The higher prevalence of extended spectrum beta-lactamases among Escherichia coli ST131 in Southeast Asia is driven by expansion of a single, locally prevalent subclone

Swaine L Chen,Partha Pratim De,Kean Lee Chew,Nuntra Suwantarat,Anucha Apisarnthanarak,Sophia Archuleta,Joshua Guo Xian Wong,Ying Ding,Tse Hsien Koh,Sharifah Faridah Syed Omar,Rukumani Devi Velayuthan,Shirin Kalimuddin,Nadia Atiya,David C Lye

doi:10.1038/s41598-019-49467-5

Abstract

The ST131 multilocus sequence type (MLST) of Escherichia coli is a globally successful pathogen whose dissemination is increasing rates of antibiotic resistance. Numerous global surveys have demonstrated the pervasiveness of this clone; in some regions ST131 accounts for up to 30% of all E. coli isolates. However, many regions are underrepresented in these published surveys, including Africa, South America, and Asia. We collected consecutive bloodstream E. coli isolates from three countries in Southeast Asia; ST131 was the most common MLST type. As in other studies, the C2/H30Rx clade accounted for the majority of ST131 strains. Clinical risk factors were similar to other reported studies. However, we found that nearly all of the C2 strains in this study were closely related, forming what we denote the SEA-C2 clone. The SEA-C2 clone is enriched for strains from Asia, particularly Southeast Asia and Singapore. The SEA-C2 clone accounts for all of the excess resistance and virulence of ST131 relative to non-ST131 E. coli. The SEA-C2 strains appear to be locally circulating and dominant in Southeast Asia, despite the intuition that high international connectivity and travel would enable frequent opportunities for other strains to establish themselves.

Highlights

The ST131 multilocus sequence type (MLST) of Escherichia coli is a globally successful pathogen whose dissemination is increasing rates of antibiotic resistance
As in other geographical areas, we found that ST131 E. coli was the most common sequence type of E. coli causing such infections, and we focused on clinical risk factors and phenotypic resistance profiles associated with ST131 infections
We found ST131 strains from all three major clades; interestingly, in Southeast Asia, C2/H30-Rx strains were all very closely related to each other; we refer to these strains as the SEA-C2 (Southeast Asia-C2) subclone of ST131

Summary

Introduction

The ST131 multilocus sequence type (MLST) of Escherichia coli is a globally successful pathogen whose dissemination is increasing rates of antibiotic resistance. ExPEC strains are generally more antibiotic resistant than other types of E. coli, and the expansion of specific ExPEC clones or multilocus sequence types (MLSTs) have been contributing to the rising rates of E. coli antibiotic resistance, such as ST38, ST405, and ST6484. Another of these ExPEC sequence types, ST131 E. coli, has been more extensively studied over the last 10 years and found to be rapidly expanding across the globe. Despite the general resistance of C2/H30-Rx strains to more antibiotics, all of Clade C/H30-R seems to be participating in the recent global expansion of ST13115

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Discussion

Conclusion