Genomic analysis of multidrug-resistant clinical Enterococcus faecalis isolates for antimicrobial resistance genes and virulence factors from the western region of Saudi Arabia

Molecular characterization and biofilm formation ability of Enterococcus faecium and Enterococcus faecalis bloodstream isolates from a Chinese tertiary hospital in Beijing

To investigate the molecular characteristics and biofilm-forming ability of 116 Enterococcus faecium (Efm) and 72 Enterococcus faecalis (Efs) isolates obtained from patients with bloodstream infections (BSI) at a Chinese hospital between July 2011 and March 2018. The presence of glycopeptide resistance genes and five virulence genes (esp, gelE, asa1, hyl, and cylA) was screened using two multiplex PCR. MLST was used to assess the clonality. Crystal violet staining was used to detect biofilms. Vancomycin resistance was detected in 30.1% of Efm and 2.8% of Efs isolates, respectively. All VRE strains carried the vanA gene. The esp, gelE, asa1, and cylA genes in 72 Efs strains were detected at 62.5%, 84.7%, 84.7%, and 69.4%, respectively. Among the 116 Efm isolates, 74.1% and 25.8% carried esp and hyl, respectively. The esp gene was significantly associated with vancomycin-resistant Efm (VREfm) compared to vancomycin-susceptible Efm (VSEfm). In total, 91.7% of Efs and 20.0% of Efm produced biofilms. Twenty-six STs were identified among the 72 Efs isolates, with ST4 (29.2%) being the predominant. In total, 116 Efm strains were grouped into 26 STs, with ST78 (46.6%) being the predominant. Both VREfm (41.7%) and VSEfm (48.8%) were dominant in ST78. There is no clear evidence suggesting that some STs are associated with vancomycin resistance or biofilm formation. Both Efm and Efs BSI isolates showed a polyclonal pattern with a dominant clone and many unique types, implying the coexistence of clonal dissemination and an influx of new clones. The horizontal transmission of resistance genes may play a more important role in VREfm prevalence than clonal expansion.

Knowledge of Antibiotic Use and Resistance Among Medical Students in Saudi Arabia

Introduction

The World Health Organization (WHO) has placed great importance on providing thorough, hands-on training to medical students regarding responsible and appropriate antibiotic prescription. Accordingly, this study aims to gain a better perspective on the knowledge of antibiotic use and resistance among medical students in Jeddah, Saudi Arabia.

Methods

A questionnaire-based cross-sectional study was conducted among medical students in Jeddah, Saudi Arabia, from 1 September to 30 November 2023. The categorical variables are presented as frequencies and percentages. Mann-Whitney and Kruskal-Wallis tests were used to compare the outcomes, and generalised linear regression models were constructed to predict the students' knowledge of antibiotics and antibiotic resistance. A p-value of < 0.05 was taken to indicate statistical significance.

Results

The study included a total of 353 medical students. First-year medical students represented 28.60% of the participants, while females represented 76.80%. Most participants (92.40%) agreed that antibiotics are effective against bacteria, whereas only 25.20% agreed about antibiotics' effectiveness against viruses. More than half of the participants (53.80%) believed that bacterial infections can be resolved without antibiotics. A significant majority (78.20%) agreed that the unnecessary use of antibiotics makes them less effective. More than half of the participants (56.90%) acknowledged that infections caused by resistant bacteria are increasing in Saudi Arabia, and two-thirds (75.10%) believed that healthcare workers could effectively reduce antibiotic resistance in Saudi Arabia. Male students had low knowledge about antibiotics [Beta = -1.429, 95% CI (-2.618, -0.241), P value = 0.019].

Conclusion

Improving the curriculum by incorporating topics like resistance mechanisms and responsible antibiotic usage can address the knowledge gap among male students. This comprehensive training, utilizing various educational methods, is essential for fostering responsible antibiotic practices among future healthcare professionals.

Medical Device-Associated Biofilm Infections and Multidrug-Resistant Pathogens

Medical devices such as venous catheters (VCs) and urinary catheters (UCs) are widely used in the hospital setting. However, the implantation of these devices is often accompanied by complications. About 60 to 70% of nosocomial infections (NIs) are linked to biofilms. The main complication is the ability of microorganisms to adhere to surfaces and form biofilms which protect them and help them to persist in the host. Indeed, by crossing the skin barrier, the insertion of VC inevitably allows skin flora or accidental environmental contaminants to access the underlying tissues and cause fatal complications like bloodstream infections (BSIs). In fact, 80,000 central venous catheters-BSIs (CVC-BSIs)-mainly occur in intensive care units (ICUs) with a death rate of 12 to 25%. Similarly, catheter-associated urinary tract infections (CA-UTIs) are the most commonlyhospital-acquired infections (HAIs) worldwide.These infections represent up to 40% of NIs.In this review, we present a summary of biofilm formation steps. We provide an overview of two main and important infections in clinical settings linked to medical devices, namely the catheter-asociated bloodstream infections (CA-BSIs) and catheter-associated urinary tract infections (CA-UTIs), and highlight also the most multidrug resistant bacteria implicated in these infections. Furthermore, we draw attention toseveral useful prevention strategies, and advanced antimicrobial and antifouling approaches developed to reduce bacterial colonization on catheter surfaces and the incidence of the catheter-related infections.

Gut microbiota and risk of endocarditis: a bidirectional Mendelian randomization study

Background

The associations between gut microbiota and cardiovascular disease have been reported in previous studies. However, the relationship between gut microbiota and endocarditis remains unclear.

Methods

A bidirectional Mendelian randomization (MR) study was performed to detect the association between gut microbiota and endocarditis. Inverse variance weighted (IVW) method was considered the main result. Simultaneously, heterogeneity and pleiotropy tests were conducted.

Results

Our study suggests that family Victivallaceae (p = 0.020), genus Eubacterium fissicatena group (p = 0.047), genus Escherichia Shigella (p = 0.024), genus Peptococcus (p = 0.028) and genus Sellimonas (p = 0.005) play protective roles in endocarditis. Two microbial taxa, including genus Blautia (p = 0.006) and genus Ruminococcus2 (p = 0.024) increase the risk of endocarditis. At the same time, endocarditis has a negative effect on genus Eubacterium fissicatena group (p = 0.048). Besides, no heterogeneity or pleiotropy was found in this study.

Conclusion

Our study emphasized the certain role of specific gut microbiota in patients with endocarditis and clarified the negative effect of endocarditis on gut microbiota.

Enterococcus species: insights into antimicrobial resistance and whole-genome features of isolates recovered from livestock and raw meat in Ghana

Introduction

Enterococcus spp. have gradually evolved from commensals to causing life-threatening hospital-acquired infections globally due to their inherent antimicrobial resistance ability and virulence potential. Enterococcus spp. recovered from livestock and raw meat samples were characterized using antimicrobial susceptibility testing and whole-genome sequencing.

Materials and methods

Isolates were confirmed using the MALDI-ToF mass spectrometer, and antimicrobial susceptibility was determined using the Kirby-Bauer disk diffusion method. Whole genome sequencing was performed on isolates resistant to two or more antibiotics. Bioinformatics analysis was performed to determine sequence types, resistance and virulence gene content and evolutionary relationships between isolates from meat and livestock samples, and other enterococci genomes curated by PATRIC. eBURST analysis was used to assign genomes to clonal complexes.

Results

Enterococcus spp. were predominantly E. faecalis (96/236; 41%) and E. faecium (89/236; 38%). Overall, isolates showed resistance to erythromycin (78/236; 33%), tetracycline (71/236; 30%), ciprofloxacin (20/236; 8%), chloramphenicol (12/236; 5%), linezolid (7/236; 3%), ampicillin (4/236; 2%) and vancomycin (1/236, 0.4%). Resistance to two or more antimicrobial agents was detected among 17% (n = 40) Enterococcus spp. Resistance genes for streptogramins [lsa(A), lsa(E), msr(C)], aminoglycosides [aac(6')-Ii, aph(3')-III, ant(6)-Ia, aac(6')-aph(2″), str], amphenicol [cat], macrolides [erm(B), erm(T), msr(C)], tetracyclines [tet(M), tet(L), tet(S)] and lincosamides [lsa(A), lsa(E), lnu(B)] were detected among the isolates. Genes for biofilm formation, adhesins, sex pheromones, cytolysins, hyaluronidase, oxidative stress resistance, quorum-sensing and anti-phagocytic activity were also identified. Potential plasmids with replicon sequences (rep1, rep2, repUS43, repUS47, rep9a, rep9b) and other mobile genetic elements (Tn917, cn_5536_ISEnfa1, Tn6009, ISEnfa1, ISEfa10) were detected. Clinically relevant E. faecium ST32 and ST416 clones were identified in meat samples.

Conclusion

The occurrence of antimicrobial-resistant Enterococcus spp. in livestock and raw meat samples, carrying multiple resistance and virulence genes, including known clones associated with hospital-acquired infections, underscores the critical need for employing robust tools like whole genome sequencing. Such tools provide detailed data essential for ongoing surveillance efforts aimed at addressing the challenge of antimicrobial resistance with a focus on one health.

Antimicrobial Potential of Different Isolates of Chaetomium globosum Combined with Liquid Chromatography Tandem Mass Spectrometry Chemical Profiling

The antimicrobial resistance of pathogenic microorganisms against commercial drugs has become a major problem worldwide. This study is the first of its kind to be carried out in Egypt to produce antimicrobial pharmaceuticals from isolated native taxa of the fungal Chaetomium, followed by a chemical investigation of the existing bioactive metabolites. Here, of the 155 clinical specimens in total, 100 pathogenic microbial isolates were found to be multi-drug resistant (MDR) bacteria. The Chaetomium isolates were recovered from different soil samples, and wild host plants collected from Egypt showed strong inhibitory activity against MDR isolates. Chaetomium isolates displayed broad-spectrum antimicrobial activity against C. albicans, Gram-positive, and Gram-negative bacteria, with inhibition zones of 11.3 to 25.6 mm, 10.4 to 26.0 mm, and 10.5 to 26.5 mm, respectively. As a consecutive result, the minimum inhibitory concentration (MIC) values of Chaetomium isolates ranged from 3.9 to 62.5 µg/mL. Liquid chromatography combined with tandem mass spectrometry (LC-MS/MS) analysis was performed for selected Chaetomium isolates with the most promising antimicrobial potential against MDR bacteria. The LC-MS/MS analysis of Chaetomium species isolated from cultivated soil at Assuit Governate, Upper Egypt (3), and the host plant Zygophyllum album grown in Wadi El-Arbaein, Saint Katherine, South Sinai (5), revealed the presence of alkaloids as the predominant bioactive metabolites. Most detected bioactive metabolites previously displayed antimicrobial activity, confirming the antibacterial potential of selected isolates. Therefore, the Chaetomium isolates recovered from harsh habitats in Egypt are rich sources of antimicrobial metabolites, which will be a possible solution to the multi-drug resistant bacteria tragedy.

Antimicrobial Resistance in Bacteria from Meat and Meat Products: A One Health Perspective

According to the 2030 Agenda of the United Nations, one of the sustainable development goals is to ensure sustainable consumption and production patterns. The need to ensure food safety includes, other than microbiological hazards, concerns with antimicrobial-resistant (AMR) bacteria. The emergence of resistant bacteria in the food industry is essentially due to the abusive, and sometimes incorrect, administration of antimicrobials. Although not allowed in Europe, antimicrobials are often administered to promote animal growth. Each time antimicrobials are used, a selective pressure is applied to AMR bacteria. Moreover, AMR genes can be transmitted to humans through the consumption of meat-harbouring-resistant bacteria, which highlights the One Health dimension of antimicrobial resistance. Furthermore, the appropriate use of antimicrobials to ensure efficacy and the best possible outcome for the treatment of infections is regulated through the recommendations of antimicrobial stewardship. The present manuscript aims to give the current state of the art about the transmission of AMR bacteria, particularly methicillin-resistant S. aureus, ESBL-producing Enterobacteriaceae, and vancomycin-resistant Enterococcus spp., along with other ESKAPE bacteria, from animals to humans through the consumption of meat and meat products, with emphasis on pork meat and pork meat products, which are considered the most consumed worldwide.

Genomic Landscape of Multidrug Resistance and Virulence in Enterococcus faecalis IRMC827A from a Long-Term Patient

We report on a highly virulent, multidrug-resistant strain of Enterococcus faecalis IRMC827A that was found colonizing a long-term male patient at a tertiary hospital in Khobar, Saudi Arabia. The E. faecalis IRMC827A strain carries several antimicrobial drug resistance genes and harbours mobile genetic elements such as Tn6009, which is an integrative conjugative element that can transfer resistance genes between bacteria and ISS1N via an insertion sequence. Whole-genome-sequencing-based antimicrobial susceptibility testing on strains from faecal samples revealed that the isolate E. faecalis IRMC827A is highly resistant to a variety of antibiotics, including tetracycline, doxycycline, minocycline, dalfopristin, virginiamycin, pristinamycin, chloramphenicol, streptomycin, clindamycin, lincomycin, trimethoprim, nalidixic acid and ciprofloxacin. The isolate IRMC827A carries several virulence factors that are significantly associated with adherence, biofilm formation, sortase-assembled pili, manganese uptake, antiphagocytosis, and spreading factor of multidrug resistance. The isolate also encompasses two mutations (G2576T and G2505A) in the 23S rRNA gene associated with linezolid resistance and three more mutations (gyrA p.S83Y, gyrA p.D759N and parC p.S80I) of the antimicrobial resistance phenotype. The findings through next-generation sequencing on the resistome, mobilome and virulome of the isolate in the study highlight the significance of monitoring multidrug-resistant E. faecalis colonization and infection in hospitalized patients. As multidrug-resistant E. faecalis is a serious pathogen, it is particularly difficult to treat and can cause fatal infections. It is important to have quick and accurate diagnostic tests for multidrug-resistant E. faecalis, to track the spread of multidrug-resistant E. faecalis in healthcare settings, and to improve targeted interventions to stop its spread. Further research is necessary to develop novel antibiotics and treatment strategies for multidrug-resistant E. faecalis infections.

An Overview of Antimicrobial Resistance in Saudi Arabia (2013-2023) and the Need for National Surveillance

Antimicrobial resistance (AMR) is a well-recognized global threat. The World Health Organization (WHO) issued a report ranking the critical types of bacterial resistance that need to be monitored. Several studies from individual institutions in Saudi Arabia have reported rates of antimicrobial resistance using automated methods. However, no national surveillance study has been conducted to date using gold standard methods for antimicrobial susceptibility testing. This review summarizes AMR rates for major bacterial pathogens in Saudi Arabia and provides a justification for the need for a national surveillance project. In Saudi Arabia, AMR rates for both Gram-positive and Gram-negative bacteria are on the rise. Surveillance studies help identify AMR trends and emergence of outbreaks. The WHO has started a program, the Global Antimicrobial Resistance Surveillance System (GLASS), encouraging its member states, including Saudi Arabia, to conduct antimicrobial surveillance studies to estimate AMR rates worldwide. Of the microbiological methods used to test antimicrobial susceptibility, only broth microdilution (BMD) is considered the "gold standard." As AMR studies in Saudi Arabia are sparse, mostly limited to single centers and were conducted using automated methods, a national AMR surveillance project is needed to evaluate the current status and to inform stewardship decisions.

First Report of a Wastewater Treatment-Adapted Enterococcus faecalis ST21 Harboring vanA Gene in Brazil

Enterococcus faecalis has emerged as an important opportunistic pathogen due to its increasing resistance to antimicrobials, mainly to vancomycin, which leads substantial cases of therapeutic failures. Wastewater treatment plants (WWTP), in turn, are considered hotpots in the spread of antimicrobial resistance according to One Health perspective. In this study, we present the first report of a vancomycin-resistant E. faecalis strain recovered from treated effluent in Brazil. For this purpose, the whole-genome sequencing (WGS) was carried out aiming to elucidate its molecular mechanisms of antimicrobial resistance and its phylogenetic relationships amongst strains from other sources and countries. According to Multilocus Sequence Typing (MLST) analysis this strain belongs to ST21. The WGS pointed the presence of vanA operon, multiple antibiotic resistance and virulence genes, and a significant pathogenic potential for humans. The phylogenomic analysis of E. faecalis 6805 was performed with ST21 representatives from the PubMLST database, including the E. faecalis IE81 strain from clinical sample in Brazil, which had its genome sequenced in this study. Our results demonstrated a strain showing resistance to vancomycin in treated effluent. To the best of our knowledge, this is an unprecedented report of vanA-carrying E. faecalis ST21. Furthermore, it is the first description of a vanA-harboring strain of this species from environmental sample in Brazil. Our data highlight the role of WWTP in the spread of AMR, since these environments are favorable for the selection of multidrug-resistant pathogens and the treated effluents, carrying antibiotic resistance genes, are directed to receiving water bodies.

A Genomic Snapshot of Antibiotic-ResistantEnterococcus faecalis within Public Hospital Environments in South Africa

Enterococci are among the most common opportunistic hospital pathogens. This study used whole-genome sequencing (WGS) and bioinformatics to determine the antibiotic resistome, mobile genetic elements, clone and phylogenetic relationship of Enterococcus faecalis isolated from hospital environments in South Africa. This study was carried out from September to November 2017. Isolates were recovered from 11 frequently touched sites by patients and healthcare workers in different wards at 4 levels of healthcare (A, B, C, and D) in Durban, South Africa. Out of the 245 identified E. faecalis isolates, 38 isolates underwent whole-genome sequencing (WGS) on the Illumina MiSeq platform, following microbial identification and antibiotic susceptibility tests. The tet(M) (31/38, 82%) and erm(C) (16/38, 42%) genes were the most common antibiotic-resistant genes found in isolates originating from different hospital environments which corroborated with their antibiotic resistance phenotypes. The isolates harboured mobile genetic elements consisting of plasmids (n = 11) and prophages (n = 14) that were mostly clone-specific. Of note, a large number of insertion sequence (IS) families were found on the IS3 (55%), IS5 (42%), IS1595 (40%), and Tn3 transposons the most predominant. Microbial typing using WGS data revealed 15 clones with 6 major sequence types (ST) belonging to ST16 (n = 7), ST40 (n = 6), ST21 (n = 5), ST126 (n = 3), ST23 (n = 3), and ST386 (n = 3). Phylogenomic analysis showed that the major clones were mostly conserved within specific hospital environments. However, further metadata insights revealed the complex intraclonal spread of these E. faecalis major clones between the sampling sites within each specific hospital setting. The results of these genomic analyses will offer insights into antibiotic-resistantE. faecalis in hospital environments relevant to the design of optimal infection prevention strategies in hospital settings.

Risk Factors and the Impact of Multidrug-Resistant Bacteria on Community-Acquired Urinary Sepsis

Risk factors for multidrug-resistant bacteria (MDRB) in nosocomial urinary tract infection (UTI) have been widely studied. However, these risk factors have not been analyzed in community-acquired urinary sepsis (US), nor have its outcomes been studied. The aim of our study is to determine risk factors for MDRB in community-acquired US and its influence on outcomes. Prospective observational study of patients with community-acquired US admitted to a university hospital. We compared epidemiological and clinical variables and outcomes of US due to MDRB and non-MDRB. Independent risk factors for MDRB were analyzed using logistic regression. A total of 193 patients were included, 33.7% of them with US due to MDRB. The median age of patients was 82 years. Hospital mortality was 17.6%, with no difference between the MDRB and non-MDRB groups. The length of hospital stay was 5 (4-8) days, with a non-significant tendency to longer hospital stays in the MDRB group (6 (4-10) vs. 5 (4-8) days, p = 0.051). Healthcare-associated US was found to be an independent risk factor for MDR bacteria by multivariate analysis. In conclusion, the impact of MDR bacteria on the outcomes of community-acquired urinary sepsis was mild. Healthcare-associated US was an independent risk factor for MDR bacteria.

Antibiotic Resistance among Gastrointestinal Bacteria in Broilers: A Review Focused on Enterococcus spp. and Escherichia coli

Chickens can acquire bacteria at different stages, and bacterial diversity can occur due to production practices, diet, and environment. The changes in consumer trends have led to increased animal production, and chicken meat is one of the most consumed meats. To ensure high levels of production, antimicrobials have been used in livestock for therapeutic purposes, disease prevention, and growth promotion, contributing to the development of antimicrobial resistance across the resident microbiota. Enterococcus spp. and Escherichia coli are normal inhabitants of the gastrointestinal microbiota of chickens that can develop strains capable of causing a wide range of diseases, i.e., opportunistic pathogens. Enterococcus spp. isolated from broilers have shown resistance to at least seven classes of antibiotics, while E. coli have shown resistance to at least four. Furthermore, some clonal lineages, such as ST16, ST194, and ST195 in Enterococcus spp. and ST117 in E. coli, have been identified in humans and animals. These data suggest that consuming contaminated animal-source food, direct contact with animals, or environmental exposure can lead to the transmission of antimicrobial-resistant bacteria. Therefore, this review focused on Enterococcus spp. and E. coli from the broiler industry to better understand how antibiotic-resistant strains have emerged, which antibiotic-resistant genes are most common, what clonal lineages are shared between broilers and humans, and their impact through a One Health perspective.

Virulence and antibiotic-resistance genes in Enterococcus faecalis associated with streptococcosis disease in fish

Enterococcus faecalis is associated with streptococcosis like infection in fish. A whole-genome sequence study was conducted to investigate the virulence factor and antibiotic-resistance genes in three fish pathogenic E. faecalis. Genomic DNA was extracted from three strains of E. faecalis isolated from streptococcosis infected Nile tilapia (strains BF1B1 and BFFF11) and Thai sarpunti (strain BFPS6). The whole genome sequences of these three strains were performed using a MiSeq sequencer (Illumina, Inc.). All three strains conserved 69 virulence factor such as genes associated with protection against oxidative stress, bacterial cell wall synthesis, gelatinase toxin, multiple biofilm-associated genes and capsule producing genes. Moreover, 39 antibiotic-resistance genes against sixteen major groups of antibiotics were identified in the genome sequences of all three strains. The most commonly used antibiotic Tetracycline resistance genes were found only in BFPS6 strain, whereas, Bacteriocin synthesis genes were identified in both BFFF11 and BFPS6 strain. Phylogenetic analysis revealed that strains BF1B1 and BFFF1 form a different cluster than BFPS6. This is one of the first whole-genome sequence study of fish pathogenic E. faecalis, unfold new information on the virulence factor and Antibiotic resistance genes linked to pathogenicity in fish.

Antibiotic Resistance in Bacteria—A Review

Background: A global problem of multi-drug resistance (MDR) among bacteria is the cause of hundreds of thousands of deaths every year. In response to the significant increase of MDR bacteria, legislative measures have widely been taken to limit or eliminate the use of antibiotics, including in the form of feed additives for livestock, but also in metaphylaxis and its treatment, which was the subject of EU Regulation in 2019/6. Numerous studies have documented that bacteria use both phenotypis and gentic strategies enabling a natural defence against antibiotics and the induction of mechanisms in increasing resistance to the used antibacterial chemicals. The mechanisms presented in this review developed by the bacteria have a significant impact on reducing the ability to combat bacterial infections in humans and animals. Moreover, the high prevalence of multi-resistant strains in the environment and the ease of transmission of drug-resistance genes between the different bacterial species including commensal flora and pathogenic like foodborne pathogens (E. coli, Campylobacter spp., Enterococcus spp., Salmonella spp., Listeria spp., Staphylococcus spp.) favor the rapid spread of multi-resistance among bacteria in humans and animals. Given the global threat posed by the widespread phenomenon of multi-drug resistance among bacteria which are dangerous for humans and animals, the subject of this study is the presentation of the mechanisms of resistance in most frequent bacteria called as “foodborne pathoges” isolated from human and animals. In order to present the significance of the global problem related to multi-drug resistance among selected pathogens, especially those danger to humans, the publication also presents statistical data on the percentage range of occurrence of drug resistance among selected bacteria in various regions of the world. In addition to the phenotypic characteristics of pathogen resistance, this review also presents detailed information on the detection of drug resistance genes for specific groups of antibiotics. It should be emphasized that the manuscript also presents the results of own research i.e., Campylobacter spp., E. coli or Enetrococcus spp. This subject and the presentation of data on the risks of drug resistance among bacteria will contribute to initiating research in implementing the prevention of drug resistance and the development of alternatives for antimicrobials methods of controlling bacteria.

Genetic Diversity, Antimicrobial Resistance, and Virulence Factors of Enterococcus Faecalis Isolates Obtained from Stool Samples of Hospitalized Patients

Background: Enterococcus faecalis rapidly develops resistance to different antibiotics, thereby resulting in serious nosocomial infections associated with high mortality rates and different problems in the healthcare systems. Objectives: This study aimed to analyze the genetic diversity, antimicrobial resistance, and virulence factors of E. faecalis isolates obtained from the stool samples of patients in a hospital in the center of Iran. Methods: In this cross-sectional descriptive-analytical study, 108 stool samples were collected from September 2019 to February 2020 from 108 patients hospitalized in a hospital in the center of Iran. Enterococcus faecalis isolates were detected using the ddlE gene detection technique, and antimicrobial resistance testing was performed using the disc agar diffusion method. Moreover, polymerase chain reaction (PCR) was used to detect antimicrobial resistance genes and virulence factors. Genetic diversity was also analyzed by enterobacterial repetitive intergenic consensus using PCR (ERIC-PCR). The BioNumerics software was used to construct a dendrogram. Results: Of 108 isolates, 50 samples were E. faecalis (46.2%). The prevalence of multidrug resistance among E. faecalis isolates was 62%, and most isolates were resistant to antibiotics tetracycline (70%), erythromycin (68%), and rifampin (60%). Among the E. faecalis isolates, the most prevalent antimicrobial resistance genes were ermB (96%), aph (2′′) Ia (66%), aac(6′)-Ie (40%), and ermC (30%), and the most prevalent virulence genes were gelE (78%), asa1 (74%), and esp (74%). The genetic diversity analysis showed 25 ERIC types in two major clusters (ie, clusters H and J) and eight minor clusters (ie, clusters A-G and I). There was no significant difference between clusters H and J in terms of antimicrobial resistance and resistance genes (P > 0.05). In contrast, the prevalence of the asa1 gene was significantly higher in cluster J than in cluster H (P < 0.05). Conclusions: This study showed the high prevalence of multidrug resistance, and high heterogeneity among the E. faecalis isolates obtained from the stool samples of hospitalized patients.

Dissemination of Quinupristin-Dalfopristin and Linezolid resistance genes among hospital environmental and healthy volunteer fecal isolates of Enterococcus faecalis and Enterococcus faecium

BACKGROUND

Streptogramins and linezolid are important in the treatment of infections caused by vancomycin-resistant enterococci.

PURPOSE

Then, we aimed to evaluate the resistance rates against these drugs and the prevalence of genes involved in hospital environmental and fecal normal-flora isolates of Enterococcus faecalis and Enterococcus faecium.

METHODS AND RESULTS

The strains were isolated from the stool samples and hospital environments by culturing on M-Enterococcus (ME) agar, and identified by phenotypic and genotypic microbiological tests. The disk agar diffusion method was used to identify the antimicrobial susceptibility pattern of the isolates. The genomic DNA extraction was done by the alkaline lysis method, and the PCR test was used to detect the resistance genes. A total of 145 enterococci isolates were taken, from which 84 (57.9%) isolates were detected as E. faecalis and 61 (42.06%) isolates were E. faecium. Moreover, 70 (83.33), 4 (4.76%), 1 (1.19%), and 40 (47.61%) isolates of E. faecalis and 20 (32.78%), 1 (1.63%), 4 (6.55%), and 26 (42.62%) E. faecium isolates were resistant against quinupristin-dalfopristin, linezolid, vancomycin, and erythromycin, respectively. Also, 112 (77.24%), 50 (34.48%), 39 (26.89%), 27 (18.62%), 19 (13.1%), 4 (2.75%), and 1 (0.68%) isolates were contained LsaA, vatD, vgbB, vatE, cfr, lsaE and optrA genes, respectively. None of the isolates carried the vgbA gene.

CONCLUSIONS

High-level streptogramin resistance rate and high prevalence of resistance genes in enterococci isolated from the stool of healthy persons and the hospital environment indicates the importance of possible transmission of resistance genes from these isolates to clinical ones.

Bacterial Community and Genomic Analysis of Carbapenem-Resistant Acinetobacter baumannii Isolates from the Environment of a Health Care Facility in the Western Region of Saudi Arabia

The escalating transmission of hospital-acquired infections, especially those due to antimicrobial-resistant bacteria, is a major health challenge worldwide. In this study, a culturomic analysis of bacterial community in a tertiary care hospital in the western region of Saudi Arabia is performed using environmental samples. The genome sequencing of four Acinetobacter baumannii was performed on isolates recovered from an intensive care unit (ICU) environment and clinical samples. A total of 361 bacterial isolates from surface and air samples were identified by MALDI-TOF technique or 16S rRNA gene sequencing. The isolates were classified into 70 distinct species, including ESKAPE pathogens. Resistance in Gram-positive isolates was mainly found to be against benzylpenicillin, azithromycin, ampicillin, and trimethoprim/sulfamethoxazole. Carbapenem- and multidrug-resistant isolates of A. baumannii and Klebsiella pneumonia were found on the ICU surfaces. Genome sequencing revealed that the carbapenem-resistant A. baumannii isolate from ICU environment was linked with those of clinical origin. The isolate Ab133-HEnv was classified as a novel sequence type (ST2528) based on a new allele of Oxf_gdhB-286. Three beta-lactam-antibiotic-resistance genes, bla_ADC-25, bla_OXA-23, and bla_OXA-66, were found in most of the analyzed genomes. Collectively, the results of this study highlight the spread of antimicrobial-resistant nosocomial pathogens in a health care facility in Saudi Arabia.

Bacterial diversity and the antimicrobial resistome in the southwestern highlands of Saudi Arabia

Soil is a reservoir of microbial diversity and the most supportive habitat for acquiring and transmitting antimicrobial resistance. Resistance transfer usually occurs from animal to soil and vice versa, and it may ultimately appear in clinical pathogens. In this study, the southwestern highlands of Saudi Arabia were studied to assess the bacterial diversity and antimicrobial resistance that could be affected by the continuous development of tourism in the region. Such effects could have a long-lasting impact on the local environment and community. Culture-dependent, quantitative polymerase chain reaction (qPCR), and shotgun sequencing-based metagenomic approaches were used to evaluate the diversity, functional capabilities, and antimicrobial resistance of bacteria isolated from collected soil samples. Bacterial communities in the southwestern highlands were mainly composed of Proteobacteria, Bacteroidetes, and Actinobacteria. A total of 102 antimicrobial resistance genes (ARGs) and variants were identified in the soil microbiota and were mainly associated with multidrug resistance, followed by macrolide, tetracycline, glycopeptide, bacitracin, and beta-lactam antibiotic resistance. The mechanisms of resistance included efflux, antibiotic target alteration, and antibiotic inactivation. qPCR confirmed the detection of 18 clinically important ARGs. In addition, half of the 49 identified isolates were phenotypically resistant to at least one of the 15 antibiotics tested. Overall, ARGs and indicator genes of anthropogenic activities (human-mitochondrial [hmt] gene and integron-integrase [int1]) were found in relatively lower abundance. Along with a high diversity of bacterial communities, variation was observed in the relative abundance of bacterial taxa among sampling sites in the southwestern highlands of Saudi Arabia.

Genetically distant bacteriophages select for unique genomic changes in Enterococcus faecalis

The human microbiota harbors diverse bacterial and bacteriophage (phage) communities. Bacteria evolve to overcome phage infection, thereby driving phage evolution to counter bacterial resistance. Understanding how phages select for genetic alterations in medically relevant bacteria is important as phages become established biologics for the treatment of multidrug‐resistant (MDR) bacterial infections. Before phages can be widely used as standalone or combination antibacterial therapies, we must obtain a deep understanding of the molecular mechanisms of phage infection and how host bacteria alter their genomes to become resistant. We performed coevolution experiments using a single Enterococcus faecalis strain and two distantly related phages to determine how phage pressure impacts the evolution of the E. faecalis genome. Whole‐genome sequencing of E. faecalis following continuous exposure to these two phages revealed mutations previously demonstrated to be essential for phage infection. We also identified mutations in genes previously unreported to be associated with phage infection in E. faecalis. Intriguingly, there was only one shared mutation in the E. faecalis genome that was selected by both phages tested, demonstrating that infection by two genetically distinct phages selects for diverse variants. This knowledge serves as the basis for the continued study of E. faecalis genome evolution during phage infection and can be used to inform the design of future therapeutics, such as phage cocktails, intended to target MDR E. faecalis.

Antimicrobial Resistance, Biofilm Formation, and Virulence Genes in Enterococcus Species from Small Backyard Chicken Flocks

Backyard birds are small flocks that are more common in developing countries. They are used for poultry meat and egg production. However, they are also implicated in the maintenance and transmission of several zoonotic diseases, including multidrug-resistant bacteria. Enterococci are one of the most common zoonotic bacteria. They colonize numerous body sites and cause a wide range of serious nosocomial infections in humans. Therefore, the objective of the present study was to investigate the diversity in Enterococcus spp. in healthy birds and to determine the occurrence of multidrug resistance (MDR), multi-locus sequence types, and virulence genes and biofilm formation. From March 2019 to December 2020, cloacal swabs were collected from 15 healthy backyard broiler flocks. A total of 90 enterococci strains were recovered and classified according to the 16S rRNA sequence into Enterococcus faecalis (50%); Enterococcus faecium (33.33%), Enterococcus hirae (13.33%), and Enterococcus avium (3.33%). The isolates exhibited high resistance to tetracycline (55.6%), erythromycin (31.1%), and ampicillin (30%). However, all of the isolates were susceptible to linezolid. Multidrug resistance (MDR) was identified in 30 (33.3%) isolates. The enterococci AMR-associated genes ermB, ermA, tetM, tetL, vanA, cat, and pbp5 were identified in 24 (26.6%), 11 (12.2%), 39 (43.3%), 34 (37.7%), 1 (1.1%), 4 (4.4%), and 23 (25.5%) isolates, respectively. Of the 90 enterococci, 21 (23.3%), 27 (30%), and 36 (40%) isolates showed the presence of cylA, gelE, and agg virulence-associated genes, respectively. Seventy-three (81.1%) isolates exhibited biofilm formation. A statistically significant correlation was obtained for biofilm formation versus the MAR index and MDR. Multi-locus sequence typing (MLST) identified eleven and eight different STs for E. faecalis and E. faecium, respectively. Seven different rep-family plasmid genes (rep1–2, rep3, rep5–6, rep9, and rep11) were detected in the MDR enterococci. Two-thirds (20/30; 66.6%) of the enterococci were positive for one or two rep-families. In conclusion, the results show that healthy backyard chickens could act as a reservoir for MDR and virulent Enterococcus spp. Thus, an effective antimicrobial stewardship program and further studies using a One Health approach are required to investigate the role of backyard chickens as vectors for AMR transmission to humans.

Prevalence of Vancomycin-Resistant Enterococcus (VRE) in Poultry in Malaysia: The First Meta-Analysis and Systematic Review

Databases such as PubMed, Scopus and Google Scholar were searched. Data extraction and assessment of study protocol was done by two independent reviewers and the results were reviewed by a third. OpenMeta analyst and comprehensive meta-analysis (CMA) were used for the meta-analysis. The random effect model was used, publication bias and between-study heterogeneity was assessed. Seventeen studies were added to the final meta-analysis. Studies were sampled from 2000–2018 and of the 8684 isolates tested, 2824 were VRE. The pooled prevalence of VRE among poultry in Malaysia was estimated at 24.0% (95% CI; 16.7–33.1%; I² = 98.14%; p < 0.001). Between-study variability was high (t² = 0.788; heterogeneity I² = 98.14% with heterogeneity chi-square (Q) = 858.379, degrees of freedom (df) = 16, and p < 0.001). The funnel plot showed bias which was confirmed by Egger’s test and estimates from the leave-one-out forest plot did not affect the pooled prevalence. Pooled prevalence of VRE in chickens and ducks were 29.2% (CI = 18.8–42.5%) and 11.2%, CI = 9.0–14.0%) respectively. Enterococcus faecalis was reported most with more studies being reported in Peninsular Malaysia Central region and used antibiotic disc diffusion as detection method. Increased surveillance of VRE in poultry in Malaysia is required.

Status of infectious disease content in the professional pharmacy curriculum in Saudi Arabia: Results of a national survey

Objectives

Antimicrobial resistance is one of the main global problems faced by healthcare institutions. Healthcare professionals as service providers must have a basic understanding of this emerging threat; additionally, considering the evolving role of pharmacists in both the community and hospital setting, it is crucial that pharmacists are part of the fight against this threat. Therefore, this study aimed to assess infectious disease subjects covered in the pharmacy curriculum in Saudi Arabia, to evaluate teaching and knowledge assessment strategies concerning infectious diseases, and to explore challenges faced by faculty members in teaching infectious disease courses.

Methods

We constructed a questionnaire with 26 items and sent it to infectious disease faculty members at 26 Saudi Arabian pharmacy colleges. It included questions regarding the faculty and institution, infectious disease topics, hours dedicated to each topic, and tools and strategies used in the courses for better understanding and assessment of students. In addition, we enquired about the faculty members' current satisfaction of, and future plans for, the curriculum.

Results

The questionnaire was completed by infectious disease faculty members, department chairs, or college deans. Among the respondent schools, 85.5% were governmental and 14.5% were private institutions. The majority of colleges (98.2%) followed a semester format schedule, with 67.3% offering solely the Doctor of Pharmacy (PharmD) program. More than 78% of respondents covered all tier 1 infectious disease topics from the American College of Clinical Pharmacy Pharmacotherapy Didactic Curriculum Toolkit. The main tool used for teaching was lectures (94.5%), while patient case application was the main teaching strategy (54.5%). Approximately 63% of respondents thought that the curricula were adequate when they were asked about their opinion of the curricula coverage, and 63.64% thought that the curriculum provided adequate baseline knowledge on infectious diseases for the following 5 years.

Conclusions

The study revealed variations in infectious disease topics covered and the time dedicated to them among pharmacy colleges in Saudi Arabia. The faculty members who responded to our questionnaire were generally satisfied with their infectious disease curriculum. To the best of our knowledge, this is the first study to assess infectious disease curricula among Saudi pharmacy colleges. Thus, the findings of this study may encourage faculty members to advocate for the standardization of infectious disease courses offered at Saudi Arabian pharmacy colleges.

Clinical impact of multidrug-resistant bacteria in older hospitalized patients with community-acquired urinary tract infection

Introduction

Previous studies have described some risk factors for multidrug-resistant (MDR) bacteria in urinary tract infection (UTI). However, the clinical impact of MDR bacteria on older hospitalized patients with community-acquired UTI has not been broadly analyzed. We conducted a study in older adults with community-acquired UTI in order to identify risk factors for MDR bacteria and to know their clinical impact.

Methods

Cohort prospective observational study of patients of 65 years or older, consecutively admitted to a university hospital, diagnosed with community-acquired UTI. We compared epidemiological and clinical variables and outcomes, from UTI due to MDR and non-MDR bacteria. Independent risk factors for MDR bacteria were analyzed using logistic regression.

Results

348 patients were included, 41.4% of them with UTI due to MDR bacteria. Median age was 81 years. Hospital mortality was 8.6%, with no difference between the MDR and non-MDR bacteria groups. Median length of stay was 5 [4–8] days, with a longer stay in the MDR group (6 [4–8] vs. 5 [4–7] days, p = 0.029). Inadequate empirical antimicrobial therapy (IEAT) was 23.3%, with statistically significant differences between groups (33.3% vs. 16.2%, p < 0.001). Healthcare-associated UTI variables, in particular previous antimicrobial therapy and residence in a nursing home, were found to be independent risk factors for MDR bacteria.

Conclusions

The clinical impact of MDR bacteria was moderate. MDR bacteria cases had higher IEAT and longer hospital stay, although mortality was not higher. Previous antimicrobial therapy and residence in a nursing home were independent risk factors for MDR bacteria.

Molecular characterization of antimicrobial resistance and virulence factors of Enterococcus faecalis from ducks at slaughterhouses

This study investigated the prevalence of antimicrobial resistant Enterococcus faecalis (E. faecalis) from ducks at slaughterhouses, analyzed antimicrobial resistance genes and virulence-associated genes of the isolates. Multilocus sequence typing (MLST) was performed to characterize their molecular characteristics. A total of 227 E. faecalis isolates (67.8%) were obtained from cecum (n = 114), cloaca (n = 50), skin (n = 59), and rinsed water (n = 4). These E. faecalis exhibited high level of resistance against tetracycline (95.6%), doxycycline (94.3%), linezolid (75.8%), erythromycin (72.2%), followed by norfloxacin (56.8%), vancomycin (38.3%), penicillin (36.1%), teicoplanin (30.8%). Lower level of resistance was found to high-level streptomycin (19.8%), imipenem (15.9%) and high-level gentamicin (5.7%). The vast majority of isolates (90.3%) were multidrug resistant (MDR). Moreover, the commonly observed resistance genes were optrA (90.7%) and ermB (90.3%), followed by aph(3’)-Ⅲ (86.8%), tetM (84.6%), acc(6’)-aph(2) (77.5%), blaZ (76.7%) and aac(6’)-Ie-aph(2”)-Ia (75.8%). The less frequently observed genes were vanC (19.8%), blaTEM (4.8%), vanM (2.6%), and vanA (0.4%). None of the strains carried aph(2”)-Ic and vanB genes. Furthermore, a high prevalence of ten virulence determinants was identified, and efaA (99.1%) was predominant, followed by eep (97.4%), srtA (96.9%), asa1 (95.6%), fsrB (92.1%), sprE (89.9%), aggA (63.9%), gelE (56.4%), esp (33.9%), and cylL (15.4%). Eleven isolates (4.9%) co-carried all of the tested virulence-associated genes. MLST analysis demonstrated that, E. faecalis isolates consisted of 12 known STs and 5 new STs, among which 6 of the identified STs were associated with nosocomial infection. Our data indicated that retail ducks serve as an important source of MDR E. faecalis with high pathogenicity potential, and suggested that transmission to humans could not be excluded.

Utility of Minimum Inhibitory Concentration values and Antibiotyping for Epidemiological study of Vancomycin Resistant Enterococci in a Tertiary Care Hospital

Vancomycin-resistant enterococci (VRE) have emerged as an important nosocomial infection. Three important vancomycin resistance types namely, VanA, VanB, VanC are very commonly found in enterococci. VanA and VanB are plasmid-encoded, transferable types of resistance and VanC is chromosomally mediated nontransferable resistance. So for infection control purpose, it is important to know the type of vancomycin resistance to prevent the spread of drug resistance. Enterococci isolated from clinical samples were tested for vancomycin resistance by disc diffusion and macro broth dilution (MIC) method. Vancomycin resistance gene was detected by the polymerase chain reaction (PCR) method. Antimicrobial susceptibility for penicillin, erythromycin, ciprofloxacin, high-level gentamicin, nitrofurantoin, tetracycline, teicoplanin and linezolid was performed by disc diffusion method. Antibiotyping of VRE strains was done based on their antimicrobial susceptibility pattern. Over a period of one year out of 246 clinical isolates of enterococci, seven (2.8%) isolates showed vancomycin resistance. Based on MICs and PCR, all the isolates demonstrated VanA type of resistance. Analysis of antibiogram showed three different antibiotype patterns for VRE labelled as 1,2,3. The majority of VRE isolates (72%) belonged to “Pattern 1”. Also clustering of cases of “Pattern 1” was observed in medicine ICU and medicine ward. These areas were identified as a potential reservoir for VRE infection and appropriate infection control measures were taken to curtail the spread of infection. The present study recommends a macro broth dilution method for detection of the type of vancomycin resistance in enterococci and “antibiotyping” as a basic typing method for VRE in resource-poor health care settings specifically in outbreak situations.

Perfil epidemiológico de la infección por Enterococcus SPP en un hospital regional

Introducción: los enterococos son responsables de múltiples infecciones y por su creciente patrón de resistencia se ha vuelto de interés en el país y en el mundo. Objetivo: caracterizar las infecciones por Enterococcus spp. Metodología: estudio descriptivo, retrospectivo observacional transversal desde enero 2015 hasta enero 2018 en un hospital regional. Resultados: la prevalencia de las infecciones por Enterococcus spp. fue de 0,154%. El E. faecalis fue el más aislado, seguido del E. faecium. La resistencia a ampicilina fue de 19% y a vancomicina de 10%; 32% de los pacientes tuvieron terapia empírica con vancomicina y 22% con piperacilina tazobactam, la mediana de antibioticoterapia fue de 10 días. Discusión: el interés por los Enterococcus spp. se ha incrementado debido a que representan una carga importante en las infecciones asociadas con la atención en salud (IAAS). La mayoría se dan en hombres con una edad mediana de 40 a 60 años, hospitalizados en UCI, con infecciones urinarias y comorbilidades como inmunosupresión y cirugías previas. Conclusión: como ha venido reportándose aumento en las tasas de resistencia a vancomicina y ampicilina, se recomienda el uso responsable de la terapia antibiótica, con la finalidad de erradicar en forma eficaz al patógeno y prevenir nuevas resistencias.

Emerging Status of Multidrug-Resistant Bacteria and Fungi in the Arabian Peninsula

Simple Summary

The incidence and developing status of multidrug-resistant bacteria and fungi, as well as their related mortality, is reviewed by a systematic published literature search from nine countries in the Arabian Peninsula. In order to analyse the emerging status and mortality, a total of 382 research articles were selected from a comprehensive screening of 1705 papers. More than 850 deaths reported since 2010 in the Arabian Peninsula due to the infection of multidrug-resistant bacteria and fungi. Multidrug-resistant bacteria Acinetobacter baumannii, Mycobacterium tuberculosis, Staphylococcus aureus, and fungi Candida auris are the most prevalent and causing high deaths. To control these infections and associated deaths in the Arabian Peninsula, continuous preventive measures, accurate methods for early diagnosis of infection, active surveillance, constant monitoring, developing vaccines, eradicating multidrug resistance modulators, and data sharing among countries are required.

Abstract

We aimed to identify the prevalence and emerging status of multidrug-resistant bacteria and fungi and their associated mortality in nine countries in the Arabian Peninsula. Original research articles and case studies regarding multidrug-resistant bacteria and fungi in the Arabian Peninsula, published during the last 10 years, were retrieved from PubMed and Scopus. A total of 382 studies were included as per the inclusion and exclusion criteria, as well as the PRISMA guidelines, from a thorough screening of 1705 articles, in order to analyse the emerging status and mortality. The emerging nature of >120 multidrug-resistant (MDR) bacteria and fungi in the Arabian Peninsula is a serious concern that requires continuous monitoring and immediate preventive measures. More than 50% (n = 453) of multidrug-resistant, microbe-associated mortality (n = 871) in the Arabian Peninsula was due to MDR Acinetobacter baumannii, Mycobacterium tuberculosis and Staphylococcus aureus infection. Overall, a 16.51% mortality was reported among MDR-infected patients in the Arabian Peninsula from the 382 articles of this registered systematic review. MDR A. baumannii (5600 isolates) prevailed in all the nine countries of the Arabian Peninsula and was one of the fastest emerging MDR bacteria with the highest mortality (n = 210). A total of 13,087 Mycobacterium tuberculosis isolates were reported in the region. Candida auris (580 strains) is the most prevalent among the MDR fungal pathogen in the Arabian Peninsula, having caused 54 mortalities. Active surveillance, constant monitoring, the development of a candidate vaccine, an early diagnosis of MDR infection, the elimination of multidrug resistance modulators and uninterrupted preventive measures with enhanced data sharing are mandatory to control MDR infection and associated diseases of the Arabian Peninsula. Accurate and rapid detection methods are needed to differentiate MDR strain from other strains of the species. This review summarises the logical relation, prevalence, emerging status and associated mortality of MDR microbes in the Arabian Peninsula.

Antimicrobial susceptibility of gram-positive and gram-negative bacteria: a 5-year retrospective analysis at a multi-hospital healthcare system in Saudi Arabia

BACKGROUND

Studying time-related changes in susceptible pathogens causing healthcare-associated infections (HAIs) is vital in improving local antimicrobial and infection control practices.

OBJECTIVES

Describe susceptibility patterns to several antimicrobials in gram-positive and gram-negative pathogens isolated from patients causing HAIs at three private tertiary care hospitals in Saudi Arabia over a 5-year period.

METHODS

Data on trends of antimicrobial susceptibility among bacteria causing HAIs events in children and adults at three tertiary private hospitals located in Riyadh and Qassim, Saudi Arabia, were collected retrospectively between 2015 and 2019 using the surveillance data datasets.

RESULTS

Over a 5-year period, 38,624 pathogens caused 17,539 HAI events in 17,566 patients. About 9450 (53.8%) of patients who suffered HAIs were females and the average age was 41.7 ± 14.3 years (78.1% were adults and 21.9% were children). Gram-negative pathogens were 2.3-times more likely to cause HAIs compared to gram-positive bacteria (71.9% vs. 28.1%). The ranking of causative pathogens in decreasing order was: Escherichia coli (38%), Klebsiella species (15.1%), and Staphylococcus aureus (12.6%). Gram-positive isolates were mostly susceptible to linezolid (91.8%) whereas they were resistant to ampicillin (52.6%), cefoxitin (54.2%), and doxycycline (55.9%). Gram-negative isolates were mostly sensitive to tigecycline (95%) whereas they were resistant to cefotaxime (49.5%) and cefixime (59.6%). During the 5 years, there were relatively stable susceptibility patterns to all tested antimicrobials, except for cefotaxime which shown a susceptibility reduction by 41.4%, among Escherichia coli and Klebsiella species. An increase in the susceptibility of Acinetobacter and Enterobacter and Citrobacter species to all studied antimicrobials was observed except for colistin that had a slight sensitivity reduction in 2019 by 4.3% against Acinetobacter species. However, we noted reduced sensitivity of MRSA, CoNS and Enterococcus species to gentamicin; and increased resistance of MRSA to linezolid and vancomycin.

CONCLUSION

The observed increase in susceptibility of gram-positive and gram-negative bacteria to studied antimicrobials is important; however, reduced sensitivity of MRSA, CoNS and Enterococcus species to gentamicin; and increased resistance of MRSA to linezolid and vancomycin is a serious threat and calls for effective antimicrobial stewardship programs.

The Role of Whole Genome Sequencing in the Surveillance of Antimicrobial Resistant Enterococcus spp.: A Scoping Review

Enterococcus spp. have arisen as important nosocomial pathogens and are ubiquitous in the gastrointestinal tracts of animals and the environment. They carry many intrinsic and acquired antimicrobial resistance genes. Because of this, surveillance of Enterococcus spp. has become important with whole genome sequencing emerging as the preferred method for the characterization of enterococci. A scoping review was designed to determine how the use of whole genome sequencing in the surveillance of Enterococcus spp. adds to our knowledge of antimicrobial resistance in Enterococcus spp. Scoping review design was guided by the PRISMA extension and checklist and JBI Reviewer's Guide for scoping reviews. A total of 72 articles were included in the review. Of the 72 articles included, 48.6% did not state an association with a surveillance program and 87.5% of articles identified Enterococcus faecium. The majority of articles included isolates from human clinical or screening samples. Significant findings from the articles included novel sequence types, the increasing prevalence of vancomycin-resistant enterococci in hospitals, and the importance of surveillance or screening for enterococci. The ability of enterococci to adapt and persist within a wide range of environments was also a key finding. These studies emphasize the importance of ongoing surveillance of enterococci from a One Health perspective. More studies are needed to compare the whole genome sequences of human enterococcal isolates to those from food animals, food products, the environment, and companion animals.

Antimicrobial Stewardship Programmes in Saudi Hospitals: Evidence from a National Survey

Saudi hospitals and healthcare facilities are facing increasing rates of antimicrobial resistance and the emergence of new multi-drug resistant strains. This is placing an unprecedented threat to successful treatments and outcomes of patients accessing those facilities. The inappropriate use of antimicrobials is fueling this crisis, warranting urgent implementation of interventions to preserve antimicrobials and reduce resistance rates. Antimicrobial stewardship programmes (ASPs) can improve antimicrobial use, treatment success rates and reduce the levels of antimicrobial resistance. The Saudi Ministry of Health (MOH) devised a national antimicrobial stewardship plan to implement ASPs in hospitals, but little is known about the progress of implementation and the factors affecting it. This study aims to assess the level and the factors affecting the adoption and implementation of ASPs in Saudi hospitals at a national level. A nationwide cross-sectional survey was conducted in 2017 using an online questionnaire sent to all MOH hospitals. Overall, 147 out 247 MOH hospitals responded to the survey (54%). Only 26% of the hospitals reported the implementation of ASPs. Hospitals lack the knowledge, technological and staff resources to adopt and implement ASPs. Alternative models of ASP adoption could be explored to improve the rates of implementation of ASPs.

Enterococcus phage Nonaheksakonda infecting clinical isolates of Enterococcus faecalis represents a new lineage in the family Siphoviridae

Enterococcus phage Nonaheksakonda was isolated from wastewater, using a vancomycin-resistant strain of the opportunistic pathogen Enterococcus faecalis (VRE) as a host. Nonaheksakonda is a lytic phage infecting E. faecalis V583 and clinical isolates with at least four different multi-locus sequence types (MLSTs). The genome is a 41.9-kb double-stranded DNA molecule (34.6% GC) with 74 coding sequences. Comparative analysis revealed only one close relative, Enterococcus phage heks. All other phages had low protein similarity and shared less than 54% nucleotide sequence identity with phage Nonaheksakonda. The most similar phages were all classified and unclassified efquatroviruses. We propose that the phages Nonaheksakonda and heks represent a novel genus within the family Siphoviridae, order Caudovirales, for which we propose the name "Nonaheksakondavirus".

Draft genome sequence of a multidrug-resistant emerging pathogenic isolate of Vibrio alginolyticus from the Red Sea

The marine ecosystem is a growing reservoir of antimicrobial-resistant bacteria, and thus an emerging risk to human health. In this study, we report the first draft genome sequence of multidrug-resistant Vibrio alginolyticus strain OS1T-47, isolated from an offshore site in the Red Sea. The draft genome of V. alginolyticus OS1T-47 is 5 157 150 bp in length and has DNA G + C content of 44.83%. Strain OS1T-47 possesses 22 antimicrobial resistance genes, including those associated with multidrug-resistant efflux pumps.

Comparative metagenomics and characterization of antimicrobial resistance genes in pasteurized and homemade fermented Arabian laban

The aim of this study was to investigate bacterial diversity and function in a fermented milk drink called laban, which is traditionally served in the Middle East, Africa, and Indian subcontinent. Pasteurized laban (LBP) and unpasteurized, homemade, raw laban (LBR) underwent 16S rRNA gene amplicon and shotgun sequencing to analyze their bacterial community, presence of antimicrobial resistance genes (ARGs), and metabolic pathways. This study highlighted relatively greater diversity in LBR bacterial populations compared to LBP, despite containing similar major taxa that consisted primarily of Firmicutes followed by Proteobacteria, Bacteroidetes, and Actinobacteria. The dominant species, Streptococcus thermophilus, was relatively more abundant in LBP (80.7%) compared to LBR (47.9%). LBR had increased diversity and higher relative abundance of several known probiotic bacteria, such as Streptococcus salivarius and Lactococcus lactis, whereas Lactobacillus acidophilus was detected at a higher abundance in LBP. Pathogens like Acinetobacter baumannii, Streptococcus pneumoniae, Streptococcus pyogenes, and Escherichia coli had lower abundance in LBP compared to LBR. Thirty-three ARGs were detected in LBR compared to nine in LBP and are responsible for resistance to 11 classes of antibiotics. A significant proportion of the metagenomes from both types of laban were assigned to housekeeping functions, such as amino acid metabolism, translation, membrane transport, and carbohydrate metabolism. LBR demonstrated increased diversity in probiotics and metabolic functions compared to LBP. However, the relatively high diversity of pathogenic and opportunistic bacteria and ARGs in LBR raises safety concerns and highlights the need for a more hygienic environment for the processing of homemade fermented dairy foods.

Drug Resistance Determinants in Clinical Isolates of Enterococcus faecalis in Bangladesh: Identification of Oxazolidinone Resistance Gene optrA in ST59 and ST902 Lineages

Enterococcus faecalis is one of the major causes of urinary tract infection, showing acquired resistance to various classes of antimicrobials. The objective of this study was to determine the prevalence of drug resistance and its genetic determinants for E. faecalis clinical isolates in north-central Bangladesh. Among a total of 210 E. faecalis isolates, isolated from urine, the resistance rates to erythromycin, levofloxacin, and gentamicin (high level) were 85.2, 45.7, and 11.4%, respectively, while no isolates were resistant to ampicillin, vancomycin and teicoplanin. The most prevalent resistance gene was erm(B) (97%), and any of the four genes encoding aminoglycoside modifying enzyme (AME) were detected in 99 isolates (47%). The AME gene aac(6′)-Ie-aph(2”)-Ia was detected in 46 isolates (21.9%) and was diverse in terms of IS256-flanking patterns, which were associated with resistance level to gentamicin. Tetracycline resistance was ascribable to tet(M) (61%) and tet(L) (38%), and mutations in the quinolone resistance-determining region of both GyrA and ParC were identified in 44% of isolates. Five isolates (2.4%) exhibited non-susceptibility to linezolide (MIC, 4 μg/mL), and harbored the oxazolidinone resistance gene optrA, which was located in a novel genetic cluster containing the phenicol exporter gene fexA. The optrA-positive isolates belonged to ST59, ST902, and ST917 (CC59), while common lineages of other multiple drug-resistant isolates were ST6, ST28, CC16, and CC116. The present study first revealed the prevalence of drug resistance determinants of E. faecalis and their genetic profiles in Bangladesh.

Comparative genomics of vancomycin-resistant Enterococcus spp. revealed common resistome determinants from hospital wastewater to aquatic environments

The rise of vancomycin-resistant Enterococcus spp. (VRE) has led to treatment challenges in hospital settings worldwide. Hospital wastewater (HW) might disseminate this threat to the aquatic environment. Thus, this study elucidates the VRE resistance quotient (RQ) of different environmental matrixes in wastewater and compares genomic determinants of VRE strains recovered from HW to water resources. Presumptive Enterococcus spp. and VRE were quantified and isolated using standard microbiological procedures. Fourteen VRE genomes were then sequenced using an Illumina HiSeq X™ Ten platform. Subsequently, VRE genomes were compared based on antibiotic resistance genes, plasmids, bacteriophages, insertion sequences, transposons, virulence and pathogenicity. Wastewater effluent showed the highest RQ among all sampled matrixes. The phylogeny of vancomycin-resistant E. faecalis (VREfs) and E. faecium (VREfm) revealed a tree structure based on their respective sequence type. A comparative genomic analysis of 14 genomes highlighted regions encoding phage protein, phage holin, phage integrase, integrase and transposase on both query genomes and the reference genome. Acquired resistance to vancomycin was conferred by vanA, vanN, vanL, vanG and the intrinsic resistance vanC operons. Plasmids were dominated by the presence of conserved areas of the replication initiating genes (rep). The Tn3-like and Tn917 transposons were present in all erythromycin-carrying erm(B) isolated VRE genomes. All VRE genomes expect one were putatively predicted as human pathogens with varying degrees of virulence. The presence of such resistant bacteria in African water resource is of great public health concern. It is, therefore, recommended that these bacteria be tracked and characterised from different environments to contribute to improved epidemiological containment action.

Insights into the Microbiological Safety of Wooden Cutting Boards Used for Meat Processing in Hong Kong's Wet Markets: A Focus on Food-Contact Surfaces, Cross-Contamination and the Efficacy of Traditional Hygiene Practices

Hong Kong's wet markets play a crucial role in the country's supply of safe, fresh meat to satisfy the dietary needs of its population. Whilst food safety regulations have been introduced over the past few years to maintain the microbial safety of foods sold from these wet markets, it remains unclear whether the hygiene maintenance that is performed on the wooden cutting boards used for meat-processing is effective. In fact, hygiene maintenance may often be overlooked, and hygiene standards may be insufficient. If so, this may lead to the spread of harmful pathogens through cross-contamination, thereby causing severe risks to public health. The aim of this study was to determine the level of microbial transfer between wooden cutting boards and swine meat of various qualities, using 16S metagenomic sequencing, strain identification and biofilm screening of isolated strains. The results established that: (a) the traditional hygiene practices used for cleaning wooden cutting boards in Hong Kong's wet markets expose the surfaces to potentially harmful microorganisms; (b) the processing of microbially contaminated meat on cutting boards cleaned using traditional practices leads to cross-contamination; and (c) several potentially pathogenic microorganisms found on the cutting boards have good biofilm-forming abilities. These results reinforce the need to review the traditional methods used to clean wooden cutting boards after the processing of raw meat in Hong Kong' wet markets so as to prevent cross-contamination events. The establishment of proper hygiene protocols may reduce the spread of disease-causing microorganisms (including antibiotic-resistant microorganisms) in food-processing environments.

Considerations and Caveats in Combating ESKAPE Pathogens against Nosocomial Infections

ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) are among the most common opportunistic pathogens in nosocomial infections. ESKAPE pathogens distinguish themselves from normal ones by developing a high level of antibiotic resistance that involves multiple mechanisms. Contemporary therapeutic strategies which are potential options in combating ESKAPE bacteria need further investigation. Herein, a broad overview of the antimicrobial research on ESKAPE pathogens over the past five years is provided with prospective clinical applications.

Prevalence of antibiotic resistance genes in cell culture liquid waste and the virulence assess for isolated resistant strains

Cell culture liquid waste containing antibiotic resistance genes (ARGs) and microbial community were still not received enough recognition, which pose potential risks to human health. Sixty-eight resistance genes and intl1 were detected in eight samples by Quantitative real-time PCR, while intl1 was only detected in hospital group. Meanwhile, the bacterial community was complex and diverse in each sample by 16S rRNA gene high-throughput sequencing, in addition, Morganella and Enterococcus presented a significant difference between two groups. Whole genome shotgun sequencing revealed that Morganella morganii had more resistance genes and virulence factors in hospital group, and three extended-spectrum beta-lactamase (ESBL) genotypes were found to be blaDHA-5, blaOXA-1, and blaTEM-1. This study provided a preliminary report on ARGs and resistant strains, which reminded people attention to the health risks of potential pathogens in this waste.

Phenotypic and genotypic characterization of glycopeptide, aminoglycoside and macrolide resistance among clinical isolates of Enterococcus faecalis: a multicenter based study

Objectives

Enterococcus faecalis as part of the normal floras of human gastrointestinal and genitourinary tracts are an important cause of nosocomial infections. The present study aimed to investigate the prevalence of genes encoding antimicrobial resistance and genetic relatedness of clinical isolates of E. faecalis among Iranian hospitalized patients.

Results

Antibiotic susceptibility testing results indicated that 53 (22.8%) out of 232 E. faecalis isolates were vancomycin resistant (MIC ≥ 256 μg/ml). All of the 53 vancomycin-resistant E. faecalis isolates carried the vanA and ermB genes; whereas aac (6′)-Ie aph (2″), msrA, and ermA gene were found in 96.2%, 30.2% and 3.8% of vancomycin-resistant isolates, respectively. ERIC-PCR typing revealed that 53 vancomycin-resistant isolates were classified into 14 ERIC types. In our results, the high level of resistance to gentamicin, erythromycin and vancomycin in enterococci isolates were mainly related to the presence of aac (6′)-Ie aph (2″), ermB and vanA genes, respectively. Meanwhile, ERIC-PCR analysis demonstrated that most of the evaluated isolates have a close genetic relatedness.