Authors: Dan Alexandru Toc, Stanca Lucia Pandrea, Alexandru Botan...

(1) Background: This paper aims to provide a description of non-faecalis non-faecium enterococci isolated from a tertiary care hospital in Romania and to briefly review the existing literature regarding the involvement of Enterococcus raffinosus, Enterococcus durans and Enterococcus avium in human infections and their antimicrobial resistance patterns; (2) Methods: We retrospectively analyzed all Enteroccocus species isolated from the “Prof. Dr. O. Fodor” Regional Institute of Gastroenterology and Hepatology from Cluj-Napoca during one year focusing on non-faecalis non-faecium Enterococci. A brief review of the literature was performed using case reports involving Enterococcus raffinosus, Enterococcus durans and Enterococcus avium; (3) Results: Only 58 out of 658 Enteroccocus isolates were non-faecalis non-faecium and met the inclusion criteria. These species were isolated more often (p < 0.05) from the surgical ward from mixed etiology infections with E. coli. In our review, we included 39 case reports involving E. raffinosus, E. durans and E. avium; (4) Conclusions: Isolation of non-faecalis non-faecium enterococci displays an emerging trend with crucial healthcare consequences. Based on the analysis of the case reports, E. avium seems to be involved more often in neurological infections, E. durans in endocarditis, while E. raffinosus displays a more heterogenous distribution.

PubMed: 35453797
DOI: 10.3390/biology11040598

Authors: Reem AlJindan, Nehal Mahmoud, Doaa M AlEraky...

BACKGROUND

Enterococcus avium (E. avium) is a Gram-positive nosocomial pathogen that is commonly isolated from the alimentary tract. The objective of this functional genomics study was to identify the resistant genes by analyzing the genome of E. avium IRMC1622a, a type of bacteria found in feces collected from a patient at a Saudi Arabian tertiary hospital.

METHODS

The bacterial strain IRMC1622a was identified by 16 S rRNA sequencing as Enterococcus sp. The resistance phenomics were performed using VITEK® 2, and morphological analysis was achieved using a scanning electron microscope (SEM). Finally, the whole bacterial genome of the bacterial strain IRMC1622a was subjected to sequencing during October 2023 using Oxford Nanopore long-read sequencing technology, and mining for resistant genes.

RESULTS

The results of antimicrobial resistant phenomics indicated that the IRMC1622a strain was sensitive to all tested antimicrobial agents except for erythromycin, and the same result was confirmed by genomic analysis in addition to other classes of antibiotics. SEM showed E. avium IRMC1622a is ovoid shape, in single cells (L 1.2797 ± 0.1490 µm), in pairs (L 1.7333 ± 0.1054 µm), and in chains (L 2.44033 ± 0.1978 µm). The E. avium IRMC1622a genome has 14 (in CARD) antimicrobial resistance genes that were identified with several mechanisms of antimicrobial resistance, such as the efflux pump and conferring antibiotic resistance. The present study revealed that the E. avium IRMC1622a genome contains a high number of genes associated with virulence factors, and 14 matched pathogenic protein families and predicted as human pathogen (probability score 0.855). We report two (ISEnfa4 and ISEfa5) mobile genetic elements for the first time in the E. avium genome.

CONCLUSIONS

The study concludes that E. avium IRMC1622a is susceptible to all tested antibacterials except erythromycin. The IRMC1622a has 14 genes encoding antimicrobial resistance mechanisms, including the efflux pump and conferring antibiotic resistance. This could indicate a potential rise in E. avium resistance in healthcare facilities. These observations may raise concerns regarding E. avium resistance in healthcare. We need more research to understand the pathophysiology of E. avium, which leads to hospital-acquired infections.

Topics: Humans; Genome, Bacterial; Anti-Bacterial Agents; Feces; Microbial Sensitivity Tests; Gram-Positive Bacterial Infections; Genomics; Saudi Arabia; Enterococcus; RNA, Ribosomal, 16S; Drug Resistance, Bacterial; Whole Genome Sequencing; Tertiary Care Centers; Cross Infection; Phenotype

PubMed: 38833914
DOI: 10.1016/j.jiph.2024.05.051

Authors: Abdelrhman Abo-Zed, Shaymaa Hegazy, Tung Phan...

Enterococci have been recognized as major pathogens causing nosocomial and community-acquired infections. The emergence of antimicrobial-resistant enterococci is one of the major public health challenges worldwide. While many enterococcal species have been identified, is rarely detected in humans. Here we present an interesting case of urinary tract infection and haematuria involving in a 72-year-old patient. The patient underwent antibiotic therapy and surgical procedures with excellent improvement. This case report highlights the important role of in clinical settings.

PubMed: 36003358
DOI: 10.1099/acmi.0.000349

Authors: So-Youn Park, Ki-Ho Park, Young Hyun Cho...

Brain abscesses can be highly lethal if appropriate treatment is not administered, and reports of such an abscess caused by Enterococcus avium are very rare. Here,we report a case of a 48-year-old man presenting with chronic otitis media. He initially presented with a headache and right otalgia. An otoscopic evaluation performed on the day of admission showed exudation of fresh pus from the right ear. Brain magnetic resonance imaging demonstrated a hypodense area in the right temporoparietal lobe, suggestive of a brain abscess. A culturing of the ear discharge and brain abscess aspirate proved of E. avium infection. Following stereotactic aspiration of the brain abscess and proper antimicrobial treatment, the patient recovered completely. In this report, we also review and discuss the available medical literature on previous cases of E. avium infection associated with brain abscess.

PubMed: 24396636
DOI: 10.3947/ic.2013.45.3.335

Authors: Yuanling Jin, Tao Zhu, Xiao Cai...

ABSTRACT

Diabetic foot ulcer (DFU) is a severe complication of diabetes. Due to conservative or delayed treatment, the majority of DFU patients frequently miss the optimal treatment window, thereby leading to amputation. Despite being a rare pathogen with low virulence, () exhibits some antibiotic resistance and can be fatal for immunocompromised patients. This report describes a DFU case, caused by infection due to exposure to poultry. Wound microbiota was dynamically monitored using bacterial culture followed by 16S rRNA gene sequencing throughout the illness. Combination of antibiotics was administered to control the secondary infection.

CASE REPORT

A 56-year-old man presented with a two-week history of redness, swelling, heat, pain, and pus discharge from a ruptured wound on his left heel. The patient was diagnosed with osteomyelitis and a Wagner grade 3 diabetic foot ulcer infection, complicated by the soft tissue infection in the left heel. Strain identification and antibiotic susceptibility tests were immediately performed after admission. The patient underwent three debridement procedures at the DFU site. However, we observed recurrent bacterial infections, based on the clinical progression. Second-generation sequencing detected various pathogens. After targeted treatment with Vacuum sealing drainage (VSD) combined with antibiotic bone cement, the patient's condition stabilised. A skin graft was subsequently performed. Antibiotics were used to control the infection and blood glucose level was controlled throughout the treatment.

CONCLUSION

Thus, this report provides a comprehensive description of a DFU case, caused by Antibiotics and surgical measures should be adjusted according to the pathogens responsible for wound infections in DFU patients. It is important to reduce the mortality and prevent irreversible amputations.

PubMed: 39760042
DOI: 10.3389/fmed.2024.1502337

Authors: Mallika Sengupta, Riya Sarkar, Soma Sarkar...

INTRODUCTION

There is increasing development of antibiotic resistance among the Enterococcus species.

OBJECTIVES

This study was performed to determine prevalence and characterize the vancomycin-resistant and linezolid-resistant enterococcus isolates from a tertiary care center. Moreover, the antimicrobial susceptibility pattern of these isolates was also determined.

MATERIALS AND METHODS

A prospective study was performed in Medical College, Kolkata, India, over a period of two years (from January 2018 to December 2019). After obtaining clearance from the Institutional Ethics Committee, Enterococcus isolates from various samples were included in the present investigation. In addition to the various conventional biochemical tests, the VITEK 2 Compact system was used to identify the Enterococcus species. The isolates were tested for antimicrobial susceptibility to different antibiotics using the Kirby-Bauer disk diffusion method and VITEK 2 Compact to determine the minimum inhibitory concentration (MIC). The Clinical and Laboratory Standards Institute (CLSI) 2017 guidelines were used to interpret susceptibility. Multiplex PCR was performed for genetic characterization of the vancomycin-resistant Enterococcus isolates and sequencing was performed for characterization of the linezolid-resistant Enterococcus isolates.

RESULTS

During the period of two years, 371 isolates of spp. were obtained from 4934 clinical isolates showing a prevalence of 7.52%. Among these isolates, 239 (64.42%) were , 114 (30.72%) , and others were , , , and . Among these, 24 (6.47%) were VRE (Vancomycin-Resistant Enterococcus) of which 18 isolates were Van A type and six isolates of and were resistant VanC type. There were two linezolid-resistant Enterococcus, and they were found to have the G2576T mutation. Among the 371 isolates, 252 (67.92%) were multi-drug resistant.

CONCLUSION

This study found an increasing prevalence of vancomycin-resistant Enterococcus isolates. There is also an alarming prevalence of multidrug resistance among these isolates.

PubMed: 36900089
DOI: 10.3390/diagnostics13050945

Authors: Xinyi Gu, Jiancun Zhao, Rongling Zhang...

() is a common bacterium inhabiting the intestines of humans and other animals. Most strains of this species can produce gamma-aminobutyric acid (GABA) the glutamate decarboxylase (GAD) system, but the presence and genetic organization of their GAD systems are poorly characterized. In this study, our bioinformatics analyses showed that the GAD system in strains was generally encoded by three genes (, , and ), together with an antiporter gene () and regulator gene (), and these genes are organized in a cluster. This finding contrasts with that for other lactic acid bacteria. SDMCC050406, a GABA producer isolated from human feces, was employed to investigate the contribution of the three genes to GABA biosynthesis. The results showed that the relative expression level of was higher than those of and in the exponential growth and stationary phases, and this was accompanied by the synchronous transcription of . After heterologous expression of the three genes in BL21 (DE3), the value of the purified GAD3 was 4.26 ± 0.48 mM, a value lower than those of the purified GAD1 and GAD2. Moreover, gene inactivation caused decreased GABA production, accompanied by a reduction in resistance to acid stress. These results indicated that plays a crucial role in GABA biosynthesis and this property endowed the strain with acid tolerance. Our findings provided insights into how strains survive the acidic environments of fermented foods and throughout transit through the stomach and gut while maintaining cell viability.

PubMed: 34566904
DOI: 10.3389/fmicb.2021.691968

Authors: Anca Farkas, Cristian Coman, Edina Szekeres...

As a consequence of global demographic challenges, both the artificial and the natural environment are increasingly impacted by contaminants of emerging concern, such as bacterial pathogens and their antibiotic resistance genes (ARGs). The aim of this study was to determine the extent to which anthropogenic contamination contributes to the spread of antibiotic resistant enterococci in aquatic compartments and to explore genetic relationships among strains. Antimicrobial susceptibility testing (ampicillin, imipenem, norfloxacin, gentamycin, vancomycin, erythromycin, tetracycline, trimethoprim-sulfamethoxazole) of 574 isolates showed different rates of phenotypic resistance in bacteria from wastewaters (91.9-94.4%), hospital effluents (73.9%), surface waters (8.2-55.3%) and groundwater (35.1-59.1%). The level of multidrug resistance reached 44.6% in enterococci from hospital effluents. In all samples, except for hospital sewage, the predominant species were and . In addition, , , , and were identified. strains carried the greatest variety of ARGs (, , , , , , , , , , ), while displayed the highest ARG frequency. Molecular typing using the ERIC2 primer revealed substantial genetic heterogeneity, but also clusters of enterococci from different aquatic compartments. Enterococcal migration under anthropogenic pressure leads to the dispersion of clinically relevant strains into the natural environment and water resources. In conclusion, ERIC-PCR fingerprinting in conjunction with ARG profiling is a useful tool for the molecular typing of clinical and environmental species. These results underline the need of safeguarding water quality as a strategy to limit the expansion and progression of the impending antibiotic-resistance crisis.

PubMed: 36139992
DOI: 10.3390/antibiotics11091213

Authors: F Depardieu, M-L Foucault, J Bell...

We studied the clinical isolates Enterococcus faecium NEF1, resistant to high levels of vancomycin (MIC, 512 microg/ml) and teicoplanin (MIC, 64 microg/ml); Enterococcus faecium BM4653 and BM4656 and Enterococcus avium BM4655, resistant to moderate levels of vancomycin (MIC, 32 microg/ml) and to low levels of teicoplanin (MIC, 4 microg/ml); and Enterococcus faecalis BM4654, moderately resistant to vancomycin (MIC, 16 microg/ml) but susceptible to teicoplanin (MIC, 0.5 microg/ml). The strains were distinct, were constitutively resistant via the synthesis of peptidoglycan precursors ending in D-alanyl-D-lactate, and harbored a chromosomal vanD gene cluster that was not transferable. New mutations were found in conserved domains of VanS(D): at T(170)I near the phosphorylation site in NEF1, at V(67)A at the membrane surface in BM4653, at G(340)S in the G2 ATP-binding domain in BM4655, in the F domain in BM4656 (a 6-bp insertion), and in the G1 and G2 domains of BM4654 (three mutations). The mutations resulted in constitutivity, presumably through the loss of the phosphatase activity of the sensor. The chromosomal Ddl D-Ala:D-Ala ligase had an IS19 copy in NEF1, a mutation in the serine (S(185)F) or near the arginine (T(289)P) involved in D-Ala1 binding in BM4653 or BM4655, respectively, and a mutation next to the lysine (P(180)S) involved in D-Ala2 binding in BM4654, leading to the production of an impaired enzyme. In BM4653 vanY(D), a new insertion sequence, ISEfa9, belonging to the IS3 family, resulted in the absence of D,D-carboxypeptidase activity. Strain BM4656 had a functional D-Ala:D-Ala ligase, associated with high levels of both VanX(D) and VanY(D) activities, and is the first example of a VanD-type strain with a functional Ddl enzyme. Study of these five clinical isolates, displaying various assortments of mutations, confirms that all VanD-type strains isolated so far have undergone mutations in the vanS(D) or vanR(D) gene, leading to constitutive resistance, but that the Ddl host ligase is not always impaired. Based on sequence differences, the vanD gene clusters could be assigned to two subtypes: vanD-1 and vanD-4.

Topics: Amino Acid Sequence; Animals; Anti-Bacterial Agents; Bacterial Proteins; Enterococcus; Enterococcus faecalis; Enterococcus faecium; Gene Expression Regulation, Bacterial; Humans; Molecular Sequence Data; Multigene Family; Mutation; Peptide Synthases; Sequence Analysis, DNA; Teicoplanin; Vancomycin; Vancomycin Resistance

PubMed: 19258279
DOI: 10.1128/AAC.01348-08

Authors: Jinpeng Yang, Yanshan Chen, Zhiyou Dong...

spp., as an opportunistic pathogen, are widely distributed in the environment and the gastrointestinal tracts of both humans and animals. Captive Asian elephants, popular animals at tourist attractions, have frequent contact with humans. However, there is limited information on whether captive Asian elephants can serve as a reservoir of antimicrobial resistance (AMR). The aim of this study was to characterize AMR, antibiotic resistance genes (ARGs), virulence-associated genes (VAGs), gelatinase activity, hemolysis activity, and biofilm formation of spp. isolated from captive Asian elephants, and to analyze the potential correlations among these factors. A total of 62 spp. strains were isolated from fecal samples of captive Asian elephants, comprising 17 (27.4%), 12 (19.4%), 8 (12.9%), 7 (11.3%), 7 (11.3%), and 11 other spp. (17.7%). Isolates exhibited high resistance to rifampin (51.6%) and streptomycin (37.1%). 50% of spp. isolates exhibited multidrug resistance (MDR), with all strains demonstrating MDR. Additionally, nine ARGs were identified, with (51.6%), (24.2%), and (21.0%) showing relatively higher detection rates. Biofilm formation, gelatinase activity, and α-hemolysin activity were observed in 79.0, 24.2, and 14.5% of the isolates, respectively. A total of 18 VAGs were detected, with being the most prevalent (69.4%). Correlation analysis revealed 229 significant positive correlations and 12 significant negative correlations. The strongest intra-group correlations were observed among VAGs. Notably, we found that vancomycin resistance showed a significant positive correlation with ciprofloxacin resistance, , and gelatinase activity, respectively. In conclusion, captive Asian elephants could serve as significant reservoirs for the dissemination of AMR to humans.

PubMed: 37954234
DOI: 10.3389/fmicb.2023.1277221