Drug Sensitivity Testing Research Articles

Clonal Diversity and Spatial Dissemination of Drug-resistant Mycobacterium tuberculosis Complex among HIV Seropositive Patients in Southwest Nigeria

Mycobacterium tuberculosis complex display relatively static genomes and 99.9% nucleotide sequence identity. Studying the evolutionary history of such monomorphic bacteria is a difficult and challenging task. Therefore, this study was undertaken to investigate the clonal diversity and spatial dissemination of drug-resistant M. tuberculosis complex among HIV seropositive clients in Southwest Nigeria. A total of two-hundred and seventeen (217) consented HIV positive (case subjects) and fifty (50) non-HIV positive controls were recruited for this study. Two Sputum samples were collected from each participant in two consecutive days. The samples were divided into two parts: one part was decontaminated using NAOH-NALC method and aseptically cultured for Mycobacteria on Lowenstein-Jensen (LJ) medium with and without pyruvate. Mycobacterial isolates were characterized using conventional and molecular methods. Anti-TB drug sensitivity test was done using 1% proportion conventional method on LJ. MTBC isolates were sequenced using Genetic Analyzer 3130xl sequencer. Genetic relatedness and clonal diversity (phylogenetic analysis) of MTBC isolates were done using Bio- Edit software and MEGA 6. Out of 217 HIV positive participants, 105(48.4%) were male, while 112(51.6%) were female. Twenty-six (26(52.0%)) of the control subjects were male, while 24(48.0%) were females. The overall prevalence of TB among PLHIV was found to be 19.1%. The prevalence of NTM among PLHIV was found to be 2.8% with M. intracellulare being the predominant organism isolated. Participants’ age was found to be significantly associated with TB (P<0.05), however there was no significant association between TB and sex of the participants (P<0.05). The prevalence of culture confirmed drug-resistant TB (DR-TB) among PLHIV was found to be 11.9%, with Rifampicin having the highest monoresistance rate of 5.5%. The overall prevalence of MDR-TB among PLHIV was found to be 9.2%. The phylogenetic analysis of M. tuberculosis strains revealed same clone of all isolates. All PLHIV should be screened for drug-resistant TB especially MDR-TB as the prevalence of primary MDR-TB is high among them. Further study like 3R gene-based studies of adaptation and evolution is needed to facilitate further epidemiological studies of these bacteria.

Abstract A006: Development of a circulating tumor cell-derived cancer organoid platform for drug screening against metastatic tumors and longitudinal monitoring of drug resistance

Abstract Metastatic disease remains the primary cause of cancer-related deaths, presenting a significant challenge in oncology drug development. Current drug screening efforts often rely on cell lines or primary tumor-derived models, which may not adequately mimic the behavior of metastatic tumors. To address this, we aimed to develop a system that more accurately reflects metastatic tumors for improved drug screening. We leveraged a specialized culture platform featuring patented coated plates and proprietary media developed by AcroCyte (Taiwan) to cultivate circulating tumor cells (CTCs) into cancer organoids without pre-selection or enrichment. Building on our previous work, where we successfully cultivated CTCs from fresh blood and cryopreserved peripheral blood mononuclear cells (PBMCs) from renal, colon, and lung cancer patients into cancer organoids, we have now demonstrated the ability to freeze these CTC- derived organoids and thaw them for new culture when needed. We also present new data extending this success to breast and prostate cancers. CTCs from five frozen PBMC samples from breast cancer patients and three from prostate cancer patients formed visible colonies, with positive immunostaining for EpCAM, cytokeratin, and CD44. The immune cells in the PBMC samples gradually died off within three weeks of culture, as confirmed by the absence of CD45- positive cells. Interestingly, CTC-derived organoids from breast and prostate cancers did not form the spheroids observed in renal, colon, and lung cancer models. Instead, they appeared as colonies or clusters of CTCs. After 6-8 weeks of active growth, these clusters exhibited a slower growth rate, although they remained viable in the proprietary culture system. We are actively evaluating various culture media supplements, tailored to breast and prostate cancers, to extend the active growth period of these CTC-derived organoids for longer durations. Importantly, these CTC-derived colonies retained drug sensitivity, demonstrating the system's potential for effective drug screening against metastatic tumors. Our platform now supports organoid development from renal, colon, lung, breast, and prostate cancers, and we are actively expanding to include all major solid tumors. Since this technology uses blood, which can be obtained non-invasively, it enables longitudinal monitoring of CTCs as a functional liquid biopsy. Additionally, frozen PBMCs can be used as a source material for CTCs, and the resulting organoids can be utilized for drug sensitivity testing. This platform could be instrumental in oncology drug development and holds promise for monitoring emerging drug resistance in clinical trials by analyzing PBMC samples collected before and after treatment, offering a functional liquid biopsy-based approach to aid in developing therapies targeting metastatic disease. Citation Format: Yi-chun Han, David Hsieh, Ruobo Zhang, Emily Miyashita-Lin, Shian-Jiun Shih. Development of a circulating tumor cell-derived cancer organoid platform for drug screening against metastatic tumors and longitudinal monitoring of drug resistance [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr A006.

Analysis of the Prevalence of Bacterial Pathogens and Antimicrobial Resistance Patterns of Edwardsiella piscicida in Largemouth Bass (Micropterus salmoides) from Guangdong, China.

To gain insights into the prevalence and antimicrobial resistance patterns of major bacterial pathogens affecting largemouth bass (Micropterus salmoides) in the Pearl River Delta (PRD) region, Guangdong, China, a study was conducted from August 2021 to July 2022. During this period, bacteria were isolated and identified from the internal organs of diseased largemouth bass within the PRD region. The antimicrobial resistance patterns of 11 antibiotics approved for use in aquaculture in China were analyzed in 80 strains of Edwardsiella piscicida using the microbroth dilution method. The results showed that 151 bacterial isolates were obtained from 532 samples, with E. piscicida (17.29%, 92/532), Aeromonas veronii (4.70%, 25/532), and Nocardia seriolae (2.26%, 12/532) being the main pathogens. Notably, E. piscicida accounted for the highest proportion of all isolated bacteria, reaching 60.92% (92/151), and mainly occurred from November to April, accounting for 68.48% (63/92) of the cases. The symptoms in largemouth bass infected with E. piscicida included ascites, enteritis, and hemorrhaging of tissues and organs. The drug sensitivity results showed that the resistance rates of all E. piscicida strains to ciprofloxacin, all sulfonamides, thiamphenicol, florfenicol, enrofloxacin, doxycycline, flumequine, and neomycin were 96.25%, 60-63%, 56.25%, 43.75%, 40%, 32.5%, 16.25%, and 1.25%, respectively. In addition, 76.25% (61/80) of these strains demonstrated resistance to more than two types of antibiotics. Cluster analysis revealed 23 antibiotic types (A-W) among the 80 isolates, which were clustered into two groups. Therefore, tailored antibiotic treatment based on regional antimicrobial resistance patterns is essential for effective disease management. The findings indicate that in the event of an Edwardsiella infection in largemouth bass, neomycin, doxycycline, and flumequine are viable treatment options. Alternatively, one may choose drugs that are effective as determined by clinical drug sensitivity testing.

DDDR-34. A SYSTEMS MEDICINE PLATFORM FOR INDIVIDUALIZED TREATMENT OF GLIOBLASTOMA

Abstract Glioblastoma is an aggressive brain cancer characterized by complex intertumoral heterogeneity. Yet, no methods have successfully stratified patients for effective individualized treatments. We aimed to use a systems medicine approach to individualize treatments for patients. From 27 patients undergoing surgery for either a newly diagnosed or a progressive glioblastoma, we collected biopsies and cultured the cells as spheroids. Drug sensitivity testing for >500 drugs from the FDA-approved oncology collection was performed. Drug efficacy was quantified using a modified area under the dose-response curve (Drug Sensitivity Score, DSS), and individualized by normalizing the DSS to the drug response in bone marrow cells from healthy donors (selective DSS, sDSS). All samples were assayed by WES, WGS, and RNA-sequencing. We found that glioblastomas can be stratified into three DSS groups. These were associated with expression of genes both known (e.g. ALDH1A1), and not known (e.g. VRK2) to be linked to drug resistance. By unsupervised clustering of sDSS, we found a robust patient stratification primarily driven by drug sensitivity to four groups of targets: i) EGFR, ii) FGFR/PDGFR/VEGFR, iii) MDM2 and iv) MEK/ERK. We found differentially expressed genes (N = 20-90 genes, varying by group) between the responders and non-responders in each group. We explored differential pathway activity between the responders and non-responders in each group to correlate drug responses to transcriptional networks to inform underlying disease mechanisms. The transcriptional networks further provide a molecular basis for drug predictions for additional treatment prioritizations. We conclude that our platform can stratify glioblastomas into subgroups, inform the underlying biology of drug sensitivity, and prioritize treatments for patients. Clinical utility is currently under evaluation in a formal trial.

DDDR-22. USE OF BIOPSY-DERIVED TUMOR ORGANOIDS FOR PERSONALIZED DRUG TESTING IN RECURRENT GLIOBLASTOMA

Abstract To date, there are no effective systemic treatment options for recurrent glioblastoma (GBM). Furthermore, often surgical resection is not possible and tumors have acquired an increased chemo- or radioresistance. Patient-derived tumor organoids (PDTOs) provide a new exciting tool to test individual treatment responses. Aim of this study was to assess the feasibility of a personalized PDTO-based drug testing even from rare material such as stereotactic biopsies. PDTOs were prepared based on single cell suspensions from tumor material obtained either from open GBM resections (reference data set, n = 37) or from stereotactic biopsies (n = 8). Drug response curves (6-9 doses) were performed for 9 drugs including commonly used drugs such as temozolomide, lomustine, etoposide and temsirolimus. Viability was measured using CellTiterGlo (Promega) to assess half-maximal inhibitory concentrations (IC50). Medical records were reviewed for survival and molecular information such as the MGMT methylation status. Drug testing on PDTOs from open resections allowed to adjust the test range for each drug. Additionally, a significant association between increased temozolomide sensitivity of PDTOs and both, MGMT methylation and increased survival was observed. However, in 59% of the cases, no sensitivity to any of the drugs was seen, and only 17% were highly sensitive to more than one drug. Subsequent drug testing on PDTOs from biopsies of recurrent GBM revealed sensitivity in 3/8 cases against one (n=2) or two (n=1) of the drugs. However, sensitivity against drugs varied substantially in a patient-individual manner. We successfully developed a workflow to test drug sensitivity on PDTO even from low starting material obtained from stereotactic biopsies. Association of clinical outcome and MGMT methylation with temozolomide sensitivity corroborated the strength of this approach. Furthermore, patient-individual treatment responses strongly suggest for a future personalized drug testing.

Distribution of Pathogenic Bacteria and Drug Resistance in ICU of a Newly Built Hospital.

This study investigated the distribution and resistance patterns of pathogens in the intensive care unit of a newly established hospital in Guizhou Province to promote the rational use of antibiotics to reduce multidrug resistance. A retrospective analysis was conducted on the distribution of pathogens and changes in drug resistance in the ICU of a newly built hospital in Guizhou Province from March 2019 to December 2023. WHONET 5.6 was used to analyze the results. A total of 2444 culture samples were received, predominantly sputum (34.66%) and blood (23.36%) samples, with a steady annual increase in specimen types. A total of 572 pathogenic strains were isolated, predominantly from respiratory specimens (54.02%), including 345 Gram-negative bacteria (60.31%), 135 Gram-positive cocci (23.60%), and 92 fungi (16.08%). The most frequent pathogens included Acinetobacter baumannii (30.77%), Candida albicans (11.71%), and Klebsiella pneumoniae (9.97%). Drug sensitivity tests indicated a fluctuating resistance rate of Acinetobacter baumannii over the past five years. Staphylococcus aureus displayed strong in vitro activity against vancomycin, tigecycline, and linezolid, with no resistant strains identified. The detection rates of carbapenem-resistant Acinetobacter baumannii (CR-AB), carbapenem-resistant Pseudomonas aeruginosa (CR-PA), methicillin-resistant Staphylococcus aureus (MRSA), and strains producing extended-spectrum beta-lactamases (ESBL) were 86.78%, 26.79%, 32.45%, 70.27%, and 23.54%, respectively. Compared with other countries in the world, China has increased its data on the prevalence of MDR pathogens and antibiotic resistance.The high resistance rate of Acinetobacter baumannii in the ICU underscores the need for effective infection control measures. Enhanced monitoring of CR-AB, ESBL-producing bacteria, and MRSA is essential, along with improved management of antibacterial drugs and the pursuit of new therapeutic options.

Comparison between Conventional Methods and Molecular Diagnosis for Candida albicans and Candida dubliniensis isolated from Cancer Patients Infected with Oral Candidiasis

Abstract Background: Two related pathogenic yeast species, Candida albicans and Candida dubliniensis share many phenotypic and microscopic diagnostic characteristics, in addition to the similarity in the characteristics of diagnosis. Objectives: The present study aimed to diagnose both yeast cells and compare them at the level of the percentage of similarities and differences according to the traditional methods and molecular approaches, which are considered more accurate and sensitive. Materials and Methods: The ability to form germ tubes was conducted for C. albicans and C. dubliniensis. The identification using biochemical tests, VITEK techniques, and molecular techniques was also conducted. Results: The results showed that both pathogenic yeast cells are similar in phenotypic and biochemical diagnosis, whereas the results of molecular diagnosis showed a difference between them, as well as the results of the drug sensitivity test, showed that the two types of yeast cells are sensitive to the antifungal drugs. The current study also showed the diagnosis of new isolates of the two species for the first time, which can be attributed to the occurrence of genetic mutations in them. Conclusion: Both types of pathogenic yeasts that were diagnosed in the current study are the important pathological types prevalent in cancer patients, especially in oral cavity infections, and they are similar to a large extent in terms of phenotypic and diagnostic characteristics.

The microbiome biomarkers of pregnant women's vaginal area predict preterm prelabor rupture in Western China.

Intraamniotic infection is crucial in preterm prelabor rupture of membranes(PPROM), a clinical condition resulting from the invasion of vaginal opportunistic microbes into the amniotic cavity. Although previous studies have suggested potential associations between infection and PPROM, the role of vaginalopportunistic bacteria in PPROM has received limited attention. This study aimed to confirm the vaginal bacterial etiology of PPROM. We investigated vaginal microbiotas using automatic analysis of vaginal discharge, microbiological tests, and 16s rRNA genehigh-throughput sequencing. The research findings revealed that the proportion of parabasal epitheliocytes, leukocytes, toxic leukocytes, and bacteria with diameters smaller than 1.5 um was significantly higher in the PPROM group than that in the normal full-term labor (TL) group. The top three vaginal opportunistic bacterial isolates in all participants were 9.47% Escherichia coli, 5.99% Streptococcus agalactiae, and 3.57% Enterococcus faecalis. The bacterial resistance differed, but all the isolates were sensitive to nitrofurantoin. Compared with the vaginal microbiota dysbiosis (VMD) TL (C) group, the VMD PPROM (P) group demonstrated more operational taxonomic units, a high richness of bacterial taxa, and a different beta-diversity index. Indicator species analysis revealed that Lactobacillus jensenii, Lactobacillus crispatus, and Veillonellaceae bacterium DNF00626 were strongly associated with the C group. Unlike the C group, the indicator bacteria in the P group were Enterococcus faecalis, Escherichia coli, and Streptococcus agalactiae. These findings provide solidevidence that an abnormal vaginal microbiome is a very crucial risk factorclosely related to PPROM. There were no unique bacteria in the vaginalmicrobiota of the PPROM group; however, the relative abundance of bacteria inthe abnormal vaginal flora of PPROM pregnancies differed. Antibiotics should bereasonably selected based on drug sensitivity testing. The findings presented in this paper enhance our understanding of Streptococcus agalactiae, Enterococcus faecalis, and Escherichia coli vaginal bacterial etiology of PPROM in Western China.

Virulence and molecular epidemiological analysis of three human blood-borne Streptococcus suis

ObjectiveTo understand the virulence genes and molecular epidemiological characteristics of human-infected strains of Streptococcus suis in Rui'an, Zhejiang Province, from 2021 to 2022, and to provide a scientific basis for diagnosis, treatment, prevention, and control. MethodsThree blood-borne strains of Streptococcus suis were analysed by morphological observation, identification, and drug sensitivity tests. We performed polymerase chain reaction (PCR) amplification of their main seven virulence factors and housekeeping genes. This was followed by virulence analysis and multilocus sequence typing. We analysed their relationships with local pathogens from previous years. ResultsThree Streptococcus suis strains were isolated from the blood samples of three patients. From these, the virulence genotypes demonstrated that the two strains were orf2+ and ef+/orf2+/sly+, respectively. The Multilocus sequence typing (MLST) typing results demonstrated that the two strains were ST25 and ST7, respectively. ConclusionThe first isolation of ST25 Streptococcus suis in Rui'an was presumed to have a close affinity with the endemic strain in North America. The other strain was an ST7 clone, consistent with the endemic strain in Sichuan, and which may have originated from Sichuan. Virulence genotype analysis demonstrated that different virulence genes of the pathogens resulted in different clinical manifestations.

Genetic framework sequencing analysis of Candida tropicalis in dairy cow mastitis and study of pathogenicity and drug resistance

Candida tropicalis (C. tropicalis) is a zoonotic pathogen that is widespread in the environment and in recent years an increasing number of dairy cows have been infected with the fungus causing mastitis in cows.In this study, 37 milk samples from the udders of cows with clinical mastitis were collected from a dairy farm in Guangxi Province, China, from which C. tropicalis was isolated and identified, and then the isolated fungi were subjected to genome frame map sequencing, genome functional analysis as well as comparative genome analysis of the sequencing results, and combined with the virulence test of the fungi and drug sensitivity test of the fungi determined in infected mice, the resistance genes and pathogenicity of the fungi were Analysis of resistance genes and pathogenicity.Our study results revealed the isolation and characterisation of C. tropicalis from diseased cows, with a genome length of approximately 14.27 Mb. Functional annotation of the genome identified 4068 genes associated with C. tropicalis. The strain exhibited a chemoresistance mutation in the gene cyp51,a virulence-enhancing mutation in the gene VTC4, and mutations in genes linked to drug resistance. Pathogenicity tests demonstrated that C. tropicalis could induce damage to the internal organs of mice, leading to different levels of cyanosis in the abdominal cavity, white necrotic foci on the surface of internal organs, lung hemorrhage, and enlargement of the spleen and thymus.Histological sections also revealed varying degrees of hemorrhage and degenerative changes in the cells of different organs in the mice. Drug sensitivity tests showed that the fungus was highly sensitive to nystatin and ketoconazole, moderately sensitive to amphotericin B, and insensitive to antibiotics such as itraconazole, gentamicin, and penicillin. In conclusion, C. tropicalis isolated from dairy cows in the Guangxi region in this study was pathogenic and resistant to azoles such as itraconazole and fluconazole, and this study provides a theoretical basis for the further screening of novel resistance genes in C. tropicalis, as well as providing a certain reference for the drugs used for the treatment of fungal cow mastitis in this region.

Expert consensus on culture of patient derived tumor organoids and organoids based drug sensitivity testing

The precision treatment of cancer has consistently been a significant issue in clinical management as well as medical research. With the rapid development and advances towards clinical application of organoids technology, the use of organoids derived from both normal and cancer tissues for pathophysiology studies, treatment regimen development, and drug screening has become increasingly prevalent. This document compiles insights from dozens of nationwide experts and scholars in the field of tumor organoids drug sensitivity testing. It discusses the entire process of tumor organoids drug sensitivity testing, with the intent to provide expert guidance for laboratories interested in conducting clinical testing and application research related to cancer precision therapy.

Tumor-infiltrating B cell-related lncRNA crosstalk reveals clinical outcomes and tumor immune microenvironment in ovarian cancer based on single-cell and bulk RNA-sequencing

BackgroundThe tumor immune microenvironment (TIME) plays a pivotal role in determining ovarian cancer (OC) prognosis. Long non-coding RNAs (lncRNAs) are key regulators of immune response and tumor progression in OC. Among these, tumor-infiltrating B cells represent an emerging target in immune response pathways. However, the specific involvement of B cell-related lncRNAs (BCRLs) in OC remains unclarified. MethodsLeveraging single-cell and bulk RNA-sequencing data, correlation analysis identified BCRLs in ovarian serous cystadenocarcinoma (OV) from the TCGA database. Subsequently, BCRLIs were filtered through COX survival analysis and the LASSO algorithm, leading to the development of a B cell-related lncRNA scoring system (BCRLss). The predictive accuracy of BCRLss for prognosis in TCGA-OV was assessed and externally validated in an independent cohort. Functional enrichment analyses were conducted to elucidate biological pathways associated with risk subgroups. Additionally, the relationship between BCRLss and TIME was investigated through multiple algorithms and consensus clustering, uncovering potential immune response targets. Drug sensitivity analyses further identified potential therapeutic options tailored to risk subgroups. The highest risk score lncRNA was selected for in vitro validation. ResultsThe BCRLss was constructed using six BCRLIs. Survival analysis revealed an improved prognosis in the low-risk group, with results corroborated by external validation in the ICGC-OV cohort. ROC analysis and nomogram construction confirmed the strong prognostic accuracy of BCRLss. Enrichment analysis highlighted associations between risk subgroups and tumor immune pathways, with the low-risk group demonstrating a more robust immune response and elevated expression of immune checkpoint-related genes. Drug sensitivity tests revealed notable differences across risk subgroups. In vitro experiments confirmed elevated LINC01150 expression in OC cells, and LINC01150 knockdown significantly inhibited the proliferation, invasion, and migration of SKOV3 cells. ConclusionsIn conclusion, BCRLss provides a reliable prognostic tool for predicting clinical outcomes and the immune landscape of patients with OC, offering valuable guidance for immunotherapy target selection and personalized treatment strategies.

Hepatocellular-Carcinoma-Derived Organoids: Innovation in Cancer Research.

Hepatocellular carcinomas (HCCs) are highly heterogeneous malignancies. They are characterized by a peculiar tumor microenvironment and dense vascularization. The importance of signaling between immune cells, endothelial cells, and tumor cells leads to the difficult recapitulation of a reliable in vitro HCC model using the conventional two-dimensional cell cultures. The advent of three-dimensional organoid tumor technology has revolutionized our understanding of the pathogenesis and progression of several malignancies by faithfully replicating the original cancer genomic, epigenomic, and microenvironmental landscape. Organoids more closely mimic the in vivo environment and cell interactions, replicating factors such as the spatial organization of cell surface receptors and gene expression, and will probably become an important tool in the choice of therapies and the evaluation of tumor response to treatments. This review aimed to describe the ongoing and potential applications of organoids as an in vitro model for the study of HCC development, its interaction with the host's immunity, the analysis of drug sensitivity tests, and the current limits in this field.

Application of high-throughput drug sensitivity testing in children with relapsed and refractory acute leukemia

To explore the current application of high-throughput drug sensitivity (HDS) testing in children with relapsed and refractory acute leukemia (RR-AL) and analyze the feasibility of salvage treatment plans. A retrospective collection of clinical data from children with RR-AL who underwent HDS testing at the Department of Children's Hematology and Oncology of the First Affiliated Hospital of Zhengzhou University from November 2021 to October 2023 was conducted, followed by an analysis of drug sensitivity results and treatment outcomes. A total of 17 children with RR-AL underwent HDS testing, including 7 cases of relapsed refractory acute myeloid leukemia and 10 cases of relapsed refractory acute lymphoblastic leukemia. The detection rate of highly sensitive chemotherapy drugs/regimens was 53% (9/17), while the detection rate of moderately sensitive chemotherapy drugs/regimens was 100% (17/17). Among the 17 RR-AL patients with highly and moderately sensitive chemotherapy drugs and regimens, the MOACD regimen (mitoxantrone + vincristine + cytarabine + cyclophosphamide + dexamethasone) accounted for 100%, with the highest inhibition rate for single-agent mitoxantrone (94%, 16/17), and the highest inhibition rate for targeted therapy being bortezomib (94%, 16/17). Nine patients adjusted their chemotherapy based on HDS testing results, with 4 undergoing hematopoietic stem cell transplantation. Four patients achieved disease-free survival, while 5 died. Eight patients received empirical chemotherapy, with 2 undergoing hematopoietic stem cell transplantation; 4 achieved disease-free survival, while 4 died. HDS testing can identify highly sensitive drugs/regimens for children with RR-AL, improving the rate of re-remission and creating conditions for subsequent hematopoietic stem cell transplantation.

Genomic Analysis and Virulence Assessment of Hypervirulent Klebsiella pneumoniae K16-ST660 in Severe Cervical Necrotizing Fasciitis

ObjectiveTo investigate the source of infection in a patient with recurrent severe neck infections caused by Klebsiella pneumoniae and to analyze the virulence of isolates obtained from different sites of the patient. MethodsWe collected preoperative neck abscess puncture fluid, intraoperative neck drainage fluid, sputum, intestinal fecal specimens, and blood samples from a patient who visited Wuxi Second People's Hospital twice between 2017 and 2018. We conducted isolation, identification, drug sensitivity tests, and string tests on the isolates. Capsule serotyping and virulence gene analysis were performed using PCR. The genetic relationship of different isolates was assessed by Multilocus Sequence Typing and virulence was evaluated using the Galleria mellonella infection model. Additionally, whole-genome sequencing was used to analyze the chromosomal and plasmid genes of one isolate. ResultsKlebsiella pneumoniae was detected in the sputum and fecal specimens from both hospitalizations, as well as the preoperative ultrasound-guided puncture fluid and intraoperative drainage fluid from the first hospitalization, resulting in six isolates. These isolates were all K16 serotype, positive in the string test, and identified as ST660 by Multilocus Sequence Typing, indicating they belonged to the same clone. Virulence gene analysis showed that wcaG, iucB, iroNB, rmpA, rmpA2, Aer, kfuBC, ureA, fimH, mrkD, uge, and peg344 were positive, while allS, cf29a, and Wzy_K1 were negative. In the Galleria mellonella virulence assay, the lethality of different isolates was dose-dependent. The K16 group showed significantly higher larval mortality compared to other control groups (including K1, K2, K5, K20, and K57 groups). Genome sequencing revealed that plasmid p17388 carried numerous virulence genes and insertion sequences, particularly ISKPN74, and showed high homology with other Klebsiella plasmids. ConclusionThis study is the first to report severe cervical necrotizing fasciitis caused by the K16-ST660 Klebsiella pneumoniae Isolate. The high virulence of these isolates was confirmed by the Galleria mellonella virulence assay and the detection of numerous virulence genes. In-depth analysis of plasmid p17388 suggests that ISKPN74 may enhance stable integration of the plasmid into the bacterial chromosome through recombinases and transposases, thereby reducing the likelihood of plasmid loss and increasing bacterial virulence. Additionally, IS5 family insertion sequences may carry extra promoters or enhancers that, when inserted upstream of mucoviscosity-associated genes such as rmpA, may increase the transcription levels of downstream genes. This ISKPN74-mediated integration or insertion reveals a complex genetic mechanism that may contribute to the severity of infections caused by ST660 isolates. Our findings offer new insights into the virulence and structure of ST660-K16 Klebsiella pneumoniae, suggesting that further investigation into the specific mechanisms by which these insertion sequences enhance virulence could aid in developing novel infection management strategies.

Establishment and Clinical Significance of the Patient-Derived Xenograft Model of Colorectal Cancer.

Patient-derived xenograft (PDX) models are widely acknowledged for their ability to reflect the heterogeneity of humancancers and can be used to improve preclinical models. In this study, we evaluatedthe factors affecting the tumor formation rate ofthe PDX colorectal cancer (CRC)model and conducted preliminary drug sensitivity tests. CRC patients who underwent elective surgery at Shaoxing People's Hospital from November 2019 to October 2020 were included. The tumor tissue obtained from surgery was transplanted to the back of NSG mice, and the PDX model was established and subcultured to the F3 generation. Factors that affected tumorigenicity were analyzed and compared histologically. Drug interventions included 5-fluorouracil, oxaliplatin, and propofol. Sixty CRC patients were included in this study, and tumorigenesis was observed in CRC tissue derived from 37 cases (62%). The primary tumor malignancy degree (tumor stage and degree of cell differentiation), preoperative carcinoembryonic antigen level, and tumor location in CRC patients could affect the tumorigenicity of the PDX model. Histopathological analysis of CRC-PDX transplanted tumor tissue was highly consistent with the patient's tumor tissue. All four chemotherapy regimens could inhibit tumor growth and cause tumor tissue damage. Propofol could inhibit diarrhea in mice and protect intestinal mucosa. The CRC-PDX model established in this study can maintain the biological characteristics of primary tumors and can be used as a reference model for the individualized treatment of CRC patients. The degree of malignancy of the primary tumor is the primary factor affecting the tumorigenesis rate of the PDX model.

Analysis of the changes of bacterial spectrum and drug resistance in sputum culture of ICU children in a hospital of pediatric in Jiangsu Province from 2017 to 2022

Objective: To investigate the changes of the distribution and drug resistance profile of bacteria from ICU children with lower respiratory tract infection (LRTI) in Suzhou City, Jiangsu Province from 2017 to 2022. Methods: From January 2017 to December 2022, a cross-sectional observational study on the bacterial spectrum analysis among intensive care unit (ICU) children with LRTI was conducted in Children's Hospital of Soochow University. The bacteria was cultivated by culture methods from sputum samples, and identified by MALDI-TOF mass spectrometry. Drug sensitivity tests were performed by the VITEK2 Compact fully automated analysis system and the paper slide method. The χ2 test or Fisher's exact probability was used to analyze the changes of the distribution of sputum culture-positive bacteria and drug resistance in ICU children. Results: The overall detection rate of sputum culture was 42.06% (1 182/2 810). Staphylococcus aureus (25.63%,303/1 182), Acinetobacter baumannii (13.62%,161/1 182) and Haemaphilus influenzae (13.28%,157/1 182) were the top three. Proportions of Acinetobacter baumannii (17.90% vs. 11.02%,χ²=11.17, P=0.001), especially carbapenem-resistant Acinetobacter baumannii (43.70% vs. 23.50%, χ²=15.21, P<0.001) increased significantly from 2020 to 2022. However, the proportions of Haemophilus influenzae (8.50% vs. 16.19%, χ²=14.27, P<0.001), Streptococcus pneumoniae (8.50% vs. 15.92%, χ²=13.42, P<0.001) and extended-spectrum-lactamase producing Escherichia coli (8.89% vs. 18.00%, χ²=5.45, P=0.025) decreased. Drug resistant results showed that Acinetobacter baumannii was obviously more resistant to imipenem (χ²=4.43, P=0.035) and levofloxacin (χ²=12.53, P<0.001), while more sensitive to minocycline (χ²=8.34, P=0.004). Escherichia coli showed a significant increase in resistance to piperacillin tazobactam (χ²=8.29, P=0.008) and cefoperazone sulbactam (χ²=5.07, P=0.024) from 2020 to 2022; Klebsiella pneumoniae consistently maintained a resistance rate of more than 60% to first and second-generation cephalosporins, and remain susceptible to quinolones and carbapenems. Staphylococcus aureus remained highly susceptible to levofloxacin (drug resistance rate: 2.31%,7/303) and sulfamethoxazole/trimethoprim (drug resistance rate: 4.95%,15/303) from 2020 to 2022. Conclusion: Higher detection and resistance rates of Acinetobacter baumannii from sputum culture in ICU children from 2020 to 2022 were explored. Resistance of Escherichia coli to β-lactamase inhibitor combinations was more serious. Regular monitoring the changes of the etiology of respiratory tract infections in ICU Children is particularly important for the prevention and treatment of multidrug-resistant bacterial infections.

Development of biomarker signatures associated with anoikis to predict prognosis in patients with esophageal cancer: An observational study.

Anoikis, a form of programmed cell death linked to cancer, has garnered significant research attention. Esophageal cancer (ESCA) ranks among the most prevalent malignant tumors and represents a major global health concern. To ascertain whether anoikis-related genes (ARGs) can accurately predict ESCA prognosis, we evaluated the predictive value and molecular mechanisms of ARGs in ESCA and constructed an optimal model for prognostic prediction. Using the Cancer Genome Atlas (TCGA)-ESCA database, we identified ARGs with differences in ESCA. ARG signatures were generated using Cox regression. A predictive nomogram model was developed to forecast ARG signatures and patient outcomes in ESCA. Gene set enrichment analysis (GSEA) was employed to uncover potential biological pathways associated with ARG signatures. Estimation of stromal and immune cells in malignant tumor tissues using expression data (ESTIMATE) and cell-type identification by estimating relative subsets of RNA transcripts analyses were used to assess differences in the immune microenvironment of the ARG signature model. Based on ARGs, the patients with ESCA were divided into high and low groups, and the sensitivity of patients to drugs in the database of genomics of drug sensitivity in cancer was analyzed. Finally, the correlation between drug sensitivity and risk score was then evaluated based on the ARG signatures. Prognostic relevance was significantly linked to the ARG profiles of 5 genes: MYB binding protein 1a (MYBBP1A), plasminogen activator, urokinase (PLAU), budding uninhibited by benzimidazoles 3, HOX transcript antisense RNA, and euchromatic histone-lysine methyltransferase 2 (EHMT2). Using the risk score as an independent prognostic factor combined with clinicopathological features, the nomogram accurately predicted the overall survival (OS) of individual patients with ESCA. Gene ontology (GO) enrichment analysis indicated that the primary molecular roles included histone methyltransferase function, binding to C2H2 zinc finger domains, and histone-lysine N-methyltransferase activity. GSEA revealed that the high-risk cohort was connected to cytokine-cytokine receptor interaction, graft-versus-host disease, and hematopoietic cell lineage, whereas the low-risk cohort was related to arachidonic acid metabolism, drug metabolism via cytochrome P450 and fatty acid metabolism. Drug sensitivity tests showed that 16 drugs were positively correlated, and 3 drugs were negatively correlated with ARG characteristic scores. Our study developed 5 ARG signatures as biomarkers for patients with ESCA, providing an important reference for the individualized treatment of this disease.

Discovery of clinical isolation of drug-resistant Klebsiella pneumoniae with overexpression of OqxB efflux pump as the decisive drug resistance factor.

Background emergence of multidrug-resistant (MDR) bacterial strains is a public health concern that threatens global and regional security. Efflux pump-overexpressing MDR strains from clinical isolates are the best subjects for studying the mechanisms of MDR caused by bacterial efflux pumps. A Klebsiella pneumoniae strain overexpressing the OqxB-only efflux pump was screened from a clinical strain library to explore reverse OqxB-mediated bacterial resistance strategies. We identified non-repetitive clinical isolated K. pneumoniae strains using a matrix-assisted laser desorption/ionization time-of-flight (TOF) mass spectrometry clinical TOF-II (Clin-TOF-II) and susceptibility test screening against levofloxacin and ciprofloxacin. And the polymorphism analysis was conducted using pulsed-field gel electrophoresis. Efflux pump function of resistant strains is obtained by combined drug sensitivity test of phenylalanine-arginine beta-naphthylamide (PaβN, an efflux pump inhibitor) and detection with ethidium bromide as an indicator. The quantitative reverse transcription PCR was performed to assess whether the oqxB gene was overexpressed in K. pneumoniae isolates. Additional analyses assessed whether the oqxB gene was overexpressed in K. pneumoniae isolates and gene knockout and complementation strains were constructed. The binding mode of PaβN with OqxB was determined using molecular docking modeling. Among the clinical quinolone-resistant K. pneumoniae strains, one mediates resistance almost exclusively through the overexpression of the resistance-nodulation-division efflux pump, OqxB. Crystal structure of OqxB has been reported recently by N. Bharatham, P. Bhowmik, M. Aoki, U. Okada et al. (Nat Commun 12:5400, 2021, https://doi.org/10.1038/s41467-021-25679-0). The discovery of this strain will contribute to a better understanding of the role of the OqxB transporter in K. pneumoniae and builds on the foundation for addressing the threat posed by quinolone resistance.IMPORTANCEThe emergence of antimicrobial resistance is a growing and significant health concern, particularly in the context of K. pneumoniae infections. The upregulation of efflux pump systems is a key factor that contributes to this resistance. Our results indicated that the K. pneumoniae strain GN 172867 exhibited a higher oqxB gene expression compared to the reference strain ATCC 43816. Deletion of oqxB led a decrease in the minimum inhibitory concentration of levofloxacin. Complementation with oqxB rescued antibiotic resistance in the oqxB mutant strain. We demonstrated that the overexpression of the OqxB efflux pump plays an important role in quinolone resistance. The discovery of strain GN 172867 will contribute to a better understanding of the role of the OqxB transporter in K. pneumoniae and promotes further study of antimicrobial resistance.

Establishment of a platform based on dual RPA combined with CRISPR/Cas12a for the detection of Klebsiella pneumoniae and its KPC resistance gene.

Carbapenem resistant Klebsiella pneumoniae (CRKP) can cause serious hospital- and community-acquired infections. Treatment for CRKP infection is limited, resulting in prolonged hospitalization and high consultation costs. The KPC genotype has the highest detection rate of CRKP, and its mortality rate is higher than the overall mortality rate of CRKP. However, traditional testing methods have disadvantages such as long time and reliance on complex and sophisticated instruments, which are not conducive to rapid screening for CRKP. Therefore, this study aimed to establish a detection platform for early screening of CRKP so that effective antimicrobial therapy could be administered promptly to prevent the widespread spread of CRKP. We integrated dual RPA with CRISPR/Cas12a to establish a dual platform for the detection of K. pneumoniae (Kp) rcsA-specific gene and KPC resistance gene. Four result reading methods were established, including fluorescence detection (FD), blue light irradiation detection (BLID), ultraviolet irradiation detection (UID), and lateral flow test strips (LFTS). For the rcsA gene, the LOD of FD was 1 × 10pg/μL, and the other three methods could detect 1 × 101pg/μL of bacterial DNA. As for the KPC gene, four resultant readout methods were able to detect 1 × 102pg/μL of bacterial DNA. In 59 clinical strains tested, the dual RPA-CRISPR/Cas12a detection of the rcsA had 100% sensitivity, specificity, and accuracy compared to the culture method. Compared with the drug sensitivity test, the sensitivity of dual RPA-CRISPR/Cas12a detection for the KPC was 85.71%, the specificity was 100%, and the accuracy was 94.92%. In summary, our dual RPA-CRISPR/Cas12a platform proved to be rapid, precise, and convenient for the efficient detection of Kp with KPC in the laboratory or at the point of care.