Genome of Multidrug-Resistant Uropathogenic Escherichia coli Strain NA114 from India

Abstract

Uropathogenic Escherichia coli (UPEC) causes serious infections in people at risk and has a significant environmental prevalence due to contamination by human and animal excreta. In developing countries, UPEC assumes importance in certain dwellings because of poor community/personal hygiene and exposure to contaminated water or soil. We report the complete genome sequence of E. coli strain NA114 from India, a UPEC strain with a multidrug resistance phenotype and the capacity to produce extended-spectrum beta-lactamase. The genome sequence and comparative genomics emanating from it will be significant in under-standing the genetic makeup of diverse UPEC strains and in boosting the development of new diagnostics/vaccines.

GENOME ANNOUNCEMENT

Pathogenic Escherichia coli constitutes a significant threat to public health, and the emergence of extended-spectrum beta-lactamase (ESBL)-producing E. coli with high virulence potential is alarming (14, 16, 20, 22, 23). Comparative genomics holds significant promise in understanding the genome organization of such bacteria and thereby identifying coordinates highly relevant in the development of intervention strategies (1). Our group has recently studied uropathogenic E. coli (UPEC) from the western Indian city of Pune (11), whereupon strain NA114 emerged as an ideal representative of the entire Pune collection. The three major characteristics of strain NA114 that make it epidemiologically and clinically significant are its affiliation with serogroup O25, its placement in phylogenetic group B2, and its sequence type, ST131 (19). The latter denotes a pandemic clone frequently associated with community-acquired antimicrobial-resistant infections (23). Motivated by these facts, we performed complete in-depth sequencing, annotation, and analysis of the genome of UPEC strain NA114, which was originally obtained from the urine of a 70-year-old male patient with prostatitis from Pune. Antibiotic sensitivity tests revealed that it was a multidrug-resistant strain refractory to several common antibiotics and was an ESBL producer (11).

(This work constitutes part of the unpublished doctoral work of Arif Hussain.)

The genome sequence was determined by Illumina Genome Analyzer (GA2x, pipeline ver. l.6) and consisted of sequence traces equivalent to 8 gigabytes of data, encompassing 54-bp paired-end reads with an insert size of 300 bp, and the genome coverage achieved was 500×. The sequence was assembled using Velvet (26), and the contigs were ordered with respect to the best-aligned positions compared to the reference genome of E. coli SE15 (25) using Mauve (5, 6). The genome alignment tools BLAT (15) and MUMmer (17) were also used to validate the aligned contigs. The genome was annotated with the help of the RAST server (2), and putative CDSs were identified by comparing outputs from Glimmer (7), Genemark (4), and EasyGene (18). Artemis (24) was used to glean the following details of the genome.

The size of the NA114 chromosome was 4,935,666 bp with a G+C content of 51.16% and a coding percentage of 88.4% with 4,875 protein coding sequences with an average length of 901 bp. The genome revealed 67 tRNA and 3 rRNA genes. We also found several virulence genes, including iha, sat, fimH, kpsM, iutA, and malX, which correspond to the genes of E. coli CFT073 (9). In addition, genes corresponding to another UPEC strain, UTI89, such as fyuA and usp etc., were located. PCR-based analysis showed that this strain carried multiple virulence genes infrequently described in a clone of this type, including sfa, aer, cnf, and an intact polyketide synthase (pks) island (12). E. coli NA114 also contains other virulence factors, such as pap, fim, and genes for iron uptake systems such as the hemin uptake system and the yersiniabactin siderophore (ybt). In addition to a 4.935-Mb chromosomal genome, strain NA114 also harbored a single plasmid of 3.5 kb which has yet to be analyzed with regard to its replicon type and resistance gene profiles, if it has any.

These observations and the comparative genomic studies emanating therefrom could be extremely useful both in improving our fundamental understanding of multidrug resistance mechanisms encoded by UPEC and in the design of effective drugs to control and manage the alarming health hazards caused by ESBL-producing bacteria in both the developing and developed parts of the world.

Nucleotide sequence accession number.

The genome sequence of E. coli NA114 has been deposited in GenBank under accession no. CP002797.