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Genome profiling of uropathogenic E. coli from strictly defined community-acquired UTI in paediatric patients: a
Sarita Mohapatra1, Dipannita Ghosh2, Perumal Vivekanandan2
1Department of Microbiology, AIIMS, New Delhi, India. drsarita2005@gmail.com.
Insights
This study found multidrug-resistant E. coli in children with urinary tract infections (UTIs), highlighting the spread of resistance genes and plasmids. Rapid identification of resistance markers is crucial to curb the spread in the community.
Area of Science:
- Microbiology
- Infectious Diseases
- Genetics
Background:
- Urinary tract infections (UTIs) are common bacterial infections in children.
- The rise of extended-spectrum beta-lactamases (ESBLs) complicates the treatment of uropathogens.
- Characterizing E. coli resistance profiles and sequence types (STs) in pediatric UTIs is critical.
Purpose of the Study:
- To characterize E. coli isolates from children with UTIs in India.
- To determine antimicrobial resistance profiles and identify circulating sequence types (STs).
- To investigate the genetic basis of antimicrobial resistance in these isolates.
Main Methods:
- Children aged 1.5-18 years with UTI symptoms were enrolled from community health centers.
- E. coli isolates were identified using MALDI-TOF MS and tested for antimicrobial susceptibility via VITEK-2.
- Whole-genome sequencing (Oxford Nanopore) was performed for phylogenetic analysis, ST identification, and detection of resistance genes and mobile genetic elements.
Main Results:
- E. coli was the predominant pathogen (86%) in pediatric UTIs.
- High susceptibility was observed against fosfomycin (100%), carbapenems (90.7%), and nitrofurantoin (88.8%).
- High-risk clones ST131 and ST167 were prevalent, carrying plasmids and multiple beta-lactamases including blaNDM-5, blaOXA-1, blaCTX-M-15, and blaTEM-4.
Conclusions:
- The study reveals horizontal transmission of resistance genes and plasmids in community-acquired pediatric UTIs in India.
- Multidrug-resistant genes like blaNDM-5 and blaCTX-M-15 are associated with high-risk clones ST131 and ST167.
- Urgent need for rapid identification of resistance markers to reduce community spread.
Background:
Urinary tract infection (UTI) in children is a common bacterial infection. The emergence of extended-spectrum beta-lactamases (ESBLs) poses a major challenge against the treatment of uropathogens. We aimed to characterize the E. coli isolates recovered from children with UTI for their resistance profile and circulating sequence types (ST).
Methods:
Children (> 1.5-18 years of age) from different community health centres of India with symptoms of UTI were enrolled. Isolates causing significant bacteriuria were identified by Matrix-Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) and tested for antimicrobial susceptibility by the automated system, VITEK-2 (Biomeriux, Durhum, US). Nineteen E. coli isolates (15 ESBL positive and 4 ESBL negative) were sequenced in Oxford Nanopore platform followed by core-genome phylogeny, accessory genome cluster analysis, identification of sequence types, mobile genetic elements, genetic antimicrobial resistance markers. The correlation between detection of antimicrobial resistance genes with phenotypic resistance profiles was also investigated.
Results:
Eleven percent of children had significant bacteriuria [male:female-1:1, > 50% were 11-18 years of age group]. E. coli was predominant (86%) followed by K. pneumoniae (11%). Susceptibility of E. coli was highest against fosfomycin (100%) followed by carbapenems (90.7%) and nitrofurantoin (88.8%). ST131 (15.8%) and ST167 (10.5%) found as high-risk clones with the presence of plasmid [IncFIB (63.1%), IncFIA (52.6%)], and composite transposon [Tn2680 (46.6%)] in many isolates. Few isolates coharboured multiple beta-lactamases including blaNDM-5 (33.3%), blaOXA-1 (53.3%), blaCTX-M-15 (60%) and blaTEM-4 (60%).
Conclusions:
This study highlights horizontal transmission of resistance genes and plasmids in paediatric patients at community centers across the nation harbouring multidrug-resistant genes such as blaNDM-5 and blaCTX-M-15 associated with high-risk clones ST131 and ST167. The data is alarming and emphasizes the need for rapid identification of resistance markers to reduce the spread in community. To our knowledge, this is the first multicentric study targeting paediatric UTI patients from the community setting of India.
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