Spread of Linezolid-Resistant Enterococcus spp. in Human Clinical Isolates in the Czech Republic

Enterococci as a One Health indicator of antimicrobial resistance

The rapid increase of antimicrobial-resistant bacteria in humans and livestock is concerning. Antimicrobials are essential for the treatment of disease in modern day medicine, and their misuse in humans and food animals has contributed to an increase in the prevalence of antimicrobial-resistant bacteria. Globally, antimicrobial resistance is recognized as a One Health problem affecting humans, animals, and environment. Enterococcal species are Gram-positive bacteria that are widely distributed in nature. Their occurrence, prevalence, and persistence across the One Health continuum make them an ideal candidate to study antimicrobial resistance from a One Health perspective. The objective of this review was to summarize the role of enterococci as an indicator of antimicrobial resistance across One Health sectors. We also briefly address the prevalence of enterococci in human, animal, and environmental settings. In addition, a 16S RNA gene-based phylogenetic tree was constructed to visualize the evolutionary relationship among enterococcal species and whether they segregate based on host environment. We also review the genomic basis of antimicrobial resistance in enterococcal species across the One Health continuum.

Global spread of the linezolid-resistant Enterococcus faecalis ST476 clonal lineage carrying optrA

OBJECTIVES

To investigate the global distribution of an optrA-harbouring linezolid-resistant Enterococcus faecalis ST476 clonal lineage.

METHODS

Comprehensive searches of the NCBI database were performed to identify published peer-reviewed articles and genomes of E. faecalis ST476. Each genome was analysed for resistome, virulome, OptrA variant and optrA genetic contexts. A phylogenetic comparison of ST476 genomes with publicly available genomes of other STs was also performed.

RESULTS

Sixty-six E. faecalis ST476 isolates from 15 countries (China, Japan, South Korea, Austria, Denmark, Spain, Czech Republic, Colombia, Tunisia, Italy, Malaysia, Belgium, Germany, United Arab Emirates and Switzerland) mainly of human and animal origin were identified. Thirty available ST476 genomes compared with genomes of 591 STs indicated a progressive radiation of E. faecalis STs starting from ST21. The closest ancestral node for ST476 was ST1238. Thirty E. faecalis ST476 genomes exhibited 3-916 SNP differences. Several antimicrobial resistance and virulence genes were conserved among the ST476 genomes. The optrA genetic context exhibited a high degree of or complete identity to the chromosomal transposon Tn6674. Only three isolates displayed an optrA-carrying plasmid with complete or partial Tn6674. The WT OptrA protein was most widespread in the ST476 lineage.

CONCLUSIONS

Linezolid-resistant optrA-carrying E. faecalis of the clonal lineage ST476 is globally distributed in human, animal and environmental settings. The presence of such an emerging clone can be of great concern for public health. Thus, a One Health approach is needed to counteract the spread and the evolution of this enterococcal clonal lineage.

Relationship Between COVID-19 and Linezolid-Resistant Enterococci: A Retrospective Single-Center Study

AIM AND OBJECTIVES

To evaluate the correlation between whether the COVID-19 pandemic turned out to be a great premise for increasing the incidence of linezolid resistance infections.

MATERIALS AND METHOD

The current retrospective study included data from March 2018 to March 2023 from a single center. The clinical records of the patients were reviewed to extract clinical data. Data gathered from medical records included demographic information, the type of specimen taken, the organism identified, and its sensitivity. Antibiotic susceptibility testing and bacterial identification are both done using the fully automated VITEK system.

RESULTS

The total number of samples collected in all the groups, i.e., Group 1 (PRE-COVID), Group 2 (COVID), and Group 3 (POST-COVID), were 201, 127, and 1315, respectively. Out of a total of 201 samples in Group 1, i.e., from March 2018 to February 2020, 47 (23.38%) samples were collected from blood, 104 (51.74%) samples were collected from urine, and the rest of the samples were collected from other sources (pus, sputum, wound, stool, pleural fluid, etc.). In Group 2, i.e., from March 2020 to February 2021, the total number of samples collected was 127, of which 21 were collected from blood, 86 were from urine, and the remaining 20 samples were from other sources. A total of 1315 samples were collected between March 2021 and February 2023, i.e., in Group 3, 598 samples were collected from blood and 548 samples from urine. The most common isolates in the study were Enterococcus faecalis (35.7%) and Enterococcus faecium (61.0%).

CONCLUSION

A new threat seems to be emerging in the era of COVID-19, the Enterococcus genus. Though the mechanism remains unidentified, the viral infection seems to cause changes in the bacterial flora, favoring Enterococcus and increasing gut permeability, which provides the perfect environment for Enterococcus bacteria to develop invasive infections. In our study, the prevalence of linezolid resistance was 18.2% for five years.

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

OBJECTIVES

In contrast to increasing reports of the emergence of linezolid-resistant enterococci (LRE) emanating from many countries in Europe, Asia, and North America, data on its status and dissemination from the African continent remain scarce, with the information available limited to countries in North Africa. This study investigated the carriage of LRE and the genetic mechanism of resistance among Enterococcus faecium and Enterococcus faecalis strains recovered from humans and animals in Makurdi, Nigeria.

METHODS

We conducted a cross-sectional study between June 2020 and July 2021 during which 630 non-duplicate human and animal faecal samples were collected and processed for the recovery of LRE. The genetic mechanisms for resistance were investigated using polymerase chain reaction (PCR) and Sanger sequencing.

RESULTS

Linezolid-resistant enterococci were recovered from 5.87% (37/630; 95% CI: 4.17-8.00) of the samples, with the prevalence in animals and humans being 6.22% [(28/450); 95% CI: 4.17-8.87] and 5.00% [(9/180); 95% CI: 2.31-9.28], respectively. All isolates remained susceptible to vancomycin. No known point mutation mediating linezolid resistance was detected in the 23S rRNA and ribosomal protein genes; however, acquisition of one or more potentially transferable genes (cfr, optrA, and poxtA) was observed in 26 of the 37 LRE isolates. Co-existence of all three transferable genes in a single isolate was found in four E. faecium strains of animal origin.

CONCLUSION

This study provides baseline evidence for the emergence and active circulation of LRE driven majorly by the acquisition of the optrA gene in Nigeria. To the best of our knowledge, our study is the first to report a co-carriage of all three transferable linezolid resistance determinants in E. faecium. Active LRE surveillance is urgently required to understand the extent of LRE spread across sub-Saharan Africa and to develop tailored mitigation strategies.

A Comprehensive Study on Antibiotic Resistance among Coagulase-Negative Staphylococci (CoNS) Strains Isolated from Ready-to-Eat Food Served in Bars and Restaurants

The present study aimed to characterize and assess the diversity of CoNS strains as potential vectors for the spread of resistance to antimicrobial agents from RTE foods served in bars and restaurants. Eighty-five CoNS strains, obtained from 198 RTE food samples, were investigated. Sixty-seven CoNS isolates (78.8%) were resistant to at least one antibiotic tested, and 37 (43.5%) were multidrug resistant (MDR-CoNS). Moreover, CoNS strains contained genes conferring resistance to antibiotics critically important in medicine, i.e., β-lactams [mecA (29.4%); blaZ (84.7%)], aminoglycosides [aac(6')-Ie-aph(2″)-Ia (45.9%); aph(2″)-Ic (3.5%)], macrolides, lincosamides and streptogramin B-MLS_B [msrA/B (68.2%); ermB (40%) and mphC (4.7%)], tetracyclines [tetK (31.8%); tetM (16.5%) and/or tetL (2.35%)]. We also found the fusB/C/D genes responsible for the acquired low-level fusidic acid resistance (17.6%) and streptogramin resistance determinant vgaA in 30.6% of isolates. In three linezolid resistant strains (2 S. epidermidis and 1 S. warneri), mutation was detected, as demonstrated by L101V and V188I changes in the L3 protein amino acid sequences. The high frequency in RTE food of MDR-CoNS including methicillin-resistant (MR-CoNS) strains constitutes a direct risk to public health as they increase the gene pool from which pathogenic bacteria can pick up resistance traits.

Emergence of OptrA Gene Mediated Linezolid Resistance among Enterococcus Faecium: A Pilot Study from a Tertiary Care Hospital, India

E. faecium is the third most common cause of nosocomial infections. Linezolid (LNZ) is a reserve antibiotic recommended for infections caused by vancomycin resistant E. faecium (VREfm).  The aim of the present study was to investigate the prevalence of optrA gene among linezolid resistant E. faecium (LREfm) and to study the molecular epidemiology using pulse field gel electrophoresis (PFGE). Clinically significant LREfm were identified and antimicrobial susceptibility was performed by disc diffusion. Minimum inhibitory concentration (MIC) of linezolid, vancomycin, daptomycin and quinupristin/dalfopristin was determined by E-test. PCR and PCR-RFPL were performed for the detection of optrA/cfr gene and G2576T mutation respectively. Molecular epidemiology was studied by PFGE. A total of 1081 clinically significant Enterococci species were isolated which included E. faecium 63.5% (n=687) and E. faecalis 36.5% (n=394). LREfm (30/687) were further studied. Multidrug resistance and vancomycin resistance was 100% and 80%, respectively. Linezolid MIC range was 8-256µg/ml and the most common mechanism of resistance was optrA gene (83.3%) followed by G2576T mutation (33.3%). PFGE analysis demonstrated 4 major clones. The optrA gene mediated linezolid resistance was high and PFGE suggests resistance was emerging in the different background strains irrespective of resistance mechanism. Studies are required to investigate factors driving the emergence of linezolid resistance. The review suggests that this is the first report of optrA-mediated resistance in E. faecium from India.

Identification of a Novel Two-Peptide Lantibiotic from Vagococcus fluvialis

Infections caused by multiresistant pathogens have become a major problem in both human and veterinary medicine. Due to the declining efficacy of many antibiotics, new antimicrobials are needed. Promising alternatives or additions to antibiotics are bacteriocins, antimicrobial peptides of bacterial origin with activity against many pathogens, including antibiotic-resistant strains. From a sample of fermented maize, we isolated a Vagococcus fluvialis strain producing a bacteriocin with antimicrobial activity against multiresistant Enterococcus faecium. Whole-genome sequencing revealed the genes for a novel two-peptide lantibiotic. The production of the lantibiotic by the isolate was confirmed by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry, which revealed distinct peaks at 4,009.4 m/z and 3,181.7 m/z in separate fractions from reversed-phase chromatography. The combination of the two peptides resulted in a 1,200-fold increase in potency, confirming the two-peptide nature of the bacteriocin, named vagococcin T. The bacteriocin was demonstrated to kill sensitive cells by the formation of pores in the cell membrane, and its inhibition spectrum covers most Gram-positive bacteria, including multiresistant pathogens. To our knowledge, this is the first bacteriocin characterized from Vagococcus. IMPORTANCE Enterococci are common commensals in the intestines of humans and animals, but in recent years, they have been identified as one of the major causes of hospital-acquired infections due to their ability to quickly acquire virulence and antibiotic resistance determinants. Many hospital isolates are multiresistant, thereby making current therapeutic options critically limited. Novel antimicrobials or alternative therapeutic approaches are needed to overcome this global problem. Bacteriocins, natural ribosomally synthesized peptides produced by bacteria to eliminate other bacterial species living in a competitive environment, provide such an alternative. In this work, we purified and characterized a novel two-peptide lantibiotic produced by Vagococcus fluvialis LMGT 4216 isolated from fermented maize. The novel lantibiotic showed a broad spectrum of inhibition of Gram-positive strains, including vancomycin-resistant Enterococcus faecium, demonstrating its therapeutic potential.

Molecular characterization of florfenicol and oxazolidinone resistance in Enterococcus isolates from animals in China

Florfenicol is widely used for the treatment of bacterial infections in domestic animals. The aim of this study was to analyze the molecular mechanisms of florfenicol and oxazolidinone resistance in Enterococcus isolates from anal feces of domestic animals. The minimum inhibitory concentration (MIC) levels were determined by the agar dilution method. Polymerase chain reaction (PCR) was performed to analyze the distribution of the resistance genes. Whole-genome sequencing and comparative plasmid analysis was conducted to analyze the resistance gene environment. A total of 351 non-duplicated enteric strains were obtained. Among these isolates, 22 Enterococcus isolates, including 19 Enterococcus. faecium and 3 Enterococcus. faecalis, were further studied. 31 florfenicol resistance genes (13 fexA, 3 fexB, 12 optrA, and 3 poxtA genes) were identified in 15 of the 19 E. faecium isolates, and no florfenicol or oxazolidinone resistance genes were identified in 3 E. faecalis isolates. Whole-genome sequencing of E. faecium P47, which had all four florfenicol and oxazolidinone resistance genes and high MIC levels for both florfenicol (256 mg/L) and linezolid (8 mg/L), revealed that it contained a chromosome and 3 plasmids (pP47-27, pP47-61, and pP47-180). The four florfenicol and oxazolidinone resistance genes were all related to the insertion sequences IS1216 and located on two smaller plasmids. The genes fexB and poxtA encoded in pP47-27, while fexA and optrA encoded in the conjugative plasmid pP47-61. Comparative analysis of homologous plasmids revealed that the sequences with high identities were plasmid sequences from various Enterococcus species except for the Tn6349 sequence from a Staphylococcus aureus chromosome (MH746818.1). The current study revealed that florfenicol and oxazolidinone resistance genes (fexA, fexB, poxtA, and optrA) were widely distributed in Enterococcus isolates from animal in China. The mobile genetic elements, including the insertion sequences and conjugative plasmid, played an important role in the horizontal transfer of florfenicol and oxazolidinone resistance.

Enterococcus Virulence and Resistant Traits Associated with Its Permanence in the Hospital Environment

Enterococcus are opportunistic pathogens that have been gaining importance in the clinical setting, especially in terms of hospital-acquired infections. This problem has mainly been associated with the fact that these bacteria are able to present intrinsic and extrinsic resistance to different classes of antibiotics, with a great deal of importance being attributed to vancomycin-resistant enterococci. However, other aspects, such as the expression of different virulence factors including biofilm-forming ability, and its capacity of trading genetic information, makes this bacterial genus more capable of surviving harsh environmental conditions. All these characteristics, associated with some reports of decreased susceptibility to some biocides, all described in this literary review, allow enterococci to present a longer survival ability in the hospital environment, consequently giving them more opportunities to disseminate in these settings and be responsible for difficult-to-treat infections.

Linezolid-Resistant Enterococcus spp. Isolates from Foods of Animal Origin-The Genetic Basis of Acquired Resistance

Enterococci are important opportunistic pathogens with the capacity to acquire and spread antibiotic resistance. At present, linezolid-resistant enterococci (LRE) pose a great challenge. Linezolid is considered as a last resort antibiotic in the treatment of enterococcal infections, so it is important to monitor the occurrence of LRE in various environments. The aim of this study was to define the genetic mechanisms of linezolid resistance in enterococci (E. faecalis, E. faecium, E. hirae, E. casseliflavus) isolated from foods of animal origin (n = 104). Linezolid resistance (LR) was shown by 26.9% of isolates. All of them displayed linezolid MICs of 8–32 µg/mL, and 96.4% of them were multidrug multidrug-resistant. The most common acquired linezolid resistance gene in LR isolates was poxtA (64%), followed by optrA (28%) and cfr (12%). According to the authors’ knowledge, this research is the first to indicate the presence of the cfr gene among isolates from food. In 28.6% of the isolates, the point mutation G2576T in the V domain of the 23S rRNA was responsible for linezolid resistance. All isolates harbored the wild-type rplC, rplD and rplV genes. The obtained results indicate that linezolid resistance among enterococci in animal-derived food may result from various genetic mechanisms. The most worrying is that this resistance is encoded on mobile genetic elements, so there is a risk of its rapid transmission, even despite the lack of selective pressure resulting from the use of antibiotics.

Phenotypic and Genotypic Evaluation of Antibiotic Resistance of Acinetobacter baumannii Bacteria Isolated from Surgical Intensive Care Unit Patients in Pakistan

Background: Carbapenem-resistant Acinetobacter baumannii (CRAB) is a significant nosocomial pathogen, causing serious threats concerning community-wide outbreaks globally, as well as in Pakistan. Antimicrobial resistance in A. baumannii is increasing day by day. Objectives: The study aimed to find out the antibiotic resistance (AMR) patterns and evaluate the AMR genes in clinical isolates from patients admitted to the surgical Intensive Care units (ICUs) at different hospitals in Lahore, Pakistan. Methods: A total of 593 clinical specimens were collected from patients admitted to the surgical ICUs of three different local hospitals in Lahore, Pakistan. From these samples, a total of 90 A. baumannii isolates were identified and further investigated to observe phenotypic resistance patterns and detect carbapenemases resistance genes. Results: The results showed that phenotypic resistance against amikacin was 27.2%, ceftriaxone 100%, ceftazidime 27.2%, cefepime 63.3%, ciprofloxacin and co-trimoxazole 100%, gentamicin 40%, imipenem 22.2%, meropenem 21.1%, piperacillin-tazobactam 27.2%, tigecycline 27.2%, and tetracycline 63.3%. All A. baumannii isolates were found to be sensitive to colistin (CT), polymixin-B (PB), and tobramycin (TOB). The PCR amplification of carbapenemases genes revealed the prevalence of blaOXA-23, blaOXA-51, and blaOXA-40 in 73, 90, and 64.4% of the isolates, respectively, along with blaNDM1 (92.2%), blaVIM (40%), blaIMP (90%), ISAba1 (85.5%), sul1 (16.6%), sul2 (20%), armA (32.2%), and PER-1 (12%) while the blaOXA-24 and blaOXA-58 genes were not detected in the isolates. The sequence analysis of the blaOXA-23 and blaOXA-51 genes showed 98% and 95% similarity with previously reported sequences in the GenBank database. Conclusions: The present study indicated that the emergence of high carbapenem resistance in CRAB isolates has increased, which may pose serious limitations in the choice of drugs for nosocomial infections.

Genomic insights of optrA-carrying linezolid-resistant Enterococcus faecium using hybrid assembly: first report from India

OBJECTIVES

Linezolid resistance in Enterococcus faecium is emerging worldwide. In this study, we aimed to characterise two linezolid-resistant E. faecium isolates using whole-genome sequencing.

METHODS

Antimicrobial susceptibility testing was performed by the broth microdilution method. A hybrid assembly approach of IonTorrent and MinION sequencing reads was used to generate the complete genome of linezolid-resistant E. faecium isolates VB3025 and VB3240.

RESULTS

VB3025 and VB3240 had minimum inhibitory concentration (MICs) for linezolid of 1024 μg/mL and 512 μg/mL, respectively. In addition, VB3025 was found to be resistant to both vancomycin and teicoplanin, while VB3240 was susceptible to these antibiotics. A hybrid assembly approach was used to generate the complete genome of VB3025 and VB3240 isolates harbouring the optrA gene. Notably, VB3025 carried two copies of optrA (chromosomal and plasmid), while in VB3240 optrA was identified on the chromosome. Interestingly, the plasmid pVB3025_2 co-carried the resistance gene clusters aph(3)-IIIa-sat4-ant(6)-Ia-ermB, the vanHAX operon and a copy of the optrA gene. Moreover, the optrA gene inserted into a Tn554 transposon carrying the ermA gene was identified in both VB3025 and VB3240 isolates. Furthermore, mutation analysis revealed the presence of a G2592T mutation in the 23S rRNA of both isolates.

CONCLUSION

This is the first study reporting optrA-positive linezolid-resistant E. faecium from India. A novel plasmid co-carrying vancomycin and linezolid resistance determinants highlights the threat for potential dissemination.