Clonal Profiles Research Articles

Profiles of Staphyloccocus aureus isolated from goat persistent mastitis before and after treatment with enrofloxacin

BackgroundStaphylococcus aureus is one of the main causative agents of mastitis in small ruminants. Antimicrobial use is the major treatment, but there are many flaws linked to resistance, tolerance or persistence. This study aimed to verify changes in resistance, virulence and clonal profiles of S. aureus isolated from persistent mastitis goat milk before and after enrofloxacin treatment.ResultsMIC increased to at least one antimicrobial in S. aureus isolates after enrofloxacin treatment compared to before. The most detected resistance genes before and after treatment were tetK, tetM, and blaZ, with more resistance genes detected after enrofloxacin treatment (p < 0.05). Occasional variations in efflux system gene detection were observed before and after treatment. Nine virulence genes (hla, fnbA, fnbB, eta, etb, sea, sec, seh, and sej) were detected at both times, and between these, the hla and eta genes were detected more in isolates after treatment. All isolates of S. aureus belonged to the same sequence type (ST) 133, except for two S. aureus isolates prior to enrofloxacin treatment which were classified as ST5 and the other as a new one, ST4966. Isolates of S. aureus 4, 8, and 100 from before and after treatment had identical pulse types, while others obtained from other animals before and after treatment were classified into distinct pulse types.ConclusionThere were occasional changes in the studied profiles of S. aureus isolated before and after treatment of animals with enrofloxacin, which may have contributed to the permanence of bacteria in the mammary gland, even when using traditional treatment, resulting in persistent mastitis.

Antibiotic Treatment and Age Are Associated With Staphylococcus aureus Carriage Profiles During Persistence in the Airways of Cystic Fibrosis Patients.

BackgroundStaphylococcus aureus is one of the most isolated pathogens from the airways of cystic fibrosis (CF) patients. There is a lack of information about the clonal nature of S. aureus cultured from CF patients and their impact on disease. We hypothesized that patients would differ in their clinical status depending on S. aureus clonal carriage profiles during persistence.MethodsDuring a 21-months prospective observational multicenter study (Junge et al., 2016), 3893 S. aureus isolates (nose, oropharynx, and sputa) were cultured from 183 CF patients (16 German centers, 1 Austrian center) and subjected to spa-sequence typing to assess clonality. Data were associated to lung function, age, gender, and antibiotic treatment by multivariate regression analysis.ResultsTwo hundred and sixty-five different spa-types were determined with eight prevalent spa-types (isolated from more than 10 patients): t084, t091, t008, t015, t002 t012, t364, and t056. We observed different carriage profiles of spa-types during the study period: patients being positive with a prevalent spa-type, only one, a dominant or related spa-type/s. Patients with more antibiotic cycles were more likely to be positive for only one spa-type (p = 0.005), while older patients were more likely to have related (p = 0.006), or dominant spa-types (p = 0.026). Two percent of isolates were identified as methicillin-resistant S. aureus (MRSA) and evidence of transmission of clones within centers was low.ConclusionThere was a significant association of antibiotic therapy and age on S. aureus carriage profiles in CF patients indicating that antibiotic therapy prevents acquisition of new clones, while during aging of patients with persisting S. aureus, dominant clones were selected and mutations in the spa-repeat region accumulated.

Exploring and analysing single cell multi-omics data with VDJView

BackgroundSingle cell RNA sequencing provides unprecedented opportunity to simultaneously explore the transcriptomic and immune receptor diversity of T and B cells. However, there are limited tools available that simultaneously analyse large multi-omics datasets integrated with metadata such as patient and clinical information.ResultsWe developed VDJView, which permits the simultaneous or independent analysis and visualisation of gene expression, immune receptors, and clinical metadata of both T and B cells. This tool is implemented as an easy-to-use R shiny web-application, which integrates numerous gene expression and TCR analysis tools, and accepts data from plate-based sorted or high-throughput single cell platforms. We utilised VDJView to analyse several 10X scRNA-seq datasets, including a recent dataset of 150,000 CD8+ T cells with available gene expression, TCR sequences, quantification of 15 surface proteins, and 44 antigen specificities (across viruses, cancer, and self-antigens). We performed quality control, filtering of tetramer non-specific cells, clustering, random sampling and hypothesis testing to discover antigen specific gene signatures which were associated with immune cell differentiation states and clonal expansion across the pathogen specific T cells. We also analysed 563 single cells (plate-based sorted) obtained from 11 subjects, revealing clonally expanded T and B cells across primary cancer tissues and metastatic lymph-node. These immune cells clustered with distinct gene signatures according to the breast cancer molecular subtype. VDJView has been tested in lab meetings and peer-to-peer discussions, showing effective data generation and discussion without the need to consult bioinformaticians.ConclusionsVDJView enables researchers without profound bioinformatics skills to analyse immune scRNA-seq data, integrating and visualising this with clonality and metadata profiles, thus accelerating the process of hypothesis testing, data interpretation and discovery of cellular heterogeneity. VDJView is freely available at https://bitbucket.org/kirbyvisp/vdjview.

Abstract PD8-05: Single-cell analysis of breast cancer metastasis using patient-derived xenograft model reveals clonal relationship between primary tumor and its metastases

Abstract Introduction Breast cancer is the most common cancer in female and triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer which shows high rate of recurrence and metastasis. Malignant cells that comprise primary tumor are heterogeneous and during disease progression selection of tumor cells occur as a mean to adapt and survive. Tumor heterogeneity can be studied by grouping cells as clones which refer to a group of cells related to each other by descent from a unitary origin. Understanding the mechanism of clonal dynamics and selection during cancer evolution is important to develop new therapeutic strategies for cancer metastasis. Moreover, it is imperative to be able to detect rare subclones that are responsible for metastasis. Thus, single-cell analysis is critical to identify cellular heterogeneity of cancer and molecular basis of metastatic phenotype in depth. Measuring genome and transcriptome in single-cell level will enable us to discover clonal dynamics during cancer metastasis and infer molecular determinants of metastasis fitness. Here, we propose to investigate the clonal dynamics, genomic, and transcriptomic profiles of human breast tumor metastasis using TNBC patient-derived xenograft (PDX) model to understand the mechanism of breast cancer progression and metastasis. Methods Tumor cells from previously established PDXs were transplanted into mammary fat pad of mice. Tumors were removed when it reached maximum allowed endpoint size (1,000mm3) and mice were monitored and allowed to grow metastasis. PDXs that developed primary tumor and metastasis were selected for subsequent single cell analysis. Single-cell whole-genome sequencing (scWGS) was performed using direct library preparation (DLP+) method which is preamplification-free single-cell genome sequencing approach. scWGS data was used to call cell-specific copy number events, which allows us to cluster cells and identify clones. Hierarchical clustering was used to identify clonal structure of each sample. Phylogenetic tree was computed using copy number data of samples from each PDX. Results Nine different TNBC PDX lines were tested and 6 PDX lines developed metastasis. We focused on 2 PDX lines of which metastatic tissues were available for single cell sequencing. SA919 developed metastatic mass near cervical or lumbar spine area. SA535 developed metastasis to lung, axillary or inguinal area and tumor recurrence at mammary fat pad site. scWGS for SA919 and SA535 was carried out and we generated libraries from single cells of primary tumor and its metastases. Hierarchical clustering using copy number data revealed clonal structure of primary tumor and metastases. SA919 showed oligoclonal primary tumor and metastasis whereas SA535 showed polyclonal metastasis from polyclonal primary tumor. scWGS data of primary tumor and its metastases in each PDX were merged to compute phylogenetic trees. Phylogenetic analysis revealed that not all clones of primary tumor contributed to metastasis in both PDXs. Different metastatic lesions of SA535 harbored different clones from primary tumor. For example, clones consisting left axillary metastasis and right axillary metastasis in SA535 were different from each other, however they both originated from primary tumor clones. Metastatic lesions from SA919 and SA535 also had newly appearing clones that were not present in primary tumor inferring clonal evolution during metastasis. Conclusion We were able to capture different patterns of metastasis in several PDXs. Phylogenetic analysis using scWGS data revealed clonal relationship between primary tumor and metastases. Further analysis of single cell genomic and transcriptomic profiles will provide deeper understanding of metastasis in breast cancer. Citation Format: Hakwoo Lee, Farhia Kabeer, Ciara O'Flanagan, Jazmine Brimhall, Justina Biele, Biexi Wang, Teresa Ruiz Algara, So Ra Lee, Daniel Lai, Michael Yuen, Simong Song, Patricia Ye, Jenifer Pham, Richard Moore, Andy J Mungall, Sohrab P Shah, Samuel Aparicio. Single-cell analysis of breast cancer metastasis using patient-derived xenograft model reveals clonal relationship between primary tumor and its metastases [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr PD8-05.

Molecular epidemiology of clinically high-risk Pseudomonas aeruginosa strains: Practical overview.

In recent years, numerous outbreaks of multidrug-resistant Pseudomonas aeruginosa have been reported across the world. Once an outbreak occurs, besides routinely testing isolates for susceptibility to antimicrobials, it is required to check their virulence genotypes and clonality profiles. Replacing pulsed-field gel electrophoresis DNA fingerprinting are faster, easier-to-use, and less expensive polymerase chain reaction (PCR)-based methods for characterizing hospital isolates. P. aeruginosa possesses a mosaic genome structure and a highly conserved core genome displaying low sequence diversity and a highly variable accessory genome that communicates with other Pseudomonas species via horizontal gene transfer. Multiple-locus variable-number tandem-repeat analysis and multilocus sequence typing methods allow for phylogenetic analysis of isolates by PCR amplification of target genes with the support of Internet-based services. The target genes located in the core genome regions usually contain low-frequency mutations, allowing the resulting phylogenetic trees to infer evolutionary processes. The multiplex PCR-based open reading frame typing (POT) method, integron PCR, and exoenzyme genotyping can determine a genotype by PCR amplifying a specific insertion gene in the accessory genome region using a single or a multiple primer set. Thus, analyzing P. aeruginosa isolates for their clonality, virulence factors, and resistance characteristics is achievable by combining the clonality evaluation of the core genome based on multiple-locus targeting methods with other methods that can identify specific virulence and antimicrobial genes. Software packages such as eBURST, R, and Dendroscope, which are powerful tools for phylogenetic analyses, enable researchers and clinicians to visualize clonality associations in clinical isolates.

Characterisation of Campylobacter spp. Isolated from Poultry in KwaZulu-Natal, South Africa

This study investigated the antibiotic resistance, virulence profiles, and clonality of Campylobacter jejuni and Campylobacter coli isolated from an intensive poultry farming system in KwaZulu-Natal, South Africa. Following ethical approval, samples were collected over six weeks using the farm-to-fork approach. Campylobacter spp. were identified using culture, confirmed and differentiated to species level by PCR, and subjected to antibiotic susceptibility testing. Selected antibiotic resistance (and mutations) and virulence genes were screened by PCR and confirmed by DNA sequencing. Genetic relatedness amongst the isolates was ascertained using pulsed-field gel electrophoresis. In all, 105 isolates were confirmed as belonging to both Campylobacter coli (60; 57%) and C. jejuni (45; 43%). The highest resistance was recorded against erythromycin and clindamycin. The gyrA mutation, A20175C/A2074G point mutation, tet(O), and cmeB, all associated with antibiotic resistance, were detected. All the virulence genes (pldA, ciaB, cdtA, cdtB, cdtC, dnaJ, except for cadF) were also detected. Isolates were grouped into five pulsotypes displaying 85% similarity, irrespective of their resistance profiles. The numerous permutations of clonality, antibiotic resistance, and virulence profiles evident in Campylobacter spp. pose a challenge to food safety and necessitate a comprehensive understanding of the molecular epidemiology of this organism to decrease its spread in the food chain.

1437Single cell RNA sequencing reveals profound changes in monocytic cell clusters in patients with mutations associated with clonal hematopoiesis

Abstract Background Monocytes and macrophages have distinct roles in cardiovascular health where they may contribute to beneficial processes like wound healing and cardiac conductance or to pathological processes like inflammation, remodeling and fibrosis. Despite their importance, the specific signatures of circulating monocytes are missing. Single cell RNA sequencing (scRNA-seq) provides a novel opportunity to define subsets of monocytes mediating inflammation in humans. Purpose To detect and study the inflammatory burden driven by subsets of monocytes in healthy individuals and subjects with chronic ischemic heart failure (CHF) using scRNA-seq. Methods and results Circulating CD31+ cells of CHF patients (n=11) along with aged matched (n=3) and young healthy controls (n=5) were sorted and scRNA-seq then performed. Unsupervised clustering of present sequencing data revealed these cells to be comprised of 19 subpopulations (primarily monocytes). Many subpopulations of cells were comprised chiefly or solely by CHF subjects. Dysregulated genes in CHF subjects, relative to healthy controls included interleukin-1b, thrombospondin-1, S100A8 and matrix metalloprotease-1, which were confirmed by FACS and qRT-PCR in a validation cohort. Given the expanded, divergent and highly inflammatory transcriptional populations of monocytes in patients with CHF, we assessed whether occurrence of somatic mutations associated with clonal hematopoiesis of indeterminate potential (CHIP), recently shown to be increased in subjects with atherosclerosis and heart failure, might occur in these subjects. Indeed, we identified patients who revealed mutations in the DNA methyltransferase DNMT3A and other CHIP-driver genes. DNMT3A mutations were associated with changes in known DNMT3A target genes such as the pro-inflammatory genes CXCL1, CXCL2 and IL6 in circulating monocytic cells. Moreover, cell fate trajectory analysis showed shared fates of cells driven by pseudotime-dependent variables from subjects harboring DNMT3A mutations. Regulated genes in this fate were associated with cell survival, migration and inflammation, appropriate for this disease phenotype. Conclusions This is the first study to show scRNA-seq profiles of monocytes in patients with CHF. Healthy subjects displayed remarkable homogeneity in their transcriptional profiles. CHF subjects show changes in inflammatory gene expression. CHF subjects with clonal hematopoiesis share signature gene expression profiles driving similar cell fates. Subjects with CHF of ischemic origin harboring DNMT3A mutations have a worse prognosis than non-CHIP carrier CHF controls. Identification of early alterations in immune cell subsets recognized by single cell sequencing and genetic testing of CHIP mutations may detect subjects with a high risk and allow for a precision treatment of the immune disorders. Acknowledgement/Funding SFB834

Abstract LB-069: Persistence of cryopreserved tumor-infiltrating lymphocyte product lifileucel (LN-144) in C-144-01 study of advanced metastatic melanoma

Abstract Adoptive cell transfer utilizing tumor-infiltrating lymphocytes (TIL) is recognized as an effective treatment in metastatic melanoma and other solid tumors eliciting durable and complete responses in heavily pretreated patients, presumably by targeting somatic mutations specific to each tumor1. We have treated patients with anti-PD-1-refractory advanced melanoma with lifileucel and reported an overall response rate of 38%2. Here, we analyzed the composition of the initial TIL products and the T cells circulating 42 days post-infusion (D42) to uncover a potential link between clonal diversity, TIL in vivo persistence, and anti-tumor activity. Since TIL products are preparations of polyclonal autologous T cells, each T cell clone expresses a unique T cell receptor (TCR) that can be identified by its complementary determining region 3 (CDR3). CDR3 of TIL products and corresponding post-infusion peripheral blood samples were subjected to RNA-seq, using iRepertoire technology (Huntsville, AL). The average number of unique TCR CDR3 sequences (uCDR3) was 17511 [3574-110797] across TIL products, with Shannon diversity indexes varying from 2.7 to 10.8. Correlation analyses revealed no association between either parameter and clinical response, suggesting that tumor-reactive T cells may be present in low and high diversity bulk TIL products. At D42, TIL clones could be detected in the circulation of all treated patients. Numbers of Shared uCDR3 ranged from 28 to 6964 unique clonotypes and represented highly variable fractions of both the TIL product and the D42 circulating T cells. A link between Shared T cell clones and clinical response was previously hypothesized3. In this study, comparable percentages of Shared uCDR3 were detected in responders and non-responders. Importantly, the majority of Shared uCDR3 were not detected in the patients’ peripheral blood at the time of enrollment, indicating that they represented intratumoral clonotypes that persisted after TIL administration. In addition, Shared uCDR3 clones represented at either high or low frequencies in the TIL product could persist for at least 6 weeks post-infusion. Finally, more than 97% of persisting clones were uniquely present in individual responding and non-responding patients, indicating a unique repertoire in each TIL preparation. Overall, the data demonstrate that a fraction of TIL clones persisted in all patients. The uniqueness of the clonal profiles associated with response highlights the challenge of identifying a single TCR as mediator of activity and supports using a polyclonal product such as bulk TILs to treat solid tumors with their associated unique, patient-specific, mutational and neoantigen spectra. 1 Rosenberg et al. CCR 2011; 2 SITC Nov2018; 3 Robbins et al. J Immunol 2004 Citation Format: Viktoria Gontcharova, Sam Suzuki, Michelle R. Simpson-Abelson, Michelle Blaskovich, Cécile Chartier. Persistence of cryopreserved tumor-infiltrating lymphocyte product lifileucel (LN-144) in C-144-01 study of advanced metastatic melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-069.

Multidrug‐resistant enterotoxigenicStaphylococcus aureuslineages isolated from animals, their carcasses, the personnel, and the environment of an abattoir in Greece

This study investigated genetic relatedness among Staphylococcus aureus from livestock, their carcass’ surfaces after slaughter, personnel, and equipment of a Greek abattoir. Genotyping was performed using PFGE, MLST, spa, and SCCmec. Antimicrobial susceptibility was determined according to EUCAST guidelines. Genes encoding staphylococcal enterotoxins (SEs) and Panton-Valentine leukocidin (PVL) were detected by PCRs. From 392 samples, 46 S. aureus were recovered, 10 from workers, 6 from animals, 10 from carcass’, and 20 from equipment’s surfaces. Resistance to tetracycline was 80.4%, whereas, 58.7% of isolates were multi-drug resistant. Eleven isolates (23.9%) were MRSA, 8 mecA- and 3 mecC-positive. Fifteen PFGE and 13 spa types were identified, classified in 10 sequence types (STs). ST80 predominated among MSSA, and ST88-IV clone among MRSA. Fifteen strains (32.6%) carried enterotoxin genes 7 of them possessed also the PVL genes. The abattoir seems to play important role in the transmission of S. aureus between animals and humans. Practical applications Antibiotic susceptibility, clonality, and toxin profiles among Staphylococcus aureus recovered from humans, animals, resulting carcasses and environmental surfaces of an abattoir were assessed. Our results showed spread of multi-resistant toxigenic strains belonging to human and animals’ origin clones, indicating that the abattoir might be the reservoir for their transmission with potential negative impact on consumers’ health. The establishment and implementation of strict hygiene rules in the farms and during the slaughtering process in the abattoirs could control spread of virulent S. aureus strains.

An epidemiological and molecular study regarding the spread of vancomycin-resistant Enterococcus faecium in a teaching hospital in Bogot\xe1, Colombia 2016

BackgroundEnterococcus faecium is ranked worldwide as one of the top ten pathogens identified in healthcare-associated infections (HAI) and is classified as one of the high priority pathogens for research and development of new antibiotics worldwide. Due to molecular biology techniques’ higher costs, the approach for identifying and controlling infectious diseases in developing countries has been based on clinical and epidemiological perspectives. Nevertheless, after an abrupt vancomycin-resistant Enterococcus faecium dissemination in the Méderi teaching hospital, ending up in an outbreak, further measures needed to be taken into consideration. The present study describes the vancomycin-resistant Enterococcus faecium pattern within Colombian’s largest installed-bed capacity hospital in 2016.MethodsThirty-three vancomycin-resistant Enterococcus faecium isolates were recovered during a 5-month period in 2016. Multilocus variable-number tandem-repeat analysis was used for molecular typing to determine clonality amongst strains. A modified time-place-sequence algorithm was used to trace VREfm spread patterns during the outbreak period and estimate transmission routes.ResultsFour clonal profiles were identified. Chronological clonal profile follow-up suggested a transitional spread from profile “A” to profile “B”, returning to a higher prevalence of “A” by the end of the study. Antibiotic susceptibility indicated high-level vancomycin-resistance in most isolates frequently matching vanA gene identification.DiscussionTransmission analysis suggested cross-contamination via healthcare workers. Despite epidemiological control of the outbreak, post-outbreak isolates were still being identified as having outbreak-related clonal profile (A), indicating reduction but not eradication of this clonality. This study supports the use of combined molecular and epidemiological strategies in an approach to controlling infectious diseases. It contributes towards a more accurate evaluation of the effectiveness of the epidemiological measures taken regarding outbreak control and estimates the main cause related to the spread of this microorganism.

Clonality and genetic profiles of drug-resistant Mycobacterium tuberculosis in the Eastern Cape Province, South Africa.

In this study, we investigated the diversity of drug‐resistant Mycobacterium tuberculosis isolates from families who own cattle in the Eastern Cape Province of South Africa using spoligotyping and mycobacterial interspersed repetitive‐unit‐variable number tandem repeat (MIRU‐VNTR) typing. The Mycobacterium tuberculosis was investigated using MIRU‐VNTR and the Mycobacterium tuberculosis families were evaluated using spoligotyping. Spoligotyping grouped 91% of the isolates into seven clusters, while 9% of the deoxyribonucleic acid (DNA) from TB isolates were unclustered from a total of 154 DNA used. Previously described shared types were observed in 89.6% of the isolates, with the Beijing family, SIT1, the principal genotype in the province, while the families T, SIT53 and X1, SIT1329 were the least detected genotypes. MIRU‐VNTR grouped 81% of the isolates in 23 clusters while 19% were unclustered. A combination of the VNTR and spoligotyping grouped 79% of the isolates into 23 clusters with 21% unclustered. The low level of diversity and the clonal spread of drug‐resistant Mycobacterium tuberculosis isolates advocate that the spread of TB in this study may be instigated by the clonal spread of Beijing genotype. The results from this study provide vital information about the lack of TB control and distribution of Mycobacterium tuberculosis complex strain types in the Eastern Cape Province of South Africa.

Molecular Characteristics and Antimicrobial Resistance of Group B Streptococcus Strains Causing Invasive Disease in Neonates and Adults.

We aimed to analyze the molecular characteristics, clonality and antimicrobial resistance profiles of group B streptococcus (GBS) isolates collected in Taiwan from invasive diseases and carriage. Multilocus sequence typing (MLST) was used to assess the genetic diversity of 225 GBS strains from neonates and adults with invasive GBS diseases. 100 GBS strains collected from colonized pregnant women during the same period were compared, and all strains were characterized for one of nine capsule genotypes. We also determined the susceptibilities of all GBS isolates to various antimicrobial agents. The most frequently identified serotypes that caused invasive disease in neonates were III (60.6%) and Ia (17.3%), whereas type VI (32.7%), Ib (19.4%), and V (19.4%) were the most common to cause invasive disease in adults. Serotype VI was the leading type that colonized pregnant women (35.0%). Twenty-six sequence types (STs) were identified, and 90.5% of GBS strains were represented by 6 STs. ST-17 and ST-1 were more prevalent in invasive diseases in neonates and adults, respectively. The majority of serotype III and VI isolates belonged to clonal complex (CC)-17 and CC-1, respectively. ST-17 strains were more likely to cause meningitis and late-onset disease than other strains. In addition, ST-12 and ST-17 GBS strains showed the highest rate of resistance to erythromycin and clindamycin (range: 75.8–100%). In conclusion, CC-17/type III and CC-1/type VI are the most important invasive pathogens in infants and non-pregnant adults in Taiwan, respectively. GBS genotypes vary between different age groups and geographical areas and should be considered during GBS vaccine development.

Immune and genomic correlates of response to anti-PD-1 immunotherapy in glioblastoma.

Immune checkpoint inhibitors have been successful across several tumor types; however, their efficacy has been uncommon and unpredictable in glioblastomas (GBM), where <10% of patients show long-term responses. To understand the molecular determinants of immunotherapeutic response in GBM, we longitudinally profiled 66 patients, including 17 long-term responders, during standard therapy and after treatment with PD-1 inhibitors (nivolumab or pembrolizumab). Genomic and transcriptomic analysis revealed a significant enrichment of PTEN mutations associated with immunosuppressive expression signatures in non-responders, and an enrichment of MAPK pathway alterations (PTPN11, BRAF) in responders. Responsive tumors were also associated with branched patterns of evolution from the elimination of neoepitopes as well as with differences in T cell clonal diversity and tumor microenvironment profiles. Our study shows that clinical response to anti-PD-1 immunotherapy in GBM is associated with specific molecular alterations, immune expression signatures, and immune infiltration that reflect the tumor's clonal evolution during treatment.

Abstract IA34: Mapping immune recognition of non-self neoantigens in human pancreatic cancer

Abstract Endogenous T-cell responses to cancer-specific mutations (neoantigens) are a common denominator of successful immunotherapies. However, endogenous neoantigen-specific T cell immunity in immunotherapy refractory tumors remains poorly characterized. Pancreatic ductal adenocarcinoma (PDAC) is the prototypical immunotherapy refractory cancer: response rates to single-agent checkpoint blockade are &amp;lt;2%, and 5-year survival with conventional therapies remains &amp;lt;7%. In these rare 7% of PDAC patients that survive &amp;gt; 5 years, T cell immunity has been linked to their exceptional outcome however the relevant antigens remained unknown. We sought to identify the landscape, antigenic potential, and T cell functional states induced by neoantigens in rare long-term pancreatic cancer survivors. Using genetic, immunologic, and computational techniques, we recently reported that tumors with the highest predicted neoantigen number and the greatest density of CD3+CD8+ infiltrates together, but neither parameter alone, could identify long-term survivors, suggesting differential inherent neoantigen immunogenicity. To investigate the specific neoantigen qualities promoting differential immunogenicity, we developed a fitness model that quantifies neoantigen immunogenicity based on estimations of the relative MHC binding affinity of each neoantigen to its wild type counterpart, as well as a nonlinear dependence on sequence similarity of neoantigens to known antigens. Our neoantigen quality fitness model identified long-term survivors in two independent PDAC datasets, as well as predicted survival in anti-CTLA4 treated melanoma patients, and anti-PD-1 treated lung cancer patients. In long-term PDAC survivors, we detected high quality neoantigen-specific intratumoral T cell clones persisting in the blood up to 12 years after primary tumor removal, with both unique clonal and phenotypic profiles. Our results identify neoantigens with unique qualities as T cell targets in both endogenous and immunotherapy treated cancers. Neoantigen quality can therefore inform rational neoantigen immunogenicity predictions that may guide patient and target selection for immunotherapies. Citation Format: Marta Luksza, Joanne P. Leung, Alexander Solovyov, David Redmond, Miriam Merad, Sacha Gnjatic, Christine Iacubuzio-Donohue, Ronald P. DeMatteo, Timothy A. Chan, Jedd Wolchock, Steven D. Leach, Benjamin D. Greenbaum, Taha Merghoub, Vinod P. Balachandran. Mapping immune recognition of non-self neoantigens in human pancreatic cancer [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr IA34.

Colistin resistance beyond carbapenems: molecular epidemiology of multi-drug resistant Klebsiella pneumoniae from an Italian hospital

Purpose: Multidrug resistant (MDR) Klebsiella pneumoniae (Kp) is a worldwide concern worsened by colistin resistance emergence. In this study, molecular epidemiology of clinical MDR Kp strains is described, assessing clonal relationships and resistance genes profiles. Prevalence of Extended-Spectrum Beta-Lactamase (ESBL) blaCTX-M, blaTEM and blaSHV genes was evaluated, as well as that associated to carbapenems (blaKPC, blaGES, blaVIM, blaIMP, blaNDM, blaOXA-48) and colistin resistance (mcr-1,2,3,4 and mgrB). Methods & Materials: Twenty-six Kp cultures were collected from “A.Cardarelli” hospital in Molise Region (Central Italy), 57.7% from Intensive Care Unit (ICU). The Minimum Inhibitory Concentration (MIC) was assessed by BD Phoenix™. Genotyping was achieved through Pulsed-Field Gel Electrophoresis (PFGE) with XbaI and MultiLocus Sequence Typing (MLST). PCRs for resistance genes detection and mgrB sequencing were performed. Results: Most (n = 20, 77%) strains were carbapenems resistant (imipenem, meropenem, ertapenem), and 53% (n = 14) to colistin. A higher prevalence of blaKPC (100%) and blaSHV (96.2%) was found compared with blaTEM (88.5%), blaVIM (69.0%) and blaCTX-M (7.7%). While none colistin-resistant (col-R) strain carried mcr-1,2,3,4 variants, 42.8% (n = 6) had an Insertion Sequence (IS) in mgrB, identified as IS5-like (5/14, 36%) and ISKpn14 (1/14, 7%). The prevalent Sequence Type was ST512 (50%), followed by ST101 (38.5%) and ST307 (11.5%). PFGE detected 12 clusters and 18 pulsotypes (95% similarity), and was more discriminating than MLST (Simpson's Index 95% vs 61%). An ICU outbreak, during November 2014-January 2015, included five ST512 strains, blaTEM/blaSHV/blaVIM/blaKPC positive, and col-R due to mgrB IS5-like. Conclusion: Molecular epidemiology study identified an outbreak caused by poor compliance with hygienic standards because of reduced personnel during Christmas holidays. Although ST258 is the most prevalent in Italy, half strains were typed as ST512 that represents its monoallelic variant. Our results confirm the endemic blaKPC distribution and blaTEM/blaSHV as the prevalent ESBLs in Kp hospital outbreaks. According to epidemiological data, plasmid mcr variants were not found in col-R strains. Conversely, IS elements prevalence in mgrB explain resistance in about half col-R strains, and was in line with Italian data. Further investigations are needed to identify mgrB mutations in IS negative col-R strains.

Evolution and mutations predisposing to daptomycin resistance in vancomycin-resistant Enterococcus faecium ST736 strains.

We recently identified a novel vancomycin-resistant Enterococcus faecium (VREfm) clone ST736 with reduced daptomycin susceptibility. The objectives of this study were to assess the population dynamics of local VREfm strains and genetic alterations predisposing to daptomycin resistance in VREfm ST736 strains. Multilocus sequence typing and single nucleotide variant data were derived from whole-genome sequencing of 250 E. faecium isolates from 1994–1995 (n = 43), 2009–2012 (n = 115) and 2013 (n = 92). A remarkable change was noticed in the clonality and antimicrobial resistance profiles of E. faecium strains between 1994–1995 and 2013. VREfm sequence type 17 (ST17), the prototype strain of clade A1, was the dominant clone (76.7%) recognized in 1994–1995. By contrast, clone ST736 accounted for 46.7% of VREfm isolates, followed by ST18 (26.1%) and ST412 (20.7%) in 2013. Bayesian evolutionary analysis suggested that clone ST736 emerged between 1996 and 2009. Co-mutations (liaR.W73C and liaS.T120A) of the liaFSR system were identified in all ST736 isolates (n = 111, 100%) examined. Thirty-eight (34.2%) ST736 isolates exhibited daptomycin-resistant phenotype, of which 13 isolates had mutations in both the liaFSR and cardiolipin synthase (cls) genes and showed high level of resistance with a daptomycin MIC50 of 32 μg/mL. The emergence of ST736 strains with mutations predisposing to daptomycin resistance and subsequent clonal spread among inpatients contributed to the observed high occurrence of daptomycin resistance in VREfm at our institution. The expanding geographic distribution of ST736 strains in other states and countries raises concerns about its global dissemination.

Single Cell RNA Sequencing and V(D)J Profiling of T-Cell Large Granular Lymphocytosis

Introduction. T-cell large granular lymphocytosis (T-LGL) is a low grade lymphoproliferative disorder, often clinically manifest as bone marrow failure. Treatment with immunosuppressive therapies is effective, but the dominant clone may persist even in responding patients. The pathogenesis of T-LGL has not been fully elucidated. In this study, we performed single cell RNA sequencing (sc-RNA seq) and V(D)J profiling to discern clonotypes and gene expression patterns of T lymphocytes from T-LGL patients who were sampled before and after treatment.Methods. Blood was obtained from patients participating in a phase 2 protocol of alemtuzumab as second line therapy (NCT00345345; Dumitriu B et al, Lancet Haematol 2016). Leukapheresis was performed in 13 patients (M/F 7/6; median age 51 years, range 26-85) before and after 3-6 months alemtuzumab administration and in 7 age-matched healthy donors. Cryopreserved blood was enriched for T cells with the EasySep Human T cell Isolation Kit (Stem cell). sc-RNA seq was performed on the 10XGenomics Chromium Single Cell V(D)J + 5' Gene Expression platform, and sequencing obtained on the HiSeq3000 Platform. Barcode assignment, alignment, unique molecular index counting and T cell receptor sequence assembly were performed using Cell Ranger 2.1.1.Results. Four hundred fifty thousand cells from 13 patients and 107,000 cells from 7 healthy donors were profiled. We measured productive TCR chains (which fully span the V and J regions, with a recognizable start codon in the V region and lacking a stop codon in the V-J region, thus potentially generating a protein). We detected at least one productive TCR α-chain in 50%, one productive TCR β-chain in 69% and paired productive αβ-chains in 47% of all cells. There was loss of TCR repertoire diversity in patients which was quantified by Simpson's diversity index; most patients showed oligoclonal or, less frequently, monoclonal expansion of the TCR repertoire (Fig. A). Regardless of clinical response, alemtuzumab treatment did not correct the low TCR repertoire diversity. TCR repertoires can be classified as “public”, when they express identical TCR sequences across multiple individuals, or “private”, when each individual displays distinct TCR clonotypes. No TCRA or TCRB CDR3 homology among patients was observed: most TCR clonotypes appeared to be private. Our data suggests that T-LGL is etiologically heterogenous disease, consistent with T cell expansion in response to a variety antigens, in diverse HLA contexts, or randomly. Despite differences of TCR among patients and healthy donors, and the presence of large clones in patients, distribution of TCR diversity followed the power law distribution in healthy donors and patients (Fig. B, showing the negative linear relationship between logarithmic expression of clone frequency and clone size). The observed distribution is consistent with a somatic evolution model, in which cell fitness depends on cellular receptor response to specific antigens and stimulation of cells by cytokine and other signals from the environment; fitted clones have higher birth-death ratios and thus expand (Desponds J et al, PNAS 2016).CD4 and CD8 T cells can be virtually separated by imputation from their transcriptomes (Fig. C). Comparison of gene expression between patients and healthy donors showed dysregulation of genes involved in pathways related to the immune response and cell apoptosis, consistent with a pathophysiology of T cell clonal expansion. We used diffusion mapping, which localizes datapoints to their eigen components in low-dimesional space, to characterize sources contributing to the gene expression phenotype: the first component was mainly from T cell activation and the second was associated with TCR expression. In LGL the T cell transcriptome appeared to be shaped by both lineage development and TCR rearrangement.Conclusion. We describe at the single cell level T clonal expansion profiles in T-LGL, pre- and post-treatment. Single cell analysis allows accurate recovery of paired α and β chains in the same cell and demonstrates a continuum of cell lineage differentiation. We found a range of differences in transcriptome and TCR repertoires across patients. Transcriptome data, coupled with detailed TCR-based lineage information, provides a rich resource for understanding of the pathology of T-LGL and has implications for prognosis, treatment, and monitoring in the clinic. [Display omitted] DisclosuresYoung:GlaxoSmithKline: Research Funding; CRADA with Novartis: Research Funding; National Institute of Health: Research Funding.

Long-Term, Clonal Tracking Comparing Autologous Transplantation of G-CSF/SCF-Primed Bone Marrow CD34+ Cells with G-CSF/SCF-Mobilized Peripheral Blood CD34+ Cells in Rhesus Macaques

Introduction:Although autologous transplantation of peripheral blood stem cells (PBSC) - mobilized with a combination of granulocyte colony-stimulating factor (G-CSF) and stem cell factor (SCF) - has been well characterized, the efficacy of G-CSF/SCF-primed bone marrow stem cell (BMSC) transplantation, however, remains unclear and controversial. In our previous lentiviral vector-mediated PBSC and BMSC transplantation study, we reported efficient and long-term hematopoietic reconstitution by PBSC but not by BMSC - the later being associated with the gradual decline of vector markings in two BMSC-transplanted animals, with a loss of marking occurring in most lineages by 26 or 32 weeks after transplant. Follow-up analysis indicated that low-level yet consistent repopulation by BMSC continued in these animals for a longer period. Here we have compared peripheral blood (PB) markings and vector integration sites (VIS) in PBSC- and BMSC-transplanted animals for up to 12 years and 6 years, respectively.Methods:Young adult rhesus macaques were treated with G-CSF (10 mg/kg of body weight/day) and SCF (200 mg/kg/day) four days before the cell harvest for transplant. Mobilized PB leukapheresis cell products from five rhesus macaques (95E132, 2RC003, RQ5427, RQ3570, and 96E035) were harvested using a CS3000 Plus blood cell separator. Bone marrow (BM) cells from two animals (95E131 and 96E041) were surgically harvested from their femurs and iliac crests under anesthesia. After harvest, PBSC and BMSC were isolated by Ficoll-Hypaque density centrifugation followed by immunoselection of CD34+ cells, and transduced with HIV-based self-inactivating lentiviral vectors expressing EGFP. Vector-marked cells were then autologously transplanted into the host after total body irradiation (10 Gy). No further priming treatment was provided after transplant. PB from the 5 PBSC- and 2 BMSC-transplanted animals were serially collected over time and cryo-preserved for PCR, flow cytometry, and VIS analyses.Results:Both PBSC- and BMSC-transplanted animals showed long-term repopulation for lymphocytes, monocytes, granulocytes, platelets, and red blood cells. PBSC animals showed an average EGFP marking that ranged from 0.32 % to 10.24 %. From these animals, a total of 141 to 4,858 VIS were recovered. We found that the total number of VIS in each animal was proportional to the average EGFP marking in the same animals, and that both of these in turn were linearly correlated with the number of EGFP+ CD34+ cells initially transplanted (1.4 x106 - 28.8 x106 per animal). BMSC-transplanted animals did not show any such patterns. In two BMSC animals, the average EGFP marking levels remained at 0.05 % and 0.10 % until the end point (5 and 6 years) despite the fact that a comparatively large number of EGFP+ CD34+ cells had been transplanted (5.2 x106 and 17.7x106)and a large number of VIS recovered (793 and 680 VIS) in these animals. Temporal VIS analysis of PBSC animals showed that different groups of a large number of PBSC clones repopulated sequentially and reached a point of maximum repopulation at different time points, with some gradually declining after this. BMSC animals also showed a wave-like sequential repopulation similar to the patterns seen in PBSC animals. Unlike PBSC, however, nearly all BMSC clones were detected at a low frequency and at a single time point, except a few larger ones that were detected at multiple time points in a rising and falling pattern. There was no notable difference between the genomic features of VIS in PBSC- and BMSC-repopulating cells.Conclusions:Our data suggest that both the BMSC and PBSC consist of highly heterogeneous stem/progenitor cells that can provide long-term polyclonal repopulation through wave-like, sequential repopulation. Unlike PBSC, however, BMSC transplant was inefficient in PB repopulation resulting in only barely detectable markings in PB. The BMSC clonal profiles reflected the clonal patterns seen in PBSC animals, aside from BMSC animals having primarily low-frequency clones. We have previously shown significant differences in immunophenotype and cell cycle status between PBSC and BMSC, where BMSC were significantly lower in Thy-1 expression and had a higher percentage of cells in the S+G2/M phase of the cell cycle than PBSC. These differences may account for the inefficient differentiation and proliferation capabilities of BMSC compared to PBSC shown in this study. DisclosuresDunbar:National Institute of Health: Research Funding.

KPC-producing Klebsiella pneumoniae bloodstream isolates from Brazilian hospitals: What (still) remains active?

This study assessed susceptibility to polymyxin B (PMB) and alternative antimicrobials, with focus on aminoglycosides and tigecycline, according to different breakpoints in KPC-producing Klebsiella pneumoniae (KPC-Kp) bloodstream isolates from Brazilian hospitals. Bloodstream K. pneumoniae isolates non-susceptible to any of the three carbapenems (meropenem, imipenem or ertapenem) from four Brazilian tertiary-care hospitals were selected. Antimicrobial susceptibility was determined and interpreted according to distinct breakpoints. Twenty-nine PMB-resistant KPC-Kp isolates were selected for molecular typing. A total of 158 KPC-Kp were analysed. MIC50/90 values for PMB were 0.25/16mg/L; 40 isolates (25.3%) were resistant to PMB. MIC50/90 values for meropenem were 32/≥256mg/L; no isolates were susceptible to meropenem according to CLSI, but 10 isolates were intermediate using EUCAST breakpoints (1, MIC=4mg/L; 9, MIC=8mg/L). MIC50/90 values for tigecycline were 2/8mg/L; 53 (33.5%) and 94 (59.5%) isolates were susceptible according to EUCAST and FDA breakpoints, respectively. MIC50/90 values were 32/≥64mg/L for amikacin and ≥16/≥16mg/L for gentamicin; 48 (30.4%), 28 (17.7%) and 16 (10.1%) were susceptible to amikacin according to CLSI, EUCAST and USCAST, respectively, but susceptibility rates to gentamicin were <7.0%. Eighteen distinct clonal profiles were identified among 29 PMB-resistant isolates by DNA macrorestriction. Most clones belonged to CC11. Elevated rates of PMB-resistant KPC-Kp bloodstream infections were found in four Brazilian hospitals, mostly of polyclonal origin. Alternative antimicrobials with the highest in vitro activity were tigecycline and amikacin, although susceptibility rates significantly decreased using criteria with stricter breakpoints (e.g. EUCAST, USCAST).

Pattern of abdominal wall hernia attended in Fishtail Hospital, Pokhara, Nepal

Introduction: All hernias are caused by a combination of pressure and an opening or weakness of muscle or fascia. The pressures push an organ or tissue through the opening or weak spot. Sometimes muscle weakness is present at birth; more often it occurs later in life. Abdominal wall hernias occur only at sites at which the aponeurosis and fascia are not covered by striated muscle. The aim of the study was to know different pattern of abdominal hernias, to analyze various clonal and demographic profiles of various abdominal wall hernias presenting to the mid-western part of Nepal and to evaluate different types of operation and complication performed in hernias patients.&#x0D; Methods: Hospital based retrospective descriptive study performed in Fishtail Hospital and Research Centre, Pokhara Nepal in October 2012 to July 2017. Ethical clearance was taken from institute and written consent was taken from all the patients who are involved in the study. All sociodemographic data were collected and analyzed by using SPSS 20 statistical software.&#x0D; Results: In this study period, 492 patients of various types of hernias were operated by various methods. Most common type of hernia is indirect inguinal hernia (94.39%) and one rare spigelian hernia was also there. Right inguinal hernia was more common (58.42%).&#x0D; Conclusion: Inguinal Hernia was the commonest type of hernia (394, 90.3%). Among inguinal hernia right side was more common (58.42%). Among inguinal hernias, most of the hernias were found in 0-9 years (38.21%). In this study we found recurrence rate 1.4%.