Disruption of an Enterococcus faecium species-specific gene, a homologue of acquired macrolide resistance genes of staphylococci, is associated with an increase in macrolide susceptibility

Multi-biome analysis identifies distinct gut microbial signatures and their crosstalk in ulcerative colitis and Crohn's disease

The integrative multi-kingdom interaction of the gut microbiome in ulcerative colitis (UC) and Crohn's disease (CD) remains underinvestigated. Here, we perform shotgun metagenomic sequencing of feces from patients with UC and CD, and healthy controls in the Japanese 4D cohort, profiling bacterial taxa, gene functions, and antibacterial genes, bacteriophages, and fungi. External metagenomic datasets from the US, Spain, the Netherlands, and China were analyzed to validate our multi-biome findings. We found that Enterococcus faecium and Bifidobacterium spp. were enriched in both diseases. Enriched Escherichia coli was characteristic of CD and was linked to numerous antibiotic resistance genes involved in efflux pumps and adherent-invasive Escherichia coli virulence factors. Virome changes correlated with shifts in the bacteriome, including increased abundances of phages encoding pathogenic genes. Saccharomyces paradoxus and Saccharomyces cerevisiae were enriched in UC and CD, respectively. Saccharomyces cerevisiae and Escherichia coli had negative associations with short-chain fatty acid (SCFA)-producing bacteria in CD. Multi-biome signatures and their interactions in UC and CD showed high similarities between Japan and other countries. Since bacteria, phages, and fungi formed multiple hubs of intra- or trans-kingdom networks with SCFA producers and pathobionts in UC and CD, an approach targeting the interaction network may hold therapeutic promise.

Investigating antimicrobial resistance genes in probiotic products for companion animals

Introduction

One of the greatest challenges of our time is antimicrobial resistance, which could become the leading cause of death globally within a few decades. In the context of One Health, it is in the common interest to mitigate the global spread of antimicrobial resistance by seeking alternative solutions, alongside appropriate drug selection and responsible use. Probiotics offer a potential avenue to reduce antibiotic usage; however, there is a scarcity of research that examines commercial products in terms of carrying antimicrobial resistance genes (ARGs) involved in resistance development through microbial vectors.

Methods

Our study investigated 10 commercially available probiotic products for cats and dogs. Initially, we conducted phenotypic testing through determination of minimum inhibitory concentration (MIC) for antibiotics important in animal and public health. Subsequently, we performed next-generation sequencing (NGS) of the products to elucidate the genetic background behind the decrease in phenotypic sensitivity.

Results

In total, 19 types of ARGs were identified, with 57.9% being found on plasmids, and in two cases, carriage as mobile genetic elements were found. One of the genes identified was the APH(3')-Ia gene, capable of inactivating aminoglycoside antibiotics through phosphotransferase enzyme production regulation, while the other was the tetS gene, capable of conferring reduced sensitivity to tetracycline antibiotics through target protection.

Discussion

Our findings underscore the importance of approaching antimicrobial resistance investigations from a broader perspective. We suggest that further studies in this area are justified and raise questions regarding the need to extend legally required studies on probiotic products from their use in economic livestock to their use in companion animals.

Genome-based taxonomic identification and safety assessment of an Enterococcus strain isolated from a homemade dairy product

The aim of this study was to explore the taxonomic identification and evaluate the safety of a bacterium, Enterococcus lactis IDCC 2105, isolated from homemade cheese in Korea, using whole genome sequence (WGS) analysis. It sought to identify the species level of this Enterococcus spp., assess its antibiotic resistance, and evaluate its virulence potential. WGS analysis confirmed the bacterial strain IDCC 2105 as E. lactis and identified genes responsible for resistance to erythromycin and clindamycin, specifically msrC, and eatAv, which are chromosomally located, indicating a minimal risk for horizontal gene transfer. The absence of plasmids in E. lactis IDCC 2105 further diminishes the likelihood of resistance gene dissemination. Additionally, our investigation into seven virulence factors, including hemolysis, platelet aggregation, biofilm formation, hyaluronidase, gelatinase, ammonia production, and β-glucuronidase activity, revealed no detectable virulence traits. Although bioinformatic analysis suggested the presence of collagen adhesion genes acm and scm, these were not corroborated by phenotypic virulence assays. Based on these findings, E. lactis IDCC 2105 presents as a safe strain for potential applications, contributing valuable information on its taxonomy, antibiotic resistance profile, and lack of virulence factors, supporting its use in food products.

Assessment of the feed additive consisting of Enterococcus lactis DSM 22502 for all animal species for the renewal of its authorisation (Chr. Hansen A/S)

Following a request from the European Commission, EFSA was asked to deliver a scientific opinion on the safety and efficacy of Enterococcus lactis DSM 22502 as a technological feed additive for all animal species. The applicant provided evidence that the additive currently on the market complies with the existing conditions of authorisation. There is no new evidence that would lead the FEEDAP Panel to reconsider its previous conclusions regarding the safety and efficacy of the additive. The FEEDAP Panel concluded that E. lactis remains safe for all animal species, consumers and environment under the authorised conditions of use. Regarding the user safety, the Panel concluded that the additive is not irritating to the skin or eyes. No conclusions can be drawn on the potential of the additive to cause skin sensitisation, but it is considered to be a respiratory sensitiser. There is no need for assessing the efficacy of the additive in the context of the renewal of the authorisation.

Antimicrobial Resistance in Enterococcus spp. Isolates from Red Foxes (Vulpes vulpes) in Latvia

Antimicrobial resistance (AMR) is an emerging public health threat and is one of the One Health priorities for humans, animals, and environmental health. Red foxes (Vulpes vulpes) are a widespread predator species with great ecological significance, and they may serve as a sentinel of antimicrobial resistance in the general environment. The present study was carried out to detect antimicrobial resistance, antimicrobial resistance genes, and genetic diversity in faecal isolates of red foxes (Vulpes vulpes). In total, 34 Enterococcus isolates, including E. faecium (n = 17), E. faecalis (n = 12), E. durans (n = 3), and E. hirae (n = 2), were isolated. Antimicrobial resistance to 12 antimicrobial agents was detected with EUVENC panels using the minimum inhibitory concentration (MIC). The presence of antimicrobial resistance genes (ARGs) was determined using whole-genome sequencing (WGS). Resistance to tetracycline (6/34), erythromycin (3/34), ciprofloxacin (2/34), tigecycline (2/34), and daptomycin (2/34) was identified in 44% (15/34) of Enterococcus isolates, while all the isolates were found to be susceptible to ampicillin, chloramphenicol, gentamicin, linezolid, teicoplanin, and vancomycin. No multi-resistant Enterococcus spp. were detected. A total of 12 ARGs were identified in Enterococcus spp., with the presence of at least 1 ARG in every isolate. The identified ARGs encoded resistance to aminoglycosides (aac(6')-I, ant(6)-Ia, aac(6')-Iih and spw), tetracyclines (tet(M), tet(L) and tet(S)), and macrolide-lincosamide-streptogramin AB (lnu(B,G), lsa(A,E), and msr(C)), and their presence was associated with phenotypical resistance. Core genome multilocus sequence typing (cgMLST) revealed the high diversity of E. faecalis and E. faecium isolates, even within the same geographical area. The distribution of resistant Enterococcus spp. in wild foxes in Latvia highlights the importance of a One Health approach in tackling AMR.

Assessment of a feed additive containing Enterococcus lactis NCIMB 11181 (Lactiferm®) for weaned piglets, calves for fattening and calves for rearing for the renewal of its authorisation (Chr. Hansen A/S)

Following a request from the European Commission, EFSA was asked to deliver a scientific opinion on the assessment of the application for renewal of the authorisation of Enterococcus lactis NCIMB 11181 (Lactiferm®) as a zootechnical additive for weaned piglets, calves for fattening and calves for rearing. The product under assessment is based on a strain originally identified as Enterococcus faecium. During the current assessment, the active agent has been reclassified as Enterococcus lactis. The additive currently authorised is marketed in two formulations: Lactiferm Basic 50 (a solid formulation to be used in feed), and Lactiferm WS200 (a solid 'water-soluble' formulation to be used in water for drinking). The applicant has provided evidence that the additive currently on the market complies with the existing conditions of authorisation. The Panel concludes that the use of Lactiferm® under the authorised conditions of use remains safe for the target species (calves up to 6 months and weaned piglets up to 35 kg), consumers and the environment. The Lactiferm WS200 formulation of the additive is not irritant to skin or eyes. Owing to the proteinaceous nature of the active agent, both formulations of the additive are considered respiratory sensitisers. It is not possible to conclude on the irritating potential for skin and eyes of the Lactiferm Basic 50 formulation or on the potential of both forms of the additive to cause skin sensitisation. There is no need for assessing the efficacy of the additive in the context of the renewal of the authorisation.

Prevalence of Enterococcus spp. and the Whole-Genome Characteristics of Enterococcus faecium and Enterococcus faecalis Strains Isolated from Free-Living Birds in Poland

Enterococci as opportunistic bacteria are important for human health. Due to the prevalence and ease of acquisition and transfer of their genes, they are an excellent indicator of environmental contamination and the spread of antimicrobial resistance. The aim of the study was to assess the prevalence of Enterococcus spp. in wild birds in Poland, determination of antimicrobial susceptibility and WGS analysis of Enterococcus (E.) faecium and E. faecalis. For this purpose, 138 samples from various species of free-living birds were tested, with 66.7% positive results. Fourteen species were detected, with E. faecalis being the most common, followed by E. casseliflavus and E. hirae. In antimicrobial susceptibility testing, 10.0% of E. faecalis and 50.0% of E. faecium showed resistance to one antimicrobial agent, in addition the MDR phenotype which was found in one E. faecium. The most common resistance phenotype included tetracycline and quinupristin/dalfopristin. The WGS analysis confirmed the significant advantage of the virulence gene diversity of E. faecalis strains over E. faecium. In addition, plasmid replicons were found in 42.0% of E. faecalis and 80.0% of E. faecium. The obtained results confirm free-living birds can be a reservoir of Enterococcus spp. with a considerable zoonotic potential.

Clinical Resistant Strains of Enterococci and Their Correlation to Reduced Susceptibility to Biocides: Phenotypic and Genotypic Analysis of Macrolides, Lincosamides, and Streptogramins

Enterococci are troublesome nosocomial, opportunistic Gram-positive cocci bacteria showing enhanced resistance to many commonly used antibiotics. This study aims to investigate the prevalence and genetic basis of antibiotic resistance to macrolides, lincosamides, and streptogramins (MLS) in Enterococci, as well as the correlation between MLS resistance and biocide resistance. From 913 clinical isolates collected from King Khalid Hospital, Hail, Saudi Arabia, 131 isolates were identified as Enterococci spp. The susceptibility of the clinical enterococcal isolates to several MLS antibiotics was determined, and the resistance phenotype was detected by the triple disk method. The MLS-involved resistance genes were screened in the resistant isolates. The current results showed high resistance rates to MLS antibiotics, and the constitutive resistance to all MLS (cMLS) was the most prevalent phenotype, observed in 76.8% of resistant isolates. By screening the MLS resistance-encoding genes in the resistant isolates, the erythromycin ribosome methylase (erm) genes that are responsible for methylation of bacterial 23S rRNA were the most detected genes, in particular, ermB. The ereA esterase-encoding gene was the most detected MLS modifying-encoding genes, more than lnuA (adenylation) and mphC (phosphorylation). The minimum inhibitory concentrations (MICs) of commonly used biocides were detected in resistant isolates and correlated with the MICs of MLS antibiotics. The present findings showed a significant correlation between MLS resistance and reduced susceptibility to biocides. In compliance with the high incidence of the efflux-encoding genes, especially mefA and mefE genes in the tolerant isolates with higher MICs to both MLS antibiotics and biocides, the efflux of resistant isolates was quantified, and there was a significant increase in the efflux of resistant isolates with higher MICs as compared to those with lower MICs. This could explain the crucial role of efflux in developing cross-resistance to both MLS antibiotics and biocides.

Antimicrobial Resistance, Virulence Factors, and Genotypes of Enterococcus faecalis and Enterococcus faecium Clinical Isolates in Northern Japan: Identification of optrA in ST480 E. faecalis

Enterococcus faecalis and E. faecium are the major pathogens causing community- and healthcare-associated infections, with an ability to acquire resistance to multiple antimicrobials. The present study was conducted to determine the prevalence of virulence factors, drug resistance and its genetic determinants, and clonal lineages of E. faecalis and E. faecium clinical isolates in northern Japan. A total of 480 (426 E. faecalis and 54 E. faecium) isolates collected over a four-month period were analyzed. Three virulence factors promoting bacterial colonization (asa1, efaA, and ace) were more prevalent among E. faecalis (46-59%) than E. faecium, while a similar prevalence of enterococcal surface protein gene (esp) was found in these species. Between E. faecalis and E. faecium, an evident difference was noted for resistance to erythromycin, gentamicin, and levofloxacin and its responsible resistance determinants. Oxazolidinone resistance gene optrA and phenicol exporter gene fexA were identified in an isolate of E. faecalis belonging to ST480 and revealed to be located on a cluster similar to those of isolates reported in other Asian countries. The E. faecalis isolates analyzed were differentiated into 12 STs, among which ST179 and ST16 of clonal complex (CC) 16 were the major lineage. Nearly all the E. faecium isolates were assigned into CC17, which consisted of 10 different sequence types (STs), including a dominant ST17 containing multidrug resistant isolates and ST78 with isolates harboring the hyaluronidase gene (hyl). The present study revealed the genetic profiles of E. faecalis and E. faecium clinical isolates, with the first identification of optrA in ST480 E. faecalis in Japan.

Vancomycin-variable enterococci in sheep and cattle isolates and whole-genome sequencing analysis of isolates harboring vanM and vanB genes

Background

Vancomycin resistance encoded by the vanA/B/M genes in enterococci is clinically important because of the transmission of these genes between bacteria. While vancomycin resistance is determined by detecting only vanA and vanB genes by routine analyses, failure to detect vanM resistance causes vancomycin resistance to be overlooked, and clinically appropriate treatment cannot be provided.

Aims

The study aimed to examine the presence of vanM-positive enterococcal isolates in Ankara, Turkey, and to have detailed information about them with sequence analyses.

Methods

Caecal samples were collected from sheep and cattle during slaughter at different slaughterhouses in Ankara, Turkey. Enterococci isolates were identified, confirmed, and analyzed for the presence of vanA/B/M genes. Antibiotic resistance profiles of isolates were determined by the broth microdilution method. A whole genome sequence analysis of the isolates harboring the vanM and vanB genes was performed.

Results

13.7% of enterococcal isolates were determined as Enterococcus faecium and Enterococcus faecalis. 15% of these isolates contained vanB, and 40% were vanM-positive. S98b and C32 isolates were determined to contain 16 CRISPR-Cas elements. 80% of the enterococci isolates were resistant to nitrofurantoin and 15% to ciprofloxacin. The first vanM-positive vancomycin-variable enterococci (VVE) isolates from food-producing animals were identified, and the S98b strain has been assigned to Genbank with the accession number CP104083.1.

Conclusion

Therefore, new studies are needed to facilitate the identification of vanM-resistant enterococci and VVE strains.

Dissemination and characteristics of high-level erythromycin-resistant Enterococcus faecalis from bulk tank milk of dairy companies in Korea

Enterococci are environmental pathogens that can cause bovine mastitis, which is treated with macrolides, one of which is erythromycin (ERY). The aim of this study was to compare the characteristics of high-level erythromycin-resistant (HLER) Enterococcus faecalis (E. faecalis) isolates from bulk tank milk of 4 dairy companies, identified as A to D, in order to assess the threat to public health. Although isolates from company D showed the highest prevalence of E. faecalis, the prevalence of HLER E. faecalis in isolates from company A showed a significant difference. A total of 149 of the 301 HLER E. faecalis isolates showed the highest rate of resistance to tetracycline. In the distribution of antimicrobial resistance genes, 147 isolates carried the ermB gene alone and 2 isolates carried both ermA and ermB genes. Also, 72 and 60 isolates carried both tetM and tetL genes and the tetM gene alone, respectively, and 38 isolates carried the optrA gene. The prevalence of both aac(6')Ie-aph(2″)-la and ant(6')-Ia genes was the highest and 104 isolates harbored the Int-Tn gene carrying the Tn916/1545-like transposon. Although the distribution of the e rmB gene showed no significant difference among dairy companies, the prevalence of other resistance genes and transposons showed significant differences among dairy companies. Virulence genes were highly conserved in the HLER E. faecalis isolates. Our results indicated that there were significant differences in phenotypic and genotypic characteristics of HLER E. faecalis isolates in milk from 4 different dairy companies. A structured management protocol by companies and constant monitoring are therefore necessary to minimize public health hazards.

Functional characterization of the ABC transporters and transposable elements of an uncultured Paracoccus sp. recovered from a hydrocarbon-polluted soil metagenome

Environmental microorganisms usually exhibit a high level of genomic plasticity and metabolic versatility that allow them to be well-adapted to diverse environmental challenges. This study used shotgun metagenomics to decipher the functional and metabolic attributes of an uncultured Paracoccus recovered from a polluted soil metagenome and determine whether the detected attributes are influenced by the nature of the polluted soil. Functional and metabolic attributes of the uncultured Paracoccus were elucidated via functional annotation of the open reading frames (ORFs) of its contig. Functional tools deployed for the analysis include KEGG, KEGG KofamKOALA, Clusters of Orthologous Groups of proteins (COG), Comprehensive Antibiotic Resistance Database (CARD), and the Antibiotic Resistance Gene-ANNOTation (ARG-ANNOT V6) for antibiotic resistance genes, TnCentral for transposable element, Transporter Classification Database (TCDB) for transporter genes, and FunRich for gene enrichment analysis. Analyses revealed the preponderance of ABC transporter genes responsible for the transport of oligosaccharides (malK, msmX, msmK, lacK, smoK, aglK, togA, thuK, treV, msiK), monosaccharides (glcV, malK, rbsC, rbsA, araG, ytfR, mglA), amino acids (thiQ, ynjD, thiZ, glnQ, gluA, gltL, peb1C, artP, aotP, bgtA, artQ, artR), and several others. Also detected are transporter genes for inorganic/organic nutrients like phosphate/phosphonate, nitrate/nitrite/cyanate, sulfate/sulfonate, bicarbonate, and heavy metals such as nickel/cobalt, molybdate/tungstate, and iron, among others. Antibiotic resistance genes that mediate efflux, inactivation, and target protection were detected, while transposable elements carrying resistance phenotypes for antibiotics and heavy metals were also annotated. The findings from this study have established the resilience, adaptability, and survivability of the uncultured Paracoccus in the hydrocarbon-polluted soil.

Comparative genomics and pangenomics of vancomycin-resistant and susceptible Enterococcus faecium from Irish hospitals

Introduction. Enterococcus faecium has emerged as an important nosocomial pathogen, which is increasingly difficult to treat due to the genetic acquisition of vancomycin resistance. Ireland has a recalcitrant vancomycin-resistant bloodstream infection rate compared to other developed countries.

Hypothesis/Gap statement. Vancomycin resistance rates persist amongst E. faecium isolates from Irish hospitals. The evolutionary genomics governing these trends have not been fully elucidated.

Methodology. A set of 28 vancomycin-resistant isolates was sequenced to construct a dataset alongside 61 other publicly available Irish genomes. This dataset was extensively analysed using in silico methodologies (comparative genomics, pangenomics, phylogenetics, genotypics and comparative functional analyses) to uncover distinct evolutionary, coevolutionary and clinically relevant population trends.

Results. These results suggest that a stable (in terms of genome size, GC% and number of genes), yet genetically diverse population (in terms of gene content) of E. faecium persists in Ireland with acquired resistance arising via plasmid acquisition (vanA) or, to a lesser extent, chromosomal recombination (vanB). Population analysis revealed five clusters with one cluster partitioned into four clades which transcend isolation dates. Pangenomic and recombination analyses revealed an open (whole genome and chromosomal specific) pangenome illustrating a rampant evolutionary pattern. Comparative resistomics and virulomics uncovered distinct chromosomal and mobilomal propensity for multidrug resistance, widespread chromosomal point-mutation-mediated resistance and chromosomally harboured arsenals of virulence factors. Interestingly, a potential difference in biofilm formation strategies was highlighted by coevolutionary analysis, suggesting differential biofilm genotypes between vanA and vanB isolates.

Conclusions. These results highlight the evolutionary history of Irish E. faecium isolates and may provide insight into underlying infection dynamics in a clinical setting. Due to the apparent ease of vancomycin resistance acquisition over time, susceptible E. faecium should be concurrently reduced in Irish hospitals to mitigate potential resistant infections.

Safety and efficacy of a feed additive consisting of Bacillus subtilis FERM BP-07462, Enterococcus lactis FERM BP-10867 and Clostridium butyricum FERM BP-10866 (BIO-THREE®) for chickens for fattening, chickens reared for laying, turkeys for fattening, turkeys reared for breeding, all avian species for rearing/fattening to slaughter and all avian species reared for laying or breeding to point of lay (TOA BIOPHARMA Co., Ltd.)

Following a request from the European Commission, the Panel on Additives and Products or Substances used in Animal Feed (FEEDAP) was asked to deliver a scientific opinion on the safety and efficacy of BIO-THREE® when used as a feed additive for chickens for fattening, chickens reared for laying, turkeys for fattening, turkeys reared for breeding, all avian species for rearing/fattening to slaughter and all avian species reared for laying or breeding to point of lay. The product under assessment is based on viable cells/spores of Bacillus subtilis FERM BP-07462, Enterococcus lactis FERM BP-10867 and Clostridium butyricum FERM BP-10866. Based on the tolerance study provided, the Panel concluded that the additive is safe for the target species under the conditions of use. The additive is safe for the consumers of products derived from animals receiving the additive. The additive is not irritant to skin and eyes. The additive is a respiratory sensitiser. No conclusions could be drawn on its potential to be a skin sensitiser. The use of the product as a feed additive is of no concern for the environment. The FEEDAP Panel was not in the position to conclude on the efficacy of BIO-THREE® for the target species. BIO-THREE® is compatible with diclazuril, decoquinate and halofuginone. No conclusions could be drawn on the compatibility of BIO-THREE® with monensin sodium, salinomycin sodium, narasin, robenidine hydrochloride and maduramicin ammonium.

Human enterococcal isolates as reservoirs for macrolide-lincosamide-streptogramin and other resistance genes

According to recent studies, the importance of MLS (macrolide-lincosamide-streptogramin) resistance phenotypes and genes in enterococci are reflected in the fact that they represent reservoirs of MLS resistance genes. The aim of this study was to investigate distribution of MLS resistance genes and phenotypes in community- and hospital-acquired enterococcal isolates and to determine their prevalence. The MLS resistance phenotypes (cMLSb, iMLSb, M/MSb, and L/LSa) were determined in 245 enterococcal isolates were characterized using the double-disc diffusion method. Specific primers were chosen from database sequences for detection of the MLS resistance genes (ermA, ermB, ermC, msrA/B, lnuA, lnuB, and lsaA) in 60 isolates of enterococci by end-point PCR. There was no linezolid-resistant enterococcal isolate. Only one vancomycin-resistant (0.6%) isolate was found and it occurred in a community-acquired enterococcal isolate. The most frequent MLS resistance phenotype among enterococcal isolates was cMLSb (79.7% community- and 67.9% hospital-acquired). The most common identified MLS resistance genes among enterococcal isolates were lsaA (52.9% community- and 33.3% hospital-acquired) and ermB (17.6% community- and 33.3% hospital-acquired). The most prevalent MLS gene combination was lnuA + lsaA (five enterococcal isolates). The ermB gene encoded cMLSb phenotype, and it was identified in only one isolate that displayed iMLSb resistance phenotype. Based on the results obtained, we can conclude that the most frequent MLS resistance phenotype among enterococcal isolates was cMLSb. Surprisingly, a vancomycin-resistant enterococcal isolate was identified in a community-acquired enterococcal isolate. This study shows that enterococci may represent a major reservoir of ermB, lsaA, and lnuA genes.

Collateral sensitivity to pleuromutilins in vancomycin-resistant Enterococcus faecium

The acquisition of resistance to one antibiotic sometimes leads to collateral sensitivity to a second antibiotic. Here, we show that vancomycin resistance in Enterococcus faecium is associated with a remarkable increase in susceptibility to pleuromutilin antibiotics (such as lefamulin), which target the bacterial ribosome. The trade-off between vancomycin and pleuromutilins is mediated by epistasis between the van gene cluster and msrC, encoding an ABC-F protein that protects bacterial ribosomes from antibiotic targeting. In mouse models of vancomycin-resistant E. faecium colonization and septicemia, pleuromutilin treatment reduces colonization and improves survival more effectively than standard therapy (linezolid). Our findings suggest that pleuromutilins may be useful for the treatment of vancomycin-resistant E. faecium infections.

Rapid, Efficient, and Cost-Effective Gene Editing of Enterococcus faecium with CRISPR-Cas12a

Considered a serious threat by the Centers for Disease Control and Prevention, multidrug-resistant Enterococcus faecium is an increasing cause of hospital-acquired infection. Here, we provide details on a single-plasmid CRISPR-Cas12a system for generating clean deletions and insertions. Single manipulations were carried out in under 2 weeks, with successful deletions/insertions present in >80% of the clones tested. Using this method, we generated three individual clean deletion mutations in the acpH, treA, and lacL genes and inserted codon-optimized unaG, enabling green fluorescent protein (GFP)-like fluorescence under the control of the trehalase operon. The use of in vivo recombination for plasmid construction kept costs to a minimum. IMPORTANCE Enterococcus faecium is increasingly associated with hard-to-treat antibiotic-resistant infections. The ability to generate clean genomic alterations is the first step in generating a complete mechanistic understanding of how E. faecium acquires pathogenic traits and causes disease. Here, we show that CRISPR-Cas12a can be used to quickly (under 2 weeks) and cheaply delete or insert genes into the E. faecium genome. This substantial improvement over current methods should speed up research on this important opportunistic pathogen.

Safety assessment and probiotic characteristics of Enterococcus lactis JDM1

OBJECTIVE

The aims of this study were to evaluate the safety and probiotic characteristics of the newly isolated Enterococcus lactis strain JDM1.

METHODS

Safety assessment of E. lactis JDM1 was accomplished by the combination of whole genome sequence information analysis and phenotypic assays, including antimicrobial susceptibility test, haemolysis assay, biogenic amine production assay, cytotoxicity assay. The bacteriostatic experiment and gastrointestinal tolerance experiment were also conducted to evaluate its applicability.

RESULTS

E. lactis JDM1 possesses good gastrointestinal tolerance and can inhibit the growth of the pathogenic bacteria Clostridioides difficile and Listeria monocytogenes. The chromosome size of JDM1 was 2,570,998 bp with a GC content of 38.46%, which contained a plasmid. One intact prophage, 13 genomic islands and 19 IS elements were predicted in the JDM1 chromosome. Five resistance-related genes and seven virulence-related genes were predicted in the genome. Most resistance genes were conserved, and virulence factors were not related to functional pathogenicity. Antimicrobial susceptibility tests showed that JDM1 was sensitive to tedizolid, ciprofloxacin, levofloxacin, penicillin, ampicillin, vancomycin, linezolid, tetracycline, high-level gentamicin and high-level streptomycin. Genes encoding putative enzymes responsible for adverse metabolites were not found and JDM1 was unable to produce the six main biogenic amines. Cytotoxicity test showed that the JDM1 supernatant had no toxic effect.

CONCLUSION

E. lactis JDM1 is expected to be developed as a probiotic, and its probiotic properties are worthy of further exploration.

Mobile Antimicrobial Resistance Genes in Probiotics

Even though people worldwide tend to consume probiotic products for their beneficial health effects on a daily basis, recently, concerns were outlined regarding the uptake and potential intestinal colonisation of the bacteria that they carry. These bacteria are capable of executing horizontal gene transfer (HGT) which facilitates the movement of various genes, including antimicrobial resistance genes (ARGs), among the donor and recipient bacterial populations. Within our study, 47 shotgun sequencing datasets deriving from various probiotic samples (isolated strains and metagenomes) were bioinformatically analysed. We detected more than 70 ARGs, out of which rpoB mutants conferring resistance to rifampicin, tet(W/N/W) and potentially extended-spectrum beta-lactamase (ESBL) coding TEM-116 were the most common. Numerous ARGs were associated with integrated mobile genetic elements, plasmids or phages promoting the HGT. Our findings raise clinical and public health concerns as the consumption of probiotic products may lead to the transfer of ARGs to human gut bacteria.

Antimicrobial Resistance of Enterococcus sp. Isolated from Sheep and Goat Cheeses

This study aimed to calculate the proportion of antibiotic resistance profiles of Enterococcus faecium, E. faecalis, and E. durans isolated from traditional sheep and goat cheeses obtained from a selected border area of Slovakia with Hungary (region Slanské vrchy). A total of 110 Enterococcus sp. were isolated from cheese samples, of which 52 strains (E. faecium (12), E. faecalis (28), E. durans (12)) were represented. After isolation and identification by polymerase chain reaction and matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry, the enterococci (E. faecium, E. faecalis, and E. durans) were submitted to susceptibility tests against nine antimicrobial agents. In general, strains of E. faecalis were more resistant than E. durans and E. faecium. A high percentage of resistance was noted in E. faecalis to rifampicin (100%), vancomycin (85.7%), teicoplanin (71.4%), erythromycin (71.4%), minocycline (57.1%), nitrofurantoin (57.1%), ciprofloxacin (14.3%), and levofloxacin (14.3%). E. durans showed resistance to rifampicin (100%), teicoplanin (100%), vancomycin (66.7%), erythromycin (66.7%), nitrofurantoin (66.7%), and minocycline (33.3%), and E. faecium showed resistance to vancomycin, teicoplanin, and erythromycin (100%). Multidrug-resistant strains were confirmed in 80% of the 52 strains in this study. Continuous identification of Enterococcus sp. and monitoring of their incidence and emerging antibiotic resistance is important in order to prevent a potential risk to public health caused by the contamination of milk and other dairy products, such as cheeses, made on farm level.

Structural basis of ABCF-mediated resistance to pleuromutilin, lincosamide, and streptogramin A antibiotics in Gram-positive pathogens

Target protection proteins confer resistance to the host organism by directly binding to the antibiotic target. One class of such proteins are the antibiotic resistance (ARE) ATP-binding cassette (ABC) proteins of the F-subtype (ARE-ABCFs), which are widely distributed throughout Gram-positive bacteria and bind the ribosome to alleviate translational inhibition from antibiotics that target the large ribosomal subunit. Here, we present single-particle cryo-EM structures of ARE-ABCF-ribosome complexes from three Gram-positive pathogens: Enterococcus faecalis LsaA, Staphylococcus haemolyticus VgaALC and Listeria monocytogenes VgaL. Supported by extensive mutagenesis analysis, these structures enable a general model for antibiotic resistance mediated by these ARE-ABCFs to be proposed. In this model, ABCF binding to the antibiotic-stalled ribosome mediates antibiotic release via mechanistically diverse long-range conformational relays that converge on a few conserved ribosomal RNA nucleotides located at the peptidyltransferase center. These insights are important for the future development of antibiotics that overcome such target protection resistance mechanisms.

The Novel Macrolide Resistance Genes mef(D), msr(F), and msr(H) Are Present on Resistance Islands in Macrococcus canis, Macrococcus caseolyticus, and Staphylococcus aureus

Chromosomal resistance islands containing the methicillin resistance gene mecD (McRI _mecD ) have been reported in Macrococcus caseolyticus Here, we identified novel macrolide resistance genes in Macrococcus canis on similar elements, called McRI _msr These elements were also integrated into the 3' end of the 30S ribosomal protein S9 gene (rpsI), delimited by characteristic attachment (att) sites, and carried a related site-specific integrase gene (int) at the 5' end. They carried novel macrolide resistance genes belonging to the msr family of ABC subfamily F (ABC-F)-type ribosomal protection protein [msr(F) and msr(H)] and the macrolide efflux mef family [mef(D)]. Highly related mef(D)-msr(F) fragments were found on diverse McRI _msr elements in M. canis, M. caseolyticus, and Staphylococcus aureus Another McRI _msr -like element identified in an M. canis strain lacked the classical att site at the 3' end and carried the msr(H) gene but no neighboring mef gene. The expression of the novel resistance genes in S. aureus resulted in a low-to-moderate increase in the MIC of erythromycin but not streptogramin B. In the mef(D)-msr(F) operon, the msr(F) gene was shown to be the crucial determinant for macrolide resistance. The detection of circular forms of McRI _msr and the mef(D)-msr(F) fragment suggested mobility of both the island and the resistance gene subunit. The discovery of McRI _msr in different Macrococcus species and S. aureus indicates that these islands have a potential for dissemination of antibiotic resistance within the Staphylococcaceae family.

Surveillance of Enterococcus spp. reveals distinct species and antimicrobial resistance diversity across a One-Health continuum

For a One-Health investigation of antimicrobial resistance (AMR) in Enterococcus spp., isolates from humans and beef cattle along with abattoirs, manured fields, natural streams, and wastewater from both urban and cattle feedlot sources were collected over two years. Species identification of Enterococcus revealed distinct associations across the continuum. Of the 8430 isolates collected, Enterococcus faecium and Enterococcus faecalis were the main species in urban wastewater (90%) and clinical human isolates (99%); Enterococcus hirae predominated in cattle (92%) and feedlot catch-basins (60%), whereas natural streams harbored environmental Enterococcus spp. Whole-genome sequencing of E. faecalis (n = 366 isolates) and E. faecium (n = 342 isolates), revealed source clustering of isolates, indicative of distinct adaptation to their respective environments. Phenotypic resistance to tetracyclines and macrolides encoded by tet(M) and erm(B) respectively, was prevalent among Enterococcus spp. regardless of source. For E. faecium from cattle, resistance to β-lactams and quinolones was observed among 3% and 8% of isolates respectively, compared to 76% and 70% of human clinical isolates. Clinical vancomycin-resistant E. faecium exhibited high rates of multi-drug resistance, with resistance to all β-lactam, macrolides, and quinolones tested. Differences in the AMR profiles among isolates reflected antimicrobial use practices in each sector of the One-Health continuum.

CRISPR-Cas9-mediated genome editing in vancomycin-resistant Enterococcus faecium

The Gram-positive bacterium Enterococcus faecium is becoming increasingly prevalent as a cause of hospital-acquired, antibiotic-resistant infections. A fundamental part of research into E. faecium biology relies on the ability to generate targeted mutants but this process is currently labour-intensive and time-consuming, taking 4 to 5 weeks per mutant. In this report, we describe a method relying on the high recombination rates of E. faecium and the application of the Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-Cas9 genome editing tool to more efficiently generate targeted mutants in the E. faecium chromosome. Using this tool and the multi-drug resistant clinical E. faecium strain E745, we generated a deletion mutant in the lacL gene, which encodes the large subunit of the E. faeciumβ-galactosidase. Blue/white screening using 5-bromo-4-chloro-3-indolyl-β-D-galactopyranoside (X-gal) could be used to distinguish between the wild-type and lacL deletion mutant. We also inserted two copies of gfp into the intrinsic E. faecium macrolide resistance gene msrC to generate stable green fluorescent cells. We conclude that CRISPR-Cas9 can be used to generate targeted genome modifications in E. faecium in 3 weeks, with limited hands-on time. This method can potentially be implemented in other Gram-positive bacteria with high intrinsic recombination rates.

Antibiotic susceptibility of plant-derived lactic acid bacteria conferring health benefits to human

Lactic acid bacteria (LAB) confer health benefits to human when administered orally. We have recently isolated several species of LAB strains from plant sources, such as fruits, vegetables, flowers, and medicinal plants. Since antibiotics used to treat bacterial infection diseases induce the emergence of drug-resistant bacteria in intestinal microflora, it is important to evaluate the susceptibility of LAB strains to antibiotics to ensure the safety and security of processed foods. The aim of the present study is to determine the minimum inhibitory concentration (MIC) of antibiotics against several plant-derived LAB strains. When aminoglycoside antibiotics, such as streptomycin (SM), kanamycin (KM), and gentamicin (GM), were evaluated using LAB susceptibility test medium (LSM), the MIC was higher than when using Mueller-Hinton (MH) medium. Etest, which is an antibiotic susceptibility assay method consisting of a predefined gradient of antibiotic concentrations on a plastic strip, is used to determine the MIC of antibiotics world-wide. In the present study, we demonstrated that Etest was particularly valuable while testing LAB strains. We also show that the low susceptibility of the plant-derived LAB strains against each antibiotic tested is due to intrinsic resistance and not acquired resistance. This finding is based on the whole-genome sequence information reflecting the horizontal spread of the drug-resistance genes in the LAB strains.

Detection of methicillin-resistant Staphylococcus aureus (MRSA) in clinical samples of patients with external ocular infection

BACKGROUND AND OBJECTIVES

Staphylococcus aureus is the main Gram-positive bacteria isolated from patients with ocular infections. Herein, we describe the pattern of antibiotic resistance, presence of resistance genes including ermA, ermB, ermC, msrA, mecA and the pvl cytotoxin gene in S. aureus isolates collected from patients with external ocular infection.

MATERIALS AND METHODS

In this study, 8 S. aureus isolates were collected from 81 patients that suffered from eye damage. Antibacterial susceptibility of isolates was determined using the Kirby-Bauer disk diffusion method. Resistance genes including ermA, ermB, ermC, msrA, mecA and the pvl virulence gene were detected by PCR method. Staphylococcal cassette chromosome mec (SCCmec) in MRSA isolates were detected by the multiplex-PCR method.

RESULTS

Three isolates were resistant to cefoxitin which is considered MRSA. The mecA gene was identified in MRSA isolates. SCCmec type IV and the pvl gene were detected in one of the MRSA isolates that was recovered from a diabetic patient.

CONCLUSION

The emergence of S. aureus isolates belonging to SCCmec type IV and pvl gene among patients with ocular infection is very serious; therefore, identify genetic characterization of MRSA isolates for empirical therapy and infection control is very important.

Enterococcus faecium SF68 as a model for efficacy and safety evaluation of pharmaceutical probiotics

As normal inhabitants of diverse ecosystems, including the human gastrointestinal tract, the enterococci, and especially the two species Enterococcus faecalis and Enterococcus faecium, can be considered ubiquitous with regard to our natural environment. E. faecium has gained special importance thanks to beneficial strains marketed as probiotics, and because of its beneficial role in traditional fermented foods such as artisanal cheeses in some Southern European countries. Yet, following reports on the increasing association of some enterococcal strains with nosocomial infections such as endocarditis and bacteraemia, it became evident that strains from clinical origin are frequently highly resistant to ‘last-defence-line’ antibiotics such as the glycopeptide derivatives. For this reason enterococci have been classified in risk group 2 in the European Directive 93/88. With this paper it is intended to clarify the uncertain situation around the safety of the species E. faecium, also with referring to intra-species heterogeneity. In fact, well established scientific and surveillance data support the safety of some probiotic E. faecium strains for both human and animal applications. As a model, summarising yet extensive information is provided on the efficacy and safety of E. faecium SF68®, a pharmaceutical probiotic with a long history of safe use. We propose the approach presented in this review as a model for the evaluation of safety of probiotic strains of this species.

Quantifying the Evolutionary Conservation of Genes Encoding Multidrug Efflux Pumps in the ESKAPE Pathogens To Identify Antimicrobial Drug Targets

Increasing rates of antibiotic-resistant bacterial infection are one of the most pressing contemporary global health concerns. The ESKAPE pathogen group represents the leading cause of these infections, and upregulation of efflux pump expression is a significant mechanism of resistance in these pathogens. This has resulted in substantial interest in the development of efflux pump inhibitors to combat antibiotic-resistant infections; however, no widespread treatments have been developed to date. Our study evaluates an often-underappreciated aspect of resistance—the impact of evolutionary selection. We evaluate selection on all annotated efflux genes in all sequenced ESKAPE pathogens, providing critical context for and insight into current and future development of efflux-targeting treatments for resistant bacterial infections.

Increasing rates of antibiotic-resistant bacterial infection are one of the most pressing contemporary global health concerns. The ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) have been identified as the leading global cause of multidrug-resistant bacterial infections, and overexpression of multidrug efflux (MEX) transport systems has been identified as one of the most critical mechanisms facilitating the evolution of multidrug resistance in ESKAPE pathogens. Despite efforts to develop efflux pump inhibitors to combat antibiotic resistance, the need persists to identify additional targets for future investigations. We evaluated evolutionary pressures on 110 MEX-encoding genes from all annotated ESKAPE organism genomes. We identify several MEX genes under stabilizing selection—representing targets which can facilitate broad-spectrum treatments with evolutionary constraints limiting the potential emergence of escape mutants. We also examine MEX systems being evaluated as drug targets, demonstrating that divergent selection may underlie some of the problems encountered in the development of effective treatments—specifically in relation to the NorA system in S. aureus. This study provides a comprehensive evolutionary context to efflux in the ESKAPE pathogens, which will provide critical context to the evaluation of efflux systems as antibiotic targets.

IMPORTANCE Increasing rates of antibiotic-resistant bacterial infection are one of the most pressing contemporary global health concerns. The ESKAPE pathogen group represents the leading cause of these infections, and upregulation of efflux pump expression is a significant mechanism of resistance in these pathogens. This has resulted in substantial interest in the development of efflux pump inhibitors to combat antibiotic-resistant infections; however, no widespread treatments have been developed to date. Our study evaluates an often-underappreciated aspect of resistance—the impact of evolutionary selection. We evaluate selection on all annotated efflux genes in all sequenced ESKAPE pathogens, providing critical context for and insight into current and future development of efflux-targeting treatments for resistant bacterial infections.

RNA-seq and Tn-seq reveal fitness determinants of vancomycin-resistant Enterococcus faecium during growth in human serum

Background

The Gram-positive bacterium Enterococcus faecium is a commensal of the human gastrointestinal tract and a frequent cause of bloodstream infections in hospitalized patients. The mechanisms by which E. faecium can survive and grow in blood during an infection have not yet been characterized. Here, we identify genes that contribute to growth of E. faecium in human serum through transcriptome profiling (RNA-seq) and a high-throughput transposon mutant library sequencing approach (Tn-seq).

Results

We first sequenced the genome of E. faecium E745, a vancomycin-resistant clinical isolate, using a combination of short- and long read sequencing, revealing a 2,765,010 nt chromosome and 6 plasmids, with sizes ranging between 9.3 kbp and 223.7 kbp. We then compared the transcriptome of E. faecium E745 during exponential growth in rich medium and in human serum by RNA-seq. This analysis revealed that 27.8% of genes on the E. faecium E745 genome were differentially expressed in these two conditions. A gene cluster with a role in purine biosynthesis was among the most upregulated genes in E. faecium E745 upon growth in serum. The E. faecium E745 transposon mutant library was then used to identify genes that were specifically required for growth of E. faecium in serum. Genes involved in de novo nucleotide biosynthesis (including pyrK_2, pyrF, purD, purH) and a gene encoding a phosphotransferase system subunit (manY_2) were thus identified to be contributing to E. faecium growth in human serum. Transposon mutants in pyrK_2, pyrF, purD, purH and manY_2 were isolated from the library and their impaired growth in human serum was confirmed. In addition, the pyrK_2 and manY_2 mutants were tested for their virulence in an intravenous zebrafish infection model and exhibited significantly attenuated virulence compared to E. faecium E745.

Conclusions

Genes involved in carbohydrate metabolism and nucleotide biosynthesis of E. faecium are essential for growth in human serum and contribute to the pathogenesis of this organism. These genes may serve as targets for the development of novel anti-infectives for the treatment of E. faecium bloodstream infections.

Electronic supplementary material

The online version of this article (10.1186/s12864-017-4299-9) contains supplementary material, which is available to authorized users.

Comparative genome analysis of multiple vancomycin-resistant Enterococcus faecium isolated from two fatal cases

Enterococcus faecium is both a commensal of the human intestinal tract and an opportunistic pathogen. The increasing incidence of enterococcal infections is mainly due to the ability of this organism to develop resistance to multiple antibiotics, including vancomycin. The aim of this study was to perform comparative genome analyses on four vancomycin-resistant Enterococcus faecium (VRE_fm) strains isolated from two fatal cases in a tertiary hospital in Malaysia. Two sequence types, ST80 and ST203, were identified which belong to the clinically important clonal complex (CC) 17. This is the first report on the emergence of ST80 strains in Malaysia. Three of the studied strains (VREr5, VREr6, VREr7) were each isolated from different body sites of a single patient (patient Y) and had different PFGE patterns. While VREr6 and VREr7 were phenotypically and genotypically similar, the initial isolate, VREr5, was found to be more similar to VRE2 isolated from another patient (patient X), in terms of the genome contents, sequence types and phylogenomic relationship. Both the clinical records and genome sequence data suggested that patient Y was infected by multiple strains from different clones and the strain that infected patient Y could have derived from the same clone from patient X. These multidrug resistant strains harbored a number of virulence genes such as the epa locus and pilus-associated genes which could enhance their persistence. Apart from that, a homolog of E. faecalis bee locus was identified in VREr5 which might be involved in biofilm formation. Overall, our comparative genomic analyses had provided insight into the genetic relatedness, as well as the virulence potential, of the four clinical strains.

Antibiotic resistance, efflux pump genes and virulence determinants in Enterococcus spp. from surface water systems

The aim of this study was to report on antibiotic susceptibility patterns as well as highlight the presence of efflux pump genes and virulence genetic determinants in Enterococcus spp. isolated from South African surface water systems. One hundred and twenty-four Enterococcus isolates consisting of seven species were identified. Antimicrobial susceptibility testing revealed a high percentage of isolates was resistant to β-lactams and vancomycin. Many were also resistant to other antibiotic groups. These isolates were screened by PCR, for the presence of four efflux pump genes (mefA, tetK, tetL and msrC). Efflux genes mefA and tetK were not detected in any of the Enterococcus spp. However, tetL and msrC were detected in 17 % of the Enterococcus spp. The presence of virulence factors in the Enterococcus spp. harbouring efflux pump genes was determined. Virulence determinants were detected in 86 % of the Enterococcus spp. harbouring efflux pump genes. Four (asa1, cylA, gel and hyl) of the five virulence factors were detected. The findings of this study have demonstrated that Enterococcus from South African surface water systems are resistant to multiple antibiotics, some of which are frequently used for therapy. Furthermore, these isolates harbour efflux pump genes coding for resistance to antibiotics and virulence factors which enhance their pathogenic potential.

Lincosamides, Streptogramins, Phenicols, and Pleuromutilins: Mode of Action and Mechanisms of Resistance

Lincosamides, streptogramins, phenicols, and pleuromutilins (LSPPs) represent four structurally different classes of antimicrobial agents that inhibit bacterial protein synthesis by binding to particular sites on the 50S ribosomal subunit of the ribosomes. Members of all four classes are used for different purposes in human and veterinary medicine in various countries worldwide. Bacteria have developed ways and means to escape the inhibitory effects of LSPP antimicrobial agents by enzymatic inactivation, active export, or modification of the target sites of the agents. This review provides a comprehensive overview of the mode of action of LSPP antimicrobial agents as well as of the mutations and resistance genes known to confer resistance to these agents in various bacteria of human and animal origin.

Effects of in-feed copper and tylosin supplementations on copper and antimicrobial resistance in faecal enterococci of feedlot cattle

AIMS

The objective was to investigate whether in-feed supplementation of copper, at elevated level, co-selects for macrolide resistance in faecal enterococci.

METHODS AND RESULTS

The study was conducted in cattle (n = 80) with a 2 × 2 factorial design of copper (10 or 100 mg kg(-1) of feed) and tylosin (0 or 10 mg kg(-1) of feed). Thirty-seven isolates (4·6%; 37/800) of faecal enterococci were positive for the tcrB and all were Enterococcus faecium. The prevalence was higher among cattle fed diets with copper and tylosin (8·5%) compared to control (2·0%), copper (4·5%) and tylosin (3·5%) alone. All tcrB-positive isolates were positive for erm(B) and tet(M) genes. Median copper minimum inhibitory concentrations (MICs) for tcrB-positive and tcrB-negative enterococci were 20 and 4 mmol l(-1) , respectively.

CONCLUSIONS

Feeding of elevated dietary copper and tylosin alone or in combination resulted in an increased prevalence of tcrB and erm(B)-mediated copper and tylosin-resistant faecal enterococci in feedlot cattle.

SIGNIFICANCE AND IMPACT OF THE STUDY

In-feed supplementation of elevated dietary copper has the potential to co-select for macrolide resistance. Further studies are warranted to investigate the factors involved in maintenance and dissemination of the resistance determinants and their co-selection mechanism in relation to feed-grade antimicrobials' usage in feedlot cattle.

Characterization of Enterococcus faecium with macrolide resistance and reduced susceptibility to quinupristin/dalfopristin in a Japanese hospital: detection of extensive diversity in erm(B)-regulator regions

Cross-resistance to macrolide, lincosamide, and streptogramin B (MLSB) antibiotics is mainly mediated by the erm (erythromycin ribosome methylation) genes that encode 23S rRNA methylases in enterococi, and various mechanisms are involved in the streptogramin B resistance. Prevalence of MLSB resistance and its genetic mechanisms were analyzed for a total of 159 strains of Enterococcus faecium isolated from clinical specimens in a university hospital in Japan from 1997 to 2006. Resistance to erythromycin (EM) and clindamycin was detected in 88.1% and 89.9% of all the strains examined, respectively, and expression of resistance was totally constitutive. Although none of the strain was resistant to quinupristin/dalfopristin (Q/D), 28 strains (17.6%) showed intermediate resistance to Q/D (MIC: 2 μg/ml). The erm(B) gene was detected in 139 strains (87.4%), and msrC was found in all the strains examined, whereas no other known MLSB resistance genes were identified. The erm(B) regulator region (RR) containing a coding region of the leader peptide was classified into 13 genetic variations (L1-L3, M, S1-S7, D, and R genotypes) in 56 strains. However, no relatedness was identified between the erm(B) RR genotype and EM resistance, or reduced susceptibility to Q/D, although most of Q/D-intermediate strains were assigned to the L1, L2, and S1 genotypes. Q/D-intermediate strains were classified into five multiple-locus variable-number tandem-repeat analysis (MLVA) types, including four types of clonal complex (CC)-C1, five sequence types (STs), including four STs of CC-17, and several resistance gene/virulence factor profiles. The present study revealed the occurrence of Q/D-intermediate E. faecium, which are composed of heterogeneous strains in Japan, and more genetic diversity in the erm(B) RRs than those reported previously.

Adaptive and mutational resistance: role of porins and efflux pumps in drug resistance

The substantial use of antibiotics in the clinic, combined with a dearth of new antibiotic classes, has led to a gradual increase in the resistance of bacterial pathogens to these compounds. Among the various mechanisms by which bacteria endure the action of antibiotics, those affecting influx and efflux are of particular importance, as they limit the interaction of the drug with its intracellular targets and, consequently, its deleterious effects on the cell. This review evaluates the impact of porins and efflux pumps on two major types of resistance, namely, mutational and adaptive types of resistance, both of which are regarded as key phenomena in the global rise of antibiotic resistance among pathogenic microorganisms. In particular, we explain how adaptive and mutational events can dramatically influence the outcome of antibiotic therapy by altering the mechanisms of influx and efflux of antibiotics. The identification of porins and pumps as major resistance markers has opened new possibilities for the development of novel therapeutic strategies directed specifically against these mechanisms.

Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing

OBJECTIVES

Antimicrobial susceptibility testing of bacterial isolates is essential for clinical diagnosis, to detect emerging problems and to guide empirical treatment. Current phenotypic procedures are sometimes associated with mistakes and may require further genetic testing. Whole-genome sequencing (WGS) may soon be within reach even for routine surveillance and clinical diagnostics. The aim of this study was to evaluate WGS as a routine tool for surveillance of antimicrobial resistance compared with current phenotypic procedures.

METHODS

Antimicrobial susceptibility tests were performed on 200 isolates originating from Danish pigs, covering four bacterial species. Genomic DNA was purified from all isolates and sequenced as paired-end reads on the Illumina platform. The web servers ResFinder and MLST (www.genomicepidemiology.org) were used to identify acquired antimicrobial resistance genes and MLST types (where MLST stands for multilocus sequence typing). ResFinder results were compared with phenotypic antimicrobial susceptibility testing results using EUCAST epidemiological cut-off values and MLST types.

RESULTS

A total of 3051 different phenotypic tests were performed; 482 led to the categorizing of isolates as resistant and 2569 as susceptible. Seven cases of disagreement between tested and predicted susceptibility were observed, six of which were related to spectinomycin resistance in Escherichia coli. Correlation between MLST type and resistance profiles was only observed in Salmonella Typhimurium, where isolates belonging to sequence type (ST) 34 were more resistant than ST19 isolates.

CONCLUSIONS

High concordance (99.74%) between phenotypic and predicted antimicrobial susceptibility was observed. Thus, antimicrobial resistance testing based on WGS is an alternative to conventional phenotypic methods.

Presence of erythromycin and tetracycline resistance genes in lactic acid bacteria from fermented foods of Indian origin

Lactic acid bacteria (LAB) resistant to erythromycin were isolated from different food samples on selective media. The isolates were identified as Enterococcus durans, Enterococcus faecium, Enterococcus lactis, Enterococcus casseliflavus, Lactobacillus salivarius, Lactobacillus reuteri, Lactobacillus plantarum, Lactobacillus fermentum, Pediococcus pentosaceus and Leuconostoc mesenteroides. Of the total 60 isolates, 88 % harbored the ermB gene. The efflux gene msrA was identified in E. faecium, E. durans, E. lactis, E. casseliflavus, P. pentosaceus and L. fermentum. Further analysis of the msrA gene by sequencing suggested its homology to msrC. Resistance to tetracycline due to the genes tetM, tetW, tetO, tetK and tetL, alone or in combination, were identified in Lactobacillus species. The tetracycline efflux genes tetK and tetL occurred in P. pentosaceus and Enterococcus species. Since it appeared that LAB had acquired these genes, fermented foods may be a source of antibiotic resistance.

Emergence of pristinamycin resistance in India

Quinupristin and dalfopristin combination has been advocated as a drug of choice for multi-drug resistant (MDR) gram-positive cocci (GPC). We are reporting two cases of neonatal septicemia, caused by the methicillin resistant Staphylococcus aureus (MRSA), showing primary in vitro pristinamycin resistance. The Minimum inhibitory concentrations (MIC) for pristinamycin in these two cases were 30 μg and 25 μg, respectively. Universal advocacy of pristinamycin for the therapy of MDR GPC infections should be re-evaluated.

Towards a compatible probiotic-antibiotic combination therapy: assessment of antimicrobial resistance in the Japanese probiotics

AIM

To determine the antimicrobial resistance of the Japanese probiotics available in the market without a pharmacist's supervision.

METHODS AND RESULTS

A total of 43 isolates were obtained from 40 samples of probiotics (30 dairy products and 10 products in tablet form). Isolates were identified using 16S rRNA gene sequencing and tested for their susceptibility to 14 antimicrobials. They were screened using PCR for some antibiotic resistance genes. Inactivation of cefepime, clarithromycin and vancomycin by different inocula of 11 strains was evaluated using the antibiotic inactivation bioassay. None of the dairy probiotics showed a level of constitutive resistance or carried inducible resistance genes, making them suitable to be administrated with macrolides. Among the probiotics in tablet form only Enterococcus faecium strains carrying the msrC gene showed an MIC(90) of 4 μg ml(-1). Extended-spectrum β-lactams, tetracyclines and ampicillin exhibited powerful germicidal activity against the vast majority of the probiotic strains.

CONCLUSIONS

There is a limited choice of the Japanese probiotics that can be administered with clinically used antibiotics.

SIGNIFICANCE AND IMPACT OF THE STUDY

Japanese probiotics are widely distributed all over the world. Through the findings of our study, we have attempted to provide guidance for clinicians interested in using the Japanese probiotics in combination with antibiotics.

Enhancement of vancomycin activity by phenothiazines against vancomycin-resistant Enterococcus faecium in vitro

The antimicrobial and resistance-reversal activities of seven phenothiazine derivatives were evaluated against vancomycin-sensitive Enterococcus faecalis ATCC 29212, vancomycin resistant E. faecalis ATCC 51299 and ten vancomycin-resistant E. faecium strains originating from human infections. Minimum inhibitory concentrations (MIC) of the compounds were determined by agar dilution method, and synergy between phenothiazines and vancomycin was investigated using Checkerboard (microbroth dilution) technique. We found that all enterococci strains, regardless of their susceptibility to vancomycin, were inhibited by phenothiazines at concentrations varying from 8 to 256 microg/ml, with thiethylperazine being the most potent inhibitory agent. Besides, all the phenothiazines showed partial synergy with vancomycin and could lessen MIC of vancomycin from 512 to 8 microg/ml at their sub-inhibitory concentrations. The highest reduction in MIC was observed with chlorpromazine (32 times); however, thiethylperazine and promethazine stood next (24 times). Although resistance modification was observed at concentrations higher than those that phenothiazines reach in vivo, the potential offered by non-antibiotics justify further animal experiments as well as clinical trials to establish their clinical relevance.

Importance of the collagen adhesin ace in pathogenesis and protection against Enterococcus faecalis experimental endocarditis

Ace is an adhesin to collagen from Enterococcus faecalis expressed conditionally after growth in serum or in the presence of collagen. Here, we generated an ace deletion mutant and showed that it was significantly attenuated versus wild-type OG1RF in a mixed infection rat endocarditis model (P<0.0001), while no differences were observed in a peritonitis model. Complemented OG1RFΔace (pAT392::ace) enhanced early (4 h) heart valve colonization versus OG1RFΔace (pAT392) (P = 0.0418), suggesting that Ace expression is important for early attachment. By flow cytometry using specific anti-recombinant Ace (rAce) immunoglobulins (Igs), we showed in vivo expression of Ace by OG1RF cells obtained directly from infected vegetations, consistent with our previous finding of anti-Ace antibodies in E. faecalis endocarditis patient sera. Finally, rats actively immunized against rAce were less susceptible to infection by OG1RF than non-immunized (P = 0.0004) or sham-immunized (P = 0.0475) by CFU counts. Similarly, animals given specific anti-rAce Igs were less likely to develop E. faecalis endocarditis (P = 0.0001) and showed fewer CFU in vegetations (P = 0.0146). In conclusion, we have shown for the first time that Ace is involved in pathogenesis of, and is useful for protection against, E. faecalis experimental endocarditis.

Enterococcus faecalis was recognized as a common cause of infective endocarditis (IE) by the early 1900s. It is still third in community-onset IE, but is the second most common cause of hospital-associated IE. Complications due to E. faecalis IE include congestive heart failure, septic emboli and death and current management involves a combination of antimicrobials, often with surgery. Emergence of antimicrobial resistance has created the need for alternative strategies (such as immunoprophylaxis) that target in vivo expressed virulence-associated surface proteins. One such E. faecalis protein is Ace, which is antigenic during human IE and mediates attachment of E. faecalis cells to host extracellular matrix proteins collagen and laminin. Using a rat model, we now show that ace contributes to E. faecalis IE pathogenesis and demonstrate that Ace is expressed at high levels during IE even though produced at low levels under laboratory conditions; both active and passive immunization based on the collagen-binding domain of Ace conferred significant protection against IE. These observations, along with data that human antibodies against Ace inhibit collagen adherence of E. faecalis, indicate that Ace is an important virulence-associated factor and a promising target for prophylactic and possibly therapeutic strategies against E. faecalis IE.

Antibiotic resistance of probiotic strains of lactic acid bacteria isolated from marketed foods and drugs

OBJECTIVE

To identify the antimicrobial resistance of commercial lactic acid bacteria present in microbial foods and drug additives by analyzing their isolated strains used for fermentation and probiotics.

METHODS

Antimicrobial susceptibility of 41 screened isolates was tested with disc diffusion and E-test methods after species-level identification. Resistant strains were selected and examined for the presence of resistance genes by PCR.

RESULTS

Distribution of resistance was found in different species. All isolates were susceptible to chloramphenicol, tetracycline, ampicillin, amoxicillin/clavulanic acid, cephalothin, and imipenem. In addition, isolates resistant to vancomycin, rifampicin, streptomycin, bacitracin, and erythromycin were detected, although the incidence of resistance to these antibiotics was relatively low. In contrast, most strains were resistant to ciprofloxacin, amikacin, trimethoprim/sulphamethoxazole, and gentamycin. The genes msrC, vanX, and dfrA were detected in strains of Enterococcus faecium, Lactobacillus plantarum, Streptococcus thermophilus, and Lactococcus lactis.

CONCLUSION

Antibiotic resistance is present in different species of probiotic strains, which poses a threat to food safety. Evaluation of the safety of lactic acid bacteria for human consumption should be guided by established criteria, guidelines and regulations.

Efflux-mediated drug resistance in bacteria: an update

Drug efflux pumps play a key role in drug resistance and also serve other functions in bacteria. There has been a growing list of multidrug and drug-specific efflux pumps characterized from bacteria of human, animal, plant and environmental origins. These pumps are mostly encoded on the chromosome, although they can also be plasmid-encoded. A previous article in this journal provided a comprehensive review regarding efflux-mediated drug resistance in bacteria. In the past 5 years, significant progress has been achieved in further understanding of drug resistance-related efflux transporters and this review focuses on the latest studies in this field since 2003. This has been demonstrated in multiple aspects that include but are not limited to: further molecular and biochemical characterization of the known drug efflux pumps and identification of novel drug efflux pumps; structural elucidation of the transport mechanisms of drug transporters; regulatory mechanisms of drug efflux pumps; determining the role of the drug efflux pumps in other functions such as stress responses, virulence and cell communication; and development of efflux pump inhibitors. Overall, the multifaceted implications of drug efflux transporters warrant novel strategies to combat multidrug resistance in bacteria.

Gene cloning and characterization of EfmA, a multidrug efflux pump, from Enterococcus faecium

A DNA fragment responsible for resistance to antimicrobial agents was cloned from chromosomal DNA of Enterococcus faecium FN-1, a clinically isolated strain. Escherichia coli KAM32, a drug-hypersusceptible mutant, was used as a host for gene cloning. Cells of E. coli KAM32 harboring a recombinant plasmid (pTFM8) carrying the DNA fragment became resistant to fluoroquinolones, macrolides, ethidium bromide, 4',6-diamidino-2-phenylindole (DAPI) and tetraphenylphosphonium chloride (TPPCl). Three complete open reading frames (ORFs) were found in the DNA insert of pTFM8, and the deduced amino acid sequences of one of the ORFs showed high similarity to Mdt(A) from Lactococcus lactis. Mdt(A) is a multidrug efflux pump belonging to a major facilitator superfamily. We designated the ORF efmA. E. coli KAM32 cells harboring the efmA showed energy-dependent efflux of DAPI and TPP(+). We also observed norfloxacin/H(+) antiport due to EfmA. The mRNA expression of efmA was observed in E. faecium FN-1 grown without any exogenously added antimicrobial agents. Thus, we conclude that efmA is constitutively expressed under laboratory growth conditions and would contribute to intrinsic resistance against multiple antimicrobial agents in E. faecium FN-1.