Dissemination of carbapenemase-producing Enterobacterales in the community of Rawalpindi, Pakistan

Abstract

Carbapenems are considered last-line beta-lactams for the treatment of infections caused by multidrug-resistant Gram-negative bacteria. However, their activity is compromised by the rising prevalence of carbapenemase-producing Enterobacterales (CPE), which are especially marked in the Indian subcontinent. In Pakistan, previous reports have warned about the possible spread of CPE in the community, but data are still partial. This study was carried out to analyse the prevalence of CPE, the genetic characterisation, and phylogenetic links among the spreading CPE in the community. In this cohort study, we collected 306 rectal swabs from patients visiting Benazir Bhutto hospital, Rawalpindi. CPEs were screened by using ertapenem-supplemented MacConkey agar. Identification was performed by using conventional biochemical tests, and genomes were sequenced using Illumina chemistry. Antibiotic resistance genes, plasmid incompatibility groups, and Escherichia coli phylogroups were determined in silico. Sequence types were determined by using MLST tool. The prevalence of CPE carriage observed was 14.4% (44/306 samples). The most common carbapenemase-encoding gene was bla-NDM-5 (n = 58) followed by blaNDM-1 (n = 7), blaNDM (non-assigned variant, n = 4), blaOXA-181 (n = 3), blaOXA-232 (n = 3) and blaNDM-7 (n = 1). Most of the CPE were E. coli (55/64, 86%), and the genomic analysis revealed a pauciclonal diffusion of E. coli with ST167 (n = 14), 405 (n = 10), 940 (n = 8), 648 (n = 6) and 617 (n = 5). We obtained a second sample from 94 patients during their hospital stay in whom carriage was negative at admission and found that 7 (7.4%) acquired a CPE. Our results indicate that the prevalence of CPE carriage in the Pakistani urban community was high and driven by the dissemination of some E. coli clones, with ST167 being the most frequent. The high CPE carriage in the community poses a serious public health threat and calls for implementation of adequate preventive measures.

Fig 1. Flowchart of the study.

Fig 2. Distribution of CPE positive and negative samples by month of collection, (January 2018 to May 2019).

Fig 3. Acquired beta-lactamase–encoding genes.

Carbapenemase-encoding genes are highlighted in red.

Fig 4. Bar plot depicting the distribution of plasmid-mediated quinolone resistance genes.

Fig 5. Bar plot depicting the distribution of aminoglycoside resistance–encoding genes.

Fig 6. Phylogeny, STs, resistance genes and plasmids of E. coli.

*: hospital-acquired isolates.

Fig 7. Pie chart of the sequence types (ST).

The distribution of STs among carbapenemase-producing E. coli from the community.

Fig 8. Phylogenetic tree of E. coli.

*: hospital-associated isolates. The dendrogram showing the phylogenetic relationship between community-acquired and hospital-associated E. coli.

Fig 9. Distribution of plasmids replicons.

Fig 10. Screening of the four reconstructed plasmids within E. coli ST167 isolates.

Fig 11. CRE relative abundance of community-acquired and hospital-acquired CRE.

Fig 12. CRE relative abundance of the different species of Enterobacterales.

Fig 13. CRE relative abundance of E. coli ST167 versus other ST of E. coli.