Klebsiella pneumoniae mutants resistant to ceftazidime/avibactam plus aztreonam, imipenem/relebactam, meropenem/vaborbactam and cefepime/taniborbactam.

Using modified Klebsiella pneumoniae clinical isolates, we show that ramR plus ompK36 mutation together with production of the V239G variant KPC-3 confirs resistance to ceftazidime/avibactam plus aztreonam, imipenem/relebactam and meropenem/vaborbactam, but not cefepime/taniborbactam. This is because the V239G variant does not generate collateral β-lactam susceptibility as do many other KPC-3 variants associated with ceftazidime/avibactam resistance. Additional mutation of ompK35 and carriage of a plasmid expressing the OXA-48-like carbapenemase OXA-232 was required to confer cefepime/taniborbactam resistance.

Localised community circulation of SARS-CoV-2 viruses with an increased accumulation of single nucleotide polymorphisms that adversely affect the sensitivity of real-time reverse transcription assays targeting Nucleocapsid protein

SummaryCurrently the primary method for confirming acute SARS-CoV-2 infection is through the use of molecular assays that target highly conserved regions within the viral genome. Many, if not most of the diagnostic targets currently in use were produced early in the pandemic, using genomes sequenced and shared in early 2020. As viral diversity increases, mutations may arise in diagnostic target sites that have an impact on the performance of diagnostic tests. Here, we report on a local outbreak of SARS-CoV-2 which had gained an additional mutation at position 28890 of the nucleocapsid protein, on a background of pre-existing mutations at positions 28881, 28882, 28883 in one of the main circulating viral lineages in Wales at that time. The impact of this additional mutation had a statistically significant impact on the Ct value reported for the N gene target designed by the Chinese CDC and used in a number of commercial diagnostic products. Further investigation identified that, in viral genomes sequenced from Wales over the summer of 2020, the N gene had a higher rate of mutations in diagnostic target sites than other targets, with 115 issues identified affecting over 10% of all cases sequenced between February and the end of August 2020. In comparison an issue was identified for ORFab, the next most affected target, in less than 1.4% of cases over the same time period. This work emphasises the potential impact that mutations in diagnostic target sites can have on tracking local outbreaks, as well as demonstrating the value of genomics as a routine tool for identifying and explaining potential diagnostic primer issues as part of a laboratory quality management system. This work also indicates that with increasing genomic sequencing data availability, there is a need to re-evaluate the diagnostic targets that are in use for SARS-CoV-2 testing, to better target regions that are now demonstrated to be of lower variability.

Jervell and Lange-Nielsen syndrome with novel KCNQ1 and additional gene mutations

We encountered a boy with Jervell and Lange-Nielsen syndrome (JLNS) with compound heterozygous KCNQ1 mutations, maternal Trp248Phe and a novel paternal mutation, Leu347Arg. His father showed long QT (LQT) and arrhythmia. His mother was asymptomatic with no ECG abnormalities. The proband and his father had an additional mutation (SNTA1 Thr372Met), which is reportedly related to SIDS. These results suggest that multiple gene mutations influence the phenotype of KCNQ1 mutation-related arrhythmia.

Clinicopathologic features and genomic analysis of pulmonary blastomatoid carcinosarcoma

Background:This study was designed to investigate the clinicopathologic features of pulmonary blastomatoid carcinosarcoma and explore the genomic profiles of epithelial and mesenchymal components in this tumor. Methods: Three cases of pulmonary blastomatoid carcinosarcoma were enrolled in this study. Clinicopathologic informationand prognostic data were retrospectively reviewed. Diagnostic immunohistochemistry was performed. The epithelial and mesenchymal components were microdissected to investigate the genomic profiles by performing capture-based targeted next generation sequencing. Results:The epithelial components in patient one consisted of low-grade and high-grade fetal lung adenocarcinoma. Low-grade epithelial cells showed nuclear expression of β-catenin and missense mutation of CTNNB1. The epithelial components in another two patients consisted of high-grade fetal lung adenocarcinoma/enteric adenocarcinoma. The epithelial cells showed membrane staining of β-cateninand harbored no mutation of CTNNB1. The mesenchymal components in all three tumors were composed of primitive round/spindle cells without definite differentiation and showed cytoplasmic dot positive of β-catenin and no corresponding mutation. Within a tumor, both components exhibited relatively comparable molecular profile. In patient one, 4 mutations: RB1, FAT3, PTCH1and LRP1Bwere shared by both epithelial and mesenchymal components. Epithelial component had additional mutations in BCOR, CTNNB1, CTCF, FAT1and DICER1. In patient two, 12 mutations were shared. The epithelial component had BRCA2mutation and the mesenchymal had mutations in CREBBP, ALK, DNMT3A, ASXL2, MYCN andRICTOR. Patient three had 6 shared mutations. The epithelial component had an additional mutation in KAT6Aand the mesenchymal had an additional mutation in APC. Collectively, we observed heterogeneity between epithelial and mesenchymal components of the same tumor. Conclusions:Blastomatoid carcinosarcoma showed characteristic morphology and immunophenotype.Parallel detection of genetic abnormalities in epithelial and mesenchymal components could provide further evidence for tumor differentiation, molecular targeting and differential diagnosis.

Clinicopathologic features and genomic analysis of pulmonary blastomatoid carcinosarcoma

Background: This study was designed to investigate the clinicopathologic features of pulmonary blastomatoid carcinosarcoma and explore the genomic profiles of epithelial and mesenchymal components in this tumor. Methods: Three cases of pulmonary blastomatoid carcinosarcoma were enrolled in this study. Clinic-pathologic information and prognostic data were retrospectively reviewed. Diagnostic immunohistochemistry was performed. The epithelial and mesenchymal components were microdissected to investigate the genomic profiles by performing capture-based targeted next generation sequencing. Results: The epithelial component in patient one was consistent of low-grade and high-grade fetal lung adenocarcinoma and displayed aberrant nuclear expression of β-catenin and missense mutation of CTNNB1 in its low-grade epithelial. The epithelial component in another two patients were consistent of high-grade fetal lung adenocarcinoma/enteric adenocarcinoma and harbored no mutation of CTNNB1. The mesenchymal components in all three tumors were primitive round/spindle cells in morphology without definite differentiation and showed cytoplasmic dot positive of β-catenin and no corresponding mutation. Within a tumor, both components exhibited relatively comparable molecular profile. In patient one, 4 mutations: RB1, FAT3, PTCH1 and LRP1B were shared by both epithelial and mesenchymal components. Epithelial had additional mutations in BCOR, CTNNB1, CTCF, FAT1 and DICER1. In patient two, 12 mutations were shared. The epithelial had BRCA2 mutations and the mesenchymal had mutations in CREBBP, ALK, DNMT3A, ASXL2, MYCN andRICTOR. Patient three had 6 shared mutations. The epithelial had an additional mutation in KAT6A and the mesenchymal had an additional mutation in APC. Collectively, we observed heterogeneity between epithelial and mesenchymal components of the same tumor. Conclusions: Parallel detection of genetic abnormalities in epithelial and mesenchymal components of blastomatoid carcinosarcoma could provide evidence for tumor differentiation, molecular targeting and further distinguish them from conventional pulmonary blastoma and carcinosarcoma.

Significant Impact of the Molecular Profile on the Prognosis of Patients with Myeloproliferative Neoplasms and Splanchnic Vein Thromboses

Introduction: Myeloproliferative neoplasms (MPN) are the most frequent underlying causes of splanchnic vein thromboses (SVT), including Budd-Chiari syndrome (BCS), portal, splenic and mesenteric vein thromboses. This subgroup of MPN patients with SVT (MPN/SVT) has been shown to have distinct clinical and molecular features like younger age and lower JAK2V617Fmutant allele burden (the most predominant driver mutation in MPN/SVT patients) and are often considered as early stages of MPN. However, there is no study that has investigated the contribution of NGS data to the risk stratification of these MPN/SVT patients. Main objective of this study was to evaluate the impact of the presence of additional mutations to the driver mutation in the long term outcome of MPN patients with SVT. Patients and methods: Over the past 10 years, a total of 286 patients with SVT have been referred to our center for diagnostic assessment of an underlying MPN. Among them, a diagnosis of MPN (WHO criteria) was finally made in 197. Full molecular analyses by NGS was available in 61 of these MPN/SVT patients. The molecular profiling of patients was performed using a Capture-based custom NGS panel provided by Sophia Genetics. This panel comprised the coding sequences of 36 genes involved in MPN. Bioinformatics analysis was performed by Sophia Genetics, with a detection limit of variants set at 1%. We compared (i) MPN/SVT patients to our local cohort of 1371 MPN patients without SVT with full NGS data available; (ii) MPN/SVT patients with and without additional mutation to the driver mutation. Results: Median follow-up of MPN/SVT patients was 11 years, 62% were females, 33% had BCS and 67% portal vein thrombosis (Table 1). All patients received anticoagulants and 58 (95%) a cytoreductive therapy after the diagnosis of MPN. The type of MPN was polycythemia vera in 69%, essential thrombocythemia in 25% and myelofibrosis in 6%. The driver mutation was JAK2V617F in 57 (93%), and CALR mutation in 4 patients, respectively, and no patient had MPL mutation. By NGS, an additional mutation was identified in 27 (44%) patients, while 34 patients had only the driver mutation. The most frequent additional mutations were in TET2 (23%), ASXL1 (8%), DNMT3A (7%), IDH1/2 (5%), and LNK (5%) genes. EZH2, SRSF2 and TP53 mutations were found in only 1 patient, respectively. When compared to NGS data from 1371 MPN patients, there was no significant difference in the frequency of each additional mutation, except a slightly lower incidence of ASXL1 mutations in MPN/SVT patients (8% vs 23% in MPN patients, p=0.07). Of note, MPN/SVT patients were younger at MPN diagnosis than the control MPN cohort (44 vs 61 years, p< 10-5). Clinical characteristics were not significantly different between MPN/SVT patients with and without additional mutations (Table 1), including age at SVT or at MPN diagnosis, type of MPN or type of SVT, use of cytoreductive therapy, and median follow-up (11 years in both groups). In contrast, MPN/SVT patients with additional mutations had a significantly higher median JAK2V617F mutant allele burden than those with only JAK2 mutation (34% vs 11%, p=0.003, Figure 1); and higher risk of hematological transformation to myelofibrosis or acute leukemia or death (30% vs 6%, p=0.017). Only few patients experienced recurrence of thrombosis during follow up, with no difference according to the mutational profile (3 (11%) and 6 (17%) in patients with and without additional mutations, respectively). Conclusion: This is to our knowledge the first study assessing the impact of molecular abnormalities in the long term outcome of MPN/SVT patients showing a possible prognostic role for NGS data in these patients. Our results suggest that MPN/SVT patients with only JAK2V617F mutation and a low mutant allele burden (below 50%) are at low risk of adverse hematological outcome. In contrast, NGS may identify a group of patients with additional mutations at very high long term risk of unfavorable hematological evolution (30% transformation or death after 11 years of median follow-up, that is unexpected in such a young MPN population). In this group, a disease modifying therapy like interferon or other targeted therapies should be proposed when possible to reduce this risk of transformation. Disclosures Kiladjian: Novartis: Honoraria, Research Funding; Celgene: Consultancy; AOP Orphan: Honoraria, Research Funding.

SF3B1 Mutations in AML, MDS and MDS/MPN-RS-T Are Accompanied By Different Other Gene Mutations: Impact for Targeted Treatment Studies

Introduction: Precision medicine aims at the molecular profiling of patients to specifically target gene mutations. Targeted therapies now enter leukemia treatment, e.g. by targeting FLT3-ITD or mutations in DNMT3A, TET2, IDH1/2 or JAK2. Recently, luspatercept, a fusion protein (ACE-536), was shown to inhibit different signaling cascades, resulting in differentiation and maturation of erythropoietic progenitors in anemic patients (Platzbecker et al., Haematologica 2015). Interestingly, only patients with myelodysplastic syndrome (MDS) and ring sideroblasts (RS) responded to luspatercept, suggesting SF3B1 to be a potential biomarker. Besides MDS, SF3B1 mutations occur also in acute myeloid leukemia (AML) and MDS/myeloproliferative neoplasms with RS and thrombocytosis (MDS/MPN-RS-T). However, concomitant gene mutations bearing prognostic information and/or also being therapeutic targets as well as the cytogenetic background may need to be addressed in addition before further investigation. Aim: To investigate the mutation pattern and cytogenetic background of patients with AML, MDS and MDS/MPN-RS-T carrying SF3B1 mutations. Patients and Methods: In a cohort of 365 patients - all showing SF3B1 mutations and the diagnosis of AML (n=51), MDS (n=263) or MDS/MPN-RS-T (n=51) - cytomorphology, cytogenetics and mutation status were available. The cohort comprised 145 females and 220 males, the median age was 75 yrs (range: 42-93 yrs). In all patients ASXL1, RUNX1, TP53 as important prognostic markers as well as DNMT3A, FLT3-TKD, IDH1/2, JAK2, K/NRAS and TET2 as optional targets were analysed for mutations. Furthermore, additional entity specific gene mutations were investigated in respective subcohorts (AML: CEBPA, FLT3-ITD, MLL-PTD, NPM1; MDS: ETV6, EZH2, SRSF2, U2AF1, ZRSR2; MDS/MPN-RS-T: MDS genes, CBL, MPL). Results: 73% of all patients (268/365) showed normal karyotypes. Addressing molecular genetics resulted in 370 mutations beside SF3B1 in 238 patients, leaving only 23% of patients (84/365) showing no other aberration than in SF3B1. The variant allele frequencies (VAF) of SF3B1 mutations were high in nearly all cases with only few (9/353) subclonal cases (VAF <10%). In AML the median VAF of SF3B1 was 45% (range: 5-70%) with 3 cases showing subclonal mutations, likewise in MDS with a VAF of 39% (range: 3-50%) and 6 subclonal cases, while in MDS/MPN-RS-T the VAF was also 39% (range: 15-50%) without any subclonal case. In detail, 63% of AML cases showed normal karyotypes. Looking at gene mutations revealed that 49/51 patients (96%) had additional gene mutations (median: 2, range: 0-4), while 28/51 cases (55%) showed mutations in at least one of the therapeutically relevant genes. Of note, 37/51 patients (73%) had a mutation known to be associated with adverse prognosis. Therefore, in AML just one patient had a sole SF3B1 mutation and only 3/51 cases (6%) showed only other targetable mutations beside SF3B1. In MDS 73% of patients showed normal karyotypes. MDS patients showed in median 1 additional mutation (range: 0-4), leaving 115/263 (44%) patients without additional mutations. Furthermore, 124/263 (47%) patients carried mutations in a therapeutically relevant gene, while only 32/263 cases (12%) had mutations worsening prognosis. This results in 74/263 MDS patients (28%) without any additional aberration and 85/263 patients (32%) showing only other targetable mutations beside SF3B1. Furthermore, 84% of MDS/MPN-RS-T showed normal karyotypes. In median 1 additional mutation (range: 0-7) was identified in MDS/MPN-RS-T patients, while 10/51 cases (20%) showed no additional mutation. Looking at therapeutically relevant gene mutations revealed in 39/51 patients a respective mutation, while 7/51 patients carried prognostically adverse mutations. Therefore, MDS/MPN-RS-T patients show also a high proportion of cases without additional aberration (9/51, 18%) and even 47% (24/51) of patients having only targetable gene mutations. Conclusion: 1) SF3B1 mutation is supposed to be in the main clone. 2) AML, MDS and MSD/MPN-RS-T differ in their respective patterns of molecular aberrations beside SF3B1 mutations. 3) MDS patients show most frequently SF3B1 mutations as sole abnormality and might therefore benefit best from SF3B1 targeting treatment. 4) Treatment decisions should in all cases consider additional targetable mutations but also those worsening prognosis. Disclosures Meggendorfer: MLL Munich Leukemia Laboratory: Employment. Jeromin:MLL Munich Leukemia Laboratory: Employment. Perglerová:MLL2 s.r.o.: Employment. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Kern:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Haferlach:MLL Munich Leukemia Laboratory: Other: Part Owner MLL Munich Leukemia Laboratory.

The impact of multiple low-level BCR-ABL1 mutations on response to ponatinib

Key Points The association between multiple BCR-ABL1 mutations and inferior response to nilotinib/dasatinib was not seen with ponatinib therapy. However, chronic phase patients with T315I plus additional mutation(s) did have poorer responses to ponatinib than those with T315I only.