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Yan Y, Li X, Yu K, Wu Z, Sun Y, Cheng Z, Zhao B, Nie C, Xia Y. Systematic evaluation of the impact of standard storage conditions on plasmid conjugation behavior in wastewater samples. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 343:123283. [PMID: 38176637 DOI: 10.1016/j.envpol.2023.123283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 11/29/2023] [Accepted: 12/30/2023] [Indexed: 01/06/2024]
Abstract
Filter mating experiment is widely used to study the conjugation behavior of plasmids and associated antibiotic resistance in environmental settings, however, the influence and biases brought by sample storage conditions (temperature and duration) were not yet systematically elaborated. This study systematically investigated the influence of standard storage conditions (4 °C, -20 °C, -80 °C) on plasmid conjugation behavior in influent (Inf) and activated sludge (AS) samples from sewage treatment plants (STP). The findings revealed a significant reduction in conjugation efficiency under all the tested storage conditions except for 1-week storage at 4 °C. Notably, storing at -80 °C maintained conjugation activities in activated sludge more effectively compared to -20 °C. However, the preservation performance was less effective for influent samples, which consist mainly of anaerobe-dominant communities. Systematic loss of IncH-type plasmids was observed in influent samples stored at 4 °C and -20 °C. Correspondingly, the plasmid-carrying resistome genotypes detected in the influent samples showed a clear downward trend with the increase in storage duration when stored at 4 °C and -20 °C. A relatively uniform composition in terms of incompatibility type and resistome profile was observed across activated sludge samples, regardless of the varied storage conditions. This study highlights the critical impact of storage conditions on plasmid conjugation behavior and resistome composition, offering valuable insights for optimal sample handling in resistome research.
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Affiliation(s)
- Yuxi Yan
- School of Environment, Harbin Institute of Technology, Harbin 150001, China; School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xiang Li
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Kaiqiang Yu
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ziqi Wu
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yuhong Sun
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Zhanwen Cheng
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Bixi Zhao
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Cailong Nie
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yu Xia
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China; State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China; Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China.
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Adedokun FL, Ajayi A, Essiet UU, Oduyebo O, Adeleye AI, Smith SI. Antibiotic Resistance and Plasmid Replicon Types of Non-Typhoidal Salmonella Serovars Isolated From Food Animals and Humans in Lagos, Nigeria. Microbiol Insights 2023; 16:11786361231181909. [PMID: 37377945 PMCID: PMC10291401 DOI: 10.1177/11786361231181909] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023] Open
Abstract
Multidrug resistance and invasiveness of non-typhoidal Salmonella (NTS) serovars have in recent times brought to the fore the public health risk associated with salmonellosis. This study was aimed at profiling NTS serovars isolated from food animals and humans for their susceptibility to antibiotics and plasmid replicon types. Forty seven NTS serovars were profiled for their susceptibility to antibiotics using the disk diffusion method. Polymerase chain reaction based replicon typing assay was used for profiling plasmid replicon types detected in Salmonella isolates. High rate of resistance were found for amoxicillin/clavulanic acid (40/47; 85.1%), cefuroxime (38/47; 80.9%) and ceftazidime (30/47; 63.8%). Thirty one (65.9%) and 33 (70.2%) showed intermediate resistance to ofloxacin and ciprofloxacin respectively. Plasmids of sizes ranging from 14.3 to 16.7 kb were detected in 24 (51.1%) of Salmonella isolates with some serovars harbouring multiple plasmids. FIA, FIB, Frep and W plasmid replicon types were detected in 11, 4, 2 and 1 of the Salmonella isolates respectively. Three of the isolates harboured both FIA and FIB replicon types. The high rate of resistance to β-lactams observed in Salmonella serovars harbouring different plasmid replicon types in this study highlight potential public health threat and the need for prudent use of antibiotics in human and veterinary medicine.
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Affiliation(s)
| | - Abraham Ajayi
- Molecular Biology and Biotechnology Department, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | - Utibeima Udo Essiet
- Molecular Biology and Biotechnology Department, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | - Oyin Oduyebo
- Department of Medical Microbiology, College Medicine University of Lagos, Idi-Araba, Lagos, Nigeria
| | | | - Stella Ifeanyi Smith
- Molecular Biology and Biotechnology Department, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
- Department of Biological Sciences, Mountain Top University, Ogun State, Nigeria
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3
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Stockdale SR, Hill C. Incorporating plasmid biology and metagenomics into a holistic model of the human gut microbiome. Curr Opin Microbiol 2023; 73:102307. [PMID: 37002975 DOI: 10.1016/j.mib.2023.102307] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 02/14/2023] [Accepted: 03/05/2023] [Indexed: 04/01/2023]
Abstract
The human gut microbiome is often described as the collection of bacteria, archaea, fungi, protists, and viruses associated with an individual, with no acknowledgement of the plasmid constituents. However, like viruses, plasmids are autonomous intracellular replicating entities that can influence the genotype and phenotype of their host and mediate trans-kingdom interactions. Plasmids are frequently noted as vehicles for horizontal gene transfer and for spreading antibiotic resistance, yet their multifaceted contribution to mutualistic and antagonistic interactions within the human microbiome and impact on human health is overlooked. In this review, we highlight the importance of plasmids and their biological properties as overlooked components of microbiomes. Subsequent human microbiome studies should include dedicated analyses of plasmids, particularly as a holistic understanding of human-microbial interactions is required before effective and safe interventions can be implemented to improve human well-being.
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4
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Kariuki S, Kering K, Wairimu C, Onsare R, Mbae C. Antimicrobial Resistance Rates and Surveillance in Sub-Saharan Africa: Where Are We Now? Infect Drug Resist 2022; 15:3589-3609. [PMID: 35837538 PMCID: PMC9273632 DOI: 10.2147/idr.s342753] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 06/16/2022] [Indexed: 01/03/2023] Open
Abstract
Introduction Although antimicrobials have traditionally been used to treat infections and improve health outcomes, resistance to commonly used antimicrobials has posed a major challenge. An estimated 700,000 deaths occur globally every year as a result of infections caused by antimicrobial-resistant pathogens. Antimicrobial resistance (AMR) also contributes directly to the decline in the global economy. In 2019, sub-Saharan Africa (SSA) had the highest mortality rate (23.5 deaths per 100,000) attributable to AMR compared to other regions. Methods We searched PubMed for articles relevant to AMR in pathogens in the WHO-GLASS list and in other infections of local importance in SSA. In this review, we focused on AMR rates and surveillance of AMR for these priority pathogens and some of the most encountered pathogens of public health significance. In addition, we reviewed the implementation of national action plans to mitigate against AMR in countries in SSA. Results and Discussion The SSA region is disproportionately affected by AMR, in part owing to the prevailing high levels of poverty, which result in a high burden of infectious diseases, poor regulation of antimicrobial use, and a lack of alternatives to ineffective antimicrobials. The global action plan as a strategy for prevention and combating AMR has been adopted by most countries, but fewer countries are able to fully implement country-specific action plans, and several challenges exist in many settings. Conclusion A concerted One Health approach will be required to ramp up implementation of action plans in the region. In addition to AMR surveillance, effective implementation of infection prevention and control, water, sanitation, and hygiene, and antimicrobial stewardship programs will be key cost-effective strategies in helping to tackle AMR.
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Affiliation(s)
- Samuel Kariuki
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya,Correspondence: Samuel Kariuki, Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya, Email
| | - Kelvin Kering
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Celestine Wairimu
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Robert Onsare
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Cecilia Mbae
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
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Epidemiology of Plasmids in Escherichia coli and Klebsiella pneumoniae with Acquired Extended Spectrum Beta-Lactamase Genes Isolated from Chronic Wounds in Ghana. Antibiotics (Basel) 2022; 11:antibiotics11050689. [PMID: 35625333 PMCID: PMC9138140 DOI: 10.3390/antibiotics11050689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/14/2022] [Accepted: 05/17/2022] [Indexed: 11/30/2022] Open
Abstract
Little information is available on the local epidemiology of mobile genetic elements such as plasmids harboring acquired beta-lactamase genes in Western African Ghana. In the present study, we screened for plasmids in three Escherichia coli and four Klebsiella pneumoniae isolates expressing extended spectrum beta-lactamases (ESBL) mediated by the blaCTX-M-15 gene from chronically infected wounds of Ghanaian patients. Bacterial isolates were subjected to combined short-read and long-read sequencing to obtain the sequences of their respective plasmids. In the blaCTX-M-15-gene-carrying plasmids of the four ESBL-positive K. pneumoniae isolates, IncFIB/IncFII (n = 3) and FIA (n = 1) sequences were detected, while in the blaCTX-M-15-gene-carrying plasmids of the three ESBL-positive E. coli isolates, IncFIA/IncFIB (n = 2) and IncFIB (n = 1) sequences were found. The three IncFIB/IncFII sequence-containing plasmids were almost identical to a K. pneumoniae plasmid reported from France. They belonged to the clonal lineages ST17, ST36 and ST39 of K. pneumoniae, suggesting transversal spread of this obviously evolutionary successful plasmid in Ghana. Other resistance gene-encoding plasmids observed in the assessed Enterobacterales harbored IncFIA/IncR and IncFII sequences. International spread was confirmed by the high genetic similarity to resistance-mediating plasmids published from Asia, Australia, Europe and Northern America, including a blaCTX-M-15-gene-carrying plasmid isolated from a wild bird in Germany. In conclusion, the study contributed to the scarcely available information on the epidemiology of third-generation cephalosporine resistance-mediating plasmids in Ghana. Furthermore, the global spread of resistance-mediating plasmids provided hints on the evolutionary success of individual resistance-harboring plasmids by transversal spread among K. pneumoniae lineages in Ghana.
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Puangseree J, Prathan R, Srisanga S, Angkittitrakul S, Chuanchuen R. Plasmid profile analysis of Escherichia coli and Salmonella enterica isolated from pigs, pork and humans. Epidemiol Infect 2022; 150:e110. [PMID: 35535461 PMCID: PMC9214845 DOI: 10.1017/s0950268822000814] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 04/16/2022] [Accepted: 04/18/2022] [Indexed: 11/17/2022] Open
Abstract
This study aimed to determine the epidemiology and association of antimicrobial resistance (AMR) among Escherichia coli and Salmonella in Thailand. The E. coli (n = 1047) and Salmonella (n = 816) isolates from pigs, pork and humans were screened for 18 replicons including HI1, HI2, I1-γ, X, L/M, N, FIA, FIB, W, Y, P, FIC, A/C, T, FIIAs, F, K and B/O using polymerase chain reaction-based replicon typing. The E. coli (n = 26) and Salmonella (n = 3) isolates carrying IncF family replicons, ESBL and/or mcr genes were determined for FAB formula. IncF represented the major type of plasmids. Sixteen and eleven Inc groups were identified in E. coli (85.3%) and Salmonella (25.7%), respectively. The predominant replicon patterns between E. coli and Salmonella were IncK-F (23.7%) and IncF (46.2%). Significant correlations (P < 0.05) were observed between plasmid-replicon type and resistance phenotype. Plasmid replicon types were significantly different among sources of isolates and sampling periods. The most common FAB types between E. coli and Salmonella were F2:A-:B- (30.8%) and S1:A-:B- (66.7%), respectively. In conclusion, various plasmids present in E. coli and Salmonella. Responsible and prudent use of antimicrobials is suggested to reduce the selective pressures that favour the spread of AMR determinants. Further studies to understand the evolution of R plasmids and their contribution to the dissemination of AMR genes are warranted.
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Affiliation(s)
- Jiratchaya Puangseree
- Research Unit for Microbial Food Safety and Antimicrobial Resistance, Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Rangsiya Prathan
- Research Unit for Microbial Food Safety and Antimicrobial Resistance, Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
- Center for Antimicrobial Resistance Monitoring in Food-borne Pathogens, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Songsak Srisanga
- Research Unit for Microbial Food Safety and Antimicrobial Resistance, Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
- Center for Antimicrobial Resistance Monitoring in Food-borne Pathogens, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
| | | | - Rungtip Chuanchuen
- Research Unit for Microbial Food Safety and Antimicrobial Resistance, Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
- Center for Antimicrobial Resistance Monitoring in Food-borne Pathogens, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
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Montelongo Hernandez C, Putonti C, Wolfe AJ. Profiling the plasmid conjugation potential of urinary Escherichia coli. Microb Genom 2022; 8:mgen000814. [PMID: 35536743 PMCID: PMC9465074 DOI: 10.1099/mgen.0.000814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 03/16/2022] [Indexed: 11/18/2022] Open
Abstract
Escherichia coli is often associated with urinary tract infection (UTI). Antibiotic resistance in E. coli is an ongoing challenge in managing UTI. Extrachromosomal elements - plasmids - are vectors for clinically relevant traits, such as antibiotic resistance, with conjugation being one of the main methods for horizontal propagation of plasmids in bacterial populations. Targeting of conjugation components has been proposed as a strategy to curb the spread of plasmid-borne antibiotic resistance. Understanding the types of conjugative systems present in urinary E. coli isolates is fundamental to assessing the viability of this strategy. In this study, we profile two well-studied conjugation systems (F-type and P-type) in the draft genomes of 65 urinary isolates of E. coli obtained from the bladder urine of adult women with and without UTI-like symptoms. Most of these isolates contained plasmids and we found that conjugation genes were abundant/ubiquitous, diverse and often associated with IncF plasmids. To validate conjugation of these urinary plasmids, the plasmids from two urinary isolates, UMB1223 (predicted to have F-type genes) and UMB1284 (predicted to have P-type genes), were transferred by conjugation into the K-12 E. coli strain MG1655. Overall, the findings of this study support the notion that care should be taken in targeting any individual component of a urinary E. coli isolate's conjugation system, given the inherent mechanistic redundancy, gene diversity and different types of conjugation systems in this population.
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Affiliation(s)
- Cesar Montelongo Hernandez
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
| | - Catherine Putonti
- Bioinformatics Program, Loyola University Chicago, Chicago, IL 60660, USA
- Department of Biology, Loyola University Chicago, Chicago, IL 60660, USA
| | - Alan J. Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
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Li IC, Wu HH, Chen ZW, Chou CH. Prevalence of IncFIB Plasmids Found among Salmonella enterica Serovar Schwarzengrund Isolates from Animal Sources in Taiwan Using Whole-Genome Sequencing. Pathogens 2021; 10:pathogens10081024. [PMID: 34451486 PMCID: PMC8399590 DOI: 10.3390/pathogens10081024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 08/12/2021] [Accepted: 08/12/2021] [Indexed: 11/22/2022] Open
Abstract
Salmonella enterica serovar Schwarzengrund is one of the most frequently isolated Salmonella serotypes responsible for human and poultry infections in Taiwan, and it has raised public health concerns. To better facilitate the understanding of transmission patterns and the dynamics of epidemics, sharing molecular data on pathogen profiles is urgently needed. The objectives of the current study were to determine and establish baseline data of S. enterica serovar Schwarzengrund isolates from 23 epidemiologically unrelated sources from year 2000 to 2018 and examine their phenotypic and genotypic characteristics. Genomic DNA of the Salmonella isolates was extracted and subjected to whole-genome sequencing using an Illumina platform. Results showed that all selected isolates exhibited multidrug resistance, and six of those were resistant to ciprofloxacin phenotypically. Genotypically, these isolates carried genes resistant to aminoglycoside (100%), phenicol (91.3%), β-lactams (69.5%), folate pathway antagonist (100%), tetracycline (82.6%), and fluoroquinolone (4.3%). Moreover, these isolates harbor integrons with five different gene cassettes identified for the first time, which are associated with resistance to trimethoprim, streptomycin, tetracycline, sulfonamide, chloramphenicol, and gentamicin. Furthermore, prevalence of IncFIB plasmid was found among studied isolates, which may increase its ability to colonize the chicken cecum and cause extra-intestinal disease. Salmonella pathogenicity islands SPI-1 to SPI-5, SPI-13, and SPI-14, as well as C63PI locus, were also detected in all isolates. This study demonstrated that a considerable high antimicrobial resistance with high virulence levels of Salmonella were found from animal sources. Sharing data on these pathogen profiles can not only help increase the reproducibility and accessibility of genomic analysis but can also support surveillance and epidemiological investigations for salmonellosis in the region.
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Affiliation(s)
- I-Chen Li
- Zoonoses Research Center, School of Veterinary Medicine, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei City 106, Taiwan;
| | - Hsiu-Hui Wu
- Animal Technology Research Center, Agricultural Technology Research Institute, No. 52, Kedong 2nd Road, Zhunan Township, Miaoli County 350, Taiwan;
| | - Zeng-Weng Chen
- Animal Technology Research Center, Agricultural Technology Research Institute, No. 52, Kedong 2nd Road, Zhunan Township, Miaoli County 350, Taiwan;
- Correspondence: (Z.-W.C.); (C.-H.C.); Tel.: +886-37-585-851 (Z.-W.C.); +886-2-3366-3861 (C.-H.C.); Fax: +886-2-2364-9154 (C.-H.C.)
| | - Chung-Hsi Chou
- Zoonoses Research Center, School of Veterinary Medicine, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei City 106, Taiwan;
- Correspondence: (Z.-W.C.); (C.-H.C.); Tel.: +886-37-585-851 (Z.-W.C.); +886-2-3366-3861 (C.-H.C.); Fax: +886-2-2364-9154 (C.-H.C.)
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Wang T, Weiss A, Ha Y, You L. Predicting plasmid persistence in microbial communities by coarse-grained modeling. Bioessays 2021; 43:e2100084. [PMID: 34278591 DOI: 10.1002/bies.202100084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 06/15/2021] [Accepted: 06/17/2021] [Indexed: 11/08/2022]
Abstract
Plasmids are a major type of mobile genetic elements (MGEs) that mediate horizontal gene transfer. The stable maintenance of plasmids plays a critical role in the functions and survival for microbial populations. However, predicting and controlling plasmid persistence and abundance in complex microbial communities remain challenging. Computationally, this challenge arises from the combinatorial explosion associated with the conventional modeling framework. Recently, a plasmid-centric framework (PCF) has been developed to overcome this computational bottleneck. This framework enables the derivation of a simple metric, the persistence potential, to predict plasmid persistence and abundance. Here, we discuss how PCF can be extended to account for plasmid interactions. We also discuss how such model-guided predictions of plasmid fates can benefit from the development of new experimental tools and data-driven computational methods.
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Affiliation(s)
- Teng Wang
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
| | - Andrea Weiss
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
| | - Yuanchi Ha
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA.,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, USA.,Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
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Sklyar T, Kurahina N, Lavrentieva K, Burlaka V, Lykholat T, Lykholat O. Autonomic (Mobile) Genetic Elements of Bacteria and Their Hierarchy. CYTOL GENET+ 2021. [DOI: 10.3103/s0095452721030099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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11
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Hassen B, Abbassi MS, Ruiz-Ripa L, Mama OM, Ibrahim C, Benlabidi S, Hassen A, Torres C, Hammami S. Genetic characterization of extended-spectrum β-lactamase-producing Enterobacteriaceae from a biological industrial wastewater treatment plant in Tunisia with detection of the colistin-resistance mcr-1 gene. FEMS Microbiol Ecol 2021; 97:5986610. [PMID: 33202005 DOI: 10.1093/femsec/fiaa231] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 11/13/2020] [Indexed: 12/14/2022] Open
Abstract
This study evaluated the occurrence of extended-spectrum β-lactamases (ESBL) and associated resistance genes, integrons, and plasmid types, as well as the genetic relatedness of enterobacterial isolates in the wastewater treatment plant (WWTP) of La Charguia, Tunis City (Tunisia). A total of 100 water samples were collected at different points of the sewage treatment process during 2017-2019. Antimicrobial susceptibility was conducted by the disc-diffusion method. blaCTX-M, blaTEM and blaSHV genes as well as those encoding non-β-lactam resistance, the plasmid types, occurrence of class1 integrons and phylogenetic groups of Escherichia coli isolates were determined by PCR/sequencing. Genomic relatedness was determined by multi-locus sequence typing (MLST) for selected isolates. In total, 57 ESBL-producer isolates were recovered (47 E. coli, eight Klebsiella pneumoniae, 1 of the Citrobacter freundii complex and 1 of the Enterobacter cloacae complex). The CTX-M-15 enzyme was the most frequently detected ESBL, followed by CTX-M-27, CTX-M-55 and SHV-12. One E. coli isolate harboured the mcr-1 gene. The following phylogroups/sequence types (STs) were identified among ESBL-producing E. coli isolates: B2/ST131 (subclade-C1), A/ST3221, A/ST8900, D/ST69, D/ST2142, D/ST38, B1/ST2460 and B1/ST6448. High numbers of isolates harboured the class 1 integrons with various gene cassette arrays as well as IncP-1 and IncFIB plasmids. Our findings confirm the importance of WWTPs as hotspot collectors of ESBL-producing Enterobacteriaceae with a high likelihood of spread to human and natural environments.
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Affiliation(s)
- Bilel Hassen
- Université de Tunis El Manar, Institut de la Recherche Vétérinaire de Tunisie, 20 rue Jebel Lakhdhar, Bab Saadoun, Tunis 1006, Tunisia
| | - Mohamed Salah Abbassi
- Université de Tunis El Manar, Institut de la Recherche Vétérinaire de Tunisie, 20 rue Jebel Lakhdhar, Bab Saadoun, Tunis 1006, Tunisia.,Université de Tunis El Manar, Faculté de Médecine de Tunis, Laboratoire de résistance aux antibiotiques LR99ES09, Tunisia
| | - Laura Ruiz-Ripa
- Departamento de Agricultura y Alimentación, Universidad de La Rioja, 26006 Logroño, Spain
| | - Olouwafemi M Mama
- Departamento de Agricultura y Alimentación, Universidad de La Rioja, 26006 Logroño, Spain
| | - Chourouk Ibrahim
- Laboratoire de Traitement et de Valorisation des rejets hydriques, Centre des Recherches et des Technologies des Eaux (CERTE), Technopole Borj-Cédria, BP 273, 8020, Soliman, Tunisia
| | - Saloua Benlabidi
- Université de Tunis El Manar, Institut de la Recherche Vétérinaire de Tunisie, 20 rue Jebel Lakhdhar, Bab Saadoun, Tunis 1006, Tunisia
| | - Abdennaceur Hassen
- Laboratoire de Traitement et de Valorisation des rejets hydriques, Centre des Recherches et des Technologies des Eaux (CERTE), Technopole Borj-Cédria, BP 273, 8020, Soliman, Tunisia
| | - Carmen Torres
- Departamento de Agricultura y Alimentación, Universidad de La Rioja, 26006 Logroño, Spain
| | - Salah Hammami
- Université de la Manouba, IRESA, École Nationale de Médecine Vétérinaire de Sidi Thabet, Sidi Thabet 2020, Sidi Thabet, Ariana, Tunisia
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12
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Genomic investigation of antimicrobial resistance determinants and virulence factors in Salmonella enterica serovars isolated from contaminated food and human stool samples in Brazil. Int J Food Microbiol 2021; 343:109091. [PMID: 33639477 DOI: 10.1016/j.ijfoodmicro.2021.109091] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 01/07/2021] [Accepted: 02/02/2021] [Indexed: 12/20/2022]
Abstract
This study investigated the antimicrobial resistance determinants, virulence factors and identified serovars in 37 Salmonella enterica strains isolated from human stool and contaminated foods linked to outbreaks that occurred in Brazil over 7 years using whole genome sequencing (WGS). Phylogenetic analysis of selected serovars (S. Typhimurium, S. Infantis, S. London, and S. Johannesburg) was performed. Ten distinct serovars were identified and, 51% of the tested strains (n = 19) showed disagreement with the previous conventional serotyping. The antimicrobial resistance (AMR) determinants or plasmids varied among the strains. Resistome analysis revealed the presence of resistance genes to aminoglycosides [aac (6')-laa, aph (3″)-lb, aph (6)-ld, aadA1 and aadA2], sulfonamides (sul1), trimethoprin (dfrA8), fosfomycin (fosA7) and tetracyclines (tetA, tetB, tetC), as well as point mutations in parC (T57S) and gyrA (S83F). Plasmidome showed the presence of IncHI2, IncHI2A, IncFIB (S), IncFII (S), IncI1 and p0111 plasmids. Eight Salmonella pathogenicity islands and up to 102 stress and/or virulence genes were identified in the evaluated genomes. Virulence genes of K88 fimbrial adhesin were first reported in S. enterica (S. Pomona, S. Bredeney and S. Mbandaka strains). pilW gene was first identified in S. Pomona. Phylogenetic analysis showed that some serovars circulated in Brazil for decades, primarily within the poultry production chain. Findings highlighted the virulence and AMR determinants in strains that may lead to recurring food outbreaks.
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Nyirabahizi E, Tyson GH, Dessai U, Zhao S, Kabera C, Crarey E, Womack N, Crews MK, Strain E, Tate H. Evaluation of Escherichia coli as an indicator for antimicrobial resistance in Salmonella recovered from the same food or animal ceca samples. Food Control 2020. [DOI: 10.1016/j.foodcont.2020.107280] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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