Genome-based characterization of Escherichia coli causing bloodstream infection through next-generation sequencing.

Rafika Indah Paramita,Linda Erlina,Nelly Puspandari,Erni Juwita Nelwan,Fadilah Fadilah,Editha Renesteen,Iddya Karunasagar

doi:10.1371/journal.pone.0244358

Rafika Indah Paramita, Linda Erlina + Show 5 more

Open Access

https://doi.org/10.1371/journal.pone.0244358

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Journal: PloS one	Publication Date: Dec 23, 2020
Citations: 16	License type: CC BY 4.0

Affiliation: University of Indonesia, Ministry of Health

Abstract

Escherichia coli are one of the commonest bacteria causing bloodstream infection (BSI). The aim of the research was to identify the serotypes, MLST (Multi Locus Sequence Type), virulence genes, and antimicrobial resistance of E. coli isolated from bloodstream infection hospitalized patients in Cipto Mangunkusumo National Hospital Jakarta. We used whole genome sequencing methods rather than the conventional one, to characterized the serotypes, MLST (Multi Locus Sequence Type), virulence genes, and antimicrobial resistance (AMR) of E. coli. The composition of E. coli sequence types (ST) was as follows: ST131 (n = 5), ST38 (n = 3), ST405 (n = 3), ST69 (n = 3), and other STs (ST1057, ST127, ST167, ST3033, ST349, ST40, ST58, ST6630). Enteroaggregative E. coli (EAEC) and Extra-intestinal pathogenic E. coli (ExPEC) groups were found dominant in our samples. Twenty isolates carried virulence genes for host cells adherence and 15 for genes that encourage E. coli immune evasion by enhancing survival in serum. ESBL-genes were present in 17 E. coli isolates. Other AMR genes also encoded resistance against aminoglycosides, quinolones, chloramphenicol, macrolides and trimethoprim. The phylogeny analysis showed that phylogroup D is dominated and followed by phylogroup B2. The E. coli isolated from 22 patients in Cipto Mangunkusumo National Hospital Jakarta showed high diversity in serotypes, sequence types, virulence genes, and AMR genes. Based on this finding, routinely screening all bacterial isolates in health care facilities can improve clinical significance. By using Whole Genome Sequencing for laboratory-based surveillance can be a valuable early warning system for emerging pathogens and resistance mechanisms.

Highlights

There is currently enlarge in the prevalence of infections worldwide due to multidrug-resistant (MDR)
The purpose of the study was to characterize the serotypes, Multi-Locus Sequence Typing (MLST) (Multi Locus Sequence Type), virulence genes, and antimicrobial resistance of E. coli isolated from bloodstream infection patients in Cipto Mangunkusumo National Hospital Jakarta
Five (22,7%) E. coli samples are belonged to ST131 and all of this five had serotype O25:H4

Summary

Introduction

There is currently enlarge in the prevalence of infections worldwide due to multidrug-resistant (MDR). Due to their correlation with a high level of mortality and morbidity which are triggered by the insufficient of potent antibiotics, Gram-negative bacteria became a critical threat to global public health [1,2,3]. Escherichia coli naturally inhabits the human gastrointestinal tract (GIT) and classified as Gram-negative commensals bacterium. Two main classification of pathogenic E. coli—diarrheagenic E. coli (DEC) and extra-intestinal pathogenic E. coli (ExPEC)—are perceived, varying in their associated clinical syndromes and virulence genes. Extraintestinal pathogenic E. coli (ExPEC) can cause a diversity of infections, including sepsis, neonatal meningitis, and urinary tract infections (UTI). Virulent E. coli strains share pathogenic, virulence, and resistance genes with avirulent or less virulent strains, allowing the appearance of pathogenesis beyond their natural characters [7]

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