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Akpınar Kankaya D, Tuncer Y. Antibiotic resistance in vancomycin‐resistant lactic acid bacteria (VRLAB) isolated from foods of animal origin. J FOOD PROCESS PRES 2020. [DOI: 10.1111/jfpp.14468] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Didem Akpınar Kankaya
- Department of Food Engineering Faculty of Engineering Süleyman Demirel University Isparta Turkey
- Department of Food Technology Gelendost Vocational School Isparta Uygulamalı Bilimler University Isparta Turkey
| | - Yasin Tuncer
- Department of Food Engineering Faculty of Engineering Süleyman Demirel University Isparta Turkey
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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.
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Rieke EL, Soupir ML, Moorman TB, Yang F, Howe AC. Temporal Dynamics of Bacterial Communities in Soil and Leachate Water After Swine Manure Application. Front Microbiol 2018; 9:3197. [PMID: 30627124 PMCID: PMC6309816 DOI: 10.3389/fmicb.2018.03197] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 12/10/2018] [Indexed: 11/17/2022] Open
Abstract
Application of swine manure to agricultural land allows recycling of plant nutrients, but excess nitrate, phosphorus and fecal bacteria impact surface and drainage water quality. While agronomic and water quality impacts are well studied, little is known about the impact of swine manure slurry on soil microbial communities. We applied swine manure to intact soil columns collected from plots maintained under chisel plow or no-till with corn and soybean rotation. Targeted 16S-rRNA gene sequencing was used to characterize and to identify shifts in bacterial communities in soil over 108 days after swine manure application. In addition, six simulated rainfalls were applied during this time. Drainage water from the columns and surface soil were sampled, and DNA was extracted and sequenced. Unique DNA sequences (OTU) associated with 12 orders of bacteria were responsible for the majority of OTUs stimulated by manure application. Proteobacteria were most prevalent, followed by Bacteroidetes, Firmicutes, Actinobacteria, and Spirochaetes. While the majority of the 12 orders decreased after day 59, relative abundances of genes associated with Rhizobiales and Actinomycetales in soil increased. Bacterial orders which were stimulated by manure application in soil had varied responses in drainage waters over the course of the experiment. We also identified a “manure-specific core” of five genera who comprised 13% of the manure community and were not significantly abundant in non-manured control soils. Of these five genera, Clostridium sensu stricto was the only genus which did not return to pre-manure relative abundance in soil by day 108. Our results show that enrichment responses after manure amendment could result from displacement of native soil bacteria by manure-borne bacteria during the application process or growth of native bacteria using manure-derived available nutrients.
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Affiliation(s)
- Elizabeth L Rieke
- Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, United States
| | - Michelle L Soupir
- Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, United States
| | - Thomas B Moorman
- National Laboratory for Agriculture and the Environment, United States Department of Agriculture-Agricultural Research Service, Ames, IA, United States
| | - Fan Yang
- Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, United States
| | - Adina C Howe
- Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, United States
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Sparo M, Delpech G, García Allende N. Impact on Public Health of the Spread of High-Level Resistance to Gentamicin and Vancomycin in Enterococci. Front Microbiol 2018; 9:3073. [PMID: 30619158 PMCID: PMC6305282 DOI: 10.3389/fmicb.2018.03073] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 11/28/2018] [Indexed: 12/18/2022] Open
Abstract
Antibiotic resistance has turned into a global public health issue. Enterococci are intrinsically resistant to many antimicrobials groups. These bacteria colonize dairy and meat products and integrate the autochthonous microbiota of mammal's gastrointestinal tract. Over the last decades, detection of vanA genotype in Enterococcus faecium from animals and from food of animal origin has been reported. Vancomycin-resistant E. faecium has become a prevalent nosocomial pathogen. Hospitalized patients are frequently treated with broad-spectrum antimicrobials and this leads to an increase in the presence of VanA or VanB vancomycin-resistant enterococci in patients' gastrointestinal tract and the risk of invasive infections. In humans, E. faecium is the main reservoir of VanA and VanB phenotypes. Acquisition of high-level aminoglycoside resistance is a significant therapeutic problem for patients with severe infections because it negates the synergistic effect between aminoglycosides and a cell-wall-active agent. The aac(6')-Ie-aph (2″)-Ia gene is widely spread in E. faecalis and has been detected in strains of human origin and in the food of animal origin. Enzyme AAC(6')-Ie-APH(2″)-Ia confers resistance to available aminoglycosides, except to streptomycin. Due to the fast dissemination of this genetic determinant, the impact of its horizontal transferability among enterococcal species from different origin has been considered. The extensive use of antibiotics in food-producing animals contributes to an increase in drug-resistant animal bacteria that can be transmitted to humans. Innovation is needed for the development of new antibacterial drugs and for the design of combination therapies with conventional antibiotics. Nowadays, semi-purified bacteriocins and probiotics are becoming an attractive alternative to the antibiotic in animal production. Therefore, a better understanding of a complex and relevant issue for Public Health such as high-level vancomycin and gentamicin resistance in enterococci and their impact is needed. Hence, it is necessary to consider the spread of vanA E. faecium and high-level gentamicin resistant E. faecalis strains of different origin in the environment, and also highlight the potential horizontal transferability of these resistance determinants to other bacteria.
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Affiliation(s)
- Mónica Sparo
- Clinical Department, Medicine School, National University of Central Buenos Aires, Tandil, Argentina
| | - Gaston Delpech
- Clinical Department, Medicine School, National University of Central Buenos Aires, Tandil, Argentina
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Hume ME, Donskey CJ. Effect of Vancomycin, Tylosin, and Chlortetracycline on Vancomycin-Resistant Enterococcus faecium Colonization of Broiler Chickens During Grow-Out. Foodborne Pathog Dis 2017; 14:231-237. [PMID: 28128649 DOI: 10.1089/fpd.2016.2217] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Broiler chickens may serve as reservoirs for human colonization by vancomycin-resistant Enterococcus (VRE). We examined the effects of vancomycin and two commonly used antimicrobial feed additives on VRE colonization in broiler chickens during grow-out. Chicks received unsupplemented feed or feed containing vancomycin, chlortetracycline, or tylosin from day of hatch to grow-out at 6 weeks. At 3 days of age, chicks received by crop gavage 107 colony-forming units (CFUs) of a human or poultry VRE isolate. Cecal contents were monitored weekly for VRE, short-chain fatty acids (SCFAs), and bacterial denaturing gradient gel electrophoresis (DGGE) profile methods. Vancomycin promoted persistent and high-level colonization with human- and poultry-derived VRE to grow-out in comparison with controls, while treatment with chlortetracycline and tylosin did not. Colonization by the poultry isolate in control, chlortetracycline, and tylosin groups persisted throughout the grow-out period with low concentrations present at 6 weeks, whereas the human isolate decreased to an undetectable level by week 6. Vancomycin resulted in significant reductions in cecal acetic acid and butyric acid in comparison with controls, but chlortetracycline and tylosin did not. DGGE profiles contained two main clusters with all vancomycin profiles in a smaller cluster and all other profiles in a larger cluster. These results demonstrate that vancomycin, but not chlortetracycline or tylosin, disrupted the indigenous microbiota and SCFA patterns of broiler chickens and promoted colonization by VRE.
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Affiliation(s)
- Michael E Hume
- 1 Food and Feed Safety Research Unit, Southern Plains Agricultural Research Center , Agricultural Research Service, U.S. Department of Agriculture, College Station, Texas
| | - Curtis J Donskey
- 2 Infectious Diseases Section, Louis Stokes Cleveland Veterans Affairs Medical Center , Cleveland, Ohio
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Oravcova V, Hadelova D, Literak I. Vancomycin-resistant Enterococcus faecium with vanA gene isolated for the first time from wildlife in Slovakia. Vet Microbiol 2016; 194:43-47. [DOI: 10.1016/j.vetmic.2015.11.027] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 11/18/2015] [Accepted: 11/19/2015] [Indexed: 11/15/2022]
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Givens CE, Kolpin DW, Borchardt MA, Duris JW, Moorman TB, Spencer SK. Detection of hepatitis E virus and other livestock-related pathogens in Iowa streams. Sci Total Environ 2016; 566-567:1042-1051. [PMID: 27318519 PMCID: PMC7111295 DOI: 10.1016/j.scitotenv.2016.05.123] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 05/17/2016] [Accepted: 05/17/2016] [Indexed: 04/14/2023]
Abstract
Manure application is a source of pathogens to the environment. Through overland runoff and tile drainage, zoonotic pathogens can contaminate surface water and streambed sediment and could affect both wildlife and human health. This study examined the environmental occurrence of gene markers for livestock-related bacterial, protozoan, and viral pathogens and antibiotic resistance in surface waters within the South Fork Iowa River basin before and after periods of swine manure application on agricultural land. Increased concentrations of indicator bacteria after manure application exceeding Iowa's state bacteria water quality standards suggest that swine manure contributes to diminished water quality and may pose a risk to human health. Additionally, the occurrence of HEV and numerous bacterial pathogen genes for Escherichia coli, Enterococcus spp., Salmonella sp., and Staphylococcus aureus in both manure samples and in corresponding surface water following periods of manure application suggests a potential role for swine in the spreading of zoonotic pathogens to the surrounding environment. During this study, several zoonotic pathogens were detected including Shiga-toxin producing E. coli, Campylobacter jejuni, pathogenic enterococci, and S. aureus; all of which can pose mild to serious health risks to swine, humans, and other wildlife. This research provides the foundational understanding required for future assessment of the risk to environmental health from livestock-related zoonotic pathogen exposures in this region. This information could also be important for maintaining swine herd biosecurity and protecting the health of wildlife near swine facilities.
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Affiliation(s)
- Carrie E Givens
- U.S. Geological Survey, 6520 Mercantile Way, Suite 5, Lansing, MI 48911, United States.
| | - Dana W Kolpin
- U.S. Geological Survey, 400 South Clinton Street, Iowa City, IA 52240, United States
| | - Mark A Borchardt
- USDA Agricultural Research Service, 2615 Yellowstone Drive, Marshfield, WI 54449, United States
| | - Joseph W Duris
- U.S. Geological Survey, 6520 Mercantile Way, Suite 5, Lansing, MI 48911, United States
| | - Thomas B Moorman
- USDA Agricultural Research Service, 2110 University Boulevard, Ames, IA 50011, United States
| | - Susan K Spencer
- USDA Agricultural Research Service, 2615 Yellowstone Drive, Marshfield, WI 54449, United States
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Haack SK, Duris JW, Kolpin DW, Focazio MJ, Meyer MT, Johnson HE, Oster RJ, Foreman WT. Contamination with bacterial zoonotic pathogen genes in U.S. streams influenced by varying types of animal agriculture. Sci Total Environ 2016; 563-564:340-350. [PMID: 27139306 DOI: 10.1016/j.scitotenv.2016.04.087] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 04/11/2016] [Accepted: 04/12/2016] [Indexed: 06/05/2023]
Abstract
Animal waste, stream water, and streambed sediment from 19 small (<32km(2)) watersheds in 12U.S. states having either no major animal agriculture (control, n=4), or predominantly beef (n=4), dairy (n=3), swine (n=5), or poultry (n=3) were tested for: 1) cholesterol, coprostanol, estrone, and fecal indicator bacteria (FIB) concentrations, and 2) shiga-toxin producing and enterotoxigenic Escherichia coli, Salmonella, Campylobacter, and pathogenic and vancomycin-resistant enterococci by polymerase chain reaction (PCR) on enrichments, and/or direct quantitative PCR. Pathogen genes were most frequently detected in dairy wastes, followed by beef, swine and poultry wastes in that order; there was only one detection of an animal-source-specific pathogen gene (stx1) in any water or sediment sample in any control watershed. Post-rainfall pathogen gene numbers in stream water were significantly correlated with FIB, cholesterol and coprostanol concentrations, and were most highly correlated in dairy watershed samples collected from 3 different states. Although collected across multiple states and ecoregions, animal-waste gene profiles were distinctive via discriminant analysis. Stream water gene profiles could also be discriminated by the watershed animal type. Although pathogen genes were not abundant in stream water or streambed samples, PCR on enrichments indicated that many genes were from viable organisms, including several (shiga-toxin producing or enterotoxigenic E. coli, Salmonella, vancomycin-resistant enterococci) that could potentially affect either human or animal health. Pathogen gene numbers and types in stream water samples were influenced most by animal type, by local factors such as whether animals had stream access, and by the amount of local rainfall, and not by studied watershed soil or physical characteristics. Our results indicated that stream water in small agricultural U.S. watersheds was susceptible to pathogen gene inputs under typical agricultural practices and environmental conditions. Pathogen gene profiles may offer the potential to address both source of, and risks associated with, fecal pollution.
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Affiliation(s)
- Sheridan K Haack
- U.S. Geological Survey, 6520 Mercantile Way, Suite 5, Lansing, MI 48911, United States.
| | - Joseph W Duris
- U.S. Geological Survey, 6520 Mercantile Way, Suite 5, Lansing, MI 48911, United States
| | - Dana W Kolpin
- U.S. Geological Survey, 400 South Clinton Street, Iowa City, IA 52240, United States
| | - Michael J Focazio
- U.S. Geological Survey, 12201 Sunrise Valley Drive, Reston, VA 20192, United States
| | - Michael T Meyer
- U.S. Geological Survey, 4821 Quail Crest Place, Lawrence, KS 66049, United States
| | - Heather E Johnson
- U.S. Geological Survey, 6520 Mercantile Way, Suite 5, Lansing, MI 48911, United States
| | - Ryan J Oster
- U.S. Geological Survey, 6520 Mercantile Way, Suite 5, Lansing, MI 48911, United States
| | - William T Foreman
- U.S. Geological Survey, P.O. Box 25585, Denver, CO 80225, United States
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Lanza VF, Tedim AP, Martínez JL, Baquero F, Coque TM. The Plasmidome of Firmicutes: Impact on the Emergence and the Spread of Resistance to Antimicrobials. Microbiol Spectr 2015; 3:PLAS-0039-2014. [PMID: 26104702 DOI: 10.1128/microbiolspec.PLAS-0039-2014] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The phylum Firmicutes is one of the most abundant groups of prokaryotes in the microbiota of humans and animals and includes genera of outstanding relevance in biomedicine, health care, and industry. Antimicrobial drug resistance is now considered a global health security challenge of the 21st century, and this heterogeneous group of microorganisms represents a significant part of this public health issue.The presence of the same resistant genes in unrelated bacterial genera indicates a complex history of genetic interactions. Plasmids have largely contributed to the spread of resistance genes among Staphylococcus, Enterococcus, and Streptococcus species, also influencing the selection and ecological variation of specific populations. However, this information is fragmented and often omits species outside these genera. To date, the antimicrobial resistance problem has been analyzed under a "single centric" perspective ("gene tracking" or "vehicle centric" in "single host-single pathogen" systems) that has greatly delayed the understanding of gene and plasmid dynamics and their role in the evolution of bacterial communities.This work analyzes the dynamics of antimicrobial resistance genes using gene exchange networks; the role of plasmids in the emergence, dissemination, and maintenance of genes encoding resistance to antimicrobials (antibiotics, heavy metals, and biocides); and their influence on the genomic diversity of the main Gram-positive opportunistic pathogens under the light of evolutionary ecology. A revision of the approaches to categorize plasmids in this group of microorganisms is given using the 1,326 fully sequenced plasmids of Gram-positive bacteria available in the GenBank database at the time the article was written.
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Haack SK, Duris JW, Kolpin DW, Fogarty LR, Johnson HE, Gibson KE, Focazio M, Schwab KJ, Hubbard LE, Foreman WT. Genes Indicative of Zoonotic and Swine Pathogens Are Persistent in Stream Water and Sediment following a Swine Manure Spill. Appl Environ Microbiol 2015; 81:3430-41. [PMID: 25769829 DOI: 10.1128/AEM.04195-14] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 03/03/2015] [Indexed: 01/31/2023] Open
Abstract
Manure spills into streams are relatively frequent, but no studies have characterized stream contamination with zoonotic and veterinary pathogens, or fecal chemicals, following a spill. We tested stream water and sediment over 25 days and downstream for 7.6 km for the following: fecal indicator bacteria (FIB), the fecal indicator chemicals cholesterol and coprostanol, 20 genes for zoonotic and swine-specific bacterial pathogens by presence/absence PCR for viable cells, one swine-specific Escherichia coli toxin gene (STII gene) by quantitative PCR (qPCR), and nine human and animal viruses by qPCR or reverse transcription-qPCR. Twelve days postspill, and 4.2 km downstream, water concentrations of FIB, cholesterol, and coprostanol were 1 to 2 orders of magnitude greater than those detected before, or above, the spill, and genes indicating viable zoonotic or swine-infectious Escherichia coli were detected in water or sediment. STII gene levels increased from undetectable before or above the spill to 10(5) copies/100 ml of water 12 days postspill. Thirteen of 14 water (8/9 sediment) samples had viable STII-carrying cells postspill. Eighteen days postspill, porcine adenovirus and teschovirus were detected 5.6 km downstream. FIB concentrations (per gram [wet weight]) in sediment were greater than in water, and sediment was a continuous reservoir of genes and chemicals postspill. Constituent concentrations were much lower, and detections less frequent, in a runoff event (200 days postspill) following manure application, although the swine-associated STII and stx2e genes were detected. Manure spills are an underappreciated pathway for livestock-derived contaminants to enter streams, with persistent environmental outcomes and the potential for human and veterinary health consequences.
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Abstract
OBJECTIVES Among European countries, Germany has one of the highest proportions of vancomycin-resistant Enterococcus faecium bloodstream infections. The aim of this study was to investigate the development of vancomycin-resistant enterococci (VRE) in German hospitals and to consider the regional distribution of VRE in Germany. METHODS Data from three components of the German national nosocomial surveillance system (KISS) from the period 2007-12 were used for analysis: ICU-KISS data on nosocomial primary bloodstream infections and urinary tract infections from intensive care units (ICUs); OP-KISS data on surgical site infections from surgical departments; and Pathogen-KISS data concentrating on VRE cases (infections and colonizations) in ICUs. Trends over time were calculated and a map according to German federal states was prepared. RESULTS Data from up to 645 ICUs and 681 surgical departments for 2 year periods from 2007 to 2012 were analysed. The proportion of VRE increased significantly for surgical site infections (526%; P < 0.01) and bloodstream infections (265%; P < 0.01) and non-significantly for urinary tract infections (278%; P = 0.07). A large subgroup of ICUs also reported VRE cases in the same period, with a significant increase of 282%. The mapping of federal states showed large variation in VRE proportions and incidence rates in a belt of states with significantly higher VRE proportions from west (North Rhine-Westphalia) to east (Saxony). CONCLUSIONS The high overall VRE proportion in Germany is mainly due to the situation in four states. There is an urgent need to analyse the epidemiology of VRE in detail to develop appropriate infection control strategies.
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Affiliation(s)
- Petra Gastmeier
- Institute of Hygiene and Environmental Medicine, Charité-Universitätsmedizin Berlin, Hindenburgdamm 27, 12203 Berlin, Germany German National Reference Centre for Surveillance of Nosocomial Infections (NRZ), Hindenburgdamm 27, 12203 Berlin, Germany
| | - Christin Schröder
- Institute of Hygiene and Environmental Medicine, Charité-Universitätsmedizin Berlin, Hindenburgdamm 27, 12203 Berlin, Germany German National Reference Centre for Surveillance of Nosocomial Infections (NRZ), Hindenburgdamm 27, 12203 Berlin, Germany
| | - Michael Behnke
- Institute of Hygiene and Environmental Medicine, Charité-Universitätsmedizin Berlin, Hindenburgdamm 27, 12203 Berlin, Germany German National Reference Centre for Surveillance of Nosocomial Infections (NRZ), Hindenburgdamm 27, 12203 Berlin, Germany
| | - Elisabeth Meyer
- Institute of Hygiene and Environmental Medicine, Charité-Universitätsmedizin Berlin, Hindenburgdamm 27, 12203 Berlin, Germany German National Reference Centre for Surveillance of Nosocomial Infections (NRZ), Hindenburgdamm 27, 12203 Berlin, Germany
| | - Christine Geffers
- Institute of Hygiene and Environmental Medicine, Charité-Universitätsmedizin Berlin, Hindenburgdamm 27, 12203 Berlin, Germany German National Reference Centre for Surveillance of Nosocomial Infections (NRZ), Hindenburgdamm 27, 12203 Berlin, Germany
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