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Zdarska V, Kolar M, Mlynarcik P. Occurrence of beta-lactamases in bacteria. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 122:105610. [PMID: 38810790 DOI: 10.1016/j.meegid.2024.105610] [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: 11/21/2023] [Revised: 05/21/2024] [Accepted: 05/25/2024] [Indexed: 05/31/2024]
Abstract
Our study highlights the escalating issue of beta-lactam resistance in nosocomial pathogens, driven by the broad spectrum of antibiotic-degrading enzymes and plasmid exchange. We catalogued known beta-lactamases across 230 bacterial genera, identified 2349 potential beta-lactamases across over 673 genera, and anticipate discovering many new types, underscoring the need for targeted gene analysis in combating resistance. This study also elucidates the complex relationship between the diversity and frequency of beta-lactamase genes across bacterial genera, highlighting the need for genus-specific approaches in combating antibiotic resistance and emphasizing these genes' significant global distribution and host-specific prevalence. We report many transcriptional regulators, transposases and other factors in the genomes of 20 different bacterial isolates, some of which are consistent with the ability of these species to adapt to different environments. Although we could not determine precisely which factors regulate the presence of beta-lactamases in specific bacteria, we found that the proportion of regulatory genes, the size of the genome, and other factors are not decisive. Further studies are needed to elucidate key aspects of this process.
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Affiliation(s)
- Veronika Zdarska
- Department of Microbiology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Hnevotinska 3, 775 15 Olomouc, Czechia.
| | - Milan Kolar
- Department of Microbiology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Hnevotinska 3, 775 15 Olomouc, Czechia.
| | - Patrik Mlynarcik
- Department of Microbiology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Hnevotinska 3, 775 15 Olomouc, Czechia.
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Abioye OE, Nontongana N, Osunla CA, Okoh AI. Antibiotic resistance and virulence genes profiling of Vibrio cholerae and Vibrio mimicus isolates from some seafood collected at the aquatic environment and wet markets in Eastern Cape Province, South Africa. PLoS One 2023; 18:e0290356. [PMID: 37616193 PMCID: PMC10449182 DOI: 10.1371/journal.pone.0290356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 08/04/2023] [Indexed: 08/26/2023] Open
Abstract
The current study determines the density of Vibrio spp. and isolates V. cholerae and Vibrio mimicus from fish-anatomical-sites, prawn, crab and mussel samples recovered from fish markets, freshwater and brackish water. Virulence and antibiotic resistance profiling of isolates were carried out using standard molecular and microbiology techniques. Vibrio spp. was detected in more than 90% of samples [134/144] and its density was significantly more in fish than in other samples. Vibrio. cholerae and V. mimicus were isolated in at least one sample of each sample type with higher isolation frequency in fish samples. All the V. cholerae isolates belong to non-O1/non-O139 serogroup. One or more V. cholerae isolates exhibited intermediate or resistance against each of the eighteen panels of antibiotics used but 100% of the V. mimicus were susceptible to amikacin, gentamycin and chloramphenicol. Vibrio cholerae exhibited relatively high resistance against polymyxin, ampicillin and amoxicillin/clavulanate while V. mimicus isolates exhibited relatively high resistance against nitrofurantoin, ampicillin and polymixin. The multiple-antibiotic-resistance-index [MARI] for isolates ranges between 0 and 0.67 and 48% of the isolates have MARI that is >0.2 while 55% of the isolates exhibit MultiDrug Resistance Phenotypes. The percentage detection of acc, ant, drf18, sul1, mcr-1, blasvh, blaoxa, blatem, blaoxa48, gyrA, gyrB and parC resistance-associated genes were 2%, 9%, 14%, 7%, 2%, 25%, 7%, 2%, 2%, 32%, 25% and 27% respectively while that for virulence-associated genes in increasing other was ace [2%], tcp [11%], vpi [16%], ompU [34%], toxR [43%], rtxC [70%], rtxA [73%] and hyla [77%]. The study confirmed the potential of environmental non-O1/non-O139 V. cholerae and V. mimicus to cause cholera-like infection and other vibriosis which could be difficult to manage with commonly recommended antibiotics. Thus, regular monitoring of the environment to create necessary awareness for this kind of pathogens is important in the interest of public health.
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Affiliation(s)
| | - Nolonwabo Nontongana
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa
| | - Charles A. Osunla
- Department of Microbiology, Adekunle Ajasin University, Akungba Akoko, Nigeria
| | - Anthony I. Okoh
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa
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Caudell MA, Ayodo C, Ita T, Smith RM, Luvsansharav UO, Styczynski AR, Ramay BM, Kariuki S, Palmer GH, Call DR, Omulo S. Risk Factors for Colonization With Multidrug-Resistant Bacteria in Urban and Rural Communities in Kenya: An Antimicrobial Resistance in Communities and Hospitals (ARCH) Study. Clin Infect Dis 2023; 77:S104-S110. [PMID: 37406050 DOI: 10.1093/cid/ciad223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023] Open
Abstract
BACKGROUND Colonization with antimicrobial-resistant bacteria increases the risk of drug-resistant infections. We identified risk factors potentially associated with human colonization with extended-spectrum cephalosporin-resistant Enterobacterales (ESCrE) in low-income urban and rural communities in Kenya. METHODS Fecal specimens, demographic and socioeconomic data were collected cross-sectionally from clustered random samples of respondents in urban (Kibera, Nairobi County) and rural (Asembo, Siaya County) communities between January 2019 and March 2020. Presumptive ESCrE isolates were confirmed and tested for antibiotic susceptibility using the VITEK2 instrument. We used a path analytic model to identify potential risk factors for colonization with ESCrE. Only 1 participant was included per household to minimize household cluster effects. RESULTS Stool samples from 1148 adults (aged ≥18 years) and 268 children (aged <5 years) were analyzed. The likelihood of colonization increased by 12% with increasing visits to hospitals and clinics. Furthermore, individuals who kept poultry were 57% more likely to be colonized with ESCrE than those who did not. Respondents' sex, age, use of improved toilet facilities, and residence in a rural or urban community were associated with healthcare contact patterns and/or poultry keeping and may indirectly affect ESCrE colonization. Prior antibiotic use was not significantly associated with ESCrE colonization in our analysis. CONCLUSIONS The risk factors associated with ESCrE colonization in communities include healthcare- and community-related factors, indicating that efforts to control antimicrobial resistance in community settings must include community- and hospital-level interventions.
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Affiliation(s)
- Mark A Caudell
- Paul G. Allen School for Global Health, Washington State University, Pullman, Washington, USA
| | - Charchil Ayodo
- Washington State University Global Health-Kenya, Nairobi, Kenya
| | - Teresa Ita
- Washington State University Global Health-Kenya, Nairobi, Kenya
| | - Rachel M Smith
- Division of Healthcare Quality Promotion, US Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Ulzii-Orshikh Luvsansharav
- Division of Healthcare Quality Promotion, US Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Ashley R Styczynski
- Division of Healthcare Quality Promotion, US Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Brooke M Ramay
- Paul G. Allen School for Global Health, Washington State University, Pullman, Washington, USA
- Center for Health Studies, Universidad del Valle de Guatemala, Guatemala City, Guatemala
| | | | - Guy H Palmer
- Paul G. Allen School for Global Health, Washington State University, Pullman, Washington, USA
- Washington State University Global Health-Kenya, Nairobi, Kenya
- University of Nairobi Institute of Tropical and Infectious Diseases, Nairobi, Kenya
| | - Douglas R Call
- Paul G. Allen School for Global Health, Washington State University, Pullman, Washington, USA
| | - Sylvia Omulo
- Paul G. Allen School for Global Health, Washington State University, Pullman, Washington, USA
- Washington State University Global Health-Kenya, Nairobi, Kenya
- University of Nairobi Institute of Tropical and Infectious Diseases, Nairobi, Kenya
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Obioha PI, Anyogu A, Awamaria B, Ghoddusi HB, Ouoba LII. Antimicrobial Resistance of Lactic Acid Bacteria from Nono, a Naturally Fermented Milk Product. Antibiotics (Basel) 2023; 12:antibiotics12050843. [PMID: 37237746 DOI: 10.3390/antibiotics12050843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/27/2023] [Accepted: 04/29/2023] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR) is one of the biggest threats to public health. The food chain has been recognised as a vehicle for transmitting AMR bacteria. However, information about resistant strains isolated from African traditional fermented foods remains limited. Nono is a traditional, naturally fermented milk product consumed by many pastoral communities across West Africa. The main aim of this study was to investigate and determine the AMR patterns of lactic acid bacteria (LAB) involved in the traditional fermentation of milk for Nono production, and the presence of transferable AMR determinants. METHODS One hundred (100) LAB isolates from Nono identified in a previous study as Limosilactobacillus fermentum, Lactobacillus delbrueckii, Streptococcus thermophilus, Streptococcus infantarius, Lentilactobacillus senioris, Leuconostoc pseudomesenteriodes, and Enterococcus thailandicus were investigated. The minimum inhibitory concentration (MIC) was determined for 18 antimicrobials using the micro-broth dilution method. In addition, LAB isolates were screened for 28 antimicrobial resistance genes using PCR. The ability of LAB isolates to transfer tetracycline and streptomycin resistance genes to Enterococcus faecalis was also investigated. RESULTS The experiments revealed variable antimicrobial susceptibility according to the LAB isolate and the antimicrobial tested. The tetracycline resistance genes tet(S) and tet(M) were detected in isolates Ent. thailandicus 52 and S. infantarius 10. Additionally, aad(E) encoding resistance to streptomycin was detected in Ent. thailandicus 52. The conjugation experiments suggested that the tet(S) and aad(E) genes were transferable in vitro from isolate Ent. thailandicus 52 to Ent. faecalis JH2-2. SIGNIFICANCE AND IMPACT Traditional fermented foods play a significant role in the diet of millions of people in Africa, yet their contribution to the burden of AMR is largely unknown. This study highlights that LAB involved in traditionally fermented foods could be potential reservoirs of AMR. It also underscores the relevant safety issues of Ent. thailandicus 52 and S. infantarius 10 for use as starter cultures as they carry transferable AMR genes. Starter cultures are an essential aspect of improving the safety and quality attributes of African fermented foods. However, AMR monitoring is an important safety aspect in the selection of starter cultures for improving traditional fermentation technologies.
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Affiliation(s)
- Promiselynda I Obioha
- Microbiology Research Unit, School of Human Sciences, London Metropolitan University, 166-220 Holloway Road, London N7 8DB, UK
| | - Amarachukwu Anyogu
- Food Safety and Security, School of Biomedical Sciences, University of West London, St. Marys Road, London W5 5RF, UK
| | - Brigitte Awamaria
- Microbiology Research Unit, School of Human Sciences, London Metropolitan University, 166-220 Holloway Road, London N7 8DB, UK
| | - Hamid B Ghoddusi
- Microbiology Research Unit, School of Human Sciences, London Metropolitan University, 166-220 Holloway Road, London N7 8DB, UK
| | - Labia Irene I Ouoba
- Microbiology Research Unit, School of Human Sciences, London Metropolitan University, 166-220 Holloway Road, London N7 8DB, UK
- Independent Senior Research Scientist & Consultant, Ouoba-Consulting, London SW16 2DY, UK
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Ahmed T, Islam MS, Haider N, Elton L, Hasan B, Nuruzzaman M, Rahman MT, Kabir SML, Khan MSR. Phenotypic and Genotypic Characteristics of Antimicrobial Resistance in Citrobacter freundii Isolated from Domestic Ducks ( Anas platyrhynchos domesticus) in Bangladesh. Antibiotics (Basel) 2023; 12:antibiotics12040769. [PMID: 37107131 PMCID: PMC10135275 DOI: 10.3390/antibiotics12040769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/13/2023] [Accepted: 04/15/2023] [Indexed: 04/29/2023] Open
Abstract
Antimicrobial resistance (AMR) in Citrobacter freundii poses a serious challenge as this species is one of the sources of nosocomial infection and causes diarrheal infections in humans. Ducks could be the potential source of multidrug-resistant (MDR) C. freundii; however, AMR profiles in C. freundii from non-human sources in Bangladesh have remained elusive. This study aimed to detect C. freundii in domestic ducks (Anas platyrhynchos domesticus) in Bangladesh and to determine their phenotypic and genotypic antibiotic susceptibility patterns. A total of 150 cloacal swabs of diseased domestic ducks were screened using culturing, staining, biochemical, polymerase chain reaction (PCR), and matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) to detect C. freundii. Phenotypic and genotypic antibiotic susceptibility patterns were done by the disk diffusion method and PCR, respectively. In total, 16.67% (25/150) of the samples were positive for C. freundii. C. freundii isolates showed a range of 20% to 96% resistance to cefotaxime, gentamicin, levofloxacin, ciprofloxacin, cotrimoxazole, tetracycline, ampicillin, and cephalexin. More than 60% of the isolates were phenotypically MDR, and the index of multiple antibiotic resistance ranged from 0.07 to 0.79. Genes encoding resistance to beta-lactams [blaTEM-1-88% (22/25), blaCMY-2-56% (14/25), blaCMY-9-8% (2/25), and blaCTX-M-14-20% (5/25)], sulfonamides [sul1-52% (13/25), sul2-24% (6/25)], tetracyclines [tetA-32% (8/25) and tetB-4% (1/25)], aminoglycosides [aacC4-16% (4/25)], and fluoroquinolones [qnrA-4% (1/25), qnrB-12% (3/25), and qnrS-4% (1/25)] were detected in the isolated C. freundii. To the best of our knowledge, this is the first study in Bangladesh to detect MDR C. freundii with their associated resistance genes from duck samples. We suggest addressing the burden of diseases in ducks and humans and associated AMR issues using the One Health approach.
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Affiliation(s)
- Tarana Ahmed
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
- Department of Livestock Services, Ministry of Fisheries & Livestock, Government of the Peoples Republic of Bangladesh, Krishi Khamar Sarak, Farmgate, Dhaka 1215, Bangladesh
| | - Md Saiful Islam
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Najmul Haider
- School of Life Sciences, Keele University, Staffordshire ST5 5BG, UK
- The Royal Veterinary College, University of London, Hertfordshire AL9 7TA, UK
| | - Linzy Elton
- Centre for Clinical Microbiology, Department of Infection, Division of Infection and Immunity, Royal Free Campus, University College London, London NW3 2PF, UK
| | - Badrul Hasan
- Department of Jobs, Precincts and Regions, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia
| | | | - Md Tanvir Rahman
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - S M Lutful Kabir
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Md Shahidur Rahman Khan
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
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Krüger GI, Pardo-Esté C, Zepeda P, Olivares-Pacheco J, Galleguillos N, Suarez M, Castro-Severyn J, Alvarez-Thon L, Tello M, Valdes JH, Saavedra CP. Mobile genetic elements drive the multidrug resistance and spread of Salmonella serotypes along a poultry meat production line. Front Microbiol 2023; 14:1072793. [PMID: 37007466 PMCID: PMC10061128 DOI: 10.3389/fmicb.2023.1072793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 02/28/2023] [Indexed: 03/18/2023] Open
Abstract
The presence of mobile genetic elements in Salmonella isolated from a chicken farm constitutes a potential risk for the appearance of emerging bacteria present in the food industry. These elements contribute to increased pathogenicity and antimicrobial resistance through genes that are related to the formation of biofilms and resistance genes contained in plasmids, integrons, and transposons. One hundred and thirty-three Salmonella isolates from different stages of the production line, such as feed manufacturing, hatchery, broiler farm, poultry farm, and slaughterhouse, were identified, serotyped and sequenced. The most predominant serotype was Salmonella Infantis. Phylogenetic analyses demonstrated that the diversity and spread of strains in the pipeline are serotype-independent, and that isolates belonging to the same serotype are very closely related genetically. On the other hand, Salmonella Infantis isolates carried the pESI IncFIB plasmid harboring a wide variety of resistance genes, all linked to mobile genetic elements, and among carriers of these plasmids, the antibiograms showed differences in resistance profiles and this linked to a variety in plasmid structure, similarly observed in the diversity of Salmonella Heidelberg isolates carrying the IncI1-Iα plasmid. Mobile genetic elements encoding resistance and virulence genes also contributed to the differences in gene content. Antibiotic resistance genotypes were matched closely by the resistance phenotypes, with high frequency of tetracycline, aminoglycosides, and cephalosporins resistance. In conclusion, the contamination in the poultry industry is described throughout the entire production line, with mobile genetic elements leading to multi-drug resistant bacteria, thus promoting survival when challenged with various antimicrobial compounds.
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Affiliation(s)
- Gabriel I. Krüger
- Laboratorio de Microbiología Molecular, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Coral Pardo-Esté
- Laboratorio de Microbiología Molecular, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Phillippi Zepeda
- Laboratorio de Microbiología Molecular, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Jorge Olivares-Pacheco
- Grupo de Resistencia Antibacteriana en Bacterias Patógenas Ambientales GRABPA, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Nicolas Galleguillos
- Laboratorio de Microbiología Molecular, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Marcia Suarez
- Laboratorio de Microbiología Molecular, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Juan Castro-Severyn
- Laboratorio de Microbiología Aplicada y Extremófilos, Departamento de Ingeniería Química, Universidad Católica del Norte, Antofagasta, Chile
| | - Luis Alvarez-Thon
- Facultad de Ingeniería y Arquitectura, Universidad Central de Chile, Santiago, Chile
| | - Mario Tello
- Laboratorio de Metagenómica Bacteriana, Centro de Biotecnología Acuícola, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Jorge H. Valdes
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Claudia P. Saavedra
- Laboratorio de Microbiología Molecular, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
- *Correspondence: Claudia P. Saavedra,
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Leinyuy JF, Ali IM, Ousenu K, Tume CB. Molecular characterization of antimicrobial resistance related genes in E. coli, Salmonella and Klebsiella isolates from broilers in the West Region of Cameroon. PLoS One 2023; 18:e0280150. [PMID: 36630464 PMCID: PMC9833522 DOI: 10.1371/journal.pone.0280150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 12/21/2022] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Antibiotic resistance has become an enduring threat to human health. This has prompted extensive research to identify the determinants responsible in a bid to fight the spread of resistance and also develop new antibiotics. However, routine procedures focus on identifying genetic determinants of resistance only on phenotypically resistant isolates. We aimed to characterise plasmid mediated resistance determinants in key Enterobacteriaceae isolates with differential phenotypic susceptibility profiles and evaluated the contribution of resistance genes on phenotypic expression of susceptibility. METHODS The study was carried out on 200 Enterobacteriaceae isolates belonging to the genera E. coli, Salmonella, and Klebsiella; 100 resistant and 100 susceptible to quinolones, aminoglycosides, and ESBL-producing as determined by disk diffusion. Reduced susceptibility in susceptible isolates was determined as an increased MIC by broth microdilution. Plasmid-borne resistance genes were sought in all isolates by endpoint PCR. We performed correlations tests to determine the relationship between the occurrence of resistance genes and increased MIC in susceptible isolates. We then used the notion of penetrance to show adequacy between resistance gene carriage and phenotypic resistance as well as diagnostic odds ratio to evaluate how predictable phenotypic susceptibility profile could determine the presence of resistant genes in the isolates. RESULTS Reduced susceptibility was detected in 30% (9/30) ESBL negative, 50% (20/40) quinolone-susceptible and 53.33% (16/30) aminoglycoside-susceptible isolates. Plasmid-borne resistance genes were detected in 50% (15/30) of ESBL negative, 65% (26/40) quinolone susceptible and 66.67% (20/30) aminoglycoside susceptible isolates. Reduced susceptibility increased the risk of susceptible isolates carrying resistance genes (ORs 4.125, 8.36, and 8.89 respectively for ESBL, quinolone, and aminoglycoside resistance genes). Resistance gene carriage correlated significantly to reduced susceptibility for quinolone and aminoglycoside resistance genes (0.002 and 0.015 at CI95). Gene carriage correlated with phenotypic resistance at an estimated 64.28% for ESBL, 56.90% for quinolone, and 58.33% for aminoglycoside resistance genes. CONCLUSIONS A high carriage of plasmid-mediated genes for ESBL, quinolone, and aminoglycoside resistance was found among the Enterobacteriaceae tested. However, gene carriage was not always correlated with phenotypic expression. This allows us to suggest that assessing genetic determinants of resistance should not be based on AST profile only. Further studies, including assessing the role of chromosomal determinants will shed light on other factors that undermine antimicrobial susceptibility locally.
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Affiliation(s)
- Jude Fonbah Leinyuy
- Research Unit of Microbiology and Antimicrobial Substances, Department of Biochemistry, University of Dschang, Dschang, Cameroon
| | - Innocent Mbulli Ali
- Research Unit of Microbiology and Antimicrobial Substances, Department of Biochemistry, University of Dschang, Dschang, Cameroon
- The Biotechnology Centre, University of Yaoundé 1, Yaoundé, Cameroon
- * E-mail:
| | - Karimo Ousenu
- Research Unit of Microbiology and Antimicrobial Substances, Department of Biochemistry, University of Dschang, Dschang, Cameroon
| | - Christopher B. Tume
- Research Unit of Microbiology and Antimicrobial Substances, Department of Biochemistry, University of Dschang, Dschang, Cameroon
- Department of Biochemistry, Faculty of Science, University of Bamenda, Bamenda, Cameroon
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Gelalcha BD, Kerro Dego O. Extended-Spectrum Beta-Lactamases Producing Enterobacteriaceae in the USA Dairy Cattle Farms and Implications for Public Health. Antibiotics (Basel) 2022; 11:antibiotics11101313. [PMID: 36289970 PMCID: PMC9598938 DOI: 10.3390/antibiotics11101313] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 09/21/2022] [Accepted: 09/22/2022] [Indexed: 11/29/2022] Open
Abstract
Antimicrobial resistance (AMR) is one of the top global health threats of the 21th century. Recent studies are increasingly reporting the rise in extended-spectrum beta-lactamases producing Enterobacteriaceae (ESBLs-Ent) in dairy cattle and humans in the USA. The causes of the increased prevalence of ESBLs-Ent infections in humans and commensal ESBLs-Ent in dairy cattle farms are mostly unknown. However, the extensive use of beta-lactam antibiotics, especially third-generation cephalosporins (3GCs) in dairy farms and human health, can be implicated as a major driver for the rise in ESBLs-Ent. The rise in ESBLs-Ent, particularly ESBLs-Escherichia coli and ESBLs-Klebsiella species in the USA dairy cattle is not only an animal health issue but also a serious public health concern. The ESBLs-E. coli and -Klebsiella spp. can be transmitted to humans through direct contact with carrier animals or indirectly through the food chain or via the environment. The USA Centers for Disease Control and Prevention reports also showed continuous increase in community-associated human infections caused by ESBLs-Ent. Some studies attributed the elevated prevalence of ESBLs-Ent infections in humans to the frequent use of 3GCs in dairy farms. However, the status of ESBLs-Ent in dairy cattle and their contribution to human infections caused by ESBLs-producing enteric bacteria in the USA is the subject of further study. The aims of this review are to give in-depth insights into the status of ESBL-Ent in the USA dairy farms and its implication for public health and to highlight some critical research gaps that need to be addressed.
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Wang H, Jia C, Li H, Yin R, Chen J, Li Y, Yue M. Paving the way for precise diagnostics of antimicrobial resistant bacteria. Front Mol Biosci 2022; 9:976705. [PMID: 36032670 PMCID: PMC9413203 DOI: 10.3389/fmolb.2022.976705] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 07/19/2022] [Indexed: 12/26/2022] Open
Abstract
The antimicrobial resistance (AMR) crisis from bacterial pathogens is frequently emerging and rapidly disseminated during the sustained antimicrobial exposure in human-dominated communities, posing a compelling threat as one of the biggest challenges in humans. The frequent incidences of some common but untreatable infections unfold the public health catastrophe that antimicrobial-resistant pathogens have outpaced the available countermeasures, now explicitly amplified during the COVID-19 pandemic. Nowadays, biotechnology and machine learning advancements help create more fundamental knowledge of distinct spatiotemporal dynamics in AMR bacterial adaptation and evolutionary processes. Integrated with reliable diagnostic tools and powerful analytic approaches, a collaborative and systematic surveillance platform with high accuracy and predictability should be established and implemented, which is not just for an effective controlling strategy on AMR but also for protecting the longevity of valuable antimicrobials currently and in the future.
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Affiliation(s)
- Hao Wang
- Institute of Preventive Veterinary Sciences & Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou, China
| | - Chenhao Jia
- Institute of Preventive Veterinary Sciences & Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou, China
- Hainan Institute of Zhejiang University, Sanya, China
| | - Hongzhao Li
- Institute of Preventive Veterinary Sciences & Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou, China
- Hainan Institute of Zhejiang University, Sanya, China
| | - Rui Yin
- Institute of Preventive Veterinary Sciences & Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou, China
| | - Jiang Chen
- Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
- *Correspondence: Jiang Chen, ; Yan Li, ; Min Yue,
| | - Yan Li
- Institute of Preventive Veterinary Sciences & Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou, China
- Hainan Institute of Zhejiang University, Sanya, China
- Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, China
- *Correspondence: Jiang Chen, ; Yan Li, ; Min Yue,
| | - Min Yue
- Institute of Preventive Veterinary Sciences & Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou, China
- Hainan Institute of Zhejiang University, Sanya, China
- Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- *Correspondence: Jiang Chen, ; Yan Li, ; Min Yue,
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High prevalence of antibiotic resistance in pathogenic foodborne bacteria isolated from bovine milk. Sci Rep 2022; 12:3878. [PMID: 35264647 PMCID: PMC8907330 DOI: 10.1038/s41598-022-07845-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 02/07/2022] [Indexed: 01/27/2023] Open
Abstract
This study aimed to investigate the prevalence of foodborne pathogenic bacteria in bovine milk, their antibiogram phenotype, and the carriage of antibiotic resistance genes. Raw bovine milk samples (n = 100) were randomly collected from different suppliers in the northwest of Iran. Antibiotic-resistant patterns and the presence of antibiotic resistance genes were evaluated in the isolates. Escherichia coli, Listeria monocytogenes, Staphylococcus aureus, and Salmonella spp. were isolated from 78%, 47%, 25%, and 21% of samples, respectively. All isolates showed high rates of resistance to amoxicillin, penicillin, and cefalexin. The blaTEM and blaSHV genes were detected in 50.0% and 6.4% of E. coli isolates, respectively. Also, 28.5% and 19.0% of Salmonella isolates were positive for blaTEM and blaSHV. The frequency of mecA and blaZ in S. aureus isolates was 20.0% and 12.0%, respectively. The high prevalence of bovine milk contamination with antimicrobial-resistant species in this study necessitates precise control on antibiotic prescription in veterinary medicine.
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Silago V, Mruma EC, Msemwa B, Mtemisika CI, Phillip S, Ndagula RA, Said MM, Mushi MF, Mshana SE. Predominance of Acinetobacter spp., Harboring the blaIMP Gene, Contaminating the Hospital Environment in a Tertiary Hospital in Mwanza, Tanzania: A Cross-Sectional Laboratory-Based Study. Pathogens 2022; 11:pathogens11010063. [PMID: 35056011 PMCID: PMC8781992 DOI: 10.3390/pathogens11010063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 12/29/2021] [Accepted: 12/30/2021] [Indexed: 02/01/2023] Open
Abstract
Data on colonization and hospital contamination of carbapenem-resistant Gram-negative bacteria (CR-GNB) are limited in low- and middle-income countries. We designed this study to determine the prevalence and co-existence of carbapenemase genes among CR-GNB isolated from clinical, colonization, and hospital environmental samples at a tertiary hospital in Mwanza, Tanzania. The modified Hodge test (MHT), the combined disk test (CDT), and the double-disk synergy test (DDST) were used for the phenotypic detection of carbapenemases. A multiplex PCR assay was used to detect blaIMP and blaKPC, and a singleplex PCR assay was used to detect blaOXA-48. Data were analyzed by STATA version 13.0. Overall, 68.8% (44/64) of the CR-GNB had at least one phenotype by phenotypic methods, whereby 60.9% (39/64) were both CDT and DDST positive and 31.3% (20/64) were MHT positive. A total of 23/64 (35.9%) had at least one of the genes tested with the predominance of blaIMP (91.3%; 21/23). In addition, 47.7% (21/44) of the CR-GNB phenotypes had at least one gene. Around 47.8% (11/23) of the CR-GNB carried multiple genes encoding for carbapenem resistance, with the maximum co-existence of blaIMP/blaKPC/blaOXA-48 (45.5%; 5/11). The majority of carbapenem-resistant genes were detected in Acinetobacter spp. (82.6%; 19/23) and isolated from bed swabs (69.6%; 16/23). Acinetobacter spp. carrying the blaIMP gene predominantly contaminated the hospital environment. Therefore, we recommend routine decontamination of inanimate hospital surfaces, including patient beds.
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Affiliation(s)
- Vitus Silago
- Department of Microbiology and Immunology, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences, Mwanza P.O. Box 1464, Tanzania; (E.C.M.); (B.M.); (C.I.M.); (S.P.); (M.M.S.); (M.F.M.); (S.E.M.)
- Correspondence:
| | - Eveline C. Mruma
- Department of Microbiology and Immunology, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences, Mwanza P.O. Box 1464, Tanzania; (E.C.M.); (B.M.); (C.I.M.); (S.P.); (M.M.S.); (M.F.M.); (S.E.M.)
| | - Betrand Msemwa
- Department of Microbiology and Immunology, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences, Mwanza P.O. Box 1464, Tanzania; (E.C.M.); (B.M.); (C.I.M.); (S.P.); (M.M.S.); (M.F.M.); (S.E.M.)
| | - Conjester I. Mtemisika
- Department of Microbiology and Immunology, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences, Mwanza P.O. Box 1464, Tanzania; (E.C.M.); (B.M.); (C.I.M.); (S.P.); (M.M.S.); (M.F.M.); (S.E.M.)
- Molecular Biology Department, Central Pathology Laboratory, Bugando Medical Centre, Mwanza P.O. Box 1370, Tanzania
| | - Shukurani Phillip
- Department of Microbiology and Immunology, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences, Mwanza P.O. Box 1464, Tanzania; (E.C.M.); (B.M.); (C.I.M.); (S.P.); (M.M.S.); (M.F.M.); (S.E.M.)
- Institute of Allied Health Sciences, Ruaha Catholic University, Iringa P.O. Box 774, Tanzania
| | - Reuben A. Ndagula
- National Public Health Laboratory, Dar es Salaam P.O. Box 9083, Tanzania;
| | - Maria M. Said
- Department of Microbiology and Immunology, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences, Mwanza P.O. Box 1464, Tanzania; (E.C.M.); (B.M.); (C.I.M.); (S.P.); (M.M.S.); (M.F.M.); (S.E.M.)
- Department of Clinical Laboratory, Kondoa District Hospital, Dodoma P.O. Box 40, Tanzania
| | - Martha F. Mushi
- Department of Microbiology and Immunology, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences, Mwanza P.O. Box 1464, Tanzania; (E.C.M.); (B.M.); (C.I.M.); (S.P.); (M.M.S.); (M.F.M.); (S.E.M.)
| | - Stephen E. Mshana
- Department of Microbiology and Immunology, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences, Mwanza P.O. Box 1464, Tanzania; (E.C.M.); (B.M.); (C.I.M.); (S.P.); (M.M.S.); (M.F.M.); (S.E.M.)
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12
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Yang X, Wu Y, Liu Q, Sun H, Luo M, Xiong Y, Matussek A, Hu B, Bai X. Genomic Characteristics of Stx2e-Producing Escherichia coli Strains Derived from Humans, Animals, and Meats. Pathogens 2021; 10:pathogens10121551. [PMID: 34959506 PMCID: PMC8705337 DOI: 10.3390/pathogens10121551] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/14/2021] [Accepted: 11/26/2021] [Indexed: 12/13/2022] Open
Abstract
Shiga toxin (Stx) can be classified into two types, Stx1 and Stx2, and different subtypes. Stx2e is a subtype commonly causing porcine edema disease and rarely reported in humans. The purpose of this study was to analyze the prevalence and genetic characteristics of Stx2e-producing Escherichia coli (Stx2e-STEC) strains from humans compared to strains from animals and meats in China. Stx2e-STEC strains were screened from our STEC collection, and whole-genome sequencing was performed to characterize their genetic features. Our study showed a wide distribution of Stx2e-STEC among diverse hosts and a higher proportion of Stx2e-STEC among human STEC strains in China. Three human Stx2e-STEC isolates belonged to O100:H30, Onovel26:H30, and O8:H9 serotypes and varied in genetic features. Human Stx2e-STECs phylogenetically clustered with animal- and food-derived strains. Stx2e-STEC strains from animals and meat showed multidrug resistance, while human strains were only resistant to azithromycin and tetracycline. Of note, a high proportion (55.9%) of Stx2e-STEC strains, including one human strain, carried the heat-stable and heat-labile enterotoxin-encoding genes st and lt, exhibiting a STEC/enterotoxigenic E. coli (ETEC) hybrid pathotype. Given that no distinct genetic feature was found in Stx2e-STEC strains from different sources, animal- and food-derived strains may pose the risk of causing human disease.
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Affiliation(s)
- Xi Yang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (X.Y.); (Q.L.); (H.S.); (Y.X.)
| | - Yannong Wu
- Yulin Center for Disease Control and Prevention, Yulin 537000, China; (Y.W.); (M.L.)
| | - Qian Liu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (X.Y.); (Q.L.); (H.S.); (Y.X.)
| | - Hui Sun
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (X.Y.); (Q.L.); (H.S.); (Y.X.)
| | - Ming Luo
- Yulin Center for Disease Control and Prevention, Yulin 537000, China; (Y.W.); (M.L.)
| | - Yanwen Xiong
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (X.Y.); (Q.L.); (H.S.); (Y.X.)
| | - Andreas Matussek
- Division of Laboratory, Medicine Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway;
- Division of Laboratory Medicine, Oslo University Hospital, 0372 Oslo, Norway
| | - Bin Hu
- Shandong Center for Disease Control and Prevention, Jinan 250014, China
- Correspondence: (B.H.); (X.B.)
| | - Xiangning Bai
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (X.Y.); (Q.L.); (H.S.); (Y.X.)
- Division of Laboratory Medicine, Oslo University Hospital, 0372 Oslo, Norway
- Correspondence: (B.H.); (X.B.)
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Agostinho Davanzo EF, dos Santos RL, Castro VHDL, Palma JM, Pribul BR, Dallago BSL, Fuga B, Medeiros M, Titze de Almeida SS, da Costa HMB, Rodrigues DDP, Lincopan N, Perecmanis S, Santana AP. Molecular characterization of Salmonella spp. and Listeria monocytogenes strains from biofilms in cattle and poultry slaughterhouses located in the federal District and State of Goiás, Brazil. PLoS One 2021; 16:e0259687. [PMID: 34767604 PMCID: PMC8589217 DOI: 10.1371/journal.pone.0259687] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 10/23/2021] [Indexed: 10/26/2022] Open
Abstract
Listeria monocytogenes and Salmonella spp. are considered important foodborne pathogens that are commonly associated with foods of animal origin. The aim of this study was to perform molecular characterization of L. monocytogenes and Salmonella spp. isolated from biofilms of cattle and poultry slaughterhouses located in the Federal District and State of Goiás, Brazil. Fourteen L. monocytogenes isolates and one Salmonella sp. were detected in poultry slaughterhouses. No isolates were detected in cattle slaughterhouses. All L. monocytogenes isolates belonged to lineage II, and 11 different pulsotypes were detected. Pulsed-field gel electrophoresis analysis revealed the dissemination of two strains within one plant, in addition to the regional dissemination of one of them. The Salmonella isolate was identified via whole genome sequencing as Salmonella enterica serovar Minnesota ST548. In the sequence analysis, no premature stop codons were detected in the inlA gene of Listeria. All isolates demonstrated the ability to adhere to Caco-2 cells, while 50% were capable of invading them. Antimicrobial resistance was detected in 57.1% of the L. monocytogenes isolates, and resistance to sulfonamide was the most common feature. The tetC, ermB, and tetM genes were detected, and four isolates were classified as multidrug-resistant. Salmonella sp. was resistant to nine antimicrobials and was classified as multidrug-resistant. Resistance genes qnrB19, blaCMY-2, aac(6')-Iaa, sul2, and tetA, and a mutation in the parC gene were detected. The majority (78.5%) of the L. monocytogenes isolates were capable of forming biofilms after incubation at 37°C for 24 h, and 64.3% were capable of forming biofilms after incubation at 12°C for 168 h. There was no statistical difference in the biofilm-forming capacity under the different evaluated conditions. Salmonella sp. was capable of forming biofilms at both tested temperatures. Biofilm characterization was confirmed by collecting the samples consistently, at the same sampling points, and by assessing biofilm formation in vitro. These results highlight the potential risk of cross-contamination in poultry slaughterhouses and the importance of surveillance and pathogen control maintenance programs within the meat production industry.
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Affiliation(s)
| | | | | | - Joana Marchesini Palma
- Faculty of Agronomy and Veterinary Medicine, University of Brasília (UnB), Brasília, DF, Brazil
| | - Bruno Rocha Pribul
- National Reference Laboratory for Bacterial Enteric Infections, Oswaldo Cruz Institute, Manguinhos, Rio de Janeiro, RJ, Brazil
| | | | - Bruna Fuga
- Laboratory of Bacterial Resistance and Therapeutic Alternatives, Biomedical Sciences Institute, University of São Paulo, São Paulo, SP, Brazil
| | - Margareti Medeiros
- Faculty of Agronomy and Veterinary Medicine, University of Brasília (UnB), Brasília, DF, Brazil
| | | | | | - Dália dos Prazeres Rodrigues
- National Reference Laboratory for Bacterial Enteric Infections, Oswaldo Cruz Institute, Manguinhos, Rio de Janeiro, RJ, Brazil
| | - Nilton Lincopan
- Laboratory of Bacterial Resistance and Therapeutic Alternatives, Biomedical Sciences Institute, University of São Paulo, São Paulo, SP, Brazil
| | - Simone Perecmanis
- Faculty of Agronomy and Veterinary Medicine, University of Brasília (UnB), Brasília, DF, Brazil
| | - Angela Patrícia Santana
- Faculty of Agronomy and Veterinary Medicine, University of Brasília (UnB), Brasília, DF, Brazil
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Rajaei M, Moosavy MH, Gharajalar SN, Khatibi SA. Antibiotic resistance in the pathogenic foodborne bacteria isolated from raw kebab and hamburger: phenotypic and genotypic study. BMC Microbiol 2021; 21:272. [PMID: 34615465 PMCID: PMC8495966 DOI: 10.1186/s12866-021-02326-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 09/27/2021] [Indexed: 11/10/2022] Open
Abstract
Background In recent years, interest in the consumption of ready-to-eat (RTE) food products has been increased in many countries. However, RTE products particularly those prepared by meat may be potential vehicles of antibiotic-resistance foodborne pathogens. Considering kebab and hamburger are the most popular RTE meat products in Iran, this study aimed to investigate the prevalence and antimicrobial resistance of common foodborne pathogens (Escherichia coli, Salmonella spp., Staphylococcus aureus, and Listeria monocytogenes) in raw kebab and hamburger samples collected from fast-food centers and restaurants. Therefore, total bacterial count (TBC), as well as the prevalence rates and antibiogram patterns of foodborne pathogens in the samples were investigated. Also, the presence of antibiotic-resistance genes (blaSHV, blaTEM,blaZ, and mecA) was studied in the isolates by PCR. Results The mean value of TBC in raw kebab and hamburger samples was 6.72 ± 0.68 log CFU/g and 6.64 ± 0.66 log CFU/g, respectively. E. coli had the highest prevalence rate among the investigated pathogenic bacteria in kebab (70%) and hamburger samples (48%). Salmonella spp., L. monocytogenes, and S. aureus were also recovered from 58, 50, and 36% of kebab samples, respectively. The contamination of hamburger samples was detected to S. aureus (22%), L. monocytogenes (22%), and Salmonella spp. (10%). In the antimicrobial susceptibility tests, all isolates exhibited high rates of antibiotic resistance, particularly against amoxicillin, penicillin, and cefalexin (79.66–100%). The blaTEM was the most common resistant gene in the isolates of E. coli (52.54%) and Salmonella spp. (44.11%). Fourteen isolates (23.72%) of E. coli and 10 isolates (29.41%) of Salmonella spp. were positive for blaSHV. Also, 16 isolates (55.17%) of S. aureus and 10 isolates (27.27%) of L. monocytogenes were positive for mecA gene. Conclusions The findings of this study showed that raw kebab and hamburger are potential carriers of antibiotic-resistance pathogenic bacteria, which can be a serious threat to public health. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02326-8.
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Affiliation(s)
- Maryam Rajaei
- Department of Food Hygiene and Aquatic, Faculty of Veterinary Medicine, University of Tabriz, Tabriz, Iran
| | - Mir-Hassan Moosavy
- Department of Food Hygiene and Aquatic, Faculty of Veterinary Medicine, University of Tabriz, Tabriz, Iran.
| | - Sahar Nouri Gharajalar
- Department of Pathobiology, Faculty of Veterinary Medicine, University of Tabriz, Tabriz, Iran
| | - Seyed Amin Khatibi
- Department of Food Hygiene and Aquatic, Faculty of Veterinary Medicine, University of Tabriz, Tabriz, Iran
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15
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Vingino A, Roberts MC, Wainstein M, West J, Norman SA, Lambourn D, Lahti J, Ruiz R, D’Angeli M, Weissman SJ, Rabinowitz P. Surveillance for Antibiotic-Resistant E. coli in the Salish Sea Ecosystem. Antibiotics (Basel) 2021; 10:antibiotics10101201. [PMID: 34680782 PMCID: PMC8532818 DOI: 10.3390/antibiotics10101201] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/23/2021] [Accepted: 09/27/2021] [Indexed: 11/26/2022] Open
Abstract
E. coli was isolated from the Salish Sea (Puget Sound) ecosystem, including samples of marine and fresh water, and wildlife dependent on this environment. E. coli isolates were assessed for phenotypic and genotypic resistance to antibiotics. A total of 305 E. coli isolates was characterized from samples collected from: marine water obtained in four quadrants of the Salish Sea; select locations near beaches; fresh water from streams near marine beaches; and fecal samples from harbor porpoises (Phocoena phocoena), harbor seals (Phoca vitulina), river otters (Lontra canadensis), and English sole (Parophrys vetulus). Isolates were evaluated using antimicrobial susceptibility typing, whole-genome sequencing, fumC, and multilocus sequence typing. Resistance and virulence genes were identified from sequence data. Of the 305 isolates from Salish Sea samples, 20 (6.6%) of the E. coli were intermediate, and 31 (10.2%) were resistant to ≥1 class of antibiotics, with 26.9% of nonsusceptible (resistant and intermediate resistant) E. coli isolates from marine mammals and 70% from river otters. The proportion of nonsusceptible isolates from animals was significantly higher than samples taken from marine water (p < 0.0001). A total of 196 unique STs was identified including 37 extraintestinal pathogenic E. coli (ExPEC)-associated STs [ST10, ST38, ST58, ST69, ST73, ST117, ST131, and ST405]. The study suggests that animals may be potential sentinels for antibiotic-resistant and ExPEC E. coli in the Salish Sea ecosystem.
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Affiliation(s)
- Alexandria Vingino
- Department of Environmental and Occupational Health Sciences (DEOHS), University of Washington, Seattle, WA 98105, USA or (A.V.); (P.R.)
| | - Marilyn C. Roberts
- Department of Environmental and Occupational Health Sciences (DEOHS), University of Washington, Seattle, WA 98105, USA or (A.V.); (P.R.)
- Correspondence: ; Tel.: +1-206-543-8001
| | | | - James West
- Washington Department of Fish and Wildlife, P.O. Box 43200, Olympia, WA 98504, USA; (J.W.); (D.L.)
| | - Stephanie A. Norman
- Marine-Med: Marine Research Epidemiology, Veterinary Medicine, Bothell, WA 98021, USA; (S.A.N.); (M.D.)
| | - Dyanna Lambourn
- Washington Department of Fish and Wildlife, P.O. Box 43200, Olympia, WA 98504, USA; (J.W.); (D.L.)
| | - Jeffery Lahti
- Washington State Department of Health, Shoreline, WA 98105, USA; (J.L.); (R.R.)
| | - Ryan Ruiz
- Washington State Department of Health, Shoreline, WA 98105, USA; (J.L.); (R.R.)
| | - Marisa D’Angeli
- Marine-Med: Marine Research Epidemiology, Veterinary Medicine, Bothell, WA 98021, USA; (S.A.N.); (M.D.)
| | - Scott J. Weissman
- Division of Infectious Disease, Seattle Children’s Hospital, Seattle, WA 98105, USA;
| | - Peter Rabinowitz
- Department of Environmental and Occupational Health Sciences (DEOHS), University of Washington, Seattle, WA 98105, USA or (A.V.); (P.R.)
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Majumder S, Jung D, Ronholm J, George S. Prevalence and mechanisms of antibiotic resistance in Escherichia coli isolated from mastitic dairy cattle in Canada. BMC Microbiol 2021; 21:222. [PMID: 34332549 PMCID: PMC8325273 DOI: 10.1186/s12866-021-02280-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 06/28/2021] [Indexed: 01/22/2023] Open
Abstract
Background Bovine mastitis is the most common infectious disease in dairy cattle with major economic implications for the dairy industry worldwide. Continuous monitoring for the emergence of antimicrobial resistance (AMR) among bacterial isolates from dairy farms is vital not only for animal husbandry but also for public health. Methods In this study, the prevalence of AMR in 113 Escherichia coli isolates from cases of bovine clinical mastitis in Canada was investigated. Kirby-Bauer disk diffusion test with 18 antibiotics and microdilution method with 3 heavy metals (copper, zinc, and silver) was performed to determine the antibiotic and heavy-metal susceptibility. Resistant strains were assessed for efflux and ß-lactamase activities besides assessing biofilm formation and hemolysis. Whole-genome sequences for each of the isolates were examined to detect the presence of genes corresponding to the observed AMR and virulence factors. Results Phenotypic analysis revealed that 32 isolates were resistant to one or more antibiotics and 107 showed resistance against at least one heavy metal. Quinolones and silver were the most efficient against the tested isolates. Among the AMR isolates, AcrAB-TolC efflux activity and ß-lactamase enzyme activities were detected in 13 and 14 isolates, respectively. All isolates produced biofilm but with different capacities, and 33 isolates showed α-hemolysin activity. A positive correlation (Pearson r = + 0.89) between efflux pump activity and quantity of biofilm was observed. Genes associated with aggregation, adhesion, cyclic di-GMP, quorum sensing were detected in the AMR isolates corroborating phenotype observations. Conclusions This investigation showed the prevalence of AMR in E. coli isolates from bovine clinical mastitis. The results also suggest the inadequacy of antimicrobials with a single mode of action to curtail AMR bacteria with multiple mechanisms of resistance and virulence factors. Therefore, it calls for combinatorial therapy for the effective management of AMR infections in dairy farms and combats its potential transmission to the food supply chain through the milk and dairy products. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02280-5.
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Affiliation(s)
- Satwik Majumder
- Department of Food Science and Agricultural Chemistry, McGill University, Macdonald Campus, 21111 Lakeshore Ste Anne de Bellevue, H9X 3V9, Quebec, Canada
| | - Dongyun Jung
- Department of Food Science and Agricultural Chemistry, McGill University, Macdonald Campus, 21111 Lakeshore Ste Anne de Bellevue, H9X 3V9, Quebec, Canada
| | - Jennifer Ronholm
- Department of Food Science and Agricultural Chemistry, McGill University, Macdonald Campus, 21111 Lakeshore Ste Anne de Bellevue, H9X 3V9, Quebec, Canada. .,Department of Animal Science, McGill University, Macdonald Campus, 21111 Lakeshore Ste Anne de Bellevue, H9X 3V9, Quebec, Canada.
| | - Saji George
- Department of Food Science and Agricultural Chemistry, McGill University, Macdonald Campus, 21111 Lakeshore Ste Anne de Bellevue, H9X 3V9, Quebec, Canada.
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Burgess SA, Aplin J, Biggs PJ, Breckell G, Benschop J, Fayaz A, Toombs-Ruane LJ, Midwinter AC. Characterisation of AmpC and extended-spectrum beta-lactamase producing E. coli from New Zealand dairy farms. Int Dairy J 2021. [DOI: 10.1016/j.idairyj.2021.104998] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Ackers-Johnson G, Kibombo D, Kusiima B, Nsubuga ML, Kigozi E, Kajumbula HM, Kateete DP, Walwema R, Ackers HL, Goodhead IB, Birtles RJ, James CE. Antibiotic resistance profiles and population structure of disease-associated Staphylococcus aureus infecting patients in Fort Portal Regional Referral Hospital, Western Uganda. MICROBIOLOGY (READING, ENGLAND) 2021; 167:001000. [PMID: 34032566 PMCID: PMC8290103 DOI: 10.1099/mic.0.001000] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 04/01/2021] [Indexed: 11/23/2022]
Abstract
Tackling antimicrobial resistance (AMR) is particularly challenging in low-resource settings such as Fort Portal Regional Referral Hospital (FPRRH) in Western Uganda. Specific knowledge of local AMR epidemiology is required to inform evidence-based improvement of antibiotic stewardship measures in the hospital. To address this, we combined existing antimicrobial susceptibility testing (AST) from FPRRH, with whole genome sequencing (WGS) of 41 Staphylococcus aureus isolates (2017-2019). AST revealed 73 % (30 of 41) of isolates were resistant to one or more antibiotics and 29 % (12 of 41) were multi-drug resistant (MDR). Resistance phenotypes were largely explained by the presence of antibiotic resistance genes in WGS data. Five isolates were methicillin-resistant S. aureus (MRSA) and MDR. Although all isolates were susceptible to clindamycin, a 24 % carriage of erm genes suggests potential for rapid development of resistance. We inferred a population structure for the S. aureus isolates by comparing their core genomes. Twenty isolates formed a tight cluster corresponding to multilocus sequence typing clonal complex (CC) 152, a CC found to be particularly prevalent in northern Africa. The frequency of genes associated with methicillin, chloramphenicol and ciprofloxacin resistance were significantly lower among CC152 strains than non-CC152 strains; thus, in keeping with previous work, we find that CC152 is almost exclusively methicillin-sensitive S. aureus (MSSA). Also, in agreement with other studies, we observed that the occurrence of Panton-Valentine leukocidin toxin-encoding genes was significantly higher among CC152 strains than non-CC152 strains. However, we also observed that the coagulase gene was over-represented in this CC, further defining the virulence strategy of this important pathogen. By generating detailed information about the epidemiology of circulating S. aureus and their antibiotic susceptibility, our study has provided, for the first time, data on which evidence-based infection and AMR interventions at FPRRH can be based.
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Affiliation(s)
- Gavin Ackers-Johnson
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Daniel Kibombo
- Fort Portal Regional Referral Hospital, Uganda, Uganda
- Infectious Diseases Institute, Kampala, Uganda
| | - Brenda Kusiima
- Fort Portal Regional Referral Hospital, Uganda, Uganda
- Infectious Diseases Institute, Kampala, Uganda
| | - Moses L. Nsubuga
- College of Health Sciences, Makerere University, Kampala, Uganda
| | - Edgar Kigozi
- College of Health Sciences, Makerere University, Kampala, Uganda
| | | | | | | | | | - Ian B. Goodhead
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Richard J. Birtles
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Chloë E. James
- School of Science, Engineering and Environment, University of Salford, Salford, UK
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Spatiotemporal Changes of Antibiotic Resistance and Bacterial Communities in Drinking Water Distribution System in Wrocław, Poland. WATER 2020. [DOI: 10.3390/w12092601] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Antibiotic resistance of bacteria is an emerging problem in drinking water treatment. This paper presents the comparison of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) prevalence during the summer and winter season in a full-scale drinking water distribution system (DWDS) supplied by two water treatment plants (WTPs). The effect of distance from WTP and physical–chemical water parameters on its microbial properties was also tested. Bacterial consortia dwelling in bulk tap water were additionally compared by means of denaturating gradient gel electrophoresis (DGGE). The results showed that among ARB, bacteria resistant to ceftazidime (CAZ) were the most abundant, followed by bacteria resistant to amoxicillin (AML), ciprofloxacin (CIP), and tetracycline (TE). Numerous ARGs were detected in tested tap water samples. Only CAZ resistant bacteria were more prevalent in the season of increased antibiotic consumption, and only AML resistant bacteria relative abundances increase was statistically significant with the distance from a WTP. The investigated tap water meets all legal requirements. It is therefore safe to drink according to the law. Nevertheless, because antibiotic resistance could pose a threat to consumer health, it should be further monitored in DWDSs.
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Urmi UL, Nahar S, Rana M, Sultana F, Jahan N, Hossain B, Alam MS, Mosaddek ASM, McKimm J, Rahman NAA, Islam S, Haque M. Genotypic to Phenotypic Resistance Discrepancies Identified Involving β-Lactamase Genes, blaKPC, blaIMP, blaNDM-1, and blaVIM in Uropathogenic Klebsiella pneumoniae. Infect Drug Resist 2020; 13:2863-2875. [PMID: 32903880 PMCID: PMC7445497 DOI: 10.2147/idr.s262493] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/16/2020] [Indexed: 12/13/2022] Open
Abstract
Introduction Klebsiella pneumoniae carbapenemase (KPC) belongs to the Group-A β-lactamases that incorporate serine at their active site and hydrolyze various penicillins, cephalosporins, and carbapenems. Metallo-beta-lactamases (MBLs) are group-B enzymes that contain one or two essential zinc ions in the active sites and hydrolyze almost all clinically available β-lactam antibiotics. Klebsiella pneumoniae remains the pathogen with the most antimicrobial resistance to KPC and MBLs. Methods This research investigated the blaKPC, and MBL genes, namely, blaIMP, blaVIM, and blaNDM-1 and their phenotypic resistance to K. pneumoniae isolated from urinary tract infections (UTI) in Bangladesh. Isolated UTI K. pneumoniae were identified by API-20E and 16s rDNA gene analysis. Their phenotypic antimicrobial resistance was examined by the Kirby-Bauer disc diffusion method, followed by minimal inhibitory concentration (MIC) determination. blaKPC, blaIMP, blaNDM-1, and blaVIM genes were evaluated by polymerase chain reactions (PCR) and confirmed by sequencing. Results Fifty-eight K. pneumoniae were identified from 142 acute UTI cases. Their phenotypic resistance to amoxycillin-clavulanic acid, cephalexin, cefuroxime, ceftriaxone, and imipenem were 98.3%, 100%, 96.5%, 91.4%, 75.1%, respectively. Over half (31/58) of the isolates contained either blaKPC or one of the MBL genes. Individual prevalence of blaKPC, blaIMP, blaNDM-1, and blaVIM were 15.5% (9), 10.3% (6), 22.4% (13), and 19% (11), respectively. Of these, eight isolates (25.8%, 8/31) were found to have two genes in four different combinations. The co-existence of the ESBL genes generated more resistance than each one individually. Some isolates appeared phenotypically susceptible to imipenem in the presence of blaKPC, blaIMP, blaVIM, and blaNDM-1 genes, singly or in combination. Conclusion The discrepancy of genotype and phenotype resistance has significant consequences for clinical bacteriology, precision in diagnosis, the prudent selection of antimicrobials, and rational prescribing. Heterogeneous phenotypes of antimicrobial susceptibility testing should be taken seriously to avoid inappropriate diagnostic and therapeutic decisions.
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Affiliation(s)
- Umme Laila Urmi
- Department of Microbiology, Jahangirnagar University, Dhaka 1342, Bangladesh
| | - Shamsun Nahar
- Department of Microbiology, Jahangirnagar University, Dhaka 1342, Bangladesh
| | - Masud Rana
- Department of Microbiology, Jahangirnagar University, Dhaka 1342, Bangladesh
| | - Fahmida Sultana
- Department of Microbiology, Jahangirnagar University, Dhaka 1342, Bangladesh
| | - Nusrat Jahan
- Department of Microbiology, Jahangirnagar University, Dhaka 1342, Bangladesh
| | - Billal Hossain
- Department of Microbiology, Jahangirnagar University, Dhaka 1342, Bangladesh
| | - Mohammed Shah Alam
- Department of Microbiology, Gono Bishwabidyalay, Savar, Dhaka 1342, Bangladesh
| | - Abu Syed Md Mosaddek
- Department of Pharmacology, Uttara Adhunik Medical College, Uttara, Dhaka, Bangladesh
| | - Judy McKimm
- Medical Education, Strategic Educational Development, Leadership for the Health Professions, Swansea University Medical School, Swansea University, Swansea, Wales SA2 8PP, UK
| | - Nor Azlina A Rahman
- Department of Physical Rehabilitation Sciences, Kulliyyah of Allied Health Sciences, International Islamic University Malaysia, Kuantan 25200, Malaysia
| | - Salequl Islam
- Department of Microbiology, Jahangirnagar University, Dhaka 1342, Bangladesh
| | - Mainul Haque
- Faculty of Medicine and Defence Health, Universiti Pertahanan Nasional Malaysia (National Defence University of Malaysia), Kuala Lumpur 57000, Malaysia
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21
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Galarce N, Sánchez F, Fuenzalida V, Ramos R, Escobar B, Lapierre L, Paredes-Osses E, Arriagada G, Alegría-Morán R, Lincopán N, Fuentes-Castillo D, Vera-Leiva A, González-Rocha G, Bello-Toledo H, Borie C. Phenotypic and Genotypic Antimicrobial Resistance in Non-O157 Shiga Toxin-Producing Escherichia coli Isolated From Cattle and Swine in Chile. Front Vet Sci 2020; 7:367. [PMID: 32754621 PMCID: PMC7365902 DOI: 10.3389/fvets.2020.00367] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 05/27/2020] [Indexed: 01/09/2023] Open
Abstract
Non-O157 Shiga toxin-producing Escherichia coli (STEC) is a zoonotic pathogen that causes bloody diarrhea and hemolytic-uremic syndrome in humans, and a major cause of foodborne disease. Despite antibiotic treatment of STEC infections in humans is not recommended, the presence of antimicrobial-resistant bacteria in animals and food constitutes a risk to public health, as the pool of genes from which pathogenic bacteria can acquire antibiotic resistance has increased. Additionally, in Chile there is no information on the antimicrobial resistance of this pathogen in livestock. Thus, the aim of this study was to characterize the phenotypic and genotypic antimicrobial resistance of STEC strains isolated from cattle and swine in the Metropolitan region, Chile, to contribute relevant data to antimicrobial resistance surveillance programs at national and international level. We assessed the minimal inhibitory concentration of 18 antimicrobials, and the distribution of 12 antimicrobial resistance genes and class 1 and 2 integrons in 54 STEC strains. All strains were phenotypically resistant to at least one antimicrobial drug, with a 100% of resistance to cefalexin, followed by colistin (81.5%), chloramphenicol (14.8%), ampicillin and enrofloxacin (5.6% each), doxycycline (3.7%), and cefovecin (1.9%). Most detected antibiotic resistance genes were dfrA1 and tetA (100%), followed by tetB (94.4%), blaTEM−1 (90.7%), aac(6)-Ib (88.9%), blaAmpC (81.5%), cat1 (61.1%), and aac(3)-IIa (11.1%). Integrons were detected only in strains of swine origin. Therefore, this study provides further evidence that non-O157 STEC strains present in livestock in the Metropolitan region of Chile exhibit phenotypic and genotypic resistance against antimicrobials that are critical for human and veterinary medicine, representing a major threat for public health. Additionally, these strains could have a competitive advantage in the presence of antimicrobial selective pressure, leading to an increase in food contamination. This study highlights the need for coordinated local and global actions regarding the use of antimicrobials in animal food production.
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Affiliation(s)
- Nicolás Galarce
- Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Fernando Sánchez
- Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Verónica Fuenzalida
- Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Romina Ramos
- Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Beatriz Escobar
- Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Lisette Lapierre
- Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Esteban Paredes-Osses
- Departamento de Salud Ambiental, Instituto de Salud Pública de Chile, Santiago, Chile
| | - Gabriel Arriagada
- Instituto de Ciencias Agroalimentarias, Animales y Ambientales, Universidad de O'Higgins, San Fernando, Chile
| | - Raúl Alegría-Morán
- Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile.,Facultad de Ciencias Agropecuarias, Universidad Pedro de Valdivia, Santiago, Chile
| | - Nilton Lincopán
- Departamento de Microbiología, Instituto de Ciências Biomedicas, Universidade de São Paulo, São Paulo, Brazil
| | - Danny Fuentes-Castillo
- Departamento de Patologia, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, Brazil
| | - Alejandra Vera-Leiva
- Laboratorio de Investigación en Agentes Antibacterianos, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Gerardo González-Rocha
- Laboratorio de Investigación en Agentes Antibacterianos, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile.,Millenium Nucleus on Interdisciplinary Approach to Antimicrobial Resistance, Santiago, Chile
| | - Helia Bello-Toledo
- Laboratorio de Investigación en Agentes Antibacterianos, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile.,Millenium Nucleus on Interdisciplinary Approach to Antimicrobial Resistance, Santiago, Chile
| | - Consuelo Borie
- Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
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22
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The gut and feed residue microbiota changing during the rearing of Hermetia illucens larvae. Antonie van Leeuwenhoek 2020; 113:1323-1344. [PMID: 32638136 DOI: 10.1007/s10482-020-01443-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 06/24/2020] [Indexed: 12/19/2022]
Abstract
Larvae of Hermetia illucens, commonly known as black soldier fly, efficiently convert organic waste into nutrient-rich supplements for different applications. Here we performed a preliminary experiment to investigate the dynamics of the H. illucens gut microbiota and changes in the composition of the bacterial community in the residue of the larval feed during rearing. We furthermore quantified the presence of antibiotic resistance and disinfectant genes in the gut and feed microbiota during the rearing process to elucidate if rearing leads to a reduction, increase, and/or transfer of resistance genes from the feed to larvae and vice versa. We found that the gut and feed residue bacterial communities were distinct throughout the rearing process. The gut microbiome remained more stable compared to the feed residue microbiome varying in both bacterial abundance and community structure during rearing. Antibiotic-resistance genes were present in both, gut and feed residues, with a significant increase in pupae and residue samples taken at the end of the rearing process. Disinfectant-resistance genes were present in the feed residue and even increased during the rearing process but were not transferred to the gut microbiome. We conclude that H. illucens larvae have a stable gut microbiome that does not change significantly over the course of larval development, whereas bacterial communities in the feed residue are strongly affected by rearing. If the presence of antibiotics and disinfectants during rearing, can promote the spread of antibiotic/disinfectant-resistance genes among feed and larvae needs to be evaluated in further experiments.
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23
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Barth SA, Weber M, Schaufler K, Berens C, Geue L, Menge C. Metabolic Traits of Bovine Shiga Toxin-Producing Escherichia Coli (STEC) Strains with Different Colonization Properties. Toxins (Basel) 2020; 12:toxins12060414. [PMID: 32580365 PMCID: PMC7354573 DOI: 10.3390/toxins12060414] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/10/2020] [Accepted: 06/17/2020] [Indexed: 01/14/2023] Open
Abstract
Cattle harbor Shiga toxin-producing Escherichia coli (STEC) in their intestinal tract, thereby providing these microorganisms with an ecological niche, but without this colonization leading to any clinical signs. In a preceding study, genotypic characterization of bovine STEC isolates unveiled that their ability to colonize cattle persistently (STECper) or only sporadically (STECspo) is more closely associated with the overall composition of the accessory rather than the core genome. However, the colonization pattern could not be unequivocally linked to the possession of classical virulence genes. This study aimed at assessing, therefore, if the presence of certain phenotypic traits in the strains determines their colonization pattern and if these can be traced back to distinctive genetic features. STECspo strains produced significantly more biofilm than STECper when incubated at lower temperatures. Key substrates, the metabolism of which showed a significant association with colonization type, were glyoxylic acid and L-rhamnose, which were utilized by STECspo, but not or only by some STECper. Genomic sequences of the respective glc and rha operons contained mutations and frameshifts in uptake and/or regulatory genes, particularly in STECper. These findings suggest that STECspo conserved features leveraging survival in the environment, whereas the acquisition of a persistent colonization phenotype in the cattle reservoir was accompanied by the loss of metabolic properties and genomic mutations in the underlying genetic pathways.
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Affiliation(s)
- Stefanie A. Barth
- Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Naumburger Str. 96a, 07743 Jena, Germany; (M.W.); (C.B.); (L.G.); (C.M.)
- Correspondence: ; Tel.: +49-3641-804-2270; Fax: +49-3641-804-2482
| | - Michael Weber
- Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Naumburger Str. 96a, 07743 Jena, Germany; (M.W.); (C.B.); (L.G.); (C.M.)
| | - Katharina Schaufler
- Free University Berlin, Institute of Microbiology and Epizootics, Robert-von-Ostertag-Str. 7-13, 14163 Berlin, Germany;
- University of Greifswald, Pharmaceutical Microbiology, Friedrich-Ludwig-Jahn-Str. 17, 17489 Greifswald, Germany
| | - Christian Berens
- Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Naumburger Str. 96a, 07743 Jena, Germany; (M.W.); (C.B.); (L.G.); (C.M.)
| | - Lutz Geue
- Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Naumburger Str. 96a, 07743 Jena, Germany; (M.W.); (C.B.); (L.G.); (C.M.)
| | - Christian Menge
- Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Naumburger Str. 96a, 07743 Jena, Germany; (M.W.); (C.B.); (L.G.); (C.M.)
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24
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Multi-drug resistant mesophilic aeromonads isolated from marketed scallops (Patinopecten yessoensis) harboring resistance genes. ACTA ACUST UNITED AC 2020. [DOI: 10.2478/aopf-2020-0001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
Antimicrobial resistance properties of 32 Aeromonas strains isolated from fresh scallops (Patinopecten yessoensis (Jay)) marketed in Korea were assessed. All the Aeromonas spp., including A. salmonicida, were mesophilic and grew very well at 37°C. The isolates were tested for susceptibility to 19 antimicrobials belonging to eight antimicrobial classes. All isolates were multi-drug resistant, which means they were resistant to five or more antimicrobials. Higher resistance rates (≥ 50%) were observed for ampicillin, piperacillin, cephalothin, imipenem, meropenem, trimethoprim-sulfamethoxazole, tetracycline, oxytetracycline, and nalidixic acid while intermediate resistance was also determined. PCR assays revealed the presence of many antimicrobial resistance genes among the isolates in varying combinations. Among them, some isolates harbored higher numbers of resistant genes, e.g., A. veronii-V1 (aac(6’)-Ib, tetE, qnrS, IntI1), A. salmonicida–SL10 (IntI1, blaCTX, aac(3’)-Ib, aac(6’)-Ib, qnrS), A. hydrophila–H13 (IntI1, blaTEM, qnrS, aac(6’)-Ib, strA-strB). However, neither the blaSHV, blaIMP, tetB, qnrA, qnrB, and aphAI-IAB genes nor class1 integrons were detected in any of the isolates. Discrepancies between phenotypic and genetic resistance traits were observed in some isolates. With respect to outcomes, scallops are proposed as a source of multi-drug resistant Aeromonas spp. that harbor antimicrobial resistant genes.
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25
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Baniga Z, Hounmanou YMG, Kudirkiene E, Kusiluka LJM, Mdegela RH, Dalsgaard A. Genome-Based Analysis of Extended-Spectrum β-Lactamase-Producing Escherichia coli in the Aquatic Environment and Nile Perch ( Lates niloticus) of Lake Victoria, Tanzania. Front Microbiol 2020; 11:108. [PMID: 32153519 PMCID: PMC7046833 DOI: 10.3389/fmicb.2020.00108] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 01/17/2020] [Indexed: 12/11/2022] Open
Abstract
Extended-spectrum β-lactamase (ESBL)-producing bacteria constitute an emerging global health issue with food products being vehicles of transmission and the aquatic environments serving as potential reservoirs. This study aimed to characterize ESBL-producing Escherichia coli in Nile perch and water from Lake Victoria in Tanzania. A total of 180 samples of Nile perch and 60 water samples were screened for ESBL-producing E. coli on MacConkey agar supplemented with 2 μg/ml of cefotaxime and confirmed by blaCTX–M and blaTEM PCR. Antimicrobial resistance was determined by the disk diffusion method, and the ESBL-producing isolates were whole genome sequencing (WGS). ESBL-producing E. coli were detected in eight of the 180 analyzed Nile perch samples, and only one water sample was positive (1.7%, n = 60). Isolates were resistant to sulfamethoxazole–trimethoprim (100%), ampicillin/cloxacillin (100%), erythromycin 72.7% (8/11), tetracycline 90.9% (10/11), and nalidixic acid 63.6% (7/11). This mostly corroborates the resistance genes that they carried for sulfonamides (sul1 and sul2), trimethoprim (dfrA and dfrB), aminoglycosides [aac(3)-IId, strA, and strB], tetracycline [tet(B) and tet(D)], and fluoroquinolones (qepA4). They harbored plasmid replicon types IncF, IncX, IncQ, and Col and carried blaCTX–M–15 and blaTEM–1B genes generally found on the same contigs as the IncF plasmid replicon. Although epidemiologically unrelated, the strains formed three separate sequence type–phylogroup–serotype-specific clusters: C1, C2, and C3. Cluster C1 included five strains (3 to 13 SNPs) belonging to ST167, phylogroup A, and serotype O9:H21; the two C2 strains (11 SNPs) belong to ST156, phylogroup B1, and serotype ONT:H28; and C3 was made up of four strains (SNPs ranged from 4 to 17) of ST636, phylogroup B2, and serotype O45:H7. The common virulence gene gad was reported in all strains. In addition, strains in C2 and C3 possessed iss, lpfA, and nfaE virulence genes, and the vat gene was found only in C3. The present study reports the occurrence of multidrug-resistant ESBL-producing E. coli carrying plasmid-mediated ESBL genes in offshore water and Nile perch in Lake Victoria. Strains formed three clonal clusters of unknown origin. This study reveals that the Lake may serve as reservoir for ESBL-producing bacteria that can be transmitted by fish as a food chain hazard of One-Health concern.
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Affiliation(s)
- Zebedayo Baniga
- Department of Veterinary Medicine and Public Health, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania.,Department of Fisheries Development, National Fish Quality Control Laboratory-Nyegezi, Mwanza, Tanzania
| | - Yaovi M Gildas Hounmanou
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Egle Kudirkiene
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lughano J M Kusiluka
- Department of Veterinary Medicine and Public Health, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania.,Mzumbe University, Mzumbe, Tanzania
| | - Robinson H Mdegela
- Department of Veterinary Medicine and Public Health, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, Singapore
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26
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Subbiah M, Caudell MA, Mair C, Davis MA, Matthews L, Quinlan RJ, Quinlan MB, Lyimo B, Buza J, Keyyu J, Call DR. Antimicrobial resistant enteric bacteria are widely distributed amongst people, animals and the environment in Tanzania. Nat Commun 2020; 11:228. [PMID: 31932601 PMCID: PMC6957491 DOI: 10.1038/s41467-019-13995-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 12/07/2019] [Indexed: 11/09/2022] Open
Abstract
Antibiotic use and bacterial transmission are responsible for the emergence, spread and persistence of antimicrobial-resistant (AR) bacteria, but their relative contribution likely differs across varying socio-economic, cultural, and ecological contexts. To better understand this interaction in a multi-cultural and resource-limited context, we examine the distribution of antimicrobial-resistant enteric bacteria from three ethnic groups in Tanzania. Household-level data (n = 425) was collected and bacteria isolated from people, livestock, dogs, wildlife and water sources (n = 62,376 isolates). The relative prevalence of different resistance phenotypes is similar across all sources. Multi-locus tandem repeat analysis (n = 719) and whole-genome sequencing (n = 816) of Escherichia coli demonstrate no evidence for host-population subdivision. Multivariate models show no evidence that veterinary antibiotic use increased the odds of detecting AR bacteria, whereas there is a strong association with livelihood factors related to bacterial transmission, demonstrating that to be effective, interventions need to accommodate different cultural practices and resource limitations.
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Affiliation(s)
- Murugan Subbiah
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA
| | - Mark A Caudell
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA.
- Food and Agriculture Organization of the United Nations, Nairobi, Kenya.
| | - Colette Mair
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Margaret A Davis
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA
| | - Louise Matthews
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Robert J Quinlan
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA
- Department of Anthropology, Washington State University, Pullman, WA, USA
| | - Marsha B Quinlan
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA
- Department of Anthropology, Washington State University, Pullman, WA, USA
| | - Beatus Lyimo
- Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | - Joram Buza
- Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | - Julius Keyyu
- Tanzania Wildlife Research Institute, Arusha, Tanzania
| | - Douglas R Call
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA
- Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
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27
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The Resistome, Mobilome, Virulome and Phylogenomics of Multidrug-Resistant Escherichia coli Clinical Isolates from Pretoria, South Africa. Sci Rep 2019; 9:16457. [PMID: 31712587 PMCID: PMC6848087 DOI: 10.1038/s41598-019-52859-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 10/25/2019] [Indexed: 12/18/2022] Open
Abstract
Antibiotic-resistant Escherichia coli is a common occurrence in food, clinical, community and environmental settings worldwide. The resistome, mobilome, virulome and phylogenomics of 20 multidrug resistant (MDR) clinical E. coli isolates collected in 2013 from Pretoria, South Africa, were characterised. The isolates were all extended-spectrum β-lactamase producers, harbouring CTX-M (n = 16; 80%), TEM-1B (n = 10; 50%) and OXA (n = 12, 60%) β-lactamases alongside genes mediating resistance to fluoroquinolones, aminoglycosides, tetracyclines etc. Most resistance determinants were found on contigs containing IncF plasmid replicons and bracketed by composite transposons (Tn3), diverse ISs and class 1 integrons (In13, In54, In369, and In467). Gene cassettes such as blaOXA,dfrA5-psp-aadA2-cmlA1a-aadA1-qac and estX3-psp-aadA2-cmlA1a-aadA1a-qac were encompassed by Tn3 and ISs; several isolates had same or highly similar genomic antibiotic resistance islands. ST131 (n = 10), ST617 (n = 2) and singletons of ST10, ST73, ST95, ST410, ST648, ST665, ST744 and ST998 clones were phylogenetically related to clinical (human and animal) strains from Egypt, Kenya, Niger, Nigeria, Tanzania, and UK. A rich repertoire of virulence genes, including iss, gad and iha were identified. MDR E. coli harbouring chromosomal and plasmid-borne resistance genes in same and multiple clones exist in South Africa, which is very worrying for clinical epidemiology and infectious diseases management.
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28
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Casaburi G, Duar RM, Vance DP, Mitchell R, Contreras L, Frese SA, Smilowitz JT, Underwood MA. Early-life gut microbiome modulation reduces the abundance of antibiotic-resistant bacteria. Antimicrob Resist Infect Control 2019; 8:131. [PMID: 31423298 PMCID: PMC6693174 DOI: 10.1186/s13756-019-0583-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 07/22/2019] [Indexed: 01/21/2023] Open
Abstract
Background Antibiotic-resistant (AR) bacteria are a global threat. AR bacteria can be acquired in early life and have long-term sequelae. Limiting the spread of antibiotic resistance without triggering the development of additional resistance mechanisms is of immense clinical value. Here, we show how the infant gut microbiome can be modified, resulting in a significant reduction of AR genes (ARGs) and the potentially pathogenic bacteria that harbor them. Methods The gut microbiome was characterized using shotgun metagenomics of fecal samples from two groups of healthy, term breastfed infants. One group was fed B. infantis EVC001 in addition to receiving lactation support (n = 29, EVC001-fed), while the other received lactation support alone (n = 31, controls). Coliforms were isolated from fecal samples and genome sequenced, as well as tested for minimal inhibitory concentrations against clinically relevant antibiotics. Results Infants fed B. infantis EVC001 exhibited a change to the gut microbiome, resulting in a 90% lower level of ARGs compared to controls. ARGs that differed significantly between groups were predicted to confer resistance to beta lactams, fluoroquinolones, or multiple drug classes, the majority of which belonged to Escherichia, Clostridium, and Staphylococcus. Minimal inhibitory concentration assays confirmed the resistance phenotypes among isolates with these genes. Notably, we found extended-spectrum beta lactamases among healthy, vaginally delivered breastfed infants who had never been exposed to antibiotics. Conclusions Colonization of the gut of breastfed infants by a single strain of B. longum subsp. infantis had a profound impact on the fecal metagenome, including a reduction in ARGs. This highlights the importance of developing novel approaches to limit the spread of these genes among clinically relevant bacteria. Future studies are needed to determine whether colonization with B. infantis EVC001 decreases the incidence of AR infections in breastfed infants. Trial registration This clinical trial was registered at ClinicalTrials.gov, NCT02457338.
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Affiliation(s)
| | | | | | | | | | - Steven A. Frese
- Evolve Biosystems, Inc, Davis, CA 95618 USA
- Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68588 USA
| | - Jennifer T. Smilowitz
- Department of Food Science and Technology, University of California, Davis, CA 95616 USA
- Foods for Health Institute, University of California, Davis, CA 95616 USA
| | - Mark A. Underwood
- Foods for Health Institute, University of California, Davis, CA 95616 USA
- Department of Pediatrics, UC Davis Children’s Hospital, Sacramento, CA 95817 USA
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Effects of two-dose ceftiofur treatment for metritis on the temporal dynamics of antimicrobial resistance among fecal Escherichia coli in Holstein-Friesian dairy cows. PLoS One 2019; 14:e0220068. [PMID: 31329639 PMCID: PMC6645674 DOI: 10.1371/journal.pone.0220068] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 07/08/2019] [Indexed: 12/15/2022] Open
Abstract
A pair-matched longitudinal study conducted on three dairy farms in the U.S. High-Plains explored the temporal effects of two-dose ceftiofur crystalline-free acid (CCFA) treatment for metritis on third-generation cephalosporin (3GC) resistance among enteric E. coli in Holstein-Friesian cows. The current 13-day slaughter withholding period does not account for rising populations of third-generation cephalosporin (3GC) resistant bacteria in feces of animals following CCFA treatment. A total of 124 matched-pairs of cows were enrolled in the study. Cows diagnosed with postpartum metritis received the product twice at the labeled dose of 6.6 mg/kg subcutaneously at the base of alternating ears. Untreated cows–absent clinical metritis–were matched on lactation number and calving date. Feces were collected per rectum on days 0 (baseline), 6, 16, 28, and 56. Environmental samples, from watering troughs as well as surface manure from fresh-cow, hospital, maternity, and milking pens, and from the compost pile were collected prior to the animal sample collection period. Historical data on metritis rates and CCFA use were compiled from herd records. On day 0, cows exhibited an overall mean difference of over 4 log10 colony forming units (CFU) comparing 3GC resistant E. coli to the general E. coli population. At the first eligible slaughter date, the difference declined to 3.31 log10 CFU among cows in the CCFA group (P<0.01 compared to control cows). Such differences were no longer observed between the treated and control groups by day 28. Results suggest a 13-day withholding period following the final treatment is insufficient to allow levels of 3GC resistant E. coli to return to baseline. This effect varied by farm and was dependent upon the starting level of resistance. A farm-specific extended slaughter-withholding period could reduce the microbial risk to food products at slaughter.
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Mancini S, Marchesi M, Imkamp F, Wagner K, Keller PM, Quiblier C, Bodendoerfer E, Courvalin P, Böttger EC. Population-based inference of aminoglycoside resistance mechanisms in Escherichia coli. EBioMedicine 2019; 46:184-192. [PMID: 31307955 PMCID: PMC6710905 DOI: 10.1016/j.ebiom.2019.07.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/27/2019] [Accepted: 07/06/2019] [Indexed: 12/17/2022] Open
Abstract
Background Interpretative reading of antimicrobial susceptibility test (AST) results allows inferring biochemical resistance mechanisms from resistance phenotypes. For aminoglycosides, however, correlations between resistance pathways inferred on the basis of the European Committee on Antimicrobial Susceptibility Testing (EUCAST) clinical breakpoints and expert rules versus genotypes are generally poor. This study aimed at developing and validating a decision tree based on resistance phenotypes determined by disc diffusion and based on epidemiological cut-offs (ECOFFs) to infer the corresponding resistance mechanisms in Escherichia coli. Methods Phenotypic antibiotic susceptibility of thirty wild-type and 458 aminoglycoside-resistant E. coli clinical isolates was determined by disc diffusion and the genomes were sequenced. Based on well-defined cut-offs, we developed a phenotype-based algorithm (Aminoglycoside Resistance Mechanism Inference Algorithm - ARMIA) to infer the biochemical mechanisms responsible for the corresponding aminoglycoside resistance phenotypes. The mechanisms inferred from susceptibility to kanamycin, tobramycin and gentamicin were analysed using ARMIA- or EUCAST-based AST interpretation and validated by whole genome sequencing (WGS) of the host bacteria. Findings ARMIA-based inference of resistance mechanisms and WGS data were congruent in 441/458 isolates (96·3%). In contrast, there was a poor correlation between resistance mechanisms inferred using EUCAST CBPs/expert rules and WGS data (418/488, 85·6%). Based on the assumption that resistance mechanisms can result in therapeutic failure, EUCAST produced 63 (12·9%) very major errors (vME), compared to only 2 (0·4%) vME with ARMIA. When used for detection and identification of resistance mechanisms, ARMIA resolved >95% vMEs generated by EUCAST-based AST interpretation. Interpretation This study demonstrates that ECOFF-based analysis of AST data of only four aminoglycosides provides accurate information on the resistance mechanisms in E. coli. Since aminoglycoside resistance mechanisms, despite having in certain cases a minimal effect on the minimal inhibitory concentration, may compromise the bactericidal activity of aminoglycosides, prompt detection of resistance mechanisms is crucial for therapy. Using ARMIA as an interpretative rule set for editing AST results allows for better predictions of in vivo activity of this drug class.
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Affiliation(s)
- Stefano Mancini
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland.
| | - Martina Marchesi
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
| | - Frank Imkamp
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
| | - Karoline Wagner
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
| | - Peter M Keller
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
| | - Chantal Quiblier
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
| | - Elias Bodendoerfer
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
| | | | - Erik C Böttger
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
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Mensah N, Tang Y, Cawthraw S, AbuOun M, Fenner J, Thomson NR, Mather AE, Petrovska-Holmes L. Determining antimicrobial susceptibility in Salmonella enterica serovar Typhimurium through whole genome sequencing: a comparison against multiple phenotypic susceptibility testing methods. BMC Microbiol 2019; 19:148. [PMID: 31266463 PMCID: PMC6604184 DOI: 10.1186/s12866-019-1520-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 06/19/2019] [Indexed: 12/12/2022] Open
Abstract
Background UK public health organisations perform routine antimicrobial susceptibility tests (ASTs) to characterise the potential for antimicrobial resistance in Salmonella enterica serovars. Genetic determinants of these resistance mechanisms are detectable by whole genome sequencing (WGS), however the viability of WGS-based genotyping as an alternative resistance screening tool remains uncertain. We compared WGS-based genotyping, disk diffusion and agar dilution to the broth microdilution reference AST for 102 Salmonella enterica serovar Typhimurium (S. Typhimurium) isolates across 11 antimicrobial compounds. Results Genotyping concordance, interpreted using epidemiological cut-offs (ECOFFs), was 89.8% (1007/1122) with 0.83 sensitivity and 0.96 specificity. For seven antimicrobials interpreted using Salmonella clinical breakpoints, genotyping produced 0.84 sensitivity and 0.88 specificity. Although less accurate than disk diffusion (0.94 sensitivity, 0.93 specificity) and agar dilution (0.83 sensitivity, 0.98 specificity), genotyping performance improved to 0.89 sensitivity and 0.97 specificity when two antimicrobials with relatively high very major error rates were excluded (streptomycin and sulfamethoxazole). Conclusions An 89.8% concordance from WGS-based AST predictions using ECOFF interpretations suggest that WGS would serve as an effective screening tool for the tracking of antimicrobial resistance mechanisms in S. Typhimurium. For use as a standalone clinical diagnostic screen, further work is required to reduce the error rates for specific antimicrobials. Electronic supplementary material The online version of this article (10.1186/s12866-019-1520-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nana Mensah
- Animal and Plant Health Agency, Weybridge, Addlestone, Surrey, UK
| | - Yue Tang
- Animal and Plant Health Agency, Weybridge, Addlestone, Surrey, UK
| | - Shaun Cawthraw
- Animal and Plant Health Agency, Weybridge, Addlestone, Surrey, UK
| | - Manal AbuOun
- Animal and Plant Health Agency, Weybridge, Addlestone, Surrey, UK
| | - Jackie Fenner
- Animal and Plant Health Agency, Weybridge, Addlestone, Surrey, UK
| | | | - Alison E Mather
- University of Cambridge, Cambridge, Cambridgeshire, UK.,Present Address: Quadram Institute Bioscience, Norwich, Norfolk, UK.,University of East Anglia, Norwich, Norfolk, UK
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Prasertsee T, Chuammitri P, Deeudom M, Chokesajjawatee N, Santiyanont P, Tadee P, Nuangmek A, Tadee P, Sheppard SK, Pascoe B, Patchanee P. Core genome sequence analysis to characterize Salmonella enterica serovar Rissen ST469 from a swine production chain. Int J Food Microbiol 2019; 304:68-74. [PMID: 31174037 DOI: 10.1016/j.ijfoodmicro.2019.05.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 05/02/2019] [Accepted: 05/25/2019] [Indexed: 02/02/2023]
Abstract
Salmonella enterica subsp. enterica serotype Rissen is the predominant serotype found in Thai pork production and can be transmitted to humans through contamination of the food chain. This study was conducted to investigate the genetic relationships between serovar Rissen isolates from all levels of the pork production chain and evaluate the ability of the in silico antimicrobial resistance (AMR) genotypes to predict the phenotype of serovar Rissen. A total of 38 serovar Rissen isolates were tested against eight antibiotic agents by a disk diffusion method and the whole genomes of all isolates were sequenced to detect AMR genetic elements using the ResFinder database.A total of 86.84% of the isolates were resistant to tetracycline, followed by ampicillin (78.96%) and sulfonamide-trimethoprim (71.05%). Resistance to more than one antimicrobial agent was observed in 78.95% of the isolates, with the most common pattern showing resistance to ampicillin, chloramphenicol, streptomycin, sulfonamide-trimethoprim, and tetracycline. The results of genotypic AMR indicated that 89.47% of the isolates carried tet(A), 84.22% carried blaTEM-1B, 78.95% carried sul3, and 78.95% carried dfrA12. The genotypic prediction of phenotypic resistance resulted in a mean sensitivity of 97.45% and specificity of 75.48%. Analysis by core genome multilocus sequence typing (cgMLST) demonstrated that the Salmonella isolates from various sources and different locations shared many of the same core genome loci. This implies that serovar Rissen has infected every stage of the pork production process and that contamination can occur in every part of the production chain.
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Affiliation(s)
- Teerarat Prasertsee
- Graduate Program in Veterinary Science, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand
| | - Phongsakorn Chuammitri
- Department of Veterinary Biosciences and Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand
| | - Manu Deeudom
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Nipa Chokesajjawatee
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand
| | - Pannita Santiyanont
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand
| | - Pakpoom Tadee
- Integrative Research Center for Veterinary Preventive Medicine, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand
| | - Aniroot Nuangmek
- Graduate Program in Veterinary Science, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand
| | - Phacharaporn Tadee
- Faculty of Animal Science and Technology, Maejo University, Chiang Mai 50290, Thailand
| | - Samuel K Sheppard
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, BA2 7BA, United Kingdom; Division of Clinical Microbiology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Ben Pascoe
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, BA2 7BA, United Kingdom; Division of Clinical Microbiology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand.
| | - Prapas Patchanee
- Integrative Research Center for Veterinary Preventive Medicine, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand.
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Li X, Gu AZ, Zhang Y, Xie B, Li D, Chen J. Sub-lethal concentrations of heavy metals induce antibiotic resistance via mutagenesis. JOURNAL OF HAZARDOUS MATERIALS 2019; 369:9-16. [PMID: 30753956 DOI: 10.1016/j.jhazmat.2019.02.006] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 01/31/2019] [Accepted: 02/03/2019] [Indexed: 05/20/2023]
Abstract
The emergence of antibiotic resistance is a growing problem worldwide. Numerous studies have demonstrated that heavy metals facilitate the spread of bacterial drug-resistance in the environment. However, the actions and mechanisms of metals at relatively low sub-lethal levels (far below the minimal inhibitory concentration [MIC]) on antibiotic resistance remain unclear. In this study, we investigated the effect of sub-lethal levels of heavy metals [Ag(I), Zn(II), and Cu(II)] on antibiotic resistance and explored the underlying mechanisms. The results demonstrated that sub-lethal levels of metal ions increased the mutation rates and enriched de novo mutants that exhibited significant resistance to multiple antibiotics. The resistant mutants exhibited hereditary resistance after 5-day of sub-culture. Whole-genome analysis revealed distinct mutations in genes involved in multiple drug and drug-specific resistance, as well as genes that are not associated with antibiotic resistance to data. The number and identities of genetic changes were distinct for mutants induced by different metals. This study provides evidence and mechanistic insights into the induction of antibiotic resistance by sub-lethal concentrations of heavy metals, which may enhance the emergence of antibiotic resistance in various environments. More consideration and regulations should be given to this potential health risk for long-standing and harmful heavy metals.
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Affiliation(s)
- Xiangyang Li
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP(3)), Department of Environmental Science and Engineering, Fudan University, Shanghai, 200433, China; College of Environment and Life Sciences, Kaili University, Kaiyuan Road, 556011, Kaili, China
| | - April Z Gu
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY, 14853, United States
| | - Ye Zhang
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP(3)), Department of Environmental Science and Engineering, Fudan University, Shanghai, 200433, China
| | - Bin Xie
- Pure and Applied Biochemistry, Department of Chemistry, Lund University, Box 124, SE, 22100, Lund, Sweden
| | - Dan Li
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP(3)), Department of Environmental Science and Engineering, Fudan University, Shanghai, 200433, China.
| | - Jianmin Chen
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP(3)), Department of Environmental Science and Engineering, Fudan University, Shanghai, 200433, China
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Day-old chicks are a source of antimicrobial resistant bacteria for laying hen farms. Vet Microbiol 2019; 230:221-227. [DOI: 10.1016/j.vetmic.2019.02.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/28/2019] [Accepted: 02/03/2019] [Indexed: 11/24/2022]
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Turchi B, Dec M, Bertelloni F, Winiarczyk S, Gnat S, Bresciani F, Viviani F, Cerri D, Fratini F. Antibiotic Susceptibility and Virulence Factors in Escherichia coli from Sympatric Wildlife of the Apuan Alps Regional Park (Tuscany, Italy). Microb Drug Resist 2019; 25:772-780. [PMID: 30676273 DOI: 10.1089/mdr.2018.0191] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Today a growing number of studies are focusing on antibiotic resistance in wildlife. This is due to the potential role of wild animals as reservoirs and spreaders of pathogenic and resistant bacteria. This study focused on isolating and identifying Escherichia coli from the feces of wild animals living in the Apuan Alps Regional Park (Tuscany, Italy) and evaluating some of their antibiotic resistance and pathogenicity traits. Eighty-five fecal samples from different species were studied. Seventy-one E. coli were identified by matrix assisted laser desorption ionization-time of flight mass spectrometry analysis, subjected to antibiograms and polymerase chain reaction for the detection of antibiotic resistance genes and pathogenicity factors. The highest resistance rates were found against cephalothin (39.4%) and ampicillin (33.8%), followed by amoxicillin/clavulanic acid (15.5%), streptomycin (12.7%), and tetracycline (5.6%). Regarding resistance genes, 39.4% of the isolates were negative for all tested genes. The remaining isolates were positive for blaCMY-2, sul2, strA-strB and aadA1, tet(B), and tet(A), encoding resistance to beta-lactams, trimethoprim/sulfamethoxazole, streptomycin, and tetracycline, respectively. With regard to virulence factors, 63.4% of the isolates were negative for all genes; 21.1% carried astA alone, which is associated with different pathotypes, 9.9% carried both escV and eaeA (aEPEC); single isolates (1.4%) harbored escV (aEPEC), escV associated with astA and eaeA (aEPEC), astA with stx2 and hlyA (EHEC) or astA and stx1, stx2, and hlyA (EHEC). These results show that wildlife from nonanthropized environments can be a reservoir for antibiotic-resistant microorganisms and suggest the need for a deeper knowledge on their origin and diffusion mechanisms through different ecological niches.
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Affiliation(s)
- Barbara Turchi
- 1 Department of Veterinary Science, University of Pisa, Pisa, Italy
| | - Marta Dec
- 2 Sub-Department of Veterinary Prevention and Avian Diseases, Institute of Biological Bases of Animal Diseases, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Lublin, Poland
| | | | - Stanisław Winiarczyk
- 3 Department of Epizootiology and Clinic of Infectious Diseases, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Lublin, Poland
| | - Sebastian Gnat
- 4 Sub-Department of Veterinary Microbiology, Institute of Biological Bases of Animal Diseases, Faculty of Veterinary Medicine, University of Life Sciences, Lublin, Poland
| | - Flavio Bresciani
- 1 Department of Veterinary Science, University of Pisa, Pisa, Italy
| | | | - Domenico Cerri
- 1 Department of Veterinary Science, University of Pisa, Pisa, Italy
| | - Filippo Fratini
- 1 Department of Veterinary Science, University of Pisa, Pisa, Italy
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Tagg KA, Francois Watkins L, Moore MD, Bennett C, Joung YJ, Chen JC, Folster JP. Novel trimethoprim resistance gene dfrA34 identified in Salmonella Heidelberg in the USA. J Antimicrob Chemother 2019; 74:38-41. [PMID: 30202900 PMCID: PMC10870229 DOI: 10.1093/jac/dky373] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 08/20/2018] [Indexed: 02/05/2023] Open
Abstract
Background Trimethoprim/sulfamethoxazole is a synthetic antibiotic combination recommended for the treatment of complicated non-typhoidal Salmonella infections in humans. Resistance to trimethoprim/sulfamethoxazole is mediated by the acquisition of mobile genes, requiring both a dfr gene (trimethoprim resistance) and a sul gene (sulfamethoxazole resistance) for a clinical resistance phenotype (MIC ≥4/76 mg/L). In 2017, the CDC investigated a multistate outbreak caused by a Salmonella enterica serotype Heidelberg strain with trimethoprim/sulfamethoxazole resistance, in which sul genes but no known dfr genes were detected. Objectives To characterize and describe the molecular mechanism of trimethoprim resistance in a Salmonella Heidelberg outbreak isolate. Methods Illumina sequencing data for one outbreak isolate revealed a 588 bp ORF encoding a putative dfr gene. This gene was cloned into Escherichia coli and resistance to trimethoprim was measured by broth dilution and Etest. Phylogenetic analysis of previously reported dfrA genes was performed using MEGA. Long-read sequencing was conducted to determine the context of the novel dfr gene. Results and conclusions The novel dfr gene, named dfrA34, conferred trimethoprim resistance (MIC ≥32 mg/L) when cloned into E. coli. Based on predicted amino acid sequences, dfrA34 shares less than 50% identity with other known dfrA genes. The dfrA34 gene is located in a class 1 integron in a multiresistance region of an IncC plasmid, adjacent to a sul gene, thus conferring clinical trimethoprim/sulfamethoxazole resistance. Additionally, dfrA34 is associated with ISCR1, enabling easy transmission between other plasmids and bacterial strains.
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Affiliation(s)
| | | | - Matthew D. Moore
- Oak Ridge Institute for Science and Education, 100 ORAU Way, Oak Ridge, TN 37830, USA
| | | | - Yoo J. Joung
- Oak Ridge Institute for Science and Education, 100 ORAU Way, Oak Ridge, TN 37830, USA
| | | | - Jason P. Folster
- Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA 30333, USA
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Springer HR, Denagamage TN, Fenton GD, Haley BJ, Van Kessel JAS, Hovingh EP. Antimicrobial Resistance in Fecal Escherichia coli and Salmonella enterica from Dairy Calves: A Systematic Review. Foodborne Pathog Dis 2018; 16:23-34. [PMID: 30481058 DOI: 10.1089/fpd.2018.2529] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The discovery of antibiotics brought with it many advances in the health and well-being of humans and animals; however, in recent years development of antimicrobial resistance (AMR) has increasingly become a concern. Much of the antibiotic use on dairy farms is for disease management in mature cattle, and AMR in fecal organisms is relatively rare in this group. However, young dairy calves often carry high levels of AMR in their fecal Escherichia coli and Salmonella enterica, which could provide a potential reservoir of AMR genes on dairy farms. To develop practical and effective antibiotic stewardship policies for dairy calf rearing, it is vital to have a solid understanding of the current state of knowledge regarding AMR in these animals. A systematic review process was used to summarize the current scientific literature regarding AMR in fecal S. enterica and E. coli and associations between management practices and AMR prevalence in dairy calves in the United States and Canada. Seven online databases were searched for literature published from 1997 to 2018. Multiple studies indicated an association between preweaned calves and increased risk of fecal shedding of resistant bacteria, compared to other animal groups on dairy farms. There also was evidence, although less consistent, of an impact of antibiotic treatment, antibiotic-containing milk replacer feeding, and feeding nonsalable or waste milk (WM) on the presence of AMR bacteria. Overall, the research summarized in this systematic review highlights the need for continued research on the impact of management practices, including antibiotic use, WM feeding, and disease prevention practices in reducing AMR in E. coli and S. enterica in dairy calves. In addition, few data were available on physiological and microbiological factors that may contribute to the high relative populations of resistant bacteria in young calves, suggesting another valuable area of future research.
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Affiliation(s)
- Hayley R Springer
- 1 Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania
| | - Thomas N Denagamage
- 1 Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania
| | - Ginger D Fenton
- 2 Penn State Extension, The Pennsylvania State University, Mercer, Pennsylvania
| | - Bradd J Haley
- 3 Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, Agricultural Research Services, United States Department of Agriculture, Beltsville, Maryland
| | - Jo Ann S Van Kessel
- 3 Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, Agricultural Research Services, United States Department of Agriculture, Beltsville, Maryland
| | - Ernest P Hovingh
- 1 Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania
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Pornsukarom S, van Vliet AHM, Thakur S. Whole genome sequencing analysis of multiple Salmonella serovars provides insights into phylogenetic relatedness, antimicrobial resistance, and virulence markers across humans, food animals and agriculture environmental sources. BMC Genomics 2018; 19:801. [PMID: 30400810 PMCID: PMC6218967 DOI: 10.1186/s12864-018-5137-4] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 10/02/2018] [Indexed: 11/13/2022] Open
Abstract
Background Salmonella enterica is a significant foodborne pathogen, which can be transmitted via several distinct routes, and reports on acquisition of antimicrobial resistance (AMR) are increasing. To better understand the association between human Salmonella clinical isolates and the potential environmental/animal reservoirs, whole genome sequencing (WGS) was used to investigate the epidemiology and AMR patterns within Salmonella isolates from two adjacent US states. Results WGS data of 200 S. enterica isolates recovered from human (n = 44), swine (n = 32), poultry (n = 22), and farm environment (n = 102) were used for in silico prediction of serovar, distribution of virulence genes, and phylogenetically clustered using core genome single nucleotide polymorphism (SNP) and feature frequency profiling (FFP). Furthermore, AMR was studied both by genotypic prediction using five curated AMR databases, and compared to phenotypic AMR using broth microdilution. Core genome SNP-based and FFP-based phylogenetic trees showed consistent clustering of isolates into the respective serovars, and suggested clustering of isolates based on the source of isolation. The overall correlation of phenotypic and genotypic AMR was 87.61% and 97.13% for sensitivity and specificity, respectively. AMR and virulence genes clustered with the Salmonella serovars, while there were also associations between the presence of virulence genes in both animal/environmental isolates and human clinical samples. Conclusions WGS is a helpful tool for Salmonella phylogenetic analysis, AMR and virulence gene predictions. The clinical isolates clustered closely with animal and environmental isolates, suggesting that animals and environment are potential sources for dissemination of AMR and virulence genes between Salmonella serovars. Electronic supplementary material The online version of this article (10.1186/s12864-018-5137-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Suchawan Pornsukarom
- Faculty of Veterinary Medicine, Rajamangala University of Technology Tawan-ok, Chonburi, Thailand
| | - Arnoud H M van Vliet
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Surrey, UK
| | - Siddhartha Thakur
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA. .,Comparative Medicine Institute, North Carolina State University, Raleigh, NC, USA.
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Ingle DJ, Levine MM, Kotloff KL, Holt KE, Robins-Browne RM. Dynamics of antimicrobial resistance in intestinal Escherichia coli from children in community settings in South Asia and sub-Saharan Africa. Nat Microbiol 2018; 3:1063-1073. [PMID: 30127495 PMCID: PMC6787116 DOI: 10.1038/s41564-018-0217-4] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 07/09/2018] [Indexed: 11/30/2022]
Abstract
The dynamics of antimicrobial resistance (AMR) in developing countries are poorly understood, especially in community settings, due to a sparsity of data on AMR prevalence and genetics. We used a combination of phenotyping, genomics and antimicrobial usage data to investigate patterns of AMR amongst atypical enteropathogenic Escherichia coli (aEPEC) strains isolated from children younger than five years old in seven developing countries (four in sub-Saharan Africa and three in South Asia) over a three-year period. We detected high rates of AMR, with 65% of isolates displaying resistance to three or more drug classes. Whole-genome sequencing revealed a diversity of known genetic mechanisms for AMR that accounted for >95% of phenotypic resistance, with comparable rates amongst aEPEC strains associated with diarrhoea or asymptomatic carriage. Genetic determinants of AMR were associated with the geographic location of isolates, not E. coli lineage, and AMR genes were frequently co-located, potentially enabling the acquisition of multi-drug resistance in a single step. Comparison of AMR with antimicrobial usage data showed that the prevalence of resistance to fluoroquinolones and third-generation cephalosporins was correlated with usage, which was higher in South Asia than in Africa. This study provides much-needed insights into the frequency and mechanisms of AMR in intestinal E. coli in children living in community settings in developing countries.
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Affiliation(s)
- Danielle J Ingle
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
- National Centre for Epidemiology and Population Health, Research School of Population Health, The Australian National University, Canberra, Australian Capital Territory, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Myron M Levine
- Departments of Pediatrics and Medicine, Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Karen L Kotloff
- Departments of Pediatrics and Medicine, Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Kathryn E Holt
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
- London School of Hygiene and Tropical Medicine, London, UK
| | - Roy M Robins-Browne
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia.
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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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Neyestani M, Dickenson E, McLain J, Robleto E, Rock C, Gerrity D. Impacts of solids retention time on trace organic compound attenuation and bacterial resistance to trimethoprim and sulfamethoxazole. CHEMOSPHERE 2017; 182:149-158. [PMID: 28494359 DOI: 10.1016/j.chemosphere.2017.04.121] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 04/18/2017] [Accepted: 04/19/2017] [Indexed: 06/07/2023]
Abstract
Bacteria can grow in the presence of trimethoprim and sulfamethoxazole by expressing antibiotic resistance genes or by acquiring thymine or thymidine from environmental reservoirs to facilitate DNA synthesis. The purpose of this study was to evaluate whether activated sludge serves as a reservoir for thymine or thymidine, potentially impacting the quantification of antibiotic resistant bacteria. This study also assessed the impacts of varying solids retention time (SRT) on trimethoprim and sulfamethoxazole removal during wastewater treatment and single and multi-drug resistance. When assayed in the presence of the antibiotics at standard clinical concentrations, up to 40% increases in the relative prevalence of resistant bacteria were observed with (1) samples manually augmented with reagent-grade thymidine, (2) samples manually augmented with sonicated biomass (i.e., cell lysate), (3) samples manually augmented with activated sludge filtrate, and (4) activated sludge samples collected from reactors with longer SRTs. These observations suggest that longer SRTs may select for antibiotic resistant bacteria and/or result in false positives for antibiotic resistance due to higher concentrations of free thymine, thymidine, or other extracellular constituents.
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Affiliation(s)
- Majid Neyestani
- Department of Civil and Environmental Engineering and Construction, University of Nevada, Las Vegas, 4505 S. Maryland Parkway, Las Vegas, NV 89154-4015, United States; Greeley and Hansen, 1120 N. Town Center Dr., Suite 120, Las Vegas, NV 89144, United States
| | - Eric Dickenson
- Applied Research and Development Center, Southern Nevada Water Authority, 1299 Burkholder Blvd., Henderson, NV 89015, United States
| | - Jean McLain
- Water Resources Research Center, University of Arizona, 350 N. Campbell Ave., Tucson, AZ 85719, United States
| | - Eduardo Robleto
- School of Life Sciences, University of Nevada, Las Vegas, 4505 S. Maryland Parkway, Las Vegas, NV 89154, United States
| | - Channah Rock
- Department of Soil, Water & Environmental Science, University of Arizona, 1177 E. 4th St., Tucson, AZ 85719, United States
| | - Daniel Gerrity
- Department of Civil and Environmental Engineering and Construction, University of Nevada, Las Vegas, 4505 S. Maryland Parkway, Las Vegas, NV 89154-4015, United States.
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Whole-Genome Sequencing of Drug-Resistant Salmonella enterica Isolates from Dairy Cattle and Humans in New York and Washington States Reveals Source and Geographic Associations. Appl Environ Microbiol 2017; 83:AEM.00140-17. [PMID: 28389536 DOI: 10.1128/aem.00140-17] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 03/27/2017] [Indexed: 01/09/2023] Open
Abstract
Multidrug-resistant (MDR) Salmonella enterica can be spread from cattle to humans through direct contact with animals shedding Salmonella as well as through the food chain, making MDR Salmonella a serious threat to human health. The objective of this study was to use whole-genome sequencing to compare antimicrobial-resistant (AMR) Salmonella enterica serovars Typhimurium, Newport, and Dublin isolated from dairy cattle and humans in Washington State and New York State at the genotypic and phenotypic levels. A total of 90 isolates were selected for the study (37 S Typhimurium, 32 S Newport, and 21 S Dublin isolates). All isolates were tested for phenotypic antibiotic resistance to 12 drugs using Kirby-Bauer disk diffusion. AMR genes were detected in the assembled genome of each isolate using nucleotide BLAST and ARG-ANNOT. Genotypic prediction of phenotypic resistance resulted in a mean sensitivity of 97.2 and specificity of 85.2. Sulfamethoxazole-trimethoprim resistance was observed only in human isolates (P < 0.05), while resistance to quinolones and fluoroquinolones was observed only in 6 S Typhimurium isolates from humans in Washington State. S Newport isolates showed a high degree of AMR profile similarity, regardless of source. S Dublin isolates from New York State differed from those from Washington State based on the presence/absence of plasmid replicons, as well as phenotypic AMR susceptibility/nonsusceptibility (P < 0.05). The results of this study suggest that distinct factors may contribute to the emergence and dispersal of AMR S. enterica in humans and farm animals in different regions.IMPORTANCE The use of antibiotics in food-producing animals has been hypothesized to select for AMR Salmonella enterica and associated AMR determinants, which can be transferred to humans through different routes. Previous studies have sought to assess the degree to which AMR livestock- and human-associated Salmonella strains overlap, as well as the spatial distribution of Salmonella's associated AMR determinants, but have often been limited by the degree of resolution at which isolates can be compared. Here, a comparative genomics study of livestock- and human-associated Salmonella strains from different regions of the United States shows that while many AMR genes and phenotypes were confined to human isolates, overlaps between the resistomes of bovine and human-associated Salmonella isolates were observed on numerous occasions, particularly for S Newport. We have also shown that whole-genome sequencing can be used to reliably predict phenotypic resistance across Salmonella isolated from bovine sources.
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Gong Y, Shen X, Huang G, Zhang C, Luo X, Yin S, Wang J, Hu F, Peng Y, Li M. Epidemiology and resistance features of Acinetobacter baumannii isolates from the ward environment and patients in the burn ICU of a Chinese hospital. J Microbiol 2016; 54:551-8. [PMID: 27480635 DOI: 10.1007/s12275-016-6146-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 06/20/2016] [Accepted: 06/29/2016] [Indexed: 01/13/2023]
Abstract
Acinetobacter baumannii is an important opportunistic pathogen that causes severe nosocomial infections, especially in intensive care units (ICUs). Over the past decades, an everincreasing number of hospital outbreaks caused by A. baumannii have been reported worldwide. However, little attention has been directed toward the relationship between A. baumannii isolates from the ward environment and patients in the burn ICU. In this study, 88 A. baumannii isolates (26 from the ward environment and 62 from patients) were collected from the burn ICU of the Southwest Hospital in Chongqing, China, from July through December 2013. Antimicrobial susceptibility testing results showed that drug resistance was more severe in isolates from patients than from the ward environment, with all of the patient isolates being fully resistant to 10 out of 19 antimicrobials tested. Isolations from both the ward environment and patients possessed the β-lactamase genes bla OXA-51, bla OXA-23, bla AmpC, bla VIM, and bla PER. Using pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST), these isolates could be clustered into 4 major PFGE types and 4 main sequence types (ST368, ST369, ST195, and ST191) among which, ST368 was the dominant genotype. Epidemiologic and molecular typing data also revealed that a small-scale outbreak of A. baumannii infection was underway in the burn ICU of our hospital during the sampling period. These results suggest that dissemination of β-lactamase genes in the burn ICU might be closely associated with the high-level resistance of A. baumannii, and the ICU environment places these patients at a high risk for nosocomial infection. Cross-contamination should be an important concern in clinical activities to reduce hospitalacquired infections caused by A. baumannii.
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Affiliation(s)
- Yali Gong
- Department of Microbiology, Third Military Medical University, Chongqing, 400038, P. R. China.,Institute of Burn Research, Southwest Hospital, Third Military Medical University, Chongqing, 400038, P. R. China
| | - Xiaodong Shen
- Department of Biochemistry and Molecular Biology, Third Military Medical University, Chongqing, 400038, P. R. China
| | - Guangtao Huang
- Institute of Burn Research, Southwest Hospital, Third Military Medical University, Chongqing, 400038, P. R. China
| | - Cheng Zhang
- Institute of Burn Research, Southwest Hospital, Third Military Medical University, Chongqing, 400038, P. R. China
| | - Xiaoqiang Luo
- Institute of Burn Research, Southwest Hospital, Third Military Medical University, Chongqing, 400038, P. R. China
| | - Supeng Yin
- Institute of Burn Research, Southwest Hospital, Third Military Medical University, Chongqing, 400038, P. R. China
| | - Jing Wang
- Department of Microbiology, Third Military Medical University, Chongqing, 400038, P. R. China
| | - Fuquan Hu
- Department of Microbiology, Third Military Medical University, Chongqing, 400038, P. R. China
| | - Yizhi Peng
- Institute of Burn Research, Southwest Hospital, Third Military Medical University, Chongqing, 400038, P. R. China.
| | - Ming Li
- Department of Microbiology, Third Military Medical University, Chongqing, 400038, P. R. China.
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Tyson GH, McDermott PF, Li C, Chen Y, Tadesse DA, Mukherjee S, Bodeis-Jones S, Kabera C, Gaines SA, Loneragan GH, Edrington TS, Torrence M, Harhay DM, Zhao S. WGS accurately predicts antimicrobial resistance in Escherichia coli. J Antimicrob Chemother 2015; 70:2763-9. [PMID: 26142410 DOI: 10.1093/jac/dkv186] [Citation(s) in RCA: 180] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 06/10/2015] [Indexed: 01/22/2023] Open
Abstract
OBJECTIVES The objective of this study was to determine the effectiveness of WGS in identifying resistance genotypes of MDR Escherichia coli and whether these correlate with observed phenotypes. METHODS Seventy-six E. coli strains were isolated from farm cattle and measured for phenotypic resistance to 15 antimicrobials with the Sensititre(®) system. Isolates with resistance to at least four antimicrobials in three classes were selected for WGS using an Illumina MiSeq. Genotypic analysis was conducted with in-house Perl scripts using BLAST analysis to identify known genes and mutations associated with clinical resistance. RESULTS Over 30 resistance genes and a number of resistance mutations were identified among the E. coli isolates. Resistance genotypes correlated with 97.8% specificity and 99.6% sensitivity to the identified phenotypes. The majority of discordant results were attributable to the aminoglycoside streptomycin, whereas there was a perfect genotype-phenotype correlation for most antibiotic classes such as tetracyclines, quinolones and phenicols. WGS also revealed information about rare resistance mechanisms, such as structural mutations in chromosomal copies of ampC conferring third-generation cephalosporin resistance. CONCLUSIONS WGS can provide comprehensive resistance genotypes and is capable of accurately predicting resistance phenotypes, making it a valuable tool for surveillance. Moreover, the data presented here showing the ability to accurately predict resistance suggest that WGS may be used as a screening tool in selecting anti-infective therapy, especially as costs drop and methods improve.
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Affiliation(s)
- Gregory H Tyson
- Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, US Food and Drug Administration, Laurel, MD, USA
| | - Patrick F McDermott
- Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, US Food and Drug Administration, Laurel, MD, USA
| | - Cong Li
- Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, US Food and Drug Administration, Laurel, MD, USA
| | - Yuansha Chen
- Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, US Food and Drug Administration, Laurel, MD, USA
| | - Daniel A Tadesse
- Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, US Food and Drug Administration, Laurel, MD, USA
| | - Sampa Mukherjee
- Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, US Food and Drug Administration, Laurel, MD, USA
| | - Sonya Bodeis-Jones
- Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, US Food and Drug Administration, Laurel, MD, USA
| | - Claudine Kabera
- Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, US Food and Drug Administration, Laurel, MD, USA
| | - Stuart A Gaines
- Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, US Food and Drug Administration, Laurel, MD, USA
| | - Guy H Loneragan
- International Center for Food Industry Excellence, Department of Animal and Food Sciences, Texas Tech University, Lubbock, TX, USA
| | - Tom S Edrington
- Food and Feed Safety Research Unit, Agricultural Research Service, US Department of Agriculture, College Station, TX, USA
| | - Mary Torrence
- Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, MD, USA
| | - Dayna M Harhay
- US Meat Animal Research Center, Agricultural Research Service, US Department of Agriculture, Clay Center, NE, USA
| | - Shaohua Zhao
- Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, US Food and Drug Administration, Laurel, MD, USA
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Fernández-Martínez M, Miró E, Ortega A, Bou G, González-López JJ, Oliver A, Pascual A, Cercenado E, Oteo J, Martínez-Martínez L, Navarro F. Molecular identification of aminoglycoside-modifying enzymes in clinical isolates of Escherichia coli resistant to amoxicillin/clavulanic acid isolated in Spain. Int J Antimicrob Agents 2015; 46:157-63. [PMID: 26022930 DOI: 10.1016/j.ijantimicag.2015.03.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 03/12/2015] [Accepted: 03/13/2015] [Indexed: 11/25/2022]
Abstract
The activity of eight aminoglycosides (amikacin, apramycin, arbekacin, gentamicin, kanamycin, neomycin, netilmicin and tobramycin) against a collection of 257 amoxicillin/clavulanic acid (AMC)-resistant Escherichia coli isolates was determined by microdilution. Aminoglycoside resistance rates, the prevalence of aminoglycoside-modifying enzyme (AME) genes, the relationship between AME gene detection and resistance phenotype to aminoglycosides, and the association of AME genes with mechanisms of AMC resistance in E. coli isolates in Spain were investigated. Aminoglycoside-resistant isolates were screened for the presence of genes encoding common AMEs [aac(3)-Ia, aac(3)-IIa, aac(3)-IVa, aac(6')-Ib, ant(2″)-Ia, ant(4')-IIa and aph(3')-Ia] or 16S rRNA methylases (armA, rmtB, rmtC and npmA). In total, 105 isolates (40.9%) were resistant to at least one of the aminoglycosides tested. Amikacin, apramycin and arbekacin showed better activity, with MIC90 values of 2mg/L (arbekacin) and 8mg/L (amikacin and apramycin). Kanamycin presented the highest MIC90 (128mg/L). The most common AME gene was aac(6')-Ib (36 strains; 34.3%), followed by aph(3')-Ia (31 strains; 29.5%), ant(2″)-Ia (29 strains; 27.6%) and aac(3)-IIa (23 strains; 21.9%). aac(3)-Ia, aac(3)-IVa, ant(4')-IIa and the four methylases were not detected. The ant(2″)-Ia gene was usually associated with OXA-1 [21/30; 70%], whilst 23/25 (92%) strains producing CTX-M-15 had the aac(6')-Ib gene. The most prevalent AME gene was aac(6')-Ib (18/41; 44%) in nosocomial isolates, whilst ant(2″)-Ia and aph(3')-Ia genes (20/64; 31%) were more frequent in strains of community origin. In 64.6% isolates the phenotypic profile correlated with the presence of commonly encountered AMEs.
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Affiliation(s)
- Marta Fernández-Martínez
- Servicio de Microbiología, Hospital Universitario Marqués de Valdecilla (IDIVAL), 39008 Santander, Spain.
| | - Elisenda Miró
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Barcelona, Spain
| | - Adriana Ortega
- Laboratorio de Antibióticos, Servicio de Bacteriología, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Germán Bou
- Servicio de Microbiología, Complejo Hospitalario Universitario A Coruña-INIBIC, A Coruña, Spain
| | | | - Antonio Oliver
- Servicio de Microbiología, Hospital Son Espases, Instituto de Investigación Sanitaria de Palma (IdISPa), Palma de Mallorca, Spain
| | - Alvaro Pascual
- Unidad de Enfermedades Infecciosas y Microbiología Clínica, Hospital Universitario Virgen Macarena, Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, Seville, Spain
| | - Emilia Cercenado
- Servicio de Microbiología, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Jesús Oteo
- Laboratorio de Antibióticos, Servicio de Bacteriología, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Luis Martínez-Martínez
- Servicio de Microbiología, Hospital Universitario Marqués de Valdecilla (IDIVAL), 39008 Santander, Spain; Departamento de Biología Molecular, Universidad de Cantabria, Santander, Spain
| | - Ferran Navarro
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Barcelona, Spain; Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain
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Murugaiyan J, Krueger K, Roesler U, Weinreich J, Schierack P. Assessment of species and antimicrobial resistance among Enterobacteriaceae isolated from mallard duck faeces. ENVIRONMENTAL MONITORING AND ASSESSMENT 2015; 187:127. [PMID: 25697309 DOI: 10.1007/s10661-015-4346-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 02/09/2015] [Indexed: 06/04/2023]
Abstract
Mallard ducks have demonstrated to be a likely reservoir for zoonotic E. coli strains; thus, it is possible that these ducks could also act as a reservoir for other Enterobacteriaceae members. The present study was initiated to evaluate the species distribution of Enterobacteriaceae other than E. coli in 175 fresh faecal samples collected from a population of mallard ducks. Sixty-four samples displayed detectable colonies of Enterobacteriaceae (excluding E. coli), which resulted in 75 pulsed-field gel electrophoresis (PFGE) types. Seventy-five single representatives of each PFGE type were subjected to identification with API 32NE and MALDI TOF MS systems due to the practical difficulties in species differentiation of Enterobacteriaceae. Those isolated were found to be from nine genera: Buttiauxella (15 %), Citrobacter (5 %), Enterobacter (32 %), Hafnia (1 %), Leclercia (1 %), Pantoea (7 %), Raoultella (21 %), Rahnella (7 %) and Serratia (11 %). Evaluation of antimicrobial resistance phenotypes using the disc method and detection of resistance genes using the microarray method revealed that these microbes possess resistance to β-lactams, aminoglycosides, macrolides, quinolones, rifamycine, sulphonamides, streptogramins and diaminopyrimidines. In conclusion, mallard ducks harbour a variety of non-pathogenic and pathogenic Enterobacteriaceae species like Enterobacter cloacae and Enterobacter amnigenus in their intestine and could act as a reservoir of resistant Enterobacteriaceae.
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Affiliation(s)
- Jayaseelan Murugaiyan
- Institute of Animal Hygiene and Environmental Health, Center for Infectious Medicine, Freie Universitaet Berlin, Robert-von-Ostertag Str. 7-13, 14163, Berlin, Germany,
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Comparative genomics of an IncA/C multidrug resistance plasmid from Escherichia coli and Klebsiella isolates from intensive care unit patients and the utility of whole-genome sequencing in health care settings. Antimicrob Agents Chemother 2014; 58:4814-25. [PMID: 24914121 DOI: 10.1128/aac.02573-14] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The IncA/C plasmids have been implicated for their role in the dissemination of β-lactamases, including gene variants that confer resistance to expanded-spectrum cephalosporins, which are often the treatment of last resort against multidrug-resistant, hospital-associated pathogens. A bla(FOX-5) gene was detected in 14 Escherichia coli and 16 Klebsiella isolates that were cultured from perianal swabs of patients admitted to an intensive care unit (ICU) of the University of Maryland Medical Center (UMMC) in Baltimore, MD, over a span of 3 years. Four of the FOX-encoding isolates were obtained from subsequent samples of patients that were initially negative for an AmpC β-lactamase upon admission to the ICU, suggesting that the AmpC β-lactamase-encoding plasmid was acquired while the patient was in the ICU. The genomes of five E. coli isolates and six Klebsiella isolates containing bla(FOX-5) were selected for sequencing based on their plasmid profiles. An ∼ 167-kb IncA/C plasmid encoding the FOX-5 β-lactamase, a CARB-2 β-lactamase, additional antimicrobial resistance genes, and heavy metal resistance genes was identified. Another FOX-5-encoding IncA/C plasmid that was nearly identical except for a variable region associated with the resistance genes was also identified. To our knowledge, these plasmids represent the first FOX-5-encoding plasmids sequenced. We used comparative genomics to describe the genetic diversity of a plasmid encoding a FOX-5 β-lactamase relative to the whole-genome diversity of 11 E. coli and Klebsiella isolates that carry this plasmid. Our findings demonstrate the utility of whole-genome sequencing for tracking of plasmid and antibiotic resistance gene distribution in health care settings.
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Roach S, Wallinga D. Commentary on genetic mechanisms of antimicrobial resistance in bacteria from U.S. food animals: ESBLs are here. Front Microbiol 2013; 4:214. [PMID: 23908648 PMCID: PMC3726830 DOI: 10.3389/fmicb.2013.00214] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 07/09/2013] [Indexed: 12/27/2022] Open
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Shi P, Jia S, Zhang XX, Zhang T, Cheng S, Li A. Metagenomic insights into chlorination effects on microbial antibiotic resistance in drinking water. WATER RESEARCH 2013; 47:111-20. [PMID: 23084468 DOI: 10.1016/j.watres.2012.09.046] [Citation(s) in RCA: 295] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 09/03/2012] [Accepted: 09/22/2012] [Indexed: 05/21/2023]
Abstract
This study aimed to investigate the chlorination effects on microbial antibiotic resistance in a drinking water treatment plant. Biochemical identification, 16S rRNA gene cloning and metagenomic analysis consistently indicated that Proteobacteria were the main antibiotic resistant bacteria (ARB) dominating in the drinking water and chlorine disinfection greatly affected microbial community structure. After chlorination, higher proportion of the surviving bacteria was resistant to chloramphenicol, trimethoprim and cephalothin. Quantitative real-time PCRs revealed that sulI had the highest abundance among the antibiotic resistance genes (ARGs) detected in the drinking water, followed by tetA and tetG. Chlorination caused enrichment of ampC, aphA2, bla(TEM-1), tetA, tetG, ermA and ermB, but sulI was considerably removed (p < 0.05). Metagenomic analysis confirmed that drinking water chlorination could concentrate various ARGs, as well as of plasmids, insertion sequences and integrons involved in horizontal transfer of the ARGs. Water pipeline transportation tended to reduce the abundance of most ARGs, but various ARB and ARGs were still present in the tap water, which deserves more public health concerns. The results highlighted prevalence of ARB and ARGs in chlorinated drinking water and this study might be technologically useful for detecting the ARGs in water environments.
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Affiliation(s)
- Peng Shi
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210046, China
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Evaluation of an expanded microarray for detecting antibiotic resistance genes in a broad range of gram-negative bacterial pathogens. Antimicrob Agents Chemother 2012; 57:458-65. [PMID: 23129055 DOI: 10.1128/aac.01223-12] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A microarray capable of detecting genes for resistance to 75 clinically relevant antibiotics encompassing 19 different antimicrobial classes was tested on 132 Gram-negative bacteria. Microarray-positive results correlated >91% with antimicrobial resistance phenotypes, assessed using British Society for Antimicrobial Chemotherapy clinical breakpoints; the overall test specificity was >83%. Microarray-positive results without a corresponding resistance phenotype matched 94% with PCR results, indicating accurate detection of genes present in the respective bacteria by microarray when expression was low or absent and, hence, undetectable by susceptibility testing. The low sensitivity and negative predictive values of the microarray results for identifying resistance to some antimicrobial resistance classes are likely due to the limited number of resistance genes present on the current microarray for those antimicrobial agents or to mutation-based resistance mechanisms. With regular updates, this microarray can be used for clinical diagnostics to help accurate therapeutic options to be taken following infection with multiple-antibiotic-resistant Gram-negative bacteria and prevent treatment failure.
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