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La prueba prenatal no invasiva es un método de cribado de aneuploidías fetales y de resultar con riesgo alto debe ser confirmado a través de prueba genética diagnóstica. Es la prueba de detección más sensible y específica para las aneuploidías fetales comunes y minimiza la realización de técnicas invasivas, solo para las gestantes con riesgo elevado. Se debe realizar asesoramiento genético pre- y poscribado. Este estudio tiene como objetivo describir los fundamentos básicos de la prueba prenatal no invasiva mediante el análisis del ácido desoxirribonucleíco libre circulante en plasma materno para cribado de aneuploidías, y de los métodos primordiales y avances en biología molecular incluyendo las tecnologías de secuenciación de nueva generación, que lo han facilitado, considerando sus beneficios y limitaciones al aplicarla en la práctica clínica, en este campo que cambia con tanta rapidez(AU)
The non-invasive prenatal test is a screening method for fetal aneuploidies and if the result is at high risk, it must be confirmed through diagnostic genetic test. It is the most sensitive and specific detection test for common fetal aneuploidies and minimizes the use of invasive techniques, only for pregnant women at high risk. Genetic counseling should be performed before and after screening. This study aims to describe the basic fundamentals of non-invasive prenatal testing by analyzing free circulating deoxyribonucleic acid in maternal plasma for aneuploidy screening, and the primary methods and advances in molecular biology, including next-generation sequencing technologies, which have facilitated it, considering its benefits and limitations when applying it in clinical practice, in this rapidly changing field(AU)
الموضوعات
Humans , Female , Pregnancy , Plasma , DNA , Mass Screening , Prevalence , Risk Factorsالملخص
Objective To explore the clinical characteristics and treatment scheme of patients with spinal infection caused by Prevotella intermedia(P.intermedia).Methods Clinical diagnosis and treatment processes of a patient with spinal infection caused by P.intermedia admitted to the spinal surgery department of a hospital were summa-rized,and relevant literature was retrieved from database for reviewing.Results The patient,a 50 year old male,was admitted to the hospital due to"lumbago pain complicated with pain in double lower extremities for 2 months".The lesion tissue was taken for metagenomic next-generation sequencing(mNGS)detection,which detected P.in-termedia,and the patient was diagnosed with P.intermedia spondylitis.After treatments with open lesion clea-rance,tube rinsing+autologous bone transplantation fusion internal fixation,intravenous drip of ceftriaxone sodium and metronidazole,as well as metronidazole rinsing,infection was under control.A total of 16 available papers were retrieved,together with this case,a total of 17 patients were included,with 7 males and 10 females.The main risk factors were diabetes and history of corticosteroid use(35.3％).The most common invasion sites were lumbar ver-tebra(n=12)and thoracic vertebra(n=6).13 cases were positive for pathogen culture,3 cases were positive for molecular detection,and 1 case was positive for staining microscopy.17 patients received anti-anaerobic bacteria treatment,with 14 cases receiving combined surgical treatment.One case died,with a mortality of 5.9％;5 cases had partial neurological impairment,with a disability rate of 29.4％.The survival rate of patients who received treatment of anti-anaerobic bacteria combined with surgery was 92.8％,3 patients only with anti-anaerobic bacteria treatment but without surgery were all cured.Conclusion P.intermedia is an opportunistic pathogeanic bacteria which often causes infection in immunocomprised individuals and is prone to be misdiagnosed.It is recommended to perform mNGS detection to identify the pathogen as early as possible and seize the opportunity for treatment to reduce mortality.
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Objective To explore the application of metagenomic next-generation sequencing(mNGS)technology in the investigation of healthcare-associated infection(HAI)outbreaks of carbapenem-resistant Acinetobacter bau-mannii(CRAB).Methods Pathogenic detection by mNGS and conventional pathogen culture were performed on 5 patients in the intensive care unit(ICU)of a hospital from June 8 to 22,2023 from whom CRAB were detected.Microbial sampling was carried out in potentially contaminated environment.Bacterial culture,identification,and antimicrobial susceptibility testing were conducted.Comprehensive control measures were taken,and the effect was evaluated.Results The time required for reporting results by mNGS was shorter than the culture time([3.92± 1.05]days vs[6.24±0.25]days,P＜0.001).CRAB was isolated from the specimens of 5 patients.mNGS de-tected OXA-23 resistance genes from all patients.After comprehensive assessment by experts,4 patients were HAI and 1 patient was due to specimen contamination.According to the definition from Guidelines for HAI outbreak control,this event was considered an outbreak of HAI.The monitoring results of environmental hygiene showed that the detection rate of CRAB in the environment during the outbreak was 51.30％(59/115),mainly from the hands of health care workers and the surface of ventilators.After implementing multidisciplinary infection control measures,clinicians'hand hygiene compliance rate and implementation rate of ventilator disinfection increased from 40.83％(49/120)and 33.33％(16/48)to 82.61％(95/115)and 83.33％(30/36),respectively.The prognosis of patients was good,and no new case emerged during subsequent monitoring.The outbreak of HAI in this hospital has been effectively controlled.Conclusion mNGS is characterized by high precision,less time consumption,and high accuracy,and can be applied to the prevention and control of HAI outbreak and the study of antimicrobial-re-sistant genomes.It is of great significance for the anti-infection treatment of patients with multidrug-resistant orga-nism infection as well as the formulation of HAI prevention and control measures.Continuous improving disinfec-tion effectiveness and hand hygiene compliance is important for preventing and controlling CRAB infection.
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Objective To explore the diagnosis and clinical characteristics of atypical severe pneumonia caused by Chlamydia abortus(C.abortus).Methods Clinical data of 4 patients diagnosed with atypical severe pneumonia caused by C.abortus in a hospital from January 2021 to November 2022 were collected.Clinical characteristics,dia-gnosis and treatment,and precautions of the disease were comprehensively analyzed.Results All 4 patients were male,aged 63-73 years old,with acute onset,high fever,cough and expectoration.Three patients had a history of contact with poultry,one patient had a history of contact with abortion goat.The interval between the emerging of clinical symptoms and the onset of acute respiratory failure in 4 patients was 1-6 days,and the oxygenation index(PaO2/FiO2)at admission was less than 200 mmHg,which gradually decreased with the progression of the disease,active support with a ventilator was necessary.Two patients had an increase in white blood cell count,4 had an in-crease in neutrophil percentage,3 had a mild decrease in platelet count.Among 4 patients,2,2,3 and 4 patients showed elevated levels of aspartate aminotransferase,alanine aminotransferase,creatine kinase,and serum creati-nine respectively,2 patients had mild hyponatremia,4 patients showed significant increase in C-reactive protein,procalcitonin,and interleukin-6 levels.Four patients'chest CT findings showed main involvement of single or mul-tiple lung lobes,with exudation and consolidation,and later involvement of multiple lobes of lung.The metageno-mic next-generation sequencing of bronchoalveolar lavage fluid detected the DNA sequence of C.abortus.Based on the clinical manifestations,contact history,chest CT,and metagenomic next-generation sequencing results of 4 pa-tients,the diagnosis was C.abortus.atypical severe pneumonia.After timely adjustment of the treatment of anti-in-fection regimen based on doxycycline,the patients'condition improved and were discharged.Conclusion C.abor-tus may also cause human pneumonia,which can lead to serious clinical outcome after infection.Patient had a histo-ry of animal contact should be alert to such diseases.Metagenomic next-generation sequencing can detect C.abortus.
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This study was aimed at performing epidemiologic investigation of the first psittacosis death case in Hangzhou City,to provide a reference for the investigation and disposal of psittacosis cases,as well as prevention and control.Epidemio-logic data were collected through field epidemiologic investigation,and close contacts and environmental samples were collected for pathogenicity testing.The first symptom in the patient was cough,which did not raise concerns at the time.Several days later,the patient developed abdominal distension and black stools,and visited two medical institutions for treatment and hospi-talization.The patient's sputum and peripheral blood were tested for Chlamydia psittaci infection by metagenomic analysis via next-generation sequencing.Samples collected from the patient's family members,close contacts,and home environment test-ed negative with real-time quantitative polymerase chain reaction.The patient later died of gastrointestinal bleeding.This article is the first report of a case of psittacosis contracted from exposure to a sick parrot in Hangzhou City,in a patient who died be-cause of an underlying disease.Operational training should be provided for medical personnel,and early diagnosis with mNGS and treatment of patients with underlying diseases should be performed as early as possible to avoid fatality.In addition,health education should be carried out to raise public awareness of the disease.
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A case of spinal cord abscess caused by Nocardia cyriacigeorgica is reported. The patient is an elderly man with a history of nephritic syndrome who presented with aggravating lower back pain and then gradually developed urinary retention, weakness and numbness in both lower extremities. Operative intervention was performed, and postoperative pathological findings suggested spinal cord abscess formation. Metagenomic next-generation sequencing of the cerebrospinal fluid identified Nocardia cyriacigeorgica as the causative pathogen. Although appropriate antibiotics were prescribed, the patient died 3 months later.
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Objective To investigate the clonal rearrangement characteristics and clinical application value of IGH gene in B-cell non-Hodgkin’s lymphoma (B-NHL). Methods Demographic and clinical data as well as IGH sequencing results of 55 patients with B-NHL who underwent next-generation sequencing (NGS) testing were collected, and IGH gene clonal rearrangement was detected. The characteristics of IGH gene clonal rearrangement, IGHV gene usage, and the clinical application value of NGS for IGH clonal rearrangement were analyzed. Results Among 55 patients with B-NHL and IGH clonal rearrangement, single dominant clones were mainly detected (85.45%, 47/55); a few patients had two (12.73%, 7/55) and three dominant clones (1.82%, 1/55). In terms of preference for IGHV gene usage, IGHV3 gene had the highest frequency of access in B-NHL, followed by IGHV4. Among the IGHV subtypes, IGHV3-23 had the highest frequency in chronic lymphocytic leukemia/small lymphocytic lymphoma, and IGHV4-34 had the highest frequency in primary central nervous system diffuse large B-cell lymphoma and not otherwise specified diffuse large B-cell lymphoma. Conclusion A preference for IGHV gene usage in clonal rearrangement of IGH genes is noted in B-NHL patients with different pathological types. Using NGS to detect IGH clonal rearrangement can identify subclones and clonal correlations, and assist in disease diagnosis.
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This case report summarizes the experience from diagnosis and treatment of a patient with repeated high fever, hepatosplenomegaly and pancytopenia. Following exclusion of bacterial, viral, fungal infections and hematological diseases, metagenomic next-generation sequencing of the patient’s peripheral blood revealed Leishmania infantum infection, and rK39 rapid diagnostic test showed positive for anti-Leishmania antibody, while microscopic examination of bone marrow smears identified Leishmania amastigotes. Therefore, the case was definitively diagnosed as visceral leishmaniasis, and given anti-infective treatment with sodium antimony gluconate and hormone, hepatoprotection, elevation of white blood cell counts and personalized nursing. Then, the case was cured and discharged from hospital. Metagenomic next-generation sequencing is of great value in etiological detection of fever patients with unknown causes, which deserves widespread clinical applications.
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@#Objective To evaluate the effect of production site change of vaccine production on the quality of live attenuated varicella vaccine at the molecular level.Methods Using next-generation sequencing(NGS),the varicella-zoster virus(VZV)Oka strain virus seed(VW-before,SYVW-after)and vaccine bulk(P-before,YZP-after)produced before and after prodution site change were subjected to DNA extraction,purification,library construction and sequencing,and the quality control of the sequencing results were performed.Taking gene sequence of Dumas strain registered in GenBank(NC＿001348)as the position reference genome,the whole gene sequences of the four samples before and after prodution site change were compared with the Oka strain virus to obtain the mutation sites,base changes and variant allele frequency(VAF),and the consistency of the samples was evaluated.Results All the sequencing depth of the four samples was more than1 500 ×,and the GC content of the virus seed and vaccine bulk was about 46%,indicating that the sequencing quality was high.The mutation sites and base composition of the gene sequences of virus seed and vaccine bulk were consistent before and after prodution site change,and the VAF was close.Pairwise comparison of correlation coefficients was highly correlated,and the correlation coefficients were significantly different(each R~2≥ 0.990,each P < 0.001).Conclusion NGS test showed that the changes in vaccine production process have no effect on the quality of live attenuated varicella vaccine.
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Objective To explore the clinical value of ultrasound bronchoscopy combined with met-agenomic next-generation sequencing(mNGS)in the etiological diagnosis of pneumonia with poor absorption and dissipation.Methods The clinical data of the patients with pneumonia with poor absorption and dissipa-tion in this hospital from January 2022 to February 2023 were retrospectively collected.Among them,73 cases received the endobronchial ultrasound guided tranbronchial needle aspiration(EBUS-TBNA)and 36 cases re-ceived endobronchial ultrasound transbronchial lung biopsy using guide sheath(EBUS-GS-TBLB).The distri-bution of causes and incidence of examination related complications were analysed.Results The results of ul-trasound bronchoscopy combined with mNGS examination showed that the benign lesions accounted for 33.03％,mainly chronic inflammation(9.17％)and infectious disease(20.18％),and tuberculosis was the main cause of infectious diseases(7.34％).The malignant lesions accounted for 57.80％,mainly adenocarcinoma(28.44％).The diagnostic positive rate was 90.83％,and no definite diagnosis accounted for 9.17％.There was no statistically significant difference in the diagnostic positive rate between the patients receiving EBUS-TBNA combined with mNGS examination and the patients receiving EBUS-GS-TBLB combined with mNGS examination(94.52％vs.83.33％,P＞0.05),and there was no statistically significant difference in the inci-dence rates of complications such as less bleeding,anoxia,pneumothorax and delayed resuscitation.No serious complications such as mediastinal emphysema,large vessel injury,shock and death were observed in all pa-tients.Conclusion Ultrasound bronchoscopy combined with mNGS has the characteristics of high diagnostic positive rate and few complications in the etiological diagnosis of pneumonia with poor absorption and dissipa-tion.It can help clinical physicians clarify the diagnosis as soon as possible,and may become a new method for diagnosing respiratory system diseases in recent years.
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Objective To analyze the clinical outcomes of early invasive fungal disease(IFD)in patients after allogenetic hematopoietic stem cell transplantation(allo-HCST)with metagenomic next-generation sequencing(mNGS).Methods A retrospective analysis was conducted on patients undergoing allo-HCST in our Bone Marrow Transplantation Center between July 2021 and October 2022.These patients experienced one of the following conditions within 100 d after transplantation:① Patients with persistent fever and negative blood culture after empiric antimicrobial therapy for 72 h or longer;② Hyperpyrexia of unknown origin occurred again after effective anti-infection in the past;③ Symptoms in lower respiratory tract associated with lung lesions on CT scan,and empiric anti-infective therapy was ineffective.Peripheral blood or bronchoscopic alveolar lavage fluid were tested with mNGS,and overall survival(OS)and non-relapse mortality(NRM)were analyzed.Results There were 60 patients enrolled in this study.For the peripheral blood samples of 47 cases and bronchoalveolar lavage fluid samples of 13 cases,mNGS found that 19 cases were negative to pathogens,30 cases were non-fungal positive,and 11 case were fungal positive,including 3 cases of aspergillus,5 cases of mucor,2 cases of Candida tropicalis,and 1 case of Trichosporon asahii.Of the 11 patients with fungal positive,8 achieved complete remission after antifungal therapy according to the mNGS results.The 1-year OS and NRM of the 60 patients were 70.0％(95％CI:64.1％～75.9％)and 20.0％(95％CI:11.9％～32.5％),respectively,while those of the fungal infection patients were 54.5％(95％CI:49.5％～69.5％)and 36.4％(95％ CI:15.5％～70.3％),respectively.No significant differences were seen in 1-year OS(P=0.487)and 1-year NRM(P=0.358)among the negative,fungal infection and non-fungal infection patients,neither OS(P=0.238)and NRM(P=0.154)between the fungal infection and the non-fungal infection patients.Conclusion mNGS can rapidly diagnose the early IFD after allo-HSCT,which is helpful for timely and effective treatment and improves the prognosis of patients.
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Objective To establish and forensically verify a 42 microhaplotypes(mircohaps,MHs)mul-tiplex assay system based on next-generation sequencing(NGS),and to explore the application value of this system in the practice of forensic genetics.Methods A total of 42 highly polymorphic MHs were selected from previous studies,and sequenced by the MiSeq FGxTM platform to verify the repeata-bility,sensitivity,specificity,stability,and mixture analysis ability of the detection system.Through population genetic investigation of 102 unrelated Chinese Han individuals in Liyang City,Jiangsu Province,China,the application value of this system in forensic genetics was evaluated.Results The sequencing repeatability of the 42-plex MHs assay was 100%and the sensitivity was as low as 0.062 5 ng.The system had the ability to withstand the interference of indigo(≤2 500 ng/μL),humic acid(≤9 ng/μL),hemoglobin(≤20 μmol),and urea(≤200 ng/μL)and to detect mixtures of 2 people(1∶19),3 people(1∶1∶9)and 4 people(1∶1∶1∶9).Based on 102 individual data,the combined power of discrimination and the combined power of exclusion were 1-3.45×10-30 and 1-3.77×10-11,respectively,and the average effect value of alleles was 2.899.Conclusion The 42-plex MHs assay was successfully established in this study and this system has high repeatability and sensitivity,good anti-jamming ability and mixture analysis ability.The 42 MHs are highly polymorphism and have good application value in individual identification and paternity testing.
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Objective To investigate the clinical features of rhino-orbital-cerebral mucormycosis(ROCM)with bilateral cranial nerve palsies as the clinical manifestation.Methods The related clinical data about ROCM with bilateral cranial nerve palsy as a clinical manifestation was collected,analyzed as well as discussed in the manuscript.And the relevant literatures were reviewed.Results This patient was a healthy young man with new-onset diabetes and diabetic ketoacidosis.The patient developed rapidly with acute onset,bilateral blindness,blepharoptosis and extraocular muscle paralysis.The presence of mucormycosis was confirmed by CSF second-generation sequencing,fungal fluorescent staining and culture.Although effective antifungal therapy was performed early,but the patient quickly presented with cerebral hemorrhage and herniation.Eventually,the patient died after discharge.Conclusions ROCM is a rare and high-mortality infectious disease.This case indicated that the clinicians should consider the presence of ROCM in patients with diabetes/diabetic ketoacidosis when the bilateral cranial nerves paralysis are the clinical symptom,whicn can not be explained by other lesions.CSF next-generation sequencing is helpful for rapid diagnosis.
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Objective To investigate the rate of germline variants in patients with pancreatic cancer and clinical characteristics related with germline variants.Methods A total of 271 patients diagnosed with pancreatic cancer were enrolled in this study.Germline variants of 21 tumor susceptibility genes were detected by next-generation sequencing,and the relationship between germline variants and clinical factors such as age of onset,family history and personal history was analyzed.Results The rate of germline P/LP variants was 6.3%in unselected pancreatic cancer patients,but was high as 17.1%in genetic high-risk group patients(those with a family or personal history of cancer,or early-onset).Genes with higher frequency of germline variants in pancreatic cancer patients were PALB2,BRCA2,and ATM.Conclusion The rate of germline variants in overall pancreatic cancer patients is not high,but it increases significantly in genetic high-risk group,proving the importance of clinical factors in the screening of hereditary pancreatic cancer.
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The incidence of spinal infections,a relatively rare infectious disease,is on the rise due to the empirical use of antibiotics that increases the chances of infection with drug-resistant bacteria,as well as advances in testing technology that have led to an increase in detection rates.Identifying the type of pathogen to target antibi-otics is the key to treatment.However,conventionaldetection methods have low detection rates and are time-consum-ing,which are not conducive to the rapid and accurate diagnosis of spinal infection.Metagenomics next-generation sequencing(mNGS)is a detection technique that can sequence all nucleic acid fragments in samples,the emer-gence of which subverts traditional detection methods and plays an important role in the diagnosis and treatment of spinal infections.This article summarizes the application of mNGS in the diagnosis and treatment of spinal infection.
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Objective To investigate the application value of single nucleotide polymorphism(SNP)linkage analysis based on next-generation sequencing(NGS)technology in preimplantation genetic testing(PGT)of families with autosomal recessive polycystic kidney disease(ARPKD).Methods A family with ARPKD was selected,where the female member had a pregnancy ultrasound revealing polycystic kidney in the fetus.Genetic testing showed compound heterozygous mutations of the polycystic kidney/polycystic liver disease 1 gene(PKHD1),c.10444C>T(paternal)and c.4303del(maternal),with the c.4303del mutation being reported for the first time.Targeting the coding region of the PKHD1 gene,335 high-density tightly linked SNP sites were selected in the upstream and downstream 2M regions using multiplex polymerase chain reaction(PCR)and NGS.The couple′s SNP risk haplotypes carrying gene mutations were constructed.After in vitro fertilization,blastocyst culture was performed.Trophoblastic cells obtained from the biopsy were subjected to whole-genome amplification,and NGS was used for linkage analysis and low-depth chromosomal aneuploidy screening of the embryos.Sanger sequencing was used to verify the results of embryo linkage analysis.Results Among the 6 biopsied embryos,4 were mutation-free and euploid,1 exhibited heterozygous for the mutation and mosaic while another unstable sequencing data,making it impossible to judge.One of the mutation-free and developmentally healthy euploid embryos was implanted into the maternal uterus,resulting in the full-term delivery of a healthy baby.Conclusion Application of NGS-based SNP linkage analysis in PGT can effectively blocking the vertical transmission of ARPKD within families,while avoiding abortion issues caused by aneuploid embryos.This study is also the first PGT report target-ing the PKHD1 gene c.4303del mutation.
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ObjectiveTo investigate the genetic polymorphism and structure of 47 autosomal microhaplotypes in the Han population in Changshu City, Jiangsu Province, and to evaluate the forensic efficiencies and forensic parameters. MethodsThe DNA library of unrelated individual samples was prepared according to MHSeqTyper47 kit manual and sequenced on the MiSeq FGx platform. Microhaplotype genotyping and sequencing depth statistics were processed using MHTyper. The genetic information of samples was then evaluated. The fixation index and genetic distance between the Jiangsu Changshu population and the reference populations in the 1000 Genomes Project phase 3 (1KG) were calculated, and forensic parameters were evaluated. ResultsThe fixation index and genetic distance between the Han population in Changshu, Jiangsu, and the CHB (Han Chinese in Beijing, China) reference population in 1KG were the lowest. The effective allele number (Ae) of each locus is also the closest between the two populations. The combined matching probability (CMP) of the Changshu Han population is close to the 5 populations of the East Asian reference super-population in 1KG, which is 1.25×10-36, and the combined probability of exclusion reached 0.999 999 999 964 1. ConclusionThis study reported the genetic polymorphism and allele frequency of 47 microhaplotypes in a Han population in Changshu City, Jiangsu Province. This information provides a data basis for 47 microhaplotypes in forensic applications. In addition, the polymorphism differences between the 1KG reference population and the Han population in Changshu, Jiangsu were compared, and the genetic structure of 47 microhaplotypes in the Han population in Changshu, Jiangsu was revealed. In general, the reference data of the East Asian super-population in 1KG is more in line with the genetic characteristics of Han population in Changshu, Jiangsu.
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Organ transplantation has become an effective treatment for multiple end-stage diseases. However, the recipients of organ transplantation need to take immunosuppressive drugs for a long time after operation, which leads to low immune function and relatively high incidence of bacterial, viral and fungal infections. Traditional microbial detection methods, such as pathogen culture, immunological detection and polymerase chain reaction, have been widely applied in infection detection, whereas these methods may cause problems, such as long detection time and presumed pathogens. Metagenomic next-generation sequencing has been widely adopted in infection prevention and control in organ transplantation in recent years due to high detection rate and comprehensive detection of pathogen spectrum. In this article, the application of metagenomic next-generation sequencing in the prevention and control of infection in solid organ transplantation was reviewed, aiming to provide reference for the diagnosis and treatment of transplantation-related infection.
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ABSTRACT Objective: The aim of this study is to investigate the molecular genetic causes of non-syndromic primary ovarian insufficiency (POI) cases with the gene panel based on next generation sequencing analysis and to establish the relationship between genotype and phenotype. Subjects and methods: Twenty three cases aged 14-40 years followed up with POI were included. Patients with a karyotype of 46, XX, primary or secondary amenorrhea before the age of 40, with elevated FSH (>40 IU/mL) and low AMH levels (<0.03 ng/mL) were included in the study. Molecular genetic analyzes were performed by the next generation sequencing analysis method targeted with the TruSightTM Exome panel. Results: Median age of the cases was 17.8 (14.0-24.3) years, and 12 (52%) cases admitted before the age of 18. Fifteen (65%) patients had consanguineous parents. In 2 (8.6%) cases, variants detected were in genes that have been previously proven to cause POI. One was homozygous variant in FIGLA gene and the other was homozygous variant in PSMC3IP gene. Heterozygous variants were detected in PROK2, WDR11 and CHD7 associated with hypogonadotropic hypogonadism, but these variants are insufficient to contribute to the POI phenotype. Conclusion: Genetic panels based on next generation sequencing analysis technologies can be used to determine the molecular genetic diagnosis of POI, which has a highly heterogeneous genetic basis.
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The objective of this study is to communicate the findings of the first whole genome sequencing of a colistin-resistant Escherichia coli isolate harboring mcr-1 gene obtained from a pig in Argentina. Genomic DNA was sequenced using the MinION Oxford Nanopore platform. The libraries were prepared using a SQK-RBK110-96 protocol. The sequencing process was conducted on a MinION Mk1C MIN 101-C, utilizing a FLO-MIN106 flow cell. The quality of the reads was evaluated using NanoPlot. De novo assembly was conducted using Canu 1.6 and the quality of contigs was evaluated using QUAST. Annotation was performed using Prokka. The CBC20 strain exhibited a colistin MIC of 4 µg/mL. The genome size was 5178653 bp with a GC content of 50,31%. The N50 value was 133,250, while the L50 value was 21. A total of 11,620 genes, 11,518 coding sequences, 77 transfer RNAs and 24 ribosomal RNAs were identified. A serotype O9:H37 with sequence type ST-297 was observed. A total of seven antimicrobial resistance genes were identified, including mcr-1.5, bla TEM-1B, bla EC-18, bla TEM-70, aph(3')-Ia, mph(A) and sul3. The presence of punctual mutations was observed in the genes encoding the proteins GyrA (S83L, D87N) and ParC (S80I). Five distinct plasmid replicon types were identified, including IncFII, IncY, IncFIB, IncX1 and Col440II. Our findings may assist in the comprehension of the mechanisms of antimicrobial resistance, genomic epidemiology and dissemination of mcr-1 gene among animals and environment, which could potentially impact human health.
El objetivo de este estudio es comunicar la primera secuenciación de genoma completo de un aislamiento de Escherichia coli resistente a colistina mediada por el gen mcr-1 obtenido de un cerdo en Argentina. El ADN genómico se secuenció utilizando la plataforma MinION Oxford Nanopore. Las bibliotecas se prepararon utilizando un protocolo SQK-RBK110-96. El proceso de secuenciación se realizó en un MinION Mk1C MIN 101-C, utilizando una flow cell FLO-MIN106. La calidad de las lecturas se evaluó mediante NanoPlot. El ensamblaje de novo se realizó utilizando Canu 1.6 y la calidad de los contigs se evaluó utilizando QUAST. La anotación se realizó utilizando Prokka. CBC20 exhibió una CIM de colistina de 4 µg/mL. El tamaño del genoma fue de 5.178.653 pb con un contenido de GC del 50.31 %. El valor N50 fue 133.250, mientras que el valor L50 fue 21. Se identificaron un total de 11.620 genes, 11.518 secuencias codificantes, 77 ARN de transferencia y 24 ARN ribosómicos. Se observó el serotipo O9:H37 con un secuenciotipo ST-297. Se identificaron siete genes de resistencia, incluyendo mcr-1.5, bla TEM-1B, bla EC-18, bla TEM-70, aph(3')-Ia, mph(A) y sul3. Se observó la presencia de mutaciones puntuales en los genes que codifican las proteínas GyrA (S83L, D87N) y ParC (S80I). Se identificaron cinco tipos distintos de plásmidos, incluidos IncFII, IncY, IncFIB, IncX1 y Col440II. Nuestros hallazgos podrían ayudar a comprender los mecanismos de resistencia antimicrobiana, la epidemiología genómica y la diseminación del gen mcr-1 entre animales y el medio ambiente, lo que potencialmente podría afectar la salud humana.