Genomic characterization of a high pathogenic Escherichia coli causing bacterial meningitis in a newborn in Italy, 2022

Introduction:The effective treatment and control of tuberculosis (TB) has been hindered due to the emergence of drug resistant TB (especially multidrug resistant TB or MDR-TB).MDR-TB (resistance to rifampicin and isoniazid) is more prevalent in low-and middle-income country (LMIC) settings.In this study, we evaluated the genetic mutations associated with rifampicin (RIF) and isoniazid (INH) resistance among patients newly diagnosed with tuberculosis using Line Probe Assay (LPA) assay at a national reference laboratory (NRL) for tuberculosis in Bhubaneswar, India during 2018 to 2023.Methods: Line Probe Assay (Hain Lifescience GmbH, Germany) testing initiated in the NRL in July, 2018.We collected retrospective data on testing of all samples from people diagnosed with tuberculosis during July, 2018 to May, 2023.The samples were received from public and private hospitals/clinics in Bhubaneswar.LPA is a qualitative in-vitro test for the detection of Mycobacterium tuberculosis (M.tb) complex, along with resistance to RIF and INH.The mutation data for rifampicin and isoniazid was entered in Excel 2010 (Microsoft office, USA) and analysed to evaluate the proportion of RIF and INH resistance along with the mutations responsible for conferring resistance.The study was approved by the Institutional Human Ethics Committee.Results: In this study, we included samples from 414 patients for whom LPA data was available.This included 69.1% (286/414) males.Pulmonary samples (sputum, bronchoalveolar lavage/ BAL, gastric aspirate) constituted 73.4% (304/414), while 26.6% (110/414) were extrapulmonary samples (cerebrospinal fluid, pleural fluid, pus/abscess, lymph node biopsy, tissue, etc).Of the 414 samples, 91.8% (380/414) were sensitive to both RIF and INH.HrTB (INH resistance only) was found in 5.3% (22/414) samples.MDR TB (resistance to both RIF and INH) was detected in 1.7% (7/414) samples.1% (4/414) samples showed inferred resistance for RIF (wild type 8/ WT8 absent, mutation bands absent), while INH was sensitive.1 sample showed inferred resistance for RIF (WT7 absent, mutation absent), and was INH resistant.Of the 7 RIF resistant samples, 1 had mut1 present (WT8 absent), while 6 samples had mut3 present (WT8 absent).For katG gene, mut1 was present in 93.3% (28/30) of INH resistant samples (12 WT present, 16 WT absent).For inhA gene, mut1 was present in 1 sample, while WT1 was absent in 1 sample.Discussion: Our study involving more than 400 M.tb positive samples found HrTB in 5.3% samples and MDR TB in 1.7% samples using LPA.LPA helps in the rapid diagnosis of MDR-TB, which is a prerequisite for appropriate therapy.In this study, we did not evaluate resistance to other anti-tubercular drugs (fluroquinolones, second-line injectable drugs, etc).Results: Genome of E. coli 1455 strain harbored a circular chromosome and two plasmids of 167.740-bp and 4.073-bp in length, respectively.E. coli 1455 belonged to the ST3, serotype O17:H18 and carried different determinants including resistance to B-lactams, tetracyclines, and quinolones.In addition, genome of E. coli 1455 strain harbored 5 integrated pro-phage regions mainly located in the chromosome, while most of the virulence factors associated to the invasiveness and clinical severity and different antimicrobial resistance determinants (blaTEM-1, tet(A) and qnrS1) were located in the 167-Kb plasmid. Conclusion:In conclusion, here we characterized the virulence factors in a E. coli causing meningitis in a newborn and provide a deeply picture of the genomic structure related to the disease severity.Taken together, our findings suggest a possible widespread of a virulence factors-carrying plasmid worldwide and highlight the importance of genomic characterization in the diffusion of public health threats.