Carriage of linezolid-resistant enterococci (LRE) among humans and animals in Nigeria: coexistence of the cfr, optrA, and poxtA genes in Enterococcus faecium of animal origin

A review of antimicrobial resistance challenges in Nigeria: The need for a one health approach

The discovery of penicillin and other antibiotics has revolutionized modern medicine. However, overreliance on antibiotics has led to a global antimicrobial resistance (AMR) crisis, jeopardizing progress made over the past decades. Antimicrobial resistance poses a critical public health challenge, affecting humans, animals, and the environment. The AMR challenge is particularly dire in Nigeria owing to the extensive antibiotic use across various sectors and ineffective antimicrobial stewardship programs. This narrative review summarizes the literature from January 2018 to December 2023, focusing on the current trends in AMR in Nigeria, including knowledge of antimicrobial usage, prescription patterns, and adherence to guidelines for humans, animals, and their shared environments. High antibiotic resistance patterns were detected in isolates recovered from healthcare settings, food supply chains, companion animals, wildlife, and the environment. Factors exacerbating the AMR crisis in Nigeria include poor regulation of antimicrobial agents, improper empirical prescriptions, inadequate infection prevention practices, arbitrary and prophylactic use of antibiotics in food-producing animals, environmental contamination, and insufficient surveillance programs. To effectively mitigate this crisis, it is essential to adopt the One Health approach, which prioritizes collaborative efforts among stakeholders, including governmental agencies, healthcare institutions, veterinary experts, farmers, and the scientific community, to address the convergence of human, animal, and environmental health. These efforts will promote transdisciplinary surveillance approaches and the establishment of policies aimed at ameliorating the impact of AMR on the Nigerian economy, the well-being of its population, and diverse ecosystems.

Multiple mechanisms drive linezolid resistance in clinical Enterococcus faecium isolates by increasing poxtA gene expression

OBJECTIVES

The poxtA gene is a transferable linezolid-resistance gene that encodes an ATP-binding cassette F protein that prevents linezolid from inhibiting protein synthesis. In enterococci, the presence of the poxtA gene does not consistently imply resistance to linezolid. The objective of this work was to analyze the role of the poxtA gene in linezolid susceptibility in a cohort of five poxtA+ clinical isolates of Enterococcus faecium.

METHODS

Three of the isolates were linezolid-resistant and two were linezolid-susceptible. The genomes of all five isolates were sequenced using short and long read sequencing. The genomes were assembled to identify the location of the poxtA gene. The presence and relative amount of the PoxtA protein was determined with a proteomics approach.

RESULTS

One of the linezolid-resistant isolates harbored a deletion in the poxtA gene promoter and a mutation in the ribosomal protein L4. Another exhibited two sets of tandem repeats of the poxtA gene within the chromosome, and the third displayed an increased copy number of the plasmid carrying the poxtA gene. Proteomic analysis detected the PoxtA protein and confirmed increased expression levels in the three resistant mutants. The highest expression was seen in the promoter deletion mutant.

CONCLUSION

The presence of the poxtA gene in clinical isolates of E. faecium does not imply resistance to linezolid, but it should be considered a significant risk factor for the development of resistance. Active molecular surveillance for intestinal poxtA gene carriers could be important to prevent dissemination.

Prevalence, Antimicrobial Resistance, and Virulence Potential of Staphylococcus aureus in Donkeys from Nigeria

BACKGROUND

Animal-associated antimicrobial-resistant staphylococci pose a One Health concern, as they can spread into the environment and cause serious infections. Yet, donkeys in Nigeria have been largely overlooked as potential reservoirs of these pathogens.

AIM/OBJECTIVES

To isolate Staphylococcus aureus from donkeys in Obollo-Afor, southeast Nigeria, assess their antimicrobial resistance profiles, and evaluate their virulence potential.

MATERIALS AND METHODS

Staphylococci were isolated from the nasal swabs of 250 donkeys, using mannitol salt agar, confirmed biochemically, with Staphylococcus aureus identified via a latex agglutination test and mass spectrometry. The resistance profiles of the isolates, including in regard to methicillin, inducible clindamycin, and β-lactamase production, were determined using disc diffusion, while vancomycin resistance was assessed through the use of agar dilution. The virulence factors were evaluated phenotypically.

RESULTS

Of the 250 samples, 11 (4.4%) contained S. aureus and 239 (95.6%) grew other Staphylococcus species. The resistance rates of the 11 S. aureus isolates to gentamicin, penicillin, tigecycline, cefoxitin, linezolid, and chloramphenicol were 45.5%, 66.7%, 54.5%, 27.3%, 36.4%, and 18.1%, respectively. The phenotypic methicillin-resistant S. aureus prevalence was 1.2%. Additionally, 23.5% of the S. aureus isolates were multidrug resistant, with a mean antibiotic resistance index of 0.25. All the S. aureus isolates exhibited virulence factors like clumping factor expression, catalase, caseinase, lecithinase, and gelatinase activity, while the occurrence of haemagglutinin, biofilm, pellicle, and hemolysin occurred in 27.3%, 54.5%, 36.4%, 72.2%, respectively.

CONCLUSION

Although a small percentage of donkeys in Nigeria may harbor S. aureus, these animals are potentially spreading antimicrobial resistance, including multidrug and methicillin resistance, to humans and the environment.

Epidemiology and genetic diversity of linezolid-resistant Enterococcus clinical isolates in Belgium from 2013 to 2021

OBJECTIVES

Linezolid-resistant opportunistic human pathogens Enterococcus faecalis and Enterococcus faecium are emerging health threats as limited therapeutic options remain. The aim of this study was to investigate the epidemiology, resistance mechanisms, and genetic diversity of linezolid-resistant enterococci (LRE) isolated between 2013 and 2021 and received at the Belgian National Reference Centre (NRC) for Enterococci.

METHODS

Linezolid susceptibility testing was performed upon request on 2458 submitted enterococci strains. Whole-genome sequencing was performed on all LRE strains.

RESULTS

Seventy-eight LRE human isolates, of which 63 (81%) E. faecalis and 15 (19%) E. faecium strains, were submitted to the Belgian NRC for Enterococci. Of the linezolid-resistant E. faecalis strains, 97% harboured the optrA gene (56% wild-type pE349) and 3% the poxtA gene. Of the linezolid-resistant E. faecium strains, 54% harboured the G2576T point mutation in the V domain of the 23S rRNA genes, 23% the poxtA, and 23% the optrA gene. Furthermore, two E. faecium strains were identified with a combination of two resistance mechanisms ([i] optrA and poxtA, and [ii] cfr(B) and G2576T point mutation, respectively). Vancomycin resistance was observed in 15% (n = 12) of the LRE. ST480 (n = 42/63 typed strains, 67%) was the most frequently detected sequence type (ST) in linezolid-resistant E. faecalis strains, while ST203 (n = 5/15 typed strains, 33%) was the most frequently detected ST in linezolid-resistant E. faecium strains.

CONCLUSIONS

E. faecalis isolates harbouring optrA were the predominant LRE in Belgium, with ST480 as the most prominent multilocus sequence typing. Linezolid resistance in E. faecium could be attributed to either chromosomal mutations or transferable resistance determinants.

Genomic epidemiology reveals multiple mechanisms of linezolid resistance in clinical enterococci in China

BACKGROUND

Infections caused by linezolid-resistant enterococci (LRE) are clinically difficult to treat and threaten patient health. However, there is a lack of studies on long time-span LRE strains in China. For this reason, our study comprehensively revealed the resistance mechanisms of LRE strains collected in a Chinese tertiary care hospital from 2011 to 2022.

METHODS

Enterococcal strains were screened and verified after retrospective analysis of microbial data. Subsequently, 65 LRE strains (61 Enterococcus faecalis and 4 Enterococcus faecium, MIC ≥ 8 µg/ml), 1 linezolid-intermediate Enterococcus faecium (MIC = 4 µg/ml) and 1 linezolid-susceptible Enterococcus faecium (MIC = 1.5 µg/ml) were submitted for whole-genome sequencing (WGS) analysis and bioinformatics analysis.

RESULTS

The optrA gene was found to be the most common linezolid resistance mechanism in our study. We identified the wild-type OptrA and various OptrA variants in 98.5% of LRE strains (61 Enterococcus faecalis and 3 Enterococcus faecium). We also found one linezolid-resistant Enterococcus faecium strain carried both optrA and cfr(D) gene, while one linezolid-resistant Enterococcus faecium only harbored the poxtA gene. Most optrA genes (55/64) were located on plasmids, with impB-fexA-optrA, impB-fexA-optrA-erm(A), fexA-optrA-erm(A), and fexA-optrA segments. A minority of optrA genes (9/64) were found on chromosomes with the Tn6674-like platform. Besides, other possible linezolid resistance-associated mechanisms (mutations in the rplC and rplD genes) were also found in 26 enterococcal strains.

CONCLUSIONS

Our study suggested that multiple mechanisms of linezolid resistance exist among clinical LRE strains in China.