Characterization of Escherichia coli involved in extraintestinal infections among patients in North-western Tanzania: circulating sequence types, risk factors and antimicrobial resistance profiles

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dc.contributor.advisorDeVinney, Rebekah
dc.contributor.advisorPitout, Johann D. D.
dc.contributor.advisorMshana, Stephen Eliatosha
dc.contributor.authorSeni, Jeremiah
dc.contributor.committeememberMeer, Franciscus Johannes van der
dc.contributor.committeememberSchryvers, Anthony Bernard
dc.date2019-06
dc.date.accessioned2018-10-30T18:00:19Z
dc.date.available2018-10-30T18:00:19Z
dc.date.issued2018-10-29
dc.description.abstractLimited information is available regarding the population structure of extraintestinal pathogenic Escherichia coli (ExPEC), and especially ST131 in Africa. Delineation of ExPEC clones among patients in Tanzania is pivotal in guiding antimicrobial therapies and infection preventive measures. A cross sectional analytical study was conducted between 2016 and 2017 in seven health care facilities (HCF) in North-western Tanzania, involving 1,828 pregnant women and 950 children under five years of age. Characterization of 226 ExPEC strains (128 from pregnant women, 15 from children and 83 from other patients) into ST-fimH clones (by the 7SNP-qPCR and gene sequencing), and ST131 clades (by multiplex PCR) was performed. The prevalence of urinary tract infections (UTIs) and blood stream infections (BSIs) among pregnant women and children was 17.7% (95%CI: 16.0-19.5%) and 14.2% (95%CI: 12.1%-16.6%), respectively, with predominance of ExPEC, Klebsiella spp. and Staphylococcus aureus. Third generation cephalosporin resistance (3rd gen Ceph-R) among Enterobacteriaceae was 16.6% (43/259) and 79.0% (75/95), respectively in the two groups; and was significantly higher in strains from a tertiary hospital [OR(95%CI): 3.27(1.02-10.49), p-value=0.046] and [4.95(1.15–21.32), p-value=0.032], among pregnant women and children, respectively compared to lower HCF. Approximately, 64.2% (n=145) of ExPEC strains were typeable using the 7SNP-qPCR and gene sequencing, with predominance of CC10 (33.1%), and ST131-fimH30/41 (17.9%). The 7-SNP qPCR correctly typed all dominant global clones in this ExPEC collection (i.e. ST131-fimH30/41, ST95-fimH41, ST73-fimH9/10 and ST69-fimH27). ST131 clades C1 (9, 34.6%) and C2 (10, 38.5%) predominated, and were associated with fluoroquinolone resistance and 3rd gen Ceph-R, respectively. Extended spectrum beta lactamases in E. coli strains were blaCTX-M-15 (89.8%, n=44), blaCTX-M-27 (n=2), blaCTX-M-24 (n=1), blaCTX-M-14 (n=1) and unknown (n=1). The pulsed field gel electrophoresis displayed heterogeneity among non-typeable strains. There is an increase in multidrug-resistant pathogens in the cascade of the referral health care system, underscoring the need to have level-specific antimicrobial stewardship. The 7-SNP qPCR and multiplex clade PCR are feasible, cost effective and simple molecular tools that can be utilized in surveillance programs to track dominant ExPEC clones, especially in low and middle income countries. This is the first report in Tanzania showing ST131 strains producing blaCTX-M-27.en_US
dc.identifier.citationSeni, J. (2018). Characterization of Escherichia coli involved in extraintestinal infections among patients in North-western Tanzania: circulating sequence types, risk factors and antimicrobial resistance profiles (Doctoral thesis, University of Calgary, Calgary, Canada). Retrieved from https://prism.ucalgary.ca. doi:10.11575/PRISM/33238en_US
dc.identifier.doihttp://dx.doi.org/10.11575/PRISM/33238
dc.identifier.urihttp://hdl.handle.net/1880/108935
dc.language.isoeng
dc.publisher.facultyCumming School of Medicine
dc.publisher.facultyGraduate Studies
dc.publisher.institutionUniversity of Calgaryen
dc.publisher.placeCalgaryen
dc.rightsUniversity of Calgary graduate students retain copyright ownership and moral rights for their thesis. You may use this material in any way that is permitted by the Copyright Act or through licensing that has been assigned to the document. For uses that are not allowable under copyright legislation or licensing, you are required to seek permission.
dc.subjectExtraintestinal pathogenic Escherichia coli
dc.subjectAntimicrobial resistance
dc.subjectNorth-western Tanzania
dc.subject.classificationBiologyen_US
dc.subject.classificationMicrobiologyen_US
dc.subject.classificationBiology--Molecularen_US
dc.subject.classificationHealth Sciencesen_US
dc.subject.classificationEpidemiologyen_US
dc.subject.classificationPublic Healthen_US
dc.titleCharacterization of Escherichia coli involved in extraintestinal infections among patients in North-western Tanzania: circulating sequence types, risk factors and antimicrobial resistance profiles
dc.typedoctoral thesis
thesis.degree.disciplineMicrobiology & Infectious Diseases
thesis.degree.grantorUniversity of Calgary
thesis.degree.nameDoctor of Philosophy (PhD)
ucalgary.item.requestcopytrue
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