Abstract
Background
Colistin resistance mediated by mcr genes poses a critical threat to antimicrobial therapy, particularly in multidrug-resistant Klebsiella pneumoniae. While mcr-1 has been previously identified in clinical Escherichia coli in Tunisia, no human clinical K. pneumoniae isolate carrying this gene has been reported to date.
Objectives
This study aims to assess colistin resistance rates in carbapenem-resistant clinical K. pneumoniae isolates, characterize genetic resistance determinants in resistant strains, and screen for the occurrence of the mcr-1 gene.
Methods
This study was conducted from January to December 2024 at Habib Thameur Hospital, Tunis and investigated colistin resistance among carbapenem-resistant K. pneumoniae isolates. Colistin resistance was assessed via broth microdilution (EUCAST criteria). Resistance genes were detected via multiplex PCR and confirmed via Sanger sequencing. Sequence identity was analysed with BLASTn database.
Results
Among the 143 carbapenem-resistant K. pneumoniae isolates, 16 [11.2% (95% CI: 6.5–17.5%)] were colistin resistant. All the isolates were multidrug resistant, with a high prevalence of the blaOXA-48-like (14/16) and blaNDM (11/16) carbapenemase genes and the β-lactamases genes blaCTX-M (14/16) and blaSHV (11/16). Additional resistance determinants included the qnrS (14/16), qnrB (15/16), and 16 S rRNA methylase genes (rmtF, rmtC, and armA). One isolate carried the mcr-1 gene, displaying moderate colistin resistance (MIC: 4 mg/L) and harbouring multiple resistance genes.
Conclusion
This study reports the first detection of the mobile colistin resistance gene mcr-1 in a clinical K. pneumoniae isolate in Tunisia. While chromosomal mechanisms remain predominant in colistin-resistant K. pneumoniae in the country, this finding underscores the urgent need for enhanced molecular surveillance and antibiotic stewardship to curb the potential risk for future dissemination of mcr-mediated resistance in North Africa.
Supplementary Information
The online version contains supplementary material available at 10.1186/s12879-026-13562-6.
Keywords: Colistin, Drug resistance, Klebsiella pneumoniae, MCR-1, Tunisia
Introduction
K. pneumoniae is a major opportunistic pathogen responsible for a broad spectrum of community- and hospital-acquired infections, including pneumonia, urinary tract infections, and septicemia, underscoring its significant clinical impact [1]. Epidemiological data indicate that K. pneumoniae accounts for 6–17% of healthcare-associated infections worldwide, with a particularly high prevalence in intensive care units (ICU) and immunocompromised patients [2].
In recent decades, the widespread use of antibiotics has driven the evolution of K. pneumoniae from multidrug-resistant (MDR) to extensively drug-resistant (XDR). This alarming trend has resulted in frequent treatment failures and high mortality rates [3]. The emergence of carbapenem resistant K. pneumoniae (CRKP) has severely limited therapeutic options, leading to the reintroduction of colistin, a last-resort treatment for these MDR pathogens [4].
Colistin is a polymyxin antibiotic and is classified by the World Health Organisation as the “highest priority critically important antimicrobial” for human medicine [5]. However, its clinical utility has been severely undermined by the discovery of the plasmid-mediated colistin resistance gene mcr-1 in 2015 [6]. Since then, mcr-1 has been detected across all five continents and in multiple reservoirs, including humans, animals, and the environment [7]. At least ten mcr variants (mcr-1 to mcr-10) have been identified, with mcr-1, mcr-3, and mcr-4 being the most frequently reported in Enterobacteriaceae causing human infections [8]. Escherichia coli remains the primary carrier, followed by K. pneumoniae, Enterobacter spp., and Salmonella [8].
Globally, mcr-positive K. pneumoniae strains from both human and animal sources have been reported [9]. In Tunisia, mcr-1-harbouring K. pneumoniae has been reported only in animal isolates [10]. To our knowledge, no clinical human isolate of K. pneumoniae carrying the mcr-1 gene has been described in Tunisia.
This study aimed to determine the prevalence of colistin resistance among carbapenem-resistant K. pneumoniae strains, perform molecular characterization of resistance genes, including the detection of the mcr-1 gene in colistin-resistant clinical isolates collected from a tertiary university hospital in Tunis, Tunisia.
Materials and methods
Study design and bacterial isolates
This study was conducted from the 1st January to 31 December 2024 at Habib Thameur Hospital, Tunis, Tunisia. The study focused on colistin-resistant K. pneumoniae (KPCR) isolates, which were identified by testing all carbapenem-resistant strains obtained from routine clinical samples for colistin susceptibility. Only isolates resistant to both carbapenems and colistin were included. Duplicate isolates from the same patient and isolates from colonization screenings were excluded from the study.
Microbiological processing and bacterial identification
All samples were processed according to standard microbiological procedures as outlined by the Référentiel en Microbiologie Médicale guidelines (REMIC) [11]. Preliminary identification was based on colony morphology, Gram staining, and oxidase testing. Further biochemical identification of K. pneumoniae isolates was performed via the API 20E identification system (bioMérieux, Marcy l’Etoile, France).
Antimicrobial susceptibility testing
The antimicrobial susceptibility of all isolates was assessed using the standard Kirby–Bauer disk diffusion method on Mueller–Hinton (MH) agar, following the 2024 recommendations of the European Committee on Antimicrobial Susceptibility Testing, EUCAST. (http://www.sfm-microbiologie.org/, accessed on 1 June 2024). Disks from Bio-Rad (Marnes–la-Coquette, France) were tested, including amoxicillin, amoxicillin/clavulanic acid, piperacillin, piperacillin/tazobactam, cefepime, ceftazidime, cefotaxime, imipenem, ertapenem, aztreonam, trimethoprim-sulfamethoxazole, ciprofloxacin, and amikacin.
The minimum inhibitory concentrations (MICs) of colistin were determined for all CRKP isolates via broth microdilution (kit (Biocentric, Bandol, France). According to the 2024 recommendations of the EUCAST, colistin resistance was defined as an MIC > 2 mg/L.
Detection and molecular characterization of antimicrobial resistance genes
For the detection of antibiotic resistance genes, a multiplex PCR–based reverse hybridization assay was performed using the CE IVD–approved MDR Direct Flow Chip Kit (VitroMaster Diagnostica, Seville, Spain). This certified kit has been validated for clinical use and allows detection of clinically relevant resistance markers, including β-lactamase genes (blaSHV, blaCTX-M, blaCMY), carbapenemase genes (blaOXA-48-like, blaNDM), plasmid-mediated quinolone resistance genes (qnrS, qnrB), aminoglycoside-modifying enzymes (aac(6’)-Ib, armA, rmtC, rmtF), sulfonamide resistance genes (sul1, sul2) and mobile colistin resistance genes (mcr-1, mcr-2) [12]. The negative control was E. coli ATCC 25,922.
Molecular detection and Sanger sequencing of the mcr-1 gene
To confirm the detection of the mcr-1 gene, standard PCR was performed. PCR amplification of the mcr-1 gene was carried out in 25 µL reaction volumes via DreamTaq DNA Polymerase (Thermo Fisher Scientific) with the primers mcr1F (5′-ATGATGCAGCATACTTCTGTG-3′) and mcr1R (5′- TCAGCGGATGAATGCGGTG-3′) [9]. The thermocycling protocol consisted of initial denaturation at 95 °C for 5 min, followed by 35 cycles of 96 °C for 60 s, 56 °C for 45 s, and 72 °C for 60 s, with a final extension at 72 °C for 10 min. Amplicons were confirmed by electrophoresis on a 1.5% agarose gel [13].
Sanger sequencing of mcr-1-positive isolates was performed via BigDye Terminator v3.1 chemistry (Applied Biosystems) on an ABI 3130 Genetic Analyser following the manufacturer’s instructions [14]. Chromatograms were trimmed and assembled via SeqMan Pro software (DNASTAR). The resulting sequences were analysed via BLASTn to identify resistance genes [15].
Statistical analysis
Statistical analyses were performed via SPSS version 22 and R software. Associations between resistance genes were assessed via the Phi (φ) coefficient from chi-square tests, with Fisher’s exact test for statistical significance. P values ≤ 0.05 were considered statistically significant.
Results
Sample collection
During the study period, 16 colistin-resistant isolates were identified, representing 11.2% (95% CI: 6.5–17.5%) of the 143 carbapenem-resistant K. pneumoniae recovered. The majority of KPCR isolates were recovered from respiratory samples (sputum and protected distal tracheal specimens) (10/16), followed by urine samples (3/16) and blood cultures (3/16).
The ICU-Emergency Unit recorded the highest number of isolates (11/16), followed by the Anaesthesia and ICU, with three isolates.
Six isolates were obtained from female patients, and 10 were obtained from male patients, yielding a sex ratio of 1.67.
Antimicrobial susceptibility pattern of KPCR
All 16 KPCR isolates were MDR. Resistance to ciprofloxacin was observed in 13 isolates, and 10/were resistant to trimethoprim-sulfamethoxazole. Only two isolates remained susceptible to amikacin, and one isolate was susceptible to cefotaxime and imipenem. Colistin MICs ranged from 4 to 64 mg/L, with eleven isolates showing MICs ≥ 16 mg/L, mainly from ICU samples. Table 1 summarised the antimicrobial susceptibility and colistin MICs of KPCR isolates according to hospital department and sample type.
Table 1.
Antimicrobial susceptibility and colistin MICs of colistin-resistant K. pneumoniae isolates (n = 16) according to hospital department and sample type
| Isolate ID | Hospital Unit | Patient -Age | Sample Type | AMC | TZP | CTX | FEP | ATM | ERT | IMP | AK | CIP | SXT | Colistin MIC (mg/L) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| K1 | ICU - Emergency | 80 | Protected Tracheal Sample | R | R | R | R | R | R | R | S | S | R | 4 |
| K2 | Anaesthesia ICU | 50 | Sputum | R | R | R | R | R | R | R | R | R | R | 32 |
| K3 | Internal Medicine | 52 | Sputum | R | R | R | R | R | R | R | R | R | R | 4 |
| K4 | ICU - Emergency | 60 | Blood Culture | R | R | R | R | R | R | R | R | R | S | 8 |
| K5 | ICU - Emergency | 62 | Sputum | R | R | R | R | R | R | R | R | R | R | 16 |
| K6 | ICU - Emergency | 70 | Sputum | R | R | R | R | R | R | R | R | R | R | 16 |
| K7 | ICU - Emergency | 64 | Protected Tracheal Sample | R | R | R | R | R | R | R | R | R | R | 64 |
| K8 | ICU - Emergency | 58 | Sputum | R | R | R | R | R | R | R | R | S | R | 64 |
| K9 | Anaesthesia ICU | 55 | Protected Tracheal Sample | R | R | R | R | R | R | R | R | R | S | 64 |
| K10 | ICU - Emergency | 43 | Sputum | R | R | R | R | R | R | R | R | R | S | 16 |
| K11 | Anaesthesia ICU | 66 | Blood Culture | R | R | R | R | R | R | R | R | R | R | 4 |
| K12 | ICU - Emergency | 75 | Urine Culture | R | R | R | R | R | R | R | R | R | R | 16 |
| K13 | ICU - Emergency | 84 | Urine Culture | R | R | R | R | R | R | R | R | R | R | 16 |
| K14 | Urology Department | 56 | Urine Culture | R | R | S | R | R | R | S | S | R | R | 4 |
| K15 | ICU - Emergency | 80 | Blood Culture | R | R | R | R | R | R | R | R | R | R | 16 |
| K16 | ICU - Emergency | 61 | Sputum | R | R | R | R | R | R | R | R | S | R | 64 |
AMC: Amoxicillin/Clavulanic acid; TZP: Piperacillin/Tazobactam; CTX: Cefotaxime; FEP: Cefepime; ATM: Aztreonam; ERT: Ertapenem, IMP: Imipenem; SXT: Trimethoprim–sulfamethoxazole; R: Resistant; S: Susceptible, ICU: intensive care unit, MIC: minimum inhibitory concentration
Molecular characterization of resistance genes in KPCR isolates
The gene encoding OXA-48-like was identified in 14 strains, followed by blaNDM, which was detected in 11 isolates. The coexistence of blaOXA-48-like and blaNDM was observed in nine isolates. Additionally, the β-lactamases genes blaSHV and blaCTX-M were detected in 11 and 14 isolates, respectively.
With respect to resistance genes from other antibiotic classes, 16 S rRNA methylase genes, including rmtF (n = 10), rmtC (n = 3), and armA (n = 1), were detected in several isolates. The fluoroquinolone resistance genes qnrS and qnrB were identified in 14 and 15 isolates, respectively, whereas the sulfonamide resistance genes sul1 and sul2 were detected in 15 and 12 isolates, respectively.
The mcr-1 gene was detected in one isolate (K14) corresponding to an overall prevalence of 0.7% (1/143) among all CRKP isolates and 6.25% (1/16) among colistin-resistant isolates specifically. This isolate also harboured blaSHV, blaOXA-48- like, sul1, qnrS, and qnrB resistance genes. The phenotypic synergy test for ESBL detection was positive. The distribution of antibiotic resistance genes is summarised in Table 2.
Table 2.
Distribution of antibiotic resistance genes in colistin-resistant Klebsiella pneumoniae isolates (n = 16)
| Resistance genes and their antibiotic classes | ||||||
|---|---|---|---|---|---|---|
| Isolate ID | β-Lactams | Carbapenem | Aminoglycosides | Fluoroquinolones | Sulfonamides | Colistin |
| K1 | bla SHV + bla CTX-M | blaOXA-48-like + blaNDM | aac(6’)-Ib + rmtF | qnrS + qnrB | sul1 + sul2 | – |
| K2 | bla SHV + bla CTX-M | blaOXA-48-like + blaNDM | aac(6’)-Ib + rmtF | qnrS + qnrB | sul1 + sul2 | – |
| K3 | bla SHV + bla CTX-M + bla CMY | bla NDM | aac(6’)-Ib + rmtF | qnrS + qnrB | sul1 + sul2 | – |
| K4 | bla SHV + bla CTX-M | blaOXA-48-like + blaNDM | aac(6’)-Ib + rmtF | qnrS + qnrB | sul1 | – |
| K5 | bla CTX-M | bla NDM | aac(6’)-Ib + rmtC | qnrS + qnrB | sul1 + sul2 | – |
| K6 | blaSHV + blaCTX-M+ blaCMY | bla OXA-48-like | aac(6’)-Ib + rmtF | qnrS + qnrB | sul1 + sul2 | – |
| K7 | bla SHV + bla CTX-M | blaOXA-48-like + blaNDM | aac(6’)-Ib + rmtF | qnrS + qnrB | sul1 + sul2 | – |
| K8 | blaCTX-M +blaCMY | blaOXA-48-like + blaNDM | aac(6’)-Ib + rmtC | qnrS + qnrB | sul1 + sul2 | – |
| K9 | blaCTX-M blaCMY | blaOXA-48-like + blaNDM | aac(6’)-Ib + rmtC | qnrS + qnrB | sul1 + sul2 | – |
| K10 | bla SHV + bla CTX-M + bla CMY | bla OXA-48-like | aac(6’)-Ib + rmtF | qnrS + qnrB | sul1 | – |
| K11 | bla SHV + bla CTX-M | blaOXA-48-like + blaNDM | aac(6’)-Ib + rmtF | qnrS + qnrB | sul1 + sul2 | – |
| K12 | bla SHV + bla CMY | bla OXA-48-like | aac(6’)-Ib + armA | qnrS | sul1 + sul2 | – |
| K13 | bla SHV + bla CTX-M | blaOXA-48-like + blaNDM | aac(6’)-Ib + rmtF | qnrS + qnrB | sul1 + sul2 | – |
| K14 | bla SHV | bla OXA-48-like | – | qnrS + qnrB | sul1 | mcr-1 |
| K15 | bla CTX-M | bla OXA-48-like | – | qnrB | – | – |
| K16 | bla CTX-M | blaOXA-48-like + blaNDM | aac(6’)-Ib + rmtF | qnrB | sul1 + sul2 | – |
Correlation analysis, as illustrated in the heatmap (Supplementary Fig. 1), revealed several associations between resistance genes. A significant positive correlation was observed between blaSHV and rmtF (φ = 0.59, p = 0.036), whereas blaNDM and aac(6’)-Ib tended to be positive (φ = 0.56, p = 0.083). Similarly, aac(6’)-Ib was strongly correlated with sul2 (φ = 0.65, p = 0.05).
Detection of the mcr-1 gene
One clinical isolate, K14, tested positive for the mcr-1 gene. Electrophoresis analysis of a 1.5% agarose gel confirmed the presence of mcr-1.
amplicon in isolate K14, as observed in comparison with the 100 bp DNA ladder (Supplementary Fig. 2).
Sanger sequencing of the mcr-1 gene
Sanger sequencing of the mcr-1 amplicon produced high-quality data, with a mean Phred score of 37.14 and over 99.7% of bases above Q20, confirming reliable base calling. The sequence corresponded to a highly conserved region of mcr-1, with no frameshifts or premature stop codons, indicating a functional gene. Alignment via BLASTn confirmed the presence of the mcr-1 gene, showing high sequence similarity with previously described mcr-1 alleles encoding a phosphoethanolamine transferase that modifies lipid A and confers colistin resistance.
Discussion
Colistin is widely regarded as a critical last-resort antibiotic for treating infections caused by MDR strains [19]. Its increasing use in clinical settings has raised significant concerns about the potential emergence and risk of dissemination of mcr genes [16].
The dissemination of the mcr-1 gene has exacerbated the AMR crisis, facilitating the rapid spread of colistin resistance across the human, animal, and environmental sectors [17]. Despite the increasing prevalence of the mcr-1 gene and the high mortality associated with MDR bacteria resistant to colistin, there is still a major lack of data on the prevalence of mcr genes in the Arab world [18].
In this context, our study focused on colistin resistance in carbapenem-resistant clinical K. pneumoniae isolates and screened for mobile colistin resistance genes (mcr-1 and mcr-2). This approach addresses the lack of regional data and provides insight into associated resistance determinants.
All 16 KPCR isolates in our study were MDR, harbouring combinations of resistance genes. Correlation analysis revealed several significant associations between resistance genes, suggesting common mechanisms of coselection or genetic linkage [19]. The β-lactamase gene blaSHV was significantly positively associated with rmtF (φ = 0.59, p = 0.036). Furthermore, a strong positive correlation was observed between blaNDM and aac(6’)-Ib (φ = 0.56, p = 0.083), indicating near-systematic co-occurrence. Overall, these findings underscore clusters of co-occurring resistance determinants that explain the multidrug-resistant phenotype observed in these isolates [19].
To our knowledge, this is the first study in Tunisia to investigate resistance genes associated with carbapenem resistance genes. Therefore, this study provides valuable insight into the local epidemiology of resistance genes.
Most importantly, we document the first clinical detection of a mcr-1-mediated colistin-resistant K. pneumoniae isolate in Tunisia. Previous studies conducted locally have attributed colistin resistance in K. pneumoniae to chromosomal mechanisms, particularly mgrB inactivation [20]. This observation is concerning, as mobile colistin resistance genes may facilitate interspecies and cross-setting dissemination [21]. However, plasmid characterization was not performed, so no conclusions on horizontal gene transfer can be drawn in this study.
To date, Tunisian reports of mcr-1 have been limited to E. coli from clinical samples [22, 23], whereas most other data concern Enterobacterales isolated from animals, including free-range chickens and food-producing livestock [10]. Our findings therefore broaden the spectrum of species and sources affected by mcr-1 in Tunisia.
The prevalence of KPCR in our study was 11.2% (16/143). Only one isolate carried mcr-1. This corresponds to a prevalence of 0.7% (1/143) among all CRKP isolates and 6.25% (1/16) among colistin-resistant isolates. These figures emphasize the rarity of mobile colistin resistance in this setting and suggest that chromosomal mechanisms are the predominant contributors to colistin resistance in our setting. A multicentre Tunisian study conducted in six university hospitals, reported that 5.02% of strains were resistant to colistin. In contrast, none of the KPCR isolates were mcr-1 positive, and four strains of E. coli harboured the mcr-1 gene. These findings suggest that different mechanisms of colistin resistance may be involved in the two species [22].
Isolate K14 was recovered during the study period from an adult male patient aged 50–59 years with a urinary tract infection. According to the patient’s history, there was no record of prior hospitalization, suggesting a possible community or zoonotic origin of this strain.
K14 was resistant to amoxicillin-clavulanic acid, piperacillin-tazobactam, ertapenem, ciprofloxacin and trimethoprim-sulfamethoxazole but remained susceptible to cefotaxime, imipenem and amikacin. The colistin MIC was 4 mg/L. Remarkably, the level of resistance to colistin was moderate consistent with typical mcr-mediated resistance. In contrast, chromosomal mutations (e.g., in mgrB) typically confer higher colistin MICs [23].
The multiplex PCR results for K14 revealed other resistance genes: blaOXA-48-like, blaSHV, qnrS, qnrB and Sul1. Sanger sequencing revealed that the mcr-1 gene from the K14 isolate corresponds to the mcr-1. The presence of blaOXA-48-like and blaSHV in our isolate is consistent with this resistance profile [19]. Notably, mcr-1 has also been reported to cotransfer with β-lactamase -encoding genes, raising concerns about the emergence of multidrug-resistant ‘superbugs’ capable of causing therapeutic failure [19]. In fact, the increasing use of colistin in both human and veterinary medicine is accelerating the spread of resistance worldwide [18].
Among the 16 KPCR isolates, five exhibited high-level resistance (MIC ≥ 32 mg/L) yet tested negative for mcr genes. This observation strongly suggests the involvement of chromosomal resistance mechanisms, which are well-documented to confer higher colistin MICs compared to plasmid-mediated mcr genes [24]. In K. pneumoniae, such high-level resistance typically arises from mutations in regulatory genes controlling lipopolysaccharide modification, particularly inactivation of mgrB (via insertions, deletions, or point mutations) or activating mutations in two-component systems (pmrAB, phoPQ, crrAB) [25]. This hypothesis aligns with recent Tunisian surveillance data demonstrating that chromosomal alterations notably mgrB disruptions combined with pmrAB/phoPQ mutations predominate among colistin-resistant clinical K. pneumoniae isolates [26]. The absence of molecular investigation into these chromosomal determinants represents a limitation of our study; however, the MIC distribution pattern (moderate resistance in the mcr-1-positive isolate versus high-level resistance in mcr-negative isolates) provides indirect evidence supporting the predominance of chromosomal mechanisms in our collection. Future studies incorporating whole-genome sequencing will be essential to confirm these putative mutations and elucidate their precise contribution to the resistance phenotype.
Finally, our study is limited by the small number of colistin-resistant isolates, the absence of plasmid characterization, and the lack of investigation into chromosomal resistance genes. Additionally, only carbapenem- and colistin-resistant K. pneumoniae isolates were analysed; colistin-resistant but carbapenem-susceptible strains were not included. These limitations reflect resource constraints in Tunisia and highlight the need for multicentre studies with larger sample sizes to comprehensively monitor colistin resistance in Tunisia [22].
Conclusion
This study reports the first clinical detection of the mcr-1 gene in a K. pneumoniae isolate in Tunisia. Although rare, this sentinel finding provides an important baseline for national colistin resistance surveillance. Our results highlight the predominance of chromosomal mechanisms in KPCR in Tunisia. While our findings represent a sentinel detection of mcr-1, further genomic studies are required to assess its actual potential for horizontal dissemination in North Africa.
Electronic Supplementary Material
Below is the link to the electronic supplementary material.
Supplementary Material 1: Supplementary Fig. 1. The heatmap displays the Phi correlation coefficients between various resistance genes identified in KPCR isolates (n = 16). Colour Scale: The colour intensity represents the strength of the correlation, ranging from − 1.0 (dark blue, perfect negative correlation) to + 0.7 (dark orange, strong positive correlation). Significance: Statistically significant correlations (p < 0.05) are highlighted with a red frame and indicated by an asterisk (*).
Supplementary Material 2: Supplementary Fig. 2. Agarose gel electrophoresis of the PCR amplification of the mcr-1 gene (expected size: 301 bp). Lane L: 100 bp DNA ladder; lanes 1–3: isolate K14 (triplicate); lane Nc: negative control; lane Pc: positive control.
Acknowledgements
The authors would like to acknowledge the kind collaboration of Dr. Manel Kaidi, Dr. Malek Houari, Mrs. Naoures Ouzari, and Mrs. Mounira Msahli for their technical support.
Abbreviations
- AMC
Amoxicillin/clavulanic acid
- AMR
Antimicrobial resistance
- ARO
Antibiotic resistance
- ATM
Aztreonam
- BLASTn
Basic local alignment search tool (nucleotide)
- CA-SFM
Comité de l’Antibiogramme de la Société Française de Microbiologie
- CE IVD
Conformité Européenne - in vitro diagnostics
- CI
Confidence interval
- CRKP
Carbapenem-resistant K. pneumoniae
- CTX
Cefotaxime
- ESBL
Extended-spectrum β-lactamase
- EUCAST
European committee on antimicrobial susceptibility testing
- FEP
Cefepime
- ICU
intensive care unit
- IMP
imipenem
- K. pneumoniae
Klebsiella pneumoniae
- KPCR
Colistin-resistant K. pneumoniae
- MCR
Mobile colistin resistance
- MDR
multidrug-resistant
- MH
Mueller‒Hinton (agar)
- MIC
Minimum inhibitory concentration
- PCR
Polymerase chain reaction
- R
Resistant
- REMIC
Référentiel en microbiologie médicale
- S
Susceptible
- SPSS
Statistical package for social sciences
- SXT
Trimethoprim–sulfamethoxazole
- TZP
Piperacillin/Tazobactam
- XDR
Extensively drug-resistant
- ϕ
Phi (statistical coefficient)
Author contributions
M.E: conceived and designed the experiments; M.E and O.I: conducted the experiments; M.E, H.BM: analysed and interpreted the data; B.O: performed the bioinformatics analysis; M.E: wrote the paper and F.B and S.C have read and approved the final manuscript.
Funding
No external funding was received for this study.
Data availability
The sequence has been deposited in the NCBI GenBank database and is publicly accessible under accession number PX400222. It can be accessed at the following link: [ https://www.ncbi.nlm.nih.gov/nuccore/3101478079 ].
Declarations
Ethical approval
This study was conducted in accordance with the ethical principles of the Declaration of Helsinki and was approved by the Ethics Committee of Habib Thameur Teaching Hospital (IRB00014475; Approval No. HTHEC-2025-32). Informed consent was obtained from all participants prior to sample collection.
Competing interests
The authors declare no competing interests.
Footnotes
Publisher’s note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
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Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Supplementary Materials
Supplementary Material 1: Supplementary Fig. 1. The heatmap displays the Phi correlation coefficients between various resistance genes identified in KPCR isolates (n = 16). Colour Scale: The colour intensity represents the strength of the correlation, ranging from − 1.0 (dark blue, perfect negative correlation) to + 0.7 (dark orange, strong positive correlation). Significance: Statistically significant correlations (p < 0.05) are highlighted with a red frame and indicated by an asterisk (*).
Supplementary Material 2: Supplementary Fig. 2. Agarose gel electrophoresis of the PCR amplification of the mcr-1 gene (expected size: 301 bp). Lane L: 100 bp DNA ladder; lanes 1–3: isolate K14 (triplicate); lane Nc: negative control; lane Pc: positive control.
Data Availability Statement
The sequence has been deposited in the NCBI GenBank database and is publicly accessible under accession number PX400222. It can be accessed at the following link: [ https://www.ncbi.nlm.nih.gov/nuccore/3101478079 ].