Isolation and characterization of enterococci from poultry reveals high incidence of Enterococcus thailandicus in Victoria, Australia

AIMS

Antibiotic resistance is a global health crisis. Roughly two-thirds of all antibiotics used are in production animals, which have the potential to impact the development of antibiotic resistance in bacterial pathogens of humans. There is little visibility on the extent of antibiotic resistance in the Australian food chain. This study sought to establish the incidence of antibiotic resistance among enterococci from poultry in Victoria.

METHODS AND RESULTS

In 2016, poultry from a Victorian processing facility were swabbed immediately post-slaughter and cultured for Enterococcus species. All isolates recovered were speciated and tested for antibiotic susceptibility to 12 antibiotics following the Clinical Laboratory Standards Institute guidelines. A total of 6 farms and 207 birds were sampled and from these 285 isolates of Enterococcus were recovered. Eight different enterococcal species were identified as follows: E. faecalis (n = 122; 43%), E. faecium (n = 92; 32%), E. durans (n = 35; 12%), E. thailandicus (n = 23; 8%), E. hirae (n = 10; 3%), and a single each of E. avium, E. gallinarum, and E. mundtii. Reduced susceptibility to older classes of antibiotics was common, in particular: erythromycin (73%), rifampin (49%), nitrofurantoin (40%), and ciprofloxacin (39%). Two vancomycin-intermediate isolates were recovered, but no resistance was detected to either linezolid or gentamicin.

CONCLUSIONS

The relatively high numbers of a recently described species, E. thailandicus, suggest this species might be well adapted to colonize poultry. The incidence of antibiotic resistance is lower in isolates from poultry than in human medicine in Australia. These results suggest that poultry may serve as a reservoir for older antibiotic resistance genes but is not driving the emergence of antimicrobial resistance in human bacterial pathogens. This is supported by the absence of resistance to linezolid and gentamicin.

Non-faecium non-faecalis enterococci: a review of clinical manifestations, virulence factors, and antimicrobial resistance

SUMMARYEnterococci are a diverse group of Gram-positive bacteria that are typically found as commensals in humans, animals, and the environment. Occasionally, they may cause clinically relevant diseases such as endocarditis, septicemia, urinary tract infections, and wound infections. The majority of clinical infections in humans are caused by two species: Enterococcus faecium and Enterococcus faecalis. However, there is an increasing number of clinical infections caused by non-faecium non-faecalis (NFF) enterococci. Although NFF enterococcal species are often overlooked, studies have shown that they may harbor antimicrobial resistance (AMR) genes and virulence factors that are found in E. faecium and E. faecalis. In this review, we present an overview of the NFF enterococci with a particular focus on human clinical manifestations, epidemiology, virulence genes, and AMR genes.

Enterococcus alishanensis sp. nov., a novel lactic acid bacterium isolated from fresh coffee beans

A coccus-shaped organism, designated ALS3T, was isolated from fresh coffee cherries collected at a farm located in the Ali Mountain region of Taiwan. Sequence analysis of its 16S rRNA gene indicated that strain ALS3T belongs to the genus Enterococcus and has more than 98.5 % sequence similarity to Enterococcus pallens and Enterococcus hermanniensis . When comparing the ALS3T genome with these two type strains, the average nucleotide identity values and digital DNA–DNA hybridization values were 72.6–73.3 and 19.2 %, respectively. The G+C content of the genomic DNA from strain ALS3T was 35.6 mol%. Results of sequence analysis, together with enzymatic activities and characteristics of carbohydrate metabolism, indicated that strain ALS3T is distinct and represents a novel species, for which the name Enterococcus alishanensis sp. nov. is proposed. The type strain is ALS3T (=NBRC 109593T=BCRC 80605T).

Slovak Local Ewe's Milk Lump Cheese, a Source of Beneficial Enterococcus durans Strain

Slovak ewe's milk lump cheese is produced from unpasteurized ewe's milk without any added culture. Because of the traditional processing and shaping by hand into a lump, this cheese was given the traditional specialty guaranteed (TSG) label. Up till now, there have existed only limited detailed studies of individual microbiota and their benefits in ewe's milk lump cheese. Therefore, this study has been focused on the beneficial properties and safety of Enterococcus durans strains with the aim to contribute to basic dairy microbiology but also for further application potential and strategy. The total enterococcal count in cheeses reached 3.93 CFU/g (log 10) ± 1.98 on average. Based on a MALDI-TOF mass spectrometry evaluation, the strains were allotted to the species E. durans (score, 1.781-2.245). The strains were gelatinase and hemolysis-negative (γ-hemolysis) and were mostly susceptible to commercial antibiotics. Among the strains, E. durans ED26E/7 produced the highest value of lactase enzyme β-galactosidase (10 nmoL). ED26E/7 was absent of virulence factor genes such as Hyl (hyaluronidase), IS 16 element and gelatinase (GelE). To test safety, ED26E/7 did not cause mortality in Balb/c mice. Its partially purified bacteriocin substance showed the highest inhibition activity/bioactivity against Gram-positive indicator bacteria: the principal indicator Enterococcus avium EA5 (102,400 AU/mL), Staphylococcus aureus SA5 and listeriae (25,600 AU/mL). Moreover, 16 staphylococci (out of 22) were inhibited (100 AU/mL), and the growth of 36 (out of 51) enterococcal indicators was as well. After further technological tests, E. durans ED26E/7, with its bacteriocin substance, can be supposed as a promising additive to dairy products.

Isolation, identification and potential probiotic characterization of lactic acid bacteria from Thai traditional fermented food

The probiotic potential of lactic acid bacteria (LAB) isolated from Thai traditional fermented food was investigated. Forty-two samples were collected from four markets in Phra Nakhon Si Ayutthaya Province. Out of 50 isolated LAB, 6 (a3, f4, f8, K1, K4 and K9) obtained from pla-ra and bamboo shoot pickle samples showed high tolerance to gastrointestinal tract conditions. These isolates were selected to identify and characterize their probiotic properties. Isolate a3 was identified as Weissella thailandensis, isolates f4 and f8 were identified as belonging to Enterococcus thailandicus and isolates K1, K4 and K9 were determined as Limosilactobacillus fermentum. All six LAB exhibited high autoaggregation ability (93.40-95.01%), while W. thailandensis isolate a3 showed potential for coaggregation in almost all the pathogenic bacteria tested. Cell-free supernatant (CFS) obtained from all isolates did not inhibit Staphylococcus aureus. CFS derived from L. fermentum isolate K4 showed the most efficient antimicrobial activity, in particular against Gram-negative bacteria, while L. fermentum isolate K4 presented high surface hydrophobicity in the presence of xylene and n-hexane. All LAB isolates were found to be resistant to clindamycin and nalidixic acid, whereas E. thailandicus isolate f8 exhibited resistance to most of the antibiotics tested. L. fermentum isolate K4 showed promise as a suitable probiotic candidate for future applications in the food industry due to tolerance to gastrointestinal tract conditions with high surface hydrophobicity and inhibited most of the pathogens tested.

Identification and safety assessment of Enterococcus thailandicus TC1 isolated from healthy pigs

Enterococci have the dual characteristics of being opportunistic pathogens and promising probiotics. The isolation from patients of CDC PNS-E2, a newly described Enterococcus species Enterococcus sanguinicola, may pose potential hazards. Enterococcus thailandicus from fermented sausage is a senior subjective synonym of E. sanguinicola. In this study, Enterococcus thailandicus TC1 was first isolated in healthy pigs in Tongcheng, China and identified by phenotypic analysis and 16S rRNA-based techniques. To evaluate the strain safety, an approach including virulence factors, antibiotic resistance, and animal experiments was adopted. The results show that cylA, gelE, esp, agg, ace, efaAfm, efaAfs, ptsD genes were undetected, and that the strain was sensitive or poorly resistant to some clinically relevant antibiotics. However, the isolated strain demonstrated β-hemolytic activity in rabbit blood agar plates. Analysis of animal experiments revealed that the isolated strain had no adverse effect on translocation and the internal organ indices, though significant differences in histology (villi height, crypts height) of ileum were observed. The data acquired suggest that E. thailandicus TC1 may be associated with a potential health risk.

Susceptibility to Enterocins and Lantibiotic Bacteriocins of Biofilm-Forming Enterococci Isolated from Slovak Fermented Meat Products Available on the Market

This study investigated eight types of Slovak dry fermented meat products (salami and sausages) that are available on the market and were produced by three different producers in different regions of Slovakia. The total counts of enterococci in these products ranged from 2.0 up to 6.0 cfu/g (log10). Three species were identified among the 15 selected enterococcal strains; Enterococcus faecium (8 strains), Enterococcus faecalis (3) and Enterococcus hirae (4). They were hemolysis-negative (γ-hemolysis) with a biofilm-forming ability, which was evaluated as low-grade biofilm formation, susceptible to conventional antibiotics and mainly susceptible to lantibiotic bacteriocins, namely, gallidermin and nisin; they even showed a higher susceptibility to gallidermin than to nisin. They were also susceptible to enterocin–durancin, but most strains showed resistance to enterocin A/P. This study indicated that bacteriocins can play a key role in preventing and/or protecting from undesirable bacterial multiplication or contamination in the food industry and that they have great potential for further experimental applications.

Enterococcus mundtii Isolated from Slovak Raw Goat Milk and Its Bacteriocinogenic Potential

Enterococci are lactic acid bacteria. Most of them can adapt well to the food system due to their salt and acid-tolerance. Moreover, many enterococcal species have been found to produce antimicrobial substances of proteinaceous character, i.e., bacteriocins/enterocins. In this study, Enterococcus mundtii EM ML2/2 with bacteriocinogenic potential was identified in Slovak raw goat milk. This strain demonstrated inhibition activity against up to 36% of Gram-positive indicator bacteria, and in concentrated form the bacteriocin substance (pH 6.3) showed the highest inhibition activity (1600 AU/mL) against the principal indicator strain E. avium EA5. Semi-purified substance (SPS) EM ML2/2 produced inhibition activity up to 3200 AU/mL. Concentrated bacteriocin substance and SPS maintained active (inhibition activity up to 100 AU/mL) for three months under −20 °C storage conditions. The strain showed susceptible antibiotic profile, and it did not form biofilm. No production of damaging enzymes was noted. It was nonhemolytic, as well as DNase, and gelatinase-negative. It grew well in skim milk, and it was salt and acid-tolerant. The bacteriocin potential of E. mundtii species isolated from Slovak raw goat milk has not previously been detected, so this is an original contribution which may stimulate addtitional research and application studies.

A newly isolated E. thailandicus strain d5B with exclusively antimicrobial activity against C. difficile might be a novel therapy for controlling CDI

Colitis induced by C. difficile is one of the most common and costly healthcare-related infections for humans. Probiotics are one of the most promising approaches for controlling CDI. Here, we presented the isolation, safety, and probiotic property evaluation of a novel E. thailandicus strain, d5B, with effective antimicrobial activity against C. difficile. Strain d5B showed strong bactericidal effects on at least 54C. difficile strains. Safety tests showed that strain d5B was sensitive to clinically important antibiotics, and had no haemolytic and cytotoxic activities. Whole genomic analysis showed strain d5B only contained one aminoglycoside resistance gene located in the chromosome. Moreover, d5B was devoid of functional virulence genes. Finally, strain d5B exhibited probiotic properties, such as tolerance to the gastrointestinal tract, and adhered well to HT-29 cells. In conclusion, the E. thailandicus strain d5B should be investigated further for useful properties as a novel candidate probiotic for controlling CDI.

Safety, beneficial and technological properties of enterococci for use in functional food applications - a review

Enterococci are ubiquitous lactic acid bacteria (LAB) that predominantly reside in the gastrointestinal tract of humans and animals but are also widespread in food and the environment due to their robust nature. Enterococci have the paradoxical position of providing several benefits of technological interest in food fermentations but are also considered as opportunistic pathogens capable of causing infection in immunocompromised patients. Several species of the genus have been correlated with disease development in humans such as bacteremia, urinary tract infections, and endocarditis. The pathogenesis of enterococci has been attributed to the increasing incidence of antibiotic resistance and the possession of virulence determinants. On the contrary, enterococci have led to improvements in the aroma, texture, and flavor of fermented dairy products, while their beneficial use as probiotic and protective cultures has also been documented. Furthermore, they have emerged as important candidates for the generation of bioactive peptides, particularly from milk, which provide new opportunities for the development of functional foods and nutraceuticals for human nutrition and health. The detection of pathogenic traits among some species is compromising their use in food applications and subsequently, the genus neither has Generally Regarded as Safe (GRAS) status nor has it been included in the Qualified Presumption of Safety (QPS) list. Nevertheless, the use of certain enterococcal strains in food has been permitted on the basis of a case-by-case assessment. Promisingly, enterococcal virulence factors appear strain specific and food isolates harbor fewer determinants than clinical isolates, while they also remain largely susceptible to clinically relevant antibiotics and thus, have a lower potential for pathogenicity. Ideally, strains considered for use in foods should not possess any virulence determinants and should be susceptible to clinically relevant antibiotics. Implementation of an appropriate risk/benefit analysis, establishment of a strain's innocuity, and consideration for relevant guidelines, legislation, and regulatory aspects surrounding functional food development, may help industry, health-staff and consumers accept enterococci, like other LAB, as important candidates for useful and beneficial applications in food biotechnology.

Enterococci Isolated from Trout in the Bukovec Water Reservoir and Čierny Váh River in Slovakia and Their Safety Aspect

The aim of this study was to investigate enterococci as lactic acid bacteria and as part of Firmicutes phylum. We focused on the virulence factor, biofilm formation, and antibiotic resistance and also on lactic acid production and enterocin gene detection. Intestinal samples were taken from 50 healthy trout (3 Salmo trutta and 47 Salmo gairdneri) collected in April 2007, 2010, and 2015 from different locations at the Bukovec water reservoir and the Čierny Váh River in Slovakia. Twenty pure colonies were identified using the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry identification system based on protein fingerprints, and then seven identified strains were also phenotyped. Based on the identification methods used, the identified enterococci (7) belong taxonomically to four different enterococcal species: Enterococcus durans, E. faecium, E. mundtii, and E. thailandicus. They were hemolysis, DNase, and gelatinase negative with acceptable enzymatic activity. They did not form biofilm and were mostly susceptible to antibiotics. All strains produced lactic acid amounting to 1.78 ± 0.33 mmol/l on average and possessed the gene for enterocin A production. This is the first study reporting more detailed properties of enterococci from trout in Slovakian wild water sources, and it produces new possibilities for studying microbiota in trout.

Maternal-neonatal transmission of Enterococcus strains during delivery

Background

Cesarean delivery (c-section) is on the rise globally. C-section is generally preferred if complications prevail in a vaginal delivery. Some private institutions conduct it unnecessarily for economic gains. This has led to a severe risk to a child’s health. The neonate’s gut microbiota has been observed to be influenced by the mode of delivery. Lactobacilli and other bacteria are very vital for developing healthy gut flora. An attempt has been made to investigate the passage of lactic acid bacteria to the infant via delivery. The vaginal swabs of the mothers and fresh meconium samples of the newborns post-delivery were examined for the presence of lactobacilli through culture techniques.

Results

The present investigation revealed that c-section-delivered infants lacked these bacteria in comparison with vaginally delivered infants. Biochemical tests and 16S rRNA sequencing showed similarity with groups 1, 2, 3, and 5 of Enterococcus genus. Phylogenetic analysis revealed more than 98% similarity with several Enterococcus species. E. canintestini, E.rivorum, and E. dispar were transferred frequently from mother to infants born via vaginal delivery. The strains were submitted to the NCBI GenBank database under accession numbers KX830968–KX830982.

Conclusion

The study supports the hypothesis of maternal-neonatal transmission of bacteria during delivery and also possibilities of isolating newer strains for probiotic use.

Antimicrobial Resistance in Enterococcus spp. of animal origin

Enterococci are natural inhabitants of the intestinal tract in humans and many animals, including food-producing and companion animals. They can easily contaminate the food and the environment, entering the food chain. Moreover, Enterococcus is an important opportunistic pathogen, especially the species E. faecalis and E. faecium, causing a wide variety of infections. This microorganism not only contains intrinsic resistance mechanisms to several antimicrobial agents, but also has the capacity to acquire new mechanisms of antimicrobial resistance. In this review we analyze the diversity of enterococcal species and their distribution in the intestinal tract of animals. Moreover, resistance mechanisms for different classes of antimicrobials of clinical relevance are reviewed, as well as the epidemiology of multidrug-resistant enterococci of animal origin, with special attention given to beta-lactams, glycopeptides, and linezolid. The emergence of new antimicrobial resistance genes in enterococci of animal origin, such as optrA and cfr, is highlighted. The molecular epidemiology and the population structure of E. faecalis and E. faecium isolates in farm and companion animals is presented. Moreover, the types of plasmids that carry the antimicrobial resistance genes in enterococci of animal origin are reviewed.

Comparative genomics of Enterococcus spp. isolated from bovine feces

Background

Enterococcus is ubiquitous in nature and is a commensal of both the bovine and human gastrointestinal (GI) tract. It is also associated with clinical infections in humans. Subtherapeutic administration of antibiotics to cattle selects for antibiotic resistant enterococci in the bovine GI tract. Antibiotic resistance genes (ARGs) may be present in enterococci following antibiotic use in cattle. If located on mobile genetic elements (MGEs) their dissemination between Enterococcus species and to pathogenic bacteria may be promoted, reducing the efficacy of antibiotics.

Results

We present a comparative genomic analysis of twenty-one Enterococcus spp. isolated from bovine feces including Enterococcus hirae (n = 10), Enterococcus faecium (n = 3), Enterococcus villorum (n = 2), Enterococcus casseliflavus (n = 2), Enterococcus faecalis (n = 1), Enterococcus durans (n = 1), Enterococcus gallinarum (n = 1) and Enterococcus thailandicus (n = 1). The analysis revealed E. faecium and E. faecalis from bovine feces share features with human clinical isolates, including virulence factors. The Tn917 transposon conferring macrolide-lincosamide-streptogramin B resistance was identified in both E. faecium and E. hirae, suggesting dissemination of ARGs on MGEs may occur in the bovine GI tract. An E. faecium isolate was also identified with two integrative conjugative elements (ICEs) belonging to the Tn916 family of ICE, Tn916 and Tn5801, both conferring tetracycline resistance.

Conclusions

This study confirms the presence of enterococci in the bovine GI tract possessing ARGs on MGEs, but the predominant species in cattle, E. hirae is not commonly associated with infections in humans. Analysis using additional complete genomes of E. faecium from the NCBI database demonstrated differential clustering of commensal and clinical isolates, suggesting that these strains may be specifically adapted to their respective environments.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-017-0962-1) contains supplementary material, which is available to authorized users.

Probiotic properties of lactic acid bacteria isolated from human milk

AIM

The objective of this study was to identify and characterize lactic acid bacteria isolated from human milk, with an emphasis on their probiotic properties.

METHODS AND RESULTS

The strains were tested for their ability to inhibit growth of Enterococcus faecalis, Salmonella enterica subsp. enterica serotype Enteritidis, Listeria monocytogenes, Staphylococcus aureus and Escherichia coli, as well as for susceptibility to antimicrobial agents and for acid pH and bile salt tolerance. Gram-positive and catalase-negative were selected and identified as Enterococcus (83·3%) after sequencing the 16S rDNA gene. All the isolates inhibited growth of Ent. faecalis and S. serotype Enteritidis, 97% inhibited growth of L. monocytogenes and Staph. aureus and 78·8% inhibited growth of E. coli. Most of the isolates were resistant to gentamicin (50%) and vancomycin (47%). Twelve isolates grew when subjected to pH 3·0 and 0·1% bile salts. At lower pH (2·5-2·0), Ent. faecalis F1 and Weissella confusa F8 were more efficient.

CONCLUSION

It was possible to isolate from human milk the lactic acid bacteria with potential for use as probiotics.

SIGNIFICANCE AND IMPACT OF THE STUDY

Lactic acid bacteria isolated of nursing mothers have probiotic properties.

Draft Genome Sequence of an Enterococcus thailandicus Strain Isolated from Bovine Feces

Here, we report the first draft genome sequence of Enterococcus thailandicus isolated from the feces of feedlot cattle in Southern Alberta.

Lactobacillus plajomi sp. nov. and Lactobacillus modestisalitolerans sp. nov., isolated from traditional fermented foods

Three Lactobacillus-like strains, NB53T, NB446T and NB702, were isolated from traditional fermented food in Thailand. Comparative 16S rRNA gene sequence analysis indicated that these strains belong to the Lactobacillus plantarum group. Phylogenetic analysis based on the dnaK, rpoA, pheS and recA gene sequences indicated that these three strains were distantly related to known species present in the L. plantarum group. DNA–DNA hybridization with closely related strains demonstrated that these strains represented two novel species; the novel strains could be differentiated based on chemotaxonomic and phenotypic characteristics. Therefore, two novel species of the genus Lactobacillus, Lactobacillus plajomi sp. nov. (NB53T) and Lactobacillus modestisalitolerans sp. nov. (NB446T and NB702), are proposed with the type strains NB53T ( = NBRC 107333T = BCC 38054T) and NB446T ( = NBRC 107235T = BCC 38191T), respectively.

Effect of in-feed administration and withdrawal of tylosin phosphate on antibiotic resistance in enterococci isolated from feedlot steers

Tylosin phosphate is a macrolide commonly administered to cattle in North America for the control of liver abscesses. This study investigated the effect of in-feed administration of tylosin phosphate to cattle at subtherapeutic levels and its subsequent withdrawal on macrolide resistance using enterococci as an indicator bacterium. Fecal samples were collected from steers that received no antibiotics and steers administered tylosin phosphate (11 ppm) in-feed for 197 days and withdrawn 28 days before slaughter. Enterococcus species isolated from fecal samples were identified through sequencing the groES-EL intergenic spacer region and subject to antimicrobial susceptibility testing, identification of resistance determinants and pulsed-field gel electrophoresis profiling. Tylosin increased (P < 0.05) the proportion of ery^R and tyl^R enterococci within the population. Just prior to its removal, the proportion of ery^R and tyl^R resistant enterococci began decreasing and continued to decrease after tylosin was withdrawn from the diet until there was no difference (P > 0.05) between treatments on d 225. This suggests that antibiotic withdrawal prior to slaughter contributes to a reduction in the proportion of macrolide resistant enterococci entering the food chain. Among the 504 enterococci isolates characterized, Enterococcus hirae was found to predominate (n = 431), followed by Enterococcus villorum (n = 32), Enterococcus faecium (n = 21), Enterococcus durans (n = 7), Enterococcus casseliflavus (n = 4), Enterococcus mundtii (n = 4), Enterococcus gallinarum (n = 3), Enterococcus faecalis (n = 1), and Enterococcus thailandicus (n = 1). The diversity of enterococci was greater in steers at arrival than at exit from the feedlot. Erythromycin resistant isolates harbored the erm(B) and/or msrC gene. Similar PFGE profiles of ery^RE. hirae pre- and post-antibiotic treatment suggest that increased abundance of ery^R enterococci after administration of tylosin phosphate reflects selection for strains that were already present within the gastrointestinal tract of cattle at arrival.

Modified 16S-23S rRNA intergenic region restriction endonuclease analysis for species identification of Enterococcus strains isolated from pigs, compared with identification using classical methods and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Fast and reliable identification of bacteria to at least the species level is currently the basis for correct diagnosis and appropriate treatment of infections. This is particularly important in the case of bacteria of the genus Enterococcus, whose resistance profile is often correlated with their species (e.g. resistance to vancomycin). In this study, we evaluated restriction endonuclease analysis of the 16S-23S rRNA gene intergenic transcribed spacer (ITS) region for species identification of Enterococcus. The utility of the method was compared with that of phenotypic methods [biochemical profile evaluation and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS)]. Identification was based on 21 Enterococcus reference strains, of the species E. faecalis, E. faecium, E. hirae, E. durans, E. casseliflavus, E. gallinarum, E. avium, E. cecorum and E. columbae, and 47 Enterococcus field strains isolated from pigs. Restriction endonuclease analysis of the ITS-PCR product using HinfI, RsaI and MboI, in the order specified, enabled species differentiation of the Enterococcus reference and field strains, and in the case of the latter, the results of species identification were identical (47/47) to those obtained by MALDI-TOF MS. Moreover, as a result of digestion with MboI, a unique restriction profile was also obtained for the strains (3/3) identified by MALDI-TOF MS as E. thailandicus. In our opinion, restriction endonuclease analysis of the 16S-23S rRNA gene ITS region of Enterococcus may be a simple and relatively fast (less than 4 h) alternative method for identifying the species occurring most frequently in humans and animals.

Transferable multiresistance plasmids carrying cfr in Enterococcus spp. from swine and farm environment

Seventy-seven porcine Enterococcus isolates with florfenicol MICs of ≥16 μg of were/ml screened for the presence of the multiresistance gene cfr, its location on plasmids, and its genetic environment. Three isolates-Enterococcus thailandicus 3-38 (from a porcine rectal swab collected at a pig farm), Enterococcus thailandicus W3, and Enterococcus faecalis W9-2 (the latter two from sewage at a different farm), carried the cfr gene. The SmaI pulsed-field gel electrophoresis patterns of the three isolates differed distinctly. In addition, E. faecalis W9-2 was assigned to a new multilocus sequence type ST469. Mating experiments and Southern blot analysis indicated that cfr is located on conjugative plasmids pW3 (∼75 kb) from E. thailandicus W3, p3-38 (∼72 kb) from E. thailandicus 3-38, and pW9-2 (∼55 kb) from E. faecalis W9-2; these plasmids differed in their sizes, additional resistance genes, and the analysis of the segments encompassing the cfr gene. Sequence analysis revealed that all plasmids harbored a 4,447-bp central region, in which cfr was bracketed by two copies of the novel insertion sequence ISEnfa4 located in the same orientation. The sequences flanking the central regions of these plasmids, including the partial tra gene regions and a ω-ε-ζ toxin-antitoxin module, exhibited >95% nucleotide sequence identity to the conjugative plasmid pAMβ1 from E. faecalis. Conjugative plasmids carrying cfr appear to play an important role in the dissemination and maintenance of the multiresistance gene cfr among enterococcal isolates and possibly other species of Gram-positive bacteria.

Inhibition of Listeria monocytogenes by Enterococcus mundtii isolated from soil

Two bacterial isolates with inhibitory activity against Listeria monocytogenes and Enterococcus faecalis were obtained from soil. Genotypic and phenotypic characterization identified them as Enterococcus mundtii, a species whose ability to compete with L. monocytogenes is relatively unexplored compared to other members of the genus. The thermal stability of the inhibitory factor and its sensitivity to proteolytic enzymes indicate that it is most likely a bacteriocin. Both isolates grew at comparable rates to L. monocytogenes at 5 °C and 10 °C in vitro. One isolate killed L. monocytogenes when it reached concentrations of 10(6)-10(8) CFU ml(-1). Minimum inocula of 10(6) and 10(5) CFU ml(-1) of E. mundtii were required to reduce and maintain L. monocytogenes concentrations beneath the level of detection at 5 °C and 10 °C, respectively. In situ experiments at 5 °C showed that E. mundtii inhibited the growth of L. monocytogenes on vacuum-packed cold smoked salmon during its four week shelf life. E. mundtii could, therefore, control the growth of L. monocytogenes at low temperatures, indicating a potential application in controlling this pathogen in chilled foods. To control growth of Listeria, the concentration of E. mundtii needs to be high, but it is possible that a purified bacteriocin could be used to achieve the same effect.

Enterococcus lactis sp. nov., from Italian raw milk cheeses

Ten atypical Enterococcus strains were isolated from Italian raw milk cheeses. The 16S rRNA gene, phenylalanyl-tRNA synthase alpha subunit (pheS), RNA polymerase alpha subunit (rpoA) and the 16S–23S rRNA intergenic transcribed spacer (ITS) sequences, randomly amplified polymorphic DNA (RAPD) PCR and the phenotypic properties revealed that the isolates represent a novel enterococcal species. On the basis of 16S rRNA gene sequence analysis, the isolates were closely related to Enterococcus hirae ATCC 8043T, Enterococcus durans CECT 411T and Enterococcus faecium ATCC 19434T, with 98.8, 98.9 and 99.4 % sequence similarity, respectively. On the basis of sequence analysis of the housekeeping gene pheS, the reference strain, BT159T, occupied a position separate from E. faecium LMG 16198. The group of isolates could be easily differentiated from recognized species of the genus Enterococcus by 16S–23S rRNA ITS analysis, RAPD-PCR and phenotypic characteristics. The name Enterococcus lactis sp. nov. is proposed, with BT159T ( = DSM 23655T = LMG 25958T) as the type strain.

Enterococcus ureasiticus sp. nov. and Enterococcus quebecensis sp. nov., isolated from water

Three enterococcal isolates, CCRI-16620, CCRI-16986T and CCRI-16985T, originating from water were characterized using morphological, biochemical and molecular taxonomic methods. 16S rRNA gene sequence analysis classified all three strains in the Enterococcus faecalis species group. The phylogenetic tree of 16S rRNA gene sequences showed that the three isolates form two separate branches. The first branch is represented by strains CCRI-16620 and CCRI-16986T and the second branch by strain CCRI-16985T. Further sequence analysis of the housekeeping genes rpoA (encoding RNA polymerase α subunit), pheS (phenylalanyl-tRNA synthase), tufA (elongation factor Tu) and atpD (ATP synthase β-subunit) as well as the results of amplified fragment length polymorphism (AFLP) DNA fingerprinting and DNA–DNA hybridization experiments confirmed the distinct status of these strains. Moreover, biochemical tests allowed phenotypic differentiation of the strains from the other species of the E. faecalis species group. On the basis of the results obtained, the names Enterococcus ureasiticus sp. nov. (type strain CCRI-16986T = CCUG 59304T = DSM 23328T = LMG 26304T) and Enterococcus quebecensis sp. nov. (type strain CCRI-16985T = CCUG 59306T = DSM 23327T = LMG 26306T) are proposed for the two hitherto undescribed species.

Enterococci as probiotics and their implications in food safety

Enterococci belong to the lactic acid bacteria (LAB) and they are of importance in foods due to their involvement in food spoilage and fermentations, as well as their utilisation as probiotics in humans and slaughter animals. However, they are also important nosocomial pathogens that cause bacteraemia, endocarditis and other infections. Some strains are resistant to many antibiotics and possess virulence factors such as adhesins, invasins, pili and haemolysin. The role of enterococci in disease has raised questions on their safety for use in foods or as probiotics. Studies on the incidence of virulence traits among enterococcal strains isolated from food showed that some can harbour virulence traits, but it is also thought that virulence is not the result of the presence of specific virulence determinants alone, but is rather a more intricate process. Specific genetic lineages of hospital-adapted strains have emerged, such as E. faecium clonal complex (CC) 17 and E. faecalis CC2, CC9, CC28 and CC40, which are high risk enterococcal clonal complexes. These are characterised by the presence of antibiotic resistance determinants and/or virulence factors, often located on pathogenicity islands or plasmids. Mobile genetic elements thus are considered to play a major role in the establishment of problematic lineages. Although enterococci occur in high numbers in certain types of fermented cheeses and sausages, they are not deliberately added as starter cultures. Some E. faecium and E. faecalis strains are used as probiotics and are ingested in high numbers, generally in the form of pharmaceutical preparations. Such probiotics are administered to treat diarrhoea, antibiotic-associated diarrhoea or irritable bowel syndrome, to lower cholesterol levels or to improve host immunity. In animals, enterococcal probiotics are mainly used to treat or prevent diarrhoea, for immune stimulation or to improve growth. From a food microbiological point of view, the safety of the bacteria used as probiotics must be assured, and data on the major strains in use so far indicate that they are safe. The advantage of use of probiotics in slaughter animals, from a food microbiological point of view, lies in the reduction of zoonotic pathogens in the gastrointestinal tract of animals which prevents the transmission of these pathogens via food. The use of enterococcal probiotics should, in view of the development of problematic lineages and the potential for gene transfer in the gastrointestinal tract of both humans and animals, be carefully monitored, and the advantages of using these and new strains should be considered in a well contemplated risk/benefit analysis.

Reevaluation of the taxonomic status of recently described species of Enterococcus: evidence that E. thailandicus is a senior subjective synonym of "E. sanguinicola" and confirmation of E. caccae as a species distinct from E. silesiacus

Several of the more recently proposed new species of Enterococcus are nearly identical based on 16S rRNA gene sequence analysis and phenotypic traits. In the present study, DNA-DNA reassociation experiments, in conjunction with sequencing of the 16S rRNA and rpoB genes, provided evidence that "Enterococcus sanguinicola" and Enterococcus thailandicus actually represent the same species. In contrast, Enterococcus caccae and Enterococcus silesiacus, two other species with nearly identical 16S rRNA gene sequences, were confirmed to be separate species.

Identification of enterococci from broiler products and a broiler processing plant and description of Enterococcus viikkiensis sp. nov

In two previous studies dealing with lactic acid bacteria (LAB) from modified-atmosphere-packaged (MAP) broiler products and a broiler processing plant, several isolates remained unidentified. According to 16S rRNA gene sequence analysis, 36 isolates were assigned to the genus Enterococcus. Numerical analysis of combined HindIII and EcoRI ribopatterns of these isolates resulted in species-specific clusters that were congruent with the clusters obtained by both DNA-directed RNA polymerase subunit A (rpoA) and phenylalanyl-tRNA synthetase α chain (pheS) housekeeping gene analyses. In the analyses, a group of five isolates distinct from any known enterococcal species clustered together. The five isolates were positioned in the Enterococcus avium group, with E. devriesei being the closest phylogenetic neighbor. The DNA-DNA hybridization levels with E. devriesei ranged from 28.8 to 54.3% and indicated that these strains represented a novel species. The name Enterococcus viikkiensis sp. nov. is proposed, with strain DSM 24043(T) (LMG 26075(T)) being the type strain. Our study demonstrated that the identification of enterococci within the E. avium phylogenetic group demands polyphasic taxonomic approaches. The rpoA and pheS gene similarities (99.0 to 99.2% and 94.3 to 95.4%, respectively) between E. viikkiensis and its closest phylogenetic neighbor, E. devriesei, were higher than those previously reported within the enterococci. In addition, the phenotypic profiles of the species in the E. avium group were also highly similar, and some traits were found to be misleading for enterococci, such as E. viikkiensis does not grow at 45°C. The numerical analysis of combined HindIII and EcoRI ribopatterns was of considerable assistance in distinguishing enterococcal species within the E. avium group.

Prospective, multicenter evaluation of the BD GeneOhm VanR assay for direct, rapid detection of vancomycin-resistant Enterococcus species in perianal and rectal specimens

The BD GeneOhm VanR assay (BD Diagnostics, San Diego, CA), a qualitative test for the rapid detection of vancomycin-resistant enterococci (VRE) from rectal and/or perianal swabs, combines integrated nucleic acid extraction and automated polymerase chain reaction for the detection of vanA and/or vanB gene sequences. We studied 1,027 perianal and rectal swab specimens from 3 geographically distinct US sites (prevalence rates, 13.1%-25.8%). Direct swab specimens were tested by the assay and compared with direct culture. The sensitivity, specificity, and positive and negative predictive values of the assay were 93.2%, 81.9%, 54.4%, and 98.1%, respectively. The specificity was limited largely due to false-positives in the vanB portion of the assay. Specificity with perianal swabs was significantly greater than with rectal swabs, 87.1% vs 74.7%, respectively (P < .0001). When used only to detect resistance conferred by vanA, the assay was 88.3% (158/179) sensitive and 95.8% (802/837) specific, with positive and negative predictive values of 81.9% and 97.4%, respectively. The assay is a simple, rapid, and acceptable method for screening for VRE in a variety of populations in which vanA is the predominant genotype. Samples positive for the vanB genotype should be confirmed by culture owing to the apparent high number of false-positive results.