Rapid Spread of Pneumococcal Nonvaccine Serotype 7C Previously Associated with Vaccine Serotype 19F, England and Wales.

We observed a sudden and rapid increase in rare invasive pneumococcal disease serotype 7C, from an annual average of 3 cases during 2000-01 through 2015-16 to 29 cases in 2016-17. The increase was caused almost entirely by clonal expansion of sequence type 177, previously associated with vaccine serotype 19F

Dari Trainer, Imam Ibadah Hingga Patronase Spiritual : Pelayanan Kbih Al-hikmah Kepada Calon/ Jamaah Haji di Kabupaten Brebes

Some people stated that the roles of KBIH and its services toward pil­grims are questionable. Several KBIHs have been changed to businessinstitution rather than social institution. There is a kind of comodi.ficationof it. This paper argues, based on field research, that KBIH al-Hikmahhas given satisfied services to pilgrims. The services were not only inthe preparation of pilgrimages (manasik), but also during the pilgrim­ages in Mecca and and after the pilgrimages in Indonesia. In the prepa­ration of pilgrimages, the role of KBIH was a trainer - making candi­dates of pilgrims are more understanding and capable for practicingthe ritual. In Mecca, KBIH was not only as guider of long journey. butalso the imam of various rituals of pilgrimages. The role of KBIH hasbecome spiritual patronages ( ecclesiasticum] of pilgrims in the rest oftheir lifes

Whole genome sequencing in the investigation of recurrent invasive Group A streptococcus outbreaks in a maternity unit

Background: The clinical manifestations of Group A streptococcus (GAS) – (Streptococcus pyogenes) are diverse, ranging from asymptomatic colonisation to devastating invasive disease. Maternity related clusters of invasive Group A streptococcus (iGAS) infection are complex to investigate and control, especially if recurrent. Aim: We report on the investigation into three episodes of emm 75 GAS/iGAS infection in maternity patients at one hospital site over a 4 year period, two with monophyletic ancestry. Methods: The episodes are described, together with whole genome sequence isolate analyses. Single nucleotide polymorphism differences were compared with contemporaneous emm 75 genomes. Findings: Seven mothers had GAS/iGAS in over a 4 year period, emm 75, S.pyogenes and one had iGAS (in year 4) emm 3, S.pyogenes (subsequently discounted as linked). Three (clinical/screening samples) of the seven babies of emm 75 positive mothers and 3 screened healthcare workers were positive for GAS emm 75. Whole genome sequence similarity suggests a shared ancestral lineage and suggested a common source transmission but directionality of transmission cannot be inferred. However the findings indicate that persistence of a particular clone in a given setting may be long-term. Conclusions: Occupational health procedures were enhanced, staff were screened and antibiotic therapy provided to GAS positive staff and patients. The definitive source of infection could not be identified, although staff/patient transmission is the most likely route. The pattern of clonal GAS transmission over 4 years suggests long-term persistence of GAS may have occurred

Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance : a retrospective cohort study

BACKGROUND : Diagnosing drug-resistance remains an obstacle to the elimination of tuberculosis. Phenotypic drugsusceptibility testing is slow and expensive, and commercial genotypic assays screen only common resistancedetermining mutations. We used whole-genome sequencing to characterise common and rare mutations predicting drug resistance, or consistency with susceptibility, for all fi rst-line and second-line drugs for tuberculosis. METHODS : Between Sept 1, 2010, and Dec 1, 2013, we sequenced a training set of 2099 Mycobacterium tuberculosis genomes. For 23 candidate genes identifi ed from the drug-resistance scientifi c literature, we algorithmically characterised genetic mutations as not conferring resistance (benign), resistance determinants, or uncharacterised. We then assessed the ability of these characterisations to predict phenotypic drug-susceptibility testing for an independent validation set of 1552 genomes. We sought mutations under similar selection pressure to those characterised as resistance determinants outside candidate genes to account for residual phenotypic resistance. FINDINGS : We characterised 120 training-set mutations as resistance determining, and 772 as benign. With these mutations, we could predict 89·2% of the validation-set phenotypes with a mean 92·3% sensitivity (95% CI 90·7–93·7) and 98·4% specifi city (98·1–98·7). 10·8% of validation-set phenotypes could not be predicted because uncharacterised mutations were present. With an in-silico comparison, characterised resistance determinants had higher sensitivity than the mutations from three line-probe assays (85·1% vs 81·6%). No additional resistance determinants were identifi ed among mutations under selection pressure in non-candidate genes. INTERPRETATION : A broad catalogue of genetic mutations enable data from whole-genome sequencing to be used clinically to predict drug resistance, drug susceptibility, or to identify drug phenotypes that cannot yet be genetically predicted. This approach could be integrated into routine diagnostic workfl ows, phasing out phenotypic drugsusceptibility testing while reporting drug resistance early.Wellcome Trust, National Institute of Health Research, Medical Research Council, and the European Union.http://www.thelancet.com/infectionhb201

Whole genome sequencing of group A Streptococcus: development and evaluation of an automated pipeline for emmgene typing

Streptococcus pyogenes group A Streptococcus (GAS) is the most common cause of bacterial throat infections, and can cause mild to severe skin and soft tissue infections, including impetigo, erysipelas, necrotizing fasciitis, as well as systemic and fatal infections including septicaemia and meningitis. Estimated annual incidence for invasive group A streptococcal infection (iGAS) in industrialised countries is approximately three per 100,000 per year. Typing is currently used in England and Wales to monitor bacterial strains of S. pyogenes causing invasive infections and those isolated from patients and healthcare/care workers in cluster and outbreak situations. Sequence analysis of the emm gene is the currently accepted gold standard methodology for GAS typing. A comprehensive database of emm types observed from superficial and invasive GAS strains from England and Wales informs outbreak control teams during investigations. Each year the Bacterial Reference Department, Public Health England (PHE) receives approximately 3,000 GAS isolates from England and Wales. In April 2014 the Bacterial Reference Department, PHE began genomic sequencing of referred S. pyogenes isolates and those pertaining to selected elderly/nursing care or maternity clusters from 2010 to inform future reference services and outbreak analysis (n = 3, 047). In line with the modernizing strategy of PHE, we developed a novel bioinformatics pipeline that can predict emmtypes using whole genome sequence (WGS) data. The efficiency of this method was measured by comparing the emmtype assigned by this method against the result from the current gold standard methodology; concordance to emmsubtype level was observed in 93.8% (2,852/3,040) of our cases, whereas in 2.4% (n = 72) of our cases concordance was observed to emm type level. The remaining 3.8% (n = 117) of our cases corresponded to novel types/subtypes, contamination, laboratory sample transcription errors or problems arising from high sequence similarity of the allele sequence or low mapping coverage. De novo assembly analysis was performed in the two latter groups (n = 72 + 117) and was able to diagnose the problem and where possible resolve the discordance (60/72 and 20/117, respectively). Overall, we have demonstrated that our WGS emm-typing pipeline is a reliable and robust system that can be implemented to determine emm type for the routine service

El Diario de Pontevedra : periódico liberal: Ano XXXIX Número 11461 - 1922 maio 27

Investigation of the not-typeable (“Serotype undetermined”) isolates from the SNP-based approach. The pileup file created during the analysis was investigated in detail to determine the aetiology behind the incomplete SNP profiles. (XLSX 19 kb

Additional file 4: Table S4. of Comparison of molecular serotyping approaches of Streptococcus agalactiae from genomic sequences

Investigation of the SNPs (previously published and novel) identified using multiple alignment of the reference cps loci using a small a small dataset of clinical samples (n = 28). SNP positions highlighted in grey represent SNPs not found in all isolates of a particular serotype. These positions were removed and the remaining SNPs represent the final set used in this study. (XLSX 23 kb