In silico characterization of chromosomally integrated blaCTX-M genes among clinical Enterobacteriaceae in Africa: insights from whole-genome analysis

Antimicrobial resistance (AMR) mediated by extended-spectrum <i>β</i>-lactamases (ESBLs) is a growing global concern, particularly among <i>Enterobacteriaceae</i>. The CTX-M-type ESBLs, encoded by the <i>bla</i> _CTX-M gene, are of significant public health importance due to their high prevalence and broad geographic distribution. Typically located on plasmids and often co-occurring with other AMR genes, <i>bla</i> _CTX-M contributes to multidrug resistance (MDR). However, increasing evidence suggests secondary chromosomal integration of <i>bla</i> _CTX-M, sometimes alongside other resistance determinants. The extent and implications of this mechanism remain poorly characterized, especially in Africa, where genomic surveillance is limited. In this study, we retrieved 295 chromosomal sequences of <i>Enterobacteriaceae</i> of African origin from the GenBank and performed <i>in silico</i> predictions of <i>bla</i> _CTX-M and other AMR genes. <i>bla</i> _CTX-M-carrying sequences were further characterized by <i>in silico</i> multilocus sequence typing and genome annotation. Chromosomal insertions were identified through alignment with reference genomes. Overall, 47 of 295 sequences (15.9%) harbored the <i>bla</i> _CTX-M gene, with the highest prevalence in <i>Klebsiella pneumoniae</i> (29/157, 18.5%), followed by <i>Escherichia coli</i> (13/72, 18.1%), <i>Enterobacter</i> spp. (4/38, 10.5%), and <i>Shigella</i> spp. (1/12, 8.3%). The most common allele was <i>bla</i> _CTX-M-15 (31/47, 66.0%), followed by <i>bla</i> _CTX-M-14 (12/47, 25.5%), <i>bla</i> _CTX-M-55 (3/47, 6.4%), and <i>bla</i> _CTX-M-27 (1/27, 3.7%). Co-occurrence of <i>bla</i> _CTX-M with additional AMR genes was frequently observed, with integration events often associated with mobile genetic elements such as IS<i>Ecp1</i> and IS26. Notably, strains from the same hospital setting were phylogenetically related and shared sequence types and AMR gene profiles, suggesting local clonal dissemination. These findings reveal a notable presence of chromosomally integrated <i>bla</i> _CTX-M among African <i>Enterobacteriaceae</i>, frequently in association with other resistance genes, thereby facilitating stable MDR propagation independent of plasmid maintenance. This evolutionary adaptation may have significant implications for the persistence and spread of MDR in clinical settings.