1
|
Zaidi SEZ, Zaheer R, Barbieri R, Cook SR, Hannon SJ, Booker CW, Church D, Van Domselaar G, Zovoilis A, McAllister TA. Genomic Characterization of Enterococcus hirae From Beef Cattle Feedlots and Associated Environmental Continuum. Front Microbiol 2022; 13:859990. [PMID: 35832805 PMCID: PMC9271880 DOI: 10.3389/fmicb.2022.859990] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 04/08/2022] [Indexed: 11/13/2022] Open
Abstract
Enterococci are commensal bacteria of the gastrointestinal tract of humans, animals, and insects. They are also found in soil, water, and plant ecosystems. The presence of enterococci in human, animal, and environmental settings makes these bacteria ideal candidates to study antimicrobial resistance in the One-Health continuum. This study focused on Enterococcus hirae isolates (n = 4,601) predominantly isolated from beef production systems including bovine feces (n = 4,117, 89.5%), catch-basin water (n = 306, 66.5%), stockpiled bovine manure (n = 24, 0.5%), and natural water sources near feedlots (n = 145, 32%), and a few isolates from urban wastewater (n = 9, 0.2%) denoted as human-associated environmental samples. Antimicrobial susceptibility profiling of a subset (n = 1,319) of E. hirae isolates originating from beef production systems (n = 1,308) showed high resistance to tetracycline (65%) and erythromycin (57%) with 50.4% isolates harboring multi-drug resistance, whereas urban wastewater isolates (n = 9) were resistant to nitrofurantoin (44.5%) and tigecycline (44.5%) followed by linezolid (33.3%). Genes for tetracycline (tetL, M, S/M, and O/32/O) and macrolide resistance erm(B) were frequently found in beef production isolates. Antimicrobial resistance profiles of E. hirae isolates recovered from different environmental settings appeared to reflect the kind of antimicrobial usage in beef and human sectors. Comparative genomic analysis of E. hirae isolates showed an open pan-genome that consisted of 1,427 core genes, 358 soft core genes, 1701 shell genes, and 7,969 cloud genes. Across species comparative genomic analysis conducted on E. hirae, Enterococcus faecalis and Enterococcus faecium genomes revealed that E. hirae had unique genes associated with vitamin production, cellulose, and pectin degradation, traits which may support its adaptation to the bovine digestive tract. E. faecium and E. faecalis more frequently harbored virulence genes associated with biofilm formation, iron transport, and cell adhesion, suggesting niche specificity within these species.
Collapse
Affiliation(s)
- Sani-e-Zehra Zaidi
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
- University of Lethbridge, Lethbridge, AB, Canada
| | - Rahat Zaheer
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Ruth Barbieri
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Shaun R. Cook
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | | | | | - Deirdre Church
- Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Calgary Laboratory Services, Calgary, AB, Canada
| | - Gary Van Domselaar
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | | | - Tim A. McAllister
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
- *Correspondence: Tim A. McAllister,
| |
Collapse
|
2
|
Kim SM, Byeon YS, Yang HL, Kim IS, Lee SD. Vagococcus allomyrinae sp. nov. and Enterococcus larvae sp. nov., isolated from larvae of Allomyrina dichotoma. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005382] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic positions of two novel strains isolated from larvae of an insect (Allomyrina dichotoma) collected in Jeju, Republic of Korea, were determined by a polyphasic approach. Strain BWB3-3T was closely related to the type strain of
Vagococcus salmoninarum
, having 97.2 % 16S rRNA gene sequence similarity, whereas strain BWM-S5T formed an independent cluster within the genus
Enterococcus
in the 16S rRNA gene phylogeny and the closest relative was the type strain of
Enterococcus canis
(98.1 % sequence similarity). The core gene analysis supported the phylogenetic positions of the isolates revealed by 16S rRNA gene phylogeny. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strain BWB3-3T and the type strain of
V. salmoninarum
were 73.2 and 20.0 %, respectively, whereas strain BWM-S5 T showed an ANI value of 70.9 % with the type strain of
Enterococcus canis
. The dDDH values between strain BWM-S5T and all the type strains of
Enterococcus
species were ≤25.1 %. On the basis of the results obtained here, the two isolates are considered to constitute two novel species of the family
Enterococcaceae
, for which the names Vagococcus allomyrineae sp. nov. and Enterococcus larvae sp. nov. are proposed, with the type strains BWB3-3T (=KCTC 43277T=CCM 9080T) and BWM-S5T (=KACC 22156T=CCM 9075T), respectively.
Collapse
Affiliation(s)
- Sung-Min Kim
- Department of Food Bioengineering, Jeju National University, Jeju 63243, Republic of Korea
| | - Yeong-Sik Byeon
- Department of Food Bioengineering, Jeju National University, Jeju 63243, Republic of Korea
| | - Hong Lim Yang
- Institute of Hallasan Ecology and Culture, Jeju 63064, Republic of Korea
| | - In Seop Kim
- Department of Biological Sciences and Biotechnology, Hannam University, Daejon 34054, Republic of Korea
| | - Soon Dong Lee
- Institute of Jeju Microbial Resources, BioPS Co., Ltd., Jeju 63243, Republic of Korea
| |
Collapse
|
3
|
Graham K, Stack H, Rea R. Safety, beneficial and technological properties of enterococci for use in functional food applications - a review. Crit Rev Food Sci Nutr 2020; 60:3836-3861. [PMID: 31924117 DOI: 10.1080/10408398.2019.1709800] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
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.
Collapse
Affiliation(s)
- Ken Graham
- Department of Biological Sciences, Cork Institute of Technology, Cork, Ireland
| | - Helena Stack
- Department of Biological Sciences, Cork Institute of Technology, Cork, Ireland
| | - Rosemary Rea
- Department of Biological Sciences, Cork Institute of Technology, Cork, Ireland
| |
Collapse
|
4
|
Abstract
The genus Enterococcus comprises a ubiquitous group of Gram-positive bacteria that are of great relevance to human health for their role as major causative agents of health care-associated infections. The enterococci are resilient and versatile species able to survive under harsh conditions, making them well adapted to the health care environment. Two species cause the majority of enterococcal infections: Enterococcus faecalis and Enterococcus faecium Both species demonstrate intrinsic resistance to common antibiotics, such as virtually all cephalosporins, aminoglycosides, clindamycin, and trimethoprim-sulfamethoxazole. Additionally, a remarkably plastic genome allows these two species to readily acquire resistance to further antibiotics, such as high-level aminoglycoside resistance, high-level ampicillin resistance, and vancomycin resistance, either through mutation or by horizontal transfer of genetic elements conferring resistance determinants.
Collapse
Affiliation(s)
- Mónica García-Solache
- Department of Medicine, Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
| | - Louis B Rice
- Department of Medicine, Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
| |
Collapse
|
5
|
Abstract
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.
Collapse
|
6
|
Harada T, Dang VC, Nguyen DP, Nguyen TAD, Sakamoto M, Ohkuma M, Motooka D, Nakamura S, Uchida K, Jinnai M, Yonogi S, Kawahara R, Kanki M, Kawai T, Kumeda Y, Yamamoto Y. Enterococcus saigonensis sp. nov., isolated from retail chicken meat and liver. Int J Syst Evol Microbiol 2016; 66:3779-3785. [DOI: 10.1099/ijsem.0.001264] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Tetsuya Harada
- Osaka Prefectural Institute of Public Health, Osaka 537-0025, Japan
| | - Van Chinh Dang
- Institute of Public Health, 159 Hung Phu, District 8, Ward 8, Ho Chi Minh City, Vietnam
| | - Do Phuc Nguyen
- Institute of Public Health, 159 Hung Phu, District 8, Ward 8, Ho Chi Minh City, Vietnam
| | - Thi Anh Dao Nguyen
- Institute of Public Health, 159 Hung Phu, District 8, Ward 8, Ho Chi Minh City, Vietnam
| | - Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Daisuke Motooka
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Shota Nakamura
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kotaro Uchida
- Osaka Prefectural Institute of Public Health, Osaka 537-0025, Japan
| | - Michio Jinnai
- Osaka Prefectural Institute of Public Health, Osaka 537-0025, Japan
| | - Shinya Yonogi
- Osaka Prefectural Institute of Public Health, Osaka 537-0025, Japan
| | - Ryuji Kawahara
- Osaka Prefectural Institute of Public Health, Osaka 537-0025, Japan
| | - Masashi Kanki
- Osaka Prefectural Institute of Public Health, Osaka 537-0025, Japan
| | - Takao Kawai
- Osaka Prefectural Institute of Public Health, Osaka 537-0025, Japan
| | - Yuko Kumeda
- Osaka Prefectural Institute of Public Health, Osaka 537-0025, Japan
| | | |
Collapse
|
7
|
Declercq AM, Chiers K, Soetaert M, Lasa A, Romalde JL, Polet H, Haesebrouck F, Decostere A. Vibrio tapetis isolated from vesicular skin lesions in Dover sole Solea solea. DISEASES OF AQUATIC ORGANISMS 2015; 115:81-86. [PMID: 26119302 DOI: 10.3354/dao02880] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Vibrio tapetis is primarily known as the causative agent for brown ring disease in bivalves, although it has been isolated from cultivated fish during mortalities on farms. Here we describe the first isolation of V. tapetis from wild-caught and subsequently captive-held Dover sole Solea solea. Pathological features consisted of multifocal circular greyish-white skin discolourations evolving into vesicular lesions and subsequent ulcerations on the pigmented side. On the non-pigmented side, multiple circular lesions-white at the center and red at the edges-were evident. Histological examination of the vesicular lesions revealed dermal fluid-filled spaces, collagen tissue necrosis and a mixed inflammatory infiltrate, with large numbers of small rod-shaped bacteria. In the deep skin lesions, loss of scales and dermal connective tissue, with degeneration and fragmentation of the myofibres bordering the ulceration, were noted. Serotyping, DNA-DNA hybridization and REP- and ERIC-PCR techniques showed that the retrieved isolates displayed a profile similar to the representative strain of genotype/serotype O2 which originally was isolated from carpet-shell clam Venerupis decussata and to which isolates obtained from wedge sole Dicologoglossa cuneata were also closely related.
Collapse
Affiliation(s)
- A M Declercq
- Department of Morphology, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium
| | | | | | | | | | | | | | | |
Collapse
|
8
|
Staley C, Dunny GM, Sadowsky MJ. Environmental and animal-associated enterococci. ADVANCES IN APPLIED MICROBIOLOGY 2014; 87:147-86. [PMID: 24581391 DOI: 10.1016/b978-0-12-800261-2.00004-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Enterococci are generally commensal bacteria inhabiting the gastrointestinal tract of humans and animals. They have, however, been implicated as the etiological agent of a variety of illnesses and nosocomial infections. In addition to pathogenic potential, there is growing concern regarding the incidence of antibiotic resistance and genetic exchange among Enterococcus spp. within and among a variety of animal hosts. While primarily considered an enteric group, extra-enteric habitats in which enterococci persist and potentially grow have been studied for decades. Although many biotic (e.g., predation) and abiotic (e.g., sunlight, nutrients, and salinity) stressors have been thought to limit the success of enterococci in these secondary habitats, a growing body of evidence suggests that certain strains may become naturalized to environmental habitats. Enterococci have also been used for decades as indicators of fecal contamination in recreational waters where increased concentrations of this group have been linked to the incidence of illness in humans following recreational use of these waters. Persistence of enterococci in secondary habitats, however, suggests that their presence in ambient waters may prove to be a poor indicator of actual risks to public health. In this chapter, we provide a review of the existing body of literature concerning animal host associations, genetic exchange is reviewed, and emphasis is placed on the growing body of evidence for the persistence and growth of enterococci in secondary habitats.
Collapse
Affiliation(s)
- Christopher Staley
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, USA
| | - Gary M Dunny
- Department of Microbiology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Michael J Sadowsky
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, USA; Department of Soil, Water and Climate, University of Minnesota, St. Paul, Minnesota, USA.
| |
Collapse
|
9
|
Neonatal piglet diarrhoea associated with enteroadherent Enterococcus hirae. J Comp Pathol 2014; 151:137-47. [PMID: 24915885 DOI: 10.1016/j.jcpa.2014.04.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 02/27/2014] [Accepted: 04/09/2014] [Indexed: 01/19/2023]
Abstract
Neonatal porcine diarrhoea of uncertain aetiology is an increasing problem in several countries. The aim of the present study was to investigate the unexpected finding of enteroadherent cocci in the small intestine of piglets selected for necropsy examination from six herds (18 diarrhoeic piglets and 11 healthy controls). Gross and microscopical lesions were characterized and selected intestinal sections were further examined by immunohistochemistry for expression of active caspase-3. The enteroadherent bacterium was characterized in situ by Gram staining, ultrastructural imaging, fluorescence in-situ hybridization (FISH) and 16S rRNA gene analysis. Species identification of enterococci from intestinal cultures was performed by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) for one diarrhoeic and one control animal per herd. Gross changes were mild. Microscopically, small intestinal colonization by gram-positive cocci was observed in diarrhoeic animals only and was accompanied by villus atrophy (4/18) and mild epithelial lesions (10/18), including increased apoptosis of enterocytes. Transmission electron microscopy revealed coccoid bacteria adjacent to the epithelium, but without effacement of microvilli. 16S rRNA gene analysis yielded a sequence identical to Enterococcus hirae and FISH identified the enteroadherent bacteria as Enterococcus spp. in all colonized animals. The proportion of bacterial isolates identified as E. hirae by MALDI-TOF MS analysis was significantly higher (P = 0.0138) in diarrhoeic pigs. Species identification was confirmed by species-specific polymerase chain reaction for one E. hirae isolate per herd. These isolates were further tested for antimicrobial susceptibility, which indicated decreased susceptibility to ciprofloxacin for one isolate (minimum inhibitory concentration >4 mg/l). These findings suggested that neonatal porcine diarrhoea was associated with small intestinal colonization by E. hirae accompanied by mucosal lesions.
Collapse
|
10
|
Abstract
Enterococci are common, commensal members of gut communities in mammals and birds, yet they are also opportunistic pathogens that cause millions of human and animal infections annually. Because they are shed in human and animal feces, are readily culturable, and predict human health risks from exposure to polluted recreational waters, they are used as surrogates for waterborne pathogens and as fecal indicator bacteria (FIB) in research and in water quality testing throughout the world. Evidence from several decades of research demonstrates, however, that enterococci may be present in high densities in the absence of obvious fecal sources and that environmental reservoirs of these FIB are important sources and sinks, with the potential to impact water quality. This review focuses on the distribution and microbial ecology of enterococci in environmental (secondary) habitats, including the effect of environmental stressors; an outline of their known and apparent sources, sinks, and fluxes; and an overview of the use of enterococci as FIB. Finally, the significance of emerging methodologies, such as microbial source tracking (MST) and empirical predictive models, as tools in water quality monitoring is addressed. The mounting evidence for widespread extraenteric sources and reservoirs of enterococci demonstrates the versatility of the genus Enterococcus and argues for the necessity of a better understanding of their ecology in natural environments, as well as their roles as opportunistic pathogens and indicators of human pathogens.
Collapse
|
11
|
Franz CMAP, Huch M, Abriouel H, Holzapfel W, Gálvez A. Enterococci as probiotics and their implications in food safety. Int J Food Microbiol 2011; 151:125-40. [PMID: 21962867 DOI: 10.1016/j.ijfoodmicro.2011.08.014] [Citation(s) in RCA: 447] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Revised: 08/03/2011] [Accepted: 08/13/2011] [Indexed: 11/29/2022]
Abstract
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.
Collapse
Affiliation(s)
- Charles M A P Franz
- Department of Safety and Quality of Fruit and Vegetables, Max Rubner-Institute, Federal Research Institute of Nutrition and Food, Haid-und-Neu-Str.9, D-76131 Karlsruhe, Germany.
| | | | | | | | | |
Collapse
|
12
|
Baele M, Stakenborg T, Lopes dos Santos Santiago G, Haesebrouck F, Vaneechoutte M. tDNA-PCR followed by automated fluorescent capillary electrophoresis for identification of bacterial species. Cold Spring Harb Protoc 2010; 2009:pdb.prot5196. [PMID: 20147139 DOI: 10.1101/pdb.prot5196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Transfer RNA intergenic spacer length polymorphism analysis (tDNA-PCR) is a simple and reproducible polymerase chain reaction (PCR) technique for identification of bacteria at the species or even subspecies level. The primers used in the PCR are based on conserved sequences located at the edges of the tRNA genes. Because the selected consensus primers are directed outwardly, the intergenic spacers are amplified rather than the genes themselves. With each PCR, several amplicons of different lengths are obtained, because several intergenic spacers are present in each bacterial genome. The patterns thus obtained are identical within species, but differ between distinct species, and as a result, can be used for identification of bacterial species. The amplicons are separated using high-resolution (1 bp) electrophoresis (e.g., fluorescent capillary electrophoresis) and immediately digitized as tables composed of numerical lengths (expressed in base pairs) and peak intensities. For identification, the resulting peak pattern can be compared with a large database of patterns of well-identified bacterial strains, using an in-house-developed software package that is available online. New patterns (linked to the correct species name, which can be obtained, e.g., after 16S rRNA gene sequence determination) can be added to expand the database further. This protocol describes tDNA-PCR, followed by automated fluorescent capillary electrophoresis to identify bacterial species.
Collapse
Affiliation(s)
- Margo Baele
- Laboratory for Veterinary Microbiology, Department of Pathology, Bacteriology and Poultry Diseases, Ghent University, 9000 Gent, Belgium
| | | | | | | | | |
Collapse
|
13
|
Bensalah F, Delorme C, Renault P. Characterisation of thermotolerant cocci from indigenous flora of 'leben' in algerian arid area and DNA identification of atypical Lactococcus lactis strains. Curr Microbiol 2009; 59:139-46. [PMID: 19484304 DOI: 10.1007/s00284-009-9411-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2008] [Revised: 03/26/2009] [Accepted: 04/02/2009] [Indexed: 10/20/2022]
Abstract
Lactic acid bacteria (LAB) are widely used in food industry and their growth performance is important for the quality of the fermented product. By combining results from conventional isolation methods and molecular investigation of 16S rRNA gene and lactococcal/enterococcal specific genes, we identify at species level catalase negative gram positive thermoresistant cocci isolated from traditional 'leben', a 24-h fermented milk in arid area of west Algeria. Forty strains phenotypically related to cocci LAB were identified as belonging to the species Lactococcus lactis ssp. lactis, Enterococcus faecalis, Enterococcus faecium, and other Enterococcus species. No Streptococcus thermophilus strain was isolated. Ten different phenotype groups were recognized, and the species content of these groups were in some cases different from the expected features usually given in genus and species descriptions. In particular, atypical lactococci, able to grow in 6.5% NaCl, at pH 9.5 and showing high resistance to thermal stresses were isolated. Lactococci, but also enterococci isolated from traditional 'leben' produced in the desert area, may be therefore of interest in milk fermentation. Further studies to assess this source of diversity within the wild microbial population should provide starter new strains for product innovation.
Collapse
Affiliation(s)
- Farid Bensalah
- Faculté des Sciences, Département de Biologie, Université Es-Sénia, Oran, 31000, Algeria.
| | | | | |
Collapse
|
14
|
Enterococcus thailandicus sp. nov., isolated from fermented sausage ('mum') in Thailand. Int J Syst Evol Microbiol 2008; 58:1630-4. [DOI: 10.1099/ijs.0.65535-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
15
|
Botina SG, Tsygankov YD, Sukhodolets VV. Identification of industrial strains of lactic acid bacteria by methods of molecular genetic typing. RUSS J GENET+ 2006. [DOI: 10.1134/s1022795406120039] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
16
|
Cauwerts K, Pasmans F, Devriese LA, Martel A, Haesebrouck F, Decostere A. Cloacal Lactobacillus isolates from broilers show high prevalence of resistance towards macrolide and lincosamide antibiotics. Avian Pathol 2006; 35:160-4. [PMID: 16595310 DOI: 10.1080/03079450600598137] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Eighty-seven Lactobacillus strains isolated from cloacal swabs of broiler chickens derived from 20 different farms in Belgium were identified to species level and tested for susceptibility to macrolide and lincosamide antibiotics. Five different Lactobacillus species were identified as being predominantly present in the cloacae of broilers: Lactobacillus crispatus, Lactobacillus salivarius subsp. salivarius, Lactobacillus amylovorus, Lactobacillus gallinarum and Lactobacillu sreuteri. Acquired resistance prevalence to macrolides and lincosamides was very high in the investigated lactobacilli: 89% of the strains were resistant to either or both lincosamide and macrolide class antibiotics. The vast majority of these resistant strains (96%) displayed constitutive resistance. More than one-half of the macrolide and/or lincosamide resistant strains carried an erm(B), erm(C), mef(A), lnu(A) gene or a combination of these genes.
Collapse
Affiliation(s)
- K Cauwerts
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B9820, Merelbeke, Belgium.
| | | | | | | | | | | |
Collapse
|
17
|
Foulquié Moreno MR, Sarantinopoulos P, Tsakalidou E, De Vuyst L. The role and application of enterococci in food and health. Int J Food Microbiol 2006; 106:1-24. [PMID: 16216368 DOI: 10.1016/j.ijfoodmicro.2005.06.026] [Citation(s) in RCA: 641] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2005] [Accepted: 06/05/2005] [Indexed: 11/21/2022]
Abstract
The genus Enterococcus is the most controversial group of lactic acid bacteria. Studies on the microbiota of many traditional cheeses in the Mediterranean countries have indicated that enterococci play an important role in the ripening of these cheeses, probably through proteolysis, lipolysis, and citrate breakdown, hence contributing to their typical taste and flavour. Enterococci are also present in other fermented foods, such as sausages and olives. However, their role in these products has not been fully elucidated. Furthermore, the production of bacteriocins by enterococci is well documented. Moreover, enterococci are nowadays used as probiotics. At the same time, however, enterococci have been associated with a number of human infections. Several virulence factors have been described and the number of vancomycin-resistant enterococci is increasing. The controversial nature of enterococci has prompted an enormous increase in scientific papers and reviews in recent years, where researchers have been divided into two groups, namely pro and contra enterococci. To the authors' impression, the negative traits have been focused on very extensively. The aim of the present review is to give a balanced overview of both beneficial and virulence features of this divisive group of microorganisms, because it is only acquaintance with both sides that may allow their safe exploitation as starter cultures or co-cultures.
Collapse
Affiliation(s)
- M R Foulquié Moreno
- Research Group of Industrial Microbiology, Fermentation Technology and Downstream Processing (IMDO), Department of Applied Biological Sciences and Engineering, Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050 Brussels, Belgium
| | | | | | | |
Collapse
|
18
|
Švec P, Vancanneyt M, Devriese LA, Naser SM, Snauwaert C, Lefebvre K, Hoste B, Swings J. Enterococcus aquimarinus sp. nov., isolated from sea water. Int J Syst Evol Microbiol 2005; 55:2183-2187. [PMID: 16166729 DOI: 10.1099/ijs.0.63722-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two enterococcal strains LMG 16607(T) and LMG 16612 originating from sea water were analysed in a polyphasic taxonomic study. Both strains, assigned as Enterococcus sp. in the BCCM/LMG culture collection, possessed analogous protein profiles, but these were different from all other enterococcal species. 16S rRNA gene sequence analysis of one strain showed the highest similarity, 96.9-96.1%, with its closest phylogenetic neighbours Enterococcus saccharolyticus, Enterococcus sulfureus, Enterococcus saccharominimus and Enterococcus italicus. Further genomic analysis by (GTG)(5)-PCR fingerprinting and sequence analysis of the housekeeping gene phenylalanyl-tRNA synthase (pheS) and distinct biochemical features confirmed that the two strains represent a novel enterococcal species for which the name Enterococcus aquimarinus sp. nov. is proposed. The type strain is LMG 16607(T) (=CCM 7283(T)).
Collapse
Affiliation(s)
- Pavel Švec
- Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Tvrdého 14, 602 00 Brno, Czech Republic
| | - Marc Vancanneyt
- BCCM/LMG Bacteria Collection, Ghent University, Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Luc A Devriese
- Laboratory of Veterinary Bacteriology and Mycology, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820 Merelbeke, Belgium
| | - Sabri M Naser
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, Ledeganckstraat 35, B-9000 Ghent, Belgium
- BCCM/LMG Bacteria Collection, Ghent University, Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Cindy Snauwaert
- BCCM/LMG Bacteria Collection, Ghent University, Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Karen Lefebvre
- BCCM/LMG Bacteria Collection, Ghent University, Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Bart Hoste
- BCCM/LMG Bacteria Collection, Ghent University, Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Jean Swings
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, Ledeganckstraat 35, B-9000 Ghent, Belgium
- BCCM/LMG Bacteria Collection, Ghent University, Ledeganckstraat 35, B-9000 Ghent, Belgium
| |
Collapse
|
19
|
Graef EM, Devriese LA, Baele M, Vancanneyt M, Swings J, Haesebrouck F, Decostere A. Identification of enterococcal, streptococcal and Weissella species in the faecal flora of individually owned dogs. J Appl Microbiol 2005; 99:348-53. [PMID: 16033466 DOI: 10.1111/j.1365-2672.2005.02588.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIMS To improve the limited information on the composition of the faecal Gram-positive coccal flora of healthy dogs by the use of a molecular identification method. METHODS AND RESULTS Faecal swabs were collected for the selective isolation of Gram-positive coccal strains. Colonies with enterococcal- and streptococcal-like morphology were identified by tRNA intergenic length polymorphism analysis (tDNA-PCR). Fourteen known species belonging to three genera (Enterococcus, Streptococcus and Weissella) and one alleged new enterococcal species were found. CONCLUSIONS The faecal flora of dogs comprises an unusually broad diversity of culturable Gram-positive coccal species with Enterococcus faecalis being most frequently present followed by not less than six other species of about equal importance. SIGNIFICANCE AND IMPACT OF THE STUDY Many human- and animal-associated enterococci and streptococci are also present in dog faeces together with the largely uncharacterized Weissella cibaria and a group of strains resembling Enterococcus dispar, but representing a distinct and hitherto unknown species. Phenotypic characteristics of the latter two species were determined and the test results were compared with the species descriptions of W. cibaria and E. dispar respectively.
Collapse
Affiliation(s)
- E M Graef
- Department of Pathology, Bacteriology and Poultry Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium.
| | | | | | | | | | | | | |
Collapse
|
20
|
Naser S, Thompson FL, Hoste B, Gevers D, Vandemeulebroecke K, Cleenwerck I, Thompson CC, Vancanneyt M, Swings J. Phylogeny and identification of Enterococci by atpA gene sequence analysis. J Clin Microbiol 2005; 43:2224-30. [PMID: 15872246 PMCID: PMC1153757 DOI: 10.1128/jcm.43.5.2224-2230.2005] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The relatedness among 91 Enterococcus strains representing all validly described species was investigated by comparing a 1,102-bp fragment of atpA, the gene encoding the alpha subunit of ATP synthase. The relationships observed were in agreement with the phylogeny inferred from 16S rRNA gene sequence analysis. However, atpA gene sequences were much more discriminatory than 16S rRNA for species differentiation. All species were differentiated on the basis of atpA sequences with, at a maximum, 92% similarity. Six members of the Enterococcus faecium species group (E. faecium, E. hirae, E. durans, E. villorum, E. mundtii, and E. ratti) showed > 99% 16S rRNA gene sequence similarity, but the highest value of atpA gene sequence similarity was only 89.9%. The intraspecies atpA sequence similarities for all species except E. faecium strains varied from 98.6 to 100%; the E. faecium strains had a lower atpA sequence similarity of 96.3%. Our data clearly show that atpA provides an alternative tool for the phylogenetic study and identification of enterococci.
Collapse
Affiliation(s)
- S Naser
- Laboratory of Microbiology, Ghent University, K. L. Ledeganckstraat 35, Ghent 9000, Belgium.
| | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Fortina MG, Ricci G, Mora D, Manachini PL. Molecular analysis of artisanal Italian cheeses reveals Enterococcus italicus sp. nov. Int J Syst Evol Microbiol 2005; 54:1717-1721. [PMID: 15388734 DOI: 10.1099/ijs.0.63190-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic positions of seven atypical Enterococcus strains, isolated from artisanal Italian cheeses, were investigated in a polyphasic study. By using 16S rRNA gene sequencing, DNA-DNA hybridization and intergenic transcribed spacer analysis, as well as by examining the phenotypic properties, the novel isolates were shown to constitute a novel enterococcal species. Their closest relatives are Enterococcus sulfureus and Enterococcus saccharolyticus, having a 16S rRNA gene sequence similarity of 96.7 %. This group of strains can be easily differentiated from the other Enterococcus species by DNA-DNA hybridization and by their phenotypic characteristics: the strains do not grow in 6.5 % NaCl, and they do not produce acid from L-arabinose, melezitose, melibiose, raffinose or ribose. The name Enterococcus italicus sp. nov. is proposed for this species, with strain DSM 15952T (= LMG 22039T) as the type strain.
Collapse
MESH Headings
- Anti-Bacterial Agents/pharmacology
- Bacterial Typing Techniques
- Carbohydrate Metabolism
- Cheese/microbiology
- DNA Fingerprinting
- DNA, Bacterial/chemistry
- DNA, Bacterial/isolation & purification
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/isolation & purification
- DNA, Ribosomal Spacer/analysis
- Enterococcus/classification
- Enterococcus/genetics
- Enterococcus/isolation & purification
- Enterococcus/physiology
- Food Microbiology
- Genes, rRNA
- Italy
- Molecular Sequence Data
- Nucleic Acid Hybridization
- Phylogeny
- Pigments, Biological/biosynthesis
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Saline Solution, Hypertonic/pharmacology
- Sequence Analysis, DNA
- Temperature
Collapse
Affiliation(s)
- M Grazia Fortina
- Department of Food Science and Microbiology - Industrial Microbiology Section, University of Milan, Via Celoria 2, 20133 Milan, Italy
| | - G Ricci
- Department of Food Science and Microbiology - Industrial Microbiology Section, University of Milan, Via Celoria 2, 20133 Milan, Italy
| | - D Mora
- Department of Food Science and Microbiology - Industrial Microbiology Section, University of Milan, Via Celoria 2, 20133 Milan, Italy
| | - P L Manachini
- Department of Food Science and Microbiology - Industrial Microbiology Section, University of Milan, Via Celoria 2, 20133 Milan, Italy
| |
Collapse
|
22
|
Carvalho MDGS, Steigerwalt AG, Morey RE, Shewmaker PL, Teixeira LM, Facklam RR. Characterization of three new enterococcal species, Enterococcus sp. nov. CDC PNS-E1, Enterococcus sp. nov. CDC PNS-E2, and Enterococcus sp. nov. CDC PNS-E3, isolated from human clinical specimens. J Clin Microbiol 2004; 42:1192-8. [PMID: 15004074 PMCID: PMC356851 DOI: 10.1128/jcm.42.3.1192-1198.2004] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
As a reference laboratory, the Streptococcus Laboratory at the Centers for Disease Control and Prevention (CDC) is frequently asked to confirm the identity of unusual or difficult-to-identify catalase-negative, gram-positive cocci. In order to accomplish the precise identification of these microorganisms, we have systematically applied analysis of whole-cell protein profiles (WCPP) and DNA-DNA reassociation experiments, in conjunction with conventional physiological tests. Using this approach, we recently focused on the characterization of three strains resembling the physiological groups I (strain SS-1730), II (strain SS-1729), and IV (strain SS-1728) of enterococcal species. Two strains were isolated from human blood, and one was isolated from human brain tissue. The results of physiological testing were not consistent enough to allow confident inclusion of the strains in any of the known enterococcal species. Resistance to vancomycin was detected in one of the strains (SS-1729). Analysis of WCPP showed unique profiles for each strain, which were not similar to the profiles of any previously described Enterococcus species. 16S ribosomal DNA (rDNA) sequencing results revealed three new taxa within the genus ENTEROCOCCUS: The results of DNA-DNA relatedness experiments were consistent with the results of WCPP analysis and 16S rDNA sequencing, since the percentages of homology with all 25 known species of Enterococcus were lower than 70%. Overall, the results indicate that these three strains constitute three new species of Enterococcus identified from human clinical sources, including one that harbors the vanA gene. The isolates were provisionally designated Enterococcus sp. nov. CDC Proposed New Species of Enterococcus 1 (CDC PNS-E1), type strain SS-1728(T) (= ATCC BAA-780(T) = CCUG 47860(T)); Enterococcus sp. nov. CDC PNS-E2, type strain SS-1729(T) (= ATCC BAA-781(T) = CCUG 47861(T)); and Enterococcus sp. nov. CDC PNS-E3, type strain SS-1730(T) (= ATCC BAA-782(T) = CCUG 47862(T)).
Collapse
Affiliation(s)
- Maria da Glória S Carvalho
- Division of Bacteria and Mycotic Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | | | | | | | | | | |
Collapse
|