1
|
Habib I, Mohamed MYI, Lakshmi GB, Ghazawi A, Khan M, Abdalla A, Anes F. High prevalence and genomic features of multidrug-resistant Salmonella enterica isolated from chilled broiler chicken on retail sale in the United Arab Emirates. Int J Food Microbiol 2024; 423:110828. [PMID: 39032201 DOI: 10.1016/j.ijfoodmicro.2024.110828] [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: 04/30/2024] [Revised: 06/22/2024] [Accepted: 07/15/2024] [Indexed: 07/22/2024]
Abstract
Non-typhoidal Salmonella represents a significant global concern for food safety and One Health. Despite the United Arab Emirates (UAE) being a leading consumer of chicken meat globally, there is a lack of comprehensive understanding regarding the prevalence and genomic characteristics of Salmonella within the country. This study aims to address this gap by conducting a thorough analysis of Salmonella prevalence, antimicrobial resistance, and genomic profiles of isolates obtained from whole broiler carcasses retailed under chilled conditions in the UAE. Our findings reveal that Salmonella was detected in 41.2 % (130/315) of the sampled chilled broiler carcasses, with notable variability observed among samples sourced from six different companies. Phenotypic antimicrobial resistance (AMR) testing, among 105 isolates, highlighted high resistance rates to tetracycline (97.1 %), nalidixic acid (93.3 %), ampicillin (92.4 %), azithromycin (75.2 %), ciprofloxacin (63.8 %), and ceftriaxone (54.3 %). Furthermore, a concerning 99 % (104/105) of the isolates exhibited multidrug resistance. Whole-genome sequencing (WGS) of 60 isolates identified five serovars, with S. infantis/Sequence Type (ST) 32 (55 %) and S. Minnesota/ST-458 (28.3 %) being the most prevalent. WGS analysis unveiled 34 genes associated with antimicrobial resistance, including mcr-1.1 (only in two isolates), conferring resistance to colistin. The two major serovars, Infantis and Minnesota, exhibited significant variation (P-values <0.001) in the distribution of major AMR genes (aadA1, blaCMY-2, blaSHV-12, qnrB19, qnrS1, sul1, and sul2). Notably, the gene qacEdelta, conferring resistance to quaternary ammonium compounds commonly found in disinfectants, was universally present in all S. Infantis isolates (n = 33), compared to only one S. Minnesota isolate. Additionally, all S. Infantis isolates harbored the IncFIB (pN55391) plasmid replicon type. Major serovars exhibited distinct distributions of antimicrobial resistance genes, underscoring the importance of serovar-specific surveillance. These findings emphasize the critical need for continuous surveillance and intervention measures to address Salmonella contamination risks in poultry products, providing valuable insights for public health and regulatory strategies not only in the UAE but also globally.
Collapse
Affiliation(s)
- Ihab Habib
- Veterinary Public Health Research Laboratory, Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain, P.O. Box 1555, United Arab Emirates; ASPIRE Research Institute for Food Security in the Drylands (ARIFSID), United Arab Emirates University, Al Ain, P.O. Box 15551, United Arab Emirates.
| | - Mohamed-Yousif Ibrahim Mohamed
- Veterinary Public Health Research Laboratory, Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain, P.O. Box 1555, United Arab Emirates; ASPIRE Research Institute for Food Security in the Drylands (ARIFSID), United Arab Emirates University, Al Ain, P.O. Box 15551, United Arab Emirates
| | - Glindya Bhagya Lakshmi
- Veterinary Public Health Research Laboratory, Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain, P.O. Box 1555, United Arab Emirates; ASPIRE Research Institute for Food Security in the Drylands (ARIFSID), United Arab Emirates University, Al Ain, P.O. Box 15551, United Arab Emirates
| | - Akela Ghazawi
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, P.O. Box 1555, United Arab Emirates
| | - Mushtaq Khan
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, P.O. Box 1555, United Arab Emirates
| | - Afra Abdalla
- Veterinary Public Health Research Laboratory, Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain, P.O. Box 1555, United Arab Emirates; ASPIRE Research Institute for Food Security in the Drylands (ARIFSID), United Arab Emirates University, Al Ain, P.O. Box 15551, United Arab Emirates
| | - Febin Anes
- Veterinary Public Health Research Laboratory, Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain, P.O. Box 1555, United Arab Emirates
| |
Collapse
|
2
|
Arnecke AL, Schwarz S, Lübke-Becker A, Jensen KC, Herre C, Bahramsoltani M. Risk Communication on Zoonoses and Antimicrobial Resistance-How Do Exotic Pet Owners Perceive the Communication of Their Veterinarians? Animals (Basel) 2024; 14:2035. [PMID: 39061497 PMCID: PMC11273538 DOI: 10.3390/ani14142035] [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: 06/01/2024] [Revised: 06/30/2024] [Accepted: 07/08/2024] [Indexed: 07/28/2024] Open
Abstract
Exotic animals traded and kept as pets can transmit a variety of diseases to humans and other animals, and vice versa. Therefore, it is essential for pet owners, particularly vulnerable groups, to be informed about associated risks. Veterinarians play a crucial role in informing pet owners about health risks associated with zoonotic pathogens and antimicrobial resistance (AMR) and should, therefore, have good communication skills to effectively transfer information to pet owners. Thus, exotic pet owners in Germany were surveyed on animal husbandry, veterinary consultation and risk communication. To evaluate the perception of communication, a self-developed questionnaire was used to derive a communication score. The perception of veterinarian communication received a high average score showing a high level of satisfaction. The duration of the veterinarian-client relationship was associated with better communication perception, and the frequency of communication on zoonoses and AMR was associated with the presence of a permanent veterinarian. However, the results indicated that the frequency of disseminated information on zoonoses and/or AMR from veterinarians was lower than desired by the pet owners. Therefore, more educational material on zoonoses and AMR should be made available, and the awareness concerning risk communication should be increased by further education and training at universities.
Collapse
Affiliation(s)
- Amelie Lisa Arnecke
- Institute of Veterinary Anatomy, School of Veterinary Medicine, Freie Universität Berlin, Koserstraße 20, 14195 Berlin, Germany; (C.H.); (M.B.)
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, School of Veterinary Medicine, Freie Universität Berlin, Robert-von-Ostertag-Straße 7, 14163 Berlin, Germany; (S.S.); (A.L.-B.)
- Veterinary Centre for Resistance Research (TZR), School of Veterinary Medicine, Freie Universität Berlin, Robert-von-Ostertag-Straße 8, 14163 Berlin, Germany
| | - Antina Lübke-Becker
- Institute of Microbiology and Epizootics, School of Veterinary Medicine, Freie Universität Berlin, Robert-von-Ostertag-Straße 7, 14163 Berlin, Germany; (S.S.); (A.L.-B.)
- Veterinary Centre for Resistance Research (TZR), School of Veterinary Medicine, Freie Universität Berlin, Robert-von-Ostertag-Straße 8, 14163 Berlin, Germany
| | - Katharina Charlotte Jensen
- Institute for Veterinary Epidemiology and Biostatistics, School of Veterinary Medicine, Freie Universität Berlin, Königsweg 67, 14163 Berlin, Germany;
| | - Christina Herre
- Institute of Veterinary Anatomy, School of Veterinary Medicine, Freie Universität Berlin, Koserstraße 20, 14195 Berlin, Germany; (C.H.); (M.B.)
| | - Mahtab Bahramsoltani
- Institute of Veterinary Anatomy, School of Veterinary Medicine, Freie Universität Berlin, Koserstraße 20, 14195 Berlin, Germany; (C.H.); (M.B.)
| |
Collapse
|
3
|
Martínez-Álvarez S, Châtre P, François P, Abdullahi IN, Simón C, Zarazaga M, Madec JY, Haenni M, Torres C. Unexpected role of pig nostrils in the clonal and plasmidic dissemination of extended-spectrum beta-lactamase-producing Escherichia coli at farm level. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 273:116145. [PMID: 38460199 DOI: 10.1016/j.ecoenv.2024.116145] [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: 12/14/2023] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 03/11/2024]
Abstract
The presence of methicillin-resistant or -susceptible S. aureus in pig nostrils has been known for a long time, but the occurrence of extended-spectrum beta-lactamase (ESBL)-producing E. coli has hardly been investigated. Here, we collected 25 E. coli recovered from nasal samples of 40 pigs/10 farmers of four farms. Nine ESBL-producing isolates belonging to ST48, ST117, ST847, ST5440, ST14914 and ST10 were retrieved from seven pigs. All blaESBL genes (blaCTX-M-32,blaCTX-M-14,blaCTX-M-1,blaCTX-M-65, and blaSHV-12) were horizontally transferable by conjugation through plasmids belonging to IncI1 (n=3), IncX1 (n=3) and IncHI2 (n=1) types. IncI1-plasmids displayed different genetic environments: i) IS26-blaSHV-12-deoR-IS26, ii) wbuC-blaCTX-M-32-ISKpn26 (IS5), and iii) IS930-blaCTX-M-14-IS26. The IncHI2-plasmid contained the genetic environment IS903-blaCTX-M-65-fipA with multiple resistance genes associated either to: a) Tn21-like transposon harbouring genes conferring aminoglycosides/beta-lactams/chloramphenicol/macrolides resistance located on two atypical class 1 integrons with an embedded ΔTn5393; or b) Tn1721-derived transposon displaying an atypical class 1 integron harbouring aadA2-arr3-cmlA5-blaOXA-10-aadA24-dfrA14, preceding the genetic platform IS26-blaTEM-95-tet(A)-lysR-floR-virD2-ISVsa3-IS3075-IS26-qnrS1, as well as the tellurite resistance module. Other plasmids harbouring clinically relevant genes were detected, such as a ColE-type plasmid carrying the mcr-4.5 gene. Chromosomally encoded genes (fosA7) or integrons (intI1-dfrA1-aadA1-qacE-sul1/intI1-IS15-dfrA1-aadA2) were also identified. Finally, an IncY plasmid harbouring a class 2 integron (intI2-dfrA1-sat2-aadA1-qacL-IS406-sul3) was detected but not associated with a blaESBL gene. Our results evidence that pig nostrils might favour the spread of ESBL-E. coli and mcr-mediated colistin-resistance. Therefore, enhanced monitoring should be considered, especially in a sector where close contact between animals in intensive farming increases the risk of spreading antimicrobial resistance.
Collapse
Affiliation(s)
- Sandra Martínez-Álvarez
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, Spain
| | - Pierre Châtre
- ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Pauline François
- ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Idris Nasir Abdullahi
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, Spain
| | - Carmen Simón
- Faculty of Veterinary Medicine, University of Zaragoza, Zaragoza, Spain
| | - Myriam Zarazaga
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, Spain
| | - Jean-Yves Madec
- ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Marisa Haenni
- ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Carmen Torres
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, Spain.
| |
Collapse
|
4
|
Anokyewaa Appau AA, Ofori LA. Antibiotic Resistance Profile of E. coli Isolates from Lettuce, Poultry Manure, Irrigation Water, and Soil in Kumasi, Ghana. Int J Microbiol 2024; 2024:6681311. [PMID: 38312829 PMCID: PMC10838198 DOI: 10.1155/2024/6681311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 01/10/2024] [Accepted: 01/18/2024] [Indexed: 02/06/2024] Open
Abstract
Inputs such as irrigation water and poultry manure used in lettuce cultivation have been found to be associated with antibiotic-resistant pathogens. The study assessed the antibiotic resistance profile of Escherichia coli isolated from lettuce, poultry manure, irrigation water, and soil in Kumasi. One hundred and fifty-six samples of lettuce, irrigation water, soil, and manure were collected from three farms over a seven-week cultivation period (seedlings to harvest stage). E. coli were enumerated using standard methods. 98% of the samples were positive for E. coli. Geometric means for lettuce, irrigation water, and soil ranged from 2.0 × 105 to 1.67 × 107 MPN/100 ml while that of manure ranged from 2.0 × 105 to 1.31 × 107 MPN/100 ml. Generally, the microbial load of all parameters on all farms across the weeks was significant and exceeded World Health Organization (WHO) and International Commission on Microbiological Specifications for Foods (ICMSF) standard recommendations for food. Using the Kirby Bauer method, antibiotic sensitivity testing was performed against 225 biochemically confirmed E. coli with twelve antibiotics. Relatively high resistance was recorded for some members of the beta-lactam class: meropenem: 94.2%, ampicillin: 91.9%, cefuroxime: 95.1%, ceftriaxone: 94.7%, and cefotaxime: 94.2%. Eighty of the isolates were screened for extended spectrum beta lactamase (ESBL) production using cefotaxime (CTX) and cefotaxime/clavulanic acid (CTX/CLA) discs and three showed positive: one each from poultry manure, irrigation water, and soil. Polymerase chain reaction (PCR) confirmed the presence of blaCTX-M gene. The occurrence of antibiotic-resistant E. coli in vegetables and their production environment is alarming and poses serious health threats to the general public. The presence of blaCTX-M gene in E. coli from a vegetable production site recorded for the first time in Ghana requires enforcement by regulatory bodies on the inappropriate use of antibiotics in the country.
Collapse
Affiliation(s)
| | - Linda Aurelia Ofori
- Department of Theoretical and Applied Biology, Kwame Nkrumah University of Science Technology, Kumasi, Ghana
| |
Collapse
|
5
|
Kim J, Cho Y, Lim SK, Seo MR, Sohn JW, Kim B, Rho M, Pai H. Comparative analyses of the faecal resistome against β-lactam and quinolone antibiotics in humans and livestock using metagenomic sequencing. Sci Rep 2023; 13:20993. [PMID: 38017092 PMCID: PMC10684531 DOI: 10.1038/s41598-023-48221-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 11/23/2023] [Indexed: 11/30/2023] Open
Abstract
To assess the prevalence and abundance of antibiotic resistance genes in human and livestock gut microbiomes, 87 humans (healthy individuals and patients with Clostridioides difficile infection (CDI)) and 108 livestock (swine, cattle, and chickens) were enrolled. Gut microbiomes and fluoroquinolone-resistant Escherichia coli isolates were sequenced, and mobile genetic elements adjacent to the β-lactamase (bla) and transferable quinolone resistance (qnr) genes were compared using metagenomic contigs. Each group of humans and livestock exhibited distinctive microbiota and resistome compositions in the gut. Concerning the resistome of bla and qnr, the prevalence rates between chickens and patients with CDI were the most similar (R2 = 0.46); blaTEM, blaOXA, blaCTX-M, and qnrS were highly prevalent in both groups. According to genomic and phylogenetic analyses, blaCTX-M and blaOXA expressed lineage specificity to either humans or livestock, while qnrS and blaTEM displayed a shared lineage between humans and livestock. A qnrS1 mobilome comprising five genes, including two recombinases, a transposase, and a plasmid gene, is commonly found in human and chicken gut microbiomes. Humans and chickens showed the most similar gut resistomes to β-lactams and quinolones. QnrS and blaTEM displayed especially strong co-occurrence between the guts of humans and livestock.
Collapse
Affiliation(s)
- Jieun Kim
- Department of Internal Medicine, College of Medicine, Hanyang University, Seoul, 04763, Republic of Korea
| | - Youna Cho
- Department of Computer Science and Engineering, Hanyang University, Seoul, 04763, Republic of Korea
| | - Suk-Kyung Lim
- Bacterial Disease Division, Animal and Plant Quarantine Agency, 177 Hyeokin 8-ro, Gimcheon-si, Gyeongsangbuk-do, 39660, Republic of Korea
| | - Mi-Ran Seo
- ConnectaGen Inc., F 203, MisaCentumbiz 2F, Jojeong-Dearo, Hanam-si, Gyeonggi-do, 12918, Republic of Korea
| | - Jang Won Sohn
- Department of Internal Medicine, College of Medicine, Hanyang University, Seoul, 04763, Republic of Korea
| | - Bongyoung Kim
- Department of Internal Medicine, College of Medicine, Hanyang University, Seoul, 04763, Republic of Korea
| | - Mina Rho
- Department of Computer Science and Engineering, Hanyang University, Seoul, 04763, Republic of Korea.
- Department of Biomedical Informatics, Hanyang University, Seoul, 04763, Republic of Korea.
| | - Hyunjoo Pai
- Department of Internal Medicine, College of Medicine, Hanyang University, Seoul, 04763, Republic of Korea.
| |
Collapse
|
6
|
Martínez-Álvarez S, Châtre P, Cardona-Cabrera T, François P, Sánchez-Cano A, Höfle U, Zarazaga M, Madec JY, Haenni M, Torres C. Detection and genetic characterization of bla ESBL-carrying plasmids of cloacal Escherichia coli isolates from white stork nestlings (Ciconia ciconia) in Spain. J Glob Antimicrob Resist 2023; 34:186-194. [PMID: 37482121 DOI: 10.1016/j.jgar.2023.07.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/17/2023] [Accepted: 07/17/2023] [Indexed: 07/25/2023] Open
Abstract
OBJECTIVES This study aimed to characterize Escherichia coli isolates from cloacal samples of white stork nestlings, with a special focus on extended-spectrum β-lactamases (ESBLs)-producing E. coli isolates and their plasmid content. METHODS Cloacal samples of 88 animals were seeded on MacConkey-agar and chromogenic-ESBL plates to recover E. coli and ESBL-producing E. coli. Antimicrobial susceptibility was screened using the disc diffusion method, and the genotypic characterization was performed by polymerase chain reaction (PCR) and subsequent sequencing. S1 nuclease Pulsed-Field-Gel-Electrophoresis (PFGE), Southern blotting, and conjugation essays were performed on ESBL-producing E. coli, as well as whole-genome sequencing by short- and long-reads. The four blaESBL-carrying plasmids were completely sequenced. RESULTS A total of 113 non-ESBL-producing E. coli isolates were collected on antibiotic-free MacConkey-agar, of which 27 (23.9%) showed a multidrug-resistance (MDR) phenotype, mainly associated with β-lactam-phenicol-sulfonamide resistance (blaTEM/cmlA/floR/sul1/sul2/sul3). Moreover, four white stork nestlings carried ESBL-producing E. coli (4.5%) with the following characteristics: blaSHV-12/ST38-D, blaSHV-12/ST58-B1, blaCTX-M-1/ST162-B1, and blaCTX-M-32/ST155-B1. Whole-genome sequencing followed by Southern blot hybridizations on S1-PFGE gels in ESBL-positive isolates proved that the blaCTX-M-1 gene and one of the blaSHV-12 genes were carried by IncI1/pST3 plasmids, while the second blaSHV-12 gene and the blaCTX-M-32 gene were located on IncF plasmids. The two blaSHV-12 genes and the two blaCTX-M genes had similar but non-identical close genetic environments, as all four genes were flanked by a variety of insertion sequences. CONCLUSION The role played by several genetic platforms in the mobility of ESBL genes allows for interchangeability on a remarkably small scale (gene-plasmid-clones), which may support the spread of ESBL genes.
Collapse
Affiliation(s)
- Sandra Martínez-Álvarez
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, Spain
| | - Pierre Châtre
- ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Teresa Cardona-Cabrera
- Health and Biotechnology (SaBio) Research Group, Institute for Game and Wildlife Research IREC (CSIC-UCLM), Ciudad Real, Spain
| | - Pauline François
- ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Alberto Sánchez-Cano
- Health and Biotechnology (SaBio) Research Group, Institute for Game and Wildlife Research IREC (CSIC-UCLM), Ciudad Real, Spain
| | - Ursula Höfle
- Health and Biotechnology (SaBio) Research Group, Institute for Game and Wildlife Research IREC (CSIC-UCLM), Ciudad Real, Spain
| | - Myriam Zarazaga
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, Spain
| | - Jean-Yves Madec
- ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Marisa Haenni
- ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Carmen Torres
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, Spain.
| |
Collapse
|
7
|
Almansour AM, Alhadlaq MA, Alzahrani KO, Mukhtar LE, Alharbi AL, Alajel SM. The Silent Threat: Antimicrobial-Resistant Pathogens in Food-Producing Animals and Their Impact on Public Health. Microorganisms 2023; 11:2127. [PMID: 37763971 PMCID: PMC10537193 DOI: 10.3390/microorganisms11092127] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 08/10/2023] [Accepted: 08/16/2023] [Indexed: 09/29/2023] Open
Abstract
The emergence of antimicrobial resistance (AMR) is a global health problem without geographic boundaries. This increases the risk of complications and, thus, makes it harder to treat infections, which can result in higher healthcare costs and a greater number of deaths. Antimicrobials are often used to treat infections from pathogens in food-producing animals, making them a potential source of AMR. Overuse and misuse of these drugs in animal agriculture can lead to the development of AMR bacteria, which can then be transmitted to humans through contaminated food or direct contact. It is therefore essential to take multifaceted, comprehensive, and integrated measures, following the One Health approach. To address this issue, many countries have implemented regulations to limit antimicrobial use. To our knowledge, there are previous studies based on AMR in food-producing animals; however, this paper adds novelty related to the AMR pathogens in livestock, as we include the recent publications of this field worldwide. In this work, we aim to describe the most critical and high-risk AMR pathogens among food-producing animals, as a worldwide health problem. We also focus on the dissemination of AMR genes in livestock, as well as its consequences in animals and humans, and future strategies to tackle this threat.
Collapse
Affiliation(s)
- Ayidh M. Almansour
- Molecular Biology Division, Reference Laboratory for Microbiology, Executive Department of Reference Laboratories, Research and Laboratories Sector, Saudi Food and Drug Authority (SFDA), Riyadh 11671, Saudi Arabia; (M.A.A.); (K.O.A.); (A.L.A.)
| | - Meshari A. Alhadlaq
- Molecular Biology Division, Reference Laboratory for Microbiology, Executive Department of Reference Laboratories, Research and Laboratories Sector, Saudi Food and Drug Authority (SFDA), Riyadh 11671, Saudi Arabia; (M.A.A.); (K.O.A.); (A.L.A.)
| | - Khaloud O. Alzahrani
- Molecular Biology Division, Reference Laboratory for Microbiology, Executive Department of Reference Laboratories, Research and Laboratories Sector, Saudi Food and Drug Authority (SFDA), Riyadh 11671, Saudi Arabia; (M.A.A.); (K.O.A.); (A.L.A.)
| | - Lenah E. Mukhtar
- Antimicrobial Resistance Division, Reference Laboratory for Microbiology, Executive Department of Reference Laboratories, Research and Laboratories Sector, Saudi Food and Drug Authority (SFDA), Riyadh 11671, Saudi Arabia;
| | - Abdulmohsen L. Alharbi
- Molecular Biology Division, Reference Laboratory for Microbiology, Executive Department of Reference Laboratories, Research and Laboratories Sector, Saudi Food and Drug Authority (SFDA), Riyadh 11671, Saudi Arabia; (M.A.A.); (K.O.A.); (A.L.A.)
| | - Sulaiman M. Alajel
- Reference Laboratory for Microbiology, Executive Department of Reference Laboratories, Research and Laboratories Sector, Saudi Food and Drug Authority (SFDA), Riyadh 11671, Saudi Arabia;
| |
Collapse
|
8
|
Ferreira M, Leão C, Clemente L, Albuquerque T, Amaro A. Antibiotic Susceptibility Profiles and Resistance Mechanisms to β-Lactams and Polymyxins of Escherichia coli from Broilers Raised under Intensive and Extensive Production Systems. Microorganisms 2022; 10:microorganisms10102044. [PMID: 36296320 PMCID: PMC9608943 DOI: 10.3390/microorganisms10102044] [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: 09/11/2022] [Revised: 10/08/2022] [Accepted: 10/10/2022] [Indexed: 01/25/2023] Open
Abstract
The intensive and extensive broiler production systems imply different veterinary interventions, including the use of antimicrobials. This study aimed to compare the antimicrobial susceptibility profiles of Escherichia coli isolated from both systems, characterize resistance mechanisms to β-lactams and polymyxins, and identify genetic elements such as integrons. E. coli isolates recovered from broiler cecal samples were assayed for antimicrobial susceptibility through the broth microdilution technique. The molecular characterization of acquired resistance mechanisms to β-lactams and colistin and the detection of integrons was performed by a multiplex PCR. For most antibiotics tested, the prevalence of reduced susceptibility is higher in commensal and extended-spectrum β-lactamases (ESBL)/AmpC producers from broilers raised in the intensive system, compared with those raised under extensive conditions. SHV-12 was the most common ESBL enzyme found in both production systems. Other ESBL variants such as CTX-M-1, CTX-M-55, CTX-M-14, CTX-M-32, CTX-M-9, TEM-52, and plasmid-encoded AmpC enzyme CMY-2 were also present. MCR-1 was identified in a colistin-resistant isolate from broilers raised under the intensive system. This study highlights the differences in E. coli antibiotic susceptibility from both production types and emphasizes that a great deal of work remains to decrease consumption and antimicrobial resistance levels.
Collapse
Affiliation(s)
- Mariana Ferreira
- Laboratory of Bacteriology and Mycology, National Reference Laboratory of Animal Health, INIAV—National Institute of Agrarian and Veterinary Research, 2780-157 Oeiras, Portugal
- University of Évora, 7004-516 Évora, Portugal
| | - Célia Leão
- Laboratory of Bacteriology and Mycology, National Reference Laboratory of Animal Health, INIAV—National Institute of Agrarian and Veterinary Research, 2780-157 Oeiras, Portugal
- MED—Mediterranean Institute for Agriculture, Environment and Development, 7006-554 Évora, Portugal
| | - Lurdes Clemente
- Laboratory of Bacteriology and Mycology, National Reference Laboratory of Animal Health, INIAV—National Institute of Agrarian and Veterinary Research, 2780-157 Oeiras, Portugal
- CIISA—Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Science, University of Lisbon, 1300-477 Lisbon, Portugal
| | - Teresa Albuquerque
- Laboratory of Bacteriology and Mycology, National Reference Laboratory of Animal Health, INIAV—National Institute of Agrarian and Veterinary Research, 2780-157 Oeiras, Portugal
| | - Ana Amaro
- Laboratory of Bacteriology and Mycology, National Reference Laboratory of Animal Health, INIAV—National Institute of Agrarian and Veterinary Research, 2780-157 Oeiras, Portugal
- Correspondence:
| |
Collapse
|
9
|
El-Tarabili RM, Ahmed EM, Alharbi NK, Alharbi MA, AlRokban AH, Naguib D, Alhag SK, El Feky TM, Ahmed AE, Mahmoud AE. Prevalence, antibiotic profile, virulence determinants, ESBLs, and non-β-lactam encoding genes of MDR Proteus spp. isolated from infected dogs. Front Genet 2022; 13:952689. [PMID: 36276974 PMCID: PMC9583872 DOI: 10.3389/fgene.2022.952689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 09/02/2022] [Indexed: 11/13/2022] Open
Abstract
This study investigated the prevalence, antibiogram, virulence, extended-spectrum β-lactamases (ESBLs), and non-β-lactam encoding genes of Proteus species isolated from infected dogs in Ismailia province, Egypt. The study was conducted on 70 fecal swabs collected from dogs with diarrhea for bacteriological identification of Proteus spp. The positive isolates were evaluated for antibiotic susceptibility, molecular tests of virulence, ESBLs, and non-β-lactam encoding genes. Prevalence of Proteus spp. was 35.7% (25/70), including Proteus mirabilis (n = 23) and Proteus vulgaris (n = 2). The Proteus spp. prevalence revealed diversity, higher in males than females, in ages < 12 weeks. Investigation of antimicrobial resistance was found against penicillin and amoxicillin (100%), amoxicillin–clavulanic acid (32%), cephalosporins: cefotaxime and ceftazidime (36%), and monobactam: aztreonam (28%) as ESBLs, in addition to tetracycline (32%) and trimethoprim sulfamethoxazole (100%). The strains retrieved by PCR revealed ureC, zapA, and rsbA virulence genes with variant prevalence as 92%, 60%, and 52%, respectively. In addition, the recovered strains contained ESBL genes with a dramatic variable prevalence of 100%, 92%, 36%, and 32%, to blaTEM, blaSHV, blaCTX-M, and blaOXA-1, respectively, and non β-lactam encoding genes with a prevalence of 100%, 48%, 44%, 20%, and 12%, to sul1, tetA, intI1, qnrA, and aadA1. Moreover, 28% (7/25) of recovering strains were MDR (multidrug-resistant) up to four classes of antimicrobials, and 48% (12/25) of the examined strains were MDR up to three antimicrobial classes. In conclusion, to the best of our knowledge, our study could be the first report recording MDR Proteus spp. in dogs in Egypt.
Collapse
Affiliation(s)
- Reham M El-Tarabili
- Department of Bacteriology, Immunology, and Mycology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt
| | - Elsayyad M Ahmed
- Department of Virology, Animal Health Research Institute (AHRI), Agriculture Research Center (ARC), Giza, Egypt
| | - Nada K Alharbi
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Maha A Alharbi
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Ahlam H AlRokban
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Doaa Naguib
- Department of Hygiene and Zoonoses, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
| | - Sadeq K Alhag
- Department of Biology, College of Science, King Khalid University, Abha, Saudi Arabia
| | - Tamer Mohamed El Feky
- Animal Health Research Institute(AHRI), Mansoura laboratory Branch, Agriculture Research Center (ARC), Giza, Egypt
| | - Ahmed Ezzat Ahmed
- Department of Biology, College of Science, King Khalid University, Abha, Saudi Arabia
- Department of Theriogenology, Faculty of Veterinary Medicine, South Valley University, Qena, Egypt
| | - Ahmed E Mahmoud
- Department of Animal Medicine, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt
| |
Collapse
|
10
|
González-Santamarina B, Weber M, Menge C, Berens C. Comparative Genomic Analysis of Antimicrobial-Resistant Escherichia coli from South American Camelids in Central Germany. Microorganisms 2022; 10:microorganisms10091697. [PMID: 36144308 PMCID: PMC9501560 DOI: 10.3390/microorganisms10091697] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/11/2022] [Accepted: 08/16/2022] [Indexed: 11/16/2022] Open
Abstract
South American camelids (SAC) are increasingly kept in Europe in close contact with humans and other livestock species and can potentially contribute to transmission chains of epizootic, zoonotic and antimicrobial-resistant (AMR) agents from and to livestock and humans. Consequently, SAC were included as livestock species in the new European Animal Health Law. However, the knowledge on bacteria exhibiting AMR in SAC is too scarce to draft appropriate monitoring and preventive programs. During a survey of SAC holdings in central Germany, 39 Escherichia coli strains were isolated from composite fecal samples by selecting for cephalosporin or fluoroquinolone resistance and were here subjected to whole-genome sequencing. The data were bioinformatically analyzed for strain phylogeny, detection of pathovars, AMR genes and plasmids. Most (33/39) strains belonged to phylogroups A and B1. Still, the isolates were highly diverse, as evidenced by 28 multi-locus sequence types. More than half of the isolates (23/39) were genotypically classified as multidrug resistant. Genes mediating resistance to trimethoprim/sulfonamides (22/39), aminoglycosides (20/39) and tetracyclines (18/39) were frequent. The most common extended-spectrum-β-lactamase gene was blaCTX-M-1 (16/39). One strain was classified as enteropathogenic E. coli. The positive results indicate the need to include AMR bacteria in yet-to-be-established animal disease surveillance protocols for SAC.
Collapse
|
11
|
Wyrsch ER, Dolejska M, Djordjevic SP. Genomic Analysis of an I1 Plasmid Hosting a sul3-Class 1 Integron and blaSHV-12 within an Unusual Escherichia coli ST297 from Urban Wildlife. Microorganisms 2022; 10:microorganisms10071387. [PMID: 35889108 PMCID: PMC9319951 DOI: 10.3390/microorganisms10071387] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 07/06/2022] [Indexed: 02/04/2023] Open
Abstract
Wild birds, particularly silver gulls (Chroicocephalus novaehollandiae) that nest near anthropogenic sites, often harbour bacteria resistant to multiple antibiotics, including those considered of clinical importance. Here, we describe the whole genome sequence of Escherichia coli isolate CE1867 from a silver gull chick sampled in 2012 that hosted an I1 pST25 plasmid with blaSHV-12, a β-lactamase gene that encodes the ability to hydrolyze oxyimino β-lactams, and other antibiotic resistance genes. Isolate CE1867 is an ST297 isolate, a phylogroup B1 lineage, and clustered with a large ST297 O130:H11 clade, which carry Shiga toxin genes. The I1 plasmid belongs to plasmid sequence type 25 and is notable for its carriage of an atypical sul3-class 1 integron with mefB∆260, a structure most frequently reported in Australia from swine. This integron is a typical example of a Tn21-derived element that captured sul3 in place of the standard sul1 structure. Interestingly, the mercury resistance (mer) module of Tn21 is missing and has been replaced with Tn2-blaTEM-1 and a blaSHV-12 encoding module flanked by direct copies of IS26. Comparisons to similar plasmids, however, demonstrate a closely related family of ARG-carrying plasmids that all host variants of the sul3-associated integron with conserved Tn21 insertion points and a variable presence of both mer and mefB truncations, but predominantly mefB∆260.
Collapse
Affiliation(s)
- Ethan R. Wyrsch
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, NSW 2007, Australia;
| | - Monika Dolejska
- CEITEC VETUNI, University of Veterinary Sciences Brno, 61242 Brno, Czech Republic;
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, 61242 Brno, Czech Republic
- Department of Clinical Microbiology and Immunology, Institute of Laboratory Medicine, University Hospital Brno, 62500 Brno, Czech Republic
| | - Steven P. Djordjevic
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, NSW 2007, Australia;
- Correspondence:
| |
Collapse
|
12
|
Aldea I, Gibello A, Hernández M, Leekitcharoenphon P, Bortolaia V, Moreno MA. Clonal and plasmid-mediated flow of ESBL/AmpC genes in Escherichia coli in a commercial laying hen farm. Vet Microbiol 2022; 270:109453. [DOI: 10.1016/j.vetmic.2022.109453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 03/09/2022] [Accepted: 05/09/2022] [Indexed: 11/29/2022]
|
13
|
Martínez-Álvarez S, Sanz S, Olarte C, Hidalgo-Sanz R, Carvalho I, Fernández-Fernández R, Campaña-Burguet A, Latorre-Fernández J, Zarazaga M, Torres C. Antimicrobial Resistance in Escherichia coli from the Broiler Farm Environment, with Detection of SHV-12-Producing Isolates. Antibiotics (Basel) 2022; 11:antibiotics11040444. [PMID: 35453196 PMCID: PMC9024766 DOI: 10.3390/antibiotics11040444] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/19/2022] [Accepted: 03/23/2022] [Indexed: 02/06/2023] Open
Abstract
Antimicrobial resistance is an important One Health challenge that encompasses the human, animal, and environmental fields. A total of 111 Escherichia coli isolates previously recovered from manure (n = 57) and indoor air (n = 54) samples from a broiler farm were analyzed to determine their phenotypes and genotypes of antimicrobial resistance and integron characterization; in addition, plasmid replicon analysis and molecular typing were performed in extended-spectrum-beta-lactamase (ESBL) producer isolates. A multidrug-resistance phenotype was detected in 46.8% of the isolates, and the highest rates of resistance were found for ampicillin, trimethoprim−sulfamethoxazole, and tetracycline (>40%); moreover, 15 isolates (13.5%) showed susceptibility to all tested antibiotics. None of the isolates showed imipenem and/or cefoxitin resistance. Twenty-three of the one hundred and eleven E. coli isolates (20.7%) were ESBL producers and carried the blaSHV-12 gene; one of these isolates was recovered from the air, and the remaining 22 were from manure samples. Most of ESBL-positive isolates carried the cmlA (n = 23), tet(A) (n = 19), and aac(6′)-Ib-cr (n = 11) genes. The following genetic lineages were identified among the ESBL-producing isolates (sequence type-phylogroup-clonotype): ST770-E-CH116−552 (n = 12), ST117-B2-CH45−97 (n = 4), ST68-E-CH26−382/49 (n = 3), ST68-E-CH26−49 (n = 1), and ST10992-A/B1-CH11−23/41/580 (n = 4); the latter two were detected for the first time in the poultry sector. At least two plasmid replicon types were detected in the ESBL-producing E. coli isolates, with IncF, IncF1B, IncK, and IncHI1 being the most frequently found. The following antimicrobial resistance genes were identified among the non-ESBL-producing isolates (number of isolates): blaTEM (58), aac(6′)-Ib-cr (6), qnrS (2), aac(3)-II (2), cmlA (6), tet(A)/tet(B) (22), and sul1/2/3 (51). Four different gene-cassette arrays were detected in the variable region of class 1 (dfrA1-aadA1, dfrA12-aadA2, and dfrA12-orf-aadA2-cmlA) and class 2 integrons (sat2-aadA1-orfX). This work reveals the worrying presence of antimicrobial-resistant E. coli in the broiler farm environment, with ESBL-producing isolates of SHV-12 type being extensively disseminated.
Collapse
Affiliation(s)
- Sandra Martínez-Álvarez
- Department of Agriculture and Food, University of La Rioja, 26006 Logroño, Spain; (S.M.-Á.); (S.S.); (C.O.); (R.H.-S.); (I.C.); (R.F.-F.); (A.C.-B.); (J.L.-F.); (M.Z.)
| | - Susana Sanz
- Department of Agriculture and Food, University of La Rioja, 26006 Logroño, Spain; (S.M.-Á.); (S.S.); (C.O.); (R.H.-S.); (I.C.); (R.F.-F.); (A.C.-B.); (J.L.-F.); (M.Z.)
| | - Carmen Olarte
- Department of Agriculture and Food, University of La Rioja, 26006 Logroño, Spain; (S.M.-Á.); (S.S.); (C.O.); (R.H.-S.); (I.C.); (R.F.-F.); (A.C.-B.); (J.L.-F.); (M.Z.)
| | - Raquel Hidalgo-Sanz
- Department of Agriculture and Food, University of La Rioja, 26006 Logroño, Spain; (S.M.-Á.); (S.S.); (C.O.); (R.H.-S.); (I.C.); (R.F.-F.); (A.C.-B.); (J.L.-F.); (M.Z.)
| | - Isabel Carvalho
- Department of Agriculture and Food, University of La Rioja, 26006 Logroño, Spain; (S.M.-Á.); (S.S.); (C.O.); (R.H.-S.); (I.C.); (R.F.-F.); (A.C.-B.); (J.L.-F.); (M.Z.)
- Department of Veterinary Sciences, University of Trás-os-Montes-and Alto Douro, 5000-801 Vila Real, Portugal
| | - Rosa Fernández-Fernández
- Department of Agriculture and Food, University of La Rioja, 26006 Logroño, Spain; (S.M.-Á.); (S.S.); (C.O.); (R.H.-S.); (I.C.); (R.F.-F.); (A.C.-B.); (J.L.-F.); (M.Z.)
| | - Allelen Campaña-Burguet
- Department of Agriculture and Food, University of La Rioja, 26006 Logroño, Spain; (S.M.-Á.); (S.S.); (C.O.); (R.H.-S.); (I.C.); (R.F.-F.); (A.C.-B.); (J.L.-F.); (M.Z.)
| | - Javier Latorre-Fernández
- Department of Agriculture and Food, University of La Rioja, 26006 Logroño, Spain; (S.M.-Á.); (S.S.); (C.O.); (R.H.-S.); (I.C.); (R.F.-F.); (A.C.-B.); (J.L.-F.); (M.Z.)
| | - Myriam Zarazaga
- Department of Agriculture and Food, University of La Rioja, 26006 Logroño, Spain; (S.M.-Á.); (S.S.); (C.O.); (R.H.-S.); (I.C.); (R.F.-F.); (A.C.-B.); (J.L.-F.); (M.Z.)
| | - Carmen Torres
- Department of Agriculture and Food, University of La Rioja, 26006 Logroño, Spain; (S.M.-Á.); (S.S.); (C.O.); (R.H.-S.); (I.C.); (R.F.-F.); (A.C.-B.); (J.L.-F.); (M.Z.)
- Correspondence:
| |
Collapse
|
14
|
Samper-Cativiela C, Diéguez-Roda B, Trigo da Roza F, Ugarte-Ruiz M, Elnekave E, Lim S, Hernández M, Abad D, Collado S, Sáez JL, de Frutos C, Agüero M, Moreno MÁ, Escudero JA, Álvarez J. Genomic characterization of multidrug-resistant Salmonella serovar Kentucky ST198 isolated in poultry flocks in Spain (2011-2017). Microb Genom 2022; 8. [PMID: 35259085 PMCID: PMC9176280 DOI: 10.1099/mgen.0.000773] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Salmonella Kentucky is commonly found in poultry and rarely associated with human disease. However, a multidrug-resistant (MDR) S. Kentucky clone [sequence type (ST)198] has been increasingly reported globally in humans and animals. Our aim here was to assess if the recently reported increase of S. Kentucky in poultry in Spain was associated with the ST198 clone and to characterize this MDR clone and its distribution in Spain. Sixty-six isolates retrieved from turkey, laying hen and broiler in 2011–2017 were subjected to whole-genome sequencing to assess their sequence type, genetic relatedness, and presence of antimicrobial resistance genes (ARGs), plasmid replicons and virulence factors. Thirteen strains were further analysed using long-read sequencing technologies to characterize the genetic background associated with ARGs. All isolates belonged to the ST198 clone and were grouped in three clades associated with the presence of a specific point mutation in the gyrA gene, their geographical origin and isolation year. All strains carried between one and 16 ARGs whose presence correlated with the resistance phenotype to between two and eight antimicrobials. The ARGs were located in the Salmonella genomic island (SGI-1) and in some cases (blaSHV-12, catA1, cmlA1, dfrA and multiple aminoglycoside-resistance genes) in IncHI2/IncI1 plasmids, some of which were consistently detected in different years/farms in certain regions, suggesting they could persist over time. Our results indicate that the MDR S. Kentucky ST198 is present in all investigated poultry hosts in Spain, and that certain strains also carry additional plasmid-mediated ARGs, thus increasing its potential public health significance.
Collapse
Affiliation(s)
- Clara Samper-Cativiela
- VISAVET Health Surveillance Centre, Complutense University of Madrid, 28040 Madrid, Spain.,Department of Animal Health, Faculty of Veterinary Medicine, Complutense University of Madrid, 28040 Madrid, Spain
| | | | - Filipa Trigo da Roza
- Department of Animal Health, Faculty of Veterinary Medicine, Complutense University of Madrid, 28040 Madrid, Spain.,Molecular Basis of Adaptation, Department of Animal Health, Faculty of Veterinary, Complutense University of Madrid, 28040 Madrid, Spain
| | - María Ugarte-Ruiz
- VISAVET Health Surveillance Centre, Complutense University of Madrid, 28040 Madrid, Spain
| | - Ehud Elnekave
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 76100 Rehovot, Israel
| | - Seunghyun Lim
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN 55455, USA.,Bioinformatics and Computational Biology Program, University of Minnesota, Rochester, MN 55455, 55455 Minnesota, USA
| | - Marta Hernández
- Molecular Biology and Microbiology Laboratory, Instituto Tecnológico Agrario de Castilla y León (ITACyL), Junta de Castilla y León, 47009 Valladolid, Spain
| | - David Abad
- Molecular Biology and Microbiology Laboratory, Instituto Tecnológico Agrario de Castilla y León (ITACyL), Junta de Castilla y León, 47009 Valladolid, Spain
| | - Soledad Collado
- Subdirección General de Sanidad e Higiene Animal y Trazabilidad, Dirección General de la Producción Agraria, Ministerio de Agricultura, Pesca y Alimentación, 28010 Madrid, Spain
| | - José Luis Sáez
- Subdirección General de Sanidad e Higiene Animal y Trazabilidad, Dirección General de la Producción Agraria, Ministerio de Agricultura, Pesca y Alimentación, 28010 Madrid, Spain
| | - Cristina de Frutos
- Laboratorio Central de Veterinaria, Ministerio de Agricultura, Pesca y Alimentación, 28110 Madrid, Spain
| | - Montserrat Agüero
- Laboratorio Central de Veterinaria, Ministerio de Agricultura, Pesca y Alimentación, 28110 Madrid, Spain
| | - Miguel Ángel Moreno
- Department of Animal Health, Faculty of Veterinary Medicine, Complutense University of Madrid, 28040 Madrid, Spain
| | - José Antonio Escudero
- VISAVET Health Surveillance Centre, Complutense University of Madrid, 28040 Madrid, Spain.,Department of Animal Health, Faculty of Veterinary Medicine, Complutense University of Madrid, 28040 Madrid, Spain.,Molecular Basis of Adaptation, Department of Animal Health, Faculty of Veterinary, Complutense University of Madrid, 28040 Madrid, Spain
| | - Julio Álvarez
- VISAVET Health Surveillance Centre, Complutense University of Madrid, 28040 Madrid, Spain.,Department of Animal Health, Faculty of Veterinary Medicine, Complutense University of Madrid, 28040 Madrid, Spain
| |
Collapse
|
15
|
Characterization of E. coli Isolates Producing Extended Spectrum Beta-Lactamase SHV-Variants from the Food Chain in Germany. Microorganisms 2021; 9:microorganisms9091926. [PMID: 34576822 PMCID: PMC8471341 DOI: 10.3390/microorganisms9091926] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/03/2021] [Accepted: 09/07/2021] [Indexed: 11/25/2022] Open
Abstract
Resistance of bacteria to 3rd generation cephalosporins mediated by beta-lactamases (ESBL, pAmpC) is a public health concern. In this study, 1517 phenotypically cephalosporin-resistant E. coli were screened for the presence of blaSHV genes. Respective genes were detected in 161 isolates. Majority (91%) were obtained from poultry production and meat. The SHV-12 beta-lactamase was the predominant variant (n = 155), while the remaining isolates exhibited SHV-2 (n = 4) or SHV-2a (n = 2). A subset of the isolates (n = 51) was further characterized by PCR, PFGE, or whole-genome sequencing and bioinformatics analysis. The SHV-12-producing isolates showed low phylogenetic relationships, and dissemination of the blaSHV-12 genes seemed to be mainly driven by horizontal gene transfer. In most of the isolates, blaSHV-12 was located on transferable IncX3 (~43 kb) or IncI1 (~100 kb) plasmids. On IncX3, blaSHV-12 was part of a Tn6 composite transposon located next to a Tn3 transposon, which harbored the fluoroquinolone resistance gene qnrS1. On IncI1 plasmids, blaSHV-12 was located on an incomplete class 1 integron as part of a Tn21 transposon. In conclusion, SHV-12 is widely distributed in German poultry production and spreads via horizontal gene transfer. Consumers are at risk by handling raw poultry meat and should take care in appropriate kitchen hygiene.
Collapse
|
16
|
Pauly N, Hammerl JA, Schwarz S, Grobbel M, Meemken D, Malorny B, Tenhagen BA, Käsbohrer A, Irrgang A. Co-occurrence of the blaVIM-1 and blaSHV-12 genes on an IncHI2 plasmid of an Escherichia coli isolate recovered from German livestock. J Antimicrob Chemother 2021; 76:531-533. [PMID: 33175149 PMCID: PMC7816165 DOI: 10.1093/jac/dkaa436] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 09/28/2020] [Indexed: 11/17/2022] Open
Affiliation(s)
- N Pauly
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - J A Hammerl
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - S Schwarz
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - M Grobbel
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - D Meemken
- Institute of Food Safety and Food Hygiene, Freie Universität Berlin, Berlin, Germany
| | - B Malorny
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - B-A Tenhagen
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - A Käsbohrer
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany.,Unit for Veterinary Public Health and Epidemiology, University of Veterinary Medicine, Vienna, Austria
| | - A Irrgang
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| |
Collapse
|
17
|
Foley SL, Kaldhone PR, Ricke SC, Han J. Incompatibility Group I1 (IncI1) Plasmids: Their Genetics, Biology, and Public Health Relevance. Microbiol Mol Biol Rev 2021; 85:e00031-20. [PMID: 33910982 PMCID: PMC8139525 DOI: 10.1128/mmbr.00031-20] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Bacterial plasmids are extrachromosomal genetic elements that often carry antimicrobial resistance (AMR) genes and genes encoding increased virulence and can be transmissible among bacteria by conjugation. One key group of plasmids is the incompatibility group I1 (IncI1) plasmids, which have been isolated from multiple Enterobacteriaceae of food animal origin and clinically ill human patients. The IncI group of plasmids were initially characterized due to their sensitivity to the filamentous bacteriophage If1. Two prototypical IncI1 plasmids, R64 and pColIb-P9, have been extensively studied, and the plasmids consist of unique regions associated with plasmid replication, plasmid stability/maintenance, transfer machinery apparatus, single-stranded DNA transfer, and antimicrobial resistance. IncI1 plasmids are somewhat unique in that they encode two types of sex pili, a thick, rigid pilus necessary for mating and a thin, flexible pilus that helps stabilize bacteria for plasmid transfer in liquid environments. A key public health concern with IncI1 plasmids is their ability to carry antimicrobial resistance genes, including those associated with critically important antimicrobials used to treat severe cases of enteric infections, including the third-generation cephalosporins. Because of the potential importance of these plasmids, this review focuses on the distribution of the plasmids, their phenotypic characteristics associated with antimicrobial resistance and virulence, and their replication, maintenance, and transfer.
Collapse
Affiliation(s)
- Steven L Foley
- Division of Microbiology, U.S. Food and Drug Administration, National Center for Toxicological Research, Jefferson, Arkansas, USA
| | - Pravin R Kaldhone
- Division of Microbiology, U.S. Food and Drug Administration, National Center for Toxicological Research, Jefferson, Arkansas, USA
- Center for Food Safety and Food Science Department, University of Arkansas, Fayetteville, Arkansas, USA
| | - Steven C Ricke
- Meat Science & Animal Biologics Discovery Program, Department of Animal and Dairy Sciences, University of Wisconsin, Madison, Wisconsin, USA
| | - Jing Han
- Division of Microbiology, U.S. Food and Drug Administration, National Center for Toxicological Research, Jefferson, Arkansas, USA
| |
Collapse
|
18
|
Ewers C, de Jong A, Prenger-Berninghoff E, El Garch F, Leidner U, Tiwari SK, Semmler T. Genomic Diversity and Virulence Potential of ESBL- and AmpC-β-Lactamase-Producing Escherichia coli Strains From Healthy Food Animals Across Europe. Front Microbiol 2021; 12:626774. [PMID: 33868190 PMCID: PMC8047082 DOI: 10.3389/fmicb.2021.626774] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 03/02/2021] [Indexed: 01/07/2023] Open
Abstract
The role of livestock animals as a putative source of ESBL/pAmpC E. coli for humans is a central issue of research. In a large-scale pan-European surveillance, 2,993 commensal Escherichia spp. isolates were recovered from randomly collected fecal samples of healthy cattle, pigs and chickens in various abattoirs. One-hundred Escherichia spp. isolates (0.5% from cattle, 1.3% pigs, 8.0% chickens) fulfilled the criteria for cefotaxime and ceftazidime non-wildtype (EUCAST). In silico screening of WGS data of 99 isolates (98 E. coli and 1 E. fergusonii) revealed blaSHV–12 (32.3%), blaCTX–M–1 (24.2%), and blaCMY–2 (22.2%) as predominant ESBL/pAmpC types. Other types were blaSHV–2 (1.0%), blaCTX–M–2/–14/–15 (1.0/6.1/1.0%), and blaTEM–52 (5.1%). Six isolates revealed AmpC-promoter mutations (position −42 (C > T) and one carried mcr-1. The majority (91.3%) of ESBL/pAmpC genes were located on plasmids. SHV-12 was mainly (50%) encoded on IncI1α plasmids (pST-3/-26/-95), followed by IncX3 (12.5%) and IncK2 (3.1%). The blaTEM–52 genes were located on IncI1α-pST-36 (60%) and IncX1 plasmids (20%). The dominant plasmid lineage among CTX-M-1 isolates was IncI1α (pST-3/-295/-317) (87.5%), followed by IncN-pST-1 (8.3%). CMY-2 was mostly identified on IncI1α (pST-12/-2) (54.5%) and IncK2 (31.8%) plasmids. Several plasmids revealed high similarity to published plasmids from human and animal Enterobacteriaceae. The isolates were assigned to phylogroups A/C (34.7/7.1%), B1 (27.6%), B2 (3.1%), D/F (9.2/10.2%), E (5.1%), and to E. clades (3.0%). With 51 known and 2 novel MLST types, a wide variety of STs was found, including STs previously observed in human isolates (ST10/38/117/131/648). ESBL/AmpC types or STs were rarely correlated with the geographic origin of the isolates or animal species. Virulence gene typing identified extraintestinal pathogenic E. coli (ExPEC; 2.0%), avian pathogenic E. coli (APEC; 51.5%), and atypical enteropathogenic E. coli (EPEC; 6.1%). In conclusion, the high diversity of STs and phylogenetic groups provides hardly any hint for clonal spread of single lineages but hints toward the dissemination of cephalosporin resistance genes in livestock via distinct, globally successful plasmid lineages. Even though a number of isolates could not be assigned to a distinct pathotype, our finding of combined multidrug-resistance and virulence in this facultative pathogen should be considered an additional threat to public health.
Collapse
Affiliation(s)
- Christa Ewers
- Department of Veterinary Medicine, Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, Giessen, Germany
| | - Anno de Jong
- European Antimicrobial Susceptibility Surveillance in Animals (EASSA) Study Group, Executive Animal Health Study Center (CEESA), Brussels, Belgium
| | - Ellen Prenger-Berninghoff
- Department of Veterinary Medicine, Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, Giessen, Germany
| | - Farid El Garch
- European Antimicrobial Susceptibility Surveillance in Animals (EASSA) Study Group, Executive Animal Health Study Center (CEESA), Brussels, Belgium
| | - Ursula Leidner
- Department of Veterinary Medicine, Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, Giessen, Germany
| | - Sumeet K Tiwari
- NG1 Microbial Genomics, Robert Koch Institute, Berlin, Germany
| | - Torsten Semmler
- NG1 Microbial Genomics, Robert Koch Institute, Berlin, Germany
| |
Collapse
|
19
|
Carvalho I, Safia Chenouf N, Cunha R, Martins C, Pimenta P, Pereira AR, Martínez-Álvarez S, Ramos S, Silva V, Igrejas G, Torres C, Poeta P. Antimicrobial Resistance Genes and Diversity of Clones among ESBL- and Acquired AmpC-Producing Escherichia coli Isolated from Fecal Samples of Healthy and Sick Cats in Portugal. Antibiotics (Basel) 2021; 10:antibiotics10030262. [PMID: 33807601 PMCID: PMC8001562 DOI: 10.3390/antibiotics10030262] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 02/28/2021] [Accepted: 03/02/2021] [Indexed: 12/26/2022] Open
Abstract
The aim of the study was to analyze the mechanisms of resistance in extended-spectrum beta-lactamase (ESBL)- and acquired AmpC (qAmpC)-producing Escherichia coli isolates from healthy and sick cats in Portugal. A total of 141 rectal swabs recovered from 98 sick and 43 healthy cats were processed for cefotaxime-resistant (CTXR) E. coli recovery (in MacConkey agar supplemented with 2 µg/mL cefotaxime). The matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) method was used for E. coli identification and antimicrobial susceptibility was performed by a disk diffusion test. The presence of resistance/virulence genes was tested by PCR sequencing. The phylogenetic typing and multilocus sequence typing (MLST) were determined by specific PCR sequencing. CTXRE. coli isolates were detected in seven sick and six healthy cats (7.1% and 13.9%, respectively). Based on the synergy tests, 11 of 13 CTXRE. coli isolates (one/sample) were ESBL-producers (ESBL total rate: 7.8%) carrying the following ESBL genes: blaCTX-M-1 (n = 3), blaCTX-M-15 (n = 3), blaCTX-M-55 (n = 2), blaCTX-M-27 (n = 2) and blaCTX-M-9 (n = 1). Six different sequence types were identified among ESBL-producers (sequence type/associated ESBLs): ST847/CTX-M-9, CTX-M-27, CTX-M-1; ST10/CTX-M-15, CTX-M-27; ST6448/CTX-M-15, CTX-M-55; ST429/CTX-M-15; ST101/CTX-M-1 and ST40/CTX-M-1. Three of the CTXR isolates were CMY-2-producers (qAmpC rate: 2.1%); two of them were ESBL-positive and one ESBL-negative. These isolates were typed as ST429 and ST6448 and were obtained in healthy or sick cats. The phylogenetic groups A/B1/D/clade 1 were detected among ESBL- and qAmpC-producing isolates. Cats are carriers of qAmpC (CMY-2)- and ESBL-producing E. coli isolates (mostly of variants of CTX-M group 1) of diverse clonal lineages, which might represent a public health problem due to the proximity of cats with humans regarding a One Health perspective.
Collapse
Affiliation(s)
- Isabel Carvalho
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal; (I.C.); (V.S.)
- Department of Genetics and Biotechnology, UTAD, 5000-801 Vila Real, Portugal;
- Functional Genomics and Proteomics Unit, UTAD, 5000-801 Vila Real, Portugal
- Laboratory Associated for Green Chemistry (LAQV-REQUIMTE), New University of Lisbon, 2829-516 Monte da Caparica, Portugal
- Area Biochemistry and Molecular Biology, University of La Rioja, 26006 Logroño, Spain; (N.S.C.); (S.M.-Á.); (C.T.)
| | - Nadia Safia Chenouf
- Area Biochemistry and Molecular Biology, University of La Rioja, 26006 Logroño, Spain; (N.S.C.); (S.M.-Á.); (C.T.)
- Laboratory of Exploration and Valuation of the Steppe Ecosystem, University of Djelfa, Djelfa 17000, Algeria
| | - Rita Cunha
- Hospital Veterinário de São Bento, 1200-822 Lisboa, Portugal;
| | - Carla Martins
- Clínica Veterinária do Vouga, 3740-253 Sever do Vouga, Portugal;
| | - Paulo Pimenta
- Hospital Veterinário de Trás-os-Montes, 5000-056 Vila Real, Portugal;
| | | | - Sandra Martínez-Álvarez
- Area Biochemistry and Molecular Biology, University of La Rioja, 26006 Logroño, Spain; (N.S.C.); (S.M.-Á.); (C.T.)
| | - Sónia Ramos
- VetRedondo, Consultório Veterinário de Monte Redondo Unipessoal Lda, Monte Redondo, 2425-618 Leiria, Portugal;
| | - Vanessa Silva
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal; (I.C.); (V.S.)
- Department of Genetics and Biotechnology, UTAD, 5000-801 Vila Real, Portugal;
- Functional Genomics and Proteomics Unit, UTAD, 5000-801 Vila Real, Portugal
- Laboratory Associated for Green Chemistry (LAQV-REQUIMTE), New University of Lisbon, 2829-516 Monte da Caparica, Portugal
| | - Gilberto Igrejas
- Department of Genetics and Biotechnology, UTAD, 5000-801 Vila Real, Portugal;
- Functional Genomics and Proteomics Unit, UTAD, 5000-801 Vila Real, Portugal
- Laboratory Associated for Green Chemistry (LAQV-REQUIMTE), New University of Lisbon, 2829-516 Monte da Caparica, Portugal
| | - Carmen Torres
- Area Biochemistry and Molecular Biology, University of La Rioja, 26006 Logroño, Spain; (N.S.C.); (S.M.-Á.); (C.T.)
| | - Patrícia Poeta
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal; (I.C.); (V.S.)
- Laboratory Associated for Green Chemistry (LAQV-REQUIMTE), New University of Lisbon, 2829-516 Monte da Caparica, Portugal
- Correspondence: ; Tel.: +351-259350466; Fax: +351-259350629
| |
Collapse
|
20
|
Trotta A, Cirilli M, Marinaro M, Bosak S, Diakoudi G, Ciccarelli S, Paci S, Buonavoglia D, Corrente M. Detection of multi-drug resistance and AmpC β-lactamase/extended-spectrum β-lactamase genes in bacterial isolates of loggerhead sea turtles (Caretta caretta) from the Mediterranean Sea. MARINE POLLUTION BULLETIN 2021; 164:112015. [PMID: 33513540 DOI: 10.1016/j.marpolbul.2021.112015] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/11/2021] [Accepted: 01/14/2021] [Indexed: 06/12/2023]
Abstract
Sea turtles are useful sentinels to monitor the dissemination of antimicrobial resistance (AMR) in the marine coastal ecosystems. Forty Gram negative bacteria were isolated from wounds of 52 injured Caretta caretta, living in the Mediterranean Sea. Bacteria were identified using 16S rRNA gene sequencing and tested for susceptibility to 15 antibiotics. In addition, NGS amplicon sequencing was performed to detect the presence of AmpC β-lactamase genes (blaAmpC) and extended-spectrum β-lactamase (ESBL) genes (blaCTX-M,blaSHV,blaTEM). Seventy-five percent of the isolates (30/40 isolates) exhibited multidrug resistance (MDR) phenotypes and 32.5% (13/40 isolates) were confirmed to be positive for at least one gene. The variants of ESBLs genes were blaCTX-M-3,blaTEM-236 and blaSHV-12. Variants of the blaAmpCβ-lactamase gene i.e., blaACT-24, blaACT-2, blaACT-17, blaDHA-4 and blaCMY-37, were also detected. In addition, 4 isolates were found simultaneously harboring CTX and AmpC genes while 2 strains harbored 3 genes (blaACT-2+TEM-236+SHV-12, and blaCTX-M-3+ACT-24+TEM-236).
Collapse
Affiliation(s)
- Adriana Trotta
- Department of Veterinary Medicine, University of Bari "Aldo Moro", Str. Prov. per Casamassima Km 3, 70010 Valenzano, BA, Italy.
| | - Margie Cirilli
- Department of Veterinary Medicine, University of Bari "Aldo Moro", Str. Prov. per Casamassima Km 3, 70010 Valenzano, BA, Italy
| | - Mariarosaria Marinaro
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Sunčica Bosak
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000 Zagreb, Croatia
| | - Georgia Diakoudi
- Department of Veterinary Medicine, University of Bari "Aldo Moro", Str. Prov. per Casamassima Km 3, 70010 Valenzano, BA, Italy
| | - Stefano Ciccarelli
- Department of Veterinary Medicine, University of Bari "Aldo Moro", Str. Prov. per Casamassima Km 3, 70010 Valenzano, BA, Italy
| | - Serena Paci
- Department of Veterinary Medicine, University of Bari "Aldo Moro", Str. Prov. per Casamassima Km 3, 70010 Valenzano, BA, Italy
| | - Domenico Buonavoglia
- Department of Veterinary Medicine, University of Bari "Aldo Moro", Str. Prov. per Casamassima Km 3, 70010 Valenzano, BA, Italy
| | - Marialaura Corrente
- Department of Veterinary Medicine, University of Bari "Aldo Moro", Str. Prov. per Casamassima Km 3, 70010 Valenzano, BA, Italy
| |
Collapse
|
21
|
Szmolka A, Wami H, Dobrindt U. Comparative Genomics of Emerging Lineages and Mobile Resistomes of Contemporary Broiler Strains of Salmonella Infantis and E. coli. Front Microbiol 2021; 12:642125. [PMID: 33717039 PMCID: PMC7947892 DOI: 10.3389/fmicb.2021.642125] [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: 02/03/2021] [Indexed: 01/06/2023] Open
Abstract
Introduction Commensal and pathogenic strains of multidrug-resistant (MDR) Escherichia coli and non-typhoid strains of Salmonella represent a growing foodborne threat from foods of poultry origin. MDR strains of Salmonella Infantis and E. coli are frequently isolated from broiler chicks and the simultaneous presence of these two enteric bacterial species would potentially allow the exchange of mobile resistance determinants. Objectives In order to understand possible genomic relations and to obtain a first insight into the potential interplay of resistance genes between enteric bacteria, we compared genomic diversity and mobile resistomes of S. Infantis and E. coli from broiler sources. Results The core genome MLST analysis of 56 S. Infantis and 90 E. coli contemporary strains revealed a high genomic heterogeneity of broiler E. coli. It also allowed the first insight into the genomic diversity of the MDR clone B2 of S. Infantis, which is endemic in Hungary. We also identified new MDR lineages for S. Infantis (ST7081 and ST7082) and for E. coli (ST8702 and ST10088). Comparative analysis of antibiotic resistance genes and plasmid types revealed a relatively narrow interface between the mobile resistomes of E. coli and S. Infantis. The mobile resistance genes tet(A), aadA1, and sul1 were identified at an overall high prevalence in both species. This gene association is characteristic to the plasmid pSI54/04 of the epidemic clone B2 of S. Infantis. Simultaneous presence of these genes and of IncI plasmids of the same subtype in cohabitant caecal strains of E. coli and S. Infantis suggests an important role of these plasmid families in a possible interplay of resistance genes between S. Infantis and E. coli in broilers. Conclusion This is the first comparative genomic analysis of contemporary broiler strains of S. Infantis and E. coli. The diversity of mobile resistomes suggests that commensal E. coli could be potential reservoirs of resistance for S. Infantis, but so far only a few plasmid types and mobile resistance genes could be considered as potentially exchangeable between these two species. Among these, IncI1 plasmids could make the greatest contribution to the microevolution and genetic interaction between E. coli and S. Infantis.
Collapse
Affiliation(s)
- Ama Szmolka
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
| | - Haleluya Wami
- Institute of Hygiene, University of Münster, Münster, Germany
| | - Ulrich Dobrindt
- Institute of Hygiene, University of Münster, Münster, Germany
| |
Collapse
|
22
|
Rochegüe T, Haenni M, Cazeau G, Metayer V, Madec JY, Ferry T, Lupo A. An inventory of 44 qPCR assays using hydrolysis probes operating with a unique amplification condition for the detection and quantification of antibiotic resistance genes. Diagn Microbiol Infect Dis 2021; 100:115328. [PMID: 33819858 DOI: 10.1016/j.diagmicrobio.2021.115328] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 01/22/2021] [Accepted: 01/24/2021] [Indexed: 01/28/2023]
Abstract
Early antibiotic resistance determinants (ARDs) detection in humans or animals is crucial to counteract their propagation. The ARDs quantification is fundamental to understand the perturbation caused by disruptors, such as antibiotics, during therapies. Forty-three qPCRs on the most diffused ARDs and integrons among human and animal Enterobacterales, and one on the 16S rDNA for bacteria quantification, were developed. The qPCRs, using hydrolysis probes, operated with a unique amplification condition and were tested analytically and diagnostically performing 435 reactions on five positive and negative controls for each qPCR. Diagnostic sensitivity and specificity were confirmed by PCR and genome sequencing of control isolates, demonstrating 100% performance for all qPCRs. An easy and rapid discrimination method for the epidemiologically relevant blaCTX-Ms is provided. This large, noncommercial qPCRs inventory could serve for precise quantification of ARDs, but also as a rapid screening tool for surveillance purposes, providing the basis for further high-throughput developments.
Collapse
Affiliation(s)
- Tony Rochegüe
- ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes (AVB), Lyon, France
| | - Marisa Haenni
- ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes (AVB), Lyon, France
| | - Géraldine Cazeau
- ANSES - Université de Lyon, Unité Epidémiologie et Appui à la Surveillance (EAS), Lyon, France
| | - Véronique Metayer
- ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes (AVB), Lyon, France
| | - Jean-Yves Madec
- ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes (AVB), Lyon, France
| | - Tristan Ferry
- Service des maladies infectieuses et tropicales, CHU de Lyon, Hôpital de la Croix-Rousse, Lyon, France; Centre International de Recherche en Infectiologie, CIRI, Inserm U1111, CNRS UMR5308, ENS de Lyon, UCBL1, Lyon, France
| | - Agnese Lupo
- ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes (AVB), Lyon, France.
| |
Collapse
|
23
|
Apostolakos I, Feudi C, Eichhorn I, Palmieri N, Fasolato L, Schwarz S, Piccirillo A. High-resolution characterisation of ESBL/pAmpC-producing Escherichia coli isolated from the broiler production pyramid. Sci Rep 2020; 10:11123. [PMID: 32636426 PMCID: PMC7341882 DOI: 10.1038/s41598-020-68036-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 05/29/2020] [Indexed: 12/16/2022] Open
Abstract
The presence of extended-spectrum β-lactamase (ESBL) or plasmid-mediated AmpC β-lactamase (pAmpC)-producing Escherichia coli (ESBL/pAmpC-EC) in livestock is a public health risk given the likelihood of their transmission to humans via the food chain. We conducted whole genome sequencing on 100 ESBL/pAmpC-EC isolated from the broiler production to explore their resistance and virulence gene repertoire, characterise their plasmids and identify transmission events derived from their phylogeny. Sequenced isolates carried resistance genes to four antimicrobial classes in addition to cephalosporins. Virulence gene analysis assigned the majority of ESBL/pAmpC-EC to defined pathotypes. In the complex genetic background of ESBL/pAmpC-EC, clusters of closely related isolates from various production stages were identified and indicated clonal transmission. Phylogenetic comparison with publicly available genomes suggested that previously uncommon ESBL/pAmpC-EC lineages could emerge in poultry, while others might contribute to the maintenance and dissemination of ESBL/pAmpC genes in broilers. The majority of isolates from diverse E. coli lineages shared four dominant plasmids (IncK2, IncI1, IncX3 and IncFIB/FII) with identical ESBL/pAmpC gene insertion sites. These plasmids have been previously reported in diverse hosts, including humans. Our findings underline the importance of specific plasmid groups in the dissemination of cephalosporin resistance genes within the broiler industry and across different reservoirs.
Collapse
Affiliation(s)
- Ilias Apostolakos
- Department of Comparative Biomedicine and Food Science, University of Padua, 35020, Padua, Italy
| | - Claudia Feudi
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, 14163, Berlin, Germany
| | - Inga Eichhorn
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, 14163, Berlin, Germany
| | - Nicola Palmieri
- Department for Farm Animals and Veterinary Public Health, University Clinic for Poultry and Fish Medicine, University of Veterinary Medicine, 1210, Vienna, Austria
| | - Luca Fasolato
- Department of Comparative Biomedicine and Food Science, University of Padua, 35020, Padua, Italy
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, 14163, Berlin, Germany
| | - Alessandra Piccirillo
- Department of Comparative Biomedicine and Food Science, University of Padua, 35020, Padua, Italy.
| |
Collapse
|
24
|
Reid CJ, Blau K, Jechalke S, Smalla K, Djordjevic SP. Whole Genome Sequencing of Escherichia coli From Store-Bought Produce. Front Microbiol 2020; 10:3050. [PMID: 32063888 PMCID: PMC7000624 DOI: 10.3389/fmicb.2019.03050] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 12/18/2019] [Indexed: 12/22/2022] Open
Abstract
The role of agriculture in the transfer of drug resistant pathogens to humans is widely debated and poorly understood. Escherichia coli is a valuable indicator organism for contamination and carriage of antimicrobial resistance (AMR) in foods. Whilst whole genome sequences for E. coli from animals and associated meats are common, sequences from produce are scarce. Produce may acquire drug resistant E. coli from animal manure fertilizers, contaminated irrigation water and wildlife, particularly birds. Whole genome sequencing was used to characterize 120 tetracycline (TET) resistant E. coli from store-bought, ready-to-eat cilantro, arugula and mixed salad from two German cities. E. coli were recovered on the day of purchase and after 7 days of refrigeration. Cilantro was far more frequently contaminated with TET-resistant E. coli providing 102 (85%) sequenced strains. Phylogroup B1 dominated the collection (n = 84, 70%) with multi-locus sequence types B1-ST6186 (n = 37, 31%), C-ST165 (n = 17, 14%), B1-ST58 (n = 14, 12%), B1-ST641 (n = 8, 7%), and C-ST88 (n = 5, 4%) frequently identified. Notably, seven strains of diverse sequence type (ST) carried genetic indicators of ColV virulence plasmid carriage. A number of previously identified and novel integrons associated with insertion elements including IS26 were also identified. Storage may affect the lineages of E. coli isolated, however further studies are needed. Our study indicates produce predominantly carry E. coli with a commensal phylogroup and a variety of AMR and virulence-associated traits. Genomic surveillance of bacteria that contaminate produce should be a matter of public health importance in order to develop a holistic understanding of the environmental dimensions of AMR.
Collapse
Affiliation(s)
- Cameron J. Reid
- The ithree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Khald Blau
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Sven Jechalke
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
- Institute for Phytopathology, Justus Liebig University Giessen, Giessen, Germany
| | - Kornelia Smalla
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Steven P. Djordjevic
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| |
Collapse
|
25
|
Maciuca IE, Cummins ML, Cozma AP, Rimbu CM, Guguianu E, Panzaru C, Licker M, Szekely E, Flonta M, Djordjevic SP, Timofte D. Genetic Features of mcr-1 Mediated Colistin Resistance in CMY-2-Producing Escherichia coli From Romanian Poultry. Front Microbiol 2019; 10:2267. [PMID: 31681191 PMCID: PMC6798173 DOI: 10.3389/fmicb.2019.02267] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 09/17/2019] [Indexed: 11/13/2022] Open
Abstract
Colistin is a last resort antibiotic used for the treatment of human infections associated with carbapenemase-producing Enterobacteriales. Here, we evaluated the occurrence of mcr-1 and -2 plasmid-mediated colistin resistance in colistin and/or carbapenem resistant human clinical Enterobacteriales and other gram-negative bacteria (n = 543) as well as third generation cephalosporin-resistant (3GCR) Escherichia coli isolates from poultry abattoir workers (n = 15) and poultry fecal samples (n = 92) collected from two geographically separate abattoirs in Romania. which revealed that mcr-1 was present within four sequence types (STs): ST744 (n = 7), ST57 (n = 7), ST156 (n = 2), and ST10 (n = 1). Within STs, serotypes were conserved and, notably, all except one of the mcr-1-positive isolates were found to exhibit fluoroquinolone-resistance (FQR) associated SNPs in both gyrA and parC. While there were variations in genotypes, all isolates belonging to ST744, ST57, and ST156 were rich in resistance determinants, carrying aminoglycoside-modifying enzymes genes, sulfonamide resistance gene bla TEM- 1 as well as bla CMY- 2 AmpC β-lactamase resistance genes. They also exhibited high similarity in carriage of virulence genes; ST10, however, only carried the mcr-1 gene. Whole genome sequencing (WGS) analysis also revealed that although the mcr-1 gene was identified in a diverse population of E. coli, two STs (ST57 and ST744) predominated and interestingly, were found in isolates across both abattoirs providing evidence for clonal transmission. Also, two main genomic contexts of mcr-1 isolates were revealed with all ST57 isolates harboring the mcr-1 gene between two copies of ISApl1 (or the Tn6330 transposon) whilst a common mcr-1 containing scaffold, highly similar to IncX type mcr-1-bearing plasmids (pWI2-mcr, Accession number: LT838201), was present among mcr-1 isolates of varying phylogenetic backgrounds (ST10, ST744 and ST156). The high prevalence of the mcr-1 gene in poultry E. coli isolates with co-resistance to cephalosporins and quinolones, in a country where antimicrobial use in food production species is poorly regulated, is concerning and the findings from this study should lead to better surveillance of antimicrobial resistance (AMR) in food-production animals in Romania.
Collapse
Affiliation(s)
- Iuliana E Maciuca
- Institute of Veterinary Science, University of Liverpool, Liverpool, United Kingdom
| | - Max L Cummins
- The ithree Institute, University of Technology Sydney, Sydney, NSW, Australia
| | - Andreea P Cozma
- Faculty of Veterinary Medicine, Ion Ionescu de la Brad, University of Agricultural Sciences and Veterinary Medicine of Iaşi, Iaşi, Romania
| | - Cristina M Rimbu
- Faculty of Veterinary Medicine, Ion Ionescu de la Brad, University of Agricultural Sciences and Veterinary Medicine of Iaşi, Iaşi, Romania
| | - Eleonora Guguianu
- Faculty of Veterinary Medicine, Ion Ionescu de la Brad, University of Agricultural Sciences and Veterinary Medicine of Iaşi, Iaşi, Romania
| | - Carmen Panzaru
- Microbiology Department, Grigore T. Popa University of Medicine and Pharmacy, Iaşi, Romania
| | - Monica Licker
- Microbiology Department, Victor Babes University of Medicine and Pharmacy, Timişoara, Romania
| | - Edit Szekely
- Microbiology Department, George Emil Palade University of Medicine, Pharmacy, Science and Technology of Târgu Mures, Târgu Mureş, Romania.,Clinical County Emergency Hospital Targu Mures, Târgu Mureş, Romania
| | - Mirela Flonta
- Clinical Hospital of Infectious Diseases, Cluj-Napoca, Romania
| | - Steven P Djordjevic
- The ithree Institute, University of Technology Sydney, Sydney, NSW, Australia
| | - Dorina Timofte
- Institute of Veterinary Science, University of Liverpool, Liverpool, United Kingdom.,Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| |
Collapse
|
26
|
Usui M, Ozeki K, Komatsu T, Fukuda A, Tamura Y. Prevalence of Extended-Spectrum β-Lactamase-Producing Bacteria on Fresh Vegetables in Japan. J Food Prot 2019; 82:1663-1666. [PMID: 31532252 DOI: 10.4315/0362-028x.jfp-19-138] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Extended-spectrum β-lactamase (ESBL)-producing bacteria are spreading rapidly, posing a threat to human and animal health. Contamination of vegetables with antimicrobial-resistant bacteria or those harboring antimicrobial resistance genes or a combination of both presents a potential route of transmission to humans. Therefore, the aim of this study was to determine the prevalence of these bacteria in fresh vegetables in Japan. A total of 130 samples of fresh vegetables were collected from seven supermarkets in Japan. The predominant genus detected was Pseudomonas spp., including 10 ESBL-producing strains, isolated from 10 (7.7%) of the vegetable samples. Two ESBL genes were detected, blaTEM-116 (n = 7) and blaSHV-12 (n = 3), and some of these strains were resistant to multiple antibiotics. Because vegetables are often consumed raw, those contaminated with ESBL producers could represent an important route of transmission to humans in Japan. Thus, more stringent hygiene measures and monitoring are required to prevent transmission via this source.
Collapse
Affiliation(s)
- Masaru Usui
- School of Veterinary Medicine, Rakuno Gakuen University, 582 Midorimachi, Bunkyodai, Ebetsu, Hokkaido 069-8501, Japan (ORCID: https://orcid.org/0000-0003-1624-1469 [M.U.])
| | - Kazuya Ozeki
- School of Veterinary Medicine, Rakuno Gakuen University, 582 Midorimachi, Bunkyodai, Ebetsu, Hokkaido 069-8501, Japan (ORCID: https://orcid.org/0000-0003-1624-1469 [M.U.])
| | - Tadasu Komatsu
- School of Veterinary Medicine, Rakuno Gakuen University, 582 Midorimachi, Bunkyodai, Ebetsu, Hokkaido 069-8501, Japan (ORCID: https://orcid.org/0000-0003-1624-1469 [M.U.])
| | - Akira Fukuda
- School of Veterinary Medicine, Rakuno Gakuen University, 582 Midorimachi, Bunkyodai, Ebetsu, Hokkaido 069-8501, Japan (ORCID: https://orcid.org/0000-0003-1624-1469 [M.U.]).,Osaka Institute of Public Health, Microbiology Section, 8-34 Tojotyo, Tennoji, Osaka 543-0026, Japan
| | - Yutaka Tamura
- School of Veterinary Medicine, Rakuno Gakuen University, 582 Midorimachi, Bunkyodai, Ebetsu, Hokkaido 069-8501, Japan (ORCID: https://orcid.org/0000-0003-1624-1469 [M.U.])
| |
Collapse
|
27
|
Darwich L, Vidal A, Seminati C, Albamonte A, Casado A, López F, Molina-López RA, Migura-Garcia L. High prevalence and diversity of extended-spectrum β-lactamase and emergence of OXA-48 producing Enterobacterales in wildlife in Catalonia. PLoS One 2019; 14:e0210686. [PMID: 31381578 PMCID: PMC6681944 DOI: 10.1371/journal.pone.0210686] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 07/02/2019] [Indexed: 11/22/2022] Open
Abstract
Most of the studies focused on antimicrobial resistance (AMR) performed in wildlife describe Escherichia coli as the principal indicator of the selective pressure. In the present study, several species of Enterobacterales with a large panel of cephalosporin resistant (CR) genes have been isolated from wildlife in Catalonia. A total of 307 wild animals were examined to determine the prevalence of CR enterobacteria, AMR phenotypes and the presence of common carbapenem and CR genes. The overall prevalence of CR-phenotype was 13% (40/307): 17.3% in wild mammals (18/104) and 11.5% in wild birds (22/191) (p<0.01). Hedgehogs showed the highest prevalence (13.5% of 104) of the mammal specimens, and raptors the highest in bird specimen (7.3% of 191). Although CR E. coli was the most frequently isolated (45%), other CR- Enterobacterales like Klebsiella pneumoniae (20%), Citrobacter freundii (15%), Enterobacter cloacae (5%), Proteus mirabilis (5%), Providencia spp (5%) and Serratia marcescens (2.5%) were also isolated. A high diversity of CR genes was identified among the isolates, with 50% yielding blaCMY-2, 23% blaSHV-12, 20% blaCMY-1 and 18% blaCTX-M-15. Additionally, resistance to carbapenems associated to OXA-48 gene was found. Most of the CR isolates, principally K. pneumoniae and C. freundii, were multi-resistant with co-resistance to fluoroquinolones, tetracycline, sulphonamides and aminoglycosides. This study reports high prevalence of Enterobacterales harbouring a variety of CR genes and OXA-48 mediated-carbapenem resistance, all of them frequently associated to nosocomial human infections, for the first time in wild mammals and wild birds. Implementation of control measures to reduce the impact of anthropogenic pressure in the environment is urgently needed.
Collapse
Affiliation(s)
- Laila Darwich
- Departament de Sanitat i Anatomia Animal, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, Spain
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- * E-mail:
| | - Anna Vidal
- Departament de Sanitat i Anatomia Animal, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, Spain
| | - Chiara Seminati
- Departament de Sanitat i Anatomia Animal, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, Spain
| | - Andreu Albamonte
- Departament de Sanitat i Anatomia Animal, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, Spain
| | - Alba Casado
- Departament de Sanitat i Anatomia Animal, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, Spain
| | - Ferrán López
- Departament de Sanitat i Anatomia Animal, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, Spain
| | - Rafael A. Molina-López
- Catalan Wildlife Service, Centre de Fauna Salvatge de Torreferrussa, Santa Perpètua de Mogoda, Barcelona, Spain
| | - Lourdes Migura-Garcia
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| |
Collapse
|
28
|
Wyrsch ER, Reid CJ, DeMaere MZ, Liu MY, Chapman TA, Roy Chowdhury P, Djordjevic SP. Complete Sequences of Multiple-Drug Resistant IncHI2 ST3 Plasmids in Escherichia coli of Porcine Origin in Australia. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2019. [DOI: 10.3389/fsufs.2019.00018] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
29
|
Hossain S, Dahanayake P, De Silva B, Wickramanayake M, Wimalasena S, Heo G. Multidrug resistantAeromonasspp. isolated from zebrafish (Danio rerio): antibiogram, antimicrobial resistance genes and class 1 integron gene cassettes. Lett Appl Microbiol 2019; 68:370-377. [DOI: 10.1111/lam.13138] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 02/14/2019] [Accepted: 02/15/2019] [Indexed: 12/13/2022]
Affiliation(s)
- S. Hossain
- Veterinary Medical Center and College of Veterinary Medicine Chungbuk National University Cheongju Korea
| | - P.S. Dahanayake
- Veterinary Medical Center and College of Veterinary Medicine Chungbuk National University Cheongju Korea
| | - B.C.J. De Silva
- Veterinary Medical Center and College of Veterinary Medicine Chungbuk National University Cheongju Korea
| | - M.V.K.S. Wickramanayake
- Veterinary Medical Center and College of Veterinary Medicine Chungbuk National University Cheongju Korea
| | - S.H.M.P. Wimalasena
- Bio‐Safety Research Institute and College of Veterinary Medicine Chonbuk National University Jeonju Korea
| | - G.‐J. Heo
- Veterinary Medical Center and College of Veterinary Medicine Chungbuk National University Cheongju Korea
| |
Collapse
|
30
|
Roy Chowdhury P, Fourment M, DeMaere MZ, Monahan L, Merlino J, Gottlieb T, Darling AE, Djordjevic SP. Identification of a novel lineage of plasmids within phylogenetically diverse subclades of IncHI2-ST1 plasmids. Plasmid 2019; 102:56-61. [PMID: 30885788 DOI: 10.1016/j.plasmid.2019.03.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 02/22/2019] [Accepted: 03/13/2019] [Indexed: 11/17/2022]
Abstract
IncHI2-ST1 plasmids play an important role in co-mobilizing genes conferring resistance to critically important antibiotics and heavy metals. Here we present the identification and analysis of IncHI2-ST1 plasmid pSPRC-Echo1, isolated from an Enterobacter hormaechei strain from a Sydney hospital, which predates other multi-drug resistant IncHI2-ST1 plasmids reported from Australia. Our time-resolved phylogeny analysis indicates pSPRC-Echo1 represents a new lineage of IncHI2-ST1 plasmids and show how their diversification relates to the era of antibiotics.
Collapse
Affiliation(s)
- Piklu Roy Chowdhury
- The Ithree Institute, University of Technology Sydney, City Campus, Ultimo, NSW 2007, Australia; NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Sydney, Australia.
| | - Mathieu Fourment
- The Ithree Institute, University of Technology Sydney, City Campus, Ultimo, NSW 2007, Australia
| | - Matthew Z DeMaere
- The Ithree Institute, University of Technology Sydney, City Campus, Ultimo, NSW 2007, Australia
| | - Leigh Monahan
- The Ithree Institute, University of Technology Sydney, City Campus, Ultimo, NSW 2007, Australia
| | - John Merlino
- Department of Microbiology and Infectious Diseases, Concord Hospital, NSW Health Pathology, Hospital Road, Concord 2139, NSW, Australia; Faculty of Medicine, University of Sydney, NSW, Australia
| | - Thomas Gottlieb
- Department of Microbiology and Infectious Diseases, Concord Hospital, NSW Health Pathology, Hospital Road, Concord 2139, NSW, Australia; Faculty of Medicine, University of Sydney, NSW, Australia
| | - Aaron E Darling
- The Ithree Institute, University of Technology Sydney, City Campus, Ultimo, NSW 2007, Australia
| | - Steven P Djordjevic
- The Ithree Institute, University of Technology Sydney, City Campus, Ultimo, NSW 2007, Australia
| |
Collapse
|
31
|
Reid CJ, Wyrsch ER, Roy Chowdhury P, Zingali T, Liu M, Darling AE, Chapman TA, Djordjevic SP. Porcine commensal Escherichia coli: a reservoir for class 1 integrons associated with IS26. Microb Genom 2019; 3. [PMID: 29306352 PMCID: PMC5761274 DOI: 10.1099/mgen.0.000143] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Porcine faecal waste is a serious environmental pollutant. Carriage of antimicrobial-resistance genes (ARGs) and virulence-associated genes (VAGs), and the zoonotic potential of commensal Escherichia coli from swine are largely unknown. Furthermore, little is known about the role of commensal E. coli as contributors to the mobilization of ARGs between food animals and the environment. Here, we report whole-genome sequence analysis of 103 class 1 integron-positive E. coli from the faeces of healthy pigs from two commercial production facilities in New South Wales, Australia. Most strains belonged to phylogroups A and B1, and carried VAGs linked with extraintestinal infection in humans. The 103 strains belonged to 37 multilocus sequence types and clonal complex 10 featured prominently. Seventeen ARGs were detected and 97 % (100/103) of strains carried three or more ARGs. Heavy-metal-resistance genes merA, cusA and terA were also common. IS26 was observed in 98 % (101/103) of strains and was often physically associated with structurally diverse class 1 integrons that carried unique genetic features, which may be tracked. This study provides, to our knowledge, the first detailed genomic analysis and point of reference for commensal E. coli of porcine origin in Australia, facilitating tracking of specific lineages and the mobile resistance genes they carry.
Collapse
Affiliation(s)
- Cameron J Reid
- 1The i3 institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Ethan R Wyrsch
- 1The i3 institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Piklu Roy Chowdhury
- 1The i3 institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Tiziana Zingali
- 1The i3 institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Michael Liu
- 1The i3 institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Aaron E Darling
- 1The i3 institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Toni A Chapman
- 2NSW Department of Primary Industries, Elizabeth MacArthur Agricultural Institute, Menangle, NSW 2568, Australia
| | - Steven P Djordjevic
- 1The i3 institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
| |
Collapse
|
32
|
Abstract
Multidrug resistance in Escherichia coli has become a worrying issue that is increasingly observed in human but also in veterinary medicine worldwide. E. coli is intrinsically susceptible to almost all clinically relevant antimicrobial agents, but this bacterial species has a great capacity to accumulate resistance genes, mostly through horizontal gene transfer. The most problematic mechanisms in E. coli correspond to the acquisition of genes coding for extended-spectrum β-lactamases (conferring resistance to broad-spectrum cephalosporins), carbapenemases (conferring resistance to carbapenems), 16S rRNA methylases (conferring pan-resistance to aminoglycosides), plasmid-mediated quinolone resistance (PMQR) genes (conferring resistance to [fluoro]quinolones), and mcr genes (conferring resistance to polymyxins). Although the spread of carbapenemase genes has been mainly recognized in the human sector but poorly recognized in animals, colistin resistance in E. coli seems rather to be related to the use of colistin in veterinary medicine on a global scale. For the other resistance traits, their cross-transfer between the human and animal sectors still remains controversial even though genomic investigations indicate that extended-spectrum β-lactamase producers encountered in animals are distinct from those affecting humans. In addition, E. coli of animal origin often also show resistances to other-mostly older-antimicrobial agents, including tetracyclines, phenicols, sulfonamides, trimethoprim, and fosfomycin. Plasmids, especially multiresistance plasmids, but also other mobile genetic elements, such as transposons and gene cassettes in class 1 and class 2 integrons, seem to play a major role in the dissemination of resistance genes. Of note, coselection and persistence of resistances to critically important antimicrobial agents in human medicine also occurs through the massive use of antimicrobial agents in veterinary medicine, such as tetracyclines or sulfonamides, as long as all those determinants are located on the same genetic elements.
Collapse
|
33
|
Liakopoulos A, van der Goot J, Bossers A, Betts J, Brouwer MSM, Kant A, Smith H, Ceccarelli D, Mevius D. Genomic and functional characterisation of IncX3 plasmids encoding bla SHV-12 in Escherichia coli from human and animal origin. Sci Rep 2018; 8:7674. [PMID: 29769695 PMCID: PMC5955891 DOI: 10.1038/s41598-018-26073-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 05/03/2018] [Indexed: 01/09/2023] Open
Abstract
The blaSHV-12 β-lactamase gene is one of the most prevalent genes conferring resistance to extended-spectrum β-lactams in Enterobacteriaceae disseminating within and between reservoirs, mostly via plasmid-mediated horizontal gene transfer. Yet, studies regarding the biology of plasmids encoding blaSHV-12 are very limited. In this study, we revealed the emergence of IncX3 plasmids alongside IncI1α/γ in blaSHV-12 in animal-related Escherichia coli isolates. Four representative blaSHV-12-encoding IncX3 plasmids were selected for genome sequencing and further genetic and functional characterization. We report here the first complete sequences of IncX3 plasmids of animal origin and show that IncX3 plasmids exhibit remarkable synteny in their backbone, while the major differences lie in their blaSHV-12-flanking region. Our findings indicate that plasmids of this subgroup are conjugative and highly stable, while they exert no fitness cost on their bacterial host. These favourable features might have contributed to the emergence of IncX3 amongst SHV-12-producing E. coli in the Netherlands, highlighting the epidemic potential of these plasmids.
Collapse
Affiliation(s)
- Apostolos Liakopoulos
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, The Netherlands. .,Institute of Biology, University of Leiden, Sylviusweg 72, 2333 BE, Leiden, The Netherlands.
| | - Jeanet van der Goot
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Alex Bossers
- Department of Infection Biology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Jonathan Betts
- Department of Bacteriology, School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Michael S M Brouwer
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Arie Kant
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Hilde Smith
- Department of Infection Biology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Daniela Ceccarelli
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Dik Mevius
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, The Netherlands.,Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| |
Collapse
|
34
|
Sadikalay S, Reynaud Y, Guyomard-Rabenirina S, Falord M, Ducat C, Fabre L, Le Hello S, Talarmin A, Ferdinand S. High genetic diversity of extended-spectrum β-lactamases producing Escherichia coli in feces of horses. Vet Microbiol 2018; 219:117-122. [PMID: 29778183 DOI: 10.1016/j.vetmic.2018.04.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 04/07/2018] [Accepted: 04/11/2018] [Indexed: 11/17/2022]
Abstract
Extended-spectrum beta-lactamases (ESBLs), especially those of the CTX-M type, represent a major public health problem throughout the world. Although the carriage of ESBL-producing Enterobacteriaceae (EPE) in feces of horses is now well recognized, little is known about the diversity of EPE after treatment of horses with antibiotics. We undertook this study to assess and follow the diversity of EP Escherichia coli isolated from horses after antibiotic treatment for an infection. Fecal samples from two horses treated and two that were untreated were tested for the presence of EPE on different days. All isolated E. coli strains were evaluated for antimicrobial resistance (AMR) and by whole-genome sequencing. Multi locus sequence typing, phylogrouping, resistance genes and plasmid content were extracted from genomic data. A phylogenetic analysis based on single nucleotide polymorphism (SNP) divergence was also performed on the core genome. We isolated 35 strains belonging to the A, B1 and C phylo-groups. All but one expressed SHV-12 enzymes and one expressed CTX-M-1. Intra- and inter-horse genetic diversity of E. coli strains was identified in the genome analysis and 10 AMR profiles. Two distinct EP E. coli-resistant populations (phylo-group B1: ST4164-AMR3 and ST155-AMR2) were found in one horse, and five other resistant populations were found in the second horse (phylo-group A: ST1250-AMR1; phylo-group B1: ST1250-AMR1, ST6981-AMR1 and phylo-group C: ST10-AMR4). Some persistent EP E. coli strains were detected at least 1 month after treatment. These results indicate that EP E. coli strains isolated from horse feces show intra- and inter-host genetic diversity, even in a region with low ESBL prevalence and in horses that are rarely treated with third-generation cephalosporins. These results also suggest that horizontal gene transfer and/or selection of resistance genes probably occurs in vivo within the horse gut microbiome. Follow-up of EP E. coli resistance profiles for at least 1 month after treatment is warranted to prevent persistence of EP E. coli.
Collapse
Affiliation(s)
- Syndia Sadikalay
- Unité Environnement Santé, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe, France
| | - Yann Reynaud
- Unité Environnement Santé, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe, France
| | | | - Mélanie Falord
- Unité Environnement Santé, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe, France
| | - Célia Ducat
- Unité Environnement Santé, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe, France
| | - Laetitia Fabre
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Centre National de Réfé.rence des Escherichia coli, Shigella et Salmonella, Paris, France
| | - Simon Le Hello
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Centre National de Réfé.rence des Escherichia coli, Shigella et Salmonella, Paris, France
| | - Antoine Talarmin
- Unité Environnement Santé, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe, France
| | - Séverine Ferdinand
- Unité Environnement Santé, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe, France.
| |
Collapse
|
35
|
Zhang PLC, Shen X, Chalmers G, Reid-Smith RJ, Slavic D, Dick H, Boerlin P. Prevalence and mechanisms of extended-spectrum cephalosporin resistance in clinical and fecal Enterobacteriaceae isolates from dogs in Ontario, Canada. Vet Microbiol 2017; 213:82-88. [PMID: 29292008 DOI: 10.1016/j.vetmic.2017.11.020] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 11/13/2017] [Accepted: 11/17/2017] [Indexed: 10/18/2022]
Abstract
There is little information on the genetic basis of resistance to the critically important extended-spectrum cephalosporins (ESCs) in Enterobacteriaceae from dogs in Canada. This study assessed the frequency of ESC resistance in Enterobacteriaceae isolated from dogs in Ontario and the distribution of major ESC resistance genes in these bacteria. A total of 542 Enterobacteriaceae were isolated from 506 clinical samples from two diagnostic laboratories in Ontario. Eighty-eight ESC-resistant Enterobacteriaceae and 217 Escherichia coli were isolated from 234 fecal samples from dogs collected at leash-free dog parks. These fecal isolates were tested for ESC resistance along with the clinical isolates. Isolates with reduced ESC susceptibility were screened for blaCMY, blaCTX-M, and blaSHV, and all CTX-M-positive isolates underwent whole-genome sequencing. The prevalence of ESC resistance in clinical Enterobacteriaceae was 10.4%. The average frequency of fecal carriage of ESC-resistant Enterobacteriaceae in healthy dogs was 26.5%. The majority of ESC-resistant isolates were E. coli and the other major Enterobacteriaceae carrying ESC resistance genes were Klebsiella pneumoniae and Proteus mirabilis. The results show that the same ESC resistance genes can be found in clinical and fecal Enterobacteriaceae in dogs. The identified E. coli sequence types (including ST131 and ST648) and CTX-M variants (including CTX-M-14, -15, and -27) support the hypothesis of transfer of resistant bacteria between humans and dogs. CTX-M-1 was frequently found in canine fecal Enterobacteriaceae, while it is still rare in human Enterobacteriaceae in Canada, thus suggesting transfer of resistant bacteria to dogs from food animals or other sources.
Collapse
Affiliation(s)
- Pauline L C Zhang
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, 50 Stone Rd. E, Guelph, Ontario, N1G 2W1, Canada
| | - Xiao Shen
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, 50 Stone Rd. E, Guelph, Ontario, N1G 2W1, Canada
| | - Gabhan Chalmers
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, 50 Stone Rd. E, Guelph, Ontario, N1G 2W1, Canada
| | - Richard J Reid-Smith
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, 50 Stone Rd. E, Guelph, Ontario, N1G 2W1, Canada; Department of Population Medicine, Ontario Veterinary College, University of Guelph, 50 Stone Rd. E, Guelph, Ontario, N1G 2W1, Canada; Centre for Food-borne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, 160 Research Lane, Suite 103, Guelph, Ontario, N1G 5B2, Canada
| | - Durda Slavic
- Animal Health Laboratory, Post Office 3612, Guelph, Ontario, N1H 6R8, Canada
| | - Hani Dick
- IDEXX Laboratories, 1345 Denison St., Markham, Ontario, L3R 5V2, Canada
| | - Patrick Boerlin
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, 50 Stone Rd. E, Guelph, Ontario, N1G 2W1, Canada.
| |
Collapse
|
36
|
Alonso CA, Alcalá L, Simón C, Torres C. Novel sequence types of extended-spectrum and acquired AmpC beta-lactamase producing Escherichia coli and Escherichia clade V isolated from wild mammals. FEMS Microbiol Ecol 2017; 93:4004838. [DOI: 10.1093/femsec/fix097] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 07/21/2017] [Indexed: 11/12/2022] Open
|