1
|
Carrasco-Acosta M, Garcia-Jimenez P. Development of Multiplex RT qPCR Assays for Simultaneous Detection and Quantification of Faecal Indicator Bacteria in Bathing Recreational Waters. Microorganisms 2024; 12:1223. [PMID: 38930605 DOI: 10.3390/microorganisms12061223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 06/05/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
In this study, we designed and validated in silico and experimentally a rapid, sensitive, and specific multiplex RT qPCR for the detection and quantification of faecal indicator bacteria (FIB) used as microbiological references in marine bathing water regulations (Escherichia coli and intestinal enterococci). The 16S rRNA gene was used to quantify group-specific enterococci and Escherichia/Shigella and species-specific such as Enterococcus faecalis and E. faecium. Additionally, a ybbW gene encoding allantoin transporter protein was used to detect E. coli. An assessment of marine coastal systems (i.e., marine water and sediment) revealed that intestinal enterococci were the predominant group compared to Escherichia/Shigella. The low contribution of E. faecalis to the intestinal enterococci group was reported. As E. faecalis and E. faecium were reported at low concentrations, it is assumed that other enterococci of faecal origin are contributing to the high gene copy number of this group-specific enterococci. Moreover, low 16S rRNA gene copy numbers with respect to E. faecalis and E. faecium were reported in seawater compared to marine sediment. We conclude that marine sediments can affect the quantification of FIBs included in bathing water regulations. Valuing the quality of the marine coastal system through sediment monitoring is recommended.
Collapse
Affiliation(s)
- Marina Carrasco-Acosta
- Department of Biology, Faculty of Marine Sciences, Instituto Universitario de Investigación en Estudios Ambientales y Recursos Naturales i-UNAT, Universidad de Las Palmas de Gran Canaria, 35017 Las Palmas de Gran Canaria, Spain
| | - Pilar Garcia-Jimenez
- Department of Biology, Faculty of Marine Sciences, Instituto Universitario de Investigación en Estudios Ambientales y Recursos Naturales i-UNAT, Universidad de Las Palmas de Gran Canaria, 35017 Las Palmas de Gran Canaria, Spain
| |
Collapse
|
2
|
Chen MY, Lira F, Liang HQ, Wu RT, Duan JH, Liao XP, Martínez JL, Liu YH, Sun J. Multilevel selection of bcrABDR-mediated bacitracin resistance in Enterococcus faecalis from chicken farms. Sci Rep 2016; 6:34895. [PMID: 27731342 PMCID: PMC5059624 DOI: 10.1038/srep34895] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 09/19/2016] [Indexed: 11/16/2022] Open
Abstract
In this study we isolated 109 Enterococcus faecalis from chicken faecal samples in 6 provinces of China to investigate the prevalence and transmission mechanism of the bacitracin resistance locus bcrABDR in E. faecalis. Thirty-seven bcrABDR-positive E. faecalis were detected with 26 different PFGE clusters. The MLST of 14 positive strains belonged to ST16 and we also detected three new sequence types. S1-PFGE analysis indicated that the locus was located on plasmids presenting different sizes, with the most prevalent size being ~50 kb (13/37). Sequence analysis revealed that 17 out of the 37 strains harbored a 5400-bp central region, in which locus bcrABDR was bracketed by two ISEnfa1 of the same orientation. Two types of bcrABDR alleles, differing in around 10% of their sequence were found. In silico analysis showed that bcrABDR is present in a variety of bacteria including the chicken commensal Enterococcus cecorum. Our results indicate that the use of bacitracin at farms might trigger the emergence and spread of the bacitracin resistance determinant bcrABDR among human bacterial pathogens. The finding of bcrABDR in the chicken commensal E. cecorum indicates that farm animals microbiota can be an important reservoir of resistance genes with relevance for human health.
Collapse
Affiliation(s)
- Mu-Ya Chen
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Felipe Lira
- Centro Nacional de Biotecnología, CSIC, Darwin 3, Madrid-28049, Spain
| | - Hua-Qing Liang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Rui-Ting Wu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Jia-Hong Duan
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Xiao-Ping Liao
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - José L Martínez
- Centro Nacional de Biotecnología, CSIC, Darwin 3, Madrid-28049, Spain
| | - Ya-Hong Liu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Jian Sun
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| |
Collapse
|
3
|
Veljović K, Popović N, Vidojević AT, Tolinački M, Mihajlović S, Jovčić B, Kojić M. Environmental waters as a source of antibiotic-resistant Enterococcus species in Belgrade, Serbia. ENVIRONMENTAL MONITORING AND ASSESSMENT 2015; 187:599. [PMID: 26314345 DOI: 10.1007/s10661-015-4814-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 08/19/2015] [Indexed: 05/13/2023]
Abstract
Despite the number of studies on antibiotic-resistant enterococci from Serbian clinical settings, there are no data about environmental contamination with these bacteria. Thus, this study investigated the prevalence of antibiotic-resistant enterococci in Belgrade, Serbia. Enterococcus species collected from ten surface water sites, including a lake, two major river systems, and springs, were tested. Among enterococci, we found single (21.7 %), double (17.4 %), and multiple antibiotic resistance patterns (56.3 %). Vancomycin-resistant strains were not found, indicating that their abundance in Belgrade is tightly linked to clinical settings. The multiple drug-resistant strains Enterococcus faecalis, Enterococcus faecium, and Enterococcus mundtii were frequently detected in the lake during the swimming season and in the rivers near industrial zones. We confirmed the presence of ermB, ermC, ant(6)-Ia, tetM, and tetL and mutations in gyrA genes. The phylogenetic analysis of 16S rRNA gene of E. faecium isolates that harbor esp gene classified them into two groups based on high-bootstraps scores in the tree analysis. Pulsed-field gel electrophoresis analysis of antibiotic-resistant enterococci revealed genomic similarity ranging from 75 to 100 %. This study indicates the importance of anthropogenic impact to the spread of antibiotic-resistant enterococci in environmental waters of Belgrade, Serbia.
Collapse
Affiliation(s)
- Katarina Veljović
- Institute of Molecular Genetics and Genetic Engineering (IMGGE), University of Belgrade, Vojvode Stepe 444a, P. O. Box 23, 11010, Belgrade, Serbia,
| | | | | | | | | | | | | |
Collapse
|
4
|
Prevalence, diversity and characterization of enterococci from three coraciiform birds. Antonie van Leeuwenhoek 2015; 107:1281-9. [DOI: 10.1007/s10482-015-0422-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 03/02/2015] [Indexed: 10/23/2022]
|
5
|
Jahan M, Zhanel GG, Sparling R, Holley RA. Horizontal transfer of antibiotic resistance from Enterococcus faecium of fermented meat origin to clinical isolates of E. faecium and Enterococcus faecalis. Int J Food Microbiol 2015; 199:78-85. [PMID: 25647243 DOI: 10.1016/j.ijfoodmicro.2015.01.013] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 01/14/2015] [Indexed: 10/24/2022]
Abstract
Enterococcus species are part of the normal intestinal flora of a large number of mammals including humans and consequently, they can be used as indicators of faecal contamination in food and water for human consumption. Their presence in large numbers in foods may indicate a lapse in sanitation and their ability to serve as a genetic reservoir of transferable antibiotic resistance is of concern. In the present study, Enterococcus spp., isolated from commercially fermented meat and human clinical specimen were studied to determine genetic relationships. SmaI pulsed-field gel electrophoresis (PFGE) patterns exhibited genomic heterogeneity within and between both groups of isolates. However, in spite of this heterogeneity there were still substantial phenotypic similarities which suggested that food might be a potential vehicle for distribution of resistant bacteria among humans. In vitro conjugation experiments demonstrated transfer of the tetracycline resistant determinant, tet(M), from Enterococcus faecium S27 isolated from fermented sausage to clinical isolates of both E. faecium and Enterococcus faecalis. The streptomycin resistance of E. faecium S27 was also transferred to a clinical strain, E. faecalis 82916, which was confirmed by the presence of the streptomycin resistance gene, aadA, in the donor and transconjugant strains. Since the aadA gene is associated with a class 1 integron, results also suggested that resistance transfer might have occurred via an integron. It appears this is the first identification of a class 1 integron in E. faecium isolated from food. The importance of food enterococci as a reservoir of antibiotic resistance genes and the potential for their genetic transfer to human strains following consumption of uncooked or undercooked contaminated meat is underlined by this work.
Collapse
Affiliation(s)
- Musarrat Jahan
- Department of Food Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - George G Zhanel
- Department of Medical Microbiology, Faculty of Medicine, University of Manitoba, Winnipeg, MB R3E 3P5, Canada
| | - Richard Sparling
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Richard A Holley
- Department of Food Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.
| |
Collapse
|
6
|
Neave M, Luter H, Padovan A, Townsend S, Schobben X, Gibb K. Multiple approaches to microbial source tracking in tropical northern Australia. Microbiologyopen 2014; 3:860-74. [PMID: 25224738 PMCID: PMC4263510 DOI: 10.1002/mbo3.209] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 07/14/2014] [Accepted: 07/25/2014] [Indexed: 11/10/2022] Open
Abstract
Microbial source tracking is an area of research in which multiple approaches are used to identify the sources of elevated bacterial concentrations in recreational lakes and beaches. At our study location in Darwin, northern Australia, water quality in the harbor is generally good, however dry-season beach closures due to elevated Escherichia coli and enterococci counts are a cause for concern. The sources of these high bacteria counts are currently unknown. To address this, we sampled sewage outfalls, other potential inputs, such as urban rivers and drains, and surrounding beaches, and used genetic fingerprints from E. coli and enterococci communities, fecal markers and 454 pyrosequencing to track contamination sources. A sewage effluent outfall (Larrakeyah discharge) was a source of bacteria, including fecal bacteria that impacted nearby beaches. Two other treated effluent discharges did not appear to influence sites other than those directly adjacent. Several beaches contained fecal indicator bacteria that likely originated from urban rivers and creeks within the catchment. Generally, connectivity between the sites was observed within distinct geographical locations and it appeared that most of the bacterial contamination on Darwin beaches was confined to local sources.
Collapse
Affiliation(s)
- Matthew Neave
- Research Institute for the Environment and Livelihoods, Charles Darwin UniversityCasuarina, Northern Territory, Australia
| | - Heidi Luter
- Research Institute for the Environment and Livelihoods, Charles Darwin UniversityCasuarina, Northern Territory, Australia
- Northern Australian Marine Research Alliance, Arafura Timor Research Facility DarwinBrinkin, Northern Territory, Australia
| | - Anna Padovan
- Research Institute for the Environment and Livelihoods, Charles Darwin UniversityCasuarina, Northern Territory, Australia
| | - Simon Townsend
- Department of Land Resource Management, Northern Territory GovernmentPalmerston, Northern Territory, Australia
| | - Xavier Schobben
- Department of Health, Northern Territory GovernmentCasuarina, Northern Territory, Australia
| | - Karen Gibb
- Research Institute for the Environment and Livelihoods, Charles Darwin UniversityCasuarina, Northern Territory, Australia
| |
Collapse
|
7
|
Liu Y, Wang Y, Dai L, Wu C, Shen J. First report of multiresistance gene cfr in Enterococcus species casseliflavus and gallinarum of swine origin. Vet Microbiol 2014; 170:352-7. [DOI: 10.1016/j.vetmic.2014.02.037] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2013] [Revised: 02/17/2014] [Accepted: 02/19/2014] [Indexed: 10/25/2022]
|
8
|
Fu LL, Li JR. Microbial Source Tracking: A Tool for Identifying Sources of Microbial Contamination in the Food Chain. Crit Rev Food Sci Nutr 2013; 54:699-707. [DOI: 10.1080/10408398.2011.605231] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
9
|
Kim JY, Lee H, Lee JE, Chung MS, Ko GP. Identification of human and animal fecal contamination after rainfall in the Han River, Korea. Microbes Environ 2013; 28:187-94. [PMID: 23666535 PMCID: PMC4070672 DOI: 10.1264/jsme2.me12187] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
We investigated the effect of rainfall on the levels and sources of microbial contamination in the Han River, Korea. Thirty-four samples were collected at two sampling sites located upstream and downstream in the river from July 2010 to February 2011. Various fecal indicator microorganisms, including total coliform, fecal coliform, Escherichia coli, Enterococcus spp., somatic and male-specific (F+) coliphage, and four major enteric viruses were analyzed. Rainfall was positively correlated with the levels of fecal coliform and norovirus at both sampling sites. Additionally, rainfall was positively correlated with the levels of total coliform, E. coli, Enterococcus spp., and F+ coliphage at the upstream site. To identify the source of fecal contamination, microbial source tracking (MST) was conducted using both male-specific (F+) RNA coliphage and the Enterococcus faecium esp gene as previously described. Our results clearly indicated that the majority of fecal contamination at the downstream Han River site was from a human source. At the upstream sampling site, contamination from human fecal matter was very limited; however, fecal contamination from non-point animal sources increased following rainfall. In conclusion, our data suggest that rainfall significantly affects the level and source of fecal contamination in the Han River, Korea.
Collapse
Affiliation(s)
- Ji Young Kim
- Department of Environmental Health, Graduate School of Public Health, Seoul National University, Seoul National University, Kwanak-ro 1, Kwanak-gu, Seoul, 151–752, Republic of Korea
| | | | | | | | | |
Collapse
|
10
|
Transferable multiresistance plasmids carrying cfr in Enterococcus spp. from swine and farm environment. Antimicrob Agents Chemother 2012; 57:42-8. [PMID: 23070165 DOI: 10.1128/aac.01605-12] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
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.
Collapse
|
11
|
Development of a DNA microarray for enterococcal species, virulence, and antibiotic resistance gene determinations among isolates from poultry. Appl Environ Microbiol 2011; 77:2625-33. [PMID: 21335389 DOI: 10.1128/aem.00263-11] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
A DNA microarray (Enteroarray) was designed with probes targeting four species-specific taxonomic identifiers to discriminate among 18 different enterococcal species, while other probes were designed to identify 18 virulence factors and 174 antibiotic resistance genes. In total, 262 genes were utilized for rapid species identification of enterococcal isolates, while characterizing their virulence potential through the simultaneous identification of endogenous antibiotic resistance and virulence genes. Enterococcal isolates from broiler chicken farms were initially identified by using the API 20 Strep system, and the results were compared to those obtained with the taxonomic genes atpA, recA, pheS, and ddl represented on our microarray. Among the 171 isolates studied, five different enterococcal species were identified by using the API 20 Strep system: Enterococcus faecium, E. faecalis, E. durans, E. gallinarum, and E. avium. The Enteroarray detected the same species as API 20 Strep, as well as two more: E. casseliflavus and E. hirae. Species comparisons resulted in 15% (27 isolates) disagreement between the two methods among the five API 20 Strep identifiable species and 24% (42 isolates) disagreement when considering the seven Enteroarray identified species. The species specificity of key antibiotic and virulence genes identified by the Enteroarray were consistent with the literature adding further robustness to the redundant taxonomic probe data. Sequencing of the cpn60 gene further confirmed the complete accuracy of the microarray results. The new Enteroarray should prove to be a useful tool to accurately genotype strains of enterococci and assess their virulence potential.
Collapse
|
12
|
Differentiation of Fecal Escherichia coli from Human, Livestock, and Poultry Sources by rep-PCR DNA Fingerprinting on the Shellfish Culture Area of East China Sea. Curr Microbiol 2011; 62:1423-30. [DOI: 10.1007/s00284-011-9870-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2010] [Accepted: 01/05/2011] [Indexed: 10/18/2022]
|
13
|
Roslev P, Bukh AS. State of the art molecular markers for fecal pollution source tracking in water. Appl Microbiol Biotechnol 2011; 89:1341-55. [DOI: 10.1007/s00253-010-3080-7] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Revised: 12/15/2010] [Accepted: 12/15/2010] [Indexed: 01/16/2023]
|