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A C, N C, A DS, A P, E Y, F G, M C. Validation of a rapid molecular detection test for gram-negative multidrug-resistant bacteria in rectal swabs upon admission of patients to the intensive care unit. Diagn Microbiol Infect Dis 2024; 109:116250. [PMID: 38479092 DOI: 10.1016/j.diagmicrobio.2024.116250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 03/05/2024] [Accepted: 03/07/2024] [Indexed: 04/30/2024]
Abstract
In ICU settings, screening patients upon admission for potential multiresistant bacteria (BMR) carriers is crucial. Traditionally, clinical decisions relied on delayed culture results, but a rapid PCR molecular test called RealCycler-Rezero-U/G (Progenie-molecular©), emerged as an alternative. This study aimed to validate its effectiveness in detecting gram-negative BMR in rectal swabs at ICU admission. Over 24 months, an observational study was conducted on 1,234 admitted patients, with 217 meeting isolation criteria and undergoing both PCR and culture tests. Results showed a 17.5 % positive rate for screening. The PCR test exhibited impressive accuracy at 98.6 % and a strong negative predictive value of 99.4 %. The area under the ROC curve (AUC) was 0.98, indicating high reliability. Notably, PCR results were available 44.5 h earlier than culture. In conclusion, PCR-based molecular testing for gram-negative BMR offers excellent diagnostic performance and a valuable negative predictive value, making it a suitable screening tool for ICU admissions.
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Affiliation(s)
- Carranza A
- Intensive Care Department, Center Hospital Universitario Clínico San Cecilio, Granada, Spain
| | - Chueca N
- Microbiology Department, Center Hospital Universitario Clínico San Cecilio, Granada, Spain; Instituto de Biomedicina de Granada. Ibs.GRANADA, Center Hospital Universitario Clínico San Cecilio, Granada, Spain; Ciber de Enfermedades Infecciosas, CIBERINFEC, Center Hospital Universitario Clínico San Cecilio, Granada, Spain
| | - De Salazar A
- Microbiology Department, Center Hospital Universitario Clínico San Cecilio, Granada, Spain; Instituto de Biomedicina de Granada. Ibs.GRANADA, Center Hospital Universitario Clínico San Cecilio, Granada, Spain; Ciber de Enfermedades Infecciosas, CIBERINFEC, Center Hospital Universitario Clínico San Cecilio, Granada, Spain
| | - Peña A
- Microbiology Department, Center Hospital Universitario Clínico San Cecilio, Granada, Spain
| | - Yuste E
- Intensive Care Department, Center Hospital Universitario Clínico San Cecilio, Granada, Spain; Instituto de Biomedicina de Granada. Ibs.GRANADA, Center Hospital Universitario Clínico San Cecilio, Granada, Spain
| | - García F
- Microbiology Department, Center Hospital Universitario Clínico San Cecilio, Granada, Spain; Instituto de Biomedicina de Granada. Ibs.GRANADA, Center Hospital Universitario Clínico San Cecilio, Granada, Spain; Ciber de Enfermedades Infecciosas, CIBERINFEC, Center Hospital Universitario Clínico San Cecilio, Granada, Spain.
| | - Colmenero M
- Intensive Care Department, Center Hospital Universitario Clínico San Cecilio, Granada, Spain; Instituto de Biomedicina de Granada. Ibs.GRANADA, Center Hospital Universitario Clínico San Cecilio, Granada, Spain
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2
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Keresztény T, Libisch B, Orbe SC, Nagy T, Kerényi Z, Kocsis R, Posta K, Papp PP, Olasz F. Isolation and Characterization of Lactic Acid Bacteria With Probiotic Attributes From Different Parts of the Gastrointestinal Tract of Free-living Wild Boars in Hungary. Probiotics Antimicrob Proteins 2023:10.1007/s12602-023-10113-2. [PMID: 37353593 DOI: 10.1007/s12602-023-10113-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2023] [Indexed: 06/25/2023]
Abstract
Lactic acid bacteria (LAB) in the microbiota play an important role in human and animal health and, when used as probiotics, can contribute to an increased growth performance in livestock management. Animals living in their native habitat can serve as natural sources of microorganisms, so isolation of LAB strains from wild boars could provide the opportunity to develop effective probiotics to improve production in swine industry. In this study, the probiotic potential of 56 LAB isolates, originated from the ileum, colon, caecum and faeces of 5 wild boars, were assessed in vitro in details. Their taxonomic identity at species level and their antibacterial activity against four representative strains of potentially pathogenic bacteria were determined. The ability to tolerate low pH and bile salt, antibiotic susceptibility, bile salt hydrolase activity and lack of hemolysis were tested. Draft genome sequences of ten Limosilactobacillus mucosae and three Leuconostoc suionicum strains were determined. Bioinformatic analysis excluded the presence of any known acquired antibiotic resistance genes. Three genes, encoding mesentericin B105 and two different bacteriocin-IIc class proteins, as well as two genes with possible involvement in mesentericin secretion (mesE) and transport (mesD) were identified in two L. suionicum strains. Lam29 protein, a component of an ABC transporter with proved function as mucin- and epithelial cell-adhesion factor, and a bile salt hydrolase gene were found in all ten L. mucosae genomes. Comprehensive reconsideration of all data helps to select candidate strains to assess their probiotic potential further in animal experiments.
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Affiliation(s)
- Tibor Keresztény
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences (MATE), 2100, Gödöllő, Hungary
- Doctoral School of Biological Sciences, Hungarian University of Agriculture and Life Sciences, 2100, Gödöllő, Hungary
| | - Balázs Libisch
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences (MATE), 2100, Gödöllő, Hungary
| | - Stephanya Corral Orbe
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences (MATE), 2100, Gödöllő, Hungary
- Doctoral School of Biological Sciences, Hungarian University of Agriculture and Life Sciences, 2100, Gödöllő, Hungary
| | - Tibor Nagy
- Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life, Sciences, 2100, Gödöllő, Hungary
| | - Zoltán Kerényi
- Hungarian Dairy Research Institute Ltd, 9200, Mosonmagyaróvár, Hungary
| | - Róbert Kocsis
- Hungarian Dairy Research Institute Ltd, 9200, Mosonmagyaróvár, Hungary
| | - Katalin Posta
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences (MATE), 2100, Gödöllő, Hungary
| | - Péter P Papp
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences (MATE), 2100, Gödöllő, Hungary
| | - Ferenc Olasz
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences (MATE), 2100, Gödöllő, Hungary.
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Kowalewicz C, Timmermans M, Fretin D, Wattiau P, Boland C. An in-house 45-plex array for the detection of antimicrobial resistance genes in Gram-positive bacteria. Microbiologyopen 2022; 12:e1341. [PMID: 36825880 PMCID: PMC9791161 DOI: 10.1002/mbo3.1341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 12/02/2022] [Indexed: 12/27/2022] Open
Abstract
Identifying antimicrobial resistance (AMR) genes and determining their occurrence in Gram-positive bacteria provide useful data to understand how resistance can be acquired and maintained in these bacteria. We describe an in-house bead array targeting AMR genes of Gram-positive bacteria and allowing their rapid detection all at once at a reduced cost. A total of 41 AMR probes were designed to target genes frequently associated with resistance to tetracycline, macrolides, lincosamides, streptogramins, pleuromutilins, phenicols, glycopeptides, aminoglycosides, diaminopyrimidines, oxazolidinones and particularly shared among Enterococcus and Staphylococcus spp. A collection of 124 enterococci and 62 staphylococci isolated from healthy livestock animals through the official Belgian AMR monitoring (2018-2020) was studied with this array from which a subsample was further investigated by whole-genome sequencing. The array detected AMR genes associated with phenotypic resistance for 93.0% and 89.2% of the individual resistant phenotypes in enterococci and staphylococci, respectively. Although linezolid is not used in veterinary medicine, linezolid-resistant isolates were detected. These were characterized by the presence of optrA and poxtA, providing cross-resistance to other antibiotics. Rarer, vancomycin resistance was conferred by the vanA or by the vanL cluster. Numerous resistance genes circulating among Enterococcus and Staphylococcus spp. were detected by this array allowing rapid screening of a large strain collection at an affordable cost. Our data stress the importance of interpreting AMR with caution and the complementarity of both phenotyping and genotyping methods. This array is now available to assess other One-Health AMR reservoirs.
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Affiliation(s)
| | | | - David Fretin
- Veterinary Bacteriology, SciensanoIxellesBelgium
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Ji X, Pan X. Intra-/extra-cellular antibiotic resistance responses to sewage sludge composting and salinization of long-term compost applied soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:156263. [PMID: 35644396 DOI: 10.1016/j.scitotenv.2022.156263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/22/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
Municipal sewage sludge, a reservoir of antibiotic resistance genes (ARGs), is usually composted as fertilizer for agricultural application especially in arid and semi-arid areas. The evolution patterns of intracellular ARGs (iARGs) and extracellular ARGs (eARGs) during composting and their responses to soil salinization after long-term compost application kept unclear previously, which were systematically studied in the current study. The variation and dissemination risk of eARGs and iARGs with the salinization of farmland soils was also evaluated. Extra/intra-cellular ARGs relative abundance varied drastically through composting process. Generally, the relative abundance of the cell-free eARGs (f-eARGs) and the cell-adsorbed eARGs (a-eARGs) were 4.62 and 3.54 folds (median) higher than that of iARGs, respectively, during the entire composting process, which held true even before the sludge composting (false discovery rate, FDR p < 0.05). There was no significant difference in relative abundance between f-eARGs and a-eARGs. The relative abundance of eARGs gradually decreased with composting time but was relatively higher than iARGs. It was worth noting that iARGs rebounded in the maturation phase. However, an over ten-year application of the eARG-rich compost led to much more severe contamination of iARGs than eARGs in soil. Soil salinization caused remarkable rise of eARGs by 943.34-fold (FDR p < 0.05). The variation of ARGs during composting and soil salinization was closely related to the change of microbial community structure. In compost, the bacterial communities mainly interacting with ARGs were the Firmicutes (54 unique and 35 shared core genera); and the bacterial communities playing major roles in ARGs during soil salinization were Proteobacteria (116 unique and 53 shared core genera) and Actinobacteria (52 unique and 27 shared core genera). These findings are important for assessing the transmission risk of ARGs in compost application to farmland in arid and semi-arid areas.
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Affiliation(s)
- Xiaonan Ji
- Xinjiang Key Laboratory of Environmental Pollution and Bioremediation, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiangliang Pan
- Xinjiang Key Laboratory of Environmental Pollution and Bioremediation, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China; Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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5
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Aljeldah MM. Antimicrobial Resistance and Its Spread Is a Global Threat. Antibiotics (Basel) 2022; 11:antibiotics11081082. [PMID: 36009948 PMCID: PMC9405321 DOI: 10.3390/antibiotics11081082] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/20/2022] [Accepted: 07/27/2022] [Indexed: 02/07/2023] Open
Abstract
Antimicrobial resistance (AMR) is a challenge to human wellbeing the world over and is one of the more serious public health concerns. AMR has the potential to emerge as a serious healthcare threat if left unchecked, and could put into motion another pandemic. This establishes the need for the establishment of global health solutions around AMR, taking into account microdata from different parts of the world. The positive influences in this regard could be establishing conducive social norms, charting individual and group behavior practices that favor global human health, and lastly, increasing collective awareness around the need for such action. Apart from being an emerging threat in the clinical space, AMR also increases treatment complexity, posing a real challenge to the existing guidelines around the management of antibiotic resistance. The attribute of resistance development has been linked to many genetic elements, some of which have complex transmission pathways between microbes. Beyond this, new mechanisms underlying the development of AMR are being discovered, making this field an important aspect of medical microbiology. Apart from the genetic aspects of AMR, other practices, including misdiagnosis, exposure to broad-spectrum antibiotics, and lack of rapid diagnosis, add to the creation of resistance. However, upgrades and innovations in DNA sequencing technologies with bioinformatics have revolutionized the diagnostic industry, aiding the real-time detection of causes of AMR and its elements, which are important to delineating control and prevention approaches to fight the threat.
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Affiliation(s)
- Mohammed M Aljeldah
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hafr Al Batin, Hafar al-Batin 31991, Saudi Arabia
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6
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Deekshit VK, Srikumar S. 'To be, or not to be' - the dilemma of 'silent' antimicrobial resistance genes in bacteria. J Appl Microbiol 2022; 133:2902-2914. [PMID: 35882476 DOI: 10.1111/jam.15738] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 07/20/2022] [Accepted: 07/22/2022] [Indexed: 11/26/2022]
Abstract
Antimicrobial resistance is a serious threat to public health that dramatically undermines our ability to treat bacterial infections. Microorganisms exhibit resistance to different drug classes by acquiring resistance determinants through multiple mechanisms including horizontal gene transfer. The presence of drug resistance genotypes is mostly associated with corresponding phenotypic resistance against the particular antibiotic. However, bacterial communities harboring silent antimicrobial resistance genes - genes whose presence is not associated with a corresponding resistant phenotype, do exist. Under suitable conditions, the expression pattern of such genes often revert and regain resistance, and could potentially lead to therapeutic failure. We often miss the presence of silent genes, since the current experimental paradigms are focused on resistant strains. Therefore, the knowledge on the prevalence, importance, and mechanism of silent antibiotic resistance genes in bacterial pathogens is very limited. Silent genes, therefore, provide an additional level of complexity in the war against drug-resistant bacteria, reminding us that not only phenotypically resistant strains but also susceptible strains should be carefully investigated. In this review, we discuss the presence of silent antimicrobial resistance genes in bacteria, their relevance, and their importance in public health.
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Affiliation(s)
- Vijaya Kumar Deekshit
- Nitte (Deemed to be University), Nitte University Center for Science Education and Research, Division of Infectious Diseases, Paneer Campus, Deralakatte, Mangaluru - 575018, Karnataka, India
| | - Shabarinath Srikumar
- Department of Food Science, College of Agriculture and Veterinary Medicine, UAE University, Al Ain, UAE
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7
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Phenotypic Adaptation to Antiseptics and Effects on Biofilm Formation Capacity and Antibiotic Resistance in Clinical Isolates of Early Colonizers in Dental Plaque. Antibiotics (Basel) 2022; 11:antibiotics11050688. [PMID: 35625332 PMCID: PMC9137571 DOI: 10.3390/antibiotics11050688] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 05/16/2022] [Accepted: 05/18/2022] [Indexed: 12/19/2022] Open
Abstract
Despite the wide-spread use of antiseptics in dental practice and oral care products, there is little public awareness of potential risks associated with antiseptic resistance and potentially concomitant cross-resistance. Therefore, the aim of this study was to investigate potential phenotypic adaptation in 177 clinical isolates of early colonizers of dental plaque (Streptococcus, Actinomyces, Rothia and Veillonella spp.) upon repeated exposure to subinhibitory concentrations of chlorhexidine digluconate (CHX) or cetylpyridinium chloride (CPC) over 10 passages using a modified microdilution method. Stability of phenotypic adaptation was re-evaluated after culture in antiseptic-free nutrient broth for 24 or 72 h. Strains showing 8-fold minimal inhibitory concentration (MIC)-increase were further examined regarding their biofilm formation capacity, phenotypic antibiotic resistance and presence of antibiotic resistance genes (ARGs). Eight-fold MIC-increases to CHX were detected in four Streptococcus isolates. These strains mostly exhibited significantly increased biofilm formation capacity compared to their respective wild-type strains. Phenotypic antibiotic resistance was detected to tetracycline and erythromycin, consistent with the detected ARGs. In conclusion, this study shows that clinical isolates of early colonizers of dental plaque can phenotypically adapt toward antiseptics such as CHX upon repeated exposure. The underlying mechanisms at genomic and transcriptomic levels need to be investigated in future studies.
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Gukowsky JC, He L. Development of a portable SERS method for testing the antibiotic sensitivity of foodborne bacteria. METHODS IN MICROBIOLOGY 2022; 198:106496. [DOI: 10.1016/j.mimet.2022.106496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/24/2022] [Accepted: 05/24/2022] [Indexed: 10/18/2022]
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9
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Staphylococcus aureus Causing Skin and Soft Tissue Infections in Companion Animals: Antimicrobial Resistance Profiles and Clonal Lineages. Antibiotics (Basel) 2022; 11:antibiotics11050599. [PMID: 35625243 PMCID: PMC9137735 DOI: 10.3390/antibiotics11050599] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/24/2022] [Accepted: 04/26/2022] [Indexed: 11/17/2022] Open
Abstract
Staphylococcus aureus is a relevant agent of skin and soft tissue infections (SSTIs) in animals. Fifty-five S. aureus comprising all SSTI-related isolates in companion animals, collected between 1999 and 2018 (Lab 1) or 2017 and 2018 (Lab 2), were characterized regarding susceptibility to antibiotics and heavy metals and carriage of antimicrobial resistance determinants. Clonal lineages were established by PFGE, MLST and agr typing. Over half of the isolates (56.4%, 31/55) were methicillin-resistant S. aureus (MRSA), and 14.5% showed a multidrug resistance (MDR) phenotype. Resistance was most frequently observed for beta-lactams (81.8%, related to blaZ and/or mecA), fluoroquinolones (56.4%) and macrolides/lincosamides (14.5%, related to erm(A) or erm(C)). The distributions of heavy-metal MICs allowed the detection of non-wild-type populations associated with several resistance genes. The collection showed genetic diversity, with prevalence of clonal lineage ST22-agrI (45.5%, 25/55), comprising only MRSA isolates, and several less frequently detected clones, including ST5-agrII (14.6%, 8/55), ST398-agrI (9.1%, 5/55) and ST72-agrI (7.3%, 4/55). This work highlights the high frequency of SSTI-related MRSA strains that reflect the clonal lineages circulating both in companion animals and humans in Portugal, reinforcing the need for a One Health approach when studying staphylococci causing infections in companion animals.
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Algarni S, Ricke SC, Foley SL, Han J. The Dynamics of the Antimicrobial Resistance Mobilome of Salmonella enterica and Related Enteric Bacteria. Front Microbiol 2022; 13:859854. [PMID: 35432284 PMCID: PMC9008345 DOI: 10.3389/fmicb.2022.859854] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/07/2022] [Indexed: 12/31/2022] Open
Abstract
The foodborne pathogen Salmonella enterica is considered a global public health risk. Salmonella enterica isolates can develop resistance to several antimicrobial drugs due to the rapid spread of antimicrobial resistance (AMR) genes, thus increasing the impact on hospitalization and treatment costs, as well as the healthcare system. Mobile genetic elements (MGEs) play key roles in the dissemination of AMR genes in S. enterica isolates. Multiple phenotypic and molecular techniques have been utilized to better understand the biology and epidemiology of plasmids including DNA sequence analyses, whole genome sequencing (WGS), incompatibility typing, and conjugation studies of plasmids from S. enterica and related species. Focusing on the dynamics of AMR genes is critical for identification and verification of emerging multidrug resistance. The aim of this review is to highlight the updated knowledge of AMR genes in the mobilome of Salmonella and related enteric bacteria. The mobilome is a term defined as all MGEs, including plasmids, transposons, insertion sequences (ISs), gene cassettes, integrons, and resistance islands, that contribute to the potential spread of genes in an organism, including S. enterica isolates and related species, which are the focus of this review.
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Affiliation(s)
- Suad Algarni
- Division of Microbiology, FDA National Center for Toxicological Research, Jefferson, AR, United States
- Cellular and Molecular Biology Graduate Program, University of Arkansas, Fayetteville, AR, United States
| | - Steven C. Ricke
- Meat Science and Animal Biologics Discovery Program, Department of Animal and Dairy Sciences, University of Wisconsin, Madison, WI, United States
| | - Steven L. Foley
- Division of Microbiology, FDA National Center for Toxicological Research, Jefferson, AR, United States
- Cellular and Molecular Biology Graduate Program, University of Arkansas, Fayetteville, AR, United States
| | - Jing Han
- Division of Microbiology, FDA National Center for Toxicological Research, Jefferson, AR, United States
- *Correspondence: Jing Han,
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11
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Microbial Community Structure and Bacterial Lineages Associated with Sulfonamides Resistance in Anthropogenic Impacted Larut River. WATER 2022. [DOI: 10.3390/w14071018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Anthropogenic activities often contribute to antibiotic resistance in aquatic environments. Larut River Malaysia is polluted with both organic and inorganic pollutants from domestic and industrial wastewater that are probably treated inadequately. The river is characterized by high biochemical oxygen demand, chemical oxygen demand, total suspended solids, ammonia, and heavy metals. In our previous study, sulfonamides (SAs) and sulfonamide resistance genes (sul) were detected in the Larut River. Hence, in this study, we further examined the microbial community structure, diversity of sulfonamide-resistant bacteria (SARB), and their resistance genes. The study also aimed at identifying cultivable bacteria potential carriers of sul genes in the aquatic environment. Proteobacteria (22.4–66.0%), Firmicutes (0.8–41.6%), Bacteroidetes (2.0–29.4%), and Actinobacteria (5.5–27.9%) were the most dominant phyla in both the effluents and river waters. SARB isolated consisted only 4.7% of the total genera identified, with SAR Klebsiella as the most dominant (38.0–61.3%) followed by SAR Escherichia (0–22.2%) and Acinetobacter (3.2–16.0%). The majority of the SAR Klebsiella isolated from the effluents and middle downstream were positive for sul genes. Sul genes-negative SAR Escherichia and Acinetobacter were low (<20%). Canonical-correlation analysis (CCA) showed that SAs residues and inorganic nutrients exerted significant impacts on microbial community and total sul genes. Network analysis identified 11 SARB as potential sul genes bacterial carriers. These findings indicated that anthropogenic activities exerted impacts on the microbial community structure and SAs resistance in the Larut River.
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12
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Gukowsky JC, Yang T, He L. Assessment of three SERS approaches for studying E. Coli O157:H7 susceptibility to ampicillin. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 264:120239. [PMID: 34358786 DOI: 10.1016/j.saa.2021.120239] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 07/14/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
Antibiotic resistant bacteria pose an increasing threat to global public health, and it is essential that effective detection methods for identifying these organisms. This study assesses the ability of three different analytical approaches that were developed using surface-enhanced Raman spectroscopy (SERS) to differentiate between antibiotic sensitive and resistant bacteria based on their responses to ampicillin exposure, using Escherichia coli O157:H7 as a model bacterium. The approaches tested in this study included a conventional SERS approach of mixing a droplet of bacterial culture with gold nanoparticles, extracellular matrix analysis, and in situ mapping of bacterial cells on a filter membrane. All three of the SERS techniques were able to differentiate between the sensitive and resistant bacterial strains based on peak intensity changes associated with compounds released by the bacteria in response to antibiotic exposure, with extracellular matrix analysis and filter mapping both observed to be more effective than the conventional approach. However, there were significant differences between the spectra obtained from the different techniques and the potential advantages and disadvantages of each approach should be considered when used in the future. This study shows that SERS can be an effective technique for rapid and efficient assessment of ampicillin sensitivity in E. coli, and more work should be done to explore these analytical approaches with other types of bacterial samples.
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Affiliation(s)
- Joshua C Gukowsky
- Department of Food Science, University of Massachusetts Amherst. 240 Chenoweth Laboratory, 102 Holdsworth Way, Amherst, MA 01003, USA
| | - Tianxi Yang
- Department of Food Science, University of Massachusetts Amherst. 240 Chenoweth Laboratory, 102 Holdsworth Way, Amherst, MA 01003, USA
| | - Lili He
- Department of Food Science, University of Massachusetts Amherst. 240 Chenoweth Laboratory, 102 Holdsworth Way, Amherst, MA 01003, USA.
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13
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Zhang C, Sun L, Wang D, Li Y, Zhang L, Wang L, Peng J. Advances in antimicrobial resistance testing. Adv Clin Chem 2022; 111:1-68. [DOI: 10.1016/bs.acc.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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14
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Wang C, Zhu W, Strong PJ, Zhu F, Han X, Hong C, Wang W, Yao Y. Disentangling the Effects of Physicochemical, Genetic, and Microbial Properties on Phase-Driven Resistome Dynamics during Multiple Manure Composting Processes. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:14732-14745. [PMID: 34689552 DOI: 10.1021/acs.est.1c03933] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Composting alters manure-derived antibiotic resistance genes (ARGs) to a certain extent, which is largely dependent upon the composting phase, manure type, microbial phylogeny, and physicochemical properties. However, little is known about how these determinants influence the fate and dynamics of ARGs as well as the mechanisms underlying the ecological process of ARGs during composting. Here, we investigated the temporal patterns of ARGs and their correlations with a series of physicochemical, genetic, and microbial properties during pilot-scale composting of chicken, maggot, bovine, and swine manure. We detected 237 ARGs, 71 of which were co-occurring across all four composting processes and accounted for >80% of the sum of resistome abundance. In support of this ARG co-occurrence, variance partition analyses demonstrated that the manure type explained less resistome variations (5.6%) than the composting phase (21.6%). During the phase-driven resistome dynamics, ARGs showed divergent variations in abundance, and certain beta-lactams and multidrug ARGs were consistently enriched across multiple manure composting processes. Correlation analyses all led to the conclusion that the divergent ARG variations during composting were attributable to the unequal effects of physicochemical properties, mobile elements, and succession of indigenous microbiota, whereas antibiotic residues' effects were marginal. Ultimately, this study determines the relative importance of various key determinants in the phase-driven divergence of ARGs during multiple manure composting processes and demonstrates a clear need to evaluate risks posed by enriched ARGs toward their receiving environments.
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Affiliation(s)
- Cheng Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Weijing Zhu
- Institute of Environmental Resources and Soil Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - P J Strong
- School of Biology and Environmental Science, Centre for Agriculture and the Bioeconomy, Queensland University of Technology, GPO Box 2432, 2 George St, Brisbane, QLD 4001, Australia
| | - Fengxiang Zhu
- Institute of Environmental Resources and Soil Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xingguo Han
- Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Universitätstrasse 16, 8092 Zurich, Switzerland
| | - Chunlai Hong
- Institute of Environmental Resources and Soil Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Weiping Wang
- Institute of Environmental Resources and Soil Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Yanlai Yao
- Institute of Environmental Resources and Soil Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
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15
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Nogueira T, Botelho A. Metagenomics and Other Omics Approaches to Bacterial Communities and Antimicrobial Resistance Assessment in Aquacultures. Antibiotics (Basel) 2021; 10:787. [PMID: 34203511 PMCID: PMC8300701 DOI: 10.3390/antibiotics10070787] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/20/2021] [Accepted: 06/22/2021] [Indexed: 12/21/2022] Open
Abstract
The shortage of wild fishery resources and the rising demand for human nutrition has driven a great expansion in aquaculture during the last decades in terms of production and economic value. As such, sustainable aquaculture production is one of the main priorities of the European Union's 2030 agenda. However, the intensification of seafood farming has resulted in higher risks of disease outbreaks and in the increased use of antimicrobials to control them. The selective pressure exerted by these drugs provides the ideal conditions for the emergence of antimicrobial resistance hotspots in aquaculture facilities. Omics technology is an umbrella term for modern technologies such as genomics, metagenomics, transcriptomics, proteomics, culturomics, and metabolomics. These techniques have received increasing recognition because of their potential to unravel novel mechanisms in biological science. Metagenomics allows the study of genomes in microbial communities contained within a certain environment. The potential uses of metagenomics in aquaculture environments include the study of microbial diversity, microbial functions, and antibiotic resistance genes. A snapshot of these high throughput technologies applied to microbial diversity and antimicrobial resistance studies in aquacultures will be presented in this review.
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Affiliation(s)
- Teresa Nogueira
- Laboratory of Bacteriology and Mycology, INIAV-National Institute for Agrarian and Veterinary Research, 2780-157 Oeiras, Portugal;
- cE3c-Centre for Ecology, Evolution and Environmental Changes, Evolutionary Ecology of Microorganisms Group, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
| | - Ana Botelho
- Laboratory of Bacteriology and Mycology, INIAV-National Institute for Agrarian and Veterinary Research, 2780-157 Oeiras, Portugal;
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16
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Falasconi I, Fontana A, Patrone V, Rebecchi A, Duserm Garrido G, Principato L, Callegari ML, Spigno G, Morelli L. Genome-Assisted Characterization of Lactobacillus fermentum, Weissella cibaria, and Weissella confusa Strains Isolated from Sorghum as Starters for Sourdough Fermentation. Microorganisms 2020; 8:E1388. [PMID: 32927810 PMCID: PMC7565839 DOI: 10.3390/microorganisms8091388] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/08/2020] [Accepted: 09/09/2020] [Indexed: 12/13/2022] Open
Abstract
Sourdough fermentation of bakery products is a well-established and widespread technique to confer an added value to the resulting food. In recent decades, gluten-free raw materials have gained more attention due to the diffusion of food disorders such as coeliac disease, but, at the same time, they present difficult manipulation and scarce technological properties because of the absence of gluten. For this reason, the present work was aimed at selecting starter cultures for sourdough application that are isolated from fermentation of sorghum flour. Three isolates of Lactobacillus fermentum, Weissella cibaria, and Weissella confusa were selected for the following properties: exopolysaccharide synthesis, acidification, CO2 production, and amylase activity. The investigated phenotypic characteristics were confirmed by genomic analyses, which also highlighted other potentially beneficial features for use in bakery products employment. These strains, together with bakery yeast, were used for bread preparation using sorghum and wheat flour and after 24 h of fermentation the resulting dough was analyzed to assess the improvement of its characteristics. The presence of lactic acid bacteria (LAB) had a great impact on the final dough, and the best preparation, from a rheological point of view, resulted in one made of sorghum and wheat flour with added LAB and bakery yeast, whose resulting characteristics were similar to all wheat flour doughs. The results of this study suggest a potential application of the selected starters in sorghum composite bread and should be validated with data from large-scale pilot tests conducted in industrial bakeries.
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Affiliation(s)
- Irene Falasconi
- Department for Sustainable Food Process (DiSTAS), Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (I.F.); (A.F.); (G.D.G.); (L.P.); (G.S.); (L.M.)
| | - Alessandra Fontana
- Department for Sustainable Food Process (DiSTAS), Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (I.F.); (A.F.); (G.D.G.); (L.P.); (G.S.); (L.M.)
| | - Vania Patrone
- Department for Sustainable Food Process (DiSTAS), Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (I.F.); (A.F.); (G.D.G.); (L.P.); (G.S.); (L.M.)
| | - Annalisa Rebecchi
- Biotechnological Research Centre, Università Cattolica del Sacro Cuore, 26100 Cremona, Italy; (A.R.); (M.L.C.)
| | - Guillermo Duserm Garrido
- Department for Sustainable Food Process (DiSTAS), Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (I.F.); (A.F.); (G.D.G.); (L.P.); (G.S.); (L.M.)
| | - Laura Principato
- Department for Sustainable Food Process (DiSTAS), Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (I.F.); (A.F.); (G.D.G.); (L.P.); (G.S.); (L.M.)
| | - Maria Luisa Callegari
- Biotechnological Research Centre, Università Cattolica del Sacro Cuore, 26100 Cremona, Italy; (A.R.); (M.L.C.)
| | - Giorgia Spigno
- Department for Sustainable Food Process (DiSTAS), Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (I.F.); (A.F.); (G.D.G.); (L.P.); (G.S.); (L.M.)
| | - Lorenzo Morelli
- Department for Sustainable Food Process (DiSTAS), Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (I.F.); (A.F.); (G.D.G.); (L.P.); (G.S.); (L.M.)
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17
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Diagnostic Accuracy of Nucleic Acid Amplification-Based Assays for Clostridium perfringens-Associated Diseases: a Systematic Review and Meta-analysis. J Clin Microbiol 2020; 58:JCM.00363-20. [PMID: 32404484 DOI: 10.1128/jcm.00363-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Timely and accurate methods for detecting Clostridium perfringens-associated diseases (CPAD) are crucial to improve patient care. A number of studies have evaluated the accuracy of nucleic acid amplification tests (NAAT) in detecting CPAD, but decisive results about their effectiveness have not been reported. We conducted a meta-analysis to evaluate the diagnostic performance of NAAT for detecting C. perfringens in clinical diarrheal samples. Five databases including PubMed, Embase, Scopus, Web of Science, and the Cochrane library were systematically probed for studies published before 6 December 2019. From 2,632 citations, we identified five eligible studies comprising 817 samples. Three studies (n = 695 samples) compared NAAT with a microbiological culture while the other three studies (n = 322 samples) compared NAAT with an immunoassay. NAAT revealed higher diagnostic accuracy against immunoassay (sensitivity, 0.53 [95% confidence interval [CI], 0.35 to 0.7]; specificity, 0.97 [95% CI, 0.95 to 0.99]; positive likelihood ratio [PLR], 23.2 [95% CI, 3.49 to 153.98]; negative likelihood ratio [NLR], 0.25 [95% CI, 0 to 245.28]; diagnostic odds ratio [DOR], 74.11 [95% CI, 2.11 to 2,593.7]) than microbiological culture (sensitivity, 0.31 [95% CI, 0.22 to 0.41]; specificity, 0.95 [95% CI, 0.93 to 0.97]; PLR, 11.56 [95% CI, 3.87 to 34.6]; NLR, 0.57 [95% CI, 0.27 to 1.21]; DOR, 18.1 [95% CI, 4.83 to 67.8]). NAAT pooled specificity was consistently ≥95% against that of applied reference standards. A meta-regression and subgroup analysis of sample condition, gene target, study design, and reference standards could not explain the heterogeneity (P > 0.05) in the diagnostic efficiency. The analysis has demonstrated that the diagnostic accuracy of NAAT is relatively insufficient to replace traditional reference standards as a single diagnostic test. NAAT can be applied in combination with microbiological culture because of the advantage of time to result and in scenarios where traditional tests are not feasible. Further investigations in this direction with larger sample sizes are still warranted to support our findings.
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Shanmugakani RK, Srinivasan B, Glesby MJ, Westblade LF, Cárdenas WB, Raj T, Erickson D, Mehta S. Current state of the art in rapid diagnostics for antimicrobial resistance. LAB ON A CHIP 2020; 20:2607-2625. [PMID: 32644060 PMCID: PMC7428068 DOI: 10.1039/d0lc00034e] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Antimicrobial resistance (AMR) is a fundamental global concern analogous to climate change threatening both public health and global development progress. Infections caused by antimicrobial-resistant pathogens pose serious threats to healthcare and human capital. If the increasing rate of AMR is left uncontrolled, it is estimated that it will lead to 10 million deaths annually by 2050. This global epidemic of AMR necessitates radical interdisciplinary solutions to better detect antimicrobial susceptibility and manage infections. Rapid diagnostics that can identify antimicrobial-resistant pathogens to assist clinicians and health workers in initiating appropriate treatment are critical for antimicrobial stewardship. In this review, we summarize different technologies applied for the development of rapid diagnostics for AMR and antimicrobial susceptibility testing (AST). We briefly describe the single-cell technologies that were developed to hasten the AST of infectious pathogens. Then, the different types of genotypic and phenotypic techniques and the commercially available rapid diagnostics for AMR are discussed in detail. We conclude by addressing the potential of current rapid diagnostic systems being developed as point-of-care (POC) diagnostic tools and the challenges to adapt them at the POC level. Overall, this review provides an insight into the current status of rapid and POC diagnostic systems for AMR.
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Affiliation(s)
- Rathina Kumar Shanmugakani
- Institute for Nutritional Sciences, Global Health, and Technology, Cornell University, Ithaca, New York, USA
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
| | - Balaji Srinivasan
- Institute for Nutritional Sciences, Global Health, and Technology, Cornell University, Ithaca, New York, USA
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
| | - Marshall J. Glesby
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Lars F. Westblade
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Washington B. Cárdenas
- Laboratorio para Investigaciones Biomédicas, Escuela Superior Politécnica del Litoral, Guayaquil, Guayas, Ecuador
| | - Tony Raj
- St. John’s Research Institute, Bangalore, Karnataka, India
| | - David Erickson
- Institute for Nutritional Sciences, Global Health, and Technology, Cornell University, Ithaca, New York, USA
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, New York, USA
| | - Saurabh Mehta
- Institute for Nutritional Sciences, Global Health, and Technology, Cornell University, Ithaca, New York, USA
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
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19
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A critical review of antibiotic resistance in probiotic bacteria. Food Res Int 2020; 136:109571. [PMID: 32846610 DOI: 10.1016/j.foodres.2020.109571] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 07/16/2020] [Accepted: 07/17/2020] [Indexed: 12/12/2022]
Abstract
Probiotics are defined as live microorganisms that, when administered in adequate amounts, confer a health benefit upon the host. At present, probiotics are gaining popularity worldwide and are widely used in food and medicine. Consumption of probiotics is increasing with further in-depth research on the relationship between intestinal flora and host health. Most people pay more attention to the function of probiotics but ignore their potential risks, such as infection and antibiotic resistance transfer to pathogenic microbes. Physiological functions, effects and mechanisms of action of probiotics were covered in this review, as well as the antibiotic resistance phenotypes, mechanisms and genes found in probiotics. Typical cases of antibiotic resistance of probiotics were also highlighted, as well as the potential risks (including pathogenicity, infectivity and excessive immune response) and corresponding strategies (dosage, formulation, and administration route). This timely study provides an avenue for further research, development and application of probiotics.
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20
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Wang B, Yan J, Li G, Zhang J, Zhang L, Li Z, Chen H. Risk of penicillin fermentation dreg: Increase of antibiotic resistance genes after soil discharge. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 259:113956. [PMID: 32023801 DOI: 10.1016/j.envpol.2020.113956] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 12/25/2019] [Accepted: 01/08/2020] [Indexed: 06/10/2023]
Abstract
Penicillin fermentation dreg (PFD) is a solid waste discharged by pharmaceutical enterprises in the fermentation production process. Due to the residual antibiotic of PFD, the risk of antibiotic resistance bacteria (ARB) generation should be considered in the disposal process. High-throughput quantitative PCR (HT-qPCR) and 16S rRNA gene sequencing were performed to investigate the effect of PFD on the dynamics of antibiotic resistance genes (ARGs) and bacterial community during a lab-scale soil experiment. After the application of PFD, the bacterial number and diversity showed an obvious decrease in the initial days. The abundances of Streptomyces and Bacillus, which are the most widespread predicted source phyla of ARGs, increased remarkably from 4.42% to 2.59%-22.97% and 21.35%. The increase of ARGs was observed during the PFD application and the ARGs carried by PFD itself contributed to the initiation of soil ARGs. The results of redundancy analysis (RDA) show that the shift in bacterial community induced by variation of penicillin content is the primary driver shaping ARGs compositions.
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Affiliation(s)
- Bing Wang
- College of Chemical Engineering, Northeast Electric Power University, Jilin, 132012, China
| | - Jianquan Yan
- College of Chemical Engineering, Northeast Electric Power University, Jilin, 132012, China
| | - Guomin Li
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150090, China
| | - Jian Zhang
- College of Chemical Engineering, Northeast Electric Power University, Jilin, 132012, China.
| | - Lanhe Zhang
- College of Chemical Engineering, Northeast Electric Power University, Jilin, 132012, China
| | - Zheng Li
- College of Chemical Engineering, Northeast Electric Power University, Jilin, 132012, China
| | - Houhe Chen
- School of Electrical Engineering, Northeast Electric Power University, Jilin, 132012, China
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21
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Monitoring of drug resistance towards reducing the toxicity of pharmaceutical compounds: Past, present and future. J Pharm Biomed Anal 2020; 186:113265. [PMID: 32283481 DOI: 10.1016/j.jpba.2020.113265] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 03/15/2020] [Accepted: 03/16/2020] [Indexed: 12/12/2022]
Abstract
Drug resistance is worldwide health care crisis which decrease drug efficacy and developing toxicities. Effective resistance detection techniques could alleviate treatment cost and mortality associated with this crisis. In this review, the conventional and modern analysis methods for monitoring of drug resistance are presented. Also, various types of emerging rapid and sensitive techniques including electrochemical, electrical, optical and nano-based methods for the screening of drug resistance were discussed. Applications of various methods for the sensitive and rapid detection of drug resistance are investigated. The review outlines existing key issues in the determination which must be overcome before any of these techniques becomes a feasible method for the rapid detection of drug resistance. In this review, the roles of nanomaterials on development of novel methods for the monitoring of drug resistance were presented. Also, limitations and challenges of conventional and modern methods were discussed.
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22
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Zhou Z, Yao H. Effects of Composting Different Types of Organic Fertilizer on the Microbial Community Structure and Antibiotic Resistance Genes. Microorganisms 2020; 8:microorganisms8020268. [PMID: 32079314 PMCID: PMC7074733 DOI: 10.3390/microorganisms8020268] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/14/2020] [Accepted: 02/14/2020] [Indexed: 12/25/2022] Open
Abstract
Organic fertilizer is a major carrier that stores and transmits antibiotic resistance genes (ARGs). In the environment, due to the application of organic fertilizers in agriculture, the increasing diversity and abundance of ARGs poses a potential threat to human health and environmental safety. In this paper, the microbial community structure and ARGs in different types of organic fertilizer treated with composting were examined. We found that the abundance and diversity of ARGs in earthworm cast organic fertilizer were the lowest and the highest in chicken manure organic fertilizer. Interestingly, the abundance and diversity of ARGs, especially beta-lactam resistance genes, sulfonamide resistance genes, and macrolide-lincosamide-streptogramin B (MLSB) resistance genes, in organic fertilizers were reduced significantly, while composting caused no significant change in mobile genetic elements (MGEs), where antibiotic deactivation and the use of efflux pumps were the two most dominant mechanisms. It was clear that removal of ARGs became more efficient with increasing reduction in the bacterial abundances and diversity of potential ARG hosts, and integron-mediated horizontal gene transfers (HGTs) played an important role in the proliferation of most ARG types. Therefore, the reduction in ARGs was mainly driven by changes in bacterial community composition caused by composting. Furthermore, rather than HGTs, the diversity and abundance of bacterial communities affected by compost physical and chemical properties were the main drivers shaping and altering the abundance and diversity of ARGs, which was indicated by a correlation analysis of these properties, antibiotic residues, microbial community structure, and ARGs. In general, high-temperature composting effectively removed antibiotic residues and ARGs from these organic fertilizers; however, it cannot prevent the proliferation of MGEs. The insights gained from these results may be of assistance in the safe and rational use of organic fertilizers by indicating the changes in microbial community structure and ARGs in different types of organic fertilizer treated with composting.
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Affiliation(s)
- Zeming Zhou
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430073, China;
| | - Huaiying Yao
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430073, China;
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, Ningbo Urban Environment Observation and Research Station, Chinese Academy of Sciences, Ningbo 315800, China
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Correspondence:
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23
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Wang Q, Duan YJ, Wang SP, Wang LT, Hou ZL, Cui YX, Hou J, Das R, Mao DQ, Luo Y. Occurrence and distribution of clinical and veterinary antibiotics in the faeces of a Chinese population. JOURNAL OF HAZARDOUS MATERIALS 2020; 383:121129. [PMID: 31546217 DOI: 10.1016/j.jhazmat.2019.121129] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/26/2019] [Accepted: 08/30/2019] [Indexed: 05/21/2023]
Abstract
Antibiotics ingested in the human gut may create selective pressure to change the composition of the gut microbiota, which could adversely effect the immune system of the host. However, the occurrence and distribution of antibiotics in the human gut remains unclear. A total population of 180 individuals, across three Chinses regions with different economic development levels, including children, adults, and elders, were sampled in 2017. A total of 19 representative antibiotics, including both clinical and veterinary antibiotics, were investigated in human faeces. While clinical use and prescriptions were the main exposure pathways for children, environmental media were the exposure pathway to adults. In addition, significant differences (P < 0.05) in antibiotic residues in human faeces were observed amongst various economic development levels, where human faeces from underdeveloped areas were mostly associated with higher levels of antibiotics. This study first to investigate the occurrence and distribution of typical antibiotics in the faeces of a Chinese population and thereby provide a reference for the intensive study of the effects and mechanisms of antibiotics on human gut microbiota.
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Affiliation(s)
- Qing Wang
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, 300071, China; Hebei Key Laboratory of Air Pollution Cause and Impact (preparatory), College of Energy and Environmental Engineering, Hebei University of Engineering, Handan, 056038, China
| | - Yu-Jing Duan
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, 300071, China
| | - Shao-Peng Wang
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, 300071, China
| | - Li-Tao Wang
- Hebei Key Laboratory of Air Pollution Cause and Impact (preparatory), College of Energy and Environmental Engineering, Hebei University of Engineering, Handan, 056038, China
| | - Ze-Lin Hou
- Hebei Key Laboratory of Air Pollution Cause and Impact (preparatory), College of Energy and Environmental Engineering, Hebei University of Engineering, Handan, 056038, China
| | - Yu-Xiao Cui
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, 300071, China
| | - Jie Hou
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, 300071, China
| | - Ranjit Das
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, 300071, China
| | - Da-Qing Mao
- School of Medicine, Nankai University, Tianjin, 300071, China
| | - Yi Luo
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, 300071, China.
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Abstract
The study of hospital wastewater (HWW) microbiology is important to understand the pollution load, growth of particular pathogenic microbes, shift and drift in microbial community, development and spread of antibiotic resistance in microbes, and subsequent change in treatment efficiencies. This chapter investigates the potential microbes such as bacteria, viruses, fungi, and parasites present in HWW along with the diseases associated and methods of treatment used. Due to the indiscriminate release of antibiotics from hospitals, HWW serves as a hotspot for emergence of antibiotic-resistance genes (ARGs) and antibiotic-resistance bacteria. This chapter discusses the ARGs occurrence in HWW, their prevalence in the environment, the molecular tools used for identification, and different mechanisms of horizontal gene transfer. Thus better understanding of the microbiology of HWW could further help in development of advanced treatment technologies for effective removal of microbes and their bioproducts (toxins and infectious nucleic acid) from HWW and contaminated water.
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25
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Abstract
Advances in precision medicine require high-throughput, inexpensive, point-of-care diagnostic methods with multiomics capability for detecting a wide range of biomolecules and their molecular variants. Optical techniques have offered many promising advances toward such diagnostics. However, the inability to squeeze light with several hundred nanometer wavelengths into angstrom-scale volume for single-nucleotide measurements has hindered further progress. This limitation has been circumvented by analyzing the relative nucleobase content with Raman spectroscopy, in an optical sequencing method. Here, we performed optical sequencing measurements on positively charged silver nanoparticles to achieve 93.3% accuracy for predicting nucleobase content in label-free DNA k-mer blocks (where k = 10) as well as measurements on RNA and chemically modified nucleobases for extensions to transcriptomic and epigenetic studies. Our high-accuracy measurements were then used with a content-scoring database searching algorithm to correctly identify a β-lactamase gene from the MEGARes antibiotic resistance database and confirm the Pseudomonas aeruginosa pathogen of origin from <12 block content measurements (<15% coverage) of the gene. These results prove the feasibility of an optical sequencing platform as a diagnostic method. With the versatile range of available plasmonic substrates offering simple data acquisition, varying resolution (single-molecule to the ensemble), and multiplexing, this optical sequencing platform has potential as the rapid, cost-effective method needed for broad-spectrum biomarker detection.
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26
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Liu Z, Klümper U, Liu Y, Yang Y, Wei Q, Lin JG, Gu JD, Li M. Metagenomic and metatranscriptomic analyses reveal activity and hosts of antibiotic resistance genes in activated sludge. ENVIRONMENT INTERNATIONAL 2019; 129:208-220. [PMID: 31129497 DOI: 10.1016/j.envint.2019.05.036] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/22/2019] [Accepted: 05/14/2019] [Indexed: 05/23/2023]
Abstract
Wastewater treatment plants (WWTPs) are a source and reservoir for subsequent spread of various antibiotic resistance genes (ARGs). However, little is known about the activity and hosts of ARGs in WWTPs. Here, we utilized both metagenomic and metatranscriptomic approaches to comprehensively reveal the diversity, abundance, expression and hosts of ARGs in activated sludge (AS) from three conventional WWTPs in Taiwan. Based on deep sequencing data and a custom-made ARG database, a total of 360 ARGs associated with 24 classes of antibiotics were identified from the three AS metagenomes, with an abundance range of 7.06 × 10-1-1.20 × 10-4 copies of ARG/copy of 16S rRNA gene. Differential coverage binning analysis revealed that >22 bacterial phyla were the putative hosts of the identified ARGs. Surprisingly, genus Mycobacterium and family Burkholderiaceae were observed as multi-drug resistant harboring 14 and 50 ARGs. Metatranscriptome analysis showed 65.8% of the identified ARGs were being expressed, highlighting that ARGs were not only present, but also transcriptionally active in AS. Remarkably, 110 identified ARGs were annotated as plasmid-associated and displayed a close to two-fold increased likelihood of being transcriptionally expressed compared to those ARGs found exclusively within bacterial chromosomes. Further analysis showed the transcript abundance of aminoglycoside, sulfonamide, and tetracycline resistance genes was mainly contributed by plasmid-borne ARGs. Our approach allowed us to specifically link ARGs to their transcripts and genetic context, providing a comprehensive insight into the prevalence, expression and hosts of ARGs in AS. Overall, results of this study enhance our understanding of the distribution and dissemination of ARGs in WWTPs, which benefits environmental risk assessment and management of ARB and ARGs.
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Affiliation(s)
- Zongbao Liu
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, PR China; Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, PR China
| | - Uli Klümper
- ESI & CLES, Biosciences, University of Exeter, Penryn Campus, Cornwall, United Kingdom; European Centre for Environment and Human Health, University of Exeter, Truro, United Kingdom
| | - Yang Liu
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, PR China
| | - Yuchun Yang
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Qiaoyan Wei
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, PR China
| | - Jih-Gaw Lin
- Institute of Environmental Engineering, National Chiao Tung University, 1001 University Road, Hsinchu City 30010, Taiwan
| | - Ji-Dong Gu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
| | - Meng Li
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, PR China.
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Chanchaithong P, Perreten V, Am-In N, Lugsomya K, Tummaruk P, Prapasarakul N. Molecular Characterization and Antimicrobial Resistance of Livestock-Associated Methicillin-Resistant Staphylococcus aureus Isolates from Pigs and Swine Workers in Central Thailand. Microb Drug Resist 2019; 25:1382-1389. [PMID: 31361580 DOI: 10.1089/mdr.2019.0011] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
This study presents molecular characteristics of livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) from pigs and swine workers in central Thailand. Sixty-three MRSA isolates were recovered from pigs (n = 60) and humans (n = 3). Two major LA-MRSA lineages, including sequence type (ST) 398 and clonal complex 9 (ST9 and ST4576, a novel single-locus variant of ST9), were identified. ST398 had spa type t034 (n = 55). ST9 and ST4576 had t337 (n = 8) and carried staphylococcal cassette chromosome mec (SCCmec) IX only. MRSA-ST398-t034 contained various SCCmec, including SCCmec V (n = 42), a novel SCCmec composite island (n = 12), and a nontypeable SCCmec (n = 1). All isolates were multidrug resistant and carried common resistance genes found in LA-MRSA. This is the first report of the presence of swine MRSA ST398 and multidrug resistance gene cfr in MRSA ST9 in Thailand. With identical molecular characteristics, pigs could be a source of MRSA ST398 spread to humans. A minor variation of genetic features and resistance gene carriage in both lineages represented a heterogeneous population and evolution of the endemic clones. A monitoring program and farm management, with prudent antimicrobial uses, should be implemented to reduce spreading. Strict hygiene and personal protection are also necessary to prevent transfer of LA-MRSA to humans.
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Affiliation(s)
- Pattrarat Chanchaithong
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Diagnosis and Monitoring of Animal Pathogen Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Vincent Perreten
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Nutthee Am-In
- Department of Obstetrics, Gynaecology and Reproduction, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Kittitat Lugsomya
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Padet Tummaruk
- Department of Obstetrics, Gynaecology and Reproduction, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Nuvee Prapasarakul
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Diagnosis and Monitoring of Animal Pathogen Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
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28
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Khemiri M, Abbassi MS, Elghaieb H, Zouari M, Dhahri R, Pomba C, Hammami S. High occurrence of enterotoxigenic isolates and low antibiotic resistance rates of Staphylococcus aureus isolated from raw milk from cows and ewes. Lett Appl Microbiol 2019; 68:573-579. [PMID: 30924159 DOI: 10.1111/lam.13152] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 03/24/2019] [Accepted: 03/25/2019] [Indexed: 11/28/2022]
Abstract
This study aimed to analyse the frequency of genes encoding virulence factors and to characterize resistance profiles of Staphylococcus aureus isolated from raw milk. In total, 47 and 9 S. aureus isolates were recovered from 150 and 100 raw bovine and ovine milk samples, respectively, in Tunisia. The majority of isolates was resistant to penicillin, and no methicillin-resistant S. aureus was detected. Eighteen and two isolates harboured etd and eta genes respectively. Sixteen enterotoxin-encoding genes were detected (n, %): sed (25, 44·6%), sec (16, 28·6%), sei (16, 28·6%), seh (13, 23·2%), seln (13, 23·2%), sell (10, 17·8%), seg (9, 16%), selu (8, 14·3%), selq (7, 12·5%), selo (7, 12·5%), selm (7, 12·5%), seb (7, 12·5%), sea (6, 10·7%), selk (3, 5·4%), ser (1, 1·8%) and selp (1, 1·8%). Ten isolates carried the tsst1 gene. All isolates carried the haemolysin toxin (hla, hld and hlg). The immune evasion cluster system-type B was predominant (20 isolates) followed by C (3 isolates), A and E (1 isolate each). The occurrence of enterotoxigenic S. aureus in raw milk constitutes a potential risk for human health. SIGNIFICANCE AND IMPACT OF THE STUDY: This paper describes the characteristics of Staphylococcus aureus isolated from raw milk samples from healthy cows and ewes collected from small family farms in Tunisia. Fifty-six strains were analysed by determining their antibiotic susceptibility and genes encoding antibiotic resistance and virulence factors. Methicillin-resistant strains were not detected, and overall low level of antimicrobial resistance was reported. However, our strains harboured several genes encoding virulence factors and 87·5% of them carried at least one gene encoding for enterotoxins showing a high risk of spread of food-borne diseases.
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Affiliation(s)
- M Khemiri
- Institut de la Recherche Vétérinaire de Tunisie, Université de Tunis El Manar, Tunis, Tunisia.,Laboratory of Antimicrobial and Biocide Resistance, CIISA, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
| | - M S Abbassi
- Institut de la Recherche Vétérinaire de Tunisie, Université de Tunis El Manar, Tunis, Tunisia.,Laboratoire de 'Résistance aux antibiotiques', Faculté de Médecine de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - H Elghaieb
- Institut de la Recherche Vétérinaire de Tunisie, Université de Tunis El Manar, Tunis, Tunisia
| | - M Zouari
- OTD Centre avicole de Mateur, Bizerte, Tunisia
| | - R Dhahri
- Complexe Sanitaire de Jebel Ouest, Zaghouan, Tunisia
| | - C Pomba
- Laboratory of Antimicrobial and Biocide Resistance, CIISA, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
| | - S Hammami
- Université de la Manouba, Ecole Nationale de Médecine Vétérinaire de Sidi Thabet, Tunis, Tunisia
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29
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Szemraj M, Kwaszewska A, Szewczyk EM. New Gene Responsible for Resistance of Clinical Corynebacteria to Macrolide, Lincosamide and Streptogramin B. Pol J Microbiol 2019; 67:237-240. [PMID: 30015464 PMCID: PMC7256696 DOI: 10.21307/pjm-2018-028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/20/2018] [Indexed: 11/11/2022] Open
Abstract
The subject of the study was phenotypic marking of the antibiotic susceptibility and MLSB resistance mechanism in Corynebacterium spp. isolated from human skin (18 isolates) and from clinical materials (19 isolates). The strains were tested for the presence of the erm(A), erm(B), erm(C), erm(X), lnu(A), msr(A), msr(B) and mph(C) genes. Clinical isolates showed wide resistance to antibiotics. In 89% clinical isolates and 72% skin microbiota a constitutive type of MLSB resistance was found. In 12 clinical isolates the erm(C) gene was detected-eight of which had erm(X) as well as erm(C), two harboured erm(X), erm(C) and erm(A) and two demonstrated only erm(C).
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Affiliation(s)
- Magdalena Szemraj
- Department of Pharmaceutical Microbiology and Microbiological Diagnostics, Medical University of Łódź,Łódź,Poland
| | - Anna Kwaszewska
- Institute of Health Sciences, State College of Applied Sciences in Skierniewice,Skierniewice,Poland
| | - Eligia M Szewczyk
- Department of Pharmaceutical Microbiology and Microbiological Diagnostics, Medical University of Łódź,Łódź,Poland
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30
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Korshoj LE, Nagpal P. BOCS: DNA k-mer content and scoring for rapid genetic biomarker identification at low coverage. Comput Biol Med 2019; 110:196-206. [PMID: 31173943 DOI: 10.1016/j.compbiomed.2019.05.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 05/23/2019] [Accepted: 05/29/2019] [Indexed: 01/10/2023]
Abstract
A single, inexpensive diagnostic test capable of rapidly identifying a wide range of genetic biomarkers would prove invaluable in precision medicine. Previous work has demonstrated the potential for high-throughput, label-free detection of A-G-C-T content in DNA k-mers, providing an alternative to single-letter sequencing while also having inherent lossy data compression and massively parallel data acquisition. Here, we apply a new bioinformatics algorithm - block optical content scoring (BOCS) - capable of using the high-throughput content k-mers for rapid, broad-spectrum identification of genetic biomarkers. BOCS uses content-based sequence alignment for probabilistic mapping of k-mer contents to gene sequences within a biomarker database, resulting in a probability ranking of genes on a content score. Simulations of the BOCS algorithm reveal high accuracy for identification of single antibiotic resistance genes, even in the presence of significant sequencing errors (100% accuracy for no sequencing errors, and >90% accuracy for sequencing errors at 20%), and at well below full coverage of the genes. Simulations for detecting multiple resistance genes within a methicillin-resistant Staphylococcus aureus (MRSA) strain showed 100% accuracy at an average gene coverage of merely 0.515, when the k-mer lengths were variable and with 4% sequencing error within the k-mer blocks. Extension of BOCS to cancer and other genetic diseases met or exceeded the results for resistance genes. Combined with a high-throughput content-based sequencing technique, the BOCS algorithm potentiates a test capable of rapid diagnosis and profiling of genetic biomarkers ranging from antibiotic resistance to cancer and other genetic diseases.
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Affiliation(s)
- Lee E Korshoj
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80303, USA; Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, CO, 80303, USA
| | - Prashant Nagpal
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80303, USA; Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, CO, 80303, USA; Materials Science and Engineering, University of Colorado Boulder, Boulder, CO, 80303, USA.
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31
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Albert E, Biksi I, Német Z, Csuka E, Kelemen B, Morvay F, Bakos Z, Bodó G, Tóth B, Collaud A, Rossano A, Perreten V. Outbreaks of a Methicillin-Resistant Staphylococcus aureus Clone ST398-t011 in a Hungarian Equine Clinic: Emergence of Rifampicin and Chloramphenicol Resistance After Treatment with These Antibiotics. Microb Drug Resist 2019; 25:1219-1226. [PMID: 31066624 DOI: 10.1089/mdr.2018.0384] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Between July 2011 and May 2016, a total of 40 Staphylococcus aureus strains originating from 36 horses were confirmed as methicillin resistant (methicillin-resistant Staphylococcus aureus [MRSA]) in a university equine clinic. An additional 10 MRSA strains from 36 samples of clinic workers were obtained in October 2017. The first equine isolate represented the sequence type ST398, spa-type t011, and SCCmec IV. This isolate was resistant to a wide spectrum of antimicrobial agents. MRSA strains with the same genotype and with very similar resistance profiles were isolated on 21 more occasions from September 2013 to September 2014. A second outbreak occurred from May 2015 until May 2016. The first isolate in this second outbreak shared the same genotype, but was additionally resistant to chloramphenicol. The second isolate from August 2015 also showed resistance to rifampicin. The clone was isolated 18 times. Most of the human isolates shared the same genotype as the isolates from horses and their resistance patterns showed only slight differences. We can conclude that the MRSA-related cases at the Department and Clinic of Equine Medicine were all nosocomial infections caused by the same clonal lineage belonging to the clonal complex 398. The clonal complex 398 of equine origin is reported for the first time in Hungary. In addition, our observation of the emergence of new resistance to antimicrobial agents within the clonal lineage after treatment with antibiotics is of concern. Strict hygiene regulations have been introduced to lower the incidence of MRSA isolation and the related clinical disease.
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Affiliation(s)
- Ervin Albert
- Diagnostic Laboratory, Department and Clinic of Production Animal Medicine, University of Veterinary Medicine Budapest, Üllő, Hungary
| | - Imre Biksi
- Diagnostic Laboratory, Department and Clinic of Production Animal Medicine, University of Veterinary Medicine Budapest, Üllő, Hungary
| | - Zoltán Német
- Diagnostic Laboratory, Department and Clinic of Production Animal Medicine, University of Veterinary Medicine Budapest, Üllő, Hungary
| | - Edit Csuka
- Diagnostic Laboratory, Department and Clinic of Production Animal Medicine, University of Veterinary Medicine Budapest, Üllő, Hungary
| | - Bernadett Kelemen
- Diagnostic Laboratory, Department and Clinic of Production Animal Medicine, University of Veterinary Medicine Budapest, Üllő, Hungary
| | - Flóra Morvay
- Department and Clinic of Equine Medicine, University of Veterinary Medicine Budapest, Üllő, Hungary
| | - Zoltán Bakos
- Department and Clinic of Equine Medicine, University of Veterinary Medicine Budapest, Üllő, Hungary
| | - Gábor Bodó
- Department and Clinic of Equine Medicine, University of Veterinary Medicine Budapest, Üllő, Hungary
| | - Balázs Tóth
- Department and Clinic of Equine Medicine, University of Veterinary Medicine Budapest, Üllő, Hungary
| | - Alexandra Collaud
- Vetsuisse Faculty, Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | - Alexandra Rossano
- Vetsuisse Faculty, Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | - Vincent Perreten
- Vetsuisse Faculty, Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
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32
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Rupp M, Pilo P, Müller B, Knüsel R, von Siebenthal B, Frey J, Sindilariu PD, Schmidt-Posthaus H. Systemic infection in European perch with thermoadapted virulent Aeromonas salmonicida (Perca fluviatilis). JOURNAL OF FISH DISEASES 2019; 42:685-691. [PMID: 30806486 DOI: 10.1111/jfd.12970] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 01/11/2019] [Accepted: 01/13/2019] [Indexed: 06/09/2023]
Abstract
In non-salmonid fish, Aeromonas salmonicidacan cause local infections with severe skin ulcerations, known as atypical furunculosis. In this study, we present a systemic infection by a virulent A. salmonicidain European perch (Perca fluviatilis).This infection was diagnosed in a Swiss warm water recirculation aquaculture system. The isolate of A. salmonicida encodes a type three secretion system (TTSS) most likely located on a plasmid similar to pAsa5/pASvirA, which is known to specify one of the main virulence attributes of the species A. salmonicida. However, the genes specifying the TTSS of the perch isolate show a higher temperature tolerance than strains isolated from cold-water fish. The function of the TTSS in virulence was verified in a cytotoxicity test using bluegill fry and epithelioma papulosum cyprinid cells.
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Affiliation(s)
- Melanie Rupp
- Centre for Fish and Wildlife Health, University of Bern, Bern, Switzerland
| | - Paola Pilo
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | - Barbara Müller
- Centre for Fish and Wildlife Health, University of Bern, Bern, Switzerland
| | | | | | - Joachim Frey
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
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33
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Tolerance to benzalkonium chloride and antimicrobial activity of Butia odorata Barb. Rodr. extract in Salmonella spp. isolates from food and food environments. Food Res Int 2019; 116:652-659. [DOI: 10.1016/j.foodres.2018.08.092] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 07/21/2018] [Accepted: 08/19/2018] [Indexed: 11/23/2022]
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34
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Contributions and Challenges of High Throughput qPCR for Determining Antimicrobial Resistance in the Environment: A Critical Review. Molecules 2019; 24:molecules24010163. [PMID: 30609875 PMCID: PMC6337382 DOI: 10.3390/molecules24010163] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 12/28/2018] [Accepted: 12/29/2018] [Indexed: 12/12/2022] Open
Abstract
Expansion in whole genome sequencing and subsequent increase in antibiotic resistance targets have paved the way of high throughput qPCR (HT-qPCR) for analyzing hundreds of antimicrobial resistance genes (ARGs) in a single run. A meta-analysis of 51 selected studies is performed to evaluate ARGs abundance trends over the last 7 years. WaferGenTM SmartChip is found to be the most widely used HT-qPCR platform among others for evaluating ARGs. Up till now around 1000 environmental samples (excluding biological replicates) from different parts of the world have been analyzed on HT-qPCR. Calculated detection frequency and normalized ARGs abundance (ARGs/16S rRNA gene) reported in gut microbiome studies have shown a trend of low ARGs as compared to other environmental matrices. Disparities in the HT-qPCR data analysis which are causing difficulties to researchers in precise interpretation of results have been highlighted and a possible way forward for resolving them is also suggested. The potential of other amplification technologies and point of care or field deployable devices for analyzing ARGs have also been discussed in the review. Our review has focused on updated information regarding the role, current status and future perspectives of HT-qPCR in the field of antimicrobial resistance.
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35
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Chen QL, An XL, Zheng BX, Ma YB, Su JQ. Long-term organic fertilization increased antibiotic resistome in phyllosphere of maize. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 645:1230-1237. [PMID: 30248848 DOI: 10.1016/j.scitotenv.2018.07.260] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/18/2018] [Accepted: 07/18/2018] [Indexed: 06/08/2023]
Abstract
Phyllosphere contains various microorganisms that may harbor diverse antibiotic resistance genes (ARGs). However, we know little about the composition of antibiotic resistome and the factors influencing the diversity and abundance of ARGs in the phyllosphere. In this study, 16S rRNA gene amplicon sequencing and high-throughput quantitative PCR approaches were employed to investigate the effects of long-term (over 10 years) organic fertilization on the phyllosphere bacterial communities and antibiotic resistome. Proteobacteria, Bacteroidetes, Actinobacteria and Firmicutes dominated in the phyllosphere bacterial communities. Long-term application of sewage sludge and chicken manure altered the phyllosphere bacterial community composition, with a remarkable decrease in bacterial alpha-diversity. A total of 124 unique ARGs were detected in the phyllosphere. The application of sewage sludge and chicken manure significantly increased the abundance of ARGs, with a maximum 2638-fold enrichment. Variation partitioning analysis (VPA) together with network analysis indicated that the profile of ARGs is strongly correlated with bacterial community compositions. These results improve the knowledge about the diversity of plant-associated antibiotic resistome and factors influencing the profile of ARGs in the phyllosphere.
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Affiliation(s)
- Qing-Lin Chen
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Xin-Li An
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Bang-Xiao Zheng
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi-Bing Ma
- Ministry of Agriculture Key Laboratory of Plant Nutrition and Nutrient Cycling, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jian-Qiang Su
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
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36
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Brilhante M, Perreten V, Donà V. Multidrug resistance and multivirulence plasmids in enterotoxigenic and hybrid Shiga toxin-producing/enterotoxigenic Escherichia coli isolated from diarrheic pigs in Switzerland. Vet J 2018; 244:60-68. [PMID: 30825896 DOI: 10.1016/j.tvjl.2018.12.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 12/04/2018] [Accepted: 12/10/2018] [Indexed: 01/08/2023]
Abstract
Enterovirulent Escherichia coli infections cause significant losses in the pig industry. However, information about the structures of the virulence and multidrug resistance (MDR) plasmids harboured by these strains is sparse. In this study, we used whole-genome sequencing with PacBio and Illumina platforms to analyse the molecular features of the multidrug-resistant enterotoxigenic E. coli (ETEC) strain 14OD0056 and the multidrug-resistant hybrid Shiga toxin-producing/enterotoxigenic E. coli (STEC/ETEC) strain 15OD0495 isolated from diarrheic pigs in Switzerland. Strain 14OD0056 possessed three virulence plasmids similar to others previously found in ETEC strains, while 15OD0495 harboured a 119-kb multivirulence IncFII/IncX1 hybrid STEC/ETEC plasmid (p15ODTXV) that co-carried virulence genes of both ETEC and STEC pathotypes, confirming the key role of plasmids in the emergence of hybrid pathotypes. All resistance genes of 14OD0056 that conferred resistance to ampicillin (blaTEM-1b), gentamicin (aac(3)-IIa), kanamycin (aph(3')-Ia), sulfonamide (sul1 and sul2), streptomycin (aph(3″)-Ib, aph(6)-Id), tetracycline (tet(B)) and trimethoprim (dfrA1) were identified on a single 207-kb conjugative MDR plasmid of incompatibility group (Inc) IncHI1/IncFIA (p14ODMR). Strain 15OD0495 carried two antimicrobial resistance plasmids (p15ODAR and p15ODMR). The 99-kb IncI1 plasmid p15ODAR harboured only aminoglycoside resistance genes (aac(3)-IIa, aph(3″)-Ib, aph(6)-Id, aph(4)-Ia), whilst the 49-kb IncN MDR plasmid p15ODMR carried genes conferring resistance to ampicillin (blaTEM-1b), sulfonamide (sul2), streptomycin (aph(6)-Id), tetracycline (tet(A)) and trimethoprim (dfrA14). Filter mating assays showed that p14ODMR, p15ODMR and p15ODAR were conjugative at room temperature and 37°C. The co-localization of multiple resistance genes on MDR conjugative plasmids such as p14ODMR and p15ODMR poses the risk of simultaneous selection of several resistance traits during empirical treatment. Thus, preventive strategies and targeted therapy following antibiotic susceptibility testing should be encouraged to avoid further dissemination of such plasmids.
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Affiliation(s)
- M Brilhante
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland; Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - V Perreten
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
| | - V Donà
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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37
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Ekwanzala MD, Dewar JB, Kamika I, Momba MNB. Systematic review in South Africa reveals antibiotic resistance genes shared between clinical and environmental settings. Infect Drug Resist 2018; 11:1907-1920. [PMID: 30425540 PMCID: PMC6203169 DOI: 10.2147/idr.s170715] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
A systematic review was conducted to determine the distribution and prevalence of antibiotic-resistant bacteria (ARB), antimicrobial-resistant genes (ARGs), and antimicrobial-resistant gene determinants (ARGDs) in clinical, environmental, and farm settings and to identify key knowledge gaps in a bid to contain their spread. Fifty-three articles were included. The prevalence of a wide range of antimicrobial-resistant bacteria and their genes was reviewed. Based on the studies reviewed in this systematic review, mutation was found to be the main genetic element investigated. All settings shared 39 ARGs and ARGDs. Despite the fact that ARGs found in clinical settings are present in the environment, in reviewed articles only 12 were found to be shared between environmental and clinical settings; the inclusion of farm settings with these two settings increased this figure to 32. Data extracted from this review revealed farm settings to be one of the main contributors of antibiotic resistance in healthcare settings. ARB, ARGs, and ARGDs were found to be ubiquitous in all settings examined.
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Affiliation(s)
| | - John Barr Dewar
- Department of Life and Consumer Sciences, University of South Africa, Johannesburg, South Africa
| | - Ilunga Kamika
- Department of Environmental, Water and Earth Sciences, Tshwane University of Technology, Pretoria, South Africa,
| | - Maggy Ndombo Benteke Momba
- Department of Environmental, Water and Earth Sciences, Tshwane University of Technology, Pretoria, South Africa,
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38
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Bannister SA, Kidd SP, Kirby E, Shah S, Thomas A, Vipond R, Elmore MJ, Telfer Brunton A, Marsh P, Green S, Silman NJ, Kempsell KE. Development and Assessment of a Diagnostic DNA Oligonucleotide Microarray for Detection and Typing of Meningitis-Associated Bacterial Species. High Throughput 2018; 7:ht7040032. [PMID: 30332776 PMCID: PMC6306750 DOI: 10.3390/ht7040032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 09/11/2018] [Accepted: 09/21/2018] [Indexed: 02/03/2023] Open
Abstract
Meningitis is commonly caused by infection with a variety of bacterial or viral pathogens. Acute bacterial meningitis (ABM) can cause severe disease, which can progress rapidly to a critical life-threatening condition. Rapid diagnosis of ABM is critical, as this is most commonly associated with severe sequelae with associated high mortality and morbidity rates compared to viral meningitis, which is less severe and self-limiting. We have designed a microarray for detection and diagnosis of ABM. This has been validated using randomly amplified DNA targets (RADT), comparing buffers with or without formamide, in glass slide format or on the Alere ArrayTubeTM (Alere Technologies GmbH) microarray platform. Pathogen-specific signals were observed using purified bacterial nucleic acids and to a lesser extent using patient cerebral spinal fluid (CSF) samples, with some technical issues observed using RADT and glass slides. Repurposing the array onto the Alere ArrayTubeTM platform and using a targeted amplification system increased specific and reduced nonspecific hybridization signals using both pathogen nucleic and patient CSF DNA targets, better revealing pathogen-specific signals although sensitivity was still reduced in the latter. This diagnostic microarray is useful as a laboratory diagnostic tool for species and strain designation for ABM, rather than for primary diagnosis.
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Affiliation(s)
| | - Stephen P Kidd
- Public Health England, Porton Down, Salisbury SP4 0JG, UK.
| | | | - Sonal Shah
- Public Health England, Porton Down, Salisbury SP4 0JG, UK.
| | - Anvy Thomas
- Public Health England, Porton Down, Salisbury SP4 0JG, UK.
| | - Richard Vipond
- Public Health England, Porton Down, Salisbury SP4 0JG, UK.
| | | | - Andrew Telfer Brunton
- Department of Clinical Microbiology, Royal Cornwall Hospitals NHS Trust, Penventinnie Lane, Treliske, Truro, Cornwall TR1 3LQ, UK.
| | - Peter Marsh
- Public Health England Laboratory Southampton, Southampton General Hospital, Tremona Road, Southampton SO16 6YD, UK.
| | - Steve Green
- Public Health England Laboratory Southampton, Southampton General Hospital, Tremona Road, Southampton SO16 6YD, UK.
| | - Nigel J Silman
- Public Health England, Porton Down, Salisbury SP4 0JG, UK.
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39
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Freitas AR, Elghaieb H, León-Sampedro R, Abbassi MS, Novais C, Coque TM, Hassen A, Peixe L. Detection of optrA in the African continent (Tunisia) within a mosaic Enterococcus faecalis plasmid from urban wastewaters. J Antimicrob Chemother 2018; 72:3245-3251. [PMID: 29029072 DOI: 10.1093/jac/dkx321] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 08/01/2017] [Indexed: 01/11/2023] Open
Abstract
Objectives Oxazolidinone resistance is a serious limitation in the treatment of MDR Enterococcus infections. Plasmid-mediated oxazolidinone resistance has been strongly linked to animals where the use of phenicols might co-select resistance to both antibiotic families. Our goal was to assess the diversity of genes conferring phenicol/oxazolidinone resistance among diverse enterococci and to characterize the optrA genetic environment. Methods Chloramphenicol-resistant isolates (>16 mg/L, n = 245) from different sources (hospitals/healthy humans/wastewaters/animals) in Portugal, Angola and Tunisia (1996-2016) were selected. Phenicol (eight cat variants, fexA, fexB) or phenicol + oxazolidinone [cfr, cfr(B), optrA] resistance genes were searched for by PCR. Susceptibility (disc diffusion/microdilution), filter mating, stability of antibiotic resistance (500 bacterial generations), plasmid typing (S1-PFGE/hybridization), MLST and WGS (Illumina-HiSeq) were performed for optrA-positive isolates. Results Resistance to phenicols (n = 181, 74%) and phenicols + oxazolidinones (n = 2, 1%) was associated with the presence of cat(A-8) (40%, predominant in hospitals and swine), cat(A-7) (29%, predominant in poultry and healthy humans), cat(A-9) (2%), fexB (2%) and fexA + optrA (1%). fexA and optrA genes were co-located in a transferable plasmid (pAF379, 72 918 bp) of two ST86 MDR Tunisian Enterococcus faecalis (wastewaters) carrying several putative virulence genes. MICs of chloramphenicol, linezolid and tedizolid were stably maintained at 64, 4 and 1 mg/L, respectively. The chimeric pAF379 comprised relics of genetic elements from different Gram-positive bacteria and origins (human/porcine). Conclusions To the best of our knowledge, we report the first detection of optrA in an African country (Tunisia) within a transferable mosaic plasmid of different origins. Its identification in isolates from environmental sources is worrisome and alerts for the need of a concerted global surveillance on the occurrence and spread of optrA.
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Affiliation(s)
- Ana R Freitas
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Houyem Elghaieb
- Université de Tunis El Manar, Institut de la Recherche Vétérinaire de Tunisie, 20 rue Jebel Lakhdhar, Bab Saadoun, Tunis, Tunisia
| | - Ricardo León-Sampedro
- Servicio de Microbiología, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain.,Centros de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBER-ESP), Barcelona, Spain
| | - Mohamed Salah Abbassi
- Université de Tunis El Manar, Institut de la Recherche Vétérinaire de Tunisie, 20 rue Jebel Lakhdhar, Bab Saadoun, Tunis, Tunisia
| | - Carla Novais
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Teresa M Coque
- Servicio de Microbiología, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain.,Centros de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBER-ESP), Barcelona, Spain
| | - Abdennaceur Hassen
- Laboratoire de Traitement des Eaux Usées, Centre des Recherches et des Technologies des Eaux (CERTE), Technopole Borj Cédria, Soliman, Tunisia
| | - Luisa Peixe
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
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Diab AM, Al-Turk IM, Ibrahim MK, Al-Zhrany KD. Tracing of Gram-negative antibiotic-resistant bacteria in hospitals final effluent at Al-Madinah Al- Mounwwarah. JOURNAL OF TAIBAH UNIVERSITY FOR SCIENCE 2018. [DOI: 10.1016/s1658-3655(12)60030-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Atef M. Diab
- Biology Department, Faculty of Science, Taibah University, Al-Madinah Al- Mounwwarah, KSA
| | - Idriss M. Al-Turk
- Biology Department, Faculty of Science, Taibah University, Al-Madinah Al- Mounwwarah, KSA
| | - Mohamed K. Ibrahim
- Biology Department, Faculty of Science, Taibah University, Al-Madinah Al- Mounwwarah, KSA
| | - Khalid D. Al-Zhrany
- Biology Department, Faculty of Science, Taibah University, Al-Madinah Al- Mounwwarah, KSA
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41
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de Lima BR, Nicoloso GF, Fatturi-Parolo CC, Ferreira MBC, Montagner F, Casagrande L. Prevotella
strains and lactamic resistance gene distribution in different oral environments of children with pulp necrosis. Int Endod J 2018; 51:1196-1204. [DOI: 10.1111/iej.12948] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 04/30/2018] [Indexed: 11/30/2022]
Affiliation(s)
- B. R. de Lima
- Post-Graduate Program in Dental Clinics; Division of Pediatric Dentistry; Federal University of Rio Grande do Sul - UFRGS; Porto Alegre Brazil
| | - G. F. Nicoloso
- Post-Graduate Program in Dental Clinics; Division of Pediatric Dentistry; Federal University of Rio Grande do Sul - UFRGS; Porto Alegre Brazil
| | - C. C. Fatturi-Parolo
- Division of Cariology; Department of Preventive and Social Dentistry; Federal University of Rio Grande do Sul - UFRGS; Porto Alegre Brazil
| | - M. B. C. Ferreira
- Department of Farmacology; Institute of Basic Health Sciences; Federal University of Rio Grande do Sul - UFRGS; Porto Alegre Brazil
| | - F. Montagner
- Post-Graduate Program in Dental Clinics; Division of Endodontics; Federal University of Rio Grande do Sul - UFRGS; Porto Alegre Brazil
| | - L. Casagrande
- Post-Graduate Program in Dental Clinics; Division of Pediatric Dentistry; Federal University of Rio Grande do Sul - UFRGS; Porto Alegre Brazil
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42
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Wullschleger S, Jans C, Seifert C, Baumgartner S, Lacroix C, Bonfoh B, Stevens MJ, Meile L. Vagococcus teuberi sp. nov., isolated from the Malian artisanal sour milk fènè. Syst Appl Microbiol 2018; 41:65-72. [DOI: 10.1016/j.syapm.2017.11.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 11/03/2017] [Accepted: 11/07/2017] [Indexed: 10/18/2022]
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Abstract
Preharvest food safety research and activities have advanced over time with the recognition of the importance and complicated nature of the preharvest phase of food production. In developed nations, implementation of preharvest food safety procedures along with strict monitoring and containment at various postharvest stages such as slaughter, processing, storage, and distribution have remarkably reduced the burden of foodborne pathogens in humans. Early detection and adequate surveillance of pathogens at the preharvest stage is of the utmost importance to ensure a safe meat supply. There is an urgent need to develop rapid, cost-effective, and point-of-care diagnostics which could be used at the preharvest stage and would complement postmortem and other quality checks performed at the postharvest stage. With newer methods and technologies, more efforts need to be directed toward developing rapid, sensitive, and specific methods for detection or screening of foodborne pathogens at the preharvest stage. In this review, we will discuss the molecular methods available for detection and molecular typing of bacterial foodborne pathogens at the farm. Such methods include conventional techniques such as endpoint PCR, real-time PCR, DNA microarray, and more advanced techniques such as matrix-assisted layer desorption ionization-time of flight mass spectrometry and whole-genome sequencing.
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44
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Jang HM, Lee J, Kim YB, Jeon JH, Shin J, Park MR, Kim YM. Fate of antibiotic resistance genes and metal resistance genes during thermophilic aerobic digestion of sewage sludge. BIORESOURCE TECHNOLOGY 2018; 249:635-643. [PMID: 29091848 DOI: 10.1016/j.biortech.2017.10.073] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 10/13/2017] [Accepted: 10/18/2017] [Indexed: 06/07/2023]
Abstract
This study examines the fate of twenty-three representative antibiotic resistance genes (ARGs) encoding tetracyclines, sulfonamides, quinolones, β-lactam antibiotics, macrolides, florfenicol and multidrug resistance during thermophilic aerobic digestion (TAD) of sewage sludge. The bacterial community, class 1 integrons (intI1) and four metal resistance genes (MRGs) were also quantified to determine the key drivers of changes in ARGs during TAD. At the end of digestion, significant decreases in the quantities of ARGs, MRGs and intI1 as well as 16S rRNA genes were observed. Partial redundancy analysis (RDA) showed that shifts in temperature were the key factors affecting a decrease in ARGs. Shifts in temperature led to decreased amounts of ARGs by reducing resistome and bacterial diversity, rather than by lowering horizontal transfer potential via intI1 or co-resistance via MRGs.
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Affiliation(s)
- Hyun Min Jang
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, Buk-gu, Gwangju 500-712, Republic of Korea
| | - Jangwoo Lee
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, Buk-gu, Gwangju 500-712, Republic of Korea
| | - Young Beom Kim
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, Buk-gu, Gwangju 500-712, Republic of Korea
| | - Jong Hun Jeon
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, Buk-gu, Gwangju 500-712, Republic of Korea
| | - Jingyeong Shin
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, Buk-gu, Gwangju 500-712, Republic of Korea
| | - Mee-Rye Park
- Department of Earth and Environmental Engineering, Columbia University, 500 West 120th Street, New York, NY 10027, United States
| | - Young Mo Kim
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, Buk-gu, Gwangju 500-712, Republic of Korea.
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45
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High diversity and abundance of cultivable tetracycline-resistant bacteria in soil following pig manure application. Sci Rep 2018; 8:1489. [PMID: 29367695 PMCID: PMC5784163 DOI: 10.1038/s41598-018-20050-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 01/12/2018] [Indexed: 11/13/2022] Open
Abstract
By performing a microcosm experiment mimicking fertilization, we assessed the dynamic distribution of tetracycline-resistant bacteria (TRB) and corresponding tetracycline resistance genes (TRGs) from pig manure (PM) to the fertilized soil, by culture-dependent methods and PCR detection. Cultivable TRB were most abundant in PM, followed by fertilized soil and unfertilized soil. By restriction fragment length polymorphism (RFLP) analysis, TRB were assigned to 29, 20, and 153 operational taxonomic units (OTUs) in PM, unfertilized soil, and fertilized soil, respectively. After identification, they were further grouped into 19, 12, and 62 species, showing an enhanced diversity of cultivable TRB in the soil following PM application. The proportions of potentially pathogenic TRB in fertilized soil decreased by 69.35% and 41.92% compared with PM and unfertilized soil. Bacillus cereus was likely widely distributed TRB under various environments, and Rhodococcus erythropolis and Acinetobacter sp. probably spread from PM to the soil via fertilization. Meanwhile, tetL was the most common efflux pump gene in both unfertilized and fertilized soils relative to PM; tetB(P) and tet36 were common in PM, whereas tetO was predominant in unfertilized and fertilized soil samples. Sequencing indicated that over 65% of randomly selected TRB in fertilized soil with acquired resistance derived from PM.
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46
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Riquelme MV, Leng W, Carzolio M, Pruden A, Vikesland P. Stable oligonucleotide-functionalized gold nanosensors for environmental biocontaminant monitoring. J Environ Sci (China) 2017; 62:49-59. [PMID: 29289292 DOI: 10.1016/j.jes.2017.08.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Revised: 08/07/2017] [Accepted: 08/08/2017] [Indexed: 06/07/2023]
Abstract
The global propagation of environmental biocontaminants such as antibiotic resistant pathogens and their antibiotic resistance genes (ARGs) is a public health concern that highlights the need for improved monitoring strategies. Here, we demonstrate the environmental stability and applicability of an oligonucleotide-functionalized gold nanosensor. The mecA ARG was targeted as model biocontaminant due to its presence in clinically-relevant pathogens and to its emergence as an environmental contaminant. mecA-specific nanosensors were tested for antibiotic resistance gene (ARG) detection in ARG-spiked effluent from four wastewater treatment plants (WWTPs). The mecA-specific nanosensors showed stability in environmental conditions and in high ionic strength ([MgCl2]<50mM), and high selectivity against mismatched targets. Spectrophotometric detection was reproducible with an LOD of 70pM (≈4×107genes/μL), even in the presence of interferences associated with non-target genomic DNA and complex WWTP effluent. This contribution supports the environmental applicability of a new line of cost-effective, field-deployable tools needed for wide-scale biocontaminant monitoring.
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Affiliation(s)
- Maria V Riquelme
- Via Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24061, United States
| | - Weinan Leng
- Via Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24061, United States
| | - Marcos Carzolio
- Department of Statistics, Virginia Tech, Blacksburg, VA 24061, United States
| | - Amy Pruden
- Via Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24061, United States
| | - Peter Vikesland
- Via Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24061, United States.
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47
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Águila-Arcos S, Álvarez-Rodríguez I, Garaiyurrebaso O, Garbisu C, Grohmann E, Alkorta I. Biofilm-Forming Clinical Staphylococcus Isolates Harbor Horizontal Transfer and Antibiotic Resistance Genes. Front Microbiol 2017; 8:2018. [PMID: 29085354 PMCID: PMC5650641 DOI: 10.3389/fmicb.2017.02018] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 10/02/2017] [Indexed: 12/11/2022] Open
Abstract
Infections caused by staphylococci represent a medical concern, especially when related to biofilms located in implanted medical devices, such as prostheses and catheters. Unfortunately, their frequent resistance to high doses of antibiotics makes the treatment of these infections a difficult task. Moreover, biofilms represent a hot spot for horizontal gene transfer (HGT) by bacterial conjugation. In this work, 25 biofilm-forming clinical staphylococcal isolates were studied. We found that Staphylococcus epidermidis isolates showed a higher biofilm-forming capacity than Staphylococcus aureus isolates. Additionally, horizontal transfer and relaxase genes of two common staphylococcal plasmids, pSK41 and pT181, were detected in all isolates. In terms of antibiotic resistance genes, aac6-aph2a, ermC, and tetK genes, which confer resistance to gentamicin, erythromycin, and tetracycline, respectively, were the most prevalent. The horizontal transfer and antibiotic resistance genes harbored on these staphylococcal clinical strains isolated from biofilms located in implanted medical devices points to the potential risk of the development and dissemination of multiresistant bacteria.
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Affiliation(s)
- Sandra Águila-Arcos
- Instituto Biofisika (UPV/EHU, CSIC), Department of Biochemistry and Molecular Biology, University of the Basque Country, Bilbao, Spain
| | - Itxaso Álvarez-Rodríguez
- Instituto Biofisika (UPV/EHU, CSIC), Department of Biochemistry and Molecular Biology, University of the Basque Country, Bilbao, Spain
| | - Olatz Garaiyurrebaso
- Instituto Biofisika (UPV/EHU, CSIC), Department of Biochemistry and Molecular Biology, University of the Basque Country, Bilbao, Spain
| | - Carlos Garbisu
- Department of Conservation of Natural Resources, Soil Microbial Ecology Group, NEIKER-Tecnalia, Derio, Spain
| | - Elisabeth Grohmann
- Life Sciences and Technology, Beuth University of Applied Sciences, Berlin, Germany
| | - Itziar Alkorta
- Instituto Biofisika (UPV/EHU, CSIC), Department of Biochemistry and Molecular Biology, University of the Basque Country, Bilbao, Spain
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48
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Shettigar K, Bhat DV, Satyamoorthy K, Murali TS. Severity of drug resistance and co-existence of Enterococcus faecalis in diabetic foot ulcer infections. Folia Microbiol (Praha) 2017; 63:115-122. [PMID: 28889401 DOI: 10.1007/s12223-017-0547-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 09/01/2017] [Indexed: 01/04/2023]
Abstract
The genes encoding aminoglycoside resistance in Enterococcus faecalis may promote collateral aminoglycoside resistance in polymicrobial wounds. We studied a total of 100 diabetic foot ulcer samples for infection and found 60 samples to be polymicrobial, 5 to be monomicrobial, and 35 samples to be culture negative. A total of 65 E. faecalis isolates were screened for six genes coding for aminoglycoside resistance, antibiotic resistance patterns, and biofilm production. Infectious Diseases Society of America/International Working Group on the Diabetic Foot system was used to classify the wound ulcers. Majority of the subjects with culture-positive wound were recommended conservative management, while 14 subjects underwent amputation. Enterococcal isolates showed higher resistance for erythromycin, tetracycline, and ciprofloxacin. Isolates from grade 3 ulcer showed higher frequency of aac(6')-Ie-aph(2″)-Ia, while all the isolates were negative for aph(2″)-Ib, aph(2″)-Ic, and aph(2″)-Id. The isolates from grade 3 ulcers showed higher resistance to aminoglycosides as well as teicoplanin and chloramphenicol. All the 39 biofilm producers were obtained from polymicrobial wound and showed higher resistance when compared to biofilm non-producers. Higher frequency of isolates carrying aac(6')-Ie-aph(2″)-Ia in polymicrobial community showing resistance to key antibiotics suggests widespread distribution of aminoglycoside-resistant E. faecalis and their role in worsening diabetic foot ulcers.
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Affiliation(s)
- Kavitha Shettigar
- Department of Biotechnology, School of Life Sciences, Manipal University, Manipal, 576104, India
| | - Deepika V Bhat
- Department of Biotechnology, School of Life Sciences, Manipal University, Manipal, 576104, India
| | - Kapaettu Satyamoorthy
- Department of Cellular and Molecular Biology, School of Life Sciences, Manipal University, Manipal, 576104, India
| | - Thokur Sreepathy Murali
- Department of Biotechnology, School of Life Sciences, Manipal University, Manipal, 576104, India.
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49
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Gao W, Li B, Yao R, Li Z, Wang X, Dong X, Qu H, Li Q, Li N, Chi H, Zhou B, Xia Z. Intuitive Label-Free SERS Detection of Bacteria Using Aptamer-Based in Situ Silver Nanoparticles Synthesis. Anal Chem 2017; 89:9836-9842. [PMID: 28803475 DOI: 10.1021/acs.analchem.7b01813] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The characteristic of an ideal bacteria-detection method should have high sensitivity and specificity, be easy to operate, and not have a time-consuming culture process. In this study, we report a new bacteria-detection strategy that can recognize bacteria quickly and directly by surface-enhanced Raman scattering (SERS) with the formation of well-defined bacteria-aptamer@AgNPs. SERS signals generated by bacteria-aptamer@AgNPs exhibited a linear dependence on bacteria (R2 = 0.9671) concentration ranging from 101 to 107 cfu/mL. The detection limit is sensitive down to 1.5 cfu/mL. Meanwhile, the bacteria SERS signal was dramatically enhanced by its specifically recognized aptamer, and the bacteria could be identified directly and visually through the SERS spectrum. This strategy eliminates the puzzling data analysis of previous studies and offers significant advantages over existing approaches, getting a critical step toward the creation of SERS-based biochips for rapid in situ bacteria detection in mixture samples.
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Affiliation(s)
- Weicun Gao
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, AMMS Changchun 130122, China.,College of Animal Sciences and Technology, Jilin Agricultural University , Changchun 130118, China
| | - Bo Li
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, AMMS Changchun 130122, China
| | - Ruizhi Yao
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University , Daqing 163000, Heilongjiang, China
| | - Zhiping Li
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, AMMS Changchun 130122, China
| | - Xiwen Wang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, AMMS Changchun 130122, China
| | - Xiaolin Dong
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, AMMS Changchun 130122, China
| | - Han Qu
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, AMMS Changchun 130122, China
| | - Qianxue Li
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, AMMS Changchun 130122, China
| | - Nan Li
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, AMMS Changchun 130122, China
| | - Hang Chi
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, AMMS Changchun 130122, China
| | - Bo Zhou
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, AMMS Changchun 130122, China
| | - Zhiping Xia
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, AMMS Changchun 130122, China
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50
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Štšepetova J, Taelma H, Smidt I, Hütt P, Lapp E, Aotäht E, Mändar R. Assessment of phenotypic and genotypic antibiotic susceptibility of vaginalLactobacillussp. J Appl Microbiol 2017; 123:524-534. [DOI: 10.1111/jam.13497] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 05/02/2017] [Accepted: 05/19/2017] [Indexed: 12/12/2022]
Affiliation(s)
- J. Štšepetova
- Department of Microbiology; Institute of Biomedicine and Translational Medicine; University of Tartu; Tartu Estonia
- Competence Centre on Health Technologies; Tartu Estonia
| | - H. Taelma
- Department of Microbiology; Institute of Biomedicine and Translational Medicine; University of Tartu; Tartu Estonia
| | - I. Smidt
- Department of Microbiology; Institute of Biomedicine and Translational Medicine; University of Tartu; Tartu Estonia
- Competence Centre on Health Technologies; Tartu Estonia
| | - P. Hütt
- Department of Microbiology; Institute of Biomedicine and Translational Medicine; University of Tartu; Tartu Estonia
| | - E. Lapp
- Department of Microbiology; Institute of Biomedicine and Translational Medicine; University of Tartu; Tartu Estonia
| | - E. Aotäht
- Tartu Health Care Colleges; Tartu Estonia
| | - R. Mändar
- Department of Microbiology; Institute of Biomedicine and Translational Medicine; University of Tartu; Tartu Estonia
- Competence Centre on Health Technologies; Tartu Estonia
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