected to be developed. In the present study, we therefore investigated whether they might be divided into the normal aging group and the pathological group with increased amyloid. We also compared the differences between the non‐accumulating group and accumulating group.MethodWe included 297 subjects from the Alzheimer’s Disease Neuroimaging Initiative database, who showed normal cognition at baseline. All subjects underwent neuropsychological test, apolipoprotein E (APOE) genotype test, brain MRI, and an average of 3.03 follow‐up 18F‐florbetapir (AV45) PET scans. The original dataset was divided by 6:4 to create a training set and a validation set. Latent Class Growth Analysis was used for statistical analysis.ResultBased on the information criterion, the model consisting of three classes was found to be the best with a high entropy of 0.979: class 1 (non‐accumulating group; n = 117, 65.7%), class 2 (accumulating group; n = 46, 25.8%), and class 3 (high accumulation group; n = 15, 8.4%) (Figure). The accumulating group had more APOE ε4 carriers and a higher tau burden than the non‐accumulating group (Table).ConclusionOur study showed that there is the heterogeneity of Aβ trajectories according to aging in the normal cognitive elderly. Heterogeneity of Aβ accumulation and early detection of accumulating group may be helpful in early diagnosis and treatment of AD.

RWD164 Real-World Prevalence of Genetic Mutations in Female Breast Cancer Patients Aged =65 Years in the US between 2014 and 2022

Genetic mutations in ERBB2, TP53, PIK3CA, BRAF, EGFR and KRAS are linked to a higher susceptibility for developing breast cancer. Thus, genetic evaluation is a critical part of patient care. This study evaluated differences in U.S. age demographics and genotype testing in a real-world population of patients with advanced breast cancer (ABC) between 2014 and 2022.

Effects of APOE genotype on amyloid PET positivity according to cognitive status and ethnicity

AbstractBackgroundAmong the various risk factors for Alzheimer disease (AD), apolipoprotein E (APOE) genotype ε4 is known to be a strong factor. On the other hand, ε2 is known to have a protective effect. It is not yet clear how amyloid positivity according to the APOE genotype differs by diagnostic criteria. Also, there were no studies showing the ethnic difference in the effects of APOE genotype on amyloid‐beta (Aβ) between American and Asian. The aim of this study was to investigate how Aβ positivity (Aβ+) according to APOE genotypes differs by ethnicity and cognition.MethodWe recruited 4,203 Korean subjects from multi‐centers in South Korea and 1,069 subjects from Alzheimer’s Disease Neuroimaging Initiative database. All subjects underwent neuropsychological tests, APOE genotype tests, and amyloid PET (FMM/FBB/AV45) scans. Subjects with the ε2/ε4 genotype were excluded due to the opposing effects of the ε4 and ε2 alleles. The degree of influence on amyloid positivity by each factor was analyzed by logistic regression.ResultThe frequency of Aβ+ in normal cognition (NC) group was higher in ADNI than in Korean group (p <0.001). Amnestic mild cognitive impairment and AD dementia (ADD) groups showed no difference in the frequency of Aβ+ between ADNI and Korean groups. Relative to APOE ε3/ε3 group, APOE ε4 carriers showed higher frequent Aβ+ regardless of cognitive status and ethnicity (Figure). ADNI and Korean groups showed APOE ε2 carriers less frequent Aβ+ in ADD but not in NC relative to APOE ε3/ε3 group.ConclusionOur findings suggested that there were no differences in effects of APOE ε4 genotype on Aβ+ between European and Korean. These findings will be helpful in predicting amyloid positivity and AD intervention according to APOE genotype and ethnicity.

Real-world experience of an in-house dihydropyrimidine dehydrogenase (DPYD) genotype test to guide fluoropyrimidine (FP) dosing at a multisite cancer hospital.

1534 Background: FPs, including 5-fluorouracil and capecitabine, are widely used to treat solid tumor malignancies like gastrointestinal (GI) cancers. One-third of patients (pts) develop severe toxicities which may lead to treatment delays or hospitalization. Toxicities can be partly due to genetic variations in DPYD. Herein, we describe the implementation of an in-house DPYD test and its impact on FP dosing at a multisite cancer hospital. Methods: This is an observational study of pts starting or continuing FP-based chemotherapy who received DPYD testing as part of routine care. Buccal swabs were collected in clinic and sent to an in-house lab for genotyping using a polymerase chain reaction-based Drug Metabolizing Enzyme assay that interrogates all 5 variants with moderate-to-strong evidence according to the Clinical Pharmacogenetics Implementation Consortium (CPIC) (c.1905+1G>A, c.2846A>T, c.1679T>G, c.1236G>A and c.557A>G). Phenotype translations and dosing were based on CPIC guidelines. Test results and dose recommendations were uploaded to the electronic medical record (EMR) and emailed to the care team. In April 2022, pre- and post-test EMR alerts were built to prompt test ordering and dose modifications. The primary objective was to evaluate the proportion of DPYD variant carriers in tested pts receiving FP. Secondarily, we evaluated turnaround time and impact on FP dosing. Results: From March 2020-December 2022, 491 pts across 14 clinics received DPYD genotyping (54% male, 74% White, 20% Black, median age 53 years). GI cancers (~50% colorectal) represented 90% of the diagnoses. The median lab turnaround time was 3 (IQR 2-6) days. Pretreatment testing was ordered in 389 (79%) pts, of which 360 (93%) had results before cycle 1. Overall, 30 pts (6.1%) were heterozygous carriers (4.9% in pretreatment and 10.8% in reactive testing groups). Variants observed were c.1236G>A (n=13), c.2846A>T (n=8), c.1905+1G>A (*2A) (n=4), c.557A>G (n=4), and c.1679T>G (*13) (n=1). FP dose was modified in 27 (90%) pts (reduced in 25, avoided in 1, discontinued in 1). Of 19 carriers with pretreatment testing, 17 (90%) received an upfront dose reduction (mean reduction 42%; 3 had subsequent dose escalations); 1 avoided FP and 1 declined chemotherapy. Of 11 carriers with reactive testing, 9 had dose reductions (mean reduction 39%) and 2 discontinued FP due to toxicity. The mean FP dose intensity at cycle 1 was 56% in pretreatment carriers, 97% in reactive carriers, and 94% in wild type pts. Conclusions: DPYD genotype-guided FP dosing is feasible at a multisite cancer hospital. In-house rapid turnaround DPYD testing identified variant carriers and resulted in treatment/dose modifications for most carriers, potentially avoiding or mitigating severe toxicities and/or hospitalization, particularly with pretreatment testing. Toxicity evaluation is ongoing.

Genetic prion diseases presenting as frontotemporal lobar degeneration: clinical features and diagnostic challenge

AbstractBackgroundElucidate the clinical and ancillary feature of genetic prion diseases (gPrDs) presenting with frontotemporal lobar degeneration (FTLD) in order to aid early identification, diagnosis, and referral for genotype testing.MethodGlobal data of gPrDs presenting with FTLD caused by prion protein gene (PRNP) mutations were collected from literature review and our records. Fifty‐one cases of typical FTLD and 136 of prion diseases admitted to our institution were included as controls. Clinical and ancillary data of the different groups were compared.ResultForty‐nine cases of gPrDs presenting with FTLD were identified, 23 of which were female. Twenty‐three mutations in PRNP have been reported to be associated with the FTLD, with P39L being the most commonly reported, seen in 4 families with 5 cases. Compared to FTLD or prion diseases, gPrDs presenting with FTLD is characterized by earlier onset age (median: 45 vs. 61/60 years) and stronger family history (81.6% vs. 27.5/13.2%). In addition, gPrDs presenting with FTLD exhibited shorter duration (median: 5 vs. 8 years), and a higher rate of clinical and ancillary features of prion diseases compared to FTLD. Compared to prion diseases, gPrDs presenting with FTLD had a longer duration of symptoms (median: 5 vs. 1.1 years), higher rates of frontotemporal atrophy (89.7% vs. 3.3%), lower rates of periodic short‐wave complexes on EEG (0% vs. 29.4%), and hyperintensity on MRI (25.0% vs. 83.0%). The frequency of the Val allele for codon 129 in PRNP carriers with FTLD was significantly higher than that reported in literature for gPrDs (33.3% vs. 19.2%).ConclusionGPrDs presenting with FTLD is characterized by early‐onset, strong family history, high frequency of the Val allele for codon 129 in PRNP. The clinical features of GPrDs presenting with FTLD is intermediate of the two distinct conditions, while the auxiliary features were closer to that of FTLD. Patients with these characteristics need to be considered for PRNP genotype testing.

HIV-1 infection in South Kivu (Democratic Republic of Congo): high genotypic resistance to antiretrovirals.

Panzi General Reference Hospital (HGR Panzi) in the Democratic Republic of Congo follows a large number of patients living with HIV-1 (PLWHIV). Although antiretrovirals (ARVs) are available, HIV-1 viral load (HIV-VL) measurement has only been implemented in the hospital since 2018. No data on ARV resistance levels and ARV dosage in plasma have yet been published for this region. We determined the prevalence of virological failure due to ARV resistance amongst patients and assessed the degree of genotypic resistance of the viral strains. We performed an HIV-VL test and determined dosage of ARVs on samples collected from 205 PLWHIV at HGR Panzi between 2017 and 2018, including 13 ARV-naive patients. Genotypic resistance testing was performed on all samples with detectable HIV-VLs, and interpreted with the Agence Nationale de Recherches sur le Sida (ANRS) 2018 algorithm. Baseline resistance to NNRTIs was found in 2 of the 13 treatment-naive individuals (15%). ARV dosage was non-optimal for 44/192 of treated patients (22.9%), with an HIV-VL ≥1000 IU/mL for 40/192 (20.8%) of them. In particular, treatment-experienced viruses presented resistance to at least one NRTI (52.5%), to at least one NNRTIs (70%) or to at least one PIs (15%). Finally, two samples contained viruses with resistance polymorphism in the integrase gene. The high level of resistance to ARVs observed during this study, mainly due to treatment compliance default, fully justifies the implementation of means for closer patient monitoring. The provision of VL tests and therapeutic education management tools in a PLWHIV follow-up remains an absolute necessity to best adapt the current treatment lines in this region.

HIV Drug Resistance among Pre-treatment Cases in Thailand: Four Rounds of Surveys during 2006-2013

In Thailand, antiretroviral therapy (ART) was initiated to treat human immunodeficiency virus infection and acquired immune deficiency syndrome (HIV/AIDS) cases using the empirical regimen with no prior genotypic test to determine drug resistance. In order to assess prevalence rate of HIV drug resistance (HIVDR) among pre-treatment cases, four rounds of survey were carried out in ART clinics, including six, eight, 33 and four ART clinics in each round during 2006-2013. For which, HIVDR testing results were available in 310, 350, 797, and 413 cases in four rounds. It was revealed that HIVDR rates among naive cases were 2.0%, 2.8%, 4.0% and 4.8%, while in experienced cases, the rates were 0, 3.3%, 11.4% and 13.9%. The rates among all cases were 1.9%, 2.9%, 4.4% and 5.6%. Resistant drugs with the highest rates among all cases in the survey round 4 were nevirapine (3.6%) and efavirenz (3.1%). The results indicated the need to continue surveillance for pre-treatment HIVDR, and posed challenges to implement activities for protecting efficacy and prolong the use of empirical first-line regimen. A strategy to apply genotyping test, in a cost-effective approach, should be considered to prepare for situation when HIVDR increases beyond a critical level.

Phenotypic and Genotypic Antimicrobial Susceptibility Testing of Chlamydia trachomatis Isolates from Patients with Persistent or Clinical Treatment Failure in Spain

The aim of this multicentre project (seven hospitals across the Spanish National Health Service) was to study the phenotypic and genotypic susceptibility of C. trachomatis to the main antimicrobials used (macrolides, doxycycline, and quinolones) in isolates from patients with clinical treatment failure in whom reinfection had been ruled out. During 2018–2019, 73 clinical isolates were selected. Sixty-nine clinical specimens were inoculated onto confluent McCoy cell monolayers for phenotypic susceptibility testing. The minimum inhibitory concentration for azithromycin and doxycycline was defined as the lowest concentration associated with an at least 95% reduction in inclusion-forming units after one passage in the presence of the antibiotic compared to the initial inoculum for each strain (control). Sequencing analysis was performed for the genotypic detection of resistance to macrolides, analysing mutations in the 23S rRNA gene (at positions 2057, 2058, 2059, and 2611), and quinolones, analysing a fragment of the gyrA gene, and searching for the G248T mutation (Ser83->Ile). For tetracyclines, in-house RT-PCR was used to test for the tet(C) gene. The phenotypic susceptibility testing was successful for 10 isolates. All the isolates had minimum inhibitory concentrations for azithromycin ≤ 0.125 mg/L and for doxycycline ≤ 0.064 mg/L and were considered sensitive. Of the 73 strains studied, no mutations were found at positions T2611C or G248T of the gyrA gene. We successfully sequenced 66 isolates. No macrolide resistance-associated mutations were found at positions 2057, 2058, 2059, or T2611C. None of the isolates carried the tet(C) gene. We found no evidence for genomic resistance in this large, clinically relevant dataset.

HIV genotyping prevalence analysis in population of Ponta Grossa

The Human Immunodeficiency Virus (HIV) has a high mutagenic degree and a high ability to integrate into the host genome, being able to create mechanisms of resistance to Antiretroviral Therapy drugs. The genotyping test is used to detect these mutations, allowing a reorganization of the therapeutic scheme and improvement of the patient's condition. The present study aimed, through the analysis of 691 medical records, to identify the prevalence of the genotyping test in the city of Ponta Grossa - Paraná, as well as the reasons why it was performed. Epidemiological findings indicated a higher prevalence of HIV in heterosexual individuals (59.04%) and men (58.61%). The prevalence of genotyping was, approximately, 10%. Of all the requests, the highest rate occurred in females, constituting 16.82% of the female sample, while in males the rate of requests was 7.44%. Regarding post-genotyping viral load, it was performed by only 5.4% of the patients (39 of the 69 who underwent the genotyping test), which reinforced the hypothesis of poor adherence to treatment as the main reason for requesting this test.