Background: The Enterobacter cloacae complex (ECC) includes opportunistic pathogens that can be carbapenem resistant, thus complicating treatment regimens. Here, we characterized a carbapenem- and colistin-resistant ECC O89H7 isolate expressing KPC carbapenemase. Case Summary: ECC O89H7 was isolated in January 2021 from an axillary swab performed during routine screening for multidrug-resistant (MDR) bacteria from a patient after 39 days of hospitalization in the intensive care unit (ICU) for severe COVID-19 pneumonia at Nini hospital (Tripoli, Lebanon). The ECC O89H7 was identified as E. roggenkampii ( Er ) belonging to sequence type (ST)422 and contained eight different plasmids as revealed by whole-genome sequencing (WGS). Er O89H7 was predicted to be a human pathogen (96.3%), harboring 51 virulence factors as well as genes conferring resistance to heavy metals and quaternary ammonium compounds. Er O89H7 was highly drug resistant, including resistance to carbapenems and colistin. The resistome revealed six β-lactamase genes: the chromosome-encoded bla _MIR-3 cephalosporinase, bla _LAP-2 and bla _SHV-12 encoded on a 115-kb IncM-1 plasmid, and bla _OXA-10 , bla _TEM-40 , and bla _KPC-2 on a mobilizable IncP-6 plasmid of 51 kb, as revealed by mating-out assays. Conclusion: Here, we have characterized a human pathogenic Er ST422 harboring bla _KPC-2 carbapenemase on an IncP-6 plasmid from Lebanon. Er O89H7 represents a major health threat due to limited therapeutic options, especially because novel β-lactam/inhibitor combinations are not available in Lebanon. Our results highlight an urgent need for improved carbapenemase screening and detection capacity in clinical laboratories and for enhanced genomic surveillance of MDR bacteria to implement intervention strategies to control their spread in Lebanon and beyond.

Plasmid-encoded colistin resistance mcr-1 genes are mainly reported in Escherichia coli worldwide. Here, we characterized a multidrug-resistant Klebsiella pneumoniae 70241 clinical isolate harbouring mcr-1.1 and bla_OXA-181, recovered from a tertiary-care hospital in Tunis, Tunisia. Antimicrobial susceptibility was tested by broth microdilution and interpreted using EUCAST 2025 criteria. Whole-genome sequencing was performed with Oxford Nanopore long-read technology. In silico analyses (MLST, resistance genes, plasmid typing) were conducted using tools from the Center for Genomic Epidemiology, while comparative plasmid analysis was performed using BLAST and PROKSEE. Conjugation assays assessed plasmid transferability. K. pneumoniae 70241 belonged to ST231 and showed a multidrug-resistant phenotype with low-level colistin resistance (MIC = 4 µg/ml). The mcr-1.1 gene was carried on a 33.3-kb IncX4 plasmid closely related to animal- and food-associated plasmids. The bla_OXA-181 gene was located within a truncated IS26-based Tn6361-like transposon on a 49.4-kb IncX3 plasmid also harboring qnrS1. Additional plasmids, a fused IncR-IncFIA(HI1) carrying qnrB6, qacE and sul1 and a large IncFIB(K) carrying bla_SHV-1 and tet(D), were also found. The mcr-1.1 harbouring IncX4 plasmid was transferred at high frequency (4 × 10^-2) to E. coli J53, confirming its self-transmissibility. This study describes the first genomic features of a K. pneumoniae ST231 clinical isolate from Tunisia co-producing Mcr-1.1 and OXA-181. The presence of highly transmissible IncX4 and IncX3 plasmids highlights the risk of horizontal spread of last-resort resistance genes across clinical and animal settings, emphasizing the need for integrated genomic surveillance within a One Health framework.

Colistin, a last-resort antibiotic, has been used in human medicine for treating infections with recalcitrant multidrug-resistant Gram-negative bacteria. However, the unregulated use of colistin in agricultural and clinical settings has accelerated the emergence and global spread of the mobile colistin resistance (mcr) genes. While mcr genes have been reported in different matrices globally, data from the Middle East and North Africa (MENA) region remain limited or absent for many countries. This knowledge gap is problematic, because conflict, overcrowding, weak regulatory frameworks, and hosting some of the world’s largest multicultural religious gatherings might collectively create conditions that amplify and spread mcr across the MENA region and beyond. Several countries in the MENA region, particularly Egypt, Lebanon, Algeria, and Tunisia, have reported different mcr genes across multiple matrices. Many mcr-positive isolates were also resistant to multiple other antibiotics and co-carried additional antibiotic resistance genes (ARGs), including those encoding extended-spectrum β-lactamases and carbapenemases. Moreover, mcr has been detected in different bacterial hosts with diverse sequence types and on various plasmid backbones. In this narrative review, we comprehensively compiled, summarized, and analyzed all available reports on mcr in the MENA region, focusing on major online search engines and databases. Our objectives were (i) map the molecular epidemiology of mcr, (ii) highlight the need for better antimicrobial stewardship programs, and (iii) emphasize the importance of implementing integrated national and regional One Health action plans. We also discuss the need for robust surveillance efforts that extend beyond clinical settings to better understand and mitigate the spread of mcr.

Background/Objectives: The emergence of plasmid-mediated mcr genes has enabled horizontal dissemination of resistance to colistin, a last-resort antibiotic against multidrug-resistant Enterobacterales. In Tunisia, genomic data on mcr-positive Escherichia coli are still limited. This study reports the genomic characterization of human clinical mcr-positive E. coli isolates from the Military Hospital of Tunis. Methods: Between August 2023 and March 2025, seven E. coli isolates with low-level colistin-resistance (MIC = 4–8 µg/mL) were collected from six patients. They were characterized by antibiotic susceptibility testing and WGS to determine resistome, MLST, genetic relatedness, and plasmid content. Results: The E. coli isolates belonged to diverse sequence types (STs), except for two isolates collected from the same patient 2.5 months apart, which were highly related. Overall, this pattern is consistent with a polyclonal spread. The mcr-1.1 gene was located on IncI2 (n = 5) or IncX4 (n = 2) plasmids, which exhibited high similarity both among themselves and in comparison with plasmids previously reported in human and livestock isolates. Most isolates were multidrug-resistant, harboring acquired resistance genes to multiple antibiotic classes, and chromosomal mutations conferring fluoroquinolone resistance. Three isolates additionally carried chromosomal insertions of the bla_CTX-M-55 gene. Resistance to cefiderocol was observed in one isolate and was associated with CirA and Fiu truncation. Conclusions: These findings highlight ongoing dissemination of mcr-1.1-positive E. coli isolates in Tunisia, primarily driven by plasmid transfer. Continuous genomic surveillance and One Health-oriented antibiotic stewardship are essential to limit the spread of colistin-resistance and the emergence of resistance to newer agents such as cefiderocol.