Molecular epidemiology of Enterococcus sp. isolated in a university hospital in Algeria

Vancomycin Resistant Enterococci Prevalence, Antibiotic Susceptibility Patterns and Colonization Risk Factors Among HIV-Positive Patients in Health-Care Facilities in Debre Berhan Town, Ethiopia

Background

The majority of multidrug-resistant organisms found in immunocompromised patients are enterococci. The rise of vancomycin-resistant enterococci (VRE) poses a significant threat to public health. There is a scarcity of information regarding the prevalence of VRE in Ethiopia.

Purpose

This study aims to determine the prevalence of VRE in fecal samples from Human Immunodeficiency Virus (HIV)-positive individuals, to identify associated factors, and to assess their susceptibility to selected commonly prescribed medications.

Patients and Methods

A cross-sectional study was conducted from April 1 to July 15, 2023, on 170 HIV-positive clients at Debre Berhan Town. A pre-tested structured questionnaire was used to collect socio-demographic and clinical data. Stool sample was collected by trained health workers, and processed by standard microbiological techniques. Kirby-Bauer disk diffusion method was used for antimicrobial susceptibility testing. Data entry and analysis was carried out by SPSS Version 25. Bivariate and multivariate logistic regressions were used to assess the associated factors. Variables with a p-value of <0.05 were considered to be significantly associated with the outcome variables and the results were displayed with tables.

Results

From the total of 170 study participants, colonization of Enterococcus species was observed among 95 (55.9%). Vancomycin resistance was found in 13 (13.8%) of them with 95% confidence interval (CI) 7.4-22.1. History of hospitalization Adjusted Odds Ratio (AOR): 11.9 (95% CI 1.11-127.53); habit of eating uncooked food (AOR: 15.34 (95% CI 2.36-99.63)) and invasive procedures (AOR: 23.07 (95% CI 3.54-150)) were among the predictors of VRE. MDR (multidrug resistance) was observed in 83 (87.4%) of the isolates. The highest rate of resistance was observed for ampicillin with 72 (74.6%).

Conclusion

Vancomycin and multidrug resistance of enterococci among HIV patients are significant in ART clinics of Debre Berhan Town. These warrant applicable infection prevention guidelines in the health facilities and health education on food hygiene.

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 frequency and diversity of Vancomycin-resistant Enterococci (VRE) in Algerian healthcare settings

The spread of vancomycin-resistant Enterococci (VRE) in Algerian hospital settings is poorly reported. Since the first report in 2006, few data have been available on the molecular mechanism of this resistance across the country. In this study, we investigate the frequency and antibiotic resistance mechanisms of Enterococci strains isolated from hospitalised patients in the Tlemcen university hospital. 191 Enterococcus spp. strains were collected from various clinical samples and were identified using MALDI-TOF-MS. The presence of van genes was investigated by standard PCR and sequencing. Results revealed that E. faecium and E. faecalis strains are the main pathogens identified in the study. Antibiotic susceptibility testing revealed that the resistance rate was high for the majority of antibiotic classes, including glycopeptides, and only linezolid was effective on all strains. Molecular analysis revealed that 52.2% of strains from intensive care unit (ICU) were positive for the vanA gene, including 44.44% E. faecium, 5.55% E. faecalis and 2.22% E. avium. 25.5% of these isolates co-harboured both the vanA and vanC genes, including E. gallinarum (n = 16) and E. faecium (n = 6). In surgical wards (SW) 29.70% of strains harboured the van genes, including 4.90% of E. faecalis harbouring the vanB gene, and of the rest of strains, (24.80%) harboured the vanC genes. Indeed, 9.90% E. gallinarum and 4.90% E. faecalis were positive for vanC1 and 9.90% of E. casseliflavus were positive for the vanC2/C3 gene. The glycopeptide resistance rate was higher among strains from the ICU and was mainly composed by E. faecium strains compared with surgical wards where resistant E. faecalis strains were predominant.

Unraveling Mechanisms and Epidemic Characteristics of Nitrofurantoin Resistance in Uropathogenic Enterococcus faecium Clinical Isolates

Purpose

Multidrug-resistant (MDR) Enterococcus faecium is an important nosocomial pathogen causing urinary tract infection, and the reapplication of nitrofurantoin (NIT) in the clinic has attracted great attention. This study aims to explore the NIT resistance mechanisms and epidemiological characteristics of E. faecium clinical isolates.

Patients and Methods

A total of 633 E. faecium clinical isolates was obtained from urine samples in a clinical teaching hospital during 2017–2018. Among them, 40 NIT-resistant strains, and a similar number of -intermediate and -susceptible strains were isolated. The minimum inhibitory concentrations (MICs) of NIT were detected by agar dilution method. The prevalence and mutations of nitroreductase-encoding genes ef0404 and ef0648 were explored by polymerase chain reaction (PCR), followed by efflux pump inhibition test and quantitative real-time PCR (qRT-PCR) to investigate the resistance mechanisms of NIT. Furthermore, the epidemiological characteristics were detected by multilocus sequence typing (MLST).

Results

The carrying rates of nitroreductase in NIT-susceptible, -intermediate, and -resistant isolates were 100%, 50%, and 20%, respectively. After exposure to the efflux pump inhibitor, the MIC of 12 E. faecium decreased by ≥4-fold. However, the efflux pump genes efrAB, emeA, and oqxAB were not overexpressed in NIT-resistant E. faecium isolates. Moreover, MLST analysis revealed that all the NIT-resistant isolates belonged to CC17, of which 30 (75%) were associated with ST78.

Conclusion

This study has established for the first time that the absence of EF0404 and EF0648 is the main mechanism of NIT resistance in E. faecium. Our findings are likely to fill the knowledge gap pertaining to the NIT resistance mechanism in E. faecium and provide important insights for molecular epidemiological characteristics analysis.

Prevalence of vancomycin-resistant enterococcus in Africa in one health approach: a systematic review and meta-analysis

Vancomycin-resistant enterococci are a global challenge currently as reported by the World Health Organization. It is also important to recognize that combating antimicrobial resistance needs to recognize the interconnections between people, animals, plants and their shared environment in creating public health, the so-called One Health approach. Although the presence of VRE has been described in many regions of the world, there is a lack of comprehensive data indicating their prevalence of in Africa. Therefore, this study aimed to aggregate the result of studies describing VRE reported across multiple regions in Africa. A literature search was conducted on PubMed, Google scholar, and Hinari with the term “Vancomycin resistance enterococcus in Africa” on August 1–3, 2019. All available articles were downloaded to “Endnote version 7.1” then to Microsoft Word 2013. Articles determined to meet our criteria for the review was extracted to Microsoft Excel 2013. Those articles that reported the prevalence of vancomycin resistance Enterococcus obtained from all sample types and published from 2010 to 2019 in the English language were included for the review. A meta-analysis was conducted with OpenMetaAnalyst version R.3.1.0 software. The effect size was determined using a binary random effect model and statically significant considered when p < 0.05. Heterogeneity determined with the inconsistency index. A leave one out analysis used to perform the sensitivity analysis. There were 151 articles identified from the database searches; of this, 36 articles included after extensive review with two independent authors. Out of 4073 samples collected, 1488 isolates identified with an overall pooled prevalence of VRE 26.8% (95% CI; 10.7–43.0%) in Africa with a one-health perspective. The analysis showed that considerable heterogeneity among the studies (I² = 99.97%; p < 0.001). Subgroup analysis in-country, African region, laboratory method, year of publication, and sample source showed that a high prevalence was identified from South Africa (74.8%), South African regions (74.8%), PCR (959.2%), 2010–2015 years (30.3%) and environmental (52.2%), respectively. This meta-analysis indicates that there was a high-pooled prevalence of vancomycin-resistant enterococci in African. A lot should be done to prevent and control the transmission of vancomycin resistance enterococci to a human being from the environment in the continent.

Emergence of high-risk multidrug-resistant Enterococcus faecalis CC2 (ST181) and CC87 (ST28) causing healthcare-associated infections in India

High-risk hospital-associated multidrug-resistant (MDR) Enterococcus faecalis clonal complexes (CCs) such as CC2 and CC87 are enriched with virulence determinants that help to accumulate, colonize, and cause serious nosocomial infections. The aim of this study was to establish the epidemiology and clonal composition of 134 clinical E. faecalis isolates and to link molecular typing data with antimicrobial resistance and virulence determinants. All isolates were identified by conventional methods and confirmed by polymerase chain reaction (PCR) (16srRNA gene and ddl genes of E. faecalis/ E. faecium) in 5-years. Disc diffusion test was performed on all strains. We screened all E. faecalis for aac(6')-aph(2″), vanA, and vanB resistance genes, and aggregation substance-asa1, cytolysin-cylA, collagen-binding protein-ace, enterococcal surface protein-esp, gelatinase-gelE, and hyaluronidase-hyl virulence genes by PCR. Representative isolates of E. faecalis were characterized by pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST). Out of 539 patients with enterococcal infections, 134 (24.9%) had E. faecalis infections, 366 (67.9%) had E. faecium infections, and 39 (7.2%) had infections due to other enterococcal species. Of the 134 isolates, 79.1% and 61.9% isolates were high-level gentamicin resistant (HLGR) and MDR. In multivariate analysis, independent predictor for infection due to MDR E. faecalis strains was a surgical intervention (OR 2.41, 95% CI 1.17-4.96, P = 0·017). Overall, the observed rate of in-hospital mortality was 11.9%. The gelE, asa1, ace, cylA, esp and hyl genes were detected in 87.3%, 78.4%, 54.5%, 53.7%, 36.6% and 3.0%, respectively in E. faecalis isolates. The asaI, cylA, and gelE genes were significantly correlated with MDR E. faecalis. The PFGE analysis showed 28 clones with four major clones. MLST analysis revealed two sequence types-ST28 (CC87) and ST181 (CC2). This is the first Indian report on the emergence of the high-risk hospital-associated worldwide-disseminated ST28 (CC87) and ST181 (CC2), which have enriched with multiple virulence determinants and resistance to antibiotics, paticularly ampicillin. This report indicates serious health concern and calls for on-going surveillance, close monitoring, and improved infection control procedures to stop further spread of these isolates.

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.

Whole Genome Sequence Analysis of the First Vancomycin-Resistant Enterococcus faecium Isolates from a Libyan Hospital in Tripoli

The purpose of the study was to investigate the molecular characteristics and genetic relatedness of the first reported cases of vancomycin-resistant enterococci (VRE) from the Tripoli Medical Center, Libya. In total, 43 VRE isolates were obtained from various clinical sites throughout the years 2013-2014, including 40 vanA-type and 2 vanB-type vancomycin-resistant Enterococcus faecium isolates and 1 vanC1-type Enterococcus gallinarum. Of the 42 E. faecium, 19 isolates were subjected to whole genome sequencing. Core genome multilocus sequence typing (cgMLST) analysis revealed three sequence clusters (SCs) of clonally related isolates, which were linked to different hospital wards. The first two VRE isolates, isolated early 2013 from patients in the medical intensive care unit, were grouped in SC1 (MLST [ST] 78, vanB) and differed in only 3 of 1423 cgMLST alleles. The SC2 (n = 16, special care baby unit, neonatal intensive care unit, pediatric surgery ward, and oncology ward) and SC3 (n = 1, antenatal ward) were all ST80 vanA-VRE, but the single SC3 isolate differed in 233 alleles compared with SC2. Within SC2, isolates differed in 1-23 alleles. Comparison with a larger database of E. faecium strains indicated that all isolates clustered within the previously defined hospital clade A1. A combination of Resfinder and mlplasmid analysis identified the presence of resistance genes on different plasmid predicted genetic elements among different SCs. In conclusion, this study documents the first isolates causing outbreaks with VRE in the Libyan health care system. Further surveillance efforts using molecular typing methods to monitor spread of multidrug-resistant bacteria in the Libyan health care system are urgently needed.

Performance of the automated multiplex PCR Unyvero implant and tissue infections system in the management of diabetic foot osteomyelitis

AIM

We evaluated the performance of Unyvero implant and tissue infections system (ITI) application (Curetis) to diagnose Diabetic Foot Osteomyelitis (DFOM).

PATIENTS & METHODS

The study was conducted in the Diabetic Foot reference center of Nîmes University Hospital (France) from 1 December 2016 to 31 May 2017. We compared the Unyvero ITI PCR to conventional culture and alternative molecular approaches.

RESULTS

A total of 79 patients with DFOM were included: 177 microorganisms were isolated by culture, 146 detected by PCR, resulting in a concordance level of 66.7% (65.0-68.4). Discrepant results were obtained for 45 samples, with 59 microorganisms being detected by PCR only (18 samples) or by culture only (27 samples).

CONCLUSION

Unyvero ITI PCR represents an interesting additional diagnosis solution to manage DFOM.

First molecular characterization of related cases of healthcare-associated infections involving multidrug-resistant Enterococcus faecium vanA in Algeria

Purpose

Vancomycin-resistant Enterococcus (VRE) faecium (VREfm) are highly resistant bacteria emerging worldwide and rarely studied using molecular tools in Algeria since their first report in 2006. The aim of the study was to investigate healthcare-associated infections (HAIs) involving the first VRE in Batna University Hospital, Algeria, and characterize isolates using molecular tools.

Patients and methods

Medical charts were reviewed for patients with VREfm. van genes were detected by multiplex polymerase chain reaction (PCR), and strains were characterized by automated repetitive sequence-based PCR (rep-PCR), multiplex rep-PCR, pulsed-field gel electrophoresis (PFGE), and multilocus sequence typing (MLST).

Results

During a 6-month period, VREfm infections occurred in four patients hospitalized in three wards. The four isolates were E. faecium vanA belonging to the hospital-adapted clonal complex 17. PCR-based methods did not discriminate the isolates but MLST and PFGE delineated a subgroup of three VREfm of identical pulsotype and sequence type (ST) 80 (yet identified for five isolates in the international PubMLST database) while the fourth isolate was of ST789 (not previously identified for a VREfm) and displayed an unrelated pulsotype. The three genotypically related isolates were recovered in patients who underwent surgery in the same department, suggesting an outbreak for which the source and route of transmission remained unidentified.

Conclusion

This first molecular epidemiology study of VRE in Algeria was useful in delimiting an outbreak involving three of the four HAI cases and revealed rarely encountered genotypes. Considering the threat and burden of VRE infections worldwide, particularly in the USA, and the late emergence in Algeria, our study supports the urgent need for improved and early adequate infection control measures to avoid VRE spread in North African hospitals.

A comparison of monomicrobial versus polymicrobial Enterococcus faecalis bacteriuria in a French University Hospital

Enterococci are of considerable relevance in the hospital setting. Their most common location is the urinary tract, where they may be responsible for both colonization and infections. They are often associated with the presence of other microorganisms. The aim was to compare monomicrobial and polymicrobial Enterococcus faecalis bacteriuria. A retrospective study was performed on the demographic, clinical, and laboratory data of 299 patients who had presented with E. faecalis bacteriuria in 2012 at a University Hospital. The bacteriuria was polymicrobial in 46.1 % of cases and in 36.4 % of cases was responsible for a urinary tract infection. Infections appeared to be more prevalent in the polymicrobial than the monomicrobial group (42 % vs 32 %, p = 0.06). Half of the patients who presented with urinary tract colonization received antibiotic treatment (54/ out of 10). A multivariate analysis adjusted for age (adjusted odds ratio [AOR] = 1.02 per year, p = 0.006), gender (AOR = 2.2, p = 0.007), and clinical classification (colonization or infection, AOR = 1.6, p = 0.091), showed that diabetes mellitus (AOR = 2.0, p = 0.04), hospital length of stay exceeding 28 days (AOR = 2.0, p = 0.03), and presence of a urinary catheter (AOR = 2.4, p = 0.001) were all factors associated with polymicrobial E. faecalis bacteriuria. A reduction in the length of hospital stay and the use of urinary catheters would appear to be required to decrease the incidence of urinary tract colonization and infections by polymicrobial E. faecalis. Improper use of antibiotics to treat urinary tract colonization remains a major concern.

Prevalence of vancomycin resistant Enterococci and associated risk factors among clients with and without HIV in Northwest Ethiopia: a cross-sectional study

BACKGROUND

Enterococci are the most important multidrug resistant organisms associated with immunocompromised patients. Data are lacking about the epidemiology of vancomycin resistant Enterococci (VRE) in Ethiopia. This study aimed to assess the prevalence of VRE, their susceptibility patterns to different antibiotics and associated risk factors in fecal samples of Human Immunodeficiency Virus (HIV) positive and HIV negative clients.

METHODS

A cross sectional study was carried out in a total of 226 (113 HIV positive and 113 HIV negative) clients, from July 1/2013 to September 30/2013 at the University of Gondar Teaching Hospital. Data on socio-demographic characteristics and risk factors were collected with a short interview guided by pre-tested structured questionnaire. The enterococci were isolated and identified from stool sample using standard bacteriological procedures. Kary Bauer disk diffusion method was used to determine the susceptibility patterns of Enterococci isolates. Data were entered and analyzed using SPSS version 20 statistical package.

RESULTS

The overall colonization of Enterococci was 88.9% (201/226) of which 11 (5.5%) were VRE. The prevalence of VRE among clients with and without HIV infections were 8(7.8%) and 3(3.1%), respectively. Ninety percent of the Enterococci isolates (181/201) were resistant to two or more antibiotics tested. Isolates of Enterococci recovered from stool samples of HIV infected patients were more resistant to amoxicillin and amoxicillin-calvulinic acid than HIV negative clients (P < 0.05). Antibiotic treatment for the last 2 weeks was found to be the risk factor that showed statistically significant association with the presence of high VRE colonization. However, the socio-demographic variables and factors such as malnutrition, leucopenia, thromobocytopenia, anaemia, duration of Highly Active Antiretroviral Therapy, CD4 cell count, stage of WHO and drinking alcohol were not associated with VRE (P > 0.05).

CONCLUSION

The high prevalence of VRE in this study signals the emergence of VRE in the study area. Prior antibiotic treatment was associated with VRE colonization. Therefore, rational use of antibiotics and more detailed study using phenotypic and genotypic methods are needed.

Enterococci in the environment

Enterococci are common, commensal members of gut communities in mammals and birds, yet they are also opportunistic pathogens that cause millions of human and animal infections annually. Because they are shed in human and animal feces, are readily culturable, and predict human health risks from exposure to polluted recreational waters, they are used as surrogates for waterborne pathogens and as fecal indicator bacteria (FIB) in research and in water quality testing throughout the world. Evidence from several decades of research demonstrates, however, that enterococci may be present in high densities in the absence of obvious fecal sources and that environmental reservoirs of these FIB are important sources and sinks, with the potential to impact water quality. This review focuses on the distribution and microbial ecology of enterococci in environmental (secondary) habitats, including the effect of environmental stressors; an outline of their known and apparent sources, sinks, and fluxes; and an overview of the use of enterococci as FIB. Finally, the significance of emerging methodologies, such as microbial source tracking (MST) and empirical predictive models, as tools in water quality monitoring is addressed. The mounting evidence for widespread extraenteric sources and reservoirs of enterococci demonstrates the versatility of the genus Enterococcus and argues for the necessity of a better understanding of their ecology in natural environments, as well as their roles as opportunistic pathogens and indicators of human pathogens.