First report of the mobile colistin resistance gene, mcr-1.26, in multidrug-resistant Escherichia coli isolated from retail chicken meat

Exploring risk factors and antimicrobial susceptibility patterns associated with bacteriuria among Syrian refugees in makeshift camps

BACKGROUND

The health and well-being of refugees are critically compromised by harsh living conditions, which foster the emergence of infectious diseases and the misuse of antimicrobial agents. This multi-centre, cross-sectional, community-based study investigated the prevalence of urine carriage of bacteria and the associated antimicrobial resistance patterns of the isolates among Syrian refugees living in makeshift camps in Lebanon, an East Mediterranean country.

METHODS

We used multi-variable logistic regression models to identify the risk factors associated with bacteriuria in this vulnerable population. Mid-stream urine samples were collected aseptically from 79 Syrian refugees; regardless of whether they exhibited symptoms of urinary tract infections. Samples were inoculated onto UriSelect™ 4 chromogenic agar, and bacterial isolates were identified using MALDI-TOF-MS. Antibiotic susceptibility testing was assessed using the Kirby-Bauer disk diffusion assay.

FINDINGS

The prevalence of bacteriuria was 30.8% (95% confidence interval: 21.6-41.7), and the aetiologic agents were primarily Escherichia coli (80%), Klebsiella pneumoniae (12%) and Enterobacter cloacae complex (8%). The Enterobacterales isolates exhibited high resistance to penicillins (64%), cephalosporins (20-48%), and quinolones (28%), with 56% showing multi-drug resistance. While the female sex and rubbish accumulation were risk factors, tea consumption, reduced chicken intake, and economic support were protective against bacteriuria.

CONCLUSIONS

This report corroborates prior anecdotal evidence regarding underdiagnosed bacteriuria among Syrian refugees in Lebanon. The data highlight the pressing need for monitoring and awareness programmes to curb the spread of infectious diseases and antimicrobial resistance in both refugee and host communities.

A Systematic Review and Comprehensive Analysis of mcr Gene Prevalence in Bacterial Isolates in Arab Countries

BACKGROUND

The resurgence of colistin has become critical in combating multidrug-resistant Gram-negative bacteria. However, the emergence of mobilized colistin resistance (mcr) genes presents a crucial global challenge, particularly in the Arab world, which includes regions with unique conditions and ongoing conflicts in some parts.

METHODS

To address this issue, a systematic review was conducted using multiple databases, including Cochrane, PubMed, Scopus, Web of Science, and Arab World Research Source.

RESULTS

A total of 153 studies were included, revealing substantial heterogeneity in the prevalence of mcr genes across 15 Arab countries, with notable findings indicating that Egypt and Lebanon reported the highest number of cases. The analysis indicated that the most prevalent sequence types were ST10, ST101, and ST1011, all of which are Escherichia coli strains linked to significant levels of colistin resistance and multiple antimicrobial resistance profiles.

CONCLUSIONS

By analyzing the diverse findings from different Arab countries, this review lays a critical foundation for future research and highlights the necessity for enhanced surveillance and targeted interventions to address the looming threat of colistin resistance in the region.

SYSTEMATIC REVIEW REGISTRATION

PROSPERO CRD42024584379.

The occurrence of the carbapenemase gene, blaNDM-5, on a transmissible IncX3 plasmid in multidrug-resistant Escherichia coli isolated from a farm dog

OBJECTIVES

In-depth phenotypic and genomic analyses on a carbapenem-resistant Escherichia coli isolate, recovered from the faeces of a farm dog in Lebanon, focusing on its antimicrobial resistance (AMR) patterns and the underlying resistome.

METHODS

E. coli strain EC-106 was identified using MALDI-TOF-MS. Analyses using Carba NP, immunochromatographic assay NG Carba5, and other antimicrobial susceptibility testing were performed. Whole-genome sequencing (WGS) using the Illumina technology and different software available at the Center of Genomic Epidemiology wwere used to predict the resistome, sequence type (ST), plasmid types, and virulence genes.

RESULTS

Susceptibility testing revealed that E. coli EC-106 was multi-drug resistant, including against newer antimicrobials such as imipenem-relebactam (MIC = 16 µg/mL), meropenem-vaborbactam (MIC = 16 µg/mL), and ceftazidime-avibactam (MIC > 32 µg/mL), but remained susceptible to aztreonam (MIC = 0.12 µg/mL), aztreonam-avibactam (MIC = 0.06 µg/mL), and cefiderocol (MIC = 0.5 µg/mL). WGS analyses showed that E. coli EC-106 carried 13 acquired resistance genes associated with resistance to β-lactams (blaNDM-5 and blaTEM-1B), aminoglycosides (aac(3)-IId, aph(3')-Ia, aadA1, and aadA2), tetracyclines (tetA), amphenicols (partial catA1), macrolides (mphA), sulphonamides (sul1 and sul3), trimethoprim (dfrA12), and quaternary ammonium compounds (partial qacE). The blaNDM-5 was located on an IncX3 plasmid. The isolate was predicted to be a human pathogen (92.9%) and belonged to ST1011.

CONCLUSION

To our knowledge, this is the first report of the detection of an IncX3 plasmid carrying the blaNDM-5 gene in animals in Lebanon, highlighting the severe AMR challenges in the country. Taken together, our current and previous findings suggest that blaNDM-5 might be spreading in different hosts and genetic backgrounds across clinical and non-clinical settings.

Longitudinal genomic surveillance of multidrug-resistant Escherichia coli carriage in critical care patients

Colonization with multidrug-resistant Escherichia coli strains causes a substantial health burden in hospitalized patients. We performed a longitudinal genomics study to investigate the colonization of resistant E. coli strains in critically ill patients and to identify evolutionary changes and strain replacement events within patients. Patients were admitted to the intensive care unit and hematology wards at a major hospital in Lebanon. Perianal swabs were collected from participants on admission and during hospitalization, which were screened for extended-spectrum beta-lactamases and carbapenem-resistant Enterobacterales. We performed whole-genome sequencing and analysis on E. coli strains isolated from patients at multiple time points. The E. coli isolates were genetically diverse, with 11 sequence types (STs) identified among 22 isolates sequenced. Five patients were colonized by E. coli sequence type 131 (ST131)-encoding CTX-M-27, an emerging clone not previously observed in clinical samples from Lebanon. Among the eight patients whose resident E. coli strains were tracked over time, five harbored the same E. coli strain with relatively few mutations over the 5 to 10 days of hospitalization. The other three patients were colonized by different E. coli strains over time. Our study provides evidence of strain diversity within patients during their hospitalization. While strains varied in their antimicrobial resistance profiles, the number of resistance genes did not increase over time. We also show that ST131-encoding CTX-M-27, which appears to be emerging as a globally important multidrug-resistant E. coli strain, is also prevalent among critical care patients and deserves further monitoring.IMPORTANCEUnderstanding the evolution of bacteria over time in hospitalized patients is of utmost significance in the field of infectious diseases. While numerous studies have surveyed genetic diversity and resistance mechanisms in nosocomial infections, time series of within-patient dynamics are rare, and high-income countries are over-represented, leaving low- and middle-income countries understudied. Our study aims to bridge these research gaps by conducting a longitudinal survey of critically ill patients in Lebanon. This allowed us to track Escherichia coli evolution and strain replacements within individual patients over extended periods. Through whole-genome sequencing, we found extensive strain diversity, including the first evidence of the emerging E. coli sequence type 131 clone encoding the CTX-M-27 beta-lactamase in a clinical sample from Lebanon, as well as likely strain replacement events during hospitalization.

Emergence of Extended-Spectrum Cephalosporin- and Colistin-Resistant Enterobacterales in Otherwise Healthy University Students

Resistance to last resort antibiotics has been increasing, particularly in low- and middle-income countries such as Lebanon, which has well established challenges in antimicrobial stewardship and other public health and environmental issues. However, data on the emergence of antibiotic resistance in the community in Lebanon are limited. In this study, we assessed resistance to last resort antibiotics in the fecal samples of 111 otherwise healthy university students in north Lebanon. The results showed that 47.7% of the samples harbored extended-spectrum cephalosporin-resistant isolates, while 2.7% of the samples yielded colistin-resistant isolates. Furthermore, molecular analyses showed that the β-lactamase gene group, blaCTX-M-1 group, was detected in the majority (93%) of screened extended-spectrum β-lactamase isolates. In addition, the colistin-resistant Escherichia coli isolates carried mcr-1, including the novel mcr-1.26 variant, which was previously reported in clinical samples as well as in domesticated animals and the environment in Lebanon. Taken together, these findings highlight the occurrence of resistance to important antibiotics in the community, perhaps suggesting diffuse sources, including clinical and environmental settings, and multiple factors driving the spread of multidrug-resistant bacteria and resistance determinants. There is a pressing need for comprehensive antimicrobial stewardship programs and the implementation of evidence-based practices in clinical and community settings to mitigate the increasing spread of antimicrobial resistance.

Prevalence and Antimicrobial Resistance of Escherichia coli Isolates from Chicken Meat in Romania

The current study was conducted in order to analyze the prevalence of Escherichia coli (E. coli) in samples of chicken meat (100 chicken meat samples), as well as to evaluate the antimicrobial susceptibility of these isolates. A total of 30 samples were positive for E. coli among the collected chicken samples. Most isolates proved to be highly resistant to tetracycline (80%), ampicillin (80%), sulfamethoxazole (73.33%), chloramphenicol (70%) and nalidixic acid (60%). Strong resistance to ciprofloxacin (56.66%), trimethoprim (50%), cefotaxime (46.66%), ceftazidime (43.33%) and gentamicin (40%) was also observed. Notably, one E. coli strain also proved to be resistant to colistin. The antimicrobial resistance determinants detected among the E. coli isolates recovered in our study were consistent with their resistance phenotypes. Most of the isolates harbored the tetA (53.33%), tetB (46.66%), blaTEM (36.66%) and sul1 (26.66%) genes, but also aadA1 (23.33%), blaCTX (16.66%), blaOXA (16.66%), qnrA (16.66%) and aac (10%). In conclusion, to the best of our knowledge, this is among the first studies analyzing the prevalence and antimicrobial resistance of E. coli strains isolated from chicken meat in Romania and probably the first study reporting colistin resistance in E. coli isolates recovered from food sources in our country.