Genomic landscape of extended-spectrum β-lactamase resistance in Escherichia coli from an urban African setting

Objectives: Efforts to treat Escherichia coli infections are increasingly being compromised by the rapid, global spread of antimicrobial resistance (AMR). Whilst AMR in E. coli has been extensively investigated in resource-rich settings, in sub-Saharan Africa molecular patterns of AMR are not well described. In this study, we have begun to explore the population structure and molecular determinants of AMR amongst E. coli isolates from Malawi. Methods: Ninety-four E. coli isolates from patients admitted to Queen’s Hospital, Malawi, were whole-genome sequenced. The isolates were selected on the basis of diversity of phenotypic resistance profiles and clinical source of isolation (blood, CSF and rectal swab). Sequence data were analysed using comparative genomics and phylogenetics. Results: Our results revealed the presence of five clades, which were strongly associated with E. coli phylogroups A, B1, B2, D and F. We identified 43 multilocus STs, of which ST131 (14.9%) and ST12 (9.6%) were the most common. We identified 25 AMR genes. The most common ESBL gene was blaCTX-M-15 and it was present in all five phylogroups and 11 STs, and most commonly detected in ST391 (4/4 isolates), ST648 (3/3 isolates) and ST131 [3/14 (21.4%) isolates]. Conclusions: This study has revealed a high diversity of lineages associated with AMR, including ESBL and fluoroquinolone resistance, in Malawi. The data highlight the value of longitudinal bacteraemia surveillance coupled with detailed molecular epidemiology in all settings, including low-income settings, in describing the global epidemiology of ESBL resistance

Optimising molecular diagnostic capacity for effective control of tuberculosis in high-burden settings

The World Health Organization's 2035 vision is to reduce tuberculosis (TB) associated mortality by 95%. While low-burden, well-equipped industrialised economies can expect to see this goal achieved, it is challenging in the low- and middle-income countries that bear the highest burden of TB. Inadequate diagnosis leads to inappropriate treatment and poor clinical outcomes. The roll-out of the Xpert® MTB/RIF assay has demonstrated that molecular diagnostics can produce rapid diagnosis and treatment initiation. Strong molecular services are still limited to regional or national centres. The delay in implementation is due partly to resources, and partly to the suggestion that such techniques are too challenging for widespread implementation. We have successfully implemented a molecular tool for rapid monitoring of patient treatment response to anti-tuberculosis treatment in three high TB burden countries in Africa. We discuss here the challenges facing TB diagnosis and treatment monitoring, and draw from our experience in establishing molecular treatment monitoring platforms to provide practical insights into successful optimisation of molecular diagnostic capacity in resource-constrained, high TB burden settings. We recommend a holistic health system-wide approach for molecular diagnostic capacity development, addressing human resource training, institutional capacity development, streamlined procurement systems, and engagement with the public, policy makers and implementers of TB control programmes.PostprintPeer reviewe

Genomic analysis of Klebsiella pneumoniae isolates from Malawi reveals acquisition of multiple ESBL determinants across diverse lineages

Objectives ESBL-producing Klebsiella pneumoniae (KPN) pose a major threat to human health globally. We carried out a WGS study to understand the genetic background of ESBL-producing KPN in Malawi and place them in the context of other global isolates. Methods We sequenced genomes of 72 invasive and carriage KPN isolates collected from patients admitted to Queen Elizabeth Central Hospital, Blantyre, Malawi. We performed phylogenetic and population structure analyses on these and previously published genomes from Kenya (n = 66) and from outside sub-Saharan Africa (n = 67). We screened for presence of antimicrobial resistance (AMR) genetic determinants and carried out association analyses by genomic sequence cluster, AMR phenotype and time. Results Malawian isolates fit within the global population structure of KPN, clustering into the major lineages of KpI, KpII and KpIII. KpI isolates from Malawi were more related to those from Kenya, with both collections exhibiting more clonality than isolates from the rest of the world. We identified multiple ESBL genes, including blaCTX-M-15, several blaSHV, blaTEM-63 and blaOXA-10, and other AMR genes, across diverse lineages of the KPN isolates from Malawi. No carbapenem resistance genes were detected; however, we detected IncFII and IncFIB plasmids that were similar to the carbapenem resistance-associated plasmid pNDM-mar. Conclusions There are multiple ESBL genes across diverse KPN lineages in Malawi and plasmids in circulation that are capable of carrying carbapenem resistance. Unless appropriate interventions are rapidly put in place, these may lead to a high burden of locally untreatable infection in vulnerable populations

Care allowance and its usage in providing social services

The topic of this thesis is a care allowance in the region of České Budejovice. The care allowance is a benefit introduced by Law No. 108/2006 Coll., Social Services, as amended with effect from 1st January 2007. Care allowance under the Act should be used to provide the necessary care to persons who are dependent on other´s assistance. It is paid in four stages according to the degree of dependence. This is a brand new benefit, novelty is its concept, which strengthens the position of active users of social services. The care allowance is designed as a subsidy at which users can purchase such social services they voluntarily choose. Since its introduction, the care allowance faced some problems - growing number of users, leading to the growth of benefits paid, which, however, compared to the original plan does not go back into the system. This is so because users mainly in the first instance elects family or other relatives as care providers, or consider care allowance for additional house hold income and does not cover social services. The theoretical part is focused on the notion of social services, their history and development. Another section is devoted to the current law on social services. .The last section of the theoretical part deals with the care allowance explanation, its function and describe the procedure of its gaining. The aim is to find out the actual use of the allowance and user satisfaction with its amount especially after the reduction from 2011. The research used quantitative methods - Secondary data analysis and questionnaire survey, which was carried out on a representative sample of users of the care allowance in the municipality České Budejovice. Basic file for secondary data analysis and questionnaire survey were the beneficiaries of care allowance in České Budejovice. According to the Municipality of České Budejovice it was in 2011, when the research was conducted, about 4400 people. The target file for the survey is therefore 330 people. In total 340 questionnaires were answered in this research. A questionnaire survey was conducted among users in the form of open and closed questions. The questionnaire contains a total of 10 questions, 8 are closed, one question is open and one question is closed with possibility of additional response. At the beginning of the questionnaire, respondents were informed about its focus and subsequent use of this information. The aim is to find out how recipients with care allowance actually use it and their satisfaction with it specially in the first stage of the reduction since 2011. I identified the following objectives and hypotheses: Objective I.: To determine how recipients treated care allowances. Objective II.: To find out how the recipients evaluate the amount of the care allowance. Hypothesis I.: Recipients of the care allowance in I. and II. degree prefer family care. Hypothesis II.: Recipients of the care allowance in the first instance are dissatisfied with the amount. Hypotheses were based on the results of preliminary research. Hypothesis I.: It was confirmed that recipients of the care allowance in I. and II. degree prefer family care, the research showed that the users of care allowance in I. and II. level prefer caregiving family or other non-registered individual in more than 60 percents Also the hypothesis II.: It was confirmed that recipients of the care allowance in the first level are dissatisfied with the amount. The results show that although it is not a rule with increasing level of the care allowance increases also user satisfaction with its amount, there is more than 60% of dissatisfied users among users of first instance of the care

Tuberculosis bacillary load, an early marker of disease severity: the utility of tuberculosis Molecular Bacterial Load Assay.

In this comparative biomarker study, we analysed 1768 serial sputum samples from 178 patients at 4 sites in Southeast Africa. We show that tuberculosis Molecular Bacterial Load Assay (TB-MBLA) reduces time-to-TB-bacillary-load-result from days/weeks by culture to hours and detects early patient treatment response. By day 14 of treatment, 5% of patients had cleared bacillary load to zero, rising to 58% by 12th week of treatment. Fall in bacillary load correlated with mycobacterial growth indicator tube culture time-to-positivity (Spearmans r=-0.51, 95% CI (-0.56 to -0.46), p<0.0001). Patients with high pretreatment bacillary burdens (above the cohort bacillary load average of 5.5log10eCFU/ml) were less likely to convert-to-negative by 8th week of treatment than those with a low burden (below cohort bacillary load average), p=0.0005, HR 3.1, 95% CI (1.6 to 5.6) irrespective of treatment regimen. TB-MBLA distinguished the bactericidal effect of regimens revealing the moxifloxacin-20 mg rifampicin regimen produced a shorter time to bacillary clearance compared with standard-of-care regimen, p=0.008, HR 2.9, 95% CI (1.3 to 6.7). Our data show that the TB-MBLA could inform clinical decision making in real-time and expedite drug TB clinical trials

Tuberculosis bacillary load, an early marker of disease severity and treatment response : the utility of tuberculosis Molecular Bacterial Load Assay

This work was supported by the European and Developing Countries Clinical Trials Partnership (EDCTP), [SP.2011.41304.008] and PreDiCT-TB consortium R [IMI Joint undertaking grant agreement number 115337], resources of which are composed of financial contribution from the European Union's Seventh Framework Programme [FP7/2007-2013] and EFPIA companies' in-kind contribution.In this comparative biomarker study, we analysed 1768 serial sputum samples from 178 patients at 4 sites in Southeast Africa. We show that tuberculosis Molecular Bacterial Load Assay (TB-MBLA) reduces time-to-TB-bacillary-load-result from days/weeks by culture to hours and detects early patient treatment response. By day 14 of treatment, 5% of patients had cleared bacillary load to zero, rising to 58% by 12th week of treatment. Fall in bacillary load correlated with mycobacterial growth indicator tube culture time-to-positivity (Spearmans r=−0.51, 95% CI (−0.56 to −0.46), p<0.0001). Patients with high pretreatment bacillary burdens (above the cohort bacillary load average of 5.5log10eCFU/ml) were less likely to convert-to-negative by 8th week of treatment than those with a low burden (below cohort bacillary load average), p=0.0005, HR 3.1, 95% CI (1.6 to 5.6) irrespective of treatment regimen. TB-MBLA distinguished the bactericidal effect of regimens revealing the moxifloxacin—20 mg rifampicin regimen produced a shorter time to bacillary clearance compared with standard-of-care regimen, p=0.008, HR 2.9, 95% CI (1.3 to 6.7). Our data show that the TB-MBLA could inform clinical decision making in real-time and expedite drug TB clinical trials.Publisher PDFPeer reviewe