Whole Genome Sequencing Reveals High Clonal Diversity of Isolated from Patients in a Tertiary Care Hospital in Moshi, Tanzania

Overview

Journal Antimicrob Resist Infect Control

Publisher Biomed Central

Specialty Infectious Diseases

Date 2018 Jul 7

PMID 29977533

Citations 16

Authors

Tolbert Sonda

Happiness Kumburu

Marco van Zwetselaar

Michael Alifrangis

Blandina T Mmbaga

Frank M Aarestrup

Gibson Kibiki

Ole Lund

Affiliations

Soon will be listed here.

Abstract

Background: Limited information regarding the clonality of circulating strains in tertiary care hospitals in low and middle-income countries is available. The purpose of this study was to determine the serotypes, antimicrobial resistance and virulence genes. Further, we carried out a phylogenetic tree reconstruction to determine relatedness of isolated from patients in a tertiary care hospital in Tanzania.

Methods: isolates from inpatients admitted at Kilimanjaro Christian Medical Centre between August 2013 and August 2015 were fully genome-sequenced at KCMC hospital. Sequence analysis was done for identification of resistance genes, Multi-Locus Sequence Typing, serotyping, and virulence genes. Phylogeny reconstruction using CSI Phylogeny was done to ascertain relatedness. Stata 13 (College Station, Texas 77,845 USA) was used to determine Cohen's kappa coefficient of agreement between the phenotypically tested and whole genome sequence predicted antimicrobial resistance.

Results: Out of 38 isolates, 21 different sequence types (ST) were observed. Eight (21.1%) isolates belonged to ST131; of which 7 (87.5.%) were serotype O25:H4. Ten (18.4%) isolates belonged to ST10 clonal complex; of these, four (40.0%) were ST617 with serotype O89:H10. Twenty-eight (73.7%) isolates carried genes encoding beta-lactam resistance enzymes On average, agreement across all drugs tested was 83.9%. Trimethoprim/sulphamethoxazole (co-trimoxazole) showed moderate agreement: 45.8%, kappa =15% and = 0.08. Amoxicillin-clavulanate showed strongest agreement: 87.5%, kappa = 74% and = 0.0001. Twenty-two (57.9%) isolates carried virulence factors for host cells adherence and 25 (65.7%) for factors that promote immune evasion by increasing survival in serum. The phylogeny analysis showed that ST131 clustering close together whereas ST10 clonal complex had a very clear segregation of the ST617 and a mix of the rest STs.

Conclusion: There is a high diversity of isolated from patients admitted to a tertiary care hospital in Tanzania. This underscores the necessity to routinely screen all bacterial isolates of clinical importance in tertiary health care facilities. WGS use for laboratory-based surveillance can be an effective early warning system for emerging pathogens and resistance mechanisms in LMICs.

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References

Mahende C, Ngasala B, Lusingu J, Butichi A, Lushino P, Lemnge M . Aetiology of acute febrile episodes in children attending Korogwe District Hospital in north-eastern Tanzania. PLoS One. 2014; 9(8):e104197. PMC: 4121319. DOI: 10.1371/journal.pone.0104197. View

Ben Zakour N, Alsheikh-Hussain A, Ashcroft M, Nhu N, Roberts L, Stanton-Cook M . Sequential Acquisition of Virulence and Fluoroquinolone Resistance Has Shaped the Evolution of Escherichia coli ST131. mBio. 2016; 7(2):e00347-16. PMC: 4850260. DOI: 10.1128/mBio.00347-16. View

Oteo J, Diestra K, Juan C, Bautista V, Novais A, Perez-Vazquez M . Extended-spectrum beta-lactamase-producing Escherichia coli in Spain belong to a large variety of multilocus sequence typing types, including ST10 complex/A, ST23 complex/A and ST131/B2. Int J Antimicrob Agents. 2009; 34(2):173-6. DOI: 10.1016/j.ijantimicag.2009.03.006. View

Valenza G, Nickel S, Pfeifer Y, Pietsch M, Voigtlander E, Lehner-Reindl V . Prevalence and genetic diversity of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli in nursing homes in Bavaria, Germany. Vet Microbiol. 2015; 200:138-141. DOI: 10.1016/j.vetmic.2015.10.008. View

Aibinu I, Odugbemi T, Koenig W, Ghebremedhin B . Sequence type ST131 and ST10 complex (ST617) predominant among CTX-M-15-producing Escherichia coli isolates from Nigeria. Clin Microbiol Infect. 2011; 18(3):E49-51. DOI: 10.1111/j.1469-0691.2011.03730.x. View

Labar A, Millman J, Ruebush E, Opintan J, Bishar R, Aboderin A . Regional dissemination of a trimethoprim-resistance gene cassette via a successful transposable element. PLoS One. 2012; 7(5):e38142. PMC: 3364232. DOI: 10.1371/journal.pone.0038142. View

Hildenwall H, Amos B, Mtove G, Muro F, Cederlund K, Reyburn H . Causes of non-malarial febrile illness in outpatients in Tanzania. Trop Med Int Health. 2015; 21(1):149-156. PMC: 4738434. DOI: 10.1111/tmi.12635. View

Moissenet D, Salauze B, Clermont O, Bingen E, Arlet G, Denamur E . Meningitis caused by Escherichia coli producing TEM-52 extended-spectrum beta-lactamase within an extensive outbreak in a neonatal ward: epidemiological investigation and characterization of the strain. J Clin Microbiol. 2010; 48(7):2459-63. PMC: 2897521. DOI: 10.1128/JCM.00529-10. View

Moyo S, Aboud S, Kasubi M, Lyamuya E, Maselle S . Antimicrobial resistance among producers and non-producers of extended spectrum beta-lactamases in urinary isolates at a tertiary Hospital in Tanzania. BMC Res Notes. 2010; 3:348. PMC: 3017072. DOI: 10.1186/1756-0500-3-348. View

10.

Mshana S, Falgenhauer L, Mirambo M, Mushi M, Moremi N, Julius R . Predictors of blaCTX-M-15 in varieties of Escherichia coli genotypes from humans in community settings in Mwanza, Tanzania. BMC Infect Dis. 2016; 16:187. PMC: 4850702. DOI: 10.1186/s12879-016-1527-x. View

11.

Shahrani M, Safarpoor Dehkordi F, Momtaz H . Characterization of Escherichia coli virulence genes, pathotypes and antibiotic resistance properties in diarrheic calves in Iran. Biol Res. 2014; 47:28. PMC: 4105491. DOI: 10.1186/0717-6287-47-28. View

12.

Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S, Lund O . Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother. 2012; 67(11):2640-4. PMC: 3468078. DOI: 10.1093/jac/dks261. View

13.

Phuc Nguyen M, Woerther P, Bouvet M, Andremont A, Leclercq R, Canu A . Escherichia coli as reservoir for macrolide resistance genes. Emerg Infect Dis. 2009; 15(10):1648-50. PMC: 2866414. DOI: 10.3201/eid1510.090696. View

14.

Larsen M, Cosentino S, Rasmussen S, Friis C, Hasman H, Marvig R . Multilocus sequence typing of total-genome-sequenced bacteria. J Clin Microbiol. 2012; 50(4):1355-61. PMC: 3318499. DOI: 10.1128/JCM.06094-11. View

15.

Afset J, Bevanger L, Romundstad P, Bergh K . Association of atypical enteropathogenic Escherichia coli (EPEC) with prolonged diarrhoea. J Med Microbiol. 2004; 53(Pt 11):1137-1144. DOI: 10.1099/jmm.0.45719-0. View

16.

Seni J, Falgenhauer L, Simeo N, Mirambo M, Imirzalioglu C, Matee M . Multiple ESBL-Producing Escherichia coli Sequence Types Carrying Quinolone and Aminoglycoside Resistance Genes Circulating in Companion and Domestic Farm Animals in Mwanza, Tanzania, Harbor Commonly Occurring Plasmids. Front Microbiol. 2016; 7:142. PMC: 4749707. DOI: 10.3389/fmicb.2016.00142. View

17.

Grimstrup Joensen K, Scheutz F, Lund O, Hasman H, Kaas R, Nielsen E . Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli. J Clin Microbiol. 2014; 52(5):1501-10. PMC: 3993690. DOI: 10.1128/JCM.03617-13. View

18.

Xiong Y, Wang P, Lan R, Ye C, Wang H, Ren J . A novel Escherichia coli O157:H7 clone causing a major hemolytic uremic syndrome outbreak in China. PLoS One. 2012; 7(4):e36144. PMC: 3338595. DOI: 10.1371/journal.pone.0036144. View

19.

Dallman T, Chattaway M, Cowley L, Doumith M, Tewolde R, Wooldridge D . An investigation of the diversity of strains of enteroaggregative Escherichia coli isolated from cases associated with a large multi-pathogen foodborne outbreak in the UK. PLoS One. 2014; 9(5):e98103. PMC: 4028294. DOI: 10.1371/journal.pone.0098103. View

20.

Torres A, Blanco M, Valenzuela P, Slater T, Patel S, Dahbi G . Genes related to long polar fimbriae of pathogenic Escherichia coli strains as reliable markers to identify virulent isolates. J Clin Microbiol. 2009; 47(8):2442-51. PMC: 2725649. DOI: 10.1128/JCM.00566-09. View