Characterization of Escherichia coli involved in extraintestinal infections among patients in North-western Tanzania: circulating sequence types, risk factors and antimicrobial resistance profiles
Bibliographic record
Abstract
Limited 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.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".