Vancomycin-ResistantEnterococcus faeciumin Tunisia: Emergence of Novel Clones

Genetic characterization of vancomycin-resistant Enterococcus faecium isolates from neutropenic patients in Tunisia: spread of the pandemic CC17 clone associated with high genetic diversity in Tn1546-like structures

AIMS

In Tunisia, limited research has focused on characterizing clinical vancomycin-resistant Enterococcus faecium (VREfm). This study aimed to bridge this knowledge gap by molecular characterization of antimicrobial resistance, determining the genetic elements mediating vancomycin-resistance, and whole-genome sequencing of one representative VREfm isolate.

METHODS AND RESULTS

Over 6 years (2011-2016), a total of eighty VREfm isolates responsible for infection or colonization were identified from hospitalized patients, with the incidence rate increasing from 2% in 2011 to 27% in 2016. All of these strains harbored the vanA gene. The screening for antimicrobial resistance genes revealed the predominance of ermB, tetM, and aac(6')-Ie-aph(2'')-Ia genes and 81.2% of strains harbored the Tn1545. Pulsed-field gel electrophoresis identified seven clusters, with two major clusters (belonging to ST117 and ST80) persisting throughout the study period. Seven Tn1546 types were detected, with type VI (truncated transposon) being the most prevalent (57.5%). Whole-genome sequencing revealed a 3 028 373 bp chromosome and five plasmids. Mobile genetic elements and a type I CRISPR-cas locus were identified. Notably, the vanA gene was carried by the classic Tn1546 transposon with ISL3 insertion on a rep17pRUM plasmid.

CONCLUSION

A concerning trend in the prevalence of VREfm essentially attributed to CC17 persistence and to horizontal transfer of multiple genetic variants of truncated vanA-Tn1546.

Epidemiology of vancomycin-resistant enterococci in the United Arab Emirates: a retrospective analysis of 12 years of national AMR surveillance data

Introduction

Enterococci are usually low pathogenic, but can cause invasive disease under certain circumstances, including urinary tract infections, bacteremia, endocarditis, and meningitis, and are associated with peritonitis and intra-abdominal abscesses. Increasing resistance of enterococci to glycopeptides and fluoroquinolones, and high-level resistance to aminoglycosides is a concern. National antimicrobial resistance (AMR) surveillance data for enterococci from the Middle East and North Africa (MENA) and the Gulf region is scarce.

Methods

A retrospective 12-year analysis of N = 37,909 non-duplicate diagnostic Enterococcus spp. isolates from the United Arab Emirates (UAE) was conducted. Data was generated by routine patient care during 2010-2021, collected by trained personnel and reported by participating surveillance sites to the UAE National AMR Surveillance program. Data analysis was conducted with WHONET.

Results

Enterococcus faecalis was the most commonly reported species (81.5%), followed by Enterococcus faecium (8.5%), and other enterococci species (4.8%). Phenotypically vancomycin-resistant enterococci (VRE) were found in 1.8% of Enterococcus spp. isolates. Prevalence of VRE (%VRE) was highest for E. faecium (8.1%), followed by E. faecalis (0.9%). A significant level of resistance to glycopeptides (%VRE) for these two species has been observed in the majority of observed years [E. faecalis (0-2.2%), 2010: 0%, 2021: 0.6%] and E. faecium (0-14.2%, 2010: 0%, 2021: 5.8%). Resistance to fluoroquinolones was between 17 and 29% (E. faecalis) and was higher for E. faecium (between 42 and 83%). VRE were associated with higher patient mortality (RR: 2.97), admission to intensive care units (RR: 2.25), and increased length of stay (six excess inpatient days per VRE case), as compared to vancomycin-susceptible Enterococcus spp.

Discussion

Published data on Enterococcus infections, in particular VRE-infections, in the UAE and MENA region is scarce. Our data demonstrates that VRE-enterococci are relatively rare in the UAE, however showing an increasing resistance trend for several clinically important antibiotic classes, causing a concern for the treatment of serious infections caused by enterococci. This study also demonstrates that VRE were associated with higher mortality, increased intensive care unit admission rates, and longer hospitalization, thus poorer clinical outcome and higher associated costs in the UAE. We recommend the expansion of current surveillance techniques (e.g., local VRE screening), stricter infection prevention and control strategies, and better stewardship interventions. Further studies on the molecular epidemiology of enterococci are needed.

High-Resolution Genotyping Unveils Identical Ampicillin-Resistant Enterococcus faecium Strains in Different Sources and Countries: A One Health Approach

Multidrug-resistant (MDR) Enterococcus faecium (Efm) infections continue to increase worldwide, although epidemiological studies remain scarce in lower middle-income countries. We aimed to explore which strains circulate in E. faecium causing human infections in Tunisian healthcare institutions in order to compare them with strains from non-human sources of the same country and finally to position them within the global E. faecium epidemiology by genomic analysis. Antibiotic susceptibility testing was performed and transfer of vancomycin-vanA and ampicillin-pbp5 resistance was performed by conjugation. WGS-Illumina was performed on Tunisian strains, and these genomes were compared with Efm genomes from other regions present in the GenBank/NCBI database (n = 10,701 Efm genomes available May 2021). A comparison of phenotypes with those predicted by the recent ResFinder 4.1-CGE webtool unveiled a concordance of 88%, with discordant cases being discussed. cgMLST revealed three clusters [ST18/CT222 (n = 13), ST17/CT948 strains (n = 6), and ST203/CT184 (n = 3)], including isolates from clinical, healthy-human, retail meat, and/or environmental sources in different countries over large time spans (10–12 years). Isolates within each cluster showed similar antibiotic resistance, bacteriocin, and virulence genetic patterns. pbp5-AmpR was transferred by VanA-AmpR-ST80 (clinical) and AmpR-ST17-Efm (bovine meat). Identical chromosomal pbp5-platforms carrying metabolic/virulence genes were identified between ST17/ST18 strains of clinical, farm animal, and retail meat sources. The overall results emphasize the role of high-resolution genotyping as provided by WGS in depicting the dispersal of MDR-Efm strains carrying relevant adaptive traits across different hosts/regions and the need of a One Health task force to curtail their spread.

Distinguishing Clinical Enterococcus faecium Strains and Resistance to Vancomycin Using a Simple In-House Screening Test

Vancomycin-resistant enterococci (VRE) are a major concern as microorganisms with antimicrobial resistance and as a public health threat contributing significantly to morbidity, mortality, and socio-economic costs. Among VREs, vancomycin-resistant Enterococcus faecium (VREfm) is frequently isolated and is resistant to many antibiotics used to treat patients with hospital-acquired infection. Accurate and rapid detection of VREfm results in effective antimicrobial therapy, immediate patient isolation, dissemination control, and appropriate disinfection measures. An in-house VREfm screening broth was developed and compared to the broth microdilution method and multiplex polymerase chain reaction for the detection of 105 enterococci, including 81 VRE isolates (61 E. faecium, 5 E. faecalis, 10 E. gallinarum, and 5 E. casseliflavus). Verification of this screening broth on 61 VREfm, 20 other VRE, and 24 non-VRE revealed greater validity for VREfm detection. The accuracy of this broth was 100% in distinguishing E. faecium from other enterococcal species. Our test revealed 93.3% accuracy, 97.5% sensitivity, and 79.2% specificity compared with broth microdilution and PCR detecting van genes. The kappa statistic to test interrater reliability was 0.8, revealing substantial agreement for this screening test to the broth microdilution method. In addition, the in-house VREfm screening broth produced rapid positivity after at least 8 h of incubation. Application of this assay to screen VREfm should be useful in clinical laboratories and hospital infection control units.

Clonal distribution of vancomycin-resistant Enterococcus faecium in Turkey and the new singleton ST733

Background

The aim of this study was to provide information about the spread and characteristics of the vancomycin‐resistant Enterococcus faecium isolates (VREfm) in Turkey.

Methods

Seventy‐one nonduplicate consecutive isolates of VREfm were obtained from various clinical specimens of inpatients treated at university or training hospitals in seven regions of Turkey. Further characteristics included antibiotic susceptibility testing, pulsed‐field gel electrophoresis (PFGE) of SmaI‐digested genomic DNA, and multilocus sequence typing (MLST) of selected isolates. The presence of vancomycin resistance and virulence genes (esp and hyl) was investigated by polymerase chain reaction (PCR).

Results

All VREfm isolates had MICs to vancomycin of ≥32 mg/L and contained the vanA gene. The presence of esp gene was identified in 64 and hyl in eight VREfm isolates. All VREfm showed the multiresistance phenotype, including ampicillin (99%), penicillin (99%), imipenem (99%), ciprofloxacin (87%), moxifloxacin (87%), erythromycin (97%), streptomycin (86%), gentamicin (82%), tetracycline (70%), and teicoplanin (99%). All were susceptible to tigecycline while quinupristin‐dalfopristin (97%) and linezolid (93%) were the most active other agents. Analysis of the PFGE profiles showed that 53 (74.6%) VREfm isolates shared a similar electrophoretic profile, designed as type 1, and were closely related (>85%). The sequence type was identified by MLST in 44 VRE isolates with unrelated or closely related PFGE patterns. MLST revealed that nosocomial spread of VREfm resulted from dissemination of lineage C1 E faecium clones. Sequence types ST78, ST203, and ST117 were the most frequently isolated. This is the first report of ST733 around the world.

Conclusions

Lineage C1 clones are disseminated among clinical VREfm isolates in seven different regions in Turkey. Regarding VREfm isolates, the worldwide epidemic strains are in circulation in Turkey.

Molecular epidemiology and mechanisms of antibiotic resistance in Enterococcus spp., Staphylococcus spp., and Streptococcus spp. in Africa: a systematic review from a One Health perspective

A systematic review of antibiotic-resistant Gram-positive bacteria in Africa from a One Health perspective is lacking. Here, we report result from a search for English-language articles on the resistance mechanisms and clonality of Gram-positive bacteria in Africa between 2007 and 2019 reported in PubMed, Web of Science, ScienceDirect, and African Journals OnLine; 172 studies from 22 different African countries were identified. Resistance genes, such as mecA, erm(B), erm(C), tet(M), tet(K), tet(L), vanB, vanA, vanC, and tet(O), were found to be common. Staphylococcus spp., Enterococcus spp., and Streptococcus spp. were the main species reported by the studies, with clones such as Staphylococcus aureus ST5 (n = 218 isolates), ST8 (n = 127 isolates), ST80 (n = 133 isolates), and ST88 (n = 117 isolates), and mobile genetic elements such as IS16 (n = 28 isolates), IS256 (n = 96), Tn916 (n = 107 isolates), and SCCmec (n = 4437 isolates) identified. SCCmec IV (n = 747 isolates) was predominant, followed by SCCmec III (n = 305 isolates), SCCmec II (n = 163 isolates), SCCmec V (n = 135 isolates), and SCCmec I (n = 79 isolates). Resistance to penicillin (n = 5926 isolates), tetracycline (n = 5300 isolates), erythromycin (n = 5151 isolates), rifampicin (n = 3823 isolates), gentamycin (n = 3494 isolates), sulfamethoxazole/trimethoprim (n = 3089 isolates), and ciprofloxacin (n = 2746 isolates) was common in most reports from 22 countries. Clonal dissemination of resistance across countries and between humans, animals, and the environment was observed. Resistance rates ranged from 1.4% to 100% for 15 of the studies; 10 were One Health-related studies. Strict infection control measures, antimicrobial stewardship, and periodic One Health epidemiological surveillance studies are needed to monitor and contain the threat of increasing antibiotic resistance in Africa.